Re: The tar paradox

On 15/12/2024 2:35 am, LDagget wrote:

On Sat, 14 Dec 2024 10:22:43 +0000, MarkE wrote:
 

On 14/12/2024 5:25 pm, erik simpson wrote:

On 12/13/24 9:51 PM, MarkE wrote:

On 14/12/2024 3:31 pm, erik simpson wrote:

Without reproduction tar is what you get for sure.  Nitrogen is high
enough concentration cause death by asphyxiation.

>
No reproduction prebiotically, therefore you're agreeing that the tar
paradox is an OoL showstopper?
>

I misprinted.  It's not a showstopper if the prebiotic reproduction is
present. It might be very slow or fail at some point.  The important
thing is that it's happening in many places.
>

>
What do you mean by "prebiotic reproduction"? Self-replicating naked
RNA? An autocatalytic set containing informational polymers?
>
In either case, these are disallowed if the tar paradox is unresolved.
And it appears to not only be unresolved, but largely unacknowledged.
>
Your statement "The important thing is that it's happening in many
places", is a vague, unsupported assertion, not an argument.

 This is a pretty goofy thread.
The initial assertion about adding energy means you produce tar is
the vague and insufficiently correct thing. Let's break it down.
 If you start with a soup of organic molecules and add in some high
energy reactants, you'll get a great deal of non-specific reactions.
I'm referring to, for example molecules prone to produce, for example,
free radicals or epoxides. These are so energetic that they will react
with the first thing they hit. That's somewhat exaggerated, but the
key point is that they won't show much discrimination so the reactions
that are "enabled" highly varied, not specific.
 With even a very modest understanding of biochemistry, you should see
that this is unlike biochemical reactions. Biochemical reactions,
especially the sorts involved with biopolymers are vastly more
specific, and require much less activation energy than exists with
free radicals and epoxides. You attach molding around a door with
finishing nails and a small hammer, not a wrecking ball.
 So the naked statement about "when you put energy into organic material
it turns into asphalt" is not very useful. In fact, the rest of that
quote runs rough over the facts as well.
 But beyond this, it presses an absurdity: it presses the idea that
scientists think abiogenesis involved strictly random chemical
processes.
I'll grant there are astrobiologists, and even some ill-informed
biologists
that might speculate that way. But serious scientists all invoke
catalysis
early. And even basic knowledge of catalysis says that the chemistry
being done is a lower activation energies and is highly specific.
 So the core question at hand is, why are you indulging in this
irrelevant aside about high energy, uncatalyzed reactions, when your
supposed focus in on OoL research?

Benner's quote refers to "organic matter", which I presume includes life's building blocks such as amino acids and nucleotides. As such, I'm thinking of simple organic molecules involved prebiotic chemistry. This stage of abiogenesis involved strictly random chemical processes. The formation of the first informational polymer must have been random, for example.
How would a transition to non-random processes occur? Autocatalytic sets sets can have a concentrating effect, so that's one hypoethesis. Although here's a skeptical comment from Jack Szostak on this:
Suzan Mazur: When we met at the Simons Foundation in April, you told me you “don’t believe” in autocatalytic sets. Why is that? Haven’t the Europeans integrated autocatalytic subsystems into their systems science?
Jack Szostak: Autocatalytic sets is one of those concepts where the people who came up with the original idea, like Stuart Kauffman, rather than admit being wrong, kept changing their story until it was basically the same concept everybody was already working on. The original idea was that there would be large numbers of compounds where one would help another to replicate, and that one would help some other one to replicate, and that somehow, out of this huge population of interacting molecules, autocatalytic replication would emerge. In my opinion, that was never chemically realistic. Now you see people talking about non-enzymatic RNA replication and calling that “autocatalytic sets.” If that’s what you want to call it, that’s fine. But it seems like the concept has lost all meaning.
Mazur, Suzan. The Origin of Life Circus: A How To Make Life Extravaganza (pp. 57-58). Kindle Edition.
Another comment on random processes in OoL:
Suzan Mazur: Pier Luigi Luisi recently told me the following: “The most popular view of origin of life by way of the RNA world, to me and to many others is and always has been a fantasy. . . . This is the story told to students and to me and is something without any scientific ground. . . Until somebody actually finds a way by which randomly produced RNA begins to self-replicate in not one single molecule but in a thermodynamically-driven process, the RNA world is baseless.”
Mazur, Suzan. The Origin of Life Circus: A How To Make Life Extravaganza (pp. 66-67). Kindle Edition.
Underlining: "a way by which randomly produced RNA begins to self-replicate in not one single molecule but in a thermodynamically-driven process"

 Establishing ways to fail doesn't mean much. Visit an undergraduate
O-chem lab. All those kids with written directions failing to produce
the correct products doesn't mean the reactions don't work. It might
mean the search for intelligent life is difficult.