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Lou FCD



Posts: 5377
Joined: Jan. 2006

(Permalink) Posted: 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.


More at the link.

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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
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Lou FCD



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(Permalink) Posted: 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.

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Louis



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(Permalink) Posted: 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.


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.

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Lou FCD



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(Permalink) Posted: 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.

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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
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Lou FCD



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(Permalink) Posted: 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.


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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
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Lou FCD



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(Permalink) Posted: 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.


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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
I think I might love you. Don't tell Deadman -Wolfhound

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Lou FCD



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(Permalink) Posted: 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.


More at the link.

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.


Edited by Lou FCD on July 16 2008,15:39

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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
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Lou FCD



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(Permalink) Posted: 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.


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.


Edited by Lou FCD on July 16 2008,18:00

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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
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Lou FCD



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(Permalink) Posted: 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.


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.


(What's up with scientists and paragraphs, by the way?  Is there a moratorium on carriage returns?)

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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
I think I might love you. Don't tell Deadman -Wolfhound

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afarensis



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(Permalink) Posted: 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.


Edit to add the link goes to the abstract in Nature.

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Church burning ebola boy

FTK: I Didn't answer your questions because it beats the hell out of me.

PaV: I suppose for me to be pried away from what I do to focus long and hard on that particular problem would take, quite honestly, hundreds of thousands of dollars to begin to pique my interest.

   
afarensis



Posts: 1005
Joined: Dec. 2006

(Permalink) Posted: July 16 2008,22:46   

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


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...

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Church burning ebola boy

FTK: I Didn't answer your questions because it beats the hell out of me.

PaV: I suppose for me to be pried away from what I do to focus long and hard on that particular problem would take, quite honestly, hundreds of thousands of dollars to begin to pique my interest.

   
Lou FCD



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Joined: Jan. 2006

(Permalink) Posted: July 16 2008,22:52   

Quote (afarensis @ July 16 2008,23:46)
Quote
Me, personally, I love links to pdfs of the original papers.


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...

Hey, thanks for that, and for hanging stuff up in this thread.

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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
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JAM



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(Permalink) Posted: 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...

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

  
afarensis



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Joined: Dec. 2006

(Permalink) Posted: 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.


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.


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Church burning ebola boy

FTK: I Didn't answer your questions because it beats the hell out of me.

PaV: I suppose for me to be pried away from what I do to focus long and hard on that particular problem would take, quite honestly, hundreds of thousands of dollars to begin to pique my interest.

   
Henry J



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Joined: Mar. 2005

(Permalink) Posted: 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

  
Arden Chatfield



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(Permalink) Posted: 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.

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"Rich is just mad because he thought all titties had fur on them until last week when a shorn transvestite ruined his childhood dreams by jumping out of a spider man cake and man boobing him in the face lips." - Erasmus

  
Nomad



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(Permalink) Posted: 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.

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.

  
Lou FCD



Posts: 5377
Joined: Jan. 2006

(Permalink) Posted: 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.

That's a lovely idea.

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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
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skeptic



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(Permalink) Posted: 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

  
hereoisreal



Posts: 745
Joined: Feb. 2006

(Permalink) Posted: 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/

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Lou FCD



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(Permalink) Posted: 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)


Edited by Lou FCD on July 22 2008,19:54

--------------
Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
I think I might love you. Don't tell Deadman -Wolfhound

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afarensis



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(Permalink) Posted: 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)

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.


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.


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.


--------------
Church burning ebola boy

FTK: I Didn't answer your questions because it beats the hell out of me.

PaV: I suppose for me to be pried away from what I do to focus long and hard on that particular problem would take, quite honestly, hundreds of thousands of dollars to begin to pique my interest.

   
Peter Henderson



Posts: 298
Joined: Aug. 2007

(Permalink) Posted: 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.

  
dvunkannon



Posts: 1377
Joined: June 2008

(Permalink) Posted: 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.



Interesting that according to this, we acquired a nucleus in response to the endosymbiosis with mitochondria. Where does that put plants?

--------------
I’m referring to evolution, not changes in allele frequencies. - Cornelius Hunter
I’m not an evolutionist, I’m a change in allele frequentist! - Nakashima

  
nadandoenloprofundo



Posts: 1
Joined: July 2008

(Permalink) Posted: 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>

  
qetzal



Posts: 309
Joined: Feb. 2006

(Permalink) Posted: 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.


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!

  
afarensis



Posts: 1005
Joined: Dec. 2006

(Permalink) Posted: 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.


--------------
Church burning ebola boy

FTK: I Didn't answer your questions because it beats the hell out of me.

PaV: I suppose for me to be pried away from what I do to focus long and hard on that particular problem would take, quite honestly, hundreds of thousands of dollars to begin to pique my interest.

   
Lou FCD



Posts: 5377
Joined: Jan. 2006

(Permalink) Posted: 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.


--------------
Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
I think I might love you. Don't tell Deadman -Wolfhound

Work-friendly photography
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dvunkannon



Posts: 1377
Joined: June 2008

(Permalink) Posted: 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.

--------------
I’m referring to evolution, not changes in allele frequencies. - Cornelius Hunter
I’m not an evolutionist, I’m a change in allele frequentist! - Nakashima

  
qetzal



Posts: 309
Joined: Feb. 2006

(Permalink) Posted: 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.

  
CeilingCat



Posts: 1663
Joined: Dec. 2007

(Permalink) Posted: 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.

Greg was never on the CB.

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Like every other academic field, philosophy of religion has its share of hacks and mediocrities.  Edward Feser

  
afarensis



Posts: 1005
Joined: Dec. 2006

(Permalink) Posted: 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.


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Church burning ebola boy

FTK: I Didn't answer your questions because it beats the hell out of me.

PaV: I suppose for me to be pried away from what I do to focus long and hard on that particular problem would take, quite honestly, hundreds of thousands of dollars to begin to pique my interest.

   
Lou FCD



Posts: 5377
Joined: Jan. 2006

(Permalink) Posted: 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."


More at the link.

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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
I think I might love you. Don't tell Deadman -Wolfhound

Work-friendly photography
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afarensis



Posts: 1005
Joined: Dec. 2006

(Permalink) Posted: 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.


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.


I haven't read this later one yet but PhysOrg says it has something to do with depression, schizophrenia and insomnia in humans...

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Church burning ebola boy

FTK: I Didn't answer your questions because it beats the hell out of me.

PaV: I suppose for me to be pried away from what I do to focus long and hard on that particular problem would take, quite honestly, hundreds of thousands of dollars to begin to pique my interest.

   
stevestory



Posts: 8882
Joined: Oct. 2005

(Permalink) Posted: Aug. 07 2008,20:20   

http://www.telegraph.co.uk/earth....106.xml

   
afarensis



Posts: 1005
Joined: Dec. 2006

(Permalink) Posted: Aug. 07 2008,21:43   

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

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...

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Church burning ebola boy

FTK: I Didn't answer your questions because it beats the hell out of me.

PaV: I suppose for me to be pried away from what I do to focus long and hard on that particular problem would take, quite honestly, hundreds of thousands of dollars to begin to pique my interest.

   
Lou FCD



Posts: 5377
Joined: Jan. 2006

(Permalink) Posted: 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.


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!


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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
I think I might love you. Don't tell Deadman -Wolfhound

Work-friendly photography
NSFW photography

   
skeptic



Posts: 1163
Joined: May 2006

(Permalink) Posted: 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.

  
deadman_932



Posts: 3094
Joined: May 2006

(Permalink) Posted: 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


-----------------
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.

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AtBC Award for Thoroughness in the Face of Creationism

  
skeptic



Posts: 1163
Joined: May 2006

(Permalink) Posted: Aug. 10 2008,09:11   

thank you much

  
Albatrossity2



Posts: 2778
Joined: Mar. 2007

(Permalink) Posted: Aug. 15 2008,13:34   

That dang designer sure keeps busy.  Here is a report of a new bird species discovered in Africa.

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Flesh of the sky, child of the sky, the mind
Has been obligated from the beginning
To create an ordered universe
As the only possible proof of its own inheritance.
                        - Pattiann Rogers

   
skeptic



Posts: 1163
Joined: May 2006

(Permalink) Posted: 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.

  
stevestory



Posts: 8882
Joined: Oct. 2005

(Permalink) Posted: Aug. 29 2008,14:37   

http://www.popularmechanics.com/blogs/science_news/4279923.html

   
Richardthughes



Posts: 10094
Joined: Jan. 2006

(Permalink) Posted: Aug. 29 2008,14:49   

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

Cool! I hope DT gives you a hat-tip when he links to that, he loves nanofabrication stuff.

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"Richardthughes, you magnificent bastard, I stand in awe of you..." : Arden Chatfield
"You magnificent bastard! " : Louis
"ATBC poster child", "I have to agree with Rich.." : DaveTard
"I bow to your superior skills" : deadman_932
"...it was Richardthughes making me lie in bed.." : Kristine

  
afarensis



Posts: 1005
Joined: Dec. 2006

(Permalink) Posted: 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.


Unfortunately a subscription is required for the entire article. link
DOI:http://dx.doi.org/10.1111/j.1558-5646.2008.00448.x

--------------
Church burning ebola boy

FTK: I Didn't answer your questions because it beats the hell out of me.

PaV: I suppose for me to be pried away from what I do to focus long and hard on that particular problem would take, quite honestly, hundreds of thousands of dollars to begin to pique my interest.

   
dvunkannon



Posts: 1377
Joined: June 2008

(Permalink) Posted: 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.

--------------
I’m referring to evolution, not changes in allele frequencies. - Cornelius Hunter
I’m not an evolutionist, I’m a change in allele frequentist! - Nakashima

  
Lou FCD



Posts: 5377
Joined: Jan. 2006

(Permalink) Posted: 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.


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.

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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
I think I might love you. Don't tell Deadman -Wolfhound

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afarensis



Posts: 1005
Joined: Dec. 2006

(Permalink) Posted: 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.


I haven't read it yet, but it is open access.

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Church burning ebola boy

FTK: I Didn't answer your questions because it beats the hell out of me.

PaV: I suppose for me to be pried away from what I do to focus long and hard on that particular problem would take, quite honestly, hundreds of thousands of dollars to begin to pique my interest.

   
Henry J



Posts: 4048
Joined: Mar. 2005

(Permalink) Posted: 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

  
afarensis



Posts: 1005
Joined: Dec. 2006

(Permalink) Posted: 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.


I have a copy, email me at afarensis1@sbcglobal.net if you would like one.

--------------
Church burning ebola boy

FTK: I Didn't answer your questions because it beats the hell out of me.

PaV: I suppose for me to be pried away from what I do to focus long and hard on that particular problem would take, quite honestly, hundreds of thousands of dollars to begin to pique my interest.

   
Dr.GH



Posts: 1954
Joined: May 2002

(Permalink) Posted: Sep. 05 2008,10:32   

New study: Bad science writing gene found in people.

Edited by Dr.GH on Sep. 05 2008,08:32

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"Science is the horse that pulls the cart of philosophy."

L. Susskind, 2004 "SMOLIN VS. SUSSKIND: THE ANTHROPIC PRINCIPLE"

   
stevestory



Posts: 8882
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(Permalink) Posted: 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

   
stevestory



Posts: 8882
Joined: Oct. 2005

(Permalink) Posted: Sep. 07 2008,17:30   

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

Canadian Writer Found to Have Dozens of Extra Mutant Copies of Said Gene

   
dvunkannon



Posts: 1377
Joined: June 2008

(Permalink) Posted: 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 ...

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I’m referring to evolution, not changes in allele frequencies. - Cornelius Hunter
I’m not an evolutionist, I’m a change in allele frequentist! - Nakashima

  
J-Dog



Posts: 4361
Joined: Dec. 2006

(Permalink) Posted: 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.

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Come on Tough Guy, do the little dance of ID impotence you do so well. - Louis to Joe G 2/10

Gullibility is not a virtue - Quidam on Dembski's belief in the Bible Code Faith Healers & ID 7/08

UD is an Unnatural Douchemagnet. - richardthughes 7/11

  
Wesley R. Elsberry



Posts: 4471
Joined: May 2002

(Permalink) Posted: 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?

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"You can't teach an old dogma new tricks." - Dorothy Parker

    
stevestory



Posts: 8882
Joined: Oct. 2005

(Permalink) Posted: 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.  


Linky

   
stevestory



Posts: 8882
Joined: Oct. 2005

(Permalink) Posted: Sep. 10 2008,17:24   

Friendly Invaders

A carl zimmer NYT article.

   
Wesley R. Elsberry



Posts: 4471
Joined: May 2002

(Permalink) Posted: 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."


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"You can't teach an old dogma new tricks." - Dorothy Parker

    
carlsonjok



Posts: 3324
Joined: May 2006

(Permalink) Posted: 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."

[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]

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It's natural to be curious about our world, but the scientific method is just one theory about how to best understand it.  We live in a democracy, which means we should treat every theory equally. - Steven Colbert, I Am America (and So Can You!)

  
stevestory



Posts: 8882
Joined: Oct. 2005

(Permalink) Posted: 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

   
blipey



Posts: 2061
Joined: June 2006

(Permalink) Posted: 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

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

ID! ID! ID!

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But I get the trick question- there isn't any such thing as one molecule of water. -JoeG

And scientists rarely test theories. -Gary Gaulin

   
blipey



Posts: 2061
Joined: June 2006

(Permalink) Posted: 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.

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But I get the trick question- there isn't any such thing as one molecule of water. -JoeG

And scientists rarely test theories. -Gary Gaulin

   
stevestory



Posts: 8882
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(Permalink) Posted: 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

   
stevestory



Posts: 8882
Joined: Oct. 2005

(Permalink) Posted: 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.”

   
afarensis



Posts: 1005
Joined: Dec. 2006

(Permalink) Posted: 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.


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.


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Church burning ebola boy

FTK: I Didn't answer your questions because it beats the hell out of me.

PaV: I suppose for me to be pried away from what I do to focus long and hard on that particular problem would take, quite honestly, hundreds of thousands of dollars to begin to pique my interest.

   
Peter Henderson



Posts: 298
Joined: Aug. 2007

(Permalink) Posted: 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.


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.


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.

  
Lou FCD



Posts: 5377
Joined: Jan. 2006

(Permalink) Posted: 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.


More at the link, paper in December's The Astrophysical Journal.

--------------
Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
I think I might love you. Don't tell Deadman -Wolfhound

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Lou FCD



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(Permalink) Posted: 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.


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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
I think I might love you. Don't tell Deadman -Wolfhound

Work-friendly photography
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afarensis



Posts: 1005
Joined: Dec. 2006

(Permalink) Posted: 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.

I have this paper if anybody wants a copy. Email me at afarensis1@sbcglobal.net

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Church burning ebola boy

FTK: I Didn't answer your questions because it beats the hell out of me.

PaV: I suppose for me to be pried away from what I do to focus long and hard on that particular problem would take, quite honestly, hundreds of thousands of dollars to begin to pique my interest.

   
Lou FCD



Posts: 5377
Joined: Jan. 2006

(Permalink) Posted: 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.

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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
I think I might love you. Don't tell Deadman -Wolfhound

Work-friendly photography
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afarensis



Posts: 1005
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(Permalink) Posted: 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.

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...

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Church burning ebola boy

FTK: I Didn't answer your questions because it beats the hell out of me.

PaV: I suppose for me to be pried away from what I do to focus long and hard on that particular problem would take, quite honestly, hundreds of thousands of dollars to begin to pique my interest.

   
Henry J



Posts: 4048
Joined: Mar. 2005

(Permalink) Posted: 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.


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

RidingHigh_402601a.jpg

Henry

  
stevestory



Posts: 8882
Joined: Oct. 2005

(Permalink) Posted: Sep. 25 2008,23:32   

Rocks may be oldest on earth

   
Louis



Posts: 6436
Joined: Jan. 2006

(Permalink) Posted: 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

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Bye.

  
Henry J



Posts: 4048
Joined: Mar. 2005

(Permalink) Posted: Sep. 26 2008,20:34   

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

Henry

  
Lou FCD



Posts: 5377
Joined: Jan. 2006

(Permalink) Posted: 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.


(My emphasis)

Pretty cool, especially given the timing.

--------------
Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
I think I might love you. Don't tell Deadman -Wolfhound

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stevestory



Posts: 8882
Joined: Oct. 2005

(Permalink) Posted: Sep. 29 2008,20:36   

fat baby girls and breast cancer

   
Richard Simons



Posts: 425
Joined: Oct. 2006

(Permalink) Posted: Sep. 29 2008,21:07   

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

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.

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All sweeping statements are wrong.

  
midwifetoad



Posts: 3553
Joined: Mar. 2008

(Permalink) Posted: 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.


http://neo.jpl.nasa.gov/news/news159.html

--------------
”let’s not make a joke of ourselves.”

Pat Robertson

  
Louis



Posts: 6436
Joined: Jan. 2006

(Permalink) Posted: 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

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

--------------
Bye.

  
Henry J



Posts: 4048
Joined: Mar. 2005

(Permalink) Posted: 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.

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.

Oh.

Never mind. :p

  
stevestory



Posts: 8882
Joined: Oct. 2005

(Permalink) Posted: Oct. 07 2008,15:45   

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

prion infection method identified.

   
khan



Posts: 1480
Joined: May 2007

(Permalink) Posted: 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

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

I've got the climate modeling one running on my desktop.

--------------
"It's as if all those words, in their hurry to escape from the loony, have fallen over each other, forming scrambled heaps of meaninglessness." -damitall

That's so fucking stupid it merits a wing in the museum of stupid. -midwifetoad

  
Reed



Posts: 274
Joined: Feb. 2008

(Permalink) Posted: 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.

  
Lou FCD



Posts: 5377
Joined: Jan. 2006

(Permalink) Posted: Oct. 08 2008,10:35   

Yes, *ahem*.



Quote
People like you find it so easy, by Roo Reynolds


--------------
Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
I think I might love you. Don't tell Deadman -Wolfhound

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stevestory



Posts: 8882
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(Permalink) Posted: Oct. 08 2008,15:42   

How the Turtle got its Shell

Irreducible Complexity Failure #10,193,883,469,093.

   
stevestory



Posts: 8882
Joined: Oct. 2005

(Permalink) Posted: Oct. 11 2008,00:25   

Chains of arthropods from half a billion years ago.

   
Henry J



Posts: 4048
Joined: Mar. 2005

(Permalink) Posted: Oct. 13 2008,13:30   

Quote
Chains of arthropods from half a billion years ago.


But did they find any missing links? :p

  
stevestory



Posts: 8882
Joined: Oct. 2005

(Permalink) Posted: Oct. 13 2008,22:09   

How ships like The Beagle dealt with lightening

   
stevestory



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(Permalink) Posted: Oct. 15 2008,00:39   

A Guiding Glow to Track the Movement of Proteins

   
Lou FCD



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(Permalink) Posted: Oct. 17 2008,05:52   

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

That's just cool.

--------------
Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
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J-Dog



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(Permalink) Posted: Oct. 19 2008,11:41   

Dude...

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

Far out.

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Come on Tough Guy, do the little dance of ID impotence you do so well. - Louis to Joe G 2/10

Gullibility is not a virtue - Quidam on Dembski's belief in the Bible Code Faith Healers & ID 7/08

UD is an Unnatural Douchemagnet. - richardthughes 7/11

  
stevestory



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(Permalink) Posted: Oct. 21 2008,18:36   

Unsustainable resource depletion began 10,000 years ago.

Interesting article. Not sure how valid the argument is.

   
stevestory



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(Permalink) Posted: 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.

   
afarensis



Posts: 1005
Joined: Dec. 2006

(Permalink) Posted: 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.


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.


--------------
Church burning ebola boy

FTK: I Didn't answer your questions because it beats the hell out of me.

PaV: I suppose for me to be pried away from what I do to focus long and hard on that particular problem would take, quite honestly, hundreds of thousands of dollars to begin to pique my interest.

   
J-Dog



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(Permalink) Posted: 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.


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.

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Come on Tough Guy, do the little dance of ID impotence you do so well. - Louis to Joe G 2/10

Gullibility is not a virtue - Quidam on Dembski's belief in the Bible Code Faith Healers & ID 7/08

UD is an Unnatural Douchemagnet. - richardthughes 7/11

  
stevestory



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(Permalink) Posted: 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.

   
stevestory



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(Permalink) Posted: Nov. 10 2008,23:16   

Good Basic Carl Zimmer Article on Genes

   
Henry J



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(Permalink) Posted: Nov. 13 2008,14:11   

Endeavour set for launch tomorrow

  
Lou FCD



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(Permalink) Posted: 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!


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.

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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
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Bob O'H



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(Permalink) Posted: 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.

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ID theorists don’t postulate a designer for their arguments. - Crandaddy
There is no connection between a peppered moth, natural selection, and religion that I can see. - FtK

   
stevestory



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(Permalink) Posted: 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.

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.

   
afarensis



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(Permalink) Posted: 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.


--------------
Church burning ebola boy

FTK: I Didn't answer your questions because it beats the hell out of me.

PaV: I suppose for me to be pried away from what I do to focus long and hard on that particular problem would take, quite honestly, hundreds of thousands of dollars to begin to pique my interest.

   
Henry J



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(Permalink) Posted: 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.

  
Lou FCD



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(Permalink) Posted: 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

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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
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Henry J



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(Permalink) Posted: Nov. 26 2008,21:46   

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


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

Henry

  
Lou FCD



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(Permalink) Posted: 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.


More, at Science.

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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
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stevestory



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(Permalink) Posted: Nov. 30 2008,12:21   

could drinking heavy water extend your life?

   
Henry J



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(Permalink) Posted: Nov. 30 2008,17:16   

Quote
could drinking heavy water extend your life?


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

Henry

  
Kristine



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(Permalink) Posted: 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.

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."

Eek!  :O

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midwifetoad



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(Permalink) Posted: 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.

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”let’s not make a joke of ourselves.”

Pat Robertson

  
Kristine



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Joined: Sep. 2006

(Permalink) Posted: 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.

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

They may just go to PDFs, which wouldn't help you.

--------------
Which came first: the shimmy, or the hip?

AtBC Poet Laureate

"I happen to think that this prerequisite criterion of empirical evidence is itself not empirical." - Clive

"Damn you. This means a trip to the library. Again." -- fnxtr

  
qetzal



Posts: 309
Joined: Feb. 2006

(Permalink) Posted: Dec. 05 2008,14:53   

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

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).


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.

  
Reed



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(Permalink) Posted: 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

  
Lou FCD



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(Permalink) Posted: 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.

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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
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Paul Flocken



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(Permalink) Posted: 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

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"The great enemy of the truth is very often not the lie--deliberate, contrived, and dishonest, but the myth, persistent, persuasive, and unrealistic.  Belief in myths allows the comfort of opinion without the discomfort of thought."-John F. Kennedy

  
midwifetoad



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(Permalink) Posted: 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.

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”let’s not make a joke of ourselves.”

Pat Robertson

  
Dr.GH



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(Permalink) Posted: Dec. 16 2008,10:41   

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

Edited by Dr.GH on Dec. 16 2008,08:42

--------------
"Science is the horse that pulls the cart of philosophy."

L. Susskind, 2004 "SMOLIN VS. SUSSKIND: THE ANTHROPIC PRINCIPLE"

   
nuytsia



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(Permalink) Posted: Dec. 17 2008,02:39   

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

But check out the comments.
Ugh!

   
keiths



Posts: 2041
Joined: Jan. 2006

(Permalink) Posted: 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

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.


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And the set of natural numbers is also the set that starts at 0 and goes to the largest number.  -- Joe G

Please stop putting words into my mouth that don't belong there and thoughts into my mind that don't belong there. -- KF

  
midwifetoad



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(Permalink) Posted: 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.


--------------
”let’s not make a joke of ourselves.”

Pat Robertson

  
ppb



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(Permalink) Posted: 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.

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"[A scientific theory] describes Nature as absurd from the point of view of common sense. And it agrees fully with experiment. So I hope you can accept Nature as She is - absurd."
- Richard P. Feynman

  
Lou FCD



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(Permalink) Posted: 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.

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.

:)

--------------
Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
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ppb



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(Permalink) Posted: 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.

:)


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.

--------------
"[A scientific theory] describes Nature as absurd from the point of view of common sense. And it agrees fully with experiment. So I hope you can accept Nature as She is - absurd."
- Richard P. Feynman

  
Lou FCD



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(Permalink) Posted: Dec. 19 2008,15:01   

I lurve me some Dr. BA, now.

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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
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Lou FCD



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(Permalink) Posted: 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.

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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
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stevestory



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(Permalink) Posted: 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.

   
Steviepinhead



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Joined: Jan. 2006

(Permalink) Posted: 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.

  
Kristine



Posts: 3037
Joined: Sep. 2006

(Permalink) Posted: 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.

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.

--------------
Which came first: the shimmy, or the hip?

AtBC Poet Laureate

"I happen to think that this prerequisite criterion of empirical evidence is itself not empirical." - Clive

"Damn you. This means a trip to the library. Again." -- fnxtr

  
Peter Henderson



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(Permalink) Posted: 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.

  
qetzal



Posts: 309
Joined: Feb. 2006

(Permalink) Posted: 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.


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.

  
Steviepinhead



Posts: 532
Joined: Jan. 2006

(Permalink) Posted: 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.

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

  
ppb



Posts: 325
Joined: Dec. 2006

(Permalink) Posted: 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.

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

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

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"[A scientific theory] describes Nature as absurd from the point of view of common sense. And it agrees fully with experiment. So I hope you can accept Nature as She is - absurd."
- Richard P. Feynman

  
J-Dog



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(Permalink) Posted: 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.

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

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!

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Come on Tough Guy, do the little dance of ID impotence you do so well. - Louis to Joe G 2/10

Gullibility is not a virtue - Quidam on Dembski's belief in the Bible Code Faith Healers & ID 7/08

UD is an Unnatural Douchemagnet. - richardthughes 7/11

  
Kristine



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(Permalink) Posted: 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.

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

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

Me, too! And what kind of chairs do they have in the Eames Theatre? ;)

--------------
Which came first: the shimmy, or the hip?

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Steviepinhead



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(Permalink) Posted: 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...!

  
utidjian



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Joined: Oct. 2007

(Permalink) Posted: 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-

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Being laughed at doesn't mean you're progressing along some line. It probably just means you're saying some stupid shit -stevestory

  
stevestory



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(Permalink) Posted: Jan. 10 2009,15:56   

self-replicating chemicals

   
stevestory



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(Permalink) Posted: Jan. 10 2009,15:58   

http://blogs.sciencemag.org/origins/

   
stevestory



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(Permalink) Posted: 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.

   
Lou FCD



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(Permalink) Posted: 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.


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.


(references removed and emphasis added)

That's just cool. (Weird, but cool.)

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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
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Henry J



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(Permalink) Posted: Jan. 15 2009,20:41   

Monkey business in Florida!

Henry

  
Henry J



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(Permalink) Posted: Jan. 16 2009,14:46   

Mars has gas!

  
Kristine



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(Permalink) Posted: 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.

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.)

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Which came first: the shimmy, or the hip?

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"Damn you. This means a trip to the library. Again." -- fnxtr

  
Henry J



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(Permalink) Posted: 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, [...]

  
Kristine



Posts: 3037
Joined: Sep. 2006

(Permalink) Posted: 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.

Obsessive-Compulsive Disorder By Bruce M. Hyman and Cherry Pedrick (a psychotherapist and a nurse, respectively)

--------------
Which came first: the shimmy, or the hip?

AtBC Poet Laureate

"I happen to think that this prerequisite criterion of empirical evidence is itself not empirical." - Clive

"Damn you. This means a trip to the library. Again." -- fnxtr

  
Henry J



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(Permalink) Posted: Jan. 29 2009,14:05   

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

Henry

  
Kristine



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(Permalink) Posted: Jan. 29 2009,17:21   

Yes - it made me think of a certain book. :)

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Which came first: the shimmy, or the hip?

AtBC Poet Laureate

"I happen to think that this prerequisite criterion of empirical evidence is itself not empirical." - Clive

"Damn you. This means a trip to the library. Again." -- fnxtr

  
stevestory



Posts: 8882
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(Permalink) Posted: Jan. 29 2009,22:22   

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

Henry

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.

   
rhmc



Posts: 340
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(Permalink) Posted: 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.

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.

  
rhmc



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(Permalink) Posted: 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.

  
Lou FCD



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(Permalink) Posted: Feb. 03 2009,19:08   

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

The paper in PLoS ONE.

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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
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Henry J



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(Permalink) Posted: 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

  
Lou FCD



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(Permalink) Posted: 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.


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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
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khan



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(Permalink) Posted: 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.

Gaack! ~40 foot snake.

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"It's as if all those words, in their hurry to escape from the loony, have fallen over each other, forming scrambled heaps of meaninglessness." -damitall

That's so fucking stupid it merits a wing in the museum of stupid. -midwifetoad

  
jeannot



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(Permalink) Posted: Feb. 06 2009,03:23   

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

http://www.sciencemag.org/content/current/

  
JLT



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(Permalink) Posted: Feb. 09 2009,15:14   

Not Exactly Rocket Science has a series of posts on evolutionary research. Nice reads so far.

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"Random mutations, if they are truly random, will affect, and potentially damage, any aspect of the organism, [...]
Thus, a realistic [computer] simulation [of evolution] would allow the program, OS, and hardware to be affected in a random fashion." GilDodgen, Frilly shirt owner

  
Erasmus, FCD



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(Permalink) Posted: 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.

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You're obviously illiterate as hell. Peach, bro.-FtK

Finding something hard to believe based on the evidence, is science.-JoeG

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I work on molecular systems with pathway charts and such.-Giggles

  
Lou FCD



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(Permalink) Posted: 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
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.


--------------
Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
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Kristine



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(Permalink) Posted: 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.

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

Whew. Curse you, Erasmus. That was a close one.  :angry:

--------------
Which came first: the shimmy, or the hip?

AtBC Poet Laureate

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afarensis



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(Permalink) Posted: 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.

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Church burning ebola boy

FTK: I Didn't answer your questions because it beats the hell out of me.

PaV: I suppose for me to be pried away from what I do to focus long and hard on that particular problem would take, quite honestly, hundreds of thousands of dollars to begin to pique my interest.

   
Lou FCD



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(Permalink) Posted: 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.


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

A really interesting read.

--------------
Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
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JLT



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(Permalink) Posted: 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.

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).


And finally accompanying commentary.

--------------
"Random mutations, if they are truly random, will affect, and potentially damage, any aspect of the organism, [...]
Thus, a realistic [computer] simulation [of evolution] would allow the program, OS, and hardware to be affected in a random fashion." GilDodgen, Frilly shirt owner

  
Steviepinhead



Posts: 532
Joined: Jan. 2006

(Permalink) Posted: 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.

  
dvunkannon



Posts: 1377
Joined: June 2008

(Permalink) Posted: 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...

--------------
I’m referring to evolution, not changes in allele frequencies. - Cornelius Hunter
I’m not an evolutionist, I’m a change in allele frequentist! - Nakashima

  
JLT



Posts: 740
Joined: Jan. 2008

(Permalink) Posted: 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]

--------------
"Random mutations, if they are truly random, will affect, and potentially damage, any aspect of the organism, [...]
Thus, a realistic [computer] simulation [of evolution] would allow the program, OS, and hardware to be affected in a random fashion." GilDodgen, Frilly shirt owner

  
J-Dog



Posts: 4361
Joined: Dec. 2006

(Permalink) Posted: 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".

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

KIDDING!  This is actully totally cool.

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Come on Tough Guy, do the little dance of ID impotence you do so well. - Louis to Joe G 2/10

Gullibility is not a virtue - Quidam on Dembski's belief in the Bible Code Faith Healers & ID 7/08

UD is an Unnatural Douchemagnet. - richardthughes 7/11

  
carlsonjok



Posts: 3324
Joined: May 2006

(Permalink) Posted: 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".

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!!!!

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It's natural to be curious about our world, but the scientific method is just one theory about how to best understand it.  We live in a democracy, which means we should treat every theory equally. - Steven Colbert, I Am America (and So Can You!)

  
Henry J



Posts: 4048
Joined: Mar. 2005

(Permalink) Posted: Feb. 23 2009,17:25   

I guess it's easy to see what that critter has on its mind...

  
ppb



Posts: 325
Joined: Dec. 2006

(Permalink) Posted: 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.

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"[A scientific theory] describes Nature as absurd from the point of view of common sense. And it agrees fully with experiment. So I hope you can accept Nature as She is - absurd."
- Richard P. Feynman

  
dvunkannon



Posts: 1377
Joined: June 2008

(Permalink) Posted: 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!

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I’m referring to evolution, not changes in allele frequencies. - Cornelius Hunter
I’m not an evolutionist, I’m a change in allele frequentist! - Nakashima

  
bystander



Posts: 301
Joined: Oct. 2005

(Permalink) Posted: 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]

ID predicted this

  
bystander



Posts: 301
Joined: Oct. 2005

(Permalink) Posted: 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...

ID Predicted this

  
JohnW



Posts: 2228
Joined: Aug. 2006

(Permalink) Posted: Mar. 03 2009,15:40   

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

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

A mutation!  And since there is no such thing as a beneficial mutation, we have learned that "p" has more CSI than "P".

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Math is just a language of reality. Its a waste of time to know it.
- Robert Byers

  
ppb



Posts: 325
Joined: Dec. 2006

(Permalink) Posted: 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]

ID predicted this

Don't worry.  The ICR is on top of it.  :D

--------------
"[A scientific theory] describes Nature as absurd from the point of view of common sense. And it agrees fully with experiment. So I hope you can accept Nature as She is - absurd."
- Richard P. Feynman

  
Lou FCD



Posts: 5377
Joined: Jan. 2006

(Permalink) Posted: 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]

ID predicted this

Don't worry.  The ICR is on top of it.  :D

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.


No, thank you.

--------------
Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
I think I might love you. Don't tell Deadman -Wolfhound

Work-friendly photography
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dvunkannon



Posts: 1377
Joined: June 2008

(Permalink) Posted: Mar. 04 2009,11:58   

The Origin of Phagocytosis and Eukaryogenesis

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

--------------
I’m referring to evolution, not changes in allele frequencies. - Cornelius Hunter
I’m not an evolutionist, I’m a change in allele frequentist! - Nakashima

  
JLT



Posts: 740
Joined: Jan. 2008

(Permalink) Posted: 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!"

Damn it.

--------------
"Random mutations, if they are truly random, will affect, and potentially damage, any aspect of the organism, [...]
Thus, a realistic [computer] simulation [of evolution] would allow the program, OS, and hardware to be affected in a random fashion." GilDodgen, Frilly shirt owner

  
JLT



Posts: 740
Joined: Jan. 2008

(Permalink) Posted: 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!"

Damn it. Didn't see that one.

Argh, I hit send too fast and now it won't let me edit my original post :(

--------------
"Random mutations, if they are truly random, will affect, and potentially damage, any aspect of the organism, [...]
Thus, a realistic [computer] simulation [of evolution] would allow the program, OS, and hardware to be affected in a random fashion." GilDodgen, Frilly shirt owner

  
dnmlthr



Posts: 565
Joined: Mar. 2008

(Permalink) Posted: 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.


Swim my darlings, swim!

--------------
Guess what? I don't give a flying f*ck how "science works" - Ftk

  
Henry J



Posts: 4048
Joined: Mar. 2005

(Permalink) Posted: 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.

Well, that answers Kristine's question - shimmies came before hips.  :p

  
Reed



Posts: 274
Joined: Feb. 2008

(Permalink) Posted: Mar. 06 2009,19:29   

Carl Zimmer has a nice post about viroids.

  
Lou FCD



Posts: 5377
Joined: Jan. 2006

(Permalink) Posted: 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.


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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
I think I might love you. Don't tell Deadman -Wolfhound

Work-friendly photography
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Kristine



Posts: 3037
Joined: Sep. 2006

(Permalink) Posted: 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.


--------------
Which came first: the shimmy, or the hip?

AtBC Poet Laureate

"I happen to think that this prerequisite criterion of empirical evidence is itself not empirical." - Clive

"Damn you. This means a trip to the library. Again." -- fnxtr

  
Kristine



Posts: 3037
Joined: Sep. 2006

(Permalink) Posted: 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.
:)

--------------
Which came first: the shimmy, or the hip?

AtBC Poet Laureate

"I happen to think that this prerequisite criterion of empirical evidence is itself not empirical." - Clive

"Damn you. This means a trip to the library. Again." -- fnxtr

  
midwifetoad



Posts: 3553
Joined: Mar. 2008

(Permalink) Posted: Mar. 11 2009,01:37   

Yeah, but did she invent COBOL?

--------------
”let’s not make a joke of ourselves.”

Pat Robertson

  
dvunkannon



Posts: 1377
Joined: June 2008

(Permalink) Posted: Mar. 11 2009,08:42   

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

That was Rear Admiral Dr. Grace Murray Hopper.

--------------
I’m referring to evolution, not changes in allele frequencies. - Cornelius Hunter
I’m not an evolutionist, I’m a change in allele frequentist! - Nakashima

  
dvunkannon



Posts: 1377
Joined: June 2008

(Permalink) Posted: 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.


Swim my darlings, swim!

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


The creationist quotemine, appearing on UD in 10, 9,...

--------------
I’m referring to evolution, not changes in allele frequencies. - Cornelius Hunter
I’m not an evolutionist, I’m a change in allele frequentist! - Nakashima

  
Albatrossity2



Posts: 2778
Joined: Mar. 2007

(Permalink) Posted: 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.

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.

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Flesh of the sky, child of the sky, the mind
Has been obligated from the beginning
To create an ordered universe
As the only possible proof of its own inheritance.
                        - Pattiann Rogers

   
Lou FCD



Posts: 5377
Joined: Jan. 2006

(Permalink) Posted: 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.


--------------
Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
I think I might love you. Don't tell Deadman -Wolfhound

Work-friendly photography
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Henry J



Posts: 4048
Joined: Mar. 2005

(Permalink) Posted: Mar. 11 2009,19:07   

Yeasts are such fun gi's. And, they don't take up mush room.

  
afarensis



Posts: 1005
Joined: Dec. 2006

(Permalink) Posted: 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.


--------------
Church burning ebola boy

FTK: I Didn't answer your questions because it beats the hell out of me.

PaV: I suppose for me to be pried away from what I do to focus long and hard on that particular problem would take, quite honestly, hundreds of thousands of dollars to begin to pique my interest.

   
Erasmus, FCD



Posts: 6349
Joined: June 2007

(Permalink) Posted: 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
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
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
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]

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.


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.

--------------
You're obviously illiterate as hell. Peach, bro.-FtK

Finding something hard to believe based on the evidence, is science.-JoeG

the odds of getting some loathsome taint are low-- Gordon E Mullings Manjack Heights Montserrat

I work on molecular systems with pathway charts and such.-Giggles

  
Henry J



Posts: 4048
Joined: Mar. 2005

(Permalink) Posted: Mar. 14 2009,20:06   

This brings to mind one of the Star Trek movies.

Henry

  
Lou FCD



Posts: 5377
Joined: Jan. 2006

(Permalink) Posted: 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


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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
I think I might love you. Don't tell Deadman -Wolfhound

Work-friendly photography
NSFW photography

   
khan



Posts: 1480
Joined: May 2007

(Permalink) Posted: 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.

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"It's as if all those words, in their hurry to escape from the loony, have fallen over each other, forming scrambled heaps of meaninglessness." -damitall

That's so fucking stupid it merits a wing in the museum of stupid. -midwifetoad

  
dvunkannon



Posts: 1377
Joined: June 2008

(Permalink) Posted: 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."


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I’m referring to evolution, not changes in allele frequencies. - Cornelius Hunter
I’m not an evolutionist, I’m a change in allele frequentist! - Nakashima

  
Henry J



Posts: 4048
Joined: Mar. 2005

(Permalink) Posted: 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

  
midwifetoad



Posts: 3553
Joined: Mar. 2008

(Permalink) Posted: 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

More a matter of when than whether.

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”let’s not make a joke of ourselves.”

Pat Robertson

  
Henry J



Posts: 4048
Joined: Mar. 2005

(Permalink) Posted: Mar. 17 2009,15:15   

When? Does that mean they used to be two, but collided in their Urals?

  
afarensis



Posts: 1005
Joined: Dec. 2006

(Permalink) Posted: 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.


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Church burning ebola boy

FTK: I Didn't answer your questions because it beats the hell out of me.

PaV: I suppose for me to be pried away from what I do to focus long and hard on that particular problem would take, quite honestly, hundreds of thousands of dollars to begin to pique my interest.

   
rhmc



Posts: 340
Joined: Dec. 2007

(Permalink) Posted: 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

  
Richardthughes



Posts: 10094
Joined: Jan. 2006

(Permalink) Posted: Mar. 22 2009,23:30   

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

Brain on the edge of chaos..

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"Richardthughes, you magnificent bastard, I stand in awe of you..." : Arden Chatfield
"You magnificent bastard! " : Louis
"ATBC poster child", "I have to agree with Rich.." : DaveTard
"I bow to your superior skills" : deadman_932
"...it was Richardthughes making me lie in bed.." : Kristine

  
Arden Chatfield



Posts: 6657
Joined: Jan. 2006

(Permalink) Posted: 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?”

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.

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"Rich is just mad because he thought all titties had fur on them until last week when a shorn transvestite ruined his childhood dreams by jumping out of a spider man cake and man boobing him in the face lips." - Erasmus

  
Erasmus, FCD



Posts: 6349
Joined: June 2007

(Permalink) Posted: 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.


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.

--------------
You're obviously illiterate as hell. Peach, bro.-FtK

Finding something hard to believe based on the evidence, is science.-JoeG

the odds of getting some loathsome taint are low-- Gordon E Mullings Manjack Heights Montserrat

I work on molecular systems with pathway charts and such.-Giggles

  
rhmc



Posts: 340
Joined: Dec. 2007

(Permalink) Posted: 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?”

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.

sounds good to me.  now where did i leave that list...

  
afarensis



Posts: 1005
Joined: Dec. 2006

(Permalink) Posted: 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.


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Church burning ebola boy

FTK: I Didn't answer your questions because it beats the hell out of me.

PaV: I suppose for me to be pried away from what I do to focus long and hard on that particular problem would take, quite honestly, hundreds of thousands of dollars to begin to pique my interest.

   
Henry J



Posts: 4048
Joined: Mar. 2005

(Permalink) Posted: 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]

  
Richardthughes



Posts: 10094
Joined: Jan. 2006

(Permalink) Posted: April 06 2009,10:22   

Privileged Planet? - notsomuch:


http://www.technologyreview.com/blog/arxiv/23309/

--------------
"Richardthughes, you magnificent bastard, I stand in awe of you..." : Arden Chatfield
"You magnificent bastard! " : Louis
"ATBC poster child", "I have to agree with Rich.." : DaveTard
"I bow to your superior skills" : deadman_932
"...it was Richardthughes making me lie in bed.." : Kristine