Thursday, July 13, 2006

Degeneracy vs Redundancy

Salvador Cordova and I have been arguing over the significance of redundancy and robustness in living systems. Salvador, has been trying to develop an "argument from redundancy" for ID creationism. It begins in an analogy between biological and engineered systems. As most ID arguments, that's where it stops as well. I'm skeptical mostly because I don't see many examples of perfect redundancy in nature.

I'm actually writing a paper on a related subject (more about that at some point) and came across an article that made the point about the difference between perfect and partial redundancy much better than I did. One of the authors is Gerald Edelman, who won the Nobel Prize for Medicine and Physiology in 1972 for his classic on the structure of antibodies. They argue that there's a difference between degeneracy in biology and redundancy in engineering:

The contrast between degeneracy and redundancy at the structural level is sharpened by comparing design and selection in engineering and evolution, respectively. In engineering systems, logic prevails, and, for fail-safe operation, redundancy is built into design. This is not the case for biological systems. Indeed, not the least of Darwin's achievements was to lay the argument by design to rest. But, for obvious economic reasons, design is by far the major component of most technical efforts in modern society. In general, an engineer assumes that interacting components should be as simple as possible, that there are no "unnecessary" or unplanned interactions, that there is an explicit assignment of function or causal efficacy to each part of a working mechanism, and that error correction is met by feedback, modeling, or other paradigms of control theory. Protection can be afforded by planned redundancy, but adventitious compensation for error is neither expected nor usual. Irrelevancy is avoided from the outset.

By contrast, in evolutionary systems, where there is no design, the term "irrelevant" has no a priori meaning. It is possible for any change in a part to contribute to overall function, mutations can prompt compensation, stochastic interactions with the environment can lead to strong selection, often there is no fixed assignment of exclusive responsibility for a given function, and, unlike the engineering case, interactions become increasingly complex [...]

Now that's what I'm talking about!

Read on

Monday, July 10, 2006

Counter Coulter II

As pointed out before, Ann Coulter has written a book of breathtaking inanity, which is now second on the New York Times non-fiction bestseller list (after topping the list for several weeks, I believe). Among the usual preposterous claims against, you guessed it, liberals (a term of abuse here in the US), she devoted two chapters to "debunking" evolution. People who have actually read the relevant chapters have not been impressed. Here's a representative sample: Darwin Central, Right Wing Professor, Talk Reason, Pharyngula, Media Matters, Loom. After that, I'm not tempted, but I'd like to comment on one passage from Coulter's book that has been quoted often:
Throw in enough words like imagine, perhaps, and might have -- and you've got yourself a scientific theory! How about this: Imagine a giant raccoon passed gas and perhaps the resulting gas might have created the vast variety of life we see on Earth. And if you don't accept the giant raccoon flatulence theory for the origin of life, you must be a fundamentalist Christian nut who believes the Earth is flat.
That's basically how the argument for evolution goes [emphasis in original].
Anyone who knows anything about science will know that this is about as ludicrous a representation of the scientific process that has led to the nearly universal acceptance of evolution as one could come up with (apparently, prompted by a misreading of an essay by Zimmer, of all people). The irony is that Coulter has actually spewed a perfect analogy for creationism, not evolution. For example, here's the Wikipedia entry describing the Zulu creation myth:
The Ancient One, known as Unkulunkulu, is the Zulu creator. He came from the reeds and from them he brought forth the people and the cattle. He created everything that is: mountains, streams, snakes, etc. He taught the Zulu how to hunt, how to make fire, and how to grow food.
Notice any similarities? This is the last one of forty-nine creation myths listed. Most of them are just as well supported by evidence as the giant racoon flatulence creation myth (the other ones are simply too vague). They are also mutually inconsistent.

Coulter should stop writing about things she doesn't understand. Better stick to something she's obviously good at, like plagiarism (for example, see here, here, here, here).

Read on

How far we have not come

A couple of weeks ago, PZ Myers brought to our attention a chilling story of anti-atheism bigotry in Oklahoma. Now, he has posted a first person account by the victim of the ordeal, Chuck Smalkowski. Here's a small excerpt to give you an idea of what his family went through:
The whole family was under constant stress. Police trying to get search warrants to the property by having ex-employees file false statements. Other cops trying to hire ex-cons to beat me up. The whole town knows of it! The Sheriff trying to have my bond pulled by the bail bondsman when there was no legal way to do it. My kids have been out of school since November. Principal's son saying should he get a gun when he sees my daughter and my son. DA has yet to reply to our concerns. The Department of Human Services comes to my place saying they received a complaint that I starve my kids. It was even obvious to them the charge was bogus.

We have become very good at using back roads. The police follow us around. Traffic tickets that when challenged were dropped in court. Not to mention the stares and whispers, the betrayal from employees, one of my healthy dogs dying. Brush fires starting up upwind.

An FBI agent even said, "You aren't kidding". When it was obvious someone followed us and was watching our meeting out in the middle of nowhere. I was told about a few things. All I can say is that some of the crooks out here now charged with crimes wore badges and guns! But he could not help my family and me. Not without witnesses willing to come forward. One scared witness left the state. The last words she spoke to me were, Chuck I don't want to end up dead in a ditch!

Just what you would expect life to be like out here in the Bible belt!

There's more: a corrupt DA, a lawyer having to remind the jury that atheists do not worship the devil, people praying in court for a conviction, whole thing appears to come straight from a Grisham novel. (One set several decades ago...) Just another Salem indeed!

Read on

Sunday, July 02, 2006

Another Devil's Chaplain

The few regular readers of this blog will have noticed that I am a great admirer of the blog Pharyngula written by the biologist PZ Myers, with its inimitable mix of evolutionary developmental biology, atheism, liberalism and cephalopods. Not only is PZ refreshing and insightful in most of what he writes, he also sustains an astonishing posting rate. I would have to blog full-time to even approach a similarly substantive output (to say nothing about quality), but perhaps I'm just an unusually slow writer. Although that is unlikely to change in the future, I thought I would improve things by posting on one of the intellectual passions I share with PZ Myers, besides evo-devo: atheism.

Recently, PZ has been tackling the thorny issue of the relationship between atheism and science in two incisive posts (here and here). He addressed the question of whether there is any difference between the scientist's and the atheist's attitudes towards religion. PZ concluded that "the scientist and atheist positions are the same". Here's a summary of his argument:
What should a scientist expect from an idea? That it be a reasonable advance in knowledge; that it be built on a foundation of evidence; that it be testable; that it should lead to new and useful questions and ideas. If we look at religion from that perspective, it doesn't help. At best, the hypothesis of the supernatural and/or a supreme being is vague, unfounded, and inapplicable in any practical fashion—deistic views, for instance, are so abstract and so carefully divorced from risk of challenge that they represent an empty hypothesis, and the most flattering thing you can say about them is that they're harmless. At worst, religion is confused, internally contradictory, and in conflict with evidence from the physical (and near as we can tell, only) world.
Now, this argument appears to upset many people. They would rather scientists keep these thoughts to themselves, and focus on teaching and practicing science at all times. Surely, people should be allowed to believe in God if they chose to. Of course they do! A better question is whether scientist-
atheists should hurt people's feelings by articulating their views in public. In fact, all atheistic and agnostic scientists I know focus exclusively on the science most of the time. I certainly don't bring up religion in my Evolutionary Biology course or at my lab meetings (and I suspect, neither does PZ). I'm much more interested in a student's understanding of linkage disequilibrium, or in how the worms (or models) behaved in the latest experiment.

The problem is that scientists are being asked to watch in silence as critics of science attack science by linking it to atheism (e.g., Ann Coulter, and the "Coultergeists" at the Discovery Institute do it all the time), while many defenders of science believe they are doing it a service by distancing science from atheism (e.g., Michael Ruse's disappointing ramblings on "evolutionism", or the talking heads at the end of the otherwise excellent Darwin exhibition). Others, such as Richard Dawkins, EO Wilson, PZ Myers and myself, believe that this is not good enough. Just because some scientists, such as Ken Miller and Francis Collins, manage to do good science while also believing that Jesus of Nazareth was the Son of God, does not mean that there is no conflict between science and religion.
By not speaking out, scientist-atheists are helping fuel most people's bigotry towards atheism.

I should note that this debate is peculiar to the US. Just the other day, I was talking to a prominent French biologist who was mystified with my account of the "debate" over evolution in this country. In Portugal, a Catholic country, Mário Soares was twice elected president with absolute majorities, despite being openly agnostic, something pollsters repeatedly show would be impossible in the US. Never before I came to the US did I think twice before including the word "evolution" in the answer to the question of what it is I actually work on. Perhaps people are just more outspoken in the US ("I have a problem with evolution..." is a common reply), but somehow I doubt it.

This debate reminds me of Jerry Coyne's review of a book by another of PZ Myers' fans, Richard Dawkins' (I would recommend
"A Devil's Chaplain" to any budding atheist, at least until his new book comes out):
[...] Atheism in early nineteenth-century Britain was blasphemy and thus illegal [...] Thankfully, such strictures are now much rarer, but a subtler form of repression prevails in places such as the United States. Scientist−atheists, bowing to prevalent notions of politically correct social inclusiveness, are unwilling to express their opinions for fear of offending religious sensibilities. But Dawkins makes a strong case that most religions are insidious and dangerous illusions. It's time for those who agree to stand up beside him.
Which I am now doing.

Read on