Sunday, April 09, 2006

The Markov Process, Evolution, and "Intelligent" "Design"

Tristero over at Hullabaloo has an interesting post on the transitions of the genetic codes of points to an article in today's NY Times:

By reconstructing ancient genes from long-extinct animals, scientists have for the first time demonstrated the step-by-step progression of how evolution created a new piece of molecular machinery by reusing and modifying existing parts.

The researchers say the findings, published today in the journal Science, offer a counterargument to doubters of evolution who question how a progression of small changes could produce the intricate mechanisms found in living cells.

"The evolution of complexity is a longstanding issue in evolutionary biology," said Joseph W. Thornton, professor of biology at the University of Oregon and lead author of the paper. "We wanted to understand how this system evolved at the molecular level. There's no scientific controversy over whether this system evolved. The question for scientists is how it evolved, and that's what our study showed."...

Discoveries like that announced this week of a fish with limblike fins have filled in the transitions between species. New molecular biology techniques let scientists begin to reconstruct how the processes inside a cell evolved over millions of years.

Dr. Thornton's experiments focused on two hormone receptors. One is a component of stress response systems. The other, while similar in shape, takes part in different biological processes, including kidney function in higher animals.

Hormones and hormone receptors are protein molecules that act like pairs of keys and locks. Hormones fit into specific receptors, and that attachment sends a signal to turn on — or turn off — cell functions. The matching of hormones and receptors led to the question of how new hormone-and-receptor pairs evolved, as one without the other would appear to be useless.

The researchers found the modern equivalent of the stress hormone receptor in lampreys and hagfish, two surviving jawless primitive species. The team also found two modern equivalents of the receptor in skate, a fish related to sharks.

After looking at the genes that produced them, and comparing the genes' similarities and differences among the genes, the scientists concluded that all descended from a single common gene 450 million years ago, before animals emerged from oceans onto land, before the evolution of bones.

I have argued in various places with creationists that this was doable, I hadn't known if it in fact had been done or not, but it seemed, uh, pretty obvious to me.

Let me explain why:

  • A trip to the NY Museum of Natural History will confirm that indeed, there are taxonomies that can be created based on the evolution of animals. This taxonomy can be of course based on DNA.

  • The DNA of different species can be arranged on a tree just like the trees arranged according to anatomical similarity or embryonic similarity.

  • The DNA trees though are of particular importance; they represent observed pieces of a what (piecewise at least) is a branching process. (Wiki link for branching process is here if it works.)

  • Now regardless of whether or not life is a true branching process or not (e.g., it could be Markov process with odd kinds of loops instead of just a simpler branching process.

  • The Markov process - let's just stick with that for now- can be represented by a graph, with nodes representing DNA of a particular species, and branches or edges representing state transitions. Such state transitions could be added too by the addition of viruses to the "junk" DNA.

  • When all species ever known/classified as to DNA are on the tree, the tree can represent a set of state transitions.

  • Finally, a we can deduce the state transitions required to go from, say, a flatwork to a human. Yes, Virginia, it's random, in a way that information theory folks and math majors will appreciate, but creationists won't.

I'll be looking at the creationist/ID blogosphere in the next few days, but Tristero over at Hullabaloo is quite wrong to think that this is a death knell for "intelligent" "design": they will simply ascribe their "designer" to the role of instigator of these state transitions. But that role is flimsier than gossamer.
Based on a probabilistic viewpoint the "ultimate cause" just doesn't matter: the states happened, and the state diagram is ultimately completely agnostic as to the "cause" just as the "cause" of a sequence of die rolls at a craps table - other than the gambler's rolling the of the die- is irrelevant.

It's all about observations, baby. Just like in Buddhism.

But Tristero is right about Behe; who has to go into denial mode to try to refute what is an obvious way to falsify evolution (which "intelligent" "design" can't do.) I await Dembski's response to this though; because it's a probability/stochastic processes exercise, and his denial should prove interesting to say the least.

The WSJ captures "Discovery Institute"'s Stephen Meyer's reaction; he says it's a "victory" for "Intelligent" "Design." Nice spinning:

One such complex structure is a hormone and its receptor. Just as a keyhole has no use without a key and vice versa, a hormone is useless without a receptor that lets it dock with a cell, and a receptor serves no purpose without hormones. Catch-22: Neither component could survive without the other, yet it strains credulity to suppose that both structures popped onto the evolutionary scene simultaneously.

To investigate this puzzle, biologists led by Joseph Thornton of the University of Oregon reconstructed an ancestral receptor. They first analyzed receptors for steroid hormones in 59 species, including primitive jawless fish and skates. Then, in a process called gene resurrection, they worked backward to infer what the gene for the ancestral receptor was, and actually made the receptor in the lab: a molecule that last existed on earth 450 million years ago.

Testing various hormones on the ancestral receptor, the scientists found that both aldosterone and another one fit. The ancestral receptor, therefore, was fully employed acting as the keyhole for this second hormone. When aldosterone appeared on the scene by random mutation, it co-opted the existing receptor, the researchers conclude in today's issue of Science.

The findings, says Christoph Adami of the Keck Graduate Institute of Applied Life Sciences, Claremont, Calif., "solidly refute" ID.

But refutation is in the eye of the beholder. No scientific discovery will end the evolution wars. For one thing, adherents of ID call the fact that scientists are studying reducible-complexity at all a victory for their side. "We're delighted they're engaging in a debate that they say doesn't exist," says Stephen Meyer of the Discovery Institute in Seattle, which pushes ID. Moreover, he says, the hormone-receptor system is not really irreducibly complex.

The trouble for ID is that this isn't the first study to show, step by step, how complex structures could have evolved. Recent experiments have shown how irreducibly complex structures such as bacterial flagella and the lens of an eye could have evolved by co-opting existing structures just as the hormone did. More such research is in the pipeline.

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