From: lambdac-AT-globalserve.net
Date: Fri, 22 Sep 2000 16:57:34 -0500
Subject: 8. The problem of the origins of Life


8. The problem of the origins of Life
Date: Sun, 17 May 1998 14:23:39 -0500
From:  lambdac-AT-globalserve.net
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Date: Sun, 17 May 1998 14:23:18 -0500
From: lambdac-AT-globalserve.net
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(c) 1998 Correa&Correa

A NIETZSCHEAN CRITIQUE OF EVOLUTIONISM, OLD AND NEW
(Doing harm to evolutionism)

8.  The problem of the origins of Life

	Neo-evolutionism evidently must uphold the principle that, if the
mutable material is not DNA , or at least not exclusively DNA - as was
once hoped - it must nevertheless be restricted to nucleic acids.  This
last redoubt is essential if we are to hold onto a revised 'central
dogma'.  Molecular biologists retrenched here - and the discovery of the
autocatalytic properties of RNA  by T. Cech went a long way to
re-establish some confidence in such a revised dogma.  Cech's discovery
even revived Crick and Orgel's late-sixties' theory that the origin of
ribosomes and transfer RNA might hold the key to the origin of life.  

	But all of a sudden, the neat and absolute separation between catalytic
metabolic functions - the enzymatic domain - on one hand, and genetic
functions - the domain of replication - on the other, began to blur. 
Enzymes still required genes, but genes or their transcripts now
appeared to become somewhat independent of enzymes - since they could be
said to have by themselves a catalytic action.  Once RNA sequences,
known as ribozymes, were shown to have ligase enzymatic action capable
of permitting their self-assemblage in complementary oligomers,
molecular geneticists were ready to do away with the world of proteins. 
This finding was immediately exploited by F. Crick - never one to miss a
good opportunity - and gave rise to the brief biological fad of the late
eighties and early nineties known as "the RNA world" (coined by
Harvard's biologist W. Gilbert).  It also provided a way out for
Crickand Orgel from having to assume their own silly variation of
Panspermia - in the words of A. Lehninger, that "genes and the genetic
code may have been brought to earth by spaceship from some other body in
the universe where intelligent life had already evolved" (Biochemistry,
p. 1052).  
	(...)
	With the revitalizing of the gene-hypothesis of life without proteins,
RNA was now seized upon as the first self-replicating molecule capable,
in Gilbert's words, of "performing the catalytic activities necessary to
assemble [itself] from a nucleotide soup" ("The RNA world", Nature,
1986, 319:618).  The 'new' hypothesis appeared to provide an escape from
the chicken-or-egg problem of which came first - proteins or their
genes? Neither DNA nor proteins had come first, but RNA, in a world all
of its own where, in the words of L. Orgel, it would have "functioned
both as a genetic material and as a source of functional enzymes
(ribozymes)", while subject to a randomistic process of Darwinian
selection.  This also appeared to tally with the fact that
deoxyribonucleotides are made from precursor ribonucleotides.

	Gone were the fears of the omnipresent RNAses which so derange bench
workers.  Gone were the considerations of the chemical fragility of RNA
and its difficulties in abiotic synthesis.  Gone were the fears now
fully justified (by C. Woese and O. Kandler) that replication of RNA is
a 'late evolutionary development'.  (...)  Decades of effort searching
for an enzyme-free polynucleotide system capable of undergoing cyclic
replication have not yielded a single successful molecular system that
could be construed as being absolutely independent from proteins.  Even
Ferris' positively charged montmorillonite clay only succeeded in
polymerizing RNA chains that were 55 nucleotides long.  The
complementary oligomers that result from such template-directed
synthesis are, in the best of cases, degenerate templates, and the
probability of forming uncontaminated RNA strands of any significant
size is thereby precluded.  Eventually, and most recently, even Orgel
abandoned the hypothesis.
	(...)
	This takes us to the real problem of interest in all this - the very
problem of the articulations between polypeptides and oligonucleotides,
a problem which has been in the mind of every biologist since the Miller
'primordial soup' experiments in 1953 demonstrated the spontaneous
catalysis of amino acids when a high voltage was passed through an
atmosphere rich in methane, ammonia and water, which was exposed to a
liquid phase to form a broth.  Since then, almost all of the essential
amino acids, as well as the purine and pyrimidine bases of DNA and RNA
have been produced in comparable simulations of prebiotic conditions.  

	The problem is succinctly summarized by Lehninger -

"Apart from the fact that all hydrophobic amino-acids are coded by
triplets whose second base is U [Uracil] there is little evidence that
the coding triplets bear any steric or chemical relationship to the
amino acids they code.  Model-building experiments have simply not
revealed a satisfactory picture of the molecular correspondence between
amino acids and their codons" ("Biochemistry", p. 1052.).

	This is precisely what led Monod and others to view the articulation
between amino-acids and their codons as a matter of absolute chance or a
'frozen accident", where no information could be imparted in reverse
from the amino-acids to ribonucleotide oligomers.  But this postulate
may be tantamount to nothing else but an acknowledgement of the
incapacity of present-day mechanistic biochemistry to account for the
specificity of codons for their amino-acids.  The problem is that the
emergence of defined cells in a broth - the differential cellularization
of the broth - already presupposes a catalytic machinery churning out
the macromolecular building blocks, the carbohydrates, the lipids,
amino-acids and nucleotides.  In other words, for cellularization to
become possible, any prebiotic soup - including all of its catalytic
surfaces - will already have to have a metabolism all its own - and one
cannot legitimately proceed to artificially isolate a class of molecules
and their reactions if the intent is to study the spontaneous
articulation between different classes of molecules which underlies the
emergence of life.  This then is the problem of the energetics and the
biochemistry of the broth.
	      (...)
	The core of the problem of evolutionism or neo-evolutionism stems from
our still poor understanding of the energetic functions of
polypeptides.  Even Monod's concept of *an absolute or essential chance*
was enunciated to somehow address  the interrelationship of these
functions.  Monod, the discoverer of induced gene transcription and
enzyme production, had to admit that 'whereas natural selection operates
*upon* the products of chance", the domain where it operates is a
"domain where chance is barred" (Chance and Necessity, p. 118), the
energetic domain of protein activity, the domain of 'necessity', the
catalytic and metabolic domains of energetic functioning through
non-covalent bonds and stereoscopic fits between enzymes and
substrates.  The essential character of chance at this level secured,
from Monod's perspective, an absolute impossibility of any direct 'flow
of information' between proteins and oligonucleotides.  Clearly,
neo-Darwinism could depart from Spencer's 'struggle for existence' with
impunity by making the differential rate of reproduction the decisive
factor in natural selection, but it had to stick to a minimalist
position - to the paradigm of an absolutely fortuitous predominance of
the teleonomic apparatus over autonomous morphogenesis.  The new limit
of the revised dogma should prevent its leakiness.  The prebiotic notion
of an RNA world fitted this criterion like a glove - and that is how, in
the words of G. Olsen, 'RNA chauvinism' came to dominate textbooks on
the origins of life.  
	(...)
	For a Lamarckian, what this implies is that one must go still further -
and seize the domain of experimentation that operates beyond chance,
even absolute chance, the domain of so-called necessity as the domain of
activity, as the plane of assemblage.  For after all, in the problem of
specific mutations during the stationary phase of bacteria and yeast,
what causes the stress condition is marked by the sign of the
laboratorial artifice; seen from another angle, from a positive
perspective, it is the stimulatory role of the substrate and its
variability that it calls into play in order to assert variation.  No
amount of autocatalytic mechanisms for the nucleic acids can avoid the
substrate-dependent specificity of postadaptive mutation: only specific
loci are affected, and the process cannot be construed as randomistic,
even if it has a discrete zone of randomness in the internal
experimentation performed by each cell's sensing and catalytic
machinery.  But, essentially, we are here confronted, as we are when we
address the problem of the origin of life, with the biophysical unknown
- how amino-acids 'talk back' (or 'act forward') upon nucleic acids -
precisely what the RNA world hypothesis sought to invalidate as a field
deserving of research.

	Furthermore, if RNA is today seen to have acquired an enzymatic action,
so have polypeptides been reported that are capable of
self-replication!  First reported by D. Lee et al in Nature, 1996
(382:525), for an a-helix 32 residue polypeptide that can catalyze with
high specificity (85% yield) its own synthesis (by isocatalytic coupling
to its template) from a peptide soup, this protein function constitutes
a replicative property not present in DNA - which relies instead upon a
web of connections with specific enzymes in order to assure its own
replication.  "The jealously conservative properties of the replicative
mechanism' (Monod, op. cit., p. 121) no longer seem so exclusive.  

	Even though biochemists still speak of reproduction at this level, it
is clear that function and formation, production and reproduction,
assemblage and replication have, at this level, become
indistinguishable.  If the prebiotic soup forms an instance of chaos,
this chaos can no longer be seen as the image of disorder - simply
because we cannot grasp its complexity.  
	(...)  
	The prebiotic machine must be understood as an energy machine - and not
just in the biochemical sense, but above all in the bioenergetic sense,
as a machine of capture of the electric energy of the aether.  Order and
disorder are the two properties of potential that coexist in the chaos
of the prebiotic soup, and we cannot effectively think the production of
bases, and their combination with sugars and phosphates independently
from the production of amino-acids, from their polymerization, folding
and self-replication.  

	One cannot afford therefore to reduce the organic of prebiotic soups to
privileged roles, whether these are negatively charged micelles (K.
Nägeli, Oparin, Fox, Orgel), clay surfaces (Ferris, Zubay), iron-pyrite
surfaces (Wächtershäuser), thioesters and coenzyme A (Miller) or still
others.  Undoubtedly, there is a critical role for coenzymes and
proto-prosthetic groups as autocatalysts and heterocatalysts of other
coenzymes - the evidence for this is remarkable..  But all these
elements will have played a role trying to wrench from the prebiotic
chaos an articulation between the catalytic action of polypeptides and
the replicative properties of nucleic acid chains in the context of
sustaining an energy flux.  

	To paraphrase A. Szent-Gyorgyi - what is missing is an electronic or
submolecular biology, and maybe even a pre-electronic (an electrostatic)
biology of prebiotic soups.  In the process of getting there, most myths
of the primordial atmosphere and its liquid phase will probably crumble:
the primordial atmosphere will be seen to have more molecular oxygen
than is assumed - and without detriment to the results of organic
synthesis obtained by Miller and Urey with methane and ammonia; aerobes
will no longer be seen to have developed from anaerobes; the
laevorotatory properties of all essential amino-acids will be explained
by the affinity of enzymatic action, including proto-enzymes like
coenzyme A for massfree negative energy, just as the electron's polar
spin stems from the same affinity; hydrocarbon and lipid layers will be
understood to form on mineral catalytic surfaces - and maybe it will
even become clear that before the age of prebiotic carbon, silicium had
already played a prebiotic role, in clay and other silicates, by
catalyzing the carbon backbones of lipids, nucleic acids and
polypeptides in the presence of high thermal energy (eg the archaic
bacteria on the edge of modern volcanoes).  
	(...)
	It is, in our view, more than likely that eventually evolutionary
biology will reach the conclusion that Life, under the conditions of the
primordial earth and the proto-atmosphere was an inevitability, and that
inevitabilities are the domain of absolute chance and prodigality - the
prodigality of the massfree Aether that forms both Matter and Life, as
well as all their functions.  As P. Cohen wrote in the New Scientist
while describing Kauffman's views-

	"The emergence of life wasn't some chance event, but something that was
bound to happen under the conditions of the primitive Earth".


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