May 5, 2017 | Tom Woodward

Darwin, Design, and the Art of Being Shocked


“Why Darwin Was Wrong about the Tree of Life” 

Dr. Thomas Woodward

by Dr. Thomas Woodward

These startling words dominated the cover of New Scientist in January, 2009, less than a month before the worldwide celebrations of the bicentennial of Charles Darwin’s birth.

Contrary to appearances, the editorial staff of New Scientist was not changing its stance on the truth of evolutionary theory, but that did nothing to diminish the surprise felt by readers when evolutionary biologist Michael Rose said, “The tree of life is being politely buried – we all know that. What’s less accepted is our whole fundamental view of biology needs to change.”

In the article several biologists took issue with Darwin’s famous branching pattern, arguing that the new picture of evolution was much more complex and messy—something like a web with endless collaborations and mergers.

In short, all is not quiet on the Darwin front. 

Five years later, in late 2014, a Nature News article asked the provocative question, “Does evolutionary theory need a major rethink?”   Two sides weighed in, and one group of eight scholars said, “Yes, urgently.”   The other group reassured readers not to worry, asserting, “No–all is well.”

Again, something called the “fact of evolution” was not questioned; both groups pledged their loyalty to the sufficiency of natural causes as explaining the rise of the living world.  Yet Darwin’s unique and pivotal ideas, which had served as the core of evolutionary theory, were coming in for brutal questioning. Meanwhile, the shadow of design theory hovered in the background.  The ghostly influence of intelligent design was even described as affecting scientific rhetoric: “Perhaps haunted by the spectre of intelligent design, evolutionary biologists wish to show a united front to those hostile to science.”[1]

Some secular scholars even went further, arguing that the philosophical foundation of naturalism needs to be rejected.  For example, atheist philosopher Thomas Nagel in late 2012 stirred the pot with his radical Oxford Press book, Mind and Cosmos.  This slender blast, with just 126 pages of text, unleashed a firestorm as it addressed the nagging mystery of the origin of life, along with rise of cognition and consciousness itself. The book’s subtitle was deliberately shocking:  “Why the Neo-Darwinist Materialist Conception of Nature Is Almost Certainly False.”

Adding insult to that injury, Nagel proposed that to explain the rise of both life and mental phenomena, we must conceptualize the universe in a new way–as having a mental dimension, which exists alongside the material aspect.  In effect, he was trying to propel science into a fundamentally altered pathway of investigation. Nagel explicitly declined the “supreme designer” hypothesis, never stating his reasons for doing so.

Why was Nagel, who had studied biological origins closely for decades, taking this drastic step?  Clearly, this move grew out of his deep grasp of where the evidence was trending,  that a paradigm shift away from neo-Darwinism was underway and nearing a critical point.   In Nagel’s mind, the plausibility of traditional Darwinian theory was not just badly damaged; it had collapsed.  Nagel’s concluding comments are blunt and biting:

“I have argued patiently against the prevailing form of naturalism, a deductive materialism that purports to capture life and mind through its neo-Darwinian extension.  … I find this view antecedently unbelievable—a heroic triumph of ideological theory over common sense. … I would be willing to bet that the present right-thinking consensus will come to seem laughable in a generation or two—though of course it may be replaced by a new consensus that is just as invalid.  The human will to believe is inexhaustible.

Small wonder then that Andrew Sullivan’s cover story on Nagel in The Weekly Standard pictured the philosopher as tied to a stake, encircled by figures with red-hooded robes.  Flames roared around his grey suit.  Similar rhetorical attacks had been unleashed against leaders of the intelligent design movement in the previous decade, but again: here we see that rage turned on a fellow atheist, who dared to say that design theorists like Michael Behe and Stephen Meyer deserve appreciation, not scorn, for pointing out unsolved mysteries.

Re-released in 2016 (click for information)

Thus, growing “doubts about Darwin” have continued to percolate unstopped and unstoppable since the release of my book Doubts about Darwin in 2003.   Indeed, discussion and debate have swirled so intensely, it has led at times to public eruptions of ferocious and frantic opposition to the controversial new theory of intelligent design.

Why such an emotional reaction to the relatively new entry of intelligent design theory (IDT)?  After all, its approach to the question of origins can be described as  “minimalist.”   Since it investigates nature by the tools, methods and data of science and science alone, without reference to the scriptures of any world religion, one would think it should be welcomed at the table where newer but potentially worthy ideas are being vetted. Yet, with its focus squarely on studying the patterns in nature that are best explained as resulting from intelligent agency, not natural processes like natural selection, it has been viewed as a very dangerous idea.

The hostility it has received is understandable. Design theory has challenged the hegemony of science’s ruling philosophy, naturalism—the view that all reality is material and natural, and that there is no “non-physical stuff” to consider as possibly real or worthy of investigation.  It is simply “a fact” and a starting point that there are no souls, no angels, no Platonic forms or ideals, no real personal-infinite god anywhere.  “To posit otherwise is to leave science!” says the naturalist referee, as he throws down his philosophical penalty flag.

Design theory, while viewed by some as a dread and a grave threat, also can be seen as supremely positive development—even a liberation of science.  How?   It may be seen as rescuing the scientific enterprise from philosophical captivity, or restoring science to its previous glory in openly engaging metaphysics.  It has opened up a new vista where science has a restored power:  the ability to show how nature bears witness to a source above nature itself.  In its pure essence, IDT grants to science the astonishing role of detecting, or inferring, the reality of a higher realm of Mind.  Not since before the Darwinian Revolution, triggered in 1859, has science been on the edge of such a restoration of explanatory power.

The New World of Darwin-Design Engagement

Yet, faced with this prospect, he authorities have acted in a way that is dead set against any such fundamental modification of the purview of science.   After 2003, when this book was first released, rhetorical assaults on intelligent design became loud and vehement. Hardly a month passed without a fresh denunciation from some prestigious body of scientists.  As the conflict grew wider and more intense, it seemed best to catalogue this second phase of IDT’s history with a separate volume.  That happened in 2006 with the publication of my sequel, “Darwin Strikes Back:  Defending the Science of Intelligent Design” (Baker 2006), still available in a kindle edition.

Now, in 2016, it may very well be a good time for a “third volume” to cover the past decade, with the flow of both continued hostility, but also positive results from laboratory tests by the Biologic Institute, and other science centers, which robustly support the predictions of design theory.  A string of stunning discoveries, including the worlds of RNA genes, epigenetics, and orphan genes, have fundamentally altered the landscape. Also, the collapse of the “junk DNA” picture of our cell has an enormous implication for the Darwin-design debate.  (See below under the “Art of Being Shocked.”)

But before that new volume is penned, it is a perfect time, some thirty years after IDT’s founding, to reexamine its momentous launch, emphasizing the first 18 years of development (1985 to 2003) which is the focus of this book.  It is time to show how newer developments can be understood only in light of the original goals of the founders of design theory.  It is especially instructive to reflect on the predictions made by design theorists when the movement was in its infancy.



To understand IDT today, one must relive the explosion of a unique “non-Genesis-based” book written by self-described agnostic Michael Denton, which helped to birth the new theory. That book, Evolution: A Theory in Crisis, was recently released in a new, fully-revised edition.  Although dozens of new arguments and lines of data have been woven into the new edition, the title only needed a slight change:  “Evolution:  Still a Theory in Crisis.”

When Denton saw his book come to light first in England (Hutchinson, 1985) and then in America (Adler and Adler, 1986), he probably had no idea what a scientific shift he was helping to trigger.  For it was his blistering critique of Darwinian macroevolution, coupled with a 1984 book on the origin of life, entitled The Mystery of Life’s Origin, by Charles Thaxton, Walter Bradley and Roger Olsen, which together fathered the movement at its inception.

It is in this spirit of seeking a clear historical frame, and gaining a narrative perspective of the present conflict, that we revisit IDT’s foundations.  All of the newest tremors coming from the world of the “design debate” are not oddities in a vacuum; they are an extension of a paradigm struggle of the highest order.

The Art of Being “Paradigm-Shocked”

In this context, let us note a clever but little-known phrase in the writings of C. S. Lewis: “The art of being shocked.”  Lewis proposed this phrase as a possible title for his inaugural BBC radio broadcasts, published originally as “Broadcast Talks.” Now these ten short chapters are the opening two sections of his celebrated book “Mere Christianity.”

The phrase was never used by BBC, and is rarely mentioned by biographers (it appears in the letter he wrote to BBC official James Welch in February, 1941).  Yet, the art of being shocked has enduring “bite”; it captures a “jarring” that can be felt when a non-theist hears for the first time a rational, compelling case for the theistic worldview.  Here the words as “bite” and “jarring” are my crude attempt to recover the original sense of “shock” in the Lewis’s phrase,[2]  as he sketched for BBC his plan for a shock treatment on the secularized public of the United Kingdom.

The key issue here is exploring the ultimate ground of reality, specifically: the existence of a higher Mind.  Is there, or is there not, any good reason to believe that an Intelligence exists above us? Is the universe governed by a concrete, objective Being with a mind, who thus has a will, and intentions, and who can plan and then realize that plan in the universe?

Lewis’s strategy was to point out what he viewed as the most powerful clue for the existence of a Mind.  A window on ultimate reality is opened up to any person who thinks carefully about his daily activity of passing judgment on right and wrong behavior around him.  Our ability as humans to discern the Rule of Right Behavior, says Lewis, points to a “Mind” which exists above us.  Lewis added that we not only discover this Mind, but we also find out (this is part of the “shock”) that we are on the wrong side of the moral balance sheet. We have fallen short of those very standards that we found embedded in the moral fabric of the universe.

Does a Mind exist above us, as the inferred cause of the natural world we see?

So Lewis’s argument from morality, used frequently, including the opening chapters of Miracles, to mention one spot, is the opening barrage in a two-phase briefing in the “art of being shocked.”   Those who would experience the second set of shocks should read Book Two of Mere Christianity.

Now, in the context of the rhetorical war raging around the theory of intelligent design, I want to apply this phrase to the history of IDT’s ongoing struggle of persuasion. In the Great Origins Debate, parallel to Lewis’s project of persuasion, the ultimate question is:  “Does a Mind exist above us, as the inferred cause of the natural world we see?”

This is not trivial.  There can be no greater question that is raised in the media, in the universities and schools, whether that question is answered by a scientific, philosophical, or religious approach.  It clearly is at the center of all cultural and worldview concerns; it sets the agenda in all other realms of philosophy, theology, and even science.

The history of intelligent design, starting with the events in this book and continuing all the way to discoveries in the science news this week, can be seen as today’s art of being shocked.  Let me mention three newer paradigm shocks that connect with the pages that follow.

  • Junk DNA…going, going, gone! The Darwinists’ much-loved “junk DNA” doctrine, which served as a rhetorical bludgeon for decades, claimed that most of our genome is the broken or non-functional leftover of a long history of aimless evolution.  Now, that theory is unraveling and is in deep trouble.  Many molecular biologists would go further and say that the “junk DNA” perspective has collapsed.  This change happened in the wake of discoveries published by researchers working at the level of molecular biology. Several hundred scientists began exploring parts of the genome that were assumed to be superfluous, since they did not code for proteins.   The astonishing result is that perhaps 80% or more of our DNA seems to play some functional role, according to published findings of the multi-national project ENCODE  (Encyclopedia of DNA Elements).  This flow of dozens of technical scientific papers, published in 2007 and 2012, have caused such a huge uproar, that they have set in motion a major rethinking of how widely our DNA is opened, read, and used.

Consider the remarks of Francis Collins, the Evangelical Christian who was formerly the head of the Human Genome Project and now leads the prestigious National Institutes of Health. Although he previously used the “junk DNA” argument in The Language of God to support his Christian Darwinism view, he changed his mind in 2011:  “It turns out that only about 1.5 percent of the human genome is involved in coding for protein. But that doesn’t mean the rest is ‘junk DNA.’  A number of exciting new discoveries about the human genome should remind us not to become complacent in our understanding of this marvelous instruction book. For instance, it has recently become clear that there is a whole family of RNA molecules that do not code for protein. These so-called non-coding RNAs are capable of carrying out a host of important functions, including modifying the efficiency by which other RNAs are translated.” (The Language of Life, 293)

  • Darwin’s Doubt, Stephen Meyer’s 2013 New York Times bestseller, exploded onto the Darwin scene on the heels of his earlier book Signature in the Cell which was named one of the top 100 books of 2009 by Britain’s secular Times Literary Supplement.

Both of these magisterial books have had massive influence in science, with Signature in the Cell addressing the origin of life enigma, while Darwin’s Doubt confronts the Cambrian explosion—the sudden appearance of complex animal fossils at the base of the geological column, without any ancestors in view.  The Cambrian mystery was named by Darwin himself as an “objection” that can be “rightly urged” against his theory.  Darwin’s Doubt garnered appreciative blurbs from several evolutionary biologists, including Cambrian fossil experts. Meyer’s analysis of every new theoretical “escape route” to account for the sudden emergence of over 20 phyla fills the second half of the 480-page tome.

Not only did these books mark a turning point in the design debate, but each has also generated a significant literature in response to Meyer’s arguments.  Meyer’s exposé of the worsening Cambrian situation has prompted enough scholarly interaction to lead a second book,  Debating Darwin’s Doubt (2015).

  • RNA, Epigenetics and 3-D Genome Packing: Another shock has come from the explosion of “RNA genes” which was alluded to in the comment of Francis Collins above.  Beginning in the late 1990s and accelerating since 2000, a myriad of functional RNA molecules were found to play previously unknown roles in the cell. Thus the origin of protein-coding genes, which neo-Darwinism is focused on, is just a subset of the much larger iceberg:  the multi-layered genome.  Several kinds of functional RNA molecules, which never leave the nucleus to be translated into proteins, play vital roles in cellular functions that were not glimpsed just two decades ago.

Parallel to the mushrooming of RNA genes is the discovery of a world of additional layers of chemically-coded information sitting beyond the DNA double helix.  (For details, see “The Mysterious Epigenome: What Lies Beyond DNA” by Dr. James Gills and myself.) Some of these code markers are tiny “methyl tags” which are directly added to some of DNA’s “C- letters” in order to switch off the gene that such a letter is part of.  Other epigenetic information is found on “tails” that protrude from the DNA spooling devices called histones, and still further information is embedded in the cell’s membrane (the so-called “cortical inheritance”) and in other structures such as microtubules.  It is as if we were told that our laptop had digital information embedded not only in the hard drive, but in practically every physical part of the laptop itself!

Beyond RNA and epigenetics, scientists recently elucidated yet another level of information that is programmed in the cell: the 3-D arrangement of genomes, both in chromosomal architecture, and in the fitting together of chromosomes in relation to each other. Such precise “fittings” set the stage for cooperative activity and conversations between chromosomes.  So the RNA and epigenetics explosions have a third partner in shocking biologists: 3-D architecture. These shocks have dramatically raised the explanatory stakes for Darwin’s blind, unguided, unintelligent process.  On the other hand, such higher order control information and genome architecture is just the sort of physical reality that finds a very plausible fit with intelligent agency.

This list of paradigm shocks could be supplemented with a discussion of “orphan genes” and truly could be extended to a dozen or more shocks.  Yet, the point has been made clearly enough:  science has been thrust into a new era that is exciting and breathtaking for design theorists, and increasingly bewildering to defenders of Darwin’s aging theory.

For the background of how this new intelligent design perspective on the universe and life arose through a powerful story unfolding after 1959, and then exploding in the mid-1980s, we must enter the story itself, the evolution of “doubts about Darwin.”

Dr. Woodward is president of the C. S. Lewis Society in Tampa, Florida


[1] Quoted from the online file as it appeared on March 3, 2016:

[2] The “art of being shocked” is somewhat similar to the German philosopher Emmanuel Kant’s comment, upon reading the philosopher David Hume, that he had been  “aroused from dogmatic slumber.”  I trace this phrase as it appears in the early IDT literature, especially in the effect Denton had on his readers.

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