Deep Homology and Front-loading

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.

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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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?

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I don't think so. I would add that that hypothesis assumes too much - it would be much better to construct a plausible scenario and make predictions from that.

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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.

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Firstly we note that neither you nor your sources present any reasoning to support this assumption.Secondly, we must note that evolution is not a goal-directed process and as such it seems somewhat unlikely that the first cell would have acquired only those genes absolutely necessary to form a cell.Thirdly we wouldn't expect the LUCA to be the first cell. And it's even less reasonable to expect there to be no ancestors shared between eukaryotes and some prokaryote since the LUCA, which could also produce deep homologies.

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...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)

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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.

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ALright. It's not reasonable, under non-teleological models, for the LUCA to have only a minimal genome and be only a minimal cell.Seriously all you have is a claim about "early hypotheses" with no indication of how they were arrived at. Where's the reasoning that would make them reasonable ?

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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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And whether FLE predicts it. That's another of your claims that is somewhat lacking in support.Edited by PaulK, : No reason given.

In order to be testable predictions they would need to differ from the assumption and differ from known natural mechanisms that you are seeking to replace. So far, you have fulfilled none of these requirements. Just like non-teleological meteorology does not predict that it has to rain on July 15th, 2016 in Dallas, TX. However, rain that day is consistent with non-teleological meteorology. In the same way, "crucial eukaryotic genes will share deep homology with functional but unnecessary (for life) prokaryotic proteins" is also consistent with non-teleological evolutionary mechanisms.It is incumbent on you to show that non-teleological mechanisms can not co-opt proteins in subsequent generations. It's not reasonable under non-teleological models for LUCA to have a minimalist genome. LUCA is a product of many rounds of evolution. LUCA will contain genes that are unnecessary for life by necessary for outcompeting other organisms in a given environment.What you label unnecessary proteins are beneficial proteins to the organism that carries them. That is why they have been preserved for 3 billion years of evolution. Can non-teleological mechanisms preserve beneficial proteins? Yes. Therefore, it is not a valid testable prediction for FLE.Can non-teleological mechanisms co-opt beneficial mutations for new purposes through random mutation and natural selection so that they are necessary genes in subsequent generations? Yes, absolutely. This too is not a valid testable prediction for FLE because it does not differentiate FLE from non-teleological processes. Yes, it is. If non-teleological mechanisms can produce the observations then FLE is not supported.

A minimal genome for what function? 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.

So, you're agreeing that the frontloaders could have designed a eukaryote. And: I think it implies that it's part of a useful system in them. But that doesn't mean that a complex eukaryote-like cell couldn't have formed in different ways, and couldn't have used different proteins for a similar function. I like this: 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?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.If they were trying to maximise the probability of metazoa, they would know that it would require something like mitochondria to power it. Surely that's what we'd expect to see frontloaded, isn't it? Any thing else seems like heavy gambling.

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:

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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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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.

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(The proteomic complexity and rise of the primordial ancestor of diversified life, 2011)Progenotes, incidentally, are even more minimal than a minimal cell.

Also:

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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.

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(A minimal estimate for the gene content of the last universal common ancestor--exobiology from a terrestrial perspective, 2006)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)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:

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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 cycleBecause 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.

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(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:

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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)That sounds like a sophisticated organism deployed for front-loading, doesn’t it?And:

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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.

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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 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.

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. 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.

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. 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.

People certainly inferred that LUCA had a minimum genome and that inferrence is consistent with the "darwinian" model. But its not necessitated. As we've uncovered more genetic evidence, we've realized that LUCA would have been bigger than we had thought. Which, too, is consistent with the model. It took me about 7 minutes to find three:

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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. Instead, a fairly complex genome similar to those of free-living prokaryotes, with a variety of functional capabilities including metabolic transformation, information processing, membrane/transport proteins and complex regulation, shared between the three domains of life, emerges as the most likely progenitor of life on Earth, with profound repercussions for planetary exploration and exobiology. source

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Thus LUCA was not a minimal organism but the first modern organism equipped with a DNA genome and the universal genetic code. source

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Results: LUCA does not appear to have been a simple, primitive, hyperthermophilic prokaryote
but rather a complex community of protoeukaryotes with a RNA genome, adapted to a broad
range of moderate temperatures, genetically redundant, morphologically and metabolically diverse.source

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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.

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.Of course if it was as useful to prokaryotes then that wouldn't be likely to happen. Of course we wouldn't expect to see only distantly related homologues in prokaryotes either. So ubiquitin hardly supports your ideas.

From Message 143: "It could have happened differently" isn't a reason to not suspect a ubiquitin homolog in prokaryotes. Why would it be lost? 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. How do you know the gene that encodes ubiquitin could have arrisen like the T-urf13 gene did?

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

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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.

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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.Even if you judge otherwise this paper at least argues that a non-minimal genome is more reasonable and calls the reasonableness of the assumption of a minimal genome into question: About the last common ancestor, the universal life-tree and lateral gene transfer: a reappraisal