Deep Homology and Front-loading

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.

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.

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

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." 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.