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, February 22, 2006

Disgruntled engineers? Or overconfident pseudo-know-it-alls?

In response to an email from a molecular biology student, regarding the common background of so many creationist website authors – one in engineering – Pogge goes on an arrogant tear. In this article:

Disgruntled Engineers Against Evolution

R. David Pogge provides some insights into the mind of the creationist engineer. Please keep in mind that most of the engineers I know - and probably the overhwelming majority of engineers worldwide - do not suffer from the delusions of superiority that creationists like Pogge do. Also keep in mind that I have nothing against engineers at all - in fact, some of my favorite relatives are engineers. Many engineers are embarrassed at the willful ignorance coupled with extreme arrogance that is seen in so many creationists with engineering backgrounds. And this article (and the previous articles by Pogge that I have rebutted ) are pretty good examples of that unattractive trait.

Pogge begins:

One of the things that makes this letter worth addressing is the fact that he at least bothered to follow some of the links on our web site. (We know this because of the reference to "writing and speaking about software development in general".) So many of the emails we get come from people who clearly haven’t read anything but the name of our corporation.
Jordan asks questions that we think he really wants answered. His questions are not purely argumentative. That makes it worthwhile to take his email seriously.
Jordan asks, "What is with you guys and hating evolution? Is it because you spend so much time designing things yourself that you just can't accept the idea that life couldn't have orginated [sic] without a designer? Spent so much time writing computer code that you think DNA couldn't have posisbly [sic] originated by chance?" Well, yes, we do!

Now that is really something….
At least Pogge admits that he believes his biologically-irrelevant background gives him unique insights into the biological world. There is not much of a rational basis for this, but at least he admits it.

Engineers build complex systems. We know from experience that designs that aren’t entirely correct fail to function. Computer programs with millions of lines of code don’t work if just a few lines are wrong. Nobody has ever soldered transistors and resistors together randomly and produced a color TV set. Since biological systems are so much more complex than the systems we build, and since the DNA code is so much more complicated than the computer programs we write, we just can’t accept the idea that they happened by chance. We have never seen a complex system arise by accident, and don’t have any good, scientific reason to believe that it is possible. We don’t have the faith necessary to believe in something that is absolutely contrary to natural observations.

Emphasis mine. Where to begin. The logical fallacies are coming on strong already. Yes, engineers build (some of them, anyway) “complex systems,” and I have little doubt that just a few lines of code can corrupt a program with millions of lines of code in it (Though Pogge had best set some of his computer programmer creationist brethren straight – I was once in a discussion with creationist computer programmer CK Lester who argued just the opposite! I guess it depends on what argument the creationist is trying to make, whether they claim that there must be near perfection (Pogge) or that the code can amass up to 30% change and still work fine (Lester)).
But Pogge’s next claim clearly demonstrates what the email writer had inferred – that Pogge and his ilk simply do not understand what they discuss when it comes to biology (This line from Pogge is most interesting:
“So many of the emails we get come from people who clearly haven’t read anything but the name of our corporation.” in its projective value). Pogge and his like-minded creationists simply cannot accept that DNA code (whatever he means by that) arose by chance. Perhaps if they bothered to find out what evolution actually posits, they might not be so predisposed to simply reject it, at least on scientific grounds. For evolution does NOT, in fact, postulate that such things arose purely by chance. Chance variation only generates the raw materials, Selection, which is anything but driven by chance, acts on that variation. It is puzzling to me that so many creationists leave that part out. Maybe they do so on purpose?

Jordan [the email author] didn’t say that 87% of the members of anti-evolution groups are theology majors. He said they were engineers. We appreciate the confirmation that so many people rejecting evolution are engineers. That’s been our observation, too, but we haven’t done a scientifically valid study to prove it. It is good, however, to have anecdotal evidence to support our observations. Creationists aren’t just dummies who don’t know anything about science. They are smart people who use their scientific knowledge to design clever, useful products.

Ummm…. Engineers may be smart people, but how that gives them special insight into evolutionary biology is a question that seems to have no legitimate answer. Designing ‘clever, useful products’ does not seem to have any bearing whatsoever on providing the creationist engineer with unique insights, special knowledge, or superior abilities when it comes to doing anything BUT designing clever, useful products. In fact, in my opinion, being an engineer with creationist tendencies may actually produce an unwarranted bias in his/her outlook on the biotic realm. They tend to assume that all things can be understood in their language; that DNA is just like computer code (just more complex), that cellular structures are just like machines and motors and so must, therefore, be the product of “intelligence”, just as actual, human-made contrivances are the products of (human) intelligence.

We don’t doubt that Jordan has done excellent work studying the genetic similarity of marsupials. No doubt they are very similar. It is our position that such work is extremely valuable if applied to practical problems. For example, if some marsupials are more prone to certain diseases than other marsupials, it would be good to know how they differ genetically. These genetic differences might be responsible for resistance or susceptibility to specific diseases. There is great value in understanding how biological systems work because many of man’s inventions (like sonar and the Sidewinder missile) are merely copies of biological systems. If we knew more about how marsupials nourish their young, it might give us insight into how we can raise healthier children. There is so much that can be learned from a study of genetics. That is why it saddens us to see talented people like Jordan wasting their time trying to figure out how a wombat turned into a wallaby or a kangaroo.

Oy… “Turned into”? It is hard to tell if Pogge is engaging is sarcastic hyperbole, or if he really just does not get it. Perhaps he does not get it and employs sarcastic hyperbole as a result? In REALITY, patterns of genetic change CAN in fact tell us about descent. Pogge and his ilk simply reject it on a priori grounds and justify these beliefs with their arrogance.

It might very well be that a wallaby and a kangaroo really are variations of one created kind, just as beagles and poodles are variations of the dog kind. If so, it is just more confirmation of microevolution, which creationists already believe. But how does one know if genetic and physical similarities are the result of a common ancestor rather than a common designer?

What is a “kind”, Mr.Pogge? Won’t you tell us all, with you special engineering insights and biblical expertise? How does one tell the difference? Quite simply – by looking at the patterns. The methodologies have been tested on knowns, and I should think that an engineer would understand the validity of tested methodologies.

Jordan has "yet to hear of a single case of hard biological evidence rejecting evolution." We wonder what his criteria for hard biological evidence is.

I have to wonder what Mr.Pogge's is.

Darwin considered the eye to be serious biological evidence against evolution.

Ah, the old creationist out-of-context issue rears its head. Paraphrasing from the link, creationists are fond of quoting Darwin thusly:

"To suppose that the eye with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, absurd in the highest degree."

And yet, if we look at the rest of the passage:

"To suppose that the eye with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of Spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, absurd in the highest degree. When it was first said that the sun stood still and the world turned round, the common sense of mankind declared the doctrine false; but the old saying of Vox populi, vox Dei ["the voice of the people = the voice of God "], as every philosopher knows, cannot be trusted in science. Reason tells me, that if numerous gradations from a simple and imperfect eye to one complex and perfect can be shown to exist, each grade being useful to its possessor, as is certain the case; if further, the eye ever varies and the variations be inherited, as is likewise certainly the case; and if such variations should be useful to any animal under changing conditions of life, then the difficulty of believing that a perfect and complex eye could be formed by natural selection, should not be considered as subversive of the theory."

We see something quite different. Do we have exact, explicit answers to the “genuine” questions Pogge asks? I don’t think so, and we may never have them, and I would venture to say that even if we did, Pogge and his ilk would still find reason to dismiss them.

Where does Jordan think the mammary glands in his marsupials came from? How did single-chambered fish hearts evolve into multi-chambered animal hearts? How did cold-blooded creatures evolve into warm-blooded creatures? What biological evidence would be sufficiently hard to disprove evolution in his eyes? These aren’t argumentative questions. We are genuinely curious.

I sincerely doubt that. Creationists typically employ 'questions' as evidence. Can't answer my particular question on evolution? Must be evolution is wrong then! Pogge is implying that because he has no satisfactory answers to these particular questions, that he is justified in rejecting evolution in favor of Divine creation.

Jordan says, "All their data about morphology, plate tectonics and amino acid interaction all correlate with our data perfectly. International conspiracy or simply science at work? You decide." We say, "None of the above." We reject the conspiracy theory because it implies sinister motives and collusion. We don’t believe that all evolutionists are evil people intent on destroying all that is good and virtuous with their evil theory. But the other option, science at work, isn’t correct either. Just because an opinion is held by a scientist doesn’t make that opinion scientific fact. We like to reserve the term "science" for knowledge obtained using the Scientific Method.

And that would include information about evolution. I wonder what 'science' Pogge can present FOR his preferred belief, young earth cvreationism? Peruse his site. You will not find a single essay or article that actually provides any such thing (I certainly have found none). It is ALL simply nitpicking and distorting evolution-based science, and it is all mere opinion, and uninformed opinion at that. An opinion on evolutionary biology held – or even firmly stated – by a creationist with no relevant biological education or experience cannot even be taken seriously, much considered as a valid position. Especially when those opinions can largely be shown to be premised on distortions and nonsense, as have all of the opinions written by Pogge that I have read have been.

Our answer is that there is correlation of data because many people are trying to make their data fit together into a pre-determined framework because they sincerely believe that framework is correct. They believe that all life evolved from a common ancestor, so they attempt to explain their observations in terms of evolution. Where there is sufficient prejudice, there is agreement.

In reality, this is what happens when someone tries to shoehorn data to fit their preconceived notions. They produce significant error and end up rejecting objective data for subjective data. That is what creationists are forced to do. We ‘believe’ that common descent occurred because that is what the data indicate.

Despite this, we don’t think there is as much agreement between the morphological data and genetic data as Jordan does. Maybe there really is good agreement between morphological data and genetic data in the marsupials Jordan studies, but that seems to be the exception, rather than the rule. We keep reading articles in Science and Nature which show there isn’t very good agreement. We have documented examples in past newsletters (Fuzz, Birds, and DNA and The DNA Dilemma ).

A few anomalies does not a trend make. As is so often the case with creationists, Pogge takes a couple of interesting cases and extrapolates them into a field wide dilemma. It is not. Indeed, Pogge makes the extremely false claim in his ‘birds’ article above “In that essay we noted that whale evolution has been controversial because the DNA analysis did not agree with the traditional fossil interpretation. This is commonly the case”. No, Pogge, it is NOT commonly the case. Your baseless and misleading claim is incorrect. But why would you care? You have a non-scientific belief system to prop up.

We hope that Jordan will continue to study marsupials. We hope he will try to explain how they all could have originated from a common ancestor. We think that the more he studies, he will discover the hard biological evidence against evolution all by himself.

Or, he could be like the creationist engineers – just start with your conclusions, then, because you are an engineer and have special overpowering insights in all fields of science even if you don’t know anything about them, proclaim the truth of your position! It is easier than thinking, and it must be real fun to pluck quotes out of context and engage in all manner of ego-gratifying falsehood spreading and misreptresentation. Right Mr.Pogge?

Where is

I have written about the misleading and shoddy work found on the site run by an electrical engineer creationist, R. David Pogge, here, here, here, here, and here.

I was getting ready to do another write up today and when double checking the link to the article that I was going to rebut, I discovered that the link was dead. Then, I tried another, and another. I then did a Google search for any mention of the site, and in each case, I was unable to get it to load.

So, what happened to Did Pogge shut down, finally realizing that his shoddy work was being exposed?

Of course not.

Instead, the creationist has simply changed domains.

Oddly, Pogge still titles the site:

Science Against EvolutionOfficial Home Page
Now, I shall have to change all my links.
I do wonder why Pogge did this.....

Tuesday, February 21, 2006

New reply to Crevo

Crevo recently replied to this post here.
His reply :

For those who want to compare whether or not my assertions about the difficulty for core functions to handle perterbations, see this paper in the most recent issue of Science (while Davidson may not agree with me on the difficulties of change in this case, he certainly points out that parts of the genome are "more core" than others, and are more constrained against change -- thus, as I said, small changes can lead
to dramatic phenotypic results, just not good ones).Read mine. Read the professor's. Read the cited literature. Decide for yourself!

Please do. Please also remind yourself of some key issues:
1. Crevo has yet to provide any rational, evidence supported explanation for why: a) Haldane's model as used by ReMine is applicable in human evolution
b) if ReMine's number is relevant, why it is a "dilemma"

Instead, Crevo wants to try to change topics. This is a common creationist tactic. While mulling over my last reply to him, something struck me that I did not comment on before. I had written:

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.

Note the part I bolded. In his reply, Crevo wrote:

How many individual changes would it take to turn achondroplasia into a beneficial mutation?

Hmmmm... Is it just me, or did I explicitly write that what I presented was NOT an example of a beneficial mutation?

Anyway, I also encourage readers to check out the Science article Crevo seems to think helps his cause.

One will note, the article deals with different levels of conserved series of gene interactions, the 'uppermost' being the 'kernels' that dictate phyletic and superphyletic basic body plan, a middle level that affects body plan at the class, order, and family level, and a lower level that dictates speciation.

Crevo, a computer programmer, wrote:

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.

in response to:

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.

So, what ARE the "large scale changes" between human and chimpanzee? The programmer is unable to say and instead tries the standard creationist tactic of trying to shift the discussion. That is OK - Crevo's hero and fellow non-biologist, Walter ReMine cannot provide the very basic information required to know whether or not the ReMine number of mutations is too few or not. They prefer engaging in prolonged bouts of mental masturbation followed by condescening quips regarding their exceptional sexual prowess...

Crevo had written above:

"..while Davidson may not agree with me on the difficulties of change in this case, he certainly points out that parts of the genome are "more core" than others, and are more constrained against change -- thus, as I said, small changes can lead to dramatic phenotypic results, just not good ones."

And who said anything different? I am fully aware that many changes are bad, I never said otherwise. The FGFR-3 mutation I mentioned may be involved in one of the GRNs that is mentioned in the paper - but in fact, that demonstrates MY point, not Crevo's - that some large number of coordinated changes are in fact NOT required to elicit alterations in phenotype.

So AGAIN I ask - what traits did the presumptive human ancestor have that would require some large number of coordinated fixed beneficial mutations to get to the modern human condition? Which level of change (ala the Davidson paper) would these mutations have to have occurred at and how do you know, Crevo?

If you cannot answer at least these fundamental questions, then you have no busieness hawking electrixcal engineer creationist ReMine's claims on the matter.

Of note, the reader will notice that Crevo has decided, apparently, not to address ANY of the questions I posed for him in my last reply. One may want to wonder why that it...

Of interest are these blog posts regarding the Davidson article and a critique of an ID advocate's take on it.

Friday, February 17, 2006

Latest response to Crevo

Crevo responded to my post on Haldane's dilemma'. My new comments in red.

" 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.

(a) sometimes they are fixed in subpopulations – that is why they can be characterized
(b) rarely is not never
But you miss my point.

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.

Sure. A few million here. A few million there. But boy that 1,667 is the nuts!

"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.

And you accuse ME of ‘circular reasoning’?

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.

And so what amount of fixed, beneficial mutation is required to get a sapien from this simian? Let’s see…

" 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.

Why is that? Please explain it, Mr.Computer-programmer-creationist-with-all-the-answers!

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.

It is quite stupid for you to have interpreted what I wrote the way you did. I know that substitutions are not entire genes. However, the point is that if all things averaged out, each gene would require many multiple substitutions. ReMine’s ignorance of development and biology dictate his foolish premise.

As a worshipper of ReMine, I should have thought that Crevo would understand at least HIS claims, but it seems that was asking a bit much. ReMine’s 500,000 claim referred to fixed, beneficial mutation. Such mutations would have to be in genes or regulatory sequence. That is, ReMine’s claim (and your de facto defense of it) implies that each gene (on average) would need to experience ~16 such substitutions, or each gene and some number of regulatory sequences would need to experience some number of such substitutions. That or a smaller number of genes and/or regulatory sequences would necessarily experience multiple fixed, beneficial substitutions

"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.

I have to wonder at how you deduced that from what I wrote. Here, let’s take a look:

“…the overwhelming majority are in noncoding regions and many that are in genes are neutral or nearly so…”

Is that a bit easier to interpret? Or doesn't correctly presenting your discussion opponant's claims matter to you?

Remember, the claim is that there are fewer than 1,667 beneficial changes separating chimps and humans from their most recent common ancestor.

No, the claim is that 1667 fixed beneficial mutations is too few to account for human evolution from an apelike ancestor according to ReMine. Don't you know your own arguments?

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.

False. Even ReMine acknowledges 10s of thousands of fixed neutral expressed substitutions. Of course, this all depends on:
1. Haldane’s model being forever and in all circumstances absolutely applicable (it is not)
2. the ancestor not having any traits that require only ‘tweaking’
(also false)
You are assuming what you conclude. Circular reasoning.

And by the way - what are these "massive" changes?

"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.

Not necessarily. Sure, big phenotypic changes can occur, but such changes are not necessitated by the DNA changes.

The issue is, though, that in order to make a _useful_ change of a core component requires that many genes change in coordination.

Assertion. In fact, my FGFR-3 scenario falsifies the claim.

How many individual changes would it take to turn achondroplasia into a beneficial mutation?

I have no idea what that means. It is not the mutations that are beneficial or not, it is their effect and the interaction of the effect with the environment. If the environment favored achondroplastic individuals, then that phenotype would become predominant. So, in the right environment, it could very well be that single mutation. But so what? I did not present it as a beneficial mutation or a mutation that could be one.

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.

Designed? What is the evidence for this? In fact, what is the actual evidence for these ‘single switch can switch on or off two different pathways’ and are they even relevant?

Creating a new pathway, however, requires much adjustment.

Assertion. Please do not assume that biological systems operate just like computer software.

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!

Indeed. Those are the ones that are weeded out by selection right away.

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.

And here comes the strawman. Again, what traits are there that we have but this presumptive ancestor did not have? And I mean traits that were non-existent or are different in kind, not degree? If you cannot address that question, then ReMine’s number is meaningless. Also, phenotype changes need not be beneficial to become fixed in a population.

Just as the achondroplasia example shows, it would take quite a number of changes in coordination to get such changes to be beneficial.

You are making some rather unjustified leaps here. You are merely asserting that there must be additional mutations and coordination. This is most likely because you are unable to divorce what you do know about (computer programming) to what you only barely understand.
What is to say that another single point mutation could not do the job? What is the say that in the appropriate environment that single mutation is sufficient? Nothing. Just empty assertions.

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.

How small is “vanishingly small” and how did you figure that out?

"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.

Nice way to avoid explaining yourself.

The "empirical studies" are simply calculating the differences between chimp and human genes.

Um, no, they are not. Please do not assume that everyone relies on the same cherry-picked handful of studies that you do.

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.

None of this seems to have anything to do with your claims of “astronomical” .

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.

You mean like assuming ‘design’ to claim that evolution did not happen? But seriously - if you are dismissing such studies, how can you say anything about the numbers involved?

"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.

It is not even that. No, it is bald-faced assertion.

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.

So, you alter DNA sequences and see what happens for a living? Or are you making the unwarranted supposition that genes operate just like computer code? Yes – that’s it!
You are not the only one - all creationists with engineering/computer backgrounds seem to think that thei filed of knowledge is universally applicable to biological structures and systems. It is a major fallacy, and one that forces those in such a position to make such silly assumptions.

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.

And yet other primates – indeed, other vertebrates – have feet and pelvi. And Gould was a paleontologist, not a developmental biologist.

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.

You are not the only creationist to have hawked that article. But like the others I have encountered, you too are gleaning way too much from what is there.

Now, there is a way to salvage the chimp/monkey common ancestor problem with regards to Haldane's dilemma.

You will first have to establish that there IS a dilemma. ReMine was unable to do this, and you have not done so either.
Maybe next time?

Monday, February 13, 2006

Bill Dembski's pseudoknowledge

Bill Dembski is a theologian and mathematian and arguably the most prolific anti-Darwinist in the so called Intelligent Design movement.

As a theologian/mathematician, he approaches issues of biology like a theologian/mathematician with no biology training would - incorrectly.

He wrote a paper on human evolution a while back that is riddled with simple errors (I may expand on that at a later date), and makes a similarly erroneous implication on his blog:

I guess that’s what happens when you assume that sequence similarity
automatically means a common ancestry (of the gene). A more likely scenario is
that both cells require a protein with the same function so they have a similar
sequence by design.
Once again, an ID perspective seems much closer to
reality than the Darwinian (Lamarckian?) just-so stories.

Now, it is claimed that this came from a "biologist colleague" of his, which if true, means probably from one of the 'biologists' affiliated with the Discovery Institute or one of his colleagues at his place of employment, the Southern Baptist Theological Seminary.

So, what is the problem?


"... assume that sequence similarity automatically means a common ancestry ..."

It is NOT the mere sequence similarity that indicates common ancestry, it is the patterns of shared mutations. Sequence similarity can certainly indicate common ancestry, and for Demski and his "biologist colleague" to dismiss that denmonstrates their ignorance of the subject.
To see some of the patterns I refer to, see this sequence alignment. The patterns are obvious and striking.

Tuesday, February 07, 2006

Crevo on Dinosaur/human co-existence

One of the necessary attributes of the young-earth creationism (YEC) position is the acceptence of the co-existence of humans and dinosaurs. Indeed, at the Creation Museum in Kentucky (where else!), one can see a display of a dinosaur wearing a saddle.
Crevo (Jonathan Bartlett, a computer programmer) takes it as a given.
He writes on his blog:

"It appears that the ancient cambodians had drawings of many common creatures in their temples. Creatures they probably saw every day. Including monkeys, deer, water buffalo, parrots, lizards, and ...... a stegasaurus."
and links to an article on this website.

Below, I present three images. The image on the left is an actual stegasaurus skeleton. On the right is an artist's rendition of what a living stegasaurus might have looked like basec on the skeletal remains. The center image is the carved 'stegasaurus' from the Cambodian temple.

While the temple carving is interesting, it does not appear to be of a stegasaurus to me. Of note is the very different heads of the carving and the actual skull.

One of the things that always intrigues me about these claims - does it not seem as though the ancients would have made a bigger fuss about these dinosaurs in their midst? By any account, dinosaurs were impressive in size and attributes (big teeth, horns, etc.). I should think that if dinosaurs and humans co-existed, they would be common in myths, drawings, inscriptions, etc.
Not to mention their bones. Archaeologists have found the remains of homes built using mammoth tusks and bones, butchery sites of large extinct mammals and the like. Why no dinosaur bones? Why no triceratops skulls found alongside stone tools?

And the creationists like to accuse evolutionists of going beyond the evidence...

On Crevo's 'information' paper

Crevo (Jonathan Bartlett, a computer programmer) referred to his article on evolution and information here.

It purports to discuss the “problem” of “information” for evolution. It is all over the map, littered with superfluous analogies and anecdotes and unnecessary background. I will quote relevant sections and discuss them below.

From the section titled “Genomic Change”:

So now, while mutation can be applied to morphological characters, it is
way more complicated than that. Not only must the morphology have changed
between organisms, but also the biochemical pathways supporting that morphology.
And the required changes must be happenstance, not directed by the organims. And
it has to be able to make these changes a small step at a time, without
destroying essential machinery. If it morphs too fast, it would cause error
catastrophe and kill the cell completely. If it morphs too slowly, nothing will
happen. In fact, if a particular adaptation requires multiple changes, it may
not be able to adapt at all if the adaptations are slow.

Did I mention that Bartlett is a computer programmer?
The biochemical pathways also have to be changed to support the morphological change? Hmmmm…
Let’s take a look at one of my favorite mutations. It is a single point mutation in the gene encoding the receptor (type 3) for fibroblast growth factor (FGFR-3). A mutation in this gene produces a type of achondroplasia, or dwarfism. The manifestations, morphological changes that can result include a loss of interphalangeal joints in the digits, disproportionate limb to trunk growth, distinctive facial features, etc. No other biochemichal changes are required to produce these functioning, albeit abnormal, limbs.
I am not presenting this as an example of evolution, nor of a beneficial mutation, nor an increase in information, or anything else. I present this to demonstrate that a suite of characteristics need not change in order to support altered morphology. That claim is the result of a computer programmer pontificating on physiology.
We also see another creationist gem – error catastrophe. Creationists like to toss around that term, most often without knowing what it actually means. It refers to an accumulation of excessive mutations during DNA replication (or, more commonly, mutations in RNA viruses). It has little relevance to evolution. But it is catchy – error catastrophe!

I stated above that this article purports to deal with “information” and evolution. I think ‘purports’ was a good choice, for it reads more like standard Apologetics with pseudoscientific use of terminology tossed in to make it look impressive. For the very next section, titled “Christian Problems with Darwinism”, opens with:

“It is important to keep in mind what, specifically, the problems Christians have with Darwinism are. Primarily it is this: that life did not need God to bring it into existence, or to order its path. Even removing origin-of-life questions, Darwinism says that purpose is unimportant for life. As Christians, we see the voice of the Lord speaking life into matter -- the life was totally dependent on the voice of the Lord to come into being.”

This is important, for it lays out the true “issues” that Christians like Bartlett have with evolution. The talk of “information theory” and error catastrophe and the like are just fluff to prop up their real problems – evolution does not require their God, thus, it is bad/wrong.

But it goes on.

The next section, titled:
“Biological and Algorithmic Problems with Darwinism

Huxley and Typewriting Monkeys -- The Probability Theorem Does Not Show Life is Inevitable”

has some gems in it. Like:

“The big scientific problem with Darwinism is the idea that information can make itself.”

This is interesting, and I will revisit it later. Bartlett recounts Huxley’s ‘monkeys at typewrites’ story, then brings up this standard creationist canard:

“First of all, to dispense with the obvious, the use of a typewriter itself imparts a huge amount of design onto what the monkeys were doing.”

This is reminiscent of the standard comeback one gets from many creationists after presenting them with experimental data that answers a question they had asked. “Well, the experiments were designed, therefore, this supports creation/intelligent design, not evolution!”
They always leave themselves an out.
Bartlett goes on with a couple of analogies, then points out that most of what the monkeys typed would be “noise” and that some intelligence would be required to produce ‘work’ distinct from the ‘noise’. Note the subtle insertion of the language of “information theory” there, and further that ‘probability’ is against it and so forth.

Of course, Bartlett is talking about abiogenesis, which is not evolution. Some refer to it as chemical evolution, but just because it has the term “evolution” in it does not mean that it is part and parcel of the theory of evolution, as initially put forth by Darwin. This is a common conflation in creationist writings. Point out the problems with abiogenesis, then extrapolate those problems to evolution as such.

The next section is titled

“The Nature of Computational Systems and Programs”

and Bartlett opens it with this line:

“Let's stop talking now about typing monkeys, and look at the biological problems of information self-creation. Cell biology is much like a machine, or more specifically, a machine being run by a computer. You have, essentially, a code, a way to replicate the code, a way to run the code, and a system that mediates the action of the code. In fact, in cell biology, you have the only naturally occurring Shannon information system. That's an interesting topic, but I don't have time to get into it here.The most interesting thing about biology is that it is coded information and algorithms. In order to understand why this is so important, we need to discuss codes, algorithms, and complexity.”

A machine being run by a computer. Did I mention that Bartlett is a computer programmer? Interesting, isn’t it, that a computer programmer will tell us that cell biology is just like a machine being run by a computer?
Bartlett then goes through a lengthy series of descriptions of various types of computing systems and what their functions/limitations are. He inserts this comment:
“It should be becoming clear why creationists often make the proposition that information cannot create itself, and evolutionists claim it can.”
Which seems something of a non-sequitur, for thus far, he has only been writing about computers.
The remainder of the essay is more computer systems/coding issues.
I cannot figure out why Bartlett linked me to this article.
Was it supposed to prove something? If anything, it appears that Bartlett can describe computing systems and toss in the typical creationist zinger, but not much else.
He mentioned towards the end what Dembski thinks about “information”, but it seems irrelevant and thrown in just to use his name.
He ends by saying he will get to how this applies to the genome at some point in a later essay.

So again I have to wonder what the point of linking to this was in the first place.

Monday, February 06, 2006

crevo and the baraminologists

This is in response to Crevo's reply in this thread.

I have now read the paper. And, again, you are confusing the assumption and the conclusion. _Nowhere_ in the paper does it say that "therefore humans and chimps are separately created kinds". That is not a conclusion of the paper. It is an _assumption_ of the paper.

It is an assumption that is "tested" in the paper. Actually, it is more of a pre-conclusion, and when the data analyses do not support their pre-conclusion, they dismiss the relevance of the data. If it is an assumption, it is an unwarranted one. For, as they indicate, only the Scriptural criterion can give the true answer. If the Scriptural criterion is above falsifiability, then it is not science at all.
Can any reader imagine the fuss that would be made if evolutionary biologists rejected data anaylses because the results did not conform to the Origin of Species/Darwinian criterion?
I am confusing nothing. I know that the baraminologists started with their conclusions then rejected data analyses that did not fit. If it were merely an assumption, why then did they justify their rejection of objective data analyses because it did not support their "assumption"? Is that how leguitimate science is performed?

Let's look at it this way. Let's say that you were friends with an artist. Let's say that artist told you, "I have made several paintings using different styles. In the 80s I used one style, in the 90s I used another, and now I am embarking on a brand new style of painting. For instance, here are two paintings I have recently completed, and here are two that I did in the 90s". Now let's say that you are tasked with determining, for each of the artists paintings, which one was painted in what decade. The best thing to do is to look at the paintings that you _know_ to be from different decades, and try and conclude what characteristics are decade-dependent, and which characteristics are not. The paintings from the current decade may be very different from each other. However, the artist himself has told you that he uses a consistent style, and it is different from a style he used to use. Therefore, it is reasonable that, if I want to know which aspects of the artists paintings differentiate them stylistically, I should compare two that are known to be different in style. In fact, it would be even better if I had a painting of the same subject done by two different styles. That would show best of all which features were stylistically important. And that is precisely what this paper does.

So, you are constructing a silly analogy to justify fruadulent science? In actual science, one does not start with THE ANSWER. There is no 'artist' that told us that humans are special creations, seperate form all other animals and that therefore, any evidence indicating otherwise is false. Even when the same data can be used to show other things are related. Special pleading and equivocation are the tools of the Apologist, not the scientist.

The Author has said that humanity is a unique root of ancestry (being formed "from the dust"). Physically, we are most similar to other primates than other animals. Therefore, if we are to know which characters are most important in defining a baramin, it would be useful to examine humans vs chimps and determine which traits are baraminically important.This is not cherry-picking data -- that would only be the case if they then turned around and said "and therefore we can be sure that the Bible is correct", which they do not do.

Right - they do something totally different:

"With the exception of the Scriptural criterion no single data set is sufficient to define the holobaramin....

It is interesting to note that the ecological and morphological criteria were the most adept at distinguishing humans and the most highly correlated, indicating that the data sets in strongest
agreement were the most reliable."

Morphological criteria that were cherry-picked and subjective and largely irrelevant ecological data are better at giving them the results they know are true based on Scripture than are objective molecular data...

True, they do not write that "therefore, the bible is true." Instead, they declare the bible true at the outset, then assume that data analyses that do not coincide with Scripture are simply unreliable.

Yup. Totally different.

There is a good case for humans and chimps being from different ancestors, but this paper is not it nor does it claim to be.

Not in the least. But I do wonder about this "good case" - what is it?

Only if it claimed to be such a paper would the objection of cherry-picking make sense.

"Crevo accepts that things like where a creature lives is more important than their genetic make-up in determining their ancestral and descendant
Why would you think that genetic make-up is necessarily good at determining ancestral relationships? Have you ever written a program? Ever used design patterns? How, specifically, would you differentiate a genomic pattern that was based on common descent versus common design (creationists have a hypothesis,
which I will get to).

Ah - the old "I am a computer guy, and therefore my insight trumps all" routine. I was wondering when that hackneyed distraction was going to make an appearance. Well, try this on: Have you ever sequenced DNA and analyzed the reults? Have you ever compared sequence alignments?
Here is how I know that genetic make-up is good at determining ancestral relationships:

Science. 1991 Oct 25;254(5031):554-8.
Gene trees and the origins of inbred strains of mice.

Atchley WR, Fitch WM.
Department of Genetics, North Carolina State University, Raleigh 27695.

Extensive data on genetic divergence among 24 inbred strains of mice provide an opportunity to examine the concordance of gene trees and species trees, especially whether structured subsamples of loci give congruent estimates of phylogenetic relationships. Phylogenetic analyses of 144 separate loci reproduce almost exactly the known genealogical relationships among these 24 strains. Partitioning these loci into structured subsets representing loci coding for proteins, the immune system and endogenous viruses give incongruent phylogenetic results. The gene tree based on protein loci provides an accurate picture of the genealogical relationships among strains; however, gene trees based upon immune and viral data show significant deviations from known genealogical affinities.

Science. 1992 Jan 31;255(5044):589-92.

Experimental phylogenetics: generation of a known phylogeny.

Hillis DM, Bull JJ, White ME, Badgett MR, Molineux IJ.

Although methods of phylogenetic estimation are used routinely in comparative biology, direct tests of these methods are hampered by the lack of known phylogenies. Here a system based on serial propagation of bacteriophage T7 in the presence of a mutagen was used to create the first completely known phylogeny. Restriction-site maps of the terminal lineages were used to infer the evolutionary history of the experimental lines for comparison to the known history and actual ancestors. The five methods used to reconstruct branching pattern all predicted the correct topology but varied in their predictions of branch lengths; one method also predicts ancestral restriction maps and was found to be greater than 98 percent accurate.

among others.
Using testable and tested methodologies is a good way to know that your results are valid, for starters. How could I tell evolution from design? Well, if patterns of nuckleotide substitution were haphazard and analyses of the same produced random trees, regardless of the liocus or amount of data, then descent would be in trouble.
Of course, design would not be. No matter what the outcome. Observable patterns of nucleotide substitution that coincide with evolution-based hypotheses? Design!
No 0bservable pattern of nucleotide substitution?
Also Design!

Also, my own data shows it clearly.
The patterns are unmistakable.
And one need not be a computer programmer to see them.

"There is a major difference here, that Crevo is glossing over. The “assumption” of human-chimp ancestry is actually a conclusion based on multiple lines of empirical evidence, while the assumption that humans are special creations separate from all other animals is premised solely on Scripture."
This isn't quite correct. You are implying that there is no evidence for the common ancestry of humans and chimps, which is incorrect.
Ummm... Actually I am saying that there IS evidence for the common ancestry of humans and apes.
So, what - other than Scripture - is the evidence that runs counter to human-ape ancestry?

Scripture is _sufficient_ reason for creationists to doubt the common ancestry of humans and chimps, but it is not the only reason, and many (including myself) think that the problems in assigning common ancestry for both groups are sufficient to doubt that such ancestry exists even in absence of scriptural authority.

Well, don't keep me guessing! What IS this amazing evidence that only you and your fellow creationosts seem to know about, and why would you keep it a secret? And how is it scientific again for a religious text to trump data analyses?

"Further, the goal of the Nachman and Crowell paper is not to ‘prove’ or support human evolution, rather it is to examine mutation rates. The baraminology paper, on the other hand, presents it’s rigged findings to support their assumptions." This is a false statement. The point of this paper has nothing at all to do with proving different ancestry. It is about finding which characters are important in determining ancestral relationships from a Biblical perspective, not in proving that such multiple roots occur.

It is not false at all. I understand that you are engaging in fellow-creationist protection here so I will not take umbrage.
As creationists like analogies, consider this one:

I think that humans and rabbits are not closely related. I produce a DNA sequence alignment which includes humans and rabbits and other mammals. I designate rabbit as the outgroup of my analyis , meaning that I tell the analysis software that humans and rabbits are not closely related. I run my analyses and, amazingly, the results show that humans and rabbits are distantly related! I then write up a paper in which I declare that my assumptions were borne out.

I understand what the stated goal of the paper is. I also understand the stated implications. I do not require explicit statements from the authors to know what they are up to.

"The authors start with Scripture, they then essentially discard the analytical results that do not conform to their assumptions."

They don't _discard_ anything. The question is, which characters are baraminically important? How better to do that than examine creatures which are close but known to be in different baramins and see which types of characters can reliably represent the difference?

And you give away the farm.

"...known to be in different baramins "

How are apes and humans "known" to be in different baramina? Why, Scripture says so! And which criterion is the only TRUE criterion by which to determine ancestor-descendant relationships? Why, the Scriptural one. The circle is complete.

As with the artist example mentioned above, how is that invalid, given the assumptions?

It is invalid for a number of reasons, among them the fact that there is no scientific reason to adopt the stated assumption.

It would only be invalid if that data were turned around and used as proof of the assumption, which it is not."No, my criticism stems from the fact that they cherry-picked data to get the results they “knew” were correct."

They did not at the outset of the study know which characters were going to be baraminically important, now they do.

Yes, those that are the most subjective and irrelevant to ancestry. Of course, those OTHER criteria - genetic data and the like - are still OK for use in non-human analyses...

What they knew beforehand was the separate ancestry of chimps and humans.

And how did they "know" this? Scripture. And Scripture cannot be incorrect, according to creationists. Therefore, when data analyses were insufficient to prop up their interpretation of Scripture, those data had to go.

I cannot understand why this is so difficult to see.

What they did not know was what characters are most important for determining

TRANSLATION: What they wanted to find were data that could be construed to prop up their Scriptural criterion.

They used what they knew beforehand to find out what they didn't. Isn't that the
whole point of analytical studies?

Typically, a legitimate researcher starts with a question, gathers data, analyzes the data, then sees if the question is answered. The baraminologists start with an answer, then seek out data and analyses that will support that.

When I do a sequence analyses my question is always "Will the patterns of nucleotide substitutions support my hypothese/hypotheses?" It has NEVER been "Which of these data sets can I use to lend credence to my assumption/conclusion/answer and which shall I disregard?"

Again, this is the same line of reasoning used in "Estimate of the Mutation Rate per Nucleotide in Humans". They used a assumption to determine an unknown fact. The difference is that in the case of the "Estimates" paper, the assumption was common ancestry, while in the paper under discussion it was separate ancestry.
Neither paper attempts to prove the assumption. Both papers use their assumption to make a conclusion. The difference is with which assumption you agree with.

This is a false statement. As I explained before, the 'Estimate...' paper assumed common descent not premised on an ancient text, but on multiple lines of evidence. There are NO lines of evidence indicating a seperate creation for apes and humans. One assumption is justified. One assumption - that is treated not as a tentative position as in science, but as a firm unyielding cconclusion - is not.

"It is true that establishing the separate baramin for humans was not a stated goal of the paper, yet it was stated clearly in their conclusions (and in the abstract) that this was a result."

This is a false statement. I will reproduce the abstract below to prove it.

Your declaration that my statement is false is itself false.

"We have found that baraminic distances based on hemoglobin amino acid sequences, 12srRNA sequences, and chromosomal data were largely ineffective for identifying the Human holobaramin. Baraminic distances based on ecological and morphological characters,
however, were quite reliable for distinguishing humans from nonhuman primates."

So, their subjective data and analyses were "quite reliable" at telling what they already "know", that the human holobaramin is 'established', i.e., delineated by 'scientific' analyses.

"In reality, the baraminologists accept descent, they just place arbitrary (i.e., premised on Scripture) limits on it."

(a) scripture is not arbitrary(b) scripture is not the only measuring stick for determining descent (though, for creationists, where it lists separate descent is a sufficient reason for believing so)

Please do not misrepresent me. I did not say scripture is arbitrary, I said that the authors arbitrarily use Scripture as a source for their limitations on what can and cannot be the product of common descent.

I have written some of my own thoughts on some of the problems with universal common descent from an information science perspective here.

It will be interested to read yet another creationist trying to address biological issues from a non-biological perspective. I shall read and rebut it in time. One of the common problems with information theory mongers is that they do not seem to be able to duiscuss the manner in a way that is relevant to biology. It is usually via some silly contrived analogy to english language sentences or computer code with no acknowledgement that genes really do not work the same way computer code or english language sentences do. We shall see how Crevo deals with it...

Todd Wood has hypothesized that, genetically, mobile elements within the genome will be the most important in defining baramins. This makes sense from a semantic perspective, as mobile elements are basically collections of entities which have semantic meaning. They would have to be different (as a group at least, though not necessarily each individual one) when applied in a different semantic environment. See Todd Wood's The AGE-ing Process: Rapid Post-Flood Intrabaraminic Diversification Caused by Altruistic Genetic Elements (AGEs).

It was quite entertaining, to say the least. Wood, like ReMine, Wells, Bergman, et al., can write an awful lot of words while saying very little and producing no original science.

"If the baraminologists are not bound by descent, why on earth are they even trying to determine baraminological relationships? If God can just poof into (and out of) existence anything He wishes, isn’t trying to define these groups and their ancestral-descendant relationships a futile effort?"

Often times people who believe in God are criticized because God, theoretically, can do anything. However, Christians don't believe in any God, they believe in Yahweh. Yahweh has made His acts and His ways known to us (at least partially), therefore, any comment about something that God did or could have done is constrained by what is in the character of Yahweh to do. In fact, modern science is premised on many of Yahweh's characteristics, specifically that He made the universe understandable to man. And cosmologists have shown over and over again that this is true in a major way.

(searches for the 'rolleyes' emoticon...)

And so what, for the baramionologist/creationist, would/could falsify their Scripture-bound descent hypothesis?

If I answer for you and say "Absolutely nothing," would I be incorrect?

Wednesday, February 01, 2006

For Mark Kennedy

This post will open a 'debate' between myself and a creationist, Mark Kennedy, on the genetic 'similarities' between humans and chimpanzees and related issues .

I await Mark's reply before making any statements.
As Mark has responded, both here and at, I will post my initial response here. My replies in Red.

Originally Posted by: SLP
Yes, I agree.

I agree that chimps and humans should be in the same genus based on their genetic identity.

Just how simular do you think their genetic identity is Professor? Last time I checked in was about 96% which is greater then it was thought to be a year ago.

I think it depends on which loci you consider. It is doubtful that an “absolute” number will ever be determined, and it is likely that such a number is, in fact, impossible to glean. The fact that individuals within a species differ from each other virtually guarantees that an absolute number will not be possible to determine.
That said, I suspect that coding and regulatory sequence are likely to be in the 98+% range, while noncoding nonregulatory sequence will be somewhat lower.


In fact, my colleagues and I wrote as much in our 2001 paper on this topic.

I would love to hear your "expert" analysis of it...

Oh the sarcasm is blinding me but, ok, I'll bite. This was the part of the abstract that caught my attention, this is the part of natural history I feel is the most important:

Hominina; at approximately 7 Ma, Hominina divided into Gorilla and Homo; and at approximately 6-5 Ma, Homo divided subgenerically into H. (Homo) for humans and H. (Pan) for common and bonobo chimpanzees.

That 'subgenetically' part would seem to indicate the the divide involved things at a molecular DNA seqeunce level. The most important changes would effect the human brain which is 2 1/2 times the size of Chimpanzees.

The term is “subgeneRically”, meaning below the taxonomic level of Genus.
Brain size is likely to be controlled by relatively few genes.

Rates of noncoding DNA evolution were assessed using a data set of noncoding gamma sequence orthologues that represented 18 catarrhines, 16 platyrrhines, 3 non-anthropoid primates (2 tarsiers and 1 strepsirhine), and rabbit (as outgroup to the primates). Results obtained with this data set revealed a faster rate of nucleotide substitutions in the early primate lineage to the anthropoid (platyrrhine/catarrhine) ancestor than from that ancestor to the present.

Speaking of rates of DNA evolution, I think it was remarkably accelerated for human evolution then the other lineages.

Any evidence for this thought? Any rationale?

In September Nature magazine printed an article that compared the entire genome of human beings to that of the chimpanzee and described the differences in great detail. What they found was approximately 35 million differences at a single-nucleotide level and among these differences there were approximately 5 million indels (insertions/deletions). In order to understand the importance of these findings you have to consider what would have had to occur for human beings to share a common ancestor with the chimpanzee. Now in order for these 35 million differences to occur there would have had to be 3.5 mutations established genome wide per year for 10 million years.

35,000,000 differences in 10,000,000 years
3,500,000 differences in 1,000,000 years
350,000 differences in 100,000 years
35,000 differences in 10,000 years
3,500 differences in 1,000 years
350 differences in 100 years
35 differences in 10 years
3.5 differences per year

According to evolutionary theory we diverged from the chimpanzee about 10 million years ago. In that time there would have had to be 35 million differences accumulated genome wide. In the article they cite, ‘High genomic deleterious mutation rates in hominids’, published in Nature in 1999. In this article they proposed that there are 4.2 amino acid altering mutations per diploid per generation which they estimate to be about 20 years. They went on to say that 38% would be eliminated by natural selection leaving 1.6 new deleterious mutations. If you do the math then that is 8 mutations every 100 years and over a period of 10 million years it could only account for 800,000 differences.

8 every 100 years
80 every 1,000 years
800 every 10,000 years
8,000 every 100,000 years
80,000 every 1,000,000 years
800,000 in 10,000,000 years

Something is just not adding up here but wait it gets better.

Yes, something is not adding up, and it is the creationist math you are employing.

The Nature article refers to ALL substitutions, while the Eyre-Walker and Keightly article (‘High genomic deleterious mutation rates in hominids’) you refer to studied substitutions only as they applied to amino-acid substitutions. So, the 8/100 years you refer to above is but a subset of the 350/year average you referred to previously.
Thus, this section of your argument is rendered irrelevant.

The most important of these changes would have had to occur in the last 2.5 million years.

Evidence? Rationale?

During that time the brain would have had to grow to 2.5 times the size of our supposed ancestors and also become 2.5 times denser.

Denser? What does that mean?

Even more recently the frontal lobes, believed to be essential for language, would have to have be developed.

Actually, the areas of the frontal lobes responsible for speech are seen in fossil endocasts of even the Taung child, as well as in modern chimps. The area, Broca’s area, appears to be involved in more than vocal communication as used by modern humans.

Rates were slower in catarrhines than in platyrrhines, slower in the cheek-pouched than in the leaf-eating cercopithecids, and slower yet in the hominids. On relating these results to data on brain sizes and life spans, it was suggested that life-history strategies that favor intelligence and longer life spans also select for decreases in de novo mutation rates.

Now that really leaves me puzzled. Rates were slower in catarrhines than in playrrhines, slower still in cerocopithecids and slower yet in hominids. Yet the expansion of the human brain is an unprecedented expansion of the brian size, function and complexity.

Since you are obviously well read on the subject perhaps you could help me with something. Human evolution included a lot of changes in protein coding and regulatory genes. Could you direct me to research into the differences of specific genes involved in brain development?

When such genes have been identified, I would be glad to do so. As the quoted portion of the abstract indicates, the rate differentials probably correlate to life ‘styles’ and histories, with species whose diets consist primarily of plant matter having generally higher mutation rates, which could be a byproduct of the increased energy demands of digesting such material.