Abstract
Intelligent design (ID)—the latest incarnation of religious creationism—posits that complex biological features did not accrue gradually via natural evolutionary forces but, instead, were crafted ex nihilo by a cognitive agent. Yet, many complex biological traits are gratuitously complicated, function poorly, and debilitate their bearers. Furthermore, such dysfunctional traits abound not only in the phenotypes but inside the genomes of eukaryotic species. Here, I highlight several outlandish features of the human genome that defy notions of ID by a caring cognitive agent. These range from de novo mutational glitches that collectively kill or maim countless individuals (including embryos and fetuses) to pervasive architectural flaws (including pseudogenes, parasitic mobile elements, and needlessly baroque regulatory pathways) that are endogenous in every human genome. Gross imperfection at the molecular level presents a conundrum for the traditional paradigms of natural theology as well as for recent assertions of ID, but it is consistent with the notion of nonsentient contrivance by evolutionary forces. In this important philosophical sense, the science of evolutionary genetics should rightly be viewed as an ally (not an adversary) of mainstream religions because it helps the latter to escape the profound theological enigmas posed by notions of ID.

Here’s an article that describes and explains the paper.

The basic concept of intelligent design comes in two parts and is as simple as it is satisfying for those unwilling to think deeply about the natural world, science, or the nature of religion. Part one, stretching way back to the ancient Greeks, notes that nature is so perfectly integrated that it must have been designed just as we see it. Part two, largely attributed to Lehigh University biologist Michael Behe, says that while some aspects of nature might certainly have changed (evolved?) over time, others are so complex that they must always have existed in the form we find them in today. Indeed, he coined the term “irreducibly complex” to explain such structures. Change anything at all in these irreducibly complex structures and they fail to work.

Both parts of ID are spectacularly wrong.