Re: Probing the Chemistry of Creation B
Sat, 21 Aug 1999 12:33:02 EDT

Here is Part Two.

> >SJ>Even Dose, another protein-first advocate, who has collaborated
> >>with Fox, cannot accept Fox's proteinoid theory.
> KO>This is incorrect. I last spoke to Dose only a month ago. We argued
> >over whether thermal protocells constitute a viable living system....
> Well that is interesting in itself! If Fox and Kevin think that Fox's
> proteinoid microspheres are "a viable living system" and Klaus
> Dose, "an outstanding exponent of the protein-first school of thought"
> (Shapiro R., "Origins", 1986, p268), does not, then why should
> *anyone* believe Fox and Kevin that they are?

Because Dose's opinion is not the final word in the "protein-first school of
thought"; because Dose has been unable to provide any evidence that
demonstrates that thermal protocells cannot be alive whereas Fox and others
have provided a great deal of evidence demonstrating that thermal protocells
are most likely alive; because Shapiro also hales Fox as an "outstanding"
figure in the origin of life field; because scientists like Linus Pauling and
Frederick Sanger have praised Fox as a leading figure in the study of protein
structure and function; because the argument Steve outlines is a logical
fallacy called appeal to authority. Take your pick. In any event, what
matters is not personal opinion, but empirical evidence. The empirical
evidence demonstrates that Dose is wrong.

> Remember this was a key point in Kevin's claim that Behe was a liar:
> ----------------------------------------------------------------
> On Sat, 24 Jul 1999 00:32:45 EDT, wrote:
> [...]
> KO>Since he [Behe] knows that such research does not produce "goo" but
> >in fact living cellular structures, he knew that his statement was
> >factually incorrect when he wrote it. What would Steve call the deliberate
> >writing of a statement that the writer knows is incorrect, if Steve
doesn't call
> >it a lie?
> [...]
> ----------------------------------------------------------------
> If Behe is charged by Kevin as being a liar because he knows that Fox's
> proteinoid microspheres are living, then to be consistent Kevin would have
> to charge Dose with being a liar too?

No, because the situation is that Behe knows that Fox and others have claimed
that thermal protocells are alive, but he pretended otherwise when he wrote
his own claim that origin of life experiments inevitably result in goo
instead of living cells. Dose has never denied that Fox and others claim
that thermal protocells are alive, and admits that he believed that once
himself; Dose also doesn't claim that origin of life experiments inevitably
result in goo instead of cellular structures. Dose still accepts that
thermal protocells are primitive cell-like structures. Dose is very candid
about what he accepts as true, what he does not accept as true, what he used
to accept as true but no longer does, and what he knows others accept as
true, and he doesn't pretend ignorance. In contrast, Behe is rather cagey
about admitting to what he accepts as true, what he does not accept as true,
what he used to accept as true but no longer does, and what he knows others
accept as true, and in this one instance he has pretended ignorance. That is
why Behe lied in that instance when Dose did not.

> KO>but he reiterated his belief that proteinoid microspheres are still the
> >best available explanation for the origin of life.
> Which is not saying much because in a major review of origin of life
> research, Dose said that "At present all discussions on principal theories
> and experiments in the field [which included Fox's proteinoids theory]
> either end in stalemate or in a confession of ignorance:

And as I have continuously explained Dose has told me that when he wrote that
he did not necessarily include thermal protocells in that statement; that it
was intended to be a critique of gene-first research only. He does NOW
believe that thermal protocells have stalemated, but he didn't at the time he
wrote that. And he still accepts that thermal protocells are the best
CURRENT model for explaining the origin of life, despite their deficiencies.
Steve can spin this all he wants, but his implication that Dose no longer
accepts the thermal protocell model as valid is not true.

> "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., 1988, p348)

The last line was meant to encourage gene-first advocates to widen their view
to include the possibility of a protein-first pre-gene world.

> Dose concluded his article:
> "The flow sheet shown in Figure 2 [of the whole origin of life process!]
> a scheme of ignorance. Without fundamentally new insights in evolutionary
> processes, perhaps involving new modes of thinking, this ignorance is
> to persist." (Dose K., 1988, p355).

Again, Dose was not specifically referring to the whole origin of life
process as Steve claims, but only to the gene-first view. The fundamental
new insights he was referring to included acceptance of proteins as the first
carriers of information.

> KO>He simply believes that someday someone will come up with a better
> >explanation.
> Which undercuts Kevin's whole argument. If proteinoids were half as good
> Kevin maintains, then Dose would not be waiting for "someone" to
> "someday...come up with a better explanation"!

Once again Steve is showing his contempt for science; in this case the idea
that any theory must be perfect or it is no good. Science is built on the
premise that any theory -- no matter how perfect it seems to be -- can
ultimately be wrong. Dose can accept that the thermal protocell is the best
CURRENT model while still accepting the (to him likely) possibility that
someday a better model might replace it. That does not invalidate thermal
protocells as a viable model for now, and if in fact they form the basis for
any new, more comprehensive theory, it will still validate them as a useful
idea, if not the whole answer.

> >SJ>Fox's proteinoid model is ignored these days in origin of life
> >>discussions because it is *irrelevant*.
> KO>Like his claim that TE/CE's are marginalized in science and theology,
> >Steve's claim that Fox's model is ignored in origin of life discussions
> >wrong.
> The fact is "Fox's model" *is* increasingly "ignored in origin of life
> discussions". For example, it is either barely mentioned, or not mentioned
> at all in the following major origin of life surveys:

None of which are truly comprehensive surveys, but are instead reviews of the
gene-first point of view. Such "surveys" are not going to discuss rival
models that have more complete answers than the models being surveyed.

> * Orgel L.E., "The origin of life - a review of facts and speculations."
> Trends In Biochemical Science, 23, December 1998, 491-495.
> * Orgel L.E., "The Origin of Life on the Earth", Scientific American, Vol.
> 271, No. 4, October 1994, 53-61.
> * Horgan J., "In The Beginning...", Scientific American, February 1991,
> 109.
> This would be simply *inconceivable* if Fox's proteinoids were only half
> good as Kevin claims.

What is inconceivable is just how dense Steve can be on this subject. These
articles discussed a narrow range of models that reflected the gene-first
view; they were not meant to discuss the whole field comprehensively.

> Kevin might argue that Orgel is biased because he is
> "shamelessly promoting" his own model....

Steve delights in putting words into peoples' mouths. I never accussed Orgel
of "shameless promotion", especially since it was Orgel who made the original
accusation. However, Orgel is convinced that a gene-first scenario is the
only viable explanation for the origin of life, not because he has empirical
evidence to prove it, but because he is professionally biased in favor of
genes as the determinators of life.

> ...but what about John Horgan, a
> *very* experienced science journalist with Scientific American.

I don't know if he "shamelessly promotes" anything, but the point of his
article was to narrowly discuss gene-first models, not to comprehensively
discuss all major models from any point of view.

In any event, the failure of three narrowly topical articles to discuss
thermal protocells in detail is not proof, nor is it even evidence, that
"'Fox's model' *is* increasingly 'ignored in origin of life discussions'."

> KO>People promoting their particular models in the popular press may not
> >mention it, but it gets discussed a great deal at scientific conferences
> >and in scientific journals.
> No doubt Fox's model "gets discussed a great deal at" origin of life
> "scientific conferences" because Fox or one of his disciples....

Character assassination. Fox doesn't have "disciples"; Fox has colleagues
who frequently disagree with him, but who have experimentally verified that
his specific model is valid and relevant.

> ...would always attend such conferences.

Fox is dead, so he cannot attend conferences anymore. And the only people
allowed to raise subjects for discussion are those invited to speak at the
conferences. Since most conferences are hosted by gene-first people, few
protein-first are invited to speak. Mere attendees cannot stand up in the
middle of a conference and suggest topics of discussion. Steve simply
doesn't understand these things.

> Whether the other delegates are interested in the
> discussions is another matter.

Since it is the researchers invited to speak that raise the issues to be
discussed, and since such issues must be approved of by the conference
organizers in advance, if a speaker raises the issue of thermal protocells it
is because the conference organizers wanted him to. And at nine out of ten
conferences there is always at least one speaker who will discuss thermal
protocells, either as part of a lecture or as the main subject of a lecture.
Since the topics to be discussed are published ahead of time, if attendees
didn't want to hear about or discuss thermal protocells, they don't have to
attend the lecture, or even the conference itself. Since no lecture or
conference has ever been cancelled due to lack of attendees -- not even
thermal protocell lectures or conferences-- I would say that most researchers
really do want to discuss this issue, whether Steve believes it is relevant
or not.

> And the same goes for origin of life "scientific journals". Fox and his
> disciples might write articles for origin of life journals but whether
> origin of life researchers are still interested as for that discuss the ,
> See above.

Steve got a little incoherent at the end here (probably from too much
righteous indignation), but if in fact thermal protocells were being ignored
as irrelevant as Steve claims, journals would not publish research reports
about them, for the very simple reason that journals get far more submissions
than they have room to publish, so they are only going to concentrate on
valid, relevant, often cutting-edge research. The fact that copious articles
on thermal protocells are being published every year (Steve has only to
subscribe to Chemical Abstracts to verify that for himself), this would
indicate that the journal editors consider the research valid, relevant and
cutting-edge, even if their readership does not. Again, Steve simply doesn't
understand how this stuff works.

Besides, "origin of life journals" account for only about one-third of the
places where thermal protocell research has been and is being published. The
other journals include general subject journals such as Science, Nature,
Annals of the New York Academy of Sciences and Naturwissenschaften,
evolutionary journals such as the Journal of Molecular Evolution, educational
journals such as the American Biology Teacher and the Journal of Chemical
Education, general chemical journals such as Pure and Applied Chemistry and
Chemical and Engineering News, biological journals such as BioSystems, the
Journal of Bacteriology, Subcellular Biochemistry and Archives of
Biochemistry and Biophysiology, and even specialty journals such as the
International Journal of Quantum Chemistry. The sheer variety of journals in
which thermal protocell research has been and still is being published
indicates that a wide variety of scientists who serve as editors on these
journals are indeed interested in publishing this research.

It should also be pointed out that Fox and his colleagues have often been and
still are invited to submit chapters to scientific books on the origin of
life, even when such books are being edited by scientists who do not accept
the thermal protocell model as realistic. These books are different from
popularizations or even more scholarly texts such as Yockey's book in that
all submissions, even those by the editors, are submitted to peer review.
This would indicate, contrary to what Steve claims, that many scientists who
do not accept Fox's model still consider it valid and relevant and are not
ignoring it, at least not in books that are meant to be comprehensive.

> Fox's proteinoids theory barely gets mentioned in a major article
> in Scientific American on the origin of life, by Horgan who cannot be
> dismissed as "promoting" his "particular model".

Perhaps not, but Horgan was "promoting" the gene-first point of view. The
point of his article was not to do a comprehensive survey of the entire
origin of life field, but to narrowly discuss one point of view, the majority
view, which at present is the gene-first view.

> KO>Whether they support it or oppose it, these scientists do not think it
> >irrelevant. All Steve has to do is subscribe to CAS and he can search
> >databases for abstracts discussing proteinoids, microspheres and thermal
> >proteins. Steve can pick up just about any origin of life conference
> >proceedings from the last twenty-five years and he should find at least
> >article that discusses proteinoids and microspheres, if not more.
> Even if that were true....

It is true; I challenge Steve to prove it is not.

> would underline that Fox's proteinoids are not as
> good as Kevin says they are. Why would "origin of life conference
> proceedings" be still *discussing* "proteinoids and microspheres" for "the
> last twenty-five years" if they were the answer?

More denseness; more contempt for science. The subject is discussed because
it is cutting-edge reseach and therefore of great interest to supporters and
critics alike. There are also people who do not want to accept that the
model is the answer, because that would invalidate their own models, not to
mention the years of research they put into proving their models. As
Rohlfing has pointed out, ego can be a powerful blinder. Other blinding
agents include close-minded bias, over-reliance on contempary models and
confusion or dispute over definitions. [Duane L. Rohlfing, "The Development
of the Proteinoid Model for the Origin of Life," _Molecular Evolution and
Protobiology_, edited by K Matsuno, K Dose, K Harada and DL Rohlfing, New
York: Plenum Publishing, 1984, pg. 41-42.] Even if everyone in the
scientific community accepted that the thermal protocell model was the
answer, it would still be discussed at conferences and in journals as people
continued to do research on it to define it better. Just because a model
becomes generally accepted does not mean that all research and all discussion
on it ceases.

> KO>High school and college students are making their own thermal
> >protocells.
> No doubt. But this is human intelligent design, which is a model of
> *creation* not prebiotic evolution.

Funny, but I wasn't aware that I had god-like powers when I was in high
school or college. Steve's objection is a ridiculous strawman; the ability
to manipulate conditions in an experiment is not the same thing as being able
to create novel physiochemical forces and mechanisms that could never exist
in nature. Experiments can only imitate what nature could do; they cannot do
what nature would never be able to do under the right circumstances.

> The questions are: a) is unaided *nature* "making...
> thermal protocells"....

What Steve means is whether nature is making thermal protocells now; as I
have stated before this is impossible to answer because wherever you could
find protocells you would also find bacteria, and protocells make excellent
bacteria chow. The more appropriate questions are whether nature could under
the right circumstances make protocells, and did those conditions exist on
the primordeal earth? Empirical evidence has demonstrated that the most
likely answer to both questions is yes.

> ...and b) are "thermal protocells" anything to do with the
> origin of life?

Since thermal protocells are the only current model that provides the
evolutionary continuity between simple chemicals and living cellular
structures, the answer to that question is an emphatic yes.

> KO>It is even being discussed in textbooks: Lehninger was the first back
> >1970 and again in 1975; the most recent has been _Principles of Cell and
> >Molecular Biology_, Second Edition (1995) by Lewis J. Kleinsmith and
> >Valerie M. Kish.
> My understanding is that Lehninger's mentioning of "proteinoids and
> microspheres" in his biochemistry textbook is unusual:
> "Sidney Fox has not merely served as a rallying point for the
> group, but has advocated the particular system of proteinoid microspheres,
> first demonstrated in his laboratory in the late 1950s, as the solution to
> the origin-of-life problem. Needless to say, this position has made him a
> center of controversy. His system has received favorable attention in the
> media and in a number of texts, most notably A. L. Lehninger's widely used
> Biochemistry, which termed it remarkable." (Shapiro R., "Origins", 1986,
> pp191-192)

Shapiro says nothing about Lehinger's treatment being unusual. His last
statement is a paraphrase of Lehninger's description of thermal protocells:
"Self-forming, cell-like structures, called *microspheres*, have been
described in great detail by Fox and his colleagues. These remarkable
bodies...." [Albert L. Lehninger, _Biochemistry_, Second Edition, New York:
Worth Publishers, 1975, pg. 1047.]

> Interestingly, Lehninger's more recent "Principles of Biochemistry" (1982)
> does not even mention Fox's proteinoid microspheres *at all* even though
> he does mention the origin of life and the Miller-Urey experiment. This
> would be inexplicable if Fox's proteinoids were even half as good as Kevin
> says they are.

Another fallacious argument: unless thermal protocells are prominantly
mentioned in every textbook ever published, they cannot be any good. In
Lehninger's previous textbook, he dovoted a whole chapter to the origin of
life; that gave him the space to discuss the basic concepts and the best
models in detail. Lehninger's later textbook was not meant to be as
comprehensive as his earlier textbook; in fact Lehninger left out or barely
mentioned a good many topics he had dealt with in greater detail in his
previous textbook. The origin of life received only a short discussion and
dealt with only the basic concepts; Lehninger didn't discuss any model, not
even the gene-first models he had discussed previously. So there is nothing
significant in Lehninger's failure to mention thermal protocells.

And of course Steve ignores the fact that an increasing number of modern
textbooks are discussing thermal protocells.

> KO>The conclusion is obvious: thermal protocell research is not irrelevant
> >to those who know and understand it, whether they support or oppose it
> So now Kevin admits that Fox's "thermal protocell" (notice how the name
> keeps changing!)....

Notice how Steve keeps bringing up trivia to hide the fact that he has no
substantial critiques of the thermal protocell model; and thermal protocell
is my name for the structures, a contraction of thermal protein (proteinoid)
microsphere protocell, which are still the scientifically accepted terms.

> ...*is* opposed by some origin of life researchers "who know
> and understand it"?

I don't recall ever denying this; at best, what I stated was I couldn't find
critiques published in the scientific literature post-1990. On the other
hand, the critics that Steve quotes do not know or understand the model.

> Why can't Behe be in that category?

Because those who do know and understand the model do not repeat the same
misconceptions that Behe does, and they present critiques that have been
validated by empirical evidence and are not simply based on theoretical or
speculative concepts. Nor do they lie by saying that origin of life
experiments produce goo instead living cells.

> Or are all these researchers who "who
> know and understand" "thermal protocell research" also liars?

Steve is starting to get belligerant here; he may be trying to get me to
loose my temper and strike back. Since as far as I know none of those
researchers who know and understand thermal protocell research have ever
stated anything that they knew was false when they stated it -- as Behe had
done -- I cannot say that any have ever lied.

And I am not claiming that Behe is liar; all I have ever claimed is that Behe
lied in one instance. One lie does not a liar make, and I have no evidence
that Behe ever lied in any other instance.

> KO>it is only irrelevant to those who don't know it or don't understand
> >>or don't want to.
> This is another example of pseudoscientific reasoning, which enables Kevin
> to dismiss anyone who claims that Fox's "thermal protocell research" is
> "irrelevant" as among "those who don't know it or don't understand it, or
> don't want to".

Except that in fact I did not simply "dismiss" anyone; so far I have been
able to **demonstrate** that all those whom Steve has quoted as supporting
his claim that thermal protocells are irrelevant in fact do not know or
understand the model; which also suggests that Steve's claim of irrelevance
is his own idea, since none of his non-creationist, non-ID theorist sources
actually claim that thermal protocells are irrelevant. Steve has chosen to
ignore my demonstrations and pretend that I am simply "dismissing" people,
because he cannot refute my arguments. And now that he has declared that he
will not even try to refute them, we can expect further mischaracterizations
on his part in a further attempt to avoid the real issue: the empirical
validity and evolutionary relevance of the model.

> Since this post seems to encapsulate in shorter form all the essential
> issues in the "God, sort of" threads, I think I will set them aside for now
> and just pursue this thread with Kevin for a short while.

Translation: I cannot deal with the evidence Kevin has presented in the
various "Re: God...Sort Of" posts; since this thread discusses no evidence, I
want to concentrate on this so Kevin cannot make me look like a fool.

Except that I have no desire to repeat the same responses to the same
objections simply because Steve will not discuss the evidence. Therefore,
unless Steve starts to actually present empirical evidence to support the
validity of his critiques or to refute my empirical evidence, I see no reason
to continue pursuing this further. Steve may have the last word; no doubt he
will do what he can to claim victory.

Kevin L. O'Brien