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 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.


Anonymous said...

This is the first time I have been invited to debate the subject on a biologists blog. I am not entirely sure what the subject matter will include because I am barely aquainted with my challenger.

I have been debating the creation/science controversy for a couple of years now and I am young earth creationist. The main issues I am concerned with are the comparitive studies of the Chimpanzee Genome Project who published their finding in Nature September 2005. I have a list of other publications that I consider directly relevant.

This is the gist of my postion on the subject and I await my hosts response to this post and the content of the subject matter.

Let us ponder the the most signifigant questions confronting the single common ancestor model in our day. What makes us human? (Nature 437, 69-87 ) What is the genetic basis for the threefold expansion of the human brain in 2 1/2 million years?(Genetics, Vol. 165, 2063-2070) What is the genetic and evolutionary background of phenotypic traits that set humans apart from our closest evolutionary relatives, the chimpanzees?(Genome Research 14:1462-1473)

One of the problems with the evolutionary expansion of the human brain from that of an ape is the size, weight and complexity. The human brian would have had to triple in size, starting 2 1/2 million years ago and ending 200 to 400 thousand years ago. The brain weight would have had to grow by 250% while the body only grows by 20%. The average brain weight would have to go from 400-450g, 2 1/2 MY ago to 1350–1450 g 0.2–0.4 MY.

"It is generally believed that the brain expansion set the stage for the emergence of human language and other high-order cognitive functions and that it was caused by adaptive selection (DECAN 1992 ), yet the genetic basis of the expansion remains elusive."

Evolution of the Human ASPM Gene, a Major Determinant of Brain Size, Genetics, Vol. 165, 2063-2070, December 2003

Jianzhi Zhang tried to determine if positive selection of amino acid substitutions that left the reading frame open are detectable in the ASPM gene. He instead found strong purifying selection and concluded that the postive selection of the ASPM gene took place time between 6–7 and 0.1 MY ago (0.5 x 10,000 generations x 20 years/generation). Researchers have determined that the gene is still evolving but I wonder how a congenital developmental defect characterized by severely reduced brain size could be an advantage.

Overall genetic differences create a problem since the size of the genetic differences is growing. Type 'DNA simularities between humans and chimpanzees' into a google search engine and you will find estimates close to 99%. Growing evidence has determined that these estimates are just plain wrong. The divergance has been found to include indels of considerable length, in the comparision of the Chimpanzee Chromosome 22 and its counterpart Human Chromosome 21 found that 83% of chimpanzee chromosome 22 proteins are different from their human counterparts.

"Sakaki said their analysis found about 68,000 insertions or deletions. "That is almost one insertion/deletion every 470 bases," he said. In addition, a small proportion of genes showed a relatively higher rate of evolution than most other genes. "We haven't known what proportion of the genes shows adaptive evolution. This study shows it to be about 2 to 3%," he said."

Chimps are not like humans Whole-chromosome comparison reveals much greater genetic differences than expected

More recently, the Chimpanzee Genome project published their highly anticipated Initial sequence of the chimpanzee genome and comparison with the human genome, Nature 437, 69-87 (1 September 2005). What they found was the the differences between the chimpanzee and human genomes have a 35 million nucleotide difference with five million insertion/deletion events, and various chromosomal rearrangements. This would include a 3 million bp divergance in the function part of the genome effecting vital functions.Even by conservative estimates the fixation of single base substitutions, insertions, deletions and polymorphisms (including chromosomal rearrangements) would have to average anywhere from 3 to 7 bp differences, fixed in the respective geneomes, per year for humans to evolve from apes.


Doppelganger said...

That is all well and good, Mark, and I will get ot that later. However, I will reply to your latest post on ChristianForums first, and paste it here.

Doppelganger said...

Our exchanges have been going on for several pages at Christianfourms, and Mark is still just presenting his "questions" as evidence.

Typical creationist.