A Book Review of
The Deeper Genome:
Why There is More to the Human
Genome than Meets the Eye
(Oxford University Press, 2015)
This article first appeared in the Christian Research Journal, volume 39, number 2 (2016). For further information or to subscribe to the Christian Research Journal please click here.
Gracing the cover of John Parrington’s almost-magisterial book from Oxford University Press is the smoothly twisting ladder of DNA. As the double helix floats in the foreground, radiating a warm red glow, one can see lurking behind it the dark, bulky mass of an iceberg. This floating mountain of ice punctures the calm ocean surface above, where its frosty tip shimmers like a distant peak in an Alaskan mountain range.
The message is clear: DNA, neatly packed into the corridors of the genetic library called the genome, is seen now by biologists in a way that shocks us. It is biology’s dark continent, whose vastness and subtle complexity had remained murky until recently, when some of its greatest secrets were pried open, one by one.
Enter Epigenetics. The Deeper Genome takes the reader on a guided tour of every major nook and cranny of the genome’s vast iceberg of complexity that has been mapped out so far. For example, the precise 3D spatial arrangements of the chromosomes that are stashed in the nuclei of our cells have been shown to add an additional layer of functional information that was not glimpsed in the earlier picture of DNA as a simple linear sequence—“beads on a string.”
During this tour of recent discoveries, the book highlights both the science and health dimensions of the genome. Medical health connections are made throughout the book, and a special chapter is devoted to diseases linked to genetics.
What is really exciting about Parrington’s tour for science junkies (I’m one) is his exposé of the new layers of “coded information” above and beyond our DNA. This area of study is referred to as “epigenetics.” (The preposition epi, meaning above, focuses our attention on the chemical signals that are clustered on or near the DNA, helping to direct its activity.) This multilayered control system, which Dr. James Gills and I sketched in The Mysterious Epigenome: What Lies beyond DNA, is a large part of the newer, deeper genome that is coming into view. Since parts of the epigenome can be shaped by our environment and habits (diet, exercise, handling of stress), that makes epigenetics one of the hottest health topics in biology.
The Professor Makes an Abstruse Topic Accessible. While Parrington’s prose often veers moderately technical, he manages to keep the flow enjoyable by weaving in many personal stories of the genome’s pioneers. In every chapter, we are treated to delightful and entertaining vignettes—such as biochemist Jacques Monod’s role as a leader in the French Resistance during France’s Nazi occupation.
One poignant revelation is that the American codiscoverer of DNA’s structure, James Watson, was prompted by the reality of a son with schizophrenia, in his effort to organize the Human Genome Project (HGP) to shed new light on such diseases. To explain a technical domain of science such as molecular genetics, it helps greatly when science’s labors are humanized by providing unforgettable glimpses of the lives of scientists along the way. In this, Parrington excels like few other science writers.
Incidentally, the author could be addressed “Professor John Parrington.” He is not only an accomplished science writer but also is writing in his field of personal expertise in teaching and research. He serves as associate professor in molecular and cellular pharmacology at the University of Oxford. Thus as a narrator of the genome’s saga, he has a command of a vast technical literature. His intimate knowledge of the debates raging within his field equips him to report accurately “why there is more to the human genome than meets the eye” (the book’s subtitle).
Parrington’s Twin Goals: Current Discovery and Natural History. I recognize that a reader of this review may have stumbled on the first sentence. There I called the book magisterial but qualified it with almost. To explain my ambivalence, I’ll focus now on Parrington’s two basic goals. First, he wants to trace the pathway of discovery that led to many revelations about the mysteries of the genomic iceberg. We learn, step-by-step, how these truths were brought to light and made useful to medical science. This storytelling task is carried off with superlative skill.
Sometimes the path to a deeper genomic understanding has been bumpy. One jarring discovery, so massive that it dominates the book, is the sudden collapse of the “junk DNA” hypothesis. This happened after the ENCODE findings were first made known in 2007, with the final reports being published in 2012.
For those not familiar with ENCODE, this is an acronym of enormous importance; it refers to the huge and controversial genetic research project, entitled “
“Encyclopedia of DNA Elements.”.” ENCODE, which involved 442 scientists from 32 institutions, shocked the scientific world repeatedly in the past decade. Perhaps the greatest shock came when some ENCODE scientists estimated that, based on their findings, at least 80 percent of the genome seems functional, and this might rise closer to 100 percent! Textbooks at the time were declaring that somewhere around 2 percent of our DNA was functional, with the rest being relegated to the category of “junk” left over by eons of evolution. Clearly, ENCODE seemed to be obliterating the junk DNA argument, which had been treasured as a rhetorical bludgeon—useful against creation or intelligent design.
In reporting the ENCODE and junk DNA debates, Parrington pulls no punches and presents a shrewd, balanced, and utterly fascinating account of this upheaval. This is arguably the finest overview of the controversy in print. He devotes five chapters to this area (6 through 10), and in this aspect, the book is truly “magisterial.” It is tied for first place with the superb focused treatment penned recently by prominent biologist Jonathan Wells: The Myth of Junk DNA (Discovery Institute Press, 2011).
Before exploring the second goal, let me also single out as outstanding his coverage of the mystery of the “fifth letter of DNA,” or “methylated C.” A quick DNA refresher may help here. High school students learn that DNA has a four-letter alphabet, and each rung of the spiral ladder has a complementary pair of letters: A with T, or C with G. In recent decades, scientists began to flesh out the sophisticated function of a tiny chemical tag that adorns some C-letters. It turns out that the addition of a “methyl tag”—a modified methane molecule (CH3 )attached to the C—effectively turns the gene off, giving it a rest. The process of adding or removing such tags across a cell’s genome functions like the cues of an orchestra director, guiding DNA’s symphony of functions. Surprisingly, the methylation pattern is changeable. One can tune up the efficiency of this system (or damage it) through life habits. Methylation is now linked to obesity, cancer, and other health problems. Parrington’s coverage of such epigenetic control is brilliant and includes the newest ENCODE discoveries.
His second goal appears to be historical, focusing on the question, “how did all this multilayered complexity arise?” Near the end of the book, this focus dominates, as the story of human evolution is tackled in a long, meandering discussion. In this history task, Parrington misses a golden opportunity for critical thinking and shrewd analysis. He frequently disappoints, hence my qualifier “almost.”
He frames his origin-proposal as an updated version of the standard evolutionary narrative, and that much was expected. Yet what was profoundly disappointing was not just his declaring allegiance to a naturalistic worldview (again, not surprising) but also this blithe assertion, as if lecturing eighth graders: “Newtonian mechanics and Darwin’s theory of natural selection are all accepted as central cornerstones of modern scientific thought” (p. 140).
Such a claim is overblown, even ludicrous, at this point in the scientific debate. Many prominent scholars have broken with Darwinian selection, no longer seeing it as a powerful source of new genetic material and innovation in living things. Stephen Meyer in Darwin’s Doubt (HarperOne, 2013) provides a devastating critique of a half dozen attempts to plug the explanatory leak in the mutation/selection theory.
Dozens of scientists are right now making known their doubts about the creative power of natural selection through books, articles, and signed statements of dissent. Parrington’s publisher, Oxford University Press, released in 2012 a bombshell, Mind and Cosmos, in which prominent atheist philosopher Thomas Nagel repudiates Darwinism. He doesn’t just say that the “materialist neo-Darwinian conception of nature is almost certainly false” (that’s the shocking subtitle); he goes beyond that and predicts that Darwin’s theory, clearly false in light of the evidence, will be laughed at in coming decades.
In light of several new levels of genomic complexity, I’d ask Parrington, “How can this iceberg of brilliant interconnected technology be crafted by selecting errors in DNA code? Can we plausibly account for even one gene this way, let alone all 23,000 genes, or our newly discovered 400,000 RNA genes? It’s no wonder that a cadre of biologists, led by Gerd Müller, Stuart Newman, and Massimo Pigliucci, have been working together since the early 2000s to hammer out a “postmodern replacement” for Darwin’s theory. This new “extended synthesis” in evolutionary biology assigns a minor role to Darwin’s cherished key of natural selection of variations. Two books published by MIT Press — Origination of Organismal Form (2003, ed. Müller and Newman) and Evolution: The Extended Synthesis (2010, ed. Pigliucci and Müller) — have been candid about the inability of Darwin’s mechanism to account for major innovations in biology. Readers unfamiliar with this development will be shocked by revelations in John Whitfield’s report in Nature: “Biological theory: Postmodern Evolution” (Sept./Oct., 2008).
As a professor teaching in the area of origins, I want my students to assess diligently the plausibility of any grand hypothesis. Sadly, when Parrington turns to the origin of the genome’s complexity, he recycles a vague story of gradual development, never reckoning with mathematical implausibilities that scream out to us. Wedded to Darwinian doctrine, he serves up a feeble series of “just so stories.”
Despite these reservations about origins storytelling, Parrington’s survey of genomic hypercomplexity is a gem, a scientific feast to savor. After his “mystery tour” of a genome that seems more astonishing with each passing month of discovery, you’ll never think of DNA the same. And the next amazing chapter is being written right now, in a genomic lab near you. —Tom Woodward
Tom Woodward (PhD, rhetoric of science, University of South Florida) is a research professor at Trinity College of Florida and directs the C. S. Lewis Society, an apologetics ministry launched originally on the Princeton campus. He authored Doubts about Darwin (Baker Books, 2003) and Darwin Strikes Back (Baker Books, 2006).