One of the major flaws in the arguments of anti-evolution writers is the conflation of the issue of prebiotic or pre-cellular evolution, and modern evolutionary theory. An example can be found in the comments of the creationist-sympathizer Judge Carnes, who demonstrated his complete ignorance of evolutionary biology with the following statement (at the LA Times, also check this post at the Panda's Thumb):
"From nonlife to life is the greatest gap in scientific theory. There is less evidence supporting it than there is for other theories. It sounds to me like evolution is more vulnerable and deserves more critical thinking..."
Leaving aside the fact that it's absurd for someone with no biology training to assume that what he sees as gaps or problems in a complex scientific theory are due to a lack of critical thinking by professional scientists and not his own ignorance, let's focus on this conflation of origins of life research and evolutionary biology, which is one of the most common misconceptions that the public has regarding evolution.
What are the differences between the two scientific fields?
Modern evolutionary biology begins where Darwin began - with the assumption of an already existing population of living cells. It makes no claims about where those first cells came from - how the first proteins came into existence, how the genetic code arose, how transcriptional and translational machinery came into being (the machinery responsible for taking the information from DNA and turning it into protein), how we got information from DNA to RNA to protein, how a metabolism arose, how a cell membrane encapsulated a replicating genome, how phenotype got linked to genotype. All of these are questions that are outstanding in the field of prebiotic evolution, or, if you will, origins of life research. If you take a class in evolutionary biology in college or high school, or read a textbook on evolutionary biology, you do not get taught the modern science of prebiotic evolution. The text may briefly mention some current scientific ideas on the origins of life (it may even include a whole chapter on it), but the textbook does not focus on the detailed content or techniques of that field. Why? Because origins of life research is not the same thing as evolutionary biology, or neo-Darwinism, or whatever you want to call it. As a biologist who is very interested in prebiotic evolution (although I have not yet done research in this field), I have to admit that most of the questions I listed above are still wide open. Scientists aren't completely empty-handed, but the transition from non-life to life is still a big, fascinating scientific question. But this is not true of evolutionary biology.
It is important to note that logically evolutionary biology does not depend on the status of the field of prebiotic evolution. Whether natural selection is a major evolutionary mechanism, whether punctuated equilibrium is correct, whether ideas about genetic drift, speciation, neutral evolution, the molecular clock, or specific phlyogenetic relationships are correct does not at all depend on any conclusions or theories about how the first cells arose. God could have poofed those first cells into existence; it would make no difference. Darwin and every major biologist since then has been clear about this. Asserting that scientists can't explain how the first molecular machines arose does not weaken the status of natural selection or any aspect of modern evolutionary biology - in other words, that which is taught in college and high schools. The idea that humans and chimps shared common ancestors (which seems to be a real problem for conservative Christians) does not depend on scientific theories of how the first cells arose. Really, this should be obvious, but everyone from Discovery Institute Fellow William Dembski to Judge Carnes to the Dover, PA school board seems to miss this point.
What this means is that when discussing how things could have evolved, we have to take note of the fact that modern evolutionary biology essentially starts with the assumption of a living population of cells - a primitive bacterium that already had a genome, transcription, translation, nutrient transporters, ion transporters, signal transduction, and gene regulation. Arguments about the sufficiency of natural selection to bring about the diversity of life we see today only have to deal with whether we can get from the structures and systems present in these early cells to the structures and systems present in today's living species. Researchers who work on issues of molecular evolution would argue that there are no holes in our understanding substantial enough to cast doubt on the idea that known evolutionary mechanisms could produce today's species diversity. This is the challenge intelligent design has to answer in its critique of evolutionary biology - the question is not could the bacterial flagellum arise from random protein subunits, but rather, could the flagellum have evolved from the machinery of a secretory system. No evidence presented by ID advocates has been able to show that this is impossible, while professional biologists argue that such a transition is fairly simple to explain with current concepts of molecular evolution. We have a reasonable understanding of how selectively advantageous mutations get fixed, we know many of the physical mechanisms of mutation in DNA, we have hundreds of examples of multi-functional proteins, as well as tremendous amounts of data on how mutations impact protein structure and function.
This misconception is so absurd, and yet it crops up again and again. You would think that before hearing arguments Judge Carnes would have actually looked at the biology textbook at issue and asked himself whether our understanding of the transition from non-life to life really has anything to do with most of the content of the book. That he didn't do so just shows how people's sympathy for conservative religion makes them approach evolution in a way that they would never consider valid for other scientific or scholarly fields.