Epigenetics: the 21st-Century Scientific Revolution

If genetics was the 20th century’s major scientific revolution, epigenetics appears to be the big revolution for the 21st.

Epigenetics refers to codes, processes and functions “above” genetics, that control and regulate the genetic code: a “code above the code,” as it were. Unlike a simple DNA strand, the epigenetic code has a multitude of players that scientists are still struggling to understand. For a good introduction, watch this 12-minute video on YouTube; for more depth, read the book The Mysterious Epigenome: What Lies Beyond DNA by Woodward and Gills (available from the C.S. Lewis Society and  Amazon.com).

One thing is becoming clear; DNA is just a bit player in a much vaster array of information. The big story now is what controls and regulates the DNA. Many things in the nucleus once considered “junk” are turning out to be the stars of the show. In addition, the findings are becoming more and more difficult to explain by neo-Darwinian mechanisms. Even more startling, epigenetics is undermining some key Darwinian principles.

The sheer number of news articles on epigenetics prevents in-depth coverage of any one, but what follows is a sampling of exciting finds in this vast, rich field of research.

Aging and epigenetics:  Let’s begin with one close to home: aging. “Epigenomes of Newborns and Centenarians Differ: New Clues to Increasing Life Span,” announced Science Daily in bold red type, alongside a photo of a grandfather holding an infant. A new study shows defects due to mutations not just to genetic code base pairs, but to some of the epigenetic marks like methyl tags that help switch genes on and off. “The results show that the centenarian presents a distorted epigenome that has lost many switches (methyl chemical group), put in charge of inappropriate gene expression and, instead, turn off the switch of some protective genes.” Understanding these epigenomic processes will, obviously, be vital to improving the health and longevity of every human who gets older.

Micro-RNA regulators of regulators:  Nature (June 28) reported that two enzymes “autoregulate” the production of micro-RNA’s (miRNA) which, in turn, regulate gene expression in many pathways (Zisoulis et al, Nature 486, pp. 541-544, doi:10.1038/nature11134). This discovery is “expanding the functions of the miRNA pathway in gene regulation,” they said.

Make space for the non-junk:  “The myth of junk DNA” continues to get exposed. New Scientist reported that mouse “junk DNA” is vital for gene regulation. Hannah Krakauer’s opening sentence gives the gist of the article: “Some junk is worth keeping.Non-coding, or junk, mouse DNA contains vast amounts of information vital to gene function – and those regulatory functions take up much more space on the genome than the all-important coding segments.”

Master regulator: PhysOrg‘s article title summarizes the message: “Forty’s a crowd: Study shows that master regulator protein brings plethora of coactivators to gene expression sites.” After a discussion of a “behemoth” protein named Mediator, this paragraph was notable:

Researchers know that all DNA-binding factors partner with other proteins to switch genes on or off. What is remarkable here is their sheer number. “It would be very interesting to find out whether this is the norm,” says Ron Conaway. “This work raises a ton of little questions about mechanism.”

Epigenetic disease: If diseases can be genetic in origin, some can be epigenetic in origin. Science Daily wrote that epigenetics alters genes implicated in rheumatoid arthritis. “It’s not just our DNA that makes us susceptible to disease and influences its impact and outcome,” the article began. “Scientists are beginning to realize more and more that important changes in genes that are unrelated to changes in the DNA sequence itself – a field of study known as epigenetics – are equally influential.”

Epigenomes and cancer: One more example of the growing interest in epigenetics over plain old genetics is seen in an article in Science, “Genetic Events That Shape the Cancer Epigenome” by Ryan and Bernstein (Science, 22 June 2012: Vol. 336 no. 6088 pp. 1513-1514, DOI: 10.1126/science.1223730).  Sure enough, “there is increasing recognition that transmissible epigenetic changes—chemical modifications to the genome or its scaffold that do not involve a change in the nucleotide sequence—may be acquired de novo, and that these “epimutations” may also contribute to carcinogenesis.” Scientists would not have understood this had they not looked above and beyond the genome into the epigenome. The Greek prefix “epi-” (above) appears poised to latch onto a number of old genetic vocabulary words.

Grammar and syntax, form and function: Remember the phrase, “The Human Genome”? It sounds almost quaint in hindsight. Not much more than a decade ago, scientists thought mapping the DNA letters would help us understand health, disease, and human evolution. The new term, according to Science Daily, is The Functional Genome – beyond mere base-pairing. Starting with the mouse genome, scientists are trying to understand the paragraphs and superstructure within the genetic code, a language above the code itself. So far, they figure they only understand 11% of the mouse functional genome. Non-coding “cis-regulatory elements,” for instance (once considered junk), regulate adjacent DNA, the article explained.

Popularly dubbed “the book of life,” the human genome is extraordinarily difficult to read. But without full knowledge of its grammar and syntax, the genome’s 2.9 billion base-pairs of adenine and thymine, cytosine and guanine provide limited insights into humanity’s underlying genetics….

As expected, the researchers identified different sequences that promote or start gene activity, enhance its activity and define where it occurs in the body during development. More surprising, said Ren, was that the structural organization of the cis-regulatory elements are grouped into discrete clusters corresponding to spatial domains. “It’s a case of form following function,” he said. “It makes sense.”

Good interference creates epigenetic memory: Why would some RNA transcripts interfere with others? It’s all part of a regulatory dance, scientists are finding out. Now, a new role for RNA interference (RNAi) was announced on PhysOrg: recognizing and silencing foreign DNA, such as strands introduced by viruses. It’s heritable, too: “Once identified, an ‘epigenetic memory’ of the foreign DNA fragments is created and can be passed on from one generation to the next, permanently silencing the gene.” This has an eerie echo of Lamarckian “inheritance of acquired characteristics.”

Once the DNA is identified as foreign and silenced, an epigenetic memory is created that silences the foreign gene from one generation to the next. While the inheritance of this memory requires further exploration, the authors showed that successive generations of C. elegans are unable to express the foreign DNA even if the corresponding piRNA is absent.

A vaster landscape:  Geneticists used to speak of the “genetic landscape” but now there’s a vaster field: the “epigenetic landscape.” James Ferrell discussed this concept in his review, “Bistability, Bifurcations, and Waddington’s Epigenetic Landscape” in Current Biology (Volume 22, Issue 11, R458-R466, 5 June 2012), saying, “Waddington’s epigenetic landscape is probably the most famous and most powerful metaphor in developmental biology.” His rather lengthy review did not contain any of the following words: Darwin, phylogeny, evolution.

In the book The Mysterious Epigenome: What Lies Beyond DNA mentioned above, Woodward and Gills describe in verbal animation what it would be like to ride a sci-fi ship into the nucleus of a cell and watch gene regulation at work. Their second-to-last chapter, “An Infinitely More Complex Genome,” is like a 4th of July Grand Finale – a rapid-fire series of new discoveries and possibilities that portend a golden age of research in the years ahead, described in vivid metaphors like air traffic control, overlapping messages, codes here there and everywhere, and functional treasure in the “junk”yard.

Two practical effects of the Epigenetic Revolution will be: (1) a realization that we are not slaves of our DNA, but that with healthy lifestyle changes, we can control the expression of genes (for instance, a vigorous workout at the gym makes observable effects on gene regulatory tags); (2) increasing pressure against Darwinism. The realization is growing that there is far more functional information in the cell than neo-Darwinists ever imagined. If the genetic code was a challenge to explain by undirected processes operating stepwise by natural selection, what will be the reaction to codes upon codes, master regulators of other regulators, and millions of molecules performing a living symphony?

Got irreducible complexity? Here, Charlie. Come and look what we brought you: a little gift for your ailing stomach.

Dr. Thomas Woodward,* a Christian theology professor, historian of science and president of the C. S. Lewis Society in Tampa, Florida, feels justifiably excited to see this vast new panorama of epigenetics as vindication par excellence for the Biblical world view. Not only that, he and co-author Dr. James P. Gills, a world-renowned ophthalmologist and modern pioneer of cataract surgery, see that world view in light of these discoveries contributing to human health: a new way to cultivate a spirit of wellness. This is not surprising, since Jesus said that a good tree produces good fruit (Matthew 7:17), and both ends of the Bible describe the Tree of Life that God planted.

Exercise: What kind of fruit has Darwin’s “tree of life” produced lately? Here’s a few possibilities to get you started: storytelling in the name of science, the Stuff Happens law, atheism, moral relativism, pride, intellectual intolerance, eugenics, abortion, infanticide, “scientific” racism, tyranny, genocide. Now read Matthew 7:15-20.