On Sat, 24 Jul 1999 00:32:45 EDT, Biochmborg@aol.com wrote:
[continued]
>MB>...with the water gone, the amino acids could join together.
>>Unfortunately, other workers had earlier shown that heating dry
>>amino acids gives a smelly, dark brown tar, but no detectable
>>proteins.
KO>This is essentially true, but Behe leaves out two important details.
Having alleged that Behe had "willfully lied" Kevin now admits that what
Behe said about "heating dry amino acids gives a smelly, dark brown tar"
was "essentially true", but incomplete, in that he left out "two important
details".
First, if incompleteness is the criterion for having "willfully lied", then
*everyone* would be a liar!
Second, Kevin fails to recognise that Behe was writing a one-page *book
review* for a weekly political magazine, not a full length article in a
scientific journal! Behe would have had to keep it simple, because of space
limitations and the level of scientific knowledge of the readers of that type
of magazine. Indeed, it is even possible that the editors changed, or even
cut out, some of Behe's words to make them more understandable to their
readership.
For Kevin to conclude that anyone (let alone a fellow Christian), is a liar in
such circumstances, and then to publicly accuse him of having "willfully
lied" on the Internet, is reckless and unwarranted, to say the least.
It is further evidence to me of the adverse effect evolutionary beliefs has
on its adherents, particularly on those Christian evolutionists like Kevin, who
seem to me to have the appearance of suffering the inevitable inner conflict
of trying to serve two opposing `masters' simultaneously (Mt 6:24), namely
materialistic-naturalism and Christian theism.
Third, the "details" that Kevin says Behe left out, do not change the
essential truth of what Behe said, that: "heating dry amino acids gives a
smelly, dark brown tar, but no detectable proteins" (see below).
KO>First,
>all the earlier experiments involved trying to thermally polymerize single
>amino acids, not mixtures. In other words, they would heat up a few
>grams of alanine all by itself to try to make poly-alanine; this is known as
>homopolymerization. Fox was the first person to try heating mixtures of
>amino acids; he called this copolymerization.
So this is the first of the "two important details" that Behe is judged by
Kevin to " had willfully lied". I am sure the readers of a *political* weekly
magazine like The Weekly Standard would be absolutely *devastated* that
they missed out on this "important detail"! ;-)
And anyway, how does this materially alter Behe's statement that Kevin
admits is "essentially true" namely that "heating dry amino acids" (note the
plural) gives a smelly, dark brown tar, but no detectable proteins"?
KO>Second, Behe neglected to mention that at the turn of the century two
>German scientists managed to get a pure mixture of aspartate to
>thermally homopolymerize into poly-aspartate, thus proving that thermal
>polymerization of amino acids is possible.
And this is the second of the "two important details" that Behe is judged by
Kevin to " had willfully lied" by omitting, namely in a one-page *book
review* in a *political* weekly magazine, that Behe "neglected to mention
that "at the turn of the century two German scientists managed to get a
pure mixture of aspartate to thermally homopolymerize into poly-
aspartate"!
And again, how would the mention of this "detail" change what Behe said
above which Kevin has already admitted was "essentially true", namely that
"...with the water gone, the amino acids could join together" but "...other
workers had earlier shown that heating dry amino acids gives a smelly, dark
brown tar, but no detectable proteins."?
KO>As such, before Fox even began his experiments he knew that
>aspartate could form thermal proteins.
So what? How does this detail change what Behe said above?
And why did the other researchers (who presumably were mostly Fox and
his colleagues) keep "heating dry amino acids" which "gives a smelly, dark
brown tar, but no detectable proteins"? Was it not because what these "two
German scientists" who "at the turn of the century" had "managed to get"
namely "a pure mixture of aspartate to thermally homopolymerize into
poly-aspartate, was *unrealistic* in an early-Earth scenario?
>MB>Fox, however, demonstrated that if an extra-large portion....
KO>Yes, Fox's proof-of-concept experiment used a mixture of amino
>acids consisting of 1/3 aspartate, 1/3 glutamate and 1/3 mixture of all
>remaining amino acids, but he supsequently discovered that as little as
>1/10 aspartate/glutamate would work as well, and others have shown
>that as little as 1/100 aspartate/glutamate can promote thermal
>polymerization of amino acids.
First, Kevin's careful choice of words that this was a "proof-of-concept
experiment" is noted! A "proof-of-concept experiment" does not mean that
it was *realistic*. The fact is, as Yockey pointed out in my previous post
that Fox's protenoids experiments depend unrealistically on the amino acids
"aspartate" and "glutamate" which are rare in chemical evolution
experiments.
Second Kevin is confusing the words "portion" (which Behe used) and
*proportion* which his "1/3" , "1/10" and "1/100" refer to. Nothing Kevin
says above refutes what Behe said about "an extra-large portion" of "one of
three different amino acids is added to a mix of purified amino acids..."
MB>...of one of three different amino acids is added to a mix of purified
>>amino acids and heated in a laboratory oven, then the amino acids do
>>join. But even then they do not join to give proteins the structure they
>>form is chemically different.
KO>Incorrect; Fox and others have proven that thermal polyamino acids
>are true polypeptides, that is, the amino acids form peptide bonds. That
>is all that is needed to make a protein.
It is Kevin who is "incorrect" here. Just producing "polypeptides" is not "all
that is needed to make a protein". All proteins are polypeptides but not all
polypeptides are proteins. Proteins are a special subset of polypeptides:
"Proteinous and non-proteinous amino acids, both D- and "would lead to
an indiscriminate production of polypeptides. These polypeptides would
have scarce resemblance to protein. Protein not only requires exclusive use
of L-amino acids, but also the use of a particular subset of only 20 amino
acids. In addition, a biofunctional protein requires a precise sequence of the
amino acids." (Thaxton C.B., Bradley W.L. & Olsen R.L., "The Mystery of
Life's Origin", 1992, pp52,55).
In fact Yockey says that "There is a chasm between the proteinoid spheres
of Fox and the simplest protein":
"...proteinoids are a heterogeneous mixture of sequences of racemic amino
acids that cannot fold to produce an active protein is a serious difficulty in
the hypothesis that proteinoids were precursors of true proteins. There is a
chasm between the proteinoid spheres of Fox and the simplest protein."
(Yockey H.P., "Information Theory and Molecular Biology", 1992, p270)
KO>In fact, Chemical Abstracts, the authoritative word in chemistry on
>nomenclature, categorizes proteinoids as proteins, under the subheading
>thermal.
Interestingly, when I searched the Chemical Abstracts Service (CAS)
database at http://www.cas.org/websearch.html for " proteinoid" and
"proteinoids" it returned "no documents found" errors. Maybe it's there
somewhere? Perhaps Kevin can check and confirm this?
But even if "proteinoid" is listed in a Chemical Abstracts Service, that is
not surprising because Fox *invented* the term " thermal protein" as a
name for proteinoids (see below), and once it is being used in the
biochemistry literature a Chemical Abstracts service would have to include
it, and where else to include "thermal protein" but under "proteins,
thermal"?
Originally Fox made it quite clear that "proteinoids are not proteins" and
"the very name indicates that they are not proteins". But he has over the
years he has gradually blurred the definitions so that what started off as
"not proteins" in 1976 had become "informed protein" by 1986:
"The description of the resemblance of thermal proteinoids to proteins has
fluctuated in time since they were first prepared. In 1975 proteinoids were
artificial proteins (Fox, 1975). Yet in two publications in 1976, Fox states
(Fox, 1976a) that proteinoids are not proteins, reiterating the assertion
(Fox, 1976b) in his comment on the work of Temussi et al. (1976), (see
Temussi's reply, 1976). In 1980 they were thermal proteins (Fox &
Nakashima, 1980). They became 'protein-like polymers' in 1981
(Hartmann, Brand & Dose, 1981). By 1984 they had again become
'thermal proteins (Fox, 1984a), but in another publication that year
(1984b), Fox states, `Proteinoids are in the main much like proteins, but
the very name indicates that they are not proteins...' However, by 1986,
Fox writes (Fox, 1986), 'Biomacromolecular information emerged at the
stage of nonrandom thermal reactions of sets of amino acids to yield
informed protein '." (Yockey H.P., 1992, p270)
So having "proteinoids" classed as "proteins, thermal" under Chemical
Abstracts, seems more a triumph for Fox's facility in inventing new names
than it does for the scientific merits of his case!
>MB>So Fox and collaborators called the structures
>>"proteinoids," then went on to show that the proteinoids had some
>>interesting properties, including modest catalytic abilities, that were
>>reminiscent of real proteins.
KO>Fox called them proteinoids to distinguish them from modern
>proteins; nonetheless they are real proteins.
See Yockey's quote above where Fox himself once admitted that
"proteinoids are not proteins" and " the very name indicates that they are
not proteins".
The ending "-oid" means only "something *resembling* a (specified)
object" (http://www.m-w.com/cgi-bin/dictionary. My emphasis). If
"proteinoids" were "real proteins" why would they need to be called
"proteinoids to distinguish them from modern proteins"?
>MB>The scientific community has remained deeply skeptical of these
>>experiments.
KO>This is a logical fallacy called a sweeping generalization. Most
>scientists have never even heard of these experiments (but then most
>have barely heard of any origin of life experiment).
Kevin is here being pedantic. Clearly Behe is talking primarily about that
part of "the scientific community" which deals with the origin of life,
although the rest of "the scientific community", to the extent it thought
about the origin of life at all, would take its cue from what the origin of life
subset of "the scientific community" thought about Fox's proteinoid
experiments.
KO>That who are familiar with proteinoids are skeptical about any form
>of abiogenic scenario, though very few question the evidence.
See above. This confirms what Behe said above about: "The scientific
community has remained deeply skeptical of these experiments."
KO>Among those who do research in abiogenesis skepticism is based
>either on a bias in favor of genetic material as the determinator of life or
>on certain misconceptions such as the belief that the first functional
>macromolecules had to be a result of random polymerization formations,
>or both.
This is too simplistic. Shapiro is a "protein-first" advocate and he is
sceptical of Fox's proteinoids, suggesting they have no more relevance to
the origin of life than a shadow image of a dog cast on a wall by a child's
fingers has any relevance to real dogs:
"One simple alternative is to presume that the properties of the
microspheres are less significant than claimed. Suppose, for example, that
our monkey had typed a sentence containing more numbers than letters,
rather than a phrase from Shakespeare. It would be nonrandom but
unimportant, indicating only that he had a preference for the upper part of
the keyboard. Similarly, the various properties shown by the microspheres-
division, weak catalytic activity, a double-layered border, electrical signals,
and the rest-may be somewhat general properties of microscopic particles
of a certain size and unrelated, or only slightly related, to the actual
processes of life. During my childhood, I learned that I could make the
shadow of a dog with my hand. I needed only to point my thumb out, bend
in my index finger, and hold my hand before a light to produce the image of
a dog's head on the wall. I could enhance the effect by moving my pinky
while making barking noises. But this form was not a dog, nor could it ever
become one; it was merely shadow play. In the same way, the properties of
the microspheres, while entertaining, may be merely shadow play."
(Shapiro R., 1986, p200).
KO>I therefore find it significant that no other scenario has the same
>degree of experimental continuity, the same degree of environmental and
>evolutionary relevance, and the same degree of success at producing
>living protocellular structures that the proteinoid model has had
First, "the proteinoid model" has had *no* "success at producing living
protocellular structures"! If it did, Fox would not have had to keep doing
the experiment. He would be able to use his original proteinoids to produce
offspring!
Second, to say that "no other scenario has the same degree of experimental
continuity...environmental and evolutionary relevance, and...success" as
"the proteinoid model" is not saying much! As Klaus Dose, a collaborator
with Fox in proteinoid experiments has admitted, "*all*...experiments in
the field either end in stalemate or in a confession of ignorance.":
"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." (Dose K.,
"The Origin of Life: More Questions Than Answers", Interdisciplinary
Science Reviews, Vol. 13, No. 4, 1988, p348)
And Behe points out below that what limited success the proteinoid
scenario has had owes more to "investigator involvement" than to
unintelligent natural causes.
Indeed, as Thaxton, et. al., point out, "most so-called prebiotic simulation
experiments actually owe their success to the crucial but illegitimate role of
the investigator":
"Over the years a slowly emerging line or boundary has appeared which
shows observationally the limits of what can be expected from matter and
energy left to themselves, and what can be accomplished only through what
Michael Polanyi has called "a profoundly informative intervention.". When
it is acknowledged that most so-called prebiotic simulation experiments
actually owe their success to the crucial but illegitimate role of the
investigator, a new and fresh phase of the experimental approach to life's
origin can then be entered. Until then however, the literature of chemical
evolution will probably continue to be dominated by reports of experiments
in which the investigator, like a metabolizing Maxwell Demon, will have
performed work on the system through intelligent, exogenous intervention.
Such work establishes experimental boundary conditions, and imposes
intelligent influence/control over a supposedly "prebiotic" earth. As long as
this informative interference of the investigator is ignored, the illusion of
prebiotic simulation will be fostered. We would predict that this practice
will prove to be a barrier to solving the mystery of life's origin." (Thaxton
C.B., et. al., 1992, p185).
KO>As with our imaginary baker, a heavy odor of investigator
>>involvement hangs over proteinoids. The special circumstance needed
>>to make them-hot, dry conditions (putatively representing rare spots
>>such as volcano rims)....
KO>Incorrect; such spots were more likely to be quite numerous, even
>common.
The simple test of this would be to "such spots" today and see if
proteinoids were forming. If protenoids were naturally occurring
phenomena, and the conditions needed to produce them were "quite
numerous, even common", they proteinoids themselves should also be
"quite numerous, even common".
>MB>...with exact amounts of already-purified amino acids
>>weighed out in advance casts dark shadows over the relevance of the
>>experiments.
KO>The amino acids don't need to be purified or of the alpha configuration, or
>even of the L stereospecificity, and proteinoids have been successfully
>made from a wide variety of amino acid mixture proportions, including those
>found in meteorites, lunar soil samples and in simulated origin of life
>experiments such as Miller-Urey.
If Kevin is saying that the output of a Miller-Urey type chemical evolution
experiment with its minor traces of amino acids and major amounts of
"goo" can be fed as is into the input of a Fox type proteinoid experiment,
and proteinoids are formed, I would request him to post the reference(s).
And again, if it was proteinoids can be made naturally from a wide range of
naturally occurring phenomena, and are "living" and therefore produce
offspring, the proteinoids themselves should be plentiful. So where are
they?
KO>And in fact no scientist has questioned the relevance
>of proteinoid microspheres simply on the basis of experimental protocol.
See my posts where the "scientists" Shapiro, Yockey, and Thaxton, et. al.
have "questioned the relevance of proteinoid microspheres".
>MB>Worse, because proteinoids are not really proteins, the
>>considerable problem of producing authentic proteins remains.
KO>As I have already pointed out, there is no problem because they are
>real proteins.
See above. Even Fox has not said that "proteinoids are not proteins" and
"Proteinoids...the very name indicates that they are not proteins". Indeed, if
"proteinoids" were "real proteins" then why are they called protein-*oids*?
[continued]
Steve
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"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)
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