Below is a slightly cleaned up version of my remarks this past Saturday during the FreedomFest 2008 debate: “Is There Scientific Evidence for Intelligent Design in Nature?” The debate took place between Discovery Institute intelligent design proponents Stephen Meyer and George Gilder and evolutionary biology proponents Michael Shermer, the executive director of the Skeptic Society, and me.

Let me begin by acknowledging that the Discovery Institute website states: "Unlike creationism, the scientific theory of intelligent design is agnostic regarding the source of design and has no commitment to defending Genesis, the Bible or any other sacred text." So far so good.

Near the end of the silly new anti-evolution film, Expelled: No Intelligence Allowed—in which fellow panelist Steve Meyer appeared—host Ben Stein asks Richard Dawkins, who is arguably the best-known living evolutionary biologist on the planet, if he could think of any circumstances under which intelligent design might have occurred. Incautiously, Dawkins brings up the idea that aliens might have seeded life on earth; so-called directed panspermia. This idea was suggested by biologists Francis Crick and Leslie Orgel back in the 1970s. In the film, Stein acts like this is a great "gotcha," like it's the silliest thing he's ever heard. Of course, the irony is that this is precisely what proponents of intelligent design are claiming—that a higher intelligence has repeatedly created life on earth.

So, since our esteemed opponents are agnostic with regard to the "source of design," and because intelligent design cannot rule out the hypothesis that super-intelligent purple space squids are not the "source of design" of life on earth, I will provisionally accept that hypothesis for the remainder of my talk.

As I understand it, intelligent design proponents—such as our distinguished Discovery Institute panelists here—fully accept the fact that the earth is around 4.5 billion years old and that some form of life has existed on earth for about 3 billion or so years. If that is the case, it would seem the record shows that the intelligent designers—which I am hypothesizing are super-intelligent purple space squids—evidently spent more than 2 billion years tinkering with single-cell algae and bacteria before they got around to creating multi-cellular species. Do intelligent design proponents have a theory to explain that? Were the space squid creators just lazy?

In addition, the record clearly shows that when more complex forms of life were created by super-intelligent purple space squids, they apparently arranged their creations in a specific order. Why did the purple space squids arrange the fossils in a sequence in which fish appear before amphibians which appear before reptiles which appear before mammals? And why did the purple space squids arrange 390 million years ago for the first amphibians to resemble Crossopterygian fish that were also alive at that time? These first amphibians had such characteristics as internal gills, fish-like skull bones, and—interestingly—eight digits just as the Crossopterygian fish did. Apparently our intelligent purple space squid creators (or whoever) found eight digits displeasing, and simply eliminated the extra three digits after they killed off the early amphibians and individually created thousands of later species of amphibians with only the now standard five digits.

Interestingly, the fossils of early reptiles—which the purple space aliens apparently created around 300 million years ago—were still rather amphibian-like in their overall structure. Their legs were splayed out sideways, bellies just barely lifted from the ground, tails dragging behind—in short, a salamander-like gait. Eventually, the creator aliens chose to produce tens of thousands of new reptile species which differed considerably from the old sticks-in-the-mud amphibians. Among their creations were much grander reptiles such as the impressively armor-plated stegosaurus (145 million years ago), and the massive apatosaurus (formerly brontosaurus), which measured 75 feet long and weighed 25 tons, and of course the largest land predator ever known, the 7-ton, 43-foot-long tyrannosaurus rex (65 million years ago).

Another puzzle—why is it that the super-intelligent purple space squid creators made the earliest mammals share so many characteristics with the therapsid reptile species that lived alongside them? Interestingly, researchers have now pieced together how the purple space squid created the mammalian inner ear over a period of 70 million years from reptilian jaw bones.

Starting with the mammal-like reptile Sphenacodon 270 million years, ago, purple space squid creators evidently spent the next 70 million years tinkering with the hinged reptilian jawbones. The squids shrank the bones, moving them back toward the ear holes in the skulls of some of the thousands of increasingly mammal-like species that squids were busy individually creating. Eventually the purple space squid creators ended up after 70 million years making a tiny mammalian-type critter called Hadrocodium which had a single jawbone (like mammals do today) and three middle-ear bones (like mammals do today). I am sure that intelligent design proponents will shortly explain why apparently intelligent purple space squid creators (or whatever creators they prefer) used this pathway for creating inner ear bones. Since, by definition, the purple space squids are intelligent and should know what they want in advance—what ID proponents call "complex specified information"—why did they piddle around so long and why not instead just create species with inner ear bones without generating a series of creatures through slow intermediate steps?

Which brings me to an even bigger puzzle—why, after going to all the trouble to finally populate the earth with millions of magnificent species, did the purple space squid creators (or whichever creator design proponents prefer) apparently allow either a five-mile wide asteroid to hit the Earth, or a huge outbreak of volcanic eruptions, or both, to wipe out at least 50 percent of the species—including the dinosaurs—living 65 million years ago? In fact, something worse occurred 250 million years ago when some event, possibly also an asteroid strike, destroyed 95 percent of all living species.

Of course, there is an alternative hypothesis that intelligent design proponents—such as the distinguished representatives from the Discovery Institute on the panel here—might fruitfully want to explore. That hypothesis is that the purple space alien squid creators actually caused asteroids to strike the earth in order to wipe the biological and ecological slate clean so that they could start over.

Perhaps like a thrifty artist who whites out an earlier painting on a canvas in order to create a masterpiece, the purple space squids destroyed most of life on earth in order to make room for new creations. Interestingly, the creator squids seem subject to a strange kind of creative conservatism. Their new, post-extinction, individually created species looked very much like earlier created species that apparently survived the massive extinction events. What hypothesis do intelligent design proponents offer to explain this interesting observation of creative conservatism? Purple space squids appear to be progressive creationists: They bring species into existence over and over again, forming each species so that it bears a striking resemblance to a species that has just gone extinct.

I have been using the phrase individually created species throughout my talk. Why? Because intelligent design proponents—such as Steve Meyer and George Gilder here on the panel—insist that micro-evolution, which I take to mean any evolutionary change below the level of species, cannot lead to macroevolution, which I take to mean any evolutionary change at or above the level of species—which means at least the splitting of a species into two new species.

Since micro-evolution, according to ID proponents such as Steve and George, cannot lead to the creation of new species, then the purple space squid creators (or whomever) must create each new species individually. Trying to figure out how super-intelligent space alien creators go about creating individual species would be a fascinating question for intelligent design researchers to look into. Do the squid creators somehow tweak genes while embryos are developing in their eggs or in their mother's wombs? Or do they work at the level of sperm and eggs before conception? Would the space squid creators use radiation to do this? Or chemical mutations? Or errors in genetic transcription? What's their favorite method for producing new species? And most crucially, how would whatever processes the purple space squid have used to create tens of millions of new species over billions of years differ from the natural processes suggested by evolutionary biology?

And there is yet another puzzle. Conservative super-intelligent purple space squid creators apparently recycle genes over and over again in new species. Biologists have found that many genes are like Animal Kingdom cassettes or Lego blocks: They can be mixed and matched across vastly different species. For example, biologists have shown that a gene crucial to building a fruit fly's eye—the Pax-6 gene—will trigger eye development in a frog and a mouse.

In addition, now that both the human and mouse genomes have been sequenced, researchers know that 99 percent of mouse genes are similar to those found in humans. Even more amazingly, 96 percent of the genes in both mice and men are present in the same order on their different genomes. Why would this be? A fascinating question for intelligent design researchers to answer is what constrains the super-intelligent purple space squid creators (or any other intelligent creator) to use the same genes over and over again in millions of species?

And here's another minor curiosity: Why did the purple space squids design humans so that we need to eat foods like oranges that provide us with vitamin C? Without vitamin C people die of the deficiency disease scurvy. It turns out that the super-intelligent squids created nearly all other mammals so that they have genes—including the GLO gene—that synthesize this vitamin in their livers. Biologists have discovered that when the purple space squids created us, they for some reason left a broken remnant of the GLO gene in our genomes. There is one group of mammals that share our inability to make vitamin C —orangutans, gorillas, chimpanzees, and macques all have broken GLO genes. Even more interestingly, biologists have found that gorillas and chimpanzees have exactly the same errors in their GLO genes that people do. So why did the purple space squids create those species along with us with exactly the same errors so that they and we could not produce vitamin C?

One other consideration: Are the intelligent designers—the super-intelligent purple space squids—finished creating new species? Are they resting from their creative labors for now? What evidence would show that intelligent designers are still at work creating new species around us? And how would we know?

The point of the foregoing is that intelligent design proponents do not have good answers to the questions I have posed. But evolutionary biologists do. In his new book, Only a Theory: Evolution and the Battle for America's Soul, Brown University biologist Kenenth Miller argues, "Design rests ultimately on the claim of ignorance, upon the hope that science cannot show evolution to be capable of producing complex organs, assemblies of molecules, or novel biological information. If evolution cannot achieve that, the argument goes, then design must be the answer.

"Since any field of biology, including evolution, is filled with unsolved problems, intelligent design can be invoked as the default explanation for any one of them," adds Miller. "The hypothesis of design is compatible with any conceivable data, makes no testable predictions, and suggests no new avenues of research."

Ultimately, the intelligent design hypothesis just leaves everything up to the ineffable whims of the moral equivalent of super-intelligent purple space squids or whoever else is the alleged "source of design."

One addendum: During his presentations, Gilder claimed several times that evolutionary biology somehow undermined the notions of freedom and economics. He just couldn't seem to get his head around the concept of bottom-up order. This so frustrated me that I eventually quipped, "Intelligent design is to evolutionary biology what socialism is to free-market economics."

Ronald Bailey is reason's science correspondent. His book Liberation Biology: The Scientific and Moral Case for the Biotech Revolution is now available from Prometheus Books.

Disclosure: I want to gratefully confess that I took many of the arguments I used in the debate from Kenneth Miller's interesting new book.