Proponents of intelligent design (ID) assert that certain complex biological systems could not emerge from a gradual evolutionary process. They argue instead that such structures are best explained via the deliberate action of an unspecified intelligent designer.

Few scientists endorse this conclusion, and they have good reasons for being skeptical. They understand that the prolonged action of natural selection can be expected to leave traces behind in the structure of modern organisms. And when scientists go looking for those traces they invariably find them in droves.

Recall that natural selection operates by preserving small, favorable variations that occur naturally in any population of organisms. Over time these variations accumulate to the point that large-scale change is the result. This implies that natural selection works by modifying structures already present in the organism. It does not craft new, complex systems from scratch.

This observation is crucial in distinguishing between those systems that could have been crafted by selection and those that could not have been. If we find that a particular organism possesses a complex system made from parts wholly distinct from anything to be found in the organism's closest evolutionary cousins, it will be difficult to explain that system via selection. But if we find that the system appears to be cobbled together from parts that were readily available, then natural selection remains a strong candidate.

Charles Darwin employed this principle in his studies of the complex systems used by orchids to attract pollinating insects. He discovered that these contrivances, as he called them, were indeed fashioned out of modified versions of parts present in closely related flowers. Stephen Jay Gould famously used the panda's "thumb" to illustrate the same principle. The panda possesses a sixth digit on its front paws that it uses to strip the leaves off of bamboo. This digit is not a true opposable thumb like that possessed by apes and humans. If it were, we would have a strong argument against natural selection in this case, since the panda's closest relatives have nothing like such a thumb. In reality, however, the panda's thumb is cobbled together from alterations in the bones found in the paws of other bears. Since examples like these are ubiquitous in nature we see that natural selection passes its first big test.

This principle extends to the biochemical realm as well. In his book Finding Darwin's God, cell biologist Kenneth Miller offers the following thoughts on the structure of the vertebrate blood clotting cascade:

The striking thing about this particular Rube Goldberg machine is how similar most of its parts are. Nearly all of the regulatory molecules belong to a single class of protein-cutting enzymes known as "serine proteases," and that...is the clue to understanding the system's evolution beginning with organisms that lacked a protein-based clotting system.

From this starting point Miller develops a scenario for the evolution of the modern blood clotting system from simple precursors found in invertebrates. An important step in his scenario involves a series of gene duplications, followed by the divergence of the duplicate copies. This explains why the individual proteins in the clotting systems are so similar. Miller goes on to describe ways of testing his scenario:

If the clotting cascade really evolved the way I have suggested, the clotting enzymes would have to be near-duplicates of a pancreatic enzyme and of each other. As it turns out, they are. Not only is thrombin homologous to trypsin, a pancreatic serine protease, but the six clotting proteases...share extensive homology as well. This is consistent with the notion that they were formed by gene duplication, just as suggested. But there is more to it than that. We could take one organism-humans for example -- and construct a branching tree based on the relative degrees of similarity and difference between each of the clotting proteases. Now, if the gene duplications that produced the clotting cascade occurred long ago in an ancestral vertebrate, we should be able to take any other vertebrate and construct a similar tree in which the relationships between the clotting proteases match the relationships between the human proteases. This is a powerful test for our scheme because it requires that sequences still undiscovered should match a particular pattern. And...it is also a test that evolution passes in one organism after another.

Many other tests and predictions can be imposed on the scheme as well...If the modern fibrinogen gene really was recruited from a duplicated ancestral gene, one that had nothing to do with blood clotting, then we ought to be able to find a fibrinogen-like gene in an animal that does not possess the vertebrate clotting pathway.

Miller goes on to describe the discovery of such a gene in a sea cucumber, thereby producing another piece of evidence for his proposed scenario.

From this description a second principle emerges. Not only does every complex system studied in detail give the appearance of a Rube Goldberg machine cobbled together from available parts, but also evolutionary scenarios for their formation invariably lead to further testable predictions.

Contrary to the protestations of anti-evolutionists, insight into the evolutionary histories of complex systems seems to come out of laboratories on almost a daily basis. For example, the March 18, 2005 issue of the professional journal Science contained a research article on the evolution of swim bladders in fish. The accompanying commentary described the article's findings as follows:

Scuba divers wear air-filled dive vests to move up and down in the water column. Researchers have now used the fish family tree to piece together how the piscine equivalent, an internal air sac called a swim bladder, evolved a complex capillary network and special hemoglobin molecule to inflate it with oxygen. Moreover, according to the proposal presented ... by Michael Berenbrink of the University of Liverpool, United Kingdom, and his colleagues, these innovations helped fish expand their species diversity. "The scenario developed presents a fascinating picture of the evolution and radiation of fish," says Bernd Pelster, an animal physiologist at the University of Innsbruck, Austria.

Shortly thereafter the March 2005 issue of the journal Genome Research published the results of recent research into the evolution of snake venom. In both cases the scientists applied logic similar to what Miller described, and they were rewarded with success in finding plausible evolutionary scenarios that were consistent with the copious data they had collected. Surely such consistent success in applying the logic of natural selection to modern complex systems counts as evidence in selection's favor.

Still, the evidence in these cases is inevitably circumstantial. It could hardly be otherwise considering that the systems whose formation we are trying to explain evolved long ago. With that in mind we might ask whether there is some "in principle" reason for rejecting natural selection as a plausible explanation. In other words, can we find some theoretical reason why natural selection is fundamentally inadequate to explain complex biological systems?

The main argument made by ID proponents in this regard is based on the idea of irreducible complexity. Michael Behe coined this term in his 1996 book Darwin's Black Box. He defined a system to be irreducibly complex if it consisted of several, well-matched parts each of which was essential for the system to function properly. It was his assertion that such a system could not evolve by gradual accretion, because any intermediate structures would have to be nonfunctional. Since there are plenty of biological systems that fit Behe's definition, the conclusion is that there are complex biological systems whose formation simply can not be attributed to prolonged selection, regardless of any other evidence.

If Behe were right, the observation of irreducible complexity would instantly trump whatever circumstantial evidence I could provide in favor of natural selection. But he is not right. Immediately after Behe's book hit the stores, scientists took up the thankless task of stating the obvious: irreducible complexity in the present tells us nothing about functional precursors in the past. This has been demonstrated in two ways: (1) by describing general schemes, based solely on known biological processes, whereby an irreducibly complex system could arise gradually (for example, irreducible complexity could result from the reduction in redundancy that occurs when subsequent mutations cause the two copies of a duplicated gene to diverge); (2) by using these schemes to produce scenarios for explaining specific biochemical machines.

In response to these observations ID proponents generally respond that the various schemes referred to in point (1) above are mere guesses, while the scenarios in point two (2) invariably lack sufficient detail to be considered definitive. Both of these objections miss the point. It is the ID proponents who are making sweeping assertions about what is possible and what is not. Scientists are simply offering an "in principle" response to an "in principle" argument. And since scientists base their scenarios solely on familiar processes, it is the ID folks who have to explain why irreducible complexity is something people should get worked up over.

ID proponents make other "in principle" arguments against natural selection, variously based on probability theory or on selection's lack of foresight, but all such arguments are completely without merit. The determination that a given system could not have evolved gradually can only be based on a detailed understanding of the structure and function of that system, not on any abstract, armchair reasoning.

There are further lines of evidence we could cite in support of natural selection's importance, but they will have to wait for future columns. Let us instead consider a different question: Circumstantial evidence notwithstanding, does ID provide a better explanation than natural selection for complex biological systems?

In considering that possibility we should begin with the observation that ID arguments are always indirect. ID proponents never argue, "We observe X. Therefore, ID." Instead they argue, "We observe X. X cannot plausibly be explained naturalistically. Therefore, ID." Since we have already seen that prolonged natural selection is capable both in theory and practice of explaining complex systems, the design hypothesis receives a serious blow right from the start.

But there is a graver objection. Design proponents try to present ID as a simple extrapolation from the actions of known intelligent agents. William Dembski expresses the argument this way in his book The Design Revolution:

It is well known that intelligence produces irreducibly complex systems. (For example, humans regularly produce machines that exhibit irreducible complexity.) Intelligence is thus known to be causally adequate to bring about irreducible complexity.

This is rather like claiming that mountains are evidence for the existence of giant moles. After all, molehills are something that moles are known to produce, and what is a mountain if not a giant molehill?

The fact is that the feats performed by the designer in ID are orders of magnitude beyond anything known intelligent agents are capable of. Human beings may possess the highest level of intelligence in the known universe, but we have no idea how to jigger with an organism's genome to bring a blood clotting cascade or a swim bladder into existence. And those are among the simpler things our hypothetical designer is called upon to do. Ask a scientist to create life, manipulate fundamental constants of the universe, or bring whole worlds into being, and he will stare at you helplessly. The fact is, if we were only extrapolating from known causes we would have to conclude that intelligence is fundamentally incapable of accomplishing what is being asked of it.

So the situation is this: On the one had we find that there is no reason in theory why evolution cannot account for complex systems. Furthermore, every one of the numerous complex systems studied in detail has just the structure it ought to have if it originated via known mechanisms. Scientists use this fact to formulate useful hypotheses about the history of these systems, and can claim one explanatory success after another as a result. For scientists the hypothesis that a system evolved by natural selection is the beginning, not the end, of their investigation.

On the other hand we find that ID proponents find it more plausible to invent out of whole cloth a designer capable of performing feats that can only be described as magical. They have not a single explanatory success to their credit, and have given no reason to believe their hypotheses can ever lead to anything useful. For ID proponents the assertion of design is the end of the investigation.

Which explanation do you think scientists should embrace?