>
> >SJ>Indeed, Davies, in his "Fifth Miracle", which Behe was reviewing,
> >>rejects Fox's proteinoids:
>
> KO>Because of three misconceptions and factual errors.
>
> >SJ>"One possible escape route from the strictures of the second law is to
> >>depart from thermodynamic equilibrium conditions. The American
> >>biochemist Sidney Fox has investigated what happens when a mixture of
> >>amino acids is strongly heated. By driving out the water as steam....
>
> KO>Misconception 1: This is not what happens during thermal
> >copolymerization, even at higher temperatures. At any temperature, the
> >mixture must first be dry. At low temperatures (under 100 degrees C),
> >glycine acts as a solid matrix that catalyzes the formation of the
peptide
> >bonds by isolating the water molecules produced by the reaction. At
> >higher temperatures (above 100 degrees C) aspartate and glutamate melt
> >and form intermediate structures that readily form peptide bonds with the
> >other amino acids, as well as catalyze the formation of peptide bonds
> >using acid catalysis, in which water actually helps the formation of
> >subsequent bonds. During this process, aspartate and glutamate revert to
> >their normal amino acid form.
>
> In the above Kevin does not contradict what Davies said. This appears to
> be a debating tactic of Kevin's to respond to an objection by saying
> something complicated and different, which looks like it is an answer, but
> is really just a change of subject!
>
It's not a change of subject, as Steve well knows. Davies was describing the
process by which thermal copolymerization was supposed to work. He
description was that, when the heat overcame the thermodynamic resistence to
the two amino acids joining, the water released during the polymerization
reaction was driven off by the heat as steam to prevent it from hydrolyzing
the new bond. This does not happen, hence Davies description is wrong. In
fact, the water created by the polymerization process is not driven off, but
retained by the molten mass, and in some cases is used to help form the next
bond. So what I said before, and what I am saying now, very definately does
contradict what Davies said. Steve didn't recognize that because he did not
understand the physiochemical processes I was describing.
>
> And while we are on the topic of "aspartate and glutamate", Yockey points
> out that Fox's `proteinoid' scenario "reaction requires a large excess of
> Asp and Glu, whereas it is well known that Gly and Ala are by far the most
> abundant amino acids under the presumed prebiotic conditions":
>
> "Sidney Fox and his disciples have championed the 'proteinoid' scenario
for
> the origin of life, a latter-day form of Oparin's coacervate paradigm.
They
> used the well-known reaction of heating amino acids to 150- 180 degrees
> C...These 'proteinoid microspheres are prepared by heating a mixture of
> amino acids that must contain a large proportion of Asp and Glu together
> with other proteinous amino acids in various proportions. This mixture is
> heated for 2-5 hours at 180 degrees C. At the end of this time a 1 %
> solution of NaCl is poured slowly over the mixture and boiled for 30
> seconds. When the solution is cooled one may see under the microscope
> numerous spheres of material'. This reaction requires a large excess of
Asp
> and Glu, whereas it is well known that Gly and Ala are by far the most
> abundant amino acids under the presumed prebiotic conditions." (Yockey
> H.P., 1992, p267).
>
> This is "Misconception 1" on Kevin's part!
>
I've already dealt with this in previous posts, posts Steve has already
received (I sent copies to him as well as to the listserv). So unless Steve
has avoided reading them yet, he is deliberately ignoring my previous
comments that clearly refute these claims.
In any event, the misconception is not mine, but Yockey's. Thermal proteins
can be synthesized at any temperature between 50 and 200 degrees; the
reaction does not require a large excess of aspartate and glutamate;
aspartate and glutamate can be made in simulated prebiotic experiments in
amounts large enough to meet the requirements of a thermal copolymerizations
reaction; and glycine itself appears to be able to catalyze the production of
thermal proteins.
The fact that Steve does not want to acknowledge these realities that refute
Yockey does not make them misconceptions on my part, despite Steve's claim.
>
> >SJ>...the linkage of amino acids into peptide chains becomes much
> >>more likely. The thermal energy flow generates the necessary entropy
> >>to comply with the second law. Fox has produced some quite long
> >>polypeptides, which he terms "proteinoids', using this method.
> >>Unfortunately, the resemblance between Fox's proteinoids and real
> >>proteins is rather superficial.
>
> KO>Misconception 2: The research demonstrates that this is incorrect.
>
> At all the critical points, Kevin just makes assertions with no *evidence*
> backed by references.
>
Since Steve already knows what this evidence is, he doesn't need me to
provide it for him. And since I have on at least three occasions now
provided references that contain the necessary evidence, I have backed up my
"assertions" with evidence from references; I just do not choose to choke my
posts with hideously long quotations when anyone can look up the references I
provide and read the evidence for themselves.
>
> *What* "research" exactly is it which "demonstrates that this is incorrect"
> i.e. "the resemblance between Fox's proteinoids and real proteins is...
> superficial"?
>
Again, Steve already knows what this evidence is, so he is being hypocritical
by pretending her doesn't. As for the rest of the group, see Fox and Dose
(1977) _Molecular Evolution and the Origin of Life_, Revised Edition, for
more details. In essence the best evidence demonstrating that thermal
proteins are real proteins is that thermal proteins are polymers of specific
sequences of amino acids linked by the peptide bond that possess specific
catalytic functions, which is the definition for any protein, contemporary or
prebiotic.
>
> Absent such evidence backed by references, this is *Kevin's* "Misconception
> 2"!
>
Again, since Steve already knows what this evidence is, and since I have
provided references that contain the evidence for anyone to read for
themselves, Steve is trying to hypocritically create a strawman argument so
that he can avoid having to discuss that evidence.
>
> >SJ>For example, real proteins are made exclusively of left-handed
> >>amino acids (see p. 42), whereas proteinoids are an equal mixture of
> >>left and right.
>
> KO>Irrelevant. **Modern** proteins are made exclusively of L-amino
> >acids, but real proteins are nothing more than chains of amino acids
linked
> >by the peptide bond. Whether the amino acids are L-, D- or a mixture of
> >both is immaterial to real proteins.
>
> Here Kevin is just redefining proteins as "modern proteins" and
polypeptides
> (ie. "chains of amino acids linked by the peptide bond") as "real
proteins".
>
No I am not, though Steve in his ignorance may think so. Proteins and
polypeptides are the same thing; both are nothing more than chains of amino
acids linked by the peptide bond. Any polymer of amino acids linked by the
peptide bond is a real protein, regardless of whether those amino acids are
all L-isomers, all D- or a mixture of the two, and regardless of whether the
peptide bond is an alpha-, beta-, gamma- or epsilon-peptide bond. Modern
proteins are real proteins that are made exclusively of L-amino acids linked
by alpha-peptide bonds, whereas thermal proteins are real proteins that can
contain D-amino acids and can be linked by beta- and epsilon-peptide bonds.
>
> Kevin would need to demonstrate that there is a distinction between
> "modern proteins" and "real proteins" made in the mainstream biochemical
> and molecular biological literature and that the majority of biochemists
> and molecular biologists agree on that distinction.
>
That would be like asking me to demonstrate that there is a distinction
between proteins and polypeptides made in the mainstream biochemical and
molecular biological literature and that the majority of biochemists and
molecular biologists agree on that distinction. Such a distinction does
exist, but it is arbitrary and seldom discussed, since in general practise
the terms are used interchangeably. In general practise the concepts of
modern protein and real protein are used interchangeably, since the only real
proteins that exist anymore are modern proteins. It is only in the cases of
materials science and abiogenesis that any distinction has to be made, and
while this distinction is not arbritary, it is taken for granted, so it is
seldom discussed. The best I can do is what I have already done:
demonstrate that the accepted definition of protein is a polymer of amino
acids linked by the peptide bond, with no mention of optical or chemical
configuration; such a definition is broad enough to encompass thermal
proteins even if it is generally used to described modern proteins.
>
> >SJ>There is a more fundamental reason why the random self-assembly of
> >>proteins seems a non-starter. This has to do not with the formation of
> >>the chemical bonds as such, but with the particular order in which the
> >>amino acids link together. Proteins do not consist of any old peptide
> >>chains; they are very specific amino acid sequences that have
specialized
> >>chemical properties needed for life. However, the number of alternative
> >>permutations available to a mixture of amino acids is super-
> >>astronomical.
> >>
> >>A small protein may typically contain 100 amino acids of 20 varieties.
> >>There are about 10^130 (which is 1 followed by a 130 zeros) different
> >>arrangements of the amino acids in a molecule of this length. Hitting
the
> >>right one by accident would be no mean feat.
>
> KO>Misconception 3: An equimixture of all 20 amino acids produces large
> >amounts of only about a dozen different proteinoids, not tiny amounts of
> >10^130. Each proteinoid has a specific sequence, and the same mixture
> >of amino acids will **always** produce the **exact same** proteinoids
> >with the **exact same** sequences. On top of that, different mixtures
> >will produce different sets of proteinoids, each with their own sequence,
> >and each specific mixture will produce only its own set of specific
> >proteinoids. This is not a random process as Davies believes, but clearly
a
> >deterministic one.
>
> This is Kevin's "Misconception 3". In the above, Davies is now talking
> about "proteins" not "proteinoids".
>
Steve's denseness has plumbed new depths. Davies is giving another example
of why "the resemblance between Fox's proteinoids and real proteins is rather
superficial." In this case, Davies has assumed that "proteinoids" are just
"any old peptide chains" created by "random self-assembly", whereas "real
proteins" are "very specific amino acid sequences that have specialized
chemical properties needed for life." However, since "the number of
alternative permutations available to a mixture of amino acids is
super-astronomical", such that a "small protein [which] may typically contain
100 amino acids of 20 varieties" can have "about 10^130 ... different
arrangements of the amino acids", "[h]itting the right one [for the protein
to be functional] by accident would be no mean feat." In other words, Davies
is saying that thermal proteins are random aggregates of amino acids that
cannot have function because there are too many possible arrangements of the
amino acids for a functional arrangement to be acquired randomly.
I was pointing out that Davies assumption is not true. Thermal proteins are
not random aggregates; like "real" proteins they have "very specific amino
acid sequences that have specialized chemical properties needed for life."
This is demonstrated by the fact that each different mixture of amino acids
produces a limited variety of thermal proteins (not 10^130), that each
mixture always produces the same limited variety, that each variety of
thermal protein has a specific sequence that is reproducible, and that each
variety has a catalytic function. In other words, I was demonstrating that
even by Davies definition, "proteinoids" are "real" proteins. Had Davies
known the research better, he would not have made these misconceptions.
>
> >SJ>Getting a useful configuration of amino acids from the squillions of
> >>useless combinations on offer can be thought of as a mammoth
> >>information retrieval problem, like trying to track down a site on the
> >>internet without a search engine."
>
> KO>Every known proteinoid is catalytically active, and a wide variety of
> >catalytic functions have been produced, further evidence that this is not
> >due to random processes.
>
> Again Kevin does not address the issue but adds his own complicated
> pseudo-explanation. Davies quote above is talking about "Getting a useful
> configuration of" "*amino acids*" on *proteins* not whether "proteinoids
> are catalytically active" or not.
>
And again Steve is being dense. Davies is simply continuing the same theme
discussed above: since "proteinoids" are made by "random self-assembly",
getting "useful configuration[s] of amino acids from the squillions of
useless combinations on offer can be thought of as a mammoth information
retrieval problem". Again, Davies claim is that "proteinoids" cannot have
"useful configurations". I was once again pointing out that this claim is
wrong; since every thermal protein has catalytic activity, every thermal
protein ("proteinoid") must also have a "useful configuration". Therefore
the "information retrieval problem" cannot be as "mammoth" as Davies believes
it to be. And the reason is because "proteinoids" are not made by "random
self-assembly", but by deterministic processes that selectively assemble
amino acids into specific, repeatable sequences with catalytic activity.
Steve cannot refute this, so he tries to pretend it is irrelevant, when in
fact it very relevantly refutes Davies claims. This is simply another
example of a critic who has not taken the trouble to understand the model.
Kevin L. O'Brien