Re: OOL X - The origin of the RNA world.


"tinyurl.com/uh3t" <rem642b@xxxxxxxxx> wrote in message news:d2ei9i$2o4h$1@xxxxxxxxxxxxxxxxxxxxxx
> (Part 2 of reply)
> > From: "Perplexed in Peoria" <jimmenegay@xxxxxxxxxxxxx>
> > Yours is a "metabolism first" theory, whereas mine is "morphology and
> > metabolism first".
>
> Actually my proposed abiogenesis/OOL scenerio is "whatever chemistry
> happens to replicate successfully", where replication and metabolism
> are a single process that can't be partitionned into separate pathways.
> For those who missed my postings a few months ago, a summary:
> High-energy input (undersea vents, UV radiation on surface, hot crashed
> meteors, lightening strikes) breaks up stable molecules to yield
> fragments that tend to react with any molecule they happen to bump into
> (much as monatomic oxygen from UV splitting of O2 in the upper
> atmosphere nowadays bumps into another O2 molecule to form ozone).

Hmmm. It sounds as though you are talking about free-radical chemistry
here. I'm not sure that thermal energy at vents, or hot meteors, are
high enough in energy to cause this kind of chemistry. Lightning
and uv certainly can.

> A cascade of chemical reactions ensues, the details of each individual
> reaction-chain depending on which other molecule the fragment first
> bumps into, and which other molecule the result of that bumps into
> next, etc.

> Every once in a while a particular random molecule A1
> appears in one of these chains, whereby
> A1 -> A2 -> A3 -> ... -> An -> A1
> (with additional chemicals as input and output of each single reaction)
> i.e. the A's form a catalyst.

Are all of these An molecules free radicals? Or, to make the question
a little more abstract, are all of these molecules highly reactive so
that each of those reactions "A(n) -> A(N+1)" proceeds at an appreciable
rate without catalysis? If so, you need to consider the possibility
that the cycle will be rapidly drained by side reactions.

> One of the additional outputs of that
> chemical reaction loop is B1, which forms a second chemical loop
> B1 -> B2 -> B3 -> ... -> Bn -> B1
> where one output from there is C1 etc. D1 etc. ... X1 etc. but one of
> the outputs from the X cycle is one of the earlier catalysts, let's say
> K. So now the spontaneous creation of A1 and the chemical cycles
> A,B,...,J are no longer necessary, the chemical cycles K,L,...,X are
> self-perpetuating, forming the first successful replicator. (Assuming
> the fecundities of A producing B, B producing C, etc. are sufficient to
> produce enough molecules of K1 to start the K,L,...,X cycle, and
> assuming the fecundities of K producing L etc. are sufficient to
> maintain that cycle with once-around fecundity greater than 1.)

A nice presentation of Eigen's "hypercycles".

> So whether you label all that as "metabolism" or not, ...
> I would just label it as "chemistry".

Well, "metabolism" is chemistry - a particular kind of chemistry. I would
say that the distinction that separates metabolism from other kinds of
chemistry is teleological. Metabolism has a "purpose", whereas other
kinds of chemistry do not. And teleological language is justified by
the existence of some kind of reproducing organism that "needs" and "uses"
the metabolism.

> Using speciation as a metaphor: Sometime later there's a speciation
> event where replication and metabolism split apart to become separate
> chemical pathways, but at this point the speciation event hasn't yet
> happened and it wastes energy to debate whether this kind of chemistry
> should be called by either post-speciation label.
>
> > I see the metabolism as working locally within organisms from the
> > start, whereas in your theory, the only organism is the ocean as a
> > whole.
>
> Ignoring for the moment multi-cellular organisms which are colonies of
> clones of single cells, and single eukaryotic cells which are
> complicated symbioses of former prokaryotes, considering only single
> prokaryotic cells and their ancestors: I see such a single cell as a
> very complicated symbiosis of various chemicals which chemically
> synthesize each other. Looking at this from the bottom upward, the key
> thing is a single species of molecule (freefloating, or attached to
> something semi-passive such as a membrane), whereby one molecule of a
> particular species undergoes some reaction with another molecule to
> yield one or more new molecules, some of which undergo additional
> reactions to yield yet more molecules, etc., until eventually some of
> the original species is created. Overall, once a replicator of any kind
> exists, this process results in exponentially increasing quantities of
> each of the fabricated molecules, within whatever ecosystem contains
> this all.
>
> (I'm assuming the fecundity of molecules tied together so that they can
> repeatedly find each other to react again is much greater than the
> fecundity of molecules that drift independently through the whole
> ocean.)
>
> Within a cell, the ecosystem is innerds&membrane the whole cell. Any
> chemicals that leak out of the cell would cease to be effective
> participants in the micro-ecosystem.
>
> With molecules attached to a membrane or glob of tar etc., the
> ecosystem might be the surface of the membrane or glob (where any
> molecules that detach from the m/g drift so far away that they get
> decomposed before they ever happen back to that or similar m/g so they
> play no further role in the ecosystem, whereas molecules that stay
> attached have good chance of reacting again before being decomposed so
> they remain effective participants of the tiny ecosystem.
>
> With molecules freefloating in the ocean, the whole ocean would usually
> be the ecosystem. But with enough local convection such as through an
> undersea vent and not much diffusion out of that convection loop to the
> ocean at large, the local convection cycle may be the effective
> ecosystem. The fecundity of the chemical cycles may be such that
> locally recirculated chemicals achieve fecundity greater than one but
> chemicals leaking out usually get decomposed before they happen to
> return.
>
> I consider the word "organism" to be a "loaded word", i.e. it misleads
> people into thinking of modern forms of life, making it difficult to
> think about the very first kinds of replicators. By comparison, the
> word "ecosystem" or "micro-ecosystem" or more specifically "chemical
> ecosystem" makes it easier to take for granted that there isn't any
> specific autonomous unit but rather the boundary between the
> self-sustaining ecosystem and some larger non-self-sustaining ecosystem
> is fuzzy with the boundary depending on where the fecundity (of the
> symbiotic chemical species(pl)) crosses the boundary from >1 (within
> the small self-sustaining system) to <1 (out in the larger ecosystem).
>
> It's possible that after the first successful replicator fills its
> local ecosystem, so much of the replicating chemicals leak out that
> they eventually fill the whole ocean too. The fecundity may be greater
> than one both locally and globally, but with different time constants,
> very quickly filling the local ecosystem, but taking much longer to
> fill the ocean, and not saturating the ocean as densely as the local
> ecosystem was saturated.
>
> Summary: I'm agnostic/undecided as to whether the first successful
> replicator had an effective ecosystem consisting of the whole ocean or
> just the surface of a bubble or targlob or just the convection cell
> driven by an undersea vent or whatever.
>
> > In a sense, you see the molecule as the organism.
>
> Not quite correct. I see any organism as essentially a local ecosystem
> consisting of several or many or very many distinct species of
> molecules that manufacture each other. Some of these molecules are in
> catalytic loops whereby they indirectly make themselves, and I would
> regard each of them (or each chemical-cycle of molecules which together
> constitute one catalyst) as a "replicator", while others are merely
> products of those hence are themselves "artifacts" rather than
> "replicators". If you must use the word "organism", then the whole
> ecosystem, which may be the whole ocean, is the "organism", but per my
> discussion above I prefer not to use that word in the first place.
>
> > A molecule reproduces by transformation through a life cycle of
> > several stages, but eventually it reaches the reproductive stage of
> > its life cycle and is cleaved into two "immature" molecules -
> > molecules at earlier stages of the cycle.
>
> No! Given that we're talking about a molecule which is a successful
> replicator (which is a special kind of catalyst), that molecule reacts
> to produce some other molecule, which produces another, etc., and once
> around the chemical loop it makes one molecule of itself most of the
> time, never more than one. But one of the side products each time
> around the chemical loop is a second catalyst. If the loop goes around
> several times before it is disrupted, then several copies of that
> second are made. Likewise the second molecule causes a chain of
> molecules around a second loop, which may go several times too,
> producing several copies of a third catalyst. CatalystA begats several
> catalystBs begats lots of catalystCs begats ... begats innumerable
> CatalystsA, not just two CatalystsA. That's assuming each link in the
> catalytic loop has fecundity greater than one. But all that is really
> needed is the product of all the fecundities around the catalytic loop
> is greater than one, which allows that some of the catalytic links
> actually have fecundity less than one (they usually don't even get
> around the chemical cycle once before they are disrupted), and in fact
> some links in the catalytic loop don't have to be catalysts at all.
> But in any case, the chance of the product of all the fecundities
> around the catalytic loop (which is the "once-around fecundity") being
> exactly two is basically zero, that product is most likely to be
> somewhere in the range 1.2 to 1.5 based on the model I calculated a few
> months ago. Even if the once-around fecundity is exactly two (like if a
> supernatural being or a very good chemical engineer designed it that
> way), the stochastic nature of these chemical reactions means that the
> number of copies of the original molecular species produced once around
> the loop, from a single starting molecule, will sometimes be 1 and
> sometimes 2 and sometimes 3 and once in a while greater than 3.

Ok. I get it. The primary cycles provide catalysis, but no growth.
It is the hypercycles that provide anaplerotic refreshment of the
cycles and which may (if fecundity > 1) provide growth.

I usually don't make that crisp of a distinction. Perhaps I should.
Your way of thinking about it IS clarifying. It will require more
thought for me to decide whether your disciplined model makes it impossible
to talk about something that may be important.


.

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