Deep Homology and Front-loading

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. 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.

Certainly it is. If it could have happened differently in the non-telic framework, then you don't have a real prediction. 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." 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 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? 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: That's from PaulK.From Taq:

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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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.

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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).

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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.

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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.

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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).

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

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? 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. 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. 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.

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.

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

I did.

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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.

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(Experimental Search for Minimal Organisms and the Last Universal Common Ancestor, 2006, Complexity: DOI 10.1002/cplx.20154)And:

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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.

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(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:

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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.

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(Evolution without speciation but with selection: LUCA, the Last Universal Common Ancestor in Gilbert's RNA world, 2003)Edited by Genomicus, : No reason given.

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? 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. 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.

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. 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 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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I did.

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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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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?

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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.

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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.

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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.

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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.

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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.

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. So does non-telic evolution.