Re: The tar paradox

On Sun, 15 Dec 2024 12:12:40 +0000, MarkE wrote:

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.

I discount anyone who asserts such "randomness".
It makes no sense at all.
This is relevant to the tar business as catalysis of the sort that
is relevant involves rather low activation energy pathways, and of
course the catalysis further lowers the activation energy.
So if you understand even the basics of how tars are formed in things
like the MIller-Urey experiment, you know that those pathways are
irrelevant. If you're going to speculate about OoL chemistry, you've
got to have a foundation in chemistry.
And the obvious supporting evidence that catalysis is necessary is
the chiral specificity of biochemistry. It simply can't be created by
completely random solution condensations. It is, however, a natural
consequence of many catalytic pathways.
This does not mean one can simply invoke catalysis and claim that all
of the challenges are solved. Indeed not. The source of the catalytic
surfaces remains unknown, although there are candidates. And
crystallization
processes can account for the stereospecificity.
But when you ignore these things and hypothesize about random chemical
reaction driven by thermal heat alone, you discredit yourself
completely.

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.

You've shown you don't understand those comments, which are more about
the sets than the catalysis. It's also a criticism of simply invoking
catalytic sets as if they magically solve the OoL problem and we can
declare things done. But this is infighting and a dick measuring contest
about who has contributed more significantly.

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"

I don't think you show any understanding of those quotes either.
The RNA World is a gross over-simplification of a thought experiment.
Fools tend to interpret it to mandate some sort of exclusivity such that
there had to have been a stage in the evolution of living systems where
__ALL__ catalysis was catalyzed by RNA and there were no functional
amino acid polymers. It's the same sort of foolishness that misconstrues
Miller-Urey type experiments to have been attempts to create actual
life in a round bottom flask.
As to the quote, the key phrase is "thermodynamically driven process".
Personally, I would add/substitute "kinetically driven process".
But ultimately, it sure seems like you are attempting to evaluate the
finer points of a chess openings while still learning how the pieces
move.

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.
>