Re: God...Sort Of #4 A
Sun, 15 Aug 1999 14:03:01 EDT

Greetings to One and All:

This latest of Steve's posts also contains nothing new, so it was tempting to
ignore it. However, Steve does raise a few issues that should be pointed
out. Because of its length, AOL has once again forced me to post it as two
separate parts. My apologies for the inconvenience and I beg everyone's

> [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"?

My apologies, I should have made my point more clear. Berlinski was writing
post-1990 (1996 to be exact), yet none of the critiques he cites is later
than 1984. Berlinski claims that Fox "has not" (present tense) persuaded the
biological community, implying that the biological community still does not
accept his model as valid. Therefore I would have expected Berlinski to cite
some post-1990 critiques. When I said I couldn't find any critiques in the
scientific literature, I meant that I couldn't find any published in
scientific journals after 1985. Books, even scholarly books like Yockey's,
are not peer reviewed before publication, so the author can in essence say
whatever he likes regardless of whether he can back it up or not. Scholastic
integrity hopefully should prevent him from making baseless assertions, but
peer review guarantees that this will not happen. Therefore, I find it
significant that there have been no critiques published in peer-reviewed
journals since 1985. More about that later.

In any event, Berlinski cannot support his claim that the biological
community at the time he wrote (1996) still would not accept the proteinoid
model as valid, considering that his most recent cited critique was published
some 12 years earlier! Nor can he claim that "criticisms of it are
overwhelming" when he could cite only 4 references covering an 8 year period,
and could cite no current critiques, not even Yockey.

> 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)

See above; I also find it interesting that apparently no further critiques
were published in peer-reviewed journals after this paper was published.
More about that later.

However, what I find even more significant is that Steve has read this paper.
He probably read it necause it was part of an anti-creationist volume, but
the point is he still read it. The reason why that is significant is
because, during all this time he has been demanding that I back up my
"assertions" with evidence quoted from references, he has known what this
evidence is all along! In other words, he knew that the claims I was making
were correct, because he already knew what evidence there was to back up my
claims. He may not believe that evidence is valid, but he knows it exists
and he knows what it is. I therefore consider disengenuous his statement
that, unless I could provide evidence in the form of quotes from references,
he would conclude that I have no evidence to back up my claims, because in
fact he knows I have such evidence and he knows what it is.

For me, this changes the whole complextion of the discussion. It is no
longer about whether I can provide evidence to support my claims; it is now
about why Steve considers that evidence to be invalid, or at least
unconvincing. If he can provide evidence of his own to show that my evidence
is invalid, or if he can at least explain why he considers the evidence
unconvincing, then our discussion can move forward.

> >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
> >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.

First of all, notice how Steve avoids my point. If the thermal protocell
model were not taken seriously in the abiogenetic community, then one would
expect at least a few papers objecting to Pappelis' and Fox's proposal. The
fact that there were none indicates that the idea is in fact no longer so
outrageous that it cannot be accepted even as a working hypothesis. In other
words, the idea is becoming more tolerable as the evidence mounts.

Secondly, there is no "mainstream origin-of-life community". There are two
rival views -- protein-first and genes-first -- and while the latter has the
most adherents, there is enough factionalism within it -- RNA world,
panspermia, clay mineral templates, peptide-initiation, to name but a few --
to keep any one model from predominating. The thermal protocell model is
largely ignored by genes-first people because it is a rival model that has
been far more successful than the different genes-first model have ever been,
not because there is anything invalid about it.

Thirdly, while I'm sure there are some scientists who consider thermal
protocells a dead issue, the real reason why there have been no critiques
published in peer-reviewed journals is because the editors of those journals
will no longer tolerate assertions that are not backed up by experimental
evidence. In other words, around about 1985 they apparently started
requiring that critiques be tested before they are published. Since most
critics have no desire to put their critiques to the test, they stopped
trying to publish them in peer-reviewed journals and started publishing them
in books, as part of letters, editorials or book reviews, or as review papers
presented at symposiums. Symposium presentations are peer-reviewed, so they
are part of the scientific literature, but review articles can present
critiques in the absence of supporting evidence as part of an historical
perspective. Books are marginally scientific literature, because while they
are not peer-reviewed, they are often based on peer-reviewed literature, and
conscientious authors will have their colleagues review the book for
scientific accuracy. As such, a book can be accepted as part of the
scientific literature if its claims are well documented and if the author is
an expert on or a researcher in the field the book discusses. In my opinion,
Yockey's book fails as being part of the scientific literature on thermal
protocells because he does not adequately document his claims and he is
himself neither an expert on nor a researcher in abiogenesis. Letters,
editorials and book reviews are not part of the scientific literature because
they are not peer-reviewed.

In any event, the point is, the most likely reason there apparently have been
no peer-reviewed critiques post-1985 is because the critics cannot back up
their critiques with experimental evidence.

> 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.

Of course not. That paper was written by a genes-first advocate to describe
the latest in genes-first evidence, research and speculation, not to
generally discuss the basic concept. In fact, it didn't mention **any**
protein-first model at all.

> >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.
> index to his book "Genesis on Planet Earth: The Search for Life's
> does not mention God or creation.

Well, in every life some crow must be eaten. However, this is due to a
rather big coincidence.

When I was in graduate school I knew a creationist named Wilson Day. He
self-published a book (pamphlet really) entitled "Genesis on Planet Earth",
in which he critiqued proteinoid microspheres. He claimed for himself
degrees that he had not earned in fields that in fact he knew nothing about.
He boasted that he had sold his book to every major scientific creationist in
the world. As such, when I saw Berlinski's reference, I assumed it was the
gentleman I knew. It was only after I discovered that both Yockey and Fox
cite a book of the same title by a **William** Day that I realized I had made
a mistake. As Steve rightly points out, this Day is not a creationist in the
sense that I meant the term. See below.


> But even if Day was "a creationist" why would that rule him out as a
> of prebiotic evolution?

I admit that this was a poor choice of words on my part. The Day I knew was
not just a creationist in the sense that he believed that God created the
Universe. He was also an anti-evolutionist (in that he rejected any
possibility that evolution in any form could explain any form of origins) and
an anti-materialist (in that he rejected any possibility that there were or
even could be materialist explanations for origins). Since I thought the Day
Berlinski was referring to was my Day, I used the term creationist to mean
anti-evolutionist and anti-materialists. I did that because most people on
this list, even the creationists, know that when an evolutionist uses the
term creationist he or she means anti-evolutionist and anti-materialist.
Whether or not list creationists agree with that definition is irrelevant;
for better or worse, that is how most evolutionists see the average

The point is, if as an anti-evolutionist and anti-materialist you would a
priori reject any possible evolutionary and/or materialistic explanation, you
are not going to examine the evidence objectively. In fact, you would have a
vested interest in discrediting the evidence if you could, so that no one
else would believe it either.

> 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*.

Any scientific theory can be validly criticized only by people who are
open-minded, who will let the evidence itself, and not their
philosophical/religious beliefs, determine whether the model being critiqued
is valid and relevant; in other words, they have to be willing to accept that
the model is valid if the evidence demonstrates that it is. To effectively
critique a model, you first have to learn all you can about it, not just what
other critics say, but what the supporters say as well. Then you identify
any weaknesses that prevent you from accepting the model completely. Then
you test those weaknesses and publish the results, regardless of whether they
support the critique or not. The ineffective way to critique a model is to
simply raise theoretical or speculative objections without testing them.
This is what Shapiro tends to do. The invalid way to critique a theory is
(to paraphrase Charles Darwin) to not take the trouble to understand the
model. This is what Yockey and Davies have done.

> Besides, if being "a creationist" makes one "hardly an unbiased observer"
> then that applies to Kevin also, because Kevin describes himself on
> of his web page as "a creationist", indeed even a "a fundamentalist":
> "As a fundamentalist, evangelical Christian, I naturally believe the
> 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."
> html

Steve has a valid point, but only in so far as the basic definition of
creationist is concerned. Nowhere in that essay do I describe myself as
either an anti-evolutionist or an anti-materialist, so I do not a priori
reject any possible evolutionary or materialistic explanation of origins. As
such, my use of the term creationist (inexact as it might be) in fact does
not apply to me.

> 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
> way they are usually defined!

This is another example of Steve's own brand of shooting the messenger,
except that it now takes on new meaning consider the revelation outlined
earlier in this post. Rather than being an excuse not to listen to my
evidence -- since after all we now know that he knows exactly what this
evidence is -- it is an attempt to convince others that I am not worth
listening to, in the hope that they will not read the references I have
provided and thus learn the evidence for themselves.

> 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).

Notice first of all that the only peer-reviewed paper listed was published in
1959, just as proteinoids were first being synthesized and before
microspheres were discovered; Jukes & Margulis is a letter and the rest are
books. Secondly, notice that the latest critique Yockey could find was 1984,
when in fact Yockey was writing this in 1992, almost 8 years later! In other
words, Yockey is depending upon outdated, possibly even obsolete critiques
rather than trying to ascertain the true state of thermal protocell research
at the time of writing. Thirdly, it should be pointed out that Fox and his
colleagues have effectively refuted all the critiques listed in the above
citations, refutations that Yockey ignores.

> Most of
> the objections to the proteinoid scenario come directly from the work of
> Fox and his followers.

Yockey must have a pretty big chip on his shoulder about thermal proteins,
because this sentence contains two simulataneous mischaracterizations.
Notice that Yockey says, "Fox and his followers" rather than Fox and his
colleagues. Elsewhere in the same section Yockey says, "Fox and his
disciples" (see a quote later in this post). Clearly Yockey is trying to
paint a picture of a group of zealots led by a fanatical leader out to
promote a particular worldview rather than a picture of a dedicated scientist
and his colleagues fascinated by an interesting phenonmenon. Such subtle ad
hominem attacks can prejudice a reader againgst an idea without him or her
being aware of it.

The second mischaracterization is when Yockey says that thermal protein
researchers have raised objections to their own model. Certainly that is
part of research, but in fact the statements that Yockey claims are
objections (see below) are in fact descriptions of the chemical and
structural nature of thermal proteins, not objections to their validity.
They are meant to show how thermal proteins are not like contemporary
proteins; they are not meant to be problems that must be overcome to validate
the model.

> 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....

This is true of lysine-rich thermal proteins (which is what Dose was
investigating), but not for all types of thermal proteins. Acidic thermal
proteins (those rich in aspartate or glutamate) and neutral thermal proteins
(those that contain equal amounts of acidic and basic amino acids or are
glysine rich) can yield 100% amino acids after 2-4 days hydrolysis. They
also have far fewer crosslinkages, with neutral thermal proteins having
virtually none. See Fox and Dose (1977) _Molecular Evolution and the Origin
of Life_, Revised Edition, for more details.

> ...such cross-links disturb most of
> the sequencing methods typically used in protein chemistry....

True, but many contemporary proteins have the same problem. Crosslinkages in
contemporary proteins can in fact be common.

> ...the optically
> active amino acids racemize during the heating process....

But the process is incomplete; see Fox and Dose (1977) _Molecular Evolution
and the Origin of Life_, Revised Edition, for more details.

> ...and no helicity was detected (Fox, 1973).

There are also contemporary proteins that produce no helices at all. The
point is, that despite Yockey's claims, thermal proteins are really not all
that different from many contemporary proteins.

> 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.

According to experimental results, polypeptides made from polynucleotides
synthesized from thermal protein templates have a high optical purity,
indicating that this racemization is no bar to the eventual production of
optically pure proteins. The reason why modern proteins are optically pure
is because the molecular machinery that synthesizes modern proteins
recognizes only L-enantiomeres. Research evidence suggests that when thermal
protocells developed the machinery to synthesize polypeptides, they would
produce optically pure proteins as well.

> The low yield of amino acids
> after prolonged hydrolysis indicates extensive cross-linkages (Folsome,
> 1976).

See above. This affects only a few types of thermal proteins; the vast
majority can in fact yield 80-100% amino acids after prolonged hydrolysis.
In many modern proteins, special agents are needed to break crosslinkages
before you can 100% hydrolysis as well.

> Andini et al. (1975) and Temussi et al. (1976) showed by nuclear
> magnetic resonance and paramagnetic resonance that thermal polypeptides
> contain only beta-peptide linkages.

This is not true. They determined that **polyaspartate** thermal polyamino
acids contained 100% beta-peptide bonds; they tested no other type of thermal
polyamino acids. However, these authors created their thermal polyamino
acids using a different method than that used to create to thermal proteins.
Since the chemical and structural nature of polyamino acids are known to be
sensitive to method conditions, it is by no means certain that Andini/Temussi
et al. (the authors in both papers were exactly the same) were even working
with real thermal proteins. On top of that, they only examined a small
fraction of the polyamino acids they prepared. Hence they might have
inadvertantly overlooked polymers that had higher propartions of alpha-amino

Meanwhile, an earlier study showed that polyaspartate thermal proteins have a
mixture of alpha- and beta-peptide bonds in a ratio of 1.0:1.3 respectively;
that translates into 45% alpha-bonds, 55% beta-bonds. Other studies have
shown that polyglutamate thermal proteins contain only alpha-bonds, whereas
some lysine-rich thermal proteins contain a small proportion of
epsilon-bonds. See Fox and Dose (1977) _Molecular Evolution and the Origin
of Life_, Revised Edition, for more details.

> 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.

As I have shown above, this conclusion was based on poorly designed and
executed experiments, and ignores other, contradictory results; it is also
based on the misconception that any real protein must be identical to modern
proteins. Even if it were true, however, the fact that the model requires
that polynucleotides be made from thermal proteins first, then used as
templates to make polypeptides means that the presence of non-alpha-bonds in
the thermal proteins would not prevent the exclusive use of alpha-bonds in
the resulting polypeptides.

> 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)

Yockey does, however, conveniently leave out Fox's refutation, as well as the
other experimental evidence that supports Fox.

> >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
> >needed to be investigated.
> This very reference has "eds. J.L.Fox"!

Is Steve for real here? This is a different Fox. The thermal protein Fox is
Sidney W. -- S.W. -- not J.L. Even if it was the same Fox, what relevance is
this suppose to have? Berlinski was implying that Dose was a critic; I was
pointing out that in fact Dose was a collaborator and a supporter, and that
his paper was not a critique, but an evaluation of where the research should
go from where it was at that point in time (1976).

> 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)

I have already dealt with this. Dose was specifically critiquing the RNA
world line of research. He has told me in a personal communication that he
believes that the thermal protocell model has also stalemated, but he also
stated that it is still the best model currently available to explain much of
the origin of life.

> >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.
> >> >>
> KO>And again, these last two articles are not really critiques at all,
> >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"?

Steve's denseness is unbelievable. It didn't say that I doubted Berlinski
had read the articles, I said that assuming he had (I have no idea whether he
did or not, but it is easier to assume he did than to assume he did not), I
tend to doubt that he understood what he was reading. The basis for this is
that he misunderstood what Folsome and Ponnamperuma were trying to do; he
characterized them as criticizing the thermal protein model when in fact they
were only pointing out what they saw as questions that needed to be answered.

And once again Steve is avoiding the real issue: Folsome and Ponnamperuma
were not critiquing the model's validity or relevance; they were suggesting
avenues of research to address specific questions.

End of Part One. Part Two will be posted when Part One has propogated.

Kevin L. O'Brien