For the record, I subscribe to the Philadelphia Inquirer and saw this letter to the editor. In response, I wrote the following. Unfortunately, it wasn't published in the paper, however I think it addresses all of his comments:
A letter writer on Wednesday, December 30, 2009, accused science of being constrained by certain presuppositions, and, by extension, not being willing to see alternate hypotheses. I think it is curious that this letter is more constrained by presuppositions than the science he criticizes.
Let us make something clear: science is the study of the natural world. Topics associated with the supernatural are not a part of scientific study. This can be anything from god to ghosts, to anything else for which we have no natural evidence. If you want to discuss the supernatural, I am not opposed to the discussion, but it is not a scientific endeavour. It may be a theological, philosophical, or fantastical discussion, but it is by definition not scientific.
This letter writer then brings up four common arguments used by proponents of creationism that attempt to discredit evolution. They are as follows:
Macroevolution. To be clear, there is no difference between microevolution and macroevolution. They are terms used by creationists to create what is ostensibly an argument from incredulity. Evolution is small changes and adaptation over a long period of time. On a long enough timeline, the adaptation that permitted the species to survive, is the one that will continue to be passed on to future generations. I believe macroevolution is used to refer to the fact that we have multi-celled organisms, in spite of the fact that everything started out as a single cell. I'm not sure I understand why this is so complicated. After a sperm cell fertilizes an egg cell of any species, it becomes a single cell that starts to reproduce and become multiple cells quite quickly, with specialized internal organs.
Lack of transitional forms. There's no lack of them. Our parents were a transitional form between our grandparents and us, just as we are a transitional form between our parents and our children. Every living thing is a transitional form between the previous generation and the following generation. Remember: this is gradual changes over a long period of time. As environment and different mutations cause common groups to diverge, that's where they cease to be able to reproduce with one another. Either they will reproduce with other animals with similar mutations, or they will die out.
Lack of any evidence for life evolving from inanimate matter. That's not what evolution is about. Evolution does not pretend to know how life first got started; it just teaches us how life came to be what it is today. That's a separate biological study and, quite frankly, we simply don't know what we don't know.
Evidence for intelligent design in all the intricate details of creation. I believe this phrase is a reference to what Darwin said could falsify his theory: something irreducibly complex. Thus far, nothing in nature has been shown to be so complex, that it cannot be reduced to something more simple. Intelligent design has not been supported within a single peer-reviewed scientific journal. It is not an alternative theory to evolution. The more we learn about life, biology, genetics, and all of the related scientific disciplines, the more credibility is lent to the theory of evolution.
Intelligent design is for wishful thinkers who prefer the far less satisfying "God did it" explanation for the beauty of life all around us. It's not for scientists or anyone else who has any appreciation for science and its methods.