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dvunkannon



Posts: 1377
Joined: June 2008

(Permalink) Posted: Jan. 11 2012,16:05   

http://www.sciencedaily.com/release....216.htm

Molecular 'Culprit' in Rise of Planetary Oxygen

Cool points include searching a database of small (single fold) proteins to find old axygen producing enzymes.

Extra cool features:
Enzyme works with single metal atom to function. (Maganese)

These small proteins that use single metal atoms (like zinc fingers) are to my mind a key piece of evidence of the way out of the RNA World into our current pattern of nucleic acid polymer for memory and amino acid polymer for enzymatic action. So many small proteins working as recognition motifs - connecting RNA and a protein, and themselves binding directly to the RNA. Small proteins templating on the nucleic acid sequence, it is one direct templating step from there to the modern genetic system.

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

  
Starbuck



Posts: 16
Joined: July 2011

(Permalink) Posted: Jan. 11 2012,23:00   

Not sure what you're talking about, small proteins are evolutionarily recent additions to the repertoires of molecules. Moreover, proteins that are part of metallomes such as the proteins harboring single metal atoms are relatively recent, especially the Zinc fingers [see paper by Dupont et al. PNAS 107: 10567 (2010)], which are gene regulatory factors that act very specifically on DNA.

There is a model that is supported by phylogenomic data on how modern biochemistry proceeded in evolution and in the model ran associated with proteins appears quite late in evolution well after metabolic protein enzymes.

  
OgreMkV



Posts: 3304
Joined: Oct. 2009

(Permalink) Posted: Jan. 12 2012,07:34   

Quote (Starbuck @ Jan. 11 2012,23:00)
Not sure what you're talking about, small proteins are evolutionarily recent additions to the repertoires of molecules. Moreover, proteins that are part of metallomes such as the proteins harboring single metal atoms are relatively recent, especially the Zinc fingers [see paper by Dupont et al. PNAS 107: 10567 (2010)], which are gene regulatory factors that act very specifically on DNA.

There is a model that is supported by phylogenomic data on how modern biochemistry proceeded in evolution and in the model ran associated with proteins appears quite late in evolution well after metabolic protein enzymes.

I'm not sure what you are talking about.  The article you cite is talking about how much MORE metaloenzymes existed in eukarotes than their ancestors.  

So they were there.  

But whatever.

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Ignored by those who can't provide evidence for their claims.

http://skepticink.com/smilodo....retreat

   
Starbuck



Posts: 16
Joined: July 2011

(Permalink) Posted: Jan. 12 2012,10:17   

Where does it say that?

  
dvunkannon



Posts: 1377
Joined: June 2008

(Permalink) Posted: Jan. 12 2012,11:49   

Quote (Starbuck @ Jan. 12 2012,11:17)
Where does it say that?

 
Quote
In contrast, despite their early appearance, most (>60%) Zn-binding FSFs evolve after 0.6 nd, a pattern shared by Cu- and Ca-binding FSFs (Fig.3). Most of the late evolving Zn-FSFs use Zn as a structural molecule (Fig S2B).


My bolding. My point was that small, single domain proteins using metal ions are effective answers to two creationist claims:

1 - proteins have to be long (150 AAs) to show function
2 - catalytic activity comes from big proteins

I'm sorry if I overstepped the evidence in my enthusiasm for zinc fingers as an example. However, as OgreMkV points out, if Eukaryotes use them a lot, they must have picked up the trick from somewhere. The interesting point is the age, not the relative frequency of different metals.

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

  
OgreMkV



Posts: 3304
Joined: Oct. 2009

(Permalink) Posted: Jan. 12 2012,12:08   

Quote (Starbuck @ Jan. 12 2012,10:17)
Where does it say that?

In the conclusion.  I don't know, but you might want to read past the abstracts.

--------------
Ignored by those who can't provide evidence for their claims.

http://skepticink.com/smilodo....retreat

   
OgreMkV



Posts: 3304
Joined: Oct. 2009

(Permalink) Posted: Jan. 12 2012,12:11   

Oh, and you might want to read this rebuttal to the Dupont paper.
http://www.pnas.org/content....ull.pdf

--------------
Ignored by those who can't provide evidence for their claims.

http://skepticink.com/smilodo....retreat

   
Starbuck



Posts: 16
Joined: July 2011

(Permalink) Posted: Jan. 12 2012,14:06   

The seeming incongruity is caused by the diversity of Zn fingers, or the small cysteine-rich Zn binding protein
folds.  There are 28 "fold superfamilies" that are small cysteine-rich Zn binding proteins and 76 protein families nested within that.   Most of these evolved very late and most are only found in eukaryotes.  But it looks like there are a select few zinc fingers and beta ribbons that evolved very early and are found in all bacteria and archaea as well.

  
midwifetoad



Posts: 3556
Joined: Mar. 2008

(Permalink) Posted: Jan. 17 2012,13:49   

Some design detection:

http://arxiv.org/PS_cach....7v1.pdf

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罵et痴 not make a joke of ourselves.

Pat Robertson

  
dvunkannon



Posts: 1377
Joined: June 2008

(Permalink) Posted: Jan. 17 2012,14:17   

http://www.nature.com/nature....24.html

Dembski's retroactive theodicy explains evolution. Growth in complexity via duplication and loss of function mutations.

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

  
Timothy McDougald



Posts: 1008
Joined: Dec. 2006

(Permalink) Posted: Jan. 18 2012,12:57   

Experimental Evolution of Multicellularity

Quote
Multicellularity was one of the most significant innovations in the history of life, but its initial evolution remains poorly understood. Using experimental evolution, we show that key steps in this transition could have occurred quickly. We subjected the unicellular yeast Saccharomyces cerevisiae to an environment in which we expected multicellularity to be adaptive. We observed the rapid evolution of clustering genotypes that display a novel multicellular life history characterized by reproduction via multicellular propagules, a juvenile phase, and determinate growth. The multicellular clusters are uniclonal, minimizing within-cluster genetic conflicts of interest. Simple among-cell division of labor rapidly evolved. Early multicellular strains were composed of physiologically similar cells, but these subsequently evolved higher rates of programmed cell death (apoptosis), an adaptation that increases propagule production. These results show that key aspects ofmulticellular complexity, a subject of central importance to biology, can readily evolve from unicellular eukaryotes.


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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.

   
noncarborundum



Posts: 320
Joined: Jan. 2009

(Permalink) Posted: Jan. 18 2012,14:33   

Quote (afarensis @ Jan. 18 2012,12:57)
Experimental Evolution of Multicellularity

 
Quote
Multicellularity was one of the most significant innovations in the history of life, but its initial evolution remains poorly understood. Using experimental evolution, we show that key steps in this transition could have occurred quickly. We subjected the unicellular yeast Saccharomyces cerevisiae to an environment in which we expected multicellularity to be adaptive. We observed the rapid evolution of clustering genotypes that display a novel multicellular life history characterized by reproduction via multicellular propagules, a juvenile phase, and determinate growth. The multicellular clusters are uniclonal, minimizing within-cluster genetic conflicts of interest. Simple among-cell division of labor rapidly evolved. Early multicellular strains were composed of physiologically similar cells, but these subsequently evolved higher rates of programmed cell death (apoptosis), an adaptation that increases propagule production. These results show that key aspects ofmulticellular complexity, a subject of central importance to biology, can readily evolve from unicellular eukaryotes.

I saw Carl Zimmer's article on this in yesterday's NYTimes. He referred to what the researchers did as "natural selection", which seems unfortunate, but other than that it was quite good.

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"The . . . um . . . okay, I was genetically selected for blue eyes. I know there are brown eyes, because I've observed them, but I can't do it. Okay? So . . . um . . . coz that's real genetic selection, not the nonsense Giberson and the others are talking about." - DO'L

  
Timothy McDougald



Posts: 1008
Joined: Dec. 2006

(Permalink) Posted: Jan. 18 2012,15:55   

Based on this bit from the PNAS article:

Quote
We used gravity to select for primitive multicellularity in the unicellular yeast Saccharomyces cerevisiae. Clusters of cells settle through liquid more quickly than do single cells, allowing us to easily select for clustering genotypes. Settling selection was chosen not because it is widespread in nature, but rather because it is an experimentally tractable method to select for larger size.Ten replicate populations of initially isogenic S. cerevisiae were grown in nutrient-rich liquid medium with shaking to stationary phase (?109 cells/replicate population) before subculturing and daily transfer to fresh medium. All replicate populations were allowed to stand for 45 min before transfer to 10 mL fresh medium, during
which time cells settled toward the bottom of the culture tube. Cells in the lower 100 ?L were then transferred to fresh medium. After the first week, we modified the settling step to be more time efficient by using 100 ラ g, 10-s centrifugations of 1.5-mL subsamples from the shaken 10-mL tube to settle population fractions for transfer to fresh medium. We expected these conditions to select for clusters of cells, whether by postdivision adhesion or by aggregation.


A case could be made that it was natural selection, although it does seem kind of borderlinish to so describe it.

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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.

   
Timothy McDougald



Posts: 1008
Joined: Dec. 2006

(Permalink) Posted: Jan. 22 2012,19:27   

This is interesting.
From the abstract:

Quote
We propose a new model of the factors influencing acceptance of evolutionary theory that highlights a novel variable unexplored in previous studies: the feeling of certainty (FOC). The model is grounded in an emerging understanding of brain function that acknowledges the contributions of intuitive cognitions in making decisions, such as whether or not to accept a particular theoretical explanation of events. Specifically, we examine the relationships among religious identity, level of education, level of knowledge, FOC, and level of evolutionary acceptance to test whether our proposed model accurately predicts hypothesized pathways. We employ widely used measures葉he CINS, MATE, and ORI擁n addition to new variables in multiple regression and path analyses in order to test the interrelationships among FOC and acceptance of evolutionary theory. We explore these relationships using a sample of 124 pre-service biology teachers found to display comparable knowledge and belief levels as reported in previous studies on this topic. All of our hypothesis tests corroborated the idea that FOC plays a moderating role in relationships among evolutionary knowledge and beliefs. Educational research into acceptance of evolutionary theory will likely benefit from increased attention to non-conscious intuitive cognitions that give rise to feeling of knowing or certainty.


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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.

   
dvunkannon



Posts: 1377
Joined: June 2008

(Permalink) Posted: Jan. 23 2012,10:50   

Very small amounts of ethanol extends the life of C. elegans

http://www.sciencedaily.com/release....540.htm

Homeopathy lovers, rejoice!

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

  
The whole truth



Posts: 981
Joined: Jan. 2012

(Permalink) Posted: Jan. 26 2012,02:04   

My local PBS TV station has been broadcasting some very interesting shows on Wednesday evenings lately. I hope you're all watching and enjoying them. They include:

Nature
Nova
Inside Nature's Giants  (with Richard Dawkins)
History Of Science (How Did We Get Here?)

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Think not that I am come to send peace on earth: I came not to send peace, but a sword. - Jesus in Matthew 10:34

But those mine enemies, which would not that I should reign over them, bring hither, and slay them before me. -Jesus in Luke 19:27

   
fnxtr



Posts: 2119
Joined: June 2006

(Permalink) Posted: Jan. 26 2012,08:47   

Quote (dvunkannon @ Jan. 23 2012,08:50)
Very small amounts of ethanol extends the life of C. elegans

http://www.sciencedaily.com/release....540.htm

Homeopathy lovers, rejoice!

and vintners, too.

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"But it's disturbing to think someone actually thinks creationism -- having put it's hand on the hot stove every day for the last 400 years -- will get a different result tomorrow." -- midwifetoad

  
dvunkannon



Posts: 1377
Joined: June 2008

(Permalink) Posted: Jan. 27 2012,10:38   

http://the-scientist.com/2012....a-trait

Was someone asking for a molecule by molecule history of the evolution of a new, beneficial mutation?

This overview article refers to two papers published in Science, one from the Lenski group. That might attract the attention of the DI crew, who would otherwise like to pretend this stuff didn't exist.

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

  
midwifetoad



Posts: 3556
Joined: Mar. 2008

(Permalink) Posted: Jan. 27 2012,20:45   

I bet evolution can't produce dFOC.

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罵et痴 not make a joke of ourselves.

Pat Robertson

  
dvunkannon



Posts: 1377
Joined: June 2008

(Permalink) Posted: Jan. 30 2012,10:58   

http://the-scientist.com/2012....d-adapt

Summarizes a study of yeast under stress and the utility of whole chromosome duplication to population survival.

My question - did the stressor cause the duplication, or was the duplication just the kind of background level variation that happens all the time?

Last para contains a quote from someone at Baylor College of Medicine "who researches the molecular basis of genome instability and evolution". Waterloo!

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

  
Henry J



Posts: 4058
Joined: Mar. 2005

(Permalink) Posted: Jan. 30 2012,12:15   

But it's still yeast!!11!!eleven!!!!

  
Quack



Posts: 1755
Joined: May 2007

(Permalink) Posted: Jan. 30 2012,16:00   

Quote
http://the-scientist.com/2012....d-adapt

Another web site added to my favourites.

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YEC creationists denigrate science without an inkling of what their lives would be without it. YEC creationism is an enrageous, abominable insult to the the human intellect.
                                                         Me.

  
dvunkannon



Posts: 1377
Joined: June 2008

(Permalink) Posted: Feb. 06 2012,16:22   

http://www.nature.com/ngeo.......ex.html

An absolutely kick ass issue of Nature Geoscience on plants and their influence on the Earth. It seems that all the articles are free.

There has already been some media buzz about one article which talks about how the colonization of land by vascularized plants drew down enough CO2 from the atmosphere to start an Ice Age. Several other articles covering how plants created rivers are equally cool.

The editorial has some 'Rare Earth' memes that could get recycled by the anti-science crowd. But the conclusion isn't that way:
Quote
Even if evolution follows a predictable path, filling all available niches in a reproducible and consistent way, the niches on any Earth analogue could be different if the composition of its surface and atmosphere are not identical to those of Earth. And if evolution is random, the differences would be expected to be even larger.


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

  
dvunkannon



Posts: 1377
Joined: June 2008

(Permalink) Posted: Feb. 09 2012,10:28   

Peppered Moths reexamined, again.

http://the-scientist.com/2012.......xamined

Confirmation of Majerus' work that peppered moths are indeed an example of variation (in color) and natural selection occuring on that variation (via bird predation).

(shout-in from Canadian rube: But they're still moths!)

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

  
dvunkannon



Posts: 1377
Joined: June 2008

(Permalink) Posted: Feb. 10 2012,16:15   

http://www.nature.com/nsmb....41.html

It makes some big claims about helping to explain an RNA World to protein world transition, but it also makes my head hurt.

Anyone want to take a shot at summarizing?

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

  
REC



Posts: 567
Joined: Sep. 2006

(Permalink) Posted: Feb. 12 2012,10:23   

Looks bad for the bacterial Arsenate-DNA study:

Quote
Absence of arsenate in DNA from arsenate-grown GFAJ-1 cells

M. L. Reaves, S. Sinha, J. D. Rabinowitz, L. Kruglyak, R. J. Redfield

Wolfe-Simon et al. reported isolation of a strain of Halomonas bacteria, GFAJ-1, which could use arsenic as a nutrient when phosphate is limiting, and which could specifically incorporate arsenic into its DNA in place of phosphorus. We have found that arsenate is not needed for growth of GFAJ-1 when phosphate is limiting. Additionally, we used mass spectrometry to show that DNA purified from cells grown with limiting phosphate and abundant arsenate does not contain detectable arsenate.


http://arxiv.org/abs....01.6643

  
REC



Posts: 567
Joined: Sep. 2006

(Permalink) Posted: Feb. 12 2012,10:41   

Quote (dvunkannon @ Feb. 10 2012,16:15)
http://www.nature.com/nsmb.......41.html

It makes some big claims about helping to explain an RNA World to protein world transition, but it also makes my head hurt.

Anyone want to take a shot at summarizing?

Quick version:

GTPases are enzymes that hydrolyze GTP to GDP. They can act as molecular switches to regulate other processes-usually the GTP-bound state being an "on" signal and following hydrolysis, the GDP-bound state is "off."

The off-to-on and on-to-off states are regulated. Canonical GTPases have a GAP (GTPase activating protein) which generally supply a catalytic residue (amino acid) in trans, which activates hydrolysis, and makes the "off" state.

Some GTPases have all needed catalytic residues built-in. One might conclude they aren't regulated-just timed by their intrinsic activity. This study claims to show another protein binding the GTPase pushes this GTPase's own catalytic residues into position, acting like a GAP, except it gives it a nudge that makes the catalysis more efficient, instead of contributing a catalytic amino acid sidechain.

The authors suggest RNA could play a similar role-in targeting RNA protein complexes in translation--for protein localization, etc. The GTPases that use the new mechanism are ancient and conserved. They suggest RNA as a GAP  predates protein GAPs-perhaps even going back pre-LUCA.

  
Starbuck



Posts: 16
Joined: July 2011

(Permalink) Posted: Feb. 14 2012,11:40   

SRP-GTPases are post-LUCA ( Leipe et al., J
Mol Biol. 2002 Mar 15;317(1):41-72.)

  
Kristine



Posts: 3037
Joined: Sep. 2006

(Permalink) Posted: Feb. 16 2012,11:57   

Just a little snippet at the Academic Minute from Inside Higher Ed about how science is presented in the media - this is not news to any of you, but it's a good summary that you educators out there may want to use: "Scientists Say".

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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

  
REC



Posts: 567
Joined: Sep. 2006

(Permalink) Posted: Feb. 16 2012,12:11   

Quote (Starbuck @ Feb. 14 2012,11:40)
SRP-GTPases are post-LUCA ( Leipe et al., J
Mol Biol. 2002 Mar 15;317(1):41-72.)

Sorry, I'm not seeing that as a conclusion of the paper you cited.

Quote
The SRP and receptor GTPases are ubiquitous in the three superkingdoms and the two corresponding parts of the phylogenetic tree follow the standard model, with distinct archaeo-eukaryotic branches (Figure 5(l)). This indicates that both these GTPases were already present in the LUCA and that the original duplication leading to the divergence of SR and FtsY occurred at an even earlier stage of evolution.164

  
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