Re: I thought this NG was about Origins?


John Wilkins wrote:
Nic <harrisondalen@xxxxxxxxxxx> wrote:

Robert Maas, see http://tinyurl.com/uh3t wrote:
Third, there may not only be isomers of the relevant species, but
larger molecules with variable properties (such as attachment sites)
in which they can be embedded.
I don't think that helps, because while the varying environment at
various sites on a large molecule will influence the activity of an
embedded catalyst, there's essentially zero chance that such a catalyst
would suddenly start manufacturing whatever large molecule it was
embedded in. So there's no way the large molecule could be replicated
and selected. So even if a really good large molecule chances into
existance and helps the auto-catalytic set for a while, after a while
it spontaneously decomposes and all benefit is forever lost. We need a
way that such a large molecule would actually synthesized by the
auto-catalytic set, which I don't see happening until after replicators
begin sticking together into polymers.
But if the catalytic molecule is constantly regenerated, and there are
something like chaperonins helping it to conform, the problem
disappears.

Where do the chaperonins come from? How do chaperonins get
manufactured? I see no mechanism by which such a chaperonin would be
manufactured by the auto-catalytic set.

I wasn't talking about chaperonins per se, but some molecule that acts
as a conformation guide. Any byproduct of a hypercycle that is reliably
able to fold by itself and act as a conformation "enforcer" will do that
job.

Anyway, the "replicator" molecule is not the only catalyst in the
hypercycle, just the most long lived and accurately reproduced.

I use the word "replicator" to refer to the entire auto-catalytic set
of chemicals, i.e. it's the system that synthesizes more copies of all
of its parts thereby replicating the complete system. Any one molecule
doesn't, all by itself without help, synthesize itself. So any one
molecule isn't a replicator.

Good point. This is, of course, also true for modern systems. DNA will
slowly denature unless it is subjected to repair and error correction.
But not all the elements of a replicating system need themselves be
reproduced with high fidelity (as they are not today). This means that a
replicator is only a subset of a larger system (which we knew), but also
that the boundary between it and the rest of the system is ill-defined.


(By comparison, with dislocation patterns of clay crystals, each such
dislocation pattern grows and then fragments thereby replicating itself
without any help. But a dislocation pattern isn't a molecule per se, so
this isn't a case of a single-molecule replicator.)

Early reaction species will not be acurately reproduced, but so long
as they exceed the threshold of accuracy needed to allow the cycles to
continue, there will be selection in a Malthusian reactor for more
accurate isomers and processes of reproduction.

We're in agreement that auto-catalytic sets will be sloppy, but all
that is needed is that sloppiness isn't so bad as to reduce effective
fecundity to less than one. (Whatever the particular set of chemicals
is, it must synthesize on the average more than one copy of itself
before the original decays.) We're in agreement that, given finite
food supply, there will be selection toward whichever replicator
achieves highest fecundity. But without a mechanism for incremental
mutation, whereby a replicator mutates to another replicator (not to
something ineffective), such natural selection reaches a "dead end"
whereby the best of existing replicators dominates the ocean and from
that point onward the only mutations are to less-fit stuff.

Unless there are equally high fidelity isoforms that can be attained. At
some point the combinatorial properties have to kick in - if not in the
base sequence, then in some manner. I have a pretty sparse knowledge of
biochemistry, but I'm thinking here of sugars, which have a number of
distinct isoforms based on different assemblies of the monosaccharides.

Prior to polymerization of replicators, the only mechanism I could
think of that might work would be micro-ecosystems of independent
replicators, whereby group selection for the micro-ecosystems would be
somewhat open-ended. If a new replicator invades such a micro-ecosystem
and becomes established, or if an old replicator goes extinct locally,
that would constitute an incremental mutation to the micro-ecosystem,
i.e. you're guaranteed to still have a set of replicators after the
mutation. That's different from a mutation of the actual chemical
species within a single isolated replicator which is most likely going
to destroy its ability to replicate. (Technically: If one of the
chemical species within a catalytic set is mutated, either it will no
longer be a catalyst at all, or it will catalyze some side reaction
that doesn't feed into the main cycle. In any case it won't catalyze
its own synthesis, so as soon as the single mutated molecule decays,
whatever effect happens will be gone.)

But is it the case that a mutant won't necessarily catalyse itself? I
mean by this (and speak from total ignorance) that if the other species
catalyse products that can catalyse the initial mutant, then there's no
reason to think that a mutant will simply evaporate.

I'm interested in whether we can have selection without a
hifi replicator, to explain why we *have* hifi replicators.

Last Summer I discussed "catalytic-type loops". The idea is that
several similar molecules act as generic catalysts for some type of
reaction, whereby different input ("food") results in different
reaction product, but all within some particular type of reaction
resulting in some particular type of reaction product. If some of the
reaction products are likewise generic catalysts, the sloppy
chemosynthesis chain extends another step. The idea is then to have a
complete loop (cycle) of such sloppy/generic catalysts.
{A1, A2, A3} -> {B1, B2, B3, B4} -> {C1, C2} -> {A1, A2, A3}
(That diagram shows only the catalysts, not the foods nor waste products
(A -> B means A catalyzes production of B, not A is converted to B.)
Note it might be more complicated than a simple loop. That's where we
get into auto-catalytic sets.

Note we have selection as soon as there is more than one different
auto-catalytic set competing for available food. That would tend to
drive all but one to extinction.

I'm not sure about this point. Have a feeling the two competing sets
would come in to equilibrium in inverse ratio to their respective
efficiencies.

Seems right to me also. But if one is more efficient than the other, and
mutants from *it* will sometimes be more efficient still, then the
result will be the same. Also, the relative efficiencies may still be
such that the more efficient one will end up at fixation.

I think Robert Maas's {A1, A2, A3} -> {B1, B2, B3, B4} -> {C1, C2} ->
{A1, A2, A3} system is very resistant to change. For a change from
say, B2 to B2' to set in and not be evanescent, there would have to be
simultaneous changes of say, C2 to C2', and A2 to A2'. You see here
all the information has to go all the way round the cycle. It would be
too much to expect that B2' causes exactly the change C2 to C2', and
that in turn causes exactly the change A2 to A2', which in turn causes
exactly the change B2 to B2', where B2' is our original mutation!

It is a very different model from having a master molecule which has a
tight loop with only itself in it - a polymer which templates itself.
Such a master molecule would have causal dead end branches off its
cycle, so that for example -> {B1, B2, B3, B4} -> {C1, C2} can happen,
where C1, C2 might be ingredients for the master molecule's template
copying process. In this way, the master molecule's information
content is directly determined by that of its predecessor, and it is
only the master molecule's (unordered)constituents that have to be in
the vicinity, albeit due indirectly to the master molecule's specific
catalytic properties.

Another point of variance between yourself and Robert Maas is that he
is entirely composing within chemical species space, whereas you are
presuming structure in actual space - a set of very slightly leaky
reaction vessels. I think this partitioning is a crucial idea. It has
to be possible for variants that aren't completely pulling their
weight, to have that fact reflected back on themselves. I.e. a lot of
little commons having their own tragedies, otherwise the whole show
couldn't go on for very long.

But there might not be direct
competition for the same food, in fact there might be a "food web"
whereby waste from one is food for another, which is beneficial to
both. So selection might eliminate some replictors while allowing
several others to survive in food webs. But until we have a mechanism
for incremetal mutation to introduce lots of new variety, this
selection wouldn't result in open-ended evolution, so it wouldn't
explain the eventual evolution of hi-fi replication.

there *has* to be an ecology from the very beginning - simple
autotrophs aren't sufficient.
I'm not sure what you mean by ecology. Normally the word presumes life
already existing. But if the chemical cascades from high-energy
sources count as an "ecology", then we're in agreement, at least in
regard to the direct production of auto-catalytic sets of chemicals, as
opposed to the theory of clay-crystals that only later undergo an
organic-chemical takeover.
If there are complex chemical reactions going on in the reactor chamber,
then the products and byproducts of other cycles will be utilised by our
target reaction cycle. This is a kind of ecology.

I don't see that happening until there are at least two different
replicators, which is not at the *very* beginning.

That depends. Why not have two from the very beginning? What makes us
have to assume that there could only be one single catalytic set? For
example, if you have an extended catalytic set where part of the set is
not strongly coupled to the products of another part, then you could
have a kind of ecological process.

So if we change your
word "very" to "near", we can be in agreement. Given a particular mix
of base chemicals, and some particular high-energy source, in some
local region, I see a particular stochastic process of exploring
various chemical cascades, eventually resulting in a catalytic chain
that closes on itself to form a loop, consuming the base chemicals and
their activated versions. If two near-simultaneous loops formed, they'd
probably compete for food, and only one would survive. But after one
replicator has grown exponentially to dominate that local habitat, it'd
drastically change the chemical content, so that later chemical
cascades would be exploring quite different kinds of reactions, so that
if and when a second catalytic loop forms it wouldn't directly compete
with the already-established first replicator for food, so it could
*also* survive. But the ecology of first and second replicator doesn't
happen until that second replicator occurs, which is a while after the
first replicator occurred, hence not at the *very* beginning (of the
age of replicators).

Two simultaneous loops would only compete if their chemistry were
identical or relied upon the same monomers for food. But I agree that is
unlikely, or at least hard to conceive. But what about very shortly
after the first catalytically closed set? If isoforms evolve in soem
kind of equilibrium, they will shortly begin to feed on each other's
products as well as the autotrophic reactions on the abiotic source
molecules. That's what I meant.


Another way that an ecology of replicators can happen is if two
different locales each generate their own first replicator, then after
each locale is totally full of copies of the corresponding replicator,
extra copies start spilling out to the ocean at large, with copies of
one replicator eventually reaching the locale of the other replicator.
Since the replicators formed in different locales, there might have
been different base chemicals in those locales, so the replicators eat
different food, so they might be able to co-exist in an ecology. But
again this doesn't happen at the *very* beginning.

It's hard to conceptualise this stuff - what counts as "the" beginning
will depend on what we think is important. I think the initial reactions
will have been very complex with different amounts of strong couplng
between reaction types.
--
John S. Wilkins, Postdoctoral Research Fellow, Biohumanities Project
University of Queensland - Blog: scienceblogs.com/evolvingthoughts
"He used... sarcasm. He knew all the tricks, dramatic irony, metaphor,
bathos, puns, parody, litotes and... satire. He was vicious."

.

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  • Re: I thought this NG was about Origins?
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