Commentary on the so-called Creation/Evolution/Intelligent Design Debate and Right-Wing nuttery in general - and please ignore the typos (I make lots!)

Wednesday, May 17, 2006

Crevo (aka 'johnnyb', aka John Bartlett), computer programmer, at it again

While checking the site meter for this blog, I traced a visit back to creationist William Dembski's blog, "Uncommon Descent", the blog after which I named this one.

The post in question is regarding electrical engineer creationist Walter ReMine's recent attempt to get a 'paper' published on the concept of genetic load/cost of evolution. It was rejected, in part because of its "non academic style" (*see the end of this post).

Anyway, someone calling himself 'russ' wrote:

I went to the Amazon listing for his book, and found a review by xxx.
I’ve “quote mined” the review here:

—————–“And, more importantly, one should wonder why ReMine’s amazing 'theory’ can only be read about in his vanity press book? Why has he not written up manuscripts to be critiqued by his fellow scientists? The answer? Creationists prefer writing in a medium wherein they receive only praise from like-minded individuals, such as ‘John Woodmorappe’, not where those that know better would demolish his flimsy, evidence-less claims.

This book belongs on the scrap heap of egomaniacal creationist rants.”—————-

This review is pretty funny when you consider ReMine’s struggle to get peer-reviewed, with two committees rejecting his paper because his theory was “wrong”, and a third rejecting it because it was “correct”, but scientists have known all that stuff for years!

Let us consider 'russ' esteemed take on this.
First, my review was written in 2002, 3 years or so before ReMine had even submitted his "paper" for review, and I was reviewing his book that was published in 1993.
Second, the paper ReMine submitted had little to do with his "theory", it had to do with his view that the definitions of 'cost' and 'load' are 'garbled and confused' and this somehow has a major impact on population genetics and evolution.

This is typical of creationists in general, and the denizens of Dembski's trash board in general - not having a basic understanding of the issues before making stupid comments.

'johnnyb' (John Bartlett) replies to russ:

It looked like xxx has also dismissed this paper out-of-hand:
He apparently had access to ReMine’s paper before it was published. Here is xxx’s comments on ReMine’s paper:
“Actually, the paper that you refer to is of substandard quality AND it says nothing new. I have read it. It was standard ReMine. Lots of finger pointing and sophomoric prose, very little of substance. Of course, ReMine’s paper did not address his baseless claims re: Haldane’s dilemma, so what we have is yet another red herring from Crevo.”

Actually, ReMine had 'published' his paper on the net, only to later remove it (I was sent a link to, if I remember correctly, CRSQ, a link which was dead last time I checked).
He does not attempt to correct anything I wrote.

russ then replies:

I skimmed xxx’s blog at your link, and it doesn’t sound like he’s actually refuting anything of substance. What’s your take?

I agree, I am not refuting anything of substance since ReMine's claims lack substance. But I don't think that is what russ meant.
So, first of all, the subtitle of this blog is "Commentary on the so-called Creation/Evolution/Intelligent Design Debate." Commentary being:

A series of explanations or interpretations.
An expository treatise or series of annotations; an exegesis. Often used in the plural.
An apt explanation or illustration: a scandal that is a sad commentary on national politics.
A personal narrative; a memoir. Often used in the plural.

In fact, in the very first post on my blog, I wrote:

While I will be commenting on such things from time to time, the purpose of this
blog is primarily to provide links to and commentary on the essays and posts of
individuals that are far more patient and eloquent than myself on these and
related issues. Please feel free to provide comments of your own, providing they
add something of value to the discussion. Thanks!

Note that the intent of this blog is not to provide 'refutations' or in-depth analyses of anything.
But russ is right - he, at best, skimmed my site. Looking at the visit length statistics, looking at all the visits betweent he time of russ' first ref to this site to the time he posted the above comment, the longest visit by someone linking in from Dembski's den was 10 minutes. This blog, while not extensive, has about 50 posts on it. I wonder how many russ read? No matter...

Bartlett replied, and I will respond to each point as I quote them:

If I remember correctly, xxx’s primary arguments are:

1) how do you know that 1,667 * 2 mutations is not enough to separate humans from chimps?

Valid question that remains unanswered.

2) experimental evidence shows that the mutation rate is much faster.

Whaaa? Bizarre memory...

#1 is fairly obvious to me.
xxx thinks that the existance of mutations that cause major problems in numerous systems is evidence that a mutation could cause just as many benefits in multiple systems.

This is a clear and, frankly, idiotic misrepresentation of my position.
Indeed - it is Barlett that does not seem to even understand the issue that he defends:

The number of mutational events that appear to have occurred between chimps and humans is in the millions. If you half that (since we are going from a common ancestor), you are still _far_ above 1,667.

You can see that it is Bartlett that equates all mutations with the fixed, beneficial mutations explored in Haldane's model. Further, Bartlett, being a computer programmer and utterly ignorant of basic genetics seems to believe that because some mutations "cause major problems" that ALL mutations must do the same. Because after all, that is what happens in computer programming:

Having done lots of design modifications myself, I find that completely contrary to experience.

So, has JohnnyB really done "design modifications" in living things? Clearly not. Yet, in the wacky world of the self-important creationist computer programmer, what he knows happens in computer programming must also happen in genetics. How can he claim to have experience in something that he clearly does not? Well, that is the creationist for you. Always claiming more "authority" than they have (or deserve). It is a common misconception with creationists with engineering backgrounds.

xxx also requires that I list specifically which mutations are needed in order to validate my point. I don’t think that this is explicitly necessary, though I have pointed to which systems I thought were the most important, and several journal papers describing multiple genes with multiple differences between humans and chimps
.And how many "fixed, beneficial" mutations did those papers describe? 10? 20? Further, I do not recall ever having made any such "requirement."
Let us take a look at what the creationist programmer actually wrote:

Likewise, I would imagine that there would need to be at least that many changes just for going to obligate bipedalism.

At least as many as:

This is silly, because we know the number of mutational events between chimps and humans.

What is this number of mutational events?

There are 35 million base substitution differences, as well as 5 million insertion/deletion events (totaling about 40 million nucleotides).

So, Bartlett thinks that "at least" 40 million nucleotide changes would have been required just to produce obligate bipedalism!!! ABSURD! What is Bartlett's supporting evidence for this laughably outrageous implication?

Why, it is the same as ReMine's - NOTHING. Nothing but a naive grasp of genetics and development and an ego the size of Montana.

Especially if we consider the fact that is takes but a single nucleotide change in one gene to produce disproportionately shortened limbs and the associated limb musculature, joint alterations, cranial changes and more in humans. The "logic" of indicating that it would take 40 million just to alter the structure of the pelvis, lower back and limb musculature is crazy ignorant.

#2 is simply circular reasoning. The paper he points to simply takes the number of differences between humans and chimps at certain spots and divides by the number of years between our supposed divergence.

Here, I guess, is what he is referring to:

...You mentioned 40 million changes in the DNA. Humans and chimps are inferred to have separated from each other about 6 million years ago. That works out to about 7 changes per year, or about 140 per generation (based on a 20 year generation time, which is what ReMine used).7 a year is astronomical? ~140 per generation is astronomical?In reality, that is very close to the number gleaned from empirical studies.

Let's see where JohnnyB is going with this...
In case you didn’t notice, this math only works if the assumption that we are separated from chimps is correct (note that the people who wrote the paper are NOT engaged in circular reasoning, because they are not using their data as evidence for the split — just extrapolating from the [IMO incorrect] assumption).

Gee, JohnnyB, I did not use the paper as evidence fo the split, either. I used it to counter your claim about "astronomical mutation rates" being required. But we shouldn't let a little thing like correctly representing the situation interfer with showing off to your pal 'russ'.

He also always wants to know exactly what the common ancestor looked like. I find this amusing.

Of course you do - you have no answer to it. UNLESS you can do this, there is no rational, logical, intellectually honest way that someone can claim that ReMine's extrapolation of Haldane's model has any relevance. And unless you can document how many mutations are "required" to produce trait Y from original trait X on top of that, the claim becomes even more ridiculous. And of course I should point out that Bartlett interprets my question regarding the traits possessed by the hypothetical ancestor as asking "what it looked like." While appearance would certainly demonstrate a large number of morphological characteristics, there are of course non-morphological traits as well, some of which have been identified as differing between chimps and humans (such as the nature of the sialic acid receptor). But the creationist is only interested in superficial arguments because anything else shows that they have no business even discussing these issues, any more than I would have discussing computer programming.

If he can’t characterize the common ancestor, what makes him so sure there was one?

What makes me so sure? Ummm.... Gee - could it be multiple lines of evidence?
I can characterize it. It had all of the traits that modern humans do - hair, pentadactyl limbs, well developed brain, etc. The differences between it and modern Homo are of degree, not kind.

I think he is trying to get me to characterize a common ancestor and then use my characterization as evidence that there was one.

Yes, that is exactly what I am doing. (*ugh*)

I point out that most evolutionary literature would have such an ancestor be more chimp-like than human-like, but there is no real evidence for its existance. I also point out that Haldane’s dilemma wouldn’t actually be a problem if chimps were merely degenerative humans, but that I don’t know any evolutionary biologist who would hold to that.

Haldane's dilemma has not actually been shown to be a problem anyway, for the reasons I have mentioned (and many others). The entire argument is little more than an assertion premised on a shallow grasp of the science.

But we can't let that stop the creationist - especially those who are computer programmers and know everything about everything - from spreading their pompous tripe.


* Here is the text of one of the reviews of ReMine's paper. I have bolded parts that highlight ReMine's egotistical and sefl-aggrandizing style, as well as outlining thew standard creationist 'I'm right and you are wrong and I don't have to support' it attitude most recently seen in Warren Bergerson at ARN:

Review of "Cost Theory and the Cost of Substitution-- a clarification" by Walter Remine.

This paper is written in a contentious, supercilious, nonacademic style, and argues that the notion of a "cost of substitution" has been misunderstood and misapplied by many workers, who have been confused. It argues that the correct definition is the reproductive excess required by a given situation.
The paper has the defect that it assumes that all authors have been attemptingto describe the same notion, and that their differences have resulted from misunderstandings of the correct concept. Remine argues strenuously against the idea that if there is too little reproductive excess the population will go extinct. Instead, he argues that too little reproductive excess to pay the cost implies that the scenario is implausible.
Remine also argues that any trait that increases in frequency in the population implies a cost, even if its increase is purely the result of genetic drift.
In fact, it is not at all clear that different researchers had the same objective in mind. Haldane (1957) did not use the phrase "cost of substitution" (his title mentions "cost of natural selection"). Ewens put forward a cost that was nonzero for pure genetic drift, other authors' costs were zero for change by genetic drift.
Remine's treatment is thus inadequate in its historical treatment of others' work, and is also inadequate internally. Take the idea that susbtitution requires reproductive excess. Suppose that we have a (haploid) species with no reproductive excess. Suppose that the environment changes so that all individuals have 20% less reproduction, except for 10% of them who have a particular allele, and those continue to barely replace themselves. A little consideration will show that the substitution will happen, and the population will end up 90% smaller. But if there is even a slight reproductive excess, then with enough time the population will ultimately recover its numbers. There is then no lower limit on the reproductive excess needed.
However, Remine defines the cost in terms of the number of copies of the allele. He adds up the reproductive excess over the generations involved,so that in the above case he would arrive at a finite total of the reproductive excess. The population may be in no difficulty, but if the researcher thinks that the change of number of copies of the gene is possible in that amount of time, they must be able to argue that there is that much reproductive excess.The problem for the population in such a scenario comes when we have, not one substitution, but a regular flow of such events. Then, if there is no reproductive excess, the population drops by 90% each time, and ends up going extinct. It is thus possible to define a cost that is the cost of avoiding extinction, in spite of Remine's strenuous arguments against such a notion.
A certain reproductive excess is necessary when there are recurring events, but it is to avoid extinction, not to allow substitution. Remine mentions that repeated substitutions are involved in several other people's definitions, but then simply declares that "that interpretation is faulty", without saying why. He sounds as if someone has issued him a certificate stating that his interpretation of the cost is the correct one and all others are wrong.
Remine's treatment of selective neutrality is also confusing. Aside from declaring that in such cases there is a cost but that there are "special mechanisms that allow high overall rates of substitution". The reader may be confused, as they may imagine that neutral substitutions just happen, as a result of randomness of mutation, birth, death, and genetic segregation. Saying that there are special mechanisms present implies that these are adaptations (or divine interventions) designed to make Motoo Kimura feel happy.
One minor matter should also be mentioned: Remine has the habit of presenting a table of frequencies of different genotypes (as on pages 11 and17) as an equation. Instead of writing p and q as the two frequencies that also add to 1, he writes p+q = 1. This is trivially true for any two frequencies of alternative genotypes, irrespective of whether they are thecorrect frequencies. (For example, 2p + (1-2p) = 1, and that statement iscorrect even when the frequencies of the two alleles are not 2p and 1-2p). This is easily corrected by replacing the summations by tables.
I conclude that, although Remine's algebra is correct, his description of how his work relates to the costs and loads defined by others is seriously wrong. Stylistics aside, it thereby makes a negative contribution to discussion ofthese issues, and I cannot recommend its publication.
I should be identified to the author.

Joe Felsenstein

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