Sarah C. P. Williams provides a concise, informative overview of epigenetics in “Core Concepts: Epigenetics” in the Proceedings of the National Academy of Sciences: “Where genetics has fallen short in explaining human biology, epigenetics is stepping up to fill in gaps.”

In the early days of the field, there was talk of a “histone code” that regulates gene expression by means of acetyl and methyl groups attached to the histones that bind DNA. In January researchers at UC San Diego announced that there does not, in fact, appear to be a single universal histone code: “Rather, the effect of epigenetics on gene expression or activity depends not only on the particular mix of histones and other epigenetic material, but also on the identity of the gene being expressed.”

Penn State researchers have found that epigenetics provides a kind of “dimmer switch” on gene expression:

Epigenetic factors act by reworking the structure in which genes reside, called chromatin. Inside chromatin, DNA is wound around proteins called histones. Several new cancer treatments interfere with the function of enzymes that chemically mark the histones to alter the readout of the DNA code and ramp the expression of genes up or down, as if with a dimmer switch. Enzymes called histone deacetylases (HDACs) erase the mark and shut off gene expression. (Emphasis added.)

Working with HDAC 3, the scientists found that mice could not survive without it, but there was no deacetylase activity unless it was activated itself by two other cofactors: “This ‘nuts and bolts’ discovery on the epigenetic control of a person’s genome has implications for cancer and neurological treatments.”

The Alpha Galileo Foundation posts a review of a paper that threatens to bring back Lamarckism, at least in part. Epigenetics appears to permit the inheritance of some acquired characteristics. In “Life Experiences Put Their Stamp on the Next Generation,” the review introduces Dr. Isabelle Mansuy, who is ready opine on a long debate:

In the most recent issue of Biological Psychiatry, Swiss researchers from the University of Zurich and Swiss Federal Institute of Technology, led by Dr. Isabelle Mansuy, discuss how the emergence of the field of epigenetics has introduced a new component to this discussion – the trans-generational transmission of changes in the regulation of gene expression.

“The question of the inheritance of acquired traits has puzzled biologists and clinicians for decades. Although it has been consistently observed as early as in the 18th century, the time has now come that sufficiently strong and convincing evidence has accumulated to firmly accept it,” said Mansuy.

She’s not claiming to explain the neck of the giraffe the way Jean-Baptiste Lamarck did, but it has become clear that some acquired epigenetic markers can be inherited by children and grandchildren, provided they occur in the germ cells. How does this affect Darwinian natural selection?

The changes in DNA structure are random events that acquire functional significance in the context of Darwin’s “natural selection” process. In contrast, the epigenetic reactions to specific environments are designed to enable that organism to cope with that context. When these traits are passed to the next generation, it is as if the newborn arrives prepared for that specific environment. Problems arise when the epigenetic processes give rise to traits that are not adaptive for the offspring, such as heightened stress reactivity, or when the environment has changed.

“This is a remarkable story with far-reaching implications,” commented Dr. John Krystal, Editor of Biological Psychiatry. “There is a suspicion that epigenetic processes may be reversed more easily than genetic traits, exemplified by the development of HDAC inhibitors. This is a rapidly evolving research area that has captured a great deal of attention.”

Did they really say that epigenetic reactions are “designed,” and that this is “in contrast” to the randomness of Darwinian natural selection? If so, unless Darwinian theorists can produce evidence that random, unguided mutations can actually produce complex structures, the only thing left in this equation is design.

Epigenetics is opening up another vista with implications closer to home. In Science, Paolo Sassone-Corsi discusses the convergence of metabolism and epigenetics. In a very real way, we can exercise some control over our own gene expression by what we put (or do not put) in our mouths. Scientists are beginning to understand how food and fasting affects the supply of epigenetic cofactors that turn certain genes on and other genes off. “As connections between epigenetics and metabolism emerge, it may be possible to consider new pharmacological interventions for a variety of pathological conditions,” he said.

In all these stories, there’s a hidden subtext of intelligent design.

This is evident not only by the lack of appeal to Darwinian theory to explain what is observed, but by the growing evidence of an elaborate epigenetic choreography in action. Enzymes, cofactors and tags that “fine tune” gene expression like a dimmer switch, that provide robustness against changing environments, that rework genetic structures in complex interactions — none of these seem amenable to being explained in terms of purposeless, gradual processes.