Group

Here is an update by creationist/IDist Walter ReMine on Haldane's Dilemma
(see tagline and below), the basic idea of which, as I understand it, is that
for a
new (e.g. beneficial) allele to completely substitute at a gene locus on a
chromosome for the existing (less beneficial) allele, all the members of the
population carrying that existing allele would have to die and be replaced by
members of the population carrying that new allele. Their `selective death' is
the `cost of substitution' and the late J.B.S. Haldane (a pioneer of
mathematical population genetics) calculated the cost to be so high that
typically it would take an average of 300 generations for such a single allele
replacement.

In addition to the tagline quote by Neo-Darwinism co-founder Mayr, here are
two brief statement of the problem by Darwinian heavyweights, Haldane's
student, the late John Maynard Smith:

"Kimura's estimate is based essentially on an argument first put
forward by Haldane 4 (Haldane J.B.S., J.Genet., Vol. 55, 1957,
p511); it is this argument which I believe to be erroneous. Haldane
bases his argument on the idea of the "cost" of natural selection.
The unit step in evolution is the substitution of one allele, say A,
for another, a, in a population. This happens because individuals
carrying the gene a are killed selectively or because they have a
lower fertility. The larger the number of selective deaths, the more
rapidly will gene frequencies change. Haldane estimated the total
number of selective deaths (that is, deaths of individuals who
would have survived had they had the optimum genotype) required
to substitute one allele for another. He concluded that, for a diploid
population with moderate selective advantage, the total 'cost" of
selection would be between 10 and 100 times the population size,
per gene substitution. Now there is an upper limit to the number of
selective deaths which can occur in one generation. Thus if, for
example, a population consisting wholly of individuals of optimal
genotype could in favourable circumstances increase by a factor R.
then the fraction of selective deaths cannot be greater than (R-1)/R
per generation. This places an upper limit on the rate of evolution."
(Smith J.M., "`Haldane's Dilemma' and the Rate of Evolution,"
Nature, Vol. 219, 1968, p.1114)

and another in a book co-authored by two other Neo-Darwinism co-
founders Dobzhansky and Stebbins:

"HALDANE'S DILEMMA Consider a population in which a gene
A1 confers on its carriers a Darwinian fitness greater than in the
carriers of A2. Natural selection acts to enhance the frequency of
A1 and to reduce that of A2. This may happen because the progeny
of A1 survive more frequently than of A2, or because the former
have a greater fecundity, sexual activity, longevity, or any
combination of these and other advantages. Whatever the cause,
one may say that carriers of A2 are eliminated by `genetic deaths.'
Substitution of more favorable for less favorable alleles by natural
selection occurs at a `cost,' and imposes upon the population a
`substitutional' genetic load. The concept of substitutional load has
a paradox at its core. Imagine a population in which every member
has a high Darwinian fitness; a new and still more favorable
mutation arises; now every member except the carrier of the
mutant has a new genetic load that must be eliminated for the
population to reach a still higher level of fitness. In 1957 Haldane
analyzed the consequences of this situation. During the passage of
a favorable mutant from its origin to fixation many individuals
have to suffer genetic death; the number of such individuals is
generally much greater than the number of individuals alive in any
one generation. Crow and Kimura (1970) give the following
example of gene substitution `if the typical allele has an initial
frequency of l0^-4, a population of one million individuals will
have to have nine million genetic deaths each generation if it is to
substitute an average of one allele per generation. Or more
probably, if there is to be a gene substitution every 100
generations, the average fitness will be lowered by 0.09.' Now, in
evolution many genes must be changed to transform one species
into another. Granted that most living species produce numbers of
progeny far in excess of those needed to have the population
survive, it is difficult to understand how evolution can happen at
such an enormous cost in genetic deaths. Haldane saw clearly that
he was confronted by a dilemma. In his words, `I am quite aware
that my conclusions will probably need a drastic revision. But I am
convinced that quantitative arguments of the kind here put forward
should play a part in all future discussions of evolution."
(Dobzhansky T., Ayala F.J., Stebbins G.L. & Valentine J.W.
"Evolution," W.H. Freeman & Co: San Francisco CA, 1977,
pp.163-164)

A creationist/IDist called Waler ReMine who is (unlike me and no doubt a
lot of other people, including I suspect most evolutionary biologists) is
able to understand the mathematics and has been pointing out the problem
that Haldane's Dilemma poses for Neo-Darwinism (e.g. in his book, "The
Biotic Message" (1993) and debating it on the Internet against all comers
for more than a decade.

ReMine claims (see below) that all the Neo-Darwinist attempts to evade
Haldane's Dilemma fail, and he eventually wrote a paper on it and
submitted it to the peer-reviewed Journal of Theoretical Biology, receiving
favourable reviews from some of the reviewers, e.g. very exciting and
potentially paradigm shifting," "The paper is hugely exciting in that it is a
glimmer of a new paradigm of population dynamics," "I agree with a very
large proportion of what ReMine says," "Its straightforward approach to
the issue of the cost of evolution may be valuable. .... Some issues raised
in the manuscript are definitely interesting," "The author's main point .... is
a good point", "I strongly recommend this paper be published. I believe it
will revitalize discussion/investigation within an area of population
biology which has otherwise become bogged down and neglected. ...
ReMine offers a fresh perspective on this old problem," "He shows this
not only clarifies the whole problem conceptually, but allows much
cleaner and more generalized computations of cost - in a way that is very
clearly connected to the real world. This paper has significantly impacted
my own understanding of the problem of substitution cost. Even those
who may take exception to ReMine's general approach, should benefit
from the resulting stimulation of dialog." Yet, after *two years*, ReMine's
paper was rejected, on the grounds that the "paper is correct, but ... it is
`not new'", which, given the reviewer's comments, is obviously FALSE.

My point here is not to argue that Haldane's Dilemma is not a problem for
evolution (in fact I have added a new subsection PE 9.2.1 "Neutral ...
Haldane's Dilemma" to my "Problems of Evolution" book outline
(http://members.iinet.net.au/~sejones/pe00cont.html)"

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http://members.iinet.net.au/~sejones/pe09mech.html#mchnsmstnsntrlhldnsdlm
"PROBLEMS OF EVOLUTION": 9. MECHANISMS [...]
2. Neutral
1. Haldane's Dilemma [...]
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but rather, my point here is one that ReMine makes:

"You've heard the accusation that creationists `do not publish in
mainstream peer-reviewed journals.' Well, my paper is a test case.
Haldane's Dilemma is an important evolutionary problem, and my
paper provides a clarification that is long overdue. My paper is
error free, and has been deemed correct by capable authorities. It
has been re-written many times to meet their recommendations.
Nonetheless, they refuse to negotiate a suitable publication of it."

So we now have the answer to evolutionist Arthur Shapiro's prediction
(albeit a different journal and two years late - ReMine's paper was
presumably submitted to JTB in 2002):

"For the moment, the authors of The Creation Hypothesis are
realistically defensive. They know their way of looking at the
world will not be generally accepted and that they will be restricted
for a while to their own journals. .... If they are successful, the day
will come when the editorial board of Science will convene in
emergency session to decide what to do about a paper which is of
the highest quality and utterly unexceptionable, of great and broad
interest, and which proceeds from the prior assumption of
intelligent design.'" (Shapiro A., Review of Moreland J.P., ed.,
"The Creation Hypothesis," InterVarsity Press, 1994, in
Creation/Evolution, 1994, in Johnson P.E., "Reason in the Balance:
The Case Against Naturalism in Science, Law, and Education,"
nterVarsity Press: Downers Grove IL, 1995, p.239)

namely, that evolutionists will *never* publish from a known
creationist/IDist a "paper which is of the highest quality and [other than
undermining Darwinism] utterly unexceptionable, of great and broad
interest, and which proceeds from the prior assumption of intelligent
design.'"

ReMine concludes:

"Their attempt, to likewise silence my paper, cannot stand. I here
announce my desire to locate a suitable peer-reviewed journal. If
you are such an editor, please contact me with your interest. My
paper is titled, "Cost Theory and the Cost of Substitution - a
clarification." Under the present environment, I might have to give
up my multi-year effort, and publish instead in a creationist
journal. I do not desire that. But if it comes to that, the fall-out will
be on evolutionary authorities heads, not mine."

Steve

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http://www1.minn.net/~science/a_tale_of_peer-review.htm
Update on Haldane's Dilemma
A Tale of Peer-Review
by Walter ReMine

January, 2005

Background: Since 1993 I have argued that the central concept in
Haldane's Dilemma [http://www1.minn.net/~science/Haldane.htm] -
known as the cost of substitution - has been widely misunderstood and
confused. All previous authors defined it using at least one (and often two
or more) of the following concepts:

Genetic death Genetic load (or substitutional load), fitness, and fitness
values Environmental change (such as environmental deterioration)
Extinction (and its avoidance) Selection - the type of selection ("soft
selection" versus "hard selection") I claim all those are confusion factors,
and unnecessary for defining or understanding the cost of substitution.
Taken in various combinations, they are sources of numerous false
"solutions" to Haldane's Dilemma, including:

Soft selection "reduces" the cost of substitution, and "solves" Haldane's
Dilemma. The total cost of substitution is 1 (not 30 as claimed by
Haldane). The cost of substitution is "an illusion." The cost of beneficial
substitution is "zero." In a non-deteriorating environment, there is no cost
of substitution. Beneficial substitutions "pay for themselves." So there is
no cost problem. "The cost of not evolving is greater than the cost of
evolving." If substitutions occur too quickly, then the cost of substitution
will make the population go extinct. Since populations obviously avoid
extinction, there really is no cost problem. For example:

J.B.S. Haldane embraced 1, & 3. James Crow's papers propound 1, & 2.
Bruce Wallace's book embraces 2, 5, & 6. Fred Hoyle's book embraces 1,
7, & 8. Joe Felsenstein actively promotes 3, 4, 10, & 11. Warren Ewens's
papers profusely use 2. Many pro-evolution websites promote the above
items, and receive no detectable objection from evolutionists. For
example, talk.origins promotes the notion that "With corrected
calculations, the cost disappears." For solutions to Haldane's Dilemma, the
most frequently recommended website promotes a smorgasbord of the
above items.1 Again, with no detectable objection from evolutionists.

During lengthy tours of the science discussion group, sci.bio.evolution, I
challenged evolutionists to address these fundamentals and resolve their
confusions and contradictions. Unfortunately, those are entrenched in the
literature, so evolutionists made little or no progress. Confusion reigns. I
attempted to show the true nature of the cost of substitution, and
evolutionists met my material with widespread ridicule and derision. They
treated my cost concept as something unfamiliar. (Link1, Link2, Link3,
Link4)2

Pause to verify that the above listed confusions occur abundantly, in the
literature and on the Internet today.

1 Note: That website abundantly misrepresents my material. As a source
of insight on my material, that website is less than worthless.)

2 Especially see the posts by wjremine, laser_thing, and Joe Felsenstein.
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Update: Three stages in the acceptance of a new idea: First they ridicule it.
Then they deny it. Then they say they already knew it.

There exists widespread confusion about the fundamentals of Haldane's
Dilemma. (See box to the left.) To remedy the situation, I wrote a paper
for the science journals. My paper identifies and rejects the confusion
factors (items 1 thru 5), and proposes a clarified cost concept on new
foundations. Directly from this new foundation it re-derives Haldane's cost
equations (for haploids, and diploids) and supplies a simpler, clearer,
physical basis for Haldane's argument (now known as Haldane's
Dilemma). My clarified cost concept works under all circumstances
(including non-constant population sizes, continuous-generation models,
and neutral substitutions) - which the traditional cost concept could not
handle. My paper shows the traditional "solutions" (items 6 thru 13) are
false. For extra emphasis, my paper directly states that (other things being
equal) "environmental change and soft-selection cannot reduce the cost
one iota." To put it bluntly, my paper runs directly contrary to the
prevailing winds.

My paper has been under peer-review for over two years. So how has it
fared?

The reviewers included well-known authorities: Warren J. Ewens, James
Crow, Alexey Kondrashov, Joe Felsenstein, and many others. Other than
one typo, no errors have ever been found. In fact, Warren Ewens
commented in detail and at length, itemizing his agreement with my paper.
My paper is correct. That will come as a shock to many people.

Reviewer #2 at the Journal of Theoretical Biology found my cost concept
to be "very exciting and potentially paradigm shifting." and "The paper is
hugely exciting in that it is a glimmer of a new paradigm of population
dynamics." At Theoretical Population Biology the four reviewers wrote of
my paper:

"I agree with a very large proportion of what ReMine says." (Warren
Ewens - His one disagreement was trivial.1)

"The author champions a clearly-defined concept of cost. .... Its
straightforward approach to the issue of the cost of evolution may be
valuable. .... Some issues raised in the manuscript are definitely
interesting." (Alexey Kondrashov)

"The author's main point .... is a good point" (James Crow, in an extremely
brief, half page review)

"I strongly recommend this paper be published. I believe it will revitalize
discussion/investigation within an area of population biology which has
otherwise become bogged down and neglected. I believe the conceptual
framework of 'genetic load' has generally led to an unfruitful morass.
ReMine offers a fresh perspective on this old problem. Instead of
understanding cost/load in terms of "genetic deaths", ReMine forcefully
argues that we should understand this issue entirely in terms of required
reproductive excess. He shows this not only clarifies the whole problem
conceptually, but allows much cleaner and more generalized computations
of cost - in a way that is very clearly connected to the real world. This
paper has significantly impacted my own understanding of the problem of
substitution cost. Even those who may take exception to ReMine's general
approach, should benefit from the resulting stimulation of dialog."
(Reviewer #4 at Theoretical Population Biology ) Nonetheless, after
several different journals, and after many reviewers, and many re-writes to
meet their recommendations ? authorities again rejected my paper. But this
time, at Theoretical Population Biology, for an entirely new, astonishing
reason. A reason not given at any previous journal, by any previous
reviewer. In fact, for a reason contradicted by every previous reviewer.
And this time it was their only reason that wasn't trivial.2 That is, Warren
Ewens and James Crow acknowledge my paper is correct, but claim it is
"not new" and that authorities knew my material at least "twenty years
ago", so my paper isn't needed. (Indeed, reviewers Ewens and Crow each
tried to personally claim priority for my material.) That's remarkable, since
my paper richly contradicts the established view, and continues far beyond
anything previously published.

I pleaded these points to them:

Their claims of priority are: extremely limited in scope, ambiguous in
nature, loaded with confusion factors, and remain confused even to this
day. Also, my paper already cites Ewens and Crow, and already allots
them priority to the full extent that can legitimately be allowed. (I
documented my points by a detailed comparison of my paper versus the
papers they cited.)

Prior authorities ALWAYS defined the cost of substitution based on
confusion factors (see the box to the left) - and my paper explicitly rejects
those confusion factors. So my cost definition is novel.

Their definition of cost is one thing. How-and-why it would limit the
substitution rate is an additional difficulty. There is a large gap in physical
reasoning between the two. Prior authorities NEVER filled-in the large
gap in physical reasoning. (To help you see that, take my challenge on
genetic death and genetic load.) In contrast, my paper provides a simple,
compelling, general purpose, physical basis for Haldane's argument, based
upon a cost definition that remains consistent throughout. No other author
does what my paper does.

They are contradicted by a world of documentation on the Internet, easily
verified with search-engines. (See the box to the left.) It overwhelmingly
documents the predominance of confusion and false "solutions." It also
documents that my cost concept (the same one Ewens and Crow claim was
widely known decades ago) is absent from evolutionist accounts, and
widely ridiculed when I advanced it on the Internet and in my book. One
benefit of suffering a decade of ridicule is that it provides abundant
evidence for the novelty of my idea.

They are directly contradicted by a highly respected genetics journal,
Heredity. In its review of my paper, Ranjan Chaudhuri (reviewer, from the
Institute of Genetics), and John Brookfield (editor) each indicated my cost
concept is "different from its previous usage in population genetics,"
Brookfield wrote, "I really believe that defining the cost of a substitution
[in the way that you do] makes this concept inconsistent with previous
uses of the concept of a cost of selection". That contradicts Ewens and
Crow.

In fact, Chaudhuri and Brookfield (at least initially) opposed my cost
concept, each of them indicating "it is not interesting that the spread of an
allele requires a reproductive excess".3 Again, that emphatically
contradicts reviewers Ewens and Crow.

That means the confusions and contradictions rise to the highest level at
leading population genetics journals - and disproves Ewens and Crow's
claim that a clarification (such as my paper) is not needed.

In addition, my paper goes much further. It contains new definitions,
clarifications, arguments, derivations, and proofs that go far beyond
anything previously published. My paper is profoundly novel. Thus, at
Theoretical Population Biology: (1) They had acknowledged my paper is
correct, and (2) Their only serious objection2 to my paper (their claim that
my paper is not new or needed) is overturned by overwhelming evidence.

Nonetheless, they still rejected my paper. Statements from the editor,
Samuel Karlin, were brief. Seeking clarification, I phoned him, and he
angrily cut me off, saying he will tolerate no further discussion. He
showed no curiosity concerning all the documented contradictions and
confusions that prevail today. Those are easy to verify, but he would have
none of it.

That is why I must open-up this review process to public scrutiny.
Haldane's Dilemma is a scandal that just keeps growing.

You've heard the accusation that creationists "do not publish in
mainstream peer-reviewed journals." Well, my paper is a test case.
Haldane's Dilemma is an important evolutionary problem, and my paper
provides a clarification that is long overdue. My paper is error free, and
has been deemed correct by capable authorities. It has been re-written
many times to meet their recommendations. Nonetheless, they refuse to
negotiate a suitable publication of it.

Do they have hidden motives? Perhaps. Perhaps they are contented that
Haldane's Dilemma remain confused and unclear, languishing in obscurity.
Or perhaps they dislike 'outsiders' - such as me. Only insiders need apply.
It's a members-only club. Perhaps. ... But there is a more likely motive in
this case; a motive that directly affects them personally. That is, the
publication of my paper (even without it saying so) would draw attention
to their epic ? many-decades-long ? negligence. Authorities had an
obligation to pursue-and-display the truth about Haldane's Dilemma,
which they failed to do. So they were at least passively negligent. That is,
perhaps they were as confused as anyone else, and they simply failed to
pursue a clarification. But the situation now appears far worse. For if
evolutionary authorities knew the truth decades ago (as Ewens and Crow
now claim), then they were knowingly negligent, and knowingly allowed
confusion and falsehood to thrive, as it does to this very day. That would
take their culpability to a whole new level. They had many opportunities,
and many decades, to clear up the confusion. But they didn't. They
remained silent.

Their attempt, to likewise silence my paper, cannot stand.

I here announce my desire to locate a suitable peer-reviewed journal. If
you are such an editor, please contact me with your interest. My paper is
titled, "Cost Theory and the Cost of Substitution - a clarification." Under
the present environment, I might have to give up my multi-year effort, and
publish instead in a creationist journal. I do not desire that. But if it comes
to that, the fall-out will be on evolutionary authorities heads, not mine.

1 Warren Ewens itemized his agreement with my paper at length, and in
detail. His only disagreement was over the word "adherent." That is, my
paper cited Ewens's papers abundantly advanced load arguments, (and his
load arguments were often better than his opponents), so my paper refers
to him as an "adherent of load arguments" (notice I said "adherent", not
"proponent"). However, Ewens did not like the term "adherent" (which he
interprets differently than I do). So I proposed a simple change in wording
to "expert user of load arguments." This shows the triviality of Ewens's
one disagreement with my paper.

2 The reviewers' second-most reason for rejection was just a different
version of the first. That is, since they felt the paper was "not new" and
already widely known at least "twenty years ago," they felt the paper was
unnecessary and therefore "overly long" and given to analytical reasoning
(in Ewens's words, "discursive"). That reason evaporates when one
recognizes that many forms of confusion are still thoroughly entrenched
today. Under those circumstances, my paper's length and analytical
reasoning are justified, and necessary.

3 I appealed Chaudhuri's decision, and that began a lengthy too-and-fro
between editor Brookfield and myself, which went about six rounds or so.
Brookfield was quite kindly, and took time to consider my pleadings and
respond. Curiously, his reasons for rejection shifted. He eventually
acknowledged that my cost concept is clearly stated and consistent, and
makes correct predictions. But he nonetheless shifted to a new reason for
rejection. That is, he did not like my new term "stochastic reproductive
excess", (which is needed to identify how the cost of neutral substitution is
actually paid). He acknowledged my term is clearly defined and
consistently used, and that he understood it, but he was afraid other readers
would not understand it. To the present date, he is the only reader who
objected to that term. Thus, I had made headway with editor Brookfield.
His initial opposition was converted to grudging acknowledgement of the
usefulness and correctness of my cost concept. He just didn't like that one
term. The paper had come a long way, only to be rejected for such a trivial
reason.

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Afternotes: Can the reviewers (Ewens and Crow) and I both be right?
Perhaps. It is conceivable some evolutionary experts knew something in
their heads (as they claim), AND that it's not clear in the literature (as I
claim). If so, it wouldn't be the first time. In fact, it is common. There is
often a disparity between what evolutionary experts know to be true, and
the way things are presented in the literature and to the public. The
disparity favors the selling of evolution ? and the disparity is maintained
by the evolutionary experts' silence. The silence allows falsehood to thrive,
often for many decades. This pattern occurs repeatedly. I need only
mention the many historical claims about "useless vestigial organs,"
embryological "recapitulation," human "gill-slits," the prevalence of
Darwinian "gradualism" and Darwinian "lineages," the relevance of
Miller-Urey style "origin-of-life" experiments. In each case, evolutionary
experts knew these were false, but their silence allowed the falsehoods to
thrive for decades thereafter.

Did that occur with Haldane's Dilemma? That depends on this: Exactly
what did evolutionary experts know, and when did they know it? We now
have their first testimony on the matter.

Copyright ¦ 2005 Saint Paul Science Inc. All Rights Reserved
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"A new selection pressure is added whenever directional selection favors
the replacement of an existing allele by a new allele. How rapidly can such
a replacement take place and how much of a "cost" does it involve?
Haldane (1957) was the first to recognize this problem and to try to supply
a quantitative answer to it. He assumed that gene substitution in a species
occurred through the "death" in each generation of a constant fraction of
individuals carrying the particular gene. On that basis he calculated that
the total number of "selective deaths" required to complete one
substitution is of the order of 30 times the population size, independent of
the intensity of selection. Haldane concluded from this that the
replacement of one gene by another had to be a slow process, requiring an
average of 300 generations per substitution. Furthermore, he and Kimura
(1960) estimated that the survival of the population would be jeopardized
if gene substitution took place at more than about a dozen loci at any one
time. The more general conclusion was that evolutionary change is an
exceedingly slow process. If two species differ at 1000 loci, Haldane
estimated that it may have taken at least 300,000 generations to complete
speciation." (Mayr E., "Populations, Species and Evolution," [1963],
Harvard University Press: Cambridge MA, 1974, reprint, p.158)
Stephen E. Jones, BSc (Biol) http://members.iinet.net.au/~sejones
Moderator: http://groups.yahoo.com/group/CreationEvolutionDesign
& http://groups.yahoo.com/group/ProblemsOfEvolution/ Book: "Problems
of Evolution" http://members.iinet.net.au/~sejones/PoE/PoE00ToC.html
& http://members.iinet.net.au/~sejones/pe00cont.html
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