The area of science that seems to cause the most discomfort for fundamentalists is evolution. The simple fact of the matter, however, is that evolution, including speciation or macro-evolution, has been directly observed. See The Talk.Origins Archive for a discussion of evolutionary biology.

Physics describes the universe in terms of relatively simple concepts (general relativity, quantum field theory, etc.; see The Physics Web). As we learn more and more physics, the structure of the universe, in some sense, seems more and more simple. But theists postulate that an infinitely complex god is necessary to explain the universe. (The conscious human mind is the most complex thing that we know about. Since God is suppose to be omniscient, he must be infinitely more complex than the human mind.) The theists' position just does not make any sense. It replaces the question "How did our simple universe get here?" with the much more difficult question "How did an infinitely complex god get here?". The principle of Ockham's Razor (don't postulate the existence of anything more than what's needed for explanation) cuts God out of the picture. To paraphrase Einstein, the more a person understands about the workings of the universe, the less likely he or she is to believe in gods. That's why 93% of the members of the National Academy of Sciences (USA) are nontheists. (The 93% figure comes from Edward J. Larson and Larry Witham: "Leading Scientists Still Reject God." Nature, 1998; 394, 313.)

There will always be unknowns in science. Many theists see these gaps in our knowledge as reasons for believing in God. The argument usually goes something like this: "We don't understand how the universe got here, therefore God must have created it." (This is today's version of the argument, years ago it was "We don't understand thunder, therefore the thunder god must have done it.") But is saying "God did it" really an explanation? No, it isn't. An explanation is a description of something we don't currently understand in terms that we do understand. Theists will usually admit that they don't understand their god, saying things like "God works in mysterious ways". Well if we don't understand how God does something, then "God did it" is just about meaningless. We will never have all the answers, but postulating an infinite god and pretending that this provides the answers is just irrational. It is much better to have the intellectual integrity to simply admit that we don't yet know.

A fairly common example of the god of the gaps fallacy described above is the argument that since we don't understand where the dimensionless constants in the equations of physics come from, and since carbon based life could not have evolved if some of the parameters varied by a small amount, a god must have chosen the parameters to produce human life. In addition to being an example of the god of the gaps fallacy, this argument is wrong for several other reasons. For example, it assumes that the dimensionless parameters are fundamentally arbitrary. In other words, it assumes that the parameters cannot be predicted with a more fundamental theory. But in string theory, for example, all dimensionless parameters are expected to be predictable. Several other problems with the argument are discussed in Cosmythology and Is God in the Details?.

For more information on science and religion, see the Secular Web's collection of Science and Religion Essays.