Re: Las universal common ancestor

On 7/23/24 4:04 PM, RonO wrote:

On 7/14/2024 7:51 AM, RonO wrote:

On 7/13/2024 11:01 AM, erik simpson wrote:

The nature of the last universal common ancestor and its impact on the early Earth system
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Abstract
The nature of the last universal common ancestor (LUCA), its age and its impact on the Earth system have been the subject of vigorous debate across diverse disciplines, often based on disparate data and methods. Age estimates for LUCA are usually based on the fossil record, varying with every reinterpretation. The nature of LUCA’s metabolism has proven equally contentious, with some attributing all core metabolisms to LUCA, whereas others reconstruct a simpler life form dependent on geochemistry. Here we infer that LUCA lived ~4.2 Ga (4.09–4.33 Ga) through divergence time analysis of pre-LUCA gene duplicates, calibrated using microbial fossils and isotope records under a new cross-bracing implementation. Phylogenetic reconciliation suggests that LUCA had a genome of at least 2.5 Mb (2.49–2.99 Mb), encoding around 2,600 proteins, comparable to modern prokaryotes. Our results suggest LUCA was a prokaryote-grade anaerobic acetogen that possessed an early immune system. Although LUCA is sometimes perceived as living in isolation, we infer LUCA to have been part of an established ecological system. The metabolism of LUCA would have provided a niche for other microbial community members and hydrogen recycling by atmospheric photochemistry could have supported a modestly productive early ecosystem.
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https://www.nature.com/articles/s41559-024-02461-1
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It has been a long time since I published in this field, and they use terminology that wasn't being used back then.  I do not know why, but they call genes "markers" and do not use gene names, but marker designations that are in the NCBI database and give you a protein sequence comparision and superfamily designation.  TIGR01032 is a member of superfamily cl00d393.  You have to use the protein alignment names to get the name of the gene.  I clicked on P47440 in the protein sequence alignment and found out that it was 50s ribosomal protein L20.
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They identified 59 single copy markers in their 700 reference genomes, and used 57 of them in their analysis.  They created a phylogeny of their 700 reference genomes by doing phylogenetic analysis on the 57 concatenated gene sequences.
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They claim to use duplicated genes whose duplication preceded LUCA. They did an analysis to identify all the gene families in their 700 reference genomes. They identified the genes and did a comparative analysis and grouped them into families.  They ended up with 5 groups of related genes whose duplication may have occurred before LUCA existed. They used analysis of these groups of related genes to estimate when LUCA may have existed.
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I do not know how accurate any estimate could be.  They do have phylogeny of their 700 reference genomes, and they do have the duplicated sequence families.  I do not know if they have enough nodes to estimate how the protein sequences have evolved over the last 4 billion years.  They have the extant sequence and are trying to recreate the sequence of the original protein gene in order to make their clock estimates.  They are trying to infer how many substitutions have occurred in 4 billion years for 700 reference genomes when it is likely that a high percentage of the amino acid positions have been substituted many times within each of their 700 lineages.
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Their estimate of 4.2 Ga for the LUCA would mean that the genetic code had evolved within 300 million years of their 4.5 Ga estimate for when the earth's surface was essentially molten.
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They reject the late heavy bombardment episode that was supposed to have occurred around 3.8 Ga that would have sterilized the planet and note that it has come into question as ever happening.
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Ron Okimoto
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 The ID perps have their take on this study.
 https://evolutionnews.org/2024/07/study-finds-lifes-origin-required-a-surprisingly-short-interval-of-geologic-time/
 They make some stupid comments like:
QUOTE:
First, it infers the genetic and phenotypic traits of LUCA by assuming that biological similarity always results from common ancestry — and never from common design. This dubious logic is seen in the opening statement from the technical paper which reads, “The common ancestry of all extant cellular life is evidenced by the universal genetic code, machinery for protein synthesis, shared chirality of the almost-universal set of 20 amino acids and use of ATP as a common energy currency.” It’s true that all life uses those components (although the genetic code is not exactly universal), but this does not provide special evidence for common ancestry because the commonality of these similar features could be explained by common design due to their functional utility.
END QUOTE:
 The stupid thing about this IDiotic notion is that the study is only possible because of descent with modification.  If it were common design there is no reason to have lineages accumulate the genetic changes that make this study possible.  Some designer could have created all lifeforms with the same genetic code and related gene sets, but this study relied on ancient gene families that started gene duplication prior to the last common bacterial ancestor and the last common Archaea ancestor.  These genes duplicated and they started changing.  The lineages of these gene families existed before LUCA, and further differentiated after the last common Archaea and bacterial common ancestors.  The phylogenies have been maintained in all the subsequent Archaea and bacterial lineages including Eukarya.  Behe and Denton understand that this pattern of evolution could not have been due to a common designer, but had to be created by descent with modification. That is why Behe started claiming that he was looking for 3 neutral mutations to alter a protein to do something different.  These 3 neutral mutations would have had to occur in a lineage that could be determined not to have them until they occurred within some Beheian time limit. Behe is a tweeker.  His designer is duplicating genes and putting in a few amino acid substitutions in them every once in a while.  For the 5 gene families used in this study the genes started duplicating before LUCA existed.
 LUCA is only the last common ancestor of both Archaea and bacteria.  As crazy as it may seem this study indicates that around a billion years after LUCA existed life was reduced to just two surviving lineages. There were likely trillions of lifeforms that started lineages before LUCA and after, but only two surviving lineages are represented by extant lifeforms.  If we had a third or a fourth surviving lineage we could have a different LUCA.  There were many different lineages of life that existed at the same time as LUCA, but LUCA identified in this study is the only one with surviving descendants.

Hey, it's just coalescence. IDers seem unable to understand coalescence, and creationists are generally worse. Also, Theobald 2010.
Theobald, D. A formal test of the theory of universal common ancestry. Nature 465, 219–222 (2010)
https://www.nature.com/articles/nature09014