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Author Topic:   Deep Homology and Front-loading
Genomicus
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Joined: 02-15-2012
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Message 151 of 172 (666825)
06-29-2012 8:56 PM
Reply to: Message 148 by PaulK
06-29-2012 2:15 PM


Re: The Ubiquitin Story
So *IF* it appeared only shortly before eukaryotes arrived it MIGHT have been lost. That doesn't mean that we don't expect to see homologues.

Umm, if the original protein had been lost, then we wouldn't find any homologs. And since it's a plausible occurrence, we can't predict deep homology or lack of deep homology from a non-telic perspective.

Of course if it was as useful to prokaryotes then that wouldn't be likely to happen.

But from a non-teleological view, we have no way of knowing if it was terribly useful to prokaryotes. And useful genes get lost in lineages all the time. That's the Darwinian explanation for why we don't see non-flagellar homologs of, say, FlgD, FliD, FliL, and a whole bunch of other flagellar proteins (that, and saturation of informative sites in protein sequences).

Edited by Genomicus, : No reason given.


This message is a reply to:
 Message 148 by PaulK, posted 06-29-2012 2:15 PM PaulK has responded

Replies to this message:
 Message 155 by PaulK, posted 06-30-2012 3:38 AM Genomicus has responded

  
Genomicus
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Posts: 844
Joined: 02-15-2012
Member Rating: 3.4


Message 152 of 172 (666826)
06-29-2012 9:12 PM
Reply to: Message 149 by New Cat's Eye
06-29-2012 2:42 PM


Re: The LUCA and the minimal genome
"It could have happened differently" isn't a reason to not suspect a ubiquitin homolog in prokaryotes.

Certainly it is. If it could have happened differently in the non-telic framework, then you don't have a real prediction.

Why would it be lost?

Because:

1. Over deep time, there's no reason why the sequence identity of the original non-coding DNA sequences would be preserved (in this context, by "non-coding DNA" I mean functionless chunks of DNA).

2. If ubiquitin was pieced together from short pieces of other proteins, again, we would not detect this homology because we wouldn't have any statistically significant matches due to the small size of the original "pieces."

Not necessarily. You could find homologous proteins without knowing their genes. It looks like you were saying that non-teleological evolution does not predict that the ubiquitin protein will have a prokaryotic homolog because the ubiquitin gene could have arrisen differently. That doesn't necessarily follow.

I'm not following you. If you find a protein that is homologous to ubiquitin, then all you have to do is track down its gene sequence, and voila! you have a gene that is homologous to the ubiquitin gene.

How do you know the gene that encodes ubiquitin could have arrisen like the T-urf13 gene did?

How do you know that it could not have? After all, what's stopping a gene that encoded ubiquitin from arising in the same manner that the T-urf13 gene did?

Who's saying that it was unreasonable to infer a minimal genome for LUCA?

Specifically, who's saying that it is unreasonable under the non-telic model for the LUCA to have a minimal genome.

I'm sure you didn't miss these:

It's not reasonable, under non-teleological models, for the LUCA to have only a minimal genome and be only a minimal cell.

That's from PaulK.

From Taq:

It's not reasonable under non-teleological models for LUCA to have a minimalist genome.

This message is a reply to:
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Genomicus
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Posts: 844
Joined: 02-15-2012
Member Rating: 3.4


Message 153 of 172 (666828)
06-29-2012 9:16 PM
Reply to: Message 150 by PaulK
06-29-2012 4:35 PM


Re: The LUCA and the minimal genome
I think that I have a paper that about qualifies - and I note that you have yet to find one paper that actually ARGUES otherwise rather than, for instance, stating that it was assumed.

You've gotten pretty close. The paper indeed argues that it is more reasonable for the LUCA to have had more than a minimal genome. Meanwhile, there are a whole bunch of other studies that argue that the LUCA had a minimal genome, that it was a simple virus-like entity, that it had an RNA genome, that did not encode tRNA genes, etc. etc. All these scenarios are fully compatible with the non-teleological framework. They are not, however, consistent with the front-loading hypothesis, and this allows us to make testable predictions from that perspective.

Edited by Genomicus, : No reason given.

Edited by Genomicus, : No reason given.


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 Message 150 by PaulK, posted 06-29-2012 4:35 PM PaulK has responded

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 Message 154 by PaulK, posted 06-30-2012 3:29 AM Genomicus has responded

  
PaulK
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Posts: 12759
Joined: 01-10-2003
Member Rating: 3.0


Message 154 of 172 (666835)
06-30-2012 3:29 AM
Reply to: Message 153 by Genomicus
06-29-2012 9:16 PM


Re: The LUCA and the minimal genome
quote:

Meanwhile, there are a whole bunch of other studies that argue that the LUCA had a minimal genome, that it was a simple virus-like entity, that it had an RNA genome, that did not encode tRNA genes, etc. etc. All these scenarios are fully compatible with the non-teleological framework. They are not, however, consistent with the front-loading hypothesis, and this allows us to make testable predictions from that perspective.

Perhaps you should find some of these studies. You don't seem to have quoted any. (And I have to say that bare front-loading is also compatible with a large number of scenarios - you need to specify what the front-loaders intended before you can say what is front-loaded).


This message is a reply to:
 Message 153 by Genomicus, posted 06-29-2012 9:16 PM Genomicus has responded

Replies to this message:
 Message 160 by Genomicus, posted 07-03-2012 12:58 PM PaulK has responded

    
PaulK
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Posts: 12759
Joined: 01-10-2003
Member Rating: 3.0


Message 155 of 172 (666836)
06-30-2012 3:38 AM
Reply to: Message 151 by Genomicus
06-29-2012 8:56 PM


Re: The Ubiquitin Story
quote:

Umm, if the original protein had been lost, then we wouldn't find any homologs. And since it's a plausible occurrence, we can't predict deep homology or lack of deep homology from a non-telic perspective.

It would be more likely to be retained than lost, therefore we have a reasonable expectation of finding homologues.

On the other hand the actual data is more consistent with a non-telic evolutionary view than it is with your front-loading.

Ubiquitin is highly conserved among eukaryotes, thus by your reasoning it must have been supplied with a mechanism to keep it adequately conserved. The only homologues known among prokaryotes are very distant, indicating that no such mechanism currently exists.

Moreover, some prokaryotes have systems similar to that where ubiquitin is used in eukaryotes, but do not use ubiquitin or homologues.

Thus we have neither a reason to believe that the importance of ubiquitin is anything more than a "frozen accident" or that it could have been supplied in a distant ancestor of eukaryotes.

quote:

But from a non-teleological view, we have no way of knowing if it was terribly useful to prokaryotes. And useful genes get lost in lineages all the time. That's the Darwinian explanation for why we don't see non-flagellar homologs of, say, FlgD, FliD, FliL, and a whole bunch of other flagellar proteins (that, and saturation of informative sites in protein sequences).

Since your whole scenario rests on useful proteins being certain to be retained - and kept intact for functions other than the one they currently serve (a more difficult proposition still!) - this rather seems to suggest that your scenario is unworkable.


This message is a reply to:
 Message 151 by Genomicus, posted 06-29-2012 8:56 PM Genomicus has responded

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Dr Adequate
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Posts: 15934
Joined: 07-20-2006
Member Rating: 3.4


(1)
Message 156 of 172 (666928)
07-01-2012 12:12 PM
Reply to: Message 137 by Genomicus
06-28-2012 2:35 PM


1. Non-teleological evolution predicts that key eukaryotic genes will share homology with functional but unnecessary proteins. Essentially then, the non-telic model predicts that the LUCA did not have a minimal genome.

Actually, no. As I have pointed out, the fact that a protein is functional but unnecessary in modern prokaryotes does not mean that it was unnecessary in LUCA. The fact that LUCA was a prokaryote in the sense of not-having-a-nucleus does not necessarily mean that its cellular economy was more like modern prokaryotes with respect to the function of (for example) histone-like proteins.

(By analogy, the first amphibians certainly had an amphibian lifestyle. But we know that in some respects they were more like modern reptiles than like modern amphibians.)

Interestingly, however, a number of papers have proposed that the LUCA did, in fact, have only a minimal genome ...

... and a number have proposed that it didn't.

... demonstrating that this is perfectly reasonable under the non-telic model.

Quite.

The designers could have engineered the minimal gene set such that it also front-loads the Metazoa we see. But this is actually quite unlikely, as you'd probably have to substantially modify the necessary genes, in which case they're no longer retaining their original function, and wouldn't be functioning as a minimal gene set.

But now you seem to be back to the error of the "giraffophile designer". (If I understand you correctly, stop me if I'm wrong.) Based on evidence which suggests that the genome was minimal, you conclude that the front-loading must have been front-loading of a minimal gene set, from which you conclude that we should have evidence that the genome was minimal.

But if it was certain (and it is far from certain) that LUCA's genome was minimal, then you couldn't hold that up as a prediction of your hypothesis when you're also using it as data to decide exactly what your hypothesis is.

You need to go: "Front loading, therefore I predict a minimal genome for LUCA"; not: "Front loading, and a minimal genome for LUCA, therefore a front-loaded minimal genome for LUCA, therefore I predict a minimal genome for LUCA."

Edited by Dr Adequate, : No reason given.


This message is a reply to:
 Message 137 by Genomicus, posted 06-28-2012 2:35 PM Genomicus has responded

Replies to this message:
 Message 167 by Genomicus, posted 07-08-2012 9:49 AM Dr Adequate has responded

  
New Cat's Eye
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Posts: 11440
From: near St. Louis
Joined: 01-27-2005
Member Rating: 2.6


Message 157 of 172 (667017)
07-02-2012 11:20 AM
Reply to: Message 152 by Genomicus
06-29-2012 9:12 PM


Re: The LUCA and the minimal genome
"It could have happened differently" isn't a reason to not suspect a ubiquitin homolog in prokaryotes.

Certainly it is. If it could have happened differently in the non-telic framework, then you don't have a real prediction.

Oh, you mean like a real temporal prediction... Sometimes when people are talking about whether a scientific theory predicts something, they're just meaning that its a valid logical consequence of the theory and not really that the theory was used to forecast a new discovery.

But if that's the case, then FLE didn't predict any of this either, did it?

I'm not following you. If you find a protein that is homologous to ubiquitin, then all you have to do is track down its gene sequence, and voila! you have a gene that is homologous to the ubiquitin gene.

Um, ubiquitin was discovered in, like, 1975. They didn't know how to "track down gene sequences" back then.

And that's the cause of a lot of your issue here. You're using the scientific inferences about the size of LUCA that were before the latest in genetic discoveries. We've learned a lot since then and the scientific position has changed. It wasn't unreasonable for those people in the past to infer a small LUCA, but today, with our current knowledge we now know that it is unreasonable. We've learned that the size of LUCA was a lot larger than we first anticipated.

But the thing is, both the small and large LUCA's are logically consistent with the model, that is, it "predicts" both of them (in the non-temporal sense). What I mean is that either one will work within the model, the model doesn't necessitate either one.

The same goes for FLE. The designers could have done it any number of ways. In your own sense, you don't have a prediction either. And in my sense, we don't have a definative case that your data suggest FLE over the traditional model.

How do you know the gene that encodes ubiquitin could have arrisen like the T-urf13 gene did?

How do you know that it could not have? After all, what's stopping a gene that encoded ubiquitin from arising in the same manner that the T-urf13 gene did?

Oh. You were saying that it could have like it was some fact. Apparently, you're just assuming that it could have. Not all genes can arrise in the same way.

Specifically, who's saying that it is unreasonable under the non-telic model for the LUCA to have a minimal genome.

I'm sure you didn't miss these:

I did miss those, and I prefer to see them in context - aren't they talking about being reasonable today rather than referring to the old inferrences from the past?

If you type [msg=152] , it will become Message 152 and you can link to specific posts within this same thread by their post number. You can also use the message ID number, the dark grey long number next to the Message # of #, with the "mid" tag like this: [mid=666826] if you want to link to messages in other threads, it'll look like this: Message 152. You can also click on the Peek button in the bottom right of any post to see the coding that was entered into the text box.


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Taq
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Posts: 6632
Joined: 03-06-2009
Member Rating: 4.1


(1)
Message 158 of 172 (667026)
07-02-2012 12:07 PM
Reply to: Message 144 by Genomicus
06-29-2012 1:54 PM


Re: The Ubiquitin Story
That Darwinian evolution can explain an observation does not mean it predicts it.

The stochastic nature of evolution predicts that you will NOT be able to predict a specific outcome millions of years in the future based on a given genome. It is incumbent on you to show that this can be done. You need start with the ancestral sequence for ubiquitin and then show, from first principles, that this sequence is front loaded so that it will become ubiquitous in future generations. You also need to show how other genes will not using those same principles. Until you do so, you are simply painting the bull's eye around the bullet hole.


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Genomicus
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Posts: 844
Joined: 02-15-2012
Member Rating: 3.4


Message 159 of 172 (667144)
07-03-2012 12:31 PM
Reply to: Message 124 by Taq
06-27-2012 2:42 PM


Re: The Ubiquitin Story
If you assume your conclusion then you can not make testable predictions. That's the problem.

You have not yet explained why we cannot make testable predictions based on the premise that the Metazoa we see today was the intended outcome of a front-loading scheme.

Those predictions exactly mirror non-teleological models. FLE states that modern genes descended from ancient genes. Non-teleological models make the SAME PREDICTION.

FLE states that modern genes descended from ancient genes that are unnecessary for life. The non-telic model does not make this specific prediction.


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 Message 124 by Taq, posted 06-27-2012 2:42 PM Taq has responded

Replies to this message:
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Genomicus
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Posts: 844
Joined: 02-15-2012
Member Rating: 3.4


Message 160 of 172 (667145)
07-03-2012 12:58 PM
Reply to: Message 154 by PaulK
06-30-2012 3:29 AM


Re: The LUCA and the minimal genome
Meanwhile, there are a whole bunch of other studies that argue that the LUCA had a minimal genome, that it was a simple virus-like entity, that it had an RNA genome, that did not encode tRNA genes, etc. etc. All these scenarios are fully compatible with the non-teleological framework. They are not, however, consistent with the front-loading hypothesis, and this allows us to make testable predictions from that perspective.

Perhaps you should find some of these studies. You don't seem to have quoted any.

I did.

quote:
Two questions that should be closely related have historically been studied with very different approaches. One is what constitutes a minimal living system, whether minimal cell or minimal self-contained ecosystem. The other is what actual system was the last universal common ancestor (LUCA) of all modern cells. As the LUCA is supposed to have been a bottleneck through which all life passed before diversifying into modern forms, it is treated as a self-sufficient organism and would be a candidate for a minimal cell.
(Experimental Search for Minimal Organisms and the Last Universal Common Ancestor, 2006, Complexity: DOI 10.1002/cplx.20154)

And:

quote:
A model has been proposed suggesting that the tRNA molecule must have originated by direct duplication of an RNA hairpin structure [Di Giulio, M., 1992. On the origin of the transfer RNA molecule. J. Theor. Biol. 159, 199-214]. A non-monophyletic origin of this molecule has also been theorized [Di Giulio, M., 1999. The non-monophyletic origin of tRNA molecule. J. Theor. Biol. 197, 403-414]. In other words, the tRNA genes evolved only after the evolutionary stage of the last universal common ancestor (LUCA) through the assembly of two minigenes codifying for different RNA hairpin structures, which is what the exon theory of genes suggests when it is applied to the model of tRNA origin. Recent observations strongly corroborate this theorization because it has been found that some tRNA genes are completely separate in two minigenes codifying for the 5' and 3' halves of this molecule [Randau, L., et al., 2005a. Nanoarchaeum equitans creates functional tRNAs from separate genes for their 5'- and 3'-halves. Nature 433, 537-541]. In this paper it is shown that these tRNA genes codifying for the 5' and 3' halves of this molecule are the ancestral form from which the tRNA genes continuously codifying for the complete tRNA molecule are thought to have evolved. This, together with the very existence of completely separate tRNA genes codifying for their 5' and 3' halves, proves a non-monophyletic origin for tRNA genes, as a monophyletic origin would exclude the existence of these genes which have, on the contrary, been observed. Here the polyphyletic origin of genes codifying for proteins is also suggested and discussed.
(The non-monophyletic origin of the tRNA molecule and the origin of genes only after the evolutionary stage of the last universal common ancestor (LUCA), 2006)

And:

quote:
Nothing concrete can be said apropos LUCA’s physical appearance, but the common ancestor can be perceived as a molecular entity invested with information qualities. For instance it can be conceived as a member of a phylogenetic line of descent without an organismal corporeal existence, without genealogy, similar to single genes of the RNA world, loosely united in a network with the evolvable gene clustering that in time encoded chaperone proteins, known as enzymes, to develop into a growing functioning metabolism. Epigrammatically, this had to be a simple genetic entity, without a real intermediary metabolism to accompany its beginning. In this view, I see LUCA as deprived of complex protein capabilities as the result of a deficient information processing apparatus. For example, complex proteins, like primases, helicases, DNA polymerases and other familiar enzymes in membrane and nuclear compartments, are out of the question. The replication process that we see in today’s eukaryotes could not have existed. Only chaperone proteins can be expected from this common and communal ancestor. It was nothing but a genetic network of RNA genetic units in total Darwinian “war” among themselves; this was the first theater of selfish genes, with little or no-intermediate metabolism. LUCA “lived” without any of the cell compartments, totally at the mercy of lateral “abuses” from nearby oligonucleotides, molecular parasites that endangered its “incipient library”.
(Evolution without speciation but with selection: LUCA, the Last Universal Common Ancestor in Gilbert's RNA world, 2003)

Edited by Genomicus, : No reason given.


This message is a reply to:
 Message 154 by PaulK, posted 06-30-2012 3:29 AM PaulK has responded

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Genomicus
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Posts: 844
Joined: 02-15-2012
Member Rating: 3.4


Message 161 of 172 (667152)
07-03-2012 1:27 PM
Reply to: Message 155 by PaulK
06-30-2012 3:38 AM


Re: The Ubiquitin Story
It would be more likely to be retained than lost, therefore we have a reasonable expectation of finding homologues.

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?

On the other hand the actual data is more consistent with a non-telic evolutionary view than it is with your front-loading.

Ubiquitin is highly conserved among eukaryotes, thus by your reasoning it must have been supplied with a mechanism to keep it adequately conserved. The only homologues known among prokaryotes are very distant, indicating that no such mechanism currently exists.

Moreover, some prokaryotes have systems similar to that where ubiquitin is used in eukaryotes, but do not use ubiquitin or homologues.

Thus we have neither a reason to believe that the importance of ubiquitin is anything more than a "frozen accident" or that it could have been supplied in a distant ancestor of eukaryotes.

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.


But from a non-teleological view, we have no way of knowing if it was terribly useful to prokaryotes. And useful genes get lost in lineages all the time. That's the Darwinian explanation for why we don't see non-flagellar homologs of, say, FlgD, FliD, FliL, and a whole bunch of other flagellar proteins (that, and saturation of informative sites in protein sequences).

Since your whole scenario rests on useful proteins being certain to be retained - and kept intact for functions other than the one they currently serve (a more difficult proposition still!) - this rather seems to suggest that your scenario is unworkable.

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.


This message is a reply to:
 Message 155 by PaulK, posted 06-30-2012 3:38 AM PaulK has responded

Replies to this message:
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Genomicus
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Posts: 844
Joined: 02-15-2012
Member Rating: 3.4


Message 162 of 172 (667160)
07-03-2012 1:56 PM
Reply to: Message 141 by bluegenes
06-28-2012 9:13 PM


Re: I predict "No LUCA"!
So, you're agreeing that the frontloaders could have designed a eukaryote.

I agree that that view is compatible with front-loading, yes. However, we should keep in mind that we have but little experience with front-loading, so we may very well find out that prokaryotes are, in fact, better front-loaders for an environment like that of the early, hostile earth.

But the front-loaders aren't going to gamble their chances on accidents.

It's exactly what you're suggesting they did do. Let's look at your scenario. The FLs design a prokaryote with the metazoa in mind. They say to themselves: "at some point in the future, two descendents of our LUCA will combine in a way that will form a more complex cell which potentially could evolve into metazoa. These two particular descendents, maybe hundreds of millions of years down the line, maybe more than a billion, will contain all the proteins that we've put into the LUCA for their use."

If that's not gambling, what is?

Well, we know that endosymbiosis events are not at all implausible occurrences. However, it's not plausible for a specific protein fold to "just happen" to evolve, given that there are many more possible protein folds that could have arisen, many of which would not have contributed to the rise of eukaryotes.

I'd suggest that the frontloaders wouldn't be able to predict anything as specific as our eukaryotes. They might well know from their own life system that endosymbiotic events that produce useful functions could happen if their prokaryotes bubble away for long enough. But what they can't know is, if they do get lucky and get a more complex cell, specifically how it would form.

I disagree. If convergent evolution has taught us anything, it is that given specified initial conditions, specific biological objectives can be front-loaded over deep-time.


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PaulK
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Posts: 12759
Joined: 01-10-2003
Member Rating: 3.0


(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.


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PaulK
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Posts: 12759
Joined: 01-10-2003
Member Rating: 3.0


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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Taq
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Posts: 6632
Joined: 03-06-2009
Member Rating: 4.1


(2)
Message 165 of 172 (667176)
07-03-2012 3:55 PM
Reply to: Message 159 by Genomicus
07-03-2012 12:31 PM


Re: The Ubiquitin Story
You have not yet explained why we cannot make testable predictions based on the premise that the Metazoa we see today was the intended outcome of a front-loading scheme.

Your predictions are the same as your assumption. That is the problem. You are assuming that ubiquitin was the goal. You then turn around and claim that it is a prediction.

FLE states that modern genes descended from ancient genes that are unnecessary for life.

So does non-telic evolution.


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