That is true, though it is trivial to demonstrate the same effect for deeper branchings. Do it for 23S ribosomal RNA and you get the same effect. As you reconstruct increasingly older nodes in trees from archaeal, eukaryal, or bacterial clades, they become more and more similar.
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Has this been done?
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Did it for my own satisfaction a few days ago.
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Nice! Can you show us your methodology and results?
Sure, will post later.
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This is puzzling, as you have elsewhere claimed that eukaryotes were seeded onto the earth at the very beginning of life here. How does that fit with the symbiotic origin of organelles? Did it happen on another planet?
Eukaryotes are characterized by their nucleus, not by the presence of mitochondria or chloroplasts. Microsporidia are also eukaryotes, even though they have secondarily lost their mitochondria. So to answer your question, I envision the seeding of first life to have happened before the acquisition of mitochondria.
I donât share your assesment, so please be specific about which commonalities youâre talking about. Did LUCA have a cell membrane? If so, what was it composed of? How did LUCA replicate its DNA? Both cell membranes and the DNA replication machinery have been hypothesized as having evolved independently in bacteria and eukaryotes due to their large differences in the two domains.
Had bacteria and eukaryotes employed fundamentally different genetic codes, I see no principled reason why it couldnât be hypothesized that the code had evolved twice, or that the codes had each diverged from the code used by LUCA.
[Edited to add a reply to @Rumraket]
Please walk me through this, as Iâm not sure I follow your logic.
So you reconstruct the ancestral 23S rRNA sequence of the ur-bacteria and the ancestral sequence of the ur-eukaryote - assuming for the sake of the argument that the phylogenetic signal of 23S rRNA is sufficient to resolve phylogenies this deep. Now what?
What would universal common ancestry predict? That if you used those two sequences to reconstruct the sequence of LUCA, it should be somewhere between the ur-bacteria and the ur-eukaryote sequences in sequence space? That follows mathematically from how ancestral sequences are reconstructed.
Now weâre getting into technical points of definition. Eukaryotes are characterized by a number of things in addition to the nucleus. What youâre talking about is some kind of proto-eukaryote that lacked some of those characteristics. This proto-eukaryote seems to be embedded within Archaea, based on recent genomic work. How does that fit your scenario?
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Or itâs a sister group:
The eocyte hypothesis, in which Eukarya emerged from within Archaea, has been boosted by the description of a new candidate archaeal phylum, âLokiarchaeotaâ, from metagenomic data. Eukarya branch within Lokiarchaeota in a tree reconstructed from the concatenation of 36 universal proteins. However, individual phylogenies revealed that lokiarchaeal proteins sequences have different evolutionary histories. The individual markers phylogenies revealed at least two subsets of proteins, either supporting the Woese or the Eocyte tree of life. Strikingly, removal of a single protein, the elongation factor EF2, is sufficient to break the Eukaryotes-Lokiarchaea affiliation. Our analysis suggests that the three lokiarchaeal EF2 proteins have a chimeric organization that could be due to contamination and/or homologous recombination with patches of eukaryotic sequences. A robust phylogenetic analysis of RNA polymerases with a new dataset indicates that Lokiarchaeota and related phyla of the Asgard superphylum are sister group to Euryarchaeota, not to Eukarya, and supports the monophyly of Archaea with their rooting in the branch leading to Thaumarchaeota.
Cunha V.D., et al., 2018, âLokiarchaea are close relatives of Euryarchaeota, not bridging the gap between prokaryotes and eukaryotesâ, PLOS Genetics 13(6):e1006810
actually i dont think that uca predict something about this. if all sequences were very different from each other the common descent theory was still ok.
Supposing that eukaryotes are the sister group of Archaea, how does that fit your scenario?
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I havenât done eukaryotes, only bacteria and archaea. Though one could do those too I suppose. Kinda tired of finding and aligning sequences now I have to admit.
The method is basically the same as that used in the paper linked. First collect a diverse set of bacterial 23s rRNA sequences, then a diverse set of archaeal sequences. Then do pairwise alignments between all members (bacteria to archaea), take the average similarity score (itâs in the 57% ish range, 23s rRNA is quite well conserved even between bacteria and archaea).
Then infer a bacterial clade phylogeny using a different set of data (than 23s rRNA) to determine a good bacterial outgroup for rooting a subset of the bacterial clade(I didnât do this, I just picked a phylogeny from the literature based on whole genome sequences for archaea, and a concatenated alignment of 31 proteins coding genes for bacteria). Now use that outgroup bacterial clade to root your internal bacterial 23s rRNA clade and infer the phylogeny and reconstruct internal nodes.
Do the exact same thing with the archaea. Now do pairwise alignments for the nodes in the archaeal tree to the bacterial sequences and nodes. If common descent is true, increasingly ancestral nodes in the bacterial clade should score increasingly higher pairwise identity to archaeal sequences and nodes. The root nodes of both trees should be the most similar to each other compared to younger nodes and extant sequences.
What would universal common ancestry predict? That if you used those two sequences to reconstruct the sequence of LUCA, it should be somewhere between the ur-bacteria and the ur-eukaryote sequences in sequence space? That follows mathematically from how ancestral sequences are reconstructed.
I agree, I obviously didnât infer a âuniversal ancestorâ node for the two clades, that would be silly and not constitute a test of the hypothesis that increasingly older nodes converge if the species really do share common descent.
Thatâs also why I didnât root my trees with outgroups from the âopposingâ clade with which I was supposed to test common ancestry, as obviously that would artificially bias my result towards that outcome. Thatâs why I used a different data set instead of 23s rRNA to determine where the deep branches in the bacterial and archeal clades were. Obviously if I just created one big tree with all 23s rRNA sequences, defined archaea as the outgroup of bacteria, then it seems to me I would have essentially forced the result.
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The original authors disagree:
https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1007080
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I donât know. Maybe archaea are reduced proto-eukaryotes (as suggested by Forterre, 2013). Maybe theyâre a third designed domain. Archaea is a much less described group than either bacteria or eukarya, so I donât have as much data to sink my toes in.
Look, Iâm very explicit that my thoughts on intelligent design are little more than a hunch pursued whenever a busy schedule allows me time. Youâve asked a good question. The answer is that I donât know yet.
Yeah, and Cunha et al. disagree with them.
In either case, I think we should wait a while before raising up one side in an ongoing debate as the concensus view to which every scenario should align.
The abstract mentions neither cell membranes or DNA replication, and the rest is behind a paywall. Besides, Iâm well aware of genomic reconstructions of LUCA. They donât pertain to my point, which is this:
Independent origins for cell membranes and DNA replication have been proposed by serious scientists who understand both biology and universal common ancestry. Their papers have been published in the scientific literature after having been reviewed by their peers, who also understand both biology and universal common ancestry.
Had bacteria and eukaryotes employed fundamentally different genetic codes, it seems entirely possible that serious scientists, understanding both biology and universal common ancestry, had published papers arguing that the code had evolved twice, or that the codes had each diverged from the code used by LUCA.
Where does this hunch come from? That is, what gives you the idea that it might be true? How is the origin of life on another planet more parsimonious than its origin here?
Sure, but the point is that they share common ancestry with eukaryotes. So where did this common ancestry happen? Where did the common ancestry of much of the eukaryote genome with eubacteria happen? On earth? On another planet?
Iâm trying to understand what your scenario is.
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Just because there is a debate in the literature doesnât mean that we shouldnât raise up one side as being most plausible. Forterre/Cuhna are outliers, itâs quite clear to most people in the field that the eocyte hypothesis is the best supported at the moment, and this support has only increased in recent years.
I thought we had already gone over this. A common genetic code is a prediction that flows from UCA if LUCA was sufficiently âadvancedâ beyond the stage of âdecidingâ its genetic code. Or you could flip that around: we observe a common genetic code, and this combined with the hypothesis of UCA makes the prediction that LUCA was sufficiently advanced beyond the point of âdecidingâ its genetic code. Either way, the predictions are correct, thatâs what the paper supports.
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I was evaluating @Krauze proposal of a human like intelligenceâŚ
As to God. Its applies to God also (Not the less work aspect). If God doesnât want to use different types of Genetic material and he doesnât need to⌠why would he?
Thatâs the point though, the outcome would be based on the whims of God - whether he âwantedâ to use different kinds of genetic material or not. We canât know this, so the hypothesis makes no specific prediction one way or the other. UCA does. Thatâs important in science.
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