Register | Sign In


Understanding through Discussion


EvC Forum active members: 65 (9162 total)
5 online now:
Newest Member: popoi
Post Volume: Total: 915,815 Year: 3,072/9,624 Month: 917/1,588 Week: 100/223 Day: 11/17 Hour: 0/0


Thread  Details

Email This Thread
Newer Topic | Older Topic
  
Author Topic:   Does gene reuse and genome plasticity have to indicate common descent?
Quetzal
Member (Idle past 5872 days)
Posts: 3228
Joined: 01-09-2002


Message 3 of 12 (26950)
12-17-2002 5:24 AM
Reply to: Message 1 by Tranquility Base
12-16-2002 8:42 PM


Hi TB:
I'm curious - you have consistently asserted that the original genes arose ex nihilo, and that all subsequent novel genes were simply "re-use" of existing structural components. What I'd like to hear is your reason for rejecting the exon theory, for instance, or the other mainstream explanations for the origin of genes. I'd like to see your arguments against, for instance, Blake et al 1987 hypothesis contained in "Proteins, exons and molecular evolution", (Biosystems 20:181-206), or Gilbert's 1997 Origin of Genes, where he tested Blake's idea. You must be familiar with the work, since you have apparently rejected it. I'd like to see your reasoning. Thanks.
quote:
Creation occurred arond 6000 years ago. Evidence? Helium retention in biotites suggests the geo-col is only 4000 to 14,000 years old. Only the flood could do this of course. Genomes could be only this old too if God created them as kinds that have since diversified.
I'm a tad surprised you bring this up again. The helium retention "evidence" you're banking on was quite significantly refuted in this thread. Do you have any new evidence that Humphrey's was actually accurate? Inquiring minds, and all that...

This message is a reply to:
 Message 1 by Tranquility Base, posted 12-16-2002 8:42 PM Tranquility Base has replied

Replies to this message:
 Message 6 by Tranquility Base, posted 12-17-2002 7:32 AM Quetzal has replied

  
Quetzal
Member (Idle past 5872 days)
Posts: 3228
Joined: 01-09-2002


Message 7 of 12 (26962)
12-17-2002 8:44 AM
Reply to: Message 6 by Tranquility Base
12-17-2002 7:32 AM


Hi TB:
quote:
Exon hypothesis. The papers I have read testing the exon hypothesis (recent stuff in the last 4 years) comes out against it. Somewhere down the track I may post you some refs. The early proposals were extrememly speculative. The analysis by structural biologists (ie people like me who understand protein folds) has shown that exons do not systematically correspond to sub-domians or anything like that. But I can't say I've read Blake who obviously comes to the opposite conclusion. The last paper I read on it was very negative and I wasn't looking for a negative one! At the least it is a controversial area.
Actually the exon theory isn't all that controversial. What is controversial is the introns early/introns late question. However, it seems the dust has mostly settled. About the only person still holding to the introns late idea is Ayala's group. Here are a couple of recent papers concerning this:
Large-scale comparison of intron positions among animal, plant, and fungal genes
Toward a resolution of the introns earlyylate debate: Only phase zero introns are correlated with the structure of ancient proteins
Intron distribution difference for 276 ancient and 131 modern genes suggests the existence of ancient introns
Anyway, that's not really important to what I was asking. I was curious as to your take on the PNA exon shuffling as producer of the first proto-gene and why you consider that to be an unacceptable answer.
On the biotite - I didn't say "you" were getting trashed. I said that Humphreys was shown to be in error. Hence, you must have additional/new data available that shows he wasn't.

This message is a reply to:
 Message 6 by Tranquility Base, posted 12-17-2002 7:32 AM Tranquility Base has replied

Replies to this message:
 Message 8 by Tranquility Base, posted 12-17-2002 5:47 PM Quetzal has replied

  
Quetzal
Member (Idle past 5872 days)
Posts: 3228
Joined: 01-09-2002


Message 11 of 12 (27154)
12-18-2002 5:46 AM
Reply to: Message 8 by Tranquility Base
12-17-2002 5:47 PM


Hi TB:
quote:
Exons. I'm actaully referring to the idea that exons correspond to 3D protein structural units becasue that is what is relevant if we are talking evolution between protein familes. Every study I've ever seen done of that has come out pretty negative.
That's nice (see below), but that wasn't the question I asked. For reference, I asked for your take on the exon theory of the origin of genes, and why you felt that it was inaccurate. Just to remind you what the theory states, it's the idea that the first genes were short strands with an intron-exon structure whose products were short polypeptides (like, 15-20 amino acids long). The intron sequences served as structural frameworks for exon shuffling, and helped with some elements of protein folding. The first shuffled exons were later fused by reverse transcription (retrotransposition) into more complicated exons. There's a growing amount of support for the "introns early" argument - some of which I posted above. There is support also for the creation of complex exons by retrotransposition (like the jingwei gene). So what's your argument against it?
As for the protein folding bit, I do appreciate the opportunity to look up some new information afforded by this discussion that I wouldn't normally have bothered with. Are you aware that there have been lab experiments that show what appears to be novel protein domains formed from disassociated exons precisely by the method predicted in the exon theory? One recent example is Riechmann L, Winter G, 2000, "Novel folded protein domains generated by combinatorial shuffling of polypeptide segments", PNAS 97:10068-10073
quote:
It has been proposed that the architecture of protein domains has evolved by the combinatorial assembly and/or exchange of smaller polypeptide segments. To investigate this proposal, we fused DNA encoding the N-terminal half of a beta-barrel domain (from cold shock protein CspA) with fragmented genomic Escherichia coli DNA and cloned the repertoire of chimeric polypeptides for display on filamentous bacteriophage. Phage displaying folded polypeptides were selected by proteolysis; in most cases the protease-resistant chimeric polypeptides comprised genomic segments in their natural reading frames. Although the genomic segments appeared to have no sequence homologies with CspA, one of the originating proteins had the same fold as CspA, but another had a different fold. Four of the chimeric proteins were expressed as soluble polypeptides; they formed monomers and exhibited cooperative unfolding. Indeed, one of the chimeric proteins contained a set of very slowly exchanging amides and proved more stable than CspA itself. These results indicate that native-like proteins can be generated directly by combinatorial segment assembly from nonhomologous proteins, with implications for theories of the evolution of new protein folds, as well as providing a means of creating novel domains and architectures in vitro.
Sure appears to me to indicate that exon shuffling as proposed in the exon theory has some experimental support. What does this do to your domaine creation ex nihilo theory?
[This message has been edited by Quetzal, 12-18-2002]

This message is a reply to:
 Message 8 by Tranquility Base, posted 12-17-2002 5:47 PM Tranquility Base has not replied

  
Newer Topic | Older Topic
Jump to:


Copyright 2001-2023 by EvC Forum, All Rights Reserved

™ Version 4.2
Innovative software from Qwixotic © 2024