Shanghai, China aerial view over Yan'an Elevated Highway.

by Evolution News and Views


Some revolutions have long onramps. Modern epigenetics has been around for well over a decade, but its impact has yet to be fully explored. Which interpretation of biology — evolution or intelligent design — stands the best chance of advancing scientific understanding of genomics through epigenetics research?

Well, it is indeed a revolution; that’s what senior reporter Heidi Ledford calls it in her Nature Outlook piece, “Epigenetics: the genome unwrapped.” She ends with remarks by Tomasz Jurkowski, a biochemist and epigeneticist at the University of Stuttgart in Germany who is racing against other researchers to untangle DNA’s secrets:

He takes the competition in stride — it is the price of entry into the fast lane. Epigenetics is on the verge of a revolution, he says. “This is just the beginning,” he says. With just a little more time, “It will develop into a completely new field.” [Emphasis added.]

Of the many epigenetic markers already identified, many have shown to affect an organism’s phenotype. Some of them have been shown to be heritable, opening up new vistas of epigenetic inheritance. Now, with the updated CRISPR-Cas9 gene editing tool, despite its potential for ethical quandaries (see discoverer Jennifer Doudna in Nature worrying about the Pandora’s box she opened), epigenetics researchers are pushing the accelerator pedal.

Ledford describes how CRISPR-Cas9 — Science Magazine’s 2015 “Breakthrough of the Year” — has already allowed one research team to speed around another team that did things the old-fashioned way.

René Maehr, an immunologist at the University of Massachusetts Medical School in Worcester and his colleagues fused an enzyme called histone demethylase, which removes methyl groups from histones, to a deactivated Cas9 enzyme, and then programmed it to target regions of DNA believed to enhance the expression of certain genes. The result was a functional map of genetic ‘enhancer’ sequences that allows researchers to determine what these enhancers do, how strongly, and — most importantly — where they are located in the genome.

Question: Why were they seeking “to determine what these enhancers do”? Answer: They didn’t believe they were junk. They watched the target gene increase its expression significantly. “That result started to convince me that the acetylation of histones may be a direct cause of gene activation.” This suggests a new layer of specified complexity that supersedes the old Central Dogma that viewed DNA as the master controller. Functional mapping now steps up from genes to the epigenetic markers that regulate them.

Four years ago, we discussed whether the epigenome is “Evolution’s Newest Nightmare.” Current Biology put up a brave front, claiming that epigenetics might promise “interesting new angles in the study of evolution.” That’s hard to support now. None of the articles quoted above had any use for evolutionary theory. Indeed, how could they? If epigenetic markers regulate genes; if they act like molecular switches; if they can be placed into functional maps — then they represent a higher level of complex specified information that defies the neo-Darwinian mutation/selection story.

Stated explicitly or not, it’s design-based thinking that leads scientists to build functional maps of epigenetic markers and motivates them to “figure out what they actually do.” Who would waste time or money on junk? The downfall of the junk-DNA concept gives scientists encouragement to seek new levels of specified complexity in epigenetic regulation. The future of epigenomics looks bright — for intelligent design.

Read the full article at Evolution News and Views.