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From: Arkalen <arkalen@proton.me>
Newsgroups: talk.origins
Subject: Re: Life: Turn it upside down!
Date: Wed, 10 Apr 2024 08:52:20 +0200
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On 09/04/2024 21:37, JTEM wrote:
>   Arkalen wrote:
> 
>>  JTEM wrote:
> 
>>> It's Faith-Based.
> 
>> No, it's based on general knowledge of chemistry and the data we have 
>> on early Earth conditions.
> 
> That is literally Faith-Based!  Because you have no idea what
> is required to spontaneously form life, or even if it were
> ever possible. Abiogenesis is not the only game in town, not
> even the only scientific game.
> 
> So it's based on beliefs. Plural.

Sorry; your reply of "it's Faith-based" was to the following:

"The alkaline hydrothermal vent hypothesis doesn't involve modern 
alkaline hydrothermal vents, in fact it relies on the assumption the 
chemistry would have worked out differently in an acidic, non-oxygenated 
ocean."

I thought the "faith" you were referring to was "our partial knowledge 
of the conditions of early Earth" but I take it you just meant the 
hypothesis overall?


The alkaline hydrothermal vent hypothesis starts out focusing on the 
proton motive force that all cells use for energy and noticing that the 
conditions for the proton gradient it involves would have existed in 
alkaline hydrothermal vents in early Earth oceans: alkaline fluid caused 
by the serpentinization reaction between water and rock seeps into the 
ocean through rocky pores, inducing a pH gradient across the walls of 
those pores that's very like the pH gradient across prokaryotic cell 
membranes today. They further noticed that the minerals in such pores 
match up with the cores of enzymes like acetyl CoA involved in carbon 
fixation, up to their crystalline structure, and have some catalytic 
activity of their own.

https://nick-lane.net/wp-content/uploads/2016/12/Sojo-et-al-Astrobiology-review.pdf


They ran experiments exploring how carbon fixation could work under such 
chemical conditions and there's been a lot of recent progress:

The paper where they actually pulled off reducing CO2 to formose IIRC:
https://www.pnas.org/doi/full/10.1073/pnas.2002659117

Exploration of the synthesis of various other relevant biomolecules:
https://www.nature.com/articles/s41467-021-26158-2
https://www.liebertpub.com/doi/10.1089/ast.2021.0125
https://www.mdpi.com/2075-1729/13/5/1177


Something about trying out simpler ATP precursors & coming up with 
insights why ATP might be use now:
https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3001437
https://link.springer.com/article/10.1007/s11084-018-9555-8


Recent years have shown a merging of this pure metabolism-first 
hypothesis with other strains of abiogenesis research, including the 
idea the earliest cells could have self-assembled from lipids, which 
this fits well with (and gives a source for the lipids!). Again with 
experiments into how that could work in the Hadean AHV conditions:

https://www.nature.com/articles/s41559-019-1015-y
https://royalsocietypublishing.org/doi/10.1098/rsfs.2019.0067


And they're even closing the circle on the biggest bootstrap problems in 
abiogenesis - after all you're metabolism first OK but then whence 
genes? And how does it resolve RNA first vs protein first? These are 
mostly computational models so far, but of course very much rooted in 
the known chemistry and ongoing experiments into that chemistry:

https://royalsocietypublishing.org/doi/10.1098/rsfs.2019.0067
https://www.mdpi.com/2075-1729/13/5/1129


The circle closes as follows: the pH gradient in those early vents would 
have reduced CO2 and basically been an ongoing reaction continuously 
generating simple organic molecules in the vent. Lipids & such would 
spontaneously form protocells, and peptides would bind to vent minerals 
& the membranes and some would catalyze the reduction of CO2, causing 
more organic molecules to be formed. This would induce a very limited 
kind of reproduction & heredity and therefore natural selection in those 
protocells: membranes with peptides that catalyzed CO2 reduction well 
would grow and split faster, causing a feedback loop that increased the 
catalysis of CO2 reduction and the resulting concentration of organic 
molecules. Nucleotides could emerge in such an environment and this in 
turn solves one of the issues with RNA World - if RNA is selected for 
speed or accuracy of replication then that pushes it towards *shorter* 
chains, not complex ones. But if RNA is selected *from the start* for 
increased CO2 reduction because it's part of a protocell that's already 
multiplying & under selective pressure for that parameter, then that's 
no longer an issue.


The most exciting aspect of the hypothesis IMO is how well it fits with 
looking at the question from the other direction: inferring the 
properties of LUCA from a phylogenetic analysis of modern life. This 
reveals that archae and bacteria have common mechanisms for most things 
- RNA replication, translation, ATP synthesis, etc, but have different 
mechanisms for all things membrane-related. They both rely on the proton 
gradient across their cells for ATP, and do it in the same way, but they 
*generate* that gradient in different ways! This is perfectly explained 
by LUCA being an organism that relied on a natural proton gradient, and 
bacteria & archaea being two branches of that tree that independently 
evolved ways of pumping protons across their membranes using the Ech 
protein, which allowed them to live outside the vents. (the first 
article I linked might get into that aspect)


You know what I just saw this review article that seems to sum 
everything up and that I should probably read because it's from 2023, so 
truly the latest dirt:
https://www.annualreviews.org/content/journals/10.1146/annurev-ecolsys-110421-101509

(Also sorry to all the non-Nick Lane folk working on this, his website 
is still my best link list in a pinch)


Anyway this is all just to say the alkaline hydrothermal vent hypothesis 
is a normal scientific hypothesis, relying on inferences from current 
knowledge, hypotheses & models on possible causes and experiments to 
test those hypotheses & models and gather further knowledge.


> 
>>> If you study non life you study things that actually exist.
> 
>> That can be true or false whether you study life or nonlife.
> 
> Working out abiogenesis is studying things that do not exist,
> including the theorized environment... not to mention HOW
> this environment could manage it.
> 
> Study non life is actually studying things that exist.


Well you might be reassured then to find that all the experimental work 
linked above is very much into non-life that exists.

> 
>> In this case while we no longer have an oxygen-less ocean we can 
>> simulate such conditions when doing experiments; those experiments 
>> involve things that actually exist.
> 
> If those experiments ever succeeded, which they haven't, that
> would prove that Creationism is real. After all, it would be
> an example of an intelligence bringing into existence life by
> intent, by design. But it wouldn't and couldn't "Prove" that
> it ever happened in nature.

That seems to assume the only possible abiogenesis experiment is "making 
a cell from scratch" but that's never how science or experiments work. 
Experiments are always about testing some testable aspect of a 
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