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Author Topic:   Deep Homology and Front-loading
Genomicus
Member (Idle past 1055 days)
Posts: 852
Joined: 02-15-2012


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.


This message is a reply to:
 Message 150 by PaulK, posted 06-29-2012 4:35 PM PaulK has responded

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

  
Genomicus
Member (Idle past 1055 days)
Posts: 852
Joined: 02-15-2012


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.


This message is a reply to:
 Message 124 by Taq, posted 06-27-2012 2:42 PM Taq has responded

Replies to this message:
 Message 165 by Taq, posted 07-03-2012 3:55 PM Genomicus has not yet responded

  
Genomicus
Member (Idle past 1055 days)
Posts: 852
Joined: 02-15-2012


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
Member (Idle past 1055 days)
Posts: 852
Joined: 02-15-2012


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

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Genomicus
Member (Idle past 1055 days)
Posts: 852
Joined: 02-15-2012


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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Genomicus
Member (Idle past 1055 days)
Posts: 852
Joined: 02-15-2012


Message 167 of 172 (667495)
07-08-2012 9:49 AM
Reply to: Message 156 by Dr Adequate
07-01-2012 12:12 PM


I'm quite busy with moving at the moment, so apologies for the extremely slow responses.

Anyhew:

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.

You're ignoring the key issue: that, under the non-telic model, LUCA could have been a simple prokaryote that did not require eukaryotic proteins. Is it not true, that under the current theory, the LUCA could easily have been only a simple prokaryote?

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.

No. As I stated in the OP, front-loading requires that the genome of the LUCA be more than a minimal genome. Indeed, some evidence indicates it was minimal. But the idea that the LUCA's genome was minimal is not compatible with front-loading, and thus we can predict that key eukaryotic proteins will share deep homology with prokaryotic proteins that are functional but unnecessary for a minimal genome, which in turn would mean that the LUCA's genome was not minimal.

Edited by Genomicus, : No reason given.


This message is a reply to:
 Message 156 by Dr Adequate, posted 07-01-2012 12:12 PM Dr Adequate has responded

Replies to this message:
 Message 168 by Dr Adequate, posted 07-08-2012 1:41 PM Genomicus has responded

  
Genomicus
Member (Idle past 1055 days)
Posts: 852
Joined: 02-15-2012


Message 169 of 172 (667572)
07-09-2012 4:42 PM
Reply to: Message 168 by Dr Adequate
07-08-2012 1:41 PM


Yes, that's perfectly true, but it's not what you said. What you said was: "Essentially then, the non-telic model predicts that the LUCA did not have a minimal genome." So I pointed out that it does not in fact make that prediction.

If I did say that, then I was dreadfully wrong. It would be more accurate to say that: "Essentially then, it is fully compatible under the non-telic model for the LUCA to have only a minimal genome, and it is also fully compatible with that model for the LUCA have more than a minimal genome."

I must have misunderstood the point I was replying to, then.

I still can't see what you were getting at here.

On the one hand, you say that: "the idea that the LUCA's genome was minimal is not compatible with front-loading" --- i.e. FLE would predict a non-minimal genome.

OTOH, you say that: "the non-telic model predicts that the LUCA did not have a minimal genome".

But weren't you meant to be looking for a prediction that FLE made and Darwinism didn't? You seem to have asserted in separate posts that both of them predict the same thing.

Okay. Let me try to explain what I'm trying to get at. The below diagram may help us visualize the situation here.

In this figure, we see two ovals: the blue one represents all the potential biological observations that are compatible with non-teleological evolution. The pink oval represents the potential biological observations that are compatible with FLE. The area of overlap between the two ovals signifies those biological observations that are compatible under both models. Areas with no overlap indicate biological observations that are only compatible in one of the models.

Now, observe that the potential biological observation of a non-minimal genome for the LUCA is compatible with both non-telic evolution and front-loading. However, the observation that the LUCA had only a minimal genome is not compatible with front-loading, while it is compatible with non-telic evolution. And this is where we can generate a testable prediction from the FLE perspective: when it comes to genomic complexity, FLE predicts that the LUCA had a non-minimal genome. Meanwhile, non-telic evolution doesn't predict this.

I have argued from the literature that it is certainly reasonable under the non-telic model for the LUCA to have only a minimal genome. You (Dr Adequate), along with Catholic Scientist, seem to be in agreement with this (i.e., that it is not unreasonable in the non-telic model for the LUCA to have only a minimal genome), while Taq, PaulK, et al., think otherwise. I'd say that the scientific literature, for the most part, supports the former contention: namely, that it is not unreasonable for the LUCA to have only a minimal genome under the current theory.

Edited by Genomicus, : No reason given.

Edited by Genomicus, : No reason given.

Edited by Genomicus, : No reason given.


This message is a reply to:
 Message 168 by Dr Adequate, posted 07-08-2012 1:41 PM Dr Adequate has responded

Replies to this message:
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