VII. The Scientific Failures
Science was the Enlightenment’s proudest achievement. Here, at last, was a method that worked: systematic observation, controlled experiment, mathematical formalization, rigorous testing. The results were undeniable. Physics, chemistry, medicine, engineering—the sciences transformed human life and demonstrated the power of disciplined reason applied to nature.
The prestige of science was not unearned. But the Enlightenment made a subtle and consequential error: it confused the success of scientific method within its proper domain with the sufficiency of scientific method for all domains. If physics could explain the motions of the planets, perhaps it could also explain the motions of the soul. If chemistry could analyze the composition of matter, perhaps it could also analyze the composition of morality. The success of science in one area became an argument for its supremacy in all areas.
This confidence has not aged well.
The institution of science, as distinct from the method, has proven vulnerable to precisely the corruptions that the Enlightenment imagined it would transcend. The guild structure of modern academia—tenure, peer review, grant funding, journal publication—was designed to ensure quality and independence. In practice, it has produced conformity and capture. The young scientist who wishes to advance must please senior scientists who control hiring, funding, and publication. Heterodox views are not refuted; they are simply not funded, not published, not hired. The revolutionary who challenges the paradigm does not receive a hearing and a refutation; he receives silence and exclusion.
The replication crisis has revealed the extent of the rot. Study after study, published in prestigious journals, approved by peer review, celebrated in the press, has proven impossible to replicate. The effect sizes shrink, the p-values evaporate, the findings dissolve upon examination. In psychology, in medicine, in nutrition science, in economics, the literature is contaminated with results that are not results at all but artifacts of bad statistics, selective reporting, and the relentless pressure to publish something—anything—novel and significant.
Peer review, that supposed guarantor of quality, has been exposed as inadequate to its function. The peers are competitors; the reviews are cursory; the incentives favor approval over scrutiny. Fraud, when it is detected, is detected years or decades after the damage is done. The process filters for conformity to existing paradigms, not for truth. The Enlightenment imagined science as a self-correcting enterprise; the corrections, it turns out, are slow, partial, and fiercely resisted by those whose careers depend on the errors.
It is in biology that the Enlightenment’s scientific project reaches its apex—and its most consequential failure.
Charles Darwin’s On the Origin of Species, published in 1859, proposed to explain the diversity of life through purely natural mechanisms: random variation and natural selection, operating over vast stretches of time, producing all the complexity we observe. No designer, no purpose, no direction—only the blind filter of differential reproduction. The theory was not merely scientific; it was the completion of the Enlightenment’s program to explain the world without recourse to anything beyond material causation.
Darwin’s idea, as Daniel Dennett observed, was “universal acid”—it ate through every traditional concept. If man is merely the product of blind variation and selection, then there is no soul, no purpose, no inherent dignity. Ethics becomes an evolved adaptation; consciousness becomes an epiphenomenon; free will becomes an illusion; man becomes a clever animal, nothing more. The stakes could not be higher. If Darwin was right, then the Enlightenment had completed its work: the world was fully explained in material terms, and everything else—meaning, value, purpose—was either reducible to matter or mere sentiment.
The scientific establishment embraced Darwin not merely as a hypothesis but as a foundation. To question evolution by natural selection was to mark oneself as a rube, a fundamentalist, an enemy of reason. The theory became unfalsifiable in practice—not because it was so well-confirmed, but because no alternative could be entertained within respectable discourse. The question was settled, and to reopen it was professional suicide.
But the question was never settled. It was merely avoided.
The mathematical problems with the theory were identified almost immediately. In 1867, Fleeming Jenkin raised an objection that Darwin never adequately answered: blending inheritance would dilute favorable variations before selection could act on them. The discovery of Mendelian genetics resolved this particular difficulty, but it raised others. The “Modern Synthesis” of the 1930s and 1940s combined Darwinian selection with Mendelian genetics and mathematical population genetics, creating the Neo-Darwinian framework that remains official orthodoxy today, even though it is honored mostly in the breach.
In 1966, mathematicians and engineers gathered at the Wistar Institute in Philadelphia to examine the mathematical foundations of the Modern Synthesis. Their verdict was devastating. The rates of mutation, the population sizes, the timescales available—the numbers did not work. The probability of generating the observed complexity through random mutation and natural selection was effectively zero.
The biologists were unimpressed. They did not engage with the mathematics; they simply noted that the mathematicians were not biologists, and continued as before. The pattern established in 1966 has held ever since: mathematically literate outsiders raise objections; biologically credentialed insiders ignore them; the textbooks remain unchanged.
The mapping of the human and chimpanzee genomes in the early 2000s provided the data necessary to test the theory quantitatively. The genetic difference between the species requires approximately forty million mutations to have become fixed in the relevant lineages since the hypothesized divergence from a common ancestor. Using the fastest fixation rate ever observed in any organism—bacteria under intense selection in laboratory conditions—and the most generous timescales proposed in the literature, the mathematics permits fewer than three hundred fixations.
The theory requires forty million. The math allows three hundred. The gap is not a matter of uncertainty or approximation; it is a difference of five orders of magnitude. No adjustment of parameters, no refinement of models, no appeal to undiscovered mechanisms can bridge such a chasm. The theory of evolution by natural selection, as an explanation for the origin of species, is mathematically impossible.
This is not a controversial claim among those who can do the arithmetic. It is simply not discussed by those whose careers depend on not discussing it. The Enlightenment’s greatest scientific achievement—the explanation of life itself through material causes alone—is empirically false. And the institution of science, that much-hallowed engine of supposed self-correction, has proven incapable of acknowledging the mathematical falsification for sixty years.