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Author | Topic: Deep Homology and Front-loading | |||||||||||||||||||||||||||||||
Genomicus Member (Idle past 1970 days) Posts: 852 Joined: |
How did you determine that ubiquitin structure was intended for use in metazoans? How did you rule out the possibility that other proteins were destined for this role, but evolution caused ubiquitin to fill this role instead. That's not really the issue IMHO. If we assume, for sake of argument, that the Metazoa we see today was the intended outcome of a front-loading scheme, we can make testable predictions regarding biotic reality. This is the point. Confirmation of those predictions strengthens the above thesis. Now, you might rightly ask why we should assume that Metazoa were the intended outcome of front-loading, instead of, say, a race of flying spaghetti monsters. But here is where fallible intuition comes into play. If we were to seed another planet with life, and front-load objectives into existence, we would likely choose plants and animals. This, of course, is not evidence that Metazoa were the intended outcome of front-loading - I am well aware of that. However, if we follow the line of thought that Metazoa were, in fact, the intended outcome of front-loading, from here we can make real predictions that are not made by the non-teleological model. The non-telic view of life does not require that prokaryotes have ubiquitin homologs. Darwinian evolution has been very comfortable with the fact that, prior to structural analyses, there were no known prokaryotic homologs of ubiquitin. Yet front-loading predicts exactly this.
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Genomicus Member (Idle past 1970 days) Posts: 852 Joined: |
There are clues that teleology has played a role in the history of life on earth, so this offers a subtle hint that maybe there was an intended outcome.
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Genomicus Member (Idle past 1970 days) Posts: 852 Joined: |
If my Rain Dance causes the rain, then I predict that it will rain after I do my dance. It did rain after I did my dance, therefore that strengthens the theory that my Rain Dance causes the rain. No, because rain is predicted from plain ole' meteorology.
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Genomicus Member (Idle past 1970 days) Posts: 852 Joined: |
I disagree. If ubiquitin is essential to eukaryotic life, and if eukaryotes and prokaryotes have a common ancestor then non-telic evolution predicts that at least some prokaryotes should have a ubiquitin homolog. And:
The reasoning as follows: If eukaryotes are descended from prokaryotes then ubiquitin must have evolved in the prokaryotic ancestors of eukaryotes (because essential proteins don't just appear at the exact moment that they are needed) If prokaryotes are descended from eukaryotes then ubiquitin must have been present in the ancestors of all prokaryotes and lost through evolution, after the divide between the two Kingdoms. Non-teleological evolution does not predict that ubiquitin will have a prokaryotic homolog because the ubiquitin gene could easily have been pieced together from different pieces of DNA, in much the same way that T-urf13 evolved. In such a scenario, given the deep-time involved and the fact that this protein would have been cobbled together from short stretches of DNA, we would almost certainly not be able to trace this homology in prokaryotes - and, of course, structural analyses wouldn't reveal any homologs of ubiquitin in prokaryotes. On the other hand, if eukaryotes were front-loaded, the designers wouldn't depend on simple accidents to "just happen" to cobble ubiquitin together from a variety of motifs, indels, chunks of functional modules, etc. The first genomes would have a structurally-related protein, such that the ubiquitin fold is already in place prior to the origin of eukaryotes.
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Genomicus Member (Idle past 1970 days) Posts: 852 Joined: |
You haven't explained why I shouldn't expect the prevalence of Ubiquitin under the standard evolutionary model. More specifically, why the current theory does not predict the presence of ubiquitin homologs in prokaryotes. See my latest reply to PaulK for reasons why we don't expect this under the standard evolutionary model. Also, in a more a global sense, FLE predicts that key eukaryotic proteins will share deep homology with prokaryotic proteins that are not part of the essential gene set. Although we can't predict exactly what proteins will share homology with functional but unnecessary prokaryotic proteins, we can predict the above in a general sense. Edited by Genomicus, : No reason given. Edited by Genomicus, : No reason given. Edited by Genomicus, : No reason given.
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Genomicus Member (Idle past 1970 days) Posts: 852 Joined: |
If you assume your conclusion then you can not make testable predictions. That's the problem. Okay, here's a simple true/false question: If the Metazoa we see today was the intended outcome of a front-loading scenario, could we make testable predictions from this premise?
Those predictions exactly mirror non-teleological models. FLE states that modern genes descended from ancient genes. Non-teleological models make the SAME PREDICTION. No, non-teleological models do not predict that crucial eukaryotic genes will share deep homology with functional but unnecessary (for life) prokaryotic proteins. I've explained why many times, but here it is again: under the non-telic model, it is completely reasonable for the LUCA to have no more than a minimal genome. I have supported this contention with references to the scientific literature. For example:"...a recent analysis of 37,402 protein families across 184 genomes inferred that a CCF [core conserved function] composed of ~1400 gene families was present in LUCA. This estimate challenged the widely held view of a minimal genome containing ~300 genes supported by previous in-silico or in-vivo analyses. ...This indicates that in contrast to early hypotheses, LUCA was far from being a minimal cell because its genome was far from a minimal genome." (emphasis added; from "Origins and Evolution of Life: An Astrobiological Perspective," Muriel Gargaud, Purificacin Lpez-Garca, Herv Martin, Cambridge University Press, 2011) Read that carefully, then tell me that it's not reasonable, under non-teleological models, for the LUCA to have only a minimal genome and be only a minimal cell.
The non-telic view of weather does not require that it rain in Dallas, TX today. However, it is certainly a possibility for non-telic meteorology, is it not? The same for ubiquitin homologs. Non-telic mechanisms are clearly capable of co-opting ancestral genes for roles in subsequent generations. The issue here really isn't whether the non-telic view of life can potentially explain the observation that crucial eukaryotic proteins share deep homology with functional but unnecessary prokaryotic proteins. The real issue is whether the non-teleological model predicts this.
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Genomicus Member (Idle past 1970 days) Posts: 852 Joined: |
If you concede that they are actually homologues, then you concede that the blind watchmaker created all (or all but a few) of the other functional parts of these various superfamilies of proteins? So why would you object to the proposition that the blind watchmaker is also responsible for the one part they have in common? Well, at this point, I'm not trying to argue against the capabilities of the blind watchmaker. I'm simply trying to develop a prediction that is made by FLE but is not made by the non-teleological model. Based on FLE, we would predict that there exists prokaryotic homologs of ubiquitin, and confirmation of that prediction is a point in favor of FLE, regardless of the possibility that the blind watchmaker could have "stumbled" upon the basic ubiquitin fold.
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Genomicus Member (Idle past 1970 days) Posts: 852 Joined: |
But as we have seen, it doesn't. The objections to this claim are as cogent this week as they were last week. AFAICT, the objections seem to revolve around the following points: 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. Interestingly, however, a number of papers have proposed that the LUCA did, in fact, have only a minimal genome, demonstrating that this is perfectly reasonable under the non-telic model. 2. 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. Edited by Genomicus, : No reason given.
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Genomicus Member (Idle past 1970 days) Posts: 852 Joined: |
A number of you seem to be under the impression that it’s really not reasonable for the LUCA to have had a minimal genome under the non-teleological model. Interestingly, the mainstream scientific literature doesn’t seem to agree with you.
For example:
quote:(Experimental Search for Minimal Organisms and the Last Universal Common Ancestor, 2006, Complexity: DOI 10.1002/cplx.20154) And:
quote:(The proteomic complexity and rise of the primordial ancestor of diversified life, 2011) Progenotes, incidentally, are even more minimal than a minimal cell. Also:
quote:(A minimal estimate for the gene content of the last universal common ancestor--exobiology from a terrestrial perspective, 2006) And:
quote:(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) So this study proposes that (a) tRNA genes arose after the LUCA, and (b) that protein-coding genes have a polyphyletic origin, which means that they similarly arose after the LUCA. This, in turn, implies that the LUCA was quite a simple organism indeed, lacking tRNA genes and other genes. Furthermore:
quote:(On the origin of genomes and cells within inorganic compartments, 2005) Thus we see that, according to this paper, the LUCA was (a) virus-like in its replication and genomic architecture, (b) LUCA was simpler than a fully-fledged prokaryotic genome. Also, if you take a look at their Figure 1, you will observe that just before the origin of the LUCA we have limited gene accretion, origin of proto-operons (that’s a far cry from encoding needless complexity), etc. And just after the origin of the LUCA, we still don’t have DNA genomes. In other words, this paper proposes that LUCA was quite simple (yet, for some odd reason — using the logic of a number of you here — this simple LUCA would have encoded globins, gephyrin, calmodulin, thymidine phosphorylase, etc.). Also:
quote:(Evolution without speciation but with selection: LUCA, the Last Universal Common Ancestor in Gilbert's RNA world, 2003) That sounds like a sophisticated organism deployed for front-loading, doesn’t it? And:
quote: Challenge: find a single paper in the scientific literature that argues that it is not reasonable under the current paradigm for the LUCA to have only a minimal genome. The PointThe point is not that the LUCA was, in fact, a simple cell with a minimal genome. The point is that it is perfectly reasonable, acceptable, and logical for the LUCA to have had a minimal genome, based on the non-teleological scenario for the origin of life. This makes comments like
LUCA did not have a single base codon system as the evidence suggests was the case for the first life. Instead, LUCA had a three base codon system, with some 3rd base wobble. Already, LUCA is not a minimalist genome, and we have only looked at the tRNA's. slightly irrelevant. The point here is not what the LUCA actually was, but what it could have logically been, under the non-telic framework.By the way, by minimal genome I am not referring to the genetic code but to the genome, Taq. There’s a difference, ya know. C’mon guys, the least you can do is admit that your view that the LUCA could not have logically had a minimal genome is contradicted by the scientific literature. Edited by Genomicus, : No reason given. Edited by Genomicus, : No reason given.
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Genomicus Member (Idle past 1970 days) Posts: 852 Joined: |
You reason seems to be: "it could have happened differently". Quite right. Under the non-teleological model, ubiquitin could have evolved from different stretches of non-coding DNA, which means that any evidence of homology would have been lost over deep-time.
That isn't a reason to not suspect a ubiquitin homolog in prokaryotes. And what makes you think that ubiquitin could have evolved like T-urf13 did? Ubiquitin is a protein and T-urf13 is a gene... wait, are you looking for a homolog to the ubiquitin protein or the ubiquitin gene? Huh? If we find a homolog to the ubiquitin protein, we automatically have found a homolog to the ubiquitin gene. "Ubiquitin is a protein and T-urf13 is a gene." Yes, and ubiquitin is encoded by a gene, which could have been pieced together in the same way that the T-urf13 gene was.
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Genomicus Member (Idle past 1970 days) Posts: 852 Joined: |
Non-teleological meteorology does not predict that it will rain in Dallas, TX today because it could just as easily not rain today. Therefore, if it rains it is due to rain fairies. Nope, because there is nothing in the "rain fairy hypothesis" that says it must rain today in Dallas, TX, and therefore that "hypothesis" doesn't predict that it will rain in Dallas today.
In the same way, evolution does not predict that specific proteins will become necessary in future generations. Rather, it accomodates such observations. Ubiquitin fits this model. Non-teleological evolution can easily co-opt a gene in ancestors to fill a necessary role in descendants. That is what it does. You are trying to falsify evolution by pointing to the very observations that it can produce. That makes no sense. Your problem is that you still think I'm looking for something that Darwinian evolution cannot explain. That's not what FLE is about. It's about making testable predictions that Darwinian evolution does not make. That Darwinian evolution can explain an observation does not mean it predicts it. And if another hypothesis predicts that observation, then that hypothesis is strengthened.
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Genomicus Member (Idle past 1970 days) Posts: 852 Joined: |
That doesn't affect my reasoning, though. HOW ubiquitin appeared is not an issue. WHEN it appeared in the evolutionary history of eukaryotes and prokaryotes is the issue. And my argument covers that. Ubiquitin could have appeared shortly before the origin of eukaryotes. In which case, it could have easily been lost in the few prokaryotic lineages in which it first arose.
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Genomicus Member (Idle past 1970 days) Posts: 852 Joined: |
It took me about 7 minutes to find three... You did not address my challenge. You provided three studies - of which I was aware - that provide evidence that the LUCA did not have a minimal genome. You did not provide any papers arguing that it is unreasonable for the LUCA to have had a minimal genome under the non-telic model. In other words, find papers that say stuff like "the idea that the LUCA had a minimal genome is not compatible with the 'Darwinian' model."
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Genomicus Member (Idle past 1970 days) Posts: 852 Joined: |
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.
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Genomicus Member (Idle past 1970 days) Posts: 852 Joined: |
"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.
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