The “God of the gaps” just got squeezed out of yet another dwelling place.

This centuries-old argument for the existence of God basically goes like this. There is no way to explain (fill in the blank: lightning . . . volcanoes . . . the creation of the sun and planets . . . the origin of species . . . ) without invoking a supernatural hand; science alone falls short. Hence there must be a God. The trouble, of course, is that science has this annoying habit of eventually accounting for such mysteries through natural, not supernatural, processes. And that leaves God one less explanatory gap to inhabit.

A current favorite refuge for those who deny that mutation and natural selection (also known as Darwinian evolution) are enough to explain the diversity of life on Earth is that highly-complicated biological structures cannot have been produced natrually. It’s basically a mouse-trap argument. A complicated structure such as, say, a receptor on a cell surface, is made of numerous components, just as a mouse trap is. No single component is of much use, just as the wooden base of a mouse trap is not much use without the bar and the spring and the other components. Since evolution confers survival only on useful components, continues the argument, it strains credulity to think that the individual parts of a receptor would have just coincidentally emerged from mutations at exactly the same time to come together in a useful structure. More likely, each component emerged, found nothing to do, and was eliminated by natural selection. Want a receptor? Ask God to make it.

Not so, say scientists who have determined, for the first time, how an ancient protein evolved step by step, refuting even more strongly a key element of the “intelligent design” argument.

In 2006 biologists reconstructed a receptor that last existed on earth 450 million years ago. Now the researchers have determined the structure of this recovered ancestor and figured out that specific mutations that, step by step, produced the modern-day glucocorticoid receptor, which allows cells to respond to the stress-hormone cortisol and therefore regulates stress. Says Joe Thornton, an evolutionary biologist at the University of Oregon who led both last year’s project and this one, “We were able to see the precise mechanisms by which evolution molded a tiny molecular machine at the atomic level, and to reconstruct the order of events by which history unfolded.” The study is being published today online in Science Express, the rapid-communication version of the journal Science.

The scientists found that just seven mutations changed the ancestral receptor gene into the gene that makes today’s glucocorticoid receptor. Some mutations would have wrecked the protein unless other mutations were in place first; this allowed the scientists to infer the sequence in which the mutations occurred. One crucial mutation resculpted a big section of the protein in a way that re-positioned a cluster of atoms; a second mutation in this region then tightened up the receptor’s embrace of cortisol. Other mutations buttressed other regions of the protein so they could withstand this remodeling. “Permissive mutations stabilized specific structural elements, allowing them to tolerate later destabilizing mutations that conferred a new function,” the authors write.

The result is “an unprecedentedly detailed view into the deep past of our genes,” Thornton told me. The discovery “provides the first fully mechanistic account of how a gene [for the ancestral receptor] evolved a new function [for the modern-day glucocorticoid receptor]. By comparing the ancestral structure to the modern structures that derived from it, we were able to see the mechanisms by which present-day receptors evolved.”

Thornton is not shy about his paper’s relevance to the unending evolution wars. The discovery, he says, “shows precisely how a complex phenotype evolved through a sequence of neutral and adaptive substitutions,” including those permissive mutations that do not themselves confer a selective advantage but pave the way for later mutations that do. A new book by the intelligent-design proponent Michael Behe argues that complex structures cannot evolve if they require two or more mutations. The new discovery shows that permissive mutations make this multi-step evolution perfectly possible—and in the case of the glucocorticoid receptor, a fact.

Chimpanzees and other great apes get all the good press when it comes to the intelligence of non-human animals. Chimps use tools and teach their offspring to do so, for instance, whether it's twirling a stick into a termite nest to extract hors d'oeuvres or selecting just the right rock to crack open a tough nut, as researchers keep discovering.

Scientists are reporting today that New Caledonian crows are no slouches when it comes to sophisticated tool use. As they report online in the journal Current Biology, the crows can spontaneously combine two tools to get a snack--and in a way that suggests they solved the problem not by trial and error, but by reasoning through analogy. That is, the crows were able to see that a novel situation was essentially the same as one they'd encountered before.

"Evidence suggests that, from the earliest human stone tools, analogical reasoning has been at the core of human innovation," Russell Gray of the University of Auckland, who led the study, said in a statement. "This hallmark of human intelligence may also be at work in both the great apes and New Caledonian crows."

In the study, the researchers put food in a hole that was unreachable unaided. They also left a stick lying around, but it was also too short to reach the food. They left one more prop: a long stick in a "toolbox." This stick was long enough to reach the food--but it, too, was out of reach. No problem. The crows used the short stick to get the long tool out of the box, then used the long stick to get the food. In fact, six out of seven crows immediately tried to get the long stick with the short stick; only one dunce did the bird-brained thing of trying to get the food directly with the short stick and realizing that wouldn't work, and that he had to use the short stick to get the long stick.

Next challenge: food still at the bottom of a deep hole, small stick inside the toolbox and long stick within the crows' reach.