On Sat, 24 Jul 1999 00:32:45 EDT, Biochmborg@aol.com wrote:
[...]
[continued]
>SJ>Berlinski cites some of the literature against Fox's proteinoid
>>hypothesis and notes that Fox " ...has not persuaded the biological
>>community of its strength" and that "criticisms of it are overwhelming":
KO>Except that none of these "criticisms" seem to have been published in
>the scientific literature, because I can't find any.
This is an indictment of either Kevin's lack of reading or his objectivity!
What does Kevin think that the references cited by Berlinski are, if
not "the scientific literature"?
Even Fox admits that there have been "Objections in the Scientific
Literature" to his proteinoids theory:
"Objections in the Scientific Literature. Some of the objections raised by
scientists to the proteinoid model are at times repeated by
creationists....Some of the objections in the scientific literature will
accordingly be answered here." (Fox S.W., "Creationism and Evolutionary
Protobiogenesis", in Montagu A., ed., "Science and Creationism", 1984,
p213)
>SJ>"There is no widely accepted, remotely plausible scenario for the
>>emergence of life on earth. The proteinoid hypothesis of Sidney Fox and
>>his colleagues (S.W. Fox, "Molecular Evolution to the First Cells," Pure
>>and Applied Chemistry 34, 1973) has not persuaded the biological
>>community of its strength.
KO>Since none of Berlinski's sources are more recent than 1983 (all of
>which have been effectively refuted by Fox and his colleagues) I hardly
>think that Berlinski knows what the current opinion of the "biological
>community" is. For example, in 1994, Aristotle Pappelis and Sidney Fox
>proposed at an origin-of-life conference the creation of a new taxonomic
>classification -- Domain Protolife -- for proteinoid microspheres and other
>protocells. There has been not a single published objection to this
>proposal from the "biological community". Apparently then more
>biologists are starting to be persuaded by the mounting evidence.
Perhaps the reason "none of Berlinski's sources are more recent than
1983" is because Fox's "proteinoid microspheres...protocells" theory has
not been taken seriously by the mainstream origin-of-life community since
the 1980's.
In the Scientific American special edition of October 1994, in a major
article on "The Origin of Life on Earth", Leslie Orgel does not even
*mention* Fox's proteinoid microspheres.
>SJ>Criticisms of it are overwhelming (W. Day, Genesis on Planet
>Earth....
KO>Day is a creationist; hardly an unbiased observer.
I would appreciate it if Kevin could substantiate his claim that "Day is a
creationist." If Day is "a creationist", then he is a most unusual one. The
index to his book "Genesis on Planet Earth: The Search for Life's Beginning"
does not mention God or creation.
Day's book has a foreword by prominent evolutionary biologist Lynn
Margulis, who praises it:
"Mitchell Rambler, my teaching fellow in Environmental Evolution at the
time, and now head of the Exobiology program at the NASA Life Sciences
Offices in Washington, picked the book off the reject pile and took it home
with him. A week later he confronted me with a firm recommendation that
we use Day's book as supplementary reading in the course for a unit of
study on the origins and early evolution of life...I took his advice and
found myself reading the book from cover to cover. Amazed that I had so
misjudged the book, I thanked Rambler profusely. We have used the book
ever since...Now, in 1984, the text has been extensively rewritten. The
flaws have receded and the book's strengths have been accentuated. The
production job is vastly improved. Retaining its original clarity and breadth,
this second edition is a fully professional work....The second edition of
Day's book stands alone as the book we sought. It is an original,
comprehensive, and comprehensible account of the scientific Genesis: the
great drama that occurred on the surface of the Earth some four billion
years ago. Furthermore it is designed, from the beginning, for students.
Students and teachers, researchers and witnesses of our space age world
will welcome this text and congratulate the Yale University Press for
making it available to a wider audience." (Margulis L., Foreword, Day W.,
"Genesis on Planet Earth: The Search for Life's Beginning", 1984, pp.xv-
xvi)
Moreover, Day accepts Darwinian evolution:
"On analysis of life's direction, we discover that it isn't man that has arrived
at a critical juncture of a long journey-it is biological evolution. Mutation
created the variety, and natural selection made the fit for organisms to
expand into every ecological niche accessible to them...Within a level of
evolutionary development the tenets of Darwinian evolution remain valid."
(Day W., "Genesis on Planet Earth, 1984, p256).
But even if Day was "a creationist" why would that rule him out as a critic
of prebiotic evolution? If evolution can only be validly criticised by
evolutionists, then the theory at its most general level would be
unfalsifiable and thus pseudoscience by Popper's criterion. *Real* science
is supposed to be able to withstand criticism from *anyone*.
Besides, if being "a creationist" makes one "hardly an unbiased observer"
then that applies to Kevin also, because Kevin describes himself on another
of his web page as "a creationist", indeed even a "a fundamentalist":
"As a fundamentalist, evangelical Christian, I naturally believe the literal
truth of the Scriptural statement, "In the beginning God created the
heavens and the earth." In that sense I proudly proclaim myself to be a
creationist." http://www.geocities.com/Tokyo/Temple/9917/evolution/kevino.html
The above page is headed "Statement from a Christian Evolutionist" which
is a testimony to Kevin's flexible use of language. Anyone who could
seriously claim to be simultaneously an "evolutionist", "creationist"
and "fundamentalist" is clearly not using one or more of those terms in the
way they are usually defined!
In any event, there are others who "have published objections to the
proteinoid scenario on chemical grounds":
"A number of authors have published objections to the proteinoid scenario
on chemical grounds, among them, Miller & Urey (1959), Bernal (1967),
Miller & Orgel (1974), Jukes & Margulis (1980), and Day (1984). Most of
the objections to the proteinoid scenario come directly from the work of
Fox and his followers. Dose (1976) points out the following: proteinoids
yield 50 % to 80 % amino acid upon hydrolysis, but contain 40 % to 60 %
fewer peptide links than typical proteins; such cross-links disturb most of
the sequencing methods typically used in protein chemistry; the optically
active amino acids racemize during the heating process; and no helicity was
detected (Fox, 1973). Fox (1975) reports that proteinoids differ from
proteins in that most of the constituent amino acids are racemized by the
heat treatment necessary for their formation. The low yield of amino acids
after prolonged hydrolysis indicates extensive cross-linkages (Folsome,
1976). Andini et al. (1975) and Temussi et al. (1976) showed by nuclear
magnetic resonance and paramagnetic resonance that thermal polypeptides
contain only B-peptide linkages. They state that their results cast serious
doubt on the role that proteinoids may have had on prebiotic polypeptide
synthesis because only a-peptide linkages are characteristic of proteins. Fox
(1976b, 1984b) is aware of the results of Andini et al. (1975) and Temussi
et al. (1976). " (Yockey H.P., "Information Theory and Molecular
Biology", 1992, p268)
>SJ>...K, Dose, "Ordering Processes and the Evolution
>>of the First Enzymes," in Protein Structure and Evolution, eds. J.L.Fox,
>>Z. Deyl, A. Blazy, 1976....
KO>At the same time Dose was writing this supposed "criticism" he was
>also co-authoring with Fox a book that supported both the validity and
>the relevance of proteinoid microsphere research. In point of fact, this
>article is no criticism; it simply points out areas that at that time still
>needed to be investigated.
This very reference has "eds. J.L.Fox"! Dose has indeed collaborated with
Fox, and no doubt did once "support both the validity and the relevance of
proteinoid microsphere research", but that support appears to have waned.
In a major review of origin-of-life scenarios, including Fox's proteinoid
microspheres, Dose summarised them all in his abstract as follows:
"More than 30 years of experimentation on the origin of life in the fields of
chemical and molecular evolution have led to a better perception of the
immensity of the problem of the origin of life on Earth rather than to its
solution. At present all discussions on principal theories and experiments in
the field either end in stalemate or in a confession of ignorance. New lines
of thinking and experimentation must be tried." (Dose K., "The Origin of
Life: More Questions Than Answers", Interdisciplinary Science Reviews,
Vol. 13, No. 4, 1988, p348)
>SJ>...C.E. Folsome, "Synthetic Organic Microstructures and the Origin
>>of Cellular Life," Die Naturwissenschaften 7, 1976; C.
>>Ponnamperuma, "Cosmochemistry and the Origin of Life," in
>>Cosmochemistry and the Origin of Life, ed. C. Ponnamperuma, 1983;
>>and so forth). " (Berlinski D., "Denying Darwin: David Berlinski and
>>Critics", Commentary, September 1996.
>>http://www.commentarymagazine.com/9609/letters.html) >>
KO>And again, these last two articles are not really critiques at all, just
>conservative statements of what still needs to be verified. Assuming
>Berlinski even read these articles, I tend to doubt he understood what he
>was reading.
On what basis does Kevin "doubt" that Berlinski had "even read these
articles" and that "he understood what he was reading"?
>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!
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!
>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.
*What* "research" exactly is it which "demonstrates that this is incorrect"
i.e. "the resemblance between Fox's proteinoids and real proteins is...
superficial"?
Absent such evidence backed by references, this is *Kevin's* "Misconception
2"!
>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".
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.
>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".
>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.
>SJ>(Davies P.F.C., "The Fifth Miracle: The Search for the Origin of
>>Life," 1998, p60).
[continued]
Steve
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"Indeed nothing remains except a tactic that ill-befits a grand
master...namely to blow thick pipe tobacco-smoke into our faces. The
tactic is to argue that although the chance of arriving at the biochemical
system of life as we know it is admitted to be utterly minuscule, there is in
Nature such an enormous number of other chemical systems which could
also support life that any old planet like the Earth would inevitably arrive
sooner or later at one or another of them. This argument is the veriest
nonsense, and if it is to be imbibed at all it must be swallowed with a jorum
of strong ale...So far from there being very many indistinguishable
chemical possibilities, it seems that we have an exceedingly distinguishable
system, the best." (Hoyle F. & Wickramasinghe C., "Evolution from
Space", [1981], Paladin: London UK, 1983, reprint, p25
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