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From: John Harshman <john.harshman@gmail.com>
Newsgroups: talk.origins
Subject: Re: Las universal common ancestor
Date: Tue, 23 Jul 2024 16:31:46 -0700
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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
>>>
>>> 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.
>>>
>>> https://www.nature.com/articles/s41559-024-02461-1
>>>
>>
>> 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.
>>
>> 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.
>>
>> 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.
>>
>> 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.
>>
>> 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.
>>
>> 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.
>>
>> Ron Okimoto
>>
>>
> 
> 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