evolution

Michael Behe provides a good introduction into the subject of intelligent design:

To a person who does not feel obliged to restrict his search to unintelligent causes, the straightforward conclusion is that many bio-chemical systems were designed.  They were designed not by the laws of nature, not by chance and necessity; rather, they were planned.  The designer knew what the systems would look like when they were completed, then took steps to bring the systems about.  Life on earth at its most fundamental level, in its most critical components, is the product of intelligent activity.

Michael Behe, Darwin’s Black Box

Within the Vicarian Domain, the evidence suggests (explored in detail in the next section) that some form of intention, planning, coordination and communication takes place, elements currently not explainable by physical and chemical processes we understand.  Even so, I would withhold judgement as to exactly what it is, with such words as ‘intelligent’ and ‘design’ a bit presumptive, because we don’t know.  Unfortunately, any serious advocate of such possibilities gets linked immediately to theological and/or supernatural advocates:

[Intelligent Design Theory] proponents generally do not publicly invoke special creation by God.  Some of them even accept certain aspects of evolution, such as development of different species from common ancestors.  They argue, however, that many biological phenomena are too complicated to have arisen by natural processes and can therefore be explained only by an intelligent designer….The designer they envision, however, is a supernatural rather than a material being.  

Douglas Futuyma, Evolution

An intelligent designer isn’t the only explanation, but it remains a possibility.  However, instead of ‘intelligent design’ I might look for something closer to ‘coordinated evolution’, perhaps.  In any case, once a full explanation is determined, it will undoubtedly be a natural one.  It could also be (and this is what I think most biologists believe) that it will simply be more of the same, in that no new processes or elements will be discovered, simply an extension of the biochemical world already in view.  

Futuyma’s book takes an unnecessarily defensive stand against Intelligent Design, unnecessarily defensive in that it remains possible that some form of intentional (or designed, or coordinated) evolution takes place:

Unless the [Intelligent Design] advocate proposes that extraterrestrial creatures are responsible (which would merely shift the problem a step back), this designer must be a supernatural rather than material being.

Douglas Futuyma, Evolution

This statement is mistaken in two ways.  First of all, whether alien-caused evolution shifts the problem back would depend entirely on the nature of the aliens.  It’s possible that aliens exist in an entirely different way than biological life on Earth, in ways we can’t imagine or comprehend.  It’s possible that such creatures have already determined how their life originated, leaving the question fully resolved.  Several such examples exist in history, where entirely unexpected realms became manifest: discovery of a round world and new continents; electricity and magnetism; radar and radio waves; cosmic radiation and quarks; microbes and bacteria.  Before their discovery, these things lay hidden in and around every living human (even the new continents, where native humans lived, unaware that they remained undiscovered). 

Secondly, it simply doesn’t follow that ‘intelligent design’ must be caused by a supernatural being.  Other possibilities exist, and will continue to exist until scientists demonstrate conclusively how complex systems evolve.  Which brings us to the next point:

But the [intelligent design] hypothesis generates no research ideas.  It stops science dead in its tracks.  

Douglas Futuyma, Evolution

This is only correct if we assume the supernatural as the source of such evolution, and not a process existing in nature, one discoverable by science.  For instance, an hypothesis that goes something like, ‘a process of intelligent design is the source of the evolution of complex biological systems’ is a valid scientific statement, because it can be falsified by demonstrating how complex biological systems actually evolve.  Research aimed at falsifying this hypothesis might be accomplished in a number of ways:

·  take a simple complex system (flagella, for instance) and determine, step by genetic step, what might be needed to take place in order to evolve the system.  Certain flagella are relatively simple, yet a functioning engine that appears irreducibly complex.  Only a couple of dozen proteins are involved, and it might be possible to model how those proteins evolve from one stable system to another, with a credible number of mutations involved.  While theories exist, they haven’t yet been validated, or accepted.  Building a model that demonstrates a potential developmental path for the evolution of flagella would be a positive step forward.

·  at a macro level, identify a complex system (pit vipers, for instance) and map a credible evolutionary path that requires a minimum of genetic change from one viable phenotype to another.  If a model of sequential genotypes could be posited that demonstrated a viable path via incremental changes, the source of the necessary genetic changes, either mutation or recombination, that would provide a decent falsification of the hypothesis.  

·  attempt to discover precisely how a novel feature comes into existence.  Humans have been breeding dogs (and other animals) for thousands of years, resulting in a wide range of types, but without ever creating one new novel feature.  Showing conclusively how a specific novel feature came into existence would be helpful.

Assume for a moment that such research is technically possible.  What if after applying existing biological/genetic/evolutionary tools in a research program designed to demonstrate a viable path to biological complexity, the effort repeatedly failed to provide even one viable explanation?  That in itself would represent new knowledge.  

But Jerry Coyne sees no point in such research:

In the main, ID [Intelligent Design] is unscientific, for it consists largely of untestable claims.  How, for example, can we determine whether mutations were mere accidents in DNA replication or were willed into being by a creator?  

Jerry Coyne, Why Evolution is True

This is a perfect example of what scientific research should address.  If we change our perspective from one that expects every explanation to adhere to known physical and chemical processes/forces to a new perspective that allows for the possibility of novel forces as yet unknown, ones that would explain biological reality as it is understood, perhaps new solutions could be discovered to the examples listed below: 

But we can still ask if there are adaptations that could not have been built by selection, and therefore required us to think of another mechanism.  Advocates of ID have suggested several such adaptations, such as the bacterial flagellum (a bacteria to propel themselves) and the mechanism of blood clotting.  Those are indeed complex features: the flagellum, for instance, is composed of dozens of separate proteins, all of which must work in concert for the hair-like “propeller” to move.

Jerry Coyne, Why Evolution is True

What doesn’t follow is the default described below:

IDer’s argue that such traits, involving many parts that must cooperate for that trait to function at all, defy Darwinian explanation.  Therefore, by default, they must have been designed by a supernatural agent.  This is commonly called the “God in the gaps” argument, and it is an argument from ignorance.  What it really says is that if we don’t understand everything about how natural selection built a trait, that lack of understanding itself is evidence for supernatural creation.

Jerry Coyne, Why Evolution is True

In my case I argue for more science, a science with a shifted perspective that allows for something new, one that shucks the shackles of basic physics and chemistry, one that recognizes new complexities at the molecular level (within the Vicarian Domain).

Jerry Coyne provides additional evidence for the existence of such scientific shackles:

But even if we agree that natural selection does work in nature, how much work can it really do?  Sure, selection can change the beaks of birds, or the flowering period of plants, but can it build complexity?  What about intricate traits like the tetrapod limb; or exquisite biochemical adaptations like blood clotting, which entails a precise sequence of steps involving many proteins; or perhaps the most complicated apparatus that ever evolved—the human brain.

 We are at somewhat of a handicap here because, as we know, complex features take a long time to evolve, and most of them did so in the distant past when we weren’t around to see how it happened.  

Jerry Coyne, Why Evolution is True

But many aspects of the natural world came about in the distant past, and yet science can figure out what took place.  Plate tectonics, for example, and the formation of large molecules in the furnaces of the stars.  You don’t have to see evolution take place to develop a viable theory and a working model; what you need is a viable explanation, something that so far doesn’t exist:

So how can we be sure that selection was involved?  How do we know that creationists are wrong when they say that selection can make small changes in organisms but is powerless to make big ones?

Jerry Coyne, Why Evolution is True

Criticism of Neo-Darwinism is not limited to creationists.  Asserting that science has yet to explain the evolution of complex biological structures is not synonymous with creationism:

But first we must ask: What’s the alternative theory?  We know of no other natural process that can build a complex adaptation.

Jerry Coyne, Why Evolution is True

We didn’t know what physical processes could move continents when Wegener made his proposal.  We didn’t know what physical processes could keep a planet in orbit around the sun prior to Newton.  The fact that we can ask such a question about evolution makes it clear that an opportunity exists to discover the natural processes that ‘build a complex adaptation.’  

Coyne emphasizes a cultural demand for supernatural explanations, demands that put defensive pressure on scientists to defend a crippled Neo-Darwinism:

The most commonly suggested alternative takes us into the realm of the supernatural.  This, of course, is creationism, known in its latest incarnation as "intelligent design".  Advocates of ID suggest that a supernatural designer has intervened at various time during the history of life, either instantly calling into being the complex adaptations that natural selection supposedly can't make, or producing "miracle mutations” that can’t occur by chance.

Jerry Coyne, Why Evolution is True

Let’s take a closer look at Neo-Darwinism.  Striking at the core of the issue, Richard Dawkins, the premier popularizer of Neo-Darwinism, writes:

We have seen that living things are too improbable and too beautifully ‘designed’ to have come into existence by chance.  How, then did they come into existence?  The answer, Darwin’s answer, is by gradual, step-by-step transformations from simple beginnings, from primordial entities sufficiently simple to have come into existence by chance.

Richard Dawkins, The Blind Watchmaker

Not far behind Dawkins in terms of public support for Neo-Darwinism, Daniel Dennett indicates that…

…having declared their allegiance to natural selection, these scientists have then proceeded to take on the burden of showing how the difficulties with their view could be overcome, and, time and time again, they have succeeded in meeting the challenge.  In the process, Darwin’s fundamental idea of natural selection has been articulated, expanded, clarified, quantified, and deepened in many ways, becoming stronger every time it overcame a challenge.  With every success, the scientists’ conviction grows that they must be on the right track.  It is reasonable to believe that an idea that was ultimately false would surely have succumbed by now to such an unremitting campaign of attacks.  [my emphasis]

Daniel Dennett, Darwin’s Dangerous Idea

This line of argument is particularly weak, as we have reviewed several major historical examples where the reigning paradigm existed for decades and even centuries before being cast aside by new discoveries.  

Dennett continues:

That is not a conclusive proof, of course, just a mighty persuasive consideration.  One of the goals of this book is to explain why the idea of natural selection appears to be a clear winner, even while there are unresolved controversies about how it can handle some phenomena.

Daniel Dennett, Darwin’s Dangerous Idea

Dennett strikes a common theme in the literature, that despite not everything related to the evolution of complex biological organisms having been fully explained, confidence that the current theory will ultimately prove out:

I cannot (yet) see how to refute this objection, or overcome this difficulty [irreducible complexity], but since I cannot imagine how anything other than natural selection could be the cause of the effects, I will have to assume that the objection is spurious; somehow natural selection must be sufficient to explain the effects.  

Daniel Dennett, Darwin’s Dangerous Idea

This is how Dawkins puts it:

The theory of evolution by cumulative natural selection is the only theory we know of that is in principle capable of explaining the existence of organized complexity.  Even if the evidence did not favor it, it would still be the best theory available!

Richard Dawkins, The Blind Watchmaker

A different view of the circumstances might interpret the gaping holes in the theory as evidence that something more fundamental is in play.  Yet scientific orthodoxy insists that...

Through endless repetition of such cycles of mutation and natural selection – a molecular form of trial and error – organisms gradually evolve.  

Alberts et al., Essential Cell Biology

One of the principle drivers of evolutionary change is called ‘the arms race.’  For instance (although countless examples exist) the faster the antelope runs, the faster the cheetah must evolve in order to catch it:

…the arms-race idea remains by far the most satisfactory explanation for the existence of the advanced and complex machinery that animals and plants possess.

Richard Dawkins, The Blink Watchmaker

No doubt such dialectical conflicts exist in nature and contribute to evolution.  But they are partial explanations at best.  More promising explanations relate to regulatory genes:

Protein sequence evolution can also be an important source of regulatory novelty in evolution.  Amino acid substitutions in transcription factors, affecting either their interactions with other regulatory proteins or their binding to cis-regulatory elements, represent an important potential source of novelty because these changes can potentially affect the expression of many downstream genes during development….it is clear that even a small number of changes in a regulatory protein can lead to important macroevolutionary novelties.  

Douglas Futuyma, Evolution

This must be right, in that the manipulation of regulatory genes have the potential to make significant changes to the phenotype with minimal changes to the genotype.  Dennett agrees:

In his account of Biomorph Land, Dawkins stresses that a tiny—indeed minimal—change in the genotype (the recipe) can produce a strikingly large change in the phenotype (the resulting individual organism), but he tends to slight one of the major implications of this: if a single step in the genotype can produce a giant step in the phenotype, intermediate steps for the phenotype may be simply unavailable, given the mapping rules.

Daniel Dennett, Darwin’s Dangerous Idea

This is a telling clue because the control of these regulatory genes can drive big changes in a species.  But do these changes in regulatory genes take place by chance mutations (and the attendant challenges with that potential solution) or is there an alternative explanation?

The principle weakness of defenses of Neo-Darwinism put forth by Dawkins and Dennett relate to the lack of molecular explanations.  Without a molecular explanation one way or another, we won’t be able to settle the question.  The proof or refutation for any theory of evolution doesn’t exist at the macro level.

Controversy about the mechanisms and principles of speciation still persists, so in one sense neither Darwin nor any subsequent Darwinian has explained the origin of species.

Daniel Dennett, Darwin’s Dangerous Idea

Even today, the origin of a new species from a pre-existing species has never been directly observed.

Michael Denton, Evolution: a Theory in Crisis

The first issue with Neo-Darwinism is the lack of direct evidence that one species evolved from a different one:

Neither Darwin nor any subsequent biologist has ever witnessed the evolution of one new species as it actually occurs.

Michael Denton, Evolution: a Theory in Crisis

Daniel Dennett agrees:

Darwin knew full well that explaining variation is not explaining speciation.  The animal-breeders he pumped so vigorously for their lore knew about how to breed variety within a single species, but had apparently never created a new species, and scoffed at the idea that their particular different breeds might have a common ancestor.

Daniel Dennett, Darwin’s Dangerous Idea

This limitation isn’t fatal to Neo-Darwinism.  It’s reasonably certain that speciation occurs.  The difficulty lies in the dependence on the theory of incremental change seeded by mutation and subject to natural selection.  Denton explains…

…that while breeding experiments and the domestication of animals had revealed that many species were capable of a considerable degree of change, they also revealed distinct limits in nearly every case beyond which no further change could ever be produced.  Here then was a very well established fact, known for centuries, which seemed to run counter to [Darwin’s] whole case, threatening not only his special theory—that one species could evolve into another—but also the plausibility of the extrapolation from micro to macroevolution, which, as we have seen, was largely based on an appeal to the remarkable degree of change achieved by artificial selection in a relatively short time.

Michael Denton, Evolution: a Theory in Crisis

Darwin insisted that the success of his theory required very small incremental changes over a great deal of time.  But this is problematic for a couple of reasons.  For one thing, we know through breeding experience that changes in a species can be achieved very quickly (in terms of geological time).  A natural example of this might be a severe change in a species’ environment or ecology that favored a select few every generation (say only the fastest 10% survived and reproduced) resulting in a rapid change in the population.

The second problem is related.  If the incremental change is too small, it’s unlikely to give any selective advantages to the individuals that possess it, limiting the change in the population.  In fact, when the environment remains relatively stable, a species will oscillate back and forth slightly over time in measurable attributes, leading essentially nowhere.  

The introduction of punctuated equilibrium provides a possible explanation for this phenomenon:

The model of evolution [Gould and Eldridge] propose, known as punctuated equilibrium, envisages evolution as an episodic process occurring in fits and starts interspaced with long periods of stasis.

 According to their model, new species arise rapidly in small peripherally isolated populations.  During the explosive phase as the new species emerges the population undergoes rapid morphological change after which it spreads over a wide geographical area and undergoes little further change.  There is a considerable amount of evidence drawn from studies of the genetics of isolated populations, such as the fruit flies of Hawaii, but many other sources as well, that this is precisely in fact how new species do arise.

Michael Denton, Evolution: a Theory in Crisis

This is almost certainly correct.  However, one of the questions raised concerns such rapid change emanating from small gene pools:

Rapidity of change is crucially affected by the size of the gene pool; large gene pools are conservative and tend to absorb innovation attempts without a trace.  

Daniel Dennett, Darwin’s Dangerous Idea

And yet the larger the gene pool, the more variation.  Smaller gene pools will necessarily consist of less variation, although be more pliable to change.

But how much change can a particular species realize?  

But this argument by uniformitarian extrapolation presents a serious difficulty…: change surely occurs in domestication, but suppose that species function like glass spheres with a modal configuration at the center and unbridgeable limits to variation representing the surface.  Artificial selection could then bring morphology from the center to the surface, but no further—and the key argument for smooth extrapolation to all change over any time would fail.  

Stephan J. Gould, The Structure of Evolutionary Theory

The possibility exists that organisms fit within certain categories that possess limits as to what can change:

According to the typological model of nature all the variations exhibited by the individual members of a particular class was merely variation on an underlying theme or design which was fundamentally invariant and immutable.

Michael Denton, Evolution: a Theory in Crisis

Denton goes on to point out that these immutable classes characterize all of nature:

Typology implied that there were absolute discontinuities between each class of organisms, that life was therefore fundamentally a discontinuous phenomenon and that sequential arrangements, whereby different classes were linked together or approached gradually through a series of transitional forms, should be completely absent from the entire realm of nature.

Michael Denton, Evolution: a Theory in Crisis

If we accept this typology as being valid, it solves one problem but then raises another.  On the one hand, this would explain the absence of intermediate organisms in the fossil record (or living on earth), but on the other hand undermines a Darwinian explanation as to how these different classes came to be.

The lack of intermediates posed a major problem for Darwin:

Why then is not every geological formation and every stratum full of such intermediate links?  Geology assuredly does not reveal any such finely graduated organic chain; and this, perhaps, is the most obvious and gravest objection which can be urged against my theory.  

Charles Darwin, quoted by Stephen J. Gould, The Structure of Evolutionary Theory 

Denton hammers this home when he writes:

…the fact that [Darwin] had absolutely no direct empirical evidence in the existence of clear-cut intermediates that evolution on a major scale had ever occurred and that any of the major divisions of nature had been crossed gradually through a sequence of transitional forms.

Michael Denton, Evolution: a Theory in Crisis

He further elaborates:

…out of all the millions of living species known to biology, only a handful can be considered to be in any sense intermediate between other well defined types.

 The lungfish is a classic example.  It has fins, gills and an intestine containing a spiral valve like any fish but lungs, heart and a larval state like an amphibian.  Another classic example of an intermediate type is the egg-laying mammals, the monotremes, such as the duck billed platypus.  In laying eggs the monotremes are reptilian, but in their possession of hair, mammary glands, and the three ear ossicles they are entirely mammalian.

 Undoubtedly, if the various anatomical and physiological systems in the lungfish and the monotremes were all strictly transitional between fish and amphibia and between reptiles and mammals respectively, then the case for them being genuine transitional types would be far clearer.  However, in the case of lungfish, its fish characteristics such as its gills and its intestinal spiral valve are one hundred per cent typical of the condition found in many ordinary fish, while its heart and the way the blood is returned to the heart from the lungs is similar to the situation found in most terrestrial vertebrates.  In other words, although the lungfish betrays a bewildering mixture of fish and amphibian character traits, the individual characteristics themselves are not in any realistic sense transitional between the two types.

 The biology of the monotremes is similar.  Again, where they are reptilian in, for example, the reproductive system an in the structure of their eggs, they seem almost fully reptilian, while where they are mammalian, as for example in the construction of their middle ear, or in the possession of hair, they are fully mammalian.  Instead of finding character traits which are obviously transitional we find them to be either basically reptilian or basically mammalian…

Michael Denton, Evolution: a Theory in Crisis

Dennett agrees:

Thousands of gradations and variations between organisms could be observed, but there were also huge gaps between them.  There were birds and mammals that swam like fish, but none with gills; there were dogs of many sizes and shapes, but no dogcats or dogcows or feathered dogs.

Daniel Dennett, Darwin’s Dangerous Idea

While the lack of intermediates, and the existence of classes separated by seemingly unbridgeable gaps, may seem overwhelmingly challenging for Darwinian theory of evolution, we possess a few telling clues that might help explain.  The first possible explanation has to do with the origination of all major classes:

It is still…overwhelmingly true that the first representatives of all major classes of organisms known to biology are already highly characteristic of their class when they make their initial appearance in the fossil record.  This phenomenon is particularly obvious in the case of the invertebrate fossil record.  At its first appearance in the ancient Paleozoic seas, invertebrate life was already divided into practically all the major groups with which we are familiar today.  Not only was every major invertebrate phyla represented, but a good many of their main subgroups were also present.  The mollusks, for example, the earliest representatives of the cephalopods (the group including the octopus and squid), of the bivalves (clams and oysters) or gastropods (snails and slugs), etc. are all highly differentiated when they burst into the fossil record.  Neither the phyla nor their main subdivisions are linked by transitional forms.  Robert Barnes summed up the current situation: “…the fossil record tells us almost nothing about the evolutionary origin of phyla and classes.  Intermediate forms are non-existent, undiscovered, or not recognized.”

 Curiously, the problem is compounded by the fact that the earliest representatives of most of the major invertebrate phyla appear in the fossil record over a relatively short space of geological time, about six hundred million years ago in the Cambrian era.  The strata lain down over the hundreds of millions of years before the Cambrian era, which might have contained the connecting links between the major phyla, are almost completely empty of animal fossils.  If transitional types between the major phyla ever existed then it is in these pre-Cambrian strata that their fossils should be found.

Michael Denton, Evolution: a Theory in Crisis

Something very special happened during the Cambrian explosion.  I suspect that extensive sharing of genetic material took place and created almost unlimited variation.  And just about everything would have worked, at least for a while.  Nothing like it has happened since.

After the explosion, each class stabilized into different branches leading in many cases to living organisms today.  

An important evolutionary concept needs to be considered.  Dogs didn’t evolve from cats, and humans didn’t evolve from chimpanzees.  In every case, any two organisms can be linked to a last common ancestor, a species that existed in the past.  As a specific example, it is believed that the LCA of humans and chimpanzees (chimpanzees being the closest living relative of humans) existed about 7 million years ago.  It would have been neither a chimp nor a human.  

All mammals evolved from some rat-like-looking thing that ran around at night trying to avoid being eaten by a dinosaur.  Every mammal on earth today, from whales to rats, share essential features of that first mammal.  In other words, a cat didn’t evolve from a bird or an insect.  In both cases, the cat has an LCA for a bird or insect that predates the first mammal.  That being the case, there will never be intermediates linking a cat and a bird, say.

Another possible explanation for the lack of intermediates brings us back to Eldridge/Gould and punctuated equilibrium:

If it is indeed true that new species evolve rapidly in localized geographical areas and that the populations involved are small, then obviously the chance of fossilization of transitional forms is very low.

Michael Denton, Evolution: a Theory in Crisis

This seems reasonable.  But then Denton continues:

…While Eldridge and Gould’s model is a perfectly reasonable explanation of the gaps between species (and, in my view, correct) it is doubtful if it can be extended to explain the larger systematic gaps.  The gaps which separate species: dog/fox, rat/mouse, etc. are utterly trivial compared with, say, that between a primitive terrestrial mammal and a whale or a primitive terrestrial reptile and an Ichthyosaur; and even these relatively major discontinuities are trivial alongside those which divide major phyla such as mollusks and arthropods.  Such major discontinuities simply could not, unless we are to believe in miracles, have been crossed in geologically short periods of time through one or two transitional species occupying restricted geographical areas.  Surely, such transitions must have involved long lineages including many collateral lines of hundreds, probably thousands of transitional species.  To suggest that the hundreds, thousands or possibly even millions of transitional species which must have existed in the interval between vastly dissimilar types were all unsuccessful species occupying isolated areas and having very small population numbers is verging on the incredible!

Michael Denton, Evolution: a Theory in Crisis

I completely agree with the problematic evolution of whales.  While a few intermediates have been discovered in recent decades, the gaps remain massive and unexplained.  However, as for the gap between mollusks and arthropods, that took place during the Cambrian explosion, and like Vegas, whatever happens in the Cambrian remains in the Cambrian.  

Seriously, if I am correct, the explosion of variation that took place in the Cambrian could have covered immense ground in a relatively short amount of time.  We know it could, because it did.

Given the dependence of evolution on occasional mutations, mainstream evolutionary scientists could demonstrate a case of evolution by taking a model genotype and demonstrate how singular changes to that genotype could lead to changes in a phenotype that are demonstrably better than the original, even if the improvement was minor, and therefore selected.  This might validate the notion that discrete mutations can drive evolutionary change.  Does such a model exist?

Another way to demonstrate a real case of evolution would be to provide extended examples of how a complex structure (cilia, the mammalian eye, the amniotic egg, a bird feather, blood clotting, etc.) could evolve one altered gene at a time, with each change an improvement in overall fitness.  This assuming that random mutation would be the source of such change.  Do such examples exist?

Or do complex structures require multiple genetic changes at any given point?  And if so, how do these multiple – and coordinated – changes in the genotype take place?

Do scientists understand the unbroken causal link between the genetic code and the development of specific features?  Sure, we know in many cases what genes affect what part of an organism’s development, but do we know each step in an unbroken causal chain?  For instance, how does my genetic code that begins in a fused sperm and egg lead step by step to ultimately drive my sexual behavior?  Isn’t there just a big black box between the genetic code and such things that we simply label ‘FM’?  (‘Fucking Magic’) 

For example (among thousands that could be cited): in pit vipers, the venom is delivered from the venom sack through hollow fangs and into the victim.  The evolution of venom seems fairly straightforward, and of course teeth can evolve into different forms, including fangs.  But how does the delivery system that includes long, hollow fangs, special muscles in the snake’s head that contracts during a strike (forcing the venom through the fangs), and the actual channel the venom passes through, evolve, one step at a time?   Why would a tooth become hollow, like a hypodermic needle, absent venom?  Or how would a regular tooth, prior, say, to selection for ever longer fangs, be able to inject venom?  And how would the source of venom ever get connected via specialized tubes that lead to the hollow fang?

Moreover, the seemingly intractable difficulty of explaining how a living system could have gradually arisen as a result of known chemical and physical processes raised the obvious possibility that factors as yet undefined by science may have played some role.

Michael Denton, Evolution: a Theory in Crisis

Neo-Darwinism fails to fully explain how evolution takes place.  Not that it’s wrong, simply incomplete.  While mutations take place, variations arise in various ways, and natural selection plays a relevant part, science has failed to demonstrate how these known mechanisms deliver new traits, structures and species.  

The current equation on how organisms evolve reads: evolution happens (fact) + mutations occur (fact) + variations arise within populations (fact) + populations are culled (via natural selection) = problem solved (Neo-Darwinism).  

Denton summarizes it well:

Undoubtedly, one of the major factors which contribute to the immense appeal of the Darwinian framework is that, with all its deficiencies, the Darwinian model is still the only model of evolution ever proposed which invokes well-understood physical and natural processes as the causal agencies of evolutionary change.  Creationist theories invoke frankly supernatural causes, the Lamarckian model is incompatible with the modern understanding of heredity, and no case has ever been observed of the inheritance of acquired characteristics; and saltational models of evolution can never be subject to any sort of empirical confirmation…Reject Darwinism and there is, in effect, no scientific theory of evolution.

Michael Denton, Evolution: a Theory in Crisis

While this formulation appeals to many scientists, justifying a commitment as it does to Neo-Darwinism, it paves over the gaping holes in current orthodoxy, and fails to acknowledge the possibility that something other than “well-understood physical and natural processes” might be at play:

There is still a possibility that living systems could possess some novel, unknown property or characteristic which might conceivably have played a role in evolution.

Michael Denton, Evolution: a Theory in Crisis

Denton goes on to offer a possibility, a starting point:

…there has been an upsurge recently of this traditional alternative to gradualism, the concept of evolution by saltation, the idea that new organs and types emerge suddenly following some sort of massive macromutation.

Michael Denton, Evolution: a Theory in Crisis

This must be true, in some form, as we have discussed the principle weakness of Neo-Darwinism in its inability to explain the evolution of complex systems, or even model in a single instance how such systems might have come about one point mutation at a time.  Gould lays it out as follows:

Charges of inconceivability took several forms, each reducible to the claim that you can’t get from here to there, however well the beginning and end points may function.  Consider the two most prominent formulations: (1) Early stages (when rudimentary) could provide no adaptive advantage, however valuable the final product (2) Major functional changes cannot occur because intermediary stages would fall into a never-never land of inviolability, with the original (and essential) function lost, and the new operation not yet established.

Stephen J. Gould, The Structure of Evolutionary Theory

This leads to the possibility, if not the certainty, that larger macro-changes are somehow spawned: 

If new Bauplane [basic body plan of an organism] often arise in an adaptive cascade following the saltational origin of a key feature, then part of the process is sequential and adaptive, and therefore Darwinian; but the initial step is not, since selection does not play a creative role in building the key feature.

Stephan J. Gould, quoted by Daniel Dennett in Darwin’s Dangerous Idea

But how?

The important steps in evolution, the construction of the Bauplan itself and the transition between Bauplane, must involve some other unknown, and perhaps, ‘internal’ mechanism.

Stephan J. Gould, quoted by Daniel Dennett in Darwin’s Dangerous Idea

This ‘internal’ mechanism must reside within the cell, and most certainly the DNA.  One interesting clue is how much of non-coding DNA is preserved.  This is relevant because random mutations on non-functioning portions of DNA generally get passed along and are easily detectable, whereas presumably mutations in functional parts of the molecule get weeded out via natural selection, the assumption being that these mutations are detrimental.  As a result, those portions of DNA are conserved: 

The functions of many of these conserved noncoding sequences [in mammalian DNA]…remains unknown.  The unexpected discovery of these mysterious conserved DNA sequences suggests that we understand much less about the cell biology of mammals than we previously imagined.

 …we can expect many more surprises that will lead to an increased understanding in the years ahead. [my emphasis]

Alberts et al., Essential Cell Biology

All this is inconclusive.  We explore the borders of scientific knowledge and peer beyond.  We mark the gaps and mysteries along the way and note any suggestive threads that might lead to an answer.  

We finish the section with an exercise of imagination:

Imagine a world in which actual hands from another galaxy supplemented the “hidden hand” of natural selection.  Imagine that natural selection on this planet was aided and abetted over the eons by visitors: tinkering, farsighted, reason-representing organism-designers, like the animal- and plant-breeders of our actual world, but not restricting themselves to “domesticated” organisms designed for human use.  (To make it vivid, we may suppose they treated Earth as their “theme park,” creating whole phyla for educational or entertainment purposes.)  These bioengineers would have actually formulated, and represented, and acted on, the rationales of their designs—just like automobile engineers or our own contemporary gene-splicers.  Then, let’s suppose, they absconded.  Now, would their handiwork be detectable by any imaginable analysis by biologists today?

 …Would a closer look at the organism designs themselves—the phenotypes—reveal some telltale discontinuities?  Gene-splicers are the most powerful cranes we have yet discovered.  Are there designs that simply could not be erected without the help of this particular crane?  If there are designs that cannot be approached by a gradual, stepwise redesign process in which each step is at least no worse for the gene’s survival chances than its predecessor, then the existence of such a design in nature would seem to require, at some point in its ancestry, a helping hand from a foresightful designer—either a gene-splicer, or a breeder who somehow preserved the necessary succession of intermediate backsliders until they could yield their sought progeny.  But could we ever conclusively establish that some design had this feature of requiring such a saltation in its ancestry?  

 …Indeed, all the biologists I have queried on this point have agreed with me that there are not sure marks of natural, as opposed to artificial, selection…It would be foolhardy, however, for any defender of Neo-Darwinism to claim that contemporary evolution theory gives one the power to read history so finely from present data as to rule out the earlier historical presence of rational designers—a wildly implausible fantasy, but a possibility after all.

Daniel Dennett, Darwin’s Dangerous Idea

Not just a possibility, I would argue, but shading towards likelihood.  While this extraterrestrial designer is possible, I think we can look closer to home for a natural solution, one that lies within the Vicarian Domain of a living cell.