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Author Topic:   Deep Homology and Front-loading
PaulK
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Posts: 17822
Joined: 01-10-2003
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(1)
Message 163 of 172 (667162)
07-03-2012 2:20 PM
Reply to: Message 160 by Genomicus
07-03-2012 12:58 PM


Re: The LUCA and the minimal genome
quote:
I did.
It certainly isn't obvious from the quotes that any of these support your ideas.
The first talks about the LUCA being a "a candidate for a minimal cell". But doesn't explain why we should think so - even in the full text. So the argument is absent, in the only paper that offers anything like your idea of the LUCA given non-telic evolution.
The second argues that the current tRNA genes came about after the last LUCA. What the consequence of this is - or the relevance to your ideas is - is unclear.
Likewise the last offers nothing like your ideas, either (and it is very unclear how it how it argues for an RNA based LUCA, even given the full text)
Now, remembering your view that the LUCA was a complex prokaryote, two of these papers pose major challenges to your view. More importantly you don't offer any argument that these scenarios would lead us to reject the idea of deep homology. The third, at the least, involves massive amounts of lateral transfer of genetic material.
None of them seem to offer an argument that the LUCA is at all likely to have been an absolutely minimal prokaryotic cell. WHich is the real point of discussion.

This message is a reply to:
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PaulK
Member
Posts: 17822
Joined: 01-10-2003
Member Rating: 2.2


Message 164 of 172 (667163)
07-03-2012 2:37 PM
Reply to: Message 161 by Genomicus
07-03-2012 1:27 PM


Re: The Ubiquitin Story
quote:
Why do you think it is more likely to be retained than lost in the few prokaryotic lineages that, potentially, it could have arisen in?
Because the appearance of completely new proteins seems to be a relatively rare event. So there's no reason to expect it to be present in only a few prokaryotic lineages.
quote:
There is a very good mechanism for keeping a protein's fold well-conserved over deep time: give it a function in which the protein's fold is of major importance.
Which only argues against your point. If the ubiquitin fold DOES have such a use then it seems to me that it would explain a large amount of the existing sequence similarity. But it does NOT give us any confidence that ubiquitin could be conserved to the degree apparently required by existing eukaryotes.
According to Wikipedia, human and yeast ubiquitin has 96% sequence identity. The homologous - maybe - ThiS has only 14% sequence similarity. That's what you have to deal with.
quote:
Actually, no, because I view the lack of non-flagellar homologs of FlgD, FliD, FliL, etc., as being the result of the flagellum's engineering. I.e., FlgD doesn't have a homologous counterpart because it never did, since it was engineered from "scratch" IMHO.
By which you mean that you REJECT the idea that useful proteins could be easily lost. - your own argument. But if your argument rests on a claim that you yourself reject it can't be considered a valid objection.

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PaulK
Member
Posts: 17822
Joined: 01-10-2003
Member Rating: 2.2


Message 170 of 172 (667575)
07-09-2012 5:06 PM
Reply to: Message 169 by Genomicus
07-09-2012 4:42 PM


I submit to you that, on the contrary, a LUCA that is a minimal prokaryote is MORE likely given FLE than non-telic evolution.
Firstly, non-telic evolution gives us no reason to presume that the LUCA was a prokaryote, while it appears to be an assumption of FLE.
Secondly I have given good reasons to expect that even if the LUCA were a prokaryote it would be very unlikely to have a strictly minimal genome - reasons that do not apply to the artificially engineered life assumed by FLE.
Thirdly your reason for assuming that the FLE LUCA could not have a minimal genome is simply an opinion without much in the way of argumentative support - and in my opinion it ignores the possibilities open to the assumed FLE engineers. It is certain that an artificial prokaryote produced by engineering would be more capable of evolving the current diversity of life than one produced by non-telic evolution, probably to a significant degree.
Finally "deep homology" does not require that the genes in question were present in the LUCA, only that they appeared prior to the split between prokaryotes and eukaryotes. They need only be present in the last common ancestor of eukaryotes and SOME prokaryotes for vertical transmission - and not even that for horizontal transmission from eukaryotes to prokaryotes.

This message is a reply to:
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