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

Tuesday, January 17, 2006

Haldane's Dilemma - another creationist takes a blind stab

*This is in draft form and will be modified as needed*

**see also This new post in response to some nonsense at Dembski's blog

**UPDATE**
See bottom of article

Over at the Creation and Evolution blog, I have made a few comments to the blog's author, a computer programmer and creationist calling himself "crevo", after comments he had made regarding his article titled Evolution, Chance, and Design.

His comment that caught my attention was this:

"...Plus, you have the cost of selection, which limits the number of mutational events (of any type, not just base pair) between man and ape's most recent ancestor as being about 1,667, which is far too few. See Haldane's Dilemma."

The link takes you to a webpage authored by Walter ReMine, an electrical engineer and creationist, whereon he hawks his book "The Biotic Message". I will be writing up an article on my encounters with ReMine and his claims later, so I will not go into his book or his specific claims now.

But, I have encountered a number of people on the internet that employ ReMine's claims without question and what I have found is that they understand as little as ReMine does about this issue (for some concise information on Haldane's dilemma, see this article).

Crevo is one of these people.

I asked the following question of Crevo in response to the above:

"Please explain why, if that number is correct, it is 'far too few'."


And classic creationist comedy ensued. Crevo's responses in red, my replies in blue.

Round 1:
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 are completely unaware of what "Haldane's dilemma" actually indicates, that much is obvious.If you are going to refer to an issue like that, it seems reasonable that you should at least have an understanding of the basics.Haldane's model dealt with fixed beneficial substitutions, not all substitutions. As an example of how out of the ballpark your take on Haldane's dilemma is, consider this:
Any two humans differ by millions of substitutions. According to your take, no two humans can be related...

Round 2:
"Haldane's model dealt with fixed beneficial substitutions, not all substitutions."

That is correct, but do you honestly think that out of the millions of differences between chimps and humans, less than 1% of them are neutral? I'm also pretty sure that the differences I am quoting from are fixed in the population, but I will have to double-check.For more information, see:
http://www.nwcreation.net/wiki/index.php?title=CB121
=============

That is correct, but do you honestly think that out of the millions of differences between chimps and humans, less than 1% of them are neutral?

Um, no - I think that most of them are neutral. Please slow down and re-think your statement.

I'm also pretty sure that the differences I am quoting from are fixed in the population, but I will have to double-check.

No, they are not. In fact, they cannot be, for as I mentioned, any two humans differ by some several million nucleotides, therefore, it is impossible to determine how many substitutions, especially neutral ones, are in fact fixed.

For more information, see: http://www.nwcreation.net/wiki/index.php?title=CB121

You may have noticed that it is on a creationist site. ReMine the electrical engineer who has been misrepresenting the issue for years. For example, he claims that 1667 fixed beneficial mutations are too few. But he does not know what traits the ancestor had!
Therefore, simple logic dictates that he cannot know how many are too few. I know this because I have asked him on many occasions and he simply ignores the question. Further, in his terrible book, he implies that it would take more than 500,000 such changes if evolution were true.* This is, of course, quite stupid - the human genome only has 25-30-,000 genes! Further still, ReMine acknowledges that neutral mutations can also contribute to phenotypic differences and that they accumulate at a higher rate than do beneficial mutations, not to mention single nucleotide polymorphisms.

Round 3: I have replied twice, but so far, my replies have not been published on Crevo's blog (as of January 20). It may be innocent - he may just have not gotten around to accepting the comments, or, he may be refusing to publish them. So, I will comment here, in black.

"Um, no - I think that most of them are neutral. Please slow down and re-think your statement."

There was a missing "not" in that statement. Thanks for pointing it out!

"In fact, they cannot be, for as I mentioned, any two humans differ by some several million nucleotides, therefore, it is impossible to determine how many substituions, especially neutral ones, are in fact fixed."

No it is not. It would be based on sequencing a wide range of humans.

Let us recall what this is in reference to - Crevo had written that he was "pretty sure" that the numbers he was referring to are fixed in the population. However, the numbers he was referring to are in fact raw estimates premised on the comparisons of only a few individuals, and notice that he has now modified his original claim - he now says the number "would be" based on sequencing a wide range of humans. Meaning, of course, that he has unwittingly acknowledged that his claim is baseless. In order to determine which neutral substitutions are fixed in genes, we would have to sequence a very large number of humans, and this does not even take into account substitutions in intergenic regions nor those that are not expressed yet are part of the total number.


If the change exists in a wide sample of humans, it would be shown to be fixed.

By definition, fixation means that it is present in 100% of the population. But this is getting off topic.

Most of the differences between chimps and humans are fixed. There are 35 million base substitution differences, as well as 5 million insertion/deletion events (totaling about 40 million nucleotides).

In reality, it is quite likely that a large - a very large - number of those differences are in fact not fixed, for at least one of the reasons I mentioned before (polymorphisms between living humans). Even if all of those changes were fixed, the overwhelming majority are in noncoding regions and many that are in genes are neutral or nearly so, and so do not fall into the "dilemma" set forth by Haldane's model. Thus, flaunting these large numbers is at best a red herring.

"You may have noticed that it is on a creationist site."

Yes. In fact, I wrote it. So what? Are creationists wrong by definition?

No, they are quite often wrong on the facts, AND they tend to view the writings of other creationists unskeptically. The piece referred to is a fairly typical creationist "hero worship" job - Crevo simply repeats ReMine's claims and denigrates a few critics of ReMine's claims.


"ReMine the electrical engineer who has been misrepresenting the issue for years."

Really? I guess that's why the editors of peer-reviewed journals have been telling him they won't publish because the issue is already well-known?

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.


"For example, he claims that 1667 fixed beneficial mutations are too few. But he does not know what traits the ancestor had!"

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

Ummm.... Ok. What does that have to do with the presumed ancestor? Surely, Crevo is not so underinformed (disinformed?) regarding evolution that he actually thinks evolution states that humans evolved FROM chimpanzees? In addition, only a tiny fraction of the mutational difference between humans and chimps represents phenotypic differences. Using Crevo's "logic" this would mean that because any two humans differ by some millions of mutations, that any two humans differ by some millions of traits. This is laughably absurd, yet Crevo is using as the crux of this portion of his argument!


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

Please name these changes. Please identify the traits that the ancestor did NOT have that the 1667 mutations must account for. But first, you will, of course, have to identify the ancestor. If you do not, how can you possibly know which traits had to be modified? Also, please explain how many beneficial mutations are required to produce a particular change.
If you cannot do at least the things I have mentioned, then claiming ANYTHING about Haldane's dilemma and numbers of required mutations is just empty rhetoric and sophistic gibberish.


"Further, in his terrible book, he implies that it would take more than 500,000 such changes if evolution were true. This is, of course, quite stupid - the human genome only has 25-30-,000 genes!"

Do you think genomes change an entire gene at a time? You should read Behe's peer-reviewed article about how long it takes just to change three _amino acids_.

No. You should read the Dover trial transcripts and see how Behe's peer-reviewed paper was shown to be little more than an academic exercise with little relevance to biology, not to mention evolution.
Of course, what we are seeing is the non-biologist's take on gene action. Non-biologists seem to believe - even insist - that any physical change requires some huge suite of 'beneficial' mutations. This is sheer ignorance.
One of my favorite refutations of this notion is the single point mutation in the FGF3-R gene that causes a form of achondroplasia (dwarfism). One little base pair substitution reduces the number of interphalangeal joints, produces disproportionate alterations in limb length, etc. Now, I am not presenting this as an example of evolution, nor as an example of a beneficial mutation. I am presenting this as evidence - proof even - that phenotypic changes do NOT in fact require large numbers of mutations. Those that claim that some huge number of mutations IS required are just telling stories to prop up their baseless claims.


In addition, the regulatory elements are not included in gene counts, and are just as important if not more so.

So perhaps that is why so many 'new' genes and the like are not really required, as creationists seem to insist?


In addition, a better count would be of proteins, not genes, which then goes into the hundreds of thousands.

If that is so, why do you even mention Haldane's dilemma? Of course, those proteins have to come from somewhere, do they not?

"ReMine acknowledges that neutral mutations can also contribute to phenotypic differences and that they accumulate at a higher rate than do beneficial mutations, not to mention single nucleotide polymorphisms."

This is true, but the rate of change would simply have to be astronomical, unlike any changes we've ever seen.

Really? Astronomical? 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.


The fact is, you are basically limited to 1,667 beneficial mutations. That's barely even enough to build a full gene, much less account for the beneficial differences between chimp and man.

The real fact is, you have no idea how many fixed, beneficial mutations would have been required to evolve humans from an apelike ancestor and continuing to claim that 1667 is too few is at best disinformative propaganda and wishful thinking.
***********************************

This morning (Jan.20) Fedmahn Kassad posted the following in Crevo's blog:

"I guess that's why the editors of peer-reviewed journals have been telling him they won't publish because the issue is already well-known?"

This is quite incorrect. Editors told him they wouldn't publish on another issue because it was on material that had been published 25 years ago. It wasn't about Haldane's Dilemma.

"The fact is, you are basically limited to 1,667 beneficial mutations. That's barely even enough to build a full gene, much less account for the beneficial differences between chimp and man."

Also quite incorrect. Since these are beneficial mutations, they are all gene modifying mutations. Walter has also acknowledged that in the same time, you could get 25,000 neutral expressed mutations. So, how many base pairs does this come out to be? I have gone a few rounds with Walter on this, using his own assumptions. Here is what Walter wrote: "Evolutionists do not get to assign the 1,667 mutations any way they please, say, as "regulatory genes" or as "mutations with a large effect". Nature does not work that way. Rather, the preponderance of mutations will be of the ordinary kind, with a small effect. Let me illustrate the concept with crude figures: about 1500 mutations with an ordinary small effect, 100 more for re-positioning genes on chromosomes (inversions and so forth), 60 as gene duplications, and 7 mutations to regulatory genes that have a larger effect "for a total of 1,667." The Human Genome Project estimates that the average gene consists of 3000 base pairs. Just taking Mr. ReMine's assumed 60 gene duplications, this would provide for 180,000 new base pairs not present in the common ancestor, and this is just from a small fraction of the 1,667 beneficial mutations. It is obvious that 1,667 beneficial mutations and 25,000 neutral mutations could add up to a great deal of base pair differences.The funny thing was that when I pointed this out to ReMine, he complained that I had misrepresented him. In dealing with him over the years, I have learned that anything he did not explicitly say - even if it is a given from his argument - amounts to misrepresentation if he doesn't like the outcome.
The Haldane argument is bunk, plain and simple. I have personally challenged ReMine to defend, and all he does is dodge and weave.

See: http://www.baptistboard.com/cgi-bin/ultimatebb.cgi/topic/36/111/4.html?

It will be interesting to see how - or if - Crevo responds.

5 comments:

crevo said...

"It appears that Crevo is, as I believed, refusing to publish my comments."

I have never deleted a comment in any of my blogs except for those annoying spam comments that are left by bots.

Doppelganger said...

I have removed the offending comment. I do wonder then, what happened, for I left - tried to leave - two comments, neither of which seemed to make it, yet when I published a link to here, there, anonymously, it appeared.

I do await your comments on this issue.

crevo said...

" As an example of how out of the ballpark your take on Haldane's dilemma is, consider this: Any two humans differ by millions of substitutions. According to your take, no two humans can be related..."

No, because our differences are (a) not fixed, and (b) rarely fitness related. There are clear benefits to being human, and while not all of the differences between human and chimps are adaptive, it is reasonable to think that a number of them are (and a number of them have been shown to be). The two that I think are notable and fairly uncontroversial are being obligate bipedals and brain function.

"No, they are not. In fact, they cannot be, for as I mentioned, any two humans differ by some several million nucleotides, therefore, it is impossible to determine how many substitutions, especially neutral ones, are in fact fixed."

Well, since, as you said, fixed means 100% of the population, it would be impossible to tell without sequencing the genome of every individual. However, we can get a general idea without knowing for sure. One often has to make judgment calls. It makes very little difference in the argument if you subtract out a few million on each side to account for variable regions.

"For example, he claims that 1667 fixed beneficial mutations are too few. But he does not know what traits the ancestor had!"

Well, first of all, this is very reasonable considering there was no ancestor. However, we can come to at least some conclusions based on evolutionary theory on what a common ancestor between the two _should_ have. It should have a diminished brain function (probably in relation to _both_ the human and the chimp), and it would be a facultative bipedal animal. These are the traits I will concentrate on. There are probably many other traits one could deduce that such an ancestor should have according to evolutionary theory.

" Further, in his terrible book, he implies that it would take more than 500,000 such changes if evolution were true.* This is, of course, quite stupid - the human genome only has 25-30-,000 genes!"

It is quite stupid for someone who is a biologist to make such a statement. A "change" is not the substitution of an entire gene. _Most_ changes are of single base pairs. Other changes are insertions, deletions, and copies. This is not restricted to the number of genes. Likewise, Haldane's calculations do not require that the change exist in a protein-coding gene. There are many regulatory regions in addition to the genes that the beneficial change could take place in.

"However, the numbers he was referring to are in fact raw estimates premised on the comparisons of only a few individuals"

If we had the benefit of complete knowledge, such discussions as these would not be needed. What we have is a reasonable estimate based on known data.

"Even if all of those changes were fixed, the overwhelming majority are in noncoding regions and many that are in genes are neutral or nearly so, and so do not fall into the "dilemma" set forth by Haldane's model."

First of all, I have to wonder at someone who assumes that a change in a non-coding region is neutral. These regions are some of the most important. Remember, the claim is that there are fewer than 1,667 beneficial changes separating chimps and humans from their most recent common ancestor. We have evidence of massive numbers of genetic changes, and massive morphological, social, mental, and other differences between chimps and humans. Yet we must have fewer than 1,667 _change events_ separating them.

"One of my favorite refutations of this notion is the single point mutation in the FGF3-R gene that causes a form of achondroplasia (dwarfism). One little base pair substitution reduces the number of interphalangeal joints, produces disproportionate alterations in limb length, etc. Now, I am not presenting this as an example of evolution, nor as an example of a beneficial mutation. I am presenting this as evidence - proof even - that phenotypic changes do NOT in fact require large numbers of mutations."

However, the notion itself still stands. If you have a complicated system, minor perterbations in the core components WILL have drastic effects. The issue is, though, that in order to make a _useful_ change of a core component requires that many genes change in coordination. How many individual changes would it take to turn achondroplasia into a beneficial mutation? In addition, there are some systems which are made with a switching mechanism, so that a single switch can switch on or off two different pathways. In such cases, both pathways are already designed, you are just switching between them. Creating a new pathway, however, requires much adjustment. This is the point of my article here. I do not deny that you can get massive body change with a single point mutation. In fact, why stop with that one. There are a huge number of mutations whose effect is so drastic that you die before birth! The question is not generating a large-scale effect, but generating a large-scale effect that was (a) not already coded in the genome, and (b) beneficial to the organism. Just as the achondroplasia example shows, it would take quite a number of changes in coordination to get such changes to be beneficial. The chances of all of those types of mutations occurring by chance in such a way, and in such sequence as that any of them can be useful is vanishingly small.

"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."

Nice exercise in circular logic. The "empirical studies" are simply calculating the differences between chimp and human genes. In order to get that rate one must ASSUME common ancestry, which is precisely what is under consideration. Such calculations are irrelevant in a question of _whether_ there is common ancestry to begin with. Don't get me wrong, I don't think that the authors of the article were engaged in circular reasoning -- they had a clear separation between their assumptions and their conclusions, and it was a very good paper. The problem is when you use the assumptions to prove the assumption. That's circular reasoning.

"The real fact is, you have no idea how many fixed, beneficial mutations would have been required to evolve humans from an apelike ancestor and continuing to claim that 1667 is too few is at best disinformative propaganda and wishful thinking."

It's not _wishful_ thinking, it's _reasoned_ thinking. As someone who creates and modifies codes on a daily basis, I know what kind of interactions are required to get large-scale changes stabilized and working. The two features I said I was focusing on were bipedalism as well as the brain. Here is what Gould says about bipedalism in "Our Greatest Evolutionary Step" (from The Panda's Thumb):

"Bipedalism is no easy accomplishment. It requires a fundamental reconstruction of our anatomy, particularly in the foot and pelvis. Moreover, it represents an anatomical reconstruction outside the general pattern of human evolution...[mentions some features that are a consequence of neoteny]...But upright posture is a different phenomenon. It cannot be achieved by the "easy" route of retaining a feature already present in juvenile stages. For a baby's legs are relatively small and weak, while bipedal posture demands enlargement and strengthening of the legs."

These are all changes that are outside the normal range of variation.

As for the brain, consider the following:

From Accelerated evolution of nervous system genes in the origin of Homo sapiens:

"...the acceleration of protein evolution is most prominent in the lineage leading from ancestral primates to humans. Thus, the remarkable phenotypic evolution of the human nervous system has a salient molecular correlate, i.e., accelerated evolution of the underlying genes, particularly those linked to nervous system development."

Positive selection on the human genome lists numerous genes which are believed to be beneficially different from chimps. I don't have the data, but I imagine that each of the genes they mention have more than one change event associated with them. The authors conclude:

"Although a fair number of genes have already been identified as targets of positive selection during the evolution of humans and/or primates, these are likely to be the tip of the iceberg. As more genes are added and as alterations in gene sequences are mapped to functional changes, the study of positively selected genes may become a mainstream approach to the dissection of human biology and disease."

So, what they have shown is just the tip of the iceberg.

Now, there is a way to salvage the chimp/monkey common ancestor problem with regards to Haldane's dilemma. That is to assume that the chimp is a degenerate form of the hypothetical common ancestor. So, the common ancestor would actually be very close to being human (if not actually human), and the chimp is degenerative from that. But I don't think that there are any evolutionary biologists that actually believe that.

Doppelganger said...

Replied via new post.

Doppelganger said...

Hi Russ,

I did not dismiss ReMnie's paper out of hand. I have dismissed his claims because they are premised on empty nonsense.

If he cannot explain what traits the ape-like ancestor had, how on earth can he declare that the number of mutations 'allowed' under Haldane's model have any direct application?

He cannot.

Yet non-scientists like Dembski and you folks at "Uncommon Descent" think he is on to something.

ReMine is a crank, and you folks are gullible enough to be taken in by him.

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