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

Saturday, January 07, 2006

The First of Many (RE: Science Against Evolution)

This is the first of what will, eventually, be a litany of creationist/Intelligent Designist arguments that are silly, hackneyed, distorted, and often just plain wrong.

The website scienceagainstevolution.org , run by David Pogge (who goes by the moniker "Do-While Jones"), a creationist engineer, is jam packed with distortions, wild extrapolations, misrepresentations, etc. - just like most anti-evolution websites. And, like many anti-evolution websites, this one purports to be all about the science (A quick glance through the archives and articles, however, provides ample evidence that it is just another religious apologist site with a phony science facade).

One of the articles there caught my attention. It is titled "98% Chimp", and came out in 2003.

There are a numbner of distortions, bizzarre interpretations, and odd antics for an author supposedly so well versed in the sciences.

Well, let's take a look.

As that web site calls itself a Public Benefit Corporation and I could find nothing on copyright, I will reproduce nearly the entire article (sans graphics and some inane drudgery) and comment on a point by point basis. My comments will be in red.
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98% Chimp

Is our DNA really more than 98% the same as chimpanzees? And, if so, what does that really mean?

You have probably heard an evolutionist claim that chimpanzees and humans are almost identical genetically. Statements like the one below are common.

We need to know two things. First, are their figures accurate? Second, if they are accurate, what does it mean? Is genetic similarity really evidence for evolution?
*One minor point of clarification – the higher (~98%) figures are for coding regions, e.g., genes. The lower figures (~85-92%) refer to all genomic regions, including the so-called ‘junk DNA’.



Accuracy

We have always been skeptical of the 98% figure because we know that 82.3% of all statistics used in debates are simply pulled out of thin air. (For the benefit of other readers who didn’t get the joke--certainly not you--we will explain the joke to them. It is very unlikely that anyone has ever done a study of debates in which statistics
were used to make a point, and then gone to the trouble to determine if the statistics are based on studies or not. So, the humor in the joke comes from the irony that someone is pulling a statistic out of the air to prove that statistics are often pulled out of the air to prove a point.)
*Interesting. So, Pogge thinks that because folks he knows use baseless statistics, everyone else does, too? Well, let's give him the benefit of a doubt and see where he goes with this 'set up'.



But the human DNA sequence was just recently decoded. (It was published in the 16 February, 2001, issue of the journal Science.) Work on decoding the DNA sequence of chimps is just beginning. (See Monkey Business, in the Evolution in the News column in this issue.) How could they have been able to calculate the similarity of two sequences “decades” ago when neither had been decoded? How can they calculate it now when only one of them has been decoded? Did they just pull 98% out of the air?
*Hmmm... Perhaps these science gurus might have actually done what any competent, intellectually honest researcher would have done - FOUND OUT. Instead, these propagandists rely on cherry-picked articles, ignore the history of the issue, and employ the time-honored 'I'm real smart and I can't understand it, therefore, it must be wrong' mentality.
For example, going to one of the most comprehensive scientific search engines, the NIH's Medline (
www.ncbi.nih.gov]) and doing a search will get you lots of relevant ionformation.

Many like these:

Mol Phylogenet Evol. 2001 Jan;18(1):14-25.
Catarrhine phylogeny: noncoding DNA evidence for a diphyletic origin of the mangabeys and for a human-chimpanzee clade.
Page SL, Goodman M.

Mol Phylogenet Evol. 1992 Jun;1(2):97-135.
Reexamination of the African hominoid trichotomy with additional sequences from the primate beta-globin gene cluster.
Bailey WJ, Hayasaka K, Skinner CG, Kehoe S, Sieu LC, Slightom JL, Goodman M.

Mol Biol Evol. 1991 Mar;8(2):155-84.
Molecular evolution of the psi eta-globin gene locus: gibbon phylogeny and the hominoid slowdown.
Bailey WJ, Fitch DH, Tagle DA, Czelusniak J, Slightom JL, Goodman M.

Science. 1987 Oct 16;238(4825):369-73.
Phylogenetic relations of humans and African apes from DNA sequences in the psi eta-globin region.
Miyamoto MM, Slightom JL, Goodman M.

All of which contain data supporting the % similarity issues. Or they could have looked at the 9 citations in the paper they quote that indicated where the numbers came form. Just because the Chimpanzee Genome Project is just beginning does not by any stretch of the imagination mean that no chimp DNA sequences are available. Using the same website and using the nucleotide search option, searching for chimpanzee, for example produces some 1.3 million entries. With that last paragraph of Pogge's alone, I am having major dounbts about the intellectual integrity of this article...




Perhaps they compared the 46 human chromosomes with the 48 chimp chromosomes. They could not possibly have done that and come up with a figure exceeding 97.8%

*And now the tomfoolery starts...



Here’s why:

Let’s compare the chromosomes of a boy and his mother. A boy gets 23 of his chromosomes from his mother and 23 from his father. Clearly, at least 23 of the chromosomes will be identical to his mother. Therefore, the similarity will be at least 50%.

But one of the chromosomes he gets from his father must be different because his mother has two X chromosomes (if she didn’t, she wouldn’t be female), and the son has one X chromosome and one Y chromosome (because he is male). Therefore, at most, 45 of the 46 (97.8%) chromosomes will be identical.

So, the boy’s Y chromosome is guaranteed to be different from his mother. What about the other 22 chromosomes he gets from his father? Societies generally try to discourage incestuous relationships, and scientists have discovered that there is a good reason for this. It reduces the chance that a baby will inherit the same defective gene from both mother and father. If the boy’s father and mother come from unrelated families, it is almost certain that most of those 22 chromosomes will have at least one different gene.

So, if you determine genetic similarity by counting identical chromosomes, the genetic similarity of a boy to his mother is likely to be closer to 50% than 100%. “Scientists” certainly could not have found that humans and chimpanzees are 98% alike by counting chromosomes. Of course we know that they didn’t count chromosomes when making the comparison.

*Then why waste so much time on irrelevant and silly diversions?

We only mention it to make the point that what you count will affect the result you get. You can use a method of counting that gives close to 50%, or you can use a different method that gives a much higher number.


*"A method of counting"? What does that mean? It appears that the author is trying to establish a falsehood - that actual scientific researchers just pick methods to employ willy-nilly as long as the results are what they want. This is a common condescension from anti-evolutionists with engineering backgrounds. In the next section, Pogge really shows the dangers of pontificating in an area not your won, especially for the purpose of 'refuting' an underlying concept.



Let’s look at some of the most recently published data comparing chimps and humans.
In this report we present the construction and analysis of a first-generation human-chimpanzee comparative genomic map based on the alignments of 77,461 chimpanzee bacterial artificial chromosome (BAC) end sequences (BESs) to human genomic sequences obtained from the public databases. To prepare the BESs, we used two independently prepared BAC libraries, PTB1 and RPCI-43. Briefly, we sequenced 64,116 BAC clones (roughly 3.3 times coverage of the currently available human contiguous genomic sequence) that produced 114,421 valid BESs. The BESs were then aligned with the RefSeq human genome contigs [National Center for Biotechnology Information (NCBI)] through NCBI-BLAST. The number of BESs having an alignment longer than 50 base pairs (bp) with 90% identity was 77,461. Out of this number, 49,160 BESs from 24,580 clones formed paired ends where each pair was derived from the same clone. Only one end could be successfully aligned from the remaining 28,301 clones. The remaining 36,960 BESs that were not mapped to the human genome were categorized into three different classes: (i) those corresponding to repeat sequences (1168 BESs) or showing hits to human sequences not included in the NT contigs (20,376 BESs), (ii) those matched only with sequences from several species other than human (515 BESs), and (iii) the 14,901 BESs that did not match with human sequences, which either correspond to unsequenced human regions or are from chimpanzee regions that have diverged substantially from humans or did not match for other unknown reasons. 3

Creationists are often accused of “carefully choosing their data.” We have never understood why evolutionists thought this was worse that carelessly choosing data, but we sometimes have trouble understanding how evolutionists think. If you understood nothing else in the paragraph quoted above, you must certainly realize that they went into great detail to justify the way in which they chose the data they actually analyzed.


As if explaining such things is bad... But I do want to re-emphasize something Pogge wrote:
"Creationists are often accused of “carefully choosing their data.”"
Look back up at the examples of papers demonstrating sequence comparisons that produce 95+% sequence identity between chimpanzees and humans and this one article that Pogge writes about. Perhaps the 'acusation' is warranted?


We aren’t criticizing them for doing that. Scientists have to choose what data they analyze. One of the services I perform at my day job is real-time data reduction. My computer programs present pertinent data to the customer in graphical form, suppressing the irrelevant data, so that the customer can tell how his test is working while the test is still in progress. This gives him the opportunity to modify the test while it is still in progress, if necessary. There is nothing fundamentally wrong with analyzing only part of the data. You usually have no choice. You can’t analyze it all.

Fujiyama and his associates chose the data they were going to analyze. What they were looking for affected what they chose to study. Their goal was clearly stated in the abstract of their paper.


The recently released human genome sequences provide us with reference data to conduct comparative genomic research on primates, which will be important to understand what genetic information makes us human. Here we present a first-generation human-chimpanzee comparative genome map and its initial analysis. The map was constructed through paired alignment of 77,461 chimpanzee bacterial artificial chromosome end sequences with publicly available human genome sequences. We detected candidate positions, including two clusters on human chromosome 21 that suggest large, nonrandom regions of difference between the two genomes. 4

They were trying “to understand what genetic information makes us human.” To do that, they looked carefully at two small parts of just one of the 46 human chromosomes. There is nothing wrong with that.

Furthermore, they picked areas “that suggest large, nonrandom regions of difference between the two genomes.” That was perhaps a poor choice of words. They probably meant “significant regions of difference”, as opposed to “irrelevant regions of difference”. Evolution is supposed to work through random changes. If the changes were “nonrandom”, that implies they were part of a conscious design. They certainly didn’t mean to imply that!


*No, and that is not what nonrandom means in science. Pogge might have known this had he any education or training in the area. Let's examine what is meant by nonrandom in this context, which apparently Pogge didn't get:

Consider transposable elements. These are segments of DNA that can insert themselves into a host’s genome. They encode their own enzymes that break a DNA strand and allow the transposon to become incorporated. They require specific DNA sequences for their enzymes to bind to. In this sense, an insertion of a transposon is nonrandom. But is it ‘designed’? As it happens, the specific sequences that these elements can bind to are found all over the place – they are fairly common. All that needs to happen is for the transposon to come into contact with one. This can happen at any one of those locations that possess the specific sequence. In that sense, it is random. So, when the authors of the paper in question referred to ‘nonrandom’ distributions, it almost certainly referred to the type of nonrandom I just described. As is so often the case, the creationist authors are merely putting a dishonest and/or uninformed spin on the issue.


They must have used their judgment to distinguish “nonrandom regions of differences” from random differences. One might wonder how they did that.


*See above. Notice how Pogge is attempting to insinuate dishonesty in the authors of the paper he is distorting. Projection is also a fairly common trait seen in anti-evolutionists.

It implies that they might have some criteria for differentiating design from random processes. Too bad we don’t have space to explore that idea in this essay!


*False premise. It has nothing to do with ‘design.’ The propagandist Pogge is merely employing his own idiosyncratic definition to suit his needs.

Let’s be perfectly clear on this point. Fujiyama et al. were perfectly justified in selecting what part of the genome to study. They were looking for differences in very similar sequences, so they picked very similar sequences that had some interesting differences. That is perfectly good science.

They were not trying to most accurately compute the similarity of chimpanzee and human DNA. But they did mention some interesting numbers in passing which do pertain to genetic similarity. If you refer back to the extremely technical paragraph we quoted earlier, you will see that they produced “114,421 valid BESs”. Of these, they found “14,901 BESs that did not match with human sequences”. That means 13% of the sequences were totally different. In other words, only 87% of the sequences showed enough similarity for them to even attempt to match them.

* Is that really what that means?
Why didn’t Pogge tell the reader what BES stands for? BES stands for Bacterial artificial chromosome End Sequence. That means that a genomic library has been made and is stored in the form of artificial chromosomes within a population of bacteria. Screening the BACs as was done in the paper looks for the end sequences of the BACs. If the BES did not match the probe, it would not bind. Does this mean what Pogge wants to think it means? NO. The technique used only looked for end sequences that were longer than 50 base pairs and exhibited greater than 90% identity.

Looking at the most similar sequences, they said, “The number of BESs having an alignment longer than 50 base pairs (bp) with 90% identity was 77,461 [out of 114,421].” So, they found that only 67.7% of the sequences were at least 90% correlated. If that is true, where does the 98% similarity figure come from?


*Pogge misrepresents the study (imagine that!). More below…


The BESs mapped with high confidence were used to calculate the difference between the chimpanzee and human genomes at the nucleotide level. The number of sites in valid alignments (nucleotide sites that have PHRED quality values q >= 30) was 19,813,086. Out of this number, 19,568,394 sites were identical to their human counterparts for a mean percent identity of 98.77. This value is consistent with previous observations; however, our calculation comes from a much larger random comparison of slightly less than 1% of the total genome. 5

That explains it. If you look at less than 1/100th of the total genome, you can find areas that are 98.77% similar!

*Hmmm… Why did the creationist Pogge leave out the section immediately preceding what he quotes above (more correctly, he does quote it but ignores/doesn't understand the implications):


The number of BESs having an alignment longer than 50 base pairs (bp) with ^90% identity was 77,461 (13). Out of this number, 49,160 BESs from 24,580 clones formed paired ends where each pair was derived from the same clone. Only one end could be successfully aligned from the remaining 28,301 clones. The remaining 36,960 BESs that were not mapped to the human genome were categorized into three different classes: (i) those corresponding to repeat sequences (1168BESs) or showing hits to human sequences not included in the NT contigs (20,376 BESs), (ii)those matched only with sequences from several species other than human (515 BESs), and (iii) the 14,901 BESs that did not match with human sequences, which either correspond to unsequenced human regions or are from chimpanzee regions that have diverged substantially from humans or did not match for other unknown reasons.

Why didn’t the creationist remind us about these exclusion criteria? Why, because it lessens the impact of his propaganda, of course!

Pogge did not tell his reader:
That the clones often did not match each other, and so were excluded.
That clones that did match human sequences, but not in the same contig clones that they were focusing on, and so were excluded.
Those hits that corresponded to repeated sequences were excluded.
Those that matched non-human species were excluded.
Those that matched unsequenced human regions were excluded.

Don’t those important exclusion criteria warrant at least a passing mention? Nah – that would lessen the impact of the spin!


But this is not always true.

For almost 30 years, researchers have asserted that the DNA of humans and chimps is at least 98.5% identical. Now research reported here last week at the American Society for Human Genetics meeting suggests that the two primate genomes might not be quite so similar after all. … The researchers assessed the resemblance between the chimp’s chromosome 22 and the equivalent human chromosome, 21. They compared 27 million bases, and “much to our surprise, we found around 57 areas of rearrangement between the human and the chimp,” says Cox.

There seemed to be no rhyme or reason to the changes; they occurred just as frequently outside coding regions as within. The density of these differences is “a little higher than anyone would have predicted,” says Eichler. “The implications could be profound,” he adds …

Locke’s and Frazer’s groups didn’t commit to new estimates of the similarity between the species, but both agree that the previously accepted 98.5% mark is too high.6

How similar is human DNA to chimp DNA? We don’t know; but the 98% number certainly doesn’t seem to be born out by recently published data.

*Yeah, I guess not…

“Here we compare ~90 kb of coding DNA nucleotide sequence from 97 human genes to their sequenced chimpanzee counterparts and to available sequenced gorilla, orangutan, and Old World monkey counterparts, and, on a more limited basis, to mouse. The nonsynonymous changes (functionally important), like synonymous changes (functionally much less important), show chimpanzees and humans to be most closely related, sharing 99.4% identity at nonsynonymous sites and 98.4% at synonymous sites.”
http://www.pnas.org/cgi/reprint/100/12/7181

The news bit Pogge refers to is from 2002, so I guess we can forgive him not citing the above study (or several others). But what is the significance of the news blurb he refers to? It is indicated that one of the major differences is in insertions and deletions, which the authors indicate are found primarily flanking duplicated regions. These regions are almost certainly one-time events, so to use the size of these deletions/insertions as an indicator of difference is misleading.

Now things get really, really silly…


Significance of Similarity

Having said all that, we admit that there is a certain amount of genetic similarity between humans and other animals. What does that mean? Is genetic similarity necessarily the result of evolution?

The answer might be found in an evaporative cooler.

Those readers who are not fortunate enough to live in the Mojave Desert probably aren’t familiar with evaporative coolers. Evaporative coolers have large fans which suck hot air (more than 100 degree F) through wet fiber pads. The hot air evaporates the water, resulting in a heat transfer which cools the air down to 80 degrees F (or lower, if you are lucky). The fan blows the cool, moist air into the house.

The lower picture is a close-up of the bracket that holds the electric motor on the evaporative cooler on the roof of my house. When both screws (and two other similar screws on the other side) are loosened, the bracket can be rotated so that the distance between the motor and the fan can be adjusted to produce the proper tension on the fan belt.

There is an almost identical bracket that holds the alternator in my truck with the proper tension against the fan belt! This bracket represents about 1% of the total mass of the cooler, but it is 98.5% similar to the bracket that holds the alternator in my truck. Not only that, the fan belts are virtually identical. (Both are cracked and liable to break at any moment.) The pulleys are identical too. There is less than 1.5% difference between an evaporative cooler and a truck!

To understand how evaporative coolers evolved into trucks, we have to study the electric motor in the cooler, and the alternator in the truck. Externally, both look very similar; but the motor is wound for a single phase, while the alternator has three phases. This is evidence of gene replication. Furthermore, the alternator has evolved a six-diode bridge, which originally had some unknown survival benefit, but was later adapted to converting alternating current to direct current.

Despite the obvious similarities, there are many differences between a truck and an evaporative cooler, which prove that it has been a very long time since trucks and coolers shared a common ancestor.

Some people might say that trucks and coolers were designed by engineers, and that the similarity in the brackets is evidence of design. After all, it is a simple and effective method for adjusting belt tension. But if trucks and coolers were consciously designed, it must be the case that the engineers conspired to make it appear that both trucks and coolers evolved from a common ancestor. Therefore, if engineers really do exist, they ought not to be trusted because they are sneaky and deceitful people.**

*Completely stupid ‘analogy.’
Brackets do not:
Accumulate change
Pass change on to offspring

Here, Jones has just employed either a very shallow understanding of genetics, evolutionary biology and science, or is being purposefully deceptive and hoping that none of his readers will be able to tell how stupid it is.




Seriously, chimps and people really do have very similar genes. But that doesn’t argue in favor of a common ancestor any more than it argues in favor of a common designer.
*That is true, the mere presence of similar genes is not what indicates descent, and if Jones took the time to understand the issues, he would not have written this piece of garbage (then again, being a creationist…).
It is the patterns of shared mutations which are found in (and not in) genes that are far more informative in indicating descent that is the fact that we share many genes.
What ‘Jones’ has done here is utterly misrepresent the entire field of study that looks at such things.

Conclusion:

Due to the extreme nature of the unwarranted extrapolations, misinterpretations, misrepresentations, and reliance upon silly, inapplicable analogies to try to prove a point, I submit that this article is utterly worthless and should be at best ignored. It serves as an indication of the quality of the other articles available at the site.

"Scienceagainstevolution.org" is a propaganda mill, pure and simple.

**Well, at least one that I know of...




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