Therefore these articles in defense of Darwinism tend to get a bit tedious because they tend to be stitched together from talking points, and exude an aura of scientific hauteur that is not matched by the arguments offered for Darwin's theory. The scientific community exhibits great indignation that anyone should doubt the decrees of science, but the result is invariably the repetitious restatement of basic fallacies present ab origo that can't pass the test anymore, because they merely show that spokesmen trained in science are unaware of the basic critique of Darwinism that has emerged. This critique has now become entangled in the revived claims for  intelligent design resulting in still further polarizing confusion. The public defense of Darwin reeks of the 'official view' in the age of Big Science, and it all looks so reasonable, so credentialed and peer-reviewed,  but Darwinists have perfected the art of restating dubious propositions as if noone could doubt them, and doing this in the context of histories of the subject that are misleading. Thus here, after summarizing the three basics in Darwinian theory, descent, speciation, natural selection, the author says

These three propositions were first articulated in 1859 by Darwin in On the Origin of Species, and they have not changed substantially, although they have been refined and supplemented by modern work. But Darwin did not propose these ideas as pure "theory"; he also provided voluminous and convincing evidence for them. The weight of this evidence was so overwhelming that it crushed creationism. Within fifteen years, nearly all biologists, previously adherents of "natural theology," abandoned that view and accepted Darwin's first two propositions. Broad acceptance of natural selection came much later, around 1930. 

 The debate constantly scrambles the issues of the 'fact' of evolution and the 'theory'. And this situation is certainly not helped by the Creationist camp, which takes an extreme position, rejecting both the fact and the theory. This tends to induce the same mistake in  Darwinists who should know better, or else feel so harried that they must take on both questions at the same time, confusing their responses. There is a complication here, which is that we can distinguish a 'theory of the evidence' from a 'theory to explain that evidence', should that theory of the evidence graduate to stable data. This subtle difference constantly confuses all discussion. Most discussions of biological evolution should be focused on arriving at the facts, with detailed records of how evolution actually happened. But that is a very difficult thing to do, and our temptation is to project a simple generalization that will apply prior to determining the facts of the case. In economics, for example, a theory of evidence would be, as a theory, that economies show cyclical behavior. A second theory to explain the first, i.e. explaining cyclical behavior, is quite another task. Note that without a detailed record we would be likely to think in the abstract about economic systems. This example shows the dilemma of Darwinian theory. We have no detailed record of the way evolution actually happened, and tend to deal only in abstractions based on Malthusian or other misleading examples. This is clearly the trap into which Darwin and Wallace fell, because they were struck by the teeming behavior of jungle populations with its clear profusion of speciation processes. They snapped out of the archaic semi-Biblical view of stable species, rightly so, but thought the survivalist drama of this spectacle of life was explained by its surface aspect, the competitive struggle in biogeographical regions.  

In any case, it is simply not true that Darwin provided voluminous and convincing evidence for this theory of natural selection, although he summarized the rising tide of data suggesting evolution. He observed innumerable cases of natural selection, none of which conclusively established a true theory of evolution.  His extrapolations from Malthus and the selective breeding of animals foisted a misleading mental image of what we mean by 'evolution' on a subject whose complexity and enigma has only increased with time. As to claims that natural selection is responsible for real evolution, say, of man, one has but to count the number of skeletons of hominids over time in the past several million years to see the extreme thinness of the record. These skeletal remains tell us very little indeed about the process of development as it actually occurred. It is merely an extravagant projection to say that natural selection produced language as an adaptation. Where's the proof of this? The evidence for evolution was indeed rapidly accepted by the public, but problems with Darwin's theory persisted.  T. H. himself Huxley had reservations about natural selection, even as he championed the broad context of the evolutionary record, the fact of evolution. Thus, by the end of the century we have the so-called 'eclipse of Darwinism', followed by the comeback called the Neo-Darwinian Synthesis. We should note that Huxley in later years saw the catch in evolutionary thinking applied to man, which is that in practice we move to contradict natural selection, because we have somehow entered some other form of evolution. So what is this missing evolution? Here again misleading ad hoc extensions to Darwin have appeared, such as the various attempts to explain, or explain away, altruism. The right approach surely is to ask how a conscious agent could have evolved who has sufficient freedom to act in a moral fashion. This is not  question of instinct, or programmatic DNA. It is hard to believe that structures as wonderously complex as what we are now seeing don't have the better potential for this superior form of evolutionary ethics done right. There are two things here, the nature of the agent, and his evolution to that state. To say that ethical freedom is the result of environmental adaptation courts disbelief, and some puzzlement at the boxed in character of biological thought. So it is the arrested thinking of Darwinists, not their actual subject matter, that is the problem here. They should start to examine the implications of the genetic revolution for the clear warnings of philosophers on this question of the real man to be explained. Figures such as Kant clearly saw this confusion early on in response to physics, what to say of the derivative methodologies of the biologists. 

Thus, the limits of the original reductionist category of explanation are fully visible in these speculative renditions of the evolution of ethics, and we should at least demand closely tracked evidence that these proposals have a sound basis in the record. In general, evolutionary reductionism has a problem with ethical issues, and more generally many of the original objections raised even by the first reviewers remain as before with this 'standard paradigm'. In any case it is simply a distortion of science to say that Darwin properly documented his theory. It is not sufficient to cite the case of bacteria in a dish undergoing selection processes. Thus the author notes,  

But we no longer need to buttress natural selection solely with analogy and logic. Biologists have now observed hundreds of cases of natural selection, beginning with the well-known examples of bacterial resistance to antibiotics, insect resistance to DDT, and HIV resistance to antiviral drugs. Natural selection accounts for the resistance of fish and mice to predators by making them more camouflaged, and for the adaptation of plants to toxic minerals in the soil. (A long list of examples may be found in Natural Selection in the Wild, by John Endler.) Moreover, the strength of selection observed in the wild, when extrapolated over long periods, is more than adequate to explain the diversification of life on Earth. 

These examples, while of great interest, simply cannot, as the author suggests, be extrapolated over long periods. How does it follow that the emergence of man is proven to be due to natural selection because of the example of germs?  It is misleading to reason so simplistically, and thinking this is sufficient blinds us to the real absence of a true evolutionary theory. In fact, the premiere case, the finches of Darwin, leaves us wondering if these are really distinct species at all. Darwin's theory, in the suggestion of the title of his book, never actually solves the problem of speciation. 

But the author rightly examines the evidence of the fossil record with its clear indications of the fact of evolution, if there are those (e.g. the Young Earthers) still who doubt the broad outlines of evolutionary descent in deep time. However, the question of the fossil record is not so simple. One of the most persistent criticisms of Darwin has always been that of the so-called gaps in the fossil record. There can be no doubt that the record is incomplete, and that something suspicious lurks in the data Darwinists give for the theory of natural selection. The fossil record isn't really homogenous, in the sense that random evolution should not show sudden changes in direction. Nonetheless, considerable progress has been made here by paleontologists. And as the author notes many of these supposed gaps have been filled, or, if not filled, given some inkling of a transitional something (e.g. dinosaurs with feathers, or the basilosaurus), so at least to a small  degree the record is filling out, although this does not add one jot to the claims for natural selection.

 Here critics of Darwin have too often fallen into confusion themselves, because the whole idea of a 'gap' in the record suffers from misdefinition, if not incoherence. Fatal theological temptations induce hallucination here in many otherwise sincere minds aware of the problems of the fossil accounts. Although it is certainly true that the fossil record is very sparse, too sparse to maintain Darwinian certainties, it is not likely that one will find 'gaps' in the record. But these critics have a point, and a refinement of the 'gaps' argument is easy to provide, and the challenge to Darwin's theory remains in some form. Indeed, conventional Darwinians such as S. J. Gould upgraded this argument with the various claims for so-called 'punctuated equilibrium', which amounts to seeing that emergence in some form is often very sudden, followed by a period of stasis where the rate of change is small, or nonexistent. Granting that such data is hard to interpret, the basic issue simply won't go away. These theories suffered from the inability to disassociate themselves from the fallacies of natural selection, as they attempted to have their cake and eat it too, by proposing various 'levels of selection'. But real evolution is altogether likely to be something different. And it might well 'punctuate', this being followed by some sort of 'equilibrium'. 

Those who propose this issue of 'gaps' in the record, then, are onto something, but need to consider that the fossil record is always going to be continuous in some sense. This does not preempt the possibility, not of 'gaps', but of some other evolutionary process that creates a real discontinuity in some definable sense on top of that continuity. Think in terms of acceleration, as artificial as physics logic might be applied to evolution. Acceleration is not a 'gaps' argument, and its discontinuous action is not in contradiction with continuous motion.  To propose discontinuity as antithetical to continuity leads to the hopeless quagmire of miraculous interventions of one kind of another in the creationist vein. We cannot say in advance what that kind of process it would be that generates this sense of discontinuity, but its existence is something that we must suspect based on the evidence that we have. 

Remarkably, the perfect example is the descent of man. There the (not very adequate) evidence of the so-called Great Explosion stands out as a mockery of the basic Darwinian claims. Something very sudden occurred in the emergence of man, or so it seems from the evidence. However, this example typifies the confusion Darwin critics often succumb to, because the evidence of some sudden crossing of a threshold for species man is not the same as man's speciation as such, nor is it incompatible with earlier continuous processes that may also have been crucial. But, in any event, the descent of man is beset with the issue of continuity/discontinuity dead-center in its data set. So much for Darwinian certainties here. The evidence for this Great Explosion, wretchedly poor as it is, is at least on a par with Darwinian presumptions in advance they have explained it all via the nearly metaphysical projection backwards of selectionist explanation. So the evolution of man shows the prime difficulty latent in all theories of the Darwinian type, if they can be called theories at all. The point is that Darwinists merely assert they have solved the issue of man's descent, when they most definitely have not.  

It is this search for the missing process that Darwinists find unacceptable, because there are no candidates for this in the thinking of reductionist science. There is something almost 'a priori' about all this reasoning, in the sense that any science is going to have a 'force' argument, this force is going to show itself in terms of its own action, archetypically 'acceleration', and this action will seemingly be short acting. Such language, like a husk, will be set aside once we have real data to examine, but the point is that Darwinists constantly remind us of the right way to do science, even as they propose a science with no substance to it.. This example of the missing 'force' uses the language of physics, but yet the basic issue must remain. The point is that Darwinism is quite anomalous as a 'science' in the sense that this process that actually 'does evolution' is missing, and the strong suspicion is always there that natural selection, however real in the survival struggles of organisms, is simply the microevolution we see in the absence of 'real evolution'. Darwinists become adamant here, or change the subject, but the sword of Damocles has always stood over Darwin's claims for this reason. It is like confusing Newton's first and second laws. 

The point is essential since the full complexity of evolution was actually better addressed by the first real evolutionary theorist, Lamarck, who proposed two levels to development. Lamarck is too often pegged with his other claims for adaptation, for which he is frequently denounced (although Darwin in his later editions himself succumbed to Lamarckism). In essence, disregarding this other issue,  Lamarck's conjecture was that these two levels correspond to environmental and progressive, or directional, aspects of evolution. The point is that the data of evolution certainly suggests the rightness of Lamarck's thinking, but the detection of this second aspect to evolution is going to be difficult. Thus as Darwin collapsed evolutionary theory the monistic one-level type, a subtle confusion entered the whole subject, because the data is being wrongly interpreted from the first step. Gould's punctuated equilibrium shows the way a working biologist is driven to reinvent this second level, with what success is not clear. 

Darwinists tend to be very much against notions of evolutionary progress, because of their ideological overtones, and misuse in discussions of cultural evolution, but we can dispense with the conventional idea of progress by adopting a simple distinction of levels to evolution, this generating the micro and macro aspects of an evolutionary record. This is a difficult route to travel, but there is probably no other alternative. Current accounts, for example, never explain what environmental adaptation led to the branching of man from a series of chimpanzee or hominid trunks. There is no such explanation, with the relevant data, that makes much sense, or offers a reason that wouldn't as well apply to all cases.  In general, Darwinists assume that branching differentiation as random evolution is the only source of evolution. But the evidence as well suggests that evolution can change direction and select via one of the branches by some unknown process, leaving these once parallel branches behind. Something is missing in our accounts. 

We can infer that something is missing in standard accounts by simple probability arguments. In a now classic text, Evolution From Space, Hoyle and Wickramasinghe give one version of this objection.

Darwinian evolution is most unlikely to get even one polypeptide right, let alone the thousands on which living cells depend for their survival. This situation is well known to geneticists and yet nobody seems prepared to blow the whistle on the theory. [Hoyle & N. Wickrmasinghe, Evolution From Space (London: Dent, 1981), p. 148]

Thus, in Hoyle and Wickramasinghe's terms, one way to state the problem with Darwinism is, not that there are 'gaps' in the record, although critical intervals of change might well exist, but that the entire record is somehow compressed (one thinks of the term from algorithmic complexity theory), that is, taken all in all, the whole thing happens much faster than it should have, if evolution were random. That this issue won't go away can also be seen from the simple fact that the onset of life itself cannot easily fall into the general account of evolution after the emergence of life. 

It is here that the current proponents of intelligent design enter with their various arguments, but it is very difficult to get much further than the simple expression of discrepancy present in the Hoyle-Wickramasinghe statement. The problem here is that to infer design from the failure of natural selection is to embark on one and the same speculative extension to the facts that Darwinists are guilty of. We can see that there is a problem with natural selection. But why should this lead us to reject methodological naturalism, to use the popular phrase for the 'materialism' of scientific methodology now under attack by religious groups? Here, of course, Darwin himself realized he had a problem.  And intelligent design authors such as Thomas Behe have produced their claims for irreducible complexity. Much of this discussion is futile since it confuses a theory of the evidence, with some theory to explain that evidence. We simply don't know enough biochemistry, or have enough evolutionary data,  to answer the question, but given what we already know it is likely to prove misleading to inject design arguments into the enigma of development. To be sure, design in some sense is the case by definition. The discussion confuses different senses of design. A body organ is in some sense 'designed' to perform some function, although a better terminology is greatly to be desired. The evolutionary process that produced that surely ought to be something more than natural selection, but just as surely something that falls within a rubric of nature. But without the theory of the evidence reaching critical thresholds as stable data, we simply can't say. If Behe's argument had been proposed solely as a critique of natural selection, proposed as a question, it might have been more successful. Instead we find the distracting issue of theology impinging on the clear limits of Darwin's theory. 

The author attempts to answer all this with what is now a standard type response (noting that Darwin himself anticipated this type of thinking): 

Thus our eyes did not suddenly appear as full-fledged camera eyes, but evolved from simpler eyes, having fewer components, in ancestral species. Darwin brilliantly addressed this argument by surveying existing species to see if one could find functional but less complex eyes that not only were useful, but also could be strung together into a hypothetical sequence showing how a camera eye might evolve. If this could be done--and it can--then the argument for irreducible complexity vanishes, for the eyes of existing species are obviously useful, and each step in the hypothetical sequence could thus evolve by natural selection. 

A giant MAYBE echoes in this statement, haunted by a very severe MAYBE NOT. This statement is, in any case, purely speculative, and not backed up by any evidence that it did in fact happen this way. The objection of Hoyle/Wichramasinghe is not easily shunted aside by this line of reasoning. Even the small steps, at the polypeptide level, are vexacious, what to say of 'large-small' steps constituting some proto-eye in a series leading to a fully developed eye. We would need to know, not just that this is possible by some naturalistic process, by that natural selection is sufficient, and that seems doubtful. And in fact, biologists are already stumbling on the answer, perhaps, in the current so-called evo-devo biology, in developmental genetics. Complex organs don't arise at all by chance, they develop in programmatic fashion via the switching mechanisms of hox genes, and the like. What is remarkable is the way that Darwinian thinking survives even in the midst of a biological revolution that would appear to contradict the Darwinian starting point. After all, we can see that it is not at all a question of chance mutations producing an eye, if it is true that such complex organs arise through the restructuring of developmental sequences. It is puzzling that biologists have remained so rigid on the issue of Darwin even as their own findings have offered them a way out of the Darwin fallacies. The problem is that these developmental sequences at the level of DNA still tell us nothing about similar developmental processes at the level of evolution in the large. And there a distinct new type of evolutionary theory would be necessary, one that is more than a matter of genetics. Instead, Darwinian biologists are proceeding with half their subject taken away by the new genetics with the same old claims about mutations in these developmental structures. There should be a call for a time-out, while the inconsistencies in these claims are sorted out, and they decide what they do mean by evolution. In fact, the discovery of DNA should have led to a complete review of Darwinian theory. Instead, the field of popular evolution veered off into a kind of genetic fundamentalism that has confused a whole generation of Darwinians. Proposing random evolution of highly teleological biochemistries is a hodgepodge, and in reality a form of retreat, we should be on the look out for evidence of the directional evolution we had missed at the level of macroevolution. The problem is that this would no longer be genetic. 

Anyone who has followed the other web pages at this site will know will know what is being suggested here, for we do in fact have evidence of this kind of macroevolutionary process in our own history. 

The clear teleological aspect of the structures discovered in current advanced biochemical research, and these often associated with developmental processes, should alert us to the fact that we have been here before, and that all of this is a rediscovery or resurfacing of issues that were on the table in the generation before Darwin. The story of this generation is never fully told in most accounts of biology, save in passing, or in a lead up to Darwin. But in many ways Darwin contracted the field of discourse by trying to foist his monistic selectionism on a subject many knew at the time to be more complex. In fact this is clear from the statements of Huxley himself whose views were influenced by this earlier research. This was the reason for his initial reservations about Darwin's theory. One is left to wonder if the scientific polish Darwin gave to his evolutionary data was not a misleading rendition of the inchoate, but broader, versions of evolutionary theory visible in his immediate predecessors. This was a rich field, if one prone to extravagant metaphysics, particularly that associated with German Classical philosophy. 

In any case, the studies of embryological development in figures such as Von Baer, or Geoffrey St. Hilaire, have found their confirmation in the new developmental genetics, leading us to wonder if the basic methodology of scientific biology is altogether unsound. The coming of Darwin was the beginning of an expanding scientific discipline, one that prided itself on its positivistic liberation from philosophy. But we should wonder if this wasn't the downfall of the whole subject, at its first step. German Classical philosophy tends to be denounced for its Hegelian renditions of transcendentalism as Nature Philosophy (Hegel was not actually a transcendentalist, more like a Spinozist), and the early Darwin of the period just after his voyage on the Beagle coincides exactly with the onset of the positivistic challenge to the great fashion of Hegelianism and the evolutionism of Schelling, this challenge almost symbolically visible in a figure such as Karl Marx, who, like Darwin, reflects the sea change that overtook culture so rapidly in the now forgotten period of the birth of modern evolutionary theory. 

But behind this lies something deeper originating in the Kantian phase, where the issues of scientific methodology, the Enlightenment, and the problems of biology were given a potentially more fruitful treatment by Kant himself, who took the measure of the rising methodology inherited from Newtonian physics, and produced a way to mediate the difficulties this was destined to create in the expansion of the sciences. And the school of Kant gave rise to the now nearly forgotten 'teleomechanists', whose careful methodology of the organism was in principle able to reconcile, or at least be wary of, the inherent contradictions of causal and teleological analysis, applied to organisms. If there is one thing that is obvious it is that current biology is hoist on its own inability to produce the net equivalent of this early, and very brilliant, version of the Kantian system. The point here, for a short discussion, is that we can proceed with great success toward the causal explication of complex structures, yet still be unable to come to grips with the organism as a whole, in an intractable teleological aspect that remains beyond our ken. This is clear if we examine the state of current biology, and the intractable Darwin debate. For it is the deceptive strategy of the intelligent design argumentation to try and seize the issue with a crypto-theological argument by design. This was clearly critiqued in the work of Kant, and never entered the work of the non-Hegelian biologists working in this vein. In general, without pursuing this further here, we should be alerted the limits of current scientific methodology as applied to biological questions, and not pretend that Darwinists have all the answers. The current Darwin debate suffers from the obsessive promotion of false emphasis on natural selection. The initial limits of Darwin's theory are returning to haunt the debate, and the educational harm done to young scientists by the excessively narrow view of biology now dominant has led to their inability to properly address the attempts from the Bible Belt to free themselves from the yoke of a bad theory. 

We have arrived in short order at the realization that all is not well with Darwin's theory, without yielding anything to the design argument, and we can also see why this is destined to arise. In the vacuum of the limited positivism of modern science the question of organismic structure, and its concealed teleological aspect, has festered to the point where open rejection of methodological naturalism has been given like a free gift to the supernaturalists of anti-evolution. The sense of the teleological, clearly evident in the structures of DNA, cannot be handled in the concepts of standard science, and give an opportunity to religious critics to inject the design argument where it probably doesn't belong. Strangely, yet understandably, modern science has yielded the ground to those who ply spiritual forms of explanation. But there is no reason that it should be this way.  After the endless promotion of Darwin, we discover that he didn't really produce a theory at all, and the whole debate is simply reverting to the design theology Darwin claimed to have superceded. It could as well backtrack for a moment to the earlier generation before Darwin where the broader scope of evolutionism was gestating, often with greater insight, if not sophistication, than what current science is capable of. Kant virtually prophesies the muddle of the current Darwin debate in the way he responds to the naive scientism of the Newtonians, if not Newton himself. It is important for scientists themselves to look critically at their subject matter, and stop this misguided promotion of natural selection as the key to both evolution and the universe. The longer they wait the greater the reaction in the end, and we are seeing the paradox of wooly-minded creationists better prepped in the flaws of Darwin than most students of science.  Intelligent design has simply flowed into the void produced by Darwinian paradigm thinking. If this is done the issue of what to teach in schools will answer itself, and it will be an issue of broadening the minds of students to the real history of science, and of biology, and center itself on the right foundation, the fact of evolution, and the limits of theory, including the imposter of intelligent design.