Sunday, June 6, 2010

Origin of Body-plan level Biodiversity

FOCUS: The next challenge for Darwinian evolutionary theory is to account, not for minor variations like moth colouration or finch beak lengths, but for new body plans, and for the information to create them. That is, for the main branches of the Darwinian tree of life. The need for novel functional body plans viable from embryological stages on, that to address the mosaic creature challenge, and the problems with several major icons often used to promote the theory highlight that this, too, is an unsolved problem. 



--> Darwinian evolution as a macro-theory ever since 1859

--> The whale & population genetics issues

--> embryological development requisites and the body plan information challenge

(a) The Darwinian Tree of Life

--> fossils: stasis, gaps & abrupt origins of body plans

--> Limited vs. universal common descent & the Cambrian top-down "explosion"

--> Stephen Jay Gould's remarks on the fossil record

(b) The functional information creation challenge

--> Mosaic creatures

(c) Other icons of evolution

--> archaeopteryx & friends

--> On ape-men and limitations of artistic reconstructions

--> The man-ape speech gap and how every presentation of or argument for Darwinian macroevolution is an example of its weaknesses

--> can open systems spontaneously create complex functional organisation?

--> the whale tale

(d) Some key questions

NEXT: Origin of Mind, Man, Morals, etc

When Darwin summed up his “one long argument” at the end of the epochal 1859 Origin of Species, he spoke as follows:

It is interesting to contemplate a tangled bank, clothed with many plants of many kinds, with birds singing on the bushes, with various insects flitting about, and with worms crawling through the damp earth, and to reflect that these elaborately constructed forms, so different from each other, and dependent upon each other in so complex a manner, have all been produced by laws acting around us. These laws, taken in the largest sense, being Growth with Reproduction; Inheritance which is almost implied by reproduction; Variability from the indirect and direct action of the conditions of life and from use and disuse: a Ratio of Increase so high as to lead to a Struggle for Life, and as a consequence to Natural Selection, entailing Divergence of Character and the Extinction of less-improved forms. Thus, from the war of nature, from famine and death, the most exalted object which we are capable of conceiving, namely, the production of the higher animals, directly follows. There is grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being evolved. [[Origin, Ch 15. Emphasis added.]

From the outset, then, Darwin's theory was a macro- evolutionary theory. That is, it claimed to explain biodiversity from pond scum to us, and all points in between. It therefore derives the major body plans -- from plants to whales to birds to bats to insects to worms to bacteria and more -- through the branching tree of life that comes about by descent with modification of one or a few primitive ancestral organisms. So, across deep time the claimed process of macro-level evolution is held to have led to the range of biodiversity in our world, starting with one or a few primitive (and, to start with, unicellular) ancestors. All these diverse forms are held to have emerged without onward intelligent guidance through variation, “the war of nature,” and its accompanying “struggle for life” and “Natural Selection.”

In the 1930's – 50's, this initial picture was further elaborated. For, the rediscovery and further development of Mendel's work on genetic inheritance, the rise of population genetics and the results of biochemical investigations -- especially the discovery of DNA and its role as an informational macro-molecule -- have contributed to the modern Neo-Darwinian Synthesis. On this view, evolutionary change, whether at the micro-level or at the macro-scale, is driven by chance variation reflected in the genetic endowment of populations, which is then acted on through the environmental culling forces that give rise to natural selection. 

This brings up a crucial distinction and point of contention.

For, it is commonly held that macro-level evolution is more or less simply the accumulated result of micro-level changes from one generation to the next that more or less add up without limit. On this view, observed small scale changes like the colour of pepper moths or the beak sizes of birds in droughts in the Galapagos islands, or bacterial resistance to antibiotics are direct evidence for the transformation of a bacterium- like organism into the vast range of life forms and body plans we see around us today.  Further, proponents of this view as a rule also directly infer that one may more or less smoothly move across what we often call the tree of life, through such small-scale  incremental changes from one generation to the next. Whale evolution is a good illustrative case (also cf. Berlinsky below, here):

Objectors point out that small scale changes of one or a few base pairs in genes are one thing, the creation of changes credibly requiring creation of tens or more of millions of new DNA bases, dozens of times over, that have to work correctly from embryological development to fitting into ecological niches and competing successfully with other organisms are utterly another.  

Now, too, an organism's body plan -- and we primarily have animals in mind here, as the most relevant case --  is first given expression through the step-by-step process of embryological development from the zygote, based on the DNA of the fertilised ovum and the existing organised structures of the egg cell. So, it is worth a moment to excerpt a basic summary of the process, using the just linked:
Embryogenesis . . .  starts with the fertilization of the ovum (or egg) by sperm. The fertilized ovum is referred to as a zygote. The zygote undergoes rapid mitotic divisions with no significant growth (a process known as cleavage) and cellular differentiation, leading to development of an embryo . . . .

Cell division with no significant growth, producing a cluster of cells that is the same size as the original zygote, is called cleavage. At least four initial cell divisions occur, resulting in a dense ball of at least sixteen cells called the morula . . . . The cells of the morula are at first closely aggregated, but soon they become arranged into an outer or peripheral layer, the trophoblast, which does not contribute to the formation of the embryo proper, and an inner cell mass, from which the embryo is developed. Fluid collects between the trophoblast and the greater part of the inner cell-mass, and thus the morula is converted into a vesicle, called the blastodermic vesicle. The inner cell mass remains in contact, however, with the trophoblast at one pole of the ovum; this is named the embryonic pole, since it indicates the location where the future embryo will be developed . . . .

During gastrulation cells migrate to the interior of the blastula, consequently forming two (in diploblastic animals) or three (triploblastic) germ layers. The embryo during this process is called a gastrula. The germ layers are referred to as the ectoderm, mesoderm and endoderm. In diploblastic animals only the ectoderm and the endoderm are present [5]. . . .

  At some point after the different germ layers are defined, organogenesis begins. The first stage in vertebrates is called neurulation, where the neural plate folds, forming the neural tube  . . .  Other common organs or structures which arise at this time include the heart and somites . . .  but from now on embryogenesis follows no common pattern among the different taxa of the animal kingdom.

In most animals organogenesis along with morphogenesis will result in a larva. The hatching of the larva, which must then undergo metamorphosis, marks the end of embryonic development. [[Source: Wikipedia article, "Embryogenesis." Emphasis added. (Cf. here for a snapshot view of gene regulatory networks in action as a sea urchin embryo develops.)]
We thus see an information-rich, step by step complex controlled process of development based on the DNA information in the zygote and the molecular machinery of the underlying egg cell:

In other words, we here see an algorithm, with a relatively similar first phases, then a threshold (as highlighted) beyond which the onward process is very distinct for each main type of organism. Thus, the first criterion of any valid theory of origin of biodiversity is that it must credibly account for the origin of the functionally specific and complex information and algorithms used to initiate the body plan starting from the zygote and ending with the embryo, larva or foetus.

When we turn to the butterfly as an iconic example of life forms that exhibit metamorphosis, the problem is "squared." For, these organisms must code for, regulate and express two body plans across one lifetime, only the second of which actually reproduces. This pattern of development of a life form strongly implies -- this word is patently not too strong -- foresight and planning, thus design. And, of course, with the 20,000 butterflies, their body plans also demonstrate long celebrated consummate artistry and obvious delight in beauty:

The information-storing macromolecule, DNA, lies at the heart of the complex biological information system that, step by step,  gives expression to the embryonic body plan. So, accounting for DNA expansion to accommodate novel body plans will have to be a key part of the story; not just a survey of the fossil record and various kinds of similarities and differences among life forms across the generally used geological timeline. 

So also, we will need to clarify whether the Darwinian vision of chance based mutations leading to diversity in a population and to culling-out of "less fit" forms as they fail in the competition for life and reproduction,  can account for the stored information in the DNA and for the algorithms that give it expression starting with embryonic development. 

Immediately, our experience of observing major and successful alterations to information systems throws up a warning. 

For, such transformative changes to existing information systems are never based on the mere adding up of small increments.  Instead, it is a commonplace of information system development planning that successful innovation requires a macro-level system-level design approach based on analysis of the situation to be addressed, technical knowledge, creative imagination and usually a fair degree of experimentation and testing to get it right.  That is, to incrementally move around within an "island" of already existing function by small changes is one thing, but to find an as yet undiscovered island of function in the vast  "sea" of possible configurations (the overwhelming majority of which will be non-functional) -- and that, without intelligent foresight, planning and action --  is utterly another.

That poses a major (but too often unacknowledged) challenge for the dominant Darwinian macro-level theory of evolution. As Dr Arthur Jones remarks on the Cichlid [["sick-lid"] family of fishes:

Similarly, there are even some thought-provoking ideas now being raised [[HT: JB] as to whether mutations --
i: i.e. the usual source cited for many of the chance variations that are held to feed into

ii: differential reproductive success (natural selection) thus

iii: yielding descent with modification across time; i.e. evolution; where

1v: we may summarise this primary Darwinian evolutionary mechanism in the "equation": 
CV + DRS/NS --> DWM = Evo

. . . are altogether a random process:

So also, the focal issue for the origin of body-plan level bio-diversity will have to be the question of the evidence for and soundness of the  Darwinian tree of life model. 

(a) The Darwinian Tree of Life

The predicted result of the gradual chance variation and cumulative culling by environmental forces is that life forms will branch out from the initial unicellular tap-root, forming a tree-like pattern

So, starting from Darwin, the body-plan level biodiversity we see in the current world and the fossil record has been viewed as the result of gradual accumulation of micro-level changes across time and place:

Fig. G.11: Darwin's Tree of Life illustration from Origin, showing 14,000 generations of hypothetical branching

The first key assumption involved was stated by the co-founder of the theory, Wallace, in his February 1858 Ternate letter: “there appears no reason to assign any definite limits [[to variability of species].” Secondly, it is implied that the variations are gradual and progressive. As a direct result the ongoing sampling of the fossil record across deep time should increasingly show gradual transitions and transformations that accumulate to account for the tree of life.

But that evidently has not happened.  (Cf. the Darwin's Dilemma Amazon page.)

Nor is this new. 

Darwin himself knew that the fossil record of his day showed a characteristic pattern of sudden appearances, stability of form and disappearance (or continuation into the modern world). Indeed, when he laid out anticipated objections in Ch 6 of Origin, the very first one was:
. . . why, if species have descended from other species by insensibly fine gradations, do we not everywhere see innumerable transitional forms? Why is not all nature in confusion instead of the species being, as we see them, well defined?

In short, he projected a gradual, incremental development of varieties that accumulate to species, genera, families and beyond, and so it would be natural to expect that the fossil record and the current world alike would commonly manifest smoothly shaded off branching sequences.  In reply he tried to portray this partly as a naive expectation on grounds that successor, superior species should replace predecessors, and the fossil record will naturally tend to gave gaps due to the want of fossilisation and the ravages of vast ages of time. Also, he argued that the fossil record at that time was but little explored and had in it many imperfections. He confidently expected that onward studies would fill in key gaps. And, starting with the Archaeopteryx toothed bird fossils in the 1860's, headlines have repeatedly triumphantly announced the discovery of “missing links.” 

The horse transitional fossils series, from the 1870's on, was also particularly emphasised:

Fig. G.11b: The horse transitional forms evolutionary sequence as was portrayed for generations, emphasising trends of toes and dentition. (However, the key issue (in light of Darwin's succession argument) that 3- and 1-toed fossils have been found in the same strata, is often not acknowledged. Nor, the challenge that elsewhere pseudo horses, per the conventional timeline, moved from 1- to 3- toed forms; raising an obvious question as to the "survival of the fittest" superiority of the 1-toe form. Where, the modern horse is still a three-toed beast, using the other toes as internal splints. And indeed, some modern horses are reportedly occasionally born with the splinting toes exposed. The "bush" model "at best" shows -- apart from an inferred [[we need to underscore: not observed] root in a more generic animal --  variation within a body plan, where one vs three toed forms show no clear "survival of the fittest" superiority.

In 1997, well known evolutionary paleontologist, Stephen Jay Gould, wrote of this key icon that is still held up in some quarters:
The evolutionary bush of horses includes many terminal tips, and each leads back to Hyracotherium through a labyrinth of branching events. No route to Hyracotherium is straight, and none of the numerous labyrinthine paths has any special claim to centrality...We run a steamroller right over a fascinatingly complex terrain when we follow the iconographic convention for displaying the pathway from Hyracotherium to Equus as a straight line . . . . Many classic ‘trends’ of evolution are stories of such unsuccessful groups - trees pruned to single twigs, then falsely viewed as culminations rather than lingering vestiges of former robustness. [[Life’s grandeur, 1997, pp.63 - 64. (That is, he emphasises the variability within the generic body plan of the horse, and implies a lack of a clear linear progression to a definite single terminus in the familiar modern horse. Let us not forget, too: Donkeys and Zebras are close "cousins" in the same genus.)] 
B. J. MacFadden is more frank about the gap between iconography presented to the public (including children in school) and the far more messy realities that have to be addressed:
Since the turn of the century, most of the foremost paleontologists involved in original research on fossil horses (e.g., Matthew, Stirton, and Simpson) have recognized that the gradual, progressive trends depicted for fossil Equidae are at best oversimplifications to illustrate general evolutionary patterns. [[--> cf. here for a different, more strongly worded view on "at best"] The problem in the interpretation of these occurs when other scientists and the lay public, themselves far removed from the original data, seize the simplified essence of these general patterns, and consequently many of the details get lost in this process . . .Trends and directionality, though firmly entrenched in the literature and thought to be prime concepts within evolutionary theory, are, at best, broad patterns or generalizations. [[Fossil horses: systematics, paleobiology, and evolution of the family Equidae, 1992, pp.216, 223. As usual, emphases are added. (It is worth previewing the remarks to follow on this iconic sequence: ". . . there are miniature horses today that are not that much larger than a dog, and horses are occasionally born with three toes, i.e. the changes are fairly modest. There is however a shortage of the “links,” sometimes three- toed and one- toed horses have been found in the same fossil beds, and similar animals from apparently similar environments in South America show one- toed pseudo- horses in layers below three- toed ones.")]
Gould's co-founder of Punctuated Equilibria (an alternative  theory of evolution that tries to account for the systematic pattern of fossil record gaps; cf. the classic joint 1972 paper here) and curator at the American Museum of Natural History, Niles Eldredge, was also quite revealing in a published interview with Luther Sunderland:
I admit that an awful lot of that has gotten into the textbooks as though it were true. For instance, the most famous example still on exhibit downstairs (in the American Museum) is the exhibit on horse evolution prepared perhaps 50 years ago. That has been presented as literal truth in textbook after textbook. Now I think that that is lamentable, particularly because the people who propose these kinds of stories themselves may be aware of the speculative nature of some of the stuff. But by the time it filters down to the textbooks, we’ve got science as truth [[ --> Cf. Lewontin's notorious "Science, as the only begetter of truth . . . "] and we’ve got a problem. [[Cited, CMI from a recorded interview reportedly dated July 17, 1979, with Luther Sunderland, published in Darwin’s Enigma: Fossils and Other Problems, Master Books, El Cajon, California, USA (1988), p. 78; cf. CMI's critique, here.  Also cf. here and here. (If you find the Bible-based creationism irritating, please discount it as a particular perspective and focus on the scientific facts, concerns and issues raised. If you are tempted to automatically reach for the rhetorical club, "quote-mining" to dismiss this statement, understand that if you call someone a liar as first resort without very good and specific evidence, that may say a lot more about you instead of your intended target.)]
Similarly, David Raup, Curator of Geology, Field Museum of Natural History, was moved to observe in 1979:
Darwin... was embarrassed by the fossil record . . . we are now about 120-years after Darwin and the knowledge of the fossil record has been greatly expanded. We now have a quarter of a million fossil species but the situation hasn't changed much. The record of evolution is still surprisingly jerky and, ironically, . . . some of the classic cases of Darwinian change in the fossil record, such as the evolution of the horse in North America, have had to be discarded or modified as a result of more detailed information. [["Conflicts between Darwin and paleontology" Field Museum of Natural History, vol.50, no. 1, Jan 1979, p.25]

So, in light of the admitted temptation to create  iconic "oversimplifications to illustrate evolutionary patterns," headlines and iconic illustrations or exhibits do not necessarily reflect the true balance of the facts

Also, dominant lawlike patterns of natural phenomena are often quite evident from the outset of investigation

In a sense, then, it should not be a surprise to learn that, 150 years later -- years in which the globe's fossil beds have been diligently explored -- with upwards of a quarter million fossil species and countless millions of fossils of all kinds in hand, the “almost unmanageably rich” fossil record still presents us with the same result: gaps, sudden appearances, stasis, disappearance.  Which tells us something is likely to be very wrong. 

For, 150 years after Darwin, we now have billions of fossils observed in situ from a span of 3.8 or so billion years on the conventional timeline, millions collected in museum shelves, and in excess of a quarter million fossil species. We have fossils of micro-organisms, of skeletons [[ --> including the allegedly 70 MY old dinosaur bones that turned out to have blood and bone cells as well as still stretchy connective tissue touched on in Fig. G.6a in the section on chronology here on], body moulds,  nests and eggs, dung, and even ephemera such as foot-prints and tunnels. So long as it is reasonable to hold that fossilisation events are un-correlated with particular body plans -- and that is obviously reasonable -- the samples are surely adequate to give us an overview of the main patterns of the history of life in the past of origins. Where, one of those major patterns is inferred to be gradual, slow, incremental development of final superior diversified forms from more primitive and generic ones all the way back to the unicellular organisms held to be the original life forms. 

So, it is plainly an inherently reasonable expectation that if the predominant mechanism for formation of the diverse body plans in the world of life is gradualistic diversification, transitional sequences much as the horse sequence was originally thought to be, should be at least fairly common, and even dominant.

Only, that is simply not the case. (Had it been so, we would be awash in indubitable examples of the gradual formation of body plans. We obviously are not.)

Worse, that goes all the way back to perhaps the worst possible case: the formation of the major multi-cellular body plans of life forms as we may see from the Cambrian fossil beds onwards. 

For this crucial case shows just the opposite of what Darwin hoped for: top down, not bottom-up variation; with the transitional forms leading up to the top level branches (phyla and sub-phyla) simply missing. Where, the same conventional timeline tells us that up to that point there were three billion years of life forms, with fossils preserved. And, in particular, with fossils of the soft-bodied Ediacaran life forms from the previous 100 MY or so.

In short, as a predominant pattern, we are seeing evidence of separate, distinct islands of functional body plans with variation within the plans. But, we are not seeing any abundance of clear transitional body plan sequences bridging them, nor -- most importantly -- going back to the proposed original unicellular forms. Nor, do we find any empirical, observational evidence that shows that the assumed or asserted smooth gradation of functional forms from unicellular ancestral form to the vast range of body plans is any more than just that: an assumption. 

Similarly, as was discussed in the introductory unit, there is no observational evidence that warrants the origin of the required degree of functionally specific, complex organisation and associated information by chance and necessity. This includes, by incremental blind -- i.e. specifically unintended and unintelligent -- chance variation and differential reproductive success that creates major body plans from a unicellular universal common ancestor, step by incrementally superior and population-dominating step.  Which is the tree of life model that we are often shown:

Fig. G.11c: A typical, popular level tree of life model/illustration. (Source.)

Fig. G.11.d: A typical popular-level view of the horse evolution "branch" -- better, given the "vertebrates" branch above, "twig" -- of the tree of life. Note that the familiar "modern" horse actually has  three toe bones internally, the other two smaller ones in effect "splinting" the main one; reportedly, from time to time modern horses are born with three visible toes. (Source.)

It is therefore worth noting the following revealing 2006 remark in the journal, PNAS, by W. Ford Doolittle and Eric Bapteste:
Darwin claimed that a unique inclusively hierarchical pattern of relationships between all organisms based on their similarities and differences [the Tree of Life (TOL)] was a fact of nature, for which evolution, and in particular a branching process of descent with modification, was the explanation. However, there is no independent evidence that the natural order is an inclusive hierarchy, and incorporation of prokaryotes into the TOL is especially problematic. The only data sets from which we might construct a universal hierarchy including prokaryotes, the sequences of genes, often disagree and can seldom be proven to agree. Hierarchical structure can always be imposed on or extracted from such data sets by algorithms designed to do so, but at its base the universal TOL rests on an unproven assumption about pattern that, given what we know about process, is unlikely to be broadly true. This is not to say that similarities and differences between organisms are not to be accounted for by evolutionary mechanisms, but descent with modification is only one of these mechanisms, and a single tree-like pattern is not the necessary (or expected) result of their collective operation . . . [[Abstract, "Pattern pluralism and the Tree of Life hypothesis," PNAS vol. 104 no. 7 2043-2049.]
 While these researchers do try to suggest a new evolutionary alternative (much as the punctuated equilibria advocates did in the 1970's), the basic message is plain. 

Namely,  the premier icon of macro-evolutionary theory, the tree of life -- one long presented in the august name of science as almost indubitable truth -- is in serious trouble and is now unlikely to be sound, once the molecular evidence has spoken. All of this grand -- even, visionary -- tree of life picture, then, has always been a sweeping, extrapolated explanatory inference; one long since projected unto a significantly recalcitrant gap-filled fossil record and now even more recalcitrant genetic/molecular evidence. 

Or, in plainer words: once the molecules have spoken, there are question-begging circularities ("there is no independent evidence . . . ") and significant conflicts between lines of evidence ("the sequences of genes, often disagree . . . "); leading to serious undermining of the plausibility of the iconic TOL ("the universal TOL rests on an unproven assumption about pattern that, given what we know about process, is unlikely to be broadly true . . . "). 

Too often, it is then presented to students in school and the general public in terms that suggest -- or blatantly state -- that these claims are as much a fact as the roundness of the earth or the orbiting of planets around the sun. (A fairer comparison would be to speculative reconstructions of the origin of the solar system, which is openly acknowledged to be highly speculative and full of unsolved puzzles.)

Where, islands of complex tightly integrated function depending on specific arrangement of well-matched parts are signs of design. 

So, while for instance, one can argue for a significant degree of common descent on a branching-tree pattern for fossils (with room for qualified acceptance of timelines), the pattern of branching plus gaps and stasis arguably points to built-in variability of major kinds at perhaps up to Family level. Similar, to what has credibly happened with dogs and wolves, or with red deer and North American elk [[discovered to be inter-fertile in New Zealand] or the cichlids, and to intelligent direction/injection of the underlying FSCO/I. So far, I think even many modern Young Earth Creationists would more or less agree; "fixity of species" being subject to the question, what is a species. (Hence, the Creationist discussion of baramins and/or created kinds.)

Beyond this level, we need to mark a distinction between causal factor at work and mechanism to implement. That starts with: there's more than one way to skin a cat-fish. That is, (a) mechanism is a means, (b) purposeful design is a cause, and (c) the two are distinct

That is why design is inferred as a causal factor on empirically tested reliable signs such as FSCO/I and associated patterns such as islands of function in large spaces of possibilities, not a mechanism. Design is compatible with the sort of limited common descent described so far, and -- as the front-loading hypothesis and the publicly stated position of leading design theorist Michael Behe alike demonstrate -- it is also compatible with universal common descent. (Which is a specific, noteworthy difference from Young Earth Creationism.)

What design theorists quite rightly spotlight, is that it is crucial is to see that the proposed Darwinian mechanism for common descent (and other unintelligent proposed mechanisms) as well as the associated models for origin of life through so-called chemical evolution, have quite serious -- and too often unacknowledged -- challenges in accounting for the origin of complex, tightly integrated biological organisation and associated information.

That is why foundational member of the ID school of thought, Michael Behe of Lehigh University, highlighted the Darwinist commitment to gradualism by citing Darwin's commitment to gradualism, and then challenged it by defining the concept of irreducible complexity then giving dozens of biological candidates. First, Darwin, in Origin:
If it could be demonstrated that any complex organ existed, which could not possibly [--> This loads the case a bit, we should read liberally as "plausibly," backed by empirical evidence]  have been formed by numerous, successive, slight modifications, my theory would absolutely break down. But I can find out no such case . . . . We should be extremely cautious in concluding that an organ could not have been formed by transitional gradations of some kind. [Origin, 6th edn, 1872, Ch VI: "Difficulties of the Theory."]
next, Dawkins, in River out of Eden (1995), explains why that is so, from the conventional Darwinist viewpoint:
 A key feature of evolution is its gradualness. This is a matter of principle rather than fact. It may or may not be the case that  some episodes of evolution take a sudden turn . . . . Evolution is very possibly not, in actual fact, always gradual. But it must be gradual when it is being used to explain the coming into existence of complicated, apparently designed objects, like eyes. For if it is not gradual in these cases, it ceases to have any explanatory power at all. Without gradualness in these cases, we are back to miracle, which is simply a synonym for the total absence of explanation.
[[NB: --> Dawkins' atheism here leads him astray into purple prose and fallacious dismissiveness. First, ever since Plato -- 2350 years ago -- in The Laws, Bk X, the obvious (and abundantly observed) alternative to blind chance and mechanical necessity as an explanation of complex functionally specific organisation is art, or design, and design is not miraculous in itself; as can be seen from a world of technology all around us. Secondly, as Paul pointed out to the largely skeptical Athenian elites at Mars Hill c. AD 50 (cf. also here and here), once a credible miracle has occurred, based on report of reliable eyewitnesses, that is -- or pretty directly leads to -- a powerful explanation of our world; as, it implies existence of entities capable of such; particularly, God. But Dawkins and others of like ilk too often seem to greatly resent even the possibility of the shadow of a Divine Foot in the door of their hallowed temple of evolutionary materialism. (Cf. Lewontin et al here on.)]
The reason eyes and wasp-pollinated orchids impress us so is that they
are improbable. The odds against their spontaneously assembling by luck
are odds too great to be borne in  the real world. Gradual evolution by small steps, each step being lucky but not too lucky, is the solution to
the riddle. But if it is not gradual, it is no solution to the riddle: it is just a restatement of the riddle.
[[The reason why this is so rests in the nature of mutation as small incremental changes in DNA, and also the appeal to gradual culling out of unsuccessful varieties through incremental differences in reproductive success leading to descent with modification held to be cumulatively unlimited -- aka natural selection; as variant sub-populations must at every step have a sufficient but limited distinction between different varieties in a population such that culling based on success/failure in environmental niches becomes possible] . . . [[River out of Eden (Basic Books, 1995), pp. 83 - 4. Emphasis and parenthesis added.]
However, as the issue of irreducibly complex systems not amenable to incremental emergence has been underscored, together with dozens of cases in point, a common rebuttal strategy has been to assert that various parts may arise for different reasons then by happy chance fall in together to form a new and successful system.

To such, Behe in Darwin's Black Box (1996) aptly and briefly notes:
What type of biological system could not be formed by “numerous successive, slight modifications?” Well, for starters, a system that is irreducibly complex. By irreducibly complex I mean a single system composed of several well-matched interacting parts that contribute to the basic function, wherein the removal of any one of the [core] parts causes the system to effectively cease functioning. [[Darwin's Black Box (Free Press, 1996), p. 39, emphases and parenthesis added. Later, he highlights the emergence of such steps by noting: “An irreducibly complex evolutionary pathway is one that contains one or more unselected steps (that is, one or more necessary-but-unselected mutations). The degree of irreducible complexity is the number of unselected steps in the pathway.” (A Response to Critics of Darwin’s Black Box, by Michael Behe, PCID, Volume 1.1, January February March, 2002;]
Even if a system is irreducibly complex (and thus cannot [[plausibly] have been produced directly), however, one can not definitively rule out the possibility of an indirect, circuitous route. As the complexity of an interacting system increases, though, the likelihood of such an indirect route drops precipitously. And as the number of unexplained, irreducibly complex biological systems increases, our confidence that Darwin's criterion of failure has been met skyrockets toward the maximum that science allows. [[Darwin's Black Box (Free Press, 1996), p. 40 . Parenthesis added. In effect, a complex, functionally specific organised system can be described by making a nodes- and- arcs 3-dimensional "drawing" or description of parts and the way they are arranged and coupled together, which in turn can be reduced to strings of bits such as is used in Drawing Packages.  This boils down to a structured string of Yes/No questions. As the string of Y/N questions -- bits -- for a functionally specific system rises to and then exceeds the threshold of functionally specific complex information and/or organisation of 500 - 1,000, the plausibility of finding such an entity by blind chance and/or mechanical necessity . . . Dawkins' Blind Watchmaker . . . rapidly diminishes to the point of vanishing.]
Angus Menuge adds some details, highlighting the celebrated case of the bacterial flagellum:

For a working [bacterial] flagellum to be built by exaptation [[--> pulling together diverse parts that work elsewhere, to form a new functional entity], the five following conditions would all have to be met:
C1: Availability. Among the parts available for recruitment to form the flagellum, there would need to be ones capable of performing the highly specialized tasks of paddle, rotor, and motor, even though all of these items serve some other function or no function.
C2: Synchronization. The availability of these parts would have to be synchronized so that at some point, either individually or in combination, they are all available at the same time.
C3: Localization. The selected parts must all be made available at the same ‘construction site,’ perhaps not simultaneously but certainly at the time they are needed.
C4: Coordination. The parts must be coordinated in just the right way: even if all of the parts of a flagellum are available at the right time, it is clear that the majority of ways of assembling them will be non-functional or irrelevant.
C5: Interface compatibility. The parts must be mutually compatible, that is, ‘well-matched’ and capable of properly ‘interacting’: even if a paddle, rotor, and motor are put together in the right order, they also need to interface correctly.
[[Agents Under Fire: Materialism and the Rationality of Science (Rowman & Littlefield, 2004), pp. 104-105 . HT: ENV.]

 The Cambrian strata "explosion" of top-level body plans is a pivotal case, as a body plan is obviously a highly complex functionally integrated entity that will require core parts for many subsystems to be there all at once on proper arrangement, to work. As Wells sums up in Ch 3 of his Icons of Evolution:
The origin of Species included only one illustration [[--> cf. Fig. G.11 above], showing the branching pattern that would result from this process of descent with modification . . . Darwin thus pictured the history of life as a tree, with the universal common ancestor as its root, and modern species as "its green and budding twigs." He called this the "great Tree of Life." [[--> The echo of the one in Genesis and the Revelation is obvious, and shows the shift in pivotal imagery and how it has affected our civilisation. This is similar to the debate about rationalist "enlightenment" vs. the Medieval "dark ages" vs. Johannine light and darkness imagery, which provides significantly unwarranted plausibility for the concept of a war of enlightening rationalistic science with benighted and oppressive religion. Cf. Pearcey's evaluation of this ill-founded metaphor.]

Of all the Icons of Evolution, the Tree of Life is the most pervasive, because descent from a common ancestor is the foundation of Darwin's theory. Neo-Darwinist Ernst Mayr boldly proclaimed in 1991 that "there is probably no biologist left today who would question that all organisms now found on the earth have descended from a single origin of life." Yet Darwin knew -- and scientists have recently confirmed -- that the early fossil record turns the evolutionary tree of life upside down. Ten years ago [[-->i.e. in the 1990's]  it was hoped that molecular evidence might save the tree, but recent discoveries [[--> of sharply divergent molecular "trees"] have dashed that hope. Although you would not learn it from reading biology textbooks, Darwin's Tree of Life has been uprooted . . . . 

Darwin believed that if we could have been there to observe the process, we would have seen the ancestral species [[--> e.g. of humans and fruit flies] split into several species only slightly different from each other. These species would then have evolved in different directions under the influence of natural selection. More and more distinct species would have appeared; and eventually at least one of them would have become so different from the others that it could be considered a different genus . . . differences would have continued to accumulate, eventually giving rise to separate families . . . .
Thus the large differences separating orders and classes would emerge only after a very long history of small differences: "As natural selection acts only by accumulating slight, successive, favourable variations, it can produce no great or sudden modifications; it can act only by short and slow steps." These "short and slow steps" give Darwin's illustration its characteristic branching-tree pattern . . . .

But in Darwin's theory, there is no way Phylum-level  differences could have appeared right at the start. Yet that is what [[--> understood on the conventional timeline] the fossil record shows. [[Icons of Evolution, 2000, pp. 29 - 35.]
For, as Wells goes on to note: "the Cambrian starts with the abrupt appearance of many phyla and classes of animals." That was seen in Darwin's day, and -- despite attempts to smear out the timeline, or suggest imperfections in the record and to put forward connexions or complex explanations suggested in order to to make the lack of sequences of incremental transitional forms seem less of a challenge to the dominant narrative -- it is just as much of a challenge today. 

With the Cambrian fossil life explosion as exhibit no 1. 

With, 3 bn year old micro-fossils and fossils of evidently soft-bodied Ediacaran forms in the preceding 100 or so Mn years to suggest that there was plenty of opportunity for the "missing" ancestral forms to have fossilised had they been there on the ground. 

Where, too, the fossils are, of course, the actual traces and facts that we must deal with. So, absence of chains of ancestral fossils in the indicated bottom-up branching tree pattern may well be telling us something.

Something that is more pervasive in the world of fossil life than we may think: a pattern of sudden appearances, stasis and disappearance of forms, rather than one where we commonly find incremental sequences of transitional forms illustrating Darwin's "short and slow steps." And yet, were Darwinian gradualism true, the dominant pattern of incremental transformation should have dominated the world of life

Which means that: we have every reason to expect that, were that so, transitional sequences should be common or even dominant in the set of snapshots provided by fossil forming events.

But, evidently, that is simply not the case.

Writing on this perhaps surprising fact, Stephen Jay Gould -- one of the founders of the alternative evolutionary theory, punctuated equilibria -- was moved to observe as follows, in his The Structure of Evolutionary Theory (2002), a technical work published just two months before his death; as a "constructive critique" of contemporary Darwinian thought:
. . . long term stasis following geologically abrupt origin of most fossil morphospecies, has always been recognized by professional paleontologists. [[p. 752.]

. . . .  The great majority of species do not show any appreciable evolutionary change at all. These species appear in the section [[first occurrence] without obvious ancestors in the underlying beds, are stable once established and disappear higher up without leaving any descendants." [[p. 753.] 
. . . . proclamations for the supposed ‘truth’ of gradualism - asserted against every working paleontologist’s knowledge of its rarity - emerged largely from such a restriction of attention to exceedingly rare cases under the false belief that they alone provided a record of evolution at all! The falsification of most ‘textbook classics’ upon restudy only accentuates the fallacy of the ‘case study’ method and its root in prior expectation rather than objective reading of the fossil record. [[p. 773.] 
Since there is a regrettable tendency to cry "quote mining" (i.e. dishonest out of context citation or misquoting . . . as opposed to error) in the face of citation of key admissions against interest, let me give a bit of context for that first, short clip:

The common knowledge of a profession often goes unrecorded in technical literature for two reasons: one need not preach commonplaces to the initiated; and one should not attempt to inform the uninitiated in publications they do not read. The longterm stasis, following a geologically abrupt origin, of most fossil morphospecies, has always been recognized by professional paleontologists, as the previous story of Hugh Falconer [c. 1862] testifies. This fact, as discussed on the next page, established a basis for biostratigraphic practice [ –> cf. ], the primary professional role for paleontology during most of its history.
But another reason, beyond tacitly shared knowledge, soon arose to drive stasis more actively into textual silence. Darwinian evolution became the great intellectual novelty of the later 19th century, and paleontology held the archives of life’s history. Darwin proclaimed insensibly gradual transition as the canonical expectation for evolution’s expression in the fossil record. He knew, of course, that the detailed histories of species rarely show such a pattern, so he explained the literal appearance of stasis and abrupt replacement as an artifact of a woefully imperfect fossil record. Thus, paleontologists could be good Darwinians and still acknowledge the primary fact of their profession — but only at the price of sheepishness or embarrassment. No one can take great comfort when the primary observation of their discipline becomes an artifact of limited evidence rather than an expression of nature’s ways. Thus, once gradualism emerged as the expected pattern for documenting evolution — with an evident implication that the fossil record’s dominant signal of stasis and abrupt replacement can only be a sign of evidentiary poverty — paleontologists became cowed or puzzled, and even less likely to showcase their primary datum . . .

Indeed, in reviewing the book for the New York Review of Books, Australian paleontologist Tim Flannery noted:
Niles Eldredge and Gould first coined the term "punctuated equilibrium" in 1971 and published it the following year. The theory seeks to explain a persistent pattern in the fossil record whereby a species suddenly appears, then persists unchanged for a very long time before going extinct. This pattern is seen in a wide variety of contexts, from marine creatures such as shellfish and sea urchins to mammals and birds. Punctuated equilibrium posits that these species come into existence relatively rapidly (over tens of thousands of years), though just how (and indeed if) this happens is hotly debated. An opposing explanation is that these species have evolved much more slowly somewhere else, and their "sudden" appearance is the result of migration. While, as Galton's polyhedron suggests, the concept of punctuated equilibrium was not entirely new to paleontology, Eldredge and Gould's formulation of it was timely and coherent. Even among its supporters, however, argument has raged over its significance, with many questioning whether it really challenges Darwin's concept of gradualism. (After all, tens of thousands of years is sufficient time for species to evolve "gradually.") Most researchers, though, recognize that the concept has been invaluable in encouraging paleontologists to examine the fossil record with a rigor and attention to detail that previously was largely lacking.

Punctuated equilibrium has forced paleontologists to focus not only on the origin of species, but also on their often long, unchanged persistence in the fossil record . . .  [["A New Darwinism?," The New York Review of Books, 49 (May 23, 2002): pp. 52–54.]

We may add to this, an older collection of nuggets containing perhaps Gould's single most famous quote, on the trade secret of paleontology (with the bonus of an internal quote from Darwin):
"The absence of fossil evidence for intermediary stages between major transitions in organic design, indeed our inability, even in our imagination, to construct functional intermediates in many cases, has been a persistent and nagging problem for gradualistic accounts of evolution." [[Stephen Jay Gould (Professor of Geology and Paleontology, Harvard University), 'Is a new and general theory of evolution emerging?' Paleobiology, vol.6(1), January 1980,p. 127.]

"The fossil record with its abrupt transitions offers no support for gradual change, and the principle of natural selection does not require it—selection can operate rapidly . . . .
[[--> this tries to make virtue out of a grave weakness, the specific functional information content of "sudden leaps" of implied scope of complexity undermines the hope of accumulating small, incremental changes to overwhelm the cliff-like challenge of Dawkins' Mt Improbable]
All paleontologists know that the fossil record contains precious little in the way of intermediate forms; transitions between major groups are characteristically abrupt. [[--> notice, "All paleontologists know . . . "] Gradualists usually extract themselves from this dilemma by invoking the extreme imperfection of the fossil record—if only one step in a thousand survives as a fossil, geology will not record continuous change  . . .
[[--> statistically, with 250,000+ fossil species notoriously in hand, millions of specimens in museums and billions observed in the field (think here of Barbados, which is built on cubic miles of fossil corals  etc. that can be seen just by walking along the roads or visiting construction sites), if gradual change were dominant, per the implications chance sampling, it should be dominant in the fossils, so that it is not is a striking concession] 
Even though we have no direct evidence for smooth transitions, [--> notice his underscoring of the "characteristically abrupt" just above] can we invent a reasonable sequence of intermediate forms—that is, viable, functioning organisms—between ancestors and descendants in major structural transitions? Of what possible use are the imperfect incipient stages of useful structures? What good is half a jaw or half a wing? The concept of preadaptation provides the conventional answer by permitting us to argue that incipient stages performed different functions. The half jaw worked perfectly well as a series of gill-supporting bones; the half wing may have trapped prey or controlled body temperature. I regard preadaptation as an important, even an indispensable, concept. But a plausible story is not necessarily true. I do not doubt that preadaptation can save gradualism in some cases, but does it permit us to invent a tale of continuity in most or all cases? I submit, although it may only reflect my lack of imagination, that the answer is no
[[--> Notice Gould's remark above, that "our inability, even in our imagination, to construct functional intermediates in many cases, has been a persistent and nagging problem for gradualistic accounts of evolution" -- especially relevant when such "preadaptation" then faces the challenge of diverse parts being required to fit together, be coupled just right (often to tiny fractions of an inch), and have all parts present and  correctly arranged at one go for irreducibly complex functional entities; e.g. to build Behe's famous bacterial flagellum which requires dozens of fairly unique proteins set up in a self-assembling functional whole . . .  where also the usual counter-example suggested rhetorically, the toxin injector of bacteria that prey on eukaryotes (which supposedly derived later from prokaryotes, that -- similar to bacteria -- don't have nuclei),  is far more plausible as a similarly irreducibly complex derivative based on one of the substructures. Likewise, at gross body plan level, loss of function on the way to becoming a wing integrated with requisite control and powering systems to achieve flight, is a classic challenge.] 
 [[Stephen Jay Gould 'The Return of Hopeful Monsters.' Natural History, vol. LXXXVI(6), June-July 1977, pp. 22 - 30 & elsewhere. Emphases, highlights and parenthetical notes on points added. This cite has been expanded in reply to an accusation of "quote-mining," and to correct a minor error in the original short highlighted clip, "transitions between the major groups are characteristically abrupt."]

"The extreme rarity of transitional forms in the fossil record persists as the trade secret of paleontology. The evolutionary trees that adorn our textbooks have data only at the tips and nodes of their branches; the rest is inference, however reasonable, not the evidence of fossils. Yet Darwin was so wedded to gradualism that he wagered his entire theory on a denial of this literal record:
[[here, I flesh out Gould's allusion to Darwin:] I have attempted to show that the geological record is extremely imperfect [[--> c. 1859]; that only a small portion of the globe [[--> Europe and North America] has been geologically explored with care; that only certain classes of organic beings have been largely preserved in a fossil state; that the number both of specimens and of species, preserved in our museums, is absolutely as nothing compared with the incalculable number of generations which must have passed away even during a single formation . . . these [[and other listed] causes taken conjointly, must have tended to make the geological record extremely imperfect, and will to a large extent explain why we do not find interminable varieties, connecting together all the extinct and existing forms of life by the finest graduated steps.
He who rejects these views on the nature of the geological record, will rightly reject my whole theory. For he may ask in vain where are the numberless transitional links which must formerly have connected the closely allied or representative species, found in the several stages of the same great formation . . . [[Cf. Origin, Ch 10, "Summary of the preceding and present Chapters," also see similar remarks in Chs 6 and 9. note, the circumstances today with 1/4 million plus fossil species, millions of fossils in museums and billions seen in the ground now make the collected record "almost unmanageably rich" but with the same basic pattern.]
Darwin's argument still persists as the favored escape of most paleontologists from the embarrassment of a record that seems to show so little of evolution. In exposing its cultural and methodological roots, I wish in no way to impugn the potential validity of gradualism (for all general views have similar roots). I wish only to point out that it was never "seen" in the rocks.

Paleontologists have paid an exorbitant price for Darwin's argument. We fancy ourselves as the only true students of life's history, yet to preserve our favored account of evolution by natural selection we view our data as so bad that we never see the very process we profess to study." [[Stephen Jay Gould 'Evolution's erratic pace'. Natural History, vol. LXXXVI95), May 1977, p.14. (Kindly note, that while Gould does put forward claimed cases of transitions elsewhere, that cannot erase the facts that he published in the peer reviewed literature in 1977 and was still underscoring in 2002, 25 years later, as well as what the theory he helped co-found, set out to do. Sadly, this needs to be explicitly noted, as some would use such remarks to cover over the points just highlighted. Also, note that this is in addition to the problem of divergent molecular trees and the top-down nature of the Cambrian explosion.)]  [[HT:]

In short, ever since Darwin's day, the general observed pattern of the fossil record, plainly, has actually always been sudden appearances, morphological stasis, and disappearance (or continuation into the modern world). 

Fazale Rana, an Old Earth Creationist, unsurprisingly, has something to say on this that we need to listen to:

Worse, the “tree” -- which is subject to considerable debate -- produced by comparing gross body plans is quite different from those produced by molecular comparisons of similar bio-molecules. Also, diverse molecules produce quite diverse trees. As Jonathan Wells, in his Icons of Evolution (Regnery, 2000),  pp. 49 - 50, summarises:
. . . the only actual data in a [[molecular difference based] phylogentic tree (with rare exceptions) come from living organisms which are the tips of the branches. The arrangement of the tips, the branches and the branch-points are all based on methodological assumptions and sequence comparisons. 

Ideally, phylogenetic trees should be approximately the same regardless of which molecules are chosen for comparison . . . . [[But that hoped for result] "began to crumble" . . . [[ for, as]  molecular biologists James Lake, Ravi Jain and Maria Rivera [[pointed out] in 1999, "when scientists started analyzing a variety of genes from different organisms and found that their relationships to each other contradicted the evolutionary tree of life derived from [[ribosomal RNA] rRNA analysis alone." According to French biologists Herve Philippe and Patrick Forterre: "with more and more sequences available, it turned out that most protein phylogenies contradicted each other as well as the rRNA tree." 
In other words, different molecules lead to very different phylogenetic trees.
Consequently, as Wells goes on to cite, biologist Carl Woese (a pioneer of the rRNA tree research) commented that: "No consistent organismal phylogeny has emerged from the many protein phylogenies so far produced. Phylogenetic incongruities can be seen everywhere in the universal tree, from its main branchings within and among the various [[groups] to the makeup of the primary groupings themselves." [[p. 50.]  

Wells then summarises how the results can be bizarre, e.g. the 1996 study of 88 protein sequences that put rabbits among the primates rather than the rodents, and a 1998 study of 13 genes across 19 animals that put sea urchins with the chordates. Another study saw cows as closer to whales than to horses. In more recent years, we have the astonishing discovery that  there are some very close similarities between Kangaroo (marsupial) and human (placental) genomes. As the Australian Broadcast Corporation science news reported in November 2008, based on remarks by Professor Jenny Graves, outgoing director of the Australian Research Council Centre for Excellence for Kangaroo Genomics (KanGO):
The tammar wallaby (Macropus eugenii), was the model kangaroo used for the genome mapping.

Like the o'possum, there are about 20,000 genes in the kangaroo's genome, Graves says.

That makes it about the same size as the human genome, but the genes are arranged in a smaller number of larger chromosomes.

"Essentially it's the same houses on a street being rearranged somewhat," Graves says.

"In fact there are great chunks of the [[human] genome sitting right there in the kangaroo genome."
 This is astonishing, for the lines of descent for placentas and marsupials are supposed to have diverged 150 million years ago. Carl Wieland of Australia-based Creation Ministries International is therefore fully warranted to respond:
. . . according to a report in Australia’s national newspaper, the 20,000–25,000 genes in the kangaroo (roughly the same number as in humans) are ‘largely the same’ as in people.1 Graves said elsewhere that ‘a lot of them are in the same order’.2
The reports made no mention of the percentage similarity. It sounds like it would be extremely high—perhaps embarrassingly so, given that unlike chimps, kangaroos are not supposed to be our ‘close relatives’ . . . . 

Evolutionists have long proclaimed that apes and people share a high percentage of DNA. Hence their surprise at these findings that ‘Skippy’ has a genetic makeup similar to ours. But even granted that chimps and humans have a high degree of shared DNA (progressively being revised downward as genomic knowledge increases), even if it were 90%, would that make them 90% human, as most interpret this? It is worth repeating what prominent evolutionist/geneticist Steve Jones has said in the context of man/chimp DNA-sharing: ‘We also share about 50% of our DNA with bananas and that doesn’t make us half bananas, either from the waist up or the waist down.’4

To all this, we must add that the Platypus is a key clue, for (as will be discussed in more details below), this creature is  an egg-laying, milk producing, duck-billed, venomous, beaver-tailed and web-footed mammal, whose 18,527 protein-encoding genes "contain alive-and-well representatives from mammals, birds and reptiles." 

That is, we are plainly seeing a pattern that strongly suggests a library of genetic and molecular parts that are adapted to particular needs for particular kinds of creatures, rather than the smoothly graded branching pattern that the Darwinist picture would lead us to expect.

In addition, the problem goes down to the common trunk and root of the proposed tree. For, recent concepts such as horizontal gene transfers and the incorporation of “symbiotic” organisms to form organelles such as mitochondria or chloroplasts – which have their own DNA -- have turned the root of the tree into much more of a web.

So much is this persistent gap between prediction and observation the case, that in his 2004 critical review paper, which according to an investigation “passed proper peer review” by “renowned scientists,” Stephen C. Meyer of the Discovery Institute remarked:

For over three billions years, the biological realm included little more than bacteria and algae (Brocks et al. 1999). [[NB: this is based on recovered fossils of such soft-bodied animals; i.e. the “soft bodied animals did not get fossilised” argument fails.] Then, beginning about 570-565 million years ago (mya), the first complex multicellular organisms appeared in the rock strata, including sponges, cnidarians, and the peculiar Ediacaran biota (Grotzinger et al. 1995). Forty million years later, the Cambrian explosion occurred (Bowring et al. 1993) . . . .

In order to explain the origin of the Cambrian animals, one must account not only for new proteins and cell types, but also for the origin of new body plans . . . Mutations in genes that are expressed late in the development of an organism will not affect the body plan. Mutations expressed early in development, however, could conceivably produce significant morphological change (Arthur 1997:21) . . . [[but] processes of development are tightly integrated spatially and temporally such that changes early in development will require a host of other coordinated changes in separate but functionally interrelated developmental processes downstream. For this reason, mutations will be much more likely to be deadly if they disrupt a functionally deeply-embedded structure such as a spinal column than if they affect more isolated anatomical features such as fingers (Kauffman 1995:200) . . . McDonald notes that genes that are observed to vary within natural populations do not lead to major adaptive changes, while genes that could cause major changes--the very stuff of macroevolution--apparently do not vary. In other words, mutations of the kind that macroevolution doesn't need (namely, viable genetic mutations in DNA expressed late in development) do occur, but those that it does need (namely, beneficial body plan mutations expressed early in development) apparently don't occur.6 [[“The origin of biological information and the higher taxonomic categories,” in Proceedings of the Biological Society of Washington 117(2):213-239. 2004 Emphases added. Cf. a more easily readable (and also peer-reviewed) but longer discussion, with illustrations, here. Also cf. Lönnig's recent [[2004] paper on "Dynamic genomes, morphological stasis, and the origin of irreducible complexity." Joseph Kuhn's 2012 short critique here (7 pp.!) will also be helpful.]

In short, organisms are based on tightly integrated systems, right from the embryological stages. For body-plan level changes to occur, integrated changes across several interacting systems will be required. It is unlikely that such tightly integrated changes would result from mere accumulation of small changes. And, it is equally unlikely that accidental duplication and random variation of DNA strands that then find themselves somehow expressed will write the relevant coordinated, complex code out of in effect molecular accident driven trial and error, i.e. lucky noise captured and turned into functional information by differences in reproductive success and competition among sub populations.

Thus, we see the significance of:

(b) The functional information creation challenge

In the same paper, Meyer observed:

One way to estimate the amount of new CSI that appeared with the Cambrian animals is to count the number of new cell types that emerged with them (Valentine 1995:91-93) . . . the more complex animals that appeared in the Cambrian (e.g., arthropods) would have required fifty or more cell types . . . New cell types require many new and specialized proteins. New proteins, in turn, require new genetic information. Thus an increase in the number of cell types implies (at a minimum) a considerable increase in the amount of specified genetic information. Molecular biologists have recently estimated that a minimally complex single-celled organism would require between 318 and 562 kilobase pairs of DNA to produce the proteins necessary to maintain life (Koonin 2000). More complex single cells might require upward of a million base pairs. Yet to build the proteins necessary to sustain a complex arthropod such as a trilobite would require orders of magnitude more coding instructions. The genome size of a modern arthropod, the fruitfly Drosophila melanogaster, is approximately 180 million base pairs (Gerhart & Kirschner 1997:121, Adams et al. 2000). Transitions from a single cell to colonies of cells to complex animals represent significant (and, in principle, measurable) increases in CSI . . . .

Thus, the sort of novel body plans observed in the Cambrian fossil life revolution reasonably required 10 – 100+ millions of functional four-state DNA bases. This is more than 100,000 times the 500 – 1,000 bit threshold at which the undirected search resources of the observed cosmos would be inadequate to carry out a credible search of the relevant configuration spaces. 

Some would doubt such a range, so let us do a fresh calculation: 50 new tissue types to make up the organs for a new body plan would easily take up probably 10 - 100 proteins [[including enzymes etc] per type, i.e we are looking at 500 - 5,000 proteins as a reasonable/ conservative estimate — VERY conservative at the low end. 500 * 300 = 1.5 *10^5 codons, or 4.5 *10^5 bases, plus regulatory, let’s say about 10% more, 1/2 mn bases.At the upper end, we would arrive at 4.5 *10^6 bases.

But this estimate is too low:
Arabidopsis thaliana [[a flowering plant] 115,409,949 DNA bases

Anopheles gambiae [[a mosquito] 278,244,063 bases

Sea urchin 8.14 x 10^8 bases

Amphibians 10^9–10^11

Tetraodon nigroviridis (a pufferfish) 3.42 x 10^8
In short, 10 – 100 million bases for a novel body plan is reasonable, even generous. And in any case the config space of 500 k bases is: 9.9 *10^301,029 possibilities.

Let us recall too, that say an insect routinely emerges from a single cell (the egg) and develops into an adult organism by a replication, specialisation and integrated body plan development process. In the case of complete metamorphosis, there is first one body plan the larva, then there is an intermediate pupal "soup" stage that refashions itself into a completely new plan, the adult.

For the explanation that this has come about by chance variation and natural selection, step by step, from a "simple" unicellular ancestor to be well-warranted, we need to see a good account with observational evidence, of how this can happen. That account has to explain how the embryological development algorithm that transforms a single cell into a complex organism based on specialised cell types, organised into tissues, organs and integrated coherent systems comprising a viable life form, came to be.

On the face of it, the bare concept that such a complex algorithm could have come about by accidental duplications and chance variations that hit on new function, then were incorporated somehow into the regulatory processes of the organism and just happening to give us a fully integrated functioning organism that unfolds from the single cell to the organism on a body plan is not plausible absent specific empirical evidence that this is what can happen and did happen. That, within the resources of our solar system over the course of the sort of window of at most several hundred millions of years to a few billion years. if the usual timelines for the Cambrian life revolution are reasonable, we may be talking about a window of maybe 2 or 3 - 10 MY, 540 or so MYA.

In fact, there is no such body of undeniable observations.

Instead, we are back to the Lewontin a priori materialistic frame of thought:
It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is absolute, for we cannot allow a Divine Foot in the door. [[From: Lewontin, R, “Billions and Billions of Demons,” NYRB, January 9, 1997. Bold emphasis added.]
No wonder ID thinker Philip Johnson so soon rebutted this line of thought as follows:

For scientific materialists the materialism comes first; the science comes thereafter. [[Emphasis original] We might more accurately term them "materialists employing science." And if materialism is true, then some materialistic theory of evolution has to be true simply as a matter of logical deduction, regardless of the evidence. That theory will necessarily be at least roughly like neo-Darwinism, in that it will have to involve some combination of random changes and law-like processes capable of producing complicated organisms that (in Dawkins’ words) "give the appearance of having been designed for a purpose."  

. . . .   The debate about creation and evolution is not deadlocked . . . Biblical literalism is not the issue. The issue is whether materialism and rationality are the same thing. Darwinism is based on an a priori commitment to materialism, not on a philosophically neutral assessment of the evidence. Separate the philosophy from the science, and the proud tower collapses. [[Emphasis added.] [[The Unraveling of Scientific Materialism, First Things, 77 (Nov. 1997), pp. 22 – 25.]

By contrast -- putting aside the Lewontinian interdict for a moment -- we observe that intelligent agents routinely create novel information systems beyond the threshold and well into the range that is reasonable for novel body plans and variations on such. On that premise, a general branching tree pattern with libraries of components re-used through directed “horizontal transfer” of information and resulting “mosaics” would also make sense.

This makes mosaic creatures such as the platypus of significant interest. For, this creature is  an egg-laying, milk producing, duck-billed, venomous, beaver-tailed and web-footed mammal, whose 18,527 protein-encoding genes "contain alive-and-well representatives from mammals, birds and reptiles":

Fig G.12: The Duck-Billed Platypus, a mosaic animal at both body-plan and genetic/molecular levels (Courtesy Wikimedia)

In addition, a recent peer-reviewed paper discloses that:
Only microbats and toothed whales have acquired sophisticated echolocation, indispensable for their orientation and foraging. Although the bat and whale biosonars originated independently and differ substantially in many aspects, we here report the surprising finding that the bottlenose dolphin, a toothed whale, is clustered with microbats in the gene tree constructed using protein sequences encoded by the hearing gene Prestin

(Ying Li, Zhen Liu, Peng Shi, and Jianzhi Zhang, "The hearing gene Prestin unites echolocating bats and whales," Current Biology, Vol. 20(2):R55-R56 (January, 2010) (internal citations removed. HT: ENV).)
 The restrained language of the journal article softens the force of the point. A Science Daily report brings out the significance more directly:
two new studies in the January 26th issue of Current Biology, a Cell Press publication, show that bats' and whales' remarkable [[sonar echolocation] ability and the high-frequency hearing it depends on are shared at a much deeper level than anyone would have anticipated -- all the way down to the molecular level.

"The natural world is full of examples of species that have evolved similar characteristics independently, such as the tusks of elephants and walruses," said Stephen Rossiter of the University of London, an author on one of the studies. "However, it is generally assumed that most of these so-called convergent traits have arisen by different genes or different mutations. Our study shows that a complex trait -- echolocation -- has in fact evolved by identical genetic changes in bats and dolphins."
A hearing gene known as prestin in both bats and dolphins (a toothed whale) has picked up many of the same mutations over time, the studies show. As a result, if you draw a phylogenetic tree of bats, whales, and a few other mammals based on similarities in the prestin sequence alone, the echolocating bats and whales come out together rather than with their rightful evolutionary cousins.

Both research teams also have evidence showing that those changes to prestin were selected for, suggesting that they must be critical for the animals' echolocation for reasons the researchers don't yet fully understand.
 Or, more directly, yet, we can plainly see the issue of common design for a common function, across highly specialised animals in widely divergent taxonomic groups. For the likelihood of "identical genetic changes" to a given gene in such divergent groups, to produce sonar systems in water-living and flying mammals being by accident is rather small. So plainly small in fact that a Current Biology journal review suggested that: 
Whales and dolphins belong to the order Cetartiodactyla, and their closest living relatives may be hippopotamuses. Nevertheless, dolphins and porpoises share at least 14 derived amino acid sites in prestin with echolocating bats, including 10 shared with the highly specialised CF bats. Consequently, dolphins and porpoises form a sister group to CF bats in a phylogenetic analysis of prestin sequences (Figure 1). This finding is arguably one of the best examples of convergent molecular evolution discovered to date, and is exceptional because it is likely to be adaptive, driven by positive selection.

(Gareth Jones, "Molecular Evolution: Gene Convergence in Echolocating Mammals," Current Biology, Vol. 20(2):R62-R64 (January, 2010) (internal citations removed). HT: ENV.)

So, it is at least as reasonable reasonable to hold that similarity and even progressive variation of key structural features may plainly reflect common design and use of relevant components, structures and programs, rather than common descent.  That is, homology -- more or less, inference to common descent based on family resemblance --  is a species of argument by analogy, and common design has the advantage of being a directly observationally warranted alternative explanation

The gradualistic evolutionary tree of life – NB: this is illustrated by the only diagram in Origin and so is Darwin's first, foremost icon of evolution – breaks down.  That is why Jonathan Wells of Discovery Institute, who has made a critical study of such icons, proposes a warning label for this common illustration:
WARNING: Darwin's tree of life does not fit the fossil record of the Cambrian explosion,  and molecular evidence does not support a simple branching-tree pattern.

(c) Other icons of evolution

The following (and similar icons of evolution) have often been headlined in newspapers or magazines, or presented in the classroom, in encyclopedia articles and museum displays or on television; but too often have been presented without a fair but critical assessment (cf. article here and Google Book preview here) of their limitations:

i] Dinosaurs: First discovered in the 1820's and commonly used to “demonstrate” the existence of long lost pre-human ages dominated by dramatically different life forms. That may well be so – issues over what dragons were and why there are so many stories of men and dragons interacting notwithstanding. However, until the above origin of bio-functional coded information challenge is resolved, the mere existence of such deep past fauna does not prove the origin of species by undirected chance variation and natural selection.

ii] The geologic column and fossils: The succession of fossil-bearing sedimentary rocks (and associated radio-dating) is held to demonstrate a datable evolutionary pattern of successive life forms across time. Leaving aside historic (or current) debates over catastrophism and global floods, the actual fossil record is dominated by: sudden appearance, stasis of body form, and disappearance. Also, we still have not addressed the source of the relevant functional bio-information and organisation implied by those fossil forms. Nor have the circularities in the various dating schemes (cf. Part II) been resolved.

iii] Archaeopteryx: This curious mosaic animal with clawed wings, a wishbone [[vital for birdlike powered flight] a toothed mouth (without a horny beak) and perching feet was discovered in Germany in 1861; two years after Origin was published. It was hailed as a reptile-bird link. However, it provided no answer to where the integrated complex components to get a flyable feathered wing and associated muscles and neurological controls come from:

Fig. G.13: The complex functional organisation of the bird wing. [[Note the assymetry of the primary flight feathers.] (SOURCE: Wikipedia, CCA, L. Shyama.)

iv] The pentadactyl limb (and other homologies):
The bird wing, the bat wing, the whale fluke, the horse's foot and the human arm etc illustrate how the five-fingered limb architecture is modified to many diverse uses. Such homologies were held to show how a common ancestral five-digit limb has evolved across time into all these diverse forms. But (as the bird wing shows) the information to functionally modify such a generic structure has to be accounted for, and design with purposeful modification is at least as good an explanation as undirected descent with modification. A helpful video:

v] The horse fossil sequence: Many museum or textbook displays of horse fossil sequences try to make the case that over the past fifty million years, horse limbs have gradually gone from three-toed to one-toed form, while the general size of the animal has increased from about that of a dog and numbers of ribs and dentition have varied somewhat more hap- hazardly. Howbeit, there are miniature horses today that are not that much larger than a dog, and horses are occasionally born with three toes, i.e. the changes are fairly modest. There is however a shortage of the “links,” sometimes three- toed and one- toed horses have been found in the same fossil beds, and similar animals from apparently similar environments in South America show one- toed pseudo- horses in layers below three- toed ones. It is worth taking a look at modern mini-horses:

Fig G.14: Modern, near- dog- sized miniature horses. (Source: Wikipedia.)

vi] Haeckel's embryos: Darwin, in Origin, identified comparative embryological development as a key evidence, "second to none" in importance; because he thought they were best explained on variation from a common ancestor. Unfortunately, the well-known sketches made by Ernst Haeckel from the 1860's on  that were presented as showing how early embryological development recapitulates evolutionary descent were both selected from cherry-picked periods of development and in some cases were altered to make the case seem stronger than it was; especially the emphasis on features like pharyngeal pouches that superficially may look like gills (and, regrettably, are still sometimes called "gill slits" today), but develop into diverse head-and throat region structures. (In addition, the "early" stage shown is not the earliest, and the earlier stages are very diverse, as can be seen from pp. 92 - 100 here.) This apparent fraud has been known for over 100 years, but the diagrams or similar illustrations have been used from that time on and astonishingly still occasionally show up in textbooks; sometimes with the modified view that similarity of embryological development path shows common ancestry. (Haeckel's recapitulation theory: "ontogeny recapitulates phylogeny," suggested that the developing embryo embryo [[ontogeny] more or less replicates adult forms of its ancestors [[phylogeny], e.g. at one stage a human embryo is effectively recognisably like a fish.) However, embryological development is plainly a step by step, tightly integrated process; based on functional, complex and specific information. So, common design of a core algorithm, with adaptations to particular cases is also a legitimate explanation; with the key advantage that it accounts for the information on the only actually directly observed source of algorithms: design.

vii] Classical ape-men: It has long been commonplace to see a drawing with a sequence of apes, reconstructed ape-men and finally a modern human; meant to illustrate descent with modification to form modern man. Neandertal man was the first to star as such an ape man, and was soon joined by the likes of Java man and Piltdown man. Nebraska man (reconstructed and lavishly illustrated in the popular press from the tooth of an extinct pig) made a brief but spectacular appearance in the 1920's. And, in the 1960's – 70's a cluster of fossils was found in or near to the Rift Valley of East Africa. But, for instance neandertal “with a bath and a suit” could “pass without comment” on a New York Subway. Java man had a “cousin” Wadjack man, who is far more modern. Some argue that the fossil -- two parts found some fifty feet apart -- is one part the skull of a large, extinct gibbon, and one part a human thigh bone. Piltdown man turned out to be a hoax based on filed-down teeth and artificially aged bones. After much fun was had twitting William Jennings Bryan on how the evidence to overturn his objections to evolutionism was found in his home state, Nebraska man turned out to be a tooth of an extinct pig after all. More broadly, the fossils seem to cluster as apes and men but -- somewhat subjective reconstructions and artistic illustrations notwithstanding -- not “ape-men.”  And (artistic diagrams and charts in museums, on TV or in textbooks notwithstanding) at no point has there been an evidence- based, step- by- step observationally verified model of the origin of man that accounts for the novel, functionally specific complex information to create a man from a chimp-like ancestor in some 6 - 10 MY, on probabilistically credible small chance variations, differential reproductive success of sub-populations in environments, and resulting demonstrated descent with modification leading to macro-evolutionary transformation. Indeed, a classic remark on the limitations of such reconstructions duly warns us --
Put not your faith in reconstructions. Some anatomists model reconstructions of fossil skulls by building up the soft parts of the head and face upon a skull cast and thus produce a bust purporting to represent the appearance of the fossil man in life. When, however, we recall the fragmentary condition of most of the skulls, the faces usually being missing, we can readily see that even the reconstruction of the facial skeleton leaves room for a good deal of doubt as to details. To attempt to restore the soft parts is an even more hazardous undertaking. The lips, the eyes, the ears, and the nasal tip leave no clues on the underlying bony parts. You can, with equal facility, model on a Neanderthaloid skull the features of a chimpanzee or the lineaments of a philosopher. These alleged restorations of ancient types of man have very little, if any, scientific value and are likely only to mislead the public. [[Earnest Albert Hooton, Up from the Ape (NY: Macmillan, 1946), p. 329.]
. . . and, for further example, there is no such step by step, empirically and probabilistically credible account for our being physically equipped to speak, while chimps etc. are not. This gap is actually a critical issue, as the ability to use complex, conceptual, abstract language is a key aspect of human intelligence. And, so, by right of fair comment, we may note that:
So long as [[Neo-]Darwinian macro-evolutionary theory lacks an empirically credible, tested and well-supported explanation of the origin and validity of human intelligence, language and associated reasoning powers, the very need to use these same human faculties to propose, discuss and analyse a theory that should but cannot account for them, turns every presentation of (or argument for) the theory into an unintended but eloquent illustration of the major and un-answered weaknesses of the theory.
viii] Spark-in gas experiments: Starting in 1953, Miller and Urey showed that in a sparked, reducing atmosphere, some of the precursor molecules for life can form, and can be trapped out with suitable apparatus. This was hailed as showing that life can “easily” form in prebiotic environments. However, by the 1970's, it was questionable whether early earth environments were ever reducing, which is required for such spark in gas experiments to work. As ENV's Casey Luskin summarises:
There are strong reasons to expect that the early earth's atmosphere did not contain significant amounts of methane, ammonia, or high concentrations of other reducing gasses. The earth's early atmosphere is thought to have been produced by outgassing from volcanoes on the early earth, and the composition of those volcanic gasses is related to the chemical properties of the earth's inner mantle. Multiple studies have found that the chemical properties of the earth's mantle would have been the same in the past as they are today.3 But today, volcanic gasses do not contain methane or ammonia, and are not reducing. A paper in Earth and Planetary Science Letters found that these chemical properties have been essentially constant over earth's history, leading to the conclusion that "Life may have found its origins in other environments or by other mechanisms."4
 And, plainly, a pile of bricks does not a three-bedroom house make. That is, the spontaneous functional organisation of even the simplest observed life form has not been demonstrated (as is discussed in Part III). Jonathan Wells comments:

ix] Open system thermodynamics: When the tendency of entropy (roughly, disorder) to rise in the universe was raised as an objection to the claimed spontaneous origin of life , it was pointed out that order can arise in open systems, e.g. a hurricane or a snow crystal or the like. From 1973 on, it has been further clarified by Orgel and others that specifically functional, complex organisation -- as is found in cell-based life forms -- is not to be equated with either the order of a crystal or a vortex, or the randomness of say an organic tar. When that organisation further embeds digital codes and algorithmic, step by step processing of information, the differences are even more stark. For instance, we can easily see the difference between: (a) randomness: hfugfiewgvf3r8 . . . , (b) order: atatatatatatatatat . . . , and (c) functionally specific complex organisation and  related information, "this is a functionally specific, complex, organised string of ASCII-coded characters." For very good reason, we routinely and only observe that type (c) objects are produced by intelligently directed configuration of components, i.e. design.  FSCI is therefore an empirically reliable sign of design. Video:

x] The Weasel computer simulation and kin: In 1986, Richard Dawkins presented a computer simulation that through “cumulative selection” was able to advance from a random initial phrase to the designated target phrase: “methinks it is like a weasel.” However, the program worked by setting up a designated, pre-loaded target and by rewarding “nonsense phrases” for getting closer to the target. So, it is a targetted search that rewards mere proximity and fails to address the spontaneous origin of functionally specific, complex information. More sophisticated genetic algorithms, similarly do not address how the genetic codes they use achieve functionality. They thus fail to deal with the search challenge of getting to isolated islands of code-based function in vast configuration space dominated by seas of non-function. And, they are in fact deliberately designed, code based algorithms, i.e. examples of intelligent design.

xi] Peppered moths: During the coal-fired British industrial revolution, it was observed that as the polluted trees etc darkened, a former minority variety of the peppered moth began to dominate the population. Then, as the pollution was cleaned up in fairly recent years, the lighter coloured moths apparently “came back.” This was held to be an outstanding example of natural selection in action; and pictures of light and dark moths resting on trees were used in many textbooks. However, the pictures were often artificially posed, sometimes with moths glued to trees. More importantly, the change introduced no true novelty: at most it illustrates that the variety dominating a population will respond to some extent to environmental forces, with the capability to swing back and forth.

xii] Darwin's Finches: On visiting the Galapagos islands in the 1830's Darwin observed finch-like birds, and suggested they would be a good illustration of adaptive radiation where, as a parent species spreads over a diverse region, different varieties dominate leading to a cluster of related species. Studies from the 1930's to the 1970's on show that: (i) while there are indeed varieties, there is no neat pattern of distribution; that (ii) different “species” are in significant cases inter-fertile; and that (iii) while even ½ mm difference in beak size can make a difference to survival in drought times (bigger beaks can crack heavier seeds), when rains return, the population swings back.

xiii] Four-winged fruit flies: Mutations can make the commonly studied fruit fly grow four full-sized wings instead of one pair and a pair of balancing stub-wing halteres. But, there are no connected powering muscles, and the resulting handicapped mutants would be eliminated in any natural environment.

xiv] Tiktaalik: In 2005, Shubin discovered fossils of a jointed lobe-finned fish with a crocodile-like head on Ellesmere Island. The jointed pectoral fins seem to have enabled this creature to do “a sort of push-up.” He announced: “[[w]hat we saw when we looked at this fossil was a real mosaic between characteristics of fish and characteristics that were previously thought to be only in land-living animals . . . . It’s showing us how creatures were assembled over evolutionary time to live on land.” However, the term “mosaic” shows the key limitation: if one looks with the eye of macro- evolutionary faith, one will see a vindication of the idea that one has "found" a missing link. But, the case, again, is not proved; especially when we consider the issue of the need to originate the bio-information to create major body plan novelties.

xv] Proto-whales: In 1994, a partial skull with whale-like elongation was discovered in Pakistan, and was announced by Gingerich as “perfectly intermediate, a missing link between earlier land mammals and later, full-fledged whales,” and an artistic reconstruction portrayed it as a proto-whale with stubby legs and tail, diving at a school of fish. However, when more complete fossils were found, Thewissen et al. (2001) acknowledged that it turned out to be “no more amphibious than a tapir.” Such a gross error of predictive reconstruction at so late a date is a clear indicator of the difficulties and subjectivity involved. More generally, Berlinski, in this video, estimates that it would take some 50,000+ changes to transform say a cow into a whale, and raises the issue of the number of co-ordinated transformations that would have to be in place, and in place at the same time, to make the change possible; also, the implication that there should be a huge range of transitional forms. We should bear in mind as well that whale populations tend to be relatively small so there is an issue of population scale and chance mutation rate to effect such a change:

xvi] Early birds and dinosaurs: Haeckel suggested that birds are dinosaur descendants. In recent years fossil finds of “feathered dinosaurs,” and various “primitive” birds have been brought forward. Currently, fossils of Anchiornis huxleyi and kin have been isotopically dated to 154 – 168 MYA, and are thus deemed to be older than Archaeopteryx. Anchiornis evidently had symmetrical flight-like feathers on not only its wings but its legs. This last is difficult to integrate with long running legs and the requisites of powered flight. A gliding habit has been suggested. This reflects the classic challenge between the two schools of thought, that a gliding tree climber or a leaping runner will run into functionality difficulties before it can get to a workable flying body plan. As an important aspect of that, birds have a one directional flow lung system, which uses air sacs to breathe in and pass air though the lungs, giving them the amount of oxygen required for sustained powered flight. Intermediates to get to such a lung – a literally vital organ – are a significant and unanswered challenge.

xvii] Ida and Ardi: In May 2009, the former -- an unusually complete fossil (a lemur with some monkey-like features) -- dated at 47 MY was announced, to global headlines. [[Most primate fossils are of “jaws and teeth.”] In September, after considerable microscopic and digital reconstruction, a fairly complete semi-arboreal, bipedal fossil ape was also announced, dated at 4.4 MY. Unfortunately, the separated “mould” fossil of Ida had been artistically retouched, reducing its scientific merits, and the promotional public announcements were made before the find was properly peer reviewed. It was also essentially a lemur. Ardi's anatomical diversity from chimps and gorillas has led to calls for sharp revisions to the proposed ancestral tree of humans, and for looking to a forest rather than savannah context. There has even been speculation on the origin of monogamy. However, in both cases it is clear that the fossils are understood based on a prevailing presumption of evolutionary ancestry from primates and apelike animals, rather than being independent evidence of such ancestry.Jonathan Wells, on the occasion of the 10th anniversary of his Icons of Evolution, comments:

Summing up: the icons of evolution on the whole provide illustrations of the already assumed evolutionary framework for interpreting biological origins, rather than independent evidence of it. In particular, at no point is there a strong empirical demonstration of the origin of functionally specific, code-based complex bio- information from forces of undirected chance and mechanical necessity. Given the origins science context: abductive explanations of a remote past that we did not directly observe, competing explanations need to be brought to bear on the evidence, and must be asked to speak to the full range of evidence, including the origin of such functional, complex coded bio-information.

(d) Some key questions:

In light of concerns and limitations of the evidence for macro-evolution, such as the above, Dr. Jonathan Wells has suggested a list of controversial questions students should bear in mind (and, if their teachers are open to it, ask). In slightly softened form:
1] ORIGIN OF LIFE. Why do many textbooks claim that the 1953 Miller-Urey experiment shows how life's building blocks may have formed on the early Earth -- when conditions on the early Earth were probably nothing like those used in the experiment, and the origin of life remains a mystery?
2] DARWIN'S TREE OF LIFE. Why don't textbooks critically discuss the "Cambrian explosion," in which major animal groups appear together in the fossil record fully formed instead of branching from a common ancestor -- thus contradicting the root-and- gradual- branching  picture given by the evolutionary tree of life?
3] HOMOLOGY. Why do textbooks often define homology as similarity due to common ancestry, then claim that it is evidence for common ancestry -- isn't that a circular argument masquerading as  evidence?
4] VERTEBRATE EMBRYOS. Why have some textbooks up to a few years ago still used drawings of similarities in vertebrate embryos as evidence for their common ancestry -- even though biologists have known for over a century that vertebrate embryos are not most similar in their early stages, and that Ernst Haeckel's drawings are faked?
5] ARCHAEOPTERYX. Why do some textbooks portray this fossil as the missing link between dinosaurs and modern birds -- even though modern birds are probably not descended from it, and its supposed ancestors do not appear until millions of years after it?
6] PEPPERED MOTHS. Why do some textbooks use pictures of peppered moths camouflaged on tree trunks as evidence for natural selection -- when biologists have known since the 1980s that the moths don't normally rest on tree trunks, and all the pictures have been staged?
7] DARWIN'S FINCHES. Why do some textbooks claim that beak changes in Galapagos finches during a severe drought can explain the origin of species by natural selection -- even though the changes were reversed after the drought ended, and no net evolution occurred?
8] MUTANT FRUIT FLIES. Why do some textbooks use fruit flies with an extra pair of wings as evidence that DNA mutations can supply raw materials for evolution -- even though the extra wings have no muscles and these disabled mutants cannot survive outside the laboratory?
9] HUMAN ORIGINS. Why are artists' drawings of ape-like humans commonly used to justify materialistic claims that we are just animals and our existence is a mere accident -- when fossil experts cannot even agree on who our supposed ancestors were or what they looked like?
10] EVOLUTION A FACT? Why are we sometimes told that Darwin's theory of evolution is a scientific "fact" -- even though (a) we cannot actually directly observe the remote past as it actually was,  (b) many of the claims are arguably based on the assumption that "blind watchmaker" evolution is true, or (c) on facts that could also be effectively explained based on common design? 

Of course, such questions are provocative, and while they should be borne in mind, they should only be raised respectfully, and with due caution . . .