Here are my responses.
1. How did life originate? We don’t know for sure, but there are plenty of good hypotheses out there, some of which are being investigated right now. Just because this question does not have an answer yet does not invalidate the rest of evolutionary theory, as claimed by one of the rebuttals. For example, the mechanism of natural selection functions just fine regardless of whether or not abiogenesis is completely understood.
2. How did the DNA code originate? Pretty much same as above. Evolution does not claim that God does not exist and did not create the DNA code. Evolution simply contradicts the creation story in the bible. Science in general, being naturalistic, cannot and should not accept supernatural explanations for observed phenomena. Science cannot accept that God created the DNA code and must search for a naturalistic explanation, as it always has. It is what makes science science and not faith, and what makes it useful.
3. How could mutations create the huge volumes of information in the DNA of living things? How could such errors create 3 billion letters of DNA information to change a microbe into a microbiologist? I do not understand what aspect of evolutionary theory the author has a problem with in regards to this question. Mutations create diversity. From that diversity, the fittest are selected via natural selection. Some lines become more complex because complexity helps them survive in their particular environment.
4. Why is natural selection, a principle recognized by creationists, taught as ‘evolution’, as if it explains the origin of the diversity of life? Who says that? Natural selection is the most interesting and important mechanism in evolution - that’s probably why it’s taught up front.
5. How did new biochemical pathways, which involve multiple enzymes working together in sequence, originate? One at a time. Each enzyme could have a different use before it was adopted into the pathway in question. Ken Miller can explain it better than I can: http://www.millerandlevine.com/km/evol/DI/clot/Clotting.html
6. Living things look like they were designed, so how do evolutionists know that they were not designed? Anything that looks designed must be designed? That seems a bit too subjective for science…. Evolutionists don’t necessarily know that living things were not designed; rather, they do not assume a designer. Scientists search for naturalistic explanations for everything, and they have found many.
7. How did multi-cellular life originate? From single-celled organisms, to colonies, to multi-cellular. They learned to cooperate because cooperation benefits everyone involved and was between organisms with very similar genetic material. Therefore the survival and reproduction of any one was beneficial to the survival of the entire lineage. Cells do not necessarily have to compete. Evolution is not about competition. It is about survival and reproduction. Sometimes cooperation helps with that. We see it often in nature and in humans.
8. How did sex originate? It originated many different times in different lineages. Genetic recombination helps fight Muller’s Ratchet, the accumulation of negative mutations over time, something that asexually reproducing organisms have to deal with. Sexual reproduction also gives rise to sexual selection, which can be a useful selective pressure. Sexual selection, in turn, tends to create genetic stability due to selection of average traits, which keeps the fitness of the population high in an unchanging environment. Sexual reproduction also creates mixtures of traits, which can yield more fit (and less fit) progeny, then the less fit are naturally selected out, leaving only the more fit. Asexual reproduction, on the other hand, creates progeny that are largely identical to the parent, meaning adaptation to new environments may be slower.
9. Why are the (expected) countless millions of transitional fossils missing? Fossilization is a rare occurrence, but we have enough to know that evolution happened. When would you consider a transitional gap to be filled? Find a fossil and there is always a gap between both the next and the previous. We have found many transitional forms. Just because we have not found all of them does not mean they did not exist. Scientific theories are built on evidence. If you don’t think the evidence for evolution is enough, yet you think the evidence for intelligent design is enough, you are biased.
10. How do ‘living fossils’ remain unchanged over supposed hundreds of millions of years? They are probably well-suited to their environment and any change would reduce their fitness. This is not an addendum to the theory of evolution; this is what it predicts. The theory of evolution does not say that everything is always evolving into something very different. I’m not sure where they got that from.
11. How did blind chemistry create mind/ intelligence, meaning, altruism and morality? By natural selection. Should we be teaching nihilism as truth? Not when there are competing secular philosophies out there.
12. Why is evolutionary ‘just-so’ story-telling tolerated? They are hypotheses that should be presented as such.
13. Where are the scientific breakthroughs due to evolution? Modern medicine, agriculture, genetic engineering, evolutionary computing, etc.
14. Why is evolution, a theory about history, taught as if it is the same as this operational science? Evolution occurs today, and it has been observed. http://en.wikipedia.org/wiki/Ring_species http://en.wikipedia.org/wiki/Speciation#Artificial_speciation
15. Why is a fundamentally religious idea, a dogmatic belief system that fails to explain the evidence, taught in science classes? It explains more evidence than competing theories such as intelligent design. It is not dogmatic. Rather, it is open to change due to its scientific nature. It is not religious because it is not based on faith and does not have rituals. It is taught in science classes because it is a very useful and profound theory with a lot of supporting evidence.
Just because some questions do not have answers does not mean evolution as a whole should be discarded. We don’t discard intelligent design just because IDers “don’t know” who the designer is. (We discard intelligent design because it is a God of the gaps argument that is not supported by the evidence).