Mr. Mooney's attack upon the scientific theory of ID has a common theme of mischaracterizing the theory and tearing down only a straw-man version of intelligent design.
This is one of the chief advantages of an ill-conceived pseudo-science... the ability to ooze out of the way of any criticisms. I've seen this same complaint lofted by IDers over an over.
So, just what is the proper definition of intelligent design, anyway? According to the Discovery Institute's web page,
The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection.
OK, so we have a definition. Hmmm... let's try to figure out what it means. First of all, what is meant by "best explained"? According to what objective measure? None... it's purely subjective, making the definition useless.
The definition also implies that intelligence is not directed by natural processes. Guess what. Science only deals with natural causes, defined as the "systematic knowledge of the physical or material world gained through observation and experimentation". That is, claims made about things outside of nature and the physical universe are not science.
And how about this elaboration on the "science" of ID;
ID theorists argue that design can be inferred by studying the informational properties of natural objects to determine if they bear the type of information that in our experience arise from an intelligent cause.
Does that say "in our experience"? Whose experience? Yours? Mine? Theirs? Science is NOT subjective... if it were, it would be called religion. The whole scientific enterprise is an attempt to find out objective truths about our universe.
Contrast that foggy definition to Wikipedia's first two sentences on evolution:
Evolution is change in the genetic material of a population of organisms from one generation to the next. Though changes produced in any one generation are normally small, differences accumulate with each generation and can, over time, cause substantial changes in the population, a process that can result in the emergence of new species.
Notice how it's stated in specific terms. We can measure the frequency of genetic alleles. We can make measurements of an organism's phenotype. How can you refute any of that... it's really more of an observation than a scientific claim. We already know that populations of organisms can change substantially. The step to "speciation" is just semantics.
Take-home message: While intelligent design proponents huff and puff about being treated unfairly by the scientific community, there is a reason for it. Their claims are not scientific. The ID movement is a sociological phenomenon, designed to allow society to hang onto antiquated irrational beliefs for one generation longer.