This post analyzes documented public intellectual debates between named individuals. It does not take a position on the existence of God or the validity of religious faith. Both scientific and theological communities contain serious, thoughtful people who have engaged these questions with rigor.
Francis Collins sequenced the human genome — arguably the most consequential act of reading in the history of biological science. Then he wrote The Language of God, in which he argued that the same genome pointed unmistakably toward a creator. His colleagues were, by and large, silent. Jerry Coyne was not.
The debate between Collins and Coyne is the most sustained, publicly documented exchange between a believing scientist and a secular scientist in recent American intellectual history. It was conducted in books, blog posts, journal responses, and media appearances over roughly a decade, and it remains largely unknown outside specialist circles. That is a failure of public discourse, because the question it addresses — can the same data set simultaneously support evolution and theism? — is not an abstract one. It is a question about whether scientific rationality and religious belief are compatible, and by extension, what kind of culture we want to be when we make decisions about biomedical research, education, and the public meaning of science.
What the Genome Project Actually Produced
The Human Genome Project completed its first working draft in June 2000. Collins stood alongside President Bill Clinton and Craig Venter to announce it. Clinton described the moment as learning the language in which God created life. Collins was more careful, but not by much. He later described the experience as humbling and awe-inspiring — and said it deepened, rather than challenged, his faith.
That faith had a history. Collins was not raised religious. He converted to evangelical Christianity at age twenty-seven, while serving as a medical resident, after a conversation with a dying patient who asked him what he believed. He described the intellectual path that followed in The Language of God (2006, Free Press): from atheism through agnosticism to Christian faith, guided in part by C.S. Lewis’s Mere Christianity and, he wrote, by a hike in the Pacific Northwest during which he encountered a triple waterfall that crystallized his sense of God’s presence.
That waterfall became a flashpoint. Harvard experimental psychologist Steven Pinker, in his public critique of Collins’s 2009 nomination to lead the NIH, described the idea that nature contains private coded messages from a supernatural being to an individual person as the antithesis of the scientific — indeed rational — mindset. Pinker’s language was sharper than most of Collins’s colleagues were willing to use publicly, but it represented a view that was, in private, widespread.
The Language of God
Collins’s book was a bestseller. It also established the intellectual framework he would build the BioLogos Foundation on: the position he called BioLogos, combining bios (Greek for life) and logos (Greek for word), the idea that theistic evolution — God working through the mechanism of natural selection — is compatible with both scientific rigor and evangelical Christianity.
The central argument of The Language of God is that the genome, read carefully, supports theism. Collins pointed to several features he regarded as evidence: the universal genetic code (one language across all life), the apparent fine-tuning of physical constants, and above all, the moral law — the sense of right and wrong that Collins argued exists in every human culture and cannot be explained by evolution alone. He called this last argument the “Moral Law argument,” borrowed explicitly from C.S. Lewis.
The genome, in Collins’s reading, is not neutral data. It is, as Clinton suggested at the announcement, a language — and a language implies an author.
Jerry Coyne’s Response
Jerry Coyne is an evolutionary biologist at the University of Chicago, a specialist in speciation, and one of the more tenacious public defenders of the view that science and religion are fundamentally incompatible. His book Faith vs. Fact: Why Science and Religion Are Incompatible (2015, Viking) is the most detailed published critique of positions like Collins’s.
Coyne’s objections to Collins’s argument operate at several levels simultaneously. At the scientific level, he argued that the Moral Law argument is empirically false: evolutionary biology can and does explain moral intuitions, including cross-cultural ones, as adaptations. Altruism, fairness, and punishment of defectors can all be modeled by kin selection and reciprocal altruism — mechanisms Darwin sketched and subsequent researchers confirmed. The existence of a moral sense does not require a supernatural source.
At the epistemological level, Coyne argued that Collins’s method is systematically flawed: he accepts scientific evidence when it confirms evolution, then switches to a different standard — personal experience, intuition, revelation — when he wants to affirm theism. Coyne maintained that this inconsistency disqualifies the argument as rational inquiry, because you cannot invoke scientific standards selectively. If extraordinary claims require extraordinary evidence — Sagan’s formulation — then the claim that the genome points to a personal God requires considerably more than a beautiful waterfall and a reading of C.S. Lewis.
On his blog Why Evolution Is True (whyevolutionistrue.com), extensively archived, Coyne engaged Collins’s arguments in detail over many years — responding to specific claims in BioLogos publications, pointing out what he regarded as logical fallacies, and arguing that organizations like BioLogos, which promote accommodation between science and religion, ultimately do a disservice to public scientific literacy by suggesting the two are compatible frameworks for understanding reality.
The NIH Nomination and the Science Magazine Controversy
In July 2009, President Barack Obama nominated Collins as director of the National Institutes of Health. The response from the scientific community was revealing precisely in its distribution: Collins drew flattering remarks from researchers and biomedical groups for his administrative and scientific track record, and quiet discomfort from those concerned about what his public religious advocacy would mean for the leadership of a federal science agency.
Sam Harris published an op-ed in the New York Times arguing that Collins was unfit for the position. Collins had written that science is not particularly effective — in fact it’s rather ineffective — in making commentary about the supernatural world. Harris’s argument was that a man who sincerely believes that a scientific understanding of human nature is impossible is not the right person to direct the most important and well-funded scientific organization on the planet.
Steven Pinker raised parallel concerns. Collins was confirmed unanimously by the Senate. He served under three presidents.
What the nomination controversy revealed was not primarily whether Collins was competent — he was, demonstrably, an exceptional scientist and administrator. It revealed that his colleagues had been conducting, in public, a civil fiction: that a scientist’s private religious beliefs are entirely separate from his public intellectual commitments. Collins had made that fiction impossible to maintain, by writing a bestselling book arguing that the genome is evidence for God and founding an organization dedicated to promoting that view among evangelical Christians.
Coyne’s position was that the fiction should never have been maintained in the first place — that the compatibility narrative is itself a form of intellectual dishonesty.
Can the Same Data Set Point Both Ways?
The question at the center of this dispute is genuinely hard: can the genome — the complete instruction set for a living organism, product of 3.8 billion years of evolution — simultaneously be the strongest evidence for natural selection and evidence for intelligent design?
Collins’s answer is yes, if you define “intelligent design” correctly. He explicitly rejected creationism and what he called “Intelligent Design” as practiced by the Discovery Institute — the idea that specific biological structures are too complex to have evolved and therefore require supernatural intervention. That, he argued, is bad theology and bad science. His position was that God created through the mechanism of evolution — that evolution is the how and theism addresses the why.
Coyne’s answer is no. The genome, read as a data set, shows precisely what you would expect from an undirected process of mutation and selection: it is full of broken genes, pseudogenes, retroviruses embedded in our DNA, and functional but inelegant solutions to engineering problems. A designer working with the genome would have been a designer who created pain, waste, and extinction on a scale that strains any conventional definition of benevolence.
You can read my review of The Selfish Gene and Dennett’s Darwin’s Dangerous Idea for the strongest versions of Coyne’s underlying framework. Both Dawkins and Dennett argue that once you understand what natural selection actually does — what the Extended Phenotype concept reveals about how genes build structures beyond individual bodies — the idea that evolution requires guidance from outside the system becomes increasingly difficult to sustain.
But this is where the argument gets philosophically subtle in a way that neither side always acknowledges. Coyne’s critique of Collins assumes that the same evidential standards apply to all claims — that you cannot use scientific evidence to support part of your worldview and then invoke personal revelation or experience for another part. This is a defensible position. It is also, strictly speaking, a philosophical position, not a scientific one. The claim that all warranted beliefs must meet scientific standards of evidence is itself not a claim that can be confirmed by scientific experiment.
Karl Popper, whose work on the demarcation problem I’ve written about here, was careful to distinguish between the domain of scientific inquiry and the broader domain of rationality. Science, he argued, is distinguished by falsifiability — the willingness to specify what observations would disprove a hypothesis. Many genuine and important questions fall outside that domain. The philosophical question of whether consciousness requires a material substrate is not falsifiable in the Popperian sense. Neither, strictly, is the question of whether the universe has a purpose.
Coyne would respond, and has, that this is exactly the kind of intellectual territory that theologians use to protect untestable claims from scrutiny. He may be right. But the response cuts both ways: the claim that all genuine questions must be scientifically answerable is also untestable by the standards of science.
The Silence of Collins’s Colleagues
What strikes me about this episode, more than the substance of the Collins-Coyne exchange, is the silence of Collins’s scientific colleagues during the years when he was publishing books and founding BioLogos. The scientific community did not, as a community, engage seriously with Collins’s theological arguments. They mostly looked away.
There are good reasons for that silence. Science, as an institution, operates through peer review of specific claims in specific domains. The question of whether the genome points to God is not a genetics question, so geneticists are not professionally obligated to address it. Religious belief is widely understood as a private matter, and publicly criticizing a colleague’s faith crosses social norms that are otherwise functional.
But the silence had a cost. Collins’s books sold millions of copies. BioLogos reached significant audiences among evangelical Christians who were seeking permission to accept evolution without abandoning faith. The intellectual quality of the engagement those audiences received — from the Collins side — was largely unchallenged in public scientific discourse until Coyne, and later Richard Dawkins in the later editions of The God Delusion, engaged it directly.
The consequence of that silence: a public that received a well-packaged argument that the genome is God’s language, and very little rigorous public response from working scientists. Coyne, whatever one thinks of his conclusions, was doing necessary work. He was saying, publicly, what many of his colleagues said privately. He deserves credit for that, even from those who disagree with his conclusions.
What the Exchange Actually Settled
The Collins-Coyne exchange settled nothing about whether God exists. It was never going to. But it did clarify the terms of the question with unusual precision.
It established, on the scientific side, that evolutionary biology does not require theistic supplement. The genome, read as data, is fully explicable by natural selection, genetic drift, and deep time. Nothing in the biology requires a designer.
It established, on the theological side — through Collins’s articulation if not Coyne’s critique — that theistic evolution is a coherent philosophical position, in the sense that it does not require rejecting any specific scientific finding. If you accept evolution fully and locate God’s action in the creation of the conditions that made evolution possible, you have not contradicted any published result in any peer-reviewed journal.
What it did not settle: which of these positions is correct. That question depends on philosophical priors — about what constitutes evidence, about what kinds of explanations are satisfying, about whether the universe is the kind of thing that can have a purpose. Those are not questions that a particle accelerator, a genome sequencer, or a series of blog posts can resolve.
They are, however, questions worth having in public. That is what the Collins-Coyne exchange demonstrated, despite its acrimony. It showed that the conversation can be had — rigorously, with primary sources, in verifiable detail — without retreating into either religious obscurantism or the reflexive contempt that makes scientific atheism occasionally as frustrating to engage with as the creationism it opposes.
The genome is three billion base pairs of molecular history, accumulated over billions of years of trial and error. What it means — beyond what it does — is a question that neither Collins nor Coyne has finally answered. Neither will we. But the asking is not optional.
Sources
- Francis Collins, The Language of God: A Scientist Presents Evidence for Belief (2006, Free Press) — publisher page
- Jerry Coyne, Faith vs. Fact: Why Science and Religion Are Incompatible (2015, Viking) — publisher page
- Jerry Coyne, Why Evolution Is True blog — whyevolutionistrue.com
- Sam Harris, op-ed on Collins NIH nomination, New York Times, July 2009 — NYT archive
- Steven Pinker, statement on Collins nomination, reported by scholarly sources, July 2009
- Jocelyn Kaiser, Science magazine coverage of Collins nomination, July 2009 — Science/AAAS
- Francis Collins, Wikipedia biographical entry — en.wikipedia.org/wiki/Francis_Collins
- BioLogos Foundation — biologos.org
- Richard Dawkins, The God Delusion (2006, Houghton Mifflin Harcourt)
