Re: Minimum Cell?


"Nic" <harrisondalen@xxxxxxxxxxx> wrote:
On 28 Nov, 02:35, "Perplexed in Peoria" <jimmene...@xxxxxxxxxxxxx>
wrote:
"Nic" <harrisonda...@xxxxxxxxxxx> wrote:
On 27 Nov, 04:38, "Perplexed in Peoria" <jimmene...@xxxxxxxxxxxxx>
wrote:
"John Wilkins" <j.wilki...@xxxxxxxxx> wrote:
Perplexed in Peoria <jimmene...@xxxxxxxxxxxxx> wrote:

"Nic" <harrisonda...@xxxxxxxxxxx> wrote...
On 26 Nov, 02:49, "Perplexed in Peoria" <jimmene...@xxxxxxxxxxxxx>
wrote:
"Nic" <harrisonda...@xxxxxxxxxxx> wrote:
[snip]
I could (in desperation) conceive of 'plain, run of the mill
chemistry' resulting in a metabolism-only system. Why not? Chemical
species space is just as valid a space as that of cellular
compartments.

There is heritable variation within a biological species or population.
I don't see how a chemical species has variation,

It doesn't, or we call it a different species. As far as I can see,
autocatalytic sets are super-stable - they aren't going anywhere
incrementally, and by the same token could not have come from
somewhere incrementally. I only mention them because you can't
literally have compartments first, can you? (That's just a line in
devils' advocacy!)

I prefer to speak of autocatalytic cycles rather than autocatalytic sets.
And cycles are not perfectly stable. Secondary cycles can arise
to parasitize the primary cycle. And then tertiary innovations can
suppress the parasites. You can have a fairly active and unpredictable
dynamics over evolutionary time.

I'm goign to expose my total lack of knowledge of chemistry here, but
isn't it possible there are isomers of components of a given
autocatalytic cycle? That is, variations in the causal reaction that
might permit the cycle *itself* to evolve over time? [This is, I hope,
agreement with PiP]

Sorry, John. Your words don't create a clear enough picture in my
mind so that I can either agree or disagree. But here is my attempt:

I would say that a cycle doesn't evolve - it is a platonic mathematical
object which can be represented by labeled nodes and arcs on a
sheet of paper. It just *exists*.

However, it is possible to have two distinct cycles which differ only in
that all of the molecular species in one cycle differ from the matching
species in the other cycle only in some trivial way - say by having an
added methyl group. Same reaction mechanisms, same catalysts -
in a sense the same reactions and even the 'same' cycle. Yes, that
could easily happen, and one could imagine an evolution from a
situation in which you start with the cycle 100% without the methyl
groups, but then a change in the nature of the feedstocks gradually
moves you through 50-50 to a cycle in which the molecules are
100% methylated.

I wan't thinking along quite those lines when I said I thought
credible autocatalytic cycles would be highly resistant to change
(i.e. so much so that it would be quicker to start over again).

I understand the idea to be something like:

A -> B -> C -> ... -> Y -> Z -> A (again)

Errr... Did you mean to have the cycle terminate with two molecules
of A? If not, then your cycle hasn't accomplished anything except
to generate heat. Or as da Vinci might have put it, "Your cycle is
naught but a machine for turning food into shit."

The 'again' in parenthesis is a sort of "which brings us back to
doh" (apologies to Julie Andrews and Homer Simpson alike). But you
make a good point - a gain slightly greater than unity is a necessity
here.

Anyway, you get what I mean, as your next comments below show.

Obviously this leaves out side branches showing fuel entering and
combustion products leaving.

In that cycle each (or some) of the '->' are catalysed by a molecule
somewhere else in the set. Eg. J -> K happens correctly just because
C and P are floating about.

Yes, I see the reason for the confusion. There are two different notions
of 'autocatalysis' floating around out there, and they are sometimes confused.

One is the idea of an 'autocatalytic set' as popularized, for example, by
Stuart Kauffman. In this one you have a set of synthetic reactions and
a set of product molecules with the property that every reaction in
the set is catalyzed by one of the product molecules in the set. But there
is no requirement that the set of products and reactions be arrangeable
in cycles. It can be a directed acyclic graph. It doesn't even need to
be connected.

Yes. Directed graph is more what I had in mind - I just did a cyclic
alphabet for symplicity's sake.

The notion of an 'autocatalytic cycle' is older and makes use of a
more general notion of catalysis. Here you have a cycle of reactions,
much like your A to Z and back to A above. That gives you a simple
catalytic cycle:
A + foodstuffs -> A + wasteproducts
Furthermore, it is assumed that each of the reactions in the cycle is
spontaneous - that is they don't require extraneous catalysts. But notice
that A is functioning as a catalyst here. When A is present, you have
the simplified net reaction
foodstuffs -> wasteproducts
This net reaction requires that A be present to run at any detectable speed.
But the reaction returns a molecule of A at the end. Hence A is functioning
as a catalyst. It is unchanged by the reaction sequence.

Now change the reaction scheme, as I suggested above, so that the total
result is:
A + foodstuffs -> 2A + wasteproducts
Again, cancel an A from both sides so that the net reaction is
foodstuffs -> A + wasteproducts
Notice that A is still functioning as a catalyst here - the reaction won't
happen unless some A is present. But now A is catalyzing its own
production. And if you look at it a bit differently, so is B and C and
... Z. Each of them serves as an "autocatalyst", as long as the reactions
of the cycle don't require catalysts in the usual sense and as long as
the foodstuffs are available.

That completes the clarification, but there is one more point I would
like to make here.

Thanks for the clarification. If I've got it, you mean there are
certain soupy conditions which may be called 'A amplifiers' even
though the chances of an A coming together spontaneously are remote,
and the amplifier's gain is paltry. Nevertheless, these conditions
can wait, as they don't depend on A. In that situation I guess the
action would happen quite quickly, especially on a planetary scale,
even with immense odds against A arising spontaneously. It would be a
case of no A at noon, one A at five past, and a planet-full by
tomorrow lunch.

You've got the idea, though of course in the real world you won't rapidly
fill the planet because you will locally exhaust the available foodstuffs
fairly quickly and will have to rely on diffusion and other abiotic processes
to replenish them.

I lump this case together with other cases of temporarily delayed
transition to inevitable stability, which is not what I think life is
about (despite or as well as remarks in other threads).


It is an odd fact of biochemistry that every set
of reactions which uses only inorganic 'foodstuffs' to build organic
molecules includes an autocatalytic cycle in the second sense. There
are no reactions in biochemistry capable of building biochemicals
'from scratch'. They all require that you add inorganics to pre-existing
biochemicals in a series of cyclic reactions with the net result being
one more biochemical than you started with. With all the enzymes
in the world available for free, you can't make a simple sugar unless
you have at least one sugar molecule to start with. This rather odd
and not-usually-empahsized 'law of biochemistry' is (IMHO) an
important clue for abiogenesis theorists.

That seems to be saying that at least one catlyst needs to be an
organic one? Or do you mean at least one foodstuff needs to be an
organic one? I guess not the later, as you seem to be against
heterotrophy-first.

One intermediate metabolite feeding into each reaction has to be
organic. There are no reactions in biochemistry in which all of
the substrates are inorganic (i.e. without any carbon-carbon bonds)
yet at least one of the products is organic. New carbon-carbon
bonds can be formed only if carbon-carbon bonds already exist
in at least one of the inputs.

And, yes, this means that the first organic molecule in abiogenesis
had to be formed abiotically - just like the first organism had to.
My autotrophy claim is (roughly) that the second and all later
organic molecules arose from the rule-breaking first molecule.

[snip]

.

Relevant Pages

  • Re: Minimum Cell?
    ... to parasitize the primary cycle. ... Same reaction mechanisms, same catalysts - ... Did you mean to have the cycle terminate with two molecules ... spontaneous - that is they don't require extraneous catalysts. ...
    (talk.origins)
  • Re: Minimum Cell?
    ... to parasitize the primary cycle. ... Same reaction mechanisms, same catalysts - ... Did you mean to have the cycle terminate with two molecules ... spontaneous - that is they don't require extraneous catalysts. ...
    (talk.origins)
  • Re: Minimum Cell?
    ... to parasitize the primary cycle. ... Same reaction mechanisms, same catalysts - ... that A is functioning as a catalyst here. ... biochemicals in a series of cyclic reactions with the net result being ...
    (talk.origins)
  • Re: Miller on Submarine Vents
    ... forced a reaction the reaction might be ... perform chemosynthesis of the next chemical in the cycle. ... temperature range, whereas the very first chemical cycles were chance ... chemicals at both ends of the link. ...
    (sci.bio.evolution)
  • Re: Minimum Cell?
    ... I don't see how a chemical species has variation, ... to parasitize the primary cycle. ... added methyl group. ... moves you through 50-50 to a cycle in which the molecules are ...
    (talk.origins)