Shapiro, JA. Rethinking the (im)possible in evolution (in press) Progress in Biophysics and Molecular Biology.
The author graciously provides an open access preprint of his forthcoming article, which is available at the link above. With considerable clarity, despite the technical aspects of the topic, Dr. Shapiro tells about the problems of evolutionary theory. Most are due to the failure of theorists to tether their opinions to what is currently known about molecular biology or any other aspect of current scientific knowledge. The theorists are more than 5 decades behind the data, which is why their opinions — based on ridiculous theories — make no sense.
One of the more important take-home messages that Dr. Shapiro provides is that: “DNA change is a non-random process in the sense that it results from well-defined biochemical operations, each leaving a characteristic signature in DNA structure.” Although he does not detail the molecular mechanisms that must be involved, they are clearly nutrient chemical-dependent and pheromone-controlled as is all adaptive evolution in species from microbes to man. There’s a model for that, and no competing models to suggest Dr. Shapiro or other clear-thinking experts are wrong.
“We know that natural genetic engineering is non-random, sensitive to external inputs, and provides all the molecular tools necessary for controlling the genome restructuring process.” — James A. Shapiro (2013)