Thank you, Wireless. Do you realize that this is the longest and fullest post that you have made in a great while about what you think?
I can kind of see what you are saying, however, evolution still doesn't necessarily follow this kind of presentation. To me, in your terms, it seems to be more of an action/reaction process than a cycle. Like in the case of malaria and Sickle cell anemia: A group is living in an area where malaria is prevalent. It has been clearly shown that carriers of this trait are infinitely more successful at overcoming malaria. Because of this, the sickle cell anemia carriers are more likely to survive than those who don't carry the trait and, therefore, are more likely to reproduce. So, you have a mutation within the hemoglobin ending up prohibiting a disease and, as a result, populations in these areas tend to be carriers of the disease by natural selection. It's a clear case of action/reaction. I actually think that many genetic diseases that are prevalent today were probably started in this exact manner and this is probably why there is autosomal dominant diseases.
I don't think that evolution is a flat time line either. I see it more as a tree branching off in many directions--far from flat. Some branches die, others move on to split again and again, while some of the trunk stays the same. There is no doubt that the earth does have cycles and it is possible to say that evolution probably does react to these larger climate cycles. One is going to find different species thriving during an ice age while others may thrive during a warm period.
I do think you are wrong, however, to think that biologists and etc think inside a box. If anything, geneticists, in particuliar, do regard DNA as rather like computer code. They are attempting to manipulate this code for a variety of reasons (the most prominent is the cessation of genetic diseases). Just because they don't say that the program is "soft" does not mean that they don't believe it is. Just like a systems administrator may look for bad code in a program that is causing problems, a geneticist also looks for bad coding in DNA to find out the same thing.
Stephanie
In every man there is something wherein I may learn of him, and in that I am his pupil.--Ralph Waldo Emerson