How Religious Thinking Fuels the Atheist Schism Over Transgender Ideology

Tensions are running high in the atheist community in the United States, where a long-brewing value conflict has now boiled over. In December, several prominent atheist scientists, Jerry Coyne, Steven Pinker, and Richard Dawkins, resigned from the honorary board of the Freedom from Religion Foundation (FFRF) in protest of FFRF’s decision to unpublish an article by Coyne that was critical of transgender ideology, leading to the dissolution of FFRF’s board.

In the wake of the split, both sides of the conflict accused the other of adopting a religious mindset, a stinging charge in a movement ostensibly dedicated to science and reason.

I do think one side in this conflict is more on the side of science and reason than the other. But there are respects in which even the more rational elements of the atheist movement have failed to break free from religious assumptions, weakening their ability to defend themselves and prolonging the controversy. There’s a notorious intellectual fad they’ve embraced that makes them look like hypocrites when they stand up against transgender ideology. They should drop the fad.

Atheist dogmatists vs. atheist heretics

Conflict among atheists about transgender ideology has been brewing for some time. In 2021, the American Humanist Association retracted a 1996 award it had given to Richard Dawkins because of a tweet raising questions about the concept of gender self-identification.¹ The trigger for the latest flare-up was an article on FFRF’s blog, “What Is a Woman?” by Kat Grant.² Grant’s answer, “A woman is whoever she says she is.”

It’s this wishing-makes-it-so definition of “woman” that most clearly prompted Jerry Coyne, a distinguished University of Chicago evolutionary biologist, to negotiate with the FFRF to publish a reply on their blog.³ Coyne’s reply triggered an angry online reaction, and because of that, FFRF removed the post.

What was it about Coyne’s reply that critics found so objectionable?

More than half of Coyne’s piece is concerned with the simple question of whether the biological concept of sex is subject to anyone’s simple say-so. Coyne argues dispassionately that the vast majority of living things, including all animals and most plants, reproduce through the combination of large and small gametes (egg and sperm), and this sexual binary helps explain sexual selection effects in evolution. He shows why none of the biological definitions of “sex” that Grant considers have the same explanatory power as the gamete-based definition.

Coyne also acknowledges that there are rare intersex individuals, but explains why these exceptions do not challenge the basic biological binary. Importantly, Coyne notes that much of Grant’s argument depends on a conflation of biological sex and gender (understood as culturally associated sex role). Here I take it Coyne is referring to the way Grant slides from refuting flawed biological definitions of sex to surveying intercultural differences in views of gender, and offering both as univocal evidence in favor of a subjective definition of “woman.” Coyne allows that gender, unlike biological sex, is a spectrum, not a binary, and doesn’t criticize those who choose to act outside the role associated with their sex. He’s even willing to call Grant by “they/them” pronouns. But he thinks none of this is relevant to the basic biological binary of sex.

While Coyne’s arguments about the biological sex binary sound plausible to me, as a non-biologist I’m not fully qualified to evaluate the debate. But I find little to no assistance from his critics. After deciding to unpublish Coyne’s piece, the FFRF offered no specific criticism apart from the claim that the piece did not align with the organization’s values.⁴ Subsequent defenders of the FFRF’s decision for the most part ignored Coyne’s arguments for the sex binary.⁵ (One tried to challenge the binary by sharing an article that admits that sex is a biological binary but which attacks its utility for failing to explain everything about the behavior of sexed individuals — a straw man if ever there was one.⁶)  

Instead of offering an argument to show why Coyne is wrong on a matter of his expertise, his critics instead focused on his remarks at the end of the piece addressing Grant’s claim that “Transgender people are no more likely to be sexual predators than other individuals.” They’ve made sensible criticisms of Coyne’s use of statistics in claiming that trans women are morelikely to be sex predators.⁷ (Notably, the study he cites draws on a very small sample size and probably classifies non-predatory behavior like consensual prostitution as a “sex offense.”) So far as I can tell, neither Coyne nor his defenders have responded to these criticisms. They should.

You might think that FFRF’s blog, Freethought Now, would be an ideal forum in which advocates of science and reason could argue about the merits of just such statistical claims and their policy implications (something that’s happened recently in another secular publication, the March 2025 edition of Free Inquiry magazine).⁸ Coyne himself acknowledged that his data were “imperfect.” His critics would contend that they are worse than that. But scientists can make honest mistakes in the use of statistics and there’s room for debate over whether his data were better than what Grant offered.

So why not then have that debate, where there seems to be room for reasonable disagreement? Coyne himself insists that he thinks the rights of transgender individuals should be protected. One critic who suggests Coyne is being disingenuous is the self-styled “Friendly Atheist” Hemant Mehta. He accuses Coyne of “spreading anti-trans rhetoric,” alleging that he is “transphobic” and “prejudiced” for claiming that trans women should not compete against biological women in sports, serve as rape counselors for biological women, or be placed in women’s prisons.⁹

Coyne’s policy proposals are eminently debatable, but it’s far from obvious that they result from prejudice or that he’s calling for a form of unjust “discrimination.” It’s far from obvious that sports leagues who base their rules on biological sex are violating anyone’s rights. Coyne is not obviously calling for a ban on trans rape counselors. And it’s even less obvious that prisoners have any right to choose the manner of their imprisonment.

If Coyne’s position and character leave the door open for reasonable debate, why would his article warrant deletion? Here it’s revealing that FFRF was unwilling to specify what about Coyne’s piece was at odds with its values. To have claimed it was a shoddy use of statistics would imply a higher estimate of his arguments for the sex binary. But that would offend the online mob that pushed FFRF to deplatform Coyne because they agreed with Grant that “a woman is whoever she says she is.” It would alienate pundits like Mehta who are quick to accuse anyone who disagrees about policy issues as a dishonest bigot.

This is why, even though Coyne’s use of statistics may be worth criticizing, there’s a real point to his defenders who say his deplatforming is the result of a “quasi-religious” approach, “complete with dogma, blasphemy, and heretics.”¹⁰ It really does look like distinguished scientists are being demonized just because they are willing to speak uncomfortable truths. Anyone who dares speak the forbidden words and violates a sacred taboo must be of unseemly character, and so must be excommunicated. To the extent that Coyne, Pinker, and Dawkins have condemned this religious dogmatism in atheist clothing, they are defending the values of science and reason.

The heretics’ residual religious assumptions

Atheist critics of Coyne and his cadre of “heretics” are otherwise critical of religious dogmatism. They must be sensitive to the criticism that they are, in effect, hypocrites. So it’s no surprise that they’ve tried to turn the table and argue that it’s actually the heretics’ promotion of the sex binary that bears the mark of religious dogma.

Their case for this charge is impressively weak. They point to Grant’s original claim that some early European missionaries settling in America were apparently perplexed by the cross-dressing behavior of members of certain indigenous tribes.¹¹ But their contention exemplifies the very conflation of sex and gender that Coyne flagged. An attitude toward a cultural practice contrary to a traditional sex role is not the same as an attitude about biological classification. And even if a belief in the sex binary was also to be found in the missionaries’ Bibles, this hardly shows it or their reaction came from the Bible. The Bible also mentions the difference between night and day, but this reflects ordinary observations (however uniformed about the underlying scientific explanation) that people have made for millennia, not religious faith.

Yet there is one respect in which the atheist heretics have failed to break free from the pull of religious attitudes, a respect none of their critics have mentioned. If only the heretics would discard this relic of their exposure to a religious culture, they could strengthen their defense of science and reason.

In recent years, atheists including Dawkins and Pinker have followed a trend in the broader rationalist community of paying homage to the value of intellectual or epistemic humility. Dawkins claims that science by its nature is “humble” insofar as it doesn’t pretend to know everything.¹² Just a few years back, the house journal of one of Dawkins’s allied organizations, Skeptical Inquirer, published a piece calling on the skeptical movement to embrace the value of humility as its “guiding credo,” as against a consistent “take-no-prisoners” approach that invites the charge of arrogance or elitism.¹³

Yet when atheists fight back against transgender ideology, they are clearly not practicing anything like the now-fashionable intellectual humility. Not only are they asserting with strident certainty the biological reality of the sex binary, they’re doing so knowing that other very intelligent atheists disagree with them. They’re also intransigent about this biological reality even though they know a whole subpopulation of vulnerable people find their assertion not only offensive but threatening to their identities.

That’s not an exercise in humility, but in pride. It’s precisely this pride that Coyne’s critics are condemning; it’s precisely humility that they’re demanding.

Unfortunately, any atheists who otherwise advocate epistemic humility but take the strident approach against transgender ideology are, frankly, hypocrites. Fortunately, there’s a rational way to escape this contradiction and reclaim the moral high ground: they should give up the humility fad.

If they give it up, they’ll be taking up the more consistently rational position. After all, praise for the value of humility derives ultimately from a well-entrenched religious approach to morality. And contrary to much confusion, it has nothing to do with scientific thinking.

As I have argued in greater detail elsewhere, much of the recent epistemic humility fad is traceable to funding from the Templeton Foundation, an American fund dedicated to spreading religious values.¹⁴ Even the Skeptical Inquirer article references fourteen Templeton-funded studies. Templeton is inspired directly by St. Augustine, who saw humility, the recognition of our alleged lowliness before God, as the foundation of all other virtues.¹⁵

An ethic of humility is also at the heart of the broader “woke” egalitarian movement of which transgender ideology is a part. As John McWhorter has argued persuasively in Woke Racism, the dogmatic religiosity of the parallel “antiracist” movement is propelled by its advocacy of “self-flagellational” white guilt, which McWhorter describes as essentially “Abrahamic” in its demand for submission to a higher power.¹⁶ The “higher power” to which the antiracists submit is the totem they fashion out of oppressed racial minorities. Transgender ideologues also totemize vulnerable transgender individuals and demand submission in their name. It seems that groups like the FFRF are motivated to appease these demands for submission, especially to the extent that they too sympathize with the idea that there is virtue in humility.

The pull of the entrenched Abrahamic worldview is so strong that even McWhorter, another secularist, himself slips into accusing the “woke” of being insufficiently humble in their strident demand for humility.¹⁷ When atheists target a religion or a quasi-religion  for being insufficiently humble, they’re speaking religion’s language and conceding some of its deepest moral premises. This concedes the premises that allow their own critics to take the moral high ground. For those interested in defending science and reason, it’s a losing strategy.

In search of scientific values

If atheists want to defend science and reason, they need to more critically scrutinize the ethical assumptions they’ve inherited as relics of their Judeo-Christian environment. They need to work harder to define a new rational moral code that they can offer as an alternative to anyone who rejects religion and still knows they need guidance for living their life.

The recent attempt to sell intellectual humility cashes in on respect for real virtues. It does this by illicitly conflating them with the original Christian demand for lowliness and submission. The real virtues are objectivity, intellectual honesty, justice, and ambitious pursuit of the truth. Scientists practice these when they recognize their fallibility, realize the difference between what they know and what they don’t, appreciate that others know more than they do about particular subjects, and desire to learn more. But these real virtues have nothing to do with “humility,” which in an ordinary definition means “a modest or low view of one’s own importance.” No one who appreciates the power of scientific reason to discover progressively more truth can see it as modest or lowly.

When Coyne and others stand up for biology against creationists or transgender ideologists, they’re practicing pride, not humility, by acknowledging the earned certainty that comes from their expertise. When and if they acknowledge real uncertainties (as they should do more consistently on the question of the statistics of sex predation), they’re also taking pride, not humility, in their love for the truth, because it conveys respect for the idea that truth does not come on the cheap.

The following proposal itself has to be weighed carefully against the balance of the evidence. Recognizing that the very practice of science involves commitment to these real virtues reveals not just a guideline for scientific practice, but the possibility of a rational code of morality. The rational commitment to truth is not just the source of our knowledge, it also helps to create the values that help us survive. Respecting the power of truth to give life means respecting the needs of the minds that pursue it, both one’s own needs and those of others. Though it goes far beyond the scope of this article, there’s an argument here that unlocks a code of moral virtues and values we need to live on earth.¹⁸

Atheists need to do the work to defend a rational moral code now more than ever. It was a major scandal for the atheist movement that its long-celebrated heroine Ayaan Hirsi Ali converted to Christianity. In her statement explaining her conversion, she argued that the West needs guidance to fight off the triple threats of resurgent authoritarianism, Islamist militancy, and “woke” ideology. “Atheism failed to answer a simple question: what is the meaning and purpose of life?” She argued that only religion can offer such guidance. Someone needs to show anyone who sympathizes with her concern that the values of the Western Enlightenment can form the basis of a powerful moral code — and that religion, by contrast, is at the root of the irrational rivals of the West.

To do that, atheists need the courage of their convictions. The latest row over transgender ideology dramatizes this for all to see. When religious-style dogmatism infiltrates atheism itself, it’s a sign of religion’s pervasive influence on our culture, and thus of the need for the courage to challenge widespread conventional assumptions like the alleged virtue of humility. As Jerry Coyne himself once observed, “Atheists have been ‘humble’ for centuries (who was more humble than Spinoza?) and it hasn’t gotten us anywhere.”¹⁹ And Coyne now says he’s “proud” to be a heretic.²⁰ It’s time to realize he’s right, drop the pose of false humility, and proudly assert the value of the scientific truth over unscrutinized feelings for faddish totems.

1. Alison Flood, “Richard Dawkins loses ‘humanist of the year’ title over trans comments,” Guardian, April 20, 2021.
2. Kat Grant, “What is a woman?,” FreeThoughtNow.org, November 7, 2024.
3. Jerry Conye, “Biology is not bigotry,” FreeThoughtNow.org, December 26, 2024 (Archive.org version).
4. Freedom From Religion Foundation, “Freedom From Religion Foundation supports LGBTQIA-plus rights,” FreeThoughtNow.org, December 27, 2024.
5. Hemant Mehta, “Atheist group faces backlash after publishing, then removing, anti-trans article,” FriendlyAtheist.com, December 28, 2024; Aaron Rabinowitz, “Biology is not ethics: A response to Jerry Coyne’s anti-trans essay,” FriendlyAtheist.com, January 2, 2025.
6. Agustín Fuentes, “Here’s Why Human Sex Is Not Binary,” Scientific American, May 1, 2023.
7. Hemant Mehta, “Atheist group faces backlash after publishing, then removing, anti-trans article,” FriendlyAtheist.com, December 28, 2024.
8. Free Inquiry, March 2025 (vol. 45 (2)).
9. Hemant Mehta, Ibid.
10. Jerry Coyne, “I resign from the Freedom from Religion Foundation,” WhyEvolutionIsTrue.org, December 29, 2024; Jerry Coyne, “Another one leaves the fold: Steve Pinker resigns from the Freedom from Religion Foundation,” Why EvolutionIsTrue.org, December 29, 2024.
11. Hemant Mehta, Ibid. cites Grant, Ibid as showing that “our society’s views on gender are steeped in religious traditions.” Grant cites Michael Lyons, “How European settlers destroyed two-spirit tradition,” November 3, 2015.
12. Richard Dawkins, “Science, the Poetry of Reality, Jewel in Humanity’s Crown,” Center For Inquiry YouTube channel, February 14, 2025.
13. Scott O. Lilienfeld, “Intellectual Humility: A Guiding Principle for the Skeptical Movement?,” Skeptical Inquirer, September/October 2020 (vol. 44 (5)).
14. Ben Bayer, “Why a Secular Commitment to Science Warrants Pride, not Humility,” New Ideal, August 7, 2024.
15. John Templeton Foundation, “Intellectual Humility.”
16. John McWhorter, Woke Racism: How a New Religion Has Betrayed Black America (New York: Portfolio/Penguin, 2021), 27, 68.
17. Ben Bayer, “The Old Morality of the New Religions,” New Ideal, January 4, 2023.
18. Onkar Ghate, “Finding Morality and Happiness Without God,” New Ideal, May 4, 2018.
19. Jerry Coyne, “Responses to Kristof’s call for a détente,” WhyEvolutionIsTrue.com, December 2, 2009.
20. Jerry Coyne,” “Losing My Nonreligion,” Wall Street Journal, March 30, 2025.