Can Darwin Fit into Designer Genes?

Humans are tinkering with DNA in ways that appear to blur the boundaries between design and nature.

1. PhysOrg reported that geneticists at the University of Nottingham have created capsules that can coax bacteria to transfer their genetic information.  The title is “Life, but not as we know it?”
2. PNAS reported that scientists at UC Santa Barbara have “rationally engineered” an aminoacyl transfer-RNA synthetase by altering its “information transfer” abilities.  Though they mentioned “copious sequence and structural information” present in the natural enzyme, they believe evolution built the information: “This role for tRNA may persist as a relic of primordial cells in which the evolution of the genetic code was driven by RNA-catalyzed amino acid�RNA pairing.”
3. Robert Deyes on Access Research Network commented on a paper in Nature Biotechnology where researchers coaxed a bacterium to play tic-tac-toe.
4. Craig Venter was interviewed on Ted Talks claiming he is just 18 months away from genetically engineering bacteria to make gasoline from carbon dioxide.

In each of these cases, humans have tampered with genetic material for purposeful ends.  The question is, are the products “natural”?

Would an unbiased alien be able to discriminate between a genetically-engineered bacterium and a natural one?
    Intelligent design makes the claim that purposeful design is distinguishable from non-design using the ordinary methods of science.  On what basis can evolutionists claim that the above examples were produced by intelligent design, but the genetic code and genetic information themselves are non-designed products of non-intelligent processes acting on matter subject to natural laws?  Consider two possible responses.
    One common argument evolutionists make is that human intelligent design is something we are familiar with, but the kind of Designer ID proponents infer is necessarily supernatural, and therefore outside of science.  The appeal to intelligent design in the genetic code, therefore, is a religious explanation.  Religion and science cannot mix.  ID, therefore, must be excluded from all scientific explanations.  But, pray tell, what is the difference in method?  If our unbiased alien inferred from the evidence, having never seen a human engineer, that an intelligent agent of some sort had designed a bacterium to play tic-tac-toe, what changes when the alien applies the same reasoning to the DNA code?  Dembski’s explanatory filter (see diagram on Evolution News) does not ask the question, “Who is the designer?”  It only asks whether design can be discriminated from chance and natural law.
    If the evolutionist agrees so far, but then persists in insisting that there is a difference between a human designer and a “supernatural” Designer (e.g., God), then explore the distinction between natural and supernatural.  Ask him if human reason is natural.  The evolutionist must believe the answer is yes.  In fact, he might explain that there is no difference in principle between what a human does altering bacteria for its purposes and what a parasite does altering a host for its purposes.  Some roundworms, for instance, alter the behavior of their insect hosts, making them climb onto the top of the leaves (which they would normally not do), where they can be spotted by birds, which are the next hosts in their life cycle.  That’s all humans are doing, he says; we alter bacteria for our purposes to make gasoline and improve our crops.  Humans are natural parasites on other organisms.
    But there are substantive differences between these cases.  The parasite cannot survive without its hosts.  Humans, on the other hand, did just fine for thousands of years before genetic engineering was invented.  What human being needs a bacterium to play tic-tac-toe?  Getting gasoline from bacteria would be nice, but we got our gas via drilling for a century, and we could get by without gas-powered transportation if need be.
    The comeback argument is actually much stronger.  If the evolutionist compares human engineering to parasite engineering and says there is no difference in principle, because humans and bacteria are products of evolution, the game is over.  He has just destroyed reason.  Human engineering is no longer intelligent design.  The words intelligent and design become meaningless.  All human activity is reduced to the deterministic or contingent activity of natural forces.  This includes reason.
    When the evolutionist uses reason, therefore, to argue against intelligent design, he refutes his own case.  Reason reduced to natural forces ceases to be reason.  Reason depends on concepts that go beyond nature into realms of rationality and the laws of logic.  Concepts are not physical.  They may revolve around physical things as their subjects, like how to design a computer.  Concepts may be communicated by physical things like voices and radios.  But the concepts themselves are independent of the physical mechanisms by which they are communicated.*  Reason reaches beyond nature for truths that are universal, timeless, necessary, and certain.  The evolutionist who appeals to reason, therefore, is a supernaturalist in spite of himself.  Think about it.