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, January 11, 2006

Pogge on Chimp-Human Differences

Ah, computer software guy David Pogge is up to his old tricks - mixing disinformation with insults and exposing his shallow grasp of science outside of his limited area of actual knowledge...
Well, grab a beer and your irony meter and let us take another gander into the mind of a creationist engineer-type. Again, as I could find no copyright information, I am reproducing the entire article here (without graphics).

This stellar essay can be found here. My comments in red.

Feature Article - October 2005

by Do-While Jones [R. David Pogge]

Chimps Are Like Us

The chimpanzee genome has been decoded and compared to the human genome. What did scientists find? They found that the genomes are very similar! What a surprise!

*NOTE: In the original, Pogge had placed side-by-side a picture of a chimpanzee and Genie Scott, director of the National Center for Science Education. Nice fella, huh?

Every time a comparison of human DNA and chimpanzee DNA appears in the technical literature, we pass that information along to you. Our previous essays have been titled “98% Chimp”, “Monkey Business”, and “More Monkey Business”. Since those essays were written, the chimpanzee genome has been completely decoded.

*Um, no Mr.Pogge - the chimpanzee genome has been sequenced. That is not the same as having been decoded.

The September 1, 2005, issue of Nature was largely devoted to articles analyzing the similarities and differences in human and chimp DNA. The September 2 issue of Science contained an analysis of the September 1 Nature analysis.

In our previous essays, we described how different methods of comparison were used to produce different percentages. The calculated values were 98%, 98.5%, 98.8%, and 99.4%. What’s the “real” value? Well, it still depends on how you measure it.

*Very disingenuous of you, Mr.Pogge. As I pointed out previously, the values depend on what is being compared, not on 'how you measure it.' For example, it makes a difference if you are comparing genes to genes, or noncoding regions to noncoding regions. Both contain relevant yet
different information, as far as phylogeny goes.

… the draft sequence was announced but not formally published in 2003. Now the team, led by Robert Waterston of the University of Washington (UW), Seattle, confirms in Nature the oft-cited statistic that on average only 1.23% of nucleotide bases differ between chimps and humans. … The total genetic difference between humans and chimps, in terms of number of bases, sums to about 4% of the genome. That includes 35 million single base substitutions plus 5 million insertions or deletions (indels), says Waterston. 1

Four Percent Difference!

That’s right. Waterston says that the total difference is 4%, which somehow confirms the 1.23% average. We are still trying to figure out that math!

*Perhaps instead of ellipsing out the intervening paragraph, Mr.Pogge may have avoided his confusion:

"...on average only 1.23% of nucleotide bases differ between chimps and humans. But as suggested by earlier work on portions of the chimp genome, other kinds of genomic variation turn out to be at least as important as single nucleotide base changes. Insertions and deletions have dramatically changed the landscape of the human and chimp lineages since they diverged. Duplications of sequence "contribute more genetic difference between the two species--70 megabases of material--than do single base pair substitutions," notes Evan Eichler, also of UW, Seattle, who led a team analyzing the duplications. "It was a shocker, even to us." The total genetic difference between humans and chimps,..."

It really is not so hard to get, Mr.Pogge - providing, of course, you actually try.

See, the 1.23% difference refers to nucleotide-by-nuclotide comparions. That is, segment by segment compariosns. But what is one of the specimens is missing a segment? You cannot do a nucleotide by nuclotide assessment then, and the 4% figure takes into account these missing or
extra segments.
It is amazing how silly you can make your opponent look when you purposefully omit important information, isn't it Mr.Pogge?

If there really is only 1.23% average difference between human DNA and chimp DNA, how much average difference is there between two different human DNA molecules? Certainly it must be much much less than 1.23%. If that is true, how can DNA evidence be used in a court of law to convict criminals?

*According to the human genome project, any two differ by about 1 nucleotide per 1250 base pairs, or about 2.5 million, or about 0.08%.

How is DNA used in courts of law? Again, instead of feigning (exhibiting?) ignorance, Pogge could have done a simple internet search. Briefly, there are several ways to do this. One way is to extract DNA from a 'foreign' sample from the victim and digest it with enzymes. These enzymes will cut the DNA strands at specific areas. The 'cut' DNA fragments can then be separated by placing them in a gelatin like substance and running an electric current through the sample. The resulting ladder-like appearance of the gel can be compared to a similarly treated sample from the suspect. Because of the polymorphisms that exist, the fragments will run through the gel at different speeds. If the suspects fragments have run through the gel at the same speed as the sample from the victim did, then there is a match. Also, direct DNA sequencing can be performed, but this is probably time and cost prohibitive. Also, samples can be tested for the presence of certain alleles. Lots of ways to do this, but the first description is, as far as I know, the most common way of doing it.

Anyway, back to Pogge's question.

0.08% of 3.2 billion is, again, about 2.5 million. That is plenty to differentiate between individuals. What was the point of his question? That remains to be seen...

The papers confirm the astonishing molecular similarity between ourselves and chimpanzees. The average protein differs by only two amino acids, and 29% of proteins are identical. The work also reveals that a surprisingly large amount of genetic material--2.7% of the genomes--has been inserted or deleted since humans and chimps went their separate evolutionary ways 6 million years ago. 2

DNA contains the biological instructions for making proteins. If 29% of the proteins are identical, that means that 71% are different, doesn’t it? If the DNA is 96% the same, why are 71% of the proteins it produces different?

*Does Mr.Pogge really understand so little basic biology? Statistics?

Seriously, we’re just having fun with the numbers. Clearly human DNA and chimp DNA is very similar. We don’t dispute that.

*Oh, I see - he is just being silly...

But, as Mark Twain once said [actually it was Leonard Henry Courtney who said it], “There are three kinds of lies: Lies; damn lies; and statistics.” Scientists can present whatever numbers they want to emphasize whatever they want.

*So can anyone else, Mr.Pogge. Like you, for instance, in this essay in which you encourage creationists to "...point out the assumptions and impossible probability of enough of these mutations happening to create a new body plan or internal organ."

Of note, you do not say what the "impossible probability" is.

But the underhanded insult is not lost on me. And all scientists.

Which numbers are the most important is really a matter of opinion. Evolutionists always present the numbers in such a way as to diminish the difference between humans and chimpanzees to make it more plausible that they have a common ancestor.

*So, the insinuation is that we routinely distort the numbers - lie with statistics - to prove our point. Nice unsupported assertion, Mr.Pogge.

Similarity can either be the result of common ancestry or common design. The 96% (or whatever) similarity alone doesn’t prove common ancestry. It might be the result of a designer making two very similar things.

*Ah, this old chestnut. This reveals more about how much (little) Pogge understands about DNA comparisons than about the weak foundation of evolutionary conclusions. For it is the patterns of shared mutations which inform evolutionists of descent. The mere similarity is a byproduct of this. For example, look at this dataset alignment. The similarity is obvious, but it is the patterns of unique shared mutations that is most striking. I suspect that Pogge has never seen DNA sequence data, as has been the case with every creationist I have thus far encountered. So,
would a 'designer' put a 'broken' gene in both humans and chimps? Would a 'designer' put so many identical insertions is both?

If the similarity is the result of a common ancestor, then one must explain how the differences came about. Evolutionists typically claim the differences came from random mutations, filtered by natural selection. This argument sounded plausible before science discovered DNA, got a better understanding of genetics, and developed the concept of information theory. The evolutionary explanation was plausible before science discovered how many differences there are between species.

*In reality, the 'discovery' of DNA and our increasing understanding of what it does and how it operates has expanded not only legitimate science's understanding of evolution, but provided ever more evidence for it. Pogge is engaging what amounts to standard creationist Orwellian

It is our opinion that the important numbers are 35 million plus 5 million. That is, if you compare human DNA with chimp DNA, there are 35 million places where the molecules differ, and there are a total of 5 million places where the human DNA either has more or fewer bases than chimp DNA. (That is, there are 5 million places where bases have been “inserted” or “deleted” if one assumes that both kinds of DNA had a common evolutionary origin.) So, there are 40 million differences, total.

Who changed?

"It's frustrating that humans and chimps are so similar," says Andrew Clark of Cornell University in Ithaca, New York. It's difficult to tell whether a DNA sequence in humans that is missing in chimps was really added during human evolution or has simply been lost in the chimp lineage. 3

Remember that evolutionists believe (by faith)

*No, Mr.Pogge - your beliefs are based on faith (and this), our's are based on actual evidence.

that humans and chimpanzees both evolved from an unknown common ancestor about 6 million years ago. If evolutionary rates were the same for both humans and chimps, those 40 million base pair differences should be evenly divided between humans and chimps. In other words, our DNA would have about 20 million differences from the mythical common ancestor, and chimp DNA would have a different 20 million differences. Vain humans, though, would rather believe that the differences are split 30/10 (or 35/5) rather than 20/20 because we are so much more “dramatically” different from the apelike “common ancestor” than chimpanzees are.

*And? Was there supposed to be something of merit to consider here? Guess not...

In some behavioral and cognitive traits, humans have changed
dramatically since their evolutionary divergence from a common ancestor shared with chimpanzees. It seems reasonable to assume that a number of these changes were driven by positive Darwinian selection. However, although positive selection has been demonstrated for several human genes, the overall patterns of evolution of chimpanzee and human genes are consistent with selective neutrality. 4

There are two important points in this paragraph. The first sentence seems to imply something more like a 30/10 split rather than a 20/20 split because “humans have changed dramatically” compared to chimpanzees.

*Wow. That is quite a bizarre leap, even for Pogge. In reality, it implies just what it said - "In some behavioral and cognitive traits, humans have changed dramatically since their evolutionary divergence from a common ancestor shared with chimpanzees." Behavioral and
cognitive traits are housed where? Somebody help Mr.Pogge out - the brain. So, simple changes in the brain can account for these behavioral and cognitive changes. Another example of the shortcomings of pontificating on things you do not understand.

If humans had 30 million mutations in 6 million years, and chimpanzees had 10 million mutations in 6 million years, then humans had an average of five mutations per year. In the last 4,000 years of recorded human history, there would have been about 20,000 mutations. Is there any evidence of that?

*Why would there be evidence of a creationist strawman fallacy? Furthermore, what does Pogge expect to see? He, of course, does not say.

The more shocking statement in the paragraph quoted above is the one about natural selection. Evolution is supposed to work primarily thorough natural selection allowing positive changes to survive. But the nine authors of this peer-reviewed article think that most of the assumed changes in human DNA have no positive value. This makes natural selection an insignificant force in human evolution. If natural selection wasn’t the mechanism, what was?

*Ummm... Neutral evolution? Just like they said? Of course, they did not say that the changes had no positive value - they said most were neutral. I suggest that Mr.Pogge read up on some basic evolutionary theory and biology, as he continues making himself look like an underinformed propagandist.

Chimpanzees exist even though they don’t have the 40 million differences that humans have. So, those differences apparently aren’t necessary for survival. If creatures can survive with or without the differences, the changes are “neutral” as far as survival goes. But Darwin thought that “positive” differences, which promote survival, are the ones that drive evolution. That’s why some evolutionary scientists are looking for another method to explain evolution.

*Like who?

Looking for differences
Of course the primary reason for decoding the chimpanzee genome was to determine what differences make us “human.”

Perhaps we will learn how small differences in the code of life enabled us--but not chimpanzees--to cook soufflés, create symphonies, translate our own voyages into maps, build ever more complicated artifacts, and write plays that reflect the social intricacies of our lives. 5

Until now, genome sequence information has shown us how many seemingly very different organisms are amazingly like humans. At a conservative estimate we share about 88% of our genes with rodents and 60% with chickens. Applying a more liberal definition of similarity, up to 80% of the sea-squirt's genes are found in humans in some form. So it's no surprise that we are still asking, "What makes us human?" To apply genomics to this quest, we need to shift the focus to look at our closest living relative, the chimpanzee. Given that we share more than 98% of our DNA and almost all of our genes, chimps are the best starting point to study not the similarities, but the minute differences that set us apart. 6

The fact that one can fiddle with the numbers in such a way as to make the similarity between humans and sea squirts 80% is further proof that someone who is(conservatively) 88% rat can make the numbers say just about anything he wants.

*'Fiddle with the numbers'. Nice. Odd that a fellow that claims that 'science is against the theory of evolution' so frequently resorts to insults and distortions.

But we really don’t want to quibble too much about the numbers. The important thing is to examine the similarities and differences between humans and chimps.

Before we tell you what differences the study found, why don’t you try to guess? Of all the organs shared by humans and chimpanzees, which do you think is the most different? We’re going to go out on a limb and say that you probably think that the study shows the biggest difference between chimps and humans is in the brain. If so, you are really, really wrong.

Two major findings stand out. First, gene expression patterns differ less between humans and chimpanzees in the brain than in the other tissues
(bootstrap test, P < 0.0001). Second, the ratio of expression divergence between species to diversity within species is higher in testis than in any other tissue (5.6 versus 1.8 to 2.5, P < 0.0001). 7

So, they say, there is roughly three times more difference (5.6 to 1.8) in our testicles than in our brains. Let’s not go there!
Individual variations
When making comparisons of DNA sequences, we have to realize that there are limitations to the data.

… most of the chromosome 22 sequence has come from just one chimpanzee, it remains formally possible that some of the same polymorphisms also occur in chimp populations. 10

In other words, we know that there are differences in the DNA of different humans. The published human DNA genome is actually an average of several individuals. Each of those individuals differs by some percentage from the average. Unfortunately we have not been able to find out the actual percentage. In May, 2004, when the quote above was published, the DNA data came from only one chimp. We don’t know how many chimps were used in the genome that was published last month, nor do we know how much variation there is in the DNA of individual chimps. We are sure, however, that there is some variation. This diversity must certainly affect the 96% (or whatever percent) calculation.

But there is a more revealing statement about diversity in the most recent report.

Unfortunately, this pattern cannot be corroborated at the DNA sequence level because human DNA sequence diversity data collected in an unbiased way are not yet available. 11

What could this statement possibly mean? First, it seems to imply that results depend upon whose DNA is sequenced. If everyone’s DNA is exactly the same, it doesn’t matter whose DNA is used. But everyone’s DNA is somewhat different, and apparently it is different enough to affect the results. We don’t have a problem with this.

*Perhaps not. But it does appear that you have a problem with context. For the previous sentence sheds some light on that quote:

"Thus, the higher ratio of gene expression divergence to diversity in testis as compared with the other tissues is indeed indicative of positive selection. Unfortunately..."

The disturbing phrase is “data collected in an unbiased way.” That implies that there is a way to collect data that would be biased to make the difference between humans and chimps appear more (or less) than it actually is; and that the biased method was the one that was used. So, we ask ourselves, “How could one bias the data?”

*Actually, Mr.Pogge, in science, 'bias' does not always mean what you think, and it certainly has nothing to do with what you imply. Again, Mr.Pogge's real problem is with context and comprehension:

"However, because realistic evolutionary models for neutral expression changes are not yet available and because environmental factors have a considerable influence on gene expression diversity, a high ratio of divergence to diversity represents an indication rather than proof of positive selection. As seen above, testis differs from other organs studied in that the ratio of expression divergence to diversity is higher (Fig. 1). If the cellular composition of testicles differed between humans and chimpanzees more than it does for other tissues, this observation could be explained by only a few genetic differences between the species. However, although human and chimpanzee testicles differ in size, there is no evidence that the cellular composition of this organ differs between the species (29). Another possibility is that the genetic component of the expression diversity in testis is not lower than expected from the expression divergence, but that gene expression patterns in testis have a smaller environmental (i.e., nongenetic) component. In that case, we would expect genes expressed in testis to be subject to as much constraint as genes expressed in tissues such as liver or heart that have a comparable expression divergence. The property of being expressed in testis should then have a similar effect on diversity levels in other tissues as the property of being expressed in, for example, liver. However, we find that among the five tissues, expression in testis is associated with the highest number of significant reductions in diversity in tissues other than testis, whereas expression in liver is associated with the highest number of significant increases of diversity in tissues other than liver (fig. S3) (15). This suggests that strong selective constraints on genes, rather than low environmental influence, account for the low extent of expression diversity in testis. Thus, the higher ratio of gene expression divergence to diversity in testis as compared with the other tissues is indeed indicative of positive selection. Unfortunately, this pattern cannot be corroborated at the DNA sequence level because human DNA sequence diversity data collected in an unbiased way are not yet available. However, we can test predictions about the chromosomal distribution of instances of positive selection in genes active in testis."

Emphasis mine. What a mouthfull... But, as one can see, the 'bias' mentioned has absolutely nothing to do with trying to get the numbers to support human-chimp ancestry as Pogge so dishonestly (or incompetently?) indicates. It has to do with examining the effects of environment versus positive selection. As far as the actual phrase used ("...because human DNA sequence diversity data collected in an unbiased way are not yet available.), this website will likely have the answers, and from a quick reading of it, I suspect that the paper's authors are referring to the fact that sequence data are not available for
representatives from all human populations, and therefore, the data available are "biased" in that they come from a limited number of populations.

If one believes in evolution, and believes that some people have evolved farther from apes than other people, what would that imply about differences in DNA? Are the results unfairly biased because of the color of the skin of the people who supplied the samples? Surely, they don’t mean that! But if they don’t mean that, what do they mean?

*Who would have thunk it? Pogge is now implying racism? What is next? Are all evolutionists Nazis, too Mr.Pogge? Or will that be saved for another of your brilliantly insightful essays?

What have we learned?
We could have told you what “scientists say” at the beginning of this essay; but if we had told you their conclusion right up front, there would have been no point in reading what we have to say. Here is what McConkey and Varki have concluded:

Can we now provide a DNA-based answer to the fascinating and fundamental question, "What makes us human?" Not at all! Comparison of the human and chimpanzee genomes has not yet offered any major insights into the genetic elements that underlie bipedal locomotion, a big brain, linguistic abilities, elaborated abstract thought, or any other unique aspect of the human phenome. 12

In all fairness, we need to say that the rest of the article we quoted above was a shameless plea for more money for research. One could argue that effective fundraisers never say, “We’ve got all the answers, now give us more money.” But that argument would rest on the assumption that scientists cast truth aside and say whatever they have to say to get more funding. Perish the thought! If one can’t believe what scientists say, what can one believe? But it isn’t just McConkey and Varki who have said that scientists haven’t found the answer yet.

Scientists produced a rough draft of the chimpanzee DNA sequence, and aligned it with the human one, and made an intimate comparison of the chimp and human genomes. "It's wonderful to have the chimp genome," says geneticist Mark Adams of Case Western Reserve University in Cleveland, Ohio, who was not on the papers. "It's the raw material ... to figure out what makes us unique."

But those hoping for an immediate answer to the question of human uniqueness will be disappointed. "We cannot see in this why we are phenotypically so different from the chimps," says Svante Pääbo of the Max Planck Institute of Evolutionary Anthropology in Leipzig, Germany, a co-author on one Nature paper and leader of a study in Science comparing gene expression in chimps and humans. 13

We still know what we always knew. Specifically, chimps look and act like humans more than other animals. Chimps’ DNA and internal organs (excluding one pair of external organs ) are very much like ours. But there is still no way to tell if that similarity is the result of descent from a common ancestor, or creation by a common designer.

*What an absurd, naive, position.

When I was in graduate school, not knowing exactly what I wanted to do, I decided to do a rotation in a lab that looked at DNA sequence data to study evolution. I had never heard of such a thing, but it interested me (in part because I did not want to do animal research). I remember the first time I saw a DNA alignment. It hit me hard. The patterns were so obvious. The simplicity of the rationale for using DNA sequence data - not to mention the fact that it has been tested - made it all so clear. Mutations happen. Sometimes, they get passed on to offspring. Over time, the patterns of these unique shared mutations can be used to infer descent. It is not faith. It is not speculation. It is testable and repeatable science. It is common sense. No 'common
designer' is needed to explain the patterns, only simple heredity.


Pogge again relies on a shallow grasp of the information - that or is quite dishonest in his treatment of it. He uses out of context quotes and ridiculous extrapolations. He uses thinly veiled insults and puts words (thoughts) into the mouths of actual scientists.

Another example of dishonest propaganda from and R. David Pogge.


Robert Rapier said...

I will never understand what it is about Creationist software/computer/electrical engineers that makes them think they are qualified to pontificate about biology. The incompetence displayed, as shown in the article you critiqued, makes me wonder how someone who is so easily confused by the concept of evolution could actually make it through their coursework and graduate. Maybe I should start a website called “Scientists Against Software”, and explain to everyone why it is impossible for software to actually work. Of course I have no qualifications, and apparently software does work, but I wouldn’t let that get in the way of making arrogant proclamations on the topic.

Doppelganger said...

Excellent points, FK. I am forwarding the url's to these articles to Pogge to see iof he will have any response. Likely, if anything, he will rant on his own website where no responses can be made by anyone and I will be put in the worst light possible.

Par for the creationist course.

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