Re: Life: Turn it upside down!

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 hypothesis. That would be like saying we never tested the theory of relativity until we put GPS satellites into orbit or something.

 

I don't know if any such spectrum is explicitly published

 Well there's your problem!
 

to my knowledge its contents are basically what you listed in your OP.

 Oh, dude; I was woafully under performing there!  We're talking
a HUGE spectrum, from the most basic forms of matter to the
most complex examples of non-living structures... onto the very
simplest forms of life...

And I'm telling you most of that spectrum is empty, shows a huge gulf. I'll give you that I could add some things to your list, most notably dissipative systems like tornadoes. But if you think the spectrum is full then you should have no trouble at all populating it better than you did there.
I mean, obviously every element of that spectrum has to have been realized at some point, or abiogenesis couldn't have happened. But you seem focused on only looking at things that exist now, so.

 Think of it like the "Electromagnetic Spectrum." We're talking
BIG here, very BIG -- the opposite of small.
 

So not exactly warranting a paper

 Lol!  It's exactly what papers need to be written about!
 THAT IS THE POINT!
 It's an approach that needs to take over, be completed in order
to make any legitimate discoveries.
 

but maybe there are review papers or subject-matter papers with good introductions that address your idea. I'll keep you posted if I look it up.

 Science is gone anyways. It's all driven by money:  Grants.
 If it doesn't have a direct military or financial benefit, it's
politics now.
 So don't hold your breath.
 

The papers I was thinking I might find anyway would either have been modern review papers saying "as you see there's a huge gulf, here's how the field failed to get anywhere from the abiotic side for decades" or old papers saying "wow, there's a huge gulf, let's investigate the abiotic side". In terms of actually solving abiogenesis I breathe easy knowing a different approach is working fine right at the moment.