Why this posting one may wonder?
On UcD our dear friend, and Nick Matzke wannabe, Casey Luskin, posted on some recent news on the similarity between chimps and humans and was quickly corrected by one of the authors he quoted. Seems Luskin had confused the various methods that can be used to measure ‘similarity’ in the genome.
The letter by Jon Cohen is too good to be quote partially
From: Jon Cohen [snip]
Sent: Saturday, October 20, 2007 12:05 PM
To: Casey Luskin
Subject: Errors in your posting
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.
Remember what Luskin had claimed
entitled “Relative Differences: The Myth of 1%,” which reported that “human and chimpanzee gene copy numbers differ by a whopping 6.4%.” The statistic of an alleged 1% difference between human and chimp DNA is thus quickly becoming a thing of the past. A recent post at Scientific American’s blog states, “humans may have as little as 99% of their genes in common with one another, and, by the same analysis, as little as 95% of their genes in common with chimpanzees.” Thus, according to the article, “Humans turn out to be as genetically different from one another as it was previously thought they were different from chimps.” (emphasis added).
So why the range of similarities from 95-99%? The answer is simple, because they measure different differences and similarities.
Now science has known this for quite some time although it seems to be ‘news’ to Luskin. See for instance this table at Wikipedia
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.
So what is meant by “gene copy number”? Wikipedia to the rescue
The gene copy number (also “copy number variants” or CNVs) is the number of copies of a particular gene in the genotype of an individual.
The group estimated that humans have acquired 689 new gene duplicates and lost 86 since diverging from our common ancestor with chimps six million years ago. Similarly, they reckoned that chimps have lost 729 gene copies that humans still have.
“The paper supports the emerging view that change in gene copy number, via gene duplication or loss, is one of the key mechanisms driving mammalian evolution,” says genomics researcher James Sikela of the University of Colorado Health Sciences Center.
Source: Human-Chimp Gene Gap Widens from Tally of Duplicate Genes, December 19, 2006 SCIAM
Now Cohen’s comments published in EVOLUTIONARY BIOLOGY: Relative Differences: The Myth of 1% Science 29 June 2007: 1836
In a groundbreaking 1975 paper published in Science, evolutionary biologist Allan Wilson of the University of California (UC), Berkeley, and his erstwhile graduate student Mary-Claire King made a convincing argument for a 1% genetic difference between humans and chimpanzees. “At the time, that was heretical,” says King, now a medical geneticist at the University of Washington, Seattle. Subsequent studies bore their conclusion out, and today we take as a given that the two species are genetically 99% the same. But truth be told, Wilson and King also noted that the 1% difference wasn’t the whole story. They predicted that there must be profound differences outside genes— they focused on gene regulation—to account for the anatomical and behavioral disparities between our knuckle-dragging cousins and us. Several recent studies have proven them perspicacious again, raising the question of whether the 1% truism should be retired.
However, how many of these differences have a phenotype impact?
Yet it remains a daunting task to link genotype to phenotype. Many, if not most, of the 35 million base-pair changes, 5 million indels in each species, and 689 extra genes in humans may have no functional meaning. “To sort out the differences that matter from the ones that don’t is really difficult,” says David Haussler, a biomolecular engineer at UC Santa Cruz, who has identified novel elements in the human genome that appear to regulate genes (Science, 29 September 2006, p. 1908).
I am confused as to how Luskin interprets these data and why he sees this as a problem for evolutionary science? Surely the finding of more duplicated genes, a source of genetic complexity, seems to help evolution and help us understand what separates us from our closest cousins, the chimps? After all even Michael Behe accepts common descent as a fact.
But in the end, it would be helpful if ID proponents would familiarize themselves a bit more in detail with the issues lest they want to be publicly corrected time after time. Certainly for a blog which ‘prides’ itself in correcting misconceptions in the media, their own error rate seems quite high.