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.
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.
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.
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.
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, Purificación López-Garcìa, Hervè 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.
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.
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.
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.
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)
quote: The last universal common ancestor represents the primordial cellular organism from which diversified life was derived. This urancestor accumulated genetic information before the rise of organismal lineages and is considered to be either a simple 'progenote' organism with a rudimentary translational apparatus or a more complex 'cenancestor' with almost all essential biological processes.
(The proteomic complexity and rise of the primordial ancestor of diversified life, 2011)
Progenotes, incidentally, are even more minimal than a minimal cell.
quote: Using an algorithm for ancestral state inference of gene content, given a large number of extant genome sequences and a phylogenetic tree, we aim to reconstruct the gene content of the last universal common ancestor (LUCA), a hypothetical life form that presumably was the progenitor of the three domains of life. The method allows for gene loss, previously found to be a major factor in shaping gene content, and thus the estimate of LUCA's gene content appears to be substantially higher than that proposed previously, with a typical number of over 1000 gene families, of which more than 90% are also functionally characterized. More precisely, when only prokaryotes are considered, the number varies between 1006 and 1189 gene families while when eukaryotes are also included, this number increases to between 1344 and 1529 families depending on the underlying phylogenetic tree. Therefore, the common belief that the hypothetical genome of LUCA should resemble those of the smallest extant genomes of obligate parasites is not supported by recent advances in computational genomics.
(A minimal estimate for the gene content of the last universal common ancestor--exobiology from a terrestrial perspective, 2006)
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)
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.
quote: However, several other components of the DNA replication machinery, such as the sliding clamp plus the clamp loader ATPase and the DNA ligase, as well as enzymes of DNA precursor biosynthesis – ribonucleotide reductase and thymidylate kinase – are homologous in all prokaryotes, which led to the proposal that LUCA had a retrovirus-like replication cycle…Because RNA molecules are fragile compared with DNA, and no RNA virus with a monopartite genome O30 kb has been described, it has been suggested that the genome of LUCA consisted of a set of co-inherited RNA segments, each coding for one or a few proteins. The retrovirus-like genetic cycle of LUCA would account for a set of multiplying, competing, functionally diversifying and recombining molecules without demanding the complexity of a fully fledged prokaryotic genome.
(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.).
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)
That sounds like a sophisticated organism deployed for front-loading, doesn’t it?
quote: The archaeal sequences are highly homologous to those of the eukaryotic Rad2 family and they cluster with genes of the FEN-1 subfamily, which are known to be involved in DNA replication and repair in eukaryotes. We argue that there is a commonality of mechanisms and protein sequences, shared between prokaryotes and eukaryotes for several modes of DNA repair, reflecting diversification from a minimal set of genes thought to represent the genome of the LUCA.
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 Point The 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.
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?
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.
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.
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."
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).
"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?
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.
It's not reasonable under non-teleological models for LUCA to have a minimalist genome.