First off, I want to make clear I'm not attacking evolution and natural selection for religious reasons. I am not a creationist or an intelligent design enthusuiast. In fact, I am a materialist and an atheist, trained in the physical sciences.

Second, I do not reject the concept of natural selection, species variation through time, and the knowledge we have gained from biology, geology, molecular biology and genetics. There is no doubt that these processes occur in nature and that they operate according to the principles first outlined by Darwin and expanded and developed by generations of biologists since. I also recognize these principles are pretty well accepted and with only a few exceptions in detail, are part of a general consensus among scientists. Having said that, the more I think about it , the more I'm convinced we're missing something.

Consider the classic case of one-trait evolution: a rabbit lives in an area where it is getting colder. Every year there is more snow, it comes earlier and stays on the ground longer. The beast has a normal variation in hair color, from dark to light, so those with light hair are favored because of the winter camouflage, and before long, all the population is snowy white because the others tend to get taken by predators more easily. Perfectly staightforward, it''s hard to see how it couldn't happen.

But a mammal is not a creature with only one trait, it has thousands of cold-weather adaptations being selected for simultaneously, from snowshoe feet to extra fat layers, to the ability to digest dead vegetation, all the way down to the molecular level. How do all of these traits evolve at the same time without interfering with or diluting each other? And recall, mammals only have a handful off pups in a litter, they mate only once a year, and are not available in large populations like insects. Even over long periods of time, how do you get such exquisitely adapted creatures when the number of genetic encounters are so limited. Even species of solitary animals with small populations and low birth rates are highly fitted to their environments. How does this happen? How are thousands, pehaps millions of anatomical and physiological traits selected for simultaneously in say, giraffes? There just aren't that many of them, they don't mate that often, and they don't have large numbers of offspring. How do you get the numbers to support the statistics you need for the species to evolve such a specialized lifestyle?

Another puzzle I feel is difficult to explain with traditional natural selection is organisms with alternating lifestyles, like ferns and Cnidarians (Coelenterates, for you old-timers). How do you evolve the different castes of social insects, where several body plans coexist at the same time in the queen's DNA, and only somatic conditions determine which one will be produced? Many creatures have multiple body plans (males and females differ considerably), others have several larval stages, like most invertebrates, and what about symbionts and parasites, who have to evolve in parallel fashion with their hosts. And what about real wierdos like colonial stromatolites and slime molds evolve? I find it difficut to see how our snow rabbit model of natural selection works in these cases. In fact, as the number of traits being modified goes up, the amount of generations needed to produce an overall adapted organism should increase geometrically, if not exponentially.

How can a glacier scrape a continent down to bedrock and only a few thousand years later highly complex ecosytems have established themselves, with millions of species perfectly adapted to the new environment? I think we're missing something really important.