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+--Forum: After the Bar Closes...
+---Topic: Science Break started by Lou FCD


Posted by: Lou FCD on July 16 2008,08:10

I've been meaning to do this for a while, but always manage to get sidetracked.

Long, long ago, before I took on the mantle of the man with the mop, I posted little interesting science bits that I'd come across in my travels about the web.  I'd give them their own threads, and sometimes they'd get some commentary and discussion, sometimes not.

Then I took to just posting them on the BW, to save from a bunch of empty threads, but then they just sort of got lost or buried amongst a big dump of trolling from PT or random matches of Mornington Crescent, or Ftk backwash or random silliness.

I'm starting this thread as a place for us all to just post links to Just Cool Science articles upon which we happen, and on which discussion may or may not take place.

It'll be nice to have a place for the occasional break from the TARD mines right here in our communal living room.

To that end, let me christen the thread with < this from LiveScience >:



---------------------QUOTE-------------------
Sexy People Sound Better
By Greg Soltis, LiveScience Staff
posted: 16 July 2008 06:54 am ET

People with voices deemed sexy and attractive tend to have greater body symmetry upon close inspection, suggesting that what we hear in a person can greatly affect what we see in them.

"The sound of a person's voice reveals a considerable amount of biological information," said Susan Hughes, an evolutionary psychologist from Albright College in Reading, Pa. "It can reflect the mate value of a person."

Hughes, whose new study is detailed in the June 2008 edition of the Journal of Nonverbal Behavior, cautions that an attractive voice does not necessarily indicate that this person has an attractive face.
---------------------QUOTE-------------------



More at the link.
Posted by: Lou FCD on July 16 2008,08:12

And let me be clear:

I intend to be ruthless to trolls here.  This thread is for real science discussion.
Posted by: Louis on July 16 2008,11:03

Great idea Lou.

I've got a few things I wouldn't mind posting, but they are all behind journal pay screens (which I can access but many probably cannot). I'll post the abstracts and hope that's enough.

Here's one of the more AtBC relevant ones from this week's Nature:



---------------------QUOTE-------------------
Nature 454, 209-212 (10 July 2008)

The evolutionary origin of flatfish asymmetry, Matt Friedman

All adult flatfishes (Pleuronectiformes), including the gastronomically familiar plaice, sole, turbot and halibut, have highly asymmetrical skulls, with both eyes placed on one side of the head. This arrangement, one of the most extraordinary anatomical specializations among vertebrates, arises through migration of one eye during late larval development. Although the transformation of symmetrical larvae into asymmetrical juveniles is well documented1, 2, 3, 4, 5, 6, 7, the evolutionary origins of flatfish asymmetry are uncertain1, 2 because there are no transitional forms linking flatfishes with their symmetrical relatives8, 9. The supposed inviability of such intermediates gave pleuronectiforms a prominent role in evolutionary debates10, 11, 12, 13, 14, 15, 16, leading to attacks on natural selection11 and arguments for saltatory change14, 15. Here I show that Amphistium and the new genus Heteronectes, both extinct spiny-finned fishes from the Eocene epoch of Europe, are the most primitive pleuronectiforms known. The orbital region of the skull in both taxa is strongly asymmetrical, as in living flatfishes, but these genera retain many primitive characters unknown in extant forms. Most remarkably, orbital migration was incomplete in Amphistium and Heteronectes, with eyes remaining on opposite sides of the head in post-metamorphic individuals. This condition is intermediate between that in living pleuronectiforms and the arrangement found in other fishes. Amphistium and Heteronectes indicate that the evolution of the profound cranial asymmetry of extant flatfishes was gradual in nature.
---------------------QUOTE-------------------



What are the "rules" for this thread (apart from no trolls and knob gags)? I'll try to link things where practical/free. DOIs are the standard I find for linking things if people don't mind. Do you just want internet links? Or are abstracts like the above appropriate? Or less technical articles? Or is it a relative free for all wrt posting scientific stuff?

Louis

P.S. WHAT THE HELL IS WRONG WITH MORNINGTON CRESCENT AND RANDOMN SILLINESS!!!!one11eleven!!!?//????/?? No wait, forget I asked.
Posted by: Lou FCD on July 16 2008,11:33

If it's science, I'm good.

Just do be sure to remember to note if it's a pdf link.  Some folks don't care much for pdfs or something.

Me, personally, I love links to pdfs of the original papers.  A short translation into Carpenter's Son English would be appreciated.
Posted by: Lou FCD on July 16 2008,12:40

From PLoS ONE:

< A 28,000 Years Old Cro-Magnon mtDNA Sequence Differs from All Potentially Contaminating Modern Sequences >

 

---------------------QUOTE-------------------
Abstract
Background

DNA sequences from ancient speciments may in fact result from undetected contamination of the ancient specimens by modern DNA, and the problem is particularly challenging in studies of human fossils. Doubts on the authenticity of the available sequences have so far hampered genetic comparisons between anatomically archaic (Neandertal) and early modern (Cro-Magnoid) Europeans.

Methodology/Principal Findings

We typed the mitochondrial DNA (mtDNA) hypervariable region I in a 28,000 years old Cro-Magnoid individual from the Paglicci cave, in Italy (Paglicci 23) and in all the people who had contact with the sample since its discovery in 2003. The Paglicci 23 sequence, determined through the analysis of 152 clones, is the Cambridge reference sequence, and cannot possibly reflect contamination because it differs from all potentially contaminating modern sequences.

Conclusions/Significance:

The Paglicci 23 individual carried a mtDNA sequence that is still common in Europe, and which radically differs from those of the almost contemporary Neandertals, demonstrating a genealogical continuity across 28,000 years, from Cro-Magnoid to modern Europeans. Because all potential sources of modern DNA contamination are known, the Paglicci 23 sample will offer a unique opportunity to get insight for the first time into the nuclear genes of early modern Europeans.
---------------------QUOTE-------------------


Posted by: Lou FCD on July 16 2008,12:42

Also from PLoS ONE:

< Major Histocompatibility Complex Based Resistance to a Common Bacterial Pathogen of Amphibians >



---------------------QUOTE-------------------
Abstract

Given their well-developed systems of innate and adaptive immunity, global population declines of amphibians are particularly perplexing. To investigate the role of the major histocompatibilty complex (MHC) in conferring pathogen resistance, we challenged Xenopus laevis tadpoles bearing different combinations of four MHC haplotypes (f, g, j, and r) with the bacterial pathogen Aeromonas hydrophila in two experiments. In the first, we exposed ff, fg, gg, gj, and jj tadpoles, obtained from breeding MHC homozygous parents, to one of three doses of A. hydrophila or heat-killed bacteria as a control. In the second, we exposed ff, fg, fr, gg, rg, and rr tadpoles, obtained from breeding MHC heterozygous parents and subsequently genotyped by PCR, to A. hydrophila, heat-killed bacteria or media alone as controls. We thereby determined whether the same patterns of MHC resistance emerged within as among families, independent of non-MHC heritable differences. Tadpoles with r or g MHC haplotypes were more likely to die than were those with f or j haplotypes. Growth rates varied among MHC types, independent of exposure dose. Heterozygous individuals with both susceptible and resistant haplotypes were intermediate to either homozygous genotype in both size and survival. The effect of the MHC on growth and survival was consistent between experiments and across families. MHC alleles differentially confer resistance to, or tolerance of, the bacterial pathogen, which affects tadpoles' growth and survival.
---------------------QUOTE-------------------


Posted by: Lou FCD on July 16 2008,14:38

Quote (Lou FCD @ July 16 2008,09:10)
To that end, let me christen the thread with < this from LiveScience >:

   

---------------------QUOTE-------------------
Sexy People Sound Better
By Greg Soltis, LiveScience Staff
posted: 16 July 2008 06:54 am ET

People with voices deemed sexy and attractive tend to have greater body symmetry upon close inspection, suggesting that what we hear in a person can greatly affect what we see in them.

"The sound of a person's voice reveals a considerable amount of biological information," said Susan Hughes, an evolutionary psychologist from Albright College in Reading, Pa. "It can reflect the mate value of a person."

Hughes, whose new study is detailed in the June 2008 edition of the Journal of Nonverbal Behavior, cautions that an attractive voice does not necessarily indicate that this person has an attractive face.
---------------------QUOTE-------------------



More at the link.
---------------------QUOTE-------------------


An earlier paper on the subject by Susan Hughes.

< Ratings of voice attractiveness predict sexual behavior and body configuration > (.pdf)

 

---------------------QUOTE-------------------
Abstract

We investigated the relationship between ratings of voice attractiveness and sexually dimorphic differences in shoulder-to-hip ratios (SHR) and waist-to-hip ratios (WHR), as well as different features of sexual behavior. Opposite-sex voice attractiveness ratings were positively correlated with SHR in males and negatively correlated with WHR in females. For both sexes, ratings of opposite-sex voice attractiveness also predicted reported age of first sexual intercourse, number of sexual partners, number of extra-pair copulation (EPC) partners, and number of partners that they had intercourse with that were involved in another relationship (i.e., were themselves chosen as an EPC partner). Coupled with previous findings showing a relationship between voice attractiveness and bilateral symmetry, these results provide additional evidence that the sound of a person’s voice may serve as an important multidimensional fitness indicator.
---------------------QUOTE-------------------




Posted by: Lou FCD on July 16 2008,16:55

< Caveman's DNA Looks Modern > at Science Now.

 

---------------------QUOTE-------------------
By Ann Gibbons
ScienceNOW Daily News
16 July 2008
When it comes to the extremely difficult task of sequencing caveman DNA, the third time may be the charm for David Caramelli. After two controversial attempts, the biological anthropologist at the University of Florence, Italy, and colleagues claim to have successfully sequenced mitochondrial DNA (mtDNA) from the fossils of a Cro-Magnon, a 28,000-year-old European ancestor of living humans. The mtDNA matches that of some modern Europeans but differs from that of Neandertals, shedding light on the fate of these ancient hominids.
---------------------QUOTE-------------------



More at the link.

ETA:  Original paper, < A 28,000 Years Old Cro-Magnon mtDNA Sequence Differs from All Potentially Contaminating Modern Sequences >, published in PLoS ONE.



---------------------QUOTE-------------------
Abstract
Background

DNA sequences from ancient speciments may in fact result from undetected contamination of the ancient specimens by modern DNA, and the problem is particularly challenging in studies of human fossils. Doubts on the authenticity of the available sequences have so far hampered genetic comparisons between anatomically archaic (Neandertal) and early modern (Cro-Magnoid) Europeans.

Methodology/Principal Findings

We typed the mitochondrial DNA (mtDNA) hypervariable region I in a 28,000 years old Cro-Magnoid individual from the Paglicci cave, in Italy (Paglicci 23) and in all the people who had contact with the sample since its discovery in 2003. The Paglicci 23 sequence, determined through the analysis of 152 clones, is the Cambridge reference sequence, and cannot possibly reflect contamination because it differs from all potentially contaminating modern sequences.

Conclusions/Significance:

The Paglicci 23 individual carried a mtDNA sequence that is still common in Europe, and which radically differs from those of the almost contemporary Neandertals, demonstrating a genealogical continuity across 28,000 years, from Cro-Magnoid to modern Europeans. Because all potential sources of modern DNA contamination are known, the Paglicci 23 sample will offer a unique opportunity to get insight for the first time into the nuclear genes of early modern Europeans.
---------------------QUOTE-------------------




Posted by: Lou FCD on July 16 2008,17:16

< Empathy is 'Hard-Wired' in Children's Brains >, at LiveScience, because the paper is behind a paywall.



---------------------QUOTE-------------------
Study author Jean Decety, a professor in the departments of Psychology and Psychiatry at the University of Chicago, reported that empathy appears to be "hard-wired" into the brains of normal children, as opposed to being solely the result of parental guidance or nurturing.

"Consistent with previous functional MRI studies of pain empathy with adults, the perception of other people in pain in children was associated with increased hemodymamic activity in the neural circuits involved in the processing of firsthand experience of pain...," Decety wrote.
---------------------QUOTE-------------------



< and the actual abstract >, from ScienceDirect:



---------------------QUOTE-------------------
Abstract

When we attend to other people in pain, the neural circuits underpinning the processing of first-hand experience of pain are activated in the observer. This basic somatic sensorimotor resonance plays a critical role in the primitive building block of empathy and moral reasoning that relies on the sharing of others' distress. However, the full-blown capacity of human empathy is more sophisticated than the mere simulation of the target's affective state. Indeed, empathy is about both sharing and understanding the emotional state of others in relation to oneself. In this functional magnetic resonance imaging (fMRI) study, 17 typically developing children (range 7–12 yr) were scanned while presented with short animated visual stimuli depicting painful and non-painful situations. These situations involved either a person whose pain was accidentally caused or a person whose pain was intentionally inflicted by another individual. After scanning, children rated how painful these situations appeared. Consistent with previous fMRI studies of pain empathy with adults, the perception of other people in pain in children was associated with increased hemodynamic activity in the neural circuits involved in the processing of first-hand experience of pain, including the insula, somatosensory cortex, anterior midcingulate cortex, periaqueductal gray, and supplementary motor area. Interestingly, when watching another person inflicting pain onto another, regions that are consistently engaged in representing social interaction and moral behavior (the temporo-parietal junction, the paracingulate, orbital medial frontal cortices, amygdala) were additionally recruited, and increased their connectivity with the fronto-parietal attention network. These results are important to set the standard for future studies with children who exhibit social cognitive disorders (e.g., antisocial personality disorder, conduct disorder) and are often deficient in experiencing empathy or guilt.
---------------------QUOTE-------------------



(What's up with scientists and paragraphs, by the way?  Is there a moratorium on carriage returns?)
Posted by: Timothy McDougald on July 16 2008,19:15

This looks interesting
< Control of segment number in vertebrate embryos >:


---------------------QUOTE-------------------
The vertebrate body axis is subdivided into repeated segments, best exemplified by the vertebrae that derive from embryonic somites. The number of somites is precisely defined for any given species but varies widely from one species to another. To determine the mechanism controlling somite number, we have compared somitogenesis in zebrafish, chicken, mouse and corn snake embryos. Here we present evidence that in all of these species a similar 'clock-and-wavefront'1, 2, 3 mechanism operates to control somitogenesis; in all of them, somitogenesis is brought to an end through a process in which the presomitic mesoderm, having first increased in size, gradually shrinks until it is exhausted, terminating somite formation. In snake embryos, however, the segmentation clock rate is much faster relative to developmental rate than in other amniotes, leading to a greatly increased number of smaller-sized somites.

---------------------QUOTE-------------------



Edit to add the link goes to the abstract in Nature.
Posted by: Timothy McDougald on July 16 2008,22:46



---------------------QUOTE-------------------
Me, personally, I love links to pdfs of the original papers.
---------------------QUOTE-------------------



I almost forgot, if you like links to pdfs you should check out the links page at PT. There are a couple of sections with links to a wide variety of downloadable pdfs. It's a work in progress...
Posted by: Lou FCD on July 16 2008,22:52

Quote (afarensis @ July 16 2008,23:46)


---------------------QUOTE-------------------
Me, personally, I love links to pdfs of the original papers.
---------------------QUOTE-------------------



I almost forgot, if you like links to pdfs you should check out the links page at PT. There are a couple of sections with links to a wide variety of downloadable pdfs. It's a work in progress...
---------------------QUOTE-------------------


Hey, thanks for that, and for hanging stuff up in this thread.
Posted by: JAM on July 16 2008,23:52

[quote=afarensis,July 16 2008,19:15]This looks interesting
< Control of segment number in vertebrate embryos >:
 

---------------------QUOTE-------------------
The vertebrate body axis is subdivided into repeated segments, best exemplified by the vertebrae that derive from embryonic somites. The number of somites is precisely defined for any given species...
---------------------QUOTE-------------------


Um...there's a slight problem there, as that claim is false.

It's false in fish:
< http://www.nature.com/nature/journal/v183/n4672/abs/1831408b0.html >

It's false in pigs:
< http://www.genome.org/cgi/content/abstract/gr.6085507v1 >

It's false in people:
< http://www3.interscience.wiley.com/journal....RETRY=0 >
Posted by: Timothy McDougald on July 17 2008,07:00

Two more, both open access from PNAS:

< Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution >:


---------------------QUOTE-------------------

Abstract

Lateral gene transfer is an important mechanism of natural variation among prokaryotes, but the significance of its quantitative contribution to genome evolution is debated. Here, we report networks that capture both vertical and lateral components of evolutionary history among 539,723 genes distributed across 181 sequenced prokaryotic genomes. Partitioning of these networks by an eigenspectrum analysis identifies community structure in prokaryotic gene-sharing networks, the modules of which do not correspond to a strictly hierarchical prokaryotic classification. Our results indicate that, on average, at least 81 ± 15% of the genes in each genome studied were involved in lateral gene transfer at some point in their history, even though they can be vertically inherited after acquisition, uncovering a substantial cumulative effect of lateral gene transfer on longer evolutionary time scales.
---------------------QUOTE-------------------



and

< A germ-line-selective advantage rather than an increased mutation rate can explain some unexpectedly common human disease mutations >



---------------------QUOTE-------------------
Abstract

Two nucleotide substitutions in the human FGFR2 gene (C755G or C758G) are responsible for virtually all sporadic cases of Apert syndrome. This condition is 100–1,000 times more common than genomic mutation frequency data predict. Here, we report on the C758G de novo Apert syndrome mutation. Using data on older donors, we show that spontaneous mutations are not uniformly distributed throughout normal testes. Instead, we find foci where C758G mutation frequencies are 3–4 orders of magnitude greater than the remaining tissue. We conclude this nucleotide site is not a mutation hot spot even after accounting for possible Luria–Delbruck “mutation jackpots.” An alternative explanation for such foci involving positive selection acting on adult self-renewing Ap spermatogonia experiencing the rare mutation could not be rejected. Further, the two youngest individuals studied (19 and 23 years old) had lower mutation frequencies and smaller foci at both mutation sites compared with the older individuals. This implies that the mutation frequency of foci increases as adults age, and thus selection could explain the paternal age effect for Apert syndrome and other genetic conditions. Our results, now including the analysis of two mutations in the same set of testes, suggest that positive selection can increase the relative frequency of premeiotic germ cells carrying such mutations, although individuals who inherit them have reduced fitness. In addition, we compared the anatomical distribution of C758G mutation foci with both new and old data on the C755G mutation in the same testis and found their positions were not correlated with one another.
---------------------QUOTE-------------------


Posted by: Henry J on July 17 2008,13:31

A mutation that's detrimental to the person, but that was advantageous to the success of the sperm that carried it? That is one weird result. :O

Henry
Posted by: Arden Chatfield on July 17 2008,22:56

It might be a good idea to pushpin this thread to the top so that it doesn't go below the fold, or whateverthefuck the hip, succinct internet term is for that concept.
Posted by: Nomad on July 17 2008,23:30

Quote (Arden Chatfield @ July 17 2008,22:56)
It might be a good idea to pushpin this thread to the top so that it doesn't go below the fold, or whateverthefuck the hip, succinct internet term is for that concept.
---------------------QUOTE-------------------


The hip Internet term would be "sticky", or to describe the process of making the thread sticky, "stickied".  Yes, another word changed into a verb.
Posted by: Lou FCD on July 18 2008,08:59

Quote (Arden Chatfield @ July 17 2008,23:56)
It might be a good idea to pushpin this thread to the top so that it doesn't go below the fold, or whateverthefuck the hip, succinct internet term is for that concept.
---------------------QUOTE-------------------


That's a lovely idea.
Posted by: skeptic on July 18 2008,20:30

Here's my current most-recent favorite:

Science 9 May 2008:
Vol. 320. no. 5877, pp. 811 - 814
DOI: 10.1126/science.1156093

Prev | Table of Contents | Next
Reports
Regulation of the Cellular Heat Shock Response in Caenorhabditis elegans by Thermosensory Neurons
Veena Prahlad, Tyler Cornelius, Richard I. Morimoto*

Temperature pervasively affects all cellular processes. In response to a rapid increase in temperature, all cells undergo a heat shock response, an ancient and highly conserved program of stress-inducible gene expression, to reestablish cellular homeostasis. In isolated cells, the heat shock response is initiated by the presence of misfolded proteins and therefore thought to be cell-autonomous. In contrast, we show that within the metazoan Caenorhabditis elegans, the heat shock response of somatic cells is not cell-autonomous but rather depends on the thermosensory neuron, AFD, which senses ambient temperature and regulates temperature-dependent behavior. We propose a model whereby this loss of cell autonomy serves to integrate behavioral, metabolic, and stress-related responses to establish an organismal response to environmental change.

here's the link in case anyone can access the archives:

< HSPs - May 2008 >
Posted by: hereoisreal on July 19 2008,21:56

Lou:

>I'm starting this thread as a place for us all to just post links to Just Cool Science articles upon which we happen, and on which discussion may or may not take place.<

………………………………......................

One Cool site:

< http://www.worldwidetelescope.org/ >
Posted by: Lou FCD on July 22 2008,18:53

I haven't located the original PNAS paper yet, but < this movie was kind of cool >.

The accompanying blurb, from LiveScience:



---------------------QUOTE-------------------
The Odorrana tormota frog opens and closes tubes in its ears when listening and calling at night. In this movie, the researchers shined a light under the frog's jaw to illuminate the inside of the mouth. The small circles of light on the side of the frog's head that brighten and dim show the opening and closing of the Eustachian tubes. Credit: National Academies of Science, PNAS (2008)
---------------------QUOTE-------------------




Posted by: Timothy McDougald on July 22 2008,20:42

Quote (Lou FCD @ July 22 2008,18:53)
I haven't located the original PNAS paper yet, but < this movie was kind of cool >.

The accompanying blurb, from LiveScience:

 

---------------------QUOTE-------------------
The Odorrana tormota frog opens and closes tubes in its ears when listening and calling at night. In this movie, the researchers shined a light under the frog's jaw to illuminate the inside of the mouth. The small circles of light on the side of the frog's head that brighten and dim show the opening and closing of the Eustachian tubes. Credit: National Academies of Science, PNAS (2008)
---------------------QUOTE-------------------


---------------------QUOTE-------------------


Yup, PNAS is bad about getting papers up on time. In the meantime, I have three that might be of interest (yes, I'm a literature hound)

< The Ascent of the Abundant: How Mutational Networks Constrain Evolution >:



---------------------QUOTE-------------------
Evolution by natural selection is fundamentally shaped by the fitness landscapes in which it occurs. Yet fitness landscapes are vast and complex, and thus we know relatively little about the long-range constraints they impose on evolutionary dynamics. Here, we exhaustively survey the structural landscapes of RNA molecules of lengths 12 to 18 nucleotides, and develop a network model to describe the relationship between sequence and structure. We find that phenotype abundance—the number of genotypes producing a particular phenotype—varies in a predictable manner and critically influences evolutionary dynamics. A study of naturally occurring functional RNA molecules using a new structural statistic suggests that these molecules are biased toward abundant phenotypes. This supports an “ascent of the abundant” hypothesis, in which evolution yields abundant phenotypes even when they are not the most fit.
---------------------QUOTE-------------------



and

< Species richness and structure of three Neotropical bat assemblages >:



---------------------QUOTE-------------------
We compared the assemblages of phyllostomid bats in three Neotropical rainforests with respect to species richness and assemblage structure and suggested a method to validate estimates of species richness for Neotropical bat assemblages based on mist-netting data. The fully inventoried bat assemblage at La Selva Biological Station (LS, 100 m elevation) in Costa Rica was used as a reference site to evaluate seven estimators of species richness. The Jackknife 2 method agreed best with the known bat species richness and thus was used to extrapolate species richness for an Amazonian bat assemblage (Tiputini Biodiversity Station; TBS, 200 m elevation) and an Andean premontane bat assemblage (Podocarpus National Park; BOM, 1000 m elevation) in Ecuador. Our results suggest that more than 100 bat species occur sympatrically at TBS and about 50 bat species coexist at BOM. TBS harbours one of the most species-rich bat assemblages known, including a highly diverse phyllostomid assemblage. Furthermore, we related assemblage structure to large-scale geographical patterns in floral diversity obtained from botanical literature. Assemblage structure of these three phyllostomid assemblages was influenced by differences in floral diversity at the three sites. At the Andean site, where understorey shrubs and epiphytes exhibit the highest diversity, the phyllostomid assemblage is mainly composed of understorey frugivores and nectarivorous species. By contrast, canopy frugivores are most abundant at the Amazonian site, coinciding with the high abundance of canopy fruiting trees. Assemblage patterns of other taxonomic groups also may reflect the geographical distribution patterns of floral elements in the Andean and Amazonian regions.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 94, 617–629.
---------------------QUOTE-------------------



and

< The origin of snakes (Serpentes) as seen through
eye anatomy >



---------------------QUOTE-------------------
Snakes evolved from lizards but have dramatically different eyes. These differences are cited widely as compelling evidence that snakes had fossorial and nocturnal ancestors. Their eyes, however, also exhibit similarities to those of aquatic vertebrates. We used a comparative analysis of ophthalmic data among vertebrate taxa to evaluate alternative hypotheses concerning the ecological origin of the distinctive features of the eyes of snakes. In parsimony and phenetic analyses, eye and orbital characters retrieved groupings more consistent with ecological adaptation rather than accepted phylogenetic relationships. Fossorial lizards and mammals cluster together, whereas snakes are widely separated from these taxa and instead cluster with primitively aquatic vertebrates. This indicates that the eyes of snakes most closely resemble those of aquatic vertebrates, and suggests that the early evolution of snakes occurred in aquatic environments. © 2004 The Linnean Society of London, Biological Journal of the Linnean Society,
2004, 81, 469–482.
---------------------QUOTE-------------------


Posted by: Peter Henderson on July 23 2008,09:55

I think this is one of the best science programmes on TV:

< http://www.bbc.co.uk/science....o.shtml >

Take a look at May's episode "we just don't know" (a phrase coined by Sir Patrick over the years).

A really fascinating discussion about the state of modern cosmology. Really worth watching. Far far better than any of the stupid reality shows that millions of brain dead people seem to watch these days e.g. Big brother, the X factor, America's got tallent, Gerry Springer, etc. etc. etc.
Posted by: dvunkannon on July 25 2008,12:34

< Origin of the nucleus and Ran-dependent transport to safeguard ribosome biogenesis in a chimeric cell >



---------------------QUOTE-------------------
Background
The origin of the nucleus is a central problem about the origin of eukaryotes. The common ancestry of nuclear pore complexes (NPC) and vesicle coating complexes indicates that the nucleus evolved via the modification of a pre-existing endomembrane system. Such an autogenous scenario is cell biologically feasible, but it is not clear what were the selective or neutral mechanisms that had led to the origin of the nuclear compartment.

Results
A key selective force during the autogenous origin of the nucleus could have been the need to segregate ribosome factories from the cytoplasm where ribosomal proteins (RPs) of the protomitochondrium were synthesized. After its uptake by an anuclear cell the protomitochondrium transferred several of its RP genes to the host genome. Alphaproteobacterial RPs and archaebacterial-type host ribosomes were consequently synthesized in the same cytoplasm. This could have led to the formation of chimeric ribosomes. I propose that the nucleus evolved when the host cell compartmentalised its ribosome factories and the tightly linked genome to reduce ribosome chimerism. This was achieved in successive stages by first evolving karyopherin and RanGTP dependent chaperoning of RPs, followed by the evolution of a membrane network to serve as a diffusion barrier, and finally a hydrogel sieve to ensure selective permeability at nuclear pores. Computer simulations show that a gradual segregation of cytoplasm and nucleoplasm via these steps can progressively reduce ribosome chimerism.

Conclusions
Ribosome chimerism can provide a direct link between the selective forces for and the mechanisms of evolving nuclear transport and compartmentalisation. The detailed molecular scenario presented here provides a solution to the gradual evolution of nuclear compartmentalization from an anuclear stage. Reviewers This article was reviewed by Eugene V Koonin, Martijn Huynen, Anthony M. Poole and Patrick Forterre.


---------------------QUOTE-------------------



Interesting that according to this, we acquired a nucleus in response to the endosymbiosis with mitochondria. Where does that put plants?
Posted by: nadandoenloprofundo on July 25 2008,14:41

Well, I am not a scientist, however I do enjoy knowing about it. So for the ones that don´t have enough time to read a lot, I post a video.


HTML
<object width="425" height="344"><param name="movie" value="http://www.youtube.com/v/Ivzs6ji7mMs&hl=en&fs=1"></param><param name="allowFullScreen" value="true"></param><embed src="http://www.youtube.com/v/Ivzs6ji7mMs&hl=en&fs=1" type="application/x-shockwave-flash" allowfullscreen="true" width="425" height="344"></embed></object>

Posted by: qetzal on July 25 2008,16:51

Here's a very interesting abstract from Cell. Ran across it on < one of the xkcd Science forums >.



---------------------QUOTE-------------------
Drummond & Wilke (2008), Mistranslation-Induced Protein Misfolding as a Dominant Constraint on Coding-Sequence Evolution. Cell 134:341-352.

Strikingly consistent correlations between rates of coding-sequence evolution and gene expression levels are apparent across taxa, but the biological causes behind the selective pressures on coding-sequence evolution remain controversial. Here, we demonstrate conserved patterns of simple covariation between sequence evolution, codon usage, and mRNA level in E. coli, yeast, worm, fly, mouse, and human that suggest that all observed trends stem largely from a unified underlying selective pressure. In metazoans, these trends are strongest in tissues composed of neurons, whose structure and lifetime confer extreme sensitivity to protein misfolding. We propose, and demonstrate using a molecular-level evolutionary simulation, that selection against toxicity of misfolded proteins generated by ribosome errors suffices to create all of the observed covariation. The mechanistic model of molecular evolution that emerges yields testable biochemical predictions, calls into question the use of nonsynonymous-to-synonymous substitution ratios (Ka/Ks) to detect functional selection, and suggests how mistranslation may contribute to neurodegenerative disease.
---------------------QUOTE-------------------



I knew that codon usage correlated with gene expression levels, but I had no idea that evolutionary rates did as well! Unfortunately, I won't have full text access 'til I'm back on work on Mon. Can't wait to read it!
Posted by: Timothy McDougald on July 25 2008,23:36

< Phylogenetic escalation and decline of plant defense strategies >



---------------------QUOTE-------------------
As the basal resource in most food webs, plants have evolved myriad strategies to battle consumption by herbivores. Over the past 50 years, plant defense theories have been formulated to explain the remarkable variation in abundance, distribution, and diversity of secondary chemistry and other defensive traits. For example, classic theories of enemy-driven evolutionary dynamics have hypothesized that defensive traits escalate through the diversification process. Despite the fact that macroevolutionary patterns are an explicit part of defense theories, phylogenetic analyses have not been previously attempted to disentangle specific predictions concerning (i) investment in resistance traits, (ii) recovery after damage, and (iii) plant growth rate. We constructed a molecular phylogeny of 38 species of milkweed and tested four major predictions of defense theory using maximum-likelihood methods. We did not find support for the growth-rate hypothesis. Our key finding was a pattern of phyletic decline in the three most potent resistance traits (cardenolides, latex, and trichomes) and an escalation of regrowth ability. Our neontological approach complements more common paleontological approaches to discover directional trends in the evolution of life and points to the importance of natural enemies in the macroevolution of species. The finding of macroevolutionary escalating regowth ability and declining resistance provides a window into the ongoing coevolutionary dynamics between plants and herbivores and suggests a revision of classic plant defense theory. Where plants are primarily consumed by specialist herbivores, regrowth (or tolerance) may be favored over resistance traits during the diversification process.
---------------------QUOTE-------------------


Posted by: Lou FCD on July 26 2008,08:04

< High Protein Bindingand Cidal Activity against Penicillin-Resistant S. pneumoniae: A Cefditoren In Vitro Pharmacodynamic Simulation >, from PLoS ONE:



---------------------QUOTE-------------------
Background

Although protein binding is a reversible phenomenon, it is assumed that antibacterial activity is exclusively exerted by the free (unbound) fraction of antibiotics.

Methodology/Principal Findings

Activity of cefditoren, a highly protein bound 3rd generation cephalosporin, over 24h after an oral 400 mg cefditoren-pivoxil bid regimen was studied against six S. pneumoniae strains (penicillin/cefditoren MICs; µg/ml): S1 (0.12/0.25), S2 (0.25/0.25), S3 and S4 (0.5/0.5), S5 (1/0.5) and S6 (4/0.5). A computerized pharmacodynamic simulation with media consisting in 75% human serum and 25% broth (mean albumin concentrations = 4.85±0.12 g/dL) was performed. Protein binding was measured. The cumulative percentage of a 24h-period that drug concentrations exceeded the MIC for total (T>MIC) and unbound concentrations (fT>MIC), expressed as percentage of the dosing interval, were determined. Protein binding was 87.1%. Bactericidal activity (?99.9% initial inocula reduction) was obtained against strains S1 and S2 at 24h (T>MIC = 77.6%, fT>MIC = 23.7%). With T>MIC of 61.6% (fT>MIC = 1.7%), reductions against S3 and S4 ranged from 90% to 97% at 12h and 24h; against S5, reduction was 45.1% at 12h and up to 85.0% at 24h; and against S6, reduction was 91.8% at 12h, but due to regrowth of 52.9% at 24h. Cefditoren physiological concentrations exerted antibacterial activity against strains exhibiting MICs of 0.25 and 0.5 µg/ml under protein binding conditions similar to those in humans.

Conclusions/Significance

The results of this study suggest that, from the pharmacodynamic perspective, the presence of physiological albumin concentrations may not preclude antipneumococcal activity of highly bound cephalosporins as cefditoren.
---------------------QUOTE-------------------


Posted by: dvunkannon on July 28 2008,17:06

My wife (who is Japanese) brought home a DVD the other day of a Japanese game show called "The Most Useful School in the World". It's a mildly educational show that is packaged inside a quiz show format that could only be dreamed up, and survive, in Japan.

In this episode, one segment was on iguanas of the Galapagos islands. The show introduced as the guest "expert" a Japanese doctor who had become a nature photographer. Interestingly, they also showed Charles Darwin's picture during the segment intro and talked about evolution. Imagine a game show trying that in the US?

The doctor showed pictures of the land iguanas eating prickly pear cactus, and showed that in areas with abundant iguanas, the prickly pear grew on a short pedestal base putting fleshy parts out of reach of the iguanas, while in areas without a lot of iguanas, it grew directly on the ground. This was given as an example of evolution.

The next film showed some of the adaptations of the sea iguanas, and asked the contestants to guess which feature had been modified the most in going to sea. The correct answer (according to the show) was that the sea iguana's claws were longer and sharper, the better to hold them against strong currents under water. (They showed great footage of the iguanas feeding underwater, gnawing seaweed off of rocks.)

Now the weird part was that they claimed that recent weather changes that had increased the foliage on the islands had given rise to the opportunity for some form of hybridization between land and sea iguanas. The result was a land iguana with claws strong enough to climb the pedestal of a prickly pear, and thereby acquire more resources.

Since this wasn't a peer reviewed game show, I was leery of accepting this story at face value, but I am trying to run down some facts. I thought I'd bring it to your attention as an example of how evolution fares in the pop culture of other countries, and also a cool example of real time evolution (if true). If I can find the show on YouTube or similar Japanese site, I will send a link.
Posted by: qetzal on July 29 2008,00:23

I had a chance to read the Cell paper I mentioned a few days back. I thought it was fascinating, and I highly recommend it.

Basically, it appears that a number of things correlate with mRNA levels across species from E. coli, yeast, worms, flies, mice, to humans. These include the fraction of optimal codon usage (i.e., the fraction of codons that correspond to the most abundant tRNA for that amino acid), the evolutionary non-synonymous substitution rate, the synonymous substitution rate, and even the relative rate of transitions to transversions.

The authors use principal component analysis to argue that all of these are related to one main underlying feature. They then argue that this feature is the need to minimize translation errors that lead to protein misfolding. In essence, they argue that misfolded proteins are cytotoxic, presumably in rough proportion to their abundance.

For low abundance proteins, occasional misfolding contributes little to the total cytotoxic burden in the cell. But for high abundance proteins, even rare misfolding may be detrimental. Thus, they argue, highly expressed genes need to use optimal codons to minimize translation errors. Even synonymous substitutions in a highly expressed gene can be detrimental, because they will tend to change an optimal codon to a suboptimal codon. This will increase the rate of translational error, resulting in more misfolded proteins, and greater cytotoxicity.

They go on to show how all of the observed correlations with gene expression level can be explained by this underlying mechanism. They do simulated evolution studies in silico that reproduce the observed correlations, but only if they include a cost associated with protein misfolding. Then they go a step further and suggest that this effect shows tissue specific features in complex organisms. For example, they suggest that neural tissue may be particularly sensitive to cytotoxicity from misfolded proteins (think Alzheimer's, Parkinsons, CJD, etc.). They note that brain-specific genes appear to evolve relatively slowly as a group, and explain how their hypothesis accounts for this.

The authors suggest that, if they're right, this has wide ranging implications for our understanding of evolution. Among other things, we would need to take into account how this affects synonymous vs. non-synonymous substituion rates when estimating divergence based on molecular data.

Here's what I really liked about this paper. 1) It proposes a new mechanism that has fundamental implications for how evolution works and is constrained. (At least, it's new to me; an editorial in the same issue of Cell seems to think it's potentially quite important as well.) 2) It provides a unifying explanation for a number of seemingly unconnected observations. (It even provides possible insight into the mechanisms of type 2 diabetes!) 3) The authors make multiple predictions based on their proposal, all of which can be tested experimentally.

To me, this is a stellar example of how science really works. The contrast with ID is stark.
Posted by: CeilingCat on July 29 2008,06:35



---------------------QUOTE-------------------
Sexy People Sound Better
By Greg Soltis, LiveScience Staff
posted: 16 July 2008 06:54 am ET

People with voices deemed sexy and attractive tend to have greater body symmetry upon close inspection, suggesting that what we hear in a person can greatly affect what we see in them.

"The sound of a person's voice reveals a considerable amount of biological information," said Susan Hughes, an evolutionary psychologist from Albright College in Reading, Pa. "It can reflect the mate value of a person."

Hughes, whose new study is detailed in the June 2008 edition of the Journal of Nonverbal Behavior, cautions that an attractive voice does not necessarily indicate that this person has an attractive face.
---------------------QUOTE-------------------


Greg was never on the CB.
Posted by: Timothy McDougald on July 30 2008,07:47

Here is one:

< Dinosaurian Soft Tissues Interpreted as Bacterial Biofilms >



---------------------QUOTE-------------------
A scanning electron microscope survey was initiated to determine if the previously reported findings of “dinosaurian soft tissues” could be identified in situ within the bones. The results obtained allowed a reinterpretation of the formation and preservation of several types of these “tissues” and their content. Mineralized and non-mineralized coatings were found extensively in the porous trabecular bone of a variety of dinosaur and mammal species across time. They represent bacterial biofilms common throughout nature. Biofilms form endocasts and once dissolved out of the bone, mimic real blood vessels and osteocytes. Bridged trails observed in biofilms indicate that a previously viscous film was populated with swimming bacteria. Carbon dating of the film points to its relatively modern origin. A comparison of infrared spectra of modern biofilms with modern collagen and fossil bone coatings suggests that modern biofilms share a closer molecular make-up than modern collagen to the coatings from fossil bones. Blood cell size iron-oxygen spheres found in the vessels were identified as an oxidized form of formerly pyritic framboids. Our observations appeal to a more conservative explanation for the structures found preserved in fossil bone.
---------------------QUOTE-------------------


Posted by: Lou FCD on Aug. 05 2008,19:36

< Phoenix Mars Team Opens Window on Scientific Process >

So the Phoenix mission team has found evidence of perchlorate salts in the Martian soil, but instead of waiting for the complete analysis, they're letting the public in on the process.



---------------------QUOTE-------------------
"The Phoenix project has decided to take an unusual step" in talking about the research when its scientists are only about half-way through the data collection phase and have not yet had time to complete data analysis or perform needed laboratory work, said Phoenix principal investigator Peter Smith of the University of Arizona, Tucson. Scientists are still at the stage where they are examining multiple hypotheses, given evidence that the soil contains perchlorate.

"We decided to show the public science in action because of the extreme interest in the Phoenix mission, which is searching for a habitable environment on the northern plains of Mars," Smith added. "Right now, we don't know whether finding perchlorate is good news or bad news for possible life on Mars."
---------------------QUOTE-------------------



More at the link.
Posted by: Timothy McDougald on Aug. 05 2008,20:24

Paging Dr. Egnor!

< Metabolic changes in schizophrenia and human brain evolution >



---------------------QUOTE-------------------
Background

Despite decades of research, the molecular changes responsible for the evolution of human cognitive abilities remain unknown. Comparative evolutionary studies provide detailed information about DNA sequence and mRNA expression differences between humans and other primates but, in the absence of other information, it has proved very difficult to identify molecular pathways relevant to human cognition.
Results

Here, we compare changes in gene expression and metabolite concentrations in the human brain and compare them to the changes seen in a disorder known to affect human cognitive abilities, schizophrenia. We find that both genes and metabolites relating to energy metabolism and energy-expensive brain functions are altered in schizophrenia and, at the same time, appear to have changed rapidly during recent human evolution, probably as a result of positive selection.
Conclusions

Our findings, along with several previous studies, suggest that the evolution of human cognitive abilities was accompanied by adaptive changes in brain metabolism, potentially pushing the human brain to the limit of its metabolic capabilities.
---------------------QUOTE-------------------



The pdf is freely downloadable.

On a related note:

< A Novel Molecular Solution for Ultraviolet Light Detection in Caenorhabditis elegans >



---------------------QUOTE-------------------
For many organisms the ability to transduce light into cellular signals is crucial for survival. Light stimulates DNA repair and metabolism changes in bacteria, avoidance responses in single-cell organisms, attraction responses in plants, and both visual and nonvisual perception in animals. Despite these widely differing responses, in all of nature there are only six known families of proteins that can transduce light. Although the roundworm Caenorhabditis elegans has none of the known light transduction systems, we show here that C. elegans strongly accelerates its locomotion in response to blue or shorter wavelengths of light, with maximal responsiveness to ultraviolet light. Our data suggest that C. elegans uses this light response to escape the lethal doses of sunlight that permeate its habitat. Short-wavelength light drives locomotion by bypassing two critical signals, cyclic adenosine monophosphate (cAMP) and diacylglycerol (DAG), that neurons use to shape and control behaviors. C. elegans mutants lacking these signals are paralyzed and unresponsive to harsh physical stimuli in ambient light, but short-wavelength light rapidly rescues their paralysis and restores normal levels of coordinated locomotion. This light response is mediated by LITE-1, a novel ultraviolet light receptor that acts in neurons and is a member of the invertebrate Gustatory receptor (Gr) family. Heterologous expression of the receptor in muscle cells is sufficient to confer light responsiveness on cells that are normally unresponsive to light. Our results reveal a novel molecular solution for ultraviolet light detection and an unusual sensory modality in C. elegans that is unlike any previously described light response in any organism.
---------------------QUOTE-------------------



I haven't read this later one yet but PhysOrg says it has something to do with depression, schizophrenia and insomnia in humans...
Posted by: stevestory on Aug. 07 2008,20:20

< http://www.telegraph.co.uk/earth....106.xml >
Posted by: Timothy McDougald on Aug. 07 2008,21:43

Quote (stevestory @ Aug. 07 2008,20:20)
< http://www.telegraph.co.uk/earth....106.xml >
---------------------QUOTE-------------------


Awesome!

< More here >

This is somewhat off topic but is really cool nonetheless. The University of Utah has a "Learn Genetics" website. < In one of the activities you can learn to extract DNA in the privacy of your own kitchen! >

All it takes is a blender and some common household chemicals...
Posted by: Lou FCD on Aug. 09 2008,09:12

Deadman posted this < here, in its own thread >, but it makes a nice addition here:

Quote (Deadman_932 @ Aug. 09 2008,09:59)
Green et al. (2008) A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing. Cell, 2008; 134 (3): 416


---------------------QUOTE-------------------
The complete mitochondrial genome of a 38,000-year-old Neanderthal has been sequenced...Analysis of the new sequence confirms that the mitochondria of Neanderthals falls outside the variation found in humans today, offering no evidence of admixture between the two lineages although it remains a possibility. It also shows that the last common ancestor of Neanderthals and humans lived about 660,000 years ago, give or take 140,000 years.
---------------------QUOTE-------------------



Science Daily write-up: < http://www.sciencedaily.com/releases/2008/08/080807130824.htm >


Journal article abstract:
< http://www.cell.com/content/article/abstract?uid=PIIS0092867408007733 >

The full article .PDF is available here:
< http://download.cell.com/pdfs/0092-8674/PIIS0092867408007733.pdf >

It’s a nice paper. Cheers!
---------------------QUOTE-------------------


Posted by: skeptic on Aug. 09 2008,20:11

I was looking for a little help and thought this was the most appropriate place.  I'm looking for some current treatment of the contrast that introns do not appear in bacterial species as opposed to eukaryotics.  I'm interested in evolutionary or mechanistic hypotheses.  I would prefer something you guys have actually read and evaluated as opposed to random links.  Thanks in advance for any assistance you guys can provide.

P.S. it goes without saying, the more current the better, thanks.
Posted by: deadman_932 on Aug. 09 2008,22:04

Uh, bacterial introns (Class I and II) are known, just oddly distributed. This is not MY field of specialization, but here's a couple of recent articles that I've read online. The first deals with hypotheses..eh, fairly heavily. Each has references and a list of recent articles that cite it:    

-----------------

Edgell, David R.; Marlene Belfort, and David A. Shub (2000) Barriers to Intron Promiscuity in Bacteria. Journal of Bacteriology, October 2000, p. 5281-5289, Vol. 182, No. 19 < http://jb.asm.org/cgi/content/full/182/19/5281 >

-----------------
Tourasse, N. J., Kolsto, A.-B. (2008). Survey of group I and group II introns in 29 sequenced genomes of the Bacillus cereus group: insights into their spread and evolution. Nucleic Acids Res 36: 4529-4548 < http://nar.oxfordjournals.org/cgi/content/full/36/14/4529 >

 

---------------------QUOTE-------------------
Group I and group II introns are well-known genetic elements that were discovered >20 years ago. They are catalytic RNAs (ribozymes) that are capable of self-splicing, i.e. excising themselves out of RNA transcripts and ligating their flanking RNA sequences (hereafter referred as exons). They are also mobile elements as they typically encode proteins that allow them to invade genomic sequences (1–10). Introns can spread into cognate (homologous) intron-less DNA sites, a process called homing, or insert into ectopic (novel) genomic locations, a process called transposition, which usually occurs at lower frequencies. Altogether, these elements are found in all three domains of life: group I introns are present in bacteria, bacteriophages and eukaryotes (organellar and nuclear genomes), while group II introns are present in bacteria, archaea and eukaryotic organelles
---------------------QUOTE-------------------



-----------------
Lixin Dai and Steven Zimmerly (2002)  Compilation and analysis of group II intron insertions in bacterial genomes: evidence for retroelement behavior. Nucleic Acids Research,  30:5, pp. 1091-1102.  

< http://nar.oxfordjournals.org/cgi/content/full/30/5/1091 >

ETA: there's some new citations on the intron wiki page here: < http://en.wikipedia.org/wiki/Intron > , many of which deal with theories of evolutionary origins. Nope, I haven't read them yet, don't have the time at the moment. Hope it helps, though.
Posted by: skeptic on Aug. 10 2008,09:11

thank you much
Posted by: Albatrossity2 on Aug. 15 2008,13:34

That dang designer sure keeps busy.  Here is a < report > of a new bird species discovered in Africa.
Posted by: skeptic on Aug. 19 2008,19:33

Anyone read "Decoding the Universe" by Seife?  I picked it up today and I'm wondering if it's worth the effort.
Posted by: stevestory on Aug. 29 2008,14:37

< http://www.popularmechanics.com/blogs/science_news/4279923.html >
Posted by: Richardthughes on Aug. 29 2008,14:49

Quote (stevestory @ Aug. 29 2008,14:37)
< http://www.popularmechanics.com/blogs/science_news/4279923.html >
---------------------QUOTE-------------------


Cool! I hope DT gives you a hat-tip when he links to that, he loves nanofabrication stuff.
Posted by: Timothy McDougald on Aug. 31 2008,10:06

Rapid Antagonistic Coevolution Between Primary And Secondary Sexual Characters In Horned Beetles

Here is the abstract:

 

---------------------QUOTE-------------------
Different structures may compete during development for a shared and limited pool of resources to sustain growth and differentiation. The resulting resource allocation trade-offs have the potential to alter both ontogenetic outcomes and evolutionary trajectories. However, little is known about the evolutionary causes and consequences of resource allocation trade-offs in natural populations. Here, we explore the significance of resource allocation trade-offs between primary and secondary sexual traits in shaping early morphological divergences between four recently separated populations of the horned beetle Onthophagus taurus as well as macroevolutionary divergence patterns across 10 Onthophagus species. We show that resource allocation trade-offs leave a strong signature in morphological divergence patterns both within and between species. Furthermore, our results suggest that genital divergence may, under certain circumstances, occur as a byproduct of evolutionary changes in secondary sexual traits. Given the importance of copulatory organ morphology for reproductive isolation our findings begin to raise the possibility that secondary sexual trait evolution may promote speciation as a byproduct. We discuss the implications of our results on the causes and consequences of resource allocation trade-offs in insects.
---------------------QUOTE-------------------



Unfortunately a subscription is required for the entire article. < link >
DOI:http://dx.doi.org/10.1111/j.1558-5646.2008.00448.x
Posted by: dvunkannon on Sep. 03 2008,12:03

John Bartlett ( "johnnyb" on UD) and I went back and forth a few times on his own blog after his recent post on UD. As part of that conversation, I found this paper by Langdon on < the Halting problem >. The basic result is that random programs don't halt, as the program length grows larger.

This upends a favorite creationist canard about computer programming, that programs are finely tuned, one error will stop them, yada yada yada. These are teleolgical arguments. It is hard to imagine a universe in which Windows ME could either evolve or survive, and so much the better!

BTW, Bartlett showed himself to be relatively Avida-friendly, so his posting rights under the big sweatertent of DDrr.. Dembski and Scooter might be threatened in the future.
Posted by: Lou FCD on Sep. 03 2008,13:19

Anybody have PNAS access? I'd like to read < this paper >, titled Genetic variation in the vasopressin receptor 1a gene (AVPR1A) associates with pair-bonding behavior in humans.

Abstract

 

---------------------QUOTE-------------------
Pair-bonding has been suggested to be a critical factor in the evolutionary development of the social brain. The brain neuropeptide arginine vasopressin (AVP) exerts an important influence on pair-bonding behavior in voles. There is a strong association between a polymorphic repeat sequence in the 5? flanking region of the gene (avpr1a) encoding one of the AVP receptor subtypes (V1aR), and proneness for monogamous behavior in males of this species. It is not yet known whether similar mechanisms are important also for human pair-bonding. Here, we report an association between one of the human AVPR1A repeat polymorphisms (RS3) and traits reflecting pair-bonding behavior in men, including partner bonding, perceived marital problems, and marital status, and show that the RS3 genotype of the males also affects marital quality as perceived by their spouses. These results suggest an association between a single gene and pair-bonding behavior in humans, and indicate that the well characterized influence of AVP on pair-bonding in voles may be of relevance also for humans.
---------------------QUOTE-------------------



Constance Holden, the reporter who < wrote the Science blurb >, done pissed me off seems to have made some interesting extrapolations from the research, given the abstract. I'd like to read the paper for myself and then possibly blog her ass back into the bronze age to compare my reading of the paper to hers.
Posted by: Timothy McDougald on Sep. 03 2008,19:07

This is interesting, and given the subject, relevant:

< Random Amino Acid Mutations and Protein Misfolding Lead to Shannon Limit in Sequence-Structure Communication >

Here is the abstract:



---------------------QUOTE-------------------
The transmission of genomic information from coding sequence to protein structure during protein synthesis is subject to stochastic errors. To analyze transmission limits in the presence of spurious errors, Shannon's noisy channel theorem is applied to a communication channel between amino acid sequences and their structures established from a large-scale statistical analysis of protein atomic coordinates. While Shannon's theorem confirms that in close to native conformations information is transmitted with limited error probability, additional random errors in sequence (amino acid substitutions) and in structure (structural defects) trigger a decrease in communication capacity toward a Shannon limit at 0.010 bits per amino acid symbol at which communication breaks down. In several controls, simulated error rates above a critical threshold and models of unfolded structures always produce capacities below this limiting value. Thus an essential biological system can be realistically modeled as a digital communication channel that is (a) sensitive to random errors and (b) restricted by a Shannon error limit. This forms a novel basis for predictions consistent with observed rates of defective ribosomal products during protein synthesis, and with the estimated excess of mutual information in protein contact potentials.
---------------------QUOTE-------------------



I haven't read it yet, but it is open access.
Posted by: Henry J on Sep. 03 2008,22:49

That leaves me wondering if one DNA three-pair code could be more reliable than another for the same amino acid?

Henry
Posted by: Timothy McDougald on Sep. 04 2008,22:29

< Natural Selection on a Major Armor Gene in Threespine Stickleback >

Here is the abstract:



---------------------QUOTE-------------------
Experimental estimates of the effects of selection on genes determining adaptive traits add to our understanding of the mechanisms of evolution. We measured selection on genotypes of the Ectodysplasin locus, which underlie differences in lateral plates in threespine stickleback fish. A derived allele (low) causing reduced plate number has been fixed repeatedly after marine stickleback colonized freshwater from the sea, where the ancestral allele (complete) predominates. We transplanted marine sticklebacks carrying both alleles to freshwater ponds and tracked genotype frequencies over a generation. The low allele increased in frequency once lateral plates developed, most likely via a growth advantage. Opposing selection at the larval stage and changing dominance for fitness throughout life suggest either that the gene affects additional traits undergoing selection or that linked loci also are affecting fitness.
---------------------QUOTE-------------------



I have a copy, email me at afarensis1@sbcglobal.net if you would like one.
Posted by: Dr.GH on Sep. 05 2008,10:32

New study:< Bad science writing gene found in people. >


Posted by: stevestory on Sep. 07 2008,17:28

< http://opa.yale.edu/news/article.aspx?id=5980 >

Yale Researchers Find “Junk DNA” May Have Triggered Key Evolutionary Changes in Human Thumb and Foot
Posted by: stevestory on Sep. 07 2008,17:30

Quote (Dr.GH @ Sep. 05 2008,11:32)
New study:< Bad science writing gene found in people. >
---------------------QUOTE-------------------


Canadian Writer Found to Have Dozens of Extra Mutant Copies of Said Gene
Posted by: dvunkannon on Sep. 08 2008,10:21

< A consensus on the evolution of the genetic code > from 2004. Nice job reminding everyone why Urey-Miller experiments are very relevant and useful

And the ID prediction is ...
Posted by: J-Dog on Sep. 10 2008,15:53

Move over Flagellum - PacMan is here!



Linky - < http://www.nature.com/news/2008/080116/full/news.2008.444.html >

PSST! - Don't let Dembski or Behe see this - they'll probably get a couple more bad books out of it. "Gee - It Looks Designed".  "No Free PacMan", and then the endless bad commentary from O'Dreary, and of course, the McCain campaign claiming sexism, because it's not Ms. Packman.
Posted by: Wesley R. Elsberry on Sep. 10 2008,16:19

< A Study on Whistles — And Only Whistles >

A study claims dophins "decrease vocal output" in larger groups, but do their data support that?
Posted by: stevestory on Sep. 10 2008,16:36



---------------------QUOTE-------------------

Biologists on the Verge of Creating New Form of Life

A team of biologists and chemists is closing in on bringing non-living matter to life.

It's not as Frankensteinian as it sounds. Instead, a lab led by Jack Szostak, a molecular biologist at Harvard Medical School, is building simple cell models that can almost be called life.

Szostak's protocells are built from fatty molecules that can trap bits of nucleic acids that contain the source code for replication. Combined with a process that harnesses external energy from the sun or chemical reactions, they could form a self-replicating, evolving system that satisfies the conditions of life, but isn't anything like life on earth now, but might represent life as it began or could exist elsewhere in the universe.  
---------------------QUOTE-------------------



< Linky >
Posted by: stevestory on Sep. 10 2008,17:24

< Friendly Invaders >

A carl zimmer NYT article.
Posted by: Wesley R. Elsberry on Sep. 11 2008,06:49

< An enzymatic vestigial function discovered >



---------------------QUOTE-------------------

"In creating these simulations of IMPDH, we observed something that hadn't been seen before," Yang said. "Previously, enzymes were believed to have a single 'pathway' through which they deliver catalytic agents to biological cells in order to bring about metabolic changes. But with IMPDH, we determined that there was a second pathway that also was used to cause these chemical transformations. The second pathway didn't operate as efficiently as the first one, but it was active nevertheless."

---------------------QUOTE-------------------


Posted by: carlsonjok on Sep. 11 2008,07:12

Quote (Wesley R. Elsberry @ Sep. 11 2008,06:49)
< An enzymatic vestigial function discovered >



---------------------QUOTE-------------------

"In creating these simulations of IMPDH, we observed something that hadn't been seen before," Yang said. "Previously, enzymes were believed to have a single 'pathway' through which they deliver catalytic agents to biological cells in order to bring about metabolic changes. But with IMPDH, we determined that there was a second pathway that also was used to cause these chemical transformations. The second pathway didn't operate as efficiently as the first one, but it was active nevertheless."

---------------------QUOTE-------------------


---------------------QUOTE-------------------


[GilDodgen]

A backup system!  Any good programmer would have designed it this way!  ID predicted this!

It is only the blind materialist dogmatist Nazi Darwinist chance worshippers that refuse to acknowledge this compelling evidence for intelligent design.

[/GilDodgen]
Posted by: stevestory on Sep. 15 2008,19:37

Viruses Collectively Decide Bacterial Cell's Fate

ScienceDaily (Sep. 15, 2008) — A new study suggests that bacteria-infecting viruses – called phages – can make collective decisions about whether to kill host cells immediately after infection or enter a latent state to remain within the host cell.

< http://www.sciencedaily.com/releases/2008/09/080915121231.htm >
Posted by: blipey on Sep. 15 2008,20:32

Quote (stevestory @ Sep. 15 2008,19:37)
Viruses Collectively Decide Bacterial Cell's Fate

ScienceDaily (Sep. 15, 2008) — A new study suggests that bacteria-infecting viruses – called phages – can make collective decisions about whether to kill host cells immediately after infection or enter a latent state to remain within the host cell.

< http://www.sciencedaily.com/releases/2008/09/080915121231.htm >
---------------------QUOTE-------------------


Wow!  That just screams intelligence.  One more for ID!

ID! ID! ID!
Posted by: blipey on Sep. 15 2008,20:37

That's actually really cool, in a creepy sort of way.  The idea would seem to generate whole new avenues of research with medicinal uses and treatment in mind.  Or at least that would be the case if all of modern science wasn't a lying ball of big liar guys.
Posted by: stevestory on Sep. 16 2008,03:06

THE FOURTH QUADRANT: A MAP OF THE LIMITS OF STATISTICS

< http://www.edge.org/3rd_culture/taleb08/taleb08_index.html >
Posted by: stevestory on Sep. 16 2008,21:48

< http://www.nytimes.com/2008....ted=all >



---------------------QUOTE-------------------
But David B. Goldstein of Duke University, a leading young population geneticist known partly for his research into the genetic roots of Jewish ancestry, says the effort to nail down the genetics of most common diseases is not working. “There is absolutely no question,” he said, “that for the whole hope of personalized medicine, the news has been just about as bleak as it could be.”

---------------------QUOTE-------------------


Posted by: Timothy McDougald on Sep. 16 2008,22:19

Two open access articles from PNAS. First:

< Molecular signatures of ribosomal evolution >

Here is the abstract:



---------------------QUOTE-------------------
Ribosomal signatures, idiosyncrasies in the ribosomal RNA (rRNA) and/or proteins, are characteristic of the individual domains of life. As such, insight into the early evolution of the domains can be gained from a comparative analysis of their respective signatures in the translational apparatus. In this work, we identify signatures in both the sequence and structure of the rRNA and analyze their contributions to the universal phylogenetic tree using both sequence- and structure-based methods. Domain-specific ribosomal proteins can be considered signatures in their own right. Although it is commonly assumed that they developed after the universal ribosomal proteins, we present evidence that at least one may have been present before the divergence of the organismal lineages. We find correlations between the rRNA signatures and signatures in the ribosomal proteins showing that the rRNA signatures coevolved with both domain-specific and universal ribosomal proteins. Finally, we show that the genomic organization of the universal ribosomal components contains these signatures as well. From these studies, we propose the ribosomal signatures are remnants of an evolutionary-phase transition that occurred as the cell lineages began to coalesce and so should be reflected in corresponding signatures throughout the fabric of the cell and its genome.
---------------------QUOTE-------------------



Second:

< Stage-specific predator species help each other to persist while competing for a single prey >

The abstract:



---------------------QUOTE-------------------
Prey in natural communities are usually shared by many predator species. How predators coexist while competing for the same prey is one of the fundamental questions in ecology. Here, we show that competing predator species may not only coexist on a single prey but even help each other to persist if they specialize on different life history stages of the prey. By changing the prey size distribution, a predator species may in fact increase the amount of prey available for its competitor. Surprisingly, a predator may not be able to persist at all unless its competitor is also present. The competitor thus significantly increases the range of conditions for which a particular predator can persist. This “emergent facilitation” is a long-term, population-level effect that results from asymmetric increases in the rate of prey maturation and reproduction when predation relaxes competition among prey. Emergent facilitation explains observations of correlated increases of predators on small and large conspecific prey as well as concordance in their distribution patterns. Our results suggest that emergent facilitation may promote the occurrence of complex, stable, community food webs and that persistence of these communities could critically depend on diversity within predator guilds.
---------------------QUOTE-------------------


Posted by: Peter Henderson on Sep. 18 2008,19:03

This is what makes science so fascinating:

< http://news.bbc.co.uk/1/hi/sci/tech/7543776.stm >



---------------------QUOTE-------------------
A new class of cosmic object has been found by a Dutch schoolteacher, through a project which allows the public to take part in astronomy research online.
Hanny Van Arkel, 25, came across the strange gaseous blob while using the Galaxy Zoo website to help classify galaxies in telescope images.
---------------------QUOTE-------------------



< http://www.physorg.com/news137157808.html >



---------------------QUOTE-------------------
Scientists working at telescopes around the world and with satellites in space were asked to take a look at the mysterious Voorwerp. "What we saw was really a mystery," said Schawinski. "The Voorwerp didn't contain any stars." Rather, it was made entirely of gas so hot — about 10,000 Celsius — that the astronomers felt it had to be illuminated by something powerful. They will soon use the Hubble Space Telescope to get a closer look.

Since there was no obvious source at hand in the Voorwerp itself, the team looked to find the source of illumination around the Voorwerp, and soon turned to the nearby galaxy IC 2497.

"We think that in the recent past the galaxy IC 2497 hosted an enormously bright quasar," Schawinski explains. "Because of the vast scale of the galaxy and the Voorwerp, light from that past still lights up the nearby Voorwerp even though the quasar shut down sometime in the past 100,000 years, and the galaxy's black hole itself has gone quiet."

"From the point of view of the Voorwerp, the galaxy looks as bright as it would have before the black hole turned off – it's this light echo that has been frozen in time for us to observe," said Chris Lintott, a co-organizer of Galaxy Zoo at Oxford University, UK. "It's rather like examining the scene of a crime where, although we can't see them, we know the culprit must be lurking somewhere nearby in the shadows." Similar light echoes have been seen around supernovae that exploded decades or centuries ago.
---------------------QUOTE-------------------



Makes a nonsense of the "where you there" argument. I'm always surprised why more scientists don't use astronomy/cosmology as proof of an ancient universe when confronting YECs.
Posted by: Lou FCD on Sep. 25 2008,18:13

< At Science >:



---------------------QUOTE-------------------
Back when our own solar system was still forming, collisions between young planets were commonplace. In fact, astronomers think our moon is the product of an encounter between Earth and a Mars-sized body. But other than occasional and relatively small-scale smash-ups, such as Comet Shoemaker-Levy's 21 pieces pelting Jupiter in 1994, no nearby worlds have been destroyed for billions of years.

Not so in a binary star system called BD+20 307, located about 300 light-years away in the constellation Aries. In 2004, a team of astronomers discovered a huge cloud of dust encircling what they thought was a young star. Now measurements using NASA's orbiting Chandra X-ray Observatory and Tennessee State University's automated ground-based instrument have revealed two old stars, each about the same age as the sun, locked in close orbit. That means the dust must have come from a collision between two planetary bodies, a collision that must have happened within the past 100,000 years or so--or even more recently, says astronomer Benjamin Zuckerman of the University of California, Los Angeles, a member of the 2004 team who led the new study.
---------------------QUOTE-------------------



More at the link, paper in December's The Astrophysical Journal.
Posted by: Lou FCD on Sep. 25 2008,18:41

< From PNAS >:



---------------------QUOTE-------------------
Abstract

Two coastal sites in Gibraltar, Vanguard and Gorham's Caves, located at Governor's Beach on the eastern side of the Rock, are especially relevant to the study of Neanderthals. Vanguard Cave provides evidence of marine food supply (mollusks, seal, dolphin, and fish). Further evidence of marine mammal remains was also found in the occupation levels at Gorham's Cave associated with Upper Paleolithic and Mousterian technologies [Finlayson C, et al. (2006) Nature 443:850–853]. The stratigraphic sequence of Gibraltar sites allows us to compare behaviors and subsistence strategies of Neanderthals during the Middle Paleolithic observed at Vanguard and Gorham's Cave sites. This evidence suggests that such use of marine resources was not a rare behavior and represents focused visits to the coast and estuaries.
---------------------QUOTE-------------------


Posted by: Timothy McDougald on Sep. 25 2008,18:46

Quote (Lou FCD @ Sep. 25 2008,18:41)
< From PNAS >:



---------------------QUOTE-------------------
Abstract

Two coastal sites in Gibraltar, Vanguard and Gorham's Caves, located at Governor's Beach on the eastern side of the Rock, are especially relevant to the study of Neanderthals. Vanguard Cave provides evidence of marine food supply (mollusks, seal, dolphin, and fish). Further evidence of marine mammal remains was also found in the occupation levels at Gorham's Cave associated with Upper Paleolithic and Mousterian technologies [Finlayson C, et al. (2006) Nature 443:850–853]. The stratigraphic sequence of Gibraltar sites allows us to compare behaviors and subsistence strategies of Neanderthals during the Middle Paleolithic observed at Vanguard and Gorham's Cave sites. This evidence suggests that such use of marine resources was not a rare behavior and represents focused visits to the coast and estuaries.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


I have this paper if anybody wants a copy. Email me at afarensis1@sbcglobal.net
Posted by: Lou FCD on Sep. 25 2008,18:50

I just popped back in as I'm wading through my feed reader and was about to < plug some guy's blog > who wrote about this.
Posted by: Timothy McDougald on Sep. 25 2008,19:07

Quote (Lou FCD @ Sep. 25 2008,18:50)
I just popped back in as I'm wading through my feed reader and was about to < plug some guy's blog > who wrote about this.
---------------------QUOTE-------------------


Aww, I like < this one better > because I mention the benefits of maritime exploitation a few days ahead of the publication of the Gibraltar paper. Serendipity can be a wonderful thing...
Posted by: Henry J on Sep. 25 2008,22:11

Going up, up, up? Want a lift?



---------------------QUOTE-------------------
Now the finest scientific minds of Japan are devoting themselves to cracking the greatest sci-fi vision of all: the space elevator. Man has so far conquered space by painfully and inefficiently blasting himself out of the atmosphere but the 21st century should bring a more leisurely ride to the final frontier.
---------------------QUOTE-------------------



< Japan hopes to turn sci-fi into reality with elevator to the stars >

< RidingHigh_402601a.jpg >

Henry
Posted by: stevestory on Sep. 25 2008,23:32

< Rocks may be oldest on earth >
Posted by: Louis on Sep. 26 2008,08:41

I just thought I'd mention < BOINC > just on the tiny chance that you chaps and chappesses were not already well aware of it.

Sign up and do science in your spare (computer) time by doing nothing! Yay!

Louis

This message was brought to you by Slackers For Science, the letter Q and the number 11. Slackers for Science is a not for profit organisation that will be going down the pub later seeing as it's POETS day. The views contained within might reflect those of someone somewhere, but not necessarily anyone you care about
Posted by: Henry J on Sep. 26 2008,20:34

"BOINC"? Not the best choice of name, given it's similarity to "boink".

Henry
Posted by: Lou FCD on Sep. 28 2008,10:52

Since we're learning about cell structure, and specifically the structure of the plasma membrane, in Biology class right now, this caught my eye, from PLoS ONE:

<
Anti-Plasmodium Activity of Angiotensin II and Related Synthetic Peptides >



---------------------QUOTE-------------------
Abstract

Plasmodium species are the causative agents of malaria, the most devastating insect-borne parasite of human populations. Finding and developing new drugs for malaria treatment and prevention is the goal of much research. Angiotensins I and II (ang I and ang II) and six synthetic related peptides designated Vaniceres 1-6 (VC1-VC6) were assayed in vivo and in vitro for their effects on the development of the avian parasite, Plasmodium gallinaceum. Ang II and VC5 injected into the thoraces of the insects reduced mean intensities of infection in the mosquito salivary glands by 88% and 76%, respectively. Although the mechanism(s) of action is not completely understood, we have demonstrated that these peptides disrupt selectively the P.gallinaceum cell membrane. Additionally, incubation in vitro of sporozoites with VC5 reduced the infectivity of the parasites to their vertebrate host. VC5 has no observable agonist effects on vertebrates, and this makes it a promising drug for malaria prevention and chemotherapy.
---------------------QUOTE-------------------



(My emphasis)

Pretty cool, especially given the timing.
Posted by: stevestory on Sep. 29 2008,20:36

< fat baby girls and breast cancer >
Posted by: Richard Simons on Sep. 29 2008,21:07

Quote (stevestory @ Sep. 29 2008,20:36)
< fat baby girls and breast cancer >
---------------------QUOTE-------------------


The title is misleading as it is size at birth, including weight and length, that they were investigating, not the fat on chubby 6-month-olds.
Posted by: midwifetoad on Oct. 07 2008,12:24



---------------------QUOTE-------------------
Small Asteroid Predicted to Cause Brilliant Fireball over Northern Sudan
Don Yeomans
NASA/JPL Near-Earth Object Program Office
October 6, 2008
A very small, few-meter sized asteroid, designated 2008 TC3, was found Monday morning by the Catalina Sky Survey from their observatory near Tucson Arizona. Preliminary orbital computations by the Minor Planet Center suggested an atmospheric entry of this object within a day of discovery. JPL confirmed that an atmospheric impact will very likely occur during early morning twilight over northern Sudan, north-eastern Africa, at 2:46 UT Tuesday morning. The fireball, which could be brilliant, will travel west to east (from azimuth = 281 degrees) at a relative atmospheric impact velocity of 12.8 km/s and arrive at a very low angle (19 degrees) to the local horizon. It is very unlikely that any sizable fragments will survive passage through the Earth's atmosphere.

Objects of this size would be expected to enter the Earth's atmosphere every few months on average but this is the first time such an event has been predicted ahead of time.

Update - 6:45 PM PDT (1 hour prior to atmospheric entry)

Since its discovery barely a day ago, 2008 TC3 has been observed extensively by astronomers around the world, and as a result, our orbit predictions have become very precise. We estimate that this object will enter the Earth's atmosphere at around 2:45:28 UTC and reach maximum deceleration at around 2:45:54 UTC. These times are uncertain by +/- 15 seconds or so. The time at which any fragments might reach the ground depends a great deal on the physical properties of the object, but should be around 2:46:20 UTC +/- 40 seconds.

---------------------QUOTE-------------------



< http://neo.jpl.nasa.gov/news/news159.html >
Posted by: Louis on Oct. 07 2008,12:51

Quote (Henry J @ Sep. 27 2008,02:34)
"BOINC"? Not the best choice of name, given it's similarity to "boink".

Henry
---------------------QUOTE-------------------


But surely you must know from "Calvin and Hobbes" that scientific progress goes "boink"?

Or in this case "boinc".

Do your part people! (The docking and protein folding studies are of particular interest, as is the quantum chemistry one. Fascinating stuff).

Louis
Posted by: Henry J on Oct. 07 2008,15:03



---------------------QUOTE-------------------
JPL confirmed that an atmospheric impact will very likely occur during early morning twilight over northern Sudan, north-eastern Africa, at 2:46 UT Tuesday morning.
---------------------QUOTE-------------------


The sky is falling!11!! The sky is fallling!one!! :O



---------------------QUOTE-------------------
It is very unlikely that any sizable fragments will survive passage through the Earth's atmosphere.
---------------------QUOTE-------------------


Oh.

Never mind. :p
Posted by: stevestory on Oct. 07 2008,15:45

< http://scienceblogs.com/neuroph....ied.php >

prion infection method identified.
Posted by: khan on Oct. 07 2008,17:41

Quote (Louis @ Oct. 07 2008,13:51)
Quote (Henry J @ Sep. 27 2008,02:34)
"BOINC"? Not the best choice of name, given it's similarity to "boink".

Henry
---------------------QUOTE-------------------


But surely you must know from "Calvin and Hobbes" that scientific progress goes "boink"?

Or in this case "boinc".

Do your part people! (The docking and protein folding studies are of particular interest, as is the quantum chemistry one. Fascinating stuff).

Louis
---------------------QUOTE-------------------


I've got the climate modeling one running on my desktop.
Posted by: Reed on Oct. 07 2008,18:04

I posted < this in the UD thread >, but it here might be a better place for it.

< http://www.astroengine.com/?p=1382 >

< Evidence for Correlations Between Nuclear Decay Rates and Earth-Sun Distance >

< Searching for modifications to the exponential radioactive decay law with the Cassini spacecraft >

Weird stuff.
Posted by: Lou FCD on Oct. 08 2008,10:35

Yes, *ahem*.





---------------------QUOTE-------------------
< People like you find it so easy >, by Roo Reynolds
---------------------QUOTE-------------------


Posted by: stevestory on Oct. 08 2008,15:42

< How the Turtle got its Shell >

Irreducible Complexity Failure #10,193,883,469,093.
Posted by: stevestory on Oct. 11 2008,00:25

< Chains of arthropods from half a billion years ago >.
Posted by: Henry J on Oct. 13 2008,13:30



---------------------QUOTE-------------------
Chains of arthropods from half a billion years ago.
---------------------QUOTE-------------------



But did they find any missing links? :p
Posted by: stevestory on Oct. 13 2008,22:09

< How ships like The Beagle dealt with lightening >
Posted by: stevestory on Oct. 15 2008,00:39

< A Guiding Glow to Track the Movement of Proteins >
Posted by: Lou FCD on Oct. 17 2008,05:52

Quote (stevestory @ Oct. 15 2008,01:39)
< A Guiding Glow to Track the Movement of Proteins >
---------------------QUOTE-------------------


That's just cool.
Posted by: J-Dog on Oct. 19 2008,11:41

Dude...

< http://www.telegraph.co.uk/news....ts.html >

Far out.
Posted by: stevestory on Oct. 21 2008,18:36

< Unsustainable resource depletion began 10,000 years ago >.

Interesting article. Not sure how valid the argument is.
Posted by: stevestory on Oct. 21 2008,18:58

I think i'm going to give that its own thread for visibility. I'm curious what some people here have to say about it.
Posted by: Timothy McDougald on Nov. 06 2008,21:19

< Copy number variation and evolution in humans and chimpanzees >. Here is the abstract:



---------------------QUOTE-------------------
Copy number variants (CNVs) underlie many aspects of human phenotypic diversity and provide the raw material for gene duplication and gene family expansion. However, our understanding of their evolutionary significance remains limited. We performed comparative genomic hybridization on a single human microarray platform to identify CNVs among the genomes of 30 humans and 30 chimpanzees as well as fixed copy number differences between species. We found that human and chimpanzee CNVs occur in orthologous genomic regions far more often than expected by chance and are strongly associated with the presence of highly homologous intrachromosomal segmental duplications. By adapting population genetic analyses for use with copy number data, we identified functional categories of genes that have likely evolved under purifying or positive selection for copy number changes. In particular, duplications and deletions of genes with inflammatory response and cell proliferation functions may have been fixed by positive selection and involved in the adaptive phenotypic differentiation of humans and chimpanzees.
---------------------QUOTE-------------------



< Initial sequence of the chimpanzee
genome and comparison with the human genome >. Here is the abstract:



---------------------QUOTE-------------------
Here we present a draft genome sequence of the common chimpanzee (Pan troglodytes). Through comparison with the human genome, we have generated a largely complete catalogue of the genetic differences that have accumulated since the human and chimpanzee species diverged from our common ancestor, constituting approximately thirty-five million single-nucleotide changes, five million insertion/deletion events, and various chromosomal rearrangements. We use this catalogue to explore the magnitude and regional variation of mutational forces shaping these two genomes, and the strength of positive and negative selection acting on their genes. In particular, we find that the patterns of evolution in human and chimpanzee protein-coding genes are highly correlated and dominated by the fixation of neutral and slightly deleterious alleles. We also use the chimpanzee genome as an outgroup to investigate human population genetics and identify signatures of selective sweeps in recent human evolution.
---------------------QUOTE-------------------


Posted by: J-Dog on Nov. 07 2008,07:27

Quote (afarensis @ Nov. 06 2008,21:19)


---------------------QUOTE-------------------
Here we present a draft genome sequence of the common chimpanzee (Pan troglodytes). Through comparison with the human genome, we have generated a largely complete catalogue of the genetic differences that have accumulated since the human and chimpanzee species diverged from our common ancestor, constituting  We also use the chimpanzee genome as an outgroup to investigate human population genetics and identify signatures of selective sweeps in recent human evolution.
---------------------QUOTE-------------------


---------------------QUOTE-------------------



It's good to see that under the New Administration, scientists are trying to find out exactly why, and what happened, to make DaveScot the way he is - so no human has to go there ever again.
Posted by: stevestory on Nov. 08 2008,21:12

< http://www.guardian.co.uk/environ....-alamos >

I knew mini nuke plants were coming, i didn't know they were coming so soon.
Posted by: stevestory on Nov. 10 2008,23:16

< Good Basic Carl Zimmer Article on Genes >
Posted by: Henry J on Nov. 13 2008,14:11

< Endeavour set for launch tomorrow >
Posted by: Lou FCD on Nov. 14 2008,06:11

Got this message on FaceBook this morning, from the Royal Society:



---------------------QUOTE-------------------
R. Soc. Journals
Today at 6:21am
Reply
The complete Royal Society journal archive, dating back to 1665, is FREE to access until 1 February 2009 - see < http://publishing.royalsociety.org/index.cfm?page=1600 > for further information.

The Archive provides a record of some key scientific discoveries from the last 340 years including: Halley's description of 'his comet' in 1705; details of the double Helix of DNA by James Watson and Francis Crick in 1954; and Edmond Stone's breakthrough in 1763 that willow bark cured fevers, leading to the discovery of salicylic acid and later the development of aspirin.

A personal favourite is the description by Captain James Cook of how he preserved the health of his crew aboard the HMS Endeavour. Have a look and see what other treasures you can find!
---------------------QUOTE-------------------



We've been discussing DNA in Biology class, and what led up to and followed the Watson and Crick paper, so the timing is simply lovely.
Posted by: Bob O'H on Nov. 17 2008,01:25

< This is just stupidly cool >.

In the last few years biologists have been studying gene expression with micro-arrays, which are horribly high-tec.  Well, some guys worked out how to do the same thing . . . on a CD.  Then you just need to play the CD to get the data off it.
Posted by: stevestory on Nov. 17 2008,01:38

Quote (Bob O'H @ Nov. 17 2008,02:25)
< This is just stupidly cool >.

In the last few years biologists have been studying gene expression with micro-arrays, which are horribly high-tec.  Well, some guys worked out how to do the same thing . . . on a CD.  Then you just need to play the CD to get the data off it.
---------------------QUOTE-------------------


I like what the nature blogger said, "They did what!?!".

Occasionally you run across an idea in science so cool all you can do is grin. This is one of those ideas.
Posted by: Timothy McDougald on Nov. 18 2008,21:10

Cave Bears!

< Deciphering the complete mitochondrial genome and phylogeny of the extinct cave bear in the Paleolithic painted cave of Chauvet >

Here is the abstract:



---------------------QUOTE-------------------
Retrieving a large amount of genetic information from extinct species was demonstrated feasible, but complete mitochondrial genome sequences have only been deciphered for the moa, a bird that became extinct a few hundred years ago, and for Pleistocene species, such as the woolly mammoth and the mastodon, both of which could be studied from animals embedded in permafrost. To enlarge the diversity of mitochondrial genomes available for Pleistocene species, we turned to the cave bear (Ursus spelaeus), whose only remains consist of skeletal elements. We collected bone samples from the Paleolithic painted cave of Chauvet-Pont d'Arc (France), which displays the earliest known human drawings, and contains thousands of bear remains. We selected a cave bear sternebra, radiocarbon dated to 32,000 years before present, from which we generated overlapping DNA fragments assembling into a 16,810-base pair mitochondrial genome. Together with the first mitochondrial genome for the brown bear western lineage, this study provides a statistically secured molecular phylogeny assessing the cave bear as a sister taxon to the brown bear and polar bear clade, with a divergence inferred to 1.6 million years ago. With the first mitochondrial genome for a Pleistocene carnivore to be delivered, our study establishes the Chauvet-Pont d'Arc Cave as a new reservoir for Paleogenetic studies. These molecular data enable establishing the chronology of bear speciation, and provide a helpful resource to rescue for genetic analysis archeological samples initially diagnosed as devoid of amplifiable DNA.
---------------------QUOTE-------------------


Posted by: Henry J on Nov. 25 2008,17:05

From nasa.gov website:



---------------------QUOTE-------------------
Mission managers gave the astronauts of space shuttle Endeavour an extra day in space as the crews of the shuttle and International Space Station continue transferring supplies and setting up new equipment inside the station.

Endeavour and seven astronauts are scheduled to return to Earth on Sunday at 12:55 p.m. EST. Endeavour is to land at NASA's Kennedy Space Center in Florida.
---------------------QUOTE-------------------


Posted by: Lou FCD on Nov. 26 2008,20:14

Dude has a new technique for genome sequencing, can do an entire human genome in about an hour.

< Science Magazine Weekly Podcast >
Posted by: Henry J on Nov. 26 2008,21:46



---------------------QUOTE-------------------
Dude has a new technique for genome sequencing, can do an entire human genome in about an hour.
---------------------QUOTE-------------------



And the people who a few years ago spent years doing it, are they laughing or crying? :)

Henry
Posted by: Lou FCD on Nov. 29 2008,11:47



---------------------QUOTE-------------------
Most Planets May Be Seeded With Life

By Phil Berardelli
ScienceNOW Daily News
26 November 2008
Astronomers have detected a building block of RNA floating within the hot, compact core of a massive star-forming region in the Milky Way. The molecule appears to have formed with all of the other stuff that makes up planets, suggesting that many other worlds are seeded with some of life's ingredients right from birth.

Two of the greatest questions of existence--Are we alone? and How did we get here?--remain unanswered. Clues keep coming, and they are tantalizing. Over the past decade, astronomers have detected organic molecules inside meteorites and even in space (ScienceNOW, 28 March). But these latter substances have not been found in the clouds of dust and gas around new stars that can form planets, making their link to life tenuous.

The new find, described this week in the journal Astro-ph, is stronger. Using the IRAM radio dish array in France, a team of European astronomers has detected glycolaldehyde--a simple sugar that makes up ribose, one of the constituents of RNA--within the core of what appears to be a coalescing disk of dust and gas in a star-forming region called G31.41+0.31, about 26,000 light-years away. The sugar molecule can apparently form in a simple reaction between carbon monoxide molecules and dust grains.
---------------------QUOTE-------------------



More, < at Science >.
Posted by: stevestory on Nov. 30 2008,12:21

< could drinking heavy water extend your life? >
Posted by: Henry J on Nov. 30 2008,17:16



---------------------QUOTE-------------------
could drinking heavy water extend your life?
---------------------QUOTE-------------------



The article that BWE referenced < here > seemed to have a different opinion.

Henry
Posted by: Kristine on Dec. 04 2008,00:20

I posted < this > jokingly at TBW but it would be my dream to work on this! :)
 

---------------------QUOTE-------------------
During his career, Gould wrote 300 consecutive essays for Natural History, the monthly magazine of the American Museum of Natural History, and more than 20 books, many of them bestsellers. He also assembled what he believed was a definitive library of the history of early paleontology, said Rhonda Shearer, Gould's widow.

Now, the collection of books, papers and artifacts that helped inform his writing and teaching is, for the most part, in the Stanford University Libraries, with the balance expected to arrive soon. It is an immense amount of material.
---------------------QUOTE-------------------


They're going to digitize much of it and make it available online!
 

---------------------QUOTE-------------------
Perhaps even more surprising than the books he collected is what he did with them.

"He actually used them, and he annotated on many of them in pencil, in the margins," Trujillo said. "He didn't really treat them as artifacts, he treated them as a working research library, and it is clear that is what he did, even though they're really quite amazing rare books."
---------------------QUOTE-------------------


Eek!  :O
Posted by: midwifetoad on Dec. 04 2008,08:59

As a hevy user of OmniPage, I have to say that hand notations in books make OCR a difficult thing.
Posted by: Kristine on Dec. 04 2008,09:08

Quote (midwifetoad @ Dec. 04 2008,08:59)
As a hevy user of OmniPage, I have to say that hand notations in books make OCR a difficult thing.
---------------------QUOTE-------------------


I'd hate to think of the EAD (encoded archival description) involved, too.

They may just go to PDFs, which wouldn't help you.
Posted by: qetzal on Dec. 05 2008,14:53

Quote (stevestory @ Nov. 30 2008,12:21)
< could drinking heavy water extend your life? >
---------------------QUOTE-------------------


The sidebar at the end of that article contains the following quote:



---------------------QUOTE-------------------
"Every single atom in the DNA of the brain of a 100-year-old man is the same atom as when he was 15 years old," says Shchepinov (BioEssays, vol 29, p 1247).
---------------------QUOTE-------------------



That's a stunningly incorrect claim, especially from someone who supposedly has expertise in isotope effects and their potential impact on free radical damage.*

If that quote is accurate (I can't access the original citation), it wouldn't encourage me to trust much of what Shchepinov says.

----

*For one thing, some of the protons (H atoms) on the DNA bases are sufficiently acidic to exchange with water at appreciable rates. Plus there are many spontaneous acid/base catalyzed reactions that alter the atoms in DNA, including cytosine deamination and depurination, to name two that are especially prevalent.

More important, the guy claims that the isotope effect will help us live longer by slowing damage from free radicals. Surely he realizes that free radical damage often changes the atoms in an affected biomolecule. Does he think DNA in the brain is somehow exempt from such alterations?

I sure hope that's a misquote.
Posted by: Reed on Dec. 09 2008,23:16

Neanderthal genome half sequenced < http://www.newscientist.com/article....ts.html >

John Hawks has some commentary < http://johnhawks.net/weblog....08.html >
Posted by: Lou FCD on Dec. 14 2008,11:16

Jeremy Mohn of Stand Up for Real Science < does a nice video on the chromosome 2 fusion in humans >  on TeacherTube.

A little over 7 minutes long.
Posted by: Paul Flocken on Dec. 16 2008,08:59

Need a physics question answered.  I am trying to contribute to a game that I play and am making my scienc-y background text for it.

Since matter warps space into positive curvature, creating gravity, is it correct to say that the cosmological constant unwarps space negatively, and that the 'natural' state of rest for space is flat?  Or am I not even wrong?

Thanks in advance.
Paul
Posted by: midwifetoad on Dec. 16 2008,09:39

I'm pretty ignorant in this area, but my understanding is the "cosmological constant" is just the gravitational effect of dark matter and dark energy. The effect would be the same if the matter was visible.
Posted by: Dr.GH on Dec. 16 2008,10:41

I have no idea, Paul. But, I like that image.


Posted by: nuytsia on Dec. 17 2008,02:39

Great article < here > on recent work on Hawai'ian Honeyeaters and there origins.

But check out the comments.
Ugh!
Posted by: keiths on Dec. 17 2008,19:30

Science investigates Heddle's brain

Two items from the January issue of Scientific American:


---------------------QUOTE-------------------
Seeing on Faith

Religion might literally influence how you view the world.  Scientists in the Netherlands compared Dutch Calvinists with Dutch atheists, looking for any effects potentially imposed on thinking by the neo-Calvinist concept of sphere sovereignty, which emphasizes that each sector of society has its own responsibilities and authorities. The researchers hypothesize that Calvinists therefore might not be as good as atheists at seeing the big picture. Participants were shown images of large rectangles or squares that each consisted of smaller rectangles or squares. In some tests, volunteers had to quickly identify the shapes of the smaller parts; in others, the larger wholes. The Calvinists scored slightly but significantly lower than atheists did in correctly identifying whole images. The investigators plan to study other religions for similar influences. See more in the November 12 PLoS ONE.
---------------------QUOTE-------------------




---------------------QUOTE-------------------

Politics of Blank Looks

How we react to faces could be linked to our political affiliations. Psychologist Jacob M. Vigil of the University of North Florida had 740 college students look at 12 photographs of faces digitally blurred to not display any clear emotion. The volunteers were then asked if these faces expressed sadness, joy, disgust, surprise, fear or anger. The students who identified themselves as Republicans were more likely than those who identified themselves as Democrats to interpret these vague faces as more threatening, as measured by anger or disgust, and less submissive, as conveyed by fear or surprise. These findings, which appeared online October 21 in Nature Precedings, are consistent with research linking conservative political views on military spending and capital punishment with heightened reactions to disturbing images and sounds. Vigil conjectures that the political ideologies we advocate could be linked with the way that we respond to ambiguous details.

---------------------QUOTE-------------------


Posted by: midwifetoad on Dec. 18 2008,07:01

< Computational modelling of evolution >



---------------------QUOTE-------------------
Computer modelling seems to be a very promising technique to study
complex systems like ecosystems or langauge. In the present paper we
briefly review such an approach and present our results in this field. In
section 1.2 we briefly discuss population dynamics of simple two-species
prey-predator systems and classical approaches in this field based on Lotka-
Volterra equations. We also argue that it is desirable to use an alternative
approach, the so-called individual based modelling. An example of such
a model is described in section 1.3. In this section we discuss results of
numerical simulations of the model concerning especially the oscillatory
behaviour.
---------------------QUOTE-------------------


Posted by: ppb on Dec. 19 2008,08:12

We are developing the capability to study the chemical composition of the atmospheres of extrasolar planets.

< Hubble finds carbon dioxide on an extrasolar planet >

When I first took up astronomy as a hobby in the late 60's our knowledge of the planets in our own solar system was still limited.  Now we can study the atmosphere of planets orbiting other stars many light-years away.

It may not be long before we detect signs of life on earth-like planets.
Posted by: Lou FCD on Dec. 19 2008,11:12

Quote (ppb @ Dec. 19 2008,09:12)
We are developing the capability to study the chemical composition of the atmospheres of extrasolar planets.

< Hubble finds carbon dioxide on an extrasolar planet >

When I first took up astronomy as a hobby in the late 60's our knowledge of the planets in our own solar system was still limited.  Now we can study the atmosphere of planets orbiting other stars many light-years away.

It may not be long before we detect signs of life on earth-like planets.
---------------------QUOTE-------------------


Yes, I was listening to a very good podcast on it yesterday, though I don't recall if it was Are We Alone, or Science Update, or maybe the Astronomy Update from Universe Today. It had been a while since I'd been able to listen to many of them at once, so they had piled up. They all sort of ran together after a few hours yesterday, so ...

It was one of those.

....unless it was another science podcast.

:)
Posted by: ppb on Dec. 19 2008,12:02

Quote (Lou FCD @ Dec. 19 2008,12:12)

Yes, I was listening to a very good podcast on it yesterday, though I don't recall if it was Are We Alone, or Science Update, or maybe the Astronomy Update from Universe Today. It had been a while since I'd been able to listen to many of them at once, so they had piled up. They all sort of ran together after a few hours yesterday, so ...

It was one of those.

....unless it was another science podcast.

:)
---------------------QUOTE-------------------



I read about it on < Phil Plait's > blog.  They did it by subtracting the spectrum of the star itself (while the planet was eclipsed) from the spectrum of the star and the planet together.  Really neat trick.
Posted by: Lou FCD on Dec. 19 2008,15:01

I lurve me some Dr. BA, now.
Posted by: Lou FCD on Dec. 20 2008,15:43

Science Friday video on < Eggnog >, complete with recipe (with booze) and an experiment.

Does the alcohol in eggnog kill the bacteria? Watch the vid.
Posted by: stevestory on Dec. 29 2008,16:29

< This is really distressing news about drugs and studies >. Assuming it's true, of course, and that the author isn't some crank.
Posted by: Steviepinhead on Jan. 05 2009,15:49

Bipedalsim -- "Lucy" Bones -- Lecture.

If any of our Seattle-area members would be interested in attending a lecture associated with* the current "Lucy's Legacy" exhibit at the Pacific Science Center, I haz TWO FREE TICKETS (a twelve dollar value!) for this Thursday evening, Jan. 8, at 7 pm.  My gf and I can't go because of another commitment (I've gone to the other lectures in the series and they've all been interesting).  

The lecture is roughly an hour long, is presented by the Burke Museum in association with the science center, and takes place in the Eames Auditorium in the Pacific Science Center complex, basically the same place you go to watch IMAX films.

Here's what Teh Lecture is about:
Jan 8, 2009, 7 p.m. - Eames Theater, Pacific Science Center
Dr. Patricia Kramer - "Lucy Walks: functional morphology and the evolution of bipedalism" - Dr. Kramer will discuss how anthropologists decipher clues from fossils to discover how and why our earliest hominid ancestors walked upright.

Dr. Kramer is a Research Assistant Professor of Anthropology at the University of Washington, and Adjunct Curator of Archaeology, Burke Museum.

If interested, please PM me!  We can hack out the ticket hand-off off-line (I live in Fremont, range as far north as Edmonds and as far south as downtown on a daily basis, and will be attending another lecture at the Seattle Art Museum the same night at the same time, so could probably swing by any location downtown north of the SAM on my way there -- for example, a location just outside the Pacific Science Center!)




__
Note that I will not be treating you to the exhibit itself, but only to the lecture.
Posted by: Kristine on Jan. 05 2009,19:38

Quote (stevestory @ Dec. 29 2008,16:29)
< This is really distressing news about drugs and studies >. Assuming it's true, of course, and that the author isn't some crank.
---------------------QUOTE-------------------


Marcia Angell was the first woman to serve as editor-in-chief of the New England Journal of Medicine and has < appeared on PBS > criticizing our health care industry. She's a critic of the pharmaceutical industry and of "alternative medicine." Yep, a depressing article, all right - and unfortunately, I trust her assessment.
Posted by: Peter Henderson on Jan. 06 2009,08:40

While arguing with some nutters over on the Premier Christian Radio forum I came across this excellent lecture to the Royal institution by our very own (she hails from Norn Iron) Professor Jocelyn Bell Burnell:

< http://vega.org.uk/video/programme/69 >

Although it's quite old (1997) it's still a good lesson on stellar evolution.
Posted by: qetzal on Jan. 06 2009,17:04

Quote (stevestory @ Dec. 29 2008,16:29)
< This is really distressing news about drugs and studies >. Assuming it's true, of course, and that the author isn't some crank.
---------------------QUOTE-------------------



Having worked on new drug development for some years, I think most of Angell's criticisms in this article are on target. I haven't agreed with some of her previous opinions on pharma, and there are some minor bits in this one that I think are wrong, but I agree with her main points: conflicts of interest and publication bias are serious problems that affect how drugs are prescribed in the US and result in significant detriment to patients.
Posted by: Steviepinhead on Jan. 06 2009,18:04

What?!?  Nobody wants to learn how Lucy's bones bespeak her bipedalism?
Quote (Steviepinhead @ Jan. 05 2009,13:49)
Bipedalsim -- "Lucy" Bones -- Lecture.

If any of our Seattle-area members would be interested in attending a lecture associated with* the current "Lucy's Legacy" exhibit at the Pacific Science Center, I haz TWO FREE TICKETS (a twelve dollar value!) for this Thursday evening, Jan. 8, at 7 pm.  My gf and I can't go because of another commitment (I've gone to the other lectures in the series and they've all been interesting).  

The lecture is roughly an hour long, is presented by the Burke Museum in association with the science center, and takes place in the Eames Auditorium in the Pacific Science Center complex, basically the same place you go to watch IMAX films.

Here's what Teh Lecture is about:
Jan 8, 2009, 7 p.m. - Eames Theater, Pacific Science Center
Dr. Patricia Kramer - "Lucy Walks: functional morphology and the evolution of bipedalism" - Dr. Kramer will discuss how anthropologists decipher clues from fossils to discover how and why our earliest hominid ancestors walked upright.

Dr. Kramer is a Research Assistant Professor of Anthropology at the University of Washington, and Adjunct Curator of Archaeology, Burke Museum.

If interested, please PM me!  We can hack out the ticket hand-off off-line (I live in Fremont, range as far north as Edmonds and as far south as downtown on a daily basis, and will be attending another lecture at the Seattle Art Museum the same night at the same time, so could probably swing by any location downtown north of the SAM on my way there -- for example, a location just outside the Pacific Science Center!)




__
Note that I will not be treating you to the exhibit itself, but only to the lecture.
---------------------QUOTE-------------------


Just bumping this again -- Free tickets to the above Seattle lecture are available!
Posted by: ppb on Jan. 07 2009,10:55

Quote (Steviepinhead @ Jan. 06 2009,19:04)
What?!?  Nobody wants to learn how Lucy's bones bespeak her bipedalism?
Quote (Steviepinhead @ Jan. 05 2009,13:49)
Bipedalsim -- "Lucy" Bones -- Lecture.

If any of our Seattle-area members would be interested in attending a lecture associated with* the current "Lucy's Legacy" exhibit at the Pacific Science Center, I haz TWO FREE TICKETS (a twelve dollar value!;) for this Thursday evening, Jan. 8, at 7 pm.  My gf and I can't go because of another commitment (I've gone to the other lectures in the series and they've all been interesting).  

The lecture is roughly an hour long, is presented by the Burke Museum in association with the science center, and takes place in the Eames Auditorium in the Pacific Science Center complex, basically the same place you go to watch IMAX films.

Here's what Teh Lecture is about:
Jan 8, 2009, 7 p.m. - Eames Theater, Pacific Science Center
Dr. Patricia Kramer - "Lucy Walks: functional morphology and the evolution of bipedalism" - Dr. Kramer will discuss how anthropologists decipher clues from fossils to discover how and why our earliest hominid ancestors walked upright.

Dr. Kramer is a Research Assistant Professor of Anthropology at the University of Washington, and Adjunct Curator of Archaeology, Burke Museum.

If interested, please PM me!  We can hack out the ticket hand-off off-line (I live in Fremont, range as far north as Edmonds and as far south as downtown on a daily basis, and will be attending another lecture at the Seattle Art Museum the same night at the same time, so could probably swing by any location downtown north of the SAM on my way there -- for example, a location just outside the Pacific Science Center!;)




__
Note that I will not be treating you to the exhibit itself, but only to the lecture.
---------------------QUOTE-------------------


Just bumping this again -- Free tickets to the above Seattle lecture are available!
---------------------QUOTE-------------------


I'd love to go.  Do they come with free airline tickets to Seattle?  :)
Posted by: J-Dog on Jan. 07 2009,11:16

Quote (Steviepinhead @ Jan. 06 2009,18:04)
What?!?  Nobody wants to learn how Lucy's bones bespeak her bipedalism?
Quote (Steviepinhead @ Jan. 05 2009,13:49)
Bipedalsim -- "Lucy" Bones -- Lecture.

If any of our Seattle-area members would be interested in attending a lecture associated with* the current "Lucy's Legacy" exhibit at the Pacific Science Center, I haz TWO FREE TICKETS (a twelve dollar value!) for this Thursday evening, Jan. 8, at 7 pm.  My gf and I can't go because of another commitment (I've gone to the other lectures in the series and they've all been interesting).  

The lecture is roughly an hour long, is presented by the Burke Museum in association with the science center, and takes place in the Eames Auditorium in the Pacific Science Center complex, basically the same place you go to watch IMAX films.

Here's what Teh Lecture is about:
Jan 8, 2009, 7 p.m. - Eames Theater, Pacific Science Center
Dr. Patricia Kramer - "Lucy Walks: functional morphology and the evolution of bipedalism" - Dr. Kramer will discuss how anthropologists decipher clues from fossils to discover how and why our earliest hominid ancestors walked upright.

Dr. Kramer is a Research Assistant Professor of Anthropology at the University of Washington, and Adjunct Curator of Archaeology, Burke Museum.

If interested, please PM me!  We can hack out the ticket hand-off off-line (I live in Fremont, range as far north as Edmonds and as far south as downtown on a daily basis, and will be attending another lecture at the Seattle Art Museum the same night at the same time, so could probably swing by any location downtown north of the SAM on my way there -- for example, a location just outside the Pacific Science Center!)




__
Note that I will not be treating you to the exhibit itself, but only to the lecture.
---------------------QUOTE-------------------


Just bumping this again -- Free tickets to the above Seattle lecture are available!
---------------------QUOTE-------------------


You could offer them to Casey Luskin and the DI - I am sure with an organization named The Discovery Institute that they are interested in ALL aspects of science....

Oh.  Right.  Never mind!

Srsly... It looks like a great time.  SOMEONE should take advantage of them!
Posted by: Kristine on Jan. 07 2009,17:23

Quote (ppb @ Jan. 07 2009,10:55)
 
Quote (Steviepinhead @ Jan. 06 2009,19:04)
What?!?  Nobody wants to learn how Lucy's bones bespeak her bipedalism?    
Quote (Steviepinhead @ Jan. 05 2009,13:49)
Bipedalsim -- "Lucy" Bones -- Lecture.

If any of our Seattle-area members would be interested in attending a lecture associated with* the current "Lucy's Legacy" exhibit at the Pacific Science Center, I haz TWO FREE TICKETS (a twelve dollar value!;) for this Thursday evening, Jan. 8, at 7 pm.  My gf and I can't go because of another commitment (I've gone to the other lectures in the series and they've all been interesting).  

The lecture is roughly an hour long, is presented by the Burke Museum in association with the science center, and takes place in the Eames Auditorium in the Pacific Science Center complex, basically the same place you go to watch IMAX films.

Here's what Teh Lecture is about:
Jan 8, 2009, 7 p.m. - Eames Theater, Pacific Science Center
Dr. Patricia Kramer - "Lucy Walks: functional morphology and the evolution of bipedalism" - Dr. Kramer will discuss how anthropologists decipher clues from fossils to discover how and why our earliest hominid ancestors walked upright.

Dr. Kramer is a Research Assistant Professor of Anthropology at the University of Washington, and Adjunct Curator of Archaeology, Burke Museum.

If interested, please PM me!  We can hack out the ticket hand-off off-line (I live in Fremont, range as far north as Edmonds and as far south as downtown on a daily basis, and will be attending another lecture at the Seattle Art Museum the same night at the same time, so could probably swing by any location downtown north of the SAM on my way there -- for example, a location just outside the Pacific Science Center!;)




__
Note that I will not be treating you to the exhibit itself, but only to the lecture.
---------------------QUOTE-------------------


Just bumping this again -- Free tickets to the above Seattle lecture are available!
---------------------QUOTE-------------------


I'd love to go.  Do they come with free airline tickets to Seattle?  :)
---------------------QUOTE-------------------


Me, too! And what kind of < chairs > do they have in the Eames Theatre? ;)
Posted by: Steviepinhead on Jan. 07 2009,18:55

You know, if I thought there was one chance in a bazillion that anyone at the DIsco Institute for the Terminally Simple would get anything out of this lecture, I would offer.  

But the odds of that being considerably less than the odds of abiogenesis ...  And even Vegas wouldn't give me odds on Luskin understanding his own zip code, much less bipedalism (which brings to mind a joke about bicycles...).

Also sorry, but I can't spring for the airline tix.  Plus, it's been very windy around here lately.  Perhaps not the time to try to land at SeaTac airport.  Though the seats in the Eames are reasonably comfy, once you get there.
Going once, going twice...!
Posted by: utidjian on Jan. 09 2009,13:11

< Self-Seplicating Chemicals Evolve in Lifelike Ecosystem >

I am afraid that much tard will come of that article. It would be nice to see the original paper.

-DU-
Posted by: stevestory on Jan. 10 2009,15:56

< self-replicating chemicals >
Posted by: stevestory on Jan. 10 2009,15:58

< http://blogs.sciencemag.org/origins/ >
Posted by: stevestory on Jan. 11 2009,21:40

< Steven Pinker on genes in the NYT >



---------------------QUOTE-------------------
The most prominent finding of behavioral genetics has been summarized by the psychologist Eric Turkheimer: “The nature-nurture debate is over. . . . All human behavioral traits are heritable.” By this he meant that a substantial fraction of the variation among individuals within a culture can be linked to variation in their genes. Whether you measure intelligence or personality, religiosity or political orientation, television watching or cigarette smoking, the outcome is the same. Identical twins (who share all their genes) are more similar than fraternal twins (who share half their genes that vary among people). Biological siblings (who share half those genes too) are more similar than adopted siblings (who share no more genes than do strangers). And identical twins separated at birth and raised in different adoptive homes (who share their genes but not their environments) are uncannily similar.
---------------------QUOTE-------------------


Posted by: Lou FCD on Jan. 15 2009,20:21

< The Bacterial Symbiont Wolbachia Induces Resistance to RNA Viral Infections in Drosophila melanogaster > in PLoS Biology.



---------------------QUOTE-------------------
Wolbachia are vertically transmitted, obligatory intracellular bacteria that infect a great number of species of arthropods and nematodes. In insects, they are mainly known for disrupting the reproductive biology of their hosts in order to increase their transmission through the female germline. In Drosophila melanogaster, however, a strong and consistent effect of Wolbachia infection has not been found. Here we report that a bacterial infection renders D. melanogaster more resistant to Drosophila C virus, reducing the load of viruses in infected flies. We identify these resistance-inducing bacteria as Wolbachia. Furthermore, we show that Wolbachia also increases resistance of Drosophila to two other RNA virus infections (Nora virus and Flock House virus) but not to a DNA virus infection (Insect Iridescent Virus 6). These results identify a new major factor regulating D. melanogaster resistance to infection by RNA viruses and contribute to the idea that the response of a host to a particular pathogen also depends on its interactions with other microorganisms. This is also, to our knowledge, the first report of a strong beneficial effect of Wolbachia infection in D. melanogaster. The induced resistance to natural viral pathogens may explain Wolbachia prevalence in natural populations and represents a novel Wolbachia–host interaction.
---------------------QUOTE-------------------



Interesting in itself, but something in the intro also caught my eye.



---------------------QUOTE-------------------
Wolbachia were first discovered infecting the mosquito Culex pipiens in 1924, but interest in these bacteria mainly arose when it was shown that infected mosquito males do not successfully breed with noninfected females. This phenomenon is termed cytoplasmic incompatibility (CI) and has, since then, been found in many other insect species infected with Wolbachia. In some hosts, Wolbachia can also cause feminization, male killing, or parthenogenesis. All these mechanisms profoundly alter the reproductive biology of their hosts and are thought to increase the success of bacterial transmission through the female germline. In the majority of known cases, Wolbachia behave like reproductive parasites of their hosts.
---------------------QUOTE-------------------



(references removed and emphasis added)

That's just cool. (Weird, but cool.)
Posted by: Henry J on Jan. 15 2009,20:41

< Monkey business in Florida! >

Henry
Posted by: Henry J on Jan. 16 2009,14:46

< Mars has gas! >
Posted by: Kristine on Jan. 21 2009,08:50

Tara Smith cans has teh famous - Aetiology made JASIST! *Whoop!* (I hear a chorus: "Jasist? What's that?")

"Scholarly hyperwriting: The function of links in academic weblogs"
María José Luzón, University of Zaragoza, Centro Politécnico Superior, Department of English and German Philology, c/María de Luna 3, 50018 Zaragoza, Spain
Journal of the American Society for Information Science and Technology, Volume 60, Issue 1, Pages 75-89

Abstract.    

---------------------QUOTE-------------------
Weblogs are gaining momentum as one of most versatile tools for online scholarly communication. Since academic weblogs tend to be used by scholars to position themselves in a disciplinary blogging community, links are essential to their construction. The aim of this article is to analyze the reasons for linking in academic weblogs and to determine how links are used for distribution of information, collaborative construction of knowledge, and construction of the blog's and the blogger's identity. For this purpose I analyzed types of links in 15 academic blogs, considering both sidebar links and in-post links. The results show that links are strategically used by academic bloggers for several purposes, among others to seek their place in a disciplinary community, to engage in hypertext conversations for collaborative construction of knowledge, to organize information in the blog, to publicize their research, to enhance the blog's visibility, and to optimize blog entries and the blog itself.
---------------------QUOTE-------------------


Aetiology was one of the blogs examined, and really, the article doesn't tell you anything you don't already know. (This is in the "Why didn't I know that they didn't know about this so I could have written it, arg!" category.)
Posted by: Henry J on Jan. 23 2009,16:03

< Newly discovered catfish species climbs rocks   >


---------------------QUOTE-------------------

Fish's pelvic fin decouples from body and moves backward and forward
Photo of a new species of climbing fish, Lithogenes wahari.
A previously unknown species of climbing catfish has been discovered in remote Venezuela, [...]

---------------------QUOTE-------------------


Posted by: Kristine on Jan. 29 2009,11:27

PANDAS:


---------------------QUOTE-------------------
Occasionally, children can suddenly develop OCD [Obsessive-Compulsive Disorder], or have a sudden worsening of existing OCD symptoms, when they have strep throat. It seems that the body forms antibodies against the streptococci bacteria. These antibodies attack certain key areas in the brain, leading to OCD symptoms or worsening of existing symptoms. Treatment of the strep infection with antibiotics results in significant improvement or even elimination fo the OCD symptoms. This relatively rare reaction to strep is called Pediatric Autoimmune Neuropsychiatric Disorders Associated with Streptococcal Infections—PANDAS.
---------------------QUOTE-------------------


Obsessive-Compulsive Disorder By Bruce M. Hyman and Cherry Pedrick (a psychotherapist and a nurse, respectively)
Posted by: Henry J on Jan. 29 2009,14:05

But, the acronym gives a rather misleading idea of what it's about before reading the excerpt. ;)

Henry
Posted by: Kristine on Jan. 29 2009,17:21

Yes - it made me think of a certain book. :)
Posted by: stevestory on Jan. 29 2009,22:22

Quote (Henry J @ Jan. 15 2009,21:41)
< Monkey business in Florida! >

Henry
---------------------QUOTE-------------------


Florida is deeply weird. Deeply. Like chromozomically, DNA-level weird. It's a part of who we are. We are deeply wrong. Malfunctional on an atomic level. But it makes sense to us. We understand why we do what we do. We understand why Fark.com has only one tag specific to a state, and we understand why that tag says Florida. We understand Adaptation. We don't even know what the big deal is. We understand Carl Hiassen and Dave Barry. It's just the same old, same old for us. A loose monkey throwing feces is hardly even newsworthy. It's SNAFU.
Posted by: rhmc on Jan. 30 2009,19:39

Quote (stevestory @ Jan. 29 2009,23:22)
Florida is deeply weird. Deeply. Like chromozomically, DNA-level weird. It's a part of who we are. We are deeply wrong. Malfunctional on an atomic level. But it makes sense to us. We understand why we do what we do. We understand why Fark.com has only one tag specific to a state, and we understand why that tag says Florida. We understand Adaptation. We don't even know what the big deal is. We understand Carl Hiassen and Dave Barry. It's just the same old, same old for us. A loose monkey throwing feces is hardly even newsworthy. It's SNAFU.
---------------------QUOTE-------------------


you people will never understand.
and if it's that bad, why do you allow your parents to move there?
situation normal, all florida up.  
us natives had to leave....those of us that are left.

or right.
Posted by: rhmc on Jan. 31 2009,09:49

perhaps i need a breathalizer attached to the keyboard.
what i though was humorous last night does not appear to be so in the light of sobriety.
Posted by: Lou FCD on Feb. 03 2009,19:08

< Proto-whales gave birth on land, not at sea > at Greg Laden's.

< The paper in PLoS ONE >.
Posted by: Henry J on Feb. 04 2009,13:45

Surely, but how long  did it take it's blow hole to move to the top of its head? Huh? Huh? :p
Posted by: Lou FCD on Feb. 04 2009,18:06

That's one < big-ass snake >.



---------------------QUOTE-------------------
Titanoboa's fossilised vertebra showed that it was a whopping 13 metres (42 feet) long. By comparison, the largest verifiable record for a living snake belongs to a 10-metre-long reticulated python, and that was probably a striking exception.  Large population surveys of reticulated pythons have failed to find individuals longer than 6 metres. By contrast, Head's team analysed vertebrae from eight different specimens of Titanoboa and found that all of them were roughly the same size. A length of 13 metres was fairly ordinary for this extraordinary serpent. Not quite Jormungandr, but amazing nonetheless.
---------------------QUOTE-------------------


Posted by: khan on Feb. 04 2009,19:01

Quote (Lou FCD @ Feb. 04 2009,19:06)
That's one < big-ass snake >.



---------------------QUOTE-------------------
Titanoboa's fossilised vertebra showed that it was a whopping 13 metres (42 feet) long. By comparison, the largest verifiable record for a living snake belongs to a 10-metre-long reticulated python, and that was probably a striking exception.  Large population surveys of reticulated pythons have failed to find individuals longer than 6 metres. By contrast, Head's team analysed vertebrae from eight different specimens of Titanoboa and found that all of them were roughly the same size. A length of 13 metres was fairly ordinary for this extraordinary serpent. Not quite Jormungandr, but amazing nonetheless.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


Gaack! ~40 foot snake.
Posted by: jeannot on Feb. 06 2009,03:23

Science has a special issue about speciation. Check it out.

< http://www.sciencemag.org/content/current/ >
Posted by: JLT on Feb. 09 2009,15:14

< Not Exactly Rocket Science > has a series of posts on evolutionary research. Nice reads so far.
Posted by: Erasmus, FCD on Feb. 12 2009,16:46

< http://www.answersingenesis.org/articles/am/v3/n4/cave-critters >

This is cutting edge research at AiG.

Wait.  No... go ahead, I won't spoil it.
Posted by: Lou FCD on Feb. 12 2009,19:43

< Ancient Virus Gave Wasps Their Sting >



---------------------QUOTE-------------------
By Rachel Zelkowitz

ScienceNOW Daily News

12 February 2009

There's no consent for these surrogate parents. Tens of thousands of wasp species lay their eggs inside caterpillars, injecting toxins that paralyze the hosts and allow their young to feast on the innards with impunity. Researchers have long wondered what exactly these toxins are and where they came from. The answers, a new genetic analysis reveals, have to do with a virus that infected wasps millions of years ago.
---------------------QUOTE-------------------





---------------------QUOTE-------------------
So in the new study, Drezen's team looked at DNA from wasp ovaries, in which the polydnaviruses are made. They analyzed DNA from three different wasp species and checked the sequences against those of known insect viruses. In one group of wasps, 22 genes matched those of an ancient family of viruses called nudiviruses, the researchers report tomorrow in Science. Further experiments showed that these genes code for key structural proteins in the wasps' polydnavirus toxins.
---------------------QUOTE-------------------


Posted by: Kristine on Feb. 12 2009,22:42

Quote (Erasmus @ FCD,Feb. 12 2009,16:46)
< http://www.answersingenesis.org/articles/am/v3/n4/cave-critters >

This is cutting edge research at AiG.

Wait.  No... go ahead, I won't spoil it.
---------------------QUOTE-------------------


Gaaaa! Quick, give me a < paper bag >!
*inhale* *exhale* *inhale* *exhale* *inhale* *exhale*

Whew. Curse you, Erasmus. That was a close one.  :angry:
Posted by: Timothy McDougald on Feb. 12 2009,23:09

Okay, since no one else has mentioned it, I'll step up. < J-dog's Genome has been decoded > - well 63% of it any way...but the rough draft is complete.
Posted by: Lou FCD on Feb. 15 2009,17:09

The Peppered Moth (with some help from lepidopterist Michael Majerus) < hands Intelligent Design Creationism Hoaxers their collective ass >.




---------------------QUOTE-------------------
Received: 29 August 2008  Accepted: 10 November 2008  Published online: 6 December 2008

Abstract  The case of industrial melanism in the peppered moth has been used as a teaching example of Darwinian natural selection in action for half a century. However, over the last decade, this case has come under attack from those who oppose Darwinian evolution. Here, the main elements of the case are outlined and the reasons that the peppered moth case became the most cited example of Darwinian evolution in action are described. Four categories of criticism of the case are then evaluated. Criticisms of experimental work in the 1950s that centered on lack of knowledge of the behavior and ecology of the moth, poor experimental procedure, or artificiality in experiments have been addressed in subsequent work. Some criticisms of the work are shown to be the result of lack of understanding of evolutionary genetics and ecological entomology on the part of the critics. Accusations of data fudging and scientific fraud in the case are found to be vacuous. The conclusion from this analysis of criticisms of the case is that industrial melanism in the peppered moth is still one of the clearest and most easily understood examples of Darwinian evolution in action and that it should be taught as such in biology classes.
---------------------QUOTE-------------------



h/t < Evolution: Education and Outreach >, < via RBH at The Thumb >.

A really interesting read.
Posted by: JLT on Feb. 17 2009,09:06

Polydnaviruses of Braconid Wasps Derive from an Ancestral Nudivirus
Science 13 February 2009: Vol. 323. no. 5916, pp. 926 - 930. DOI: 10.1126/science.1166788 < Link >

For some < background: Not merely bioweaponized, but mutualistic bioweaponized wasps (Mystery rays from outer space) >

The abstract:
 

---------------------QUOTE-------------------
Many species of parasitoid wasps inject polydnavirus particles in order to manipulate host defenses and development. Because the DNA packaged in these particles encodes almost no viral structural proteins, their relation to viruses has been debated. Characterization of complementary DNAs derived from braconid wasp ovaries identified genes encoding subunits of a viral RNA polymerase and structural components of polydnavirus particles related most closely to those of nudiviruses—a sister group of baculoviruses. The conservation of this viral machinery in different braconid wasp lineages sharing polydnaviruses suggests that parasitoid wasps incorporated a nudivirus-related genome into their own genetic material. We found that the nudiviral genes themselves are no longer packaged but are actively transcribed and produce particles used to deliver genes essential for successful parasitism in lepidopteran hosts.
---------------------QUOTE-------------------


And a bit from the article itself:
 

---------------------QUOTE-------------------
Comparative genomic studies have highlighted the role of symbiotic associations in evolution (1). Polydnaviruses (PDVs) are virus-like particles associated with wasp species that parasitize lepidopteran larvae. PDV particles are injected along with the eggs of the wasp into the lepidopteran larvae (or eggs) and express proteins that interfere with host immune defenses, development, and physiology; this interference enables wasp larvae to survive and develop within the host (2). Viral particle production occurs exclusively in a specialized region of the wasp ovaries (the calyx), and the vertically transmitted virus does not initiate particle production in the infected host tissues (3). The viral genome packaged in the particles is composed of multiple double-stranded DNA (dsDNA) circles, and it is surprising that it encodes almost no viral structural proteins, although it harbors immunosuppressive genes that are expressed in the host and are essential for successful parasitism (4, 5) (see PDV description at www.ictvonline.org). Because of this lack of genes coding for structural proteins, it has been debated whether PDVs are of viral origin or a "genetic secretion" of the wasp (6, 7).
PDVs are classified as either bracoviruses or ichnoviruses, when associated with braconid or ichneumonid wasps, respectively. Detailed phylogenetic studies have shown that the bracovirus-associated wasps form a monophyletic group known as the microgastroid complex (8), and it has been hypothesized that there has been a single integration event of a viral genome, as a provirus, in the microgastroid lineage. This predicts that vertically transmitted viral DNA may have been maintained because of its contribution to successful parasitism and that PDVs have contributed to the diversification of the microgastroid complex of at least 17,500 species (8).
---------------------QUOTE-------------------



And finally accompanying < commentary. >
Posted by: Steviepinhead on Feb. 17 2009,16:25

One of the local rags, the Seattle Times, did a write-up on < stickleback fish research > for the Sunday paper that came out closest in time to the 200th anno of Darwin's birthday...

Not bad, and a nice call-out for the researchers involved.
Posted by: dvunkannon on Feb. 18 2009,14:06

< A report of an omnivorous early dinosaur > has created two new gaps in the fossil record.

So when the lion lies down with the lamb, this guy can lie down in between, eat the lamb's lunch for the salad course, then eat both the lion and the lamb...
Posted by: JLT on Feb. 23 2009,15:54

This must be < the strangest fish > (YouTube video) I've seen so far:
< Macropinna microstoma: A deep-sea fish with a transparent head and tubular eyes > (press release by Monterey Bay Aquarium Research Institute).

The greenish globes inside the head are the eyes. The black spots at the front are the fish equivalent of "nostrils".

[edit]The video was removed from YouTube but can now be found at the press release link[/edit]
Posted by: J-Dog on Feb. 23 2009,16:37

Quote (JLT @ Feb. 23 2009,15:54)
This must be < the strangest fish > (YouTube video) I've seen so far:
< Macropinna microstoma: A deep-sea fish with a transparent head and tubular eyes > (press release by Monterey Bay Aquarium Research Institute).

The greenish globes inside the head are the eyes. The black spots at the front are the fish equivalent of "nostrils".
---------------------QUOTE-------------------


Thanks - that is a beautiful fish.  I think I will like it even more with tarter sauce! MMMMM!

KIDDING!  This is actully totally cool.
Posted by: carlsonjok on Feb. 23 2009,16:46

Quote (JLT @ Feb. 23 2009,15:54)
This must be < the strangest fish > (YouTube video) I've seen so far:
< Macropinna microstoma: A deep-sea fish with a transparent head and tubular eyes > (press release by Monterey Bay Aquarium Research Institute).

The greenish globes inside the head are the eyes. The black spots at the front are the fish equivalent of "nostrils".
---------------------QUOTE-------------------


ID predicted this.  Any good designer would have gone through at least a few different eye designs before finding the best solution.  It is clear that this is one of those eye prototypes.  

Take that Darweenies!!!!
Posted by: Henry J on Feb. 23 2009,17:25

I guess it's easy to see what that critter has on its mind...
Posted by: ppb on Mar. 02 2009,12:48

If you're not a Real Scientist ™, but are a scientist wanna-be like me, here's a web site that lets you analyze galaxy images and provide useful data for working astronomers.  It's called < Galaxy Zoo >, and it shows you pictures of galaxies and asks you a series of questions about them.  

It turns out that our brains do a better job of classifying galaxies than computers currently do.  Galaxy Zoo takes images from the robotic < Sloan Digital Sky Survey > and uses people's responses to sort the galaxies into categories for further study.  It is an easy and fun way to contribute to our growing knowledge of the universe.
Posted by: dvunkannon on Mar. 02 2009,22:15

I just joined < Folding@Home >. Now my spare CPU cycles fold proteins for scientific and medical research. Dang! Science is more addicting than TARD!

Everyone should do this. Certainly everyone with a PS3 should do this. Please join!
Posted by: bystander on Mar. 03 2009,15:26

Quote (JLT @ Feb. 24 2009,08:54)
This must be < the strangest fish > (YouTube video) I've seen so far:
< Macropinna microstoma: A deep-sea fish with a transparent head and tubular eyes > (press release by Monterey Bay Aquarium Research Institute).

The greenish globes inside the head are the eyes. The black spots at the front are the fish equivalent of "nostrils".

[edit]The video was removed from YouTube but can now be found at the press release link[/edit]
---------------------QUOTE-------------------


ID predicted this
Posted by: bystander on Mar. 03 2009,15:27

Quote (dvunkannon @ Feb. 19 2009,07:06)
< A report of an omnivorous early dinosaur > has created two new gaps in the fossil record.

So when the lion lies down with the lamb, this guy can lie down in between, eat the lamb's lunch for the salad course, then eat both the lion and the lamb...
---------------------QUOTE-------------------


ID Predicted this
Posted by: JohnW on Mar. 03 2009,15:40

Quote (bystander @ Mar. 03 2009,13:26)
ID predicted this
---------------------QUOTE-------------------


Quote (bystander @ Mar. 03 2009,13:27)
ID Predicted this
---------------------QUOTE-------------------


A mutation!  And since there is no such thing as a beneficial mutation, we have learned that "p" has more CSI than "P".
Posted by: ppb on Mar. 03 2009,15:45

Quote (bystander @ Mar. 03 2009,16:26)
 
Quote (JLT @ Feb. 24 2009,08:54)
This must be < the strangest fish > (YouTube video) I've seen so far:
< Macropinna microstoma: A deep-sea fish with a transparent head and tubular eyes > (press release by Monterey Bay Aquarium Research Institute).

The greenish globes inside the head are the eyes. The black spots at the front are the fish equivalent of "nostrils".

[edit]The video was removed from YouTube but can now be found at the press release link[/edit]
---------------------QUOTE-------------------


ID predicted this
---------------------QUOTE-------------------


Don't worry.  The < ICR > is on top of it.  :D
Posted by: Lou FCD on Mar. 03 2009,15:58

Quote (ppb @ Mar. 03 2009,16:45)
Quote (bystander @ Mar. 03 2009,16:26)
   
Quote (JLT @ Feb. 24 2009,08:54)
This must be < the strangest fish > (YouTube video) I've seen so far:
< Macropinna microstoma: A deep-sea fish with a transparent head and tubular eyes > (press release by Monterey Bay Aquarium Research Institute).

The greenish globes inside the head are the eyes. The black spots at the front are the fish equivalent of "nostrils".

[edit]The video was removed from YouTube but can now be found at the press release link[/edit]
---------------------QUOTE-------------------


ID predicted this
---------------------QUOTE-------------------


Don't worry.  The < ICR > is on top of it.  :D
---------------------QUOTE-------------------


This gave me a chuckle:



---------------------QUOTE-------------------

Ethical Use Policy

Nothing on our website may be reprinted or reproduced for other websites and media in whole or in part beyond these guidelines without obtaining permission from ICR. This applies to the website pages, content, graphics, audio and video, etc.

Guidelines:
1. You may print out pages in whole as evangelistic tools for churches, schools, etc. Our copyright notice and website address (© 2009 Institute for Creation Research. All Rights Reserved. < http://icr.org) > must be included with no exceptions.

2. You may quote up to 100 words,

(blah blah blah - snipped)

Example Footnotes:

[1] Henry Morris, Ph.D. Henry Morris, Ph.D. "Willingly Ignorant", Institute for Creation Research, < http://icr.org/article/491/ > (accessed July 29, 2008).

Thank you.

---------------------QUOTE-------------------



No, thank you.
Posted by: dvunkannon on Mar. 04 2009,11:58

< The Origin of Phagocytosis and Eukaryogenesis >

Or as Tommy Lee Jones said in Men In Black, "Eat me!"
Posted by: JLT on Mar. 04 2009,16:29

Quote (dvunkannon @ Mar. 04 2009,17:58)
< The Origin of Phagocytosis and Eukaryogenesis >

Or as Tommy Lee Jones said in Men In Black, "Eat me!"
---------------------QUOTE-------------------


< Damn it. >
Posted by: JLT on Mar. 04 2009,16:37

Quote (JLT @ Mar. 04 2009,22:29)
 
Quote (dvunkannon @ Mar. 04 2009,17:58)
< The Origin of Phagocytosis and Eukaryogenesis >

Or as Tommy Lee Jones said in Men In Black, "Eat me!"
---------------------QUOTE-------------------


< Damn it. > Didn't see that one.
---------------------QUOTE-------------------


Argh, I hit send too fast and now it won't let me edit my original post :(
Posted by: dnmlthr on Mar. 06 2009,13:01



---------------------QUOTE-------------------
ARGONNE, Illinois — In the basement of a nondescript building here at Argonne National Laboratory, nickel particles in a beaker are building themselves into magnetic snakes that may one day give clues about how life originally organized itself.

These chains of metal particles look so much like real, living animals, it is hard not to think of them as alive. (See exclusive video below.) But they are actually bits of metal that came together under the influence of a specially tuned magnetic field.
---------------------QUOTE-------------------



< Swim my darlings, swim! >
Posted by: Henry J on Mar. 06 2009,14:18



---------------------QUOTE-------------------
they can generate different types of systems. Besides the hunter, they've generated single- and multiple-snake systems, chains that stay still but pump water, and others that just shimmy in place.
---------------------QUOTE-------------------


Well, that answers Kristine's question - shimmies came before hips.  :p
Posted by: Reed on Mar. 06 2009,19:29

Carl Zimmer has a < nice post about viroids >.
Posted by: Lou FCD on Mar. 10 2009,15:51

< In PLoS ONE >:



---------------------QUOTE-------------------
Free-Ranging Macaque Mothers Exaggerate Tool-Using Behavior when Observed by Offspring

Abstract

The population-level use of tools has been reported in various animals. Nonetheless, how tool use might spread throughout a population is still an open question. In order to answer that, we observed the behavior of inserting human hair or human-hair-like material between their teeth as if they were using dental floss in a group of long-tailed macaques (Macaca fascicularis) in Thailand. The observation was undertaken by video-recording the tool-use of 7 adult females who were rearing 1-year-old infants, using the focal-animal-sampling method. When the data recorded were analyzed separately according to the presence/absence of the infant of the target animal in the target animal's proximity, the pattern of the tool-using action of long-tailed adult female macaques under our observation changed in the presence of the infant as compared with that in the absence of the infant so that the stream of tool-using action was punctuated by more pauses, repeated more often, and performed for a longer period during each bout in the presence of the infant. We interpret this as evidence for the possibility that they exaggerate their action in tool-using so as to facilitate the learning of the action by their own infants.
---------------------QUOTE-------------------


Posted by: Kristine on Mar. 10 2009,22:08

I can haz Ken Milleh at my skool! :)



---------------------QUOTE-------------------
Finding Darwin’s God: A Scientist’s Search for Common Ground Between God and Evolution

Dr. Kenneth Miller, Professor of Biology
Brown University

7:00 PM
Wednesday, April 8, 2009
Jeanne d’Arc Auditorium
College of St. Catherine
2004 Randolph Avenue
St. Paul, MN   55105

The lecture is free and open to the public, but tickets are required to assure seating.  Tickets are available from Lynne Linder in Mendel 112: lelinder@stkate.edu  or 651-690-6203.  Please direct any questions about Dr. Miller’s visit to Cindy Norton, Endowed Professor in the Sciences: cgnorton@stkate.edu  or 651-690-6631.

Dr. Miller’s visit is sponsored by the Myser Initiative on Catholic Identity, the Endowed Professorship in the Sciences, the President’s Office, and the Student Senate at the College of St. Catherine.
---------------------QUOTE-------------------


Posted by: Kristine on Mar. 10 2009,22:46

< First Woman > to Earn Computer Science Ph.D. in U.S. Wins Turing Award
 

---------------------QUOTE-------------------
Barbara Liskov, the first woman in the United States to earn a Ph.D. from a computer-science department and a professor at the Massachusetts Institute of Technology, has been awarded the A.M. Turing Award for 2008.

Ms. Liskov was chosen for the $250,000 prize, given by the Association for Computing Machinery, for her contributions to the computer programs that “form the infrastructure of our information-based society,” an association statement said.
---------------------QUOTE-------------------

:)
Posted by: midwifetoad on Mar. 11 2009,01:37

Yeah, but did she invent COBOL?
Posted by: dvunkannon on Mar. 11 2009,08:42

Quote (midwifetoad @ Mar. 11 2009,02:37)
Yeah, but did she invent COBOL?
---------------------QUOTE-------------------


That was Rear Admiral Dr. Grace Murray Hopper.
Posted by: dvunkannon on Mar. 11 2009,08:50

Quote (dnmlthr @ Mar. 06 2009,14:01)


---------------------QUOTE-------------------
ARGONNE, Illinois — In the basement of a nondescript building here at Argonne National Laboratory, nickel particles in a beaker are building themselves into magnetic snakes that may one day give clues about how life originally organized itself.

These chains of metal particles look so much like real, living animals, it is hard not to think of them as alive. (See exclusive video below.) But they are actually bits of metal that came together under the influence of a specially tuned magnetic field.
---------------------QUOTE-------------------



< Swim my darlings, swim! >
---------------------QUOTE-------------------




---------------------QUOTE-------------------
But when the magnetic field is tuned just right, something strange happens.
---------------------QUOTE-------------------



The creationist quotemine, appearing on UD in 10, 9,...
Posted by: Albatrossity2 on Mar. 11 2009,10:52

Highly conserved pathways used in yeast for mating factor export and in fruitflies for export of a chemoattractant molecule necessary for germ cell migration to the developing gonad.

< Ricardo and Lehman >, at NYU Med School, show that a membrane-bound transport protein, needed for export of a lipophilic (geranlygeranlylated) chemoattractant peptide in Drosophila, is related to another transport protein in yeast. In flies, the chemoattractant peptide is necessary for migration of germ cells to the presumptive gonad in developing embryos; in yeast the same system (probably using a different chemoattractant) allows production and secretion of lipophilic mating factors. The yeast protein can functionally substitute in fly embryos missing the regular fly protein. The authors conclude    

---------------------QUOTE-------------------
The use of a prenylated signal may thus be an ancient mechanism of cell communication. It is striking that this pathway is used in yeast and flies to facilitate the migration and adhesion of germ cells, the essential cells for reproduction.
---------------------QUOTE-------------------


More speculatively, the lipid synthesis pathway that produces the lipophilic isoprene-based moieties that are attached to these pheromones is the same pathway that produces the sterols, and thus the steroid hormones that are so important in sex determination in eukaryotes. This ancient pathway is probably derived from the < hopanoid > biosynthetic system in prokaryotes, the difference being that hopanoid synthesis can happen in anaerobic conditions, while sterol synthesis requires molecular oxygen. These lipids all have functions in assuring the integrity of biomembranes, but it appears that some of the products of the pathway were co-opted early on in the evolution of sex.
Posted by: Lou FCD on Mar. 11 2009,18:53

< Peking Man older than thought >, from Nature News:



---------------------QUOTE-------------------
Researchers have sifted the sands of time to show that Homo erectus  lived at China's most famous anthropology site at least 250,000 years earlier than was thought.

The new date means that this early human ancestor — the first lineage to migrate out of Africa — prospered in an earlier, colder climate, and its physical development in China matched that in Africa, where the species first evolved.

Discovered in 1918, the Zhoukoudian caves near Beijing have yielded surprises for nearly a century. Layers in the hillside cave system overlooking a river valley have produced some 17,000 stone artefacts and fossils of 50 H. erectus individuals, including six skulls. The species had a distinctive barrel-shaped torso and stood 145–180 centimetres tall, walking upright in a similar way to modern humans (Homo sapiens).

Now, work by a team of scientists based in China and the United States reveals that the Zhoukoudian cave fossils are about 770,000 years old — much more ancient than previous estimates of 230,000–500,000 years.
---------------------QUOTE-------------------


Posted by: Henry J on Mar. 11 2009,19:07

Yeasts are such fun gi's. And, they don't take up mush room.
Posted by: Timothy McDougald on Mar. 12 2009,21:30

From PLoS One:

< Identification of Coevolving Residues and Coevolution Potentials Emphasizing Structure, Bond Formation and Catalytic Coordination in Protein Evolution >

The abstract:



---------------------QUOTE-------------------
The structure and function of a protein is dependent on coordinated interactions between its residues. The selective pressures associated with a mutation at one site should therefore depend on the amino acid identity of interacting sites. Mutual information has previously been applied to multiple sequence alignments as a means of detecting coevolutionary interactions. Here, we introduce a refinement of the mutual information method that: 1) removes a significant, non-coevolutionary bias and 2) accounts for heteroscedasticity. Using a large, non-overlapping database of protein alignments, we demonstrate that predicted coevolving residue-pairs tend to lie in close physical proximity. We introduce coevolution potentials as a novel measure of the propensity for the 20 amino acids to pair amongst predicted coevolutionary interactions. Ionic, hydrogen, and disulfide bond-forming pairs exhibited the highest potentials. Finally, we demonstrate that pairs of catalytic residues have a significantly increased likelihood to be identified as coevolving. These correlations to distinct protein features verify the accuracy of our algorithm and are consistent with a model of coevolution in which selective pressures towards preserving residue interactions act to shape the mutational landscape of a protein by restricting the set of admissible neutral mutations.
---------------------QUOTE-------------------


Posted by: Erasmus, FCD on Mar. 14 2009,17:29

behind wall

i snipped some

Science 13 February 2009:
Vol. 323. no. 5916, pp. 880 - 881

Should Whales Be Culled to Increase Fishery Yield?
Leah R. Gerber, Lyne Morissette,Kristin Kaschner Daniel Pauly

 

---------------------QUOTE-------------------
Science and international politics play complicated roles in the global arena of whale conservation and the management of the resources of the world's oceans. The International Whaling Commission (IWC), charged with the global conservation of whales and the management of whaling, introduced a moratorium on commercial whaling in 1986 because of the widespread depletion of whale species and stocks. Despite a lack of scientific data to indicate that many whale stocks have recovered, every year a heated debate takes place at the IWC meeting about the future of commercial whaling. Recently, whaling countries have introduced a new argument for resuming whaling by blaming whale populations for the decline in commercial fish stocks.

Couched in terms of "ecosystem management," whaling countries, including Japan, advocate the culling of whales as a solution to recover overexploited fish stocks and to increase fishery yield (1, 2). Some developing countries, which may benefit economically and politically by supporting pro-whaling nations at IWC (3-7), have also supported the "whales-eat-fish" assertion. The Caribbean-driven St. Kitts Declaration at the 58th Annual Meeting of the IWC stated: "scientific research has shown that whales consume huge quantities of fish making the issue a matter of food security for coastal nations" (6). This issue was also claimed to be one of global concern at a 2008 symposium of IWC members in the Northwest Africa region (8).
---------------------QUOTE-------------------





---------------------QUOTE-------------------
The rationale for whaling as the solution to depleted fisheries has been questioned by many in the scientific community in light of documented overfishing in oceans globally (15), a lack of spatially explicit overlap of resource exploitation between fisheries and whales (2), and the unpredictable consequences of culling (16, 17). Based on stomach content analyses of whales caught during the Japanese scientific whaling program and available data on whale abundance, Japanese scientists estimate that whales consume several times as much food as the combined global fisheries catch in recent years (18). However, the methodology used by Japanese researchers to support their claim that whales' consumption of fish is an important component of fish declines has been repeatedly criticized (19-22). Although these discussions have been insightful, they have not stimulated movement within the IWC to break the current deadlock.

One of the obstacles in scientific studies of whales is that there are few data and models available to inform policy discussions. This is particularly true in the tropical waters bordering many of the developing countries that support the resumption of commercial whaling, although these areas are known to be primarily breeding (not feeding) grounds for baleen whales (23-27). We conducted an extensive literature search to compile and make use of all available sources of local data to provide a scientific starting point to the discussion (9). We also sought to actively involve scientific advisers of delegates who support Japan's position at the IWC meetings and to foster regional collaboration and active dissemination of our findings to inform discussions in local communities among scientists, managers, and other local experts (e.g., 2008 "Whales-Eat-Fish" regional workshops held in Senegal and Barbados, < link >
---------------------QUOTE-------------------



 

---------------------QUOTE-------------------
Using data available from the literature, and e.g., the Sea Around Us Project (www.seaaroundus.org) and obtained during our regional stakeholder workshops, we developed ecosystem models to examine the potential increase in the biomass of commercially important fish stocks that would result from a reduction in whale abundance in the Northwest African and Caribbean ecosystems (9). Any discussion about the interactions between whales and fisheries must be considered in an ecosystem context, which allows investigation of the complex indirect effects of trophic relationships that would otherwise be very difficult to study. Although the IWC Scientific Committee maintains that "Ecosystem modelling cannot be used to predict interactions between marine mammals and fisheries" (28-30), other studies provide evidence to the contrary that mammals and fisheries can be studied with ecosystem models (31-32).

Our approach to addressing concerns about scientific uncertainty was to conduct extensive sensitivity analyses to explore the results emerging from a range of assumptions about ecosystem structure and the quality of our input data (table S2). For a wide range of assumptions about whale abundance, feeding rates, and fish biomass, even a complete eradication of baleen whales in these tropical areas does not lead to any appreciable increase in the biomass of commercially exploited fish. In contrast, just small changes in fishing rates lead to considerable increases in fish biomass *(see figure, p. 880). We found little overlap between fisheries and whale consumption in terms of prey types, and we also found that fisheries remove far more fish biomass than whales consume (9). Moreover, because some whale prey species compete with commercially targeted fish for plankton and prey occupying a lower trophic level in the food web, it is possible that removing whales from marine ecosystems could result in fewer fish available to the fisheries (9).
---------------------QUOTE-------------------



 

---------------------QUOTE-------------------
Here, we offer a set of recommendations for rational decision-making by effectively applying ecosystem management concepts to managing whales.

First, the question of "who is eating our fish" should be considered in a larger context (with respect to foreign fleets, ecosystem collapses, and climate change). Indirect social and economic benefits of whales in tropical ecosystems [e.g., tourism (36, 37)] should also be taken into account.

Second, despite complicated politics, science should be an integral component of the discussions about managing whale and fishery interactions. An effort must be made to actively engage scientists and managers from countries that support Japan's claims (3-5) to help them investigate this issue within an ecosystem context in their own regions. In many cases, fisheries officers in tropical areas, such as the Caribbean, do not necessarily believe the whales-eat-fish arguments. Rather, the arguments are endorsed for reasons related to their aid relationship with Japan, especially in the fisheries sector.

Third, ecosystem modeling tools should be developed in order to bring the best available science to decision-making about the conservation of whales. Research aimed at filling the gaps on key scientific parameters (e.g., abundance, consumption rates, and diet information for key marine organisms) should be supported.

Finally, it is important to recognize that the goal of ecosystem-based management is to manage the whole system for long-term sustainability rather than modifying particular trophic levels in an attempt to maximize fishery yield (38). Broad-based, ecosystem management can and should increase an ecosystem's value so that it can provide benefits for future generations.
---------------------QUOTE-------------------

[/quote]

interesting problem.  like shooting wolves, except they swim  and poop and eat and sing over hundreds of thousands of square miles.  

you are usually on safe ground to be skeptical of top down regulation of some large population or assemblage but following Erasmus' Rule**  there will always be exceptions.  in this case erring on the side of caution seems prudent, despite the creationist like mewling about social and economic persecution by those big bad guys (here the bad guys are different, ie not the EAC necessarily, but it's all part of the dichotomy of these sorts of mythical narratives to have your emmanual goldstein or jonas brothers)

surely in such a large heterogeneous contingent set of biologies referenced in the claim "whales deplete fisheries" these nonlinear relationships exist are at present unpredictable.  



---------------------QUOTE-------------------
Could whales have maintained a high abundance of krill?
Willis J  2007 EVOLUTIONARY ECOLOGY RESEARCH    Volume: 9    Issue: 4    Pages: 651-662      

---------------------QUOTE-------------------
Abstract: Question: Several million large whales were killed between 1900 and 1970. All these whales preyed on krill (Euphausia superba). Why has krill population abundance declined after the elimination of their primary predator?

Hypothesis: Krill have changed their behaviour due to the absence of whales and this change in behaviour has resulted in a decrease in krill abundance.

Methods: I reproduced a computer model of krill life history. I then extended the model as an individual-based model to show the effects of habitat choice on individual lifetime reproductive success and abundance.

Conclusions: In the context of our current understanding of krill physiology, predator-invoked behaviour may lead to increased population abundance and, without the predator, natural selection may favour behaviour that would lead to lower abundance. This reverses the predictions of mass balance ecosystem models.
---------------------QUOTE-------------------


---------------------QUOTE-------------------



whale wars?

hey zero as i am typing this there are whales on my TV on some pacific life commercial during the PAC 10 game.  spoooooky


*my bolding

**Shit varies, it matters, sometimes.
Posted by: Henry J on Mar. 14 2009,20:06

This brings to mind one of the Star Trek movies.

Henry
Posted by: Lou FCD on Mar. 15 2009,16:37

Sweet counterpoint to Behe's drivel at UNCW a few weeks ago:

< Darwin's Legacy 2009 Conference >



---------------------QUOTE-------------------
Darwin's Legacy: Evolution's Impact on Science and Culture
March 19-21, 2009

UNCW's Evolution Learning Community will be hosting "Darwin's Legacy: Evolution's Impact on Science and Culture," a multidisciplinary student conference on March 19-21, 2009.

The conference will be a unique opportunity for undergraduate and graduate students in the natural sciences, social sciences, humanities and arts who are conducting research or creative endeavors related to evolution to present their research, investigate graduate study opportunities, network, enhance their resumes, and enrich the body of knowledge surrounding evolution.

With the exception of the four keynote speakers, all presentations will be made by students.

Keynote Speakers:

Dr. David Buss, University of Texas

Dr. Peter Carruthers, University of Maryland

Dr. David Mindell, California Academy of Sciences

Dr. Kevin Padian, University of California, Berkeley
---------------------QUOTE-------------------


Posted by: khan on Mar. 15 2009,19:42

< Indonesia's psychedelic fish >

A funky, psychedelic fish that bounces on the ocean floor like a rubber ball has been classified as a new species, a scientific journal reported.
Posted by: dvunkannon on Mar. 16 2009,18:11

< Isaac Asimov Memorial Debate >

This is sig-worthy:
 

---------------------QUOTE-------------------
The whole debacle has painted a new picture of how planetary scientists operate.

"I think this has been one of the more disappointing episodes for science with regard to the IAU," Stern said. "Now school kids see science as voting, and that's not the best way to do science."

"I like to call it the Irrelevant Astronomical Union," Stern added. He summed up the messiness of the scientific process as being "like cats herding themselves."

---------------------QUOTE-------------------


Posted by: Henry J on Mar. 17 2009,14:41

But, the status of Pluto is a question of terminology, not of basic facts. What to use as official terminology is something that can be decided by a vote.

I wonder if geologists have ever held a debate about whether Europe and Asia are two continents, or one.  :p

Henry
Posted by: midwifetoad on Mar. 17 2009,14:51

Quote (Henry J @ Mar. 17 2009,14:41)
But, the status of Pluto is a question of terminology, not of basic facts. What to use as official terminology is something that can be decided by a vote.

I wonder if geologists have ever held a debate about whether Europe and Asia are two continents, or one.  :p

Henry
---------------------QUOTE-------------------


More a matter of when than whether.
Posted by: Henry J on Mar. 17 2009,15:15

When? Does that mean they used to be two, but collided in their Urals?
Posted by: Timothy McDougald on Mar. 18 2009,19:23

This is interesting. < Positive Darwinian selection and the birth of an olfactory receptor clade in teleosts >. Here is the abstract:



---------------------QUOTE-------------------
Trace amine-associated receptors (TAARs) in mammals recently have been shown to function as olfactory receptors. We have delineated the taar gene family in jawless, cartilaginous, and bony fish (zero, 2, and >100 genes, respectively). We conclude that taar genes are evolutionary much younger than the related OR and ORA/V1R olfactory receptor families, which are present already in lamprey, a jawless vertebrate. The 2 cartilaginous fish genes appear to be ancestral for 2 taar classes, each with mammalian and bony fish (teleost) representatives. Unexpectedly, a whole new clade, class III, of taar genes originated even later, within the teleost lineage. Taar genes from all 3 classes are expressed in subsets of zebrafish olfactory receptor neurons, supporting their function as olfactory receptors. The highly conserved TAAR1 (shark, mammalian, and teleost orthologs) is not expressed in the olfactory epithelium and may constitute the sole remnant of a primordial, nonolfactory function of this family. Class III comprises three-fourths of all teleost taar genes and is characterized by the complete loss of the aminergic ligand-binding motif, stringently conserved in the other 2 classes. Two independent intron gains in class III taar genes represent extraordinary evolutionary dynamics, considering the virtual absence of intron gains during vertebrate evolution. The dN/dS analysis suggests both minimal global negative selection and an unparalleled degree of local positive selection as another hallmark of class III genes. The accelerated evolution of class III teleost taar genes conceivably might mark the birth of another olfactory receptor gene family.
---------------------QUOTE-------------------


Posted by: rhmc on Mar. 19 2009,17:51

not sure if these qualify as "science" but...  


Bill Would Allow Texas School to Grant Master's Degree in Science for Creationism


A Texas legislator is waging a war of biblical proportions against the science and education communities in the Lone Star State as he fights for a bill that would allow a private school that teaches creationism to grant a Master of Science degree in the subject.

State Rep. Leo Berman (R-Tyler) proposed House Bill 2800 when he learned that The Institute for Creation Research (ICR), a private institution that specializes in the education and research of biblical creationism, was not able to receive a certificate of authority from Texas' Higher Education Coordinating Board to grant Master of Science degrees.

Berman's bill would allow private, non-profit educational institutions to be exempt from the board’s authority.

“If you don’t take any federal funds, if you don’t take any state funds, you can do a lot more than some business that does take state funding or federal funding,” Berman says. “Why should you be regulated if you don’t take any state or federal funding?”

HB 2800 does not specifically name ICR; it would allow any institution that meets its criteria to be exempt from the board's authority. But Berman says ICR was the inspiration for the bill because he feels creationism is as scientific as evolution and should be granted equal weight in the educational community....

more here:

< http://www.foxnews.com/story/0,2933,509719,00.html >


and then we have:

Creation Museum: Darwin Not Entirely Wrong
Thursday, March 19, 2009  

LOUISVILLE, Ky. —  A controversial Kentucky museum that trumpets the Bible story of creation and rejects evolution is making room for an odd guest: Charles Darwin.

A new exhibit at the Answers in Genesis Creation Museum argues that natural selection — Darwin's explanation for how species develop new traits over time — can coexist with the creationist assertion that all living things were created by God just a few thousand years ago.

"We wanted to show people that creationists believe in natural selection," said Ken Ham, founder of the Christian ministry Answers in Genesis and frequent Darwin critic...

more here:

< http://www.foxnews.com/story/0,2933,509800,00.html >
Posted by: Richardthughes on Mar. 22 2009,23:30

< http://www.physorg.com/news156767725.html >

Brain on the edge of chaos..
Posted by: Arden Chatfield on Mar. 22 2009,23:45

Quote (rhmc @ Mar. 19 2009,15:51)
“Why should you be regulated if you don’t take any state or federal funding?”
---------------------QUOTE-------------------


By that reasoning, if I owe taxes every April 15th and don't work for the government, I should be able to have people killed and drive as fast as I want.
Posted by: Erasmus, FCD on Mar. 24 2009,21:04

See how long < this lasts >.



---------------------QUOTE-------------------
WASHINGTON - Dozens of mountaintop coal-mining permits are being put on hold until the projects’ impacts on streams and wetlands can be reviewed, the Environmental Protection Agency said Tuesday.

Announced by EPA Administrator Lisa Jackson, the move targets a controversial practice by coal mining companies that blasts away whole peaks and sends mining waste into streams and wetlands. It does not apply to existing mines, but to requests for new permits, a number estimated to be as high as 200.

EPA spokeswoman Adora Andy said the agency does not expect problems with the overwhelming majority of permits.
Story continues below ?advertisement | your ad here

The EPA also urged the Army Corps of Engineers not to issue permits for two new projects unless their impacts were reduced. The projects would allow companies to fill thousands of feet of streams with mining waste at two sites in West Virginia and Kentucky.

"The two letters reflect EPA’s considerable concern regarding the environmental impact these projects would have on fragile habitats and streams," Jackson said in a statement.

"I have directed the agency to review other mining permit requests" as well, she added. "EPA will use the best science and follow the letter of the law in ensuring we are protecting our environment."

The EPA said the letters stated that the projects "would likely cause water quality problems in streams below the mines, would cause significant degradation to streams buried by mining activities, and that proposed steps to offset these impacts are inadequate."

The agency said it had also "recommended specific actions be taken to further avoid and reduce these harmful impacts and to improve mitigation."

The EPA said it would be actively involved in the review of the long list of permits awaiting approval by the Corps, a signal that the agency under the Obama administration will exercise its oversight. The EPA has the authority to review and veto any permit issued by the Corps under the Clean Water Act, but under the Bush administration it did that rarely.

"If the EPA didn't step in and do something now, all those permits would go forward," said Joe Lovett, executive director for the Appalachian Center for the Economy and the Environment. "There are permits that will bury 200 miles of streams pending before the Corps," he claimed.
---------------------QUOTE-------------------



Bolding mine.  This is the bullshit clause.  Inasmuch as science can provide "should" or "ought" directives and imperatives, there is absolutely no justification for this type of resource destruction.  I personally do not hold the view that science gives us the means to answer those types of questions, but I do hold the view that there is no possible conceivable justification for this sort of mechanized resource extraction under any possible scenario.  Global economies certainly don't provide justification.

Recent studies have documented massive shifts in aquatic insect assemblages downstream of MTR and surface mines.  This is a big "No Shit" to anyone paying attention, but the interface between University Science and Corporate Resource Extraction is a nebulous incestuous nepotist affair.  At these same universities documenting the unimaginable community and ecosystem level effects of MTR, you have individuals attempting to find technological means to continue MTR that alleviate the concerns raised by ecologists and conservationists.

I recall recently a researcher nearby at the university of tennessee was taking money from coal companies to plant hybrid blight-resistant chestnut trees on MTR spoil.  Of course it was a failure, but the coal companies thumped their chests about their green initiative.  See, they are doing the right thing, etc etc.  What a bunch of soulless lackwit antihuman traitorious luchre worshippers.  any self respecting moral and ethical biologist would never take money for such a project.

I do wonder what Obama has in mind.  i doubt he has anything in mind, but this could throw the wrench in the works for a lot of rich powerful people.  as much as i love to see it all hit the fan, I fear the retributions on the next cycle.  MTR sucks, and I am trying to be optimistic, but given the history of union busting, ponzi schemes, mob incitement and callous disregard for the law and human dignity exhibited by King Coal it seems that our people are in for some more trouble.
Posted by: rhmc on Mar. 25 2009,17:45

Quote (Arden Chatfield @ Mar. 23 2009,00:45)
Quote (rhmc @ Mar. 19 2009,15:51)
“Why should you be regulated if you don’t take any state or federal funding?”
---------------------QUOTE-------------------


By that reasoning, if I owe taxes every April 15th and don't work for the government, I should be able to have people killed and drive as fast as I want.
---------------------QUOTE-------------------


sounds good to me.  now where did i leave that list...
Posted by: Timothy McDougald on Mar. 26 2009,22:00

Based on some of the posts I have read at AtBC over the years I am convinced that quite a few of you will find this interesting. :p  It's from December of 2008, so it's little old, but I just discovered it.



< Phytochemical and genetic analyses of ancient cannabis from Central Asia >

Here is the abstract:



---------------------QUOTE-------------------
The Yanghai Tombs near Turpan, Xinjiang-Uighur Autonomous Region, China have recently been excavated to reveal the 2700-year-old grave of a Caucasoid shaman whose accoutrements included a large cache of cannabis, superbly preserved by climatic and burial conditions. A multidisciplinary international team demonstrated through botanical examination, phytochemical investigation, and genetic deoxyribonucleic acid analysis by polymerase chain reaction that this material contained tetrahydrocannabinol, the psychoactive component of cannabis, its oxidative degradation product, cannabinol, other metabolites, and its synthetic enzyme, tetrahydrocannabinolic acid synthase, as well as a novel genetic variant with two single nucleotide polymorphisms. The cannabis was presumably employed by this culture as a medicinal or psychoactive agent, or an aid to divination. To our knowledge, these investigations provide the oldest documentation of cannabis as a pharmacologically active agent, and contribute to the medical and archaeological record of this pre-Silk Road culture.
---------------------QUOTE-------------------


Posted by: Henry J on Mar. 27 2009,13:31

[not me]
But how do you knows what those people thousands off year ago did with that stuff? Were you THERE?? !!!1111!one!
[/not me]
Posted by: Richardthughes on April 06 2009,10:22

Privileged Planet? - notsomuch:


< http://www.technologyreview.com/blog/arxiv/23309/ >
Posted by: J-Dog on April 06 2009,11:55

Quote (Richardthughes @ April 06 2009,10:22)
Privileged Planet? - notsomuch:


< http://www.technologyreview.com/blog/arxiv/23309/ >
---------------------QUOTE-------------------


Poor , poor ID :(

After all this time, they get expelled by an old friend - thermodynamics.

RIP Dr. Gonzales... Baya con Dios.
Posted by: Richardthughes on April 08 2009,09:34

I'm sure this is ID research, somehow:

< http://www.sciencedaily.com/releases/2009/04/090402143457.htm >
Posted by: ppb on April 08 2009,10:57

Quote (Richardthughes @ April 08 2009,10:34)
I'm sure this is ID research, somehow:

< http://www.sciencedaily.com/releases/2009/04/090402143457.htm >
---------------------QUOTE-------------------


If it spits out 42 for an answer we could be certain that Slarty Bartfast is the Designer.
Posted by: midwifetoad on April 08 2009,12:42

< http://www.sciencealert.com.au/news/20090604-18994.html >



---------------------QUOTE-------------------
Murdoch University scientists have developed an improved theory of evolution – a groundbreaking hypothesis which finally reconciles evolutionary theory with the fossil record.
---------------------QUOTE-------------------



And the author isn't I. Lirpa, although he may be related to Mi Tu.
Posted by: dvunkannon on April 08 2009,14:47

Quote (J-Dog @ April 06 2009,12:55)
Quote (Richardthughes @ April 06 2009,10:22)
Privileged Planet? - notsomuch:


< http://www.technologyreview.com/blog/arxiv/23309/ >
---------------------QUOTE-------------------


Poor , poor ID :(

After all this time, they get expelled by an old friend - thermodynamics.

RIP Dr. Gonzales... Baya con Dios.
---------------------QUOTE-------------------


I thought they had gone back and done more sensitive analysis of Miller's results and found all 20 amino acids. This paper still says only 10.
Posted by: midwifetoad on April 08 2009,15:18

I think the others drop off a cliff in quantity.
Posted by: Schroedinger's Dog on April 15 2009,03:56

He's done it!!!

< NASA to name ISS treadmill after Colbert >
Posted by: Richardthughes on April 16 2009,09:39

Brace for ID spin:

< http://seedmagazine.com/content/print/the_body_politic/ >
Posted by: Erasmus, FCD on April 16 2009,11:07



---------------------QUOTE-------------------
The deep symbiosis between bacteria and their human hosts is forcing scientists to ask: Are we organisms or living ecosystems?
---------------------QUOTE-------------------



as opposed to dead ecosystems?

yeah they're forced to ask that.
Posted by: ppb on April 22 2009,13:31

Interesting new fossil discovered that fills in some of the detail in the transition from land animals to ocean dwelling mammals like seals and walruses.  It's been named Puijila darwini.  Puijila means "young sea mammal" in the Inuktitut language spoken where the fossil was found in the far north of Canada.  You know where darwini comes from.  Read all about it here:

< http://nature.ca/puijila/index_e.cfm >

I just heard Neil Shubin talk about < Tiktaalik roseae > last week.  This is sort of Tiktallik in reverse!

ETA: I've taken a closer look at their web site, and it is really nicely done.  They have a cool interactive picture of the skull that lets you rotate it while reading about the skull's pinniped-like characteristics.
Posted by: rhmc on April 22 2009,19:50

molly mating mystery

Researchers have proposed an explanation for how three species of tiny fish manage to coexist despite having seemingly incompatible modes of reproduction, according to a study published in Oikos last week.

The Amazon molly (Poecilia formosa) is an asexually reproducing species in which females produce only female clones via parthenogenesis. To initiate embryogenesis, however, Amazon mollies require sperm from the males of one of two closely related, but sexually reproducing, species sharing their habitats in southern Texas and northern Mexico -- the sailfin molly (Poecilia latipinna) or the shortfin molly (Poecilia mexicana).

Ecological theory predicts that such species living as a complex in nature are doomed because population growth in the asexual species should overwhelm the metapopulation with females. That in turn would lead to a shortage of sperm and a collapse of the entire system. The ecological model proposed in the study suggests that with the right mating behavior in males, the arrangement could work.

"It's an interesting paper in terms of highlighting this problem," Laurence Loewe, a University of Edinburgh evolutionary biologist, told The Scientist. "But I'm not so sure they solved it."

While the model may not completely answer the question of how the mollies defy ecological theory and manage to coexist, it is one of the few solutions yet proposed.

Hanna Kokko, an evolutionary ecologist at Helsinki University in Finland who led the research, based her mathematical model on the idea that if male members of the two sexual species are able to discriminate between females of their own species and females of the asexual species, the complex has a better chance of persisting. Males would mate with their own females more often than providing sperm for their asexual cousins. The model additionally suggests that if males are also relatively efficient -- that is, they can continue servicing both sexual and a few asexual females as population numbers rise -- the three species should be able to get along.

And get along they do, though the system does collapse, with molly species going locally extinct on the average of once every four years, Kokko told The Scientist. Populations rebuild themselves, though, and the asexually and sexually reproducing species continue their mate sharing, an arrangement that has persisted for as long as 25,000 years. The Amazon molly, likely the result of a hybridization event between its two host species, has already existed for about as long as an asexual species is predicted to hang around, Kokko explained. Asexual species should theoretically accumulate deleterious mutations at a much faster rate than sexually reproducing species due to a lack of gene recombination.

Another important factor in keeping the species complex going may be how the fish species share their watery habitats. Spatially complex structures, such as tree limbs and rock bottoms, may provide molly species with the opportunity to divide up their local habitats and limit interaction between males and asexual females. Kokko said that although her current model does not account for this spatial partitioning, she and her colleagues did address that aspect in a paper published last year in Proceedings of the Royal Society B. That model suggested that the coexistence of asexual and sexual mollies could be explained by habitat partitioning alone.

But all three factors -- male discrimination, male efficiency, and spatial factors -- likely play a role, according to Kokko. "My gut feeling is that the spatial aspect could actually prove quite important," she said. The two sexual species also have broader home ranges, one stretching northward into the US and the other southward into Central America, where the asexual species do not occur. "That would mean there would be a reservoir of sexual species that the asexuals could not endanger," Loewe said.




< http://www.the-scientist.com/blog/display/55611/ >
Posted by: dvunkannon on April 24 2009,13:05

< Titanium Infused Spider SIlk >

Sometimes I read something like this, and I think Kurzweil is right, the Singularity is around the corner. Other times, I just giggle about living in the future.
Posted by: Richardthughes on April 24 2009,13:43

Quote (dvunkannon @ April 24 2009,13:05)
< Titanium Infused Spider SIlk >

Sometimes I read something like this, and I think Kurzweil is right, the Singularity is around the corner. Other times, I just giggle about living in the future.
---------------------QUOTE-------------------


Probably better to cite Venge?
Posted by: rhmc on April 29 2009,18:02

"Chemical 'caterpillar' points to electronics-free robots

A chemical gel that can walk like an inchworm, or looper caterpillar has been demonstrated in a Japanese robotics lab.

The video above shows the material in action. It was created in the Shuji Hashimoto applied physics laboratory at Waseda University, Tokyo.

Shingo Maeda and colleagues made the colour-changing, motile gel by combining polymers that change in size depending on their chemical environment. This is based on an oscillating chemical reaction called the Belousov–Zhabotinsky (BZ) reaction. The result is an autonomous material that moves without electronic stimulation.

The BZ reaction is one of a class of chemical systems in which the concentration of one or more compounds periodically increases and decreases. As well as producing stunning patterns (video), it can even be used to perform calculations using a dish containing the pulsing patterns as a chemical brain...."

< http://www.newscientist.com/article....ts.html >
Posted by: ppb on April 30 2009,08:54

Watched the PBS Nova program called < "Alien From Earth" > about Homo floresiensis, the "hobbit" fossils found in Indonesia.  The debate rages on about whether they are a separate species, but further research seems to support this.  Comparison with other human ancestors raises the possibility that H. floresiensis may be descended from australopithecines (like Lucy) rather than Homo erectus as earlier speculated.  If so, this is the first evidence of migration out of Africa of anything pre H. erectus.

There is a good article on this in < The New York Times >.
Posted by: mitschlag on April 30 2009,15:46

Intelligent machines!

Two papers in Sciencemag.org, April 3, 2009:

Page 81 describes an algorithm that derives fundamental equations of motion from raw data (e.g., Hamiltonian and Lagrange equations)

Page 85 describes a robot that conducted experiments on yeast metabolism with little human intervention, then  reasoned about its results and planned appropriate next experiments. The robot, Adam, identified orphan enzymes that were confirmed (by humans) to function in yeast metabolism, solving problems that have baffled humans for the past 50 years.

The Perspective on p 43 is also worth reading, if you have access.
Posted by: dvunkannon on April 30 2009,15:46

Quote (Richardthughes @ April 24 2009,14:43)
Quote (dvunkannon @ April 24 2009,13:05)
< Titanium Infused Spider SIlk >

Sometimes I read something like this, and I think Kurzweil is right, the Singularity is around the corner. Other times, I just giggle about living in the future.
---------------------QUOTE-------------------


Probably better to cite Venge?
---------------------QUOTE-------------------


I love Marooned In Real Time! I have a friend who owns the oil painting used for the original hardcover cover art. Is there an SF thread on this board?

I think more people associate the Singularity with Kurzweil than Vinge.
Posted by: Reed on May 02 2009,23:43

Interesting bit on the evolution design of capsaicin in chili peppers < http://www.smithsonianmag.com/science....rs.html >
Posted by: jeannot on May 09 2009,17:49

This is hardly a breakthrough but we've got a paper published in PNAS this week about speciation, more specifically the blurry frontier between what we may call subspecies and species. Of course, there's no strict boundary, as well as there is no qualitative difference between micro- and macroevolution, if this is relevant to the anti-evolution debate.

The work is done on an aphid species complex. Feel free to give you opinion on this. Full access requires subscription, but I can provide a pdf for those interested.

< http://www.pnas.org/content/106/18/7495.abstract >
Posted by: Timothy McDougald on May 09 2009,21:45

Quote (jeannot @ May 09 2009,17:49)
This is hardly a breakthrough but we've got a paper published in PNAS this week about speciation, more specifically the blurry frontier between what we may call subspecies and species. Of course, there's no strict boundary, as well as there is no qualitative difference between micro- and macroevolution, if this is relevant to the anti-evolution debate.

The work is done on an aphid species complex. Feel free to give you opinion on this. Full access requires subscription, but I can provide a pdf for those interested.

< http://www.pnas.org/content/106/18/7495.abstract >
---------------------QUOTE-------------------


I'd like a copy please. You can send it to afarensis1@sbcglobal.net
Posted by: rhmc on May 14 2009,20:34

Chemists see first building blocks to life on Earth

< http://news.yahoo.com/s....3210508 >

PARIS (AFP) – British scientists said on Wednesday that they had figured out key steps in the process by which life on Earth may have emerged from a seething soup of simple chemicals.

Genetic information in living organisms today is held in deoxyribonucleic acid (DNA), the famous "double helix" molecule of sugar, phosphate and a base.

But DNA is too sophisticated to have popped up in an instant, and one avenue of thought says its single-stranded cousin, ribonucleic acid, or RNA, came first.

RNA plays a key role in making proteins and, in viruses, is used to store genetic code.

It is chemically similar to DNA but is simpler and tougher in structure, and thus looks like a good candidate for Earth's first information-coding nucleic acid.

But for all its allure, the "RNA first" theory has run into practical problems.

Its three ingredients -- the base, ribose sugar and phosphate -- must have formed separately and then combined to form the molecule, according to conventional thinking.

Critics, though, say that RNA, while somewhat simpler than DNA, is still a complex molecule and could not have been assembled spontaneously.

These doubters have been comforted by the failure to find any feasible chain of chemical events to explain how the three components all came together.

But a paper published in the British journal Nature by University of Manchester chemists puts forward a different explanation.

The team, led by Professor John Sutherland, venture that an RNA-like synthesis took place through a series of chemical reactions and an important intermediate substance.

Their lab model uses starting materials and environmental conditions that are believed to have been around in early Earth and are also used in the standard "RNA first" scenario.

Their theory starts with a simple sugar called glycolaldehyde, which reacts with cyanmide (a compound of cyanide and ammonia) and phosphate to produce an intermediate compound called 2-aminooxazole.

Gentle warming from the Sun and cooling at night help purify the 2-aminooxazole, turning it into a plentiful precursor which contributes the sugar and base portions of the new ribonucleotide molecule.

The presence of phosphate and ultraviolet light from the Sun complete the synthesis.

In a commentary also published by Nature, US molecular biologist Jack Szostak hailed the research as an elegant explanation as to why the sugar and base would not have to form separately before forming the new molecule.

"It will stand for years as one of the great advances in prebiotic chemistry," the term for the study of the chemical processes that led to life on Earth, he enthused.

Opinions vary as to when the first organisms appeared on Earth.

One estimate, based on fossilised mats of bacteria found in Australia, is that this happened around 3.8 billion years ago, around 700 million years after the planet was formed.
Posted by: Erasmus, FCD on May 14 2009,21:41

Quote (jeannot @ May 09 2009,18:49)
This is hardly a breakthrough but we've got a paper published in PNAS this week about speciation, more specifically the blurry frontier between what we may call subspecies and species. Of course, there's no strict boundary, as well as there is no qualitative difference between micro- and macroevolution, if this is relevant to the anti-evolution debate.

The work is done on an aphid species complex. Feel free to give you opinion on this. Full access requires subscription, but I can provide a pdf for those interested.

< http://www.pnas.org/content/106/18/7495.abstract >
---------------------QUOTE-------------------


pffft its still an aphid.  wake me up when one turns into a blue whale or summtin.  evilutionists

hey jean i noticed that at least some of those plants are tag-alongs with humans (clover, afalfa, peas, vetch)  i didn't recognize some of the others but i wouldn't.  

wondering if you had any idea of what the ancestral host preference mighta been?  i'm not swift enough to figure out if the biotypes that can switch hosts prefer hosts that have been strongly domesticated.  would make sense that selection for being tasty for people or livestock, if it reduces any defense complexes, might make you tastier for insects.

in one fell swoop you have generated more science than the entire ID movement in 2008 AND 2009.  Cheers!
Posted by: Henry J on May 14 2009,22:27

So we came from ammonia and cyanide, rather than from goo? Is that good or bad?

Henry
Posted by: Erasmus, FCD on May 14 2009,23:46

anyone into this sort of thing...



---------------------QUOTE-------------------
Olivier Rieppel.  2008.  Species as a Process.  Acta Biotheoretica Sep 2008.  

Abstract  Species are generally considered to be the basic units of evolution, and hence to constitute spatio-temporally bounded entities. In addition, it has been argued that species also instantiate a natural kind. Evolution is fundamentally about change. The question then is how species can remain the same through evolutionary change. Proponents of the species qua individuals thesis individuate species through their unique evolutionary origin. Individuals, or spatio-temporally located particulars in general, can be bodies, objects, events, or processes, or a combination of these. It is here argued that species are best understood as open or closed, causally integrated processual systems that also instantiate an historically conditioned homeostatic property cluster natural kind.

Keywords  Species - Systems - Presentism - Eternalism - Endurance - Perdurance - Futuralism
---------------------QUOTE-------------------



here is a bit



---------------------QUOTE-------------------
Eternalism takes time as a fourth dimension that is on par with the three dimensions of space. Space-time forms a four-dimensional continuum, as is required by the space-time ontology of modern physics (Rea 2003). On that account, all the space-time slices of an object, past, present, and future, ‘co-exist’ in four dimensions. A perduring object then forms a space-time worm (Loux 2003, p. 223), as do species on a perdurantist–eternalist account (Hull 1989, p. 187; Brogaard 2004, p. 226). Species cannot be extinct, they can only be ‘far away’. Nor can species evolve in the Darwinian sense of the word, since they have no future that could bring about genuine change.
---------------------QUOTE-------------------



any physicists care to comment on this view of time?

contrast with



---------------------QUOTE-------------------
As was emphasized by Rea (2003, p. 274), presentism is in strong accord with intuition, whereas eternalism seeks empirical support from contemporary theories of physics (Sklar 2006). Where the presentist has a problem to identify the duration of the present, the eternalist has the problem of identifying the ‘thickness’ of the temporal parts (space—time slices) of the perduring object. For some philosophers such as Whitehead (1920), time obtains from the passing of nature. But if we cannot keep time from passing, we also cannot hold nature still: “There is no holding nature still and looking at it” (Whitehead 1920, p. 14). A perduring object, or species, thus threatens to disintegrate into a series of theoretically infinitely thin time-slices, i.e., fleeting Whiteheadian ‘occasions’ (Whitehead 1979) that are spatio-temporally located parts of processes whose moment “of becoming is also their moment of perishing” such that they themselves neither change nor move (Sherburne 1966, pp. 210, 222). If the question is how one and the same (numerically identical) species can persist through temporal change, an ontology premised on the notion that nothing exists for any substantial length of time would not solve the problem. Identity conditions for persistence through time would lose their relevance (Haslanger 2003, p. 335). Herein lies a strong motivation for four-dimensionalism that results from an eternalist account of time, as was employed by Whitehead (1979) in his process philosophy—an account that was also adopted by Hennig (1950, 1966; see Rieppel 2007b).

Some authors take a four-dimensional space-time worm to be “the mereological fusions of instantaneous temporal parts or stages located at different times” (Crisp 2003, p. 216). Such a space-time worm stands in contrast to one whose segments are events or processes, which naturally extend through time. Organisms (Bertalanffy 1932, 1941; Hennig 1950, 1966; Rieppel 2007a) as well as evolving species take part in processes, indeed can be seen to be processes themselves (see further discussion below, and in Rieppel 2007b); Hennig (1950, 1966) realized with respect to his concept of the semaphoront that instantaneous temporal parts or stages are not a suitable ontology to capture developing organisms (Rieppel 2003, 2007b), and the same is true for evolving species. Such a radical, indeed Whiteheadian interpretation of the perdurantist–eternalist account contrasts with another possible interpretation of four-dimensionalism, which does not take time as another dimension on par with space, but which takes a persisting object to be identical with its history (Gallois 2005, p. 8). On that account, the species is a sequence of events that is identical with its history, i.e., a process that extends through space and time. History has not only a past and a present, but also a future, distinctions that are denied on the perdurantist–eternalist account. A species that is a four-dimensional space-time worm (Hull 1989, p. 187; Brogaard 2004, p. 226) has no past, nor any future: it just is (Hull 1989, p. 187). Accordingly, and for Hull (1989 , p. 187), “the species name Cygnus olor” refers “both to a spatio-temporally extended lineage and to a time-slice of that lineage.” This is why Løvtrup (1979, p. 390) contrasts Hull’s (1976) views with his own, where species (‘terminal taxa’ in Løvtrup’s (1977, 1979) axiomatic system) remain active players in the arena of evolution, making history.

Presentism yields a non-dimensional species concept (Mayr 1963, 1982) that fails to capture the species as an evolutionary process. Eternalism likewise cannot capture the species as an evolutionary process, as there is no past, nor any potential for future change and innovation. As will be illustrated by a brief excursion into the history of biology, a ‘third way’, a new metaphysics of change is required to capture species that are “evolution in the making” (Løvtrup 1977, p. 50).
---------------------QUOTE-------------------



i do not know many young biologists who are concerned with these issues.  yet they seem grave enough to warrant consideration.  these concepts form the foundation for discussing "speciation" and macroevolution, yet there are deep schisms between schools of thought that cannot be addressed by simply "following the evidence".
Posted by: Erasmus, FCD on May 14 2009,23:47

Quote (Henry J @ May 14 2009,23:27)
So we came from ammonia and cyanide, rather than from goo? Is that good or bad?

Henry
---------------------QUOTE-------------------


why, goooooooood, of course!
Posted by: jeannot on May 15 2009,09:43

Quote (Erasmus, FCD @ May 14 2009,21:41)
Quote (jeannot @ May 09 2009,18:49)
This is hardly a breakthrough but we've got a paper published in PNAS this week about speciation, more specifically the blurry frontier between what we may call subspecies and species. Of course, there's no strict boundary, as well as there is no qualitative difference between micro- and macroevolution, if this is relevant to the anti-evolution debate.

The work is done on an aphid species complex. Feel free to give you opinion on this. Full access requires subscription, but I can provide a pdf for those interested.

< http://www.pnas.org/content/106/18/7495.abstract >
---------------------QUOTE-------------------


pffft its still an aphid.  wake me up when one turns into a blue whale or summtin.  evilutionists

hey jean i noticed that at least some of those plants are tag-alongs with humans (clover, afalfa, peas, vetch)  i didn't recognize some of the others but i wouldn't.  

wondering if you had any idea of what the ancestral host preference mighta been?  i'm not swift enough to figure out if the biotypes that can switch hosts prefer hosts that have been strongly domesticated.  would make sense that selection for being tasty for people or livestock, if it reduces any defense complexes, might make you tastier for insects.

in one fell swoop you have generated more science than the entire ID movement in 2008 AND 2009.  Cheers!
---------------------QUOTE-------------------


We don't know the ancestral host. It could be an annual vetch related to broad bean, which is suitable for all biotypes. But we don't have the data to test this.

Artificial selection for/against plant defenses is an interesting question. But pea and broad bean, which do not grow in the wild, are far from being deprived of anti-insect defenses.
In fact, host fidelity seems a bit stronger in some biotypes feeding on wild plants, like broom, restharrow and meadow vetchling. But these biotypes may have diverged more anciently.
Posted by: Erasmus, FCD on May 15 2009,10:10

i never thought it before but how old are peas?  are there new and old world peas?

can you date those divergences in the aphids molecularly?

is domestication of wild pea lineages likely to have played a role in the extinction of the ancestral pea?  

perhaps if there were never peas would call them some other sort of aphid.  if only there were poison ivy aphids.

i just picked a gallon or so of peas in my garden and i am tickled about it

we planted some storebought 'alaska' spring peas and 'little marvel' bush peas.  i  should have picked them the first time several weeks ago but we'll probably get another good pick out of these two patches.  

peas don't do very well here but its not aphids its heat.  in fact i have never seen an aphid on them but that doesn't mean anything.  they don't seem to have much insect damage at all.

thanks for posting that very cool
Posted by: Richard Simons on May 15 2009,13:18

Quote (Erasmus @ FCD,May 15 2009,10:10)
i never thought it before but how old are peas?  are there new and old world peas?

can you date those divergences in the aphids molecularly?

is domestication of wild pea lineages likely to have played a role in the extinction of the ancestral pea?  

perhaps if there were never peas would call them some other sort of aphid.  if only there were poison ivy aphids.

i just picked a gallon or so of peas in my garden and i am tickled about it

we planted some storebought 'alaska' spring peas and 'little marvel' bush peas.  i  should have picked them the first time several weeks ago but we'll probably get another good pick out of these two patches.  

peas don't do very well here but its not aphids its heat.  in fact i have never seen an aphid on them but that doesn't mean anything.  they don't seem to have much insect damage at all.

thanks for posting that very cool
---------------------QUOTE-------------------


Off the top of my head: Peas are amongst the oldest crops from the Fertile Crescent (the higher ground around what was Mesopotamia) together with wheat, barley and lentils. I seem to recall the suggestion that they came from Anatolia. The ancestral form quite likely became extinct because it was swamped by the crop and the hybrids could not survive in the wild. It is thought that the same thing happened to onions.

I would be pleased if I had just picked a gallon of them, too. There's nothing quite like fresh-picked peas. Unfortunately, our garden will be just about ready to sow peas in about a week.

Edit to change silly mistake.
Posted by: Erasmus, FCD on May 15 2009,13:33

thanks richard that is good stuff.  i wonder how long that hybridization/backcross process lasts til extinction?  it must be a complex sequence of events, patchy in space and sensitive to human interactions with domestication.

probably different for different critters but it must not always happen...  thinking about blueberries potatoes bananas and tame blackberries but i reckon it is similar for any domesticated thing if there is gene flow between cultivars and wild types

you must be far north of that sunny state of tennessee.  i wish we could grow peas longer.  i am going to try a fall crop this year but i dunno if i can time it right
Posted by: jeannot on May 15 2009,15:41

I am not sure that the wild ancestor of pea is extinct. I thought it was Pisum fulvum.

But the wild ancestor of broad bean, which is as old as cultivated pea, is unknown/extinct.
Posted by: Erasmus, FCD on May 15 2009,16:01

jean there are new and old world beans right?
Posted by: jeannot on May 15 2009,18:29

The broad bean is Vicia faba, one of the first crops. I guess new world beans belong to Phaseolus sp. Both genera are unrelated. In fact Vicia is paraphyletic in respect to Pisum, Lens and Lathyrus. Its "sister" genus may be Trifolium (clovers), but phylogenies are not very robust in the Viciae tribe.

The tree of life web project has detailed entries on legumes, thanks to Martin Wojciechowski, the authority.
Posted by: Timothy McDougald on May 15 2009,20:22

This is pretty cool. < Description of an early Cretaceous termite (Isoptera: Kalotermitidae) and its associated intestinal protozoa, with comments on their co-evolution >. Here is the abstract:



---------------------QUOTE-------------------
Background: The remarkable mutualistic associations between termites and protists are in large part responsible for the evolutionary success of these eusocial insects. It is unknown when this symbiosis was first established, but the present study shows that fossil termite protists existed in the Mesozoic.

Results: A new species of termite (Kalotermes burmensis n. sp.) in Early Cretaceous Burmese amber had part of its abdomen damaged, thus exposing trophic stages and cysts of diverse protists. Some protists were still attached to the gut intima while others were in the amber matrix adjacent to the damaged portion. Ten new fossil flagellate species in the Trichomonada, Hypermastigida and Oxymonadea are described in nine new genera assigned to 6 extant families. Systematic placement and names of the fossil flagellates are based on morphological similarities with extant genera associated with lower termites. The following new flagellate taxa are established: Foainites icelus n. gen. n. sp., Spiromastigites acanthodes n. gen. n. sp., Trichonymphites henis n. gen., n. sp., Teranymphites rhabdotis n. gen. n. sp., Oxymonas protus n. sp., Oxymonites gerus n. gen., n. sp., Microrhopalodites polynucleatis n. gen., n. sp., Sauromonites katatonis n. gen., n. sp., Dinenymphites spiris n. gen., n. sp., Pyrsonymphites cordylinis n. gen., n. sp. A new genus of fossil amoeba is also described as Endamoebites proterus n. gen., n. sp. Fourteen additional trophic and encystid protist stages are figured and briefly characterized.

Conclusion: This represents the earliest fossil record of mutualism between microorganisms and animals and the first descriptions of protists from a fossil termite. Discovering the same orders, families and possibly genera of protists that occur today in Early Cretaceous kalotermitids shows considerable behaviour and morphological stability of both host and protists. The possible significance of protist cysts associated with the fossil termite is discussed in regards the possibility that coprophagy, as well as proctodeal trophallaxis, was a method by which some termite protozoa were transferred intrastadially and intergenerationally at this time.
---------------------QUOTE-------------------



The article is open access.
Posted by: Henry J on May 15 2009,22:01



---------------------QUOTE-------------------
A perduring object, or species, thus threatens to disintegrate into a series of theoretically infinitely thin time-slices, i.e., fleeting Whiteheadian ?occasions? (Whitehead 1979) that are spatio-temporally located parts of processes whose moment ?of becoming is also their moment of perishing? such that they themselves neither change nor move (Sherburne 1966, pp. 210, 222).
---------------------QUOTE-------------------



So a species is a quantum waveform in a four dimensional space? Such that taking one kind of measurement makes look like a single thing, but another type of measurement makes it look like a wave that's spread out in several directions? Also with the problem that the act of trying to measure it causes uncertainty in the result. :lol:

Henry
Posted by: Erasmus, FCD on May 15 2009,22:38

yeah i'm not so sure that is helpful in thinking about species are.  but it might be if i knew wtf it was supposed to mean.

and it seems like all of it requires that you forget about the delimitation part.  just believe that there even is such a thing as a matter of faith.  

works good enough for picking blackberries

ETA and it just occurred to me that i could wiki the beans thing.  i suck at internetz but thats purty cool
Posted by: Richard Simons on May 15 2009,23:09

Quote (jeannot @ May 15 2009,15:41)
I am not sure that the wild ancestor of pea is extinct. I thought it was Pisum fulvum.

But the wild ancestor of broad bean, which is as old as cultivated pea, is unknown/extinct.
---------------------QUOTE-------------------


You could be right about the pea. It is a long time since I've done any reading on the topic and I don't have my material on the subject handy.

Regarding New World vs Old World beans; faba beans (=broad beans, horse beans) and of course soya beans are Old World species and Phaseolus is a New World group (mainly Central/South America). There was a lot of work studying the origins of Phaseolus beans and things may have changed, but many beans are regarded as one species - green, wax, white, haricot, navy, black, black-eyed, pinto and kidney beans. Lima/butter beans are different and so are runner beans - but still Phaseolus.

It's interesting to think about what food plants people did not have available. I've tried one or two of the traditional leafy vegetables that fell out of favour and it's easy to tell why they were dropped.
Posted by: ppb on May 21 2009,08:46

I know you guys tend more towards the biological sciences, but since Creationists think evolution covers the Big Bang and is pretty much the Theory of Everything (evil), I thought I would share < this item > from the good Dr Phil's Bad Astronomy blog.  It is a video of the center of the Milky Way Galaxy rising over the Texas Star Party.

It was taken with a Canon EOS-5D with filter modifications to record hydrogen alpha at 656 nm.  An EF 15mm f/2.8 lens was used, and the exposures were controlled by a timer, 20 seconds of exposure followed by 40 seconds off.

The results are spectacular.  I've seen the Milky Way under really dark skies, but it was nothing quite like this!
Posted by: dvunkannon on May 26 2009,11:19

Quote (Henry J @ May 15 2009,23:01)


---------------------QUOTE-------------------
A perduring object, or species, thus threatens to disintegrate into a series of theoretically infinitely thin time-slices, i.e., fleeting Whiteheadian ?occasions? (Whitehead 1979) that are spatio-temporally located parts of processes whose moment ?of becoming is also their moment of perishing? such that they themselves neither change nor move (Sherburne 1966, pp. 210, 222).
---------------------QUOTE-------------------



So a species is a quantum waveform in a four dimensional space? Such that taking one kind of measurement makes look like a single thing, but another type of measurement makes it look like a wave that's spread out in several directions? Also with the problem that the act of trying to measure it causes uncertainty in the result. :lol:

Henry
---------------------QUOTE-------------------


I haz confuze. How does Sherburne 1966 quote Whitehead 1979?
Posted by: Henry J on May 26 2009,23:35

Well, I was describing an analogy (perhaps an overly loose one) that occurred to me on reading that. I can't help it if the two concepts got published in the wrong order. :D

Henry
Posted by: Erasmus, FCD on May 27 2009,00:00

it's not like the original is easy to read anyway.  there is a stone in the soup but i almost can't be arsed to find it
Posted by: khan on May 28 2009,17:32

< Meteoric organics >
Posted by: Lou FCD on May 28 2009,19:20

Quote (ppb @ May 21 2009,09:46)
I know you guys tend more towards the biological sciences, but since Creationists think evolution covers the Big Bang and is pretty much the Theory of Everything (evil), I thought I would share < this item > from the good Dr Phil's Bad Astronomy blog.  It is a video of the center of the Milky Way Galaxy rising over the Texas Star Party.

It was taken with a Canon EOS-5D with filter modifications to record hydrogen alpha at 656 nm.  An EF 15mm f/2.8 lens was used, and the exposures were controlled by a timer, 20 seconds of exposure followed by 40 seconds off.

The results are spectacular.  I've seen the Milky Way under really dark skies, but it was nothing quite like this!
---------------------QUOTE-------------------


I'm looking for just such a filter for my new Canon EOS Rebel XS. I'm trying to avoid the duct tape route, but hey, a man's gotta do...

ETA: Near as I can tell to this point, there's no front end filter to just screw on, it requires serious surgery on the camera. I'd like to avoid that, too.


Posted by: ppb on May 28 2009,22:57

Quote (Lou FCD @ May 28 2009,20:20)
ETA: Near as I can tell to this point, there's no front end filter to just screw on, it requires serious surgery on the camera. I'd like to avoid that, too.
---------------------QUOTE-------------------


That's the impression I had from the description.  Not something that I would want to do to my camera.
Posted by: Nerull on May 29 2009,00:53

If this is the procedure I think it is, it consists of removing the factory installed IR filter in front of the CMOS sensor, and replacing it with clear to improve sensitivity. It does require surgery inside the camera and is a bit of a delicate operation.

Canon made a series of 20Ds that never had the filter installed for a while, but they were discontinued.
Posted by: nuytsia on May 29 2009,07:53

Quote (Richard Simons @ May 15 2009,15:09)
     
Quote (jeannot @ May 15 2009,15:41)
I am not sure that the wild ancestor of pea is extinct. I thought it was Pisum fulvum.

But the wild ancestor of broad bean, which is as old as cultivated pea, is unknown/extinct.
---------------------QUOTE-------------------


You could be right about the pea. It is a long time since I've done any reading on the topic and I don't have my material on the subject handy.

-snip-
---------------------QUOTE-------------------


I had to attend a meeting at a plant breeding institute a few years ago and was told at the time that the pea was domesticated twice once in the middle east and once in Ethiopia. I got the distinct impression that these were from different species but must admit my memory is rather fuzzy on the detail and I certainly don't have any refs. :(

In regard to the synthesis of RNA article, I found this comment on the < Nature page > interesting.
     

---------------------QUOTE-------------------
What is most promising is that it may lead us to be able to show, definitively, that man did not in fact ascend or evolve from apes [as I had always found odd] but rather we evolved along a seperate, but similar strain of the same... for lack of a better term, primordial ooze. Like the other prehistoric beasts, some went inland and some went back to the seas, and others still made for the trees. This is a wonderful study and I hope to read more.
---------------------QUOTE-------------------


WTF?  ???
Posted by: Quack on May 29 2009,09:13

Quote (nuytsia @ May 29 2009,07:53)

In regard to the synthesis of RNA article, I found this comment on the < Nature page > interesting.
               

---------------------QUOTE-------------------
What is most promising is that it may lead us to be able to show, definitively, that man did not in fact ascend or evolve from apes [as I had always found odd] but rather we evolved along a seperate, but similar strain of the same... for lack of a better term, primordial ooze. Like the other prehistoric beasts, some went inland and some went back to the seas, and others still made for the trees. This is a wonderful study and I hope to read more.
---------------------QUOTE-------------------


WTF?  ???
---------------------QUOTE-------------------


There goes common descent down the drain - or maybe the 'tree of life'?

Ed. modified statement.
Posted by: JLT on June 04 2009,07:37



---------------------QUOTE-------------------

< FOXP2 and Human Cognition >

Our restless species strives ceaselessly to invent ever more useful devices, improve our social systems, and create new works of art. Our creative ability derives from motor and cognitive flexibility that allows us to form a potentially unbounded number of new words and sentences as well as tools, art, dance forms, and music; it is a fundamental defining attribute of Homo sapiens that presumably derives from a suite of neural capabilities absent or greatly reduced in other species. The archaeological record, however, reveals few signs of creativity earlier than not, vert, similar200,000 years ago in Africa, with a burst of creativity appearing in Homo sapiens during the Upper Paleolithic, not, vert, similar50,000 years ago ([Klein, 1999] and McBrearty and Brooks, 2000 S. McBrearty and A.S. Brooks, J. Hum. Evol. 39 (2000), pp. 453–563. Abstract |  PDF (2416 K)  | View Record in Scopus | Cited By in Scopus (314)[McBrearty and Brooks, 2000]). Something must have modified the brains of our ancestors in that distant time, the period associated with both the appearance of the immediate ancestors of modern humans and the amino acid substitutions that differentiate the human form of the FOXP2 gene from that of chimpanzees. Now, Enard, Paabo and their colleagues shed new light on the role of the FOXP2 gene on the evolution of human language and cognition (Enard et al., 2009).

They report, in this issue, the results of introducing into mice the human version of the Foxp2 gene. The mice exhibited alterations in ultrasonic vocalizations and exploratory behavior as well as changes in brain dopamine concentrations. The neurological consequences provide an explanation for why human speech, language, and cognitive capacity transcend those of living apes, as well as the cognitive abilities of our distant hominid ancestors that can be inferred from the archaeological record. In mice with a “humanized” Foxp2 gene, the medium spiny neurons of the basal ganglia show increased synaptic plasticity and dendrite length. Such changes enhance the efficiency of neural cortico-basal ganglia circuits, the brain mechanisms that in humans are known to regulate motor control including speech, word recognition, sentence comprehension, recognition of visual forms, mental arithmetic, and other aspects of cognition (Figure 1).

[....]
This brings us to the signal achievements of Enard and his colleagues (Enard et al., 2009). The FOXP2 story started with the discovery of a mutation in this gene in an extended family in the UK that resulted in extreme speech motor-control deficits, deficits in language comprehension, and lower scores on standardized intelligence tests. Neuroimaging studies revealed anomalies in basal ganglia morphology and activity. Embryological studies then showed that both the mouse and human versions of this gene modulate development of the basal ganglia and other subcortical structures. Moreover, the two amino acid substitutions that differentiate the human form of FOXP2 from that of chimpanzees occurred and were fixed within the past 200,000 years, the period associated with the appearance of the immediate ancestors of modern humans and Neanderthals. However, it has not been clear whether the behavioral deficits associated with the aberrant missense mutation in the affected family members have any bearing on the effects of the human form of FOXP2 on the brain. With their new study, Enard and coworkers resolve this issue. They demonstrate that the amino acid substitutions that mark the human form of FOXP2 would have played a key role in the evolution of the human brain by increasing synaptic plasticity and dendrite length and connectivity in the basal ganglia.

The proximate “tinkering” logic of evolution has often been pointed out. In a sense, we can view the effects of the human form of FOXP2 as a sort of “tuning” that brought the cortico-striatal circuits that humans inherited from other species to a state of higher efficiency. Synaptic plasticity is the key to how neurons code and process information. Dendrites connect the neuronal map, channeling information between neurons. Neurophysiological texts contain hundreds of references to studies that note the roles of synaptic plasticity and neuronal connectivity in forming new associations and new action patterns—the Hebbian (Hebb, 1949) “computational” processes of the brain that appear to underlie virtually all aspects of cognition.

As is the case for all significant discoveries, the new work addresses seemingly unrelated issues and raises further questions. The earliest surviving hominid fossils that could have had tongues capable of producing fully modern speech date back 50,000 years to the Upper Paleolithic (Lieberman and McCarthy, 2007). In earlier Middle Pleistocene fossils, in which the neck segment is equal to the mouth segment, neck lengths were too short to accommodate a human tongue. Tongue proportions that facilitate speech came at the cost of increasing the risk of choking—the fourth leading cause of accidental death in the U.S. Therefore, a human tongue would be worse than useless unless the hominid in question also had cortico-basal ganglia circuits capable of executing the rapid, complex motor gestures that are necessary to produce articulate speech. The presence of a human tongue in Upper Paleolithic hominids thus serves as an index for the presence of these neural circuits. But as Enard et al., 2009 W. Enard, S. Gehre, K. Hammerschmidt, S.M. Hölter, T. Blass, M. Somel, M.K. Brückner, C. Schreiweis, C. Winter and R. Sohr et al., Cell (2009) this issue.Enard et al. (2009) show, cortico-basal ganglia circuits could have evolved before the appearance of the modern human tongue, explaining the presence of some Upper Paleolithic artifacts in Africa >50,000 years ago.

Finally, these results argue against Noam Chomsky's views concerning the neural bases of human language. In all versions of Chomskian theory, the central claim is that humans possess a species-specific, innate, neural “organ,” devoted to language and language alone. Language in Chomsky's theories, moreover, is equated with syntax, the means by which distinctions in meaning are conveyed in a sentence. Cortico-basal ganglia circuits clearly are involved in sentence comprehension, but enhanced human cortico-basal ganglia circuit efficiency clearly would be expressed in cognitive acts beyond language and motor control. With the study by Enard and his colleagues, we have reached a new milestone in the journey toward understanding the evolution of human cognition.
---------------------QUOTE-------------------



< Enard et al., A Humanized Version of Foxp2 Affects Cortico-Basal Ganglia Circuits in Mice
Cell, Volume 137, Issue 5, 29 May 2009, Pages 961-971 >

< Short video summary of Enard's and Pääbo's results >

ETA: The original article is open access. If the above link isn't working < try this one >.
Posted by: J-Dog on June 04 2009,08:14

I just received a jpeg of the FOXP2 mouse they experimented on...< FOXP2 Mouse >
Posted by: Wesley R. Elsberry on June 04 2009,10:45

If you want to try something without the cost and modification headaches of the hydrogen alpha filter, just slap a 25A (deep red) filter on your lens and do some time exposures. If that looks like the sort of thing you like, you can decide whether to step up to the hydrogen alpha filter. The 25A will get you much of the benefit of the narrow-band hydrogen alpha filter by dropping out blue and green light contributions. Unless what you are battling is sodium-arc light pollution, it should do a pretty decent job. Drive further out into the country to get away from the light pollution.
Posted by: dvunkannon on June 04 2009,12:31

Quote (JLT @ June 04 2009,08:37)
 

---------------------QUOTE-------------------

< FOXP2 and Human Cognition >

The proximate “tinkering” logic of evolution has often been pointed out. In a sense, we can view the effects of the human form of FOXP2 as a sort of “tuning” that brought the cortico-striatal circuits that humans inherited from other species to a state of higher efficiency.
---------------------QUOTE-------------------


---------------------QUOTE-------------------



Hmm, I'm going to have to skim it again. I didn't see "efficiency" the first time through. I'm pretty sure mice had a highly efficient FoxP2 gene and cortical neurons for their niche. If they are less jittery and more thoughtful mice, thay are worse mice, no matter what that tells us about humans.
Posted by: JLT on June 04 2009,18:09

Quote (dvunkannon @ June 04 2009,18:31)
 
Quote (JLT @ June 04 2009,08:37)
   

---------------------QUOTE-------------------

< FOXP2 and Human Cognition >

The proximate “tinkering” logic of evolution has often been pointed out. In a sense, we can view the effects of the human form of FOXP2 as a sort of “tuning” that brought the cortico-striatal circuits that humans inherited from other species to a state of higher efficiency.
---------------------QUOTE-------------------


---------------------QUOTE-------------------



Hmm, I'm going to have to skim it again. I didn't see "efficiency" the first time through. I'm pretty sure mice had a highly efficient FoxP2 gene and cortical neurons for their niche. If they are less jittery and more thoughtful mice, thay are worse mice, no matter what that tells us about humans.
---------------------QUOTE-------------------


How do you know they are worse mice?

*





* You're right, of course. That's a very anthropocentric view.
Posted by: Lou FCD on June 05 2009,16:29

Quote (Wesley R. Elsberry @ June 04 2009,11:45)
If you want to try something without the cost and modification headaches of the hydrogen alpha filter, just slap a 25A (deep red) filter on your lens and do some time exposures. If that looks like the sort of thing you like, you can decide whether to step up to the hydrogen alpha filter. The 25A will get you much of the benefit of the narrow-band hydrogen alpha filter by dropping out blue and green light contributions. Unless what you are battling is sodium-arc light pollution, it should do a pretty decent job. Drive further out into the country to get away from the light pollution.
---------------------QUOTE-------------------


Thanks, Wesley. I'll give that a go.
Posted by: Richardthughes on June 08 2009,16:10

< http://www.physorg.com/news163328877.html >


Brace for Quotemining from DO'L.
Posted by: Gunthernacus on June 08 2009,16:27

Quote (Richardthughes @ June 08 2009,17:10)
< http://www.physorg.com/news163328877.html >


Brace for Quotemining from DO'L.
---------------------QUOTE-------------------


Bradford at Tardic Thoughts beat you (and DO'L) < to it >.
Posted by: Lou FCD on June 08 2009,21:00

Quote (Gunthernacus @ June 08 2009,17:27)
Quote (Richardthughes @ June 08 2009,17:10)
< http://www.physorg.com/news163328877.html >


Brace for Quotemining from DO'L.
---------------------QUOTE-------------------


Bradford at Tardic Thoughts beat you (and DO'L) < to it >.
---------------------QUOTE-------------------


Slimey Sal jumps in there to yap at oleg's ankles.
Posted by: Richardthughes on June 09 2009,10:47

Related: Quantum woo:

< http://www.physorg.com/news163670588.html >
Posted by: Lou FCD on June 09 2009,10:55

Quote (Richardthughes @ June 09 2009,11:47)
Related: Quantum woo:

< http://www.physorg.com/news163670588.html >
---------------------QUOTE-------------------


Oh, this smacks of something familiar:



---------------------QUOTE-------------------
Marin lays out each player’s role and perspective in the controversy, and argues that studying the original interpretations of quantum mechanics can help scientists better understand the theory, and could also be important for the public in general.
---------------------QUOTE-------------------



I hope the article gets better as I go along.

Unrelated: WTF is up with physicists and hair?
Posted by: Richardthughes on June 09 2009,11:06

Quote (Lou FCD @ June 09 2009,10:55)
*snip*

Unrelated: WTF is up with physicists and hair?
---------------------QUOTE-------------------


HAR HAR HEDDLE AND OLEG.
Posted by: KCdgw on June 09 2009,11:09

Quote (Richardthughes @ June 09 2009,11:06)
Quote (Lou FCD @ June 09 2009,10:55)
*snip*

Unrelated: WTF is up with physicists and hair?
---------------------QUOTE-------------------


HAR HAR HEDDLE AND OLEG.
---------------------QUOTE-------------------


Physicists and hair? What about biologists?

Steven Pinker:




Kevin Padian:



KC
Posted by: Lou FCD on June 09 2009,11:17

Quote (KCdgw @ June 09 2009,12:09)
Quote (Richardthughes @ June 09 2009,11:06)
 
Quote (Lou FCD @ June 09 2009,10:55)
*snip*

Unrelated: WTF is up with physicists and hair?
---------------------QUOTE-------------------


HAR HAR HEDDLE AND OLEG.
---------------------QUOTE-------------------


Physicists and hair? What about biologists?

Steven Pinker:




Kevin Padian:



KC
---------------------QUOTE-------------------


Point taken.

May I amend the question to "Scientists and hair"?
Posted by: Wesley R. Elsberry on June 09 2009,11:25

Kevin is a camera-shy guy. I think I could get a better pic, but I don't know that it is going to happen.
Posted by: Gunthernacus on June 09 2009,15:04


To hair is human...


Two hair is divine.
Posted by: Richardthughes on June 10 2009,10:30

Brain wiring optimality:

< http://www.newscientist.com/article....iq.html >
Posted by: Henry J on June 10 2009,20:41

If brain wiring is optimized, how do you explain creationists?

(Did I say that?)
Posted by: JLT on June 11 2009,05:38

Reconstructing the Evolution of Laughter in Great Apes and Humans
Davila Ross, M., Owren, M. J. & Zimmermann, E. Curr. Biol. (2009).< doi:10.1016/j.cub.2009.05.028 >



---------------------QUOTE-------------------
Human emotional expressions, such as laughter, are argued to have their origins in ancestral nonhuman primate displays [1], [2], [3], [4], [5] and [6]. To test this hypothesis, the current work examined the acoustics of tickle-induced vocalizations from infant and juvenile orangutans, gorillas, chimpanzees, and bonobos, as well as tickle-induced laughter produced by human infants. Resulting acoustic data were then coded as character states and submitted to quantitative phylogenetic analysis. Acoustic outcomes revealed both important similarities and differences among the five species. Furthermore, phylogenetic trees reconstructed from the acoustic data matched the well-established trees based on comparative genetics. Taken together, the results provide strong evidence that tickling-induced laughter is homologous in great apes and humans and support the more general postulation of phylogenetic continuity from nonhuman displays to human emotional expressions. Findings also show that distinctively human laughter characteristics such as predominantly regular, stable voicing and consistently egressive airflow are nonetheless traceable to characteristics of shared ancestors with great apes.
---------------------QUOTE-------------------



I really hope this link works: < movie of a ticklish gorilla >
Posted by: Timothy McDougald on June 15 2009,19:45

A new paper with some interesting implications for OOL research. < Self-Assembling Sequence-Adaptive Peptide Nucleic Acids >

Here is the abstract:



---------------------QUOTE-------------------
Several classes of nucleic acid analogs have been reported, but no synthetic informational polymer has yet proven responsive to selection pressures under enzyme free conditions. Here, we introduce an oligomer family that efficiently self-assembles via reversible covalent anchoring of nucleobase recognition units onto simple oligo-dipeptide backbones [thioester peptide nucleic acids (tPNA)] and undergoes dynamic sequence modification in response to changing templates in solution. The oligomers specifically self-pair with complementary tPNA strands and cross-pair with RNA and DNA in Watson-Crick fashion. Thus, tPNA combines base-pairing interactions with the side chain functionalities of typical peptides and proteins. These characteristics might prove advantageous for the design or selection of catalytic constructs or biomaterials that are capable of dynamic sequence repair and adaptation.
---------------------QUOTE-------------------



And a link to Science Daily on the same article:

< Simple Chemical System Created That Mimics DNA >
Posted by: Timothy McDougald on June 16 2009,20:16

Scooooooooore!

PNAS has three volumes (so far) - all open access -devoted to Darwin.

< Volume 1 > - which has an article co-written by Lenski which should get Conservapedia all riled up.

< Volume 2 >

< Volume 3 >
Posted by: Richardthughes on June 17 2009,10:10

Quotemining in 3...2...1...

< http://www.sciencedaily.com/releases/2009/06/090616103205.htm >



---------------------QUOTE-------------------
Cells Are Like Robust Computational Systems, Scientists Report
ScienceDaily (June 17, 2009) — Gene regulatory networks in cell nuclei are similar to cloud computing networks, such as Google or Yahoo!, researchers report today in the online journal Molecular Systems Biology. The similarity is that each system keeps working despite the failure of individual components, whether they are master genes or computer processors.


---------------------QUOTE-------------------



This is an argument for design, no doubt. But so is IC. Hmmmmmm
Posted by: dvunkannon on June 17 2009,14:29

< Speciation through a single base mutation >
Posted by: Erasmus, FCD on June 17 2009,15:32



---------------------QUOTE-------------------
The researchers also used stuffed taxidermic mounts to test the birds' ability to recognize their own subspecies and found that the two groups of flycatchers consistently preferred their own kind. Together, these results indicate that the single genetic swap probably set speciation in motion, Uy said.
---------------------QUOTE-------------------



NICE TRY CHANCE WORSHIPPER.  WATCH THIS

FLYCATCHER MATE PREFERENCE = F(IMMATERIAL MIND) = CANNOT BE MEASURED = CANNOT BE QUANTIFIED= SUPERNATURAL

SUCK IT DARWINIST HOMOS.  MAYBE THERE ARE INUIT FLYCATCHERS.  GO BURN A CHURCH  -  DT
Posted by: GCUGreyArea on June 17 2009,15:43

Quote (dvunkannon @ June 17 2009,14:29)
< Speciation through a single base mutation >
---------------------QUOTE-------------------


IT'S STILL A BIRD!!!!!!BIRD IS SPECIES!!!!!ID IZ SCIENCE
Posted by: dvunkannon on June 17 2009,20:05

Quote (Erasmus @ FCD,June 17 2009,16:32)
 

---------------------QUOTE-------------------
The researchers also used stuffed taxidermic mounts to test the birds' ability to recognize their own subspecies and found that the two groups of flycatchers consistently preferred their own kind. Together, these results indicate that the single genetic swap probably set speciation in motion, Uy said.
---------------------QUOTE-------------------



NICE TRY CHANCE WORSHIPPER.  WATCH THIS

FLYCATCHER MATE PREFERENCE = F(IMMATERIAL MIND) = CANNOT BE MEASURED = CANNOT BE QUANTIFIED= SUPERNATURAL

SUCK IT DARWINIST HOMOS.  MAYBE THERE ARE INUIT FLYCATCHERS.  GO BURN A CHURCH  -  DT
---------------------QUOTE-------------------


how do they know what they looklike?! huh?? answer that darwinist!!1! no pocket mirrors in the Malay jungle
besides both subspecies actually preferred the BLOND flycatchers, even ones with dark roots ha i kill myself
"flycatchers" who is gonna believe that anyway sounds gay and gays species go extinct faster than debbie gibson's hairstyle -dt

Posted by: dvunkannon on June 20 2009,09:41

< Extending the lifetime of the biosphere >

Thes folks argue that life naturally reduces the partial pressure of nitrogen over time by sequestering it. Is that right?
Posted by: nuytsia on June 21 2009,07:00

Not a paper but < this presentation at TEDS > on the geckos tail I thought was rather cool.
Posted by: jeannot on June 21 2009,07:49

Quote (GCUGreyArea @ June 17 2009,15:43)
Quote (dvunkannon @ June 17 2009,14:29)
< Speciation through a single base mutation >
---------------------QUOTE-------------------


IT'S STILL A BIRD!!!!!!BIRD IS SPECIES!!!!!ID IZ SCIENCE
---------------------QUOTE-------------------


"Speciation through a single base mutation" still remains highly misleading and does not reflect the orignal article title. Although cannot have access full-text articles from Am. Nat., I do not see unambiguous evidence that this mutation has promoted reproductive isolation between these birds. Moreover, the populations are allopatric, which makes the question of reproductive isolation partly irrelevant.

In this new era of speciation genomic, it should be stressed that a mutation that is shown to cause reproductive incompatibilities may not have historically promoted speciation. There are certainly thousands of genetic incompatibilities and millions of fixed mutations differentiating humans and our sister species (chimps). Obviously, not every single one is a "speciation gene". This partly applies to related species fruit flies, in which some claim to have identified such genes.

One has to infer how reproductive barriers have evolved. But this is essentially impossible when speciation is complete and when many types of reproductive barriers prevent successful hybridation.
Posted by: Henry J on June 21 2009,17:03

Not to mention that the original cause might have simply been geographic isolation.

Henry
Posted by: jeannot on June 22 2009,09:40

Quote (Henry J @ June 21 2009,17:03)
Not to mention that the original cause might have simply been geographic isolation.

Henry
---------------------QUOTE-------------------


Allopatry surely permit speciation in birds and many other animals, but it is not considered as a reproductive barrier, since geography is not a trait.
Plumage color may well determine mate choice in these birds; but in allopatric populations, reproductive barriers are irrelevant.
Posted by: Henry J on June 22 2009,10:38

True, the geographic isolation isn't by itself a speciation event; it just allows accumulation of differences which might eventually add up to a reproductive barrier.

Henry
Posted by: Henry J on June 22 2009,10:39

The < T.O. Post of the Month > is fascinating.
Posted by: Richardthughes on June 23 2009,10:51

< http://www.technologyreview.com/blog/arxiv/23748/ >


Quotemine in 3....2.....1
Posted by: keiths on June 24 2009,01:58

< From the Telegraph >:


---------------------QUOTE-------------------
Inside Nature's Giants: A gory attempt to disprove 'intelligent design' theories

A new Channel 4 series shows the dissection of giant animals. Ajesh Patalay reports.

By Ajesh Patalay
Published: 5:13PM BST 23 Jun 2009

Of the many extraordinary sights revealed in Channel 4’s upcoming four-part series Inside Nature’s Giants, which uses dissection to take us inside the bodies of an elephant, giraffe and crocodile, the most remarkable is surely afforded by an autopsy carried out on a 65-foot long, 60-ton fin whale (a species second only in size to the blue whale) beached off the coast of Ireland.

“I am always awed by how magnificently large and streamlined whales are,” says Dr Joy Reidenberg, the comparative anatomist who oversaw the in situ dissection amid gales, driving rain and hail. Working against the effects of rapid decomposition and an advancing tide that threatened to engulf the whale, Reidenberg’s team had only a few hours to complete the dissection. “It’s a messy operation,” Reidenberg explains. “You have to dissect it from the inside out. At one point I crawled under the ribcage to get to the heart. All you could see were my boots sticking out.”

The team excised over 200 feet of guts, which were loaded onto dumper trucks and laid out on tarp sheets the size of an Olympic swimming pool. Other markers of the whale’s immensity included jaws weighing three tons each, a heart the size of a small car and a windpipe wide enough, says Reidenberg, “that I could actually wear it like a dress”.

Inside Nature’s Giants, which starts on Monday, is the brainchild of producer David Dugan of Windfall Films (also behind The Operation: Surgery Live). “I had been reading about Darwin and early animal dissections carried out by his friend Richard Owen,” Dugan says. “Each animal’s evolutionary past is hidden within its anatomy. These dissections gave us the chance to show how natural selection created these animals.”

Collaborating with the Royal Veterinary College, Dugan recruited a team of experts including the evolutionary biologist Richard Dawkins (the author of The God Delusion) who, says Dugan, got “terribly excited” by the prospect of dissecting a giraffe. Its anatomy is key in proving evolution over intelligent design (the belief that the complexity of living things demonstrates the existence of a creator). Rather than passing a few inches directly between the larynx and the brain, the giraffe’s recurrent laryngeal nerve (which stimulates the voice box) takes a huge detour up and down the neck. This, says Dawkins, is not the work of Intelligent Design: “A designer can go back to the drawing board and come back with something more sensible. Evolution can’t. Evolution has no foresight.”

The dissection goes on to show how the giraffe’s neck, despite its length, contains only seven vertebrae (the same as humans) and how in order to maintain its high blood pressure the giraffe has evolved a thick heart wall muscle and tight skin around its legs that act like pressure stockings.

Before the workings of the elephant can be dissected, the team has to release the build-up of gases caused by decomposition and fermentation (elephants produce 2,000 litres of methane a day, enough to fill a weather balloon). The resultant hiss of escaping gas is deafening. Having unpacked the elephant’s massive guts, the team examines its trunk (a marvel of engineering that saves the elephant from having to lower its weighty head to pick up food), its ears (flooded with blood vessels to aid cooling) and its feet, which bear up to three tons each and are cushioned with chunky insoles of fat that mimic a pogo-stick in propelling the elephant forward as it runs.

With the series’s deluge of blood and guts, the obvious question is whether viewers will prove too squeamish to endure. “It’s a worry,” says Dugan. “But when you get inside the head of an anatomist and start looking at it as a problem of engineering or evolution, you stop noticing the gore and it becomes so interesting.”

Reidenberg hopes that the series will not only educate viewers about evolution but also give them “an appreciation of how special these animals are”. She adds: “Whenever I see an animal like this, I feel sad that it’s dead but there’s also this marvellous opportunity to open up a present and see what’s inside. Every animal is unique. I hope people come to love and understand some of the natural beauty there and not be grossed out by it.”

Inside Nature’s Giants begins on Monday on Channel 4 at 9.00 pm.

---------------------QUOTE-------------------


Posted by: Henry J on June 25 2009,13:11

< Crop circles explained > (well, some of them, anyway).

Henry
Posted by: dvunkannon on June 29 2009,17:30

An update on the Steyr 2007 paper:
< Evolution and the second law of thermodynamics >

the money quote
   

---------------------QUOTE-------------------
If we compare this value with the rate of entropy production due to sunlight in Eq. (3), we find that the second law, in the form of Eq. (1), is satisfied as long as the time required for life to evolve on Earth is at least
delta t =|deltaSlife|/(dS/dt)sun ~ 10^7 s, (6)
or less than a year. Life on Earth took four billion years to evolve, so the second law of thermodynamics is safe.
---------------------QUOTE-------------------



Steyr 2007 was blogged by PZ Myers, which was picked up by PT. This paper tries to be a bit more rigorous, even though there is still a lot of hand waving in parts.

Nakashima mentioned the paper on UD, with no apparent response.
Posted by: Henry J on July 01 2009,10:15

Shuttle Endeavour is preparing to launch tonight, 739 PM Eastern.
Posted by: Reed on July 01 2009,19:29

Quote (Henry J @ July 01 2009,08:15)
Shuttle Endeavour is preparing to launch tonight, 739 PM Eastern.
---------------------QUOTE-------------------


Launch window opens July 11. There was a tanking test today.

< http://spaceflightnow.com/shuttle/sts127/090701tanking/ >

Unrelated but cool and sciencey < http://news.bbc.co.uk/earth/hi/earth_news/newsid_8127000/8127519.stm >
Posted by: khan on July 01 2009,20:33

@Astro_127 on twitter

< http://twitter.com/Astro_127 >
Posted by: Henry J on July 01 2009,21:27

Oh well, tanks for that.

Henry
Posted by: JLT on July 03 2009,09:57

How to Think, Say, or Do Precisely the Worst Thing for Any Occasion
Daniel M. Wegner
Science 3 July 2009:
Vol. 325. no. 5936, pp. 48 - 50
< DOI: 10.1126/science.1167346 >
   

---------------------QUOTE-------------------
Ironic lapses of mental control often appear when we attempt to be socially desirable, as when we try to keep our minds out of the gutter. People instructed to stop thinking of sex, for example, show greater arousal (as gauged by finger skin conductance) than do those asked to stop thinking about a neutral topic. Indeed, levels of arousal are inflated during the suppression of sex thoughts to the same degree that they inflate during attempts to concentrate on such thoughts (8). In research on sexual arousal per se, male participants instructed to inhibit erections as they watched erotic films found it harder than they had hoped, so to speak—particularly if they imbibed a mental load in the form of a couple of alcoholic drinks (30). Ironic effects also may underlie the tendency of homophobic males to show exaggerated sexual arousal to homoerotic pictures (31).
---------------------QUOTE-------------------


LOL.
Klinghoffer should read this*. Or maybe he knows already...

Ref 31:

< Is homophobia associated with homosexual arousal? >
Adams HE, Wright LW Jr, Lohr BA.
J Abnorm Psychol. 1996 Aug;105(3):440-5.
   

---------------------QUOTE-------------------
The authors investigated the role of homosexual arousal in exclusively heterosexual men who admitted negative affect toward homosexual individuals. Participants consisted of a group of homophobic men (n = 35) and a group of nonhomophobic men (n = 29); they were assigned to groups on the basis of their scores on the Index of Homophobia (W. W. Hudson & W. A. Ricketts, 1980). The men were exposed to sexually explicit erotic stimuli consisting of heterosexual, male homosexual, and lesbian videotapes, and changes in penile circumference were monitored. They also completed an Aggression Questionnaire (A. H. Buss & M. Perry, 1992). Both groups exhibited increases in penile circumference to the heterosexual and female homosexual videos. Only the homophobic men showed an increase in penile erection to male homosexual stimuli. The groups did not differ in aggression. Homophobia is apparently associated with homosexual arousal that the homophobic individual is either unaware of or denies.
---------------------QUOTE-------------------




* His latest homophobic diatribes: < 1** >, < 2 >, < 3 >, < 4 >)

** That's the post that started it all. Klinghoffer reposted a comment from a reader that he found "brilliantly insightful". I think it's friggin' hilarious.
 

---------------------QUOTE-------------------
The social history behind this piece is clear: once they've experienced sex with other men, Catullus tells us, men are unsatisfied with what their new wives provide them. Notice that the poet is unconcerned about the husband's dallying with other women -- it's the other men around that threaten the marital union. [...]

And so now we come back to the idyllic day of free choice and tolerance envisioned by the gay and lesbian movement. It turns out that that day has winners and losers. The winners -- big time -- are homosexual men, because the historical record shows that they can expect their potential pool of partners to expand exponentially. Of note here is that this expanded pool of partners accrues to gay men, but not to homosexual women. At the risk of getting too explicit, I leave it the reader's basic grasp of anatomy to figure out why in ancient Rome a man who found pleasure in a woman, could also find pleasure in a man, while the record shows that a heterosexual woman rarely found sexual satisfaction in the company of another woman.

The losers from all this will be the vast majority of women. With full social sanction given to homoerotic activity, the historical precedent suggests that tomorrow's women will have a harder time finding and holding on to suitable men. As women will suffer, so will the vitality and stability of the nuclear family.[...]

But there is a utilitarian argument as well: full social sanction for the homoerotic bond is opposed not for God's sake, but for the sake of tomorrow's women.
---------------------QUOTE-------------------


tl;dr: If homosexuality becomes socially acceptable, all men will become gay and women won't find someone to marry.
Posted by: dvunkannon on July 03 2009,11:10

Quote (JLT @ July 03 2009,10:57)
How to Think, Say, or Do Precisely the Worst Thing for Any Occasion
Daniel M. Wegner
Science 3 July 2009:
Vol. 325. no. 5936, pp. 48 - 50
< DOI: 10.1126/science.1167346 >
   

---------------------QUOTE-------------------
Ironic lapses of mental control often appear when we attempt to be socially desirable, as when we try to keep our minds out of the gutter. People instructed to stop thinking of sex, for example, show greater arousal (as gauged by finger skin conductance) than do those asked to stop thinking about a neutral topic. Indeed, levels of arousal are inflated during the suppression of sex thoughts to the same degree that they inflate during attempts to concentrate on such thoughts (8). In research on sexual arousal per se, male participants instructed to inhibit erections as they watched erotic films found it harder than they had hoped, so to speak—particularly if they imbibed a mental load in the form of a couple of alcoholic drinks (30). Ironic effects also may underlie the tendency of homophobic males to show exaggerated sexual arousal to homoerotic pictures (31).
---------------------QUOTE-------------------


LOL.
Klinghoffer should read this*. Or maybe he knows already...

Ref 31:

< Is homophobia associated with homosexual arousal? >
Adams HE, Wright LW Jr, Lohr BA.
J Abnorm Psychol. 1996 Aug;105(3):440-5.
   

---------------------QUOTE-------------------
The authors investigated the role of homosexual arousal in exclusively heterosexual men who admitted negative affect toward homosexual individuals. Participants consisted of a group of homophobic men (n = 35) and a group of nonhomophobic men (n = 29); they were assigned to groups on the basis of their scores on the Index of Homophobia (W. W. Hudson & W. A. Ricketts, 1980). The men were exposed to sexually explicit erotic stimuli consisting of heterosexual, male homosexual, and lesbian videotapes, and changes in penile circumference were monitored. They also completed an Aggression Questionnaire (A. H. Buss & M. Perry, 1992). Both groups exhibited increases in penile circumference to the heterosexual and female homosexual videos. Only the homophobic men showed an increase in penile erection to male homosexual stimuli. The groups did not differ in aggression. Homophobia is apparently associated with homosexual arousal that the homophobic individual is either unaware of or denies.
---------------------QUOTE-------------------




* His latest homophobic diatribes: < 1** >, < 2 >, < 3 >, < 4 >)

** That's the post that started it all. Klinghoffer reposted a comment from a reader that he found "brilliantly insightful". I think it's friggin' hilarious.
   

---------------------QUOTE-------------------
The social history behind this piece is clear: once they've experienced sex with other men, Catullus tells us, men are unsatisfied with what their new wives provide them. Notice that the poet is unconcerned about the husband's dallying with other women -- it's the other men around that threaten the marital union. [...]

And so now we come back to the idyllic day of free choice and tolerance envisioned by the gay and lesbian movement. It turns out that that day has winners and losers. The winners -- big time -- are homosexual men, because the historical record shows that they can expect their potential pool of partners to expand exponentially. Of note here is that this expanded pool of partners accrues to gay men, but not to homosexual women. At the risk of getting too explicit, I leave it the reader's basic grasp of anatomy to figure out why in ancient Rome a man who found pleasure in a woman, could also find pleasure in a man, while the record shows that a heterosexual woman rarely found sexual satisfaction in the company of another woman.

The losers from all this will be the vast majority of women. With full social sanction given to homoerotic activity, the historical precedent suggests that tomorrow's women will have a harder time finding and holding on to suitable men. As women will suffer, so will the vitality and stability of the nuclear family.[...]

But there is a utilitarian argument as well: full social sanction for the homoerotic bond is opposed not for God's sake, but for the sake of tomorrow's women.
---------------------QUOTE-------------------


tl;dr: If homosexuality becomes socially acceptable, all men will become gay and women won't find someone to marry.
---------------------QUOTE-------------------


Any single woman in new York City could tell you that all the desirable men were either gay or taken.
Posted by: JLT on July 03 2009,12:50



---------------------QUOTE-------------------
Any single woman in new York City could tell you that all the desirable men were either gay or taken.
---------------------QUOTE-------------------


Well. The only difference, if you still live in a place were homosexuality is a no no, is that it's not gay or taken but gay, taken, or both.
BTW, we all know who's fault it is that there are so many gays. Pornography!
 

---------------------QUOTE-------------------
Some of Dr. Manning’s patients report first encountering pornography at the very young age of 5 or 6. One patient—now a grown man—is struggling with same-sex attraction. He firmly believes he is straight, and wants to get married and have a family. But his first sexual experience was with homosexual pornography—at the age of 9.
---------------------QUOTE-------------------


From < here >, linked to < by DO'L >.
Posted by: sledgehammer on July 03 2009,13:22



---------------------QUOTE-------------------
At the risk of getting too explicit, I leave it the reader's basic grasp of anatomy to figure out why in ancient Rome a man who found pleasure in a woman, could also find pleasure in a man, while the record shows that a heterosexual woman rarely found sexual satisfaction in the company of another woman.

---------------------QUOTE-------------------


And I leave it to the reader to grasp that the author of this statement has a very poor understanding of female sexual arousal, much less female anatomy and ingenuity!
Posted by: Richardthughes on July 06 2009,08:49

< http://www.dailygalaxy.com/my_webl....on.html >




---------------------QUOTE-------------------
Although It has taken homo sapiens several million years to evolve from the apes, the useful information in our DNA, has probably changed by only a few million bits. So the rate of biological evolution in humans, Stephen Hawking points out in his Life in the Universe lecture,  is about a bit a year.

"By contrast," Hawking says, "there are about 50,000 new books published in the English language each year, containing of the order of a hundred billion bits of information. Of course, the great majority of this information is garbage, and no use to any form of life. But, even so, the rate at which useful information can be added is millions, if not billions, higher than with DNA."


This means Hawking says that we have entered a new phase of evolution. "At first, evolution proceeded by natural selection, from random mutations. This Darwinian phase, lasted about three and a half billion years, and produced us, beings who developed language, to exchange information."

But what distinguishes us from our cave man ancestors is the knowledge that we have accumulated over the last ten thousand years, and particularly, Hawking points out, over the last three hundred.

"I think it is legitimate to take a broader view, and include externally transmitted information, as well as DNA, in the evolution of the human race," Hawking said.

....



---------------------QUOTE-------------------


Posted by: dvunkannon on July 06 2009,13:55

< Spores Spill Evolution's Secrets >




---------------------QUOTE-------------------
Developmental "noise" -- the imprecision in molecular pathways that leads to minor slip-ups in development -- creates fodder for evolution. That's the conclusion of a paper published online yesterday (July 5) in Nature, which shows that a single mutation in bacterial spore formation that affect individuals in different ways generates morphological diversity that can then be genetically fine-tuned to maximize an organism's fitness.

---------------------QUOTE-------------------



I'm guessing Mendel's Accountant doesn't do partial penetrance.
Posted by: sledgehammer on July 06 2009,17:15

Quote (Richardthughes @ July 06 2009,06:49)
< http://www.dailygalaxy.com/my_webl....on.html >
     

---------------------QUOTE-------------------
Although It has taken homo sapiens several million years to evolve from the apes, the useful information in our DNA, has probably changed by only a few million bits. So the rate of biological evolution in humans, Stephen Hawking points out in his Life in the Universe lecture,  is about a bit a year.

...<snip>

---------------------QUOTE-------------------


---------------------QUOTE-------------------


Does anybody have even an estimate for how much "useful information" separates H. sapiens from say, A. afarensis, as compared to the genetic variation within the current human population, much less from "apes"?
I suspect it's even less than "only a few million bits".

Anyway, a more useful number genetically, would probably be bits/generation*population rather than bits/year.

Not to disparage the Great Stephen, but HINAB, and I think his main point was to contrast genetic and cultural evolution, so I'm inclined to give him the benefit of the doubt.
Posted by: Henry J on July 06 2009,17:23

Quote (sledgehammer @ July 06 2009,16:15)
Does anybody have even an estimate for how much "useful information" separates H. sapiens from say, A. afarensis, as compared to the genetic variation within the current human population, much less from "apes"?
---------------------QUOTE-------------------


Useful to who?

:)
Posted by: Albatrossity2 on July 08 2009,09:50

< Monkeys can learn grammar >.

Is there hope for Denyse?
Posted by: Erasmus, FCD on July 08 2009,10:42

Quote (dvunkannon @ July 06 2009,14:55)
< Spores Spill Evolution's Secrets >


 

---------------------QUOTE-------------------
Developmental "noise" -- the imprecision in molecular pathways that leads to minor slip-ups in development -- creates fodder for evolution. That's the conclusion of a paper published online yesterday (July 5) in Nature, which shows that a single mutation in bacterial spore formation that affect individuals in different ways generates morphological diversity that can then be genetically fine-tuned to maximize an organism's fitness.

---------------------QUOTE-------------------



I'm guessing Mendel's Accountant doesn't do partial penetrance.
---------------------QUOTE-------------------


some of these creationist morons lately have been yammering about SNPs and how they are all deleterious.  fortunately i have already forgotten which creationist moron and where.  

nice
Posted by: Erasmus, FCD on July 22 2009,16:34

< Hand Of God, Wing of Buzzard, both lose >



---------------------QUOTE-------------------
 Robin Lloyd
LiveScience Senior Editor
LiveScience.com robin Lloyd
livescience Senior Editor
livescience.com – Wed Jul 22, 1:46 pm ET

Airplane passengers who like to gaze out at Earth's surface from the window seat have probably noticed this weird phenomenon - many valleys and ridges seem to be evenly spaced. Badlands National Park in South Dakota is a good example.

For decades, scientists have suspected that this strange but widespread regularity emerges from a geological tug-of-war between streams carving rock to create valleys and soil gradually creeping or falling downhill due to disturbances.

A new study by MIT geologist Taylor Perron and his colleagues has worked out a mathematical equation to describe this process and figure out which force is winning the tug-of-war - and by how much.

Their approach also allows them to predict the spacing between valleys and ridges. In fact, Perron and his colleagues tested their primary equation on five landscapes throughout the United States, and correctly predicted the valley and ridge spacings there. The sites included Gabilan Mesa and Napa Valley in the California Coast Ranges; the Dragon's Back pressure ridge along the San Andreas fault in the Carrizo Plain, California; Point of the Mountain in Salt Lake Valley, Utah; and Eaton Hollow in southwestern Pennsylvania.

In all five sites, the equal spacing between valleys is not a result of any structures in the underlying bedrock, such as fractures or faults. The sites are comprised of different a range of rock types, including sandstones, siltstones, conglomerate rocks, and even coal, and have different kinds of vegetation.

Perron said he was surprised to find that the mechanism controlling valley spacing is so simple.

"It was like disassembling a complicated machine, only to discover that it's controlled by a single knob!" he told LiveScience.
---------------------QUOTE-------------------



clearly he has not tuned into BA^77's youtube channel, which also only has a single knob.  which is polished daily.
Posted by: Timothy McDougald on July 24 2009,19:00

< Ants are more rational than Richardthughes > from the abstract:



---------------------QUOTE-------------------
Our results confirm that ants are more rational than Richardthughes.
---------------------QUOTE-------------------

- okay I made that quote up, here is the real abstract:



---------------------QUOTE-------------------
Economic models of animal behaviour assume that decision-makers are rational, meaning that they assess options according to intrinsic fitness value and not by comparison with available alternatives. This expectation is frequently violated, but the significance of irrational behaviour remains controversial. One possibility is that irrationality arises from cognitive constraints that necessitate short cuts like comparative evaluation. If so, the study of whether and when irrationality occurs can illuminate cognitive mechanisms. We applied this logic in a novel setting: the collective decisions of insect societies. We tested for irrationality in colonies of Temnothorax ants choosing between two nest sites that varied in multiple attributes, such that neither site was clearly superior. In similar situations, individual animals show irrational changes in preference when a third relatively unattractive option is introduced. In contrast, we found no such effect in colonies. We suggest that immunity to irrationality in this case may result from the ants’ decentralized decision mechanism. A colony's choice does not depend on site comparison by individuals, but instead self-organizes from the interactions of multiple ants, most of which are aware of only a single site. This strategy may filter out comparative effects, preventing systematic errors that would otherwise arise from the cognitive limitations of individuals.
---------------------QUOTE-------------------


Posted by: midwifetoad on July 24 2009,23:56

I feel a bit guilty foisting this website on innocents, but it's the weekend, so what the hey.

< http://tvtropes.org/pmwiki/pmwiki.php/Main/EvolutionaryLevels >

< http://tvtropes.org/pmwiki/pmwiki.php/Main/YouFailBiologyForever >

Edit: it occurs to me that teachers could do worse than slyly let a link to this site slip out. Maybe with a warning about adult content.
Posted by: Reed on July 25 2009,00:23

Quote (midwifetoad @ July 24 2009,21:56)
I feel a bit guilty foisting this website on innocents, but it's the weekend, so what the hey.

---------------------QUOTE-------------------


< As well you should >!

ETA:
Someone recently pointed me to Bob Altemeyer's < The Authoritarians > (Yeah, I'm probably behind the times.) Anyway, despite some doubts about whether his results merit the significance he attaches to them... his profile of the kind of people attracted to the religious right should be eerily familiar to anyone who has spent any time watching UD or attempting discussion with likes of FTK, Daniel Smith etc.
Posted by: dvunkannon on July 30 2009,10:31

< String Theory Does Something Useful >

Explaining some aspect of high temperature superconductivity -


---------------------QUOTE-------------------
Because of Zaanen's interest in string theory, he and string theoreticist Koenraad Schalm soon became acquainted after Schalm's arrival in Leiden. Zaanen had an unsolved problem and Schalm was an expert in the field of string theory. Their common interest brought them together, and they decided to work jointly on the research. They used the aspect of string theory known as AdS/CFT correspondence. This allows situations in a large relativistic world to be translated into a description at minuscule quantum physics level. This correspondence bridges the gap between these two different worlds. By applying the correspondence to the situation where a black hole vibrates when an electron falls into it, they arrived at the description of electrons that move in and out of a quantum-critical state.

---------------------QUOTE-------------------



Sorry BA^77, not teleportation...
Posted by: Richardthughes on Aug. 06 2009,16:44

< http://www.upi.com/Science....9509244 >
Posted by: midwifetoad on Aug. 07 2009,22:37

Hope this qualifies as science.

< http://www.eurekalert.org/pub_releases/2008-05/sicp-tmp050308.php >

Edit: Crap. Saw this on another board and didn't check the date.

Nevermind.
Posted by: Lou FCD on Aug. 11 2009,08:37

dude.

rats.

< Big-ass pitcher plant discovered in the Philippines >.



---------------------QUOTE-------------------
"The plant is among the largest of all carnivorous plant species and produces spectacular traps as large as other species which catch not only insects, but also rodents as large as rats," says McPherson.
---------------------QUOTE-------------------


Posted by: ppb on Aug. 12 2009,10:38

OMG!!!

< Zombie Ants! >

We're doomed!
Posted by: Richardthughes on Aug. 18 2009,16:36

Get ready for mega-quotemine and Tard jubilation:

< http://www.newscientist.com/article....ne-news >



---------------------QUOTE-------------------
STATISTICAL method that picks out the most significant words in a book could help scholars decode ancient texts like the Voynich manuscript - or even messages from aliens.

Humans find it easy to identify the words that capture the theme of a text - for example, that "whale" is a key word in Moby Dick - but this is a difficult task for computers. Now Marcelo Montemurro, a systems biologist at the University of Manchester, UK, and colleagues have developed a method to identify word importance based on a branch of mathematics called information theory. "It seems that what we call semantics or meaning has a signature at the level of the statistics of words," says Montemurro.


---------------------QUOTE-------------------





---------------------QUOTE-------------------
For a more detailed analysis, the team calculated the "entropy" of each word, a measure of how evenly distributed it is, in both the original text and in a scrambled version in which the words appeared in a random stream. From the difference between the two entropies multiplied by the frequency of the word, the team generated that word's "information value" in the text.

Connective words are fairly uniformly distributed in both the scrambled text and the original, so their information value is low. Significant words have a high value, because they tend to clump in the original and are relatively common. When the team applied the technique to On the Origin of Species, the top 10 words included: species, varieties, hybrids, forms, islands, selection and genera (www.arxiv.org/abs/0907.1558).

Similar methods could have applications in biology, perhaps to identify genes that carry "value". "That's the place where the most direct application of this stuff is," says Marcelo Magnasco at Rockefeller University in New York. "When you're looking at the genome, it's really an alien language."


---------------------QUOTE-------------------


Posted by: J-Dog on Aug. 18 2009,16:46

Quote (Richardthughes @ Aug. 18 2009,16:36)
Get ready for mega-quotemine and Tard jubilation:

 

---------------------QUOTE-------------------
STATISTICAL method that picks out the most significant words in a book could help scholars decode ancient texts like the Voynich manuscript - or even messages from aliens.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


Cliff notes:

If you ran any UD posts and/or comments through this filter, chances of finding Tard are 100%.
Posted by: Erasmus, FCD on Aug. 18 2009,17:00

most informative words for UD

herring
oil
soaked
strawman
right
reasoning
always
linked
evolution
can't
objective
morality
Dawkins
onlookers
provisional
common
design
darwinbots
Posted by: Henry J on Aug. 18 2009,19:47



---------------------QUOTE-------------------


---------------------QUOTE-------------------
Similar methods could have applications in biology, perhaps to identify genes that carry "value". "That's the place where the most direct application of this stuff is," says Marcelo Magnasco at Rockefeller University in New York. "When you're looking at the genome, it's really an alien language."
---------------------QUOTE-------------------


---------------------QUOTE-------------------



Wonder what subjects this guy knows. After reading that, I wouldn't trust his judgment in either genetics or linguistics.

Henry
Posted by: Quack on Aug. 19 2009,04:24

Quote (Lou FCD @ Aug. 11 2009,08:37)
dude.

rats.

< Big-ass pitcher plant discovered in the Philippines >.

 

---------------------QUOTE-------------------
"The plant is among the largest of all carnivorous plant species and produces spectacular traps as large as other species which catch not only insects, but also rodents as large as rats," says McPherson.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


Link is doubled, < fixed here >
Posted by: Richardthughes on Aug. 19 2009,19:04

< http://www.technologyreview.com/blog/editors/24010/?a=f >

evolving robots
Posted by: Timothy McDougald on Aug. 19 2009,20:07

< Advance in understanding endosymbiosis >
Posted by: Lou FCD on Aug. 21 2009,18:33

< Epicycles, the Idea that Just Won't Die >.



---------------------QUOTE-------------------
Current thinking about how spiral galaxies form traces back to an idea nearly 2 millennia old, to 2nd-century Egyptian mathematician Ptolemy. Trying to describe how the five planets in the night sky followed seemingly irregular paths, Ptolemy hit upon an idea he called epicycles. Basically, the theory posits that, as an object orbits, it performs little loops that make it appear to wobble. The idea was revived in the 1920s to explain similar irregular movements among the stars in the Milky Way and later still to describe the formation of galactic spiral arms. But there have been little data to support it.
---------------------QUOTE-------------------


Posted by: ppb on Aug. 25 2009,14:17

This looks interesting.  A researcher in Canada wants to manipulate developing chicken embryos to resurrect ancient dinosaur features.

< http://www.ctvbc.ctv.ca/servlet....biaHome >

Hans Larsson, a paleontologist at McGill University, got the idea from discussions with Jack Horner.

It will be interesting to see how much genetic information remains to be turned back on.
Posted by: Albatrossity2 on Aug. 25 2009,15:48

Quote (ppb @ Aug. 25 2009,14:17)
This looks interesting.  A researcher in Canada wants to manipulate developing chicken embryos to resurrect ancient dinosaur features.

< http://www.ctvbc.ctv.ca/servlet....biaHome >

Hans Larsson, a paleontologist at McGill University, got the idea from discussions with Jack Horner.

It will be interesting to see how much genetic information remains to be turned back on.
---------------------QUOTE-------------------


In 1980 a couple of scientists reported that teeth could be induced to grow from the right combination of mouse mesenchyme and chicken jaw epithelium. (Kollar E.J. & Fisher C., "Tooth induction in chick epithelium: expression of quiescent genes for enamel synthesis," Science, Vol. 207, February 29, 1980, pp.993-5). The hypothesis was that long-dormant chicken genes were activated by some signal in the mouse tissue; those were dinosaur molars!

In 2006 another pair of scientists published a paper in Current Biology (summarized < here) >, reporting some progress in identifying the signaling pathways that might be involved in chicken tooth production.
Posted by: Henry J on Aug. 25 2009,20:16



---------------------QUOTE-------------------
A researcher in Canada wants to manipulate developing chicken embryos to resurrect ancient dinosaur features.
---------------------QUOTE-------------------



Goody; research somebody can sink their teeth into!

Henry
Posted by: Quack on Aug. 26 2009,00:43

Quote (Henry J @ Aug. 25 2009,20:16)
     

---------------------QUOTE-------------------
A researcher in Canada wants to manipulate developing chicken embryos to resurrect ancient dinosaur features.
---------------------QUOTE-------------------



Goody; research somebody can sink their teeth into!

Henry
---------------------QUOTE-------------------


Another case of < thunder thievery - S-F coming true? >
Posted by: Lou FCD on Aug. 27 2009,20:12



---------------------QUOTE-------------------
August 26, 2009—With needle-sharp poisonous fangs and powerful limbs sprouting from its head, you probably won't find this crab cousin floating in a creamy bisque anytime soon.

The newfound eyeless crustacean was recently discovered in the world's longest underwater lava tube, on the island of Lanzarote in the Spanish-ruled Canary Islands. (See map.)
---------------------QUOTE-------------------



< More here >, at NatGeo.
Posted by: Henry J on Aug. 27 2009,21:40



---------------------QUOTE-------------------
Element 112 shall be named copernicium
Proposed name honours astronomer Nicolaus Copernicus

In honour of scientist and astronomer Nicolaus Copernicus (1473-1543), the discovering team around Professor Sigurd Hofmann suggested the name copernicium with the element symbol Cp for the new element 112, discovered at the GSI Helmholtzzentrum f?r Schwerionenforschung (Center for Heavy Ion Research) in Darmstadt.
---------------------QUOTE-------------------



< http://www.webelements.com/ >

Henry
Posted by: sledgehammer on Aug. 28 2009,12:12

< Evidence of recent evolution in Deer Mice >
Deer mice of the Sand hills in Nebraska have recently (in the last 4000 years) evolved a new, lighter color coat, that better matches their environment.

New coat color? Pfft.  Micro-evolution. No big deal.

Not so fast there, Poindexter.  The color change is a manifestation of a brand new gene, Agouti, that developed in around 8000 generations.  From the article:  

---------------------QUOTE-------------------
"The light gene wasn't in existence, so the mice had to "wait" until a particular mutation occurred and then selection had to act on that new mutation," says team member Professor Hopi Hoekstra, also of Harvard University.

"It's a two part process. First the mutation has to occur and second, selection has to increase its frequency."

The researchers say it is the first time that it has been possible to document the appearance of a gene, its selection and subsequent spread through a population of wild animals.

And that has allowed them to estimate the "strength" of the natural selection pressure.

Having light coloured fur gives the paler Sand Hills mice a 0.5% survival advantage.

"It doesn't seem that much, but multiplied over thousands of individuals over hundreds of years, it makes a huge difference," says Prof Hoekstra.

"Ours is a very complete story," adds Dr Linnen.

"We've been able to connect changes at DNA level to the ability of deer mice to survive in nature."
---------------------QUOTE-------------------


Now how many bits of "FSCI" does this new gene represent?  More than 140?  Must have been a direct intervention by god! :p
Posted by: Erasmus, FCD on Aug. 28 2009,13:34

they're still just mice.

yawn.

wake me up when one gives birth to a dog-cat.
Posted by: ppb on Aug. 28 2009,13:52

Quote (Erasmus @ FCD,Aug. 28 2009,14:34)
they're still just mice.

yawn.

wake me up when one gives birth to a dog-cat.
---------------------QUOTE-------------------


Will you accept a dog-racoon?


Posted by: Timothy McDougald on Aug. 28 2009,19:19

Quote (Erasmus, FCD @ Aug. 28 2009,13:34)
they're still just mice.

yawn.

wake me up when one gives birth to a dog-cat.
---------------------QUOTE-------------------


I'm holding out for a fishungulant myself - part barracuda, part moose, and all Sarah Palin!
Posted by: bfish on Aug. 29 2009,02:55

Quote (sledgehammer @ Aug. 28 2009,10:12)
< Evidence of recent evolution in Deer Mice >
Deer mice of the Sand hills in Nebraska have recently (in the last 4000 years) evolved a new, lighter color coat, that better matches their environment.
---------------------QUOTE-------------------


Dude, were you there?

[QUOTE]
The color change is a manifestation of a brand new gene, Agouti, that developed in around 8000 generations.  From the article:          

---------------------QUOTE-------------------
"The light gene wasn't in existence, so the mice had to "wait" until a particular mutation occurred and then selection had to act on that new mutation," says team member Professor Hopi Hoekstra, also of Harvard University.

"It's a two part process. First the mutation has to occur and second, selection has to increase its frequency."
---------------------QUOTE-------------------



I think this isn't quite correct. I don't have access to the article from home, but < agouti > is a pretty well-known gene. I think she's using sloppy "popular science" speak, whereby what she means to say is that the light mutation of the already existing Agouti gene wasn't present in the population.

I'm curious to know the nature of the mutation. It would be deliciously ironic if it were a mutation in Agouti regulation rather than in coding sequence (see < this > for explanation). I'll bet it's a coding mutation, though. Damn cool stuff, too.

Anyone who has access to the article, please let me know if I'm wrong about any of this.

ETA: my lameness in not being able to make the block quotes work.
Posted by: Timothy McDougald on Aug. 29 2009,08:24

Quote (bfish @ Aug. 29 2009,02:55)
Quote (sledgehammer @ Aug. 28 2009,10:12)
< Evidence of recent evolution in Deer Mice >
Deer mice of the Sand hills in Nebraska have recently (in the last 4000 years) evolved a new, lighter color coat, that better matches their environment.
---------------------QUOTE-------------------


Dude, were you there?

[QUOTE]
The color change is a manifestation of a brand new gene, Agouti, that developed in around 8000 generations.  From the article:            

---------------------QUOTE-------------------
"The light gene wasn't in existence, so the mice had to "wait" until a particular mutation occurred and then selection had to act on that new mutation," says team member Professor Hopi Hoekstra, also of Harvard University.

"It's a two part process. First the mutation has to occur and second, selection has to increase its frequency."
---------------------QUOTE-------------------



I think this isn't quite correct. I don't have access to the article from home, but < agouti > is a pretty well-known gene. I think she's using sloppy "popular science" speak, whereby what she means to say is that the light mutation of the already existing Agouti gene wasn't present in the population.

I'm curious to know the nature of the mutation. It would be deliciously ironic if it were a mutation in Agouti regulation rather than in coding sequence (see < this > for explanation). I'll bet it's a coding mutation, though. Damn cool stuff, too.

Anyone who has access to the article, please let me know if I'm wrong about any of this.

ETA: my lameness in not being able to make the block quotes work.
---------------------QUOTE-------------------


Yeah, I don't have access either, but would love to have a copy. Especially since one of the coauthors of the paper I mention below is involved in the new paper. This is pretty common in mice, a previous study on < mainland vs beach dwelling forms > indicates that an interaction between Mc1r and Agouti is responsible for the lighter color in beach forms. Be interesting to see if this is the case in the new paper also...
Posted by: bfish on Aug. 30 2009,02:25

OK, I've seen the paper now.

They begin with the observation that the mice who live in the Sand Hills have lighter-colored coats than nearby mice of the same species who live on darker soils, and the knowledge that the Sand Hills are geologically young (apparently can't be older than the date of the last glacial retreat). This leads to the inference that the lighter coat has evolved relatively recently (i.e. no more than two times the age of the universe, according to Ken Ham).
They want to know the genetic cause of the color difference. Sequencing is getting cheaper and faster, but it's still neither cheap enough nor fast enough that you could sequence the entire genomes of the several population groups that they want to sample. So they need to zero in on a target for their search. They looked at the agouti gene specifically because it is known to be involved in hair color phenotype in mice. This allowed them to sequence only the region near agouti. They found several sequence differences between light and dark mice, and concluded that one of them, an amino acid deletion (Dang. I was hoping for regulatory sequence) is probably responsible for the coat color phenotype.
They then calculated the selection coefficent and used population genetics to estimate that the light coat color allele should achieve fixation (all mice in the Sand Hills would carry the allele) in roughly half the life span of the Sand Hills. Since not all the mice do, they infer (with the support of several other observations) that the mutation causing the amino acid deletion did not exist in the initial mice population.

All good stuff.

It is important to note, though, that their beak sizes did not change at all.

If I have represented any of this wrongly, please correct me here.
Also, if any mice people see this, could they use homologous recombination to replace the amino acid deletion with the pre-mutation sequence, in order to prove that the deletion is sufficient to cause the light coat color? (i.e. returning the gene to it's prior state should cause the coat color to darken).
Posted by: sledgehammer on Aug. 30 2009,11:59

Thanks bfish, for digging up the details.  I apologize for taking the BBC blurb a little too literally. I should know better.
 I am but a humble physicist, and although I had learned of the agouti gene in mice, it's not a fact I use everyday. it's been a while since undergrad genetics and my memory is getting old and decrepit.
 So what are the odds of that protein island, in the middle of the vast sea on non-functional sequences, arising by chance mutations?  A bazillion-gazillion-to-one???!!!111!!! (technical physics terminology)
God must love those meeces to pieces, to make that change just for them!
Posted by: Henry J on Aug. 30 2009,17:29



---------------------QUOTE-------------------
It is important to note, though, that their beak sizes did not change at all.
---------------------QUOTE-------------------


They also didn't grow wings or start talking. :)

Henry
Posted by: jeannot on Sep. 01 2009,10:57

Quote (afarensis @ Aug. 28 2009,19:19)
 
Quote (Erasmus @ FCD,Aug. 28 2009,13:34)
they're still just mice.

yawn.

wake me up when one gives birth to a dog-cat.
---------------------QUOTE-------------------


I'm holding out for a fishungulant myself - part barracuda, part moose, and all Sarah Palin!
---------------------QUOTE-------------------


Talking about hybridization, there's a bizarre paper on the early edition of PNAS.

"Caterpillars evolved from onychophorans by hybridogenesis"

< http://www.pnas.org/content/early/2009/08/25/0908357106.abstract >

Yes, you read it right. (for your info, onychophorans are not even arthropods)
I find it quite disturbing. The author (Donald Williamson) proposes that some larvae and their adults do not have a shared ancestry, but that larvae (namely caterpillars) were acquired by hybridization with distant taxa.
Although the hypothesis is testable, it seem extremely far-fetched, and in any case, not tested in the paper. So the title is highly misleading.
This reminds me of some JAD's paper, the guy does not seem to like Darwin either.

How could such paper pass through the editorial board?  
???
Posted by: qetzal on Sep. 01 2009,20:56

Quote (jeannot @ Sep. 01 2009,10:57)
Quote (afarensis @ Aug. 28 2009,19:19)
   
Quote (Erasmus @ FCD,Aug. 28 2009,13:34)
they're still just mice.

yawn.

wake me up when one gives birth to a dog-cat.
---------------------QUOTE-------------------


I'm holding out for a fishungulant myself - part barracuda, part moose, and all Sarah Palin!
---------------------QUOTE-------------------


Talking about hybridization, there's a bizarre paper on the early edition of PNAS.

"Caterpillars evolved from onychophorans by hybridogenesis"

< http://www.pnas.org/content/early/2009/08/25/0908357106.abstract >

Yes, you read it right. (for your info, onychophorans are not even arthropods)
I find it quite disturbing. The author (Donald Williamson) proposes that some larvae and their adults do not have a shared ancestry, but that larvae (namely caterpillars) were acquired by hybridization with distant taxa.
Although the hypothesis is testable, it seem extremely far-fetched, and in any case, not tested in the paper. So the title is highly misleading.
This reminds me of some JAD's paper, the guy does not seem to like Darwin either.

How could such paper pass through the editorial board?  
???
---------------------QUOTE-------------------


Must be because it's PNAS, and it was communicated by Lynn Margulis. PNAS gives academy members special rights to communicate papers and more-or-less bypass 'normal' peer review. From the < PNAS Info for Authors > page:



---------------------QUOTE-------------------
An Academy member may “communicate” for others up to 2 manuscripts per year that are within the member's area of expertise. Before submission to PNAS, the member obtains reviews of the paper from at least 2 qualified referees, each from a different institution and not from the authors' or member's institutions. Referees should be asked to evaluate revised manuscripts to ensure that their concerns have been adequately addressed. The names and contact information, including e-mails, of referees who reviewed the paper, along with the reviews and the authors' response, must be included. Reviews must be submitted on the PNAS review form, and the identity of the referees must not be revealed to the authors. The member must include a brief statement endorsing publication in PNAS along with all of the referee reports received for each round of review. Members should follow National Science Foundation (NSF) guidelines to avoid conflict of interest between referees and authors (see Section iii). Members must verify that referees are free of conflicts of interest, or must disclose any conflicts and explain their choice of referees. These papers are published as “Communicated by" the responsible editor.
---------------------QUOTE-------------------



I assume Margulis is an NAS member. Still, it's pretty bizzare that she would agree to communicate such nonsense, or that she was able to find two qualified referees to agree that it should be published!
Posted by: jeannot on Sep. 02 2009,00:56

Yes, I noticed that it was a communicated paper. No way it could have been otherwise. But this should be examined by the editorial board anyway.  
But it seems that Margulis has published with this author. She must be seduced by anything controversial or something.
It is not good for PNAS's reputation, and their submitting procedure for NAS member could be criticized.

At the end of the paper, the author proposes crossing an insect and an onychophoran! I almost laughed. On can barely cross related species, that's called (postmating) reproductive isolation.
The predictions about gene content are ridiculous too. Gene content can vary greatly between related species, due to polyploidization, etc.
Posted by: Erasmus, FCD on Sep. 02 2009,01:16

i've never heard such stuff as that.  should be fun.
Posted by: Richardthughes on Sep. 02 2009,09:49

Brace for quotemine:

< http://www.newscientist.com/article....am.html >



---------------------QUOTE-------------------
I'm an empirical kind of guy, and there is just no evidence of an artificial toehold in sentience. It is often forgotten that the idea of mind or brain as computational is merely an assumption, not a truth. When I point this out to "believers" in the computational theory of mind, some of their arguments are almost religious.
---------------------QUOTE-------------------


Posted by: sledgehammer on Sep. 03 2009,23:00

< Origins:  The Zinc Link? >
 

---------------------QUOTE-------------------
This work puts forward an evolutionary scenario that satisfies the known constraints by proposing that life on Earth emerged, powered by UV-rich solar radiation, at photosynthetically active porous edifices made of precipitated zinc sulfide (ZnS) similar to those found around modern deep-sea hydrothermal vents. Under the high pressure of the primeval, carbon dioxide-dominated atmosphere ZnS could precipitate at the surface of the first continents, within reach of solar light. It is suggested that the ZnS surfaces (1) used the solar radiation to drive carbon dioxide reduction, yielding the building blocks for the first biopolymers, (2) served as templates for the synthesis of longer biopolymers from simpler building blocks, and (3) prevented the first biopolymers from photo-dissociation, by absorbing from them the excess radiation. In addition, the UV light may have favoured the selective enrichment of photostable, RNA-like polymers. Falsification tests of this hypothesis are described in the accompanying article (A.Y. Mulkidjanian, M.Y. Galperin, Biology Direct 2009, 4:27).
---------------------QUOTE-------------------


< Abstr. Part 2 >
< and PDFs too! >
< and PDF two >
Posted by: Henry J on Sep. 04 2009,14:17

< Pandamonium! >

Oh, and it's a boy.
Posted by: Bob O'H on Sep. 04 2009,15:46



---------------------QUOTE-------------------
I'm curious to know the nature of the mutation. It would be deliciously ironic if it were a mutation in Agouti regulation rather than in coding sequence (see this for explanation). I'll bet it's a coding mutation, though. Damn cool stuff, too.
---------------------QUOTE-------------------


She has found < mutations in regulatory sequences that affected coat colour > in the past.
Posted by: Timothy McDougald on Sep. 04 2009,18:53

Quote (Bob O'H @ Sep. 04 2009,15:46)


---------------------QUOTE-------------------
I'm curious to know the nature of the mutation. It would be deliciously ironic if it were a mutation in Agouti regulation rather than in coding sequence (see this for explanation). I'll bet it's a coding mutation, though. Damn cool stuff, too.
---------------------QUOTE-------------------


She has found < mutations in regulatory sequences that affected coat colour > in the past.
---------------------QUOTE-------------------


There is some interesting stuff on < her publication page. >
Posted by: bfish on Sep. 04 2009,20:01

Quote (afarensis @ Sep. 04 2009,16:53)
Quote (Bob O'H @ Sep. 04 2009,15:46)
 

---------------------QUOTE-------------------
I'm curious to know the nature of the mutation. It would be deliciously ironic if it were a mutation in Agouti regulation rather than in coding sequence (see this for explanation). I'll bet it's a coding mutation, though. Damn cool stuff, too.
---------------------QUOTE-------------------


She has found < mutations in regulatory sequences that affected coat colour > in the past.
---------------------QUOTE-------------------


There is some interesting stuff on < her publication page. >
---------------------QUOTE-------------------


Yes, and #16 on the list

# *Hoekstra, H.E. and J.A. Coyne. 2007. The locus of evolution: evo devo and the genetics of adaptation.  Evolution. 61(5):995-1016.

is what I was alluding to when I said it would be ironic if the adaptive coat color change was caused by regulatory sequence. In that paper they list 35 examples of adaptations caused by changes in protein coding sequence while maintaining that there are (or were in 2007) zero proven examples of adaptations caused by changes in regulatory sequence. They argue that one must meet the standard of showing what the specific mutation is AND demonstrating it's adaptive value.

In the new paper they show a specific mutation AND they measure the adaptive value of a phenotype they believe is caused by that mutation. So it would have been fun if it had been a regulatory mutation. I wonder, though, if they met there own standard in this paper, because I'm not sure they PROVE that the mutation they focus on causes the phenotype. That's why I asked if it would be possible for them to take mice from the native population and replace, in their progeny, the new version of the gene with a version of the gene that repairs the amino acid deletion. Then you could see if the dark phenotype was rescued, which would be very convincing evidence that the deletion caused the light color phenotype. I'm not a mouse person, so I don't know if that is technically feasible.
Posted by: Timothy McDougald on Sep. 04 2009,20:59

Quote (bfish @ Sep. 04 2009,20:01)
Quote (afarensis @ Sep. 04 2009,16:53)
 
Quote (Bob O'H @ Sep. 04 2009,15:46)
 

---------------------QUOTE-------------------
I'm curious to know the nature of the mutation. It would be deliciously ironic if it were a mutation in Agouti regulation rather than in coding sequence (see this for explanation). I'll bet it's a coding mutation, though. Damn cool stuff, too.
---------------------QUOTE-------------------


She has found < mutations in regulatory sequences that affected coat colour > in the past.
---------------------QUOTE-------------------


There is some interesting stuff on < her publication page. >
---------------------QUOTE-------------------


Yes, and #16 on the list

# *Hoekstra, H.E. and J.A. Coyne. 2007. The locus of evolution: evo devo and the genetics of adaptation.  Evolution. 61(5):995-1016.

is what I was alluding to when I said it would be ironic if the adaptive coat color change was caused by regulatory sequence. In that paper they list 35 examples of adaptations caused by changes in protein coding sequence while maintaining that there are (or were in 2007) zero proven examples of adaptations caused by changes in regulatory sequence. They argue that one must meet the standard of showing what the specific mutation is AND demonstrating it's adaptive value.

In the new paper they show a specific mutation AND they measure the adaptive value of a phenotype they believe is caused by that mutation. So it would have been fun if it had been a regulatory mutation. I wonder, though, if they met there own standard in this paper, because I'm not sure they PROVE that the mutation they focus on causes the phenotype. That's why I asked if it would be possible for them to take mice from the native population and replace, in their progeny, the new version of the gene with a version of the gene that repairs the amino acid deletion. Then you could see if the dark phenotype was rescued, which would be very convincing evidence that the deletion caused the light color phenotype. I'm not a mouse person, so I don't know if that is technically feasible.
---------------------QUOTE-------------------


Yeah, I don't think they prove that either, granted what they do have strongly suggests that it does, but they didn't seal the deal. I'll have to download the paper your talking about (among others), sigh, too many science papers, too little time to blog about them...
Posted by: jeannot on Sep. 05 2009,13:55

Some update on pea aphids:

Post-Pleistocene radiation of the pea aphid complex revealed by rapidly evolving endosymbionts

Jean Peccoud, Jean-Christophe Simon, Heather J. McLaughlin, and Nancy A. Moran

< http://www.pnas.org/content/early/2009/09/03/0905129106.abstract >

Basically, our pea aphid races and species have a very recent origin that may be linked to the domestication of some of their host plants.

I can send the pdf to anyone interested.
Posted by: jeannot on Sep. 05 2009,14:05

Quote (bfish @ Aug. 29 2009,02:55)
I'm curious to know the nature of the mutation. It would be deliciously ironic if it were a mutation in Agouti regulation rather than in coding sequence.
---------------------QUOTE-------------------


When I read "cis-acting mutation" in the abstract, I thought "how ironic", since the term reminded me the work of Sean Caroll on cis-regulatory sequences.
Posted by: Timothy McDougald on Sep. 06 2009,13:49

Speaking of botany there is a new paper called Xylem heterochrony: an unappreciated key to angiosperm origin and diversifications in the Botanical Journal of the Linnean Society, 2009; 161 (1): 26 DOI: 10.1111/j.1095-8339.2009.00991.x. Here is the abstract:



---------------------QUOTE-------------------
All angiosperms can be arranged along a spectrum from a preponderance of juvenile traits (cambial activity lost) to one of nearly all adult characters (cambium maximally active, mature patterns realized rapidly early in ontogeny). Angiosperms are unique among seed plants in the width of this spectrum. Xylem patterns are considered here to be indicative of contemporary function, not relictual. Nevertheless, most families of early-divergent angiosperms exhibit paedomorphic xylem structure, a circumstance that is most plausibly explained by the concept that early angiosperms had sympodial growth forms featuring limited accumulation of secondary xylem. Sympodial habits have been retained in various ways not only in early-divergent angiosperms, but also among eudicots in Ranunculales. The early angiosperm vessel, relatively marginal in conductive abilities, was improved in various ways, with concurrent redesign of parenchyma and fibre systems to enhance conductive, storage and mechanical capabilities. Flexibility in degree of cambial activity and kinds of juvenile/adult expressions has been basic to diversification in eudicots as a whole. Sympodial growth that lacks cambium, such as in monocots, provides advantages by various features, such as organographic compartmentalization of tracheid and vessel types. Woody monopodial eudicots were able to diversify as a result of production of new solutions to embolism prevention and conductive efficiency, particularly in vessel design, but also in parenchyma histology. Criteria for paedomorphosis in wood include slow decrease in length of fusiform cambial initials, predominance of procumbent ray cells and lesser degrees of cambial activity. Retention of ancestral features in primary xylem (the 'refugium' effect) is, in effect, a sort of inverse evidence of acceleration of adult patterns in later formed xylem. Xylem heterochrony is analysed not only for all key groups of angiosperms (including monocots), but also for different growth forms, such as lianas, annuals, various types of perennials, rosette trees and stem succulents. Xylary phenomena that potentially could be confused with heterochrony are discussed. Heterochronous xylem features seem at least as important as other often cited factors (pollination biology) because various degrees of paedomorphic xylem are found in so many growth forms that relate in xylary terms to ecological sites. Xylem heterochrony can probably be accessed during evolution by relatively simple gene changes in a wide range of angiosperms and thus represents a current as well as a past source of variation upon which diversification was based. Results discussed here are compatible with both current molecular-based phylogenetic analyses and all recent physiological work on conduction in xylem and thus represent an integration of these fields.
---------------------QUOTE-------------------



It does require a subscription....

Edited to correct some typos
Posted by: Albatrossity2 on Sep. 10 2009,11:29

One of the great old-time biologists, < Henry Fitch >, has passed away at the ripe old age of 99. He was still working (at the biological preserve named after him) up to the age of 96!
Posted by: dvunkannon on Sep. 10 2009,11:51

Quote (sledgehammer @ Sep. 04 2009,00:00)
< Origins:  The Zinc Link? >
 

---------------------QUOTE-------------------
This work puts forward an evolutionary scenario that satisfies the known constraints by proposing that life on Earth emerged, powered by UV-rich solar radiation, at photosynthetically active porous edifices made of precipitated zinc sulfide (ZnS) similar to those found around modern deep-sea hydrothermal vents. Under the high pressure of the primeval, carbon dioxide-dominated atmosphere ZnS could precipitate at the surface of the first continents, within reach of solar light. It is suggested that the ZnS surfaces (1) used the solar radiation to drive carbon dioxide reduction, yielding the building blocks for the first biopolymers, (2) served as templates for the synthesis of longer biopolymers from simpler building blocks, and (3) prevented the first biopolymers from photo-dissociation, by absorbing from them the excess radiation. In addition, the UV light may have favoured the selective enrichment of photostable, RNA-like polymers. Falsification tests of this hypothesis are described in the accompanying article (A.Y. Mulkidjanian, M.Y. Galperin, Biology Direct 2009, 4:27).
---------------------QUOTE-------------------


< Abstr. Part 2 >
< and PDFs too! >
< and PDF two >
---------------------QUOTE-------------------


I just finished reading the first article yesterday. I think they did a great job of bringing together multiple streams of evidence to support their hypothesis, as well as bridging the RNA-world and metabolism first divide.

Definitely something to wave in front of GERM of TIKI the next time he goes on about the always linked improbabilities of OOL. It looks like you don't need plate tectonics to get started, though tides might help.
Posted by: Henry J on Sep. 10 2009,14:12

I zinc, therefore I am?
Posted by: sledgehammer on Sep. 10 2009,16:20

Quote (dvunkannon @ Sep. 10 2009,09:51)
   
Quote (sledgehammer @ Sep. 04 2009,00:00)
< Origins:  The Zinc Link? >
       

---------------------QUOTE-------------------
This work puts forward an evolutionary scenario that satisfies the known constraints by proposing that life on Earth emerged, powered by UV-rich solar radiation, at photosynthetically active porous edifices made of precipitated zinc sulfide (ZnS) similar to those found around modern deep-sea hydrothermal vents. Under the high pressure of the primeval, carbon dioxide-dominated atmosphere ZnS could precipitate at the surface of the first continents, within reach of solar light. It is suggested that the ZnS surfaces (1) used the solar radiation to drive carbon dioxide reduction, yielding the building blocks for the first biopolymers, (2) served as templates for the synthesis of longer biopolymers from simpler building blocks, and (3) prevented the first biopolymers from photo-dissociation, by absorbing from them the excess radiation. In addition, the UV light may have favoured the selective enrichment of photostable, RNA-like polymers. Falsification tests of this hypothesis are described in the accompanying article (A.Y. Mulkidjanian, M.Y. Galperin, Biology Direct 2009, 4:27).
---------------------QUOTE-------------------


< Abstr. Part 2 >
< and PDFs too! >
< and PDF two >
---------------------QUOTE-------------------


I just finished reading the first article yesterday. I think they did a great job of bringing together multiple streams of evidence to support their hypothesis, as well as bridging the RNA-world and metabolism first divide.

Definitely something to wave in front of GERM of TIKI the next time he goes on about the always linked improbabilities of OOL. It looks like you don't need plate tectonics to get started, though tides might help.
---------------------QUOTE-------------------


Except for the extent of plate tectonics being resposible for undersea vents?
Also, for part 2 abstract and PDF, change the ref number inthe URL's from "26" to "27"
i.e
< Abstr. Part 2 >
< and PDF two >

My bad.
Posted by: dvunkannon on Sep. 10 2009,17:52

Quote (sledgehammer @ Sep. 10 2009,17:20)
Quote (dvunkannon @ Sep. 10 2009,09:51)
   
Quote (sledgehammer @ Sep. 04 2009,00:00)
< Origins:  The Zinc Link? >
       

---------------------QUOTE-------------------
This work puts forward an evolutionary scenario that satisfies the known constraints by proposing that life on Earth emerged, powered by UV-rich solar radiation, at photosynthetically active porous edifices made of precipitated zinc sulfide (ZnS) similar to those found around modern deep-sea hydrothermal vents. Under the high pressure of the primeval, carbon dioxide-dominated atmosphere ZnS could precipitate at the surface of the first continents, within reach of solar light. It is suggested that the ZnS surfaces (1) used the solar radiation to drive carbon dioxide reduction, yielding the building blocks for the first biopolymers, (2) served as templates for the synthesis of longer biopolymers from simpler building blocks, and (3) prevented the first biopolymers from photo-dissociation, by absorbing from them the excess radiation. In addition, the UV light may have favoured the selective enrichment of photostable, RNA-like polymers. Falsification tests of this hypothesis are described in the accompanying article (A.Y. Mulkidjanian, M.Y. Galperin, Biology Direct 2009, 4:27).
---------------------QUOTE-------------------


< Abstr. Part 2 >
< and PDFs too! >
< and PDF two >
---------------------QUOTE-------------------


I just finished reading the first article yesterday. I think they did a great job of bringing together multiple streams of evidence to support their hypothesis, as well as bridging the RNA-world and metabolism first divide.

Definitely something to wave in front of GERM of TIKI the next time he goes on about the always linked improbabilities of OOL. It looks like you don't need plate tectonics to get started, though tides might help.
---------------------QUOTE-------------------


Except for the extent of plate tectonics being resposible for undersea vents?
Also, for part 2 abstract and PDF, change the ref number inthe URL's from "26" to "27"
i.e
< Abstr. Part 2 >
< and PDF two >

My bad.
---------------------QUOTE-------------------


While the article explains the hydrothermal precipitation of ZnS with reference to what we see today at the mid ocean ridges caused by plate tectonics, it also makes clear (deep in the article) that the huge ZnS outflows such as the Pilbara Craton of the early Earth took place at the continental surface as the result of volcanic hot spots and high atmospheric pressure working together - hydrothermal does not imply deep ocean in this case.

Plate tectonics would still be important later in sequestering carbon, but just to get life started, they are argunig not necessary.
Posted by: sledgehammer on Sep. 10 2009,18:25

Quote (dvunkannon @ Sep. 10 2009,15:52)
   
Quote (dvunkannon @ Sep. 10 2009,09:51)
     
While the article explains the hydrothermal precipitation of ZnS with reference to what we see today at the mid ocean ridges caused by plate tectonics, it also makes clear (deep in the article) that the huge ZnS outflows such as the Pilbara Craton of the early Earth took place at the continental surface as the result of volcanic hot spots and high atmospheric pressure working together - hydrothermal does not imply deep ocean in this case.

Plate tectonics would still be important later in sequestering carbon, but just to get life started, they are argunig not necessary.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


Yes I see that now.  Thanks for clearing that up.  From the abstract in part 2:
   

---------------------QUOTE-------------------
Results
If  life  started within  photosynthesizing  ZnS compartments,  it  should  have  been  able  to  evolve under  the  conditions  of  elevated  levels  of  Zn2+  ions,  byproducts  of  the  ZnS-mediated photosynthesis.  Therefore,  the  Zn  world  hypothesis  leads  to  a  set  of  testable  predictions regarding  the  specific  roles  of Zn2+  ions  in modern  organisms,  particularly  in RNA  and  protein structures  related  to  the  procession  of RNA  and  the  “evolutionarily  old”  cellular  functions.   We checked  these  predictions  using  publicly  available  data  and  obtained  evidence  suggesting  that the  development  of  the  primeval  life  forms  up  to  the  stage  of  the  Last  Universal  Common Ancestor  proceeded  in  zinc-rich  settings.   Testing  of  the  hypothesis  has  revealed  the  possible supportive role of manganese sulfide in the primeval photosynthesis.  In addition, we demonstrate the explanatory power of the Zn world concept by elucidating several points that so far remained without  acceptable  rationalization.    In  particular,  this  concept  implies  a  new  scenario  for  the separation of Bacteria and Archaea and the origin of Eukarya.  
---------------------QUOTE-------------------


I also notice that Gene Koonin was one of the reviewers. Here's (part of) what he had to say:
   

---------------------QUOTE-------------------
...The idea of the pivotal role  of  Zn  ions  (and  ZnS  in  particular)  in  the  earliest  stages  of  the  evolution  of  life  is  highly attractive and generally plausible. However, in this manuscript, Mulkidjanian and Galperin put the plank very high by formulating several predictions that they claim to serve as Popperian tests of the “Zn world” hypothesis. In principle, the intention to test the hypothesis in a formal Popperian setting  is  indeed  commendable.  In  practice,  it  is well  known  that  it  is  hard  to  strictly  adhere  to Popperian criteria,  and  this paper  is no exception...
---------------------QUOTE-------------------


I think it is very cool that the reviewers comments and the responses by the authors are included in the manuscript.  Is this common in biology?  I've not seen this in the physics realm, unless I was one of the reviewers.
Posted by: Timothy McDougald on Sep. 10 2009,21:45

In light of the recent paper - and fuss- on the appendix this paper is topical. < Relaxed selection in the wild > here is the abstract:


---------------------QUOTE-------------------
Natural populations often experience the weakening or removal of a source of selection that had been important in the maintenance of one or more traits. Here we refer to these situations as relaxed selection, and review recent studies that explore the effects of such changes on traits in their ecological contexts. In a few systems, such as the loss of armor in stickleback, the genetic, developmental and ecological bases of trait evolution are being discovered. These results yield insights into whether and how fast a trait is reduced or lost under relaxed selection. We provide a prospectus and a framework for understanding relaxed selection and trait loss in natural populations. We also examine its implications for applied issues, such as antibiotic resistance and the success of invasive species.
---------------------QUOTE-------------------



It is a really fascinating paper that I strongly recommend. I'll be doing a post on it - hopefully this weekend. For those who don't have access a pdf can be found < here >.
Posted by: Zachriel on Sep. 11 2009,10:13

Quote (afarensis @ Sep. 10 2009,21:45)
In light of the recent paper - and fuss- on the appendix this paper is topical. < Relaxed selection in the wild > here is the abstract:


---------------------QUOTE-------------------
Natural populations often experience the weakening or removal of a source of selection that had been important in the maintenance of one or more traits. Here we refer to these situations as relaxed selection, and review recent studies that explore the effects of such changes on traits in their ecological contexts. In a few systems, such as the loss of armor in stickleback, the genetic, developmental and ecological bases of trait evolution are being discovered. These results yield insights into whether and how fast a trait is reduced or lost under relaxed selection. We provide a prospectus and a framework for understanding relaxed selection and trait loss in natural populations. We also examine its implications for applied issues, such as antibiotic resistance and the success of invasive species.
---------------------QUOTE-------------------



It is a really fascinating paper that I strongly recommend. I'll be doing a post on it - hopefully this weekend. For those who don't have access a pdf can be found < here >.
---------------------QUOTE-------------------


Excellent paper. Thanks.

I noticed they cited some obscure scientist; Darwin, C. (1859) The Origin of Species.
Posted by: mammuthus on Sep. 11 2009,10:33

Quote (sledgehammer @ Aug. 28 2009,12:12)
Deer mice of the Sand hills in Nebraska have recently (in the last 4000 years) evolved a new, lighter color coat, that better matches their environment.

New coat color? Pfft.  Micro-evolution. No big deal.

Not so fast there, Poindexter.  The color change is a manifestation of a brand new gene, Agouti, that developed in around 8000 generations.
---------------------QUOTE-------------------



It's a really great paper.  I suspect the response from creationists will be similar to their response to another Hoekstra paper:

< http://www.oeb.harvard.edu/faculty/hoekstra/PDFs/HoekstraSCI2006.pdf >

to which Georgia Purdom argued:



---------------------QUOTE-------------------
From a creationist perspective, this research provides us with yet another example of a beneficial outcome of a mutation in a given environment allowing an organism a selectable advantage. Mutations lead to loss of information, and while the organism may be more well suited for its current environment, it may have lost the ability to adapt to other environments. The mutation described in this Science paper does not address the origin of the melanin gene or pigmentation, only the loss of them, thus it is not relevant to the discussion of molecules-to-man evolution.
---------------------QUOTE-------------------



< http://www.answersingenesis.org/article....ptation >
Posted by: Timothy McDougald on Sep. 11 2009,19:04

Quote (Zachriel @ Sep. 11 2009,10:13)
Quote (afarensis @ Sep. 10 2009,21:45)
In light of the recent paper - and fuss- on the appendix this paper is topical. < Relaxed selection in the wild > here is the abstract:
 

---------------------QUOTE-------------------
Natural populations often experience the weakening or removal of a source of selection that had been important in the maintenance of one or more traits. Here we refer to these situations as relaxed selection, and review recent studies that explore the effects of such changes on traits in their ecological contexts. In a few systems, such as the loss of armor in stickleback, the genetic, developmental and ecological bases of trait evolution are being discovered. These results yield insights into whether and how fast a trait is reduced or lost under relaxed selection. We provide a prospectus and a framework for understanding relaxed selection and trait loss in natural populations. We also examine its implications for applied issues, such as antibiotic resistance and the success of invasive species.
---------------------QUOTE-------------------



It is a really fascinating paper that I strongly recommend. I'll be doing a post on it - hopefully this weekend. For those who don't have access a pdf can be found < here >.
---------------------QUOTE-------------------


Excellent paper. Thanks.

I noticed they cited some obscure scientist; Darwin, C. (1859) The Origin of Species.
---------------------QUOTE-------------------


One of the parts that caught my attention was in the section on constitutive costs where they discuss insecticide resistance in mosquitoes and the Ace.I gene. I've been tracking down some of the literature on the subject and, leaving aside the health implications, there is an interesting story about how evolution works...
Posted by: keiths on Sep. 14 2009,20:32

< Snake with clawed foot found in China >

How thoughtful of the Designer to give snakes a latent ability to grow clawed feet!
Posted by: Richardthughes on Sep. 15 2009,10:33

IDiots wont like this one:

< http://www.sciencedaily.com/releases/2009/09/090914172644.htm >
Posted by: Lou FCD on Sep. 15 2009,16:26

Quote (keiths @ Sep. 14 2009,21:32)
< Snake with clawed foot found in China >

How thoughtful of the Designer to give snakes a latent ability to grow clawed feet!
---------------------QUOTE-------------------


Apparently, the snake kind lost a bunch of FSCI sometime before the Garden of Eden. But now they've found it again?




...or something.
Posted by: Richardthughes on Sep. 15 2009,16:29

Quote (Lou FCD @ Sep. 15 2009,16:26)
Quote (keiths @ Sep. 14 2009,21:32)
< Snake with clawed foot found in China >

How thoughtful of the Designer to give snakes a latent ability to grow clawed feet!
---------------------QUOTE-------------------


Apparently, the snake kind lost a bunch of FSCI sometime before the Garden of Eden. But now they've found it again?




...or something.
---------------------QUOTE-------------------


It's the snake that put its foot in its mouth in the garden of eden, obviously.
Posted by: khan on Sep. 15 2009,16:31

Adam blamed Eve.
Eve blamed the snake.
And the snake didn't have a leg to stand on.
Posted by: jeannot on Sep. 16 2009,04:17

This week in PNAS:

The reducible complexity of a mitochondrial molecular machine

  Abigail Clements, Dejan Bursac, Xenia Gatsos, Andrew J. Perry, Srgjan Civciristov, Nermin Celik, Vladimir A. Likic, Sebastian Poggio, Christine Jacobs-Wagnerd, Richard A. Strugnell and Trevor Lithgow



---------------------QUOTE-------------------
Molecular machines drive essential biological processes, with the component parts of these machines each contributing a partial function or structural element. Mitochondria are organelles of eukaryotic cells, and depend for their biogenesis on a set of molecular machines for protein transport. How these molecular machines evolved is a fundamental question. Mitochondria were derived from an ?-proteobacterial endosymbiont, and we identified in ?-proteobacteria the component parts of a mitochondrial protein transport machine. In bacteria, the components are found in the inner membrane, topologically equivalent to the mitochondrial proteins. Although the bacterial proteins function in simple assemblies, relatively little mutation would be required to convert them to function as a protein transport machine. This analysis of protein transport provides a blueprint for the evolution of cellular machinery in general.
---------------------QUOTE-------------------



They even quote Behe. Waiting for his rebutal.
Posted by: Bob O'H on Sep. 17 2009,06:20

This is one to wave at the Design Detectors:



---------------------QUOTE-------------------
< Were crocodiles responsible for the stones we call tools?

Patrick Dempsey >

Sir

Could Nature have been unknowingly publishing papers for the past 80 years about crocodilian gastroliths (stomach stones) instead of stones concluded to be 2.5-million-year-old hominid tools? This possibility could cast doubt, for example, on the nature of the Oldowan specimens described by Michael Haslam and colleagues in their Review of primate archaeology (Nature 460, 339–344; 2009).

Palaeontologists use a simple eyeball test to distinguish stone tools from gastroliths. If a specimen has wear marks on its outer surface but none on its inner surfaces, this indicates that the stone has been grinding away in some prehistoric stomach or other and is a gastrolith. But wear on both inner and outer surfaces indicates that it has been used for some sort of pounding or battering and can confidently be considered a tool. A quick look at the three Oldowan specimens reveals wear on only the extended surfaces, so they should be considered as gastroliths, not tools.

Identification of the Oldowan specimens as tools is based on the fact that the soft relict sands of Olduvai Gorge contain no natural stones of their own, so any stone found there must have been moved from distant river beds by some unknown animal transporter — concluded by high science to be Homo habilis. But crocodiles have the curious habit of swallowing rocks: these account for 1% of their body weight, so for a 1-tonne crocodile that's 10 kg of stones in its stomach at all times. Surprisingly, science has never even considered the crocodile as transporter.

Crocodiles and hippos have always lived happily together. Hippo herds would naturally trample riverside gravel stones into the shape of Oldowan cutting tools, quantities of which the crocodile would then swallow and transport to other places.

The crocodile lives and dies at the water's edge. So far, all East African Oldowan specimens have come from the same waterside environments where crocodiles are known to have dwelt. Millions, perhaps trillions, of transported crocodile stomach stones must remain where the old crocodiles left them, deep in relict East African sediments, though none has ever been reported.
---------------------QUOTE-------------------


Posted by: Timothy McDougald on Sep. 17 2009,18:53

Quote (Bob O'H @ Sep. 17 2009,06:20)
This is one to wave at the Design Detectors:

 

---------------------QUOTE-------------------
< Were crocodiles responsible for the stones we call tools?

Patrick Dempsey >

Sir

Could Nature have been unknowingly publishing papers for the past 80 years about crocodilian gastroliths (stomach stones) instead of stones concluded to be 2.5-million-year-old hominid tools? This possibility could cast doubt, for example, on the nature of the Oldowan specimens described by Michael Haslam and colleagues in their Review of primate archaeology (Nature 460, 339–344; 2009).

Palaeontologists use a simple eyeball test to distinguish stone tools from gastroliths. If a specimen has wear marks on its outer surface but none on its inner surfaces, this indicates that the stone has been grinding away in some prehistoric stomach or other and is a gastrolith. But wear on both inner and outer surfaces indicates that it has been used for some sort of pounding or battering and can confidently be considered a tool. A quick look at the three Oldowan specimens reveals wear on only the extended surfaces, so they should be considered as gastroliths, not tools.

Identification of the Oldowan specimens as tools is based on the fact that the soft relict sands of Olduvai Gorge contain no natural stones of their own, so any stone found there must have been moved from distant river beds by some unknown animal transporter — concluded by high science to be Homo habilis. But crocodiles have the curious habit of swallowing rocks: these account for 1% of their body weight, so for a 1-tonne crocodile that's 10 kg of stones in its stomach at all times. Surprisingly, science has never even considered the crocodile as transporter.

Crocodiles and hippos have always lived happily together. Hippo herds would naturally trample riverside gravel stones into the shape of Oldowan cutting tools, quantities of which the crocodile would then swallow and transport to other places.

The crocodile lives and dies at the water's edge. So far, all East African Oldowan specimens have come from the same waterside environments where crocodiles are known to have dwelt. Millions, perhaps trillions, of transported crocodile stomach stones must remain where the old crocodiles left them, deep in relict East African sediments, though none has ever been reported.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


Is that the entire piece or is there more? Any idea how nature chooses items for the Correspondence section? I ask because if this was peer reviewed someone goofed....
Posted by: Lou FCD on Sep. 17 2009,20:23

< Gene Therapy Gives Monkeys Color Vision > at Science.



---------------------QUOTE-------------------
By Gisela Telis
ScienceNOW Daily News
16 September 2009
Squirrel monkeys can now see your true colors, thanks to gene therapy. Researchers have given the colorblind primates full color vision as adults by injecting their eyes with a human gene. The result raises questions about how the brain understands color, and it could eventually lead to gene-therapy treatments for colorblindness and other visual disorders in humans.

In the world of squirrel monkeys, seeing colors is for girls. Whereas some females enjoy full color vision, males of the South American genus see only blues and yellows (see picture). They lack a gene that allows color-sensitive cells in the eye, called cones, to distinguish red and green from gray--the same distinction that confounds most colorblind humans.
---------------------QUOTE-------------------



More at the link.
Posted by: Lou FCD on Sep. 17 2009,20:28

< Googling Food Webs: Can an Eigenvector Measure Species' Importance for Coextinctions? > in PLoS Computational Biology:



---------------------QUOTE-------------------
Stefano Allesina1*, Mercedes Pascual2,3,4

1 National Center for Ecological Analysis and Synthesis, Santa Barbara, California, United States of America, 2 Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America, 3 Santa Fe Institute, Santa Fe, New Mexico, United States of America, 4 Howard Hughes Medical Institute

Abstract

A major challenge in ecology is forecasting the effects of species' extinctions, a pressing problem given current human impacts on the planet. Consequences of species losses such as secondary extinctions are difficult to forecast because species are not isolated, but interact instead in a complex network of ecological relationships. Because of their mutual dependence, the loss of a single species can cascade in multiple coextinctions. Here we show that an algorithm adapted from the one Google uses to rank web-pages can order species according to their importance for coextinctions, providing the sequence of losses that results in the fastest collapse of the network. Moreover, we use the algorithm to bridge the gap between qualitative (who eats whom) and quantitative (at what rate) descriptions of food webs. We show that our simple algorithm finds the best possible solution for the problem of assigning importance from the perspective of secondary extinctions in all analyzed networks. Our approach relies on network structure, but applies regardless of the specific dynamical model of species' interactions, because it identifies the subset of coextinctions common to all possible models, those that will happen with certainty given the complete loss of prey of a given predator. Results show that previous measures of importance based on the concept of “hubs” or number of connections, as well as centrality measures, do not identify the most effective extinction sequence. The proposed algorithm provides a basis for further developments in the analysis of extinction risk in ecosystems.
---------------------QUOTE-------------------


Posted by: Erasmus, FCD on Sep. 17 2009,21:34

Science 4 September 2009:
Vol. 325. no. 5945, pp. 1269 - 1272
DOI: 10.1126/science.1176960

Differential Sensitivity to Human Communication in Dogs, Wolves, and Human Infants
József Topál,1,* György Gergely,2 Ágnes Erdhegyi,3 Gergely Csibra,2 Ádám Miklósi3




---------------------QUOTE-------------------
Ten-month-old infants persistently search for a hidden object at its initial hiding place even after observing it being hidden at another location. Recent evidence suggests that communicative cues from the experimenter contribute to the emergence of this perseverative search error. We replicated these results with dogs (Canis familiaris), who also commit more search errors in ostensive-communicative (in 75% of the total trials) than in noncommunicative (39%) or nonsocial (17%) hiding contexts. However, comparative investigations suggest that communicative signals serve different functions for dogs and infants, whereas human-reared wolves (Canis lupus) do not show doglike context-dependent differences of search errors. We propose that shared sensitivity to human communicative signals stems from convergent social evolution of the Homo and the Canis genera.
---------------------QUOTE-------------------



that shit is BAD ASS
Posted by: qetzal on Sep. 18 2009,13:56

Remember the PNAS paper that argued that caterpillars and butterflies used to be different species? Jeannot first linked it < here >.

Turns out PNAS is changing their submission policies so that papers like this can no longer avoid standard peer review. See < this post > at Sandwalk for more details.
Posted by: jeannot on Sep. 18 2009,16:50

I was just reading the story.
There's a link to a Sci Am article discussing the caterpillar paper. As expected, it didn't go unnoticed and it appears that Margulis's reputation is already affected.

I still find hard to believe that the paper was not rejected by the editorial board at PNAS, as comprises respectable researchers like Futuyma, Ayala, etc.
Posted by: qetzal on Sep. 18 2009,17:17

I think they couldn't reject it as long as Margulis could submit two favorable reviews. I don't have access to the Science article, but Larry Moran at Sandwalk quotes it as saying the following:



---------------------QUOTE-------------------
He {Williamson} also says he knows that Margulis sent his paper to a half-dozen academy reviewers. Williamson says that he thinks they were all positive reviews, but Margulis told Scientific American last week that she canvassed six or seven reviewers to find the two positive reviews necessary to push the paper through.
---------------------QUOTE-------------------



Sounds like their hands were tied under their existing policies, which is no doubt why they're changing them.
Posted by: jeannot on Sep. 21 2009,10:25

Larry Moran comments on the story.
< http://sandwalk.blogspot.com/2009....od.html >
Posted by: ppb on Sep. 24 2009,09:34

This is from Pharyngula.  It is a bit dated, but very entertaining and informative.  < Julia Child makes primordial soup. >
Posted by: Richardthughes on Sep. 24 2009,15:46

MarkCC (Good math Bad math)

Information vs meaning:

< http://scienceblogs.com/goodmat....hp#more >
Posted by: sledgehammer on Sep. 25 2009,00:18

< Feathered dinosaur fossils from China >

 

---------------------QUOTE-------------------
Exceptionally well preserved dinosaur fossils uncovered in north-eastern China display the earliest known feathers.

The creatures are all more than 150 million years old.

The new finds are indisputably older than Archaeopteryx, the oldest recognised bird discovered in Germany.

Professor Xu Xing and colleagues tell the journal Nature that this represents the final proof that dinosaurs were ancestral to birds.
---------------------QUOTE-------------------


Posted by: Timothy McDougald on Sep. 28 2009,19:37

Some archaeology news that is very interesting. < It seems the British can't figure out where the Battle of Bosworth was fought! >
Posted by: Bob O'H on Sep. 29 2009,03:54

From The Loom:

< The Continuing Adventures of the Blind Locksmith: You Can’t Get There From Here >



---------------------QUOTE-------------------
Three years ago, I wrote a series of blog posts about how scientists at the University of Oregon reconstructed the 450-million-year history of a protein. ...  What was particularly elegant about the study was how the scientists recreated the ancestral protein as it existed over 400 million years ago, to see how it functioned. Then they  pinpointed the mutations that transformed the protein, shifting it from an old function to a new one.

Recently, the scientists tried to run their experiment backwards. They tried to turn the new protein back into the old one. And they failed. In that failure, they’ve discovered something important. They argue that when it comes to evolution, you can’t go home again.
---------------------QUOTE-------------------



IOW, the protein was latched!!!!!one!!!  Someone alert kairosfocus.
Posted by: Timothy McDougald on Oct. 01 2009,22:14

< Ardipithecus! > you can download them all for free if you register. It's paleoanthropological heaven! I am sooo excited! OMG!OMG! Did I mention how excited I was? OMG!ZOMG!OMG! It is very cool! And did I mention how excited I am, stoked, or I would even say chuffed! Wooooohoooooooooooo!
Posted by: ppb on Oct. 02 2009,05:58

Quote (afarensis @ Oct. 01 2009,23:14)
< Ardipithecus! > you can download them all for free if you register. It's paleoanthropological heaven! I am sooo excited! OMG!OMG! Did I mention how excited I was? OMG!ZOMG!OMG! It is very cool! And did I mention how excited I am, stoked, or I would even say chuffed! Wooooohoooooooooooo!
---------------------QUOTE-------------------


I can understand why you're so excited, afarensis.  She does look pretty hot!


Posted by: midwifetoad on Oct. 02 2009,13:33

Is this news to anyone here?

< http://www.sciencenews.org/view....osphere >





---------------------QUOTE-------------------
Viruses aren’t supposed to be visible under a light microscope; they are typically far too small. But mimivirus (“mimi” for mimicking microbe) isn’t just big for a virus, it’s bigger than some bacteria. Analyses of its DNA, cataloged in 2004, revealed that it also has more genetic material than some bacteria and certainly more than any other previously seen virus. The mimivirus genome contains genes for more than 900 proteins. (In contrast, T4—which, pre-mimi, was considered a large virus—has about 77 genes.) Some of the mimivirus genes appear to be involved in processes thought to be conducted only by cellular creatures—the virus’s hosts—such as translating messenger RNA into proteins.  All in all, mimivirus seriously unsettled the world of virus research.
---------------------QUOTE-------------------


Posted by: Dr.GH on Oct. 02 2009,17:47

Quote (ppb @ Oct. 02 2009,03:58)
 
Quote (afarensis @ Oct. 01 2009,23:14)
< Ardipithecus! > you can download them all for free if you register. It's paleoanthropological heaven! I am sooo excited! OMG!OMG! Did I mention how excited I was? OMG!ZOMG!OMG! It is very cool! And did I mention how excited I am, stoked, or I would even say chuffed! Wooooohoooooooooooo!
---------------------QUOTE-------------------


I can understand why you're so excited, afarensis.  She does look pretty hot!

---------------------QUOTE-------------------


I posted an item at < http://www.examiner.com/examine....schools > about Ardipithecus and the crappy headlines at NatGeo and CNN. I then moved to creato-stupid questions teacher might face.

My scientific qualms are about the sesamoid bone, and the environmental determinist interpretations. The site was obviously as reconstructed- a riparian forest. However, White et al concluded that this is the environment that Ar ramidus evolved in, as opposed to some other environment. Riparian locations facilitate fossilization. What is needed prior to asserting that this is where humans evolved is some comparitive data from non-riparian environments. That is not likely to be found, certainly not when you keep looking in the same place.

(Apparently you will need to c'n'p' the URL from AtBC. The link works at other sites BTW). Well, that didn't work either.

weird.

Try from here
< http://www.examiner.com/Los_Angeles-Education_and_Schools.html >


Posted by: khan on Oct. 04 2009,15:02

Don't know if this belongs here:

< 3.6 million pounds of thrust >
Posted by: Henry J on Oct. 05 2009,15:19

Now that's what you call rocket science!
Posted by: deadman_932 on Oct. 05 2009,23:32

< http://www.scielo.org.ar/cgi-bin/wxis.exe/iah/ >

That link gives access to papers like these:

Ramos, Victor A. (2009) Darwin at Puente del Inca: observations on the formation of the Inca's bridge and mountain building. Rev. Asoc. Geol. Argent., Mar 2009, vol.64, no.1, p.170-179. ISSN 0004-4822

Vizcaíno, Sergio F., Fariña, Richard A. and Fernicola, Juan Carlos (2009) Young Darwin and the ecology and extinction of pleistocene south american fossil mammals. Rev. Asoc. Geol. Argent., Mar 2009, vol.64, no.1, p.160-169. ISSN 0004-4822

Fernicola, Juan Carlos, Vizcaíno, Sergio F. and De Iuliis, Gerardo (2009) The fossil mammals collected by Charles Darwin in South America during his travels on board the HMS Beagle. Rev. Asoc. Geol. Argent., Mar 2009, vol.64, no.1, p.147-159.

Iriondo, Martin and Kröhling, Daniela (2009) From Buenos Aires to Santa Fe: Darwin's observations and modern knowledge. Rev. Asoc. Geol. Argent., Mar 2009, vol.64, no.1, p.109-123.

Martínez, Oscar A., Rabassa, Jorge and Coronato, Andrea (2009) Charles Darwin and the first scientific observations on the patagonian shingle formation (Rodados Patagónicos). Rev. Asoc. Geol. Argent., Mar 2009, vol.64, no.1, p.90-100.

Giambiagi, Laura, Tunik, Maisa, Ramos, Victor A. et al. (2009) The High Andean Cordillera of central Argentina and Chile along the Piuquenes Pass-Cordon del Portillo transect: Darwin's pioneering observations compared with modern geology. Rev. Asoc. Geol. Argent., Mar 2009, vol.64, no.1, p.43-54.

Aguirre-Urreta, Beatriz and Vennari, Verónica (2009) On Darwin's footsteps across the Andes: Tithonian-Neocomian fossil invertebrates from the Piuquenes pass. Rev. Asoc. Geol. Argent., Mar 2009, vol.64, no.1, p.32-42.

AND 11 OTHER QUALITY PAPERS ON DARWIN'S WORK (just click the "texto en inglés" link next to each title)
Posted by: deadman_932 on Oct. 05 2009,23:40

Free science journals: (admittedly not very good ones, but , hey, they're free you cheap &@%#&)  http://www.meetscience.net/science_publications.html

< http://www.biobooke.blogspot.com/ > Offers full ebook-format (.pdf or .djvu) textbooks ranging from The Lehninger "Principles of Biochemistry" (Cox and Nelson)  to O'Reilly Books "Developing Bioinformational Computer Skills " for free download from Megaupload and Rapidshare sources. Pretend you're at the bookstore reading one, then delete the ebook when your conscience nags you for being a total thief, you *&%#@  

The two most-often-used formats for ebooks are .pdf and .djvu

Foxit Reader is a free PDF document viewer, small size, fast launch speed < http://www.foxitsoftware.com/pdf/reader/ >

For a free .djvu reader:
< http://windjview.sourceforge.net/ >

< http://djvu.sourceforge.net/ >
Posted by: Dr.GH on Oct. 12 2009,12:09

Molecule by molecule, mutation by mutation with full selection

Behe and Dembski have both made famous demands for what they would accept at an evolutionary explanation;

Jamie T. Bridgham, Eric A. Ortlund & Joseph W. Thornton
“An epistatic ratchet constrains the direction of glucocorticoid receptor evolution” Nature Vol 461|24 September 2009

So, I guess they will become good Darwinists now.
Posted by: midwifetoad on Oct. 12 2009,13:09

Never assume that Behe will accept reality:

< http://www.arn.org/blogs...._dollo_ >
Posted by: Dr.GH on Oct. 12 2009,14:27

Quote (midwifetoad @ Oct. 12 2009,11:09)
Never assume that Behe will accept reality:

< http://www.arn.org/blogs...._dollo_ >
---------------------QUOTE-------------------


Gosh! Are you as schocked and surprised as I am!!!1!1!111eleven

(Thanks for the link).
Posted by: Albatrossity2 on Oct. 13 2009,09:51

< Vegetarian spider > found in Costa Rica. This must be a spider species that is unchanged since before the Fall!
Posted by: Henry J on Oct. 13 2009,15:21

Really. Given how spiders digest their food, I wouldn't have expected that. Interesting.
Posted by: ppb on Oct. 14 2009,13:43

Another < gap is filled. >  Darwinopterus modularis is another of those transitional forms that creationists prefer to remain ignorant about.  It fits nicely between between earlier non-pterodactyloids and later pterodactyloids.

It's amazing what you can find if you actually go out and do some science.
Posted by: Dr.GH on Oct. 14 2009,17:14

Quote (ppb @ Oct. 14 2009,11:43)
Another < gap is filled. >  Darwinopterus modularis is another of those transitional forms that creationists prefer to remain ignorant about.  It fits nicely between between earlier non-pterodactyloids and later pterodactyloids.

It's amazing what you can find if you actually go out and do some science.
---------------------QUOTE-------------------


No, no!

It is now two gaps taht need to be filed. Science just took a step backwards.
Posted by: Henry J on Oct. 14 2009,18:13

Bee sides, those pterodactyloids still didn't tern into birds!
Posted by: sledgehammer on Oct. 14 2009,18:32

Sparrow us your puns. I don't swallow it.
Posted by: Reed on Oct. 14 2009,18:46

Quote (ppb @ Oct. 14 2009,11:43)
Another < gap is filled. >  Darwinopterus modularis is another of those transitional forms that creationists prefer to remain ignorant about.  It fits nicely between between earlier non-pterodactyloids and later pterodactyloids.

---------------------QUOTE-------------------


< What will the creationists say this time > ?
Posted by: JLT on Oct. 17 2009,03:42

Quote (Dr.GH @ Oct. 12 2009,18:09)
Molecule by molecule, mutation by mutation with full selection

Behe and Dembski have both made famous demands for what they would accept at an evolutionary explanation;

Jamie T. Bridgham, Eric A. Ortlund & Joseph W. Thornton
“An epistatic ratchet constrains the direction of glucocorticoid receptor evolution” Nature Vol 461|24 September 2009

So, I guess they will become good Darwinists now.
---------------------QUOTE-------------------


< Thornton responds to Behe's take on his work. >

A very good take-down of Behe that shows not only how Behe misrepresents Thornton's current work but also why Behe (and ID) suck in general.

 

---------------------QUOTE-------------------
Finally, Behe erroneously equates “evolving non-deterministically” with “impossible to evolve.”  He supposes that if each of a set of specific evolutionary outcomes has a low probability, then none will evolve.  This is like saying that, because the probability was vanishingly small that the 1996 Yankees would finish 92-70 with 871 runs scored and 787 allowed and then win the World Series in six games over Atlanta, the fact that all this occurred means it must have been willed by God.
---------------------QUOTE-------------------


Posted by: Dr.GH on Oct. 17 2009,11:17

Quote (JLT @ Oct. 17 2009,01:42)
< Thornton responds to Behe's take on his work. >

A very good take-down of Behe that shows not only how Behe misrepresents Thornton's current work but also why Behe (and ID) suck in general.
---------------------QUOTE-------------------


Thanks for the link.
Posted by: OgreMkV on Oct. 19 2009,08:14

< http://www.sciencedaily.com/releases/2009/10/091016121827.htm >  Seeing Blue: Fish Vision Discovery Makes Waves In Evolutionary Biology

Interesting article about a single deletion event that removed the ability of the fish to see UV light.

The only problem with this article is that it's ripe for being misinterpretted.  

"The researchers found that adaptive changes occur by a small number of amino acid substitutions, but most substitutions do not lead to functional changes."

and

"Evolutionary biology is filled with arguments that are misleading, at best," Yokoyama says. "To make a strong case for the mechanisms of natural selection, you have to connect changes in specific molecules with changes in phenotypes, and then you have to connect these changes to the living environment."

I predict great amounts of quote mining from this article.
Posted by: Reed on Oct. 19 2009,17:48

Ho hum < 32 more exoplanets >. This proves we are the special creation of god unspecified telic entity, right ?
Posted by: OgreMkV on Oct. 19 2009,19:31

Quote (Reed @ Oct. 19 2009,17:48)
Ho hum < 32 more exoplanets >. This proves we are the special creation of god unspecified telic entity, right ?
---------------------QUOTE-------------------


I'm actually really curious as to what happens when we find life on other planets.

I especially want to see us meet an intelligent life form on another planet, ask it read the Bible, then laugh it's ass off and everything humans have done to each other in the name of some unknowable entity that is omni-everything.  (This, BTW, doesn't have to be directed at the Bible, all holy texts I can think of right off the top of my head are included here).
Posted by: Lou FCD on Oct. 19 2009,19:50

Quote (OgreMkV @ Oct. 19 2009,20:31)
Quote (Reed @ Oct. 19 2009,17:48)
Ho hum < 32 more exoplanets >. This proves we are the special creation of god unspecified telic entity, right ?
---------------------QUOTE-------------------


I'm actually really curious as to what happens when we find life on other planets.

I especially want to see us meet an intelligent life form on another planet, ask it read the Bible, then laugh it's ass off and everything humans have done to each other in the name of some unknowable entity that is omni-everything.  (This, BTW, doesn't have to be directed at the Bible, all holy texts I can think of right off the top of my head are included here).
---------------------QUOTE-------------------


They'll probably quarantine our planet until the infection passes.

ETA: ...unless they already have, that is.


Posted by: midwifetoad on Oct. 20 2009,09:58

We'll be lucky if they aren't spreading their own infection.
Posted by: FrankH on Oct. 20 2009,10:10

Quote (midwifetoad @ Oct. 20 2009,09:58)
We'll be lucky if they aren't spreading their own infection.
---------------------QUOTE-------------------


Personally, I'm not so sure they'll be "much better" than us.

I have a feeling that a certain amount of arrogance and ignorance are going to be a defining feature of technological intelligences.
Posted by: Lou FCD on Oct. 20 2009,21:03

< Nasty-Big Orb Weaving Spider > discovered.



---------------------QUOTE-------------------
Description: Female paratype: Total length 39.7. Prosoma 14.3 long, 10.9 wide, 8.7 high at head region; dark red-black. High head region, low thoracic region. Carapace densely covered with thin white hairs; mid-carapace humps large and rounded. Carapace lateral edge at thoracic region ridged. Sternum 6.9 long, 5.5 wide, widest anteriorly, with paired sternal humps adjacent to coxae 1–4, the third paired hump enlarged; a large unpaired projection on anterior sternum. Sternum dark red-brown (in alcohol) with a small yellow spot at each paired hump. Labium black, yellow frontally and medially. Maxillae black, medially white. Clypeus height 1.25. Legs and palp unicolor dark red (in alcohol). Leg formula 1, 2, 4, 3. Coxae 3 and 4 with a conspicuous ventral bulge. Femora with sparse warts. Tibiae 1, 2 and 4 with a conspicuous distal tuft of setae. Leg I length 75.4 (femur 21.7, patella 5.1, tibia 18.9, metatarsus 25.4, tarsus 4.3). Opisthosoma massive, widest anteriorly, 27.3 long, 12.4 wide (frontally), 12.7 high, extended 4.9 beyond spinnerets. Dorsum (in ethanol) brown with a broad anterior yellow notched pattern, a mid-posterior paired and a caudal unpaired yellow patch; lateral opisthosoma brown with yellow spots and stripes; venter brown, with two irregularly shaped conspicuous yellow transverse bands. Epigynum a protruding sclerotized area and a posterior transverse plate with slit-like, medially converging copulatory openings (Fig. 2C–D). Round spermathecae juxtaposed medially. Copulatory ducts complex and long, fertilization ducts massive.
---------------------QUOTE-------------------


Posted by: JohnW on Oct. 21 2009,11:49

Quote (Lou FCD @ Oct. 20 2009,19:03)
Total length 39.7
---------------------QUOTE-------------------


Millimetres.  Phew.
Posted by: Henry J on Oct. 21 2009,13:02

That was only millimeters? Shucks, that makes it only around half the length of finger.
Posted by: Richardthughes on Oct. 22 2009,20:28

Kicking the privileged planet

< http://media4.obspm.fr/exoplanets/base/carte3d.php >

(see how many are in habitable zones)
Posted by: deadman_932 on Oct. 24 2009,05:11

For people that like to keep learning, lots of universities and colleges offer free courses, assignments, and lectures over the intertubes, using streaming video, podcasts, and downloadable lecture notes.

A collection of free online class courses ranging from physics to nursing, chemistry, theology, geology, etc:
< http://oedb.org/library....nything >

MIT offers a load of courses online (as many as 1,800), from Aeronautics to Writing:
< http://ocw.mit.edu/OcwWeb/web/courses/courses/index.htm >

UCLA: < http://www.bruincast.ucla.edu/ >

U.C. Berkeley has ...I dunno, maybe 50 classes available: < http://webcast.berkeley.edu/courses.php >

U.C. Irvine < http://ocw.uci.edu/courses/ > has free and open digital publication of high quality university-level educational materials, often including syllabi, lecture notes, assignments and exams in subjects ranging from business to physical and social sciences. There's also free online tutorial services.

Stanford allows you to download podcast courses, faculty lectures, interviews using iTunes for Mac or PC, which you can burn to CD. < http://itunes.stanford.edu/ >

Yale also uses iTunes: < http://opa.yale.edu/netcasts.aspx >

Johns Hopkins' Bloomberg School of Public Health has online coursework here: < http://ocw.jhsph.edu/ >
and includes a listing of major Open Coursework Consortium Colleges and Universities here:  < http://ocw.jhsph.edu/otherocw.cfm >
( Tufts, Carnegie Mellon, Utah, Notre Dame )

Other free sites can be found here:
< http://www.openculture.com/2007/07/freeonlinecourses.html >
< http://universitiesandcolleges.org/free-online-college-courses/# >
< http://www.docnmail.com/ >
< http://www.jimmyr.com/blog/2_Top_10_University_Podcasts.php >
< http://diyscholar.wordpress.com/best-webcasts-podcasts/ >
Posted by: Kattarina98 on Oct. 24 2009,05:43

Quote (Albatrossity2 @ Oct. 13 2009,09:51)
< Vegetarian spider > found in Costa Rica. This must be a spider species that is unchanged since before the Fall!
---------------------QUOTE-------------------


The latest issue of Creation magazine ...

< http://www.youtube.com/watch?v=pOp_z5zPaq0 >
Posted by: Albatrossity2 on Oct. 24 2009,09:07

Quote (Kattarina98 @ Oct. 24 2009,05:43)
Quote (Albatrossity2 @ Oct. 13 2009,09:51)
< Vegetarian spider > found in Costa Rica. This must be a spider species that is unchanged since before the Fall!
---------------------QUOTE-------------------


The latest issue of Creation magazine ...

< http://www.youtube.com/watch?v=pOp_z5zPaq0 >
---------------------QUOTE-------------------


That's an outrage! Do I need to sue to recover my "intellectual" property rights?
Posted by: JLT on Oct. 26 2009,14:24

Quote (JLT @ Oct. 17 2009,09:42)
   
Quote (Dr.GH @ Oct. 12 2009,18:09)
Molecule by molecule, mutation by mutation with full selection

Behe and Dembski have both made famous demands for what they would accept at an evolutionary explanation;

Jamie T. Bridgham, Eric A. Ortlund & Joseph W. Thornton
“An epistatic ratchet constrains the direction of glucocorticoid receptor evolution” Nature Vol 461|24 September 2009

So, I guess they will become good Darwinists now.
---------------------QUOTE-------------------


< Thornton responds to Behe's take on his work. >

A very good take-down of Behe that shows not only how Behe misrepresents Thornton's current work but also why Behe (and ID) suck in general.

     

---------------------QUOTE-------------------
Finally, Behe erroneously equates “evolving non-deterministically” with “impossible to evolve.”  He supposes that if each of a set of specific evolutionary outcomes has a low probability, then none will evolve.  This is like saying that, because the probability was vanishingly small that the 1996 Yankees would finish 92-70 with 871 runs scored and 787 allowed and then win the World Series in six games over Atlanta, the fact that all this occurred means it must have been willed by God.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


And now < Behe responds > to Thornton's response to Behe's reaction to Thornton's work.... in several posts!
I'm soo excited. More TARD to come!

ETA: and tard it is, < here > and < here >.
Posted by: bfish on Oct. 28 2009,23:15

Well..... um....... it's not squirrels or horses, but......

< um...... >

*runs away*
Posted by: bfish on Oct. 28 2009,23:19

Oh no they di'n't!

I can't believe they put a music soundtrack with the video. I can't believe they HAD a video.
Posted by: Dr.GH on Oct. 29 2009,09:33

Quote (bfish @ Oct. 28 2009,21:19)
Oh no they di'n't!

I can't believe they put a music soundtrack with the video. I can't believe they HAD a video.
---------------------QUOTE-------------------


She might be licking her vagina. Great sound track though. Maybe certain porno experts can tell us the original source.

Back in the late '70s I helped data code Eric Phoebus's dissertation videos of monkey's fucking. Hours and hours and hours of monkey fuck video.


Posted by: dvunkannon on Nov. 01 2009,18:29

< http://tinyurl.com/yby7sqq >

Murata Seiko - the practical benefits of a unicycling robot remain unclear...

Hitachi Wooo gesture controlled TV - what Tom Cruise was using in Minority Report

Nissan collision avoidance for cars - uses the same algorithm as a school of fish... sounds safe, unless the 18 wheeler behind you is using the same algorithm as a leopard seal...

Yamaha's Mimi - a singing robotic receptionist dressed like a Final Fantasy cosplay... what your home needs...
Posted by: ppb on Nov. 05 2009,12:29

< Hubble's back! >  Better than ever too.  Some great pictures at Phil's place.  Check 'em out.
Posted by: OgreMkV on Nov. 08 2009,21:31

Not sure where else to put this.  This is a link to a debate on "Is the Catholic Church a Force for Good in the World?"  Broadcast on the BBC.

< http://www.youtube.com/view_play_list?p=F821DBF3CE3374A3 >

Funny, funny stuff.  

Spoiler Alert...








Catholicism got its collective butt kicked.
Posted by: Raevmo on Nov. 09 2009,02:49

Thanks for the link, Ogre. Great stuff! One of the socks should post it in a UD thread where StephenB is claiming the moral high ground.
Posted by: midwifetoad on Nov. 10 2009,01:12



---------------------QUOTE-------------------
"We have demonstrated for the first time that we can make uracil, a component of RNA, non-biologically in a laboratory under conditions found in space," said Michel Nuevo, research scientist at NASA's Ames Research Center, Moffett Field, Calif. "We are showing that these laboratory processes, which simulate occurrences in outer space, can make a fundamental building block used by living organisms on Earth."
---------------------QUOTE-------------------



< http://www.astrobio.net/pressrelease/3304/uracil-made-in-the-lab >
Posted by: Richardthughes on Nov. 13 2009,14:15

On November 18, 2009, join us for our first Cornell on the Road webinar, featuring a presentation on biodiversity by Ecology & Evolutionary Biology professor Anurag Agrawal.

In this webinar, you will learn about biodiversity and coevolution:
What factors allow the coexistence of similar species and the diversification of species.
How insect herbivores evolve new strategies for attack, and plants counter with their own unique defenses.

What factors cause this evolutionary "arms race" to slow down.
Date:  Wednesday, November 18, 2009

Time:  12:00PM - 1:00PM EDT

Cost:  $10 per person; if you are not completely satisfied with the presentation, you will be fully refunded.


This is an online event. To participate in the web seminar you will need internet and a phone. Log-in and dial-in information will be sent a day before the event. If you have any questions, contact Francine Darling at francine.darling@cornell.edu or 607-254-7147.
Posted by: Lou FCD on Nov. 21 2009,22:03

< That's just cool >.



---------------------QUOTE-------------------
Epibulus insidiator, the slingjaw wrass, “possesses the most extreme jaw protrusion ever measured in fishes.” Individuals can protrude their jaw up to half the body length to capture crabs, shrimps, and small fishes.   This occurs through multiple structural novelties, as the video above can attest to, involving fundamentally reorganizing the way the bones and ligaments interact in the jaw linkage (Westneat 1991).

At the American Museum of Natural History website, you can view and interact with fish skulls that illustrate how the bones move in this process.
---------------------QUOTE-------------------


Posted by: Richardthughes on Nov. 23 2009,10:46

J-Dog's home movies:

< http://www.youtube.com/watch?v....#at=102 >
Posted by: J-Dog on Nov. 23 2009,12:27

Quote (Richardthughes @ Nov. 23 2009,10:46)
J-Dog's home movies:

< http://www.youtube.com/watch?v....#at=102 >
---------------------QUOTE-------------------


Thanks for finding the early days - we thought those were lost!

Please note that before all you hairless little freaks invaded us, how uncrowded the land was, and how nice the environment was.

My Uncle warned that we should not teach all you Homos how to survive in Europe.  And I guess Dad was right - He told us all to "keep your penus, in your genus"*

But we just wouldn't listen.  Here's why:


Posted by: Richardthughes on Nov. 26 2009,01:28

Acute stress leaves epigenetic marks on the hippocampus

< http://www.physorg.com/news178271825.html >

"Scientists are learning that the dynamic regulation of genes -- as much as the genes themselves -- shapes the fate of organisms. Now the discovery of a new epigenetic mechanism regulating genes in the brain under stress is helping change the way scientists think about psychiatric disorders and could open new avenues to treatment.

..."
Posted by: Reed on Nov. 26 2009,04:05

Mars meteorite ALH84001: It's < baaaaaaaaaaaaaaaack > (< PDF paper >)

I have no idea how sound this conclusion is, but I'm sure it's evidence of design either way ;)
Posted by: Timothy McDougald on Nov. 27 2009,15:15

< Interesting news n the OOL front >:



---------------------QUOTE-------------------
Now, Ernesto Di Mauro and colleagues found that ancient molecules called cyclic nucleotides can merge together in water and form polymers over 100 nucleotides long in water ranging from 40-90 °C -- similar to water temperatures on ancient Earth.

Cyclic nucleotides like cyclic-AMP are very similar to the nucleotides that make up individual pieces of DNA or RNA (A, T, G and C), except that they form an extra chemical bond and assume a ring-shaped structure. That extra bond makes cyclic nucleotides more reactive, though, and thus they were able to join together into long chains at a decent rate (about 200 hours to reach 100 nucleotides long).

This finding is exciting as cyclic nucleotides themselves can be easily formed from simple chemicals like formamide, thus making them plausible prebiotic compounds present during primordial times. Thus, this study may be revealing how the first bits of genetic information were created.
---------------------QUOTE-------------------



The paper can be found < here > for those who have access...
Posted by: Dr.GH on Nov. 28 2009,13:45

Quote (afarensis @ Nov. 27 2009,13:15)
< Interesting news n the OOL front >:



---------------------QUOTE-------------------
Now, Ernesto Di Mauro and colleagues found that ancient molecules called cyclic nucleotides can merge together in water and form polymers over 100 nucleotides long in water ranging from 40-90 °C -- similar to water temperatures on ancient Earth.

Cyclic nucleotides like cyclic-AMP are very similar to the nucleotides that make up individual pieces of DNA or RNA (A, T, G and C), except that they form an extra chemical bond and assume a ring-shaped structure. That extra bond makes cyclic nucleotides more reactive, though, and thus they were able to join together into long chains at a decent rate (about 200 hours to reach 100 nucleotides long).

This finding is exciting as cyclic nucleotides themselves can be easily formed from simple chemicals like formamide, thus making them plausible prebiotic compounds present during primordial times. Thus, this study may be revealing how the first bits of genetic information were created.
---------------------QUOTE-------------------



The paper can be found < here > for those who have access...
---------------------QUOTE-------------------


Interesting reference. Thanks.

I am glad I chose to go fishing intstead of back to shcool.
Posted by: Richardthughes on Dec. 01 2009,10:21

< http://www.newscientist.com/article....ve.html >
Posted by: Richardthughes on Dec. 01 2009,11:08

< http://philosophy.hku.hk/think/sci/ >
Posted by: Richardthughes on Dec. 01 2009,11:18

MOAR!

< http://philosophy.hku.hk/think/sci/induction.php >



---------------------QUOTE-------------------
TUTORIAL S02: Choosing among theories
Scientific reasoning is often about choosing the theory from a set of alternatives that we think is most likely to be true. But how do we decide which theory is the best one that is most likely to be true? Here are some relevant criteria.
Predictive power
The minimum requirement for a scientific theory is that it can help us make predictions and explain our observations. If a hypothesis generates no testable prediction, it fails the minimal requirement for a scientific hypothesis.

When we evaluate the predictive power of a theory, we consier both the quantity and the quality of the predictions. How many predictions can the theory make? How accurate and precise are they?

Mechanism
In general, we want theories that can explain the connections between events by revealing the underlying causal mechanisms. This can help us generate more predictions to test the theory and make other discoveries.

Fruitfulness
This is about whether a theory helps us make surprising or unexpected predictions which turn out to be correct, and whether the theory helps us detect and explain connections which we would not have noticed otherwise.
Simplicity
A simple theory is (roughly) one with fewer assumptions, and which posits less entities than its competitors. Many scientists believe strongly that we should search for simple theories if feasible.

Coherence
A theory should be internally coherent in the sense that it is logically consistent. If not, there is something wrong with the theory as it stands, and so there is a need to revise the theory to come up with a better version.

The other aspect of coherence is that we should look for theories that fit together with other well-confirmed facts and scientific theories. Widely accepted theories are already well-confirmed, so if a hypothesis is incompatible with existing science, the default response should be that the hypothesis is mistaken. An extraordinary claim incompatible with scientific knowledge should require very strong evidence before it can be accepted.


---------------------QUOTE-------------------


Posted by: ppb on Dec. 01 2009,15:30

This one's for Carlsonjok.  < Domestic Horse Ridden Further Back in Time. >
Posted by: ppb on Dec. 02 2009,11:40

There's a paper in the November 25 PLoS ONE that should interest Wes.  It's about variation in raptor talons and how they are used to restrain and imobilize prey.  

< http://www.plosone.org/article....0007999 >

ETA: It even made < Blog Pick of the Month > on the PLoS ONE Community Blog.
Posted by: Richardthughes on Dec. 08 2009,12:00

FYI, CHATTERBOX:

< Monkey language >
Posted by: Kattarina98 on Dec. 08 2009,12:55

Yet another example of beginning speciation observed ("Were you there?")

Human Feeding Creates New Population of Birds

< http://www.livescience.com/animals/091203-birdfeeding-evolution.html >
Posted by: JohnW on Dec. 08 2009,13:14

Quote (Kattarina98 @ Dec. 08 2009,10:55)
Yet another example of beginning speciation observed ("Were you there?")

Human Feeding Creates New Population of Birds

< http://www.livescience.com/animals/091203-birdfeeding-evolution.html >
---------------------QUOTE-------------------


Yeah, but they're still birds.  Unless they turn into plants, it doesn't count.
Posted by: Kattarina98 on Dec. 08 2009,14:36

Quote (JohnW @ Dec. 08 2009,13:14)
Quote (Kattarina98 @ Dec. 08 2009,10:55)
Yet another example of beginning speciation observed ("Were you there?")

Human Feeding Creates New Population of Birds

< http://www.livescience.com/animals/091203-birdfeeding-evolution.html >
---------------------QUOTE-------------------


Yeah, but they're still birds.  Unless they turn into plants, it doesn't count.
---------------------QUOTE-------------------


What do you mean?

Posted by: Richardthughes on Dec. 09 2009,16:18

Dark Matter?

< http://www.newscientist.com/blogs....er.html >
Posted by: Schroedinger's Dog on Dec. 09 2009,18:22

Quote (Richardthughes @ Dec. 09 2009,22:18)
Dark Matter?

< http://www.newscientist.com/blogs....er.html >
---------------------QUOTE-------------------


Well, Sir Terry Pratchett tells us that dark matter is actually the paperwork of the universe, accounting for the position of any atom at anytime. Makes sense...

Also, < Lawrence Krauss > has nice things to say about dark matter in his AAI 2009 lecture (to be found on Richard Dawkin's youtube channel).
Posted by: ppb on Dec. 10 2009,09:16

This is just too cool.  

There is a < hexagonal weather pattern > around Saturn's north pole.

It is apparently some sort of standing wave thingie.  
Posted by: Richardthughes on Dec. 22 2009,13:31

Does ID predeict this?:

< http://www.newscientist.com/article....fe.html >
Posted by: J-Dog on Dec. 22 2009,14:52

Quote (Richardthughes @ Dec. 22 2009,13:31)
Does ID predeict this?:

< http://www.newscientist.com/article....fe.html >
---------------------QUOTE-------------------


I'm predicting that ID will say that they predicted this.
Posted by: Albatrossity2 on Dec. 23 2009,11:45

Someone needs to ask the Udiots why teh dezinner didn't give humans the same fancy genitalia that ducks have!

< Carl Zimmer explains duck penises >, with videos.
Posted by: Reg on Dec. 23 2009,12:29

Quote (Richardthughes @ Dec. 22 2009,13:31)
Does ID predeict this?:

< http://www.newscientist.com/article....fe.html >
---------------------QUOTE-------------------


Of course. The life will have been designed, which required intelligence, thus ID.
Posted by: fnxtr on Dec. 23 2009,13:39

Quote (Albatrossity2 @ Dec. 23 2009,11:45)
Someone needs to ask the Udiots why teh dezinner didn't give humans the same fancy genitalia that ducks have!

< Carl Zimmer explains duck penises >, with videos.
---------------------QUOTE-------------------


They just show the little guy some duck porn and whispered dirty duck stories in his ear.
Posted by: Thought Provoker on Dec. 28 2009,11:15

Thanks for having this thread Lou.

At the risk of appearing lost in hero worship...

I have noticed Penrose has been having some interesting ideas lately on the origins of the Big Bang.

Here is a video of a recent lecture...
< http://www.youtube.com/watch?v=OutKE3tyG94 >

As I understand it, the short version is that because of the discovery of Hawking Radiation the presumption is that near the end of the universe there will be nothing left but evaporating Black Holes.  And once the last of the Black Holes totally evaporate all that will be left is photons traveling along the null geodesics which literally means the end of time.

Again, if I am understanding correctly, Penrose is suggesting this null-time state matches the Big Bang state.  Therefore, another Big Bang occurs and another universe is started.

Penrose is suggesting that this idea might be supportable by analysing the Big Bang echo for ripples corresponding to point sources of photons.  Similar to ripples in a pond caused by raindrops.

I welcome the opinions of others (especially Oleg).
Posted by: fnxtr on Dec. 28 2009,14:43

Well, I can see how it means the end of clocks by which to  measure time, but the end of time? And will it also mean the end of space? There will still be distance between photons which didn't exist in the first big bang, won't there?  Won't there? What will become of dark matter and it's effect on the dimensions of space?

eta correct italic tags.
Posted by: Thought Provoker on Dec. 28 2009,15:58

Hi Fnxtr,

I expect Oleg to jump on me with both feet any time now (I say that with all due respect).

Therefore, I will try not to make too much a fool out of myself.

Sir Roger Penrose wrote< The Road to Reality: A Complete Guide to the Laws of the Universe >.  It is around 1000 pages long.

In it, Penrose walks the reader through thinking about the geometry of the universe and Quantum Mechanics as he, a mathematician, looks at it.

About half way through the book, he gets to Minkowskian geometry.  This is the space-time concept we learned in school.

Most people think of the universe similar to a movie but in 3D.  Each 3D frame being a slice in time as time marches on.

This concept does not match observations.  Minkowskian geometry has time as a fourth dimension and it mathematically explains things like the Twin Paradox (Special Relativity).

But is this reality or just a mathematical trick?

Even Oleg has indicated Minkowskian geometry has become so accepted that it is much more than just math.

At this point in his book, Penrose starts the process of combining General Relativity and Quantum Mechanics into a single reality.  The result, Twistor space.

In Twistor Space, null geodesics are single points.

To me, this has explanatory power for Quantum Experiments where photons seem to interact with each other even when separated in space and time.  They are the same point in Twistor Space.

By this view, if all that’s left in the universe is photons then the universe has no volume in Twistor Space.

But is Twistor Space just a mathematical trick or is it real?

Twistor Space is providing explanatory power to modern string theory.  I suspect it is also helping Penrose picture how the Big Bang may have worked.

Oleg may have a different opinion.
Posted by: Reed on Dec. 29 2009,01:34

Mars madness! < A special issue of  Icarus > is dedicated to MROs HiRISE camera, with full text available online.
Posted by: fnxtr on Dec. 29 2009,01:48

Thanks, TP, I'll see if our library has it.
Posted by: Richardthughes on Dec. 31 2009,10:28

< http://www.newscientist.com/article....lf.html >



---------------------QUOTE-------------------
FIRST it was planes, trains and automobiles that benefited from computer-aided design technology. Now, as synthetic biologists attempt to build artificial life forms, a CAD system has been developed to allow them to redesign the stuff of life much faster and more easily.

...
---------------------QUOTE-------------------


Posted by: Richardthughes on Dec. 31 2009,13:29

< http://periodictable.com/ >

Cool, good for teachers?
Posted by: sledgehammer on Dec. 31 2009,17:56

Quote (Richardthughes @ Dec. 31 2009,11:29)
< http://periodictable.com/ >

Cool, good for teachers?
---------------------QUOTE-------------------


Tres Cool  But they left off Unobtanium, an element crucial to many perpetual motion machines.

Happy New Decadium, AtBC!
Posted by: Lou FCD on Dec. 31 2009,18:18

Quote (sledgehammer @ Dec. 31 2009,18:56)
Quote (Richardthughes @ Dec. 31 2009,11:29)
< http://periodictable.com/ >

Cool, good for teachers?
---------------------QUOTE-------------------


Tres Cool  But they left off Unobtanium, an element crucial to many perpetual motion machines.

Happy New Decadium, AtBC!
---------------------QUOTE-------------------


Also Warp Drives, which I mentioned on Facebook just this morning. :)
Posted by: Badger3k on Dec. 31 2009,18:58

Quote (Lou FCD @ Dec. 31 2009,18:18)
Quote (sledgehammer @ Dec. 31 2009,18:56)
Quote (Richardthughes @ Dec. 31 2009,11:29)
< http://periodictable.com/ >

Cool, good for teachers?
---------------------QUOTE-------------------


Tres Cool  But they left off Unobtanium, an element crucial to many perpetual motion machines.

Happy New Decadium, AtBC!
---------------------QUOTE-------------------


Also Warp Drives, which I mentioned on Facebook just this morning. :)
---------------------QUOTE-------------------


Floating mountains too, from what I hear.
Posted by: J-Dog on Dec. 31 2009,19:01

I cracked the firewall at Discovery and found this:


Posted by: fnxtr on Dec. 31 2009,19:58

Quote (Badger3k @ Dec. 31 2009,16:58)
Quote (Lou FCD @ Dec. 31 2009,18:18)
Quote (sledgehammer @ Dec. 31 2009,18:56)
 
Quote (Richardthughes @ Dec. 31 2009,11:29)
< http://periodictable.com/ >

Cool, good for teachers?
---------------------QUOTE-------------------


Tres Cool  But they left off Unobtanium, an element crucial to many perpetual motion machines.

Happy New Decadium, AtBC!
---------------------QUOTE-------------------


Also Warp Drives, which I mentioned on Facebook just this morning. :)
---------------------QUOTE-------------------


Floating mountains too, from what I hear.
---------------------QUOTE-------------------


You're thinking of upsidaisium.

Ve must get sqvirrel!
Posted by: Quack on Jan. 01 2010,04:37



---------------------QUOTE-------------------
To me, this has explanatory power for Quantum Experiments where photons seem to interact with each other even when separated in space and time.  They are the same point in Twistor Space.
---------------------QUOTE-------------------

If mathematics is required in order to (really) understand the universe, I haven't got a chance. But I am interested anyway. And since Laughlin's "A Different Universe" is quite an entertaining read, you have at least made me pick it up once again. I know entanglement is mentioned.

For the rest of you, have phun.
Posted by: Henry J on Jan. 01 2010,17:02



---------------------QUOTE-------------------
If mathematics is required in order to (really) understand the universe,
---------------------QUOTE-------------------


Well, the math is needed to compute predictions from the theory. Some of the ideas can be loosely described without making specific predictions.

Henry
Posted by: Quack on Jan. 02 2010,08:59

Quote (Henry J @ Jan. 01 2010,17:02)


---------------------QUOTE-------------------
If mathematics is required in order to (really) understand the universe,
---------------------QUOTE-------------------


Well, the math is needed to compute predictions from the theory. Some of the ideas can be loosely described without making specific predictions.

Henry
---------------------QUOTE-------------------


Guess I can live with that.
Posted by: sledgehammer on Jan. 02 2010,20:49

Prion evolution: <
'Lifeless' prion proteins are 'capable of evolution' >
"Scientists have shown for the first time that "lifeless" prion proteins, devoid of all genetic material, can evolve just like higher forms of life."

So prions replicate by inducing configuration changes in "normal" proteins?  (IANOB)

Fascinating.
Posted by: Richardthughes on Jan. 04 2010,09:09

< http://discovermagazine.com/2009....than-us >

One for SassanFrancis.
Posted by: Richardthughes on Jan. 04 2010,09:10

Quote (sledgehammer @ Jan. 02 2010,20:49)
Prion evolution: <
'Lifeless' prion proteins are 'capable of evolution' >
"Scientists have shown for the first time that "lifeless" prion proteins, devoid of all genetic material, can evolve just like higher forms of life."

So prions replicate by inducing configuration changes in "normal" proteins?  (IANOB)

Fascinating.
---------------------QUOTE-------------------




---------------------QUOTE-------------------
"This means that this pattern of Darwinian evolution appears to be universally active.


---------------------QUOTE-------------------



Quotemine THAT, bitches.
Posted by: sledgehammer on Jan. 04 2010,09:52

Quote (Richardthughes @ Jan. 04 2010,07:10)
 
Quote (sledgehammer @ Jan. 02 2010,20:49)
Prion evolution: <
'Lifeless' prion proteins are 'capable of evolution' >
"Scientists have shown for the first time that "lifeless" prion proteins, devoid of all genetic material, can evolve just like higher forms of life."

So prions replicate by inducing configuration changes in "normal" proteins?  (IANOB)

Fascinating.
---------------------QUOTE-------------------


 

---------------------QUOTE-------------------
"This means that this pattern of Darwinian evolution appears to be universally active.


---------------------QUOTE-------------------



Quotemine THAT, bitches.
---------------------QUOTE-------------------


Yeah, yeah, but they're still just proteins.
Posted by: Timothy McDougald on Jan. 04 2010,18:55

Quote (Richardthughes @ Jan. 04 2010,09:09)
< http://discovermagazine.com/2009....than-us >

One for SassanFrancis.
---------------------QUOTE-------------------


I've seen it. Hawks takes it down quite nicely < here > and < here >.

< This is much more interesting > and via Bob O'H I have the article from Current Biology...
Posted by: ppb on Jan. 05 2010,22:24

Hubble shows < stuff happening > 13.2 billion years ago.  That takes us back to within half a billion years of the Big Bang.
Posted by: dvunkannon on Jan. 06 2010,13:38



---------------------QUOTE-------------------
Researchers report in this week's issue of Nature that bornaviruses, a group of negative sense RNA viruses, integrated into the DNA of humans and other primates, rodents, and elephants millions of years ago. These snippets represent a source of additional mutation in the mammal genomes they inhabit and a potential source of genomic innovation, the authors suggest.

---------------------QUOTE-------------------



Is it too much to ask that there be a bornavirus 77?
Posted by: Richardthughes on Jan. 06 2010,15:18

Quote (ppb @ Jan. 05 2010,22:24)
Hubble shows < stuff happening > 13.2 billion years ago.  That takes us back to within half a billion years of the Big Bang.
---------------------QUOTE-------------------


by 13.2 you mean 0.0000006
Posted by: ppb on Jan. 07 2010,10:34

Quote (Richardthughes @ Jan. 06 2010,16:18)
Quote (ppb @ Jan. 05 2010,22:24)
Hubble shows < stuff happening > 13.2 billion years ago.  That takes us back to within half a billion years of the Big Bang.
---------------------QUOTE-------------------


by 13.2 you mean 0.0000006
---------------------QUOTE-------------------


13.2 billion years or 6 thousand.  It's somewhere in that range.

What difference does several orders of magnitude make among friends?
Posted by: Lou FCD on Jan. 09 2010,07:06

< What came first in the origin of life? >



---------------------QUOTE-------------------
ScienceDaily (Jan. 9, 2010) — A new study published in Proceedings of National Academy of Sciences rejects the theory that the origin of life stems from a system of self-catalytic molecules capable of experiencing Darwinian evolution without the need of RNA or DNA and their replication.
---------------------QUOTE-------------------



I'd love to read the paper, if anyone has access.



---------------------QUOTE-------------------
Vera Vasasa, Eörs Szathmáry and Mauro Santosa. Lack of evolvability in self-sustaining autocatalytic networks: A constraint on the metabolism-first path to the origin of life. PNAS, January 4, 2010 DOI: 10.1073/pnas.0912628107
---------------------QUOTE-------------------


Posted by: bfish on Jan. 10 2010,01:01

Quote (Lou FCD @ Jan. 09 2010,05:06)
I'd love to read the paper, if anyone has access.
---------------------QUOTE-------------------


PDF winging it's way to your gmail address.
Posted by: Lou FCD on Jan. 10 2010,11:47

Quote (bfish @ Jan. 10 2010,02:01)
Quote (Lou FCD @ Jan. 09 2010,05:06)
I'd love to read the paper, if anyone has access.
---------------------QUOTE-------------------


PDF winging it's way to your gmail address.
---------------------QUOTE-------------------


Thou rocketh.
Posted by: Kristine on Jan. 10 2010,14:17

Quote (fnxtr @ Dec. 28 2009,14:43)
Well, I can see how it means the end of clocks by which to  measure time, but the end of time? And will it also mean the end of space? There will still be distance between photons which didn't exist in the first big bang, won't there?  Won't there? What will become of dark matter and it's effect on the dimensions of space?

eta correct italic tags.
---------------------QUOTE-------------------


Just a quest/ion: ;) What is time apart from its measurement? Phenomena exist apart from memory and our ability to measure, but does time? Is time a phenomenon, like chemical interactions, or a way that we organize phenomena, like "species"?
Posted by: Erasmus, FCD on Jan. 10 2010,16:32

< http://www.sciencemag.org/cgi/content/full/327/5962/148 >



---------------------QUOTE-------------------
Despite much debate in the United States ( 4), surprisingly little attention has been given to the growing scientific evidence of the negative impacts of MTM/VF. Our analyses of current peer-reviewed studies and of new water-quality data from WV streams revealed
serious environmental impacts that mitigation practices cannot successfully address. Published studies also show a high potential for
human health impacts.
---------------------QUOTE-------------------





---------------------QUOTE-------------------
U.S. rules have considered stream creation a valid form of
mitigation while acknowledging the lack of science documenting its ef?cacy (30). Senior of? cials of the U.S. Army Corps of Engineers
(ACOE) have testi? ed that they do not know of a successful stream creation project in conjunction with MTM/VF
---------------------QUOTE-------------------



MTM= mountain top mining (mountaintop removal)
VF=  valley fill) dumping of mine spoil in streams and watercourses

money shot



---------------------QUOTE-------------------
Clearly, current attempts to regulate MTM/ VF practices are inadequate. Mining permits are being issued despite the preponderance of scienti?c evidence that impacts are pervasive and irreversible and that mitigation cannot compensate for losses. Considering environmental impacts of MTM/VF, in combination with evidence that the health of people living in surface-mining regions of the central Appalachians is compromised by mining activities, we conclude that MTM/VF permits should not be granted unless new methods can be subjected to rigorous peer review and shown to remedy these problems. Regulators should no longer ignore rigorous science. The United States should take leadership on these issues, particularly since surface mining in many developing
countries is expected to grow extensively ( 32).(2007).
---------------------QUOTE-------------------




ouch
Posted by: fnxtr on Jan. 10 2010,17:17

Quote (Kristine @ Jan. 10 2010,12:17)
 
Quote (fnxtr @ Dec. 28 2009,14:43)
Well, I can see how it means the end of clocks by which to  measure time, but the end of time? And will it also mean the end of space? There will still be distance between photons which didn't exist in the first big bang, won't there?  Won't there? What will become of dark matter and it's effect on the dimensions of space?

eta correct italic tags.
---------------------QUOTE-------------------


Just a quest/ion: ;) What is time apart from its measurement? Phenomena exist apart from memory and our ability to measure, but does time? Is time a phenomenon, like chemical interactions, or a way that we organize phenomena, like "species"?
---------------------QUOTE-------------------


If the universe were massless, would it still have dimensions? Can there just be space, with nothing in it?
Posted by: Henry J on Jan. 10 2010,22:55



---------------------QUOTE-------------------
What is time apart from its measurement? Phenomena exist apart from memory and our ability to measure, but does time? Is time a phenomenon, like chemical interactions, or a way that we organize phenomena, like "species"?
---------------------QUOTE-------------------


Imnsho, the fact that measurements of time intervals can be made, plus the fact that interactions aren't generally observed between things at different "points" in time, implies that the measurements are of something analogous to distances, but along a dimension that behaves somewhat differently than do dimensions of space.

Or something like that.

Henry
Posted by: fnxtr on Jan. 11 2010,11:05

That's sort of what I was obliquely referring to. If time is another dimension, it (too) may exist without any kind of ruler.  

It could be an anarcho-syndicalist commune.
Posted by: Lou FCD on Jan. 12 2010,12:46

Autotrophy in Kingdom Animalia:

< Green Sea Slug steals chloroplasts intact from the algae it eats >.



---------------------QUOTE-------------------
Scientists have shown that once a young slug has slurped its first chloroplast meal from one of its few favored species of Vaucheria algae, the slug does not have to eat again for the rest of its life. All it has to do is sunbathe.
---------------------QUOTE-------------------



Cool.
Posted by: Quack on Jan. 12 2010,14:30

Quote (Lou FCD @ Jan. 12 2010,12:46)
Autotrophy in Kingdom Animalia:

< Green Sea Slug steals chloroplasts intact from the algae it eats >.

 

---------------------QUOTE-------------------
Scientists have shown that once a young slug has slurped its first chloroplast meal from one of its few favored species of Vaucheria algae, the slug does not have to eat again for the rest of its life. All it has to do is sunbathe.
---------------------QUOTE-------------------



Cool.
---------------------QUOTE-------------------


Grand design.
Posted by: Richardthughes on Jan. 12 2010,15:27

Wasn't there some speculation on GNOME CHOMPSKY'S view on evolution?

< http://www.chomsky.info/debates/20060301.htm >



---------------------QUOTE-------------------
CHOMSKY: You could be an intellectually respectable atheist in the 17th century, or in the fifth century. In fact, I don’t even know what an atheist is. When people ask me if I’m an atheist, I have to ask them what they mean. What is it that I’m supposed to not believe in? Until you can answer that question I can’t tell you whether I’m an atheist, and the question doesn’t arise.

I don’t see anything logical in being agnostic about the Greek gods. There’s no agnosticism about ectoplasm [in the non-biological sense]. I don’t see how one can be an agnostic when one doesn’t know what it is that one is supposed to believe in, or reject. There are plenty of things that are unknown, but are assumed reasonably to exist, even in the most basic sciences. Maybe 90 percent of the mass-energy in the universe is called “dark,” because nobody knows what it is.

Science is an exploration of very hard questions. Not to underrate the theory of evolution, that’s a terrific intellectual advance, but it tells you nothing about whether there’s whatever people believe in when they talk about God. It doesn’t even talk about that topic. It talks about how organisms evolve.


---------------------QUOTE-------------------


Posted by: Kristine on Jan. 12 2010,16:05

Quote (fnxtr @ Jan. 11 2010,11:05)
That's sort of what I was obliquely referring to. If time is another dimension, it (too) may exist without any kind of ruler.  

It could be an anarcho-syndicalist commune.
---------------------QUOTE-------------------


Ah, I see (said the blind woman)! I'm getting this (I think), but if (a) dimension(s) exist(s) without a ruler, what's the difference between that and a singularity?

*brainfahrt*! :p
Posted by: Henry J on Jan. 12 2010,17:24



---------------------QUOTE-------------------
the slug does not have to eat again for the rest of its life. All it has to do is sunbathe.
---------------------QUOTE-------------------


But that could lead to a sluggish lifestyle for the creature!

Henry
Posted by: fnxtr on Jan. 12 2010,17:29

Quote (Kristine @ Jan. 12 2010,14:05)
Quote (fnxtr @ Jan. 11 2010,11:05)
That's sort of what I was obliquely referring to. If time is another dimension, it (too) may exist without any kind of ruler.  

It could be an anarcho-syndicalist commune.
---------------------QUOTE-------------------


Ah, I see (said the blind woman)! I'm getting this (I think), but if (a) dimension(s) exist(s) without a ruler, what's the difference between that and a singularity?

*brainfahrt*! :p
---------------------QUOTE-------------------


"Hmm. Tricky." -- Deep Thought.

I should of course read a little more on the subject, but as I understand it a singularity is infinitely dense (like Byers), a condition of the spacetime curvature, erm, disappearing into itself. (But does the matter that disappeared into the singularity still exist?)

Space devoid of matter and energy would be just the opposite, infinitely flat. Or so I understand it.

But yeah, I also understand the perspective that if there's nothing in the universe, it doesn't matter how big it is.

More sparks in the head. Damn you.

This means a trip to the library. Again. :-)
Posted by: RDK on Jan. 12 2010,17:31

Quote (Henry J @ Jan. 12 2010,17:24)
 

---------------------QUOTE-------------------
the slug does not have to eat again for the rest of its life. All it has to do is sunbathe.
---------------------QUOTE-------------------


But that could lead to a sluggish lifestyle for the creature!

Henry
---------------------QUOTE-------------------


The heathen!  Don't the 7 Deadly Sins speak out against being a sloth?
Posted by: fnxtr on Jan. 12 2010,17:36

So now slugs and slothes(!) are the same "kind"?

At first glance it seems like a pretty cushy lifestyle, but then, it'd be pretty boring.
Posted by: Quack on Jan. 13 2010,02:37

Is it possible that space (or maybe rather the space-time continuum) and matter are linked - you can't have the one without the other, or vice versa?
Posted by: Henry J on Jan. 13 2010,10:40



---------------------QUOTE-------------------
Is it possible that space (or maybe rather the space-time continuum) and matter are linked
---------------------QUOTE-------------------


The impression I get from what I've read on that is that matter is a form of energy, and energy is a vibration of space (whatever space might be). If that's not too far off, then matter/energy would have no separate existence, and space sitting without vibrating seems unlikely.

Henry
Posted by: sledgehammer on Jan. 13 2010,11:56

From Carl Zimmer (NYT/Science):
< "Hunting Fossil Viruses in Human Genome" >

 An interesting side plot: apparently placental mammals co-opted a retrovirus to produce a viral protein (syncytin) that is crucial to placental formation. From page 2 of the NYT article: (links can be found in the original)

"Mammal genomes contain thousands of stretches of DNA called LINEs. LINEs sometimes make copies of themselves that get reinserted back into the genome. Dr. Tomonaga’s research indicates that LINEs grabbed the genes of borna viruses and pulled them into their genome.

The discovery raises the possibility that LINEs have kidnapped other viruses floating near their host’s DNA, like flu viruses.

Two of the four copies of the borna virus gene carry crippling mutations. It’s impossible for our cells to make proteins from them. But the other two genes look remarkably intact, perhaps suggesting that our bodies use them for our own benefit. Exactly what they do isn’t clear though.

Studies on other captive viruses have revealed that some help ward off viral invasions. One virus protein, syncytin, is essential for our being born at all.

“The only place it’s expressed is in the placenta,” Dr. Heidmann said. To understand its function, he and his colleagues disabled the gene in mice. Without syncytin, mice developed deformed placentas, and their embryos died.

Syncytin started as a surface protein on retroviruses that fused them to cells. When mammals captured the gene, they used it in the placenta to create a layer of fused cells through which mothers can send nutrients to their embryos.

Dr. Heidmann and his colleagues have discovered that over the past 100 million years, mammals have repeatedly harnessed viruses to make syncytin. “Wherever we search for them, we find them,” Dr. Heidmann said.

But the syncytin genes we use today may have actually replaced an ancestral one that a virus bequeathed to the very first placental mammals. In fact, that infection may have made the placenta possible in the first place. “It was a major event for animal evolution,” Dr. Heidmann said."


Where is the intelligence behind this macro-evolutionary change?
None of this would make any sense without common descent, including HGT.

ETA: attribution and correction
Posted by: dvunkannon on Jan. 13 2010,14:01

The Scientist is bring a volley of great articles on evolution.

< New Clues to Y Evolution >

< Are Mutations Really Random? >

< Should Evolutionary Theory Evolve? > - Altenberg 16 story!

< The Maverick Bacterium >
Posted by: Quack on Jan. 13 2010,14:46

What can I say? I read all of them but had to skip most of the fascinating Listeria story. A bit overwhelming and I have no use for it... But great stuff, I wonder if creationists bother reading such articles?
Posted by: Henry J on Jan. 13 2010,16:39



---------------------QUOTE-------------------
An interesting side plot: apparently placental mammals co-opted a retrovirus to produce a viral protein
---------------------QUOTE-------------------



Well that's uncommonly descent of those usually pesky viruses, huh?

Henry
Posted by: dvunkannon on Jan. 14 2010,09:59

< Elastic, not plastic species: Frozen plasticity theory and the origin of adaptive evolution in sexually reproducing organisms >

For extra credit - find the positive reference to JAD!! Since the author is Czech, have we found the real VMartin?
Posted by: Quack on Jan. 16 2010,07:07

< BMC Microbiology >
 

---------------------QUOTE-------------------
Polar bears living in the pristine Svalbard area of Norway have a low diversity of bacteria in their feces, harboring mostly anaerobic bacteria from the genus Clostridia, and very few ampicillin resistance blaTEM alleles.
---------------------QUOTE-------------------


Posted by: Alan Fox on Jan. 16 2010,07:18

Quote (Quack @ Jan. 16 2010,02:07)
< BMC Microbiology >
   

---------------------QUOTE-------------------
Polar bears living in the pristine Svalbard area of Norway have a low diversity of bacteria in their feces, harboring mostly anaerobic bacteria from the genus Clostridia, and very few ampicillin resistance blaTEM alleles.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


I did wonder how the hell you go about collecting fecal samples from polar bears!



---------------------QUOTE-------------------
Bears were caught by remote injection of a dart Palmer Cap-Chur Equipment) containing the drug Zoletil® (Virbac, Carros Cedex, France) fired from a helicopter [41].
---------------------QUOTE-------------------



Cowards!
Posted by: fnxtr on Jan. 16 2010,13:35

[grampa]
We never had no fancy-shmancy sleeper darts when I was a boy, no sir! We used to just fist the buggers! Grab a big handful of fewmets, then head for the igloo and hope to outrun the other guy.
[/grampa]
Posted by: Henry J on Jan. 16 2010,14:22

Or, how about just taking some polar-oid pictures from a safe distance? :)

Henry
Posted by: Erasmus, FCD on Jan. 18 2010,01:22

< sometimes you gotta follow them around and pick up the poop >

2:15
Posted by: fnxtr on Jan. 18 2010,10:06

Quote (Erasmus @ FCD,Jan. 17 2010,23:22)
< sometimes you gotta follow them around and pick up the poop >

2:15
---------------------QUOTE-------------------


That's even bigger than the < Camberwell Carrot >!
Posted by: Richardthughes on Jan. 21 2010,20:54

Design?

< http://www.youtube.com/watch?v....bedded# >
Posted by: JLT on Jan. 26 2010,10:48

< Floreano D, Keller L (2010) Evolution of Adaptive Behaviour in Robots by Means of Darwinian Selection. PLoS Biol 8(1): e1000292 >
 

---------------------QUOTE-------------------
Ever since Cicero's De Natura Deorum ii.34., humans have been intrigued by the origin and mechanisms underlying complexity in nature. Darwin suggested that adaptation and complexity could evolve by natural selection acting successively on numerous small, heritable modifications. But is this enough? Here, we describe selected studies of experimental evolution with robots to illustrate how the process of natural selection can lead to the evolution of complex traits such as adaptive behaviours. Just a few hundred generations of selection are sufficient to allow robots to evolve collision-free movement, homing, sophisticated predator versus prey strategies, coadaptation of brains and bodies, cooperation, and even altruism. In all cases this occurred via selection in robots controlled by a simple neural network, which mutated randomly.
---------------------QUOTE-------------------


Posted by: fnxtr on Jan. 27 2010,09:34

Quote (Thought Provoker @ Dec. 28 2009,13:58)
Hi Fnxtr,

I expect Oleg to jump on me with both feet any time now (I say that with all due respect).

Therefore, I will try not to make too much a fool out of myself.

Sir Roger Penrose wrote< The Road to Reality: A Complete Guide to the Laws of the Universe >.  It is around 1000 pages long.
---------------------QUOTE-------------------


Yeah, I just got this from the local library. It makes "The Structure of Evolutionary Theory" look like a Marvel comic.

Fins: check! Mask: check! O2: check!

Okay, down we go...
Posted by: Richardthughes on Jan. 29 2010,10:08

Coolness!

< http://www.popsci.com/science....hniques >

Evolving robots!



Wait for the ID spin..
Posted by: bfish on Jan. 29 2010,14:43

Quote (Richardthughes @ Jan. 29 2010,08:08)
Coolness!

< http://www.popsci.com/science....hniques >

Evolving robots!



Wait for the ID spin..
---------------------QUOTE-------------------


They're still robots...
Posted by: Richardthughes on Feb. 04 2010,12:11

This will tripple the mining shifts in Tardistan.

< http://www.newscientist.com/article....ll=true >
Posted by: midwifetoad on Feb. 04 2010,14:51

Quote (Richardthughes @ Feb. 04 2010,12:11)
This will tripple the mining shifts in Tardistan.

< http://www.newscientist.com/article....ll=true >
---------------------QUOTE-------------------




---------------------QUOTE-------------------
These analogies are telling. Skinner's theory, though once fashionable, is now widely agreed to be unsustainable, largely because Skinner very much overestimated the contribution that the structure of a creature's environment plays in determining what it learns, and correspondingly very much underestimated the contribution of the internal or "endogenous" variables - including, in particular, innate cognitive structure.
---------------------QUOTE-------------------



Actually what Skinner wrote was that operant conditioning builds upon the behavioral traits inherited via biological evolution. But let's not let facts get in the way of a good story.

He specifically mentioned that laboratory experiments in conditioning always started with hard-wired behavior appropriate for a species -- pecking for pigeons, bar pressing for rats.

I get kind of pissed when this is distorted by pop-science writers.
Posted by: midwifetoad on Feb. 04 2010,15:00



---------------------QUOTE-------------------
There never were any winged pigs because there's no place on pigs for the wings to go. This isn't environmental filtering, it's just physiological and developmental mechanics.
---------------------QUOTE-------------------



I'm glad I'm not a biologist. I'd hate to be part of a tribe too effing stupid to notice that physics and developmental constraints affect the direction of evolution. :angry:
Posted by: midwifetoad on Feb. 05 2010,06:45

Interesting site.

Is it new or just new to me?

< http://www.scienceclarified.com/ >
Posted by: sledgehammer on Feb. 05 2010,14:34

Quote (Richardthughes @ Feb. 04 2010,10:11)
This will tripple the mining shifts in Tardistan.

< http://www.newscientist.com/article....ll=true >
---------------------QUOTE-------------------


 

---------------------QUOTE-------------------
It's a main claim of our book that, when phenotypic traits are endogenously linked, there is no way that selection can distinguish among them: selection for one selects the others, regardless of their effects on fitness.
---------------------QUOTE-------------------


What crap.
Selection still applies, if only for a group of linked traits.  Think sickle cell anemia and malaria resistance.
A population can still exhibit all varieties and combinations of linked traits in varying degrees, and selection drives the percentages.

Apparently Jerry Fodor is no stranger to UD:
< Fodor on NS >

ETA: UD linky
Posted by: Kristine on Feb. 06 2010,15:23

Ye gonads, guys, I had no idea that Biological databases were so darned complex! ;) Reading this stuff is like curling up by a warm fire and kitty on your lap with a volume of Chemical Abstracts:


---------------------QUOTE-------------------
The phrase biology databases is deliberately vague so as to cover a wide range of data types. There is no good estimate as to the number of databases that are publicly accessible and have some aspect of molecular
biology/genomics in their contents, but it is easily double the number included in the Nucleic Acids database issue. The 2003 issue included approximately 400 titles, so there could easily be 800 to 1,000 databases. While numerous, the databases do cluster based on the type of
data they include, or by some other scheme, such as organization, institution, or species. Various articles about these resources have generated categorizations.

Another resource sorted them into: biological literature, sequences, expression, protein interaction measurements, and metabolic expression (Marcotte and Date 2001). Another variation is: pathway, genome, protein, enzyme, chemical, and literature. Some of the databases have print counterparts; most are purely electronic. There are hybrid databases, combining data from multiple sources. KEGG, the Kyoto Encyclopedia of Genes and Genomes, is an example of such a combination. “KEGG is a suite of databases and associated software, integrating our current knowledge on molecular interaction networks in biological processes, the information about the universe of
genes and proteins, and the information about the universe of chemical compounds and reactions” (http://www.genome.ad.jp/kegg/kegg.html).

Other databases are subsets from the larger databases with local valueadded content. This article focuses on four core database examples: sequence, microarray, protein, and literature databases. The last example needs no explanation for librarians. The sequence databases are the next easiest to explain–they contain DNA sequences and documentation on how thatsequence was created, and often, links to articles and other information related to that sequence. The microarray data come from experiments
looking at the ‘interdependence of genes’ (Hung and Kim 2000). The protein data come from both experiments and computational modeling of protein sequences and their structures.
---------------------QUOTE-------------------


Got all that? Okay, what kills me (and I attended a workshop on this last July at ALA, and almost had my mind stretched beyond the point of snapping back) is the fact that biologists don't search the literature necessarily - they search the abstracts and citations. It's called data mining, and there is such a thing as a data (or database) curator.


---------------------QUOTE-------------------
With many large sequence datasets completed, the research has moved to the next phase. As touched on in the introduction, this sequence of effort is unusual in the life sciences world of hypothesis-driven experiments. In the classical experiment-based process, a scientist generates a hypothesis, devises an experiment, collects data, and analyses those data in order to determine, with some level of statistical confidence, whether the null hypothesis can be rejected. Then one more bit of knowledge enters the discipline. But much of the current data collection runs independent of any experiment driven by any hypothesis. The analysis of these data is referred to as in silico biology, or hypothesis free. The former term is considerably less assumptive than the latter. The goal is, as it has always been, to extract significance from the data: an action, a function, a role in a pathway. But the approach must differ from classical methods simply because there is so much data. The only way to extract any sense from them is to apply highly computational approaches.
---------------------QUOTE-------------------


(Chiang, Katherine S.(2004) 'Biology Databases for the New Life Sciences', Science & Technology
Libraries, 25: 1, 139 — 170) Yes, I am reading this article for my class (Reference Sources in the Sciences).

I think I need to see these search algorithms in action before I completely get it.
Posted by: fnxtr on Feb. 06 2010,19:10

Quote (Kristine @ Feb. 06 2010,13:23)
 

---------------------QUOTE-------------------
(snip) ... of any experiment driven by any hypothesis. The analysis of these data is referred to as in silico biology, or hypothesis free. The former term is considerably less assumptive than the latter. The goal is, as it has always been, to extract significance from the data: an action, a function, a role in a pathway. But the approach must differ from classical methods simply because there is so much data. The only way to extract any sense from them is to apply highly computational approaches.
---------------------QUOTE-------------------


(Chiang, Katherine S.(2004) 'Biology Databases for the New Life Sciences', Science & Technology
Libraries, 25: 1, 139 — 170) Yes, I am reading this article for my class (Reference Sources in the Sciences).

I think I need to see these search algorithms in action before I completely get it.
---------------------QUOTE-------------------


Erm, yeah. Don't you need some kind of hypothesis on which to base your search algorithms in the first place?
Posted by: Kristine on Feb. 08 2010,12:50

Quote (fnxtr @ Feb. 06 2010,19:10)
         
Quote (Kristine @ Feb. 06 2010,13:23)
           

---------------------QUOTE-------------------
(snip) ... of any experiment driven by any hypothesis. The analysis of these data is referred to as in silico biology, or hypothesis free. The former term is considerably less assumptive than the latter. The goal is, as it has always been, to extract significance from the data: an action, a function, a role in a pathway. But the approach must differ from classical methods simply because there is so much data. The only way to extract any sense from them is to apply highly computational approaches.
---------------------QUOTE-------------------


(Chiang, Katherine S.(2004) 'Biology Databases for the New Life Sciences', Science & Technology
Libraries, 25: 1, 139 — 170) Yes, I am reading this article for my class (Reference Sources in the Sciences).

I think I need to see these search algorithms in action before I completely get it.
---------------------QUOTE-------------------


Erm, yeah. Don't you need some kind of hypothesis on which to base your search algorithms in the first place?
---------------------QUOTE-------------------


Yes, and therein lies the rub.
         

---------------------QUOTE-------------------
Current activities are in a chaotic phase. The ability of researchers to collect data outstrips the availability of techniques to analyze them. Bioinformatics researchers looking at the citation literature, at sequences, and at gene expression are trying to reduce the amount of data in an intelligent way so as to bubble up ‘interesting data’ that can then drive experiments. Researchers are trying to create high-level overviews of the data, “ideally in ways that impart additional information about its structure” (Slonim 2002). Several examples of this dry work of computational in silico data mining have been presented. The results of those efforts are intended to focus the subsequent work of the wet laboratory experiments. Bioinformaticians are inventing techniques for data analysis. Theyare creating so many approaches to data analysis that the scene is reminiscentof the Wild West. There are multiple approaches to the same goals. The literature is full of articles describing new and better algorithmsfor data mining. Authors rarely cite anything outside of the field, and sometimes cite comparable approaches, even though much of the analysis (at least superficially) has parallels to data analysis in other domains.

Most likely, a settling period will follow just as sequence comparisons have settled around some quasi-standard tools such as BLAST. Meanwhile, authors jostle and engage in subtle salesmanship for their approach. In the proof-of-concept papers, phrases such as ‘the advantage of,’ ‘a novel computational method,’ and ‘unlike other literature-based tools, the work we present here’ appear...

All of the articles introducing techniques acknowledge the need for validation. In some cases, each approach is validated by comparing it against known results. For example, if it is an automated annotation technique, the researcher will strip the known annotations out of a
dataset. They use their algorithm to create a set of annotations, then compare the results to the original annotations. In other cases, researchers are relying on the collective evaluative power of their colleagues. One article simply says: “Such links must be validated by the international research community” (Dicks 2000). Phrases like ‘we rely on the fact,’ ‘the method is based on the assumption,’ ‘our primary assumptions’ still abound in this world.

As bioinformatics approaches proliferate and the field matures, the question of validity will be answered in some form or another... Parallel assessments of the validity of thecurrent crop of algorithmic approaches will need to be developed and applied in the -omics (genomics, proteomics, bibliomics) world. Questions such as the following need to be asked.

Compared to other approaches making the same claim, what is the quality of a particular data clustering or mining approach? Does the approach even do what it claims to do? Does the algorithm in the approach incorporate the theory adequately? Is the algorithm valid for the theory it assumes? Is the theory valid, given the data to which it is being applied? Do the data justify the inference being used on them?

Researchers will develop increasingly sophisticated computational methods that should compensate somewhat for heterogeneous data, and additional calculations for confidence measures are likely to develop as the bioinformatics field matures. But conclusions will still be only as reliable as the weakest data. Perhaps, eventually, certain clustering will ‘win’ and become the de facto standard manipulation for a particular function. Over time, that algorithm could be incorporated into the commonly used software and become invisible to users. At a simplistic level, the concept of a mean in linear statistics, and how it is calculated, and the embedding of that calculation into spreadsheet and statistical software packages is an example of this transition. It could be envisioned as an in silica recapitulation of evolutionary survival–the survival of the most efficient, most predictive/productive algorithmic approach.
---------------------QUOTE-------------------


Whew! Sorry for the long quotes. (I'm the one who had to read the whole shebang for a class!;)

It's a big, wonderful, strange in silico world out there. I wonder if successful algorithms could be considered selection, with the literature as phenotype?
Posted by: fnxtr on Feb. 08 2010,14:13

That was a bender, all right.

Those algorithms most suited to their environment will prevail...

(Wayne Campbell)H'yeah, right.(/Wayne Campbell)

That's how we got VHS. And Windows.

It might be more like sexual selection: the best advertiser will win.
Posted by: Timothy McDougald on Feb. 08 2010,20:19

< This is pretty cool: >



---------------------QUOTE-------------------
"Records of ancient seawater chemistry allow us to unravel past changes in climate, plate tectonics and evolution of life in the oceans. These processes affect ocean chemistry and have shaped our planet over millions of years," said Dr Rosalind Coggon, formerly of NOCS now at Imperial College London.

"Reconstructing past ocean chemistry remains a major challenge for Earth scientists, but small calcium carbonate veins formed from warm seawater when it reacts with basalts from the oceanic crust provide a unique opportunity to develop such records," added co-author Professor Damon Teagle from SOES.
---------------------QUOTE-------------------


Posted by: ppb on Feb. 10 2010,15:00

This is my kind of science!  Turns out that < beer may be good for building bones. >

It is a very good source of dietary silicon.

I knew there was a reason for drinking it.  :)
Posted by: Quack on Feb. 10 2010,15:47

Quote (ppb @ Feb. 10 2010,15:00)
This is my kind of science!  Turns out that < beer may be good for building bones. >

It is a very good source of dietary silicon.

I knew there was a reason for drinking it.  :)
---------------------QUOTE-------------------


So that's the reason my teeth and bones still are so good? But does it have any effect on cartilage?
Posted by: Henry J on Feb. 10 2010,20:01

"Beer bad" - Xander Harris.
Posted by: fnxtr on Feb. 10 2010,20:27

Quote (Henry J @ Feb. 10 2010,18:01)
"Beer bad" - Xander Harris.
---------------------QUOTE-------------------


"Smart women are so hot." -- Ibid.
Posted by: Schroedinger's Dog on Feb. 11 2010,07:20

It's snowing in Nice right now, an event that last occured on this scale more than 10 years ago.

The weather is getting a bit looney, isn't it?
Posted by: Schroedinger's Dog on Feb. 11 2010,07:34











All taken from my flat...
Posted by: fnxtr on Feb. 11 2010,11:12

Quote (Schroedinger's Dog @ Feb. 11 2010,05:34)
(snip)





All taken from my flat...
---------------------QUOTE-------------------


Meanwhile Vancouver is having to truck in snow in preparation for some of the winter Olympic events. Of all the places in Canada to hold them, IOC chose the warmest.  Genius.
Posted by: Schroedinger's Dog on Feb. 11 2010,13:44

It seems snow has finally fallen on Vancouver and affiliated snow parks...
Posted by: fnxtr on Feb. 11 2010,17:56

VANOC has friends in high places, it would seem.

I keep thinking of that ERV image about bacteria nukleatin' yer snowz.
Posted by: fnxtr on Feb. 11 2010,18:01

Equivocal.  15cm of new snow but a high of +4 C.

Cypress is historically, and to my memory, the slushiest of the nearby mountains. I guess they outbid Grouse and Seymour. Whistler is wet, too, btw.
Posted by: dvunkannon on Feb. 12 2010,06:53

Not a science link, but a quick question for y'all -

Is it possible to calculate the time that has passed since the stellar explosion that created the atoms now present in the earth?

As I understand it, some star had to explode in order to cook up the atoms that are above iron in size. These atoms would be floating around for a while in space. Then another nearby explosion would start the process of collapse of the gas cloud, leading to the formation of the sun and our planet.

Radioactive atoms such as uranium must have been decaying into lead the whole time since they were created. Some lead would have been formed directly by the explosion. Is it possible to tease these factors apart and make an estimate (for example) that our atoms are 6 billion years old? At least our heavier atoms anyway. Our hydrogen has probably been around since right after the Big Bang.

All part of a back of the envelope calculation of whether we are among the first intelligent life that has had time to evolve.
Posted by: dvunkannon on Feb. 12 2010,07:00

Quote (Schroedinger's Dog @ Feb. 11 2010,08:34)


All taken from my flat...
---------------------QUOTE-------------------


You have a flat in Nice with an ocean view and haven't invited us all over to crash for several weeks? For shame sir!
Posted by: fnxtr on Feb. 12 2010,10:14

Quote (dvunkannon @ Feb. 12 2010,04:53)
Not a science link, but a quick question for y'all -

Is it possible to calculate the time that has passed since the stellar explosion that created the atoms now present in the earth?

As I understand it, some star had to explode in order to cook up the atoms that are above iron in size. These atoms would be floating around for a while in space. Then another nearby explosion would start the process of collapse of the gas cloud, leading to the formation of the sun and our planet.

Radioactive atoms such as uranium must have been decaying into lead the whole time since they were created. Some lead would have been formed directly by the explosion. Is it possible to tease these factors apart and make an estimate (for example) that our atoms are 6 billion years old? At least our heavier atoms anyway. Our hydrogen has probably been around since right after the Big Bang.

All part of a back of the envelope calculation of whether we are among the first intelligent life that has had time to evolve.
---------------------QUOTE-------------------


You mean how long it would take supernova shrapnel to re-coagulate?

There was probably a lot of the stellar equivalent of horizontal gene transfer.  Those remnants blow out at quite a velocity.

Later they mix with the rest of the interstellar medium (always loved that expression), which may or may not end up as a stellar nursery like those cool columns in the Hubble images.

Also, not all stars have the same expected lifetime.  Low mass stars (red and brown dwarves) live billions of years longer than blue giant and supergiant stars. But low mass stars don't go nova anyway. (Ours won't, it'll just get swollen and red and then gradually sort of evaporate into a white dwarf.)

So, IANAA, but my guess on the first question is probably not.  We have no idea how many generations of stars contributed to our current chemistry.

Those "are we alone" and "are we the first" speculations are full of uncertainty on all levels. Cosmologically, there's no reason we'd have to be the first, there's also no reason we couldn't be first.
Posted by: Richardthughes on Feb. 15 2010,09:46

ID in action:

< http://www.newscientist.com/article....ed.html >


(By Humans.)
Posted by: Peter Henderson on Feb. 15 2010,10:24

The YECs are quotemining this one for all it's worth:

< http://www.sciencedaily.com/releases/2010/02/100209183335.htm >



---------------------QUOTE-------------------
Science News

Bird-from-Dinosaur Theory of Evolution Challenged: Was It the Other Way Around?
ScienceDaily (Feb. 10, 2010) — A new study just published in the Proceedings of the National Academy of Sciences provides yet more evidence that birds did not descend from ground-dwelling theropod dinosaurs, experts say, and continues to challenge decades of accepted theories about the evolution of flight.


A new analysis was done of an unusual fossil specimen discovered in 2003 called "microraptor," in which three-dimensional models were used to study its possible flight potential, and it concluded this small, feathered species must have been a "glider" that came down from trees. The research is well done and consistent with a string of studies in recent years that pose increasing challenge to the birds-from-dinosaurs theory, said John Ruben, a professor of zoology at Oregon State University who authored a commentary in PNAS on the new research.

The weight of the evidence is now suggesting that not only did birds not descend from dinosaurs, Ruben said, but that some species now believed to be dinosaurs may have descended from birds.

"We're finally breaking out of the conventional wisdom of the last 20 years, which insisted that birds evolved from dinosaurs and that the debate is all over and done with," Ruben said. "This issue isn't resolved at all. There are just too many inconsistencies with the idea that birds had dinosaur ancestors, and this newest study adds to that."

Almost 20 years of research at OSU on the morphology of birds and dinosaurs, along with other studies and the newest PNAS research, Ruben said, are actually much more consistent with a different premise -- that birds may have had an ancient common ancestor with dinosaurs, but they evolved separately on their own path, and after millions of years of separate evolution birds also gave rise to the raptors. Small animals such as velociraptor that have generally been thought to be dinosaurs are more likely flightless birds, he said.

"Raptors look quite a bit like dinosaurs but they have much more in common with birds than they do with other theropod dinosaurs such as Tyrannosaurus," Ruben said. "We think the evidence is finally showing that these animals which are usually considered dinosaurs were actually descended from birds, not the other way around."

Another study last year from Florida State University raised similar doubts, Ruben said.

In the newest PNAS study, scientists examined a remarkable fossil specimen that had feathers on all four limbs, somewhat resembling a bi-plane. Glide tests based on its structure concluded it would not have been practical for it to have flown from the ground up, but it could have glided from the trees down, somewhat like a modern-day flying squirrel. Many researchers have long believed that gliders such as this were the ancestors of modern birds.

"This model was not consistent with successful flight from the ground up, and that makes it pretty difficult to make a case for a ground-dwelling theropod dinosaur to have developed wings and flown away," Ruben said. "On the other hand, it would have been quite possible for birds to have evolved and then, at some point, have various species lose their flight capabilities and become ground-dwelling, flightless animals -- the raptors. This may be hugely upsetting to a lot of people, but it makes perfect sense."

In their own research, including one study just last year in the Journal of Morphology, OSU scientists found that the position of the thigh bone and muscles in birds is critical to their ability to have adequate lung capacity for sustained long-distance flight, a fundamental aspect of bird biology. Theropod dinosaurs did not share this feature. Other morphological features have also been identified that are inconsistent with a bird-from-dinosaur theory. And perhaps most significant, birds were already found in the fossil record before the elaboration of the dinosaurs they supposedly descended from. That would be consistent with raptors descending from birds, Ruben said, but not the reverse.

OSU research on avian biology and physiology has been raising questions on this issue since the 1990s, often in isolation. More scientists and other studies are now challenging the same premise, Ruben said. The old theories were popular, had public appeal and "many people saw what they wanted to see" instead of carefully interpreting the data, he said.

"Pesky new fossils...sharply at odds with conventional wisdom never seem to cease popping up," Ruben wrote in his PNAS commentary. "Given the vagaries of the fossil record, current notions of near resolution of many of the most basic questions about long-extinct forms should probably be regarded with caution."
---------------------QUOTE-------------------



for obvious reasons.
Posted by: dvunkannon on Feb. 15 2010,15:51

Pimp My Ribosome!

< Reprogramming the Genetic Code >
Posted by: Richardthughes on Feb. 15 2010,16:08

Quote (dvunkannon @ Feb. 15 2010,15:51)
Pimp My Ribosome!

< Reprogramming the Genetic Code >
---------------------QUOTE-------------------


Oi, Dvk ... two posts above your post, phone-it-in-monkey!
Posted by: Henry J on Feb. 15 2010,16:41

I have to ask this: why exactly should anybody be upset by the notion of raptors being descended from avians? Whichever one came first, if one is descended from the other, that's still evolution! (Or evilution, whichever.)

Henry
Posted by: dheddle on Feb. 15 2010,17:01

On the topic of entropy--a question.

Do you think only the difference in entropy has physical significance? I've been thinking a great deal about this. The conventional answer is "yes" (I once argued about this Mark Perakh on PT and he dismissed me out of hand—arrogant bastard—I don’t mind being dissed by superstar physicists but not garden-variety physicists—but I digress.)

I’m teaching thermo and have been thinking about this a great deal. Of course, all the equations involving entropy can be cast in terms of the difference in entropy—but that’s not exactly what I am asking. (For example, we can add a constant momentum to everything, and Newton’s 2nd Law still applies, but we don’t go about carefully stating that only changes in momentum are relevant.)

I’m thinking, of course, of the quantum basis for entropy—which unlike the classical basis is not mysterious at all. Every microstate (because of Heisenberg) has a finite volume in phase space, therefore we only have a finite (though typically ginormous) number of microstates for each macrostate. That is certainly a well defined absolute quantity: the number of macrostates. It is a positive definite integer. In order to free ourselves from dealing with enormous numbers—numbers with exponents in the exponents, we shrink ‘em down—and make them additive rather multiplicative by taking the log—and give that quantity the name entropy. Nothing mysterious.

The number of microstates is clearly a well defined quantity—so why not the entropy, which is just a smoothing thereof? We define absolute zero and an absolute temperature scale—as if temperature has some absolute meaning—but in fact all those formulae that demand that you insert an absolute temperature can be recast in terms of  a temperature difference. And entropy is more fundamental than temperature.

Anyway, I think the language is simply a carryover from classical thermodynamics. And I think it is wrong—I think it at least makes a certain sense to say that S=0 when the number of microstates = 1, and that this is not arbitrary in the same sense that the zero of a potential energy is arbitrary.

If Louis cares to chime in he may not use enthalpy. The friggin' chemists and their friggin' enthalpy really piss me off!
Posted by: Tony M Nyphot on Feb. 17 2010,18:24

I have been personally introduced to an affliction known as < Pine Mouth >.

< Here is an 2001 article from the European Journal of Emergency Medicine >.

After eating 2 handfuls of pine nuts last Thursday, I woke up Sunday to find that regardless of what I eat, it all is incredibly bitter.

Between meals, there is no sense of bitterness, but anytime I eat or drink, my mouth is overwhelmed with bitterness...chocolate, cheese, bread, salsa, beer, fruit juice...even brushing my teeth. I can't even enjoy a good glass of port.

While palate-ly horrible, it is a most curious experience from an intellectual stand point.

If anyone knows of more recent information, it would be appreciated. There's nothing like a good spoonful of alum, but I've had enough.
Posted by: REC on Feb. 17 2010,18:38

I've never heard of pine nuts as taste disturbing.

The best example I can think of is miraculin, a glycoprotein from "miracle fruit' that binds and alters taste receptors.  Everything tastes sweet for hours after exposure.  You can buy the stuff online, or in Asian groceries for kicks.
Posted by: Tony M Nyphot on Feb. 17 2010,19:03

Quote (REC @ Feb. 17 2010,17:38)
Everything tastes sweet for hours after exposure.
---------------------QUOTE-------------------


Only hours? Apparently, I get to experience bitter for up to 2 weeks.
Posted by: Richardthughes on Feb. 22 2010,10:20

< http://www.cosmosmagazine.com/news/3325/life-evolution-a-test-tube >

"For the first time, scientists have synthesized RNA enzymes – ribonucleic acid enzymes also known as ribozymes - that can replicate themselves without the help of any proteins or other cellular components.

What’s more, these simple nucleic acids can act as catalysts and continue the process indefinitely."
Posted by: Louis on Feb. 22 2010,11:43

Quote (Tony M Nyphot @ Feb. 18 2010,00:03)
Quote (REC @ Feb. 17 2010,17:38)
Everything tastes sweet for hours after exposure.
---------------------QUOTE-------------------


Only hours? Apparently, I get to experience bitter for up to 2 weeks.
---------------------QUOTE-------------------


I've been bitter for years....oh wait...different thing right?

Louis
Posted by: fnxtr on Feb. 22 2010,11:44

Quote (Louis @ Feb. 22 2010,09:43)
Quote (Tony M Nyphot @ Feb. 18 2010,00:03)
Quote (REC @ Feb. 17 2010,17:38)
Everything tastes sweet for hours after exposure.
---------------------QUOTE-------------------


Only hours? Apparently, I get to experience bitter for up to 2 weeks.
---------------------QUOTE-------------------


I've been bitter for years....oh wait...different thing right?

Louis
---------------------QUOTE-------------------


I'm not bitter, I'm just tangy.
Posted by: sledgehammer on Feb. 22 2010,11:52

Quote (Richardthughes @ Feb. 22 2010,08:20)
< http://www.cosmosmagazine.com/news/3325/life-evolution-a-test-tube >
---------------------QUOTE-------------------


Way cool!  Lincoln and Joyce are on a roll.

Predictalbly from the comments :
 

---------------------QUOTE-------------------
And I tend to a agree with you, what have we really achieved here? I'll start believing its actually evolution when it starts to become something more than building blocks.
Submitted by Visitor on 21 February 2010 - 3:30pm.


---------------------QUOTE-------------------


Translation: Yawn.  But it's still a ribosyme.  Wake me up when it turns into a banana.
Posted by: Henry J on Feb. 22 2010,14:14

Quote (sledgehammer @ Feb. 22 2010,10:52)
Wake me up when it turns into a banana.
---------------------QUOTE-------------------


Cause that's when it would have a peel?
Posted by: Tony M Nyphot on Feb. 23 2010,01:06

Quote (fnxtr @ Feb. 22 2010,10:44)
 
Quote (Louis @ Feb. 22 2010,09:43)
 
Quote (Tony M Nyphot @ Feb. 18 2010,00:03)
   
Quote (REC @ Feb. 17 2010,17:38)
Everything tastes sweet for hours after exposure.
---------------------QUOTE-------------------


Only hours? Apparently, I get to experience bitter for up to 2 weeks.
---------------------QUOTE-------------------


I've been bitter for years....oh wait...different thing right?

Louis
---------------------QUOTE-------------------


I'm not bitter, I'm just tangy.
---------------------QUOTE-------------------


HAR, HAR, THIS IS FNXTR


Posted by: Richardthughes on Feb. 23 2010,14:56

Fine tuning - not that fine:


< http://web.mit.edu/newsoffice/2010/multiple-universes.html >

< http://www.scientificamerican.com/article....tiverse >
Posted by: J-Dog on Feb. 23 2010,16:37

Quote (Richardthughes @ Feb. 23 2010,14:56)
Fine tuning - not that fine:


< http://web.mit.edu/newsoffice/2010/multiple-universes.html >

< http://www.scientificamerican.com/article....tiverse >
---------------------QUOTE-------------------


Yeah!  I want to go to the multiverse that does not include Casey Luskin, Dr. Dr. Dembski and IDCists!

Now that would be a real privileged planet...
Posted by: dvunkannon on Feb. 23 2010,17:17

Quote (sledgehammer @ Feb. 22 2010,12:52)
Quote (Richardthughes @ Feb. 22 2010,08:20)
< http://www.cosmosmagazine.com/news/3325/life-evolution-a-test-tube >
---------------------QUOTE-------------------


Way cool!  Lincoln and Joyce are on a roll.

Predictalbly from the comments :
   

---------------------QUOTE-------------------
And I tend to a agree with you, what have we really achieved here? I'll start believing its actually evolution when it starts to become something more than building blocks.
Submitted by Visitor on 21 February 2010 - 3:30pm.


---------------------QUOTE-------------------


Translation: Yawn.  But it's still a ribosyme.  Wake me up when it turns into a banana.
---------------------QUOTE-------------------


Don't tell KF that Tracey Lincoln is one hot Jamaican chica that has avoided being barefoot and pregnant under his protection.
Posted by: fnxtr on Feb. 23 2010,19:59

Quote (Tony M Nyphot @ Feb. 22 2010,23:06)
Quote (fnxtr @ Feb. 22 2010,10:44)
 
Quote (Louis @ Feb. 22 2010,09:43)
   
Quote (Tony M Nyphot @ Feb. 18 2010,00:03)
   
Quote (REC @ Feb. 17 2010,17:38)
Everything tastes sweet for hours after exposure.
---------------------QUOTE-------------------


Only hours? Apparently, I get to experience bitter for up to 2 weeks.
---------------------QUOTE-------------------


I've been bitter for years....oh wait...different thing right?

Louis
---------------------QUOTE-------------------


I'm not bitter, I'm just tangy.
---------------------QUOTE-------------------


HAR, HAR, THIS IS FNXTR


---------------------QUOTE-------------------


Is this from engrish.com?
Posted by: Henry J on Feb. 23 2010,23:15

< abydosaurus >



---------------------QUOTE-------------------
Abydosaurus (meaning "Abydos lizard") is a genus of brachiosaurid sauropod dinosaur known from skull and postcranial material found in upper Lower Cretaceous rocks of northeastern Utah, United States.
---------------------QUOTE-------------------





---------------------QUOTE-------------------
Kingdom: Animalia
Phylum: Chordata
Class: Reptilia
Superorder: Dinosauria
Order: Saurischia
Suborder: Sauropodomorpha
Infraorder: Sauropoda
Family: Brachiosauridae
Genus: Abydosaurus

---------------------QUOTE-------------------


Posted by: OgreMkV on Feb. 25 2010,08:24

5 nucleotide rybozyme.  That's a short ribozyme.

Money quote "To see this, consider that, to pick every possible RNA pentamer sequence from arbitrary pentamers (with probability 0.9975), one needs only accumulate 4.1 × 10?18 gm of RNA. To possess every tetramer (with probability 0.9975) from a pool of arbitrary tetramers, one would need 3.4 × 10?18 gm RNA. In a real polymerization, one would have a distribution of lengths; nonetheless, with only attograms of total RNA of distributed short lengths from some geochemical source, one would have not only our ribozyme, but every activity of comparable size."

< Science Daily Report >

< PNAS Paper >
Posted by: OgreMkV on Feb. 25 2010,08:35

Not an epically cool science like the 5-nt ribozyme, but a "Things that make you go hmmm..." science.

< Liberals and Atheists smarter? >
Posted by: Dr.GH on Feb. 25 2010,09:49

Quote (OgreMkV @ Feb. 25 2010,06:24)
5 nucleotide rybozyme.  That's a short ribozyme.

< Science Daily Report >

< PNAS Paper >
---------------------QUOTE-------------------


Nice. Thanks for the "heads up."
Posted by: Richardthughes on Feb. 25 2010,17:07

Another human vanity squashed:

< http://www.miller-mccune.com/culture....er-8507 >

Gil will no doubt find the performance "mechanical".
Posted by: Richardthughes on Feb. 26 2010,13:10

Coolness:

< http://www.evolutionarymodel.com/ervs.htm >
Posted by: ppb on Feb. 26 2010,13:18

Quote (Richardthughes @ Feb. 25 2010,18:07)
Another human vanity squashed:

< http://www.miller-mccune.com/culture....er-8507 >

Gil will no doubt find the performance "mechanical".
---------------------QUOTE-------------------


But we're still the only species that can write apps for the iPhone, so there!
Posted by: Reciprocating Bill on Feb. 26 2010,17:58

Quote (Richardthughes @ Feb. 25 2010,18:07)
Another human vanity squashed:

< http://www.miller-mccune.com/culture....er-8507 >

Gil will no doubt find the performance "mechanical".
---------------------QUOTE-------------------


There's no programming frilly shirtness.
Posted by: fnxtr on Feb. 26 2010,18:44

Quote (Richardthughes @ Feb. 25 2010,15:07)
Another human vanity squashed:

< http://www.miller-mccune.com/culture....er-8507 >

Gil will no doubt find the performance "mechanical".
---------------------QUOTE-------------------




---------------------QUOTE-------------------
“All the computer is is just an extension of me,” Cope says. “They’re nothing but wonderfully organized shovels. I wouldn’t give credit to the shovel for digging the hole. Would you?”
---------------------QUOTE-------------------



Waters said a similar thing in "Live at Pompeii".
Posted by: bfish on Feb. 26 2010,18:49

Quote (fnxtr @ Feb. 26 2010,16:44)
Quote (Richardthughes @ Feb. 25 2010,15:07)
Another human vanity squashed:

< http://www.miller-mccune.com/culture....er-8507 >

Gil will no doubt find the performance "mechanical".
---------------------QUOTE-------------------




---------------------QUOTE-------------------
“All the computer is is just an extension of me,” Cope says. “They’re nothing but wonderfully organized shovels. I wouldn’t give credit to the shovel for digging the hole. Would you?”
---------------------QUOTE-------------------



Waters said a similar thing in "Live at Pompeii".
---------------------QUOTE-------------------


Is he saying he's smuggling in design?
Posted by: ppb on Mar. 02 2010,10:01

Does it seem to you like the days are just whizzing by?
< Now we know why. >
Posted by: Albatrossity2 on Mar. 02 2010,13:29

< Dinosaur-eating snake described. >

Gotta wonder how they kept those guys apart on the Ark...
Posted by: J-Dog on Mar. 02 2010,13:45

Quote (Albatrossity2 @ Mar. 02 2010,13:29)
< Dinosaur-eating snake described. >

Gotta wonder how they kept those guys apart on the Ark...
---------------------QUOTE-------------------


Alby - I read the link, and those darned scientists don't even mention if it was one of them there talkin' snakes that was a-sellin' apples to Adam & Eve. :(
Posted by: Henry J on Mar. 02 2010,17:00



---------------------QUOTE-------------------
those darned scientists don't even mention if it was one of them there talkin' snakes that was a-sellin' apples to Adam & Eve.
---------------------QUOTE-------------------


Since snakes can't hear, how would a talking snake know if a person answered it?

Henry
Posted by: Occam's Aftershave on Mar. 02 2010,17:12

Quote (Henry J @ Mar. 02 2010,17:00)


---------------------QUOTE-------------------
those darned scientists don't even mention if it was one of them there talkin' snakes that was a-sellin' apples to Adam & Eve.
---------------------QUOTE-------------------


Since snakes can't hear, how would a talking snake know if a person answered it?

Henry
---------------------QUOTE-------------------


Everyone knows talking snakes can read lips, silly.
Posted by: midwifetoad on Mar. 02 2010,17:29

And speak in forked tongues.
Posted by: 1of63 on Mar. 02 2010,19:13

Quote (Albatrossity2 @ Mar. 02 2010,13:29)
< Dinosaur-eating snake described. >

Gotta wonder how they kept those guys apart on the Ark...
---------------------QUOTE-------------------


So THAT'S what happened to the dinosaurs!

A lot of them got ON the ARK but all that got off were a bunch of well-fed snakes.  (Duh, duh DUU-UU-UMMM!!)
Posted by: fnxtr on Mar. 02 2010,19:15

Quote (Richardthughes @ Feb. 25 2010,15:07)
Another human vanity squashed:

< http://www.miller-mccune.com/culture....er-8507 >

Gil will no doubt find the performance "mechanical".
---------------------QUOTE-------------------


Sure it's great for Eno/Glass material, but can it play "Bad to the Bone"? I'm guessing not.
Posted by: ppb on Mar. 10 2010,13:06

Einstein was right...< again >.

New research shows Einstein's General Relativity Theory works even at the scale of galaxy clusters.
Posted by: keiths on Mar. 11 2010,00:11

< An interesting study >:

---------------------QUOTE-------------------
MINNEAPOLIS / ST. PAUL (03/10/2010) —High school and college students who understand the geological age of the Earth (4.5 billion years) are much more likely to understand and accept human evolution, according to a University of Minnesota study published in the March issue of the journal Evolution.

The finding could give educators a new strategy for teaching evolution, since the Earth’s age is typically covered in physical rather than biological science classes.

Researchers Sehoya Cotner and Randy Moore, professors in College of Biological Sciences, and D. Christopher Brooks, of the university’s Office of Information Technology, surveyed 400 students enrolled in several sections of a University of Minnesota introductory biology course for non-majors.

The survey included questions about knowledge of evolution and whether students were taught evolution or creationism in high school as well as questions about religious and political views. Participation was voluntary and had no effect on grades for the course.

The researchers extracted six variables from the survey to explore factors that contributed to students’ views about the age of the Earth and origins of life and the relation of those beliefs to students’ knowledge of evolution and their vote in the 2008 presidential election.

Using that information, they created a model that shows, for example, when a student’s religious and political views are liberal, they are more likely to believe that the Earth is billions, rather than thousands, of years old and to know more about evolution. Conversely, students with conservative religious and political views are more inclined to think the Earth is much younger (20,000 years or less) and to know less about evolution.

“The role of the Earth’s age is a key variable that we can use to improve education about evolution, which is important because it is the unifying principle of biology,” said lead author Sehoya Cotner, associate professor in the Biology Program, which provides general biology classes for University of Minnesota undergraduates.

Through this and previous surveys, Cotner and her colleagues have learned that 2 percent of students are taught creationism only, 22 percent are taught evolution and creationism, 14 are taught neither and 62 percent evolution only.

“In other words, about one in four high school biology teachers in the upper Midwest are giving students the impression that creationism is a viable explanation for the origins of life on Earth,” Cotner says. “That’s just not acceptable. The Constitution prohibits teaching creationism in schools.”

The researchers noted that understanding the Earth’s age is a difficult concept; even Darwin found it challenging. Teaching and understanding creationist views of about the Earth’s age and life’s origins are much easier.

The paper cites a 2009 Gallup poll that coincided with the 200th anniversary of Darwin’s birth reporting that only four out of 10 people in the U.S. believe in evolution. The poll also reported that 16 percent of biology teachers believe God created humans in their present form at some time during the last 10,000 years.

The complete study, "Is the age of the Earth one our 'sorest troubles?' Students' perceptions about deep time affect their acceptance of evolutionary theory," can be accessed < here >.
---------------------QUOTE-------------------


Posted by: midwifetoad on Mar. 11 2010,09:42



---------------------QUOTE-------------------
The finding could give educators a new strategy for teaching evolution, since the Earth’s age is typically covered in physical rather than biological science classes.
---------------------QUOTE-------------------



Well duh. Darwin had more training in geology than biology.
Posted by: Albatrossity2 on Mar. 15 2010,15:28

At least some Canadians can think and do experiments.

< Canadian teenager finds bacteria that degrade plastic bags. >
Posted by: Schroedinger's Dog on Mar. 15 2010,15:51

Quote (Albatrossity2 @ Mar. 15 2010,21:28)
At least some Canadians can think and do experiments.

< Canadian teenager finds bacteria that degrade plastic bags. >
---------------------QUOTE-------------------


I am genuinely impressed! The boy knows his science process all right!

(But the first word of the article was "WATERLOO". I expected something ID-related :))
Posted by: Thought Provoker on Mar. 15 2010,16:00

Hi Albatrossity2,

That is impressive.  Thanks for sharing it.

At the risk of being overly cynical, why wasn't this discovered earlier?

Was it because prevailing thinking assumed there weren't any natural bacteria which would eat plastic?

Is this a case of someone successfully doing something because he didn't know it couldn't be done?
Posted by: Albatrossity2 on Mar. 15 2010,16:30

Quote (Thought Provoker @ Mar. 15 2010,16:00)
Hi Albatrossity2,

That is impressive.  Thanks for sharing it.

At the risk of being overly cynical, why wasn't this discovered earlier?

Was it because prevailing thinking assumed there weren't any natural bacteria which would eat plastic?

Is this a case of someone successfully doing something because he didn't know it couldn't be done?
---------------------QUOTE-------------------


TP

Beats me.

And here's a chance for you to shine as well. DARPA is < soliciting > proposals "in the area of quantum effects in a biological environment. Proposed research should establish beyond any doubt that manifestly quantum effects occur in biology, and demonstrate through simulation proof-of concept experiments that devices that exploit these effects could be developed into biomimetic sensors."

Time for you (or Penrose) to get a grant submitted and get to work!
Posted by: ppb on Mar. 15 2010,16:34

Quote (Albatrossity2 @ Mar. 15 2010,16:28)
At least some Canadians can think and do experiments.

< Canadian teenager finds bacteria that degrade plastic bags. >
---------------------QUOTE-------------------


Way to go Canada!

You'd think if a Canadian high-school student can do good quality science, some of those ID elites could figure it out too, if they wanted to.
Posted by: Thought Provoker on Mar. 15 2010,16:56

OH MY GOD!!!!!

(I ask forgiveness from the atheists in the room)

From the DARPA solicitation Albatrossity2 mentioned...



---------------------QUOTE-------------------
Recent research on biological sensor systems such as photosynthesis, magnetoreception, and olfaction, has uncovered tantalizing evidence that they operate using “manifestly” quantum effects.  The Fenna-Matthews-Olson (FMO) complex forms a portion of the photosynthetic apparatus of purple bacteria.  It was shown that at low temperatures and upon photon absorption, the excitons in the FMO complex migrate via quantum coherence.  Recent evidence indicates that this coherence still exists at physiological temperatures.  Whether it is of biological relevance is still an unanswered question.  One of the prevailing theories for magnetoreception in birds invokes long-lived interconverting singlet/triplet excited states of the cryptochrome protein.  There is strong evidence that the cryptochrome is involved in the magnetoreception in insects but the nature and mechanism of that involvement has not been fully established.  Finally, it has been speculated that odor receptors use phonon-assisted tunneling to sense the vibrational spectra of odorants.

For the purposes of this BAA, “manifestly” quantum effects are defined as those that are intrinsically quantum mechanical in nature, and novel and surprising for a biological system to exhibit.  Examples include quantum coherence, superposition, the quantum Zeno effect, and entanglement.  Excluded are expected effects such as chemical bonding involving orbitals or van der Waals forces.
---------------------QUOTE-------------------



The funny thing is that I'm a part owner of a small engineering company that has been subcontracted on a successful DARPA project in the past.

Except for the fact we have no relevant experience in Quantum Mechanics or Biological Engineering it is right up our ally </sarcasm>

I guess I could see if a team could use some data acquisition and computer modeling experts.

I will have to look into this.

Albatrossity2, I don't know whether to thank you or curse you.

I guess I can do both.

Thank you  (I reserve the right to curse you later).
Posted by: midwifetoad on Mar. 15 2010,17:05

Solid state electronics would be impossible without quantum theory.
Posted by: Albatrossity2 on Mar. 15 2010,17:20

Quote (Thought Provoker @ Mar. 15 2010,16:56)
OH MY GOD!!!!!

(I ask forgiveness from the atheists in the room)

From the DARPA solicitation Albatrossity2 mentioned...

 

---------------------QUOTE-------------------
Recent research on biological sensor systems such as photosynthesis, magnetoreception, and olfaction, has uncovered tantalizing evidence that they operate using “manifestly” quantum effects.  The Fenna-Matthews-Olson (FMO) complex forms a portion of the photosynthetic apparatus of purple bacteria.  It was shown that at low temperatures and upon photon absorption, the excitons in the FMO complex migrate via quantum coherence.  Recent evidence indicates that this coherence still exists at physiological temperatures.  Whether it is of biological relevance is still an unanswered question.  One of the prevailing theories for magnetoreception in birds invokes long-lived interconverting singlet/triplet excited states of the cryptochrome protein.  There is strong evidence that the cryptochrome is involved in the magnetoreception in insects but the nature and mechanism of that involvement has not been fully established.  Finally, it has been speculated that odor receptors use phonon-assisted tunneling to sense the vibrational spectra of odorants.

For the purposes of this BAA, “manifestly” quantum effects are defined as those that are intrinsically quantum mechanical in nature, and novel and surprising for a biological system to exhibit.  Examples include quantum coherence, superposition, the quantum Zeno effect, and entanglement.  Excluded are expected effects such as chemical bonding involving orbitals or van der Waals forces.
---------------------QUOTE-------------------



The funny thing is that I'm a part owner of a small engineering company that has been subcontracted on a successful DARPA project in the past.

Except for the fact we have no relevant experience in Quantum Mechanics or Biological Engineering it is right up our ally </sarcasm>

I guess I could see if a team could use some data acquisition and computer modeling experts.

I will have to look into this.

Albatrossity2, I don't know whether to thank you or curse you.

I guess I can do both.

Thank you  (I reserve the right to curse you later).
---------------------QUOTE-------------------


You're welcome, for now.

I reserve the right to recurse you  :p
Posted by: fnxtr on Mar. 15 2010,21:36

Quote (Schroedinger's Dog @ Mar. 15 2010,13:51)
Quote (Albatrossity2 @ Mar. 15 2010,21:28)
At least some Canadians can think and do experiments.

< Canadian teenager finds bacteria that degrade plastic bags. >
---------------------QUOTE-------------------


I am genuinely impressed! The boy knows his science process all right!

(But the first word of the article was "WATERLOO". I expected something ID-related :))
---------------------QUOTE-------------------


Sure, praise him now, but when these things get loose and become the plastic-eating equivalent of the Ringworld silicon bug, you'll....

< blame Canada! >
Posted by: Richardthughes on Mar. 19 2010,10:19

Fuck off Guinnea Worm

< http://www.telegraph.co.uk/health....xt.html >


Fuck off for ever.
Posted by: FrankH on Mar. 19 2010,10:32

Quote (Richardthughes @ Mar. 19 2010,10:19)
Fuck off Guinnea Worm

< http://www.telegraph.co.uk/health....xt.html >


Fuck off for ever.
---------------------QUOTE-------------------


You rat bastard.

All of god's creatures are special.  He designed all of them in his own image.  How dare you want to destroy what he has created!

I thought all you tree huggers (or buggers) want to promote diversity!  What happens to diversity when one of god's special creatures goes extinct?

Hell, if we can't build a golf course because of some damn lizard, why is this worm's fate any less deserving?
Posted by: Doc Bill on Mar. 19 2010,10:45

The price of Guinnea Worm soup is going to skyrocket!  Better stock up now.
Posted by: rhmc on Mar. 20 2010,10:31

Japanese researchers have managed to engineer mosquitoes into “flying vaccinators” that could theoretically be used to deliver protein-based vaccines against diseases such as leishmaniasis and malaria through their bite. The team, from the Jichi Medical University in Japan, report on the development of a transgenic mosquito that can express foreign proteins in its saliva...

more here:  http://www.genengnews.com/news/bnitem.aspx?name=78153298

around here, it's not a matter of if i'll get skeeter bit when i go out, it's a matter of how many times.

no malaria here anymore but equine encephalitis and west nile virus show up every year...
Posted by: FrankH on Mar. 20 2010,10:53

Quote (rhmc @ Mar. 20 2010,10:31)
Japanese researchers have managed to engineer mosquitoes into “flying vaccinators” that could theoretically be used to deliver protein-based vaccines against diseases such as leishmaniasis and malaria through their bite. The team, from the Jichi Medical University in Japan, report on the development of a transgenic mosquito that can express foreign proteins in its saliva...

more here:  http://www.genengnews.com/news/bnitem.aspx?name=78153298

around here, it's not a matter of if i'll get skeeter bit when i go out, it's a matter of how many times.

no malaria here anymore but equine encephalitis and west nile virus show up every year...
---------------------QUOTE-------------------


Watch out, Jenny McCarthy and her boyfriend will demand that those mosquitoes be destroyed or there will be more cases of autism.
Posted by: Henry J on Mar. 20 2010,11:26

About the engineered mosquitoes:

But that tactic would leave them with no control over the dosage. They'd have to design the vaccine so that overdosing wouldn't cause problems.
Posted by: Dr.GH on Mar. 20 2010,15:33

I have not noticed this mentioned here as yet:

Meredith RW, Gatesy J, Murphy WJ, Ryder OA, Springer MS 2009 "Molecular Decay of the Tooth Gene Enamelin (ENAM) Mirrors the Loss of Enamel in the Fossil Record of Placental Mammals."  PLoS Genet 5(9): e1000634. doi:10.1371/journal.pgen.1000634

Summary: Enamel is the hardest substance in the vertebrate body. One of the key proteins involved in enamel formation is enamelin. Most placental mammals have teeth that are capped with enamel, but there are also lineages without teeth (anteaters, pangolins, baleen whales) or with enamelless teeth (armadillos, sloths, aardvarks, pygmy and dwarf sperm whales). All toothless and enamelless mammals are descended from ancestral forms that possessed teeth with enamel. Given this ancestry, we predicted that mammalian species without teeth or with teeth that lack enamel would have copies of the gene that codes for the enamelin protein, but that the enamelin gene in these species would contain mutations that render it a nonfunctional pseudogene. To test this hypothesis, we sequenced most of the protein-coding region of the enamelin gene in all groups of placental mammals that lack teeth or have enamelless teeth. In every case, we discovered mutations in the enamelin gene that disrupt the proper reading frame that codes for the enamelin protein. Our results link evolutionary change at the molecular level to morphological change in the fossil record and also provide evidence for the enormous predictive power of Charles Darwin's theory of descent with modification.
Posted by: midwifetoad on Mar. 26 2010,07:41

< http://www.causeweb.org/wiki/chance/index.php/Chance_News_61 >
Posted by: Albatrossity2 on Mar. 27 2010,14:46

< Gravity is an emergent phenomenon. >

And I just can't wait for the self-proclaimed "Isaac Newton of Information" to comment on this bit:



---------------------QUOTE-------------------
Some physicists are convinced that the properties of information do not come from the behaviour of information carriers such as photons and electrons but the other way round. They think that information itself is the ghostly bedrock on which our universe is built.
---------------------QUOTE-------------------



No details on whether or not the information is CSI...
Posted by: Thought Provoker on Mar. 27 2010,15:05

oooh neat.

Thanks for the information.

It is more like a confirmation of what I have been understanding from reading Penrose's stuff.
Posted by: Henry J on Mar. 27 2010,16:09



---------------------QUOTE-------------------
No details on whether or not the information is CSI...
---------------------QUOTE-------------------


Insufficient data for conclusion about information? :)
Posted by: midwifetoad on Mar. 30 2010,12:33

< Judge Invalidates Human Gene Patent >
Posted by: Albatrossity2 on April 01 2010,12:05

From < here >, scientists discover gene (WTF1) and brain region (inferior supra-credulus) involved in gullibility!
Posted by: Schroedinger's Dog on April 01 2010,14:44

Quote (Albatrossity2 @ April 01 2010,18:05)
From < here >, scientists discover gene (WTF1) and brain region (inferior supra-credulus) involved in gullibility!
---------------------QUOTE-------------------




---------------------QUOTE-------------------
When Morris studied individual neurons within the supra-credulus, he found that gullibility was associated with the activity of a single gene called WTF1. The less active it was, the more feckless people were.
---------------------QUOTE-------------------



Ok, if this is not a April's Fool, I don't know what it is.

WTF1 gene?

:D   :D   :D





ps: Dave, did I just kill your joke? if so, please accept apologies and virtual beers!
Posted by: Thought Provoker on April 01 2010,15:15

Oh I am sure...

"The findings could have massive implications for treating the growing number of people who fall wide-eyed for sensationalist media reports."

"Honest"
Posted by: midwifetoad on April 02 2010,07:36

< Emergence from Symmetry: A New Type of Cellular Automata >
Posted by: Richardthughes on April 02 2010,10:38

Coolness:

< http://www.nytimes.com/2009/09/29/science/29grid.html?_r=1 >
Posted by: Richardthughes on April 05 2010,09:46

< http://www.kongregate.com/games/BryceSummer/walkinator >

Evo game. Quite good!
Posted by: qetzal on April 07 2010,09:14

Anaerobic multicellular animals!

Here's the abstract:

 

---------------------QUOTE-------------------
Background
Several unicellular organisms (prokaryotes and protozoa) can live under permanently anoxic conditions. Although a few metazoans can survive temporarily in the absence of oxygen, it is believed that multi-cellular organisms cannot spend their entire life cycle without free oxygen. Deep seas include some of the most extreme ecosystems on Earth, such as the deep hypersaline anoxic basins of the Mediterranean Sea. These are permanently anoxic systems inhabited by a huge and partly unexplored microbial biodiversity.

Results
During the last ten years three oceanographic expeditions were conducted to search for the presence of living fauna in the sediments of the deep anoxic hypersaline L'Atalante basin (Mediterranean Sea). We report here that the sediments of the L'Atalante basin are inhabited by three species of the animal phylum Loricifera (Spinoloricus nov. sp., Rugiloricus nov. sp. and Pliciloricus nov. sp.) new to science. Using radioactive tracers, biochemical analyses, quantitative X-ray microanalysis and infrared spectroscopy, scanning and transmission electron microscopy observations on ultra-sections, we provide evidence that these organisms are metabolically active and show specific adaptations to the extreme conditions of the deep basin, such as the lack of mitochondria, and a large number of hydrogenosome-like organelles, associated with endosymbiotic prokaryotes.

Conclusions
This is the first evidence of a metazoan life cycle that is spent entirely in permanently anoxic sediments. Our findings allow us also to conclude that these metazoans live under anoxic conditions through an obligate anaerobic metabolism that is similar to that demonstrated so far only for unicellular eukaryotes. The discovery of these life forms opens new perspectives for the study of metazoan life in habitats lacking molecular oxygen.
---------------------QUOTE-------------------



< Link to full text >

ETA:
< Link to some commentary >

< Link to more commentary >

HT: < The Scientific Activist >
Posted by: FrankH on April 07 2010,09:52

Quote (qetzal @ April 07 2010,09:14)
Anaerobic multicellular animals!

Here's the abstract:

---------------------QUOTE-------------------
Background
Several unicellular organisms (prokaryotes and protozoa) can live under permanently anoxic conditions. Although a few metazoans can survive temporarily in the absence of oxygen, it is believed that multi-cellular organisms cannot spend their entire life cycle without free oxygen. Deep seas include some of the most extreme ecosystems on Earth, such as the deep hypersaline anoxic basins of the Mediterranean Sea. These are permanently anoxic systems inhabited by a huge and partly unexplored microbial biodiversity.

Results
During the last ten years three oceanographic expeditions were conducted to search for the presence of living fauna in the sediments of the deep anoxic hypersaline L'Atalante basin (Mediterranean Sea). We report here that the sediments of the L'Atalante basin are inhabited by three species of the animal phylum Loricifera (Spinoloricus nov. sp., Rugiloricus nov. sp. and Pliciloricus nov. sp.) new to science. Using radioactive tracers, biochemical analyses, quantitative X-ray microanalysis and infrared spectroscopy, scanning and transmission electron microscopy observations on ultra-sections, we provide evidence that these organisms are metabolically active and show specific adaptations to the extreme conditions of the deep basin, such as the lack of mitochondria, and a large number of hydrogenosome-like organelles, associated with endosymbiotic prokaryotes.

Conclusions
This is the first evidence of a metazoan life cycle that is spent entirely in permanently anoxic sediments. Our findings allow us also to conclude that these metazoans live under anoxic conditions through an obligate anaerobic metabolism that is similar to that demonstrated so far only for unicellular eukaryotes. The discovery of these life forms opens new perspectives for the study of metazoan life in habitats lacking molecular oxygen.
---------------------QUOTE-------------------

< Link to full text >

ETA:
< Link to some commentary >

< Link to more commentary >

HT: < The Scientific Activist >
---------------------QUOTE-------------------


Excellent!  Yet more proof (I'd say at least 151) that those anaerobic animals were specifically designed, by some intelligence of course, to live "just so" in their environment.

Another case (of Bud) for ID!
Posted by: Timothy McDougald on April 07 2010,18:52

< How to challenge the consensus view and not be thought a quack >


---------------------QUOTE-------------------
In the study, U-M evolutionary biologist Jianzhi "George" Zhang and colleagues Ben-Yang Liao and Meng-Pin Weng set out to systematically test a hypothesis proposed by molecular biologist Sean Carroll in 2005. Carroll posited that changes in morphology (such things as shape, color and structure of external and internal parts) occur through different genetic mechanisms than changes in physiology (inner workings). Carroll backed up his assertion with examples, but the idea, which challenged previous dogma, was controversial, Zhang said.
---------------------QUOTE-------------------


Posted by: FrankH on April 08 2010,07:04

Quote (afarensis @ April 07 2010,18:52)
< How to challenge the consensus view and not be thought a quack >

---------------------QUOTE-------------------
In the study, U-M evolutionary biologist Jianzhi "George" Zhang and colleagues Ben-Yang Liao and Meng-Pin Weng set out to systematically test a hypothesis proposed by molecular biologist Sean Carroll in 2005. Carroll posited that changes in morphology (such things as shape, color and structure of external and internal parts) occur through different genetic mechanisms than changes in physiology (inner workings). Carroll backed up his assertion with examples, but the idea, which challenged previous dogma, was controversial, Zhang said.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


Wow, in other words produce the work and show the evidence that backs up you claim instead of claiming something and expecting others to:

A:  Fall in line

or

B:  PROVE you're wrong (but of course you're right until they prove it)
Posted by: Henry J on April 12 2010,13:29

< http://www.webelements.com/ >



---------------------QUOTE-------------------
Element 117 discovered?

A paper just accepted for publication (5 April 2010) in Physical Review Letters by Yu. Ts. Oganessian and others claims the synthesis of a new element with atomic number 117. The abstract states "The discovery of a new chemical element with atomic

number Z=117 is reported. The isotopes 293 117 and 294 117 were produced in fusion reactions between 48 Ca and 249 Bk.

[...]
---------------------QUOTE-------------------


Posted by: Richardthughes on April 20 2010,23:03

SETI / Evolution:

< http://www.cnn.com/2010....?hpt=C1 >
Posted by: Albatrossity2 on April 21 2010,06:26

Neanderthal genes may still be < found in modern humans. >
Posted by: Dr.GH on April 21 2010,07:34

Quote (Albatrossity2 @ April 21 2010,04:26)
Neanderthal genes may still be < found in modern humans. >
---------------------QUOTE-------------------


Wow.
Posted by: dvunkannon on April 21 2010,12:05

< Evolved Self Replication >


---------------------QUOTE-------------------
Abstract

Cellular automata models have historically been a major approach to studying the information-processing properties of self-replication. Here we explore the feasibility of adopting genetic programming so that, when it is given a fairly arbitrary initial cellular automata configuration, it will automatically generate a set of rules that make the given configuration replicate. We found that this approach works surprisingly effectively for structures as large as 50 components or more. The replication mechanisms discovered by genetic programming work quite differently than those of many past manually designed replicators: There is no identifiable instruction sequence or construction arm, the replicating structures generally translate and rotate as they reproduce, and they divide via a fissionlike process that involves highly parallel operations. This makes replication very fast, and one cannot identify which descendant is the parent and which is the child. The ability to automatically generate self-replicating structures in this fashion allowed us to examine the resulting replicators as their properties were systematically varied. Further, it proved possible to produce replicators that simultaneously deposited secondary structures while replicating, as in some past manually designed models. We conclude that genetic programming is a powerful tool for studying self-replication that might also be profitably used in contexts other than cellular spaces.

---------------------QUOTE-------------------



Self replication in a way that even genius humans never thought of.
Posted by: Albatrossity2 on April 22 2010,17:04

The latest issue of Science has a < nice paper > that demonstrates the principle, unknown to IDiots, that a new functionality can be generated by a loss of "information". Nakagawa et al. demonstrate that the enzyme known as "dicer", which is normally a ribonuclease, is converted by proteolysis to become a DNA-degrading enzyme during apoptosis. Mammalian cells have a DNAase that is used during apoptosis; this study was done in the nematode Caenorhabditis elegans, which does not have a homologous DNAase.

New functions generated by loss of protein "information"!

I'm sure that Casey will be covering this on EN&V quite soon.
Posted by: keiths on April 22 2010,18:25

< New Caledonian crow uses three different tools in succession to retrieve food. >
Posted by: REC on April 27 2010,17:11

Carl Zimmer writes on deep homology and medicine:

"The scientists took advantage of a peculiar feature of our evolutionary history. In our distant, amoeba-like ancestors, clusters of genes were already forming to work together on building cell walls and on other very basic tasks essential to life. Many of those genes still work together in those same clusters, over a billion years later, but on different tasks in different organisms. "

< http://www.nytimes.com/2010....ted=all >

Original Report here:

< http://www.pnas.org/content/107/14/6544.long >

"Biologists have long used model organisms to study human diseases, particularly when the model bears a close resemblance to the disease. We present a method that quantitatively and systematically identifies nonobvious equivalences between mutant phenotypes in different species, based on overlapping sets of orthologous genes from human, mouse, yeast, worm, and plant (212,542 gene-phenotype associations). These orthologous phenotypes, or phenologs, predict unique genes associated with diseases. Our method suggests a yeast model for angiogenesis defects, a worm model for breast cancer, mouse models of autism, and a plant model for the neural crest defects associated with Waardenburg syndrome, among others."
Posted by: OgreMkV on April 29 2010,08:25

Two good ones ripe to beat IDistsists over the head with:

< Alaskan Megaflood > - unfortunately for YECs it was 17,000 years ago and caused by a lake breaking through an ice dam.  But still, 1400 cubic km of water is a lot... even if it didn't rain.

< How mathematics and evolution should work together > - "Building on classical competition models for single traits, they designed their mathematical theory to gauge the evolutionary impact of multiple traits in concert, and found that adding this layer of complexity significantly lowered the threshold for the maintenance of diversity and the evolution of new species."


Both are layman articles with links to the original research papers.
Posted by: ppb on April 29 2010,08:48

Quote (OgreMkV @ April 29 2010,09:25)
< Alaskan Megaflood > - unfortunately for YECs it was 17,000 years ago and caused by a lake breaking through an ice dam.  But still, 1400 cubic km of water is a lot... even if it didn't rain.
---------------------QUOTE-------------------


Hey, the picture in the article is of Wasilla, Alaska.  
Sarah Palin could see The Flood from her house.
Posted by: Paul Flocken on April 30 2010,08:21

I have to get my science from the popular media, so this may be old hat to all of you, but it is really cool to me.
< Horizontal Gene Transfer in Pea Aphids >
Posted by: Albatrossity2 on April 30 2010,15:20

One of the unanticipated joys of being a department head is the sporadic arrival of screamingly hilarious scientific "papers" that arrive in the mailbox. Papers announcing cures for cancer, theories of everything, and other non-peer-reviewed manuscripts are a regular occurrence for me these days.

Today's mail brought something that could have been written by the love child of AFDave and Denyse O'Leary, if that love child had been raised on another planet and with some horizontal gene transfer from Bobby Byers and FL. I've put a PDF version of it < here >; enjoy it in lieu of the regular Friday meltdown. I particularly love the fact that the writer claims to have a BA in Biology from Brown University. Maybe Ken Miller knows him!
Posted by: Richardthughes on April 30 2010,15:45

Quote (Albatrossity2 @ April 30 2010,15:20)
One of the unanticipated joys of being a department head is the sporadic arrival of screamingly hilarious scientific "papers" that arrive in the mailbox. Papers announcing cures for cancer, theories of everything, and other non-peer-reviewed manuscripts are a regular occurrence for me these days.

Today's mail brought something that could have been written by the love child of AFDave and Denyse O'Leary, if that love child had been raised on another planet and with some horizontal gene transfer from Bobby Byers and FL. I've put a PDF version of it < here >; enjoy it in lieu of the regular Friday meltdown. I particularly love the fact that the writer claims to have a BA in Biology from Brown University. Maybe Ken Miller knows him!
---------------------QUOTE-------------------


Could be the best paper ever. Up there with "Time Cube".
Posted by: Tracy P. Hamilton on April 30 2010,15:53

Quote (Henry J @ April 12 2010,13:29)
< http://www.webelements.com/ >



---------------------QUOTE-------------------
Element 117 discovered?

A paper just accepted for publication (5 April 2010) in Physical Review Letters by Yu. Ts. Oganessian and others claims the synthesis of a new element with atomic number 117. The abstract states "The discovery of a new chemical element with atomic

number Z=117 is reported. The isotopes 293 117 and 294 117 were produced in fusion reactions between 48 Ca and 249 Bk.

[...]
---------------------QUOTE-------------------


---------------------QUOTE-------------------


Used that in my general chemistry exam - how many neutrons were produced?

I wonder if any of CSI whizzes can calculate even that.
Posted by: Tracy P. Hamilton on April 30 2010,15:54

Quote (Albatrossity2 @ April 22 2010,17:04)
The latest issue of Science has a < nice paper > that demonstrates the principle, unknown to IDiots, that a new functionality can be generated by a loss of "information". Nakagawa et al. demonstrate that the enzyme known as "dicer", which is normally a ribonuclease, is converted by proteolysis to become a DNA-degrading enzyme during apoptosis. Mammalian cells have a DNAase that is used during apoptosis; this study was done in the nematode Caenorhabditis elegans, which does not have a homologous DNAase.

New functions generated by loss of protein "information"!

I'm sure that Casey will be covering this on EN&V quite soon.
---------------------QUOTE-------------------


It is just microdicing.
Posted by: Badger3k on April 30 2010,19:16

Quote (Albatrossity2 @ April 30 2010,15:20)
One of the unanticipated joys of being a department head is the sporadic arrival of screamingly hilarious scientific "papers" that arrive in the mailbox. Papers announcing cures for cancer, theories of everything, and other non-peer-reviewed manuscripts are a regular occurrence for me these days.

Today's mail brought something that could have been written by the love child of AFDave and Denyse O'Leary, if that love child had been raised on another planet and with some horizontal gene transfer from Bobby Byers and FL. I've put a PDF version of it < here >; enjoy it in lieu of the regular Friday meltdown. I particularly love the fact that the writer claims to have a BA in Biology from Brown University. Maybe Ken Miller knows him!
---------------------QUOTE-------------------


Holy crap, warn a guy first!  My roommate nearly died of shock, and if I hadn't started to read with my eyelashes, I'd be dead, or believe in ID.   Or think that O'Leary makes sense.

Anyway, you owe me a new camera.  Send it through the intertubes.  I'll have my ear to the wire until I hear it.  Unless....do sin proteins wait in the ear as well?  I didn't get that far!
Posted by: fnxtr on April 30 2010,19:41

Quote (Albatrossity2 @ April 30 2010,13:20)
One of the unanticipated joys of being a department head is the sporadic arrival of screamingly hilarious scientific "papers" that arrive in the mailbox. Papers announcing cures for cancer, theories of everything, and other non-peer-reviewed manuscripts are a regular occurrence for me these days.

Today's mail brought something that could have been written by the love child of AFDave and Denyse O'Leary, if that love child had been raised on another planet and with some horizontal gene transfer from Bobby Byers and FL. I've put a PDF version of it < here >; enjoy it in lieu of the regular Friday meltdown. I particularly love the fact that the writer claims to have a BA in Biology from Brown University. Maybe Ken Miller knows him!
---------------------QUOTE-------------------


That's what Mary Baker Eddy's "Science and Health with Key to the Scriptures" always looked like to me.
Posted by: Albatrossity2 on April 30 2010,20:48

Quote (Badger3k @ April 30 2010,19:16)
Holy crap, warn a guy first!  My roommate nearly died of shock, and if I hadn't started to read with my eyelashes, I'd be dead, or believe in ID.   Or think that O'Leary makes sense.

Anyway, you owe me a new camera.  Send it through the intertubes.  I'll have my ear to the wire until I hear it.  Unless....do sin proteins wait in the ear as well?  I didn't get that far!
---------------------QUOTE-------------------


Sorry about your roommate. I was reading it out loud to one of the folks in my office and she was laughing so hard I thought she might pee. I think it was the part about the observation that "people that form melanin need to take a chewable flintstone vitamin" to "elevate the cyclic ring in the brain". I was gonna ask Louis about that, but I think he's asleep over there in Albion...
Posted by: Henry J on April 30 2010,22:14



---------------------QUOTE-------------------
Used that in my general chemistry exam - how many neutrons were produced?

I wonder if any of CSI whizzes can calculate even that.
---------------------QUOTE-------------------


I've no idea what a CSI whiz might do, but I figure that the 294 isotope left 3 neutrons unclaimed, and the 293 left 4.

But in a general chemistry test? I wouldn't have expected chemistry class to bother with elements of which only a few atoms have momentarily existed, during physics experiments.

Henry
Posted by: Reed on May 03 2010,02:43

Another < mammoth challenge > to the Darwinist paradigm.
Posted by: fnxtr on May 03 2010,09:37

Quote (Reed @ May 03 2010,00:43)
Another < mammoth challenge > to the Darwinist paradigm.
---------------------QUOTE-------------------


So i wonder if the genetic deterioration that led to the loss of this low-temperature haemoglobin happened after Teh Fall, or just after Teh Flood?
Posted by: Quack on May 04 2010,16:22

Quote (afarensis @ April 07 2010,18:52)
< How to challenge the consensus view and not be thought a quack >
   

---------------------QUOTE-------------------
In the study, U-M evolutionary biologist Jianzhi "George" Zhang and colleagues Ben-Yang Liao and Meng-Pin Weng set out to systematically test a hypothesis proposed by molecular biologist Sean Carroll in 2005. Carroll posited that changes in morphology (such things as shape, color and structure of external and internal parts) occur through different genetic mechanisms than changes in physiology (inner workings). Carroll backed up his assertion with examples, but the idea, which challenged previous dogma, was controversial, Zhang said.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


Lovely, and to think that this was not predicted by ID?

I've got to say this, ToE still continues to surprise and amaze me every day. After pondering for years about a pathway for the evolution of the human larynx - and speech, I realized on rereading Jeffrey K. McKee's "The Riddled Chain" that bipedalism/upright stance must have been the trigger.

Fascinating work on computer simulations too.

Isn't science wonderful?
Posted by: midwifetoad on May 06 2010,15:24

< http://www.sciencemag.org/cgi....1188021 >

A Draft Sequence of the Neandertal Genome
Posted by: J-Dog on May 06 2010,17:06

Quote (midwifetoad @ May 06 2010,15:24)
< http://www.sciencemag.org/cgi....1188021 >

A Draft Sequence of the Neandertal Genome
---------------------QUOTE-------------------


I looked, and I looked, but no Dembski, Behe, Wells or  other IDer could I find.  No doubt, the Evil Darwinist Truth, Not Fantasy Cabal is still in action.

However, I did find this link too, and I see that some of your ancestors got lucky...

< Some Homos Got Lucky >
Posted by: Timothy McDougald on May 06 2010,19:08

Quote (J-Dog @ May 06 2010,17:06)
Quote (midwifetoad @ May 06 2010,15:24)
< http://www.sciencemag.org/cgi....1188021 >

A Draft Sequence of the Neandertal Genome
---------------------QUOTE-------------------


I looked, and I looked, but no Dembski, Behe, Wells or  other IDer could I find.  No doubt, the Evil Darwinist Truth, Not Fantasy Cabal is still in action.

However, I did find this link too, and I see that some of your ancestors got lucky...

< Some Homos Got Lucky >
---------------------QUOTE-------------------


ALL RIGHT, LISTEN UP 'CAUSE I'M TALKING! ALTHOUGH ALL THE NEANDERBABES BEGGED TO HAVE MY CHILDREN i REFUSED BECAUSE ACCORDING TO THE GEICO COMMERCIALS NEANDERBABES IS UGLIER THAN INUIT WOMEN SO i SAVED MY HAPLOID DIPLOID HOUSEBOAT COMMANDOS FOR BILL!!!111!1! SO IT WASN'T ME, HOMOS dt
Posted by: Reed on May 06 2010,19:13

Quote (midwifetoad @ May 06 2010,13:24)
< http://www.sciencemag.org/cgi....1188021 >

A Draft Sequence of the Neandertal Genome
---------------------QUOTE-------------------


As usual, John Hawks has some < interesting commentary >.
Posted by: midwifetoad on May 06 2010,20:13



---------------------QUOTE-------------------
I looked, and I looked, but no Dembski, Behe, Wells or  other IDer could I find.
---------------------QUOTE-------------------



ID performance is measured in zettaflops.
Posted by: J-Dog on May 06 2010,21:10

Quote (afarensis @ May 06 2010,19:08)
ALL RIGHT, LISTEN UP 'CAUSE I'M TALKING! ALTHOUGH ALL THE NEANDERBABES BEGGED TO HAVE MY CHILDREN i REFUSED BECAUSE ACCORDING TO THE GEICO COMMERCIALS NEANDERBABES IS UGLIER THAN INUIT WOMEN SO i SAVED MY HAPLOID DIPLOID HOUSEBOAT COMMANDOS FOR BILL!!!111!1! SO IT WASN'T ME, HOMOS dt
---------------------QUOTE-------------------



Beautiful sentiments, artfully expressed!  I can almost hear the Cheesy Poofs crunching in the background. (Snif & sob for The Old Days)...

Do you want your Post Of Teh Week Award sent to your houseboat in TX, or your Rift Valley Ranch?
Posted by: ppb on May 07 2010,14:54

Quote (J-Dog @ May 06 2010,18:06)
 
Quote (midwifetoad @ May 06 2010,15:24)
< http://www.sciencemag.org/cgi....1188021 >

A Draft Sequence of the Neandertal Genome
---------------------QUOTE-------------------


I looked, and I looked, but no Dembski, Behe, Wells or  other IDer could I find.  No doubt, the Evil Darwinist Truth, Not Fantasy Cabal is still in action.

However, I did find this link too, and I see that some of your ancestors got lucky...

< Some Homos Got Lucky >
---------------------QUOTE-------------------


No offense J-Dog, but I don't understand the attraction to Neandertal chicks.
To me they are loud and obnoxious, they smell bad.  Not a brain in their head.

Take < this one > for instance... Please!
Posted by: Timothy McDougald on May 07 2010,19:05

< How to challenge scientific findings and not be thought a quack >.

The important part:





---------------------QUOTE-------------------
The research, which was supported by NASA, the National Science Foundation and the Agouron Institute, counters previous work of co-author Roger Summons, an EAPS professor of geobiology, who first proposed in 1999 that 2-methylhopanoids could be a biomarker for cyanobacteria. That work was called into question in 2007 when researchers in the lab of co-author Dianne K. Newman, the John and Dorothy Wilson Professor of Biology and Geobiology, in collaboration with Alex Sessions at the California Institute of Technology, discovered a type of bacterium that doesn’t produce oxygen but does produce 2-methylhopanoids.

To determine whether this was a chance finding or whether different kinds of bacteria produce 2-methylhopanoids, Summons, Newman, Sessions and several postdoctoral researchers joined forces to figure out which genes and proteins are involved in making the lipids. Knowing this gene, the researchers could then search the genome databases for other bacteria that also produce these molecules. They could also learn more about the purpose of the molecules, such as whether they emerged in response to some sort of environmental stress billions of years ago.
---------------------QUOTE-------------------



The research is published in < PNAS > and sounds like an excellent example of how to test a hypothesis. Unfortunately, I don't have access ???
Posted by: Kristine on May 12 2010,10:51

Well, guys, I'm going to plug myself here. For my Reference Sources in the Sciences class I had to create a page of online resources. Unlike everyone else, who chose a specialty, I wanted to implement science communication techniques and so I created a transdiciplinary introductory science page.

I chose online tutorials that were interactive, attractive, and had clear language. Actually, for the assignment I eliminated some vetted links that I would like to incorporate later, or in another guide. It's amazing to see what scientists, educators, and designers are doing to bring science to the public.

Here it is, my pride and joy: < Concepts, Scales, and Measures in Science >

I am finished with classes, have earned my Master's (just need to get the grades), and just submitted my first paper for peer review. :)
Posted by: JohnW on May 12 2010,12:24

Quote (Kristine @ May 12 2010,08:51)
Well, guys, I'm going to plug myself here. For my Reference Sources in the Sciences class I had to create a page of online resources. Unlike everyone else, who chose a specialty, I wanted to implement science communication techniques and so I created a transdiciplinary introductory science page.

I chose online tutorials that were interactive, attractive, and had clear language. Actually, for the assignment I eliminated some vetted links that I would like to incorporate later, or in another guide. It's amazing to see what scientists, educators, and designers are doing to bring science to the public.

Here it is, my pride and joy: < Concepts, Scales, and Measures in Science >

I am finished with classes, have earned my Master's (just need to get the grades), and just submitted my first paper for peer review. :)
---------------------QUOTE-------------------


That's terrific, Kristine.  Extra points for including "Powers Of Ten".

I think the section on "Ask Me Services" is incomplete without "Ask A Bitter, Frustrated Creationist With Two Doctorates Who Can't Get a Real Position And Is Stuck In A Backwoods Bible School".
Posted by: Robin on May 12 2010,12:37

Quote (Kristine @ May 12 2010,10:51)

---------------------QUOTE-------------------




---------------------QUOTE-------------------
Well, guys, I'm going to plug myself here. For my Reference Sources in the Sciences class I had to create a page of online resources. Unlike everyone else, who chose a specialty, I wanted to implement science communication techniques and so I created a transdiciplinary introductory science page.

I chose online tutorials that were interactive, attractive, and had clear language. Actually, for the assignment I eliminated some vetted links that I would like to incorporate later, or in another guide. It's amazing to see what scientists, educators, and designers are doing to bring science to the public.

Here it is, my pride and joy: < Concepts, Scales, and Measures in Science >

I am finished with classes, have earned my Master's (just need to get the grades), and just submitted my first paper for peer review. :)
---------------------QUOTE-------------------



Congrats Kristine! Nicely done!
Posted by: Dr.GH on May 12 2010,13:45

Quote (Kristine @ May 12 2010,08:51)
I am finished with classes, have earned my Master's (just need to get the grades), and just submitted my first paper for peer review. :)
---------------------QUOTE-------------------


Congratulation. Shimmy on!
Posted by: dvunkannon on May 12 2010,18:37

Quote (Kristine @ May 12 2010,11:51)
Well, guys, I'm going to plug myself here. For my Reference Sources in the Sciences class I had to create a page of online resources. Unlike everyone else, who chose a specialty, I wanted to implement science communication techniques and so I created a transdiciplinary introductory science page.

I chose online tutorials that were interactive, attractive, and had clear language. Actually, for the assignment I eliminated some vetted links that I would like to incorporate later, or in another guide. It's amazing to see what scientists, educators, and designers are doing to bring science to the public.

Here it is, my pride and joy: < Concepts, Scales, and Measures in Science >

I am finished with classes, have earned my Master's (just need to get the grades), and just submitted my first paper for peer review. :)
---------------------QUOTE-------------------


Congratulations!

May I recommend to you the Molecular Workbench program
< http://mw.concord.org/modeler/ >

and Sodaplay
< http://sodaplay.com/ >

in the area of interactive science education?
Posted by: Kristine on May 12 2010,18:45

Thank you all! :)

Quote (JohnW @ May 12 2010,12:24)

That's terrific, Kristine.  Extra points for including "Powers Of Ten".
---------------------QUOTE-------------------



I love that film - in which science, art, music, design, and wonder combine. I was so thrilled to find it again.

Man, if anyone can tell me where to find old science films on the web, let me know! We saw these strange, and incredibly funny, films from the 1950s in chemistry and physics class, and I could not tell you who produced them, but I remember the guy in the Bozo the Clown hair who had a creative way of saying "solution," and this weird, really cool and mind-bending physics film about special relativity, featuring The Professor and His Assistant.

Quote (JohnW @ May 12 2010,12:24)
I think the section on "Ask Me Services" is incomplete without "Ask A Bitter, Frustrated Creationist With Two Doctorates Who Can't Get a Real Position And Is Stuck In A Backwoods Bible School".
---------------------QUOTE-------------------



How about a link called "To Behe or not to Behe"? :p
Posted by: Kristine on May 12 2010,18:50

Quote (dvunkannon @ May 12 2010,18:37)
Quote (Kristine @ May 12 2010,11:51)
Well, guys, I'm going to plug myself here. For my Reference Sources in the Sciences class I had to create a page of online resources. Unlike everyone else, who chose a specialty, I wanted to implement science communication techniques and so I created a transdiciplinary introductory science page.

I chose online tutorials that were interactive, attractive, and had clear language. Actually, for the assignment I eliminated some vetted links that I would like to incorporate later, or in another guide. It's amazing to see what scientists, educators, and designers are doing to bring science to the public.

Here it is, my pride and joy: < Concepts, Scales, and Measures in Science >

I am finished with classes, have earned my Master's (just need to get the grades), and just submitted my first paper for peer review. :)
---------------------QUOTE-------------------


Congratulations!

May I recommend to you the Molecular Workbench program
< http://mw.concord.org/modeler/ >

and Sodaplay
< http://sodaplay.com/ >

in the area of interactive science education?
---------------------QUOTE-------------------


These are wild! Thank you.
Posted by: fnxtr on May 12 2010,23:34

Quote (Kristine @ May 12 2010,16:45)
Thank you all! :)

 
Man, if anyone can tell me where to find old science films on the web, let me know!
---------------------QUOTE-------------------


It's not old, but it's fun:

< http://www.youtube.com/watch?v=3JdWlSF195Y >


Congratulations, Kristine.
Posted by: JLT on May 13 2010,03:54

< A formal test of the theory of universal common ancestry >

Douglas L. Theobald

Nature 465: 219–222
doi:10.1038/nature09014
 

---------------------QUOTE-------------------
In the conclusion of On the Origin of Species, Darwin proposed that “all the organic beings which have ever lived on this earth have descended from some one primordial form”. This theory of UCA—the proposition that all extant life is genetically related—is perhaps the most fundamental premise of modern evolutionary theory, providing a unifying foundation for all life sciences. UCA is now supported by a wealth of evidence from many independent sources, including: (1) the agreement between phylogeny and biogeography; (2) the correspondence between phylogeny and the palaeontological record; (3) the existence of numerous predicted transitional fossils; (4) the hierarchical classification of morphological characteristics; (5) the marked similarities of biological structures with different functions (that is, homologies); and (6) the congruence of morphological and molecular phylogenies. Although the consilience of these classic arguments provides strong evidence for the common ancestry of higher taxa such as the chordates or metazoans, none expressly address questions such as whether bacteria, yeast and humans are all genetically related. However, the ‘universal’ in universal common ancestry is primarily supported by two further lines of evidence: various key commonalities at the molecular level (including fundamental biological polymers, nucleic acid genetic material, l-amino acids, and core metabolism) and the near universality of the genetic code. Notably, these two traditional arguments for UCA are largely qualitative, and typical presentations of the evidence do not assess quantitative measures of support for competing hypotheses, such as the probability of evolution from multiple, independent ancestors.
The inference from biological similarities to evolutionary homology is a feature shared by several of the lines of evidence for common ancestry. For instance, it is widely assumed that high sequence resemblance, often gauged by an E value from a BLAST search, indicates genetic kinship. However, a small E value directly demonstrates only that two biological sequences are more similar than would be expected by chance. [...] Sequence similarity is an empirical observation, whereas the conclusion of homology is a hypothesis proposed to explain the similarity. Statistically significant sequence similarity can arise from factors other than common ancestry, such as convergent evolution due to selection, structural constraints on sequence identity, mutation bias, chance, or artefact manufacture. For these reasons, a sceptic who rejects the common ancestry of all life might nevertheless accept that universally conserved proteins have similar sequences and are ‘homologous’ in the original pre-Darwinian sense of the term (homology here being similarity of structure due to “fidelity to archetype”). Consequently, it would be advantageous to have a method that is able to objectively quantify the support from sequence data for common-ancestry versus competing multiple-ancestry hypotheses.
Here I report tests of the theory of UCA using model selection theory, without assuming that sequence similarity indicates a genealogical relationship. [...]
The theory of UCA allows for the possibility of multiple independent origins of life. If life began multiple times, UCA requires a ‘bottleneck’ in evolution in which descendants of only one of the independent origins have survived exclusively until the present (and the rest have become extinct), or, multiple populations with independent, separate origins convergently gained the ability to exchange essential genetic material (in effect, to become one species). All of the models examined here are compatible with multiple origins in both the above schemes, and therefore the tests reported here are designed to discriminate specifically between UCA and multiple ancestry, rather than between single and multiple origins of life. Furthermore, UCA does not demand that the last universal common ancestor was a single organism, in accord with the traditional evolutionary view that common ancestors of species are groups, not individuals. Rather, the last universal common ancestor may have comprised a population of organisms with different genotypes that lived in different places at different times.
The data set consists of a subset of the protein alignment data from ref. 27, containing 23 universally conserved proteins for 12 taxa from all three domains of life, including nine proteins thought to have been horizontally transferred early in evolution. The conserved proteins in this data set were identified based on significant sequence similarity using BLAST searches, and they have consequently been postulated to be orthologues. The first class of models I considered (presented in Table 1 and Fig. 1) constrains all the universally conserved proteins in a given set of taxa to evolve by the same tree, and hence these models do not account for possible horizontal gene transfer (HGT) or symbiotic fusion events during the evolution of the three domains of life. Hereafter I refer to this set of models as ‘class I’. The class I model ABE, representing universal common ancestry of all taxa in the three domains of life and shown in Fig. 1a, can be considered to represent the classic three-domain ‘tree of life’ model of evolution.
Among the class I models, all criteria select the UCA tree by an extremely large margin (score differences ranging from 6,569 to 14,057), even though nearly half of the proteins in the analysis probably have evolutionary histories complicated by HGT. For all model selection criteria, by statistical convention a score difference of 5 or greater is viewed as very strong empirical evidence for the hypothesis with the better score (in this work higher scores are better). All scores shown are also highly statistically significant (the estimated variance for each score is approximately 2–3). According to a standard objective Bayesian interpretation of the model selection criteria, the scores are the log odds of the hypotheses. Therefore, UCA is at least 10^2,860 times more probable than the closest competing hypothesis. Notably, UCA is the most accurate and the most parsimonious hypothesis. Compared to the multiple-ancestry hypotheses, UCA provides a much better fit to the data (as seen from its higher likelihood), and it is also the least complex (as judged by the number of parameters).
The extraordinary strength of these results in the face of suspected HGT events suggests that the preference for the UCA model is robust to the extent of HGT. To test this possibility, the analysis was expanded to include models that allow each protein to have a distinct, independent evolutionary history. I refer to this set of models, which rejects a single tree metaphor for genealogically related taxa, as ‘class II’. Representative class II models are shown in Fig. 2. Within each set of genealogically related taxa, each of the 23 universally conserved proteins is allowed to evolve on its own separate phylogeny, in which both branch lengths and tree topology are free parameters. [...] Overall, the model selection tests show that the class II models are greatly preferred to the class I models. For instance, the class II UCA hypothesis ([ABE]II) versus the class I UCA hypothesis (ABE) gives a highly significant LLR of 3,557, a ?AIC of 2,633 and an LBF of 2,875. The optimal class II models represent an upper limit to the degree of HGT, as many of the apparent reticulations are probably due to incomplete lineage sorting, hidden paralogy, recombination, or inaccuracies in the evolutionary models. Nonetheless, as with the class I non-HGT hypotheses, all model selection criteria unequivocally support a single common genetic ancestry for all taxa. Also similar to the class I models, the class II UCA model has the greatest explanatory power and is the most parsimonious.
Several hypotheses have been proposed to explain the origin of eukaryotes and the early evolution of life by endosymbiotic fusion of an early archaeon and bacterium. A key commonality of these hypotheses is the rejection of a single, bifurcating tree as a proper model for the ancestry of Eukarya. For instance, in these biological hypotheses certain eukaryotic genes are derived from Archaea whereas others are derived from Bacteria. The class II models freely allow eukaryotic genes to be either archaeal-derived or bacterial-derived, as the data dictate, and hence class II hypotheses can model several endosymbiotic ‘rings’ and HGT events. [...] In all cases, these bounds show that multiple-ancestry versions of the constrained class II models are overwhelmingly rejected by the tests (model selection scores of several thousands), indicating that common ancestry is also preferred for all specific HGT and endosymbiotic fusion models. In terms of a fusion hypothesis for the origin of Eukarya, the data conclusively support a UCA model in which Eukarya share an ancestor with Bacteria and another independently with Archaea, and in which Bacteria and Archaea are also genetically related independently of Eukarya (see Table 3).
[...]
What property of the sequence data supports common ancestry so decisively? When two related taxa are separated into two trees, the strong correlations that exist between the sequences are no longer modelled, which results in a large decrease in the likelihood. Consequently, when comparing a common-ancestry model to a multiple-ancestry model, the large test scores are a direct measure of the increase in our ability to accurately predict the sequence of a genealogically related protein relative to an unrelated protein. The sequence correlations between a given clade of taxa and the rest of the tree would be eliminated if the columns in the sequence alignment for that clade were randomly shuffled. In such a case, these model-based selection tests should prefer the multiple-ancestry model. In fact, in actual tests with randomly shuffled data, the optimal estimate of the unified tree (for both maximum likelihood and Bayesian analyses) contains an extremely large internal branch separating the shuffled taxa from the rest. In all cases tried, with a wide variety of evolutionary models (from the simplest to the most parameter rich), the multiple-ancestry models for shuffled data sets are preferred by a large margin over common ancestry models (LLR on the order of a thousand), even with the large internal branches. Hence, the large test scores in favour of UCA models reflect the immense power of a tree structure, coupled with a gradual Markovian mechanism of residue substitution, to accurately and precisely explain the particular patterns of sequence correlations found among genealogically related biological macromolecules.
---------------------QUOTE-------------------



If IDists were actually interested in testing ID, they'd write articles like this.

ETA: < Nick Matzke at PT about this article >

ETA: That's 10^2,860:
Therefore, UCA is at least 10^2,860 times more probable than the closest competing hypothesis.
Posted by: Quack on May 13 2010,06:39



---------------------QUOTE-------------------
If IDists were actually interested in testing ID, they'd write articles like this.

---------------------QUOTE-------------------


I know what I think but don't quite find the words to use...

-----------
ETA qualifications...
Posted by: midwifetoad on May 20 2010,14:12

Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome

< http://www.sciencemag.org/cgi/content/abstract/science.1190719 >
Posted by: khan on May 25 2010,10:20

< http://www.sott.net/article....Species >



---------------------QUOTE-------------------

Using its fins to walk, rather than swim, along the ocean floor in an undated picture, the pink handfish is one of nine newly named species described in a recent scientific review of the handfish family.
---------------------QUOTE-------------------


Posted by: midwifetoad on May 25 2010,10:25

Quote (khan @ May 25 2010,10:20)
< http://www.sott.net/article....Species >



---------------------QUOTE-------------------

Using its fins to walk, rather than swim, along the ocean floor in an undated picture, the pink handfish is one of nine newly named species described in a recent scientific review of the handfish family.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


Good eating, but an hour later, you're dead.
Posted by: Richardthughes on May 25 2010,12:16

< http://sfmatheson.blogspot.com/ >
Posted by: J-Dog on May 25 2010,13:38

Quote (Richardthughes @ May 25 2010,12:16)
< http://sfmatheson.blogspot.com/ >
---------------------QUOTE-------------------


Good stuff!  -  I'm always impressed when a DI fellow gets blasted by a TE - and your link is one of the best I've seen.
Posted by: Kristine on May 26 2010,15:12

Quote (J-Dog @ May 25 2010,13:38)
Quote (Richardthughes @ May 25 2010,12:16)
< http://sfmatheson.blogspot.com/ >
---------------------QUOTE-------------------


Good stuff!  -  I'm always impressed when a DI fellow gets blasted by a TE - and your link is one of the best I've seen.
---------------------QUOTE-------------------


Yes, thank you. Very informative.

I continue to be astonished at the way these IDists conduct themselves.
Posted by: Timothy McDougald on May 27 2010,18:35

< Teh designer is a termite >:



---------------------QUOTE-------------------
The real king of the savanna appears to be the termite, say ecologists who've found that these humble creatures contribute mightily to grassland productivity in central Kenya via a network of uniformly distributed colonies. Termite mounds greatly enhance plant and animal activity at the local level, while their even distribution over a larger area maximizes ecosystem-wide productivity.
---------------------QUOTE-------------------


Posted by: Henry J on May 28 2010,14:06

The Designer was a termite? is that what caused the Fall - when the Designer ate the supporting beams? :p
Posted by: midwifetoad on May 28 2010,14:41

< http://arstechnica.com/science....ent.ars >



---------------------QUOTE-------------------
It's hardly a secret that large segments of the population choose not to accept scientific data because it conflicts with their predefined beliefs: economic, political, religious, or otherwise. But many studies have indicated that these same people aren't happy with viewing themselves as anti-science, which can create a state of cognitive dissonance. That has left psychologists pondering the methods that these people use to rationalize the conflict.

A study published in the Journal of Applied Social Psychology takes a look at one of these methods, which the authors term "scientific impotence"—the decision that science can't actually address the issue at hand properly. It finds evidence that not only supports the scientific impotence model, but suggests that it could be contagious. Once a subject has decided that a given topic is off limits to science, they tend to start applying the same logic to other issues.

The paper is worth reading for the introduction alone, which sets up the problem of science acceptance within the context of persuasive arguments and belief systems. There's a significant amount of literature that considers how people resist persuasion, and at least seven different strategies have been identified. But the author, Towson University's Geoffrey Munro, attempts to carve out an exceptional place for scientific information. "Belief-contradicting scientific information may elicit different resistance processes than belief-contradicting information of a nonscientific nature," he argues. "Source derogation, for example, might be less effective in response to scientific than nonscientific information."

---------------------QUOTE-------------------


Posted by: Richardthughes on June 01 2010,10:43

< http://people.cohums.ohio-state.edu/tennant9/thagard_JP1978.pdf >

well, Philosophy of science break.
Posted by: JLT on June 08 2010,10:21

Those are the rules...

This editorial in the current Nature Immunology spells out nicely why most IDist don't stand a chance at getting an article published in a peer-reviewed scientific journal.

 

---------------------QUOTE-------------------
< Dogmas, paradigms and proving hypotheses >
Nature Immunology 11: 455(2010)
doi:10.1038/ni0610-455

Strong hypotheses stand the test of time because of rigorous experimentation by authors and the scientific community.

From time to time a manuscript arrives accompanied by a cover letter in which the authors state that the new work being submitted “overturns existing dogma” on some immunological process. Others suggest their work is “paradigm changing” and go on to describe how they prove their hypothesis. Naturally, such bold claims capture our attention, but unfortunately, more often than not, they fall short. Why is this so?

Part of the problem is the authors' choice of words to describe the hypothesis addressed in the study and why this question is relevant to a large cross-section of the community. A 'dogma' is defined as a principle or set of principles laid down by an authority and held to be incontrovertibly true. However, immunology is an experimental science and rarely if ever can dogmatic claims be made in science. Moreover, a paradigm (a word derived from the Greek paradeiknynai, meaning 'to show side by side') is defined as an outstandingly clear or typical example or archetype. Perhaps better stated, a paradigm is a current model supported by abundant experimental evidence. For example, one immunological paradigm at present might be the hypothesis that innate immunity triggered by pattern-recognition receptors initiates and shapes adaptive immune responses through the expression of proinflammatory cytokines. For authors who seek to claim “paradigm-changing” results, the onus is on them to explain why the previous theory cannot explain the present findings. They also need to put forth a new or unifying hypothesis that can account for both the previous work and the new experimental data. Admittedly, the bar is higher for authors claiming to “change” a paradigm.
[...]

Alternative interpretations of the same data set give rise to competing hypotheses. Here, as with the posing of any hypothesis, authors should strive to test the robustness of their model and determine how well its predictions hold true after perturbation of the system. A weak test to demonstrate the desired result is not strong support for a favored hypothesis. Instead, the challenge is to design the most stringent test possible to disprove the hypothesis and then see if the new data rule out or support the hypothesis. In the process of peer review, referees will often voice concerns that additional experimentation is needed to rule out alternative interpretations. Such referee concerns are not intended to hold back publication of the work but to provide additional support that the authors' hypothesis is the most likely explanation of the data set and to show how the hypothesis fits in the broader framework of previous findings. Often such control experiments have already been done by the authors, as they too recognize the need to rule out trivial or alternative explanations for the data obtained, but these have not been included in the submitted manuscript. Such data can readily be incorporated into a revision and serve to increase the validity of the authors' conclusions.
[...]

Scientific advancement does not occur by proclamation of dogmatic theories. Immunologists, like other scientists, gather data sets from which hypotheses can be posed to explain the findings obtained. The challenge is how to design rigorous tests for a favorite hypothesis—and by doing so, researchers help to truly advance the field.
---------------------QUOTE-------------------


Especially the bit I highlighted in blue is the part that IDists just don't get.

IMO it's a useful article one can point to in case yet another ID proponent claims ID is unfairly excluded from being published in peer-reviewed journals when all ID has is the claim that every protein that has both a function and is longer than 35 aminoacids can't have evolved because it has more than 150 bits of dFSCI or whatever the newest creation is (seems that each IDiot nowadays makes up his own acronym, the more letters the better; maybe they think that'll increase the information content of their undefined mess and if they keep it up it will at some point suddenly become useful).
Posted by: J-Dog on June 08 2010,14:47

Quote (JLT @ June 08 2010,10:21)
For authors who seek to claim “paradigm-changing” results, the onus is on them to explain why the previous theory cannot explain the present findings. They also need to put forth a new or unifying hypothesis that can account for both the previous work and the new experimental data. Admittedly, the bar is higher for authors claiming to “change” a paradigm.
[...]
---------------------QUOTE-------------------


You make Teh Baby Billy Dembski cry, and sing the blues...

And I like it.
Posted by: Dr.GH on June 08 2010,15:10



---------------------QUOTE-------------------
Often such control experiments have already been done by the authors, as they too recognize the need to rule out trivial or alternative explanations for the data obtained, but these have not been included in the submitted manuscript. Such data can readily be incorporated into a revision and serve to increase the validity of the authors' conclusions.
---------------------QUOTE-------------------



This part caught my eye. We used to joke about whether a paper had a LPU, or Least Publishable Unit. The less data you could get away with in a publication meant the more publications you could squeeze out of a project.
Posted by: Quack on June 09 2010,05:22

I don't know if I can contribute anything of interest here, but I found this very interesting, and yet another reason to ask what the heck does the designer think he is doing? Anyway, just an excerpt I've tried to translate:

 

---------------------QUOTE-------------------
It is done by making a complete DNAanalysis of the radiolarian with all its contents.

Even if the parasites cannot be identified with a microscope, DNA analysis shows that they are there.

We don’t know the numbers, but there may be many parasites in radiolarians. Each day we discover some new ones.

It is just the discovery of parasites in radiolarians that makes it possible to solve the mystery of the unknown, biological diversity in the oceans.

It is explained by the strong correlation between DNA-samples from a single radiolarian and DNA-samples of seawater.

Now we know that all sequences inside of the radiolarians are identical with the unknown sequences in the oceans.

We therefore may conclude that large proportions of the unknown strands of DNA in water are from parasites.

- We now are going to map DNA from a number of radiolarians and parasites in order to learn the interplay between them says Kamran Shalchian Tabrizi. (leader of the interdisciplinary group Microbial Evolution Research Group (MERG) at Universitetet i Oslo (UiO) who has for many years been researching at University of Oslo.)

To reach their goal, the researchers wish to sequence the entire genome, i.e. the complete genetic mass, of both radiolarians and their parasites. The problem is the enormous genomes. Incredibly enough the genome of radiolarians may be up to a hundred times larger than the human.

---------------------QUOTE-------------------


My bold and italics.
Posted by: Schroedinger's Dog on June 09 2010,05:56

< Quite old news >, but it seems science has mad a further small step towards abiogenesis. I find this colour of panspermia* theory quite attractive.



*Well, not exactly panspermia, but this type of "contamination" is definitely an interesting thought...
Posted by: Quack on June 09 2010,07:16

Quote (Schroedinger's Dog @ June 09 2010,05:56)
< Quite old news >, but it seems science has mad a further small step towards abiogenesis. I find this colour of panspermia* theory quite attractive.
*Well, not exactly panspermia, but this type of "contamination" is definitely an interesting thought...
---------------------QUOTE-------------------


   

---------------------QUOTE-------------------
"We wanted to test whether pyrimidine can survive in space, and whether it can undergo reactions that turn it into more complicated organic species, such as the nucleobase uracil."
---------------------QUOTE-------------------


What, without an intelligent source for fCSI?
Posted by: Schroedinger's Dog on June 14 2010,11:55

< Mmmmh..Interesting... >

What I like there:



---------------------QUOTE-------------------
"Titan's atmospheric chemistry is cranking out organic compounds that rain down on the surface so fast that even as streams of liquid methane and ethane at the surface wash the organics off, the ice gets quickly covered again," Clark said. "All that implies Titan is a dynamic place where organic chemistry is happening now."
---------------------QUOTE-------------------



And:



---------------------QUOTE-------------------
"Scientific conservatism suggests that a biological explanation should be the last choice after all non-biological explanations are addressed," Allen said. "We have a lot of work to do to rule out possible non-biological explanations. It is more likely that a chemical process, without biology, can explain these results - for example, reactions involving mineral catalysts."
---------------------QUOTE-------------------




But yeah, sure, science is *very dogmatic* and will settle on any explanation that fits its political agenda...

DI will probably FUQ it (fill it in their "Frequently Unanswered Questions"*)




*Thank you, leastIcouldDo
Posted by: Richardthughes on June 14 2010,13:17

Oleg:

< http://www.sciencenews.org/view....Feynman >
Posted by: Schroedinger's Dog on June 14 2010,13:27

Quote (Richardthughes @ June 14 2010,19:17)
Oleg:

< http://www.sciencenews.org/view....Feynman >
---------------------QUOTE-------------------


Is their server a 52ko hosted in Narnia? I can't reach the page...
Posted by: Timothy McDougald on June 14 2010,20:48

< This is interesting. > From the abstract:



---------------------QUOTE-------------------
Pathogenic Gram-negative bacteria use a type three secretion system (TTSS) to deliver virulence factors into host cells. Although the order in which proteins incorporate into the growing TTSS is well described, the underlying assembly mechanisms are still unclear. Here we show that the TTSS needle protomer refolds spontaneously to extend the needle from the distal end. We developed a functional mutant of the needle protomer from Shigella flexneri and Salmonella typhimurium to study its assembly in vitro. We show that the protomer partially refolds from ?-helix[alpha helix - afarensis] into ?-strand [beta strand - afarensis] conformation to form the TTSS needle. Reconstitution experiments show that needle growth does not require ATP. Thus, like the structurally related flagellar systems, the needle elongates by subunit polymerization at the distal end but requires protomer refolding. Our studies provide a starting point to understand the molecular assembly mechanisms and the structure of the TTSS at atomic level.
---------------------QUOTE-------------------


Posted by: dvunkannon on June 15 2010,12:16

< Article on a protein that mutates quickly and drives speciation. >



---------------------QUOTE-------------------
It’s logical then to ask what specifies or controls hotspot location. Scientists have gathered evidence that three different mechanisms are involved in controlling location and activity. First, the genomic sequence around each hotspot seems to be important; for example, 40 percent of human hotspots are associated with a repeating 13-basepair motif. However, because only a portion of hotspots correlates with a specific sequence, other factors must be involved. For example, evidence is accumulating that hotspot locations are associated with certain histone modifications. The third proposed mechanism implies that a soluble factor or protein must control the location and distribution of hotspots.

Remarkably, a single protein appears to satisfy all three conditions.



Read more: Sticky fingers - The Scientist - Magazine of the Life Sciences < http://www.the-scientist.com/article/display/57466/#ixzz0qwWLH2d2 >

---------------------QUOTE-------------------


Posted by: dvunkannon on June 15 2010,14:49

A query to y'all sciency types:

I was reading Nick Lane's "The 10 Great Inventions of Evolution" last week. At one point he is describing the historical path to understanding how RNA led to protein formation, and the realization that amino acids didn't just attach to random spots on the mRNA chain, instead the ribsome mediated the growth of the protein as it walked the length of the messenger RNA.

I was suddenly struck by the question of whether any protein folding algorithm actually works the same the way the ribosome does.

My general impression of ab initio protein folding algorithms is that they start with the whole linear string of peptides floating freely in a solvent, and then let the whole string twist and collapse under the influence of local force fields. They don't, to my knowledge, build up the protein one AA at a time from one end which is tethered to a large object (ribosome + mRNA). Not surprisingly, they often don't fold into the native conformation.

Reinforcing my general impression, a google search on 'incremental protein folding algorithm' didn't generate any decent hits.

So I ask you - do you know of any such algorithm? Is this an idea that has been tried and discarded? It would seem to me to be much faster in some ways. Any suggestions on where/who could provide better insights?
Posted by: REC on June 15 2010,15:02

Quote (dvunkannon @ June 15 2010,14:49)
A query to y'all sciency types:

I was reading Nick Lane's "The 10 Great Inventions of Evolution" last week. At one point he is describing the historical path to understanding how RNA led to protein formation, and the realization that amino acids didn't just attach to random spots on the mRNA chain, instead the ribsome mediated the growth of the protein as it walked the length of the messenger RNA.

I was suddenly struck by the question of whether any protein folding algorithm actually works the same the way the ribosome does.

My general impression of ab initio protein folding algorithms is that they start with the whole linear string of peptides floating freely in a solvent, and then let the whole string twist and collapse under the influence of local force fields. They don't, to my knowledge, build up the protein one AA at a time from one end which is tethered to a large object (ribosome + mRNA). Not surprisingly, they often don't fold into the native conformation.

Reinforcing my general impression, a google search on 'incremental protein folding algorithm' didn't generate any decent hits.

So I ask you - do you know of any such algorithm? Is this an idea that has been tried and discarded? It would seem to me to be much faster in some ways. Any suggestions on where/who could provide better insights?
---------------------QUOTE-------------------


The search you're looking for is "algorithm cotranslational protein folding"

Since co-translational folding is a known (but fought over) mechanism, that makes solution folding of a whole denatured protein and the folding of a nascent peptide during translation different, this is important.

< http://www.jbc.org/content/275/22/16597.full >

And people are starting to work on it:

< http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1523309/ >

"Molecular Simulations of Cotranslational Protein Folding: Fragment Stabilities, Folding Cooperativity, and Trapping in the Ribosome"
Posted by: dvunkannon on June 16 2010,06:36

Quote (REC @ June 15 2010,16:02)
 
Quote (dvunkannon @ June 15 2010,14:49)
A query to y'all sciency types:

I was reading Nick Lane's "The 10 Great Inventions of Evolution" last week. At one point he is describing the historical path to understanding how RNA led to protein formation, and the realization that amino acids didn't just attach to random spots on the mRNA chain, instead the ribsome mediated the growth of the protein as it walked the length of the messenger RNA.

I was suddenly struck by the question of whether any protein folding algorithm actually works the same the way the ribosome does.

My general impression of ab initio protein folding algorithms is that they start with the whole linear string of peptides floating freely in a solvent, and then let the whole string twist and collapse under the influence of local force fields. They don't, to my knowledge, build up the protein one AA at a time from one end which is tethered to a large object (ribosome + mRNA). Not surprisingly, they often don't fold into the native conformation.

Reinforcing my general impression, a google search on 'incremental protein folding algorithm' didn't generate any decent hits.

So I ask you - do you know of any such algorithm? Is this an idea that has been tried and discarded? It would seem to me to be much faster in some ways. Any suggestions on where/who could provide better insights?
---------------------QUOTE-------------------


The search you're looking for is "algorithm cotranslational protein folding"

Since co-translational folding is a known (but fought over) mechanism, that makes solution folding of a whole denatured protein and the folding of a nascent peptide during translation different, this is important.

< http://www.jbc.org/content/275/22/16597.full >

And people are starting to work on it:

< http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1523309/ >

"Molecular Simulations of Cotranslational Protein Folding: Fragment Stabilities, Folding Cooperativity, and Trapping in the Ribosome"
---------------------QUOTE-------------------


Thanks, REC!

From a recent publication:
 

---------------------QUOTE-------------------
BMC Bioinformatics. 2010 Apr 7;11:172.

Directionality in protein fold prediction.
Ellis JJ, Huard FP, Deane CM, Srivastava S, Wood GR.

Department of Statistics, Macquarie University, Sydney, NSW 2109, Australia.

Abstract
BACKGROUND: Ever since the ground-breaking work of Anfinsen et al. in which a denatured protein was found to refold to its native state, it has been frequently stated by the protein fold prediction community that all the information required for protein folding lies in the amino acid sequence. Recent in vitro experiments and in silico computational studies, however, have shown that cotranslation may affect the folding pathway of some proteins, especially those of ancient folds. In this paper aspects of cotranslational folding have been incorporated into a protein structure prediction algorithm by adapting the Rosetta program to fold proteins as the nascent chain elongates. This makes it possible to conduct a pairwise comparison of folding accuracy, by comparing folds created sequentially from each end of the protein. RESULTS: A single main result emerged: in 94% of proteins analyzed, following the sense of translation, from N-terminus to C-terminus, produced better predictions than following the reverse sense of translation, from the C-terminus to N-terminus. Two secondary results emerged. First, this superiority of N-terminus to C-terminus folding was more marked for proteins showing stronger evidence of cotranslation and second, an algorithm following the sense of translation produced predictions comparable to, and occasionally better than, Rosetta. CONCLUSIONS: There is a directionality effect in protein fold prediction. At present, prediction methods appear to be too noisy to take advantage of this effect; as techniques refine, it may be possible to draw benefit from a sequential approach to protein fold prediction.
---------------------QUOTE-------------------


Posted by: Albatrossity2 on June 16 2010,06:58

Good news (from the IEEE Spectrum) for intelligent-designer-philes like Sal! < Engineer/computer geek develops sex robots. >
 

---------------------QUOTE-------------------
Hines devised the skin by encasing a woman—a fine-art model—in silicone and cutting the material away after it solidified. “Roxxxy has three inputs and motors where it counts,” explains Hines. “There’s a lot of heat buildup, so we installed a convection system. Other motors simulate a heartbeat and responsive gestures.”
---------------------QUOTE-------------------


Chunkdz will have to wait for a bit.
 

---------------------QUOTE-------------------
A male version, Rocky, is planned by year’s end. “My wife wants to be a beta tester, which is just desserts for my spending time in the middle of the night with girls covered in silicone,” he says.
---------------------QUOTE-------------------


Posted by: ppb on June 16 2010,15:51

Quote (Albatrossity2 @ June 16 2010,07:58)
Good news (from the IEEE Spectrum) for intelligent-designer-philes like Sal! < Engineer/computer geek develops sex robots. >
   

---------------------QUOTE-------------------
Hines devised the skin by encasing a woman—a fine-art model—in silicone and cutting the material away after it solidified. “Roxxxy has three inputs and motors where it counts,” explains Hines. “There’s a lot of heat buildup, so we installed a convection system. Other motors simulate a heartbeat and responsive gestures.”
---------------------QUOTE-------------------


Chunkdz will have to wait for a bit.
   

---------------------QUOTE-------------------
A male version, Rocky, is planned by year’s end. “My wife wants to be a beta tester, which is just desserts for my spending time in the middle of the night with girls covered in silicone,” he says.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


It's just more proof of ID theory.  Sex couldn't have evolved.  It requires a designer!   :)
Posted by: skeptic reborn on June 16 2010,23:46

Quote (dvunkannon @ June 15 2010,12:16)
< Article on a protein that mutates quickly and drives speciation. >

 

---------------------QUOTE-------------------
It’s logical then to ask what specifies or controls hotspot location. Scientists have gathered evidence that three different mechanisms are involved in controlling location and activity. First, the genomic sequence around each hotspot seems to be important; for example, 40 percent of human hotspots are associated with a repeating 13-basepair motif. However, because only a portion of hotspots correlates with a specific sequence, other factors must be involved. For example, evidence is accumulating that hotspot locations are associated with certain histone modifications. The third proposed mechanism implies that a soluble factor or protein must control the location and distribution of hotspots.

Remarkably, a single protein appears to satisfy all three conditions.



Read more: Sticky fingers - The Scientist - Magazine of the Life Sciences < http://www.the-scientist.com/article/display/57466/#ixzz0qwWLH2d2 >

---------------------QUOTE-------------------


---------------------QUOTE-------------------


Wonderful stuff!  Studies like these are just the beginning.  One of these days, fifty years from now, we'll be able to tell our great-grandchildren (hopefully) that we once believed evolution was random.  As the famous chaos theorisist once said, "life finds a way."
Posted by: sledgehammer on June 17 2010,00:29

Quote (skeptic reborn @ June 16 2010,21:46)

Wonderful stuff!  Studies like these are just the beginning.  One of these days, fifty years from now, we'll be able to tell our great-grandchildren (hopefully) that we once believed evolution was random.  As the famous chaos theorisist once said, "life finds a way."
---------------------QUOTE-------------------


Who is "we", kimosabe?  Random is not a word currently used to describe evolution, except by creato strawmakers.
Posted by: Richardthughes on June 18 2010,23:54

Self replication in Conway's Life:

< http://www.newscientist.com/article....or.html >
Posted by: OgreMkV on June 21 2010,07:46

Oh boy.  I can hear the creationist yelling "victory" over this one.

< Canyon carved in just three days >

"ScienceDaily (June 20, 2010) — In the summer of 2002, a week of heavy rains in Central Texas caused Canyon Lake -- the reservoir of the Canyon Dam -- to flood over its spillway and down the Guadalupe River Valley in a planned diversion to save the dam from catastrophic failure. The flood, which continued for six weeks, stripped the valley of mesquite, oak trees, and soil; destroyed a bridge; and plucked meter-wide boulders from the ground. And, in a remarkable demonstration of the power of raging waters, the flood excavated a 2.2-kilometer-long, 7-meter-deep canyon in the bedrock."

Michael P. Lamb, Mark A. Fonstad. Rapid formation of a modern bedrock canyon by a single flood event. Nature Geoscience, 2010; DOI: 10.1038/ngeo894
Posted by: Wesley R. Elsberry on June 25 2010,07:18

Some of you may have heard of the TransOcean/BP/Halliburton/Macondo Prospect/Mississippi Canyon 252 incident/oil spill currently ongoing in the Gulf of Mexico.

I've been pitching an idea around concerning acoustic monitoring of snapping shrimp. If you don't already know, these are small shrimp that use one oversized claw to "snap", an abrupt motion that causes a cavitation event. This can stun or kill outright small prey items. The snaps are also very, very loud. Where there are snapping shrimp, there tend to be quite high numbers of them: in seagrass, in rocks, in coral reefs. Thus, in the near-shore, structured environments favored by snapping shrimp, there is usually a pervasive noise from the collective snapping of the whole population of these shrimp. The noise is broadband, with a peak frequency up around 50kHz. But because the energy is broadband, there's plenty to be heard in the usual human audio range of 20Hz to 20kHz.

I'm aiming toward a citizen scientist project based on acoustic monitoring of snapping shrimp. The first installment on that is < here >.
Posted by: fnxtr on June 25 2010,17:37

Quote (Wesley R. Elsberry @ June 25 2010,05:18)
Some of you may have heard of the TransOcean/BP/Halliburton/Macondo Prospect/Mississippi Canyon 252 incident/oil spill currently ongoing in the Gulf of Mexico.

I've been pitching an idea around concerning acoustic monitoring of snapping shrimp. If you don't already know, these are small shrimp that use one oversized claw to "snap", an abrupt motion that causes a cavitation event. This can stun or kill outright small prey items. The snaps are also very, very loud. Where there are snapping shrimp, there tend to be quite high numbers of them: in seagrass, in rocks, in coral reefs. Thus, in the near-shore, structured environments favored by snapping shrimp, there is usually a pervasive noise from the collective snapping of the whole population of these shrimp. The noise is broadband, with a peak frequency up around 50kHz. But because the energy is broadband, there's plenty to be heard in the usual human audio range of 20Hz to 20kHz.

I'm aiming toward a citizen scientist project based on acoustic monitoring of snapping shrimp. The first installment on that is < here >.
---------------------QUOTE-------------------


When does the Snapping Shrimp Orchestra CD come out? Christmas?
Posted by: Wesley R. Elsberry on June 25 2010,19:14

Some people like rain forest sounds. For myself, a nice chorus of snapping shrimp is about as soothing as it gets.
Posted by: carlsonjok on June 25 2010,19:30

Quote (Wesley R. Elsberry @ June 25 2010,19:14)
Some people like rain forest sounds. For myself, a nice chorus of snapping shrimp is about as soothing as it gets.
---------------------QUOTE-------------------


For some reason, all I can think of is the < prologue to West Side Story >.
Posted by: rhmc on June 25 2010,20:16

Quote (carlsonjok @ June 25 2010,20:30)
For some reason, all I can think of is the < prologue to West Side Story >.
---------------------QUOTE-------------------


and that reminds me of:
when you're a jet you're a jet all the way.
from your first cigarette til your last dying day...

alice cooper.  school's out.
Posted by: rhmc on June 25 2010,20:25

Quote (Wesley R. Elsberry @ June 25 2010,08:18)
Some of you may have heard of the TransOcean/BP/Halliburton/Macondo Prospect/Mississippi Canyon 252 incident/oil spill currently ongoing in the Gulf of Mexico.

I've been pitching an idea around concerning acoustic monitoring of snapping shrimp. If you don't already know, these are small shrimp that use one oversized claw to "snap", an abrupt motion that causes a cavitation event. This can stun or kill outright small prey items. The snaps are also very, very loud. Where there are snapping shrimp, there tend to be quite high numbers of them: in seagrass, in rocks, in coral reefs. Thus, in the near-shore, structured environments favored by snapping shrimp, there is usually a pervasive noise from the collective snapping of the whole population of these shrimp. The noise is broadband, with a peak frequency up around 50kHz. But because the energy is broadband, there's plenty to be heard in the usual human audio range of 20Hz to 20kHz.

I'm aiming toward a citizen scientist project based on acoustic monitoring of snapping shrimp. The first installment on that is < here >.
---------------------QUOTE-------------------


That's interesting stuff.  
I collect biological specimens for an ichthyologist  at the University of Miami.
We fish, seine and throw a cast net alot and send samples, two by two if possible.  
East of Savannah.

We see a little bit of everything.

Wife has participated in some of the Caretta Research projects monitoring egg laying on the nearby barrier islands.

Caretta caretta is an awesome critter.

The UGA Skidaway Institute is not far from here and we do some stuff with them.

They've not broken out a hydrophone yet.  Perhaps I should mention such?

I'll see if I can send some of those folks to your site.  Or is there a better place to send such marine folk?
Posted by: Wesley R. Elsberry on June 26 2010,04:25

I don't know offhand of a better place to send them. If I knew of some group doing recordings to assess invertebrate populations, I'd be trying to help them out.
Posted by: Wesley R. Elsberry on June 26 2010,13:50

I'll make some comments about gear for recording snapping shrimp.

At the minimal, low-cost end, one can demonstrate that snapping shrimp are active at a particular place and time with just an audio recording. For this level of documentation, one should have an audio recorder and either a hydrophone or a water-resistant microphone. If you already have an audio recorder (cassette tape, DAT, digital recorder, voice recorder, video camcorder, etc.) and a hydrophone, you are set.

You can make a hydrophone or water-resistant microphone inexpensively.

If you go with making a microphone water-resistant, it is best to think of it as a disposable item. In other words, think Coby, not Sennheiser, when picking a microphone to deploy in saltwater, unless you have cash to burn. A common way to make a microphone water-resistant is to slide it into an unlubricated condom and seal the condom's open end to the microphone cable. This can be done with alternating layers of good electrical tape (i.e., 3M Scotch Super 33+) and a sealing compound (i.e., 3M Scotchkote (preferred) or rubber cement (OK in a pinch)). I'd do at least two layers of seal. Obviously, a dynamic microphone rather than an electret will be easier to deal with, since the electret mics require a battery or phantom power. Let's say that you buy a dynamic mic for $20 or less, the Scotchkote is about $20 at Home Depot the last time I got it there, and Super 33+ is about $4 a roll. I don't recall the cost on unlubricated condoms, but let's just call this do-it-yourself project about $50 for the first one, and less than $25 each for subsequent ones.

A do-it-yourself hydrophone can be prepared using a piezoelectric element with cabling, sealed against saltwater intrusion. < Here > is a source of piezo disks, 6 for $1.50. You'll need a cable, so make one of suitable length. Coax is better for the small signals coming out of the piezo disk. You need to solder the cable at one end to each side of the disk; for the disks linked above, that would be one solder connection anywhere on the metal backing, and one on the visible disk material. For a somewhat more sophisticated project, add a preamplifier circuit and a line for power for it. Putting a preamplifier right with the transducer helps reduce transmission loss, especially if you want to use a long cable. Another unlubricated condom can be used to cast the disk and exposed cable connections (and pre-amp, if it is used) with some casting material (urethane, epoxy, or silicone caulk in order of preference). At the other end, add a signal connector for your equipment. You will likely need an amplifier to go between a piezo disk hydrophone and a recorder. Radio Shack's < Mini Audio Amplifier > has adjustable gain, a speaker, and a headphone jack for $15. If you use it, you'll want to put an 1/8" mini-plug end on the hydrophone, and get a 1/8" mini-plug cable to go to your recorder. The RS amp is also useful to check out function of components simply by listening to the speaker output. Toting up, let's say $5 for piezo disks and shipping, $10 for coax cable, $15 for the mini amp, $5 for the plug for the cable, $5 for a connecting cable, and $10 for casting material. That's about $50 for a do-it-yourself hydrophone system.

I'll discuss getting better recordings and how the price goes up for that later.
Posted by: Richardthughes on June 30 2010,11:20

Quote mine in 3...2...1

< http://www.eurekalert.org/pub_releases/2010-06/afot-tbt062910.php >



---------------------QUOTE-------------------
Turning back the cellular clock
Tel Aviv University develops method for tracking adult stem cells as they regress
 
Cell reprogramming calls The Curious Case of Benjamin Button to mind.

---------------------QUOTE-------------------





Reprogramming = computer!!!!11111one
Posted by: Reed on July 10 2010,21:20

< A new endosymbiotic relationship appears in fruit flies > ?

I'm sure ID predicted this.
Posted by: Timothy McDougald on July 10 2010,23:50

< Yikes, us primates are doomed, doomed I tells ya >



---------------------QUOTE-------------------
Researchers first recorded the incident in 2005 when a group of eight pied tamarins were feeding in a ficus tree. They then observed a margay emitting calls similar to those made by tamarin babies. This attracted the attention of a tamarin "sentinel," which climbed down from the tree to investigate the sounds coming from a tangle of vines called lianas. While the sentinel monkey started vocalizing to warn the rest of the group of the strange calls, the monkeys were clearly confounded by these familiar vocalizations, choosing to investigate rather than flee. Four other tamarins climbed down to assess the nature of the calls. At that moment, a margay emerged from the foliage walking down the trunk of a tree in a squirrel-like fashion, jumping down and then moving towards the monkeys. Realizing the ruse, the sentinel screamed an alarm and sent the other tamarins fleeing.
---------------------QUOTE-------------------



Apparently the behavior occurs in a wide variety of South American felines. I think they are transitional species to LOL cats....

Edit to add: Okay a quick search reveals this was actually published in Neotropical Primates last year. I'm not sure why it is just now hitting Science Daily.
Posted by: Reed on July 12 2010,02:00

< The Earth is younger than previously thought! >

Is the Darwinist tent is big enough to include the Young Earth Darwinists (4.467 billion) and the Old Earth Darwinsts (4.537 billion) ?
Posted by: OgreMkV on July 12 2010,12:45

< Standards Framework for K-12 Science - Public Comments Open >

This link takes you to a proposed draft document for national level science standards.  The document is open for public comment from now until August 2nd.

A survey will be posted in a few days.

I would appreciate any with strong interest and/or training in science or education reading this (long) document and making any comments for improvement that you can find.

Wes, might it be possible to post this to the PT main page?

Thanks
Posted by: Raevmo on July 12 2010,17:35

< The end of gravity? >

Now is the time to buy those mcdonalds stock options, before the rest of the world learns that weight is just an illusion...
Posted by: Henry J on July 12 2010,22:20



---------------------QUOTE-------------------
Is the Darwinist tent is big enough to include the Young Earth Darwinists (4.467 billion) and the Old Earth Darwinsts (4.537 billion) ?
---------------------QUOTE-------------------


What's 60 million years between friends? (If I did the math right.)

Henry
Posted by: midwifetoad on July 13 2010,19:32

< http://www.youtube.com/watch?v=gFwgblszf6s >
Posted by: Timothy McDougald on July 13 2010,21:19

< Similar patterns of cortical expansion during human development and evolution >

Here is the abstract:


---------------------QUOTE-------------------
The cerebral cortex of the human infant at term is complexly folded in a similar fashion to adult cortex but has only one third the total surface area. By comparing 12 healthy infants born at term with 12 healthy young adults, we demonstrate that postnatal cortical expansion is strikingly nonuniform: regions of lateral temporal, parietal, and frontal cortex expand nearly twice as much as other regions in the insular and medial occipital cortex. This differential postnatal expansion may reflect regional differences in the maturity of dendritic and synaptic architecture at birth and/or in the complexity of dendritic and synaptic architecture in adults. This expression may also be associated with differential sensitivity of cortical circuits to childhood experience and insults. By comparing human and macaque monkey cerebral cortex, we infer that the pattern of human evolutionary expansion is remarkably similar to the pattern of human postnatal expansion. To account for this correspondence, we hypothesize that it is beneficial for regions of recent evolutionary expansion to remain less mature at birth, perhaps to increase the influence of postnatal experience on the development of these regions or to focus prenatal resources on regions most important for early survival.
---------------------QUOTE-------------------



The article is open access.
Posted by: Schroedinger's Dog on July 14 2010,03:37

Quote (midwifetoad @ July 14 2010,01:32)
< http://www.youtube.com/watch?v=gFwgblszf6s >
---------------------QUOTE-------------------


WTF?!?

Ok, the "Evil Owl" is pretty disturbing...
Posted by: Albatrossity2 on July 14 2010,09:22

Quote (Schroedinger's Dog @ July 14 2010,03:37)
Quote (midwifetoad @ July 14 2010,01:32)
< http://www.youtube.com/watch?v=gFwgblszf6s >
---------------------QUOTE-------------------


WTF?!?

Ok, the "Evil Owl" is pretty disturbing...
---------------------QUOTE-------------------


Not evil! It is merely trying to disguise itself as a dead snag or stick. The squinty eyes are a nice touch.

BTW, I've finally been able to ID this owl. It is the Southern White-faced Owl (Ptilopsis granti), native to the southern half of Africa.
Posted by: OgreMkV on July 14 2010,22:31

Quote (Albatrossity2 @ July 14 2010,09:22)
Quote (Schroedinger's Dog @ July 14 2010,03:37)
Quote (midwifetoad @ July 14 2010,01:32)
< http://www.youtube.com/watch?v=gFwgblszf6s >
---------------------QUOTE-------------------


WTF?!?

Ok, the "Evil Owl" is pretty disturbing...
---------------------QUOTE-------------------


Not evil! It is merely trying to disguise itself as a dead snag or stick. The squinty eyes are a nice touch.

BTW, I've finally been able to ID this owl. It is the Southern White-faced Owl (Ptilopsis granti), native to the southern half of Africa.
---------------------QUOTE-------------------


Thank you, that's been buggin the heck out me for weeks.
Posted by: Richardthughes on July 15 2010,08:46

Look at all that FSCCSCFCSCI:

< http://www.newscientist.com/article....ne-news >
Posted by: rhmc on July 17 2010,21:00

i'm taking the 100' seine out in the morn to one of the barrier islands (tybee) to see what we can see.

hand to hand combat with edible stuff.  :)


on the hydrophone front, the state has shutdown the program i wanted to broach that idea to.

perhaps next year....
Posted by: Kattarina98 on July 21 2010,04:45


Gymnocephalus ambriaelacus - Ammersee-Barsch
< http://tinyurl.com/37x3vqc >
The student has not yet published his thesis, so you must excuse this quote from a Bavarian rag. The article says they have discovered a new species found only in this glacial lake - that means the species can't be older than 10 000 years.
We Bavarians always had a special relationship with God - the Creator - the Designer, but imagine he-she-it-they descended to Bavaria just to create our very own species - whow!
Posted by: Schroedinger's Dog on July 21 2010,04:52



---------------------QUOTE-------------------
but imagine he-she-it-they descended to Bavaria just to create our very own species
---------------------QUOTE-------------------



And probably try out some of your oh-so-delicious beers. If not, he/she/it/they're not half the Creator they should be!
Posted by: Kattarina98 on July 21 2010,05:27

Quote (Schroedinger's Dog @ July 21 2010,04:52)
 

---------------------QUOTE-------------------
but imagine he-she-it-they descended to Bavaria just to create our very own species
---------------------QUOTE-------------------



And probably try out some of your oh-so-delicious beers. If not, he/she/it/they're not half the Creator they should be!
---------------------QUOTE-------------------


The Creator's choice:
< http://www.augustiner-braeu.de/enabfrage.html >
Posted by: Schroedinger's Dog on July 21 2010,05:30

Quote (Kattarina98 @ July 21 2010,11:27)
Quote (Schroedinger's Dog @ July 21 2010,04:52)
 

---------------------QUOTE-------------------
but imagine he-she-it-they descended to Bavaria just to create our very own species
---------------------QUOTE-------------------



And probably try out some of your oh-so-delicious beers. If not, he/she/it/they're not half the Creator they should be!
---------------------QUOTE-------------------


The Creator's choice:
< http://www.augustiner-braeu.de/enabfrage.html >
---------------------QUOTE-------------------


I have to try the Maximator and Heller Bock...
Posted by: qetzal on July 21 2010,13:26

Quote (Kattarina98 @ July 21 2010,04:45)
The article says they have discovered a new species found only in this glacial lake - that means the species can't be older than 10 000 years.
---------------------QUOTE-------------------


I hate to be pedantic,* but since this is the Science Break thread, I feel compelled to point out that the above species could actually be very old and merely died out everywhere else after colonizing that lake.


*OK, yes, I actually enjoy being pedantic, to the frequent annoyance of my wife.
Posted by: ppb on July 21 2010,14:14

Quote (Kattarina98 @ July 21 2010,05:45)

Gymnocephalus ambriaelacus - Ammersee-Barsch
< http://tinyurl.com/37x3vqc >
The student has not yet published his thesis, so you must excuse this quote from a Bavarian rag. The article says they have discovered a new species found only in this glacial lake - that means the species can't be older than 10 000 years.
We Bavarians always had a special relationship with God - the Creator - the Designer, but imagine he-she-it-they descended to Bavaria just to create our very own species - whow!
---------------------QUOTE-------------------


I did my best reading the newspaper article using my rusty German, then did some googling and found the actual paper < here >, in English.
It's in the July 2010 issue of SPIXIANA, published by the Zoologische Staatssammlung München.

ETA: When I lived in Tübingen, my favorite brew was Dinkelacker CD-Pils.  Sadly, I can't seem to find it anymore here in the US.
Posted by: Kattarina98 on July 21 2010,15:56

Quote (ppb @ July 21 2010,14:14)
I did my best reading the newspaper article using my rusty German, then did some googling and found the actual paper < here >, in English.
It's in the July 2010 issue of SPIXIANA, published by the Zoologische Staatssammlung München.

ETA: When I lived in Tübingen, my favorite brew was Dinkelacker CD-Pils.  Sadly, I can't seem to find it anymore here in the US.
---------------------QUOTE-------------------


Great Google-Fu! Obviously, I gave up too early.

And quetzal, thanks for being pedantic; actually it makes sense. So the Creator allowed the species to survive in the Ammersee just for us.
Posted by: fnxtr on July 22 2010,14:20

A few of my long-suffering friends are hoping this can help them:

< Botanical progesterone??? >
Posted by: Richardthughes on July 23 2010,13:11

I like Kurzweil, but I'm not a fan of making your own laws up:

< http://www.kurzweilai.net/kurzwei....returns >

Even if they do violates teh_slot.
Posted by: ppb on July 27 2010,08:41

Sean B. Carroll has a nice article in the New York Times about Ediacaran fossils.

< http://www.nytimes.com/2010....science >
Posted by: dvunkannon on July 27 2010,09:42

Quote (Richardthughes @ July 23 2010,14:11)
I like Kurzweil, but I'm not a fan of making your own laws up:

< http://www.kurzweilai.net/kurzwei....returns >

Even if they do violates teh_slot.
---------------------QUOTE-------------------


He is just renaming FSCI as order!
Posted by: dvunkannon on July 27 2010,09:44

Gentle reminder from Riccardo Poli...

[QUOTE]Hi,  I'm a co-editor of a special issue of the Journal of Genetic Programming and Evolvable Machines which looks back at past progress and future possibilities in this amazing area of computer science and machine intelligence. Among lots of goodies it includes a review of human competitive results obtained via genetic programming! The special issue is FREE for people to download **until the end of July**.
Please, see  http://www.springerlink.com/content/h46r77k291rn/?p=bfaf36a87f704d5cbcb66429f9c8a808&pi=0

Many thanks
Riccardo

PS: if you are interested in learning more about genetic programming have a look at the FREE BOOK entitled "A field guide to genetic programming" which is available from www.gp-field-guide.org.uk
Posted by: Richardthughes on July 28 2010,10:45

< http://vimeo.com/13457383 >

Coolness!
Posted by: Richardthughes on July 28 2010,12:19

< http://ia360702.us.archive.org/23....ife.mp3 >
Posted by: Schroedinger's Dog on July 28 2010,12:22

Quote (Richardthughes @ July 28 2010,16:45)
< http://vimeo.com/13457383 >

Coolness!
---------------------QUOTE-------------------


Yeah, right. Do you have anything cooler to watch? Like, anything? Say, a drunk stripper skydiving while playing the banjo?

Because short of that, this is one of the coolest things I've ever seen!

Fluids mechanics rulez big time!!!

Thanks a lot for the linkk Rich!

EDIT: although it reminds me a lot of Cinema 4D's dynamics pluggin...
Posted by: Richardthughes on July 30 2010,13:33

< http://www.springerlink.com/content/60814261078l485q/ >
Posted by: fnxtr on July 30 2010,16:33

Quote (Richardthughes @ July 30 2010,11:33)
< http://www.springerlink.com/content/60814261078l485q/ >
---------------------QUOTE-------------------


AUGHHHHHHHHHHHHHH!!!!

Sorry I have zero patience for the "how do we know anything is true" onanism.
Posted by: midwifetoad on Aug. 03 2010,14:30

Don't know if this has been posted before. but the link comes via ERV.

< http://www.plospathogens.org/article....1001005 >

Can't wait to see Hunter's take.
Posted by: skeptic reborn on Aug. 03 2010,19:15

Quote (midwifetoad @ Aug. 03 2010,14:30)
Don't know if this has been posted before. but the link comes via ERV.

< http://www.plospathogens.org/article....1001005 >

Can't wait to see Hunter's take.
---------------------QUOTE-------------------


OH, how I love OpenAccess!  Thanks for this link.
Posted by: JLT on Aug. 11 2010,07:34

< Brainless slime mould makes decisions like humans >
Posted by: J-Dog on Aug. 11 2010,08:01

Quote (JLT @ Aug. 11 2010,07:34)
< Brainless slime mould makes decisions like humans >
---------------------QUOTE-------------------


Rats... I expected an article about Sal Cordova...
Posted by: Albatrossity2 on Aug. 11 2010,08:39

Quote (J-Dog @ Aug. 11 2010,08:01)
Quote (JLT @ Aug. 11 2010,07:34)
< Brainless slime mould makes decisions like humans >
---------------------QUOTE-------------------


Rats... I expected an article about Sal Cordova...
---------------------QUOTE-------------------


Hey, that's an insult to slime molds!
Posted by: dvunkannon on Aug. 11 2010,10:45

Driving to work today, I was thinking about vesicle division - what would drive the splitting of a big vesicle into two small ones. By vesicles here, I'm considering the protocells of some chemistry bounded by a lipid bi-layer, such as is mooted as an early step in OOL.

First, it wasn't obvious to me why a vesicle would ever split at all. Why not keep growing?

The first process I thought of was something that would expel a good amount of the volume of the vesicle while leaving the lipid surface intact. As volume goes down, splitting into two spheres makes energetic sense. Perhaps some regulatory circuit detects that the interior of the vesicle is getting too watery, and in response water is pushed out.

It might work, but I didn't think it was too realistic. When bacteria divide, do the daughter cells have significantly less volume than the parent?

So my second idea was simply that the vesicle produces too much of the lipid 'skin' in relation to its rate of production of the vesicle contents. Assume there is a primitive genome that codes for proteins that build lipids or are vesicle contents. In the genome, there is a fixed ratio of lipid to content protein genes. But as the vesicle grows, it needs less and less skin for a given amount of content (cube/square law in action). If the vesicle continues to produce lipids and contents in arithmetic rather than geometric ratio, it will be making too much skin. At some point, the best use of all that skin is to invaginate and split.

I like this second explanation because it is very simple and mechanical in nature. The vesicle is just minimizing the energy of the physical system when it splits, no fancy  awareness of accumulating resources hitting some magic level that says "it is now safe to split."

Comments? I have no idea if this is already a commonplace idea.
Posted by: midwifetoad on Aug. 11 2010,11:46

In the spirit of BA77 I would point out that Szostac has a video on this.

< http://www.youtube.com/watch?v=U6QYDdgP9eg >
Posted by: Henry J on Aug. 11 2010,14:17

At a guess, if a cell just keeps growing instead of splitting, then when it dies, there's no descendants. If it splits, chances of descendants being around for a while goes up.

Henry
Posted by: dvunkannon on Aug. 11 2010,15:16

Quote (midwifetoad @ Aug. 11 2010,12:46)
In the spirit of BA77 I would point out that Szostac has a video on this.

< http://www.youtube.com/watch?v=U6QYDdgP9eg >
---------------------QUOTE-------------------


Well, it is CDK007's video about Szostak's work, but we are splitting vesicles, not hairs!
Posted by: ppb on Aug. 11 2010,15:23

Looks like Afarensis figured out that you need to bang the rocks together.


< Lucy species used stone tools >.

ETA: Nature article < here >.
Posted by: Timothy McDougald on Aug. 11 2010,18:49

That's right! We gave you bipedalism, a trend of increasing brain size, and tools and sent you out into the world to earn your fortune and do we get as much as a phone call or a card :angry:    Homos!
Posted by: J-Dog on Aug. 11 2010,21:29

Quote (afarensis @ Aug. 11 2010,18:49)
That's right! We gave you bipedalism, a trend of increasing brain size, and tools and sent you out into the world to earn your fortune and do we get as much as a phone call or a card :angry:    Homos!
---------------------QUOTE-------------------


Amen & tell it brother!
Posted by: ppb on Aug. 12 2010,07:43

Quote (afarensis @ Aug. 11 2010,19:49)
That's right! We gave you bipedalism, a trend of increasing brain size, and tools and sent you out into the world to earn your fortune and do we get as much as a phone call or a card :angry:    Homos!
---------------------QUOTE-------------------


Bipedalism?  That's so last eon.  What have you done for us lately grandpa?

Ha ha, this is you!


Posted by: dvunkannon on Aug. 13 2010,11:57

< What has Neptune got in his Trojan? >
Posted by: Henry J on Aug. 13 2010,21:39

A trident?
Posted by: Richardthughes on Aug. 17 2010,15:38

Oleg: You're next!

< http://www.youtube.com/watch?v=yiPsU13M6ek&feature=related >
Posted by: Quack on Aug. 18 2010,11:11

Quote (ppb @ Aug. 11 2010,15:23)
Looks like Afarensis figured out that you need to bang the rocks together.


[URL=http://news.yahoo.com/s/ap/20100811/ap_on_sc/us_sci_earliest_tools;_ylt=AsEi_Hka6b0j6S7HUOjDqB0PLBIF;_ylu=X3oDMTJtYmtsbDRmBGFzc2V0A2FwLzIwMTAwODExL3VzX3NjaV9lYXJsaWVzdF90b29scwRjcG9zAzEEcG9zAzIEc2

VjA3luX3RvcF9zdG9yeQRzbGsDbHVjeXNwZWNpZXN1]Lucy species used stone tools[/URL].

ETA: Nature article < here >.
---------------------QUOTE-------------------


A chimp at zoo in Stockholm collecting pile of rocks in the morning in preparation for visitors.
Posted by: midwifetoad on Aug. 25 2010,14:00

< http://www.cosmosmagazine.com/news....eretics >



---------------------QUOTE-------------------
SYDNEY: In the hallowed pages of this week's edition of Nature is a paper destined to reignite the flames of a fiery debate that has troubled every generation of biologists since Charles Darwin.

Paying short shrift to the idea of 'kin selection' - which has formed the cornerstone of sociobiological theory for almost half a century - the authors of the offending article propose a contentious new model to explain the evolution of 'eusociality'.

---------------------QUOTE-------------------


Posted by: Henry J on Aug. 25 2010,21:40

I wonder if multicellularity could be regarded as a side effect of kin selection?

Henry
Posted by: Timothy McDougald on Sep. 04 2010,10:03

Oh, sure but can they LOL? < Researchers Create 'Quantum Cats' Made of Light >:



---------------------QUOTE-------------------
The NIST experiments, described in a forthcoming paper, repeatedly produced light pulses that each possessed two exactly opposite properties -- specifically, opposite phases, as if the peaks of the light waves were superimposed on the troughs. Physicists call this an optical Schrödinger's cat. NIST's quantum cat is the first to be made by detecting three photons at once and is one of the largest and most well-defined cat states ever made from light. (Larger cat states have been created in different systems by other research groups, including one at NIST.)
---------------------QUOTE-------------------


Posted by: OgreMkV on Sep. 06 2010,22:06

Where's the intelligent design in this?  When did the intelligent designer act?  

This is a novel new structure that has not existed before.

< http://news.nationalgeographic.com/news....th-eggs >

Some members of the species of yellow-bellied three-toed skink has developed a placenta-like structure and is giving birth to live young rather than laying eggs as the rest of the species does.

This is so cool.
Posted by: Schroedinger's Dog on Sep. 07 2010,01:38

Already covered < here >, with the mandatory link to UD's "debunking"...

:)
Posted by: dvunkannon on Sep. 07 2010,13:10

< Definitions of evolution that fit in a Tweet >
Posted by: Schroedinger's Dog on Sep. 08 2010,19:13

< New dino-freak discovered. >
Posted by: dvunkannon on Sep. 09 2010,05:38

< Great White Sharks: Not just for breakfast anymore! >

Nice example of animal learning and communication.
Posted by: Albatrossity2 on Sep. 09 2010,06:53

< The Designer Universe >

Can't wait until Sal hears about this!
Posted by: dheddle on Sep. 09 2010,07:23

Quote (Albatrossity2 @ Sep. 09 2010,06:53)
< The Designer Universe >

Can't wait until Sal hears about this!
---------------------QUOTE-------------------


That article sho' is sciency. I like the certainty with which it declares:

Despite the colossal amount of energy contained in every atom of matter, it is precisely balanced by the negativity of gravity.

I am the only one who is perpetually annoyed by gravity's incessant negativity? Anyhow, that was some impressive cosmological survey (that I must have missed reading about) that concluded the total energy of the universe is precisely zero.
Posted by: carlsonjok on Sep. 09 2010,07:50

Quote (dheddle @ Sep. 09 2010,07:23)
That article sho' is sciency. I like the certainty with which it declares:

Despite the colossal amount of energy contained in every atom of matter, it is precisely balanced by the negativity of gravity.

I am the only one who is perpetually annoyed by gravity's incessant negativity?
---------------------QUOTE-------------------


Gravity is alot like The Man ™.  Always keeping you down.
Posted by: Richardthughes on Sep. 09 2010,08:57

Quote (carlsonjok @ Sep. 09 2010,07:50)
Quote (dheddle @ Sep. 09 2010,07:23)
That article sho' is sciency. I like the certainty with which it declares:

Despite the colossal amount of energy contained in every atom of matter, it is precisely balanced by the negativity of gravity.

I am the only one who is perpetually annoyed by gravity's incessant negativity?
---------------------QUOTE-------------------


Gravity is alot like The Man ™.  Always keeping you down.
---------------------QUOTE-------------------




Posted by: dvunkannon on Sep. 10 2010,22:40

I just posted a version of the following on one of the threads on Cornelius Hunter's blog. The context was discussion of the Nilsson and Pelger model of eye evolution. I'd appreciate comments here or there.




OK, lets try to build an eye!

As a target our eye will be a ball of cells, roughly spherical, about 1,000 cells in radius. A ball of cells that size is just under 2^32 cells (4 gigacells, FWIW). The surface area of one hemisphere (about 6 and a quarter megacells) will be the retina.

Starting from one 'stem cell', we would have to double the cells 32 times. Since we can count up to 32 in 5 bits, we can use 5 cell signals to handle growing the ball of cells.

In addition we want to keep track of where we started (the tip of a nerve, lets say), so we nned another signal to create a gradient from the nerve ending to the surface of the body. We'll also want a gradient that goes from the center of the ball outwards.

The stem cells can differentiate into pigment cells, opsin cells, or crystallin cells.

After 32 doublings, the back hemisphere surface of the ball expresses the dark pigment (and recruits some blood vessels and more nerve endings). The pigment layer prevents light from entering the eye from the back, which might happen if the rest of the animal's body is thin or transparent.

The next inward layer of cells from these pigment cells differeniates into opsin loaded retinal cells that will transduce the light entering the eye from the front.

The lens forms at the far end of the gradient that began at the nerve ending.

Once the lens, retina, and pigment layer have formed, the rest of the cells in the interior of the ball get the signal to die, and thus form the clear ocular fluid.

So the basic substance of the eye can be made with less than a dozen signals and a stem cell that can differentiate into three daughter types, each of which specializes in producing one of three proteins.

The nerves that attach to the retina also need to be patterned. A very simple pattern can be created with two gradients (up-down, and left-right), but you could also overlay that with a counter based gradient. With 10 signals, we can count up to 1,000 (2^10 = 1024). We'll need 20 signals then, 10 for each axis. These same signals can get reused in the brain, where we will lay out a pattern of nerves that matches the pattern at the back of the retina, and makes the transduced image available to the rest of the brain for further processing.

That is a brief sketch. It assumes the genetic signalling and protein making functions are already available, what is really evolving is the developmental network.
Posted by: Henry J on Sep. 10 2010,23:38

I'd think the target would be in terms of effectiveness in identifying objects or motion, rather than size of the equipment used to do so.

Henry
Posted by: dvunkannon on Sep. 11 2010,07:18

Quote (Henry J @ Sep. 11 2010,00:38)
I'd think the target would be in terms of effectiveness in identifying objects or motion, rather than size of the equipment used to do so.

Henry
---------------------QUOTE-------------------


Nilsson and Pelger's paper does use visual acuity to drive the selection process across all scales of eye evolution.

What I'm trying to bring out here is that evolving an eye doesn't mean evolving the placement of each cell individually, and that the developmental program which puts one cell in the right place can be scaled up to one that puts several million in the right place through stepwise refinements.
Posted by: skeptic reborn on Sep. 11 2010,21:05

unless the heavy lifting is done in the paper, I see some rather vague hand-waving here.  I think you need to tighten this up quite a bit before it's really usable for discussion.
Posted by: dvunkannon on Sep. 12 2010,22:06

Quote (skeptic reborn @ Sep. 11 2010,22:05)
unless the heavy lifting is done in the paper, I see some rather vague hand-waving here.  I think you need to tighten this up quite a bit before it's really usable for discussion.
---------------------QUOTE-------------------


Could you be clearer about which portions need to be more precise?

Nilsson and Pelger's paper is clear about the calculation of visual acuity for selection, but outlines a different model entirely for eye evolution. In that paper, no effort is made to sketch the developmental program of the eye, or how it must have changed gradually. Instead, they focus (sorry for the pun) entirely on the final morphology of the eye, and assume it could change gradually from generation to generation.
Posted by: midwifetoad on Sep. 14 2010,12:37



---------------------QUOTE-------------------
BOSTON – An infectious-disease nightmare is unfolding: Bacteria that have been made resistant to nearly all antibiotics by an alarming new gene have sickened people in three states and are popping up all over the world, health officials reported Monday.

The U.S. cases and two others in Canada all involve people who had recently received medical care in India, where the problem is widespread. A British medical journal revealed the risk last month in an article describing dozens of cases in Britain in people who had gone to India for medical procedures.
...
Scientists have long feared this — a very adaptable gene that hitches onto many types of common germs and confers broad drug resistance, creating dangerous "superbugs."


---------------------QUOTE-------------------



< http://news.yahoo.com/s/ap/20100914/ap_on_he_me/us_med_superbug_gene >
Posted by: Richardthughes on Sep. 16 2010,16:42

User's guide to Design Arguments:

< http://commonsenseatheism.com/wp-cont....nts.pdf >
Posted by: dheddle on Sep. 16 2010,17:07

Quote (Richardthughes @ Sep. 16 2010,16:42)
User's guide to Design Arguments:

< http://commonsenseatheism.com/wp-cont....nts.pdf >
---------------------QUOTE-------------------


Arggh.

Why doesn't anyone listen to me when I get on my soapbox and shout: the fine-tuning argument is strongest when the probability of the constants is high (especially unity) not when low. Low probability is what the multiverse predicts. How can that be good for the fine tuning argument?

Also--another unfair bias will show here--I have long proposed a Bayes's Theorem theorem--which is that with sufficiently inscrutable assumptions anything can be demonstrated with Bayes's theorem.

Like the Heisenberg Uncertainty Principle, it should be illegal for theologians, philosophers, and F1 drivers to invoke Bayes's Theorem.

And it should be Bayes's, not Bayes'. It's Gauss's Law, not Gauss'. Oh, and another thing...
Posted by: dheddle on Sep. 16 2010,17:13

< Some REAL science news. >
Posted by: Rob R. on Sep. 16 2010,17:56

Quote (dheddle @ Sep. 16 2010,17:13)
< Some REAL science news. >
---------------------QUOTE-------------------


Your brother?
Posted by: dheddle on Sep. 16 2010,19:02

Quote (Rob R. @ Sep. 16 2010,17:56)
Quote (dheddle @ Sep. 16 2010,17:13)
< Some REAL science news. >
---------------------QUOTE-------------------


Your brother?
---------------------QUOTE-------------------


No--I don't know him. I started getting email intended for him.
Posted by: Rob R. on Sep. 16 2010,19:24

Quote (dheddle @ Sep. 16 2010,19:02)
Quote (Rob R. @ Sep. 16 2010,17:56)
Quote (dheddle @ Sep. 16 2010,17:13)
< Some REAL science news. >
---------------------QUOTE-------------------


Your brother?
---------------------QUOTE-------------------


No--I don't know him. I started getting email intended for him.
---------------------QUOTE-------------------


Okay... but,

<a href=http://www.pcs.cnu.edu/faculty/heddle/>original Heddle</a>

<a href=http://www.riken.go.jp/engn/r-world/research/lab/asi/heddle/index.html>other Heddle</a>

You can see, besides the name, how I was confused.  Same little peanut head.  Just sayin'.

:p
Posted by: dvunkannon on Sep. 17 2010,08:35

< Self editing proteins >

Another OOL way for proteins to kickstart life without much reliance on nucleotides?
Posted by: Richardthughes on Sep. 17 2010,09:28

Quote (dheddle @ Sep. 16 2010,17:07)
Why doesn't anyone listen to me when I get on my soapbox and shout: the fine-tuning argument is strongest when the probability of the constants is high (especially unity) not when low.
---------------------QUOTE-------------------


Well high probability doesn't speak to "not by chance" very much...  ???
Posted by: Reciprocating Bill on Sep. 17 2010,10:20

Quote (Richardthughes @ Sep. 16 2010,17:42)
User's guide to Design Arguments:

< http://commonsenseatheism.com/wp-cont....nts.pdf >
---------------------QUOTE-------------------


I have several times remarked on the tensions underscored in this paper.

Thanks, RTH.
Posted by: Richardthughes on Sep. 17 2010,10:36

Quote (Reciprocating Bill @ Sep. 17 2010,10:20)
Quote (Richardthughes @ Sep. 16 2010,17:42)
User's guide to Design Arguments:

< http://commonsenseatheism.com/wp-cont....nts.pdf >
---------------------QUOTE-------------------


I have several times remarked on the tensions underscored in this paper.

Thanks, RTH.
---------------------QUOTE-------------------


Always welcome. I'd be remiss if I didn't share this with you:

< http://philosophicaldisquisitions.blogspot.com/2010....st.html >
Posted by: Richardthughes on Sep. 17 2010,11:13

< http://www.theaustralian.com.au/news....5241955 >
Posted by: dvunkannon on Sep. 17 2010,12:13

Quote (Reciprocating Bill @ Sep. 17 2010,11:20)
Quote (Richardthughes @ Sep. 16 2010,17:42)
User's guide to Design Arguments:

< http://commonsenseatheism.com/wp-cont....nts.pdf >
---------------------QUOTE-------------------


I have several times remarked on the tensions underscored in this paper.

Thanks, RTH.
---------------------QUOTE-------------------


I like the paper's approach, and it does a good job of putting this tension on display.

I disagree that if any definite value could be defined for the probability they discuss, then theistic apologists would be on better ground. There would just be a regress to the prior assumptions, such as why a personal agent is more explanatory than an impersonal agent, and why the vague sense of "good" that we as humans have can be imputed to God's actions. Given the facts of the world, it is just as possible, or more possible, that God's idea of good is more aligned with what good means to termites, or praying mantises, or bacteria, than with humans.
Posted by: Henry J on Sep. 17 2010,13:04



---------------------QUOTE-------------------
termites, or praying mantises, or bacteria,
---------------------QUOTE-------------------


And beetles! don't forget beetles!  :)
Posted by: fnxtr on Sep. 17 2010,13:41

Quote (Henry J @ Sep. 17 2010,11:04)


---------------------QUOTE-------------------
termites, or praying mantises, or bacteria,
---------------------QUOTE-------------------


And beetles! don't forget beetles!  :)
---------------------QUOTE-------------------


Especially Ringo. He was the nice, quiet boy.
Posted by: Lou FCD on Sep. 17 2010,18:44

< Heart Sickening >

Oil spill news: Species-by-species tally released



---------------------QUOTE-------------------
Oil spill news: Species-by-species tally released

This week we were encouraged to see that the U.S. Fish and Wildlife Service has begun posting counts of bird species  that have been recovered in the Gulf of Mexico during the oil spill. The first such report lists 4,676 individuals representing some 85 species, plus another 19 categories for incompletely identified birds.
---------------------QUOTE-------------------



More at the link.
Posted by: Lou FCD on Sep. 17 2010,18:57

Quote (Henry J @ Sep. 17 2010,14:04)


---------------------QUOTE-------------------
termites, or praying mantises, or bacteria,
---------------------QUOTE-------------------


And beetles! don't forget beetles!  :)
---------------------QUOTE-------------------


"An inordinate fondness" is such a wonderful turn of phrase...
Posted by: skeptic reborn on Sep. 19 2010,00:43

Quote (Reciprocating Bill @ Sep. 17 2010,10:20)
Quote (Richardthughes @ Sep. 16 2010,17:42)
User's guide to Design Arguments:

< http://commonsenseatheism.com/wp-cont....nts.pdf >
---------------------QUOTE-------------------


I have several times remarked on the tensions underscored in this paper.

Thanks, RTH.
---------------------QUOTE-------------------


Very nice post.  This will occupy me for a good day or two.  Thanks.

One thing I'm seeing after the premises are defined could be a quick resolution.  I'll lay it out now for discussion and see if it still rings true by the time I finish the rest of the paper.

Namely, the tension is one of false definition.  Whether through intent of the authors or selection of the source definitions, the prospect that P© and P(B) are inversely proportional is incorrect.  In fact, they are correlated and BDA is merely a subset of FTA.  The misconception lies in the belief that the BDA requires an inhospitable universe, it does not.  The existance of complex life anywhere still begs the questions How and further supports the FTA.  By virtue of the hypothetical fine-tuning the possiblity of complex life proceeds from 0 towards 1.  Any increase in the P(B) does not in any way diminish P© because the range of fundamental values follows an infinite continuum and impact conditions that, while including those required for complex life, define the entire structure of the universe.  Any alteration of the value set for the fundamental properties would decrease the P(B), or at least in our current understanding of life.  Any other proposed forms of life are completely hypothetical and beyond assignment of quantitative probability.

So, in short, P(B) is only defined when C has occurred.  Or said differently, if the universe were not fine-tuned for life, i.e. possessing certain fundamental values making life possible, then the possibility of biologically complex life, as we know it, would be zero.  In the truest sense P(B) is a boolean quantity.  Further, in order to prove otherwise, one would need to compile alternate values referred to by the FTA and contemplate life forms under those conditions, and assess the probability of those life forms emerging.  The lack of credible relavent information renders this impossible but the exercise may be interesting, none the less.

Personally, this is where I see the failure of all such fine-tuning or design arguments.  Ultimately, they always become circular alternate data sets do not occur and their completely hypothetical and untestable nature renders any comparison impossible.  As a consequence, the strength of the FTA (+BDL) is completely undercut in the same way irreducible complexity et. al. are lacking.

Anyway, these are my immediate thoughts 11 pages in, I'll see how they compare at the end.
Posted by: Schroedinger's Dog on Sep. 24 2010,05:52

< Red sea parting explained??? >

Sadly, some more fuel for the literalist creotards...
Posted by: dvunkannon on Sep. 27 2010,11:51

< Evolution of lignin biosynthesis >

Besides being cool, this got me thinking about carbon sequestration. Lignin is a great way to sequester carbon. That's what the Carboniferous period was all about - plants evolved lignin and nothing was around that could eat it, so it just piled up and got buried.

Why can't we insert those lignin producing genes in a bacteria, amp them up a bit so that they are hard to eat (again), and start dumping it into a handy marine trench? Send my Nobel Prize to dvunkannon at Science Break dot Antievolution dot com. :)
Posted by: midwifetoad on Sep. 28 2010,20:11

< http://arxiv.org/PS_cache/arxiv/pdf/1009/1009.2634v1.pdf >

Evolution of National Nobel Prize Shares in the 20th Century
Posted by: fnxtr on Sep. 28 2010,23:25

Quote (Schroedinger's Dog @ Sep. 24 2010,03:52)
< Red sea parting explained??? >

Sadly, some more fuel for the literalist creotards...
---------------------QUOTE-------------------


That's some stretch.

Next: The Air-Bag of Turin: Fact or Forgery?
Posted by: sledgehammer on Sep. 28 2010,23:38

< Genome-wide analysis of a long-term evolution experiment with Drosophila >

Last week in Nature, a Lenski-style selection experiment  w/ (sexually reproducing) D.melanogaster by  Molly K. Burke, Michael R. Rose and Anthony D. Long at UC Irvine distinguishes "soft" selection of traits involving 100s of genes from "hard sweeps" of single allele frequencies.
 From the abstract:        

---------------------QUOTE-------------------
Signatures of selection are qualitatively different than what has been observed in asexual species; in our sexual populations, adaptation is not associated with ‘classic’ sweeps whereby newly arising, unconditionally advantageous mutations become fixed.
---------------------QUOTE-------------------


Nick Wade at NYT quotes Lenski and < discusses > discusses the study w/ Michael Rose:        

---------------------QUOTE-------------------
The debate about whether evolution proceeds by altering one or many genes started 90 years ago among the three founders of population genetics, Ronald Fisher, Sewall Wright and J. B. S. Haldane. Haldane favored the single mutation mechanism, but Fisher and Wright backed multiple gene change. The fruit fly experiment “is a total vindication of Wright and Fisher and a major defeat for Haldane and a lot of conventional geneticists who have sided with him,” Dr. Rose said.

The demise of the Haldane view “is very bad news for the pharmaceutical industry in general,” Dr. Rose said. If disease and other traits are controlled by many genes, it will be hard to find effective drugs; a single target would have been much simpler.
---------------------QUOTE-------------------


and includes this subtitle for Michael Egnor's benefit        

---------------------QUOTE-------------------
A new exploration of how evolution works at the genomic level may have a significant impact on drug development and other areas of medicine.
---------------------QUOTE-------------------


Posted by: Tony M Nyphot on Sep. 30 2010,23:39

Dazed from Duvel and blithely trundling through the channels, I stumbled upon < Charlie Rose: The Brain Series >. The episode on the tube was quite fascinating. I then watched 2 more online.

Perhaps one of yarny brethren might pass the link along to the Canadian morphodyke...maybe she could learn about actual brain science and the people behind it.
Posted by: dvunkannon on Oct. 01 2010,14:42

< Cold Spring Harbor Perspectives Collection on The Origin of Life >

19 great review articles written by the best and brightest minds in OOL.
Posted by: Thought Provoker on Oct. 08 2010,16:13

Another OOL viewpoint...

< How did LUCA make a living? Chemiosmosis in the origin of life >

This sounds good to me from a quick read.

I would appreciate hearing other opinions on it.
Posted by: Lou FCD on Oct. 20 2010,18:12

Anopheles gambiae M and S strains (the mosquitoes that carry the malaria parasite) < are apparently diverging > enough to be on the verge of a speciation event.
Posted by: REC on Oct. 26 2010,10:03

Here's yet another article showing that the genome is less transcribed than earlier studies indicated. Along with the mouse studies deleting swaths of the genome with no ill effect, this kinda blows the every nucleotide is precious, there is no junk story for ID.

Most “Dark Matter” Transcripts Are Associated With Known Genes



---------------------QUOTE-------------------
We conclude that, while there are bona fide new intergenic transcripts, their number and abundance is generally low in comparison to known exons, and the genome is not as pervasively transcribed as previously reported.
---------------------QUOTE-------------------



< Link >
Posted by: keiths on Nov. 08 2010,21:59

The IDers will love this one.

< Evolution by Religious Selection: Mexican Cavefish Develop Resistance to Toxin >
Posted by: Richardthughes on Nov. 09 2010,09:22

< http://www.sciencenews.org/view....central >



---------------------QUOTE-------------------
WASHINGTON — Text messagers and computer gamers aren’t alone in the willful misspelling department. RNA molecules do it too.

RNA molecules aren’t always faithful reproductions of the genetic instructions contained within DNA, a new study shows. The finding seems to violate a tenet of genetics so fundamental that scientists call it the central dogma: DNA letters encode information and RNA is made in DNA’s likeness. The RNA then serves as a template to build proteins.

But a study of RNA in white blood cells from 27 different people shows that, on average, each person has nearly 4,000 genes in which the RNA copies contain misspellings not found in DNA.


---------------------QUOTE-------------------



I'm sure ID predicted this: The RNA of Babel.
Posted by: Henry J on Nov. 09 2010,10:21

If cells really were computers, they'd have spell checkers!!111!!!one!!!
Posted by: sledgehammer on Nov. 15 2010,10:34

To the "Information is neither matter nor energy" crowd: take note: < "Maxwell's Demon" experiment converts information to energy >  

---------------------QUOTE-------------------
For the first time, scientists have converted information into pure energy, experimentally verifying a thought experiment first proposed 150 years ago...The researchers describe their results in the Nov. 14 online edition of the journal Nature Physics.
In an accompanying essay in the same issue of the journal, physicist Christian Van den Broeck of the University of Hasselt in Belgium, who was not involved in the new study, called it "a direct verification of information-to-energy conversion."
---------------------QUOTE-------------------


I can't wait to see how some IDer will twist this into "Therefore God"

ETA: < link to pdf >
Posted by: Albatrossity2 on Nov. 15 2010,11:41

I predict the IDiots will completely misrepresent and misunderstand < this paper > in the Nov. 5 Science (may be behind a firewall for some).


---------------------QUOTE-------------------
Mutational Robustness of Ribosomal Protein Genes
Peter A. Lind, Otto G. Berg, Dan I. Andersson

The distribution of fitness effects (DFE) of mutations is of fundamental importance for understanding evolutionary dynamics and complex diseases and for conserving threatened species. DFEs estimated from DNA sequences have rarely been subject to direct experimental tests. We used a bacterial system in which the fitness effects of a large number of defined single mutations in two ribosomal proteins were measured with high sensitivity. The obtained DFE appears to be unimodal, where most mutations (120 out of 126) are weakly deleterious and the remaining ones are potentially neutral. The DFEs for synonymous and nonsynonymous substitutions are similar, suggesting that in some genes, strong fitness constraints are present at the level of the messenger RNA.
---------------------QUOTE-------------------


Posted by: dvunkannon on Nov. 15 2010,13:00

Quote (Albatrossity2 @ Nov. 15 2010,12:41)
I predict the IDiots will completely misrepresent and misunderstand < this paper > in the Nov. 5 Science (may be behind a firewall for some).
 

---------------------QUOTE-------------------
Mutational Robustness of Ribosomal Protein Genes
Peter A. Lind, Otto G. Berg, Dan I. Andersson

The distribution of fitness effects (DFE) of mutations is of fundamental importance for understanding evolutionary dynamics and complex diseases and for conserving threatened species. DFEs estimated from DNA sequences have rarely been subject to direct experimental tests. We used a bacterial system in which the fitness effects of a large number of defined single mutations in two ribosomal proteins were measured with high sensitivity. The obtained DFE appears to be unimodal, where most mutations (120 out of 126) are weakly deleterious and the remaining ones are potentially neutral. The DFEs for synonymous and nonsynonymous substitutions are similar, suggesting that in some genes, strong fitness constraints are present at the level of the messenger RNA.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


< Done There, Been That >
Posted by: Albatrossity2 on Nov. 15 2010,13:31

Quote (dvunkannon @ Nov. 15 2010,13:00)
Quote (Albatrossity2 @ Nov. 15 2010,12:41)
I predict the IDiots will completely misrepresent and misunderstand < this paper > in the Nov. 5 Science (may be behind a firewall for some).
   

---------------------QUOTE-------------------
Mutational Robustness of Ribosomal Protein Genes
Peter A. Lind, Otto G. Berg, Dan I. Andersson

The distribution of fitness effects (DFE) of mutations is of fundamental importance for understanding evolutionary dynamics and complex diseases and for conserving threatened species. DFEs estimated from DNA sequences have rarely been subject to direct experimental tests. We used a bacterial system in which the fitness effects of a large number of defined single mutations in two ribosomal proteins were measured with high sensitivity. The obtained DFE appears to be unimodal, where most mutations (120 out of 126) are weakly deleterious and the remaining ones are potentially neutral. The DFEs for synonymous and nonsynonymous substitutions are similar, suggesting that in some genes, strong fitness constraints are present at the level of the messenger RNA.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


< Done There, Been That >
---------------------QUOTE-------------------


Oooh, that'll teach me. I should read UD more often.

Well, in the true spirit of ID pre(post)dictions everywhere, the fact that my prediction came true before I predicted it means GODDIDIT!
Posted by: Richardthughes on Nov. 16 2010,13:49

E-coli solves suduku

< http://www.newscientist.com/article....ku.html >
Posted by: sledgehammer on Nov. 16 2010,16:33

Quote (Richardthughes @ Nov. 16 2010,11:49)
E-coli solves suduku

< http://www.newscientist.com/article....ku.html >
---------------------QUOTE-------------------


From the article:  

---------------------QUOTE-------------------
"If you consider an ant colony, an individual ant isn't very useful," he told New Scientist. "But if you put millions of ants together they're suddenly capable of very rich, very complex population-level behaviour. That's what we're trying to harness."
---------------------QUOTE-------------------


Something Sal will, apparently, never understand.
Posted by: ppb on Nov. 17 2010,07:56

Quote (Richardthughes @ Nov. 16 2010,14:49)
E-coli solves suduku

< http://www.newscientist.com/article....ku.html >
---------------------QUOTE-------------------


So, if you're working on a tough Sudoku puzzle, it's best to go with your gut.
Posted by: dvunkannon on Nov. 17 2010,17:06

< One pot OOL synthesis - formamide to RNA >

The money shot:


---------------------QUOTE-------------------
The production in the same chemical frame of acyclonucleotides (Saladino et al. 2003), the abiotic phosphorylation of nucleosides to yield cyclic nucleotides (Costanzo et al. 2007), their nonenzymatic polymerization to yield long RNA chains (Costanzo et al. 2009), and the non-enzymatic terminal ligation of oligomers (Pino et al. 2008; Costanzo et al. 2009) show that the whole series of events leading from a one-carbon atom precursor (NH2COH) to RNA polymers may be accomplished within a single chemical frame.
---------------------QUOTE-------------------




Big shout out of thanks to NASA for the virtual OOL workshop (read about it on PT). Many fantastic lectures available online.
Posted by: dvunkannon on Nov. 22 2010,15:09

< Bone Marks - By Design or By Chance? >

Homework question - why haven't these scientists used the Explanatory Filter?
Posted by: Henry J on Nov. 22 2010,16:55

Quote (dvunkannon @ Nov. 22 2010,14:09)
Homework question - why haven't these scientists used the Explanatory Filter?
---------------------QUOTE-------------------


They did use it, but then they flushed and went back to the lab to do some more work.
Posted by: dvunkannon on Nov. 23 2010,12:46

Quote (dvunkannon @ Nov. 22 2010,16:09)
< Bone Marks - By Design or By Chance? >

Homework question - why haven't these scientists used the Explanatory Filter?
---------------------QUOTE-------------------


< More data for the Explanatory Filter to filter >

Apparently, these elephants mining salt in a cave on Mt Elgon in Kenya fooled some 19th century biologists about the origin of the marks on the wall of the cave. Did they use the Explanatory Filter to correct themselves?

(Since the elephants visit the cave at night, direct observation of how the marks were made was difficult.)
Posted by: midwifetoad on Nov. 23 2010,13:24



---------------------QUOTE-------------------
Homework question - why haven't these scientists used the Explanatory Filter?
---------------------QUOTE-------------------



No.

EF can only be used to discern the work of imaginary entities having no attributes.
Posted by: dvunkannon on Nov. 23 2010,13:36

What could be more natural than applying the Explanatory Filter to the 9-11 Truth Movement? Building 7, was the collapse natural or designed? Come on, DDr.. Dembski, the accolades of an entirely new wing of the wingnut universe is waiting for the answer...
Posted by: Quack on Nov. 23 2010,16:26

Quote (Henry J @ Nov. 22 2010,16:55)
 
Quote (dvunkannon @ Nov. 22 2010,14:09)
Homework question - why haven't these scientists used the Explanatory Filter?
---------------------QUOTE-------------------


They did use it, but then they flushed and went back to the lab to do some more work.
---------------------QUOTE-------------------


flushed? I'd have thought they should have blushed.
Posted by: Henry J on Nov. 23 2010,21:52



---------------------QUOTE-------------------
flushed? I'd have thought they should have blushed.
---------------------QUOTE-------------------


Hey, I didn't say what they used it for! ;)

Henry
Posted by: Quack on Nov. 24 2010,12:22

Quote (Henry J @ Nov. 23 2010,21:52)
 

---------------------QUOTE-------------------
flushed? I'd have thought they should have blushed.
---------------------QUOTE-------------------


Hey, I didn't say what they used it for! ;)

Henry
---------------------QUOTE-------------------


LOL...
Posted by: Thought Provoker on Nov. 24 2010,13:10

DNA = Quantum Computers?

Some 2010 papers on that...

< DNA Replication via Entanglement Swapping >

< The relevance of continuous variable entanglement in DNA >

< Enol Tautomers of Watson-Crick Base Pair Models Are Metastable Because of Nuclear Quantum Effect >

EDIT - fixed title of third paper
Posted by: Richardthughes on Nov. 30 2010,10:59

Place your bets on the forthcomming NASA press conference:

< http://kottke.org/10/11/has-nasa-discovered-extraterrestrial-life >
Posted by: midwifetoad on Nov. 30 2010,11:09

Quote (Richardthughes @ Nov. 30 2010,10:59)
Place your bets on the forthcomming NASA press conference:

< http://kottke.org/10/11/has-nasa-discovered-extraterrestrial-life >
---------------------QUOTE-------------------




---------------------QUOTE-------------------
Update: According to Alexis Madrigal, the answer to the hyperbolic question in the headline is "no".

I'm sad to quell some of the @kottke-induced excitement about possible extraterrestrial life. I've seen the Science paper. It's not that.
---------------------QUOTE-------------------


Posted by: REC on Nov. 30 2010,11:34

Exciting! My guess is they found something "weird" here on earth.

Felisa Wolfe-Simon and Steven Benner are authors on a paper outlining the search for weird life and shadow biospheres-life on earth we wouldn't easily recognize as life. Something without DNA, or ribosomes, something not sharing common ancestry with the rest of life.

James Elser fits this too, as a biogeologist.

Davies, P. C. W. , Benner, S.A., Cleland, C.E., Lineweaver,C.H., McKay,C.P. and Wolfe-Simon, F. Signatures of a Shadow Biosphere (2009) Astrobiology. 9(2): 241-249.

doi:10.1089/ast.2008.0251.
Posted by: Thought Provoker on Nov. 30 2010,11:37

< I like this summary for my guess. >

Interesting findings which support the possibility the origin of life could have been extraterristial.

EDIT- Kudos to Richard for posting this.
Posted by: qetzal on Nov. 30 2010,16:01

Quote (Thought Provoker @ Nov. 24 2010,13:10)
DNA = Quantum Computers?

Some 2010 papers on that...

< DNA Replication via Entanglement Swapping >

< The relevance of continuous variable entanglement in DNA >

< Enol Tautomers of Watson-Crick Base Pair Models Are Metastable Because of Nuclear Quantum Effect >

EDIT - fixed title of third paper
---------------------QUOTE-------------------


Interesting papers; thanks for the links!

However, I'm not sure what they have to do with quantum computers. They describe how quantum effects may be important in base pairing, replication, & duplex stability. I don't see the relevance to quantum computing, other than perhaps "computing" which bases should pair with one another.
Posted by: keiths on Nov. 30 2010,18:47



---------------------QUOTE-------------------
< Complexity not so costly after all, analysis shows >

ANN ARBOR, Mich.—The more complex a plant or animal, the more difficulty it should have adapting to changes in the environment. That's been a maxim of evolutionary theory since biologist Ronald Fisher put forth the idea in 1930.

But if that tenet is true, how do you explain all the well-adapted, complex organisms—from orchids to bower birds to humans—in this world?

This "cost of complexity" conundrum puzzles biologists and offers ammunition to proponents of intelligent design, who hold that such intricacy could arise only through the efforts of a divine designer, not through natural selection.

A new analysis by Jianzhi "George" Zhang and coworkers at the University of Michigan and Taiwan's National Health Research Institutes reveals flaws in the models from which the cost of complexity idea arose and shows that complexity can, indeed, develop through evolutionary processes. In fact, a moderate amount of complexity best equips organisms to adapt to environmental change, the research suggests. The findings will be published online in the Proceedings of the National Academy of Sciences during the week of Sept. 27.
---------------------QUOTE-------------------


Posted by: Thought Provoker on Nov. 30 2010,19:01

Qetzal,

Quantum computers are good at searching unsorted databases.  From Wikipedia...
   

---------------------QUOTE-------------------
Grover's algorithm is a quantum algorithm for searching an unsorted database with N entries in O(N1/2) time and using O(log N) storage space (see big O notation). It was invented by Lov Grover in 1996.

In models of classical computation, searching an unsorted database cannot be done in less than linear time (so merely searching through every item is optimal). Grover's algorithm illustrates that in the quantum model searching can be done faster than this; in fact its time complexity O(N1/2) is asymptotically the fastest possible for searching an unsorted database in the quantum model.
---------------------QUOTE-------------------


Dembski's No Free Lunch argument is based on the presumption of an unsorted search using classical algorithms.  Quantum computing does what is impossible classically.

In 2001, Apoorva D. Patel wrote a paper titled < Quantum algorithms and the genetic code >


---------------------QUOTE-------------------
Over the last few years, Grover's algorithm has been studied in detail. I just summarise some of the important features:
...
 The algorithm is known to be optimal [10], going from |s> to |b> along a geodesic. No other algorithm, classical or quantum, can locate the desired object in an unsorted database with a fewer number of queries.
 The iterative steps of the algorithm can be viewed as the discretised evolution of the state vector in the Hilbert space, governed by a Hamiltonian containing two terms, |b> <b| and |s> <s|. The former represents a potential energy attracting the state towards |b>, while the latter represents a kinetic energy diffusing the state throughout the Hilbert space. The alteration between Ub and Us in the discretised steps is reminiscent of Trotter’s formula used in construction of the transfer matrix from a discretised Feynman’s path integral [11].
...
With the use of superposition of all possibilities at the start, the quantum algorithm performs a directed walk to the final result and achieves the square-root speed-up.
 The result in eq. (3) depends only on |<b|s>|; the phases of various components of |s> can be arbitrary, i.e. they can have the symmetry of bosons, fermions or even anyons.

To come back to the genetic code, let us look at two of the solutions of eq. (3) for small Q. The only exact integral solution is Q = 1,N = 4. Base-pairing during DNA replication can be looked upon as a yes/no query, either the pairing takes place through molecular bond formations or it does not, and its task is to distinguish between 4 possibilities. The other interesting solution is Q = 3, N = 20:2. The well-known triplet code of DNA has 3 consecutive nucleotide bases carrying 21 signals [12], 20 for the amino acids plus a STOP [13]. 3 base-pairings between t-RNA and m-RNA transfer this code to the amino acid chain [5].

These solutions are highly provocative. This is the first time they have come out of an algorithm that performs the actual task accomplished by DNA. It is fascinating that they are the optimal solutions [14]. Indeed it is imperative to investigate whether DNA has the quantum hardware necessary to implement the quantum search algorithm.
---------------------QUOTE-------------------


Patel's observation was mostly disregarded because the concept of the "quantum hardware necessary" existing in a biological environment was just too incredible to accept without more empirical evidence.

A lot has changed since 2001, especially lately which is why the three papers I linked to were something I noticed.
Posted by: qetzal on Nov. 30 2010,19:54

Thought Provoker,

Sorry, I still don't see how any of that suggests that DNA is any sort of quantum computer.

BTW, we discussed that Patel paper in a previous thread. I can't speak to the math, but the biochemistry & molecular biology are incredibly wrong. Makes it hard for me to take any of the rest seriously.
Posted by: Richardthughes on Dec. 01 2010,11:57

< http://scienceblogs.com/startsw....bui.php >
Posted by: midwifetoad on Dec. 02 2010,13:12

< http://www.nasa.gov/multimedia/nasatv/index.html >

Live
Posted by: Thought Provoker on Dec. 04 2010,16:06

The abstract of < Speculation on Quantum Mechanics and the Operation of Life Giving Catalysts >

---------------------QUOTE-------------------
The origin of life necessitated the formation of catalytic functionalities in order to realize a number of those capable of supporting reactions that led to the proliferation of biologically accessible molecules and the formation of a proto-metabolic network. Here, the discussion of the significance of quantum behavior on biological systems is extended from recent hypotheses exploring brain function and DNA mutation to include origins of life considerations in light of the concept of quantum decoherence and the transition from the quantum to the classical. Current understandings of quantum systems indicate that in the context of catalysis, substrate-catalyst interaction may be considered as a quantum measurement problem. Exploration of catalytic functionality necessary for life’s emergence may have been accommodated by quantum searches within metal sulfide compartments, where catalyst and substrate wave function interaction may allow for quantum based searches of catalytic phase space. Considering the degree of entanglement experienced by catalytic and non catalytic outcomes of superimposed states, quantum contributions are postulated to have played an important role in the operation of efficient catalysts that would provide for the kinetic basis for the emergence of life.

---------------------QUOTE-------------------



< Magnetism, FeS colloids, and Origins of Life > is freely available on-line.  It includes...

---------------------QUOTE-------------------
Today, clear signatures of quantum processing in biology are coming in ((Engel et al. 2007), aided by femtosecond laser-based 2D spectroscopy and coherent control approaches, showing how phase relationships in nano-structures modulate the course of bio-reactions (Nagya et al 2006). As to decoherence evading mechanisms, the role of a gel-state; quasicrystalline order; (Jibu et al 1994; Hagan et al. 2002); are amongst proposed order maintaining mechanisms in a wet environment, while 'screening effect', or 'cocooning' structural mechanisms are seen as providing insulation against interactions with the environment [Patel (2001); Davies (2003, 2004)] (see also Sect. 3.9). Indeed, it seems that Nature has quietly been using these strategies all along, i.e. leading to creation of biological language itself, as the Grover-Patel search numbers match those used by Nature! Using Grover's quantum search method for a marked item in an unsorted database, Patel (2001) hit upon the base-pairing logic of nucleic acids in transcription and translation as an excellent quantum search algorithm { a directed walk through a superposition of all possibilities - resulting in a 2-fold increase in sampling efficacy over its classical counterpart (which at best permits a random walk).
...
This possibility seems intriguing in the light of Patel's findings, where quantum searches seem to be responsible for the creation of biological language itself. Moreover, Russell et al have argued that life's hatchery could have been busy by 3.8 Gyr, evolving fast enough for a branch to have reached the ocean surfaces by 3.5 Gyr, as evidenced by photosynthetic signatures. The gestation period of life had to have been less than the umbilical mound's delivery of the formative hydrothermal solution, i.e., certainly less than 3 million years, and probably less than 30,000 years (Fruh-Green et al. 2003). Indeed, a magnetic start to Life could provide the ingredients for an intelligent Ancestor, along the lines envisaged by Lloyd (2006) for a computing universe. Again, it seems to be a physically feasible embodiment (Mitra-Delmotte and Mitra 2007; 2009) of Paul Davies's Q-Life proposal (2008), as also acknowledged by him in Merali (2007). A magnetic basis of assembly could also offer robustness to an `open' system against interference from a decohering environment. On the other hand, as evidence of quantum processing effects in biology trickles in, it appears that Nature is equipped for tackling environmental intrusion.

---------------------QUOTE-------------------


I linked to this paper over at Telic Thoughts but I doubt anyone is going to run with it as a Pro-ID argument.

Let me know if you are tired of arguing with JoeG and others like him and I will post a thread and try to defend the concepts offered by this paper.
Posted by: midwifetoad on Dec. 09 2010,17:47

< http://www.newscientist.com/blogs....go.html >

World's oldest computer recreated in Lego
Posted by: sledgehammer on Dec. 09 2010,20:22

Evolution Texts Survive Challenge in Louisiana
< John Roach writes >: The theory of evolution has survived the latest attack in the struggle to insert creationism-flavored themes into science classrooms.
On Tuesday, a committee of Louisiana's school board recommended in a 6-to-1 vote that the state approve purchase of industry-standard textbooks on evolution, which have been attacked by Christian conservatives for failing to teach the "controversy" about evolution.

"That sent a strong signal from the Louisiana board of education that they want accurate science taught in the classrooms, and that publishers don't need to put in these creationists' critiques," Joshua Rosenau, the programs and policy director of the National Center for Science Education, told me.
Posted by: Wesley R. Elsberry on Dec. 10 2010,05:46

< The Worms Turn... and a Patient Recovers >

My take on a CNN article about an ulcerative colitis patient self-medicating with Trichuris trichuria nematodes.
Posted by: Richardthughes on Dec. 13 2010,16:11

< http://www.technologyreview.com/blog/arxiv/26132/?ref=rss >

Astronomers Find Evidence Of Other Universes In Cosmic Microwave Background

ID will not pleased.
Posted by: Albatrossity2 on Dec. 13 2010,16:17

< Adult stem cells > take on a whole new level of meaning. Stem cells derived from liposuctioned fat could be used for breast augmentation, replacing silicone implants.

Gordon Mullings, GEM of Talky, will not be pleased.
Posted by: Schroedinger's Dog on Dec. 13 2010,16:17

Quote (Richardthughes @ Dec. 13 2010,22:11)
< http://www.technologyreview.com/blog/arxiv/26132/?ref=rss >

Astronomers Find Evidence Of Other Universes In Cosmic Microwave Background

ID will not pleased.
---------------------QUOTE-------------------


[head explodes]

Beside that, I've always been convinced that our universe is just one bubble in the large cup of moccaccino some fat ass is sipping down in Xxtrublub.

Take a look at a cup of hot coffee.

I mean, have you ever really looked at your hand?!?




Ok, I think it's time for me to go to sleep...
Posted by: Wesley R. Elsberry on Dec. 13 2010,21:40

Just got my copy of <i>Nature</i> 9 December 2010 today... it features a version of Haeckel's embryo drawings on the cover and an article supporting a phylotypic developmental stage with molecular evidence. It turns out that the lowest divergence in gene expression and the oldest genes are the ones associated with the phylotypic stage, as tested across six Drosophila spp.

How long until the DI hissy-fit?


Posted by: bfish on Dec. 14 2010,12:55

Quote (Wesley R. Elsberry @ Dec. 13 2010,19:40)
Just got my copy of <i>Nature</i> 9 December 2010 today... it features a version of Haeckel's embryo drawings on the cover and an article supporting a phylotypic developmental stage with molecular evidence. It turns out that the lowest divergence in gene expression and the oldest genes are the ones associated with the phylotypic stage, as tested across six Drosophila spp.

How long until the DI hissy-fit?
---------------------QUOTE-------------------


Hey, I know one of those dudes. He didn't tell me they were getting the cover.

ETA: The guy I know is the corresponding author, and it turns out he has already contacted < Panda's Thumb. >
Posted by: OgreMkV on Dec. 14 2010,18:46

< IBM Computer to Play Jeopardy >

So IBM thinks they have a computer that can figure out the clues well enough to actually play a game of Jeopardy.

I'll take AI for a million dollars Alex.
Posted by: Henry J on Dec. 15 2010,13:03

That... does... not... compute! Danger Will Robinson! Or something like that.
Posted by: OgreMkV on Dec. 18 2010,21:00

Anyone have any references for the development of DNA?
Posted by: Sol3a1 on Dec. 19 2010,06:59

Greetings all,

I see that the DI mill has been running OT despite their continuing to get their butts handed to them.  Good job.  OBTW, kudos to Dr. Wes for helping Dr. Eugene, I didn't know that.

I have a question about Chirality.  Right now, it is my understanding that of course it doesn't matter to Evolution, but the effect it has on Abiogenesis I'm still not clear about.

I know that amino acids are produced in the dust cloud that formed the solar system and that radiation made one selected over the other (and as early Earth was bombarded with comets with these selected Amino Acids) and gave rise to the chirality that we see today.  Oh yes, I forget if we're left or right handed proteins.

Any help or things to read would be appreciated.
Posted by: Dr.GH on Dec. 19 2010,13:51

Quote (Sol3a1 @ Dec. 19 2010,04:59)
Greetings all,

I have a question about Chirality.  Right now, it is my understanding that of course it doesn't matter to Evolution, but the effect it has on Abiogenesis I'm still not clear about.
---------------------QUOTE-------------------


I have a short outline at:

< A Short Outline of the Origin of Life >.
Posted by: Amadan on Dec. 20 2010,03:58

< Cool! >



---------------------QUOTE-------------------
THE FACT that dawn sunlight will beam into the passage grave at Newgrange tomorrow at the very moment that a full moon begins to pass out of a total lunar eclipse is a remarkable and rare coincidence, according to Prof Tom Ray, an astronomer at the Dublin Institute for Advanced Studies.

“It is the first time it has happened in about 450 years so that is a coincidence enough. The Tudors were in power in England at the time,” he said.

It is even more remarkable that light from the sun and the moon will appear together, with the first sunbeams at dawn coming just as the moon emerges from eclipse.

“That will happen at exactly eight minutes to nine. The two happen to coincide to within a minute.”

This kind of connection is unbelievably rare, Prof Ray said. “It would not have occurred since Newgrange was built.”
---------------------QUOTE-------------------



Of course, we all know that < this was prophesised in thuh Babble >
Posted by: dvunkannon on Dec. 20 2010,07:38

Quote (Sol3a1 @ Dec. 19 2010,07:59)
Greetings all,

I see that the DI mill has been running OT despite their continuing to get their butts handed to them.  Good job.  OBTW, kudos to Dr. Wes for helping Dr. Eugene, I didn't know that.

I have a question about Chirality.  Right now, it is my understanding that of course it doesn't matter to Evolution, but the effect it has on Abiogenesis I'm still not clear about.

I know that amino acids are produced in the dust cloud that formed the solar system and that radiation made one selected over the other (and as early Earth was bombarded with comets with these selected Amino Acids) and gave rise to the chirality that we see today.  Oh yes, I forget if we're left or right handed proteins.

Any help or things to read would be appreciated.
---------------------QUOTE-------------------


I think a few of the presentations at the recent NASA virtual conference had findings that there was a definite preference for one chirality over another in RNA/protein systems. So you don't need to buy into a space based origin of the amino acids, RNA bases, etc to have an explanation of chirality. A few rounds of normal chemistry will amplify the preference to a preponderence to a necessity.
Posted by: dvunkannon on Dec. 20 2010,07:52

Quote (Amadan @ Dec. 20 2010,04:58)
< Cool! >

 

---------------------QUOTE-------------------
THE FACT that dawn sunlight will beam into the passage grave at Newgrange tomorrow at the very moment that a full moon begins to pass out of a total lunar eclipse is a remarkable and rare coincidence, according to Prof Tom Ray, an astronomer at the Dublin Institute for Advanced Studies.

“It is the first time it has happened in about 450 years so that is a coincidence enough. The Tudors were in power in England at the time,” he said.

It is even more remarkable that light from the sun and the moon will appear together, with the first sunbeams at dawn coming just as the moon emerges from eclipse.

“That will happen at exactly eight minutes to nine. The two happen to coincide to within a minute.”

This kind of connection is unbelievably rare, Prof Ray said. “It would not have occurred since Newgrange was built.”
---------------------QUOTE-------------------



Of course, we all know that < this was prophesised in thuh Babble >
---------------------QUOTE-------------------


I'm not getting the distinction in rarities that the professor is making.

Newgrange * dawn * solstice * lunar eclipse  = once in 450 yrs

?? = not since Newgrange was built

Plus, exactly what is the force of

---------------------QUOTE-------------------
light from the sun and the moon will appear together, with the first sunbeams at dawn coming just as the moon emerges from eclipse
---------------------QUOTE-------------------



If you were in the Newgrange chamber, you wouldn't see the moon. It would be setting behind you, with tons of rock and dirt between you and that horizon.

I take it that precession of the equinoxes does not affect sites such as Newgrange. The solstice dawn hapens at the same point on the horizon, no matter what day the solstice happens to be.
Posted by: George on Dec. 20 2010,08:14

Quote (dvunkannon @ Dec. 20 2010,07:52)
Quote (Amadan @ Dec. 20 2010,04:58)
< Cool! >

 

---------------------QUOTE-------------------
THE FACT that dawn sunlight will beam into the passage grave at Newgrange tomorrow at the very moment that a full moon begins to pass out of a total lunar eclipse is a remarkable and rare coincidence, according to Prof Tom Ray, an astronomer at the Dublin Institute for Advanced Studies.

“It is the first time it has happened in about 450 years so that is a coincidence enough. The Tudors were in power in England at the time,” he said.

It is even more remarkable that light from the sun and the moon will appear together, with the first sunbeams at dawn coming just as the moon emerges from eclipse.

“That will happen at exactly eight minutes to nine. The two happen to coincide to within a minute.”

This kind of connection is unbelievably rare, Prof Ray said. “It would not have occurred since Newgrange was built.”
---------------------QUOTE-------------------



Of course, we all know that < this was prophesised in thuh Babble >
---------------------QUOTE-------------------


I'm not getting the distinction in rarities that the professor is making.

Newgrange * dawn * solstice * lunar eclipse  = once in 450 yrs

?? = not since Newgrange was built

Plus, exactly what is the force of  

---------------------QUOTE-------------------
light from the sun and the moon will appear together, with the first sunbeams at dawn coming just as the moon emerges from eclipse
---------------------QUOTE-------------------



If you were in the Newgrange chamber, you wouldn't see the moon. It would be setting behind you, with tons of rock and dirt between you and that horizon.

I take it that precession of the equinoxes does not affect sites such as Newgrange. The solstice dawn hapens at the same point on the horizon, no matter what day the solstice happens to be.
---------------------QUOTE-------------------


What I think is really cool, if my last tour guide there is to be believed, is that sunlight doesn't hit the back wall of Newgrange, but lands on the floor a little in front.  However, when first constructed, it did hit the back wall, but the position of the Earth relative to the sun has changed in the intervening 6000 years.
Posted by: Amadan on Dec. 20 2010,10:07

Quote (dvunkannon @ Dec. 20 2010,13:52)
Quote (Amadan @ Dec. 20 2010,04:58)
< Cool! >

 

---------------------QUOTE-------------------
THE FACT that dawn sunlight will beam into the passage grave at Newgrange tomorrow at the very moment that a full moon begins to pass out of a total lunar eclipse is a remarkable and rare coincidence, according to Prof Tom Ray, an astronomer at the Dublin Institute for Advanced Studies.

“It is the first time it has happened in about 450 years so that is a coincidence enough. The Tudors were in power in England at the time,” he said.

It is even more remarkable that light from the sun and the moon will appear together, with the first sunbeams at dawn coming just as the moon emerges from eclipse.

“That will happen at exactly eight minutes to nine. The two happen to coincide to within a minute.”

This kind of connection is unbelievably rare, Prof Ray said. “It would not have occurred since Newgrange was built.”
---------------------QUOTE-------------------



Of course, we all know that < this was prophesised in thuh Babble >
---------------------QUOTE-------------------


I'm not getting the distinction in rarities that the professor is making.

Newgrange * dawn * solstice * lunar eclipse  = once in 450 yrs

?? = not since Newgrange was built

Plus, exactly what is the force of  

---------------------QUOTE-------------------
light from the sun and the moon will appear together, with the first sunbeams at dawn coming just as the moon emerges from eclipse
---------------------QUOTE-------------------



If you were in the Newgrange chamber, you wouldn't see the moon. It would be setting behind you, with tons of rock and dirt between you and that horizon.

I take it that precession of the equinoxes does not affect sites such as Newgrange. The solstice dawn hapens at the same point on the horizon, no matter what day the solstice happens to be.
---------------------QUOTE-------------------


What's rare is the coincidence of the eclipse and solstice dawn. As the eclipse ends you'll just have enough time to get inside, scramble down the passage and turn around to see the sun light up the inside.

Mind you, you have to be lucky to win a place in there for the morning of the solstice. (There's a lottery of some sort, places are liable to be gazumped by visiting dignitaries etc etc) The rest of us mere peasants have to make do with the simulated dawn they do with electric lights six times a day on the tours.
Posted by: dvunkannon on Jan. 11 2011,07:01

< http://www.sciencedaily.com/releases/2011/01/110106145311.htm >

A very cool result, and challenge to the "tiny island of function in a sea of useless" argument for ID.

De novo gene sequences code for completely non-natural proteins (apparently the sequences were chosen based on some probability that they would fold). Insert these sequences into bacteria with some necessary genes knocked out, and the novel proteins substitute for the lacking natural proteins.

So the space of functional proteins is larger than the space of proteins sampled so far by evolution. Perhaps far larger, since this was pretty easy to do.

Our friend at UD, KF-san, often argues that micro-evolution can climb the slope of the island, but that finding the island in the first place is the problem (especially for abiogenesis). He appears to be mistaken. There are lots of islands, but evolution is very conservative. Perhaps more conservative than BarryA!
Posted by: midwifetoad on Jan. 11 2011,09:23

< http://www.plosone.org/article/info:doi/10.1371/journal.pone.0015364 >
Posted by: fnxtr on Jan. 11 2011,10:00

Quote (midwifetoad @ Jan. 11 2011,07:23)
< http://www.plosone.org/article/info:doi/10.1371/journal.pone.0015364 >
---------------------QUOTE-------------------


Amazing.

This is the kind of real work that is anathema to the armchair wankers of ID.  But just watch them turn it into another "intelligence was involved" pedantic circle jerk.
Posted by: dvunkannon on Jan. 11 2011,11:37

Quote (midwifetoad @ Jan. 11 2011,10:23)
< http://www.plosone.org/article/info:doi/10.1371/journal.pone.0015364 >
---------------------QUOTE-------------------


Thanks for providing the link to the original article. It is wonderfully clear and direct.

The polar patterning space they were exploring is vastly smaller than the full random 20^102 space of the strawman argument. They only scratched the surface with one million sequences and only tested four possible functions. And yet, they got hits on all four. That is impressive.
Posted by: midwifetoad on Jan. 11 2011,12:24

As an ignorant bystander to this kind of work, I'd sure like to know how the library of sequences was designed.

Some preview of the sure to be upcoming Corny Hunter blog would be interesting.
Posted by: dvunkannon on Jan. 11 2011,13:10

Quote (midwifetoad @ Jan. 11 2011,13:24)
As an ignorant bystander to this kind of work, I'd sure like to know how the library of sequences was designed.

Some preview of the sure to be upcoming Corny Hunter blog would be interesting.
---------------------QUOTE-------------------


Details here:
< http://peds.oxfordjournals.org/content/18/4/201.full.pdf >
Posted by: fnxtr on Jan. 11 2011,17:08

Quote (midwifetoad @ Jan. 11 2011,10:24)
As an ignorant bystander to this kind of work, I'd sure like to know how the library of sequences was designed.

Some preview of the sure to be upcoming Corny Hunter blog would be interesting.
---------------------QUOTE-------------------


Second paragraph of the introduction may help. Is that what you were asking?

If I'm reading it correctly, they used their PNPetc... codon pattern to insert sequences that would code for a specific protein shape (my bold):

 

---------------------QUOTE-------------------
For example, to design a helical bundle comprising ?-helices with hydrophilic faces exposed to aqueous solvent and hydrophobic faces buried in the interior of a protein, the binary pattern of polar (P) and nonpolar (N) residues should be PNPPNNPPNPPNNP, consistent with the structural repeat of 3.6 residues per alpha-helical turn [9], [10]. For the current studies, we used the binary code strategy to design and construct a library of sequences designed to fold into 102-residue 4-helix bundles. Our strategies for protein design and selecting biological function are summarized in Figure 1. Details describing the construction and biophysical characterization of the library are presented elsewhere [11], [12].


---------------------QUOTE-------------------



Apparently any of the polar/nonpolar amino acids in that order will make the protein shape they wanted.
Posted by: Steverino on Jan. 11 2011,18:04

This is off topic but, what's the latest/up to date evidence on Dino-Bird evolution?

Was the merits of Evolution with a creationist who used this article (below) as proof that the dino-bird evolution lineage is not as strong as previously thought.

I've tried to find a more up to date information but seem to have hit a wall.

Any suggestions?


article referenced:

Jones, T. D. and J. A. Ruben. Respiratory structure and function in theropod dinosaurs and some related taxa. In: New perspectives on the origins and evolution of birds. Pp. 443-461. Gauthier, J. and Gall, L. F., eds.,Yale University Press, New Haven.
Posted by: dvunkannon on Jan. 11 2011,19:07

Quote (Steverino @ Jan. 11 2011,19:04)
This is off topic but, what's the latest/up to date evidence on Dino-Bird evolution?

Was the merits of Evolution with a creationist who used this article (below) as proof that the dino-bird evolution lineage is not as strong as previously thought.

I've tried to find a more up to date information but seem to have hit a wall.

Any suggestions?


article referenced:

Jones, T. D. and J. A. Ruben. Respiratory structure and function in theropod dinosaurs and some related taxa. In: New perspectives on the origins and evolution of birds. Pp. 443-461. Gauthier, J. and Gall, L. F., eds.,Yale University Press, New Haven.
---------------------QUOTE-------------------


I think the latest pub from Ruben's group is talked about here:
< http://www.sciencedaily.com/releases/2009/06/090609092055.htm >
(This is the pop-sci version, the article has the direct cite at the bottom.)

Basically, the OSU group under Ruben is still the lonely outlier, and is resorting to insinuations of politics and "more and more people agree with us every day". Pretty familiar tactics.

I think I read through Quick's article at the time, and came to the conclusion that it doesn't say what Ruben says it says, but she just wanted to finish her doctorate and get the hell out. At best it says dinosaurs did not start as good long distance fliers. Duh.

Your creationist friend is out of date, perhaps quoting the last pub on Ruben's own OSU page. Not that anything Ruben holds is in any way supportive of YEC. He is not saying birds are a "kind" or that they poofed into existence 6,000 years ago. Ruben holds that birds evolved from some previous lineage, just not theropod dinosaurs. This happened 100 million years ago according to Ruben, so why your friend thinks this supports their position is beyond me. Just another example of latching on to any controversy to yelp that Evilution Is Teh Dying!

< http://en.wikipedia.org/wiki/Origin_of_birds >
is good, and you'll see that even the debate section doesn't deal with Ruben's position by name, just that some hold birds derived from archosaurs, not theropods.
Posted by: dvunkannon on Jan. 12 2011,17:19

More goodness on Dinos and birds:
< http://scienceblogs.com/tetrapo....urs.php >
Posted by: Wesley R. Elsberry on Jan. 12 2011,18:13

Quote (dvunkannon @ Jan. 11 2011,07:01)
< http://www.sciencedaily.com/releases/2011/01/110106145311.htm >

A very cool result, and challenge to the "tiny island of function in a sea of useless" argument for ID.

De novo gene sequences code for completely non-natural proteins (apparently the sequences were chosen based on some probability that they would fold). Insert these sequences into bacteria with some necessary genes knocked out, and the novel proteins substitute for the lacking natural proteins.

So the space of functional proteins is larger than the space of proteins sampled so far by evolution. Perhaps far larger, since this was pretty easy to do.

Our friend at UD, KF-san, often argues that micro-evolution can climb the slope of the island, but that finding the island in the first place is the problem (especially for abiogenesis). He appears to be mistaken. There are lots of islands, but evolution is very conservative. Perhaps more conservative than BarryA!
---------------------QUOTE-------------------


IIRC, some of Kirk Durston's argumentation rested on the assumption that what protein families living things had discovered comprised all the functional proteins possible. This seems a nice rebuttal of that.
Posted by: midwifetoad on Jan. 12 2011,18:23



---------------------QUOTE-------------------
IIRC, some of Kirk Durston's argumentation rested on the assumption that what protein families living things had discovered comprised all the functional proteins possible.
---------------------QUOTE-------------------



I'd sure like to see a link to that.
Posted by: dvunkannon on Jan. 13 2011,06:26

Please excuse my use of this thread to record a research proposal, rather than report one.

Thinking about the series of Miller-Urey experiments, one of the most productive was simulating the effect of lightning in a volcanic eruption. A spark was passed through superheated steam in a model atmosphere. This experiment yielded abundant organic molecules.
< http://www.sciencemag.org/content/322/5900/404 >
< http://www.sciencedaily.com/releases/2008/10/081016141411.htm >

I hypothesize that it should be able to confirm this result by collecting dust and ash from volcanos erupting today. While the current atmosphere contains abundant oxygen, the outgassing of a volcano may contain much less until thouroughly mixed. Therefore, lightning passing through the cloud produced by a volcano may be close to the conditions of the Miller-Bada experiment using steam.

In order to minimize contamination and degradation, my specific proposal is to collect samples from a volcano erupting through snow and ice, such as the Icelandic or Antarctic volcanos. In these conditions (dust and ash falling on new snow) the cold, dry environment would help preserve any molecules produced, and the background level of organics would be minimized.

My expectation is that the organic molecules would attach to the dust and ash particles through electrostatic forces, and be carried to the ground with them. Spectroscopy or some other form of analysis should then be able to detect them.

In summary, one criticism of abiogenesis that is sometimes heard is that if it happened in the past, why isn't it still happening today? This experiment would confirm that a reasonable mechanism that could have been at work in the past is in fact still at work today producing organic molecules. Of course, in the present these molecules do not have the chance to accumulate that they had in the deep past, due to the presence of oxygen and living creatures ready to absorb them.

I would be very happy to get comments on this proposal.
Posted by: Wesley R. Elsberry on Jan. 13 2011,07:53

Quote (midwifetoad @ Jan. 12 2011,18:23)


---------------------QUOTE-------------------
IIRC, some of Kirk Durston's argumentation rested on the assumption that what protein families living things had discovered comprised all the functional proteins possible.
---------------------QUOTE-------------------



I'd sure like to see a link to that.
---------------------QUOTE-------------------


I have a comment < here > about Durston using a number of proteins found in PFAM to fill in for "functional configurations", which is pretty close, I think.
Posted by: OgreMkV on Jan. 13 2011,10:47

Quote (dvunkannon @ Jan. 13 2011,06:26)
Please excuse my use of this thread to record a research proposal, rather than report one.

Thinking about the series of Miller-Urey experiments, one of the most productive was simulating the effect of lightning in a volcanic eruption. A spark was passed through superheated steam in a model atmosphere. This experiment yielded abundant organic molecules.
< http://www.sciencemag.org/content/322/5900/404 >
< http://www.sciencedaily.com/releases/2008/10/081016141411.htm >

I hypothesize that it should be able to confirm this result by collecting dust and ash from volcanos erupting today. While the current atmosphere contains abundant oxygen, the outgassing of a volcano may contain much less until thouroughly mixed. Therefore, lightning passing through the cloud produced by a volcano may be close to the conditions of the Miller-Bada experiment using steam.

In order to minimize contamination and degradation, my specific proposal is to collect samples from a volcano erupting through snow and ice, such as the Icelandic or Antarctic volcanos. In these conditions (dust and ash falling on new snow) the cold, dry environment would help preserve any molecules produced, and the background level of organics would be minimized.

My expectation is that the organic molecules would attach to the dust and ash particles through electrostatic forces, and be carried to the ground with them. Spectroscopy or some other form of analysis should then be able to detect them.

In summary, one criticism of abiogenesis that is sometimes heard is that if it happened in the past, why isn't it still happening today? This experiment would confirm that a reasonable mechanism that could have been at work in the past is in fact still at work today producing organic molecules. Of course, in the present these molecules do not have the chance to accumulate that they had in the deep past, due to the presence of oxygen and living creatures ready to absorb them.

I would be very happy to get comments on this proposal.
---------------------QUOTE-------------------


Would you be collecting the material directly from the vent outgassing or from the ground around the vent?

I think it would be very difficult to distinguish between material made within the vent outgassing ('new material' if you will) and material that has been formed outside of that system.

That being said, depending on the volcano, you might be able to look at the ratios of various isotopes and look for signatures that would be more appropriate to recent eruptions rather than surface/recycled material.  

Personally, I would think collecting gases directly from the vent (no helicopters!!) would be the best bet.  Keep them sealed, then run some electricity through them and see what results.
Posted by: dvunkannon on Jan. 13 2011,11:18

Quote (OgreMkV @ Jan. 13 2011,11:47)
Quote (dvunkannon @ Jan. 13 2011,06:26)
Please excuse my use of this thread to record a research proposal, rather than report one.

Thinking about the series of Miller-Urey experiments, one of the most productive was simulating the effect of lightning in a volcanic eruption. A spark was passed through superheated steam in a model atmosphere. This experiment yielded abundant organic molecules.
< http://www.sciencemag.org/content/322/5900/404 >
< http://www.sciencedaily.com/releases/2008/10/081016141411.htm >

I hypothesize that it should be able to confirm this result by collecting dust and ash from volcanos erupting today. While the current atmosphere contains abundant oxygen, the outgassing of a volcano may contain much less until thouroughly mixed. Therefore, lightning passing through the cloud produced by a volcano may be close to the conditions of the Miller-Bada experiment using steam.

In order to minimize contamination and degradation, my specific proposal is to collect samples from a volcano erupting through snow and ice, such as the Icelandic or Antarctic volcanos. In these conditions (dust and ash falling on new snow) the cold, dry environment would help preserve any molecules produced, and the background level of organics would be minimized.

My expectation is that the organic molecules would attach to the dust and ash particles through electrostatic forces, and be carried to the ground with them. Spectroscopy or some other form of analysis should then be able to detect them.

In summary, one criticism of abiogenesis that is sometimes heard is that if it happened in the past, why isn't it still happening today? This experiment would confirm that a reasonable mechanism that could have been at work in the past is in fact still at work today producing organic molecules. Of course, in the present these molecules do not have the chance to accumulate that they had in the deep past, due to the presence of oxygen and living creatures ready to absorb them.

I would be very happy to get comments on this proposal.
---------------------QUOTE-------------------


Would you be collecting the material directly from the vent outgassing or from the ground around the vent?

I think it would be very difficult to distinguish between material made within the vent outgassing ('new material' if you will) and material that has been formed outside of that system.

That being said, depending on the volcano, you might be able to look at the ratios of various isotopes and look for signatures that would be more appropriate to recent eruptions rather than surface/recycled material.  

Personally, I would think collecting gases directly from the vent (no helicopters!!) would be the best bet.  Keep them sealed, then run some electricity through them and see what results.
---------------------QUOTE-------------------


I think it would be cool to fly through a lightning charged cloud collecting gases, but I'm not sure I could afford the insurance. So second best is to collect the dust and ash samples after they fell to the ground.

I agree that the problem of contamination is a big issue, that is why I propose the mitigation strategy of collecting samples from new snow. The control samples would come from samples collected at the same time, but upwind of the volcano. That would give a baseline of how much organic material (and of what isotopes, as you mention) happen to be landing on the snow. Subtract that baseline, and you have a shot at seeing what the volcano is producing in the way of organics.

In the case of sampling an Antarctic volcano it would be really, really cool to look at an ice core taken from downwind of one, and look back thousands of years in order to add up the output over that time frame.
Posted by: OgreMkV on Jan. 13 2011,12:04

That's the thing... I'm not sure that anywhere on Earth would be clean enough for you to accurately determine if the material was from the volcano or contamination.  

I really think that they only way to do this would be to collect the hot gases directly from the vent and add the 'lightening' later in a lab.

IIRC, there were organics in NASA's high altitude material captures.

Whatever the original source, the Earth's atmosphere is full of organic debris.  Unless there is a very good isotope signature, I don't see how to determine if material is formed from the volcano or living systems.

Alternately, you could use the gases in the same ratio as modern volcanos generate them (see link below) and run them through a Miller-Urey-like apparatus.  If you get positive results, then a field study might be more likely to be funded.
< volcanic Gases USGS >
Posted by: Richardthughes on Jan. 13 2011,13:38

DNA teleportation WTF:

< http://www.popsci.com/science....inks-so >
Posted by: dvunkannon on Jan. 13 2011,14:00

Quote (OgreMkV @ Jan. 13 2011,13:04)
That's the thing... I'm not sure that anywhere on Earth would be clean enough for you to accurately determine if the material was from the volcano or contamination.  

I really think that they only way to do this would be to collect the hot gases directly from the vent and add the 'lightening' later in a lab.

IIRC, there were organics in NASA's high altitude material captures.

Whatever the original source, the Earth's atmosphere is full of organic debris.  Unless there is a very good isotope signature, I don't see how to determine if material is formed from the volcano or living systems.

Alternately, you could use the gases in the same ratio as modern volcanos generate them (see link below) and run them through a Miller-Urey-like apparatus.  If you get positive results, then a field study might be more likely to be funded.
< volcanic Gases USGS >
---------------------QUOTE-------------------


Thanks for the link to the gases page, good stuff!

Well, I got an e-mail back from Dr Bada, saying that the oxygen in the atmosphere would stop any organics from forming in the first place. So unless the lightning reaches a very unmixed part of the outgassing cloud, there will be no organic molecules to find, in his opinion. Dang.
Posted by: dvunkannon on Jan. 13 2011,14:05

Quote (Richardthughes @ Jan. 13 2011,14:38)
DNA teleportation WTF:

< http://www.popsci.com/science....inks-so >
---------------------QUOTE-------------------


Did BA^77 write that article?
Posted by: Seversky on Jan. 13 2011,17:42

Quote (Richardthughes @ Jan. 13 2011,13:38)
DNA teleportation WTF:

< http://www.popsci.com/science....inks-so >
---------------------QUOTE-------------------


Sounds like a variant of Jacques Benveniste's claims about water 'memory'.
Posted by: qetzal on Jan. 13 2011,21:55

Quote (Seversky @ Jan. 13 2011,17:42)
 
Quote (Richardthughes @ Jan. 13 2011,13:38)
DNA teleportation WTF:

< http://www.popsci.com/science....inks-so >
---------------------QUOTE-------------------


Sounds like a variant of Jacques Benveniste's claims about water 'memory'.
---------------------QUOTE-------------------


Not teleportation. Just plain old vanilla cross-contamination in their PCR. (The only other conceivable explanation is deliberate fraud.)

Montagnier has previous published claims wherein highly diluted DNA supposedly emits "electromagnetic signals" when placed inside a special apparatus. According to that paper, the apparatus was based on a design by none other than Jacques Benveniste!

Not sure if this device is the same one, but it sounds similar.

Sadly, it seems that Montagnier has gone down the same path as Pauling and Duesberg - once-brilliant scientists who become cranks in their old age.
Posted by: Badger3k on Jan. 14 2011,00:02

Quote (dvunkannon @ Jan. 13 2011,11:18)
Quote (OgreMkV @ Jan. 13 2011,11:47)
 
Quote (dvunkannon @ Jan. 13 2011,06:26)
Please excuse my use of this thread to record a research proposal, rather than report one.

Thinking about the series of Miller-Urey experiments, one of the most productive was simulating the effect of lightning in a volcanic eruption. A spark was passed through superheated steam in a model atmosphere. This experiment yielded abundant organic molecules.
< http://www.sciencemag.org/content/322/5900/404 >
< http://www.sciencedaily.com/releases/2008/10/081016141411.htm >

I hypothesize that it should be able to confirm this result by collecting dust and ash from volcanos erupting today. While the current atmosphere contains abundant oxygen, the outgassing of a volcano may contain much less until thouroughly mixed. Therefore, lightning passing through the cloud produced by a volcano may be close to the conditions of the Miller-Bada experiment using steam.

In order to minimize contamination and degradation, my specific proposal is to collect samples from a volcano erupting through snow and ice, such as the Icelandic or Antarctic volcanos. In these conditions (dust and ash falling on new snow) the cold, dry environment would help preserve any molecules produced, and the background level of organics would be minimized.

My expectation is that the organic molecules would attach to the dust and ash particles through electrostatic forces, and be carried to the ground with them. Spectroscopy or some other form of analysis should then be able to detect them.

In summary, one criticism of abiogenesis that is sometimes heard is that if it happened in the past, why isn't it still happening today? This experiment would confirm that a reasonable mechanism that could have been at work in the past is in fact still at work today producing organic molecules. Of course, in the present these molecules do not have the chance to accumulate that they had in the deep past, due to the presence of oxygen and living creatures ready to absorb them.

I would be very happy to get comments on this proposal.
---------------------QUOTE-------------------


Would you be collecting the material directly from the vent outgassing or from the ground around the vent?

I think it would be very difficult to distinguish between material made within the vent outgassing ('new material' if you will) and material that has been formed outside of that system.

That being said, depending on the volcano, you might be able to look at the ratios of various isotopes and look for signatures that would be more appropriate to recent eruptions rather than surface/recycled material.  

Personally, I would think collecting gases directly from the vent (no helicopters!!) would be the best bet.  Keep them sealed, then run some electricity through them and see what results.
---------------------QUOTE-------------------


I think it would be cool to fly through a lightning charged cloud collecting gases, but I'm not sure I could afford the insurance. So second best is to collect the dust and ash samples after they fell to the ground.

I agree that the problem of contamination is a big issue, that is why I propose the mitigation strategy of collecting samples from new snow. The control samples would come from samples collected at the same time, but upwind of the volcano. That would give a baseline of how much organic material (and of what isotopes, as you mention) happen to be landing on the snow. Subtract that baseline, and you have a shot at seeing what the volcano is producing in the way of organics.

In the case of sampling an Antarctic volcano it would be really, really cool to look at an ice core taken from downwind of one, and look back thousands of years in order to add up the output over that time frame.
---------------------QUOTE-------------------


New snow is still going to be contaminated from the air - there's all kinds of stuff floating around the atmosphere (picked up as the snow forms and floats down), and on the ground itself.  I agree with the others that the best defense against contamination would be to get freshly outgassed...er...gas - something that has not even had time to mix with the atmosphere now.  That way you can try to limit the atmospheric contamination.

ETA - just saw the oxygen post above.  Collecting it fresh from the source seems to be the only likely avenue.  Has anyone looked to see if oxygen is part of the gasses released?  Is the composition now different than what it was in the past?  Has oxygen in the soil translated into oxygen in volcanic gasses?  Obviously I'm completely unfamiliar with this and just tossing out my 2 pennies worth.
Posted by: dvunkannon on Jan. 14 2011,07:17

Quote (Badger3k @ Jan. 14 2011,01:02)
New snow is still going to be contaminated from the air - there's all kinds of stuff floating around the atmosphere (picked up as the snow forms and floats down), and on the ground itself.  I agree with the others that the best defense against contamination would be to get freshly outgassed...er...gas - something that has not even had time to mix with the atmosphere now.  That way you can try to limit the atmospheric contamination.

ETA - just saw the oxygen post above.  Collecting it fresh from the source seems to be the only likely avenue.  Has anyone looked to see if oxygen is part of the gasses released?  Is the composition now different than what it was in the past?  Has oxygen in the soil translated into oxygen in volcanic gasses?  Obviously I'm completely unfamiliar with this and just tossing out my 2 pennies worth.
---------------------QUOTE-------------------


The gases page that the Big CyberTank linked to doesn't list oxygen, does list CO2, H2O and other goodness.

In re contamination, two points:
1 - I thought that subtracting the control samples was a good response to that. If the control shows 20 of X and the dust sample shows 22 of X, the volcano made the 2. Are you saying that you think the difference will always fall in the error bar? If it did that would certainly be a problem, but I think you'd have to do the experiment to find that out.

2 - Let's say you were trying to measure glycine. Is it possible to measure the presence of glycine, not the presence of bigger proteins that incorporate glycine? The volcano is (possibly maybe (an Icelandic volcano, lol)) making the free amino acid, while the contamination is a virus, a frozen bacteria, or some other bit of a living system. Any glycine present in the control sample is likely part of a much larger molecule. So we wash, spin, filter, etc to eliminate the big molecules. This is another way I would try to differentiate the volcanic output from the background material.
Posted by: dvunkannon on Jan. 14 2011,08:07

Check out Fig 2 in
< http://www.suagm.edu/umet/pdf/Cardona99CJS.pdf >

I was researching island pygmies of the Caribbean for an eventual KF joke when I cam across this pygmy sperm whale.  Or is it a great white shark that never saw an orthodontist? Dang, that is the sharkiest looking whale I ever saw.

I'm tempted to call this protective mimicry, but maybe its convergent evolution. The shape of the nose could conceivably be functional, but false gill markings?? We report, you decide.
Posted by: OgreMkV on Jan. 14 2011,09:52

And from the 'throwing one out there department'

< http://www.pnas.org/content....7210112 > (abstract only, full version behind a paywall for now)

full version (draft): < http://www.life.illinois.edu/ccheng....ine.pdf >

Evolution of an antifreeze protein by neofunctionalization under escape from adaptive conflict

From the abstract:
"We report here clear experimental evidence for EAC-driven evolution of type III antifreeze protein gene from an old sialic acid synthase (SAS) gene in an Antarctic zoarcid fish. We found that an SAS gene, having both sialic acid synthase and rudimentary ice-binding activities, became duplicated. In one duplicate, the N-terminal SAS domain was deleted and replaced with a nascent signal peptide, removing pleiotropic structural conflict between SAS and ice-binding functions and allowing rapid optimization of the C-terminal domain to become a secreted protein capable of noncolligative freezing-point depression."

There you go. Clear, unambiguous evidence that what Behe says can't happen does happen.

Just a warning, this paper is thick (i.e. heavily detailed with very technical information).
Posted by: Seversky on Jan. 14 2011,14:29

Quote (qetzal @ Jan. 13 2011,21:55)
Quote (Seversky @ Jan. 13 2011,17:42)
   
Quote (Richardthughes @ Jan. 13 2011,13:38)
DNA teleportation WTF:

< http://www.popsci.com/science....inks-so >
---------------------QUOTE-------------------


Sounds like a variant of Jacques Benveniste's claims about water 'memory'.
---------------------QUOTE-------------------


Not teleportation. Just plain old vanilla cross-contamination in their PCR. (The only other conceivable explanation is deliberate fraud.)
---------------------QUOTE-------------------


Benveniste made claims about being able to make digital recordings of some sort of EM 'signal' emanating from these solutions, < transmitting the files over the Internet >, and then inducing an effect in water exposed to these recordings at the other end.

Professor Madeleine Ennis conducted some research, when challenged by Benveniste to test his claims, using four independent labs which produced < some intriguing results. >

Unfortunately, an < attempt to replicate these results >, conducted for BBC TV's science documentary series Horizon failed to find any effect.
Posted by: midwifetoad on Jan. 14 2011,14:55

Suffering from decline, no doubt.
Posted by: fnxtr on Jan. 14 2011,16:46

Quote (Seversky @ Jan. 14 2011,12:29)
Benveniste made claims about being able to make digital recordings of some sort of EM 'signal' emanating from these solutions, < transmitting the files over the Internet >, and then inducing an effect in water exposed to these recordings at the other end.
---------------------QUOTE-------------------


Coincidentally, this is exactly the procedure used to add the correct amount of Vermouth to a martini.
Posted by: Badger3k on Jan. 14 2011,19:40

Quote (midwifetoad @ Jan. 14 2011,14:55)
Suffering from decline, no doubt.
---------------------QUOTE-------------------


Nah - it was done by skeptics, and everyone knows skeptics change the biomorphologicalquantumancientchinesesecret field, causing such experiments to fail.

Happens all the time.  Strange... ???
Posted by: Badger3k on Jan. 14 2011,19:44

Quote (dvunkannon @ Jan. 14 2011,07:17)
Quote (Badger3k @ Jan. 14 2011,01:02)
New snow is still going to be contaminated from the air - there's all kinds of stuff floating around the atmosphere (picked up as the snow forms and floats down), and on the ground itself.  I agree with the others that the best defense against contamination would be to get freshly outgassed...er...gas - something that has not even had time to mix with the atmosphere now.  That way you can try to limit the atmospheric contamination.

ETA - just saw the oxygen post above.  Collecting it fresh from the source seems to be the only likely avenue.  Has anyone looked to see if oxygen is part of the gasses released?  Is the composition now different than what it was in the past?  Has oxygen in the soil translated into oxygen in volcanic gasses?  Obviously I'm completely unfamiliar with this and just tossing out my 2 pennies worth.
---------------------QUOTE-------------------


The gases page that the Big CyberTank linked to doesn't list oxygen, does list CO2, H2O and other goodness.

In re contamination, two points:
1 - I thought that subtracting the control samples was a good response to that. If the control shows 20 of X and the dust sample shows 22 of X, the volcano made the 2. Are you saying that you think the difference will always fall in the error bar? If it did that would certainly be a problem, but I think you'd have to do the experiment to find that out.

2 - Let's say you were trying to measure glycine. Is it possible to measure the presence of glycine, not the presence of bigger proteins that incorporate glycine? The volcano is (possibly maybe (an Icelandic volcano, lol)) making the free amino acid, while the contamination is a virus, a frozen bacteria, or some other bit of a living system. Any glycine present in the control sample is likely part of a much larger molecule. So we wash, spin, filter, etc to eliminate the big molecules. This is another way I would try to differentiate the volcanic output from the background material.
---------------------QUOTE-------------------


re point 1 - that sounds plausible.  You'd just need to make sure you have enough samples to get a good baseline control.  You'd have to time it right, too - determine what would be considered "freshly fallen" - ie, could it be on the ground for 1 minute, 10, 20? - you get the idea.  But it seems ok at a glance.  I have to admit I'm not skilled enough to judge it beyond that.  Maybe someone else?

re 2 - that's also beyond me.  I don't see why it wouldn't be possible, unless there is something that would make the glycine bond immediately without inducing it.
Posted by: dvunkannon on Jan. 15 2011,09:38

< http://onlinelibrary.wiley.com/doi....pdf >

And now for something completely different...

One of the common OOL related arguments you hear from creationists is about how everything has to be 100-150 units in length before anything interesting happens, and such long sequences are soooo specific and soooo improbable to be built by chance processes, that, therefore, Jimbo. Or Jebus. Or something.

Another argument you'll hear (as in Signature in the Cell) is that the entire protein-mRNA-DNA transcription/translation system is waaay too complex to have sprung up by chance, see the argument above.

So one of the points I like to make about the  RNA world is that there was plenty of opportunity for proteins and RNA polymers to work together even when both were short, randomly assembled sequences. As this relates to the formation of the genetic code, the idea is called the stereochemical hypothesis. Nakashima regularly flogged the work of Michael Yarus when discussing this on UD.

I bring the paper above to your attention because it can be read as addressing the same set of issues, from a slightly different perspective.

One of the questions we might ask about protein-RNA interaction is how hard is it to find? Modern gene regulatory networks often work through transcription factors, which are proteins that bind to the DNA. The DNA binding domain of these proteins is actually rather small, common domains are less than 25 AA in length. They also have a fairly 'generic' architecture, such as helix-turn-helix. As we saw this past week with the announcement of the creation of functional proteins by simply stringing 4 helices together, functional helix-turn-helix shouldn't be that hard for a random process to make.

The referenced paper shows that is true for proteins binding to RNA, which is more directly relevant OOL and RNA World discussions. The RNA recognition motif, RRM, is one of several common ways for proteins and RNA to interact in our cells today. The AA sequences that are conserved across many uses and species of eukaryote, prokaryote, and virus are short, only 6 and 8 AA long. Even these are variable in content.

These variable but conserved sequences can then be embedded in a wide variety of larger proteins to be more or less specific in modern cells. Read the paper for all the goodness.

What this says to me, relavent to OOL, is that protein binding to RNA is easy to accomplish, even from random starting points. If these small binding domains are further attached to sequences with enzymatic function, then the RNA World is not going to limp along relying on the self catalytic properties of RNA for very long. Once amino acids and RNA are in the same pot, they will start to interact in a process of molecular co-evolution.

In summary, this paper shows how short and variable sequences of amina acids can have important function, creating interactions directly with strands of RNA. These findings contradict creationist arguments that rely on the length and specificity of proteins to argue that functional proteins could not arise naturally, through normal chemical processes.

PS - Just one quote:


---------------------QUOTE-------------------
To date, more than 30 RRM structures have been
determined either by NMR or X-ray crystallography
and reveal unexpected variations as shown in Fig. 2.
The loops between the secondary structure elements
(loops 1–5 as indicated in Figs 1 and 2) can have
different lengths and are often disordered in the free
form.
---------------------QUOTE-------------------


While it is easy, in the context of the argument I am making above, to focus on the variability mentioned in this quote, I am drawn to the mention of 'disordered'. To me, proteins that work even when they haven't folded right are important clues to some very old process. The recent NASA virtual conference had an example of this in discussing a protein in the ribosome.  The newer end of the protein, on the outside of the ribosome was folded normally, the end on the interior, the most ancient part of the ribosome, was not folded.
Posted by: OgreMkV on Jan. 15 2011,09:47

I paper last year (or maybe the year before) found that very, very short RNA chains could catalyze metabolic reactions.

Like 5 nucleotides long (with a 3 nucleotide active site).  I'll dredge up the paper if you like.

Kinda nukes the entire long RNA/protein argument anyway.
Posted by: dvunkannon on Jan. 18 2011,15:54

Quote (OgreMkV @ Jan. 15 2011,10:47)
I paper last year (or maybe the year before) found that very, very short RNA chains could catalyze metabolic reactions.

Like 5 nucleotides long (with a 3 nucleotide active site).  I'll dredge up the paper if you like.

Kinda nukes the entire long RNA/protein argument anyway.
---------------------QUOTE-------------------


< http://www.sciencedaily.com/releases/2010/02/100222162009.htm >

Yup, 5 bases. But the universe won't find it.
Posted by: dvunkannon on Jan. 20 2011,14:18

< http://www.dpreview.com/news/1101/11011915curvilinearcamera.asp >

CHanging the shape of the detector (retina) at the same time as the lens allows "zoom" feature with simple lens.

Now why didn't teh designer think of that?
Posted by: Henry J on Jan. 20 2011,14:40

It does sound like something Oscar Goldman might have done...
Posted by: midwifetoad on Jan. 20 2011,14:50

< http://www.pnas.org/content/early/2010/02/12/0912895107.full.pdf >
Posted by: dvunkannon on Jan. 21 2011,14:54

Extremophile uses metabolic pathway it 'tinkered together', mostly from gene transfer, as it adapted to a saltier and saltier environment.

< http://www.sciencedaily.com/releases/2011/01/110121103537.htm >
Posted by: dvunkannon on Jan. 22 2011,16:03

< http://www.agu.org/meetings/fm10/lectures/lecture_videos/B14B.shtml >

Carl Sagan lecture from the 2010 meeting of the American Geophysical Union. Topic is the use of isotopic geochemistry to understand the history of Mars wrt water and perhaps life.

I thought it was a good lecture, well spoken and presented. It is amazing what kind of things we know, and the outlook for knowing more in the future!
Posted by: OgreMkV on Jan. 24 2011,12:15

< Salt and a New Metabolic Pathway for Archea >

Talks about how Archea took genes from a variety of sources, then 'tweaked' them to meet their needs.

I haven't absorbed the full paper yet, but it's interesting.
Posted by: OgreMkV on Jan. 24 2011,17:06

For Mad Panda

< http://www.zooborns.com/zooborns/2011/01/firefoxes-on-white.html >
Posted by: MadPanda, FCD on Jan. 24 2011,21:18

Coolness!  Always nice to see a few more pics of the wahs.

Thanks much!


The MadPanda, FCD
Posted by: OgreMkV on Jan. 24 2011,22:02

Is that one in the middle yours?  Looks just like you :)
Posted by: MadPanda, FCD on Jan. 24 2011,22:04

I'm not sure.  My av is from Fuzhou...


The MadPanda, FCD
Posted by: OgreMkV on Jan. 25 2011,10:10

Question time.

Is speciation a process, a result, or both?  No specific type of speciation (allopatric or sympatric), but generic 'speciation'?

My initial thoughts are that it is a result of evolutionary processes.  I can see that it could be considered a process, if one is referring to a specific type of speciation, but the generic speciation?  I think it's an event or a result, not the process.

Thoughts?
Posted by: MadPanda, FCD on Jan. 25 2011,10:23

From a layman's perspective, I would guess that it's both, in that the process and the results cannot be easily separated into discrete boxes.  (This may also be part of the reason why there are so many working definitions of 'species' out there.  :)  )

I would start muttering a bit about Hegel's Dialectic* here for a few minutes, as I am prone to doing, but someone might think I actually know what I'm talking about and take me for an authority.


The MadPanda, FCD


* Yes, I know, but it's still an interesting model if you can get around the original author's fundamental error in assuming a final perfect form.
Posted by: midwifetoad on Jan. 25 2011,10:55

Language doesn't precisely reflect reality when describing change. Is birth a process or a result? How about reproduction in general?

What is the *result* of speciation? Absolute reproductive isolation? Probabilistic reproductive isolation?
Posted by: dvunkannon on Jan. 25 2011,12:28

Quote (midwifetoad @ Jan. 25 2011,11:55)
Language doesn't precisely reflect reality when describing change. Is birth a process or a result? How about reproduction in general?

What is the *result* of speciation? Absolute reproductive isolation? Probabilistic reproductive isolation?
---------------------QUOTE-------------------


That is an interesting way of arriving at an answer to the original question.

If speciation is the process, isolation is the result.

If X is the process, speciation is the result.

I have trouble filling in X, so I prefer the first version!
Posted by: OgreMkV on Jan. 25 2011,12:43

Quote (dvunkannon @ Jan. 25 2011,12:28)
Quote (midwifetoad @ Jan. 25 2011,11:55)
Language doesn't precisely reflect reality when describing change. Is birth a process or a result? How about reproduction in general?

What is the *result* of speciation? Absolute reproductive isolation? Probabilistic reproductive isolation?
---------------------QUOTE-------------------


That is an interesting way of arriving at an answer to the original question.

If speciation is the process, isolation is the result.

If X is the process, speciation is the result.

I have trouble filling in X, so I prefer the first version!
---------------------QUOTE-------------------


OK, but couldn't it just as easily be

Isolation is the process and speciation is the result?

Where isolation equals physical, anatomical, behavioral, etc?
Posted by: midwifetoad on Jan. 25 2011,17:03

How about incremental change is the process; isolation is the result; speciation is the applied term?
Posted by: Henry J on Jan. 25 2011,17:13

How about look at the definition of "speciation", and see if it describes the process or the result.

Of course, if there are multiple definitions of "speciation", both answers might be produced depending on which definition is selected.

(Whether that selection is natural or artificial doesn't matter here.)
Posted by: Richardthughes on Jan. 26 2011,10:18

Free Lunch?

< http://www.physorg.com/news/2011-01-scientists-erase-energy.html >

"Scientists show how to erase information without using energy"
Posted by: OgreMkV on Jan. 26 2011,10:26

Quote (Henry J @ Jan. 25 2011,17:13)
How about look at the definition of "speciation", and see if it describes the process or the result.

Of course, if there are multiple definitions of "speciation", both answers might be produced depending on which definition is selected.

(Whether that selection is natural or artificial doesn't matter here.)
---------------------QUOTE-------------------


Well, in a scientific sense, speciation is divided into 'types' (like sympatric speciation and allopatric speciation) by the process that results in the speciation.

That's why my thought was the 'speciation' by itself should be a result instead of a process.
Posted by: sledgehammer on Jan. 28 2011,13:52

< 13% of H.S. Biology Teachers Advocate Creationism in Class >
 

---------------------QUOTE-------------------
The majority of high-school biology teachers don't take a solid stance on evolution with their students, mostly to avoid conflicts, and fewer than 30 percent of teachers take an adamant pro-evolutionary stance on the topic, a new study finds. Also, 13 percent of these teachers advocate creationism in their classrooms.
---------------------QUOTE-------------------


This is sad.  Not unexpected, but sad nonetheless
Posted by: Lou FCD on Jan. 28 2011,16:06

Quote (sledgehammer @ Jan. 28 2011,14:52)
< 13% of H.S. Biology Teachers Advocate Creationism in Class >
 

---------------------QUOTE-------------------
The majority of high-school biology teachers don't take a solid stance on evolution with their students, mostly to avoid conflicts, and fewer than 30 percent of teachers take an adamant pro-evolutionary stance on the topic, a new study finds. Also, 13 percent of these teachers advocate creationism in their classrooms.
---------------------QUOTE-------------------


This is sad.  Not unexpected, but sad nonetheless
---------------------QUOTE-------------------


Given my own experiences with my kids' history teachers, I'm only shocked the percentage is so low.
Posted by: Erasmus, FCD on Jan. 28 2011,20:33

you might remember that cool story blogged on the Loom a few years ago about < canine transmissible venereal tumors >.  Macroevolution in human observed time.

Last week in < Science > is a sweet phylogeny that suggests CTVT mitochondrial capture events have happened multiple times, even in house dogs, wolves and coyotes.  What a freak show
Posted by: Timothy McDougald on Jan. 29 2011,13:29

This is really cool! < A novel resource–service mutualism between bats and pitcher plants >. Here is the abstract:



---------------------QUOTE-------------------
Mutualistic relationships between vertebrates and plants apart from the pollen and seed-dispersal syndromes are rare. At first view, carnivorous pitcher plants of the genus Nepenthes seem to be highly unlikely candidates for mutualistic interactions with animals, as they form dimorphic terrestrial and aerial pitchers that trap arthropods and small vertebrates. Surprisingly, however, the aerial pitchers of Nepenthes rafflesiana variety elongata are poor insect traps, with low amounts of insect-attractive volatile compounds and low amounts of digestive fluid. Here, we show that N. rafflesiana elongata gains an estimated 33.8 per cent of the total foliar nitrogen from the faeces of Hardwicke's woolly bats (Kerivoula hardwickii hardwickii) that exclusively roost in its aerial pitchers. This is the first case in which the faeces-trapping syndrome has been documented in a pitcher plant that attracts bats and only the second case of a mutualistic association between a carnivorous plant and a mammal to date.
---------------------QUOTE-------------------


Posted by: Sol3a1 on Jan. 29 2011,13:58

Quote (Lou FCD @ Jan. 28 2011,16:06)
Quote (sledgehammer @ Jan. 28 2011,14:52)
< 13% of H.S. Biology Teachers Advocate Creationism in Class >

---------------------QUOTE-------------------
The majority of high-school biology teachers don't take a solid stance on evolution with their students, mostly to avoid conflicts, and fewer than 30 percent of teachers take an adamant pro-evolutionary stance on the topic, a new study finds. Also, 13 percent of these teachers advocate creationism in their classrooms.
---------------------QUOTE-------------------

This is sad.  Not unexpected, but sad nonetheless
---------------------QUOTE-------------------

Given my own experiences with my kids' history teachers, I'm only shocked the percentage is so low.
---------------------QUOTE-------------------


If I'm correct Lou, you live in the south as I do. At least I live by 4 major Universities which helps quell the TARD to Reality Index, TTRI
Posted by: sledgehammer on Jan. 29 2011,13:59

Very cool!
I always thought the "pitchers" looked like elongated chamberpots.  Apparently the bats do as well.
Posted by: fnxtr on Jan. 29 2011,16:31

Quote (afarensis @ Jan. 29 2011,11:29)
This is really cool! < A novel resource–service mutualism between bats and pitcher plants >. Here is the abstract:

 

---------------------QUOTE-------------------
Mutualistic relationships between vertebrates and plants apart from the pollen and seed-dispersal syndromes are rare. At first view, carnivorous pitcher plants of the genus Nepenthes seem to be highly unlikely candidates for mutualistic interactions with animals, as they form dimorphic terrestrial and aerial pitchers that trap arthropods and small vertebrates. Surprisingly, however, the aerial pitchers of Nepenthes rafflesiana variety elongata are poor insect traps, with low amounts of insect-attractive volatile compounds and low amounts of digestive fluid. Here, we show that N. rafflesiana elongata gains an estimated 33.8 per cent of the total foliar nitrogen from the faeces of Hardwicke's woolly bats (Kerivoula hardwickii hardwickii) that exclusively roost in its aerial pitchers. This is the first case in which the faeces-trapping syndrome has been documented in a pitcher plant that attracts bats and only the second case of a mutualistic association between a carnivorous plant and a mammal to date.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


Let me beat Henry J to saying that's some batshit crazy stuff.
Posted by: Lou FCD on Jan. 30 2011,09:21

Quote (Sol3a1 @ Jan. 29 2011,14:58)
Quote (Lou FCD @ Jan. 28 2011,16:06)
Quote (sledgehammer @ Jan. 28 2011,14:52)
< 13% of H.S. Biology Teachers Advocate Creationism in Class >

---------------------QUOTE-------------------
The majority of high-school biology teachers don't take a solid stance on evolution with their students, mostly to avoid conflicts, and fewer than 30 percent of teachers take an adamant pro-evolutionary stance on the topic, a new study finds. Also, 13 percent of these teachers advocate creationism in their classrooms.
---------------------QUOTE-------------------

This is sad.  Not unexpected, but sad nonetheless
---------------------QUOTE-------------------

Given my own experiences with my kids' history teachers, I'm only shocked the percentage is so low.
---------------------QUOTE-------------------


If I'm correct Lou, you live in the south as I do. At least I live by 4 major Universities which helps quell the TARD to Reality Index, TTRI
---------------------QUOTE-------------------


You're correct. I live across the street from my uni in Wilmington, NC, so it's a bit attenuated here, but my son still lives in Jacksonville, home to the largest Marine Corps base in the world and lots and lots of seriously deranged Christians.
Posted by: George on Feb. 03 2011,07:38

While I'm here, I have to add the pitcher plant - bat mutualism story is way cool.
Posted by: dvunkannon on Feb. 03 2011,10:24

Let's talk planets!!

< http://www.nasa.gov/mission_pages/kepler/news/kepler_data_release.html >

5 near Earth-like planets in their habzones! Extrapolating from our own solar system, at least one of those should be closer to an Earth than a Venus or Mars.

Can someone tell me which way Kepler is pointed? Is it looking inwards toward the galactic center, or along a tangent to Sol's radius from the galactic center?
Posted by: sledgehammer on Feb. 03 2011,10:32

Here's a link to the < Nature > article.

ETA  

---------------------QUOTE-------------------
The mean velocity of -57.16 kms-1 is measured relative to the Solar System barycenter; compared to the local velocity dispersion of ~30 kms-1, this Galactic velocity suggests that Kepler-11 is a member of the thick disk of the Milky Way.
---------------------QUOTE-------------------


Here's a non-paywalled .pdf of < Supplementary Data > on the Kepler-11 system that might help.
Posted by: dvunkannon on Feb. 05 2011,22:19

< http://cshperspectives.cshlp.org/cgi/collection/rna_worlds >

If you liked the Cold Spring Harbor subject collection on the origins of life, this collection on RNA World topics will also make you happy.

For the KrisBob trolls out there, here's a quote from Steven Benner's article "Setting the Stage: The History, Chemistry, and Geobiology behind RNA"

 

---------------------QUOTE-------------------
No community-accepted scientific methods are available today to guide studies on what role RNA played in the origin and early evolution of life on Earth. Further, a definition-theory for life is needed to develop hypotheses relating to the “RNA First” model for the origin of life. Four approaches are currently at various stages of development of such a definition-theory to guide these studies. These are (a) paleogenetics, in which inferences about the structure of past life are drawn from the structure of present life; (b) prebiotic chemistry, in which hypotheses with experimental support are sought that get RNA from organic and inorganic species possibly present on early Earth; ( c) exploration, hoping to encounter life independent of terran life, which might contain RNA; and (d) synthetic biology, in which laboratories attempt to reproduce biological behavior with unnatural chemical systems.
---------------------QUOTE-------------------



Science, he's doin it rite.
Posted by: Sol3a1 on Feb. 06 2011,08:49

Howdy people,


I ran into this: "Trisha Gura, "Bones, Molecules or Both?" and when I typed it in to get a search, holy deep quote mine batman, in addition to the site of the magazine, Nature, that published it, it seems that this is a "major find" for every ID or Creation website out there.

Even though I am not a biologist, after reading what the writer stated and then what the ID sites think she said there's is a reach. I think that the ID and YEC sites are in the words of the great philosopher Inigo Montoya

---------------------QUOTE-------------------
You keep using that word. I do not think it means what you think it means
---------------------QUOTE-------------------

or am I the one missing something?
Posted by: dvunkannon on Feb. 06 2011,22:33

Quote (Sol3a1 @ Feb. 06 2011,09:49)
Howdy people,


I ran into this: "Trisha Gura, "Bones, Molecules or Both?" and when I typed it in to get a search, holy deep quote mine batman, in addition to the site of the magazine, Nature, that published it, it seems that this is a "major find" for every ID or Creation website out there.

Even though I am not a biologist, after reading what the writer stated and then what the ID sites think she said there's is a reach. I think that the ID and YEC sites are in the words of the great philosopher Inigo Montoya  

---------------------QUOTE-------------------
You keep using that word. I do not think it means what you think it means
---------------------QUOTE-------------------

or am I the one missing something?
---------------------QUOTE-------------------


Yes, the YEC sites are grasping at straws. IMHO, Gura's article (science journalism, not peer reviewed research) exaggerated issues that existed at the time.

Gura's article was taken up almost immediately by the ID crowd. If you go a page or two down into the Google search, you'll find an NCSE site hit. The DI had referenced the Gura article in a bibliography they submitted to the Ohio State BOE, back in 2002. The NCSE site shows that Gura responded to their request for answers to a questionnaire asking if the author agrees that their article questions evolution. (Gura is not quoted by the NCSE, however.)

The ID crowd (Casey Luskin, for example) is never going to engage on the level of incongruence in phylogenies vs the overwhelming level of congruence in those same phylogenies. Its not like one method groups dogs and starfish, while the other doesn't. The incongruences are at the twig level compared to the overall tree of life. Places where the data is spotty on both the molecular and morphological sides.

And in the end, what is the scientific response to incongruences?
< http://elibrary.unm.edu/sora/Auk/v115n01/p0127-p0141.pdf >
Buckle down and find out why, not throw up your hands and say Goddidit.
Posted by: OgreMkV on Feb. 12 2011,08:57

GM Crops.  yeah or nay?
Posted by: Albatrossity2 on Feb. 12 2011,09:10

The problem with GM crops is not biological. If GM crops could be wrested away from the seed and chemical conglomerates (yeah, we're looking at you, Monsanto), there would be some real benefits (salt-tolerant plants, for one). Sadly, that seems very unlikely.
Posted by: Lou FCD on Feb. 12 2011,09:23

I'm moving the troll's comments and responses to them to the BW.



< Religious Vomit >, taken by me just for this purpose, on Flickr.
Posted by: OgreMkV on Feb. 15 2011,10:49

Epic  

< Great Balls of Evolution >

link to paper at the end of the blog post.
Posted by: dvunkannon on Feb. 15 2011,11:41

Quote (OgreMkV @ Feb. 15 2011,11:49)
Epic  

< Great Balls of Evolution >

link to paper at the end of the blog post.
---------------------QUOTE-------------------


Dang, the big cybertank beats me by less than 1 hour.

Yes, epic. A little selection pressure goes a long way. Then serendipity takes over, and you get bacteria that skip all that messy chemistry and head into the realm of Edison. We don't need no stinkin' protons! Electrical bacteria.
Posted by: OgreMkV on Feb. 15 2011,11:50

Quote (dvunkannon @ Feb. 15 2011,11:41)
Quote (OgreMkV @ Feb. 15 2011,11:49)
Epic  

< Great Balls of Evolution >

link to paper at the end of the blog post.
---------------------QUOTE-------------------


Dang, the big cybertank beats me by less than 1 hour.

Yes, epic. A little selection pressure goes a long way. Then serendipity takes over, and you get bacteria that skip all that messy chemistry and head into the realm of Edison. We don't need no stinkin' protons! Electrical bacteria.
---------------------QUOTE-------------------


It was very lucky for me.  I happened to be writing an item about chemosynthesis at the time for the AP test.
Posted by: dvunkannon on Feb. 15 2011,12:17

Satisfy your drool for OOL.

Clay-Armored Bubbles May Have Formed First Protocells: Minerals Could Have Played a Key Role in the Origins of Life

< http://www.sciencedaily.com/releases/2011/02/110207073744.htm >

We've all heard for donkey's ears about montmorillonite, a common clay, and how helpful it can be as a catalyst and tethering spot for long chain molecules. Now it appears that scientists have found a way for it to form vesicles that may help concentrate longer molecules. Short precursors enter the clay shell through pores. This happens more easily than long molecules escape, leading to a natural buildup of long biologically useful molecules.
Posted by: dvunkannon on Feb. 15 2011,12:40

Darwin was wrong (again) (about something he couldn't have known about) (again)!!1!

< http://www.plosgenetics.org/article....1001284 >

The real story, of course, is that Darwin was right. Since Darwin didn't know anything about how traits were passed down, evolution is not the RM+NS creationist shorthand meme. Variation and selection, yes, but variation has many sources. HGT means that even an asexually reproducing bacteria can have two parents.

We can now make the exciting prediction that Lenski's E. coli cultures aren't going to change in any exciting ways, but if you started with a dozen species of archaea, bacteria, and virus, the results would be very different.
Posted by: dvunkannon on Feb. 17 2011,12:04

Yikes! Another electrical bacteria story...

< http://spectrum.ieee.org/biomedi....etworks >

Hmmm... biomass fuel cell... where have I heard this idea before?
Posted by: dvunkannon on Feb. 17 2011,12:14

Paging Roger Penrose...

< http://spectrum.ieee.org/biomedi....roscope >

A very cool experiment in which flies are shown to differentiate between two versions of a chemical, one normal, the other where the hydrogen atoms have been swapped out for deuterium. If smell equalled the molecular shape and charge surface, they shouldn't be able to do that.

I put the shout out to Penrose up top because he has speculated that free will arises from quantum fluctuations in the human brain. This study is about a quantum phenomena in an extension of the brain. I can't wait for this to be picked up by the Spiritual Brain Drain herself.
Posted by: midwifetoad on Feb. 17 2011,13:09

From another site:



---------------------QUOTE-------------------
Binding is a function of molecular shape, polarity and the strength of interactions like hydrogen bonding. On H/D substitution neither shape nor polarity change noticeably, but the hydrogen bonds involving deuterium could indeed vary in energy from those based on normal hydrogen.
Cf. "Effect of Deuterium on the Strength of Hydrogen Bonds", by Melvin Calvin, Jan Hermans Jr., Harold A. Scheraga J. Am. Chem. Soc., 1959, 81 (19), pp 5048–5050
---------------------QUOTE-------------------


Posted by: keiths on Feb. 17 2011,21:45

< Hudson River fish resist PCBs through gene variant >


---------------------QUOTE-------------------
Because the tomcod is resistant to the toxic effects of PCBs they are able to accumulate the industrial chemical in larger amounts than nonresistant creatures without becoming ill or dying, explained Wirgin. His findings were reported Thursday in the online edition of the journal Science.

The resistance is provided by a variant in a single gene that prevents the chemical from binding onto cells in the fish, Wirgin explained.

That variant, he said, is found in about 95 percent of the tomcod in the Hudson. It appears in about 5 percent of tomcod in two smaller streams in Connecticut and on Long Island, and "if you go further from the Hudson you don't see it at all."

...Pollution of the Hudson by PCBs is traced to 1947 and continued for 30 years before being banned. During that period, General Electric Co. plants discharged an estimated 1.3 million pounds of PCBs into the river. Cleanup is continuing.
---------------------QUOTE-------------------


Posted by: Henry J on Feb. 18 2011,09:11



---------------------QUOTE-------------------
On H/D substitution neither shape nor polarity change noticeably, but the hydrogen bonds involving deuterium could indeed vary in energy from those based on normal hydrogen.
---------------------QUOTE-------------------


Really? I thought I read someplace that the angle in a water molecule was different with D's than with H's.
Posted by: midwifetoad on Feb. 18 2011,21:51

Classic Selective Sweeps Were Rare in Recent Human Evolution

< http://www.sciencemag.org/content....78b4aee >
Posted by: dvunkannon on Feb. 23 2011,19:26

< http://www.biology-direct.com/content/pdf/1745-6150-6-14.pdf >

Origin of the genetic code, stereochemical hypothesis yada yada blah blah blah...

Exactly what Stephen Meyer is pretending doesn't exist in Signature in the Cell.
Posted by: Dr.GH on Feb. 24 2011,10:54

Quote (dvunkannon @ Feb. 23 2011,17:26)
< http://www.biology-direct.com/content/pdf/1745-6150-6-14.pdf >

Origin of the genetic code, stereochemical hypothesis yada yada blah blah blah...

Exactly what Stephen Meyer is pretending doesn't exist in Signature in the Cell.
---------------------QUOTE-------------------




---------------------QUOTE-------------------
Conclusion: Taken together, our findings necessarily imply that primordial tRNAs, tRNA aminoacylating ribozymes, and (later) the translation machinery in general have been co-evolving to ‘‘fit’’ the (likely already defined) genetic code, rather than the opposite way around.
---------------------QUOTE-------------------



What?
Posted by: Henry J on Feb. 24 2011,15:08



---------------------QUOTE-------------------
Astronauts In Astrovan Heading to Launch Pad
Thu, 24 Feb 2011 11:04:56 AM MST

The six astronauts of STS-133 are riding in the Astrovan headed to Launch Pad 39A. The countdown is proceeding smoothly this afternoon for a liftoff at 4:50 p.m. EST. Weather forecasters call for a 90 percent chance of acceptable conditions at launch time. For continuous coverage of the countdown, check out NASA's launch blog at < http://www.nasa.gov/mission_pages/shuttle/launch/launch_blog.html >
---------------------QUOTE-------------------


Posted by: dvunkannon on Feb. 26 2011,22:20

Quote (Dr.GH @ Feb. 24 2011,11:54)
Quote (dvunkannon @ Feb. 23 2011,17:26)
< http://www.biology-direct.com/content/pdf/1745-6150-6-14.pdf >

Origin of the genetic code, stereochemical hypothesis yada yada blah blah blah...

Exactly what Stephen Meyer is pretending doesn't exist in Signature in the Cell.
---------------------QUOTE-------------------




---------------------QUOTE-------------------
Conclusion: Taken together, our findings necessarily imply that primordial tRNAs, tRNA aminoacylating ribozymes, and (later) the translation machinery in general have been co-evolving to ‘‘fit’’ the (likely already defined) genetic code, rather than the opposite way around.
---------------------QUOTE-------------------



What?
---------------------QUOTE-------------------


Good question. The paper has some hefty ESL problems. I think they mean that the code (or parts of it) are defined stereochemically, and that the development of the tRNA mechanisms are constrained by this.
Posted by: dvunkannon on Feb. 26 2011,22:24

From the News (to me) Dept.

Energy density of lasers could cause virtual particles to be created, thus disrupting the laser - aka there is a limit to attainable energy densities.
< http://theastronomist.fieldofscience.com/2010/08/limits-on-lasers.html >

Might be useful for beating creationists (like StephenB) over the head with when they start bleating objections to virtual particles.
Posted by: Henry J on Feb. 27 2011,18:04



---------------------QUOTE-------------------
Might be useful for beating creationists (like StephenB) over the head with when they start bleating objections to virtual particles.
---------------------QUOTE-------------------


They'd probably just proceed to claim that the Intelligent Designer used LASERs to implement the designs.

Henry
Posted by: Richardthughes on Mar. 01 2011,13:58

< http://b3ta.com/challenge/kittenscience/popular/ >
Posted by: OgreMkV on Mar. 06 2011,08:03

Alien Life in Meteorites?  A new report was published online late Friday night.

< My blog has a report and links to the original article and popular treatment at Yahoo. >

< Original Report (for us hard corer science geeks) >
Posted by: OgreMkV on Mar. 06 2011,09:29

And PZ slaps it down here: < http://scienceblogs.com/pharyng....ter.php >
Posted by: dvunkannon on Mar. 09 2011,14:53

< http://www.the-scientist.com/news/display/58044/ >

Big brains and spineless penises
How DNA deletions may have produced uniquely human traits

Cue the pen15 jokes in 3, 2,...
Posted by: dvunkannon on Mar. 18 2011,12:26

A very readable review article on transposable elements and their role in evolution.
< http://www.biology-direct.com/content/pdf/1745-6150-6-19.pdf >


Does anyone have a good recent article on the subject of virus-bacteria competition as a driver of early evolution (2-3 Gya)? Many thanks!
Posted by: dvunkannon on Mar. 18 2011,15:06

< http://www.the-scientist.com/news/display/58057/ >

A new article based on the Lenski E.coli studies. Sure to incite the masses at UD!
Posted by: Richardthughes on Mar. 18 2011,15:37

no doubt " long-term evolvability" will equal front-loading for them. Somehow.
Posted by: keiths on Mar. 22 2011,19:37

< Religion may become extinct in nine nations, study says >


---------------------QUOTE-------------------
A study using census data from nine countries shows that religion there is set for extinction, say researchers.

The study found a steady rise in those claiming no religious affiliation.

The team's mathematical model attempts to account for the interplay between the number of religious respondents and the social motives behind being one.

The result, reported at the American Physical Society meeting in Dallas, US, indicates that religion will all but die out altogether in those countries.
---------------------QUOTE-------------------


Posted by: dvunkannon on Mar. 22 2011,19:42

< http://www.sciencedaily.com/releases/2011/03/110321161904.htm >

Re-analysis of another Miller experiment, this time from 1958, yields more rich amino acid mixtures.
Posted by: Henry J on Mar. 22 2011,22:21

Ah, but how much information is in those mixtures!!111!!!eleven!!!
Posted by: Steverino on Mar. 24 2011,07:27

Gerneal question I was sent in response to humam chromosome 2:



---------------------QUOTE-------------------

Honestly ... is there any similar two species ... with the same 99% gene relation such as the man-chimp ... with one having a combined chromosomes 6 or 8 or whatever ... there must be evidence that combination of chromosomes can lead to evolutionary speciation. Because as far what I know; combining genes results to two things only.
---------------------QUOTE-------------------




Anyone?
Posted by: Louis on Mar. 24 2011,07:36

Quote (Henry J @ Mar. 23 2011,04:21)
Ah, but how much information is in those mixtures!!111!!!eleven!!!
---------------------QUOTE-------------------


2.

I defy any IDCist to demonstrate my calculation of the quantity of information in the mixtures is wrong.

Louis
Posted by: OgreMkV on Mar. 24 2011,09:28

Quote (Steverino @ Mar. 24 2011,07:27)
Gerneal question I was sent in response to humam chromosome 2:

 

---------------------QUOTE-------------------

Honestly ... is there any similar two species ... with the same 99% gene relation such as the man-chimp ... with one having a combined chromosomes 6 or 8 or whatever ... there must be evidence that combination of chromosomes can lead to evolutionary speciation. Because as far what I know; combining genes results to two things only.
---------------------QUOTE-------------------




Anyone?
---------------------QUOTE-------------------


I don't think enough species have been sequenced yet to be able to answer that.

I'd think that the condition is at least somewhat rare, but that's based on a very limited sample size.  Two chromosomes have to combine in such a way that both retain their (hah) information and (double hah) functionality.  

It could be an extremly rare thing, it could be common.  

Honestly, though, it doesn't matter.  It happened once and there are many pieces of evidence to support that.  So, we know it can happen.  That supports common descent and effectively disproves special creation of humans.
Posted by: Erasmus, FCD on Mar. 24 2011,09:55

hard to understand if the question doesn't mistake genes for chromosomes or what.  evolution along chromosomes at least in theory can partly explain some speciation events

i think everyone can see this one

< http://www.hummingbirds.arizona.edu/Courses....001.pdf >

this one has good refs

< http://www.indiana.edu/~ensiweb/chrom.spec.html >
Posted by: dvunkannon on Mar. 24 2011,13:11

Quote (Steverino @ Mar. 24 2011,08:27)
Gerneal question I was sent in response to humam chromosome 2:

 

---------------------QUOTE-------------------

Honestly ... is there any similar two species ... with the same 99% gene relation such as the man-chimp ... with one having a combined chromosomes 6 or 8 or whatever ... there must be evidence that combination of chromosomes can lead to evolutionary speciation. Because as far what I know; combining genes results to two things only.
---------------------QUOTE-------------------




Anyone?
---------------------QUOTE-------------------


I agree with OgreMkV, with the caveat that you can see the possible fusion site at the "banding of the chromosome" level of analysis, you don't need fully sequenced genomes. Then sequence just the apparent fusion site and look for the mirrored telomere sequences.

There was a recent UD post on "interstitial telomeric sequences". Googling that phrase, "Robertsonian translocation", and "chromosome fusion" got some interesting hits.

Some assert that fusion is common. Maybe it is.

Robertsonian translocation seems to happen frequently in humans, 1 of 1000 live births. While the chimp 2a and 2b chromosomes look like candidates for Robertsonian translocation due to their long/short arms, the fusion that separates humans from chimps is not Robertsonian, because the short arms survived the fusion. However, your correspondent may be lumping the categories together as evidenced by the last sentence.

The point of the UD post was that there are a lot of ITS sites inside the human genome. A good number are associated with inversions, which makes sense. If the end of a chromosome breaks off, flips around and reattaches, you get an inversion with associated ITS, assuming the end gets a new telomere and you survive. That is not completely relevant to the situation at the fusion site, which has a mirrored ITS.

Bottom line: the fusion of 2a and 2b preserved all genetic material. Other common fusion types, such as Robertsonian translocation, do not. Humans rarely mate with close relatives. Other primates may, given their close social groups. So a need to "marry your sister" to make a fusion event viable is not insurmountable.
Posted by: dvunkannon on Mar. 31 2011,13:17

< http://www.scientificamerican.com/article....roteins >

A nice article in the print edition of SciAm on proteins that don't need to fold completely to show function. There is a section towards the end of the article on evolution and how unfolded proteins could have been functional in early life. Makes the point that light, hydrophilic AAs seem to have entered the genetic code early, and these are the AAs that show up preferentially in in unfolded proteins. Conclusion is that unfolded proteins could have been catalytic in the RNA World.
Posted by: fnxtr on April 01 2011,09:08

< Bwahahaha! >

The best part is the comments section, a veritable Poe-puree.  :-)
Posted by: dvunkannon on April 02 2011,21:34

< http://www.sciencedaily.com/releases/2011/03/110330131310.htm >

In silico, whole cell simulation.
Posted by: REC on April 05 2011,15:28

I'm not sure if this was posted here yet (I had missed it!):

Experimental support for the evolution of symmetric protein architecture from a simple peptide motif

Jihun Lee and Michael Blaber (2011)
PNAS  108(1):126-13
doi: 10.1073/pnas.1015032108      



---------------------QUOTE-------------------
The majority of protein architectures exhibit elements of structural symmetry, and “gene duplication and fusion” is the evolutionary mechanism generally hypothesized to be responsible for their emergence from simple peptide motifs. Despite the central importance of the gene duplication and fusion hypothesis, experimental support for a plausible evolutionary pathway for a specific protein architecture has yet to be effectively demonstrated. To address this question, a unique “top-down symmetric deconstruction” strategy was utilized to successfully identify a simple peptide motif capable of recapitulating, via gene duplication and fusion processes, a symmetric protein architecture (the threefold symmetric ?-trefoil fold). The folding properties of intermediary forms in this deconstruction agree precisely with a previously proposed “conserved architecture” model for symmetric protein evolution. Furthermore, a route through foldable sequence-space between the simple peptide motif and extant protein fold is demonstrated. These results provide compelling experimental support for a plausible evolutionary pathway of symmetric protein architecture via gene duplication and fusion processes.
---------------------QUOTE-------------------



Great support for the idea that longer peptides with complex folds may have evolved from shorter peptides with simple folds. The symmetry around protein motifs we see indicates molecular fossils of simpler translation motifs, or folding units. And each step of gene duplication and fusion seems thermodynamically viable-showing a putative evolutionary path.

Needless to say, the big big numbers crowd won't like this.
Posted by: Henry J on April 06 2011,10:00

Big big numbers crowd? And here I thought those guys didn't like numbers much larger than 6000 or so...
Posted by: dvunkannon on April 06 2011,14:49

< http://www.the-scientist.com/news/display/58105/ >

Retinas from Stem Cells

Actual article is in Nature. We were talking about eye development recently on another thread, and I hypothesized that simple differential growth rates on one side or the other of a film would bow it inward to form an optical cup, or outward as in the arthropod eye. So it was nice to see this


---------------------QUOTE-------------------
"Certain mechanical forces were involved to shape the cup," Tsonis said, but the details of that process are still unclear.
---------------------QUOTE-------------------


Posted by: Lou FCD on April 06 2011,16:04

Quote (dvunkannon @ April 06 2011,15:49)


---------------------QUOTE-------------------
but the details of that process are still unclear.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


Obvious joke is obvious.
Posted by: REC on April 14 2011,17:31

Hey RNA-world kids-

Ribozyme-Catalyzed Transcription of an Active Ribozyme
Science 8 April 2011:  Vol. 332 no. 6026 pp. 209-212
DOI: 10.1126/science.1200752

The authors evolve a ribozyme, selected from a previous study, into an efficient polymerase, capable of transcribing many different sequences from a complementary template. The evolved ribozyme was shown to be able to synthesize a naturally occurring ribizyme, called the hammerhead ribozyme. All with in vitro selection and evolution.
Posted by: midwifetoad on April 15 2011,05:13

Phonemic Diversity Supports a Serial Founder Effect Model of Language Expansion from Africa

< http://www.sciencemag.org/content/332/6027/346.abstract >

< http://www.nytimes.com/2011....al-home >



---------------------QUOTE-------------------
The finding fits well with the evidence from fossil skulls and DNA that modern humans originated in Africa. It also implies, though does not prove, that modern language originated only once, an issue of considerable controversy among linguists.

The detection of such an ancient signal in language is surprising. Because words change so rapidly, many linguists think that languages cannot be traced very far back in time. The oldest language tree so far reconstructed, that of the Indo-European family, which includes English, goes back 9,000 years at most
---------------------QUOTE-------------------


Posted by: Henry J on April 15 2011,23:11

Ah, so the tower of Babel is slightly older than previously thought? ;)

Henry
Posted by: Albatrossity2 on April 16 2011,11:30

< Evolutionary analysis applied to languages. >

Common descent is a good explanatory framework.
Posted by: Kristine on April 16 2011,13:29

I just attended the science teachers workshop, "Fossils, Bones & Primates:  Enriching High School Teaching," open to the public, at the American Association of Physical Anthropologists annual meeting in Mpls. Great presentations, resources, and exchange of ideas; I met Dr. Andrew Petto, of the University of Wisconsin-Milwaukee, along with many educators and grad students, and I hope to turn this into another article with resources and links.  

(Oh, I forgot to say, my article on the Brooklyn Public Library's "Human Genome Project Community Conversations" program will be published soon in Public Libraries.)
Posted by: fnxtr on April 16 2011,18:38

Quote (Kristine @ April 16 2011,11:29)
I just attended the science teachers workshop, "Fossils, Bones & Primates:  Enriching High School Teaching," open to the public, at the American Association of Physical Anthropologists annual meeting in Mpls. Great presentations, resources, and exchange of ideas; I met Dr. Andrew Petto, of the University of Wisconsin-Milwaukee, along with many educators and grad students, and I hope to turn this into another article with resources and links.  

(Oh, I forgot to say, my article on the Brooklyn Public Library's "Human Genome Project Community Conversations" program will be published soon in Public Libraries.)
---------------------QUOTE-------------------


Brava, again. :-)
Posted by: Kristine on April 17 2011,11:09

Quote (fnxtr @ April 16 2011,18:38)
Quote (Kristine @ April 16 2011,11:29)
I just attended the science teachers workshop, "Fossils, Bones & Primates:  Enriching High School Teaching," open to the public, at the American Association of Physical Anthropologists annual meeting in Mpls. Great presentations, resources, and exchange of ideas; I met Dr. Andrew Petto, of the University of Wisconsin-Milwaukee, along with many educators and grad students, and I hope to turn this into another article with resources and links.  

(Oh, I forgot to say, my article on the Brooklyn Public Library's "Human Genome Project Community Conversations" program will be published soon in Public Libraries.)
---------------------QUOTE-------------------


Brava, again. :-)
---------------------QUOTE-------------------


< A summation and some photos >.

When am I going to get paid for doing this? ;)
Posted by: Dr.GH on April 17 2011,12:18

Quote (Kristine @ April 17 2011,09:09)
When am I going to get paid for doing this? ;)
---------------------QUOTE-------------------


That is a profound question my wife has often asked me.
Posted by: Kristine on April 17 2011,12:58

Quote (Dr.GH @ April 17 2011,12:18)
Quote (Kristine @ April 17 2011,09:09)
When am I going to get paid for doing this? ;)
---------------------QUOTE-------------------


That is a profound question my wife has often asked me.
---------------------QUOTE-------------------


If I only had a dollar for every time an editor said to me in the past year, "You do realize that scholarly publication is gratis, and that we cannot pay you?" Yes, we know. :)

Money isn't important. I need it, but it is not of prime importance.
Posted by: Timothy McDougald on April 23 2011,08:56

< I'm sure Robert Byers would say that this is just a lizard >



---------------------QUOTE-------------------
“This rainforest skink has an almost identical giant, hammer-tooth in its dentition and in this case we know what it’s used for: crushing the hard shells of snails, one of the main foods of this rainforest skink,” says Dr Hocknull.

"It appears Malleodectes evolved millions of years ago to exploit the ecological niche occupied today by these specialised lizards," says Dr Arena.

The researchers say the similarity between the teeth of the fossil marsupials and the living skink is a remarkable example of evolutionary convergence.
---------------------QUOTE-------------------


Posted by: Albatrossity2 on April 23 2011,20:51

Do ya think that the "author" of The Spatula Brain cares about Buddhist monks?
< http://www.bbc.co.uk/news/world-us-canada-12661646 >
Coffee!!!
Posted by: Kristine on April 26 2011,16:38

< Challenger Center webcasts >
Posted by: dvunkannon on April 28 2011,13:49

A guy that is also in my SF club sent around a YouTube video on Fibonacci, therefore Jebus.
< http://www.youtube.com/watch?v=e9MwNm0gXd8 >

My response:


---------------------QUOTE-------------------
I've seen this appeal to the Fibonacci sequence before in jousting with anti-evolution and anti-science folks on the internet. You can hear and see that as the presentation gets away from organic growth and talks about waves and galaxies, the language gets more soft. People have especially criticized seeing Fibonacci spirals in galaxies as an example of pareidolia - seeing patterns where we want to see them.

Nautilus spirals and Fibonacci Numbers - Busted!
< http://www.shallowsky.com/blog/science/fibonautilus.html >
Busted and Stomped On!
[URL=http://www.lhup.edu/~dsimanek/pseudo/fibonacc.htm
---------------------QUOTE-------------------



Until I googled it, I had gone along with the Nautilus-Fibonacci linkage. Now I see this is just another example of careful picking of evidence to support the case, and wrong at that.

Giving it a little more thought, a logarithmic (Fibonacci) spiral is space filling, and the shell reinforces itself. Other spiral patterns (seen in fossils) don't, and therefore would be more likely to break, affecting the expected survival of the organism. So these spirals are under evolutionary pressure, and the surviving patterns are examples of evolutionary arms races and selection pressures, not Jebus-doodles.

(The video misses an opportunity to link fingerprints and Fibonacci by failing to note the whorls in fingerprints and zooming in on a suitably spiral shaped picture.)
Posted by: Kristine on April 28 2011,20:56

This Saturday I shall be in a group of about 15 people heading out to rural MN to launch a balloon with payloads into the atmosphere, and retrieving it after it parachutes when the balloon bursts. I did not make up a payload (a lot of this was over my head), but I will be photographing and writing about the event. :)

We will be tracking the payload via radio frequency, and I think someone scrounged up a camera to launch. Another guy is writing up the curriculum to give to schools.

ETA - We had to cancel due to weather. Alternate date: end of May


Posted by: Kristine on April 29 2011,12:46

< Electrical Oscillations Found to be Critical > for Storing Spatial Memories in Brain.



---------------------QUOTE-------------------
"This important result shows that, in general, you can eliminate a substantial amount of incoming information to a brain circuit without that brain circuit losing a majority of its functionality," he adds. "The implication of this finding is that restoring memory function does not require that we exactly reassemble damaged neural circuitry, rather we can regain function by preserving or restoring key components."
---------------------QUOTE-------------------


Posted by: dvunkannon on May 03 2011,14:26

Apparently, not only did the Good Lord see fit to hide bone shaped rocks deep in the Earth, but He also hid bone proteins in some of them.

< http://www.plosone.org/article....0019445 >
Posted by: Henry J on May 03 2011,14:29

Is that why some people think they have a bone to pick...
Posted by: dvunkannon on May 03 2011,16:49

Speculative question: Does a black hole have a hab zone?

The accretion disc goes from cold gas to x-ray emitting plasma. Somewhere inbetween, it is room temperature.
Posted by: Henry J on May 03 2011,17:09

But do objects stay in that zone for enough time to matter, or do they just fall through it?
Posted by: dvunkannon on May 04 2011,05:50

Quote (Henry J @ May 03 2011,18:09)
But do objects stay in that zone for enough time to matter, or do they just fall through it?
---------------------QUOTE-------------------


According to the Wikipedia article on accretion discs, particles travel in a tight spiral, almost circular orbits. Also, radiation pressure and eddies push some material outward temporarily. So I think residence time could be pretty high.
Posted by: Albatrossity2 on May 04 2011,06:42

Interesting news about < thylacines. >
Posted by: OgreMkV on May 04 2011,07:57

Quote (dvunkannon @ May 04 2011,05:50)
Quote (Henry J @ May 03 2011,18:09)
But do objects stay in that zone for enough time to matter, or do they just fall through it?
---------------------QUOTE-------------------


According to the Wikipedia article on accretion discs, particles travel in a tight spiral, almost circular orbits. Also, radiation pressure and eddies push some material outward temporarily. So I think residence time could be pretty high.
---------------------QUOTE-------------------


Depends on what you mean by habitable.  The density of material around the black hole is probably high enough with enough energy to create a fair bit of frictional drag, so I doubt the residence time would be all that much.

Too, the infalling matter causes jets of x-rays and other nastiness, so that might be a problem.

OTOH, there are black holes at the center of galaxies and they are obviously long-lived structures.
Posted by: OgreMkV on May 04 2011,08:32

Quote (Albatrossity2 @ May 04 2011,06:42)
Interesting news about < thylacines. >
---------------------QUOTE-------------------


Someone needs to let Robert Byers know...
Posted by: Henry J on May 04 2011,23:07

Letting that guy know something is not one of my skills.

Henry
Posted by: midwifetoad on May 05 2011,06:01

A facepalm enabled wolf.
Posted by: dvunkannon on May 10 2011,20:11

< http://www.sciencedaily.com/releases/2011/05/110509113254.htm >

Calculation of the "Hoyle nucleus" of Carbon

This story should get some coverage over on UD. The Hoye nucleus is that state of the carbon nucleus with very similar energy to three helium nuclei. The similarity allows fusion in stars to create carbon readily, and from there, the rest of the larger atomic nuclei up to iron. (Nuclei bigger than iron only get formed when stars explode.)

Hoyle considered the similarity to be an example of cosmic fine tuning, without which we would not exist. As this article points out, this was pretty much an assertioin for the last 50 years, but now we are in a position to actually calculate whether it does depend sensitively on other physical constants, and if so, what they are and over what range.

Several years ago, I asked an astrophysicist if the resonance was necessary or just helpful. In our normal model of stellar evolution, as the star ages and uses up hydrogen in the core, it starts fusing helium nuclei. Two He-4 nuclei form an unstable Beryllium-8, but if another He-4 comes along they can form a stable C-12. Everyone agrees the process proceeds faster because of the resonance. My question was - if the resonance didn't exist, would a similar amount of carbon be formed, just later, when the core had reached a higher temperature?

If you do have to wait, that by itself would knock down the total amount of carbon in the universe, since some smaller stars would never reach that temperature without the help of fusing larger and larger nuclei. Their fusion proces would stall, and they would evolve towards red dwarfdom, as small stars do in the real physics of our universe. But we are the result of large stars blowing up, so I discount this effect in deciding whether there would be enough carbon for life.

On the other hand, you can't just tinker with the resonance without explaining why it would be different than it is. Changing whatever underlies the resonance of C-12 and 3 He-4 would necessarily change other things as well, perhaps in the direction of producing Carbon by a different route through a new or strengthened alernative resonance. This is of course never considered by fine tuning enthusiasts. Now we are starting to put the tools together to test these ideas.
Posted by: dvunkannon on May 11 2011,15:04

Quote (dvunkannon @ May 10 2011,21:11)
< http://www.sciencedaily.com/releases/2011/05/110509113254.htm >

Calculation of the "Hoyle nucleus" of Carbon

This story should get some coverage over on UD. The Hoye nucleus is that state of the carbon nucleus with very similar energy to three helium nuclei. The similarity allows fusion in stars to create carbon readily, and from there, the rest of the larger atomic nuclei up to iron. (Nuclei bigger than iron only get formed when stars explode.)

Hoyle considered the similarity to be an example of cosmic fine tuning, without which we would not exist. As this article points out, this was pretty much an assertioin for the last 50 years, but now we are in a position to actually calculate whether it does depend sensitively on other physical constants, and if so, what they are and over what range.

Several years ago, I asked an astrophysicist if the resonance was necessary or just helpful. In our normal model of stellar evolution, as the star ages and uses up hydrogen in the core, it starts fusing helium nuclei. Two He-4 nuclei form an unstable Beryllium-8, but if another He-4 comes along they can form a stable C-12. Everyone agrees the process proceeds faster because of the resonance. My question was - if the resonance didn't exist, would a similar amount of carbon be formed, just later, when the core had reached a higher temperature?

If you do have to wait, that by itself would knock down the total amount of carbon in the universe, since some smaller stars would never reach that temperature without the help of fusing larger and larger nuclei. Their fusion proces would stall, and they would evolve towards red dwarfdom, as small stars do in the real physics of our universe. But we are the result of large stars blowing up, so I discount this effect in deciding whether there would be enough carbon for life.

On the other hand, you can't just tinker with the resonance without explaining why it would be different than it is. Changing whatever underlies the resonance of C-12 and 3 He-4 would necessarily change other things as well, perhaps in the direction of producing Carbon by a different route through a new or strengthened alernative resonance. This is of course never considered by fine tuning enthusiasts. Now we are starting to put the tools together to test these ideas.
---------------------QUOTE-------------------


< http://physics.aps.org/pdf/10.1103/PhysRevLett.106.192501.pdf >

The money quote, at least for Hoyle worshipers.
   

---------------------QUOTE-------------------
We note the 17 MeV reduction in the ground state binding energy and 12 MeV reduction for the Hoyle state while less than half as much binding correction for the spin-2 state. This degree of freedom in the energy spectrum suggests that at least some fine-tuning of parameters is needed to set the Hoyle state energy near the 8Be-alpha threshold. It would be very interesting to understand which fundamental parameters in nature control this fine-tuning. At the most fundamental level there are only a few such parameters, one of the most interesting being the masses of the up and down quarks.
---------------------QUOTE-------------------



Emboldenation by mois.
Posted by: Albatrossity2 on May 11 2011,16:55

< Missing link discovered > between "fungi and the rest of the kingdom of life."

Or, as the IDiots would observe - Two new gaps!
Posted by: dvunkannon on May 11 2011,16:59

Quote (dvunkannon @ May 11 2011,16:04)
   
Quote (dvunkannon @ May 10 2011,21:11)
< http://www.sciencedaily.com/releases/2011/05/110509113254.htm >

Calculation of the "Hoyle nucleus" of Carbon

This story should get some coverage over on UD. The Hoye nucleus is that state of the carbon nucleus with very similar energy to three helium nuclei. The similarity allows fusion in stars to create carbon readily, and from there, the rest of the larger atomic nuclei up to iron. (Nuclei bigger than iron only get formed when stars explode.)

Hoyle considered the similarity to be an example of cosmic fine tuning, without which we would not exist. As this article points out, this was pretty much an assertioin for the last 50 years, but now we are in a position to actually calculate whether it does depend sensitively on other physical constants, and if so, what they are and over what range.

Several years ago, I asked an astrophysicist if the resonance was necessary or just helpful. In our normal model of stellar evolution, as the star ages and uses up hydrogen in the core, it starts fusing helium nuclei. Two He-4 nuclei form an unstable Beryllium-8, but if another He-4 comes along they can form a stable C-12. Everyone agrees the process proceeds faster because of the resonance. My question was - if the resonance didn't exist, would a similar amount of carbon be formed, just later, when the core had reached a higher temperature?

If you do have to wait, that by itself would knock down the total amount of carbon in the universe, since some smaller stars would never reach that temperature without the help of fusing larger and larger nuclei. Their fusion proces would stall, and they would evolve towards red dwarfdom, as small stars do in the real physics of our universe. But we are the result of large stars blowing up, so I discount this effect in deciding whether there would be enough carbon for life.

On the other hand, you can't just tinker with the resonance without explaining why it would be different than it is. Changing whatever underlies the resonance of C-12 and 3 He-4 would necessarily change other things as well, perhaps in the direction of producing Carbon by a different route through a new or strengthened alernative resonance. This is of course never considered by fine tuning enthusiasts. Now we are starting to put the tools together to test these ideas.
---------------------QUOTE-------------------


< http://physics.aps.org/pdf/10.1103/PhysRevLett.106.192501.pdf >

The money quote, at least for Hoyle worshipers.
       

---------------------QUOTE-------------------
We note the 17 MeV reduction in the ground state binding energy and 12 MeV reduction for the Hoyle state while less than half as much binding correction for the spin-2 state. This degree of freedom in the energy spectrum suggests that at least some fine-tuning of parameters is needed to set the Hoyle state energy near the 8Be-alpha threshold. It would be very interesting to understand which fundamental parameters in nature control this fine-tuning. At the most fundamental level there are only a few such parameters, one of the most interesting being the masses of the up and down quarks.
---------------------QUOTE-------------------



Emboldenation by mois.
---------------------QUOTE-------------------


OK, I hope you don't think I'm being a dick about this for posting three times on the same article, but I think this is important.

Why? Because of Hoyle's approach and use of anthropic reasoning, and the subsequent uptake by fine tuning anti-science folk, that's why. Besides, this is damn hard for me to understand, and I'd like to make sure I do understand it.

So, Hoyle says this resonance _must_ exist because we exist, and further, this shows that the universe has been mightily fine tuned.

So what is this amazing fine tuning?

Look at table 1 in the paper.

Be-8 + He-4 = -84.8 MeV
C-12 = -92.16 MeV

Difference? 8%

As a result of which, 4 out of 10,000 Be-8 and He-4 collisions go on to become C-12.

I gotta say, I'm way disappointed. I thought I was going to hear that the difference was only 0.000000...8%, not 8%, and that C-12 production was 9,000 out of 10,000, not 4.

What is Hoyle saying? If it was 8.00001%, then the successful collision rate would crash to 4 in a billion? If it was 7.9999999% the rate would shoot up to 4 out of 10? That in one case no star could evolve synthesize carbon, and in the other the universe would be awash in carbon? I've never heard a numerical guess like that attributed to him, just that the existence of the resonance convinced him a deity exists.

The paper does speculate that the resonance depends on the ratio of the mass of the up and down quarks. Cool, that is a step towards understanding it. But if we imagine the fine tuning in these terms, changing this ratio will also change the energy levels of Be-8 and He-4. A resonance at one energy level might disappear, while one at another level will be created. Hoyle didn't work all that out, did he? No, he just asserted that changing some unknown parameter by any amount would wreck the known resonance, and nothing would replace it.

That is not science.
Posted by: Henry J on May 11 2011,17:15



---------------------QUOTE-------------------
Missing link discovered between "fungi and the rest of the kingdom of life."
---------------------QUOTE-------------------


Kingdom of life? i thought "kingdom" described groups that are a subset of a domain, as plants, animals, and fungi are each a subset of the Eucaryote domain.
Posted by: OgreMkV on May 16 2011,13:03

< http://www.sciencedaily.com/releases/2011/05/110511162538.htm >

Research shows that highly complex evolutionary adaptations are more difficult (i.e. more rare) to reverse.

From the blindingly obvious department, but it's good to see someone putting some numbers on this.
Posted by: midwifetoad on May 16 2011,13:12

Quote (OgreMkV @ May 16 2011,13:03)
< http://www.sciencedaily.com/releases/2011/05/110511162538.htm >

Research shows that highly complex evolutionary adaptations are more difficult (i.e. more rare) to reverse.

From the blindingly obvious department, but it's good to see someone putting some numbers on this.
---------------------QUOTE-------------------


Do I get banned for suggesting that this is a possible approach to calculating CSI?  :p
Posted by: J-Dog on May 16 2011,13:15

BLAST FROM THE PAST!!

Orac does DCA Update - DaveScot Still Wrong! :)

< DCA Update >
Posted by: OgreMkV on May 16 2011,14:04

Quote (midwifetoad @ May 16 2011,13:12)
Quote (OgreMkV @ May 16 2011,13:03)
< http://www.sciencedaily.com/releases/2011/05/110511162538.htm >

Research shows that highly complex evolutionary adaptations are more difficult (i.e. more rare) to reverse.

From the blindingly obvious department, but it's good to see someone putting some numbers on this.
---------------------QUOTE-------------------


Do I get banned for suggesting that this is a possible approach to calculating CSI?  :p
---------------------QUOTE-------------------


Only at UD.  I've got the paper and will read it when I have time... which unfortunately means sometime in late August probably.
Posted by: Erasmus, FCD on May 16 2011,14:19

Quote (J-Dog @ May 16 2011,14:15)
BLAST FROM THE PAST!!

Orac does DCA Update - DaveScot Still Wrong! :)

< DCA Update >
---------------------QUOTE-------------------


i sure do wish he would chugalug the houseboat over to within reach of a wireless router and chime in.  what the fuck does it take?
Posted by: paragwinn on May 16 2011,14:43

Quote (Erasmus @ FCD,May 16 2011,12:19)
Quote (J-Dog @ May 16 2011,14:15)
BLAST FROM THE PAST!!

Orac does DCA Update - DaveScot Still Wrong! :)

< DCA Update >
---------------------QUOTE-------------------


i sure do wish he would chugalug the houseboat over to within reach of a wireless router and chime in.  what the fuck does it take?
---------------------QUOTE-------------------


Maybe he's off fighting Somali pirates or searching for Capt Jack Sparrow to join his crew.
Posted by: dvunkannon on May 16 2011,16:48

Quote (paragwinn @ May 16 2011,15:43)
Quote (Erasmus @ FCD,May 16 2011,12:19)
 
Quote (J-Dog @ May 16 2011,14:15)
BLAST FROM THE PAST!!

Orac does DCA Update - DaveScot Still Wrong! :)

< DCA Update >
---------------------QUOTE-------------------


i sure do wish he would chugalug the houseboat over to within reach of a wireless router and chime in.  what the fuck does it take?
---------------------QUOTE-------------------


Maybe he's off fighting Somali pirates or searching for Capt Jack Sparrow to join his crew.
---------------------QUOTE-------------------


While we're reminiscing about DT and waiting for the Rapture/Zombie Apocalypse...

Does anyone know how the owner of the Floating Command Center first hooked up with permanent student and occasional professor, Dr Dr WmAD? Its got to be a story worth telling, especially if it involves the bathroom of the Riesel YMCA during the break in the middle of an AA (Arrogance Anonymous) meeting, a bodily appendage coyly referred to a 'Single Malt', and a Canadian friend introduced as 'Dennis' O'Leary.
Posted by: J-Dog on May 16 2011,19:50

Quote (dvunkannon @ May 16 2011,16:48)
Quote (paragwinn @ May 16 2011,15:43)
Quote (Erasmus @ FCD,May 16 2011,12:19)
 
Quote (J-Dog @ May 16 2011,14:15)
BLAST FROM THE PAST!!

Orac does DCA Update - DaveScot Still Wrong! :)

< DCA Update >
---------------------QUOTE-------------------


i sure do wish he would chugalug the houseboat over to within reach of a wireless router and chime in.  what the fuck does it take?
---------------------QUOTE-------------------


Maybe he's off fighting Somali pirates or searching for Capt Jack Sparrow to join his crew.
---------------------QUOTE-------------------


While we're reminiscing about DT and waiting for the Rapture/Zombie Apocalypse...

Does anyone know how the owner of the Floating Command Center first hooked up with permanent student and occasional professor, Dr Dr WmAD? Its got to be a story worth telling, especially if it involves the bathroom of the Riesel YMCA during the break in the middle of an AA (Arrogance Anonymous) meeting, a bodily appendage coyly referred to a 'Single Malt', and a Canadian friend introduced as 'Dennis' O'Leary.
---------------------QUOTE-------------------


Hey!  I can finally say yes to that Buy My Book question!

Do I get a deal for pre-ordering?  

And something tells me I am right in assuming that the Real True ID Story™ will not be for sale in your basic Church Basement...
Posted by: dvunkannon on May 16 2011,20:44

< http://www.sciencedaily.com/releases/2011/05/110516080124.htm >

Gliese 581d habitable!

Now we know where the Rapture is going to take all those folks in a few days...

Tidally locked, the side facing the sun would be a great place for the Heavenly Throne. The Deity would have this natural backlight for a halo effect.

On the other hand, its a red dwarf. Dank, murky atmosphere on one side, eternal darkness and ice on the other, guys named Dante wandering the surface... maybe that's not the Rapture, maybe its.... SATAN!
Posted by: dvunkannon on May 16 2011,21:29

Quote (J-Dog @ May 16 2011,20:50)
Quote (dvunkannon @ May 16 2011,16:48)
Quote (paragwinn @ May 16 2011,15:43)
 
Quote (Erasmus @ FCD,May 16 2011,12:19)
   
Quote (J-Dog @ May 16 2011,14:15)
BLAST FROM THE PAST!!

Orac does DCA Update - DaveScot Still Wrong! :)

< DCA Update >
---------------------QUOTE-------------------


i sure do wish he would chugalug the houseboat over to within reach of a wireless router and chime in.  what the fuck does it take?
---------------------QUOTE-------------------


Maybe he's off fighting Somali pirates or searching for Capt Jack Sparrow to join his crew.
---------------------QUOTE-------------------


While we're reminiscing about DT and waiting for the Rapture/Zombie Apocalypse...

Does anyone know how the owner of the Floating Command Center first hooked up with permanent student and occasional professor, Dr Dr WmAD? Its got to be a story worth telling, especially if it involves the bathroom of the Riesel YMCA during the break in the middle of an AA (Arrogance Anonymous) meeting, a bodily appendage coyly referred to a 'Single Malt', and a Canadian friend introduced as 'Dennis' O'Leary.
---------------------QUOTE-------------------


Hey!  I can finally say yes to that Buy My Book question!

Do I get a deal for pre-ordering?  

And something tells me I am right in assuming that the Real True ID Story™ will not be for sale in your basic Church Basement...
---------------------QUOTE-------------------


It is all right here in the Gospel According To Chunkdz, which angels revealed to Sal Cordova during a lucid dream. Written on thin premium latex with ridges for extra sensation, a sample of the Gospel According To Chunkdz:

Chapter 3
17 "Davey, you must be the only Marine I've ever met that doesn't know how to hold your liquor. I guess I'm gonna have to give  you a lesson in how to take a shot of Single Malt." 18 The Good Doctor smiled wickedly at his friend Dennis, who was blushing under his beard. "Or if you like blended, we've got some Canadian Club too." 19 Dennis patted his skin tight denims, where he must have been hiding a flask.
20 Davey felt butterflies in his stomach. "Its just because I'm an autodidact. I never had a real professor give me a lesson. Two doctorates, wow, I really look up to you."
21 "Get on your knees, son, and you can look up to me all night long."
Posted by: Henry J on May 16 2011,21:56

Space Shuttle Endeavour took off this morning!



---------------------QUOTE-------------------
The crew members for space shuttle Endeavour's STS-134 mission are Commander Mark Kelly, Pilot Gregory H. Johnson and Mission Specialists Michael Fincke, Greg Chamitoff, Andrew Feustel and European Space Agency astronaut Roberto Vittori.

During the 16-day mission, Endeavour and its crew will deliver the Alpha Magnetic Spectrometer (AMS) and spare parts including two S-band communications antennas, a high-pressure gas tank and additional spare parts for Dextre.
---------------------QUOTE-------------------



Henry
Posted by: Hermagoras on May 19 2011,15:17

I, Hermagoras, have published a paper in Science!  < Inquiry-Based Writing in the Laboratory Course > (with Cary Moskovitz).  

Complete with random meme duplication and mutation on the second page.  Compositor error, post-galley-proofs.  We've sent a request for correction.
Posted by: Reciprocating Bill on May 19 2011,15:49

Quote (Hermagoras @ May 19 2011,16:17)
I, Hermagoras, have published a paper in Science!  < Inquiry-Based Writing in the Laboratory Course > (with Cary Moskovitz).  

Complete with random meme duplication and mutation on the second page.  Compositor error, post-galley-proofs.  We've sent a request for correction.
---------------------QUOTE-------------------


Hey, congratulations!!
Posted by: dvunkannon on May 24 2011,06:53

Just discovered this blog:
Small Things Considered
< http://schaechter.asmblog.org/schaechter/ >

Many cool articles on microbes.
Posted by: fusilier on May 24 2011,07:33

Quote (Hermagoras @ May 19 2011,16:17)
I, Hermagoras, have published a paper in Science!  < Inquiry-Based Writing in the Laboratory Course > (with Cary Moskovitz).  

Complete with random meme duplication and mutation on the second page.  Compositor error, post-galley-proofs.  We've sent a request for correction.
---------------------QUOTE-------------------


Missed this in the run-up to summer semester.

Congratulations!

(May I hate you now?)
Posted by: paragwinn on May 24 2011,22:17

Quote (Hermagoras @ May 19 2011,13:17)
I, Hermagoras, have published a paper in Science!  < Inquiry-Based Writing in the Laboratory Course > (with Cary Moskovitz).  

Complete with random meme duplication and mutation on the second page.  Compositor error, post-galley-proofs.  We've sent a request for correction.
---------------------QUOTE-------------------


Congratulations!

is it ready for quote-mining?
Posted by: Richardthughes on May 25 2011,14:39

Hat Tip Bob O':

< http://www.guardian.co.uk/science....omments >

Evolution in action. With mechanisms. Joe G - have fun with this one.
Posted by: OgreMkV on May 25 2011,15:03

Quote (Richardthughes @ May 25 2011,14:39)
Hat Tip Bob O':

< http://www.guardian.co.uk/science....omments >

Evolution in action. With mechanisms. Joe G - have fun with this one.
---------------------QUOTE-------------------


Epic.  Joe will only see the word 'may' and suddenly everything is a neofascist attempt to find out where he lives... or something.
Posted by: dvunkannon on May 26 2011,07:04

Electron Surprisingly Spherical
< http://www.sciencedaily.com/releases/2011/05/110525131707.htm >

Back in the day, when I walked to school uphill both ways, wrote my PDP-8 Basic programs on paper tape and Fortran IV on punched cards, electrons were point particles. You could calculate an interaction probability within a certain cross sectional area, but you didn't imagine that the electron was an object with extension in space.

Now the world has gone anti-pear shaped.
Posted by: dvunkannon on May 26 2011,20:04

Evolution Overturned!!

Again!!

A giant Ordovician anomalocaridid
< http://www.nature.com/nature/journal/v473/n7348/full/nature09920.html >

ID... um... predicted this!
Posted by: OgreMkV on May 26 2011,21:46

Quote (dvunkannon @ May 26 2011,20:04)
Evolution Overturned!!

Again!!

A giant Ordovician anomalocaridid
< http://www.nature.com/nature/journal/v473/n7348/full/nature09920.html >

ID... um... predicted this!
---------------------QUOTE-------------------


Oh... My... God.

You've got to be fucking kidding me.  A giant Ordivician anomalocaridid!!!  Holy Crap!!!











ummm... what's an anomalocaridid?
Posted by: Henry J on May 26 2011,22:26

If electrons are spherical, what about neutrinos and quarks? Does that also apply to them? I know they're sometimes described as point particles, but then I also recall reading about collisions, which strike me as unlikely for things with zero size and with no net attractive force between them.

Henry
Posted by: Occam's Aftershave on May 26 2011,22:26

Quote (OgreMkV @ May 26 2011,21:46)
 
Quote (dvunkannon @ May 26 2011,20:04)
Evolution Overturned!!

Again!!

A giant Ordovician anomalocaridid
< http://www.nature.com/nature/journal/v473/n7348/full/nature09920.html >

ID... um... predicted this!
---------------------QUOTE-------------------


Oh... My... God.

You've got to be fucking kidding me.  A giant Ordivician anomalocaridid!!!  Holy Crap!!!

ummm... what's an anomalocaridid?
---------------------QUOTE-------------------


Big assed shrimp-like thingie



Now where's the cocktail sauce?
Posted by: paragwinn on May 26 2011,23:00

Quote (Occam's Aftershave @ May 26 2011,20:26)
 
Quote (OgreMkV @ May 26 2011,21:46)
   
Quote (dvunkannon @ May 26 2011,20:04)
Evolution Overturned!!

Again!!

A giant Ordovician anomalocaridid
< http://www.nature.com/nature/journal/v473/n7348/full/nature09920.html >

ID... um... predicted this!
---------------------QUOTE-------------------


Oh... My... God.

You've got to be fucking kidding me.  A giant Ordivician anomalocaridid!!!  Holy Crap!!!

ummm... what's an anomalocaridid?
---------------------QUOTE-------------------


Big assed shrimp-like thingie



Now where's the cocktail sauce?
---------------------QUOTE-------------------


According to the Editor's Summary:  

---------------------QUOTE-------------------
One of the Ordovician anomalocaridids was a metre or so in length, ...
---------------------QUOTE-------------------



That's 3.281 feet (for the diametrically opposed)
Posted by: dvunkannon on May 27 2011,12:45

Deciphering the splicing code

< http://www.nature.com/nature/journal/v465/n7294/full/nature09000.html >

It's not a "code", but we're now stuck with the word, just as we're stuck with -ome.

Since the simplicity and near optimality of the genetic code is proof of its Intelligent Design, the complexity and messiness of the 'splicing code' must be proof of... Intelligent Design!
Posted by: dvunkannon on May 27 2011,14:47

Currently reading Carl Zimmer's E.coli book. Wonderful as would be expected.

He mentions that bacteria maintain a high internal pressure, which he credits with helping chemical reactions proceed more quickly. However, it also forces bacteria to wear a corset, and if this is pierced, they explode.

On the web, I saw the actual internal pressure quoted as 3-5 atmospheres.

Here's a hypothesis - the internal pressure of bacteria is approximately the atmospheric pressure under which they evolved. If so, the corset evolved later as a way to maintain high pressure and chemical activity, even as atmospheric pressure dropped (due to CO2 being used by life and then sequestered, etc.). Sort of like how people argue that blood is the salinity of the ocean.

What think you?
Posted by: fnxtr on May 27 2011,16:05

Quote (dvunkannon @ May 27 2011,12:47)
Currently reading Carl Zimmer's E.coli book. Wonderful as would be expected.

He mentions that bacteria maintain a high internal pressure, which he credits with helping chemical reactions proceed more quickly. However, it also forces bacteria to wear a corset, and if this is pierced, they explode.

On the web, I saw the actual internal pressure quoted as 3-5 atmospheres.

Here's a hypothesis - the internal pressure of bacteria is approximately the atmospheric pressure under which they evolved. If so, the corset evolved later as a way to maintain high pressure and chemical activity, even as atmospheric pressure dropped (due to CO2 being used by life and then sequestered, etc.). Sort of like how people argue that blood is the salinity of the ocean.

What think you?
---------------------QUOTE-------------------


Or they developed in water 20-30 meters deep.
Posted by: noncarborundum on May 27 2011,16:08

Quote (dvunkannon @ May 27 2011,14:47)
Currently reading Carl Zimmer's E.coli book. Wonderful as would be expected.

He mentions that bacteria maintain a high internal pressure, which he credits with helping chemical reactions proceed more quickly. However, it also forces bacteria to wear a corset, and if this is pierced, they explode.

On the web, I saw the actual internal pressure quoted as 3-5 atmospheres.

Here's a hypothesis - the internal pressure of bacteria is approximately the atmospheric pressure under which they evolved. If so, the corset evolved later as a way to maintain high pressure and chemical activity, even as atmospheric pressure dropped (due to CO2 being used by life and then sequestered, etc.). Sort of like how people argue that blood is the salinity of the ocean.

What think you?
---------------------QUOTE-------------------


I plan to keep an eye on < this >.
Posted by: Schroedinger's Dog on May 27 2011,16:12



---------------------QUOTE-------------------
Currently reading Carl Zimmer's E.coli book. Wonderful as would be expected.
---------------------QUOTE-------------------



Because nothing spells "wonderful" like potentially deadly bacterias living in one's colon. Aaaah, the poetry of science!

:)

ETA: I'm not talking about Joe G here. Or Luskin...
Posted by: dvunkannon on May 27 2011,18:24

Quote (noncarborundum @ May 27 2011,17:08)
Quote (dvunkannon @ May 27 2011,14:47)
Currently reading Carl Zimmer's E.coli book. Wonderful as would be expected.

He mentions that bacteria maintain a high internal pressure, which he credits with helping chemical reactions proceed more quickly. However, it also forces bacteria to wear a corset, and if this is pierced, they explode.

On the web, I saw the actual internal pressure quoted as 3-5 atmospheres.

Here's a hypothesis - the internal pressure of bacteria is approximately the atmospheric pressure under which they evolved. If so, the corset evolved later as a way to maintain high pressure and chemical activity, even as atmospheric pressure dropped (due to CO2 being used by life and then sequestered, etc.). Sort of like how people argue that blood is the salinity of the ocean.

What think you?
---------------------QUOTE-------------------


I plan to keep an eye on < this >.
---------------------QUOTE-------------------


That is frickin' brilliant. We live in an amazing time, when we can afford to investigate the most wonderful mysteries of how life started.

MY TAX DOLLARS AT WORK!!1!
Posted by: Henry J on May 27 2011,21:40

So one way to kill invasive bacteria would be to puncture their girdles? Er, corsets?

Henry
Posted by: Badger3k on May 27 2011,22:58

Quote (Henry J @ May 27 2011,21:40)
So one way to kill invasive bacteria would be to puncture their girdles? Er, corsets?

Henry
---------------------QUOTE-------------------


Maybe we can get them to trip on their stiletto heels, puncturing their corsets?  Seriously, do they use whalebone or what?  And who manufactures them - whoever it is, boy do they mass-produce.
Posted by: dvunkannon on May 28 2011,07:27

Quote (Henry J @ May 27 2011,22:40)
So one way to kill invasive bacteria would be to puncture their girdles? Er, corsets?

Henry
---------------------QUOTE-------------------


Yes.

< http://www.iop.org/news/oct10/page_44964.html >
Posted by: Wesley R. Elsberry on May 28 2011,09:31

Quote (Henry J @ May 27 2011,21:40)
So one way to kill invasive bacteria would be to puncture their girdles? Er, corsets?

Henry
---------------------QUOTE-------------------


One mechanism shared by many antibiotic agents is disturbing bacterial cell wall production. Once the bacterium tries to reproduce itself, its inability to complete the cell wall in each part results in it opening the inside of both to the outside. At least, that's what they told us back in the dark ages.
Posted by: Schroedinger's Dog on May 28 2011,09:51

Sounds a bit nasty to the bacteria. I like it!
Posted by: noncarborundum on May 30 2011,01:53

< Industrial Melanism in British Peppered Moths Has a Singular and Recent Mutational Origin >

I think there's a typo in the title.  They wrote "Peppered Moths" where they meant "Icon of Evolution".
Posted by: Kristine on June 06 2011,10:45

For what it's worth:

Harley, K. (June, 2011). Book reviews. The Indexer 29(2), p. 93-94. I review Melanie J. Norton's book, Introductory Concepts in Information Science, Second Edition.
   

---------------------QUOTE-------------------
In fact, this reviewer recommends that any novice, whether indexer or information science student, read the last four chapters only with caution. Norton, in Chapter 9 on bibliometrics, uses percentages to describe Lotka’s frequency distribution, which is misleading. Care must be exercised in drawing conclusions from Lotka’s pattern as it is neither a mathematical formula nor statistically rigorous; Norton neglects to say this. She apparently does not understand that Bradford’s Law describes a pattern after intentionally dividing journals into three categories of diminishing citation frequencies (core and scatter), which is likewise not statistically accurate. She does not explain which allegedly ‘qualitative’ research methods are used in bibliometrics, and the reviewer is not aware of any. Chapter 10, on economics, does not even mention the concept of return on investment or the so-called ‘crisis’ in scholarly publication.

In Chapter 11, Norton seems to erroneously credit NASA with an inadvertent development of Velcro in the 1960s, when it was intentionally patented in the 1950s. The text subheaded ‘Value in context’ could have been shortened and integrated with the rest of the chapter; setting out this section achieves a Zeno’s paradox of abstract tortuousness.
---------------------QUOTE-------------------


I know it's boring, but it's exciting to me, because I'm new at scholarly writing.
Posted by: noncarborundum on June 06 2011,11:39

Quote (Kristine @ June 06 2011,10:45)


---------------------QUOTE-------------------
The text subheaded ‘Value in context’ could have been shortened and integrated with the rest of the chapter; setting out this section achieves a Zeno’s paradox of abstract tortuousness.
---------------------QUOTE-------------------


I know it's boring, but it's exciting to me, because I'm new at scholarly writing.
---------------------QUOTE-------------------


And here I always thought Zeno's paradoxes involved concrete tortoiseness.
Posted by: Henry J on June 06 2011,23:48

It's turtles all the way down!  :p
Posted by: BWE on June 07 2011,00:52

yertle the king of all he could see...
Posted by: Richardthughes on June 07 2011,10:02

< http://forums.gottadeal.com/showthr....-Amazon >
Posted by: Kristine on June 07 2011,15:47

Okay, I swear that I will not turn this thread into shimmy whoring, but my latest article (< TOC here >) is about the Human Genome Project curriculum at the Brooklyn Public Library.

Not my fault that after oodles of rejection letters over the years I get published twice in one week!
Posted by: Richardthughes on June 09 2011,09:42

< http://www.news.ucdavis.edu/search/news_detail.lasso?id=9921 >
Posted by: Kristine on June 13 2011,16:45

A < new study > suggests something that I have often suspected: that it is not the particular political position taken by the student that makes the student resist what a professor teaches, or see bias in that professor. It is how rigidly that student holds his or her political views.
Posted by: dvunkannon on June 14 2011,11:55

BUT THEY ARE STIL JUST BIRDS!!1!

< http://www.sciencedaily.com/releases/2011/06/110610131906.htm >
Posted by: Henry J on June 15 2011,09:55

Not only are they still birds, but they're also still dinosaurs, reptilian, vertebrate, chordate, bilateral, metazoan eukaryotes.
Posted by: dvunkannon on June 16 2011,11:38

BUT THEY ARE STIL JUST FLIES!!1!

< http://www.pnas.org/content/early/2011/05/17/1105937108 >

More kick ass evo-devo from Sean Carroll et al.
Posted by: Schroedinger's Dog on June 23 2011,14:37

< Darwin's notes online >

Full link since it seems to not work:

[URL=http://www.dailymail.co.uk/sciencetech/article-2007170/The-origin-On-The-Origin-Species-Darwins-research-notes-scribbled-730-books-library-online

.html?ito=feeds-newsxml]http://www.dailymail.co.uk/science....newsxml[/URL]

ETA: just remove the <br> tag in the adress...


Posted by: Quack on June 23 2011,15:44

How about using TinyURL?
Posted by: Schroedinger's Dog on June 23 2011,15:58

Quote (Quack @ June 23 2011,21:44)
How about using TinyURL?
---------------------QUOTE-------------------


I could do that, but I'm just too damn lazy at the moment...
Posted by: Kristine on June 29 2011,20:14

< University of Minnesota Engineering Researchers > Discover Source for Generating 'Green' Electricity.


---------------------QUOTE-------------------
To create the material, the research team combined elements at the atomic level to create a new multiferroic alloy, Ni45Co5Mn40Sn10. Multiferroic materials combine unusual elastic, magnetic and electric properties. The alloy Ni45Co5Mn40Sn10 achieves multiferroism by undergoing a highly reversible phase transformation where one solid turns into another solid. During this phase transformation the alloy undergoes changes in its magnetic properties that are exploited in the energy conversion device.

During a small-scale demonstration in a University of Minnesota lab, the new material created by the researchers begins as a non-magnetic material, then suddenly becomes strongly magnetic when the temperature is raised a small amount. When this happens, the material absorbs heat and spontaneously produces electricity in a surrounding coil. Some of this heat energy is lost in a process called hysteresis. A critical discovery of the team is a systematic way to minimize hysteresis in phase transformations. The team’s research was recently published in the first issue of the new scientific journal Advanced Energy Materials.
---------------------QUOTE-------------------


Posted by: fnxtr on June 29 2011,21:55

Quote (Kristine @ June 29 2011,18:14)
< University of Minnesota Engineering Researchers > Discover Source for Generating 'Green' Electricity.
 

---------------------QUOTE-------------------
To create the material, the research team combined elements at the atomic level to create a new multiferroic alloy, Ni45Co5Mn40Sn10. Multiferroic materials combine unusual elastic, magnetic and electric properties. The alloy Ni45Co5Mn40Sn10 achieves multiferroism by undergoing a highly reversible phase transformation where one solid turns into another solid. During this phase transformation the alloy undergoes changes in its magnetic properties that are exploited in the energy conversion device.

During a small-scale demonstration in a University of Minnesota lab, the new material created by the researchers begins as a non-magnetic material, then suddenly becomes strongly magnetic when the temperature is raised a small amount. When this happens, the material absorbs heat and spontaneously produces electricity in a surrounding coil. Some of this heat energy is lost in a process called hysteresis. A critical discovery of the team is a systematic way to minimize hysteresis in phase transformations. The team’s research was recently published in the first issue of the new scientific journal Advanced Energy Materials.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


"Spontaneously" may be a bit misleading.

If I remember my physics, it's the sudden alignment of the magnetic field that would generate an electric current, but only while the field is changing strength, so they'd probably have to keep the material fluctuating above and below the critical temperature fairly rapidly to generate any useful current. Be hard to do with any respectable mass.

Innerestin', tho...
Posted by: Henry J on June 29 2011,22:45



---------------------QUOTE-------------------
so they'd probably have to keep the material fluctuating above and below the critical temperature fairly rapidly to generate any useful current.
---------------------QUOTE-------------------


That may depend on what it's used for; even if it's too weak to power something, it might be useful as a sensor (in a thermostat, perhaps).

Henry
Posted by: Dr.GH on June 30 2011,09:00

Quote (Kristine @ June 07 2011,13:47)
Not my fault that after oodles of rejection letters over the years I get published twice in one week!
---------------------QUOTE-------------------


congratulations  :D
Posted by: Kristine on June 30 2011,09:04

Quote (Dr.GH @ June 30 2011,09:00)
Quote (Kristine @ June 07 2011,13:47)
Not my fault that after oodles of rejection letters over the years I get published twice in one week!
---------------------QUOTE-------------------


congratulations  :D
---------------------QUOTE-------------------


Thanks - another is coming! I'm really proud of this one.
Posted by: fnxtr on July 01 2011,00:27

Quote (Henry J @ June 29 2011,20:45)


---------------------QUOTE-------------------
so they'd probably have to keep the material fluctuating above and below the critical temperature fairly rapidly to generate any useful current.
---------------------QUOTE-------------------


That may depend on what it's used for; even if it's too weak to power something, it might be useful as a sensor (in a thermostat, perhaps).

Henry
---------------------QUOTE-------------------


Yes. That. Hardly "Green energy", though, you can do the same thing with garden-variety thermocouple.
Posted by: dvunkannon on July 05 2011,13:21

< http://www.biology-direct.com/content/6/1/35 >

Nick Lane explaining (once again) his view of eukaryotic origins via endosymbiosis, and the follow on effects. Part of a number of Biology Direct articles on the "Tree of Life" just published.
Posted by: dvunkannon on July 06 2011,14:37

< http://www.biomedcentral.com/1471-2148/11/194/abstract >

A look at what drives speciation in salamander ring species. Ring species are great topics for discussion with anti-evos. This paper shows that reproductive isolation in the salamanders is mostly driven by genetics, not ecology.
Posted by: dvunkannon on July 07 2011,09:31

Superconductivity, Theory and Practice

< http://spectrum.ieee.org/semicon....ulators >

This article brings up the interesting point that for 50 years we had no explanation for the phenomenon of superconductivity. This could be a good discussion point for anti-evos talking about non-materialist explanations in science. Did any useful non-materialist explanation get put forward in 50 years? Was Darwinism suppressing these?
Posted by: dvunkannon on July 07 2011,13:33

Finger Length Related to Penis Size!!1!

< http://news.yahoo.com/finger-length-linked-penis-size-131801200.html >

Since I'm getting no uptake on the real science, we'll switch gears and go for the National Enquirer-level reporting.

If I was smart, I'd write an iPhone App that you could use to take a pic of a guy's hand in a bar, and it would advise on penis size to expect (or avoid being disappointed by) later in the evening. It would even analyze skin color to apply a scale factor appropriate to ethnicity. Then I could retire on my new fortune as thousands of women and gay men downloaded my masterpiece.
Posted by: Henry J on July 07 2011,13:34



---------------------QUOTE-------------------
This article brings up the interesting point that for 50 years we had no explanation for the phenomenon of superconductivity. This could be a good discussion point for anti-evos talking about non-materialist explanations in science. Did any useful non-materialist explanation get put forward in 50 years? Was Darwinism suppressing these?
---------------------QUOTE-------------------



I wouldn't know, as I'm not entirely sure what "non-materialist" even means. In the context in which I've seen that term used lately, it seems to mean ignoring the relevant evidence, which doesn't seem to me like a good thing.

But maybe I missed something?  :O
Posted by: dvunkannon on July 07 2011,14:34

Quote (Henry J @ July 07 2011,14:34)


---------------------QUOTE-------------------
This article brings up the interesting point that for 50 years we had no explanation for the phenomenon of superconductivity. This could be a good discussion point for anti-evos talking about non-materialist explanations in science. Did any useful non-materialist explanation get put forward in 50 years? Was Darwinism suppressing these?
---------------------QUOTE-------------------



I wouldn't know, as I'm not entirely sure what "non-materialist" even means. In the context in which I've seen that term used lately, it seems to mean ignoring the relevant evidence, which doesn't seem to me like a good thing.

But maybe I missed something?  :O
---------------------QUOTE-------------------


Cornelius Hunter is currently making a big thing of this. Check his blog or the thread here.
Posted by: Erasmus, FCD on July 07 2011,23:46

Quote (dvunkannon @ July 07 2011,14:33)
Finger Length Related to Penis Size!!1!

< http://news.yahoo.com/finger-length-linked-penis-size-131801200.html >

Since I'm getting no uptake on the real science, we'll switch gears and go for the National Enquirer-level reporting.

If I was smart, I'd write an iPhone App that you could use to take a pic of a guy's hand in a bar, and it would advise on penis size to expect (or avoid being disappointed by) later in the evening. It would even analyze skin color to apply a scale factor appropriate to ethnicity. Then I could retire on my new fortune as thousands of women and gay men downloaded my masterpiece.
---------------------QUOTE-------------------


DAYUM

with ideas like that you don't need to know how to do shit.  call perez hilton's programmer immediately!
Posted by: Schroedinger's Dog on July 12 2011,07:44

< Happy revolution around the Sun, Neptune! >
Posted by: dvunkannon on July 15 2011,10:20

Quick question for the masses reading this thread:

I'm considering purchase of "The Chemistry of Evolution", 2006, RJP Williams and da Silva. I can only get it hardcopy and it is expensive. Is it worth it? I looked at the table of contents online (BN) and it seemed valuable to have at least the first half of the book. These chapters cover physical chemistry, abiogenesis, oxidation of the Earth's surface through to anerobic prokaryote life.

After that, I'm not sure how valuable the book will be. If I understand the argument laid out in the preface, the authors conceive of life as being classifiable into chemotypes, based on the kinds of energy and chemical processes species use. Sounds cool, but then I would expect the book to focus on things like methanogens, and other relatively exotic chemistry. Instead, anerobic prokaryotes lead to aerobic prokaryotes, eukaryotes, metazoans, complex brains, and finally man - all as an 'inevitable' directed sequence.

It all sounds ripe for quote mining by cosmic fine tuners. Are they really going to argue that metazoans are a new chemotype compared to single celled eukaryotes?

If you have the book, or others by the same pair of authors, I'd appreciate your opinion.
Posted by: dvunkannon on July 15 2011,12:21

< http://www.naturalgenome.at/pdf/talks/Forterre.komp.pdf >

An entertaining slide deck captured as PDF from Patrick Forterre. Viruses are apparently responsible for all that is interesting about cellular life. Amusing English  written as if it were a dialect of Surrenderese, as a bonus.

Should probably crosspost to the Abiogenesis thread, but its Friday.
Posted by: Kristine on July 19 2011,11:22

There is an < important discussion > going on at Inside Higher Ed re opening up peer-review to an online "Wiki" model. I weigh in with my mixed feelings.
Posted by: midwifetoad on July 19 2011,12:49

Quote (Kristine @ July 19 2011,11:22)
There is an < important discussion > going on at Inside Higher Ed re opening up peer-review to an online "Wiki" model. I weigh in with my mixed feelings.
---------------------QUOTE-------------------


Looks to me like they are advocating something like rottentomatoes.com, where you have all critics and top critics. Maybe you get to filter on your own selection of top critics.

I think given a couple of decades, something like this will happen. Don't know if it will be a good thing, but it seems like the way things are going.
Posted by: Kristine on July 19 2011,21:41

Quote (midwifetoad @ July 19 2011,12:49)
 
Quote (Kristine @ July 19 2011,11:22)
There is an < important discussion > going on at Inside Higher Ed re opening up peer-review to an online "Wiki" model. I weigh in with my mixed feelings.
---------------------QUOTE-------------------


Looks to me like they are advocating something like rottentomatoes.com, where you have all critics and top critics. Maybe you get to filter on your own selection of top critics.

I think given a couple of decades, something like this will happen. Don't know if it will be a good thing, but it seems like the way things are going.
---------------------QUOTE-------------------


I disagree. I think a rottentomatoes model is already out of date. If we are talking a "paradigm change" (gawd, I have come to hate that phrase!;) then let's have a real transformation that addresses the problems of scholarly publication (e.g., the publishers themselves, costs, and zero-sum signing away rights to one's work).

Scientific collaboratories and the Zooniverse are already taking us into different online collaborative areas than just "add Amazon.com comments and stir." These provide controls and parameters that are not mere popularity contests.

It's an important discussion, but the underlying ethics and methodologies of peer review are not the issue and should not change.
Posted by: midwifetoad on July 19 2011,21:48

I wasn't thinking about a free-for all. I was thinking about a model where your view of critical comments would be filtered. I don't know how the filters would be developed, but I assume that commenters would be sorted according to qualifications.
Posted by: Kristine on July 19 2011,22:50

Quote (midwifetoad @ July 19 2011,21:48)
I wasn't thinking about a free-for all. I was thinking about a model where your view of critical comments would be filtered. I don't know how the filters would be developed, but I assume that commenters would be sorted according to qualifications.
---------------------QUOTE-------------------


Oh, I see. I think another problem, though, is actually getting qualified people to show up and comment.

Open access online repositories ran into this problem with faculty; faculty agreed with depositing their work with the university in theory, but balked at actually doing it because they thought it would mean more work for them.
Posted by: dvunkannon on July 22 2011,08:33

< http://www.biology-direct.com/content/6/1/39 >



---------------------QUOTE-------------------
Of Woods and Webs: Possible alternatives to the tree of life for studying genomic fluidity in E. coli

Julie Beauregard-Racine , Cedric Bicep , Klaus Schliep , Philippe Lopez , Francois-Joseph Lapointe  and Eric Bapteste

Biology Direct 2011, 6:39doi:10.1186/1745-6150-6-39


Published: 20 July 2011

Abstract (provisional)

Background
We introduce several forest-based and network-based methods for exploring microbial evolution, and apply them to the study of thousands of genes from 30 strains of E. coli. This case study illustrates how additional analyses could offer fast heuristic alternatives to standard tree of life (TOL) approaches.

Results
We use gene networks to identify genes with atypical modes of evolution, and genome networks to characterize the evolution of genetic partnerships between E. coli and mobile genetic elements. We develop a novel polychromatic quartet method to capture patterns of recombination within E. coli, to update the clanistic toolkit, and to search for the impact of lateral gene transfer and of pathogenicity on gene evolution in two large forests of trees bearing E. coli. We unravel high rates of lateral gene transfer involving E. coli (about 40% of the trees under study), and show that both core genes and shell genes of E. coli are affected by non-tree-like evolutionary processes. We show that pathogenic lifestyle impacted the structure of 30% of the gene trees, and that pathogenic strains are more likely to transfer genes with one another than with non-pathogenic strains. In addition, we propose five groups of genes as candidate mobile modules of pathogenicity. We also present strong evidence for recent lateral gene transfer between E. coli and mobile genetic elements.

Conclusions
Depending on which evolutionary questions biologists want to address (i.e. the identification of modules, genetic partnerships, recombination, lateral gene transfer, or genes with atypical evolutionary modes, etc.), forest-based and network-based methods are preferable to the reconstruction of a single tree, because they provide insights and produce hypotheses about the dynamics of genome evolution, rather than the relative branching order of species and lineages. Such a methodological pluralism - the use of woods and webs - is to be encouraged to analyse the evolutionary processes at play in microbial evolution. This manuscript was reviewed by: Ford Doolittle, Tal Pupko, Richard Burian, James McInerney, Didier Raoult, and Yan Boucher

---------------------QUOTE-------------------



An article ripe for misunderstanding by DeNews. But note that even these critics of TOL consider LGT and gene webs to be 'atypical' evolutionary modes.
Posted by: OgreMkV on July 27 2011,08:30

If I understand non-duality, all that there is is made from one energy, so it seems obvious there would be patterns repeated throughout; the universe and the mind are modeled on the same pattern - can we perceive a limit to our minds? Can we see the edge? Is there ever any expansion? Some people claim to be able to imagine being outside of themselves (or even actually traveling outside themselves!) and so it seems, in reflecting back on the universe, why not more than just the habitually egocentric ONE that we repeatedly revise, as the article points out? Wrong about the sun, wrong about the galaxy... typical of man to wonder are we the only ones; to have that thought creates the likelihood of the answer being, no,stupid, we're not alone at all.

[/QUOTE]

That one is particularly... ummm... yeah...
Posted by: Robin on July 28 2011,08:42

Found this bit on the < new specimen > found in China interesting. I'm surprised that the ID folks haven't jumped all over this, but then maybe I just missed it. Of course, it's a bit early to make any firm conclusions, but it is interesting still.

The specimen is called Xiaotingia zhengi.

Some interesting comments btw.

ETA: Spoke too soon. < News > has predictably misrepresented it.
Posted by: midwifetoad on July 28 2011,08:54



---------------------QUOTE-------------------
I'm surprised that the ID folks haven't jumped all over this...
---------------------QUOTE-------------------



But what's its baramin?
Posted by: Henry J on July 28 2011,11:44

But would it taste like chicken?
Posted by: Dr.GH on July 29 2011,10:24

< "Cilia-Like Beating of Active Microtubule Bundles" >

If you build it, it will wiggle
Posted by: Hermagoras on July 30 2011,07:54

Our paper in Science generates controversy!  Mwahahahaha!  

"Lab Course Goals: Science or Writing?," < letter > by Michael Groggin critiquing our (Moskovitz & Kellogg) recent < paper > in Science, along with our response.

Science 29 July 2011: Vol. 333 no. 6042 p. 524
DOI: 10.1126/science.333.6042.524-a?
Posted by: OgreMkV on Aug. 02 2011,09:16

In case anyone is curious,

"A Framework for K-12 Science Education: Practices, Crosscutting Concepts, and Core Ideas" is available here for free download.

< http://www.nap.edu/catalog.php?record_id=13165 >

This is still a draft copy, but only in the fact that it hasn't had the final copy-edit done yet.  They are very late, hence the pre-publication status.

So far it looks pretty good.  Just reading Chapter 3 points to some of the major problems that many creationists and other anti-science people have with science.  i.e. they were educated poorly or not at all.

It is believed that if states adopt this document as the principle science curriculum, then much of that will be dealt with through proper science education.  Of course, we can't help those poor kids in private schools (especially those with a history of lying to and/or abusing children in their care).
Posted by: midwifetoad on Aug. 07 2011,22:25

< http://atlasobscura.com/place/blood-falls >
Posted by: Quack on Aug. 08 2011,07:04

In an article at < Science Daily >, I find        

---------------------QUOTE-------------------
The study's results also help to explain two puzzles: the persistence of schizophrenia, despite the fact that those with the disease do not tend to pass down their mutations through children; and the high global incidence of the disease, despite large environmental variations.
---------------------QUOTE-------------------


I am curious about the reason why they do not tend to pass down their mutations to their children.

That is of course a good tendency, but there has to be a mechanism.
Posted by: Schroedinger's Dog on Aug. 08 2011,07:17

Quote (Quack @ Aug. 08 2011,13:04)
In an article at < Science Daily >, I find        

---------------------QUOTE-------------------
The study's results also help to explain two puzzles: the persistence of schizophrenia, despite the fact that those with the disease do not tend to pass down their mutations through children; and the high global incidence of the disease, despite large environmental variations.
---------------------QUOTE-------------------


I am curious about the reason why they do not tend to pass down their mutations to their children.

That is of course a good tendency, but there has to be a mechanism.
---------------------QUOTE-------------------


I like to think that the schizo-gene-carrying spermatozoids don't have a clue who they really are and what they have to do, so instead of running for the egg, they just sit in a confy corner and have a nice chat with themselves.

DISCLAIMER: Not a scientific hypothesis.
Posted by: Quack on Aug. 08 2011,07:51

Quote (Schroedinger's Dog @ Aug. 08 2011,07:17)
 
Quote (Quack @ Aug. 08 2011,13:04)
In an article at < Science Daily >, I find            

---------------------QUOTE-------------------
The study's results also help to explain two puzzles: the persistence of schizophrenia, despite the fact that those with the disease do not tend to pass down their mutations through children; and the high global incidence of the disease, despite large environmental variations.
---------------------QUOTE-------------------


I am curious about the reason why they do not tend to pass down their mutations to their children.

That is of course a good tendency, but there has to be a mechanism.
---------------------QUOTE-------------------


I like to think that the schizo-gene-carrying spermatozoids don't have a clue who they really are and what they have to do, so instead of running for the egg, they just sit in a confy corner and have a nice chat with themselves.

DISCLAIMER: Not a scientific hypothesis.
---------------------QUOTE-------------------


I could have opted for that except for the reference to 'their children'. Unless we are talking about hypothetical children.
Posted by: midwifetoad on Aug. 08 2011,08:37



---------------------QUOTE-------------------
I am curious about the reason why they do not tend to pass down their mutations to their children.
---------------------QUOTE-------------------



Schizophrenic men tend to have fewer children. I don't think this applies to women. But as a former protective services worker, I can say that schizophrenic women are less likely to successfully raise children (or maintain custody).

Intelligent schizophrenic men, however, can be very successful at manipulating courts and agencies.

I'm afraid my evidence is anecdotal.
Posted by: Quack on Aug. 08 2011,10:33

Quote (midwifetoad @ Aug. 08 2011,08:37)
 

---------------------QUOTE-------------------
I am curious about the reason why they do not tend to pass down their mutations to their children.
---------------------QUOTE-------------------



Schizophrenic men tend to have fewer children. I don't think this applies to women. But as a former protective services worker, I can say that schizophrenic women are less likely to successfully raise children (or maintain custody).

Intelligent schizophrenic men, however, can be very successful at manipulating courts and agencies.

I'm afraid my evidence is anecdotal.
---------------------QUOTE-------------------


Yes, I would have thought so.

Whereas my question possibly may be based on just another case of journalistic  distortion.


ETA: lost word.
Posted by: Timothy McDougald on Aug. 08 2011,22:01

< This is pretty cool. > An interesting application of Allen's Rule:



---------------------QUOTE-------------------
Focusing on 10 species and subspecies of tidal salt marsh sparrow, the team measured 1,380 specimens and found that the variation in the sparrows' bill size was strongly related to the variation in the daily high summer temperatures of their salt marsh breeding habitats -- the higher the average summer temperature, the larger the bill. Birds pump blood into tissue inside the bill at high temperatures and the body's heat is released into the air. Because larger bills have a greater surface area than smaller bills, they serve as more effective thermoregulatory organs under hot conditions. On average, the study found the bills of sparrows in marshes with high summer temperatures to be up to 90 percent larger than those of the same species in cooler marshes.
---------------------QUOTE-------------------


Posted by: Kristine on Aug. 18 2011,15:26

Whoa! British libraries go all anti-truck system on < both Elsevier and Wile-E-Blackwelly >.
 

---------------------QUOTE-------------------
If the libraries cancel their big deals, they intend to make savings by buying only high-use journals from the publishers. Articles from lower-use journals will be shared between them in an electronic version of an inter-library loan. Prosser admitted that the publishers might react by putting up the price of high-use journals, but predicted that such a move would fall foul of competition authorities. He said he expected that libraries would already be talking to researchers about the titles that could be dropped with the least impact.

"It is not a question of whether we drop journals, it is a question of which we drop," he said.
---------------------QUOTE-------------------


Gobbler and Cobbler naturally have "no comment" for once. Wiley-Blackwell really astonished me. All I did was subscribe to < JASIST > and I received via snail mail glossy ads for Quantum Soil Erosion Quarterly and I-Am-Lewontin-Yellow science catalogs.  :angry:
Posted by: paragwinn on Aug. 20 2011,22:42

Quote (Kristine @ Aug. 18 2011,13:26)
Whoa! British libraries go all anti-truck system on < both Elsevier and Wile-E-Blackwelly >.
   

---------------------QUOTE-------------------
If the libraries cancel their big deals, they intend to make savings by buying only high-use journals from the publishers. Articles from lower-use journals will be shared between them in an electronic version of an inter-library loan. Prosser admitted that the publishers might react by putting up the price of high-use journals, but predicted that such a move would fall foul of competition authorities. He said he expected that libraries would already be talking to researchers about the titles that could be dropped with the least impact.

"It is not a question of whether we drop journals, it is a question of which we drop," he said.
---------------------QUOTE-------------------


Gobbler and Cobbler naturally have "no comment" for once. Wiley-Blackwell really astonished me. All I did was subscribe to < JASIST > and I received via snail mail glossy ads for Quantum Soil Erosion Quarterly and I-Am-Lewontin-Yellow science catalogs.  :angry:
---------------------QUOTE-------------------


What? They didn't offer you Picogram Dilution Wellness Weekly?
Posted by: dvunkannon on Aug. 25 2011,04:09

How will DeNews spin this?

< http://www.sciencedaily.com/release....520.htm >
Engineers Discover Nanoscale Balancing Act That Mirrors Forces at Work in Living Systems

Basic physical forces govern the self assembly of large systems of uniform building blocks, similar to viral self assembly. The point of the story is another nail in the coffin of ID, but it will probably be spun as evidence for cosmic fine tuning and how human scientists can always learn something from the Great Designer.
Posted by: OgreMkV on Aug. 25 2011,07:40

Quote (dvunkannon @ Aug. 25 2011,04:09)
... human scientists can always learn something from the Great Designer.
---------------------QUOTE-------------------


you mean evolution right?
Posted by: Henry J on Aug. 25 2011,22:39



---------------------QUOTE-------------------
you mean evolution right?
---------------------QUOTE-------------------


It's not about what's right, it's about what's left! ;)

Henry
Posted by: Schroedinger's Dog on Aug. 27 2011,11:58

I've found the perfect < wedding ring > for Alicja.

I might need a bit of help to get it, though...
Posted by: Henry J on Sep. 01 2011,11:20

But it's still carbon - it hasn't evolved into another element!!!111!!eleven!!
Posted by: Reed on Sep. 04 2011,16:09

An interesting proposal from John Hawks: < http://johnhawks.net/malapa.....11.html >


---------------------QUOTE-------------------
I am pleased to announce a new open science initiative, focused on a discovery that is unique in paleoanthropology. Together we are going to find out if the Malapa site has preserved evidence of soft tissue from an ancient hominin species.

---------------------QUOTE-------------------


Maybe our ID friends can calculate the probability that these specimens were actually deposited in a flood four thousand years ago!
Posted by: Seversky on Sep. 04 2011,17:10

Quote (Schroedinger's Dog @ Aug. 27 2011,11:58)
I've found the perfect < wedding ring > for Alicja.

I might need a bit of help to get it, though...
---------------------QUOTE-------------------


Sweet!  But don't we have anything similar here on Earth?

Either that or you'd better get that warp drive finished, Dr Cochrane.
Posted by: Timothy McDougald on Sep. 05 2011,12:10

< An interesting woolly rhino fossil > has been discovered. If anybody has access to the < article in Science > can you send me a copy? PM me for my email address...
Posted by: noncarborundum on Sep. 08 2011,14:30

< Rethinking human evolution > once again!!!!11!

Won't those slimy Darwinists ever decide what they believe, once and for all?  All this revision in the light of new evidence makes my poor head spin.
Posted by: midwifetoad on Sep. 08 2011,14:38

Quote (noncarborundum @ Sep. 08 2011,14:30)
< Rethinking human evolution > once again!!!!11!

Won't those slimy Darwinists ever decide what they believe, once and for all?  All this revision in the light of new evidence makes my poor head spin.
---------------------QUOTE-------------------


This is really mucking with the myth of punk eek.
Posted by: Timothy McDougald on Sep. 09 2011,18:52

< But they are still pupfish! > - even if it does make conservation harder...
Posted by: OgreMkV on Sep. 15 2011,14:32

Take a good long look at the reference list.

< http://mbe.oxfordjournals.org/content....40.full >
Posted by: George on Sep. 15 2011,15:11

Quote (OgreMkV @ Sep. 15 2011,14:32)
Take a good long look at the reference list.

< http://mbe.oxfordjournals.org/content....40.full >
---------------------QUOTE-------------------


You mean?


---------------------QUOTE-------------------
Tolkien, J. R. R. 1954. The lord of the rings. George Allen and Unwin, London.
---------------------QUOTE-------------------



I thought I was doing well to cite LoTR in my PhD thesis.  But a journal paper?  Well done that man!
Posted by: OgreMkV on Sep. 15 2011,18:29

Quote (George @ Sep. 15 2011,15:11)
Quote (OgreMkV @ Sep. 15 2011,14:32)
Take a good long look at the reference list.

< http://mbe.oxfordjournals.org/content....40.full >
---------------------QUOTE-------------------


You mean?


---------------------QUOTE-------------------
Tolkien, J. R. R. 1954. The lord of the rings. George Allen and Unwin, London.
---------------------QUOTE-------------------



I thought I was doing well to cite LoTR in my PhD thesis.  But a journal paper?  Well done that man!
---------------------QUOTE-------------------


Yeah, those guys got mad cult powers.
Posted by: Timothy McDougald on Sep. 18 2011,15:48

Since there was a recent discussion about online gaming I thought I would mention < this. >

Apparently, online gamers solved a vexing problem in AIDs research.
Posted by: midwifetoad on Sep. 19 2011,06:40

< http://ns.msu.edu/index.p....minants >
Posted by: keiths on Sep. 20 2011,11:44

< Lizards show evolution in action >

Of course, to our ID friends, this is merely the loss of the loss of a juvenile function.  No information gained whatsoever.
Posted by: Dr.GH on Sep. 20 2011,17:34

New species of sparrow joins < the List. >
Posted by: Seversky on Sep. 22 2011,17:47

<Mr Spock>

< Fascinating! >

</Mr Spock>

I wonder how long it will take UD to spin this into another Death Knell for Darwinism and materialist science?

Come to think of it, that's another good nickname for DeNews - Death Nell for Darwinism.

And she sort of reminds me of les tricoteuses the French working women who sat knitting under Madame la Guillotine cheering at the next head to fall.
Posted by: midwifetoad on Sep. 22 2011,18:18

DeNews has her sights set on physics too.
Posted by: Seversky on Sep. 22 2011,21:11

Quote (Seversky @ Sep. 22 2011,17:47)
I wonder how long it will take UD to spin this into another Death Knell for Darwinism and materialist science?
---------------------QUOTE-------------------


< Not long. >

These people are so predictable.
Posted by: Schroedinger's Dog on Sep. 23 2011,04:10

Neutrinos detected as travelling 0.002% faster than speed of light:

Sorry, < link > in French only...
Posted by: Dr.GH on Sep. 23 2011,13:24

Quote (Seversky @ Sep. 22 2011,15:47)
<Mr Spock>

< Fascinating! >

</Mr Spock>
---------------------QUOTE-------------------



One approach (assuming the result is real) is that the neutrinos are traveling at the speed if light, and something else is slowing down all the other measurements a 60 billionth of a sec.

I am trying to think how this could fit with the measurement of the < Fine Structure Constant. >


Posted by: Cubist on Sep. 23 2011,14:29

Quote (Schroedinger's Dog @ Sep. 23 2011,04:10)
Neutrinos detected as travelling 0.002% faster than speed of light:

Sorry, < link > in French only...
---------------------QUOTE-------------------


< Google Translate > is your friend. The mechanized translation is of course not as good as one that was done by a skilled human translator, but it does give non-francophones a decent idea of what the article was about.
Posted by: midwifetoad on Sep. 25 2011,00:56

< http://www.newscientist.com/article....ne-news >

Resurrected ancient protein is a potent antibiotic
Posted by: Quack on Sep. 26 2011,08:54

Quote (midwifetoad @ Sep. 25 2011,00:56)
< http://www.newscientist.com/article....ne-news >

Resurrected ancient protein is a potent antibiotic
---------------------QUOTE-------------------


See? No limits to what an Intelligent Designer can do...
Posted by: fnxtr on Sep. 26 2011,10:02

Quote (Quack @ Sep. 26 2011,06:54)
Quote (midwifetoad @ Sep. 25 2011,00:56)
< http://www.newscientist.com/article....ne-news >

Resurrected ancient protein is a potent antibiotic
---------------------QUOTE-------------------


See? No limits to what an Intelligent Designer can do...
---------------------QUOTE-------------------


Wasn't there a brief flurry of interest in carbohydrate tags a couple years back? It was supposed to be the new protieomics, or something.
Posted by: Louis on Oct. 05 2011,09:58

Since it is Nobel week and today is the Chemistry Prize, I thought I'd offer you the story of the 2011 prize winner. It's a good one.

< Here > is one reference, < here > is the Nobel committee's scientific explanation, and < here > is the prize announcement.

Dan Shechtman made a discovery that people generally thought was impossible back in the 1980s. He was expelled* from his lab, was publicly ridiculed, was regularly taken apart in the literature by no lesser an authority on crystallography  than Linus Pauling.

But he was right.

Go and read about quasicrystals. It's not my field but it's an interesting story about mathematics, Penrose tiling, chemistry and solid state physics and Moorish art.

Louis

* OH NOES TEH DARWIZMUS! Wait....Darwin was not a crystallographer....OH NOES TEH BRAGGIZMUS! For any creationists reading, this is how you do it. You go out, work hard, and GET THE FUCKING DATA. I cannot emphasise that last bit enough. Stop whining and lying and do some work, pissants.
Posted by: OgreMkV on Oct. 05 2011,10:03

Quote (Louis @ Oct. 05 2011,09:58)
Since it is Nobel week and today is the Chemistry Prize, I thought I'd offer you the story of the 2011 prize winner. It's a good one.

< Here > is one reference, < here > is the Nobel committee's scientific explanation, and < here > is the prize announcement.

Dan Shechtman made a discovery that people generally thought was impossible back in the 1980s. He was expelled* from his lab, was publicly ridiculed, was regularly taken apart in the literature by no lesser an authority on crystallography  than Linus Pauling.

But he was right.

Go and read about quasicrystals. It's not my field but it's an interesting story about mathematics, Penrose tiling, chemistry and solid state physics and Moorish art.

Louis

* OH NOES TEH DARWIZMUS! Wait....Darwin was not a crystallographer....OH NOES TEH BRAGGIZMUS! For any creationists reading, this is how you do it. You go out, work hard, and GET THE FUCKING DATA. I cannot emphasise that last bit enough. Stop whining and lying and do some work, pissants.
---------------------QUOTE-------------------


Can I put this as a guest post on my blog?
Posted by: Louis on Oct. 05 2011,10:22

Quote (OgreMkV @ Oct. 05 2011,16:03)
Quote (Louis @ Oct. 05 2011,09:58)
Since it is Nobel week and today is the Chemistry Prize, I thought I'd offer you the story of the 2011 prize winner. It's a good one.

< Here > is one reference, < here > is the Nobel committee's scientific explanation, and < here > is the prize announcement.

Dan Shechtman made a discovery that people generally thought was impossible back in the 1980s. He was expelled* from his lab, was publicly ridiculed, was regularly taken apart in the literature by no lesser an authority on crystallography  than Linus Pauling.

But he was right.

Go and read about quasicrystals. It's not my field but it's an interesting story about mathematics, Penrose tiling, chemistry and solid state physics and Moorish art.

Louis

* OH NOES TEH DARWIZMUS! Wait....Darwin was not a crystallographer....OH NOES TEH BRAGGIZMUS! For any creationists reading, this is how you do it. You go out, work hard, and GET THE FUCKING DATA. I cannot emphasise that last bit enough. Stop whining and lying and do some work, pissants.
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Can I put this as a guest post on my blog?
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NO! THAT IS VERBOTEN!

Oh all right. ;-)

However, I don't see why you need to make it a guest post, I would hardly aspire to those lofty heights. It's all public information and a (relatively) well known story.

Louis
Posted by: Dr.GH on Oct. 05 2011,10:52

Thanks Louis.

I found I needed to read < the "popular" explanation first. >
Posted by: dheddle on Oct. 05 2011,13:44

Jason Rosenhouse of JMU and EvolutionBlog fame will speak at Christopher Newport University on Tuesday, Nov. 15 at 4:00 pm in Forbes 1022 and on Wednesday, Nov. 16 at 3:00 pm in Gosnold 202.

Tuesday's talk will be on The Creationism v. Evolution Wars and is sponsored jointly by the Departments of Mathematics and Biology.

Wednesday's talk is a Mathematics colloquium on the Monty Hall Problem.

Any AtBC'ers in the Hampton Roads area* are welcome to attend.

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* The Hampton Roads area includes Yorktown. All you Brits have heard of Yorktown, right? Louis?
Posted by: Louis on Oct. 05 2011,13:58

Quote (dheddle @ Oct. 05 2011,19:44)
Jason Rosenhouse of JMU and EvolutionBlog fame will speak at Christopher Newport University on Tuesday, Nov. 15 at 4:00 pm in Forbes 1022 and on Wednesday, Nov. 16 at 3:00 pm in Gosnold 202.

Tuesday's talk will be on The Creationism v. Evolution Wars and is sponsored jointly by the Departments of Mathematics and Biology.

Wednesday's talk is a Mathematics colloquium on the Monty Hall Problem.

Any AtBC'ers in the Hampton Roads area* are welcome to attend.

=========
* The Hampton Roads area includes Yorktown. All you Brits have heard of Yorktown, right? Louis?
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Ahhh yes. Yorktown. I remember it well. It was where the Cheating Colonials aided by the Perfidous French Harlots scraped a lucky home turf win over Our Brave Boys (TM Patent Pending) by not wearing red, marching in easy to shoot lines, and fighting at night and during tea time.

No bloody manners, that's your problem.

Louis
Posted by: Henry J on Oct. 05 2011,16:06



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No bloody manners, that's your problem.
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We're trying!
Posted by: Louis on Oct. 05 2011,17:11

Quote (Henry J @ Oct. 05 2011,22:06)


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No bloody manners, that's your problem.
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We're trying!
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Very.

Louis
Posted by: Timothy McDougald on Oct. 07 2011,18:16

< Sweet! >:



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“He’s trying to see how different this particular strain of organisms is compared with present-day varieties of the bacteria,” Schaffner said. “We may find to our surprise that the bacteria are somewhat different.”

The widespread use of antibiotics, beginning with the 1928 discovery of penicillin, has had a lasting impact on lots of bacteria, particularly on their genes. Blaser told the Journal that he and his team will be looking for how these drugs might have affected Clostridium perfringens.

“We’ve had 70 years of antibiotics, so the question is, have there been new changes in the bacterial genome from the time of that organism,” he said.
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Posted by: dvunkannon on Oct. 13 2011,15:23

< http://www.sciencedaily.com/release....655.htm >

Genome comparison across 29 species reveals many areas related to control of transcription.

Evolution credited with guiding research useful to medicine. Don't tell Dr (only one, sorry) Michael Egnor and Evilution News and Spews.
Posted by: Timothy McDougald on Oct. 15 2011,22:44

Quote (dvunkannon @ Oct. 13 2011,15:23)
< http://www.sciencedaily.com/release....655.htm >

Genome comparison across 29 species reveals many areas related to control of transcription.

Evolution credited with guiding research useful to medicine. Don't tell Dr (only one, sorry) Michael Egnor and Evilution News and Spews.
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Even cooler, the article is open access!
Posted by: fnxtr on Oct. 18 2011,12:33

Quote (afarensis @ Oct. 15 2011,20:44)
Quote (dvunkannon @ Oct. 13 2011,15:23)
< http://www.sciencedaily.com/release....655.htm >

Genome comparison across 29 species reveals many areas related to control of transcription.

Evolution credited with guiding research useful to medicine. Don't tell Dr (only one, sorry) Michael Egnor and Evilution News and Spews.
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Even cooler, the article is open access!
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I'm in the middle of Kirschner and Gerhart's "The Plausibility of Life".

It's all about regularity... er, regulation.


eta: 360 Megabases in the newly-discovered conserved regions... out of circa 3.4 Gigabases total. Still lots of mystery/junk left. :-)
Posted by: Henry J on Oct. 19 2011,12:19



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It's all about regularity... er, regulation.
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Eat more fiber?
Posted by: Dr.GH on Oct. 19 2011,22:11

I have been waiting for someone else to mention;

"Acceleration of Emergence of Bacterial Antibiotic Resistance in Connected Microenvironments" Qiucen Zhang, Guillaume Lambert, David Liao, Hyunsung Kim, Kristelle Robin,    Chih-kuan Tung, Nader Pourmand, Robert H. Austin, Science 23 September 2011: Vol. 333 no. 6050 pp. 1764-1767



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It is surprising that four apparently functional SNPs should fix in a population within 10 hours of exposure to antibiotic in our experiment. A detailed understanding of the order in which the SNPs occur is essential, but it is unlikely that the four SNPs emerged simultaneously; in all likelihood they are sequential (21–23). The device and data we have described here offer a template for exploring the rates at which antibiotic resistance arises in the complex fitness landscapes that prevail in the mammalian body. Furthermore, our study provides a framework for exploring rapid evolution in other contexts such as cancer (24).
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Multi-site mutations, functional mutations, TEN HOURS, why sequential mutations are functional, and more likely, and with medical applications.

ID is DEAD HaHaHeeheeHaHa HoHo
Dead as the cat down the well, HaHa
Dead is as Dead as ID, HeeHee HaHo
Posted by: Quack on Oct. 20 2011,06:36



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Multi-site mutations, functional mutations, ..., why sequential mutations are functional
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As you all know, IANAS, but I have expected that to be true for a long time.

Glad to chalk up another 'confirmed' on my blackboard.
Posted by: Richardthughes on Oct. 30 2011,20:25

ID PREDICTS THIS:

< http://www.eurekalert.org/pub_rel....511.php >

With it's 'abundant universe" hypothesis.
Posted by: Timothy McDougald on Nov. 15 2011,22:10

< This is pretty cool. > In case you haven't read it here is the abstract:



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Locomotor strategies in terrestrial tetrapods have evolved from the utilisation of sinusoidal contractions of axial musculature, evident in ancestral fish species, to the reliance on powerful and complex limb muscles to provide propulsive force. Within tetrapods, a hindlimb-dominant locomotor strategy predominates, and its evolution is considered critical for the evident success of the tetrapod transition onto land. Here, we determine the developmental mechanisms of pelvic fin muscle formation in living fish species at critical points within the vertebrate phylogeny and reveal a stepwise modification from a primitive to a more derived mode of pelvic fin muscle formation. A distinct process generates pelvic fin muscle in bony fishes that incorporates both primitive and derived characteristics of vertebrate appendicular muscle formation. We propose that the adoption of the fully derived mode of hindlimb muscle formation from this bimodal character state is an evolutionary innovation that was critical to the success of the tetrapod transition.
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Posted by: Kristine on Nov. 17 2011,16:10

< This > is an important bioethical ruling.



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Minnesota’s highest court ruled Wednesday that parents will have a say in how the government handles the DNA of their newborn babies.

In Minnesota, unless a family opts out when a baby is born, blood is taken and sent to a lab to be tested for dozens of disorders. When the testing is done, the sample is sent to the Minnesota Department of Health for storage, and can sometimes be used for studies.

After years of legal battles, parents will have more of a say in that last step.

Until now, parents had to ask for the form after giving birth to opt out of the storage program.

On Wednesday, a ruling by the Minnesota Supreme Court said that doesn’t go far enough and written informed consent is required for the use, storage or dissemination of any remaining blood samples or test results after the completion of the newborn screening.
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Of course, the World Nut Daily twists it again: "Court tells gov