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From: RonO <rokimoto557@gmail.com>
Newsgroups: talk.origins
Subject: Re: Las universal common ancestor
Date: Sun, 14 Jul 2024 07:51:16 -0500
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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