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.