I recently finished reading Thomas Nagel’s Mind and Cosmos: Why the Materialist Neo-Darwinian Conception of Nature is Almost Certainly False, published by Oxford Press in 2012.

Nagel, who earned his PhD from Harvard and now teaches at New York University, is widely considered to be one of America’s most prominent philosophers. He is also an avowed atheist, known for delivering this famous nugget:

“I want atheism to be true and am made uneasy by the fact that some of the most intelligent and well-informed people I know are religious believers. It isn’t just that I don’t believe in God and, naturally, hope that I’m right in my belief. It’s that I hope there is no God! I don’t want there to be a God; I don’t want the universe to be like that.”

I was therefore surprised to come across these lines, in reference to contemporary debates over the mind/body problem and the broader cosmological implications of evolutionary biology, from his Introduction to Mind and Cosmos:

“Even if one is not drawn to the alternative of an explanation by the actions of a designer, the problems that these iconoclasts [religious intelligent design theorists] pose for the orthodox scientific consensus should be taken seriously. They do not deserve the scorn with which they are commonly met. It is manifestly unfair” (10).

Nagel advances his own thesis against this “orthodox scientific consensus”—what he calls psychophysical reductionism—by arguing that it is incapable of robustly accounting for realities such as consciousness, intentionality, meaning, purpose, thought and value.

Throughout the book, Nagel makes it clear that he finds the hypothesis of an intelligent designer neither plausible nor philosophically sound. He does, however, conclude that it is likely that natural teleological principles guide and govern the unfolding of nature, and can make better sense of the aforementioned features of our existence than the present alternative.

Being an atheist, Nagel’s hypothesis cannot be dismissed as pseudo-scientific religious philosophy. Being a foremost contributor to contemporary mind/body philosophy, he’s no lightweight thinker.

Nagel has long been suggesting that he finds the contemporary scientific orthodoxy unsatisfactory. He even published an article in a prominent philosophy journal in which he argued that it can be entirely constitutional—and more importantly, completely scientifically responsible—to include intelligent design in science class discussions about the evidence for and against scientific theories meant to cover the data of evolutionary biology well, and fully.

Whatever one thinks of Nagel’s own proffered answers to the questions he raises in Mind and Cosmos, he has done academic freedom a great service by publicly challenging the dogmas of scientists who smuggle philosophical views (such as psychophysical reductionism) into the science classroom.

Academic freedom in the fields of evolutionary biology, cosmology and physics is somewhat endangered anymore. Ever since a fear of fundamentalism invaded the academy, any interpretation of data that deviates from strictly atheistic readings is anathema to scientists who have brought their own emotionalism into the debate, hoping to construe the data such that biology especially proves to be the “intellectual superhighway to atheism,” as Richard Dawkins has said.

Indeed, anyone who has sat through philosophy 101 and who has read any of Dawkins’ work notices instantly that the majority of his public literature is not primarily scientific at all but is philosophical (the same is true of Stephen Hawking, whose recent The Grand Design betrays a stunning ignorance of basic philosophical competency). As Al Plantinga has (rather humorously) pointed out,

“Dawkins is not a philosopher (he’s a biologist). Even taking this into account, however, much of the philosophy he purveys is at best jejune. You might say that some of his forays into philosophy are at best sophomoric, but that would be unfair to sophomores; the fact is (grade inflation aside), many of his arguments would receive a failing grade in a sophomore philosophy class.”

The bad news for academic freedom is that the “orthodox scientific consensus” decidedly includes philosophical interpretations of experimentation. Since the majority of scientists in the academy hold to the philosophy that Nagel attacks in Mind and Cosmos, the academic freedom to not deduce atheism from a study of biology is sacrificed on the altar of “academic integrity” that is, in reality, determined by the philosophical biases of the majority—thus entirely defeating the purpose and undermining the logic of academic freedom.

Exhibit A: Ball State University (BSU), a public university in Muncie, Indiana. There, Eric Hedin, a professor in the Department of Astronomy and Astrophysics, created a national controversy this summer by including on the syllabus for his “Boundaries of Science” honors science elective the writings of thinkers who suggested that there are, in fact, boundaries to what science—as an academic discipline—can and cannot determine.

Ball State president Jo Ann Gora announced late this summer that, after further review, Hedin’s course would be discontinued at the university: He was charged with teaching philosophy (and “Christian religion”) in the science classroom and even with “proselytization” by some of his more vocal critics. Why?

Hedin believes that the physical structure of the universe bespeaks the sort of teleological principles that Nagel also detects, although Hedin believes that one can responsibly, additionally posit the activity of a supreme intelligence without contradicting any data.

In explaining the cancellation of Hedin’s class, Gora revealed that his course had been judged unsuitable to the standards of “academic integrity” by his peers in the sciences (she was referencing statements released by numerous national scientific councils and foundations on the matter of how one may “read” cosmological data).

Nevermind that a cursory glimpse at Hedin’s CV instantly punctures such a claim; a much more alarming occurrence, one that garnered less media attention, was unfolding simultaneously in Muncie.

When Ball State hired a man named Guillermo Gonzalez this summer on June 12 as a tenure-track assistant faculty in the Department of Astronomy and Physics, the Madison-based Freedom From Religion Foundation, as well as peer science faculty at BSU, publicly and voraciously criticized his hire.

You can probably guess whence the criticisms. Gonzalez coauthored a 2004 book in which he argued that the facts of the universe bespeak a teleology or intentionality. Not so different a thought from Thomas Nagel, a man whose academic credentials have never been questioned (except for the people like Daniel Dennett).

Gonzalez was denied tenure at Iowa State University (ISU) in 2006, allegedly because his work was not up to snuff and he did not meet the requisite academic and publishing standards for tenure.

When he was denied tenure, he was told that he had not produced an adequate amount of scientific research. An interesting claim, given that he outperformed all ISU astronomy faculty in normalized publications from 2003 to 2006 (not to mention that he authored an astronomy textbook published by the University of Cambridge during that same time). A brief look at his own CV reveals a scientist whose competency and achievements are unquestionable. Furthermore, Gonzalez has never taught intelligent design in a classroom (nobody claims that he has) and has publicly announced that he has no intention to do so at BSU.

Yet the same atheist professor-blogger who drew national media fire to the Hedin case lamented of Gonzalez hire, ”If the university wants to retain any scientific credibility, they should start hiring scientists who will teach real science and not religious apologetics.”

Gonzalez’s story is not alarming because he was denied tenure simply for holding certain academic views and not others: It’s no secret that politics and ideology determine many tenure appointments. His story is alarming because he is being persecuted at BSU now not for his academic credentials (they are unquestionable), not for what he has or has not taught in a classroom, but simply for the fact that he is an astrophysicist who publicly admits to believing in God on rational grounds. For a man in his field, that apparently can amount to professional suicide: It is an indication that one is a faulty scientist.

The philosophy of science is distinct from science itself, yes. But if the BSU controversies are an issue of keeping philosophy of science in the philosophy classroom and not the science classroom, why do the Jerry Coynes of the world get to proclaim their theological and philosophical views in the name of Science? Why are scientists who see faith and reason as being symphonic rather than antinomic denied tenure and attacked not even for what they teach, but simply what they believe? And how can academic scientists dismiss as “religious obscurantism” (Sam Harris’s term) objections to the present orthodoxy when some of the objectors are atheists themselves?

The purpose of academic freedom is to ensure that public university environments remain true to their etymological roots in welcoming a diversity of professional opinions in all disciplines, especially in fields that are controversial. Academic freedom exists to prevent majoritarian thought-regimes from determining whose opinion meets standards of “academic integrity” and whose does not. Of course, the relationship between academic freedom and academic integrity can be a tense and nuanced one, but they need not and should not be pitted against one another.

Nevertheless, when it comes to the present orthodoxy of cosmology, biology and physics, what we have in many university systems is the suppression of academic freedom in the name of a sham academic integrity. When this is the case, something is wrong either with how we understand one of those terms, or with how we understand the disciplines in the name of which we invoke them.

Nagel’s book has opened afresh the discussion on the nature of evolutionary biology: its limits, its achievements and viable alternative explanations. For those who believe the present scientific orthodoxy to be fundamentally wrong in its atheistic absolutism, this is happy news indeed.

Every university student has a right to be taught sound science without being force-fed her professor’s philosophical and religious views. In this regard, it is not Eric Hedin and Guillermo Gonzalez who are the guilty parties. Unfortunately, the guilty party is more often than not the one wielding the gavel.