This will be the fifth of my in depth responses to Steve's reply to my post.
It deals with whether proteinoid experiments also produce goo.
>
> In any event, it seems that there is "goo" in at least some proteinoid
> microsphere experiments.
>
Having failed to provide any direct experimental evidence that a Miller-Urey
type of experiment produces goo rather than or even as part of a mixture of
soluble and insoluble organic products (personal opinion does not count as
direct experimental evidence), Steve is now trying to claim that proteinoid
microsphere experiments also produce goo. The question is, does he have any
actual direct experimental evidence to back up this new claim, or will he
simply present personal opinion as he has so far done?
>
> "It is vitally important to draw attention to the fact that these model
> experiments carried out on the laboratory bear little resemblance to what
> could have occurred on the primeval earth.
>
I find it interesting that there is no reference for this claim. That would
mean this is not only Croft's own personal claim rather than a paraphrase of
someone else's claim, but that it also has no scientific support. In other
words, this is simply Croft's opinion based on speculation.
>
> The primeval soup, by
> definition, had to be a complex mix of thousands upon thousands of
> different molecules.
>
Again, no reference, and the wording ("had to be" rather than "is") further
reinforces the fact that this is opinion that is based on speculation rather
than evidence.
>
> If this soup had dried up on exposed volcanic rocks it
> is extremely doubtful if amino acids could have polymerized as might be
> suggested from these simple experiments. The most likely product would
> have been a horrible tarry 'goo'." (Croft L.R., "How Life Began", 1988,
> p48)
>
Again, no references to support his conclusion, and again the wording
("extremely doubtful if amino acids could have" rather than "demonstrated
that amino acids could not have"; "the most likely product product would have
been" rather than "the only product produced was") indicates that this is
still opinion based on speculation and not experimental evidence. So far no
real evidence.
Croft's critique is based on theoretical considerations, but as I quoted
Rohlfing in an earlier post, for a critique to be valid its theoretical
considerations must be tested, which apparently they have not in this case,
or Croft would have provided references. Meanwhile there is plenty of
evidence to demonstrate that Croft's critique is invalid. See Sidney Fox and
Klaus Dose, _Molecular Evolution and the Origin of Life_, Revised Edition,
Marcel Dekker Publisher, 1977.
>
> Yockey cites Fox's collaborator Klause Dose saying of Fox's microspheres
> that:
>
Actually Dose is talking about proteinoids, not microspheres. And its
"Klaus".
>
> "Side reactions lead to largely unknown substances (tar) that are linked
to
> the polymerized amino acids (Dose, 1976)."(Yockey H.P., 1992, p269)
>
First of all, Dose did not say "(tar)" in his paper, so unless my copy of the
article has a typo, this looks like something Yockey himself threw in. As
such, there can be no claim that Dose himself believed that proteinoid
experiments produced tar or goo.
Secondly, as with the Miller-Urey type of experiments, what Yockey and Steve
want to label as tar or goo are long-chain insoluble polymers. No one ever
claimed that thermal copolymerization produced ONLY proteinoids, and in fact
had Steve bothered to read the scientific literature he would have discovered
that researchers have been very candid that thermal copolymerization produces
other kinds of polymers in addition to proteinoids. At the same time,
however, to my knowledge no one who has actually done these experiments has
ever called the non-proteinoid products tar or goo; that is a term used
virtually exclusively by critics of proteinoid research (though to my
knowledge never in scientific papers).
Thirdly, the fact that large yields of proteinoids are always obtained
indicates that these insoluble polymers do not interfere with proteinoid
synthesis, and the fact that one can actually observe through a microspcope
the formation of microspheres when the copolymerization product is exposed to
water also indicates that these insoluble polymers do not interfere with
microsphere formation either.
So again, there is no direct experimental evidence that proteinoid
experiments produce goo.
>
> Nobel laureate biochemist Christian De Duve said that "the resulting
> material" from heating "a dry mixture of amino acids for three hours at
170
> degrees C" has "more in common with primeval `goo' than with proteins":
>
> "For Fox, this discovery initiated a lifelong avocation. He found that
> proteinoids spontaneously form microscopic vesicles, or "microspheres,"
> which he saw as the first cells, and spent his whole career pursuing these
> studies. Few origin-of-life experts are as sanguine as Fox concerning the
> significance of his results.
>
I would not call one-quarter of those dedicated to abiogenesis research
"few"; more like a significant minority. Enough at least to demonstrate that
this is a real phenonemon and not just one man's deluded obsession. In any
event, De Duve should know that the validity of a scientific concept is not
determined by how many people consider it significant, but by the quality of
its evidence.
>
> It has been objected that the conditions required
> for the formation of proteinoids are not likely to have obtained on the
> prebiotic Earth....
>
These objections have been refuted by experimental evidence. See Sidney Fox
and Klaus Dose, _Molecular Evolution and the Origin of Life_, Revised
Edition, Marcel Dekker Publisher, 1977.
>
> ...that the resulting material has more in common with
> primeval "goo" than with proteins....
>
Again, there is direct experimental evidence that refutes this objection,
namely chemical and structural analysis of proteinoids which reveals their
proteinaceous nature. See Sidney Fox and Klaus Dose, _Molecular Evolution
and the Origin of Life_, Revised Edition, Marcel Dekker Publisher, 1977 for
details.
>
> ...and that the microspheres are a far cry
> from anything that could be called a cell. I tend to share these
> misgivings..." (de Duve C.R., "Vital Dust: Life as a Cosmic Imperative",
> 1995, p29)
>
And again, there is direct experimental evidence that refutes this claim.
See Sidney Fox and Klaus Dose, _Molecular Evolution and the Origin of Life_,
Revised Edition, Marcel Dekker Publisher, 1977 for details.
In any event with no references this is still just De Duve's opinion (his use
of the term "misgivings" is also significant; had he any direct experimental
evidence he would have said something like "conclusions"). Still no evidence
that proteinoid experiments produce goo.
>
> Origin-of-life specialist Robert Shapiro says that when *realistic* ratios
> of amino acids are heated "the result was pyrolysis to a dark brown tar
> with a disagreeable odor":
>
In point of fact, Shapiro does not "state" this at all, and neither does Day.
Steve is the one saying whether certain amino acid mictures are "realistic"
or not, and this is based on his previous claims that asparate and glutamate
are not made in large enough amounts under prebiotic conditions to justify
the amounts used in proteinoid synthesis. As I have already demonstrated,
this claim is invalid: not only are aspartate and glutamate two of the most
common amino acids produced under simulated prebiotic conditions (after
glycine and alanine), there are many experiments that can produce more than
enough to account for the amounts used in proteinoid synthesis.
>
> This remedy, when tried, had been found wanting, however. "Biochemists
> knew that when a mixture of amino acids in the ratio found in proteins was
> heated, the result was pyrolysis to a dark brown tar with a disagreeable
> odor," commented chemist William Day." (Shapiro R., "Origins: A
> Skeptic's Guide to the Origin of Life", 1986, p193).
>
With this and the following quotes, Steve is trying to make the claim that
another reason why Fox's use of large proportions of aspartate or glutamate
is unrealistic is because modern proteins do not contain large proportions of
aspartate or glutamate, and that if you use mixtures of amino acids that
represent the actual proportions found in modern proteins you get tar or goo
instead of proteinoids. This is incorrect for three reasons. The first and
most important is that this is not even what Shapiro is talking about in this
case. Shapiro is discussing the history of research that led up to Fox's
proof of concept experiment demonstrating that amino acids could thermally
copolymerize. More about that below. So in point of fact Steve has
misquoted Shapiro to make it appear as if he was making one claim when in
fact he was discussing something entirely different.
The second reason is that there is experimental evidence that refutes Steve's
newest claim. For one thing there are many modern proteins that contain
large proportions of aspartate and glutamate. One example is calmodulin,
which contains 50% aspartate and glutamate. Further examples include
ferredoxin, which contain 30% aspartate/glutamate, casein, which contains
24%, albumin and beta-galactosidase, which contain 23%, prolactin and enolase
22%, methionyl-tRNA synthetase, pencillinase, thyroglobulin and creatine
kinase 21%, and carbonic anhydrase B, glycerol-3-P dehydrogenase, thrombin,
invertase and deoxyribonuclease B 20% aspartate/glutamate. (It should be
pointed out that these percentages can vary between species, but usually by
less than 10%.) In E. coli proteins, glutamate and aspartate are the second
and third most frequent amino acids after alanine (glycine was fifth). Most
proteins contain less than 20% aspartate/glutamate, but most of these still
contain more than 10%. All of these percentages have been produced in one
kind or another of prebiotic experiment, and mixtures of amino acids that
have contained these percentages have all made proteinoids.
The third reason is that amino acid analysis of proteinoids has revealed
that, regardless the mixture, proteinoids contain amino acid proportions very
similar, if not identical to, those of numerous modern proteins. While
proteinoids made from mixtures high in glycine, or aspartate/glutamate, or
lysine will contain large proportions of glycine, or aspartate/glutamate, or
lysine, the proteinoid proportions are still a close match for proportions
found in modern proteins. In other words, it doesn't matter whether you
start with a "realistic" mixture or not, the resulting proteinoids will
contain "realistic" proportions of amino acids. See Sidney Fox and Klaus
Dose, _Molecular Evolution and the Origin of Life_, Revised Edition, Marcel
Dekker Publisher, 1977 for details.
>
> Only when *unrealistic* ratios of amino acids are used was the result
> "clean" but then "the products obtained were not natural proteins":
>
> "At this point Sidney Fox made a contribution. Fox set aside the usual
> recipes and added extra amounts of any of three special amino acids.
>
As I explained above and in previous posts, there is nothing "*unrealistic*"
about either the mixture amino acid ratios or the amino acid ratios of the
resulting proteinoids. Besides, as I also pointed out, this is not what
Shapiro is talking about. He is describing the history of how Fox developed
and tested the idea of thermal copolymerization, and while the account is
fairly accurate, it is nonetheless somewhat imprecise as stated.
Almost from the moment scientists discovered that proteins were made of amino
acids, some of them started trying to take amino acids and assemble them into
proteins. This was based on organic chemistry methodology that demanded that
the ultimate test of whether the structure of a compound was understood was
whether you could make a chemical with the same structure that had the same
properties as the natural compound. Unfortunately, it proved to be more
difficult to synthesize a protein from amino acids than it was to synthesize
even a complex organic compound. Based on these experiments, plus research
investigating the properties of amino acids, a consensus developed that it
would be virtually impossible to synthesize proteins by any physical method,
especially if it involved heat. The thing is no one actually tried to test
whether that was true; it was a collective opinion based on research, but no
one really tried to do the actual experiment to see if the opinion was
correct.
Fortunately, in science there are always mavericks who in essence say, "I
don't care what the consensus is, I'm going to do the experiment and see what
happens." The first attempts were done using aqueous solutions, which of
course failed, but then people decided to work with dry mixtures. Mixtures
of different kinds amino acids hadn't work with other methods, so these same
researchers decided to try heating just one type of amino acid. The
reasoning went that, with a mixture of amino acids there was bound to be such
a wide variety of cross reactions that they would interfere and prevent
polymerization, whereas by limiting the mixture to a single amino acid type,
you also limited the reactions a single or a very limited variety of
reactions. They called this process homopolymerization. Most of the
reactions were undoubtedly failures, but at the turn of the century at least
one lab managed to thermally homopolymerize glycine and at least two labs
managed to thermally homopolymerize aspartate. However, since these were the
only two successes, most researchers abandoned the idea of trying to
thermally polymerize amino acids into proteins.
Fox started out doing work in protein sequencing, but the more he learned the
more he was convinced that it should be possible to thermally polymerize
amino acids. Since homopolymerization did not work, he considered it likely
that copolymerization of two or more types of amino acids should. Remember,
this was contrary to conventional thinking, but Fox also knew that no one had
really tested that thinking to see if it was right. When he discovered the
earlier successes with glycine and aspartate, he realized that it was
possible in principle to thermally polymerize amino acids. He also realized
that if glycine and aspartate could homopolymerize, they might also be able
to copolymerize with other amino acids. So he began by first repeating the
thermal homopolymerization of aspartate, then he tried mixing aspartate with
leucine or valine. Both mixtures produced copolymers. Fox then demonstrated
that glutamate could also copolymerize with other amino acids, then finally
he performed the classical experiment in which he mixed equal amounts of
aspartate and glutamate with an equimixture of all remaining amino acids, and
got the first proteinoids. Later, one of his collaborators (Kaoru Harada)
demonstrated that lysine could also copolymerize other amino acids in the
absence of aspartate or glutamate, and finally Saunders and Rohlfing
demonstrated that glycine could copolymerize other amino acids as well. See
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 for more details.
Though Fox started out with a mixture of amino acids consisting of 2/3
aspartate/glutamate, he experimented with other mixtures and discovered that
as long as there was at least 5% glycine, aspartate, glutamate or lysine,
copolymerization could occur. See Sidney Fox and Klaus Dose, _Molecular
Evolution and the Origin of Life_, Revised Edition, Marcel Dekker Publisher,
1977 for more details.
So when William Day states that biochemists "knew that when a mixture of
amino acids in the ratio found in proteins was heated, the result was
pyrolysis to a dark brown tar with a disagreeable odor", he was referring to
the consensus opinion that stated that amino acids could not be thermally
polymerized. And when Shapiro states that "Fox set aside the usual recipes",
he was rerring to the fact that Fox tried copolymerizing other amino acids
with aspartate. In any event, this has nothing to do with the question of
whether amino acid proportions in modern proteins are more realistic than the
mixture proportions used to make proteinoids.
>
> These
> mixtures, when heated in the dry state well above the boiling point of
> water, gave clean preparations, in which the amino acids had united with
> one another. The products obtained were not natural proteins, however,
> even though they were made from amino acids.
>
What Shapiro means in this case is that they are not like biotically
synthesized proteins. He is not using natural in the everyday sense of
normal, but in the scientific sense of made by nature. Nor is he using clean
to imply the absence of other, insoluble polymers, but to connote that
proteinoids were made and could be solublized out of the insoluble material
produced as well.
>
> The special amino acids
> mentioned above contained either an extra amino or an extra acid group. In
> normal proteins, these extra groups do not take part in chain formation,
but
> this had occurred in the heating process. Unnatural chains, even branched
> chains, had been produced." (Shapiro R., 1986, p193).
>
Again, Shapiro is not using unnatural in the everyday sense of abnormal, but
in the scientific sense of not like that made by nature. His reference to
normal proteins is meant to connote modern proteins. His choice of terms is
unfortunate, but it not meant to imply that proteinoids are not real proteins.
In any event, Steve's claim that "realistic" amino acid ratios based on amino
acid proportions in modern proteins produce goo whereas "unrealistic" ratios
do not is not supported by Shapiro's statement or the known experimental
evidence. Again, there is no direct evidence here.
In conclusion, Steve has once again failed to produce any direct experimental
evidence to back up his claims. All he can produce is personal opinion based
on speculation, that in many cases is also based on miscomprehensions or even
outright ignorance, if not bias. I find it significant that these people
quoted by Steve have only voiced their objections in popularization books
rather than scientific articles. In a book, even a scientific one, you can
say whatever you like, because there is no peer review. If, however, they
tried to make the same objections in a journal article, the journal editors
would ask, "Where is your evidence to support these objections?" When they
would admit that they had none, that they were simply voicing "misgivings"
with the established proteinoid microsphere research, the editors would
reply, "Sorry, but without evidence to support your objections, they are
simply speculation. Feel free to resubmit when you have some evidence." The
only exceptions to this are letters to the editor, book reviews and
conference reports, and I have one or two examples of each that contain
objections, but I have never found a single journal article that offered any
substantial objections backed by actual experimental evidence. And the
reason for this simple: they have no actual evidence that demonstrates that
proteinoid microsphere research is either invalid or irrelevant to
abiogenesis; their objections are based mainly on their personal biases for
alternative models or against proteinoid microspheres.
In light of this, I consider it hypocritical of Steve to demand that I back
up my claims with "*deatils* of the research" in the form of quotes from
specific references, when all he can provide are his own unsubstantiated
assertions and the speculative opinions of others. I have backed up my
statements with references, which is all that is really necessary; I now
request that Steve stop offerring personal opinion and provide references to
actual data that demonstrates either the invalidity or the irrelevance of
proteinoid microsphere research to abiogenesis. He doesn't have to provide
quotes, though he should summarize the research described in those
references; once I have the references I can acquire them and read them for
myself.
Kevin L. O'Brien