In correspondence and comments on some of my blogs, there have been confusions or questions as to what I mean by "natural genetic engineering" (NGE). I will use this blog to spell out what my understanding of NGE is.

Did Wallace and Darwin hit the nail on the head and identify the crucial process of biological diversification? To most people, and especially to the evolutionist profession, the answer is so obviously "Yes" that even to pose the question subjects the person asking to abuse.

In the pre-DNA era, students were all taught that genetic change is random and accidental. Because the molecular details were inaccessible, this was the default assumption. But once we learned about DNA carrying hereditary information, we could research the details of how changes occur.

McClintock predicted that we would focus on how the genome responds to challenge. Clearly, unraveling the molecular basis of epigenetic regulation is an integral part of that revolutionary research agenda.

Two postings back, I promised a commenter called Sierkovitz that I would discuss epigenetics. This is an important subject with major implications for understanding natural genetic engineering in evolution.

Let's look at how we would "fish" for complex genomic novelty through natural genetic engineering. I can think of two approaches. There will definitely turn out to be more.

I have argued that natural genetic engineering is the real creative process in evolutionary innovation. A central but undocumented feature of my argument is that cells can coordinate separate DNA-change events to produce functional new genome structures.

A major advance in our understanding of heredity and genetics is recognizing that organism characters are produced by networks and not by individual "gene products."

A few blogs ago I asked, "Where, in fact, do 'the good ones' really come from?" By "good ones" I meant useful genome changes in evolution. This question stimulated some debate about whether it was possible to distinguish good changes from bad changes before they occur.

While most population biology is highly theoretical and conjectural, the Grants have been following what has actually been going on in the wild. Theirs is an exciting scientific and human story, including raising and educating their daughters in a tent while making field observations.

A good way to see how natural genetic engineering facilitates the evolutionary process is to review what we have learned about protein evolution.

How could natural selection operate so that "the good ones spread in the population" if there were no positive variants in the first place? That is why I am confounded by Jerry Coyne's comment that he can explain natural genetic engineering by "garden variety natural selection."

In a very complimentary blog entitled "Seeing Past Darwin II: James A. Shapiro," James Barham poses the following question and then chides me gently for not answering it: "But if natural selection cannot explain natural genetic engineering, what can?"

The curious responses to my position exposed a fundamental difference in understanding of biological functions between molecular geneticists and these particular proponents of population genetics. Because I can only speak for the molecular side, let me elaborate.

One of the Creationists' main tools is the argument that evolutionists are simply militant atheists in drag, who care more about dissing religion than about understanding evolution. Pro-evolution debaters will enjoy far more success by active engagement with evolution doubters.

In a recent posting on his Why Evolution Is True website, "Jim Shapiro continues his misguided attack on neo-Darwinism," Jerry Coyne attacks me again. Let us examine some of his arguments.

This posting will discuss how further targeted natural genetic engineering refines antibody specificity and directs antibodies to the right place in your body to deal with each infection.

Was Darwin simply mistaken about the gradual nature of hereditary variation? Such ignorance would be unavoidable before we knew about Mendelian genetics and DNA. Or was there a deeper flaw in the theory that he (and Alfred Russell Wallace) propounded?

Your life depends on purposeful, targeted changes to cellular DNA. Although conventional thinking says directed DNA changes are impossible, the truth is that you could not survive without them.