This will be the first of my detailed replies to Steve's response to my post.
It deals specifically with the Yockey quote.
>
> KO>anhydrous mixtures of amino acids that contain at least 1%
> >glycine, aspartate, glutamate or lysine can, upon being heated between
> >50 and 200 degrees C, selectively copolymerize into nonrandom polyamino
> >acids called proteinoids or thermal proteins. These spontaneously form,
> >when rehydrated, hollow double-layer membraned spheroids called
> >microspheres of uniform size and shape.
>
> Yockey points out that Fox's protenoids' dependance on the amino acids
> "aspartate" and "glutamate" is unrealistic since Glycine and Alanine
> are by far the most abundant amino acids formed by chemical evolution
> experiments:
>
> "Amino acids decompose at the temperature needed, 150-180 degrees
> C....
>
Two points regarding this. First of all, only one amino acid decomposes at
any temperature less than 200 C -- glutamine; the rest have decomposition
temperatures above 200 and four have decomposition temperatures above 300.
The following table gives the decomposition tempertures for each amino acid;
the values are obtained from The CRC Handbook of Chemistry and Physics
(Physical Constants of Organic Compounds, C-65 to C-576).
Amino Acid Temperature
-------------- ---------------
Alanine 314
Arginine 244
Asparagine 236
Aspartic Acid/
Aspartate 324
Cysteine 240
Glutamic Acid/
Glutamate 225
Glutamine 185
Glycine 262
Histidine 284
Isoleucine 285
Leucine 295
Lysine 225
Methionine 283
Phenylalanine 283
Proline 220
Serine 228
Threonine 235
Tryptophan 290
Tyrosine 342
Valine 315
What Yockey probably meant by "decompose" was that they react at these
temperatures to form long-chain, often branched, non-peptidic polymers that
aggregate into opaque solid masses that resemble tar. Strictly speaking,
however, this is not decomposition, which involves the breakdown of the amino
acids into different chemical structures by reacting with themselves. Amino
acids that form tar polymers are for the most part still amino acids, so no
true decomposition has occurred.
Even so, this ad hoc version of decomposition doesn't work either. It is
true only if the amino acids are heated individually, or in the absence of
glycine, aspartate, glutamate or lysine, and only under certain conditions.
Amino acids with decomposition temperatures near or above 300 simply do not
react with themselves at temperatures below 200, so by themselves they cannot
form tar polymers at these low temperatures. They can, however, react with
other amino acids, so they can be incorporated into tar polymers made from
amino acids with lower decomposition temperatures. Glycine, lysine and
aspartate by themselves do not form tar, but long-chain polypeptides. In the
presence of other amino acids, glycine will form di- and tripeptides, that
can in turn grow into polypeptides in a manner similar to solid phase
synthesis. Asparate and glutamate form pyroaspartate and pyroglutamate,
respectively, which are cyclic compounds formed when the secondary carboxyl
acid group in the R chain reacts with the primary amino group of the same
molecule. These pyroamino acids can only react with other amino acids, and
they can only form polypeptides, and after reacting they convert back into
amino acids. The mechanism by which lysine promotes copolymerization is
unknown, but since it has a secondary amino group in its R chain that could
react with its primary carboxyl acid group, it seems likely that it too can
form a pyroamino acid.
To summarize then, amino acids -- with one exception -- do not decompose at
temperatures under 200 C. Less than half of the amino acids will, when
heated alone in the absence of any other amino acid, form polymers, and three
of these are known to form polypeptides instead of tar. Mixtures of amino
acids will form tar polymers only in the absence of glycine, aspartate,
glutamate or lysine. Glycine catalyzes copolymerization by solid phase
synthesis, while aspartate, glutamate and lysine catalyze copolymerization by
the formation of pyroamino acids that in turn react with with other amino
acids. See the following references for complete details of methods, results
and discussions:
S.W. Fox and K. Dose (1977) Molecular Evolution and the Origin of Life,
Revised Edition, Marcel Dekker Publisher.
D.L. Rohlfing (1984) "The Development of the Proteinoid Model for the Origin
of Life" in K. Matsuno, K. Dose, K. Harada and D.L. Rohlfing, eds., Molecular
Evolution and Protobiology, Plenum Publishing.
K. Dose (1995) "On the Origin of Biological Information" in C. Ponnamperuma
and J. Chela-Flores, eds., Chemical Evolution: Structure and Model of the
First Cell, Kluwer Academic Publishers.
Secondly, 150-180 C is not the temperature range needed to thermally
copolymerize amino acids. The temperature range traditionally used is
120-200 to insure that the amino acids are anhydrous, but D.L. Rohlfing was
able to copolymerize amino acids at temperatures as low as 65 C. He used
mixtures rich in glycine, in dicarboxylic amino acids (aspartate and
glutamate) and in lysine; all produced roughly the same amount of proteinoid.
So in fact, it is reasonable to expect that thermal copolymerization can
occur within a range of temperature from 50 to 200 C.
D.L. Rohlfing (1976) "Thermal Polyamino Acids: Synthesis at Less Than 100
C", Science, 193, 68-70.
>
> ...so that the heating period must be artificially short.
>
Since amino acids do not decompose at temperatures under 200 C, the heating
period is not kept short to avoid this. The heating period is kept short
because copolymerization proceeds much more quickly at 200 C than at 65 C.
It only takes a couple of hours to obtain the same amount of proteinoid at
200 C that one would obtain after 81 days at 65 C. The only concern with
heating at temperatures above 100 C is thermal breakdown of the resulting
proteinoids, but this takes longer than a couple of hours to have any
significant result.
D.L. Rohlfing (1976) "Thermal Polyamino Acids: Synthesis at Less Than 100
C", Science, 193, 68-70.
>
> Furthermore, since
> Gly and Ala are by far the most abundant amino acids formed by chemical
> evolution, it is doubtful that the appropriate amounts of Glu and Asp,
> required by the proteinoid synthesis, existed in the lagoons as postulated.
>
First of all, Fox and other researchers have shown that, regardless of
whether you use a gaseous phase or an aqueous phase, whether you use
electrical discharges, ultraviolate light, ionizing radiation, optical
radiation, or thermal energy, you get exactly the kind of mixture of amino
acids, hydrocarbons, saccharides, nucleic acids, phosphated nucleotides,
porphyrins and other biologically significant compounds predicted by the
"primordial soup" hypothesis and a number of other scenarios.
S.W. Fox and K. Dose (1977) Molecular Evolution and the Origin of Life,
Revised Edition, Marcel Dekker Publisher.
Secondly, glycine and alanine are not the only amino acids produced in large
amounts. As Fox and Dose explain: "When we examine all of the relevant
experiments comparatively, we find that the compounds most common to
organisms, i.e., adenine, alanine, aspartic acid, glycine, etc., are those
that appear mosty frequently and in largest proportion in 'origin'
experiments." Note that they state that aspartate is one of the most common
biologically significant compounds produced under simulated prebiotic
conditions. How much you get of any amino acid does depend upon the method
you use, though. Electrical discharge experiments produce only about 1% the
amount of aspartate as compared to glycine, but ionizing radiation like
x-rays can produce 50% the amount of aspartate as compared to glycine and
thermal energy can produce 13% to 63% the amount of aspartate as compared to
glycine.
S.W. Fox and K. Dose (1977) Molecular Evolution and the Origin of Life,
Revised Edition, Marcel Dekker Publisher.
Thirdly, since glycine by itself can catalyze copolymerization in the absence
of dicarboxylic amino acids, how much or how little aspartate or glutamate is
produced in simulated prebiotic experiments is largely inconsequential as
long as large amounts of glycine are also produced.
M.A. Saunders and D.L. Rohlfing (1972) "Polyamino acids: preparation from
reported proportions of 'prebiotic' and extraterrestrial amino acids",
Science, 176, 172-173.
>
> 'Prebiotic' experiments show conclusively that mixtures of pure a-amino
> acids, similar to the experiments of Fox, did not exist on the primeval
> Earth.
>
This statement is factually true; simulated prebiotic experiments do not
produce just proteinous alpha-amino acids, though according to Dose
"[b]ecause of the good solubility of most amino acids in water and their
electrochemical properties, plausible geological accumulation mechanisms can
bee seen in weathering of prebiotic organic materials, separation of the
dissolved amino acids from other solutes by the ion exchange properties of
minerals (for an instance, zeolites or montmorillonites) and ultimate
concentration by evaporation of water." However, as Yockey should know, the
use of purified alpha-amino acids is done for experimental expediency and
precision, not to accurately reproduce prebiotic conditions. After all,
these experiments are meant to *simulate* what are believed to be *plausible*
prebiotic conditions, to see what kind of result occurs. Pure alpha-amino
acids may not accurately reproduce the exact prebiotic conditions that
prevailed on the Earth, but if amino acids cannot be polymerized into
polypeptides using heat under *any* conditions -- natural or artificial --
then no amount of manipulation or control by Fox or anyone else could force
purified alpha-amino acids to thermally copolymerize. These experiments
serve as proof of concept; they establish that there are natural mechanisms
by which amino acids can self-orgainize into nonrandom peptidic polymers.
K. Dose (1995) "On the Origin of Biological Information" in C. Ponnamperuma
and J. Chela-Flores, eds., Chemical Evolution: Structure and Model of the
First Cell, Kluwer Academic Publishers.
In another more important sense, however, the statement is false, because it
implies that thermal copolymerization is possible only if the amino acids are
pure, of the alpha configuration and concentrated. See below for details.
>
> The proposed polymerization would certainly be stopped by a
> variety of molecules that have been shown to be formed in simulation
> experiments (Horowitz & Hubbard, 1974).
>
At the time this statement was written, that supposition might have been
reasonable, but we now know that this concern is unwarrented. Proteinoids
can be formed by the thermal copolymerization of beta, gamma, even omega
amino acids. As Fox explains: "In fact, the du Pont chemist Wallace
Carothers thought of heat when he wanted to make, in the 1930s, a substitute
for the protein silk fibroin, the essense of silk. Knowing that heating the
alpha-amino acids would give unwanted products according to the convential
wisdom, Carothers heated the other kind of amino acid, an omega-amino acid.
This was successful in its own way and led into the whole family of silk
substitutes, the nylons."
S.W. Fox (1988) The Emergence of Life, Basic Books.
Proteinoids can also be formed by the thermal copolymerization of D- as well
as L-amino acids. For one thing, as Dose points out: "L-Amino Acids are
largely racemized during heating." For another, as Fox et al. points out:
"In examining the functions of chiral amino acids in thermal polymers in
protobiogenesis, we do not see total prohibition of functions in polymers
from racemic, or partly racemic, amino acids." In other words, racemic
mixtures of amino acids can thermally copolymerize into functional
proteinoids.
K. Dose (1995) "On the Origin of Biological Information" in C. Ponnamperuma
and J. Chela-Flores, eds., Chemical Evolution: Structure and Model of the
First Cell, Kluwer Academic Publishers.
S.W. Fox et al. (1995) "Experimental Retracement of the Origins of a
Protocell" in C. Ponnamperuma and J. Chela-Flores, eds., Chemical Evolution:
Structure and Model of the First Cell, Kluwer Academic Publishers.
Proteinoids can also be formed by the thermal copolymerization of
nonproteinous amino acids. As Saunders and Rohlfing explain: "...
nonproteinous amino acids can be incorporated into polyamino acids during
thermal polymerization; the copresence of proteinous or even of alpha-amino
acids is not necessary." In other words, nonproteinous amino acids could
have formed their own proteinoids, or they could have been incorporated into
proteinoids formed by proteinous amino acids.
M.A. Saunders and D.L. Rohlfing (1974) "Inclusion of nonproteinous amino
acids in thermally prepared models for prebiotic protein", BioSystems, 6,
81-92.
Proteinoids can also be formed by thermal copolymerization in the presence of
inorganic contaminants, such as basalt or sea sand. As Rohlfing reported:
"The ... sets of amino acids polymerized in the presence of all tested
proportions of added inorganic material," which went as high as 8 times as
much basalt as amino acids. Rohlfing also reported that "the presence of sea
sand results in a statistically significant increase in yield of polymer."
In other words, some inorganic materials can actually enhance proteinoid
production rather than inhibit it.
D.L. Rohlfing (1974) "Evolution of Models for Evolution" in K. Dose, S.W.
Fox, G.A. Deborin and T.E. Pavlovskaya, eds., The Origin of Life and
Evolutionary Biochemistry, Plenum Publishing.
Finally, proteinoids can also be formed by thermal copolymerization in the
presence of a wide variety of organic material such as hydrocarbons,
saccharides, nucleic acids, phosphated nucleotides, porphyrins and other
biologically significant or insignificant compounds, as described by Fox and
Dose.
S.W. Fox and K. Dose (1977) Molecular Evolution and the Origin of Life,
Revised Edition, Marcel Dekker Publisher.
In summary, there is no longer any reason to believe that any product of a
simulated prebiotic experiment would prevent thermal copolymerization, though
some might inhibit it. In any event, so far no one has found any compound
that can.
>
> A glaring weakness of the
> proteinoid scenario is that it requires a highly concentrated and intimate
> mixture of a specific selection of amino acids as noted by Ponnamperuma
> (1983)." (Yockey H.P., 1992, p269)
>
As has been demonstrated above and earlier, this assessment by Yockey is not
correct. Furthermore, Fox and Dose report: "Also, since amino acids pass
from a solid state [after dehydration] to a molten mixture [after heating] of
polymer with oligomers and monomers ... no question of an act of
concentrating amino acids from a solvent need arise. Also, as stated
earlier, an aqueous solution may be heated until the dry amino acids left by
evaporation condense. The amino acids are at infinite concentration in the
dry state. An infinitesimal amount of amino acid can polymerize on heating
as indicated, providing the small but sufficient proportion of nonneutral
amino acid is present." So in fact the very act of drying out the amino
acids by evaporation is by itself enough to concentrate even very dilute
solutions of amino acids sufficiently to permit thermal copolymerization.
Finally, a wide variety of amino acid compositions have been tested, and as
long as they contain at least a small but significant proportion of glycine,
aspartate, glutamate or lysine, all have produced proteinoids, so no
"intimate mixture of a specific selection of amino acids" is actually
necessary.
S.W. Fox and K. Dose (1977) Molecular Evolution and the Origin of Life,
Revised Edition, Marcel Dekker Publisher.
In conclusion, the dependance of proteinoids on the amino acids "aspartate"
and "glutamate" is by no means unrealistic, and in fact proteinoids do not
even depend solely on aspartate or glutamate, but can be formed using lysine
or glycine as well. And since glycine is the most abundant amino acid
produced by any simulated prebiotic experiment, we can be sure that there
would be enough around to produce loads of proteinoids.
Kevin L. O'Brien