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« Links Mentioned on the 3/11/16 Show | Main | What Should You Do When Your Church Is Moving Away from Biblical Views? »

March 12, 2016


Minor point: The fish with vestigial eyes are no worse off than their sighted ancestors. So the term 'devotion' is misleading because it implies a non-existent distinction.

Major point:

Everyone agrees that genuine vestigial structures started out functional and then became non-functional.
Such agreement poses a risk for the creationist position.

What are the limits of this agreement?

Do we agree on the history, the process, through which we got fish with sightless eyes?

Was selection pressure against blindness gradually removed, generation by generation, from the population of fish as they gradually moved, generation by generation, fully into the caves?

Did the fish gradually, generation by generation, move into the caves while they gradually, mutation by mutation, lost their sight?

Did mutations occur, one by one, over the generations through mechanisms having nothing to do with sight or the lack of it?

Do you agree that this was the process?

If not, then why not?

If you agree with the process, can it happen in the reverse direction?

If not, then why not?

What would happen, under this agreement, if these fish were gradually exposed to selection pressure that initially favored sensitivity to light and later favored acute vision?

Second major point: What other changes occurred along with the loss of sight?

Third major point: Everyone agrees. Whales have vestigial legs. What, then, shall we say to these things? Are whales tetrapods?

(It doesn't work to say these bones have a function today. The fossil record is evidence that they ARE vestigial legs and, anyway, it is perfectly fine, as far as evolutionary theory is concerned, for an organ to acquire a new function.)

Another clear example of why it's important to distinguish microevolution (proven fact) from the philosophy of evolution from a common ancestor (not proven, lack of evidence). Thanks for the post!

Vestigial whale limbs and so on.

This is interesting.

For several reasons.

Before getting to Reduction of Whale Limbs and so on, which will be looked at a bit more in the comment (post) which follows this comment (post), first there is the proverbial lens in question, a sort of singular “Archetype” by which all lines seem to be, whether we like it or not, defined:

While the debate over the “nature” of Eden is nothing new, it is of course an entirely theological discussion and we find that the entire anthology of physics – and Hawking etc. – affirm that the current state of physics is by no means – at all – anything which any thinking person can attempt to label “the only physics/universe possible”. Far from it. Such merges with the theological discussion on the nature of Eden and of course the physicalist hasn’t the tools to participate in that discussion. Natural Selection’s canopy is red with Tooth and Claw and we find therein – from the ground up – all the pains of privation should we take Genesis seriously as to Eden’s topography of possible worlds. Dualism from the get-go, so to speak, which, of course, isn’t surprising should the evidence lead us there. Stephen Webb makes an attempt with his “The Dome of Eden” though (at first glance at least) he seems to ignore (which is problematic) what several other brands of theistic evolutionists ignore – the inescapable landscape of Genesis with respect to the nature of Eden vis-à-vis Eden’s necessary nature of something that is neither a World soaked through with Eternal Life nor a World soaked through with Good and Evil (Privation). But, again, such is a purely theological debate which happens to be immune to scient-ism while simultaneously enjoying the luxury of being perfectly cohesive with the physical sciences.

Final causes (teleos) immersed within privation (good-minus-some-thing) describes and prescribes the reality we all awake to find ourselves within and our Non-Theist friends faithfully affirm the all-encompassing metaphysical landscape of Genesis and they do so both when observing nature’s unmistakable straining along that incline towards E Pluribus Unum from the ground up through eons of the evils of Tooth and Claw morphing towards reciprocity, and they do so when observing the schizophrenic array of causations within the Privation of Good through those same eons. Their thoroughness in describing such a painful mess is uncanny as they affirm Christianity's metaphysical landscape.

Reality seems soaked through with the Red of blood and pain in and through Natural Selection’s Tooth and Claw. An entire Paradigm, an entire World – Universe – soaked through with Tooth and Claw, soaked through with Privatized Good (good minus some-thing) and thereby Evil, Lack, Brokenness, Thirst, Striving – from A to Z – and soaked through with Final Causes and thereby Good, Reach, Teleos, Hope, Becoming, Actualizing – from A to Z – is precisely the World we all affirm, both Non-Theist and Christian.

Though Christianity’s ontology predicts it, it is still uncanny that evil’s argument in and through the Red of Tooth and Claw (from the ground up) forces our hand to embrace its peculiar “EAAE” with respect to the causations in-play within evolution and that entire state of affairs not only affirms Genesis’s topography with respect to the trio of natures subsumed by Eden / Privation / Eternal Life but evil’s argument also converges and then merges with Plantinga’s EAAN.

But, of course, the Christian paradigm predicts said truths via said correspondence.

All the rants of our Non-Theist friends testify on behalf of Scripture's God as whatever mechanism of creation we find employed, including presenting the entire show of natural selection as, simply, all the pains of Good and Evil (vis-à-vis final causes and an obviously paradigm shifting privation) in and around Christianity’s internal discussion as to the nature of Eden, well the Non-Theist just cannot speak coherently about *any* of it *even* on his own terms, whether from the perspective of pain, or suffering, or “design and the good”, or “design and good-minus-some-thing”, or the inescapable reductio ad absurdum which the entire materialist project suffers within inherent intentionality, qualia, and Mind, or teleos vis-à-vis purpose, and so on. The Non-Theist cannot comment on any nuance, at all, which necessitates either inherent intentionality or which necessitates design of any degree as even the phrases good design, bad design, stupid design, or great design fall into incoherence as the Non-Theist is forced to use as his metric for “design” the absurdity that is the Un-Designed Designer there within what just is the non-rationally and non-intentionally conditioned wads of neurons inside Man’s skull.

The Non-Theist’s epistemic is insolvent and hence his entire epistemological body just does ride upon the coattails of the only genre on Planet Earth wherein such terms and definitions are actually solvent. That singular genre being, obviously, none other than the singular metanarrative of the Christian paradigm.

We find here that there is a convergence of all things when it comes to Christianity’s metaphysical landscape, necessity, science, and facts. By that we mean two things.


When it comes to our “respective terminus of explanation” with respect to actuality’s irreducible causation(s) and when it comes to inherent intentionality within said irreducible causation(s) – as opposed to as-if intentionality – (and therefore to any intelligible explanatory terminus of the terms “design / design-ing / design-er” – within our respective causal paradigms with respect to those same irreducible causations, and when it comes to Final Causes in actuality’s irreducible causation(s), we find this:

“The universe, however physics and scientific cosmology end up describing it – even if it turned out to be a universe without a temporal beginning, even if it is a four-dimensional block universe, even if Hawking’s closed universe model turned out to be correct, even if we should really think in terms of a multiverse rather than a single universe – will, the Aristotelian argues, necessarily exhibit just these features (potentialities needing actualization, composition, contingency, etc.). And thus it will, as a matter of metaphysical necessity, require a cause outside it. And only that which is pure actuality devoid of potentiality, only what is utterly simple or non-composite, only something whose essence or nature just is existence itself, only what is therefore in no way contingent but utterly necessary – only that, the classical theist maintains, could in principle be the ultimate terminus of explanation, whatever the specific scientific details turn out to be.” (E. Feser)


Regarding the landscape of Adam, Eden, and World, our ultimate terminus of explanation, whatever the specific scientific details turn out to be, finds only two options in a universe such as ours:

[1] It is a universe void of inherent intentionality (as per E. Feser’s discussions of As-If intentionality), it is a universe void of inherent design.

[2] It is a universe constituted of, soaked through with, Final Causes.

As for the Non-Theist’s endless intoxication with the ultimately absurd, well we can grant him whatever cascade of molecules which the ebb and flow of his capricious fancy happens to find inebriating for on the questions within [1] and [2] the Non-Theist must appeal to this or that unavoidable reductio ad absurdum which forces an ultimately deflationary view of truth-value in any causal paradigm constituted as [1] which is just any Non-Theistic paradigm.

E. Feser takes a look at Teleology verses Teleonomy vis-à-vis irreducible causality. From the ground up (literally) we find that reality’s evil and reality’s good present us with ends which outdistance the Non-Theist’s meager means as we find the obvious:

“Hence to write many paragraphs about the scientific banishment of teleology from everywhere else in nature while insisting that teleology is real in the case of human beings, and then casually to insinuate that the history of that banishment gives hope that someday a scientific explanation of the teleology of human consciousness will also be possible… to do that is something of a conjuring trick, a bit of sleight of hand.”

Whale limbs and Etc:

In the comment to follow we’ll meander through a few more extrapolations within the Non-Theist’s current intoxication with the ultimately absurd as we grant him his current drug of choice there within the cascade of molecules which the ebb and flow of his capricious fancy happens to find inebriating there amid vestigial structures. Oddly, we can either grant the Non-Theist his “take” on such, or, we can meander down the route of Denton’s “take” and, well, either way we find that neither [1] nor [2] from earlier will mind the journey. Christianity’s metaphysical reach enjoys the luxury of simply sitting back, collecting new information as it arrives, and allowing the physical sciences to comment on, well, physicality.

The Reduction of Whale Hind Limbs Etc:

Here we’ll meander through a few more extrapolations within the Non-Theist’s current intoxication with the ultimately absurd as we grant him his current drug of choice there within the cascade of molecules which the ebb and flow of his capricious fancy happens to find inebriating there amid vestigial structures. Oddly, we can either grant the Non-Theist his “take” on such, or, we can meander down the route of Denton’s “take” here in this post/comment, and, well, either way we find that neither [1] nor [2] from the previous comment/post will mind the journey. Christianity’s metaphysical reach enjoys the luxury of simply sitting back, collecting new information as it arrives, and allowing the physical sciences to comment on, well, physicality.


The reduction of the hind limb of extant cetaceans is another example where a non-adaptive trend appears to have shaped an evolutionary transition. At the Dover trial, Kevin Padian described the transitional sequence starting with Ambulocetus:

“Ambulocetis means “walking whale”… It still has legs, and… it’s perfectly OK getting around on land, but… the limbs are large and paddle-like… the hands and feet are clearly already being broadened and are apparently of some use to the animal in getting around in the water… The next slide shows you protocetids, which are ancient whale relatives that are a little bit closer [to modern whales than Ambulocetus is]. Even though these animals are quite aquatic and have a lot of whale features, they still have ankle bones that are very much like the ankle bones in the hoofed mammals from which they evolved… These animals are spending more and more time in water, but they can still deal okay [with land]… [In the] basilosaurids, the next step toward living whales… the hind limb bones are now not just decoupled from the back bone; they’ve become extremely reduced… [but] that pulley-shaped bone… is the ankle… [it] is still like the ankle of a terrestrial animal, a hoofed mammal, from which they evolved, even though this animal couldn’t any more walk on land than it could fly. So what we are seeing here is the progression of features more and more whale-like… the final thing we have here is the living cetacean [modern whale].”

But can we infer that the causal mechanism of the successive modifications was cumulative selection alone, or were other factors also involved? The succession of whale ancestors do indeed exhibit increasing adaptations for marine life and gradual diminishing of the size of the hind limbs. But was the jump between Ambulocetus and Protocetus and that between Protocetus and Basilosaurus the result of gradual cumulative selection? Some argue that these great morphological changes appeared so rapidly in the fossil record (within less than 10 million years) that they could not possibly have arisen and been fixed by Darwinian selection. One aspect of the transition is certainly hard to account for in adaptive terms: the final stages in the reduction of the hind limbs from tiny but almost complete hind limbs to mere vestigial remnants in most modern whales. These final stages of their elimination, when the reduced limbs were entirely encased in the immensity of the whale’s body, are obviously problematical.

Gould comments:

“What conceivable pressure of natural selection could account for gradual stages in the disappearance of a functionless organ—for loss of function should remove a structure from the domain of selection entirely, and knowledge about an eventually adaptive state could not be invoked to guide an explanation for intermediary states along such a functionless path.”

The reduction of whale hind limbs troubled the great Darwinist August Weismann, who debated the issue with Herbert Spencer in the 1890s. As Spencer points out in his correspondence, a Greenland Right Whale, weighing 44,800 pounds, has a femur which weighs only three and a half ounces, and a Razorback (Finback) weighing 56,000 pounds, has a femur of one ounce, “so that these vanishing remnants of hind limbs weighed but 1/896,000 part of the animal.” Weismann was forced to concede the point:

“To use Herbert Spencer’s striking illustration, how could the balance between life and death, in the case of a colossus like the Greenland whale, be turned one way or another by the difference of a few inches in the length of the hind-leg... Further reduction to their modern state of great degeneration and absolute concealment within the flesh of the animal cannot be referred even to negative selection.”

Moreover, many large marine vertebrates retained their hind limbs: ichthyosaurs, plesiosaurs, and of course modern seals, which are almost as well-suited for life in the oceans as whales but have retained their hind limbs for tens of millions of years, a period about as long as that covering the entire evolution of the whales. If seals have retained their hind limbs for adaptive reasons, why did the whales lose theirs? A host of additional questions are raised when the morphological changes are considered in detail. One intriguing detail—the teeth of one group of primitive whales, the basilosaurids, are fairly typical of primitive mammals and very seal-like, while the teeth of dolphins and killer whales are unique in mammals, simple pegs. Was the change adaptive? Seals are able to catch fish efficiently with standard mammalian teeth and presumably so did the basilosaurids.

It is no wonder that so many paleontologists interpreted such trends as examples of orthogenesis. Henry Fairfield Osborn, one the giants of American paleontology, expressly rejected the pan-adaptationist paradigm. One phenomenon he alluded to is the peculiar occurrence in diverse mammalian lines of recurrent patterns of dental cusps. These are the small tubercles on the upper surface of the molars and premolars in mammals. Osborn’s studies convinced him that there were very striking non-adaptive trends in the evolution of cusp patterns. And the evidence is certainly convincing, as anyone who consults Osborn’s work will concur. He wrote:

“My study of teeth in a great many [groups] of mammalia in past times has convinced me that there are fundamental predispositions to vary in certain directions; that the evolution of teeth is marked out beforehand by hereditary influences which extend back hundreds of thousands of years. These predispositions are aroused under certain exciting causes and the progress of tooth development takes a certain form converting into actuality what has hitherto been potentiality… Philosophically, predeterminate variation and evolution brings us upon dangerous ground. If all that is involved in the Tertiary molar tooth is included in a latent or potential form in the Cretaceous molar tooth, we are nearing the emboitement hypothesis of Bonnet or the archetype of Owen and Oken.”

The literature on trends is vast, but now largely ignored because of its anti-Darwinian ethos.However, there is no doubt that what appear to be non-adaptive trends do occur in the fossil record, and these undermine further the Darwinian claim that natural selection was the major causal agency of macroevolution. Many years ago Osborn, in characteristic regal style, summed up the situation, and no discoveries since have materially challenged his verdict:

“In all the research since 1869 on the transformations observed in successive phyletic series no evidence whatsoever, to my knowledge, has been brought forward by any paleontologist, either of the vertebrated or invertebrated animals, that the fit originates by selection from the fortuitous.”

Osborn continued in a strikingly structuralist vein:

“As in the domain of inorganic nature, so in the domain of organic nature fortuity is wanting, and the fit originates… through laws which are in the main similar to growth—laws the modes of which we see and measure, the causes of which we do not and may never understand, but nevertheless laws and not fortuities or chance happenings.”

The existence of long-term trends in the history of life irreducible to any credible functionalist explanation represents another important strand in the consilience of structuralist evidence against Darwinian functionalism presented in this book, evidence showing that the functionalist paradigm cannot in itself provide a comprehensive explanation for the development of life on earth. Causal factors beyond selection—including the developmental constraints now being elucidated by researchers in evo-devo—must have been involved. Indeed, many of the trends can be looked on as providing powerful support for the new evo-devo “developmental constraints paradigm” discussed in Chapter 5. Admittedly, in the case of some of the trends, including the reduction of the gametophyte generation and the gradual loss of aortic arches in vertebrates, it is hard to envisage what developmental constraints might have brought them about. But whatever causal factors were responsible, the trends themselves provide an obvious challenge to Darwinian panadaptationism.

This brings us to the final section of this book, in which I consider the structuralist alternative to Darwinian functionalism—the traditional typological notion of life’s basic forms as built into nature, the result of the long-sought-after “laws of biological form”—and show that it is supported not only by the failure of Darwinian functionalism, i.e., by default, but also by another consilience of evidence, one arising from many recent advances in various fields. These advances are pointing back to the nineteenth century, to Owen, to laws of form, and to the reaffirmation of the reality of the Type. And it is not only advances in biology, but also advances in cosmology, which have revealed the universe to be fine-tuned for life on earth…….

…….Despite the evidence, many evolutionary biologists make statements that appear to directly contradict the claim that the Types are real and defined by unique taxa-defining novelties, by alluding to “transitional forms” leading from one Type to another.

Jerry Coyne, for example, claims:

“We have many examples of transitional fossils between what anyone would consider different kinds: fish and amphibians (like Tiktaalik…), between amphibians and reptiles, between reptiles and mammals, between reptiles and birds, between land animals and whales, and of course, between early and modern humans, with early fossils showing intermediacy between the features of apelike ancestors and modern humans.”

Such claims seem to imply that there are no distinct Types or Type-defining novelties. Yet, as we have seen in Chapter 3, it is the view of many researchers that there are indeed unique Type-defining novelties and that accounting for their origin is one of the major tasks of evolutionary theory. This is what Gould, for example, says about transitional forms: “Can we invent a reasonable sequence of intermediate forms—that is, viable, functional organisms—between ancestors and descendants in major structural transitions?... I submit, although it may only reflect my lack of imagination, that the answer is no....” About one relatively simple novelty—rodent cheek pouches—

Gould comments:

“The… pocket gophers and… kangaroo rats and pocket mice… have invaginated their cheeks to form external fur-lined pouches with no connection to the mouth or pharynx. What good is an incipient groove or furrow on the outside? Did such hypothetical ancestors run about three-legged while holding a few scraps of food in an imperfect crease with their fourth leg? Charles A. Long has recently considered a suite of preadaptive possibilities (external grooves in burrowing animals to transport soil, for example) and rejected them all in favour of discontinuous transition. These tales, in the “just-so story” tradition of evolutionary natural history, do not prove anything. But the weight of these, and many similar cases, wore down my faith in gradualism long ago.”

In the same vein, Gould elsewhere comments, as mentioned in Chapter 1: “The extreme rarity of transitional forms in the fossil record persists as the trade secret of paleontology.”

How can Coyne’s claim be reconciled with Gould and the many other researchers who do acknowledge the existence of Type-defining novelties? The explanation is that Coyne and Gould are referring to different things.

When Coyne talks of intermediates between fish and amphibians, he cannot be alluding to the origin of the tetrapod limb, which defines the Tetrapoda, and unambiguously separates fish (all fish) from amphibians, and is not led up to via transitional forms. If his intention is to claim this, then his claim is massively misleading. What he is claiming, I think, is that there are some fish—lobe-finned fish—that are closer to amphibians than the ancestral groups of fish from which they were derived and can be deemed intermediate in the loose sense that they possess certain characteristics possessed by amphibians but not by other fish.

Every cladogram illustrates transitional forms in this loose sense. For example, frogs lack many of the defining traits of mammals, but do share limbs with the mammals, while no fish possesses this particular homolog. So you can argue, with Coyne, that frogs are in this loose sense intermediate or transitional between mammals and fish, and so forth. Again, you can claim that reptiles share with mammals the amniotic membrane, while no amphibian possesses this homolog. But as mammals also possess many unique traits not possessed by reptiles, you can loosely describe reptiles as being intermediate or transitional between amphibians and mammals. If descent with modification involves the acquisition along a lineage of a succession of novel homologs, this is bound to lead to organisms which possess a mixture of the “older” homologs of the ancestral clade from which they were derived and the new homologs which define the clade to which they belong. Such species are termed mosaics, possessing a mixture of new and old traits.

Coyne gives a good example in his Why Evolution is True of an ant, which combines older defining features (synapomorphies) of the Hymenoptera and newer taxa-defining novelties of the ants.8 Many other mosaics could be cited: Archaeopteryx (reptilian teeth, long tail, wings and flight feathers), Platypus (egg-laying, mammary glands, hair), Australopithecus (small ape brain, bipedal human stance).

Gould, however, is claiming along with other researchers (including Rupert Riedl, Gareth Nelson, Massimo Pigliucci, Günter Wagner, and other authors cited in Chapter 3) that the novelties themselves are not led up to via transitional forms and are genuine novelties.

Thus, there is no contradiction between the claims of Coyne and Gould. Under a typological viewpoint, there are “transitional forms” between man and fish, which in a loose sense form a linear evolutionary series of forms increasingly resembling a human being and sharing an increasing number of the taxa-defining novelties possessed by mammals. But there are no transitional forms leading to the actualization of each novelty. The successive appearance of novel homologs is the key series of events which generated the overall pattern of life on earth, a series which, in the words of Owen in the last paragraph of On the Nature of Limbs, guided life “from the first embodiment of the vertebrate idea under its old Ichthic vestment, until it became arrayed in the glorious garb of Human form.”

The other example of transitional forms widely cited as evidence for evolution are those many cases in the fossil record where there is an obvious incremental sequence of morphological changes in the successive members of a particular lineage. The classic case is the evolution of the horse, which evolved from a five-toed ancestral species Eohippus via three-toed intermediate proto-horses to the modern horse over a period of fifty million years. Many other similar evolutionary sequences exist and are depicted in standard texts of paleontology as evidence for evolution.

Many of these sequences are not quite as linear as often made out. Nonetheless, they do show an evolutionary trend in a particular morphological feature. Thus, such trends support the notion of descent with modification; and because they often involve what are clearly adaptive changes, they may be construed to support Darwinian adaptive evolution—e.g., in the case of the horse, the changes may have facilitated more efficient running on drier land.

At the same time, when examined in detail, these “trends” either involve change to an adaptive mask and not to an underlying homolog or, in the case of many long-term trends, give no hint that they might have arisen to serve some environmental constraint, thus they provide a major challenge to Darwinism.

Intriguingly, perhaps the most widely cited functional transformation alluded to as “evidence for evolution” is the functional transformation of three skeletal components of the upper and lower jaw in primitive fishes into the three ear ossicles—the malleus, incus, and stapes, respectively—in mammals. These skeletal components are Meckel’s cartilage, the palatoquadrate (formed from the ventral and dorsal parts of the first pharyngeal arch, the mandibular), and the hyomandibular bone from the dorsal part of the second pharyngeal arch (the hyoid), which played a role in bracing the two parts of the jaw together. In reptiles, these three skeletal components are called the quadrate (which articulates with the articular bone in the lower jaw); the articular bone in the lower jaw; and the stapes (which transmits sound from the outer to the inner ear in all tetrapods). So these three elements of the first and second pharyngeal arches were utilized firstly to form the jaws and a bracing hinge in primitive fishes; they were utilized secondly in reptiles to form the stapes in the middle ear and part of the lower jaw and the joint linking the lower jaw to the skull; and they were utilized thirdly in mammals to form the three bones in the middle ear.

But yet again, although these changes do support the notion of descent with modification, when these transformations are considered in depth, it is clear that a series of adaptive masks have been imposed on a changeless underlying Bauplan. As Riedl comments:

“The extent to which these three units have retained their relationship over a period of 400 million years is striking, for it is in spite of all sorts of adaptive selection demonstrated by their complete change of function, structure and position. We can therefore raise the old question more specifically: what is this superimposed coherence which so steadfastly keeps them together?”

The co-option of the same three bones for very different purposes during vertebrate evolution illustrates descent with modification, but, ironically, it also provides one of the most stunning examples of invariance of an underlying Bauplan.

There is a tree of life. There is no doubt that all extant life forms are related and descended from a primeval ancestral form at the base of the tree. But there is no evidence to support the Darwinian claim that the tree is a functional continuum where it is possible to move from the base of the trunk to all the most peripheral branches in tiny incremental adaptive steps. On the contrary, all of the evidence as reviewed in these first six chapters implies that nature is clearly a discontinuum. The tree is a discontinuous system of distinct Types characterized by sudden and saltational transitions and sudden origins of taxa-defining novelties and homologs, exactly as I claimed in Evolution thirty years ago. The claim has weathered well.

The grand river of life that has flowed on earth over the past four billion years has clearly not meandered slowly and steadily across some flat and featureless landscape, but tumbled constantly through a rugged landscape over endless cataracts and rapids. No matter how unfashionable, no matter how at odds with current thinking in evolutionary biology, there is no empirical evidence for believing that organic nature is any less discontinuous than the inorganic realm. There is not the slightest reason for believing that the major homologs were achieved gradually via functional continuums. It is only the a priori demands of Darwinian causation that have imposed continuity on a basically discontinuous reality.

No matter how “unacceptable,” the notion that the organic world consists of a finite set of distinct Types, which have been successively actualized during the evolutionary history of life on earth, satisfies the facts far better that its Darwinian rival.

Firstly, the absence of transitional sequences leading from antecedent structures to the each of the thousands of Type-defining homologs actualized during phylogeny is far more consonant with typology than Darwinism. The Darwinian claim that all the homologs were gradually achieved over millions of generations by incremental functionalism—the genetic code, human language, the flower, the diaphragm eevtc.—is a phantasm. The near-universal absence of intermediates leading from antecedent structures to the homologs speaks volumes. Secondly, as we saw in Chapter 4, on any Darwinian account, one must assume that previously plastic forms, “the homologs in the making,” became fixed for some absolutely mysterious reason at specific points in phylogeny and thereafter remained invariant. This is a curiously non-adaptive specter, and highly incongruous in the context of a biology wedded to pan-adaptationism and a biological worldview which posits all living forms as part of an ever-mutating continuum. Thirdly, and perhaps most importantly, in the case of many of the homologous patterns—and particularly the Bauplans like the tetrapod limb—there is no evidence that they are basically adaptive forms. Certainly in the vast majority of cases, they have never been shown to serve some functional end. Self-evidently, in accounting for the evolutionary emergence of homologs that serve no specific adaptive function, structural explanations win hands down……….

I view the Types as being in some sense analogous to the stable atoms of the periodic table. And I view their actualization in the course of phylogeny to have come about in many cases in a relatively saltational manner; thus, the organic realm can be considered like the periodic table of elements: a genuine natural discontinuum of stable material forms. Although I do believe that the origin of many of the homologs occurred by saltation (as this is where the evidence points), I have no fixed view of how saltational were the jumps or whether in many cases their actualization, like the formation of stable atoms (such as lead) may have come about via unstable and elusive short-lived transitional forms (analogous to the radioisotopes of Uranium), which are currently empirically unknown and often theoretically hard to envisage. It is in this sense, viewing the jumps as analogous to those between stable atoms, that I am using the terms “discontinuous,” “discontinuum,” etc. throughout the book.

Stucturalists have long viewed the origin of life and of the major Types in discontinuous or saltational terms. But it is important to point out that structuralism and the notion that organic forms are the product of natural processes do not necessitate saltation. Natural forms and processes may be glacially slow or spectacularly fast: A continent slides at one centimeter a year across the globe and a stalactite may take a million years to grow a few centimeters, while a supernova explodes in a fraction of a second.

While Darwinism demands absolute gradualism if selection is to be the agent of change, structuralism is perfectly compatible with either mode of origin. My own saltationalism is based not on any logical necessity of structuralism but on the empirical facts that the homologs are not led up to via transitional forms and that many, like Owens’s “primal patterns,” give every appearance of being abstract non-adaptive patterns.

Whatever the mode of transition, according to the strong version of structuralism I am defending here, the origin of these homologs was determined primarily by internal causal factors, ultimately derived from the basic properties of biomatter and not by the external action of natural selection via long series of functional intermediates as Darwinism implies. I do not deny a causal role for selection in some or perhaps many of the transitions, but I believe that its role was secondary to the primary internal and natural causal factors which drew life, to cite Owen, “nomogenously” from chemistry to its cellular stirrings in the primeval ocean to the diverse forms which grace the world today.

As to how the successive emergence of the taxa-defining homologs actually occurred as evolution unfolded, I take the view that all the various vertebrate homologs actualized during the course of evolution—limbs, amnion, hair, mammary glands, feathers—were in some sense prefigured into the design of the vertebrate Type, what one might call the Urvertebrate. However, in envisaging that the entire subsequent unfolding of vertebrate evolution from jawless fish to primates was in some sense prefigured in the Urvertebrate, I do not see this as a simple kind of preformism, i.e., that all the information for the actualization of the successive vertebrate taxa-defining homologs was already present in the Urvertebrate in the way gene-centrists claim all the information necessary for development is in the egg or in DNA sequences.

Rather, on the typological view I am inclined to favor, phylogeny is emergent and analogous to epigenesis in ontogeny. Just as all the various organs and structures of an organism emerge from the initial egg in a developmental process that is profoundly epigenetic—involving all manner of emergent self-organizing processes, which arise successively as embryogenesis proceeds—so I see the vertebrate homologs as arising in analogous fashion during the course of evolution.

In this model, the Urvertebrate may be thought of as a ball poised at the top of a slope in a complex natural multidimensional landscape that contains a prefigured set of facilitated paths to the valley bottom. On this naturalistic view, phylogeny is strictly analogous to the folding of a protein into its native form where the amino acid sequence is drawn through a set of preferred structures to the emergent vastly complex 3-D arrangement of the atoms in the native form of the protein. In this model the evolutionary pathways are in nature, not in the Urvertebrate itself. The facilitated paths are part of nature’s deep causal structure, prefigured into the order of things from the beginning, drawing the various vertebrate subtypes from the Urvertebrate during the course of evolution.

Typology has the merit of unifying all biological becoming within the same lawful framework. The folding of a protein, the ontogeny of an individual organism, and the grand march of phylogeny are all seen on this view to be analogous and inevitable emergent ends of nature’s deep structure. Moreover, the same paradigm unifies both the inorganic and organic realm and makes intelligible the discovery of the extraordinary fine-tuning of the laws of nature and the structure of the cosmos for the carbon-based life forms that exist on earth. Typology holds out the immensely beautiful possibility of a completely scientific explanation of the phenomenon of life based on natural law rather than the vagaries of contingency, a goal which is surely at least worthy of respect. For it is, after all, the same end which all science and rationality has sought since the beginning of the scientific revolution.

In these first six chapters, I have presented my reasons for viewing the biological realm as a discontinuum of isolated Types and pointed out that many of the Type-defining homologs give no indication of being adaptive. I have argued that this empirical picture is incompatible with Darwinism but supportive of typology. Standing on their own, I think the evidence and arguments offered in these first six chapters are sufficient to make a very strong case for my thesis. In the rest of the book, I will provide further evidence for this view by considering in depth the origin of a number of specific novelties. Near the end in Chapter 13 I will also present additional positive evidence for typology.

End Quotes/Excerpts.

(by Michael Denton, “Evolution: Still a Theory in Crisis”)

The difference between microevolution and macroevolution is simple; time. Enough mirco changes eventually leads to marco changes. So you have species A1 then A2 then A3 then A4, etc. Eventually you get species A100 (not to mention all the branches off of each Ax) which is so different from A1 it is recognized as B1. This has been going on for 3.8 billion years which is represented in what is known as the tree of life.

No, vestigial X’s are not evidence of evolution.


Sure, gradualism (the Neo-Darwinian paradigm) does have its advocates.

Unfortunately “If evolution has occurred as conceived of by Darwin, invariant taxa-defining novelties, not led up to via long sequences of transitional forms from some antecedent structure, should not exist. But exist they do….” (Denton).

Gradualism is, of late, underpowered. Non-Theist’s own Evo-Devo and the evidence in the arena of Denton’s analysis and more weigh in upon [Gene X mutates / Gene X gets selected] and inform us that such just won’t do any more. That is not to say that evolutionary biologists are looking outside of their own Philosophical Naturalism. Why should they? One’s a priori takes precedence (apparently) over pesky evidence, after all. Rather, it simply means that the last 100 years of gradualism and, more specifically, [Gene X mutates / Gene X gets selected], which is simply the Neo-Darwinian paradigm, has been mistaken and underpowered given what it is telling us “it” can and does account for. Notice the reaction of Non-Theists in this thread to the adventures of Gene X within the question at hand. Interesting. Again, the Non-Theist need never abandon his philosophical naturalism for just as in the teleos of consciousness and therein within reasoning itself and his intoxication with the ultimately absurd, evidence ought not interfere with his crusade to avoid – at all costs – the irreducible / rock bottom causations in-play within our current causal paradigm.

The answer to the OP (opening piece) is:

Gradualism and “….did mutations occur, one by one, over the generations through mechanisms having nothing to do with sight or the lack of it?” (etc.) are simply not the whole show – and such is from within the evolutionary biologist’s own camp. Hence one cannot claim A is evidence of B given what “B” is supposed to (in whole) “be”. Denton’s book adds more nuance and facts of course, and such is mentioned here only to dispel the notion that the micro arena just grants (without evidence and also in spite of evidence) the marco arena. More specifically – the Neo-Darwinian paradigm is underpowered, which is, for the Christian, neither here nor there in any conclusive sense as the Christian is happy to just grant the Non-Theist whatever cascade of molecules within temporal becoming (space-time) which the ebb and flow of the Non-Theist’s capricious fancy happens to find inebriating.


“In Homology, Genes, and Evolutionary Innovation (2014), Günter Wagner, a leading researcher in the field of evo-devo, makes his sympathies with pre-Darwinian notions of the Type obvious. Questioning the notion that the homologs are “nominal kinds… simple arbitrary summaries of phenotypic structure and variation,” Wagner asks whether they are instead “natural kinds,” a possibility which he describes as “highly controversial.” Controversial or not, the very use of the term “natural kinds” by a leading mainstream researcher interested in evolutionary causation is illustrative of just how far skepticism of classic Darwinism has gone in some quarters.

Richard Prum and Alan Brush, the researchers who elucidated the development of the feather, speak for many workers in the evo-devo field when they write:

“Recently, Wagner and colleagues... proposed that research on the origin of evolutionary novelties should be distinct from research on standard microevolutionary change, and should be restructured to ask fundamentally different questions that focus directly on the mechanisms of the origin of qualitative innovations. This view underscores why the traditional neo-Darwinian approaches to the origin of feathers, as exemplified by Bock (1965) and Feduccia (1985, 1993, 1999), have failed. By emphasizing the reconstruction of a series of functionally and microevolutionarily plausible intermediate transitional states, neo-Darwinian approaches to the origin of feathers have failed to appropriately recognize the novel features of feather development and morphology, and have thus failed to adequately explain their origins. This failure reveals an inherent weakness of neo-Darwinian attempts to synthesize micro and macroevolution. In contrast, the developmental theory of the origin of feathers focuses directly on the explanation of the actual developmental novelties involved in the origin and diversification of feathers (Prum 1999). Restructuring the inquiry to focus directly on the explanation of the origin of the evolutionary novelties of feathers yields a conceptually more appropriate and productive approach.”

Günter Wagner, mentioned earlier, is equally skeptical of the micro-evolution to macroevolution extrapolation and claims that the origin of major novelties may be inexplicable via gradualistic, bit-by-bit, Darwinian steps. One of his main points in Homology, Genes, and Evolutionary Innovation is that while microevolutionary changes may throw light on the origin of small-scale novelties, they may do nothing to explain macroevolutionary novelties such as the major higher-taxa-defining novelties discussed in this book. Wagner writes:

“The question of how complex body plans arise is not within the reach of population genetics [defined as the change in gene frequencies in populations, i.e., microevolution] neither are the questions on how complex organisms can arise from random mutation and selection.”

Another key point in Wagner’s book is the claim (echoing Owen’s distinction between homologs or “primal patterns” and their adaptive masks) that the processes which lead to major evolutionary novelties are different from those that cause adaptive modifications. Wagner argues:

“Novelties likely require large scale reorganizations of the gene regulatory network. Gene regulatory network reorganization involves… the creation of novel cis-regulatory elements. In contrast adaptive modifications often involve only the modification of existing cis-regulatory elements.”

An additional dissenting voice is Scott Gilbert, who confessed recently:

“I’m on record in a 1996 paper saying that if the population genetics model of evolutionary biology isn’t revised by developmental genetics, it will be as relevant to biology as Newtonian physics is to current physics.”

Many recent publications touch on aspects of the current ferment, including Pigliucci and Müller’s Evolution, the Extended Synthesis, Wallace Arthur’s Evolution: A Developmental Approach, Suzan Mazur’s The Altenberg 16 , and Fodor and Piattelli-Palmarini’s What Darwin Got Wrong. Part One of the last-named book provides a highly critical review of the present status of classic Darwinism. The authors cite many current researchers in evo-devo to establish that there is widespread dissatisfaction with the micro- to macro- extrapolation, and argue that natural selection “can’t be the whole story about how phenotypes evolve.”

They go on to say:

“In fact, as we read the current literature… that isn’t seriously in dispute these days.”

Basing their skepticism on the “evo-devo constraints paradigm” that informs so much research in evolutionary biology today, they write:

“Contrary to traditional opinion, it needs to be emphasized that natural selection among traits generated at random cannot by itself be the basic principle of evolution. Rather there must be strong, often decisive, endogenous constraints… on the phenotypic options that exogenous selection operates on.”

Fodor and Piattelli-Palmarini conclude in words which echo the position I will defend throughout this work (also echoing Owen’s distinction between homolog [the melody] and adaptive mask [tuning the piano]):

“We think of natural selection as tuning the piano, not as composing the melodies. That’s our story, and we think it’s the story that modern biology tells when it’s properly constructed.”

End quote/excerpts. (by Michael Denton, “Evolution: Still a Theory in Crisis”)

The answer to the OP (opening piece) is:

Gradualism and “….did mutations occur, one by one, over the generations through mechanisms having nothing to do with sight or the lack of it?” (etc.) are simply not the whole show – and such is from within the evolutionary biologist’s own camp. Hence one cannot claim A is evidence of B given what “B” is supposed to (in whole) “be”.

A slightly different approach to the same question echoes the same concerns forced on us by modern evolutionary biologists with respect to evo-devo and other emerging data relative to the formula of [Gene X Mutates] + [Gene X’s Mutation Is Selected] as, well, simply a rather underpowered Neo-Darwinian paradigm:


“The neo-Darwinian paradigm is a synthesis of two overarching theses: the Thesis of Common Ancestry and the Thesis of Random Mutation and Natural Selection as the means of evolutionary development. The evidence for these two theses is anything but compelling; indeed, the theory involves a enormous extrapolation from evidence of very limited ranges to conclusions far beyond the evidence. We know that in science such extrapolations often fail (take, for example, Albert Einstein’s failed attempt to extrapolate a general principle of relativity that would relativize acceleration and rotational motion just as his special principle had successfully relativized uniform motion). Such failures make very pressing the question: how do we know that the extrapolation from local instances of evolutionary development to the grand story of evolution is a valid one?

…..Notice that just the single phylum of the vertebrates (Chordata) includes all fish, mammals, birds, reptiles, etc. Seen in the context of the wider picture, typical examples of evolutionary change are seen to be microevolutionary changes. The evolutionary development of whales, horses, and elephants you mention are trivialities compared to the grand scenario envisioned by the theory. The transition from lower primates to humans is nothing compared to what the theory postulates on the grand scale.

But even that illustration obscures the fact of how trivial in the grand scheme of things such a development would be, for it would have taken place entirely within the class of Mammalia (mammals) in the phylum of Chordata. Even the evolution of amphibians from fish or birds from reptiles is miniscule compared to whole tree of life postulated by the theory, for it still only involves evolutionary development within a single phylum.

……By contrast, what is the evidence that a bat and a sponge are descended via mutation and natural selection from a common ancestor? And now reflect that the above chart shows only some of the phyla within the Animal Kingdom, which is only a part of the domain of the Eukarya, which also includes the whole of the Plant Kingdom, and that in addition to the domain of the Eukarya we’ve also got the domains of the Bacteria and the Archaea to account for! Clearly we’re dealing with a mind-boggling extrapolation from limited instances of microevolutionary change to conclusions that far outstrip the evidence. Caution certainly seems appropriate here.

In any event, as I emphasized, the Thesis of Common Ancestry is really the less important of the two claims of the neo-Darwinian paradigm: far more important is the Thesis of Random Mutation and Natural Selection. As you note, theorists like Michael Behe embrace the Thesis of Common Ancestry. Their bone to pick (no pun intended) is with the postulated explanatory mechanisms of the neo-Darwinian synthesis. Here you had nothing to say to show that the staggering biological complexity which our world exhibits could have been created by such mechanisms in the span of four billion years. Recall Barrow and Tipler’s claim that there are at least ten steps in the evolution of homo sapiens, each of which is so improbable that before it would have occurred the sun would have ceased to be a main sequence star and incinerated the Earth! Here is where my greatest hesitation about the neo-Darwinian paradigm lodges. I haven’t seen any evidence that the hypothesis of random mutation and natural selection has the sort of explanatory power which the neo-Darwinian paradigm attributes to it.”

End quote.

Again: None of this means the Non-Theist need ever abandon his philosophical naturalism for just as in the teleos of consciousness and therein within reasoning itself and his intoxication with the ultimately absurd, evidence ought not interfere with his crusade to avoid – at all costs – the irreducible / rock bottom causations in-play within our current causal paradigm.

“Hence to write many paragraphs about the scientific banishment of teleology from everywhere else in nature while insisting that teleology is real in the case of human beings, and then casually to insinuate that the history of that banishment gives hope that someday a scientific explanation of the teleology of human consciousness will also be possible… to do that is something of a conjuring trick, a bit of sleight of hand.” (by E. Feser here)

Again: Denton’s and Craig’s quotes etc. add this or that nuance and facts and so on, but such are mentioned here only to dispel the notion that the micro arena just grants (without evidence and also in spite of evidence) the marco arena. More specifically – the Neo-Darwinian paradigm is underpowered, which is, for the Christian, neither here nor there in any conclusive sense as the Christian is happy to just grant the Non-Theist whatever cascade of molecules within temporal becoming (space-time) which the ebb and flow of the Non-Theist’s capricious fancy happens to find inebriating.


I'm not qualified to answer most of your questions, but I think the answer to one of your major questions is pretty straightforward, given what Tim says in the main post:

Do you agree that this was the process? If not, then why not? If you agree with the process, can it happen in the reverse direction? If not, then why not?

Suppose that we agree that this (devolution of eyes) was the process as you describe. If we agree that devolution is a plausible process, where information is lost, we could still answer your other question "can it happen in the reverse direction?" with the following answer: no. Why? Because there is nothing about the ability of a biological organism to randomly lose genetic information that would cause us to think that the biological organism can randomly gain genetic information. The processes are not necessarily symmetrical.


It doesn't logically follow that if microevolution is possible that macroevolution must be possible. Your statement that macroevolution will result from microevolution so long as we have enough time assumes that there is a plausible step by step path from A to B. But the fact that A can evolve into A1 and A2 and A3 does not, in itself, lead us to believe that A4 or some other variation down the line will qualify as B.

Genomic Information – gaining and losing:

On losing and gaining information, two books by D. Johnson may (or may not) be helpful and they are [1] Programming of Life and its supplement [2] or “prerequisites". The following review introduces the topic:

"This is currently the best book covering the relationship between genome and computer architectures." - JOHNATHAN BARTLETT, Author / Publisher / Speaker / Director of Technology ----- This book highlights the informational aspects of life that are generally overlooked or ignored in chemical and biological evolutionary scenarios. Each cell of an organism has millions of interacting computers reading and processing digital information, using digital programs and digital codes to communicate and translate information. Life is an intersection of physical science and information science. Both domains are critical for any life to exist, and each must be investigated using that domain's principles. Yet most scientists have been attempting to use physical science to explain life's information domain, a practice which has no scientific justification. -- As you can tell by the preceding words this research is a fascinating approach to the question of the origin of life. - (PUBLISHER) ----- "Programming of Life is an excellent freshman level review of the formal programming, coding/decoding, integration, organization, Prescriptive Information (PI), memory, regulation and control required for a physical object to find itself 'alive.'”

Along a similar theme:

The link here ( ) E. Feser comments on David Oderberg’s recent essays on causation, teleology, and intentionality:

“Readers interested in final causality and its relationship to the current debate in analytic metaphysics about the purported “physical intentionality” of causal powers will definitely find it of interest.”

David Oderberg obviously has many essays on many topics (here: ) although the two which Feser introduces are these links to the respective PDFs:

[1] “Finality revived: powers and intentionality”

[2] “Contemporary Perspectives on Natural: Law as a Limiting Concept Natural Law” with the PDF of chapter 16 which is “Teleology: Inorganic and Organic, by David S. Oderberg”

Such are helpful supplements to this:

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