Re: PiP OOL 1 - Origin of Life == Emergence of Biochemistry

On Nov 28, 5:01 am, "Rolf" <r...@xxxxxxxx> wrote:
"Vend" <ven...@xxxxxxxxxxx> wrote in message

news:02f4b400-a466-4153-8cf8-2616ab7fcb01@xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx





On 27 Nov, 20:09, "Perplexed in Peoria" <jimmene...@xxxxxxxxxxxxx>
wrote:
This is the first of a planned series of postings in which I will
present some
details of my vision of an autotrophic, metabolism-first,
membrane-centric
account of abiogenesis. As has been the case with previous planned
posting series, this one may not reach completion if my motivation
peters out, but ... here goes. Blame Howard Hershey for getting me
started.

I want to begin by taking a fresh look at that old chestnut of a
question:
"What is an appropriate definition of life, for purposes of talking
about
the origin of life?". I'm going to provide a somewhat 'flip' answer to
this question. "'Life' originates at the same point in time at which
biochemistry emerges from chemistry." That is, if we were observing
the origin of life by using a time machine, we could say that life has
originated at the stage in the process where a chemist studying the
process would say "This ain't just chemistry anymore. What is
happening here is outside my field. We need to call in a biochemist."
Bear with me on this - my answer may grow on you.

Or maybe the process might undergo a kind of chemistry that nobody is
currently familiar with.
Organic chemistry is very complex, and scientists tend to specialize
to sub-fields of it that have some practical relevance. If life or
proto-life went through a kind of organic chemistry that is not widely
studied today, everybody would be puzzled.

The discipline of biochemistry is certainly based on chemistry, and
it reduces to chemistry. But it is not a subset of nor specialization
within chemistry. It is a separate discipline with its own methods
and traditions and with its own notion of what is important in the
phenomenon being studied.

And chemistry has different methods and traditions and notions of
importance than physics, nevertheless chemistry is epistemologically
just a sub-field of physics.

I think that the differences in practice and traditions exist for
historical and practical reasons, they don't necessarly denote a
difference in the goal and basic methodology.

Chemistry seeks to develop universal
laws - laws which should be applicable everywhere in the universe.
Biochemistry seeks to find local and contingent laws - it studies
life-as-we-know-it. Chemists eschew consideration of 'final cause'.
The molecules in their systems have no function or purpose - they
only have characteristic behaviors. Biochemists embrace a kind
of half-assed final cause or teleology - they are always ready to
ask (and answer) the question of "What is the function of this
molecule, this reaction, this process?" Biochemists can think in
terms of function only because the systems they study have been
selected by natural selection to have functions. Biochemical
systems are a tiny subset of the plethora of possible chemical
systems. Biochemical systems have a contingent evolutionary
history which is an important aspect of the explanation of those
systems. Chemists, for the most part, don't worry about history.

Ok.

An abiotic molecule exists because the laws of chemistry naturally
lead to its formation. A biochemical molecule exists because its
synthesis serves a function for some organism.

You sound like an IDist. :D

Its formation
requires both the laws of chemistry plus the vital interests of
some naturally selected organism. Chemists are interested in
all molecular species. Biochemists are interested mostly in
that rare subset of molecular species which also qualify as
'biochemicals'.

Many chemists are intersted in just some molecular species.

Now, it might be objected that my flip answer just transfers
the problem (of drawing a line of demarkation on a slippery
slope) from one viewpoint to another. There probably wasn't
a clear-cut point in time when you could say with assurance
"Formerly there was no life here; now there is life; life has
originated". And it is still probably the case that you can't say,
"This used to be ordinary chemistry, but now it is biochemistry."
But this objection misses the point.

The reason we want to look at the "What is life?" question is
not to draw a line of demarkation on a slippery slope. It
is instead to provide some illumination of the slope as a whole.
And the reason that I suggest that we think about the question
of "What is biochemistry, that we should be mindful of it?" is
because thinking about this question can provide a fresh
perspective on the sequence of steps leading from non-life to
life.

How does it do this? Well, let us simply produce a listing of
the 'laws of biochemistry" and then attempt to address the
question of how and when (ie. in what order) these laws
became laws. In fact, you get a pretty good sketch of a
testable hypothesis of abiogenesis just by listing some laws
that apply to life-as-we-know-it and hypothesizing some
particular order in which these laws actually became laws
in the course of abiogenesis.

I begin the process of doing so in my next posting - "Laws
of Biochemistry".

Ok.
But let me premptively warn about defining biochemistry as a sort of
teleological or pseudo-teleological chemistry.
I can identify the functions of the parts in my computer, I can even
identify the purpose, but I don't think that my computer is alive.

Put a computer inside a 'robot', make a program so it will find a live AC
outlet whenever its battery needs a recharge, and you will have life. The
only thing missing is reproduction. For reproductive life it takes
chemistry. Mechanical life probably never may reach a stage where
reproduction is possible. Cellular life probably is the only kind of
self-sustaining life possible. Simpler forms of life, like virus also
depends on cells for reproduction.

Although modern viruses and viroids are parasites that require a
living cell in order to replicate, one should keep in mind that the
simplest ones (like Q-beta phage) can replicate in cell-free systems
provided with a source of NTPs and a *single* enzyme function, the RNA
replicase (and the appropriate temperature, ionic conditions, etc.).
The RNA replicase, however, is composed of 4 protein subunits, the
alpha subunit is host-provided ribosome protein S1, the beta subunit
is phage encoded RNA replicase, the gamma and delta are host-provided
elongation factors Tu and Ts. It is likely that only part of each of
the host-provided proteins are relevant to phage replication.

In addition, there is another host-encoded protein called HF-I (host
factor I), which is required. It is involved, in the host, in rpoS
translation into an RNA polymerase regulatory sigma protein involved
in the stress response. However, in bacteria which have had this gene
deleted, q-beta phage can evolve to replicate efficiently (both in
vivo and in vitro) in the absence of HF-I, as the last reference below
shows.

A Muffler, D Fischer, R Hengge-Aronis - Genes and Development, 1996 -
Cold Spring Harbor Lab
M Kajitani, A Ishihama - Nucleic Acids Research, 1991 -
pubmedcentral.nih.gov

http://www.pnas.org/cgi/content/abstract/94/19/10239

That means a *known* genome that requires (currently) a minimum of 4
proteins (3 of them host proteins) acting together to produce a single
enzymatic *function*.

In fact, these phage 'evolve' in acellular systems (rich in NTPs) in
ways that favor even smaller viruses. Viruses (especially the simpler
ones) and viroids typically only need a very small subset of cellular
*functions* for their replication. It might be worthwhile to
consider, rather than the requirement for a living cell, the
functional requirements for their replication.

It is also worth pointing out that many of the enzymatic *functions*
(RNA polymerase, PNK, RNA ligase) that viruses need to replicate can
be found in ribozymes as well as in proteins. And can be found in
randomly generated oligonucleotide sequences.

So, if you consider viruses to be "living systems", the proper answer
to how many enzymatic functions you need to replicate a minimal
'living system' that was like a virus would be somewhere between one
(the entire multimeric structure) and four (the four independent
units) if the RNAs acted as both genome and enzyme.

[snip]

.

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