A Tale of Peer-Review

Background: 

Since 1993 I have argued that the central concept in Haldane's Dilemma - 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:

1. Genetic death
2. Genetic load (or substitutional load), fitness, and fitness values
3. Environmental change (such as environmental deterioration)
4. Extinction (and its avoidance)
5. 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:

6. Soft selection "reduces" the cost of substitution, and "solves" Haldane's Dilemma.
7. The total cost of substitution is 1 (not 30 as claimed by Haldane).
8. The cost of substitution is "an illusion."
9. The cost of beneficial substitution is "zero."
10. In a non-deteriorating environment, there is no cost of substitution. 
11. Beneficial substitutions "pay for themselves." So there is no cost problem. 
12. "The cost of not evolving is greater than the cost of evolving." 
13. 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.

Update:

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, and many others.¹ 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.²)
  
• "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.³ 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: 

1. 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.)
   
2. 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.
   
3. 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. 
   

4. 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.
   

5. 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".⁴  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. 
   

6. 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 objection³ to my paper (their claim that my paper is not sufficiently 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    Some of the reviewers disagreed with technical points in my paper, especially initially, and later relented after some discussion. Dr. John Brookfield is an example of that. However, reviewer Joe Felsenstein, in particular, continued his disagreement, though he did not identify any error -- rather, he refused to deal with the arguments in my paper. He may as well have read my paper with his eyes closed. I will discuss that here.

²    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. 

³    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.  

⁴    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.  

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. 

Note added March 13, 2005:  Dr. James Crow recently posted some relevant comments on the Internet.  See my discussion of it here.