One of the reasons evolutionists are convinced their theory is true is because of the way the species compare to each other. The patterns we find amongst the species, say the evolutionists, prove Darwin’s idea beyond a shadow of a doubt. Such arguments pervade the evolution genre—from textbooks to popular literature—but what exactly do they mean? To understand this we must understand the evolutionary mind. These arguments have circuitous histories and baked-in assumptions that are now long forgotten. But they are worth remembering. Here is one example.

In the early years of modern science it was argued that motion was caused by contact between masses. In this mechanical philosophy, influences in the natural world were assumed to be transmitted only by direct mechanical contact. And while this may seem intuitive, the related assumption that there can be no vacuum was less obvious. But it was taken to be a fact. As Rene Descartes wrote in 1644, “some make the mistake of imagining [the heavens] to be a totally empty space … there can be no such vacuum in nature.”

For Descartes the planets moved around the sun because they floated in a cosmic whirlpool. And although Isaac Newton later disproved any such Cartesian whirlpool effect, the Lutheran philosopher and mathematician Gottfried Leibniz later promoted Descartes’ ideas. As Leibniz explained in 1715, the principle of plenitude disproves the existence of vacuums in nature:

Now let us fancy a space wholly empty. God could have placed some matter in it without derogating in any respect from all other things. Therefore he has actually placed some matter in that space; therefore there is no space wholly empty; therefore all is full.

It was a good example of how rationalism can produce certainty in even the most obscure notions. Empirical evidence gives one a healthy respect for nature’s complexities, but thought experiments lead to tidy conclusions.

Not surprisingly this mechanical philosophy objected to Newton’s idea that gravitational attraction acted at a distance, and even through a vacuum. How could Newton, Leibniz asked, “have the sun to attract the globe of the earth through an empty space?” Such a notion, Leibniz objected, took on occult qualities.

Another theological objection was that Newton’s solar system was, ultimately, not stable. Over eons to time it could occasionally become chaotic. While Newton allowed that God could fix things when needed, this was unacceptable to the rationalists. God was not an unskilled designer who would create a faulty machine. Therefore God would not use miracles to fix nature, and whoever thinks otherwise, Leibniz said, “must have a very mean notion of the wisdom and power of God.”

Despite the many theological objections Newton’s new physics was compelling. But as Newton cautioned, while it explained the motion we observe, it did not explain the origin of that motion. Newton could explain how the planets moved, but not how they got going. That question was attempted by a series of brilliant thinkers in the eighteenth century.

In 1734 Daniel Bernoulli wrote an award winning paper on the origin of the solar system. His explanation, that the sun’s atmosphere caused the planetary motions and alignments, was reminiscent of Descartes’ whirlpools. And while Bernoulli’s explanation was eventually discarded, he introduced a powerful argument that became crucial in evolutionary thought and remains pervasive today.

The planetary orbits were aligned so as to form a striking pattern. Surely this could not have arisen by chance, argued the great mathematician. Bernoulli posited random design as the null hypothesis. Either the planets fell into their orbits by chance or some mechanism caused their alignment. Bernoulli used a calculation to show the long odds of random design, thus proving beyond a shadow of a doubt that a mechanical cause did the job. He who would deny this, the Christian argued, “must reject all the truths, which we know by induction.”

Twenty years later Immanuel Kant elaborated Bernoulli’s argument. Why do planets revolve about the sun in the same direction? “It is clear,” explained the great philosopher, “that there is no reason why the celestial bodies must organize their orbits in one single direction.” If God had directly arranged their orbits then we would expect them to reveal deviations and differences:

Thus, God’s choice, not having the slightest motive for tying them to one single arrangement, would reveal itself with a greater freedom in all sorts of deviations and differences.

Theology was not discarded in the Enlightenment, as is often said, it was internalized. Buffon and Laplace followed with their versions of Bernoulli’s random design null hypothesis calculation, and cosmic evolution became accepted fact. The details were yet to be worked out, but it was a fact. Sound familiar?

Not surprisingly Bernoulli’s random design null hypothesis became a key argument in Darwin’s new theory of biological evolution. For like the planets, the species show striking patterns. Over and over, they are “aligned.” As Darwin pointed out, “We never find the bones of the arm and forearm, or of the thigh and leg, transposed.” If God created the species, the evolution inventor pointed out, then we should find “a sudden leap from structure to structure?”

Such rationalism was rampant in Darwin’s thought, and it is pervasive in the literature today. Biological patterns, and there are many, disprove creation and therefore prove evolution. Mark Ridley, in his textbook Evolution, explains to the student that protein comparisons between 11 different species should not reveal the patterns we find if they did not evolve:

If the 11 species had independent origins, there is no reason why their [traits] should be correlated.

This is nothing more than seventeenth century rationalism in the guise of twentieth century molecular biology.

This is but one example of the many metaphysical arguments motivating and mandating evolution. Why don’t the historians explain this, you might wonder. The answer, it seems, is that historians allow themselves to analyze the evolutionists, but not their arguments—at least not from a theory-neutral perspective.

One helpful exception is Neal Gillespie’s Charles Darwin and the Problem of Creation. Gillespie reveals many of Darwin’s metaphysical arguments, and he explores their context to a limited extent. But the Enlightenment and earlier influences, and the place and importance of metaphysics in today’s theory, are outside the scope of Gillespie’s fine work. And of course those subjects would have raised awkward questions about the theory’s scientific status—and that is not allowed.

What is evolution? Is it natural selection acting on random biological variation? Is it gradualism or punctuated equilibrium? Is it the slow accumulation of neutral changes that eventually become useful? No, these are all sub hypotheses of evolution. Evolution is the theory that naturalistic causes are sufficient to explain the origin of species.

The idea that the world must have arisen naturally became increasingly popular before and during the Enlightenment period a century before Darwin. Christian thinkers such as Malebranche, Cudworth, Burnet, Ray, Leibniz, Wolf and Kant argued for a naturalistic origins. These traditions grew and by Darwin's day were increasingly accepted in the Anglican broad church, and Victorian society in general.

For instance Henry Peter Brougham, Lord Chancellor of England and one of the most famous people in England when Darwin was a young man, argued for such a naturalistic origins. It is hardly a shocker that Darwin and Alfred Wallace would independently "discover" that, you guessed it, the species had arisen naturally. Funny how this new "discovery" just happened to scratch old itches.

Of course Darwin and Wallace didn't know quite how this could have happened, and so they were willing to negotiate the details. As Darwin once pointed out:

Whether the naturalist believes in the views given by Lamarck, by Geoffroy St. Hilaire, by the author of the ‘Vestiges,’ by Mr. Wallace or by myself, signifies extremely little in comparison with the admission that species have descended from other species, and have not been created immutable ...

Darwin and Wallace knew the species arose naturally because they knew the species did not arise supernaturally. Darwin did not provide incontrovertible evidence that naturalism worked, but rather that supernaturalism did not work. Their arguments against supernaturalism were, not surprisingly, straight out of that earlier Enlightenment period, but applied to biology. Yesterday's theology and philosophy had become today's science.

The greater god (it is beneath god's dignity to manually create the species), problem of evil (god wouldn't create this gritty world) and intellectual necessity (naturalism is needed for good science) were a few of the non scientific arguments that were shaping today's science.

The common thread, and key to evolution, was naturalism. This is why evolutionists refer to their idea as a fact and a theory. The "fact" is that the species arose from strictly naturalistic causes. The "theory" is how this is supposed to have happened--the details behind the fact.

And this is why evolution can sustain substantial empirical contradictions. Such contrary evidence doesn't falsify evolution, it merely falsifies sub hypotheses. A recent paper by evolutionist Stuart Newman demonstrates how well protected evolution is from the empirical evidence. Early in the paper Newman reiterates the need for naturalistic explanations for all things:

The program of advancing materialism against supernaturalism and superstition is clearly a necessary one.

This is not a call for atheism, but merely naturalistic explanations. But how can naturalism be advanced in the face of apparent scientific problems? After all:

when it comes to the innovation of entirely new structures (‘‘morphological novelties’’) such as segmentally organized bodies (seen in earthworms, insects, and vertebrates such as humans, but not jellyfish or molluscs), or the hands and feet of tetrapods (vertebrates with four limbs), Darwin’s mechanism comes up short. This is a reality that is increasingly acknowledged by biologists, particularly those working in the field of evolutionary developmental biology, or “EvoDevo.”

Contrary to the expectations of the Darwinian model, the fossil record is deficient in transitional forms between organisms distinguished from one another by the presence or absence of major innovations. Niles Eldredge and the late Stephen Jay Gould emphasized this point when they propounded their scenario of ‘‘punctuated equilibria’’ almost four decades ago. And although our current knowledge of the cellular and genetic mechanisms of the development of animal forms is relatively sophisticated, it is difficult to come up with plausible scenarios involving incremental changes in developmental processes that would take an organism from one adult form (e.g., an unsegmented worm) to one embodying an innovation (a segmented worm).

And these are not the only apparent problems with evolution:

Gregor Mendel, in performing his remarkable experiments on various plants, carefully picked traits to study whose different versions were uniquely tied to alternative states of specific genes. Much genetic research in the first half of the 20th century, using a similar strategy, also identified strict gene-trait correlations (particularly with regard to simple biochemical pathways) in other organisms. This led to a deep-seated conviction that the Mendelian mode of inheritance was essentially applicable to all traits in all organisms at all stages of their evolutionary histories. But even Mendel himself, who cautiously described his most famous findings as ‘‘the law valid for peas,’’ did not suggest this, and it is demonstrably not the case.

The Mendelian paradigm deals with factors, or genes, that are associated with biological characters. As such, it focuses on the logic of intergenerational transmission of traits (the alternative forms of characters) rather than the mechanisms of character generation.

Unfortunately many evolutionists continue to insist that this failed paradigm is one of the most powerful ideas ever produced by science.

Evolution has led to many false expectations, and failures to inquire into important observations such as the incredible ability of organisms and populations to adjust to their environment:

Phenotypic plasticity, a relatively common property of developing organisms, which was appreciated by many 19th century biologists and which provided the basis for Jean-Baptiste Lamarck’s (generally mischaracterized and not entirely incorrect) pre-Darwinian evolutionary concepts, is only now reentering biology after becoming an all-but-taboo subject within evolutionary theory during the 20th century.

Darwin’s theory, in holding that the competition between individuals marginally different from one another with respect to the small, inherited, morphological, physiological, or behavioral variations encountered in any natural population, has been sufficient to generate the entire array of biologically distinct types seen on the face of planet, avoided cases in which the same organism could take on different forms under different conditions. Indeed, a major impact of Darwin’s theory of evolution by natural selection was to marginalize the concept of phenotypic plasticity. Once the theory’s scientific hegemony was established, all phenomena that fit this description were consigned to a theoretical limbo.

Given scientific problems such as these, how can evolutionists promote their naturalistic agenda? For starters Newman encourages his fellow evolutionists to be more forthcoming about problems with their theory. A century ago physicists had the courage to acknowledge that the old ideas were not adequate, but:

The present-day neo-Darwinists provide a poor contrast to this, insofar as they persist in the hand-waving consignment of all problematic aspects of the origination of complex subcellular entities to the putative universal mechanism of random variation and natural selection. ... Unless the discourse around evolution is opened up to scientific perspectives beyond Darwinism, the education of generations to come is at risk of being sacrificed for the benefit of a dying theory.

While such truth in advertising is certainly laudable, note what is not on the table. For the evolutionist, sub hypotheses can be freely discarded but the core theory is not testable. After all, it is a fact, regardless of the science. Religion drives science and it matters.

Steven Pinker, Harvard professor of psychology, is the latest evolutionist to become unglued over Stephen Meyer's op-ed piece in the Boston Globe. Pinker writes:

SHAME ON you for publishing two creationist op-eds in two years from the Discovery Institute, a well-funded propaganda factory that aims to sow confusion about evolution. Virtually no scientist takes "intelligent design’’ seriously, and in the famous Dover, Pa., trial in 2005, a federal court ruled that it is religion in disguise.

Where do we begin? We could reassure Pinker that the Discovery Institute surely is not a "propaganda factory that aims to sow confusion about evolution." Or we could politely explain to the evolutionists that Meyer's op-ed is not "creationist" as Meyer's claims and the creationist's claims do not line up. And we could point out that federal courts, while very good at ruling on interstate trade and kidnapping cases, are not always equipped to deal with more nuanced cases involving the history and philosophy of thought, as was abundantly revealed in the Dover case.

Such responses would be intended to clear the air of the false notions evolutionists carry around. The responses would be made under the assumption that evolutionists are interested in facts and objective inquiry into such matters. Unfortunately, that is typically not the case. Evolutionists are certainly not interested in understanding intelligent design--then the evolutionists wouldn't be able to brand ID proponents as creationists.

Of course such explanations and reassurances would never be considered. They would never open the mind of an evolutionist like Pinker. But what is worse is they would mask the more serious problem. Trying to explain errors of logic or erroneous assumptions would miss the utter hypocrisy that fuels the evolutionist's vitriol.

Intelligent design is an inference from the data. Agree or disagree with it, there are no religious assumptions. It may be all wrong, but its arguments are based on the evidences of nature, logic, mathematics, and so forth. In other words, it is a scientific argument.

Evolutionists have always branded skeptics as guilty of being driven by religious motivations. Surely there must be religious convictions behind anything the skeptics say. If the skeptics don't admit to their sin, then they are liars as well.

But while evolutionists stand in self-righteous judgment of anyone who disagrees, it is in fact the evolutionists who have founded and promoted a religious theory. Their hypocrisy is plain for all to see. For they commit the very crime for which they castigate others. There is no scientific argument for their claim that evolution is a fact just like gravity--it is a religious argument based on deep metaphysics. Consider Pinker's very next paragraph.

The judge referred to the theory’s "breathtaking inanity,’’ which is a fine description of Stephen Meyer’s July 15 op-ed "Jefferson’s support for intelligent design.’’ Well, yes, Thomas Jefferson died 33 years before Darwin published "The Origin of Species.’’ And Meyer’s idea that the DNA code implies a code maker is just a rehash of the ancient "argument from design’’ - that an eye implies an eye maker, a heart implies a heart maker, and so on. Darwin demolished this argument 150 years ago.

And how did Darwin demolish the argument from design? How did Darwin show that the eye evolved rather than was designed? Did Darwin demonstrate a reasonable evolutionary pathway leading to the eye? Did he convince us that vision plausibly arises on its own? Of course not.

Darwin had no such evidence. But he did have something more powerful--religion. In Chapter 6 of Origin Darwin argued that the evolution of vision is the superior view because otherwise we must say that "the Creator works by intellectual powers like those of men." Have we any such right?

This anthropomorphic warning was straight out of the theological pronouncements of Enlightenment philosopher David Hume. And it was one of hundreds of religious arguments that mandated evolution, one way or another.

Religion drives science, and it matters.