Friday, October 06, 2006

That's Avida!

Mark Chu-Carroll has written an excellent post over at Good Math, Bad Math addressing creationist attacks on some research using the artificial life model system known as Avida. A descendant of Tom Ray's Tierra, Avida is used by several labs around the world, notably those of Chris Adami at Caltech and Richard Lenski at Michigan State University, to study a wide range of problems in evolutionary biology and ecology: from the evolution of robustness to adaptive radiation, from the evolution of sex to phylogenetic reconstruction. And, of course, the evolution of complexity.

On the face of it, work on these digital organisms (think of them as tame computer viruses) has grown into a vibrant research field in its own right, at the intersection between evolutionary biology and computer science. A quick search reveals at least 9 high profile papers on Avida in the last decade, including some of the ones I've already linked to. What do I mean by "high profile"? As a crude benchmark, those are papers with more than 10 citations each in other scientific papers (indeed, they were cited 37 times each on average). To put these numbers in perspective consider that the same database, the Institute for Scientific Information's (ISI) Web of Knowledge, tells us that William Dembski, none other than the Isaac Newton of information theory, has co-authored a total of 5 papers, cited 5 times in total (i.e., once each on average). So, there are Newtons and then there are Newtons...

So what do creationists think about all this work on Avida? Surely they would welcome an actual test of Behe's ideas on irreducible complexity, right? Wrong. They didn't like it one bit. So what did they do about it? Publish a rebuttal in the pages of Nature? Submit their own test to another journal? No. Instead they got Eric Anderson to sneer at the paper in one of their best journals, the Progress in Complexity, Information, and Design.

That might sound fair enough, but only if you don't know your scientific journals. The problem is that PCID, despite its impressive sounding description ("quarterly, cross-disciplinary, online journal that investigates complex systems apart from external programmatic constraints like materialism, naturalism, or reductionism") is not even up to the standard required for listing in the ISI. But is that really so bad? Well, the ISI currently lists 6088 science journals, including such obscure titles as Wool Technology and Sheep Breeding (impact factor 0.02), the Journal of the South African Institute of Mining and Metallurgy (impact factor 0.08) and Hazard Waste Consultant (impact factor 0, yes zero). So, yes, that is pretty bad. Publishing in journals not listed by the ISI counts for next to nothing in tenure decisions which could go some way towards explaining some of the problems Chapman listed in his pathetic apologia for the dismal state of scientific research on intelligent design.

And who, exactly, is Eric Anderson? The paper is not helpful in this respect, as no affiliation is listed. A search in ISI reveals no one of that name with a track record of publication in either evolution or computer science. For all we know, it might be a pseudonym for one (or more) of those "ID-friendly scientists" working at undisclosed locations that populate Chapman's dream world. Of course, anyone, credentialled or not, is entitled to comment on scientific matters. It's just that if you're going to fight evolutionary heavyweights like Lenski, Ofria and Adami, then you'd better make sure that you know what you're talking about. Specially when they have teamed up with Pennock, a philosopher, to make damn sure their argument was watertight. By now you've probably guessed it: Eric Anderson made a dog's breakfast of his critique. Let's turn to Mark for the details. Commenting on the abstract to Anderson's paper he says:
So the authors Avida are at best oblivious to the properties of the work they're doing; at worst, they're liars. And their work is based on on circular assumptions, which support Behe's notion of irreducible complexity. He's making an incredibly strong accusation against the Avida team: that either they're stupid and don't understand their own work; or they're liars.
In other words, not a promising start. And it gets worse. Not only does Anderson adopt an incredibly obnoxious and patronizing tone throughout, but he confuses hypotheses and assumptions and then accuses Lenski et al. of circular reasoning. Here's Mark's summary of the problem:

Now, here's where it gets really interesting. He says that he's going to examine the "key assumptions" built into Avida. But that's not really what he's going to do. What you'll see as I go through his paper is that he repeatedly tries to make it look like Avida is using circular reasoning. In fact, what they're doing is describing an experiment.

How do you do an experiment in real science? You start by developing a hypothesis. Using your hypothesis, you make a prediction. Then you perform the test, and see if the results match the prediction. If they do, then the experiment confirms the hypothesis (note, confirms not proves); if they don't, then the experiment disproves the hypothesis.

What the Avida team did was develop a hypothesis that an evolutionary system, working within the constraints of Behe's model of evolution could produce an irreducibly complex system. They proceed to describe their model, and the predictions it makes. Then they show their results, which confirm their hypothesis. Mr. Anderson tries to argue that because they stated their hypothesis up front, and then the test confirmed it, that they were cheating and being circular. He's pretending that the hypothesis is actually a set of assumptions; and that therefore, the experiment confirming the hypothesis is invalid.

Nicely put, hm? You get the idea.

Now, if you want to learn more about Avida, you could turn to Carl Zimmer's excellent piece in Discover. Here's one of my favorite passages:
One of the hallmarks of life is its ability to evolve around our best efforts to control it. Antibiotics, for example, were once considered a magic bullet that would eradicate infectious diseases. In just a few decades, bacteria have evolved an arsenal of defenses that make many antibiotics useless.

Ofria has been finding that digital organisms have a way of outwitting him as well. Not long ago, he decided to see what would happen if he stopped digital organisms from adapting. Whenever an organism mutated, he would run it through a special test to see whether the mutation was beneficial. If it was, he killed the organism off. "You'd think that would turn off any further adaptation," he says. Instead, the digital organisms kept evolving. They learned to process information in new ways and were able to replicate faster. It took a while for Ofria to realize that they had tricked him. They had evolved a way to tell when Ofria was testing them by looking at the numbers he fed them. As soon as they recognized they were being tested, they stopped processing numbers. "If it was a test environment, they said, 'Let's play dead,'" says Ofria. "There's this thing coming to kill them, and so they avoid it and go on with their lives."

This is yet another example of what has been called Leslie Orgel's Second Law: "Evolution is smarter than you are".