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But Doesn't Intelligent Design Refer to Something Supernatural?

From an ID perspective, the natural-vs.-supernatural distinction is irrelevant. The real contrast is not between natural laws and miracles, but between undirected natural causes and intelligent ones.

Mathematician and philosopher of science William Dembski puts it this way: "Whether an intelligent cause is located within or outside nature (i.e., is respectively natural or supernatural) is a separate question from whether an intelligent cause has operated."

Human actions are a case in point: "Just as humans do not perform miracles every time they act as intelligent agents, so there is no reason to assume that for a designer to act as an intelligent agent requires a violation of natural laws."

On the other hand, even if an object were miraculously created, it could still be studied. Take the flagellum, for example. No matter what its origins, a flagellum is a flagellum. We can take it apart, we can examine its components, we can modify it, we can figure out how it works. And we can do that whether it evolved over eons or popped into existence two seconds ago.

In the world of human technology, this is called reverse engineering. But the same process is also used in biology.

"That’s basically what everybody at the bench is doing," said Scott Minnich, a microbiologist at the University of Idaho. "We don’t have the blueprints in the true sense. We have the DNA code for a lot of organisms, but in terms of the assembly of these molecular machines, it’s a matter of breaking them apart and trying to put them back together to figure out how they function."

This is also the kind of work that will be done with the human genome. Speaking to the New York Times in late June, when the human genome breakthrough was announced, Harold Varmus, former director of the National Institutes of Health commented, "The important thing is having pieces of DNA in your hand, and being able to figure out how they work by modifying and mutating them. That's where the game is now."

Fittingly, the metaphor he used to describe this process was examining a clock: "You can take the clock apart, lay the pieces out in front of you, and then try to understand what makes it tick by putting it back together again."

ARN Recommends: For further study on the important distinction between natural laws and naturalism see:
The Wedge of Truth Phillip E. Johnson
Darwinism: Science or Naturalistic Philosophy Debate at Stanford University between William B. Provine and Phillip E. Johnson.

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