Re: Minimum Cell?


"hersheyh" <hersheyhv@xxxxxxxxx> wrote:
"Perplexed in Peoria" <jimmene...@xxxxxxxxxxxxx> wrote:
"hersheyh" <hershe...@xxxxxxxxx> wrote:
PiP wrote:
[snip]
If one is thinking of metabolism first model, even that pathway to a
"living system" would probably involve a form of 'replication'. One
that was probably more along the line of prion 'replication' or the
replication of the cortex subunits of paramecia. That is, something
more akin to crystal formation or multimeric protein assembly than the
template-copy mechanism of nucleotides.

It is interesting that the only kind of informational systems you can
imagine have something to do with geometry and/or conformation.

Actually, chemical or physical affinity is involved in the attraction
to produce multimers in modern transmembrane proteins. That is what
is also involved in crystal formation. The geometry of such
affinities is determined by the chemical or physical affinities. I
would imagine the same in abiogenic proteins/proteinoids and lipids.

True. I'm not saying that stereochemistry is unimportant. Only that
the *information inheritance* need not be based on some kind of
geometric or tesselation principle.

Our imaginations are indeed constrained by what we already know
about how things work today.

The prion model strikes me as a non-starter. The prion is a macro-molecule
which does nothing to catalyze the formation of its own primary sequence -
it only catalyzes the formation of its own secondary structure - and provides
only one bit of heritable information in doing so. You would need lots and
lots of different specific macromolecular sequences with this fairly special
property to somehow be produced abiotically to have lots and lots of
bits of info in your genome.

Not necessarily. Most amino acid sequences that have biological
relevance do not produce random structures. They form alpha helixes
or beta sheets. These often have affinities that are not completely a
function of particular aa sequence. So a system that can force
particular secondary structures that meet particular needs when
sequences differ slightly and can be forced may be important. We are
talking about abiogenic (and at least quasi-random) sequences at this
point. Secondary (and tertiary) structure is more relevant to
function even in today's proteins.

And I claim that there was never a stage in abiogenesis in which abiogenic,
quasi-random sequences were important, or even present. Life originated
with essentially no macromolecules - in fact, without any condensation
(ie. hydrolyzable) bonds between 'building blocks'. Or at least, very few.

And nucleotides, of course, *naturally* hydrogen bond appropriately in
a template-copy fashion at certain temperatures, even in the absence
of enzymes. That is, in fact, what much of molecular biology gene
synthesis technology has relied on.

Yes. But I claim that things like WC base-pairing require the prior
presence of a biological metabolism producing lots and lots of
precisely 'machined', interchangeable parts thingies. Almost all
'good' thingies and almost no 'bad' thingies. Abiotic processes
cannot produce the 'quality control' to make this 'natural' bonding
work. Selection of a few kinds of 'good' molecular species from a huge
library of mixed good and bad molecules is not a 'natural geological
process'.

[snip]

My current favorite scheme for pre-RNA 'genetics' is quite simple and
has nothing to do with geometry. The genome is simply the set of
active autocatalytic cycles. (If the molecular species constituting the
elements of the cycle are present, the cycle 'cycles' (is 'active') and
you continually refresh the presence of the cycle elements. But if
those molecular species are not present, then the cycle is inactive
and will remain inactive until some fluke 'mutation' makes at least
one molecule of those species available within the restricted region
of space constituting the 'organism'.)

I certainly do not regard such a "metabolism first" system as
impossible. But because a membrane-based system (which would be
abiogenic in a metabolism-first model)

I wouldn't call it abiogenic. I'm talking about an autotrophic system.
Something like what Wachtershauser proposes. No absorption of
abiogenic lipids from a 'soup'.

requires some combination of
lipids and proteins or proteinoids (to be semi-permeable)

Why do you keep suggesting that semipermeability requires the presence
of peptides? Just not so. If a membrane with carbon chains of length
16 is too impermeable for you, try one with carbon chains of length
14. Or one in which some ether molecules are dissolved. Blanket claims
that lipids just don't give you enough selective permeability - you have
to have some peptides from day one - such claims must be based on the
properties of laboratory membranes made from refined modern phospho-lipids.

and has to
have some ability to 'selectively' reproduce, I would suggest that the
ability to accumulate particular types of proteins (not necessarily
identical sequences) because of a 'natural' affinity of certain
protein secondary (tertiary?) structures for each other in the
floating sea of a lipid bilayer would be crucial. IOW, pre-biotic
metabolism has to be based on specific enzymatically useful
macromolecules if you want it to be a result of a transmembrane
(specifically a semi-permeable membrane) proton or other type of
gradient.

No it doesn't. I claim life started without macromolecules of any
kind. More on this below.

And, needless to say, it must be capable of being co-opted
by and replaced by a genetic system at some point.

Of course. I see this as being similar to the RNA-world co-option
of ribozymes by enzymes. Same metabolic reactions are taking
place, but a better, more efficient or more specific catalyst is used.

[snip]
However, I do not concede that the only possible kind of biological
information requires the presence of individual information-bearing
molecules. I think that there is another way - a more primitive way.
A way in which the information is a collective property of the organism
as a whole and cannot be reduced to individual molecules.

Only if one is thinking of a "system" that self-assembles in the
fashion of a multimeric protein or a transmembrane pore. That
probably requires that random polymerization (of proteinoids or
nucleotides or whatever has the ability to metabolize) is less
'random' than the random sequences that are generated in modern labs.
That certainly is possible.

Another unwarranted assumption here. That metabolism requires the
presence of specific macromolecules to serve as catalysts.

As opposed to...? Metabolism not based on macromolecules?

Yes.

Or not based on specific catalytic activities?

No. Pretty good effective specificities from day 1. About the only way in
which it is not specific is that there is not much difference between a lipid
with (say) a 14-carbon hydrophobic tail and one with a 15-carbon tail. All
metabolic reactions take place at the hydrophilic surface of the lipid
membrane (hydrophilic end of the molecules). And that is where the
specificity is most important.

If the former and if you are
proposing a metabolism based on the inside/outside differences of semi-
permeable membranes, I would think that macromolecules would be needed
to generate a semi-permeable membrane. And I don't think lipids alone
would work well.

Disagree.

And metabolism certainly doesn't involve random
activities; it requires specific activities.

Fully agree.

[snip remainder]

Howard, if you are interested in continuing, I can provide more details on
my viewpoint on abiogenesis. But it should probably appear in another
thread. If you can provide some specific questions and objections to
what you have seen so far, that might help to structure my presentation.

Or, we can just agree to disagree.

.

Relevant Pages

  • Re: Minimum Cell?
    ... to produce multimers in modern transmembrane proteins. ... sequences differ slightly and can be forced may be important. ... Or one in which some ether molecules are dissolved. ... metabolism has to be based on specific enzymatically useful ...
    (talk.origins)
  • Re: Minimum Cell?
    ... to produce multimers in modern transmembrane proteins. ... sequences differ slightly and can be forced may be important. ... Or one in which some ether molecules are dissolved. ... metabolism has to be based on specific enzymatically useful ...
    (talk.origins)
  • Re: Minimum Cell?
    ... 'reproduction' and metabolism. ... (activated nucleotides) ... to produce multimers in modern transmembrane proteins. ... But any model of abiogenesis would ...
    (talk.origins)
  • Re: Minimum Cell?
    ... Lipid bilayers, *if* ... 'reproduction' and metabolism. ... Organisms reproduce; molecules (or maybe ... was more likely to be a mixed proteinoid/lipid membrane that naturally ...
    (talk.origins)
  • Re: News: Telepathic Genes Recognize Similarities In Each Other
    ... similarities in each other from a distance, without any proteins or other ... biological molecules aiding the process, ... This new study shows that genes -- which are parts of double-stranded DNA ...
    (sci.bio.evolution)