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sledgehammer



Posts: 531
Joined: Sep. 2008

(Permalink) Posted: Aug. 28 2009,12:12   

Evidence of recent evolution in Deer Mice
Deer mice of the Sand hills in Nebraska have recently (in the last 4000 years) evolved a new, lighter color coat, that better matches their environment.

New coat color? Pfft.  Micro-evolution. No big deal.

Not so fast there, Poindexter.  The color change is a manifestation of a brand new gene, Agouti, that developed in around 8000 generations.  From the article:  
Quote
"The light gene wasn't in existence, so the mice had to "wait" until a particular mutation occurred and then selection had to act on that new mutation," says team member Professor Hopi Hoekstra, also of Harvard University.

"It's a two part process. First the mutation has to occur and second, selection has to increase its frequency."

The researchers say it is the first time that it has been possible to document the appearance of a gene, its selection and subsequent spread through a population of wild animals.

And that has allowed them to estimate the "strength" of the natural selection pressure.

Having light coloured fur gives the paler Sand Hills mice a 0.5% survival advantage.

"It doesn't seem that much, but multiplied over thousands of individuals over hundreds of years, it makes a huge difference," says Prof Hoekstra.

"Ours is a very complete story," adds Dr Linnen.

"We've been able to connect changes at DNA level to the ability of deer mice to survive in nature."

Now how many bits of "FSCI" does this new gene represent?  More than 140?  Must have been a direct intervention by god! :p

--------------
The majority of the stupid is invincible and guaranteed for all time. The terror of their tyranny is alleviated by their lack of consistency. -A. Einstein  (H/T, JAD)
If evolution is true, you could not know that it's true because your brain is nothing but chemicals. ?Think about that. -K. Hovind

  
Erasmus, FCD



Posts: 6349
Joined: June 2007

(Permalink) Posted: Aug. 28 2009,13:34   

they're still just mice.

yawn.

wake me up when one gives birth to a dog-cat.

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

  
ppb



Posts: 325
Joined: Dec. 2006

(Permalink) Posted: Aug. 28 2009,13:52   

Quote (Erasmus @ FCD,Aug. 28 2009,14:34)
they're still just mice.

yawn.

wake me up when one gives birth to a dog-cat.

Will you accept a dog-racoon?



--------------
"[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

  
Timothy McDougald



Posts: 1014
Joined: Dec. 2006

(Permalink) Posted: Aug. 28 2009,19:19   

Quote (Erasmus, FCD @ Aug. 28 2009,13:34)
they're still just mice.

yawn.

wake me up when one gives birth to a dog-cat.

I'm holding out for a fishungulant myself - part barracuda, part moose, and all Sarah Palin!

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

   
bfish



Posts: 267
Joined: Feb. 2006

(Permalink) Posted: Aug. 29 2009,02:55   

Quote (sledgehammer @ Aug. 28 2009,10:12)
Evidence of recent evolution in Deer Mice
Deer mice of the Sand hills in Nebraska have recently (in the last 4000 years) evolved a new, lighter color coat, that better matches their environment.

Dude, were you there?

[QUOTE]
The color change is a manifestation of a brand new gene, Agouti, that developed in around 8000 generations.  From the article:          
Quote
"The light gene wasn't in existence, so the mice had to "wait" until a particular mutation occurred and then selection had to act on that new mutation," says team member Professor Hopi Hoekstra, also of Harvard University.

"It's a two part process. First the mutation has to occur and second, selection has to increase its frequency."


I think this isn't quite correct. I don't have access to the article from home, but agouti is a pretty well-known gene. I think she's using sloppy "popular science" speak, whereby what she means to say is that the light mutation of the already existing Agouti gene wasn't present in the population.

I'm curious to know the nature of the mutation. It would be deliciously ironic if it were a mutation in Agouti regulation rather than in coding sequence (see this for explanation). I'll bet it's a coding mutation, though. Damn cool stuff, too.

Anyone who has access to the article, please let me know if I'm wrong about any of this.

ETA: my lameness in not being able to make the block quotes work.

  
Timothy McDougald



Posts: 1014
Joined: Dec. 2006

(Permalink) Posted: Aug. 29 2009,08:24   

Quote (bfish @ Aug. 29 2009,02:55)
Quote (sledgehammer @ Aug. 28 2009,10:12)
Evidence of recent evolution in Deer Mice
Deer mice of the Sand hills in Nebraska have recently (in the last 4000 years) evolved a new, lighter color coat, that better matches their environment.

Dude, were you there?

[QUOTE]
The color change is a manifestation of a brand new gene, Agouti, that developed in around 8000 generations.  From the article:            
Quote
"The light gene wasn't in existence, so the mice had to "wait" until a particular mutation occurred and then selection had to act on that new mutation," says team member Professor Hopi Hoekstra, also of Harvard University.

"It's a two part process. First the mutation has to occur and second, selection has to increase its frequency."


I think this isn't quite correct. I don't have access to the article from home, but agouti is a pretty well-known gene. I think she's using sloppy "popular science" speak, whereby what she means to say is that the light mutation of the already existing Agouti gene wasn't present in the population.

I'm curious to know the nature of the mutation. It would be deliciously ironic if it were a mutation in Agouti regulation rather than in coding sequence (see this for explanation). I'll bet it's a coding mutation, though. Damn cool stuff, too.

Anyone who has access to the article, please let me know if I'm wrong about any of this.

ETA: my lameness in not being able to make the block quotes work.

Yeah, I don't have access either, but would love to have a copy. Especially since one of the coauthors of the paper I mention below is involved in the new paper. This is pretty common in mice, a previous study on mainland vs beach dwelling forms indicates that an interaction between Mc1r and Agouti is responsible for the lighter color in beach forms. Be interesting to see if this is the case in the new paper also...

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

   
bfish



Posts: 267
Joined: Feb. 2006

(Permalink) Posted: Aug. 30 2009,02:25   

OK, I've seen the paper now.

They begin with the observation that the mice who live in the Sand Hills have lighter-colored coats than nearby mice of the same species who live on darker soils, and the knowledge that the Sand Hills are geologically young (apparently can't be older than the date of the last glacial retreat). This leads to the inference that the lighter coat has evolved relatively recently (i.e. no more than two times the age of the universe, according to Ken Ham).
They want to know the genetic cause of the color difference. Sequencing is getting cheaper and faster, but it's still neither cheap enough nor fast enough that you could sequence the entire genomes of the several population groups that they want to sample. So they need to zero in on a target for their search. They looked at the agouti gene specifically because it is known to be involved in hair color phenotype in mice. This allowed them to sequence only the region near agouti. They found several sequence differences between light and dark mice, and concluded that one of them, an amino acid deletion (Dang. I was hoping for regulatory sequence) is probably responsible for the coat color phenotype.
They then calculated the selection coefficent and used population genetics to estimate that the light coat color allele should achieve fixation (all mice in the Sand Hills would carry the allele) in roughly half the life span of the Sand Hills. Since not all the mice do, they infer (with the support of several other observations) that the mutation causing the amino acid deletion did not exist in the initial mice population.

All good stuff.

It is important to note, though, that their beak sizes did not change at all.

If I have represented any of this wrongly, please correct me here.
Also, if any mice people see this, could they use homologous recombination to replace the amino acid deletion with the pre-mutation sequence, in order to prove that the deletion is sufficient to cause the light coat color? (i.e. returning the gene to it's prior state should cause the coat color to darken).

  
sledgehammer



Posts: 531
Joined: Sep. 2008

(Permalink) Posted: Aug. 30 2009,11:59   

Thanks bfish, for digging up the details.  I apologize for taking the BBC blurb a little too literally. I should know better.
 I am but a humble physicist, and although I had learned of the agouti gene in mice, it's not a fact I use everyday. it's been a while since undergrad genetics and my memory is getting old and decrepit.
 So what are the odds of that protein island, in the middle of the vast sea on non-functional sequences, arising by chance mutations?  A bazillion-gazillion-to-one???!!!111!!! (technical physics terminology)
God must love those meeces to pieces, to make that change just for them!

--------------
The majority of the stupid is invincible and guaranteed for all time. The terror of their tyranny is alleviated by their lack of consistency. -A. Einstein  (H/T, JAD)
If evolution is true, you could not know that it's true because your brain is nothing but chemicals. ?Think about that. -K. Hovind

  
Henry J



Posts: 4098
Joined: Mar. 2005

(Permalink) Posted: Aug. 30 2009,17:29   

Quote
It is important to note, though, that their beak sizes did not change at all.

They also didn't grow wings or start talking. :)

Henry

  
jeannot



Posts: 1200
Joined: Jan. 2006

(Permalink) Posted: Sep. 01 2009,10:57   

Quote (afarensis @ Aug. 28 2009,19:19)
 
Quote (Erasmus @ FCD,Aug. 28 2009,13:34)
they're still just mice.

yawn.

wake me up when one gives birth to a dog-cat.

I'm holding out for a fishungulant myself - part barracuda, part moose, and all Sarah Palin!

Talking about hybridization, there's a bizarre paper on the early edition of PNAS.

"Caterpillars evolved from onychophorans by hybridogenesis"

http://www.pnas.org/content/early/2009/08/25/0908357106.abstract

Yes, you read it right. (for your info, onychophorans are not even arthropods)
I find it quite disturbing. The author (Donald Williamson) proposes that some larvae and their adults do not have a shared ancestry, but that larvae (namely caterpillars) were acquired by hybridization with distant taxa.
Although the hypothesis is testable, it seem extremely far-fetched, and in any case, not tested in the paper. So the title is highly misleading.
This reminds me of some JAD's paper, the guy does not seem to like Darwin either.

How could such paper pass through the editorial board?  
???

  
qetzal



Posts: 309
Joined: Feb. 2006

(Permalink) Posted: Sep. 01 2009,20:56   

Quote (jeannot @ Sep. 01 2009,10:57)
Quote (afarensis @ Aug. 28 2009,19:19)
   
Quote (Erasmus @ FCD,Aug. 28 2009,13:34)
they're still just mice.

yawn.

wake me up when one gives birth to a dog-cat.

I'm holding out for a fishungulant myself - part barracuda, part moose, and all Sarah Palin!

Talking about hybridization, there's a bizarre paper on the early edition of PNAS.

"Caterpillars evolved from onychophorans by hybridogenesis"

http://www.pnas.org/content/early/2009/08/25/0908357106.abstract

Yes, you read it right. (for your info, onychophorans are not even arthropods)
I find it quite disturbing. The author (Donald Williamson) proposes that some larvae and their adults do not have a shared ancestry, but that larvae (namely caterpillars) were acquired by hybridization with distant taxa.
Although the hypothesis is testable, it seem extremely far-fetched, and in any case, not tested in the paper. So the title is highly misleading.
This reminds me of some JAD's paper, the guy does not seem to like Darwin either.

How could such paper pass through the editorial board?  
???

Must be because it's PNAS, and it was communicated by Lynn Margulis. PNAS gives academy members special rights to communicate papers and more-or-less bypass 'normal' peer review. From the PNAS Info for Authors page:

Quote
An Academy member may “communicate” for others up to 2 manuscripts per year that are within the member's area of expertise. Before submission to PNAS, the member obtains reviews of the paper from at least 2 qualified referees, each from a different institution and not from the authors' or member's institutions. Referees should be asked to evaluate revised manuscripts to ensure that their concerns have been adequately addressed. The names and contact information, including e-mails, of referees who reviewed the paper, along with the reviews and the authors' response, must be included. Reviews must be submitted on the PNAS review form, and the identity of the referees must not be revealed to the authors. The member must include a brief statement endorsing publication in PNAS along with all of the referee reports received for each round of review. Members should follow National Science Foundation (NSF) guidelines to avoid conflict of interest between referees and authors (see Section iii). Members must verify that referees are free of conflicts of interest, or must disclose any conflicts and explain their choice of referees. These papers are published as “Communicated by" the responsible editor.


I assume Margulis is an NAS member. Still, it's pretty bizzare that she would agree to communicate such nonsense, or that she was able to find two qualified referees to agree that it should be published!

  
jeannot



Posts: 1200
Joined: Jan. 2006

(Permalink) Posted: Sep. 02 2009,00:56   

Yes, I noticed that it was a communicated paper. No way it could have been otherwise. But this should be examined by the editorial board anyway.  
But it seems that Margulis has published with this author. She must be seduced by anything controversial or something.
It is not good for PNAS's reputation, and their submitting procedure for NAS member could be criticized.

At the end of the paper, the author proposes crossing an insect and an onychophoran! I almost laughed. On can barely cross related species, that's called (postmating) reproductive isolation.
The predictions about gene content are ridiculous too. Gene content can vary greatly between related species, due to polyploidization, etc.

  
Erasmus, FCD



Posts: 6349
Joined: June 2007

(Permalink) Posted: Sep. 02 2009,01:16   

i've never heard such stuff as that.  should be fun.

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

  
Richardthughes



Posts: 10304
Joined: Jan. 2006

(Permalink) Posted: Sep. 02 2009,09:49   

Brace for quotemine:

http://www.newscientist.com/article....am.html

Quote
I'm an empirical kind of guy, and there is just no evidence of an artificial toehold in sentience. It is often forgotten that the idea of mind or brain as computational is merely an assumption, not a truth. When I point this out to "believers" in the computational theory of mind, some of their arguments are almost religious.


--------------
"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

  
sledgehammer



Posts: 531
Joined: Sep. 2008

(Permalink) Posted: Sep. 03 2009,23:00   

Origins:  The Zinc Link?
 
Quote
This work puts forward an evolutionary scenario that satisfies the known constraints by proposing that life on Earth emerged, powered by UV-rich solar radiation, at photosynthetically active porous edifices made of precipitated zinc sulfide (ZnS) similar to those found around modern deep-sea hydrothermal vents. Under the high pressure of the primeval, carbon dioxide-dominated atmosphere ZnS could precipitate at the surface of the first continents, within reach of solar light. It is suggested that the ZnS surfaces (1) used the solar radiation to drive carbon dioxide reduction, yielding the building blocks for the first biopolymers, (2) served as templates for the synthesis of longer biopolymers from simpler building blocks, and (3) prevented the first biopolymers from photo-dissociation, by absorbing from them the excess radiation. In addition, the UV light may have favoured the selective enrichment of photostable, RNA-like polymers. Falsification tests of this hypothesis are described in the accompanying article (A.Y. Mulkidjanian, M.Y. Galperin, Biology Direct 2009, 4:27).

Abstr. Part 2
and PDFs too!
and PDF two

--------------
The majority of the stupid is invincible and guaranteed for all time. The terror of their tyranny is alleviated by their lack of consistency. -A. Einstein  (H/T, JAD)
If evolution is true, you could not know that it's true because your brain is nothing but chemicals. ?Think about that. -K. Hovind

  
Henry J



Posts: 4098
Joined: Mar. 2005

(Permalink) Posted: Sep. 04 2009,14:17   

Pandamonium!

Oh, and it's a boy.

  
Bob O'H



Posts: 1991
Joined: Oct. 2005

(Permalink) Posted: Sep. 04 2009,15:46   

Quote
I'm curious to know the nature of the mutation. It would be deliciously ironic if it were a mutation in Agouti regulation rather than in coding sequence (see this for explanation). I'll bet it's a coding mutation, though. Damn cool stuff, too.

She has found mutations in regulatory sequences that affected coat colour in the past.

--------------
It is fun to dip into the various threads to watch cluelessness at work in the hands of the confident exponent. - Soapy Sam (so say we all)

   
Timothy McDougald



Posts: 1014
Joined: Dec. 2006

(Permalink) Posted: Sep. 04 2009,18:53   

Quote (Bob O'H @ Sep. 04 2009,15:46)
Quote
I'm curious to know the nature of the mutation. It would be deliciously ironic if it were a mutation in Agouti regulation rather than in coding sequence (see this for explanation). I'll bet it's a coding mutation, though. Damn cool stuff, too.

She has found mutations in regulatory sequences that affected coat colour in the past.

There is some interesting stuff on her publication page.

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

   
bfish



Posts: 267
Joined: Feb. 2006

(Permalink) Posted: Sep. 04 2009,20:01   

Quote (afarensis @ Sep. 04 2009,16:53)
Quote (Bob O'H @ Sep. 04 2009,15:46)
 
Quote
I'm curious to know the nature of the mutation. It would be deliciously ironic if it were a mutation in Agouti regulation rather than in coding sequence (see this for explanation). I'll bet it's a coding mutation, though. Damn cool stuff, too.

She has found mutations in regulatory sequences that affected coat colour in the past.

There is some interesting stuff on her publication page.

Yes, and #16 on the list

# *Hoekstra, H.E. and J.A. Coyne. 2007. The locus of evolution: evo devo and the genetics of adaptation.  Evolution. 61(5):995-1016.

is what I was alluding to when I said it would be ironic if the adaptive coat color change was caused by regulatory sequence. In that paper they list 35 examples of adaptations caused by changes in protein coding sequence while maintaining that there are (or were in 2007) zero proven examples of adaptations caused by changes in regulatory sequence. They argue that one must meet the standard of showing what the specific mutation is AND demonstrating it's adaptive value.

In the new paper they show a specific mutation AND they measure the adaptive value of a phenotype they believe is caused by that mutation. So it would have been fun if it had been a regulatory mutation. I wonder, though, if they met there own standard in this paper, because I'm not sure they PROVE that the mutation they focus on causes the phenotype. That's why I asked if it would be possible for them to take mice from the native population and replace, in their progeny, the new version of the gene with a version of the gene that repairs the amino acid deletion. Then you could see if the dark phenotype was rescued, which would be very convincing evidence that the deletion caused the light color phenotype. I'm not a mouse person, so I don't know if that is technically feasible.

  
Timothy McDougald



Posts: 1014
Joined: Dec. 2006

(Permalink) Posted: Sep. 04 2009,20:59   

Quote (bfish @ Sep. 04 2009,20:01)
Quote (afarensis @ Sep. 04 2009,16:53)
 
Quote (Bob O'H @ Sep. 04 2009,15:46)
 
Quote
I'm curious to know the nature of the mutation. It would be deliciously ironic if it were a mutation in Agouti regulation rather than in coding sequence (see this for explanation). I'll bet it's a coding mutation, though. Damn cool stuff, too.

She has found mutations in regulatory sequences that affected coat colour in the past.

There is some interesting stuff on her publication page.

Yes, and #16 on the list

# *Hoekstra, H.E. and J.A. Coyne. 2007. The locus of evolution: evo devo and the genetics of adaptation.  Evolution. 61(5):995-1016.

is what I was alluding to when I said it would be ironic if the adaptive coat color change was caused by regulatory sequence. In that paper they list 35 examples of adaptations caused by changes in protein coding sequence while maintaining that there are (or were in 2007) zero proven examples of adaptations caused by changes in regulatory sequence. They argue that one must meet the standard of showing what the specific mutation is AND demonstrating it's adaptive value.

In the new paper they show a specific mutation AND they measure the adaptive value of a phenotype they believe is caused by that mutation. So it would have been fun if it had been a regulatory mutation. I wonder, though, if they met there own standard in this paper, because I'm not sure they PROVE that the mutation they focus on causes the phenotype. That's why I asked if it would be possible for them to take mice from the native population and replace, in their progeny, the new version of the gene with a version of the gene that repairs the amino acid deletion. Then you could see if the dark phenotype was rescued, which would be very convincing evidence that the deletion caused the light color phenotype. I'm not a mouse person, so I don't know if that is technically feasible.

Yeah, I don't think they prove that either, granted what they do have strongly suggests that it does, but they didn't seal the deal. I'll have to download the paper your talking about (among others), sigh, too many science papers, too little time to blog about them...

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

   
jeannot



Posts: 1200
Joined: Jan. 2006

(Permalink) Posted: Sep. 05 2009,13:55   

Some update on pea aphids:

Post-Pleistocene radiation of the pea aphid complex revealed by rapidly evolving endosymbionts

Jean Peccoud, Jean-Christophe Simon, Heather J. McLaughlin, and Nancy A. Moran

http://www.pnas.org/content/early/2009/09/03/0905129106.abstract

Basically, our pea aphid races and species have a very recent origin that may be linked to the domestication of some of their host plants.

I can send the pdf to anyone interested.

  
jeannot



Posts: 1200
Joined: Jan. 2006

(Permalink) Posted: Sep. 05 2009,14:05   

Quote (bfish @ Aug. 29 2009,02:55)
I'm curious to know the nature of the mutation. It would be deliciously ironic if it were a mutation in Agouti regulation rather than in coding sequence.

When I read "cis-acting mutation" in the abstract, I thought "how ironic", since the term reminded me the work of Sean Caroll on cis-regulatory sequences.

  
Timothy McDougald



Posts: 1014
Joined: Dec. 2006

(Permalink) Posted: Sep. 06 2009,13:49   

Speaking of botany there is a new paper called Xylem heterochrony: an unappreciated key to angiosperm origin and diversifications in the Botanical Journal of the Linnean Society, 2009; 161 (1): 26 DOI: 10.1111/j.1095-8339.2009.00991.x. Here is the abstract:

Quote
All angiosperms can be arranged along a spectrum from a preponderance of juvenile traits (cambial activity lost) to one of nearly all adult characters (cambium maximally active, mature patterns realized rapidly early in ontogeny). Angiosperms are unique among seed plants in the width of this spectrum. Xylem patterns are considered here to be indicative of contemporary function, not relictual. Nevertheless, most families of early-divergent angiosperms exhibit paedomorphic xylem structure, a circumstance that is most plausibly explained by the concept that early angiosperms had sympodial growth forms featuring limited accumulation of secondary xylem. Sympodial habits have been retained in various ways not only in early-divergent angiosperms, but also among eudicots in Ranunculales. The early angiosperm vessel, relatively marginal in conductive abilities, was improved in various ways, with concurrent redesign of parenchyma and fibre systems to enhance conductive, storage and mechanical capabilities. Flexibility in degree of cambial activity and kinds of juvenile/adult expressions has been basic to diversification in eudicots as a whole. Sympodial growth that lacks cambium, such as in monocots, provides advantages by various features, such as organographic compartmentalization of tracheid and vessel types. Woody monopodial eudicots were able to diversify as a result of production of new solutions to embolism prevention and conductive efficiency, particularly in vessel design, but also in parenchyma histology. Criteria for paedomorphosis in wood include slow decrease in length of fusiform cambial initials, predominance of procumbent ray cells and lesser degrees of cambial activity. Retention of ancestral features in primary xylem (the 'refugium' effect) is, in effect, a sort of inverse evidence of acceleration of adult patterns in later formed xylem. Xylem heterochrony is analysed not only for all key groups of angiosperms (including monocots), but also for different growth forms, such as lianas, annuals, various types of perennials, rosette trees and stem succulents. Xylary phenomena that potentially could be confused with heterochrony are discussed. Heterochronous xylem features seem at least as important as other often cited factors (pollination biology) because various degrees of paedomorphic xylem are found in so many growth forms that relate in xylary terms to ecological sites. Xylem heterochrony can probably be accessed during evolution by relatively simple gene changes in a wide range of angiosperms and thus represents a current as well as a past source of variation upon which diversification was based. Results discussed here are compatible with both current molecular-based phylogenetic analyses and all recent physiological work on conduction in xylem and thus represent an integration of these fields.


It does require a subscription....

Edited to correct some typos

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

   
Albatrossity2



Posts: 2779
Joined: Mar. 2007

(Permalink) Posted: Sep. 10 2009,11:29   

One of the great old-time biologists, Henry Fitch, has passed away at the ripe old age of 99. He was still working (at the biological preserve named after him) up to the age of 96!

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

   
dvunkannon



Posts: 1377
Joined: June 2008

(Permalink) Posted: Sep. 10 2009,11:51   

Quote (sledgehammer @ Sep. 04 2009,00:00)
Origins:  The Zinc Link?
 
Quote
This work puts forward an evolutionary scenario that satisfies the known constraints by proposing that life on Earth emerged, powered by UV-rich solar radiation, at photosynthetically active porous edifices made of precipitated zinc sulfide (ZnS) similar to those found around modern deep-sea hydrothermal vents. Under the high pressure of the primeval, carbon dioxide-dominated atmosphere ZnS could precipitate at the surface of the first continents, within reach of solar light. It is suggested that the ZnS surfaces (1) used the solar radiation to drive carbon dioxide reduction, yielding the building blocks for the first biopolymers, (2) served as templates for the synthesis of longer biopolymers from simpler building blocks, and (3) prevented the first biopolymers from photo-dissociation, by absorbing from them the excess radiation. In addition, the UV light may have favoured the selective enrichment of photostable, RNA-like polymers. Falsification tests of this hypothesis are described in the accompanying article (A.Y. Mulkidjanian, M.Y. Galperin, Biology Direct 2009, 4:27).

Abstr. Part 2
and PDFs too!
and PDF two

I just finished reading the first article yesterday. I think they did a great job of bringing together multiple streams of evidence to support their hypothesis, as well as bridging the RNA-world and metabolism first divide.

Definitely something to wave in front of GERM of TIKI the next time he goes on about the always linked improbabilities of OOL. It looks like you don't need plate tectonics to get started, though tides might help.

--------------
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: 4098
Joined: Mar. 2005

(Permalink) Posted: Sep. 10 2009,14:12   

I zinc, therefore I am?

  
sledgehammer



Posts: 531
Joined: Sep. 2008

(Permalink) Posted: Sep. 10 2009,16:20   

Quote (dvunkannon @ Sep. 10 2009,09:51)
   
Quote (sledgehammer @ Sep. 04 2009,00:00)
Origins:  The Zinc Link?
       
Quote
This work puts forward an evolutionary scenario that satisfies the known constraints by proposing that life on Earth emerged, powered by UV-rich solar radiation, at photosynthetically active porous edifices made of precipitated zinc sulfide (ZnS) similar to those found around modern deep-sea hydrothermal vents. Under the high pressure of the primeval, carbon dioxide-dominated atmosphere ZnS could precipitate at the surface of the first continents, within reach of solar light. It is suggested that the ZnS surfaces (1) used the solar radiation to drive carbon dioxide reduction, yielding the building blocks for the first biopolymers, (2) served as templates for the synthesis of longer biopolymers from simpler building blocks, and (3) prevented the first biopolymers from photo-dissociation, by absorbing from them the excess radiation. In addition, the UV light may have favoured the selective enrichment of photostable, RNA-like polymers. Falsification tests of this hypothesis are described in the accompanying article (A.Y. Mulkidjanian, M.Y. Galperin, Biology Direct 2009, 4:27).

Abstr. Part 2
and PDFs too!
and PDF two

I just finished reading the first article yesterday. I think they did a great job of bringing together multiple streams of evidence to support their hypothesis, as well as bridging the RNA-world and metabolism first divide.

Definitely something to wave in front of GERM of TIKI the next time he goes on about the always linked improbabilities of OOL. It looks like you don't need plate tectonics to get started, though tides might help.

Except for the extent of plate tectonics being resposible for undersea vents?
Also, for part 2 abstract and PDF, change the ref number inthe URL's from "26" to "27"
i.e
Abstr. Part 2
and PDF two

My bad.

--------------
The majority of the stupid is invincible and guaranteed for all time. The terror of their tyranny is alleviated by their lack of consistency. -A. Einstein  (H/T, JAD)
If evolution is true, you could not know that it's true because your brain is nothing but chemicals. ?Think about that. -K. Hovind

  
dvunkannon



Posts: 1377
Joined: June 2008

(Permalink) Posted: Sep. 10 2009,17:52   

Quote (sledgehammer @ Sep. 10 2009,17:20)
Quote (dvunkannon @ Sep. 10 2009,09:51)
   
Quote (sledgehammer @ Sep. 04 2009,00:00)
Origins:  The Zinc Link?
       
Quote
This work puts forward an evolutionary scenario that satisfies the known constraints by proposing that life on Earth emerged, powered by UV-rich solar radiation, at photosynthetically active porous edifices made of precipitated zinc sulfide (ZnS) similar to those found around modern deep-sea hydrothermal vents. Under the high pressure of the primeval, carbon dioxide-dominated atmosphere ZnS could precipitate at the surface of the first continents, within reach of solar light. It is suggested that the ZnS surfaces (1) used the solar radiation to drive carbon dioxide reduction, yielding the building blocks for the first biopolymers, (2) served as templates for the synthesis of longer biopolymers from simpler building blocks, and (3) prevented the first biopolymers from photo-dissociation, by absorbing from them the excess radiation. In addition, the UV light may have favoured the selective enrichment of photostable, RNA-like polymers. Falsification tests of this hypothesis are described in the accompanying article (A.Y. Mulkidjanian, M.Y. Galperin, Biology Direct 2009, 4:27).

Abstr. Part 2
and PDFs too!
and PDF two

I just finished reading the first article yesterday. I think they did a great job of bringing together multiple streams of evidence to support their hypothesis, as well as bridging the RNA-world and metabolism first divide.

Definitely something to wave in front of GERM of TIKI the next time he goes on about the always linked improbabilities of OOL. It looks like you don't need plate tectonics to get started, though tides might help.

Except for the extent of plate tectonics being resposible for undersea vents?
Also, for part 2 abstract and PDF, change the ref number inthe URL's from "26" to "27"
i.e
Abstr. Part 2
and PDF two

My bad.

While the article explains the hydrothermal precipitation of ZnS with reference to what we see today at the mid ocean ridges caused by plate tectonics, it also makes clear (deep in the article) that the huge ZnS outflows such as the Pilbara Craton of the early Earth took place at the continental surface as the result of volcanic hot spots and high atmospheric pressure working together - hydrothermal does not imply deep ocean in this case.

Plate tectonics would still be important later in sequestering carbon, but just to get life started, they are argunig not necessary.

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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

  
sledgehammer



Posts: 531
Joined: Sep. 2008

(Permalink) Posted: Sep. 10 2009,18:25   

Quote (dvunkannon @ Sep. 10 2009,15:52)
   
Quote (dvunkannon @ Sep. 10 2009,09:51)
     
While the article explains the hydrothermal precipitation of ZnS with reference to what we see today at the mid ocean ridges caused by plate tectonics, it also makes clear (deep in the article) that the huge ZnS outflows such as the Pilbara Craton of the early Earth took place at the continental surface as the result of volcanic hot spots and high atmospheric pressure working together - hydrothermal does not imply deep ocean in this case.

Plate tectonics would still be important later in sequestering carbon, but just to get life started, they are argunig not necessary.

Yes I see that now.  Thanks for clearing that up.  From the abstract in part 2:
   
Quote
Results
If  life  started within  photosynthesizing  ZnS compartments,  it  should  have  been  able  to  evolve under  the  conditions  of  elevated  levels  of  Zn2+  ions,  byproducts  of  the  ZnS-mediated photosynthesis.  Therefore,  the  Zn  world  hypothesis  leads  to  a  set  of  testable  predictions regarding  the  specific  roles  of Zn2+  ions  in modern  organisms,  particularly  in RNA  and  protein structures  related  to  the  procession  of RNA  and  the  “evolutionarily  old”  cellular  functions.   We checked  these  predictions  using  publicly  available  data  and  obtained  evidence  suggesting  that the  development  of  the  primeval  life  forms  up  to  the  stage  of  the  Last  Universal  Common Ancestor  proceeded  in  zinc-rich  settings.   Testing  of  the  hypothesis  has  revealed  the  possible supportive role of manganese sulfide in the primeval photosynthesis.  In addition, we demonstrate the explanatory power of the Zn world concept by elucidating several points that so far remained without  acceptable  rationalization.    In  particular,  this  concept  implies  a  new  scenario  for  the separation of Bacteria and Archaea and the origin of Eukarya.  

I also notice that Gene Koonin was one of the reviewers. Here's (part of) what he had to say:
   
Quote
...The idea of the pivotal role  of  Zn  ions  (and  ZnS  in  particular)  in  the  earliest  stages  of  the  evolution  of  life  is  highly attractive and generally plausible. However, in this manuscript, Mulkidjanian and Galperin put the plank very high by formulating several predictions that they claim to serve as Popperian tests of the “Zn world” hypothesis. In principle, the intention to test the hypothesis in a formal Popperian setting  is  indeed  commendable.  In  practice,  it  is well  known  that  it  is  hard  to  strictly  adhere  to Popperian criteria,  and  this paper  is no exception...

I think it is very cool that the reviewers comments and the responses by the authors are included in the manuscript.  Is this common in biology?  I've not seen this in the physics realm, unless I was one of the reviewers.

--------------
The majority of the stupid is invincible and guaranteed for all time. The terror of their tyranny is alleviated by their lack of consistency. -A. Einstein  (H/T, JAD)
If evolution is true, you could not know that it's true because your brain is nothing but chemicals. ?Think about that. -K. Hovind

  
Timothy McDougald



Posts: 1014
Joined: Dec. 2006

(Permalink) Posted: Sep. 10 2009,21:45   

In light of the recent paper - and fuss- on the appendix this paper is topical. Relaxed selection in the wild here is the abstract:
Quote
Natural populations often experience the weakening or removal of a source of selection that had been important in the maintenance of one or more traits. Here we refer to these situations as relaxed selection, and review recent studies that explore the effects of such changes on traits in their ecological contexts. In a few systems, such as the loss of armor in stickleback, the genetic, developmental and ecological bases of trait evolution are being discovered. These results yield insights into whether and how fast a trait is reduced or lost under relaxed selection. We provide a prospectus and a framework for understanding relaxed selection and trait loss in natural populations. We also examine its implications for applied issues, such as antibiotic resistance and the success of invasive species.


It is a really fascinating paper that I strongly recommend. I'll be doing a post on it - hopefully this weekend. For those who don't have access a pdf can be found here.

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

   
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