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

Tuesday, March 11, 2008

Casey Luskin, propagandist for Christ

The Energizer Bunny of the Anti-Evolution movement, Casey Luskin, is up to his usual pathetic antics.

He was recently on a 'chat' for a San Francisco newspaper and he made the following claim, (about 1/3 of the way down) in response to a question asking him what evidence compelled him to espouse ID:

(4) Genetics: Genetic research continues to uncover functions for "junk-DNA,"
include functionality for pseudogenes, introns, LINE, and ALU elements. ID
proponents have long said that DNA was designed, then junk-DNA will turn out to
have function, whereas neo-Darwisms's support for junk-DNA would turn out to be
a science-stopping view. It turns out, ID proponents were right!
Ah, yes - "neo-Darwinism" is a science stopper when it comes to 'junk DNA'. Right - so, when we look into this matter, the publications - if any - should be dominated by Intelligent Design creationist 'scientists', right? We should see predictions by creationists or IDists going back decades espousing function for all junk DNA, and we should see evolutionists claiming that it was totally junk and useless and actively discouraging research on it, right?

But wait - Luskin takes this further. A few questions later, he writes a screed laced with innuendo, nonsense, and that oh-so-creationist tendency to ignore reality.
It is a lot of garbage to wade through.

ID proponents long-predicted the death of the junk-DNA paradigm, while most (but
not all) neo-Darwinsists were defending it. (please see
for details).
I dissect that article at the link Luskin provided below. Suffice it to say, Luskin's take on junk DNA is a bit misguided, at best.

Regarding the percent-similarity between human and chimp-DNA, the 98% statistic
is often based upon studies of functional-proteins, so I'm not sure if junk-DNA
would apply here.
In fact, the numbers generally refer to ALL DNA, 'junk' and not. Of course, the fact that Luskin refers only to 'similarity' indicates a rather shallow grasp of what the analyses actually show.

Nonetheless, it's worth commenting on this statitistic by asking 2 questions: 1)
Is the ~99% Human/Chimp DNA-similarity statistic accurate? While recent studies
have confirmed that certain stretches of human and chimp DNA are on average
about 1.23% different, this is merely an estimate with huge caveats.

Actually, recent studies have confirmed that most functional genes are much more similar than that - closer to 99.4% similar or only 0.6% different.

A recent news article in Science observed that the 1% figure "reflects only base
substitutions, not the many stretches of DNA that have been inserted or deleted
in the genomes." (see Jon Cohen, "Relative Differences: The Myth of 1%,"
Science, Vol. 316:1836 (June 29, 2007).) In other words, when the chimp genome
has no similar stretch of human DNA, such DNA sequences are ignored by those
touting the statistic that humans and chimps are only 1% genetically different.
For this reason, the aforementioned Science news article was subtitled "The Myth
of 1%," and printed the following language to describe the 1% statistic: -
"studies are showing that [humans and chimps] are not as similar as many tend to
believe"; - the 1% statistic is a "truism [that] should be retired"; - the 1%
statistic is "more a hindrance for understanding than a help"; - "the 1%
difference wasn't the whole story"; - "Researchers are finding that on top of
the 1% distinction, chunks of missing DNA, extra genes, altered connections in
gene networks, and the very structure of chromosomes confound any quantification
of 'humanness' versus 'chimpness.'" Indeed, due to the huge caveats in the 1%
statistic, some scientists are suggesting that a better method of measuring
human/chimp genetic differences might be counting individual gene copies. When
this metric is employed, human and chimp DNA is over 5% different.

True, however, what Luskin fails to note is that if we are to adopt this "new" method of comparison, than ALL DNA 'similarity' numbers between ALL species will have to be increased, not just the human-chimp numbers. Of course, what Luskin fails to note - and likely understand - is that there is a good rationale for not counting the individual nucleotide differences in insertions and deletions - they are one-time events. That is, when a "chunk of [missing] DNA" is removed from a genome, it happens all at once. A 1000 base deletion does not take 1000 events in which a single nucleotide is lost, it is ALL lost in one event. Thus, most researchers had 'counted' such occurrences on par with single nucleotide substitutions. Luskin also fails to mention that any two humans have different numbers of genes! I guess humans must not be related to each other... Poor humans... And, what is more, the author of the article Luskin quotes from, Jon Cohen, caught wind of this Luskin article and wrote the following letter to him:

From: Jon Cohen [snip]
Sent: Saturday, October 20, 2007 12:05 PM
To: Casey
Cc: [Snip]
Subject: Errors in your posting
Mr. Luskin,

I wrote the Science news article that you refer to in your recent posting on the
Discovery Institute’s “Evolution News and Views.” Given that “misreporting of
the evolution issue is one key reason” for that site, which complains that “much
of the news coverage has been sloppy, inaccurate, and in some cases, overtly
biased,” I wanted to point out that your own post contains several errors and
apparent misunderstandings. I realize that you are largely reporting what others
have written, but you do it selectively and out of context–and you also fail to scrutinize what the original reports said.
As I wrote in my article, chimps and humans do differ genetically by more than 1%, but our genes–in contrast to what the Scientific American posting states–are only 1.23% different. The bulk of the differences between chimps and humans exist in noncoding regions of the genome that regulate our genes and in gene copy number variation/segmental duplication, which ultimately determine how much product (typically protein) they produce.

You also state that my article “reports” that copy numbers differ by 6.4%. Not only does this misleadingly imply that humans thus differ from chimps by 6.4% (it’s probably closer to 5%), you fail to note that my article was not the source of this figure: I was citing a report that was done by a computational genomics researcher. In other words, it’s a model, which is another way of saying it’s an estimate, not a hard fact. (The 1.23% is a hard fact: It’s based on sequencing the entire human genome and the chimpanzee genome.)
The claim that humans are as different from each other as was previously thought we were different from chimps also is misleading and inaccurate. No credible study that I know of ever suggested that one human’s genes differ from another human’s gene by 1.23%. The Scientific America posting–which is referring to an AP story in USA Today that’s referring to the PLoS Biology paper about Craig Venter’s genome–does not explain that Venter reported a 0.5% difference between his inherited genome from his mother and father, which once again is measuring not simply gene differences but differences in noncoding regions that include inserts and deletions (that may sometimes contain copied or deleted genes or may impact regulation).
None of the original studies I cited in my article or Venter’s genome paper suggest in
any way that their findings challenge Darwinian evolution, and I doubt that any
of those researchers would support that conclusion from their data. And indeed,
the fact that we differ genetically by more than 1%, largely for gene regulatory
reasons, was predicted in Science more than 30 years ago (again as my article
notes)–and the 1975 article was co-authored by one of the world’s leading
evolutionary biologists at the time, Allan Wilson.
The bottom line is that your post is so distant from the sources that you have completely garbled the data to support Intelligent Design. It’s sloppy, inaccurate, and overtly biased.
Your are welcome to post my e-mail in its entirety, but given the
errors that you made in your post by selectively quoting from other posts,
please do not excerpt this for a public posting. I’m also attaching original
papers that discuss these issues. It’s complicated stuff, and I hope these
papers help clarify the details.
Jon Cohen

Of interest is the date of Cohen's letter - October 20, 2007. Recall that the 'chat' in which Luskin took part occurred just a few days ago - Mar. 11, 2008. So Luskin is STILL using disinformation that had been corrected for him. Will the good little IDcreationists out there in listener/reader land care? Doubt it... Luskin posted a 'response' to Cohen's letter here (no comments allowed, of course), which I will take a look at in a later posting.

But new findings in genetics show that gene-coding DNA might not even be the
right place to seek differences between humans and chimps. But there is a deeper
question: (2) If humans and chimps were truly only 1% different at the genetic
level, why should that demonstrate common ancestry?
Perhaps because that is not all that such studies indicate? I predict that Luskin has never seen DNA sequence data, certainly never analyzed any. The reporting of % similarity is interesting and informative in and of itself, but it is only part of the story - in reality, what indicates descent is not just the similarity between any two sequences (genomes), it is the patterns of unique shared mutations among many species' genomes.(see the section on cladistics).
The next section of Luskin's gibberish merely provides more evidence that he does not truly understand what the "% similarity" figures truly mean, and does not understnad what phylogenetic analyses entail.

Similarities in key genetic sequences may be explained as a
result of functional requirements and common design rather than mere common
descent. We might reasonably ask the evolutionist why the 1% difference value is
considered powerful evidence for Darwinian evolution, and at what point does the
comparison cease to support Darwinian evolution? What about 2% different? 3%?
5%? 10%? Is there an objective metric for falsification here, or are Darwinists
putting forth a fallacious argument for human / chimp common ancestry? In my
view, intelligent design is certainly compatible with human/ape common ancestry,
but the truth is that the percent difference says nothing about whether humans
and chimps share a common ancestor. The percent genetic similarity between
humans and apes does not demonstrate Darwinian evolution, unless one excludes
the possibility of intelligent design. Just as intelligent agents 're-use'
functional components that work over and over in different systems (e.g., wheels
for cars and wheels for airplanes), genetic similarities between humans and
chimps could also be explained as the result of the re-usage of common genetic
programs due to functional requirements of the hominid body plan.

It could be, but then, so could de-novo genetic elements. With a Designer, any and all phenomena are explained by His - oops, I mean "it's" - folly and whim.
See? Just spewing goo for the rubes. Luskin is clueless, or is being purposefully deceptive. All for his beliefs.


Luskins IDEA center article, linked to in the 'chat', my comments interspersed:

Two recent news articles are discussing the death of the junk-DNA icon of Neo-Darwinism.

One, what does he mean by 'icon of Neo-Darwinism'? Apparently, Luskin is trying to indicate that this is a major issue for evolution. As he frames it, it is not.

Wired Magazine has an article pejoratively titled "One Scientist's Junk Is a Creationist's Treasure" that emphasizes the positive point that intelligent design has
made successful predictions on the question of "junk-DNA."
That's funny - I cannot wait to see these 'predictions' . The article only quotes Discovery Institute hack Stephen Meyer as claiming that function in junk DNA is an 'empirical' prediction of ID and it disconfirms evolution, which noit only shows what a sleaze Meyer is, but that he is an out and out liar, to boot. But I digress.

The article reports: [A] surprising group is embracing the
results: intelligent-design advocates. Since the early '70s, many scientists
have believed that a large amount of many organisms' DNA is useless junk. But
recently, genome researchers are finding that these "noncoding" genome regions
are responsible for important biological functions.The Wired Magazine
article then quotes Discovery
Institute's Stephen Meyer explaining that this is a prediction of intelligent
design that was largely unexpected under neo-Darwinian thought:
"It is a
confirmation of a natural empirical prediction or expectation of the theory of
intelligent design, and it disconfirms the neo-Darwinian hypothesis," said
Stephen Meyer, director of the Center for Science and Culture at the Discovery
Institute in Seattle.The Wired Magazine
article openly and unashamedly
confuses intelligent design with creationism,

Indeed - ID advocates are creationists, whether Luskin wants ot admit it or not. Of course, the article glosses over some important facts - like the little fact that it was evolutionists that discovered that some junk DNA has funcxtion, and that even the originators of the phrase "junk DNA" did not assert that all noncoding DNA was useless, and mistakenly gives the creationists more credit - much more credit - than they deserve. And Collins - I just wish that guy would keep his mouth shut.
Anyway, these 'predictions' by ID creationists - where were they published? They weren't. What we really see is creationists taking papers indicating function for some junk DNA and claiming that they would 'expect' this. 'Expecting' something after the fact is not a prediction.

Well, it goes on and on, and frankly, like all lies, it takes much longer to correct them than to make them, and I don't have the time or pateince to go through each of this person's distortions and contortions.

But you get the picture.

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