Tuesday, July 07, 2009

Tracing human evolution via mistakes

Kenneth Chang has post on Tierney Lab about the role of natural mistakes that have provided some of the strongest evidence for evolution. Some simple conceptual predictions - and fantastic confirmations. Science at its best. Here Chang quotes from a recent talk by Ken Miller. If you don't want to read the whole thing, I have also embedded below a relevant segment from the NOVA episode about the Dover trial, Judgment Day: Intelligent Design on Trial:

Dr. Miller told an anecdote of how he caught two students plagiarizing.

Two of my students cheated on a written assignment by submitting the same paper. And I called them in and said, “Guys, I caught you.”

They said, “Well, our papers aren’t that similar. We have different titles. We begin in a different way.”

What they had done was rearrange all of the paragraphs and put in new words and stuff like that. At superficial glance, they looked entirely different. And they said, “Our thinking is the same, because we’re roommates, of course. And we had discussed this, we talked about it, so it’s not surprising we come to the same conclusion. But look, none of the paragraphs in our two papers match.”

And they were right about that. So they said, “How would you think we copied?”

I said, “I ran your papers through a program that looks for unusual matching strings. You guys misspelled the same six words in the same six ways. And when you have matching mistakes, there is no other explanation other than a common ancestor for the paper.” And they broke down, and they threw themselves on the mercy of the court.

In the same way that the spelling errors pointed to the students’ copying from an earlier paper (or one another), Dr. Miller said, genetic errors point to the lineage of different species.

The human genome includes five copies of the gene that produces beta-globin. In the middle of these genes is a stretch of genetic code that clearly was once a sixth beta-globin gene. But this so-called pseudogene now contains mistakes that prevent it from producing RNA that can be transcribed into beta-globin protein. Dr. Miller continued:

It turns out that there is an organism that has matching mistakes in its beta-globin pseudogene. That organism actually turns out to be the chimpanzee, and also the gorilla – beta-globin pseudogenes with exact matching errors. And there is only one explanation for that at the molecular level, which is common ancestor.
But perhaps, even a dramatic evidence comes from human chromosome number 2 - evidence for which was also presented during the Dover trial. Here is Ken Miller again:

In 2005, a couple of weeks before the start of the Kitzmiller vs. Dover Area School District trial in Pennsylvania over the teaching of “intelligent design” in public schools, the journal Nature published the full chimpanzee genome. Humans and chimps share about 98 percent of the DNA and most of the genes. That general fact had been known for some time and by itself is not immensely convincing. But there are stronger arguments in the details, and Dr. Miller discussed one argument presented at the trial. Again, the evidence centers around a glitch.

We had to put this into terms – no offense intended here – that were so simple that even an attorney could understand them. And I want to show you how we did this.

We humans have 46 chromosomes – 23 pairs. All of the other great apes have 24 pairs of chromosomes. So how is it that we are missing a pair of chromosomes that all these recent relatives actually have?

Is it possible that a pair of chromosomes just got lost in our lineage? Well, no. There are so many important genes on every chromosome that the loss of both members of a homologous pair would be fatal, wouldn’t even get past embryonic development. So the only possibility is two chromosomes that are still separate in other primates must have gotten accidentally stuck together to form a single fused chromosome in us. And that’s the explanation that exists in evolution. Here is why evolution is science and not conjecture. If that’s true, we want to be able to find that fused chromosome. So if we can, that is a powerful confirmation of an evolutionary prediction.

Well, can we find it? It turns out it is much easier to recognize a fused chromosome than you might think. The tips of all chromosomes are covered with a very special DNA sequence, in a region called the telomere. It is really easy to recognize. Near the center of every chromosome is an equally recognizable region called the centromere. If one of our chromosomes was formed by the fusion of two primate chromosomes, you know what it would have? It would have telomere DNA at the center, and it would have two centromeres. Should be very easy to recognize.

We scanned the human genome. Do we have a chromosome like that? The answer is, you bet we do.
It is called human chromosome number two. Our second chromosome has telomere DNA at the center. It has two centomeres. We have placed it as being from primate chromosomes 12 and 13 and so exact is the correspondence that people who work on the chimpanzee genome now call the chromosomes they used to call 12 and 13 2A and 2B, because they correspond to those two halves of the human second chromosome.

Is there any question, to explain these facts – and these are facts, this is not hypothesis or conjecture – any way to explain these facts in light of the view that our species was uniquely designed or intelligently created? The answer is no. You can only explain this by evolutionary common ancestry. About the only thing you could say is maybe the designer wanted to fool us into thinking we evolved and he rigged chromosome number two to make it look that way.

And the only thing I can tell you is if that was his intent, he did a heck of a job. Because the marks of evolution are literally all over our chromosome.
And here is the Nova segment relevant for the role of the second human chromosome (you should watch the full episode here - it is fantastic and it also won a 2008 Peabody award). This is also great about the nature of science and it clears up some of the confusion about the way scientists use the word theory. Of equal importance, the documentary successfully conveys the notion that science is primarily driven by unanswered questions. Enjoy.


Atif Khan said...

Thanks for sharing such nice piece of info.

Don said...

I screened this for Charlene's tutorial last fall, but the two most interested people in the room were the two of us. It was too bad, because it really was a well done documentary on the trial.

Everett said...

FYI, Salman, the Miller material is also accessible via his most recent book, _Only a Theory_, which is both more focused in terms of content and more widely targeted in terms of audience than _Finding Darwin's God_--while still overlapping here and there.

Farhan said...

And the only thing I can tell you is if that was his intent, he did a heck of a job. Because the marks of evolution are literally all over our chromosome.

LOL! How nicely put. Great article by the way.

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