Atheist legal commentator Timothy Sandefur believes that the discussion of the weaknesses (in addition to the strengths) of Darwin’s theory of evolution in public schools is an unconstitutional violation of the Establishment Clause. Yet he sees no Establishment Clause problem with the public funding of research in evolutionary biology that asks the same questions that he believes are constitutionally proscribed in public schools.
For example, Mr. Sandefur apparently believes that teaching public school students that there are large inadequately explained gaps in the fossil record is a violation of the Establishment Clause. Yet, as it happens, there is substantial publicly funded ongoing research being conducted by evolutionary biologists on these large inadequately explained gaps. Mr. Sandefur has no Establishment Clause objections to the public funding of the research on this topic; he only objects to publicly funded teaching on this topic. Yet the teaching and the research both address the same premise — that there are large unexplained gaps in the fossil record.
Mr. Sandefur asserts:

…the Constitution places no specific limit against the use of taxpayer money to fund secular activities and the propagation of scientific facts–while it absolutely forbids the spending of taxpayer money for religious activities and the propagation of such religious viewpoints as creationism…

Actually, Mr. Sandefur grossly exaggerates the constraints imposed by the Establishment Clause. The government funds all kinds of “religious activities” and routinely funds “the propagation of such religious viewpoints as creationism,” and always has. Churches, synagogues, and mosques are effectively subsidized by tax exemptions. “In God We Trust” adorns our money. School children pledge allegiance to “One Nation, under God.” Military cemeteries plant crosses and Stars of David on soldiers’ graves. Presidents invoke God in speeches. Legislative bodies routinely open with prayers. Presidents and witnesses in court are sworn on Bibles. Military and police chaplains are paid by the government to carry out their religious duties. Atheist ideology is propagated in public school biology classes at public expense. (Mr. Sandefur will no doubt disagree with the last example).
Worst of all (for Mr. Sandefur), some public school textbooks reproduce this phrase — surely “the propagation of such religious viewpoints as creationism”:

We hold these truths to be self-evident, that all men are created equal, that they are endowed by their Creator with certain inalienable rights, that among these are Life, Liberty and the pursuit of Happiness. –That to secure these rights, Governments are instituted among Men…

Our Creator is the Source of our rights.
How does an atheist like Mr. Sandefur insulate his personal Creation Myth from scrutiny in public schools, when the Founding Fathers explicitly stated that the rights Mr. Sandefur invokes to censor scrutiny of Darwinism are endowed… by our Creator?
You have to love the irony.
Thus, Mr. Sandefur’s atheist angst. Mr. Sandefur, who eschews theism but not worship , no doubt reflects: ‘What would Howard Roark do?” He would refuse to be tied down by cognitive dissonance. Mr. Sandefur endorses censorship of science in public schools based on his own idiosyncratic interpretation of the Establishment Clause. The Establishment Clause (notice how infrequently Mr. Sandefur actually quotes it) merely says this: “Congress shall make no law respecting an establishment of religion…” followed by the Free Exercise Clause, “or prohibiting the free exercise thereof.” The Establishment Clause prohibits the government from establishing religion. Discussing the strengths and weaknesses of Darwin’s theory does not establish religion in any way, shape or form. Rather, to paraphrase Mr. Sandefur, it pertains to a secular activity of the scientific investigation of various scientific claims and facts. Discussing the strengths and weakness of a scientific theory is merely science. Science is the discussion of weaknesses and strengths of theories about nature. As the U.S. Supreme Court stated in the case Edwards v. Aguillard, it is not impermissible to “require that scientific critiques of prevailing scientific theories be taught.” What Mr. Sandefur is demanding isn’t enforcement of the Establishment Clause, which the Supreme Court has ruled does not prohibit critiques of prevailing scientific theories. Mr. Sandefur is demanding censorship of a scientific discussion of which he disapproves.
Now back to the issue of public funding for the research and teaching of Darwin’s theory.
Research in evolutionary biology is inherently research on the weaknesses of Darwinian theory. That’s what ‘research’ means. Research addresses problems that are not yet adequately addressed by the prevailing understanding of the science. Publicly-funded scientific research that does not address scientific questions (weaknesses) goes by another name: fraud.
It’s noteworthy that Mr. Sandefur does not infer that the publicly-funded research on the weaknesses of evolutionary theory is unconstitutional, yet he infers that publicly-funded teaching of the weaknesses of evolutionary theory is unconstitutional. In Mr. Sandefur’s view, it’s perfectly constitutional to spend taxpayer money on research on questions in evolutionary biology, but it’s unconstitutional for public schools to teach those same questions to students. Mr. Sandefur is highly selective in his Establishment Clause angst.
Taken together, Mr. Sandefur’s constitutional ‘interpretations’ advance Darwinism at public expense. It is unsurprising to note that this comports nicely with Mr. Sandefur’s atheist beliefs, which seem to benefit from his remarkably flexible Constitutional interpretation.
In Mr. Sandefur’s view, Darwinists may receive public funds to study scientific questions that the public is not permitted ask in public schools. Whether constitutional or not, this clearly advances Darwinism and the atheist metaphysics in which Darwinism is grounded.
Mr. Sandefur is demanding censorship of objective discussion of a scientific theory — Darwinism — that is central to his own personal religious belief — atheism. He is using the First Amendment, which was intended to protect freedom of inquiry, to stifle freedom of inquiry.