Visualizing the Similarity of Human and Chimp DNA

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Source: Visualizing the Similarity of Human and Chimp DNA

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

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

Remember what Luskin had claimed

Luskin Wrote:

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

Cohen explains

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.

According to

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.

12 Comments

Now you’re thinking with portals!

Excellent post. And an excellent example of a scientist fighting back against the misuse of their work.

Rhetorical question: Did we expect any more out of Luskin?

Yet it remains a daunting task to link genotype to phenotype

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.

still shocking to me that apparently NONE of the sci blogs bothered to take advantage of the recent (Oct. 16) NOVA special on epigenetics to explore exactly that.

You still can do it, Pim.

Yet it remains a daunting task to link genotype to phenotype

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.

still shocking to me that apparently NONE of the sci blogs bothered to take advantage of the recent (Oct. 16) NOVA special on epigenetics to explore exactly that.

You still can do it, Pim.

PvM Wrote:

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.

You’re not confused. The goal is to get the target audience to think that evolution can’t produce changes that fast. From that, some will infer that the designer originated the 2 lineages independently, and others will agree with Behe that it was all an “in-vivo” process, just not “evolutionary.” Also, some will infer that the “design actuation event” occurred millions of years ago, and others will infer mere thousands. But more importantly, the emphasis on (quote-mined) “weaknesses” of “Darwinism,” coupled with a complete absence of a potential alternate explanation, will distract audience members from recognizing, let alone critiquing, their own irreconcilable differences.

Luskin must try harder. Sequencing the Neandertal genome shows that they are more like us than chimps (even if the material now is suspected of more contamination than they estimated), something that is not dreamt of in his philosophy but is predicted by evolution.

I guess he should Gish gallop faster.

It is just obvious smoke. They do not want the rubes who believe them to understand the issues. It is the mushroom treatment. Feed their followers shit and keep them in the dark.

Who would think that this was an argument once they realize that the relative genetic distances between species stay the same. Not only that, but the number of mutational events to go from around 1% difference in the single copy sequence to 5% difference once the deletion/insertions are accounted for doesn’t even come close to even doubling. You can change thousands of base-pairs in a single event by duplicating a gene. The 1.2% difference in the genes is mainly due to single base-pair substitutions that change one nucleotide pair at a time. We haven’t even hit the maximum difference between the genomes. We do not have an accurate means to sequence highly repetitive tandem repeats (the sequence that makes up most of the heterochromatin). Once we get a handle on this fraction of the genome the difference between humans and chimps is going to more than double that 5% difference figure.

The main point to understand is that all these changes are relative. The relative distance between species isn’t really going to change. We knew that there were going to be insertions and deletions encompassing large continuous stretches of DNA. We just couldn’t get a good handle on it until we had the genome sequences. We know that heterochromatin regions are the fastest changing regions of the genome. Just find that comparison between human and other ape chromosomes and look at the chromosome ends. We can’t yet get a good handle on the difference of this type of sequence because they are mostly short low complexity tandem repeats, and we can’t sequence through the entire repeat that might be hundreds of thousands of base-pairs or even greater in a single pass so we can’t get a good idea of how many repeats there are in any cluster. Once technology improves enough to sequence really large pieces of DNA in a single pass we will start getting these answers. The fact will remain that chimps will still be our closest living relatives by genetic distance.

The mushroom treatment only works on the rubes that want to believe the ID scam artists. Scientists that are doing the work know better. What I can’t understand is how many of the rubes keep going back to the trough even though they know what they are being fed. It has to be an acquired taste. What happened to the ID scam? Why are the ID perps running a replacement scam where ID can’t even be mentioned in the public face of the scam (only in back rooms and with winks and nods) if they seriously had an argument? Can anyone deny that the same perps that ran the ID scam are running the replacement? Why do they need a replacement? Have you looked at the replacement scam? Isn’t it just smoke and obfuscation with no central argument except that we do not understand everything about nature? Why can’t ID or creationism be mentioned as one of the scientific controversies?

Any ID supporter that wants to answer any of those quetions? Any that have seriously asked themselves those obvious questions? What are your answers?

Ron,

I have been using your phrase “replacement scam” in hopes that it would catch on. Given my luck with other favorite phrases like “postmodern synthesis” (what I call that odd hybrid of ID and YEC) don’t expect much success.

Anyway, it occurred to me that “the” replacement scam (“teach the controversy” or “critical analysis”) is actually the 3rd or later generation replacement. It replaced the “don’t ask, don’t tell” strategy that morphed into ID (via “cdesign proponentsists”), which replaced “scientific” creationism, which replaced Biblical creationism. As you know, at each step it was less about honest belief and more about deliberate misrepresentation and evasion.

Venus Mousetrap:

Now you’re thinking with portals!

The cake is a lie!

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).

The sequencing of new human genomes has uncovered a startling fact which so far the internet hasn’t covered much. Humans differ among themselves in genomic sequence by quite a bit. The J. Cohen letter above says 0.5% between his maternal and paternal genomes which would be 15 million base pairs. Another source stated that his genome differed from the government reference genome by 4.1 million base pairs.

This range in variation between H. sapiens isn’t as high as between humans and chimps. But it is much higher than was thought before we had multiple human sequences.

We are still considering the implications of this data. 1. It is support that much of noncoding DNA is ephemeral, it is there, very rapidly evolving and not doing much of anything important.

2. The rate of mutation in humans is high enough to provide a lot of variation between individuals and from generation to generation. I’ve proposed many times that what is rate limiting in evolution is not mutation rates or variation (RM=random mutation) but NS, natural selection pressures.

I guess he should Gish gallop faster.

It’s hard to gallop faster when seated backwards on the horse.

Ichthyic Wrote:

It’s hard to gallop faster when seated backwards on the horse.

Which means that the apparatus whereby Luskin speaks is facing forwards.

About this Entry

This page contains a single entry by PvM published on November 1, 2007 9:49 PM.

Intelligent Design ‘flunked’: Crowther and “Judgment Day” was the previous entry in this blog.

Dumbest Attack on Genetic Algorithms. Ever. is the next entry in this blog.

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