Friday, January 27, 2006

Genetics and Genesis

Let us close the week's blogging with a brief consideration of this amusing take on Science magazine's decision to spotlight progress in evolutionary biology as their scientific breakthrough of the year. It was written by Regis Nicoll and posted at Breakoint's website.

Actually, it was really only the closing paragraphs that caught my eye:

To the contrary, one could lift the basis for Mendel’s laws right off the opening chapter of Genesis, where flora and fauna are created “according to their kinds” and are bid to “be fruitful and multiply.” There we find the source of life’s origin, variety and fecundity. God creates life and endows it with the ability to adapt and proliferate in a decaying world.

But the Genesis account also informs us of an inherent limit to that adaptability. While the avian gene pool can produce everything from the Galapagos finch to the Andean condor, it will produce nothing other than a bird, “according to its kind.” And since the beginning, no evidence, fossil or otherwise, has demonstrated the contrary—“Breakthrough of the Year” notwithstanding.

If the basis for Mendel's laws is there right in the opening chapter of Genesis, one wonders why it took so long for people to formulate those laws.

Of course, the real bases for Mendel's laws are the ideas of particulate inheritance and the basic principles of probability theory. I'm afraid I must have overlooked the part of Genesis that discusses these ideas.

And I love Mr. Nicoll's take on what constitutes evidence.

A vague reference in Genesis to creatures being created according to their kind is taken as evidence for basic principles of genetics. Nicoll sees here an important statement about how on the one hand God equipped animals with the ability to adapt to their surroundings (thereby anticipating principles of microevolution that scientists would not establish for several centuries), while on the other hand He described a clear limitation on that ability. Not too shabby for half a Bible verse.

But confront him with the entirety of the fossil record, the anatomical homologies throughout the animal kingdom, the molecular and genetical similarities, the embryological evidence for common descent, the evidence from biogeography, the clear evolutionary orgins of numerous complex systems, various strategically placed retroviral scars, the entirety of mathematical population genetics and the numerous field studies of natural selection, the successful game-theoretical models of ethologists, the countless successful predictions made by biologists taking evolution as their starting point; in short, the mountains of data that pour in on a daily basis from every branch of the life sciences, and all Nicoll sees is a lot of groundless speculation and empty theorizing.

Where can I get a pair of glasses like that?

Thursday, January 26, 2006

Design's Last Stand

I finally finished Leonard Susskind's book The Cosmic Landscape: String Theory and the Illusion of Intelligent Design. Susskind's main argument is that the universe as we know it is just one small piece of a vastly larger landscape inhabited by something like 10^500 different pocket universes. The laws of physics can vary from universe to universe. If this is correct, it provides a satisfying explanation for the apparent examples of fine-tuning we find in the fundamental constants of our own universe. Why does our universe appear to be so well-suited for life? Because if it weren't we wouldn't be here to ask the question. And if you get 10^500 tries to get it right, there is bound to be some corner of the landscape where the constants will work out the right way.

I won't attempt a full review of the book. Overall I liked it quite a bit, but there are also a lot of small problems along the way. My main criticism is that as an explainer of difficult ideas from physics, Susskind can't hold a candle to Brian Greene.

But his main argument strikes me as very satisfying on two fronts. First, the main rival to Susskind's idea is that the fine-tuning of the universe represents the action of an intelligent designer. This idea is based on nothing more than people's desire that it be true. Susskind's idea, by contrast, arises naturally from modern String Theory. Susskind writes (in a discussion of the idea of Eternal Inflation):

The bubbling up of an infinity of pocket univerdses is as certain as the bubbling of an opened bottle of champagne. There are only two assumptions: the existence of a Landscape and the fact that the universe started with a very high density of energy, i.e., that it started at high altitude. The first may prove to be no assumption at all. The mathematics of String Theory seems to make the Landscape unavoidable. And the second - high energy density - is a feature of every scientific cosmology that begins with the Big Bang. (p. 304)

I also liked this:

In any case the difficulties in testing the Landscape, Eternal Inflation, and the Anthropic Principle are real, but there are many ways to test a theory. Mathematical consistency may not impress the most hard-nosed experimental physicist, but it should not be underestimated. Consistent theories that combine quantum mechanics and general relativity are far from common. Indeed, this is the reason that String Theory has so little competition. If no alternatives show up and if String Theory proves to have as varied a Landscape as it seems, then the populated Landscape will be the default position - the theory to beat, so to speak. (p. 375)

So the choice between ID and the Landscape is the choice between an explanation made up out of whole cloth for its emotional value on the one hand and an explanation that makes sense out of such data as we have on the other. String theory can hardly claim to have proven itself correct, but it has a lot going for it.

The second reason I find the Landscape appealing is that it fits so well with everything else we have learned from science over the years. Everything science has been telling us has been in the direction of downplaying the metaphysical significance of our existence. Comparative anatomy reveals to us that there is nothing in our physical make-up to distinguish us from the animals. Neuroscience can find nothing to support the idea that the mind exists separately from the brain. Evolution shows that we are just one more species among many, formed by the same processes that formed every other species. And we did not arise in a puff of smoke in one moment of creation, but rather as one end result of a billion year process; a process, no less, that gives no indication of having had us in mind. Astronomy shows that the Earth is not the center of it all. Rather we are just an unremarkable planet orbiting a nondescript star; one of countless solar systems in countless galaxies that litter the universe.

And now here comes the Landscape to show us that even our universe is not distinguished in any important way. That is why I have titled this blog entry the way that I have. The relentless march of science over the last few centuries has been paralleled by one ignominious retreat after another for the design argument. Today design advocates can only play one, last, desperate card - the fine-tuning of the constants. Upon this one puzzling phenomenon they base their conclusion that despite all the evidence to the contrary, humans are still the point of it all. Can any thoughful person seriously believe such a thing?

And is there any argument at all - I'll take one! - for rejecting the Landscape, or more generally, the megaverse? Can the other side offer any actual reason for thinking that we are not part of a vast Landscape? It certainly can't be that we have no direct evidence of the existence of other universes. After all, we have no direct evidence for the existence of God either, but ID folks are quick to assure us that it is the height of rationality to believe it nonetheless.

Susskind himself points out some unsolved problems with the Landscape, and he also points to ways we might possibly, someday, be able to experimentally test various aspects of his theories. So it is possible that String Theory and its logical correlates will eventually fail the only test that matters - fit with experimental data. But until that day comes the Landscape has to be regarded as vastly more probable than ID. Even if some people find that idea unpleasant.

Wednesday, January 25, 2006

Good Stuff from CSICOP and Free Inquiry

Be sure to have a look at Chris Mooney's excellent summary of the significance of the Dover decision:

Over the course of a lengthy trial, Jones looked closely at the scientific merits of “intelligent design”--the contention that Darwinian evolution cannot explain the biological complexity of living organisms, and that instead some form of intelligence must have created them. And in the end, the judge found ID utterly vacuous. “[ID] cannot be adjudged a valid, accepted scientific theory,” Jones wrote, “as it has failed to publish in peer-reviewed journals, engage in research and testing, and gain acceptance in the scientific community.”

ID critics have been making these same observations for years; so have leading American scientific societies. Meanwhile, investigative reporters and scholars studying the ID movement have demonstrated that it is, indeed, simply creationism reincarnated--all religion and no science. On the intellectual merits, ID was dead a long time ago. But before Judge Jones came along, it's astonishing how hard it was to get that acknowledged, unequivocally, in public discussion of the issue.

Meanwhile, the current issue of Free Inquiry has an excellent essay from Christopher Hitchens, not available online. Here's an excerpt:

It must be obvious even to the laziest observer that we now have at least a semi-official “religious test” for appointment to the Supreme Court. The test is not the one that the framers of the Constitution feared: the question of “What religion are you?” It is, rather, a test to make sure that the candidate does have a religion. In all the arguments about John Roberts, Harriet Myers, and Samuel Alito, one lement was consistent. Their religious affiliation was bannered as if it were a guarantee, in itself, of integrity. (In the case of Ms. Miers, it was the only thing that was bannered, apart from her devotion to the person of the president.)

However, along with this affirmation came a prohibition. It was, said the Right, quite outrageous to ask any furhter questions about the way in which a confessed allegiance might influence the application of the law. Any such line of inquiry would be construed as anti-Catholic (in the case of Roberts and Alito) or anti-evangelical (in the case of Miers). Rather than be accused of offending any faith-based “community,” the Democrats duly abstained from asking about abortion, creationism, and other salient issues that are well-understood to be of doctrinal as well as legal salience. Quite a neat trick, when you think of it. And now ask yourself what would happen to a nominee for the highest court who, superbly trained, educated, and qualified, announced that he or she had no belief in any deity and thought that an ethical life could be lived without religion. It must say quite a lot that we already know the answer to that question. (Emphasis in original)

MikeGene on Me on Krauze

MikeGene offers up these thoughts on my recent exchanges with Krauze.

I will only reply briefly to two of MikeGene's points. He writes:

Rosenhouse talks about lots of evolutionary theories prior to Darwin, undercutting his previous claim that it was Darwin who got people to embrace common descent. But these other evolutionary theories were speculations. And yes, some of us have used ID to speculate about biotic reality.

I talked about no such thing. Actually I talked about lots of proposed evolutionary mechanisms in the time between Darwin and the modern synthesis. This was in response to Krauze's assertion that there were no such theories. My point was that while you had to wait 60+ years between Darwin's publication of The Origin and a well-substantiated explanation for how evolution occurs, that long period of time was marked by continual research and prgress. ID can claim nothing similar.

MikeGene writes:

He first misrepresents Krauze, telling us that Krauze believes ID is an infant science “that simply requires time to blossom fully.” I didn’t see this claim in Krauze’s blog. Then, Rosenhouse wants Krauze, an obscure internet persona, to tell other people how to title their books, what to say, and what to do. But this is ridiculous. Krauze, like me, has already told ID proponents to stop trying to teach ID in schools. And while I have not seem him instruct people about the other things, I have never seen him equate ID with revolution nor equate an ID proponent with Galileo, Newton and Einstein. Neither does he argue that evolution is a dying theory. On the contrary, both Krauze and I like to explore the reality of evoluion from an ID perspective.

Let me see if I understand the situation. Krauze writes an essay for a pro-ID blog in which he argues that big ideas take time. This is offered specifically as a cautionary note to those who challenge ID on the grounds that it has produced no useful research. He then draws an analogy with the early days of evolution, and attempts to liken the current state of ID with those early days.

But I wasn't meant to conclude from this that Krauze believes that ID is a big idea that just needs time to develop?

As for the rest of it, I have explained twice already that the leading ID proponents are not arguing that they need time to develop their ideas. They are claiming to already have the goods. If Krauze is concerned that people on my side are not giving ID folks enough time to make their case, then he should also criticize Behe, Dembski and the rest for cliaming that they have already made their case.

And I am not asking Krauze to tell anyone what to do. I am asking him to criticize leading ID proponents for the things they have already done. He chides people on my side for demanding results from the ID folks. He conveniently ignores the fact that my side makes such demands solely in response to the bloated, falacious claims of ID's leading advocates.

I note that neither Krauze nor MikeGene has disputed my contention that irreducible complexity and complex specified information are worthless ideas. And both seemed bothered that I would attribute to one of them the view that the triumph of ID is a matter of time. I'm glad to hear it.

Tuesday, January 24, 2006

Chapman in Harpers

The February issue of Harpers contains a lengthy report on the big Dover trial, by Matthew Chapman. In addition to being a first-rate writer, Chapman is also a great-great-grandson of Charles Darwin.

Sadly, the article does not seem to be available online. I recommend running down to the local newsstand to pick up a copy. But there are a few places where Chapman so completely nails it that I felt compelled to transcribe a few portions. Early on we find:

Having said that, I suppose I should declare my bias at the start. My great-great-grandfather was Charles Darwin. This was not something I thought much about growing up in England. Evolution was fully accepted. Darwin was a historical figure. If I did think about my connection to him, it was only negatively. The pressure to succeed academically and the unlikelihood of doing so in comparison to my ancestor was such that I decided to turn my back on academia and pursue a course of willful ignorance. When I finally moved to Hollywood in the early Eighties, I had gone about as far as I could in that direction.

I then discovered that many Americans not only rejected the theory of evolution; they reviled it. I had come here in part because I never felt comfortable in England. I hated the snobbery and thought of America as being less weighed down by its past, more advanced. Sir Francis Drake might have been the first man to sail around the world, but it was an American who first set foot on the moon. Now here I was in the New World faced with a willful ignorance that went far beyond anything I had ever attempted.

True, I did not know much about evolution, but a quick study of the subject showed that 99 percent of scientists believed in it. Why would one doubt them? Did the pedestrian question the theory of gravity? Did the farmer who went to the doctor question his diagnosis? Why in this one area of science did nonexperts feel compelled to disagree with those who clearly knew better?

Willful ignorance. Exactly right. I've been to enough creationist conferences to know that a great many of the people in the audience eagerly want to be deceived.

Chapman's description of Behe is likewise perfect:

On the stand, Behe sat forward in his chair, earnest and concentrated. Only once did I see him lose his composure. This was when Rothschild revealed that Behe's own department at Lehigh had issued a statement saying it fully supported evolutionary theory and that:

The sole dissenter from this position, Professor Michael Behe, is a well-known proponent of intelligent design. While we respect Professor Behe's right to express his views, they are his alone and are in no way endorsed by the department. It is our collective position that intelligent design has no basis in science, has not been tested experimentally, and should not be regarded as scientific.

Behe put his hands behind his head and leaned back in his chair, smiling defiantly. He looked like a naughty child who had told his mother he'd seen a ghost and wouldn't budge from the story no matter what. I couldn't help wondering what Behe would be without intelligent design. The scientific community may despise him, but he is beloved on the other side. He gets invited to talk all over the country, and he has sold a lot of books.

The answer is that Behe would be just another competent scientist toiling away at esoteric problems only a handful of people in the world would care about. I used to feel some sympathy for ID advocates who had made sacrifices in their careers to defend their beliefs. Then at some point it dawned on me that they were laughing all the way to the bank. There is a good living to be made in the propagation of popular crankery.

One more excerpt:

Heather Geesey, a school board member who supported Bonsell and Buckingham, fell squarely into the repellant category, however, without mitigation. I found her the most terrifying of all the witnesses. A woman who seemed to think - against all evidence - that everything she did or said was astonishingly cute and funny, she clearly relished being on the same team as “President Alan,” as she referred to Bonsell, and grinned relentlessly throughout....

[ACLU attorney Vic Walczak] asked Geesey if she supported the teaching of intelligent design. “Yes.” “Because it gave a balanced view of evolution?” “Yes.” “It presented an alternative theory?” “Yes.” “And the policy talks about gaps and problems in evolution?” “Yes.” “Yes. You don't know what those gaps and problems refer to, do you?” “No.” “But it's good to teach about those gaps and problems.” “That's our mission statement, yes.” “But you have no idea what they are?” “It's not my job, no.” “Is it fair to say you didn't know much about intelligent design in October of 2004?” “Yes.” “And you didn't know much about the book Of Pandas and People either, did you. “Correct.” “So you had never participated in any discussions of the book?” “No.” “And you made no effort independently to find out about the book?” “No.”...“And no one ever explained to you what intelligent design was about?” “No.” This went on for quite a while, Geesey grinning throughout as if her ignorance was just the cutest thing, until, finally, still smiling happily, she stated that she had relied on the curriculum committee - Bill Buckingham and Alan Bonsell - to make the decision. “And do you know whether Buckingham has a background in science?” “No, I do not.” “Do you know that in fact he doesn't have a background in science?” “I don't know. He's law enforcement, so I would assume he had to take something along the way.”

So this was the genesis of the whole thing: an auto repairman appointed an OxyContin-addicted biblical literalist without a shred of knowledge to decide which books the kids should learn from, and a woman who had no curiosity about anything, even her own most deeply held beliefs, seconded the whole idea.

And unless one doubted two seemingly decent professional reporters and a host of other witnesses, she would happily lie.

Ouch. That's rather harsh, but the unbelievable arrogance of these people simply has to be exposed.

Anyway, Chapman's article is quite long and nearly perfect. Go read the whole thing!

Monday, January 23, 2006

Round Two with Krauze

Last Thursday, Krauze, of the pro-ID blog Telic Thoughts, posted this essay in which he argued that big scientific ideas require time to come to fruition. He illustrated this idea with the early days of evolutionary theory, pointing out that it was more than sixty years after Darwin published the Origin that the neo-Darwinian synthesis was developed. This was intended as a rebuttal to those who criticize ID for not producing any peer-reviewed research. ID has only been around for a decade, you see.

I replied here. I made four main points in reply.

The first was that, unlike ID, evolution had a solid foundation in empirical fact. A biologist of the late nineteenth century could be confident that the search for a mechanism of evolution was leading somewhere, because the fact of common descent had been adequately established by Darwin. ID, by contrast, has only proposed arguments that are completely false. Consequently, there is no reason to believe an ID research program wull ever get anywhere.

My second point was to correct Karuze's history. In his initial post he said that no theory of evolution had been proposed prior to the syntheiss of the thirties and forties. I pointed out that that was not correct.

My third point was that ID has not evolved at all in the decade or so that it has been around. This was in response to Krauze's contention that ID was developing in a manner similar to how evolution developed in its early days.

Finally, my fourth point was that people on my side would be perfectly happy to give ID proponents all the time they want. The trouble is, the leading ID proponents do not act like people who simply want time to develop their ideas. Instead, they run around claiming that they already have the goods, that they have made discoveries that should place them right along Galileo and Newton, and that they have revolutionized science.

Krauze replied here. Since he seems to have missed every important point, I thought I'd take another stab at it.

Krauze begins by stating that the title of my blog entry, “Is ID Just a Matter of Time?” overstated his point. He was not suggesting that ID was just a matter of time, rather his point was simply that new sciences take time to develop. He writes:

I think there are some subtle clues that point to intelligent design, but when dealing with natural history, there’s always a possibility that a closer look reveals another picture. If it turns out that there’s nothing to intelligent design, all the time in the world won’t make a difference. The point in my post was much more subtle: Sciences don’t spring up fully formed, as Athena from Zeus’ forehead. Critics should keep this in mind when demanding to see intelligent design turned into a research program.

Of course, there's no controversy that new branches of science take time to come to fruition. But the demand that ID advocates produce some significant reasearch in defense of their claims is merely a response to the conduct of its leading proponents. People like William Dembski and Michael Behe claim to already have the goods. I think it's perfectly reasonable for people on my side to point out that, actually, they don't.

We will consider this further below. But let's turn now to Krauze's bullet point replies (to my bullet-point criticisms):

Rosenhouse claims that intelligent design rests entirely on the pillars of irreducible complexity and complex specified information: “Nothing the ID folks build upon such a foundation will ever produce anything but poisonous fruit.” I don’t presume to have Rosenhouse’s gift to see into the future, so let’s instead look at the past. As I said in the comments, we have yet to see a work comparable to Darwin’s Origin of the Species on intelligent design. How was the state of evolution prior to the publication of Darwin’s great work? As Mike explained, the road was paved by Robert Chambers’ Vestiges of the Natural History of Creation. Michael Ruse describes it as “the Big Mac of popular science”, in that it was “very tasty, very filling, very accessible, and (in the opinion of the authorities) of very dubious value to one’s health. Vestiges was the archetype of pseudoscience.” (P. 48) The archetype of pseudoscience. Yet on this foundation a prosperous research program was eventually built.

I note that Krauze does not dispute my contention that arguments based on irreducible complexity or complex specified information are hopelessly flawed. Instead he points to Robert Chambers' Vestiges of the Natural History of Creation and identifies it as the rotten foundation that nonetheless led to fruitful research in evolution.

Sadly, that's ridiculous. Chambers' work has some historical significance today, but it was rightly dismissed by the scientists of the time, including Darwin. It did not form the foundation of any important scientific research. Modern evolutionary theory begins with Darwin, and his work was a solid foundation indeed for a new science.

Krauze claims that ID has not yet produced its own Origin. I certainly agree, but I'm surprised that an ID supporter would make that claim. I was under the impression that Dembski's The Design Inference and No Free Lunch, and Behe's Darwin's Black Box were supposed to be precisely those seminal works. In fact, in this paragraph Krauze seems to be saying that the combined works of ID proponents to date is at the level of Chambers' work. And since he is happy to describe Chambers' work as the archetype of pseudoscience...

In reply to my point that there were a great many proposed theories for evolution's mechanism prior to the synthesis, Karuaze writes:

Rosenhouse claims that it’s “manifestly untrue … that there were no proposed theories of evolution prior to the synthesis”, citing Lamarckism and mutationism (the proposition that evolution was driven solely by mutations, with no input from natural selection). Here’s the definition of a “theory” from the National Academy of Science, embraced by ID critics at Dover:

Theory: In science, a well-substantiated explanation of some aspect of the natural world that can incorporate facts, laws, inferences, and tested hypotheses.

Although I agree that there were some observations that were seen as providing support for Lamarckism and mutationism, I disagree that either of those were “well-substantiated”. In fact, they would seem to fit better under NAS’ definition of a hypothesis (“A tentative statement about the natural world leading to deductions that can be tested”).

In my original blog entry I made a clear distinction between a well-developed theory and a proposed theory. Krauze here argues that instead of “proposed theory” I should have said “hypothesis.” Fine. The fact remains that there were many possible meachanisms of evolution in the late nineteenth and early twentieth centuries and all could claim a considerable amount of support. And these hypotheses led to clear avenues of research. ID, alas, does not even have a hypothesis. It has nothing at all beyond falacious logic and distortions of modern science. This is what Krauze will have to come to terms with if he wants to draw any comparisons between modern ID and the early days of evolution.

Krauze next writes:

According to Rosenhouse, “The idea that ID has evolved over the years is nonsense. ID is today what it has always been: A political and legal strategy for uniting various schools of creationism under one banner acceptable to all.” We’ll ignore the Wedge-centrism, and get straight to the point. Ruse explains how evolution became a professional science by shedding its metaphysical baggage of progressionism, and the teleological approach has also evolved, shedding its commitment to religious apologetic. Young-earth creationism was wedded to a particular interpretation of the first chapters of Genesis, whereas even agnostics like me can contemplate intelligent design. Furthermore, ID has made the integration of evolution and design possible, something that could never have happened with young-earth creationism.

It is completely false that Young-Earth creationism is wedded to a particular interpretation of Genesis. Not if you take the Young-Earth proponents at their word anyway. They claim that all of their major conclusions (young Earth, sudden and simultaneous creation of all kinds, global flood) are justified by the best available scientific data. They are also happy to announce their faith in the Bible, and to trumpet the consonance of the scientific data with the story in Genesis. But the fact remains that scientific creationism was supposed to be a purely scientific enterprise.

More to the point, it's pure fantasy to say that ID has made the integration of evolution and design possible. To the extent that evolution and design can be integrated, it was theistic evolution that did the integrating, and that integration happened long ago. A theory in which God is constantly intervening to direct the development of life over time is not evolution. It is creationism. The theory in which God set up the initial conidtions of the universe and then allowed them to play out over the course of natural history is theistic evolution. Krauze will have to explain how, exactly, ID has made possible the integration of anything.

As for Ruse, I'd be surprised if he can really back up his claim that it was the shedding of progressionism that led to progress in evolution in the early twentieth century. There are certainly simpler explanations for evolution's sudden leap forward: progress in genetics, the quantitative approach pioneered by Fisher, the fact that all branches of science were becoming larger and more professional in the twentieth century...

Finally, Krauze writes:

Now, it just so happened that I have voiced my disapproval of teaching intelligent design in schools. But it really doesn’t matter, as I fail to see how me performing the tasks on Rosenhouse’s laundry list influences the matter at hand: In my post, I pointed out an aspect of reality. Whether Rosenhouse chooses to acknowledge this aspect or not is entirely up to himself.

Oh, please. Krauze's essay was intended as a cautionary tale about why it is unreasonable for critics of ID to demand too much from ID proponents at this early stage of its development. In that context it was perfectly reasonable for me to point out that the demands coming from people on my side are offered entirely as counters to rival claims made by ID proponents. It is the Behes and Dembskis of the world who claim they have the goods. My side is merely asking them to back that up with something other than their standard gobbledygook.

Krauze's initial post made a trivial point about reality (that big ideas take time), implied a fantasy (that ID has promise as a research program) and backed up the implication with a lot of spurious history (that there is any important parallel between the early days of evolution and modern ID). His reply disputes neither my claim that modern ID arguments are nonsense nor my claim that ID is nothing but a political movement (ignoring an argument is not the same as disputing it). He clearly implied that modern ID is at the level of Chambers' Vestiges, which he describes as a work of pseudoscience. I suspect Behe and Dembski are having a Get Off My Side moment right now.