Opposition to intelligent design
Opposition to intelligent design (ID) is largely motivated by entrenched distaste for its philosophical implications.
A living organism fulfills the definition of a machine all the way down to the molecular level. And yet, because of the philosophical and religious implications of life resulting from Intelligent Design, a surprisingly large portion of the intelligentsia seek to find a mechanism by which life may arise naturally by random chance. 
The question that ID poses is not "might there be an intelligent designer?" so much as "is there evidence of intelligent design?" Yet the first thing ID opponents always bring up is that design implies a designer. For atheists, such a designer could only be God. (Or as Richard Dawkins said in Expelled, since God almost certainly does not exist, the designer must be an alien from outer space who was himself naturalistically evolved. Obviously, Dawkins brought up that alternative to dismiss it.)
Why are scientists, who supposedly only care about the physical world, up in arms about the religious implications of their work?
The point is that atheists and materialists in the mainstream of modern science reject any suggestion that the material world is all there is. If evolution were to lose credibility, atheism would accordingly lose support. This would lead to what is for them an outrageous alternative.
The problem is the ideological refusal to separate science from ideology. Supposedly, pure science just explores what is and does its best to explain observed facts with theories. Physical science uses natural law for its explanations, and it has down spectacularly well, especially in the last 400 years. Pasteur's germ theory of disease is an outstanding example of a very useful discovery which has saved countless lives.
But when it comes to the question of human origins, there is no escape from the implications of any theory. It is generally agreed that there are only two possibilities:
- that life "evolved" entirely because of physical causes; or,
- that some other cause is responsible for life's existence
In the physical sciences, methodological naturalism is the favored approach. Scientists choose to consider only physical forces and principles. Natural selection is one such principle, and all biologists accept it - even those who disbelieve completely in evolution (such as Young Earth Creationists).
But at the boundary of science and philosophy, we are forced to consider whether physical science has all the answers. In criminology (a social science), investigators must give a scientific opinion as to whether an occurrence such as a fire or a human death was caused naturally, by human error, or by a deliberate act. A building might catch on fire due to an accident that is no one's fault; it might be the result of culpable negligence, or it may have been set on purpose; see Arson. Likewise, a death might be accidental (the brakes failed), the result of negligence (the other driver ran a stop sign); or it could be suicide (he drove straight into a tree); see also Murder.
Some attempts have been made to identify "science" with physical science, as if all the other areas of study were not scientific at all. This comes as news to doctors, psychologists, anthropologists, economists and professors of political science. Some philosophers of science may wish to make a sharp distinction between real science and "the fuzzy subjects", but in academia there has traditionally been less of a cliff than a spectrum. In fact, it is only in one relatively obscure part of the life sciences, i.e., biology, that anyone has put forth this idea.