This is my latest refutation of Fred Williams' claims - what he refers to as an 'informal debate' . [ NOTE: While Williams refers to this as a debate, albeit informal, I do not nor did I ever do so. I do not think Williams' specious claims worthy of investing the requisite time and effort into. I see this as more of an expanded internet discussion board post. I do not, nor would I, consider such a venue to be the proper place for any sort of scientific discussion, and so my responses are not indicative of the sort of effort and demeanor I would employ in a 'formal' debate or in any type of legitimate sientific exchange.] In keeping with the quoting scheme Williams uses, any previous posts will be in blue, my last reply in maroon. My new responses will be green and bold.
Williams begins:
[snip posturing by Williams]
Hairsplitting and semantics games
In my opening rebuttal, I mistakenly[sic] used “ape” instead of “monkey” when I wrote “The authors of the genetics study are arriving at their estimate of 10 generations by first assuming that man and ape share a common ancestor”. Page made note of this in his first rebuttal: “Chimpanzees ('ape') are not Old World monkeys”. Fine. I accommodated his nit-pick in my subsequent rebuttal by instead using the term “simian” (a more encompassing term).
I am unsure why the creationist believes that using the correct terminology should be considered a 'nit-pick.' Would the creationist mind if I claim that he is an old-earth creationist snake-handler? After all, some Christians that are creationists are snake-handlers. .. Close enough, right?
You would think this would be the end of it, but it became a focal point for Dr Page in his latest installment! He called it the “crux” of his dispute!!! (Wait, I thought the dispute, our debate, is whether or not Page's citations have anything to say about Haldane's Dilemma!)
That is interesting, since Williams wrote in his last installment:
"This particular debate is not on the merits of Haldane's argument. "
In addition, this is what I actually wrote:
"...the 'crux' of my dispute is that Williams switches terminology as it suits him, which confuses the debate. This is one of the many reasons that it is very difficult to discuss such issues with creationists. "
Not quite how the creationist depicts it.... As is so often the case....
Dr. Page has now tried to shift the reader's attention away from the debate and on to a silly nit-pick! He reminds the reader of this “ape” vs. “simian” hairsplit at least five times throughout his latest rebuttal, all the while complaining along the way about my revised use of “simian”!
Again, the 'silly nit pick' is about the wishy-washy and improper use of terminology by the creationist.
Note the desperation of Page's argument when he writes:
“First, Williams refers to Old World monkeys as apes in his original rebuttal. I point out that Old World monkeys are not apes. Williams then re-writes his original 'challenge' and presents it as he did above, using the word 'simian' instead of ape. Old World monkeys are, at least by laymen, considered to be simians. Williams has reworded his claim so as to prevent it from being rendered moot and shown to be inaccurate, and now bases his 'new' argument on this reformulated claim.”
Dearest Dr. Page, I did not “re-formulate” my argument. I simply changed one word, ape, to “simian” to appease your nit-pick.A nit-pick extraordinaire indeed!
Using proper terminology - especially when using the wrong term totally changes the meaning of a claim - is hardly a nit-pick, nor is it a sign of 'desperation'. Again, Old World monkeys are not apes.
Whether or not the simian used in the study was an ape or a monkey has no bearing on whether or not your use of the citation was circular reasoning. I wonder how else you think I should have responded. I suppose you would have preferred me to exclaim “Yep, I should have said monkey and not ape, so you win the debate on a technicality!”
No, I would prefer to 'debate' with someone that has sufficient background knowledge so as to use proper terminology. This would at least ensure that the usual type of defensive evasion being offered by the creationist here could be avoided. And, as I have already demonstrated, my use of a peer-reviewed scientific paper is not circular reasoning. But let us examine Williams' attempt at handwaving.
"Whether or not the simian used in the study was an ape or a monkey...blah blah blah."
What it does have import in is whether or not Willaims ORIGINAL claims (and his continued attempts at defending them via underhanded tactics) were accurate depictions. As I have already demonstrated, and reiterate with additional examples below, they were not.
Next, Dr. Page calls my use of the term “analogous” instead of “homologous” a “fundamental error”. This is quite an exaggeration. From a creationist perspective the sequences could be called analogous because creationists do not believe apes (oops, I mean “simians” J), are related to humans via decent. Nevertheless, to speak in evolutionary terms “homologous” would indeed be the appropriate term. Yet another silly nit-pick on Page's part.
No, it IS a fundamental error. In evolutionary biology, which Williams implies that he is conversant enough in to hold his own here, an Analogy (analogous character) is a character that is similar, for the purposes of this discussion, by 'accident'. The wing of a bird is analogous to the wing of an insect. They are both wings, yet they are distinct structures. The wing of a bird is Homologous to the wing of a bat. Why? Because they are both the forelimbs of a tetrapod. A fundamental error. Again we see the creationist hide the misuse of terminology due yto an ignorance of the subject matter behind his differing 'worldview.' Unfortunately, these sorts of 'personal definitions' or 'redefinitions' make it very difficult to have any reasoned discourse with a creationist arguing well outside of his field.
Equivocation of the word "evolution"
I originally wrote:
This fixation rate is in stark contrast to Haldane's calculation of 300 generations, so that's why Dr. Page cites this study. But Haldane's cost argument is a mathematical model that is not based on the assumption that simian/man ancestry (or any other form of large-scale evolution) is true.
Page replies with:
“Williams can re-write this as many times as he wants to, and it will still be bogus. Haldane assumed evolution when he formulated his model. If Haldane had simply set out to produce a purely mathematical model, devoid of evolutionary assumptions and constraints, as Williams suggests (insists?), then one should be curious as to why the formulae employed by Haldane contain a variable called the selection coefficient. For, what good is the concept of selection except in an evolutionary context?”
Here Dr. Page is equivocating on the definition of 'evolution' . In my preceding comment that he responded to, I explicitly stated that Haldane's model is not based on the assumption that simian/man ancestry (or any other form of large-scale evolution) is true. I am not referring to population genetics (also called evolutionary biology) where concepts such as selection coefficients are used. Creationists have no problem with natural selection, and in fact proposed selection before Darwin1. So I ask Dr. Page yet again, to provide any evidence whatsoever that Haldane's model requires the assumption that simian/man ancestry (or any other form of large-scale evolution) is true.
To equivocate:
1 : to use equivocal language especially with intent to deceive
2 : to avoid committing oneself in what one says
synonym see LIE
Hmmm...So I am a liar because I know that Haldane's model presupposed evolution? To the population geneticist - which Haldane was - there is no distinction between the 'small scale' evolution that the creationist allows for (indeed - needs LOTS of to keep the Ark from sinking)(microevolution) and "large-scale evolution" (macroevolution; see Mayr on this topic). So, Haldane, an evolutionist population geneticist, produces a model of what amounts to what must occur to replace an allele (evolution). His model contains a variable called the 'selection coefficient', which has to do with (for ease of explanation) the 'need' for the allele to become fixed (as in response to an environmental pressure, for example). Because Haldane did not write "My model is premised on the assumption that humans and apes are related via descent" or something similar, Williams believes - insists - that it is a purely mathematical construct, devoid of any evolutionary underpinning, and therefore is immune from any criticism or reformulation due to additional information (Haldane's model was formulated in the 1950's). I do not believe that I ever claimed that Haldane's model "requires" any such thing; if I did, please point it out to me. What I did say was that Haldane assumed evolution - which of course he did. It is the creationist that is equivocating because as a layman, one that has fed from the trough of propaganda, there really is a big distinction between 'microevolution' and 'macroevolution.'
However, since it is the creationist's assertion that Haldane's model contradicts evolution ("...a mathematical model that contradicts evolution (Haldane's Dilemma)..."), perhaps the creationist can explain how this is so...
Of course, the creationist originally wrote:
Haldane's estimate of 300 generations per substitution is based on a mathematical model that need not rely on such assumptions of the validity of evolution.
Perhaps the creationist or one of his supporters can point out where, in his ORIGINAL charge, we see anything about specific types of evolution. No, the criteria that Williams points to above were later additions - AFTER it was made clear that Haldane premised his model on evolution.
Another common creationist tactic - add additional criteria to a challenge when the original criteria are met. That way, you can never have to concede a point!
In addition, the creationist went on in his original installment:
...conclude it refutes a mathematical model [Haldane's] that contradicts the initial assumption of man/ape shared ancestry.
Emphasis mine. The 'contradiction? See Below..
Red Herrings Galore
Following are several Red Herrings that have nothing to do with our debate:
Williams calls this a debate. I never agreed to any debate, I merely responded to a collection of haphazard extrapolations. But lets see what transpires...
Williams' continued claims that Haldane's model contradicts human/ape ancestry is premised on his personal disbelief that 1667 fixed beneficial mutations can account for human evolution from an ape-like ancestor. Willaims has never been able to provide a shred of evidence that that position has merit.
Our debate is not on the merits of Haldane's Dilemma. As I stated in my previous post, even if Haldane's model is wrong, it still doesn't rescue Dr Page from his circular reasoning error.
And yet Williams uses Haldane's model to claim that Wu and Rice are wrong. As I have already demonstrated, I did not employ circular reasoning. But that mustn't stop the creationist from repeating the charge over and over. Just like the creationist continues to make the false claim that I tried to 'get help' in this 'debate' (see below).
Page then pulls out the chimp-bonobo red herring. What does this have to do with our debate? Absolutely nothing.
Easier to call it a red herring than to deal with it, I suppose. I also did not realise that this "debate" had a set limit of topics. Since we are not engaged in any sort of 'debate', I am free to bring up any topic I wish. The creationist has every right not to address the topics. Just like the creationist has the right to claim that "directed mutations" can account for the mutational distance between related species like chimps and bonobos without presenting any supporting evidence for the claim, or claim to be writing 'an article' on the topic as an excuse not to present such evidence on discussion boards (we are still waiting - more than a year - for this amazing article...).
The chimp-bonobo scenario shows how out of the loop the creationist's claims are. That is probably why the creationist wants to brush it aside as a 'red herring.'
Dr Page then expands his chimp-bonobo red herring by offering several lengthy citations regarding non-random mutations. Again, what does this have to do with our debate? Again, absolutely nothing. The simple fact is, Dr Page cannot defend his use of the Genetics study, so instead tries to bury the reader with a bunch of boring and lengthy citations that have no bearing on this debate.
As I have previously outlined the merits of my use of the studies I cited, the creationist's repeated claims to the contrary are simply rhetorical ploys - what was it Goebbels supposedly said? Repeat a lie enough and people will believe it? The reason I produced documentation regarding non-random mutations is because it takes the wind out of the sails of the creationists - including Williams - that want to use it as an 'answer' to Haldane's dilemma when applied to issues such as the bonobo-chimp issue. No wonder Williams want to blow it off.
Revisiting Dr Page's Core Error
Page writes:
I cited the Genetics paper as recent data-based evidence that the rate of change is much faster than originally estimated by Haldane (1957). Williams expends a considerable amount of energy trying to convince the reader that 1. the authors engaged in circular reasoning (an assumption of common descent), and so 2. my citation of it and use of it is also circular and 'faulty logic.
'
For the second time Dr. Page, I did not accuse the authors of circular reasoning, I accused you of circular reasoning. It is you who tried to apply a study that requires the assumption of simian/human ancestry, to a mathematical model (Haldane) that does not require the assumption of simian/human ancestry. I repeat, if the assumption of simian/human ancestry is wrong, then the Genetics study is useless. To apply such a study to a mathematical model void of assumptions about human/simian ancestry is faulty logic, plain and simple. It's textbook circular reasoning. I will explain it again. You believe evolution. You get a rate of change from a study (Wu, et al) that begins with the assumption that evolution is true (specifically common decent, or man/simian ancestry). You contrast this rate of change to a mathematical model (Haldane) where the rate of change is so small as to make evolution untenable. Since the rates don't jive, you claim the Haldane mathematical model is refuted, and evolution is defended! The circle is complete!
Yes, it is complete. Make claim. Repeat claim. Repeat it again. It must be true!
I think I finally get it - since Haldane did not explicitly write that his model requires the assumption of human-ape ancestry, it must not have any evolutionary assumptions and is therefore immune to revision based on data! Marvelous!
Consider: a mathematical model (premised on evolution) is made, however, at the time the model is constructed, no actual DNA sequence data is available. When such data is available, analyses indicate that the model is in error (actually, the model was shown to be in error in the early seventies1). Williams would have us believe that we should go with the math, data be damned!
Even better - the creationist claims that Haldane's model reduces the speed of evolution so much so as to make it "untenable" - what is Williams rationale for claiming this?
His personal disbelief! He cannot believe that a mere "1667 beneficial mutations" can account for human evolution from an ape-like ancestor2, therefore, it cannot (providing, of course, that Haldane's model is impenetrably correct in all applications in all situations; see 1 below...)
More Population Genetics Errors by Dr Page
Page: Williams then writes that all those lacking the mutation and all of their descendants had to be removed from the population. As worded – and probably as understood by Williams – it sounds as though all non-mutation holding organisms must be literally removed. This is incorrect.
Me: No, it is entirely correct, unless you believe our ancestors are all still alive!
Page: How ridiculous. I was clearly referring to a time-dependant explanation.
What? Dr. Page, frankly you do not know what you are talking about. Check Futuyma, Evolutionary Biology, p 299. When an allele becomes fixed, it becomes monomorphic, its frequency is 1 (100%). That means the wild type is GONE, and ALL prior descendants who had the wild type (did not receive the new allele) over time had to be removed from the population. My statement is entirely correct, and I am surprised you would question it.
Looks like one of those 'shortcomings of the medium' issues. "Time dependant" means that there is a time factor, that is, at any given time (prior to fixation), the wild type can still be present. What is a "prior descendant"? Sounds like jumbo shrimp... Looks like this section should have been called "More Undue extrapolations by the Creationist "...
In Response to my Bike Analogy
Page responds:
In a 'harmful mutation environment', reducing the number of them that become fixed in the population, via whatever means, is a benefit, no matter how you look at it.
Notice Page switches the goal posts. He now admits it's a benefit to evolution, providing its a "harmful mutation environment"! But a harmful mutation environment is itself an obvious and huge disadvantage to evolution! Perhaps Dr Page is finally getting my point without realizing it!
Switches the goal posts? Whaaa???? Amazing - Williams claims that I now admit that being able to reduce the number of harmful mutations is good for evolution? When did I ever say anything otherwise? It was the creationist Williams that wrote that an increased accumulation of beneficial mutations and a decreased accumulation of harmful mutations in sexual species is NOT an advantage (except, the creationist writes, when contrasted to asexual species)! What poppycock! Does Williams believe that the mechanism suddenly stops when the organisms are removed from a 'harmful mutation environment'? Amazing! I wonder if Williams also believes that one need not breath oxygen when put in an oxygen-free environment...
We need lungs to get oxygen to our tissues - the more oxygen, the better.
Person A lost a lung to cancer.
Person B has two lungs.
Two lungs are a benefit, as it is easier to get oxygen to the tissues with more lung volume.
But only when compared to someone that lost one lung to cancer...
Page: I did not present it [Rice study] as “evidence for evolution” – I presented it as evidence that the typical claims of harmful mutations accumulating fast enough to prevent evolution – as is often implied by Williams and his ilk – is in error. And in this it succeeds.
No, it does not succeed. You continue to validate my claim that the Rice study is misleading, because it has surely misled you into believing something that is not true. I repeat, the Rice study merely shows the advantage of recombination when contrasted with an asexual species in a harmful mutation environment, period. Nothing more. It does nothing, I repeat, nothing to reduce the mutation problem. Here is my article on the mutation rate problem. Please explain to the audience how the Rice study has any impact whatsoever on this problem.
You can repeat and repeat all you want to, and you will still be wrong. I think I see the problem here - you simply do not comprehend the point that I am making. I do not know how much easier I can make it for you. The Rice study demonstrates the benefit of sex (which creationists claim is an 'enigma' and all that) - it helps to increase the accumulation of beneficial mutations while decreasing the accumulation of deleterious ones. If the comparison was not made to asexual organisms, then there would have been no basis on which to conclude the benefits of sex!
Since creationists like analogies, and Williams likes bikes, here is one:
You have two men who want to travel across a terrain. Both are given bikes that are the same. Bike 'A' has thin “street” tires, bike 'B' has the same. The optimum surface for efficiency is a flat surface. In a race on such a surface bike 'A' will have the same advantage that bike B does. But as you add bumps to the surface, bike 'A' begins to lose ground, and so does bike 'B'. As you make the surface bumpier, at some point both bikes are kaput, as their tires are for street riding. With nothing to contrast the bikes' tires performance to, no conclusions can be drawn about how well the tires allow the bikes to perform. However, if we put wide “off-road” tires on bike B, something happens. The optimum surface for efficiency is a flat surface. In a race on such a surface bike 'A' will be have a distinct advantage every time. But as you add bumps to the surface, bike 'A' begins to lose ground, and bike 'B' starts to gain ground. As you make the surface bumpier, at some point bike 'B' becomes the faster and thus more efficient of the two bikes. So under bad race conditions, bike 'B' (analogous to a sexual species) is the better bike, under good race conditions, bike 'A' (the asexual species) is the better bike. But even when bike 'B' is the better bike, it still cannot go as fast as it would if it were racing on a smoother surface. It is still impeded in its progress, but not as much as bike B is impeded. (thank you Fred)
So, with no options to compare, no conclusions can be drawn. Why the creationist thinks that he has made a point by harping on the conditions of the study is a mystery.
Dr Page's Response to List of Errors I Presented Him
(my original claim is in blue)
* [Me] Mistakenly claiming that Haldane based his substitution estimate on the observation of peppered moths (Haldane did the opposite, see Haldane 1957, p521)
Page: You sure like p.521. In my copy of Haldane's 1957 paper, on p.521. there is nothing at all about what he based his estimate on. You should notice that on the first page, p. 511, Haldane expends some time explaining the observations seen in peppered moths, and how he will attempt to estimate "the effect of natural selection in depressing the fitness of a species." I committed an error of omission, and should have included the fact that he considered some Drosophila experiments and such as well. However, your claim that he "did the opposite" seems to have no basis in reality.
On page 521 Haldane writes: "...This represents, in my opinion fairly intense selection, of the order of that found in Biston betularia [peppered moth]... I doubt if such high intensities of selection have been common in the course of evolution. I think n=300...is a more probable figure". Dr. Page, it is quite clear that Haldane did NOT base his substitution rate on the peppered moth observation (which you now implicitly admit above), and in fact did the opposite (low intensity as opposed to high intensity selection).
So, you are now claiming that Haldane did not consider peppered moths at all? What, pray tell, is the "exact opposite" of considering peppered moths? I dare say it would be not considering them at all, which is clearly false. As your quote above clearly indicates, he considered them in his formulation! "Implicitly admit"? I came right out and said I made an error of omission! What is implicit about that! Amazing, Mr.Williams, that you can actually quote something and still manage to garble and mangle its meaning...
* [Me] Implying that a large population is a bad assumption for evolution (Haldane did the opposite; see Haldane 1960, p351)
Page: You are recklessly misrepresenting me. I claimed no such thing. Quoting from my solid refutation of your original bombast, the times I mentioned population size or Haldane's use of it: "…premised on unrealistic assumptions (such a s a constant population size), made using observations of phenotypic variation in Peppered moths." "Williams writes "entire population" for a reason - the connotation of "entire population" is that the population is extremely large, such as the human population of today. This is an unreasonable allusion." I did, however, say that a constant population size is an unrealistic assumption. But 'constant' does not mean 'large.' Misrepresentation.
I do not accept your explanation. Why did you write that an extremely large population is an "unreasonable allusion"? It sure sounds to me that you believe its a bad (unfavorable) assumption for evolution, or you would not have wrote [sic] "unreasonable allusion". It is clear you were unaware that Haldane believed it was a favorable assumption for evolution (1960, p 351).
Frankly, I do not care what you accept. Do you know what the word "allusion" means? Here is what I actually wrote:
"Williams writes “entire population” for a reason – the connotation of “entire population” is that the population is extremely large, such as the human population of today. This is an unreasonable allusion."
As is clear from the context (see my last installment) and from my quote above, I was not referring to Haldane's model at all, rather I was responding to Williams' statement. This odd transferrence seems to occur frequently in creationist writings.
* [Me] Claiming that a wild-type allele can still persist in a population even after its mutant allele reaches 100% fixation in the same population!
Page: I see you don't understand what fixation means, or perhaps are unaware of what a dominant allele is.
Dr. Page, I again refer you to Futuyma, Evolutionary Biology, p 299. If that is not good enough, check his glossary: "Fixation: Attainment of a frequency of 1 (ie. 100%), by an allele in a population, which thereby becomes monomorphic for the allele" [emphasis in original]. It is quite clear it is you who does not understand what fixation means.
An example of a response to an out of context point.... Keep reading.
Page continues: If 100% of a population has a DOMINANT allele, they can still be heterozygous - the individuals can still have a recessive allele for the same locus, and yet they all would exhibit the dominant phenotype.
Strawman. This is not what you claimed. Regardless, even this a very bad argument, because using your new explanation, if 100% of the population has the dominant allele, it is extremely likely that any remaining recessive alleles are by now virtually extinct, at a frequency very near zero.
Yes, strawman. If you say so. As written, my arguemnt is correct. It is the creationist that is now wanting to add qualifiers and such.
* [Me] Because of his previous error, reaches the erroneous conclusion that a dominate[sic] allele does not need to be replaced, which implies it has no reproductive cost.
Page: More misrepresentation. If the members of a population are homozygous for the wild type, then the replacement of one allele with a dominant mutant will incur your beloved cost. However, the impact of the cost - under realistic assumptions - is not what you continue to claim it is.
Wrong again! Perhaps this figure from Futuyma, p 298 will help:
The diagram above should help illustrate that a new allele from a mutated wild-type, be it recessive or dominant, will have to incur reproductive costs over the life of the fixation. Haldane assumed ALL of his mutations were dominant, since the cost of recessive mutation is exponentially higher.
Strawman AND a non sequitur. The reader shall notice that the creationist's reply has nothing to do with what he is supposedly responding to. I did not say, as the creationist seems to be implying, that no cost is incurred. Indeed, I explicitly stated that a cost will be incurred. However, I qualified that with the basis of reality - that under realistic conditions, the cost is not what the cost-mongers will have you believe, as evidenced by the references I provide in 1 below. But what does "...cost of recessive mutation is exponentially higher." actually mean? According to Haldane (1957), recessive mutant alleles occur in a population at a rate some 200 times that of dominant ones (p.514). On p. 517, Haldane expands on the costs for dominant and recessive substitutions. He gives the cost D for dominants of between 9.9 and 79; for recessives, D= ~105. 105 is not an exponential increase unless one only considers his low value of 9.9, which the creationist must have done (Haldane put the average at 30). That is, he makes a worse case scenario.
On an interesting side note, in his follow-up paper4, Haldane explains:
"... we can see precisely how the cost falls off as the intensity of selection increases." (in reference to - gasp! - peppered moth data).
But more importantly, on the first page, Haldane writes:
"Haldane (1957) gave expressions for the "cost" of natural selection...which must occur in a population of constant size..."
and
"These expressions were not precise unless the intensity of selection is weak."
Emphasis mine. This goes to some of the earlier criticisms of Haldane's model, as well as those used by some reviewing ReMine's book, that Haldane used unrealistic assumptions in his original model, as he here 'admits' (much of the paper is on the evolution of peppered moths and how selection was intense in some populations, thus rendering his original application of his model to the peppered moth issue moot). Please present us all with some real live concrete examples of natural populations that remain at a constant size. Indeed, Haldane writes in his conclusion:
"Thus it is important that Kimura's theory and my own should not be extended to cover biological situations to which they do not in fact apply."
One should hope that the creationists that like to hang their hat on "Haldane's Dilemma" would have read and understood this at some point...
But apparently not...
* [Me] Claiming that a beneficial mutation will spread through a population in a sexual species "as well" as it would in an asexual species, even given an environment free of deleterious mutations.
Page: I really wish that you would put a lid on your shameless attempts at revisionism. That or learn some common colloquial english: http://www.m-w.com/cgi-bin/dictionary "as well 1 : in addition : ALSO...I am unsure whether you are purposely trying to be annoying, if you are so self-deluded that you simply ignore the context, or that your english really is that poor. Either way, all you are doing is pointing out your incompetence.
Dr Page should consider accessing a more complete dictionary next time before accusing me of "poor english" and "incompetence". Note definition #2, apparently missing from Page's dictionary, in the Webster Collegiate Dictionary:
- as well 1 : in addition : ALSO 2 : to the same extent or degree : as much
However, I take Dr Page at his word that his intended use was '1', so I hereby retract my original claim (stated above in blue).
Hmmmm... Perhaps the reason that I only cited one definition was BECAUSE THAT IS THE USAGE I HAD EMPLOYED, as should have been obvious from the context. Indeed, it should be obvious from the examples given in the online dictionary definiton, which Williams quotes above, that the only logical way to interpret what I wrote was to use "as well" in the first sense.
No, Mr.Williams, having engaged you and other creationists for some time, I have learned to recognize the difference between 'honest' misunderstanding/misinterpretation and the all too common misrepresentation/incompetent reasoning skills.
* [Me] Claims that Wu's study dos *not* assume human/simian ancestry in its determination of the substitution rate.
Page: That is a fact... [NOTE ADDED HERE: Observe that Williams then changed his phrasing to “simian and human” ancestry, which is correct, then made a stink about how I was 'misrepresenting' him!] That or provide the exact quotations from their paper pointing out their assumption of human-ape ancestry - as per your ORIGINAL claim - and how it was pivotal in their mutation rate analyses.
I already did, in my previous post in this debate. I'll copy it here:
Let's look at an important passage from the study, emphasis mine. Particularly note the word “divergence”, which refers to the monkey/man split, and “positive selection” which is derived from the “divergence” data: [snip irrelevant quote]
If Dr Wu has arrived at this substitution rate of 1 per 200 years without contrasting DNA between old-world monkeys and humans, as Dr Page is essentially saying, then Dr. Wu needs to re-write his study. But I suspect he will not need to re-write it, because he is indeed contrasting simian/human DNA, and hence assuming simian/man ancestry to arrive at this rate.
And I will cut and paste my refutation of your attempt to save face:
After Williams had pasted the quote used in his 'concluding' installment and in installment 2:
I think that at this point, the reader can see that Williams is just trying to save his ego. I am duly impressed that Williams can cut and paste segments of the paper in question. However, once again, Williams purposely tries to bury his original claims (as happens frequently in creationist discussions) in a sea of quotation.
AGAIN, Williams' original claim, that I rebutted and that now Williams is desperately trying to deny, was that an assumption of human/ape ancestry was used in determining the degree of divergence. Yet as he actually quotes above, it was human and Old World monkey genes that were compared. Note that Williams is trying to put words in my mouth to save his position:
“If Dr Wu has arrived at this substitution rate of 1 per 200 years without contrasting DNA between old-world monkeys and humans, as Dr Page is essentially saying…”
I am not 'essentially saying' any such thing. I AM saying that a comparison of human and APE genes did not occur in the analyses used in the Genetics paper. Why Williams is having such a hard time with this, I am unsure.
I think I now see where Williams' confusion stems from. The young earth creationist seems unable to distinguish between the results of the data comparisons (Old World monkey and human) and their application to the human-ape issue. The mutation rates were derived NOT from the use of human-ape ancestry, as Williams insists, but from human-Old World monkey comparisons. Doubtless, the creationist will label this another 'red herring' or some such drivel, however it should be clear that my point here is that, once again, Williams the electrical engineer shines through, as his 'argument' here relies on a confusion of terms.
Dr. Page, you are simply in error here. If not, then get Dr. Wu, whom you admit to have contacted regarding this debate, to substantiate your claim!
I cannot believe the amount of misrepresentation employed by the young earth creationist.
CHRONOLOGY
I make a guestbook entry at Williams 'satirical' website on January 23, 2002, consisting of evidence that had been presented to him several times in the past and that he had deigned to ignore.
Williams interprets this as, or at least treats it as some sort of 'debate' and responds on Feb.10, a date which must be inaccurate, as the reader will see. His response contains the accusations of poor logic and deception.
I email Drs. Wu and Rice to inform them of the libelous rant of Williams on Feb.8, the text of the message I sent to Dr.Wu was reproduced verbatim in my last installment, appended here again:
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Dear Dr.Wu,
I have used your recent paper "Positive and Negative Selection on the Human Genome" as an example, on several occasions, of how the old estimates of mutation accumulation (e.g., Haldane) were in error.
Creationist Fred Williams took my citation of your paper and has written what he calls a 'refutation' of it on his website:
http://www.evolutionfairytale.com/
He and I have a long history of ill will between each other, so his claims against me are immaterial. However, he accuses you and your co-authors of, among other things, circular reasoning.
I am planning to write a rebuttal and post it on my own website, but I thought you or one of your co-authors might want to take a look at Williams' essay as well.
Thank you for your time.
Warm regards,
Scott Page.
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I write my refutation of Williams on Feb. 19.
I 'admit' that I contacted Wu and Rice to inform them of Williams' hatchet job, of course. However, Williams repeatedly insinuated that I had in actuality tried to enlist their help in writing a response. My message to Wu should be clear evidence that this accusation is false.
I do not need to contact anyone to substantiate MY claim. Indeed, the quote you provided substantiates it for me.
WILLIAMS' CLAIM:
To have provided the exact quotations from their paper pointing out their assumption of human-ape ancestry - as per your ORIGINAL claim - and how it was pivotal in their mutation rate analyses
REALITY:
The quote Williams provides - and in fact the part he places emphasis on:
The A/S ratio from divergence is estimated from 182 orthologous human and old world monkey genes
Emphasis mine. Again:
WILLIAMS: man/ape descent assumed in Wu paper, writes in his latest installment, "I already did (substantiate my claim that the paper relies upon an assumption of human-ape descent) , in my previous post in this debate. I'll copy it here:"
FROM WILLIAMS' "SUBSTANTIATION":
The A/S ratio from divergence is estimated from 182 orthologous human and old world monkey genes
For the umpteenth time - and it is no nit-pick - Old World monkeys are NOT apes.
This is key to the entire debate! This is your only hope, that Dr Wu engaged in poor writing skills when he wrote his paper and that his estimate really did not rely on simian/man ancestry. Come on, you and I and every reader can clearly see from the excerpt above that simian/man ancestry is an important assumption in the study!
Williams' comedy of errors continues unabated and despite repeated correction. Truly astounding. Look at what Williams writes above:
"...on simian/man ancestry."
Look at what Williams claimed to have substantiated with his quote:
their assumption of human-ape ancestry
Only by conflating and haphazardly interchanging terms does Williams have a prayer of substantiating his claims. As has been established in previous exchanges3, whenever Williams commits to a straightforward position, he is usually quite wrong. The only logical conclusions that can be drawn from the preceeding comedy of errors are:
1. Williams still believes that terminology is unimportant, and that since in his 'worldview' there are no evolutionary distinctions, pointing out the improper use of terms is a rhetorical ploy, or
2. Williams simply doesn't get it.
Williams best defense is what he has been employing above - adopt ambiguous terminology while still insisting that his original specification has merit. It apparently works wonders on fellow creationists, but to any objective reader, the tactic is all too obvious.
Conclusion
To conclude, I have clearly shown in this debate that Dr. Page was mistaken to cite the Genetics study (Wu, et al) and the Science article (Rice, et al) as implied refutations of Haldane's Dilemma. In the Genetics study he clearly engaged in circular reasoning. To make matters worse for Dr. Page, the study actually worsens the mutational cost problem! (required offspring per breeding couple increases to at least 60 instead of 40; see first post in debate, and my article on the mutation problem for evolution). In the Rice study, Page admitted that the evolutionary "benefit" described by the study pertains to a "harmful mutation environment", which by its very description is a huge disadvantage to evolution!
Clearly, Williams has convinced himself that he has accomplished something here. He is alone. Let us look at what prompted Williams to write his 'rebuttal' in this 'informal debate':
The following papers:
J. C. Fay, G. J. Wyckoff and C.-I. Wu: Positive and Negative Selection on the Human Genome, Genetics 158, 1227-1234. 2001.
and
Sexual Recombination and the Power of Natural Selection William R. Rice* and Adam K. Chippindale 2001 Science 294:555-559
severely impact the various claims of creationists who insist that because of 'Haldane's dilemma', among other things, human evolution from an ape-like ancestor is impossible.
This 'conclusion' is premised primarily on personal opinions, for there is, at present, no information at all regarding the numbers of fixed beneficial mutations required to explain various adaptations and traits in extant organisms.
Nonetheless, the argument regarding the human question goes something like this:
According to an extrapolation of Haldane's 1957 paper, no more than 1667 fixed, beneficial mutations could accrue in the lineage leading to humans from an ape-like ancestor.
1667 is too few to account for this (unsupported assertion), therefore, humans must not have evolved at all.
According to the first paper mentioned, the number is off - way off. We cannot blame Haldane - he was working more than a decade before and sequence data was available to him. This paper demonstrates that there have been approximately one beneficial allele substitution every 200 years since the split between Old and New world primates some 30 million years ago.
This amounts to 150,000 in 30 million years. The estimated split between the lineage leading to humans from that leading to chimps is around 5-6 million years ago.
We'll go with 5. That allows for some 25,000. That is 14 times what was allowed under Haldane's model.
Considering the fact that HGP analysis and others put the total gene number in the human genome at between 30 and 60,000, and if we consider that each of these genes may be influenced by at least one regulatory region, 25,000 substitutions - by anyone's standards - should be seen as more than enough to acocunt for the differences.
Of course, since it is a fact that it has not been shown that 1667 fbms is too few, I am still not convinced that it cannot be explained by the lower number.
I suppose it all rests on one's point of view, and whether or not one is willing to accommodate new discoveries into their lexicon.
From the second paper, emphases mine:
"Our results experimentally verify a counteracting advantage of recombining compared to clonal lineages: reduced accumulation of harmful mutations and increased accumulation of beneficial mutations.The magnitude of this benefit will accrue over geological timeand promote the superior persistence of recombining lineages at both the level of species within communities (clonal versus sexual species) and genes within chromosomes (nonrecombining Y-linked versus recombining X-linked genes)."
I don't think that needs any more explanation.
Comments appreciated.
I am not quite sure how pitting data against an evolution-based mathematical model is circular reasoning, especially if the assumptions that Williams decries are valid due to a wealth of evidence. Williams seems to be relying on that old creationist canard regarding scientific exploration: If you use assumptions in your work, then the outcomes are invalid. Apparently, the creationist thinks all experimentation should be done devoid of assumptions, regardless of the merit (of course, this does not apply to the creationist, whose all-encompassing assumption is that the bible is literally true and that therefore evolution could not have occurred). What Williams is arguing against is really not my supposedly employing 'circular reasoning', rather it is with the entire lexicon of scientific pursuit.
Willaims can use as many exclamation points as he wishes to, it will not lend validity to his specious claims. As for the Rice paper, I explain above how Williams' treatment of it is flawed.
This did not leave Dr Page with anything substantive to offer in his latest rebuttal, so the recourse he chose was to distract the reader with 1) hairsplitting (ape vs monkey), 2) equivocation of the definition of evolution, and 3) numerous red-herrings.
The substance of my response was to demonstrate the ineptitude of your positions. And I succeeded.
I truly believe Dr Page now knows, or at least suspects, his citations are not valid weapons against the Haldane substitution problem, nor do they support the theory of evolution in any way (as I mentioned earlier, the Wu study in fact provides evidence against evolution).
I was unaware that Williams was such a clever student of Goebbellian doctrine. Haldane's 'substitution problem' is not what its creationist proponants claim it to be - indeed, as I quote Haldane above, even he admitted that his numbers were in error. And to claim that neither paper I cited originally supports evolution in any way is just an amazing position to take. Especially entertaining is Williams last sentence, the part in parentheses. Only a committed dogmatic creationist with no relevant knowledge, education or background could come to such a conclusion. Of course, there were many 'solutions' to the 'Haldane problem' long ago. Curious that the Haldane-advocating creationist is so unaware of such information.
Certainly the authors of these studies did not think their findings had a bearing on such an important issue as Haldane's Dilemma, or you would think they would have mentioned it. Despite direct correspondence with at least one of the authors, Page was unable to get any of them to join him in his circular reasoning foray.
Why would they make such mention, as Haldane's dilemma is not considered a dilemma in the world of practicing biologists? And how many times shall Williams make his clearly false representations of my correspondance? And Williams wanted to characterize one of my replies as 'desperate' - how does the characterization 'desperate and dishonest' sound, directed at the appropriate target, of course...
To Page's credit, I have not seen him trumpeting on the net either study since our debate began. Unfortunately however, there are several other evolutionists on the net who have now picked up his flawed nugget and are running with it. I ask Dr Page to take the time to correct the error he started whenever it re-appears on the net.
What utter nonsense. As I wrote in my earlier replies, I have taken on additional duties at work and have not taken part in nearly as many internet discussions as I had in the past. Hence, I have had less opportunity to 'trumpet' anything. And should the topic come up again, I would gladly cite the studies. Repeated assertions to the contrary are no match for actual scientific research.
It should be more clear than before that Williams is more interested in boosting his ego and propping up his religious beliefs than actually engaging in any sort of reasoned discourse. Should Williams reply to this, I will again have to point out his confusion and conflation of terms which make his positions so incoherent and untenable.
Some of the things I found most interesting, however, are not what Williams did reply to, but what he did not. His handwave of the chimp-bonobo conundrum for creationism is a case in point. He seems to be of the 'attack, never explain' mindset. Other things Williams deigned to ignore:
His erroneous defense of ReMine's claims (re: 500,000 changes...)
His continued reliance upon papers that also assume evolution (e.g., Eyre-Walker and Keightly's paper), indicating some hypocrisy in his position
His inability to understand that Haldane's model was premised on evolution being true (accusations of equivocation notwithstanding)
My mention of his ignored Baptist Board posts, specifically, my question regarding his beloved 'X-number of offspring per couple' schtick
Accusations of positing 'red herrings' and repeated false charges are no way to engage in 'debate', informal or not. Considering the tone and content of Williams' web site, not to mention in this discussion (though it was refreshing that Williams did not call me a "knucklehead" or a "complete moron" for not agreeing with his piffle, as his his usual tact), one should be hard pressed to accept that he wants to be taken seriously, I for one no longer think he does.
Games, it would appear, are best left to children and creationists.
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1For example, in no particular order:
Powell and Richmond, 1974. Founder Effects and Linkage Disequilibria in Experimental Populations of Drosophila. PNAS 71(5) 1663-1665.
Grant and Flake, 1974. Solutions to the Cost-of-Selection Dilemma. PNAS 71(10) 3863-3865.
Darlington, 1977. The cost of evolution and the imprecision of adaptation. PNAS 74(4) 1647-1651.
Interestingly, none of these was cited in ReMine's book, "The Biotic Message", of which a central theme was the 'evolution busting' "Haldane's Dilemma."
2Williams is not alone in his 'personal incredulity.' His source for most information that he uses in this line of 'reasoning' is Walter ReMine's book "The Biotic Message", wherein ReMine, also an elctrical engineer and creationist, writes:
“Take an ape-like creature from 10 million years ago, substitute a maximum of 500,000 selectively significant nucleotides and would you have a poet philosopher? What does that sound like to you?” (p.209)
“Think about it again. Is 1,667 selectively significant nucleotides enough to make a sapien out of a simian?” (p. 217)
Gee - ReMine doubts it, and he wrote a book, so I guess I should doubt it too...
Not a single citation or even logical argument ensues in ReMine's book supporting his implicit claims.
3On the OCW discussion board, Williams had claimed first that SNPs (single nucleotide polymorphisms) were removed from phylogenetic studies. I and others asked how this was done. I and others pointed out that typically only a single specimen from each taxon is used in such analyses, and that therefore there is nothing to compare the individual taxon's sequence to to determine what changes would qualify as SNPs. Williams continued to claim that he was correct, and upon again being asked how SNPs were discovered in such analyses, Williams again claimed 'genetic analyses'. When asked what those genetic analyses were, he refused to respond. There are only so many ways to interpret such antics. HINT: There are no 'genetic analyses' that can assess from a single sequence which loci are SNPs. Draw your own conclusions.
4Haldane, J.B.S. More Precise Expressions for the Cost of Natural Selection. Date and additional citation information unavailable at this time.
