Intelligent designer argument

Some people are arguing that life is to complex to have evolved, so it must have had an intelligent designer. They do not say that the designer is God, but it is generally assumed. Others are arguing against intelligent design, saying that nature has too many flaws and extinctions to have been designed intelligently. From the NYTIMES:

While there is much that is marvelous in nature, there is also much that is flawed, sloppy and downright bizarre. Some nonfunctional oddities, like the peacock’s tail or the human male’s nipples, might be attributed to a sense of whimsy on the part of the designer. Others just seem grossly inefficient. In mammals, for instance, the recurrent laryngeal nerve does not go directly from the cranium to the larynx, the way any competent engineer would have arranged it. Instead, it extends down the neck to the chest, loops around a lung ligament and then runs back up the neck to the larynx. In a giraffe, that means a 20-foot length of nerve where 1 foot would have done. If this is evidence of design, it would seem to be of the unintelligent variety.Such disregard for economy can be found throughout the natural order. Perhaps 99 percent of the species that have existed have died out. Darwinism has no problem with this, because random variation will inevitably produce both fit and unfit individuals. But what sort of designer would have fashioned creatures so out of sync with their environments that they were doomed to extinction?

The truth is:

Philosophy is like being in a dark room and looking for a black cat.
Metaphysics is like being in a dark room and looking for a black cat that isn’t there.
Theology is like being in a dark room and looking for a black cat that isn’t there and shouting “I found it!”