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Critique of Intelligent Design

Evolution vs. Creationism

The Art of ID Stuntmen

Faith vs Reason

Anthropic Principle

Autopsy of the Bible code

Science and Religion

Historical Notes


Serious Notions with a Smile


Letter Serial Correlation

Mark Perakh's Web Site

Meanwhile, trait no. 31 (which had to make it onto the list if he was to keep his total of 53 reversing ones) had five missing slots (actually seven, if you tossed in those due to the excluded Adelobasileus and the Kuehneotheriidae).

Exactly as in the first chart, there seemed no consistency to how he had arrived at the 28 "progressive" items (which you may note he misprinted as "53 of 81 of 82" in the heading of his own chart).

Now while he clearly had "normalized" the Mammalness column (the numbers there were mainly within a point or so either way from the spreadsheet figures) it turns out he had also done that to the "progressive" column, exactly as he said he hadn't. And there were some numerical oddities even then (off by as much as a dozen points, as in the case of Sinoconodon). Of course, had he not pulled this fast one, the totals for the "progressive" list and also the full unfiltered 82 would have looked significantly less chasm-like to suit his apologetic purposes.

ID Number


The 28 Progressive Characters Normalized

Mammalness Index Progressive Characters
(53 of 81 of 82)

Sum of the 28 Progressive Characters

Sum of the Full 82 Character Set









































































Thus the "great gulf" of progressive characters between items 17-19 and 20-21 is not between 7 and 34 & 54, but between 2 and 8 & 15.  And if you look at the full set of data, the numbers shift from 14-28 to 45 & 61. Likewise the change to the earliest mammals isn't a jump to 104-131, but to 24-36 for the progressive features, and 75 to 107 for the full 82.

But as we saw with the earlier charts, such number play is meaningless because it is sidestepping the details of what is changing, and over what considerable time frame all this is taking place.

That Woodmorappe was getting wound a bit too tight here is made plain by what he penned a couple of paragraphs farther on in his piece. I reprint it exactly as written (his emphases, ellipses and inclusions), including the superscripts for his notes 34 & 35 (the content of which are given below) and the one time he correctly spelled Tritheledontidae:

And, ironic to the fallacious argument about mammalian traits appearing in correct "stratomorphic" sequence,34 we have a situation where one of the presumed sister groups (Tritylodontidae) is actually more mammalian than the first recognized mammals! Consider the following unenviable dilemma faced by evolutionists:

"The main difficulty with the tritylodontid-mammal hypothesis is that too many apopmorphic features of tritylodontids are more derived than the corresponding features in primitive mammals such as Sinoconodon and Adelobasileus... . By contrast, the main weakness of the trithelodontid-mammal hypothesis is that far too many trithelodontid characters are primitive ... [emphasis added]."35

"Primitive" and "derived", of course, are in comparison with the presumed earliest mammals, though neither the trithelodonts nor the tritylodonts are capable of being connected to the inferred earliest mammals in an ancestor-descendent lineage. Table 3 shows that a near doubling of characters (in fact, tripling if Tritheledontidae is chosen as the sister-group) is necessary to bridge the chasm between the sister-group cynodonts and the inferred primitive mammals. For evolutionists who portray the sister-group cynodonts as "almost mammals", this is a sobering result.

Woodmorappe's first note was not a reference, but merely a redundant premonition of the rest of his own sentence:

34.  As noted earlier, the numerous reversing characters that are prominent throughout the chain of mammal-like reptiles soundly refute the claim that mammalian traits appear in a straightforward stratomorphic sense. The fact that the ancestor Tritylodontids are more mammalian than their presumed early-mammalian successors only drives the final nail into the coffin.

Having repeated this claim twice, however, the "bottom falls out" when we wonder how the Tritylodontidae's 78 points (or 34, if we take the progressive value) could be construed as "more mammalian" than 100 or 104 (the lowest corresponding mammal values, that of Sinoconodon). One simple possibility presents itself: that Woodmorappe's vision glazed over yet again and he jumped a few rows to confuse "the ancestor Tritylodontids" with item 24, the mammal Triconodontidae (whose Woodmorappe-calculated values were indeed higher than their fellows).

Beyond Woodmorappe's evident numerical and analytical eccentricities looms a more general scholarly defect pertaining to his note 35, which actually was a reference, to Luo (1994, 111). As one might have suspected given the long tradition of selective creationist apologetics, Woodmorappe was being mighty careful about what he quoted. Here is the full passage, with Woodmorappe's extractions highlighted in bold:

Both hypotheses of mammalian relationships are supported by a number of apomorphies, but neither hypothesis is without problems. The main difficulty with the tritylodontid-mammal hypothesis is that too many apomorphic features of tritylodontids are more derived that the corresponding features in primitive mammals such as Sinoconodon and Adelobasileus (e.g., greatly reduced rate of tooth replacement and the hypertrophied paroccipital process). By contrast, the main weakness of the tritheledontid-mammal hypothesis is that too many tritheledontid characters are primitive (e.g., the orbit and braincase). For a solution to this sister-taxon controversy, we shall have to obtain more evidence on the critical taxa, such as Sinoconodon, Adelobasileus, and Haldanodon, and more anatomical information through more detailed studies, such as serial sectioning, on the existing taxa.[49]

Although Woodmorappe had explained in his note 8 that "An apomorphy is a trait that appears for the first time at a given position in the cladogram," he surgically removed any reference to what Luo had been talking about in this specific instance. This returns us to the cladogram issue noted above. If you looked at the specimens involved it would take quite an expert to tell them apart ... the "primitive" and "derived" traits did not represent any vast "gulf" between them and the mammals. Only the most miniscule diagnostic features were distinguishing them, as Luo quite plainly stated on the same page as the paragraph Woodmorappe had vacuumed.

It's worth quoting this part in full too, as it illustrates how cladistic analysis weighs competing models, and how this was not even slightly what Woodmorappe was doing in his "cladistic analysis":

Based on the character matrix (Table 6.1. Appendix 6.1), the tritheledontid-mammal hypothesis has consistently fewer transformational steps than the tritylodontid-mammal hypothesis, regardless of different permutations in the arrangement of the out-groups. Nevertheless, the difference between the two hypotheses is quite small. Given the same out-group arrangement proposed by Rowe (1988), there are only six more steps required for the cladogram in Figure 6.8A (tritylodontid-mammal hypothesis) than for the cladogram in Figure 6.8B (tritheledontid-mammal hypothesis). Given the out-group arrangement proposed by Kemp (1983), the former hypothesis (Figure 6.8C) involves only two steps more than the latter hypothesis (Figure 6.8D). Given the out-group arrangement proposed by Wible (1991) (Figure 6.8E,F), the tritheledontid-mammal hypothesis is also favored by only two steps less.[50]

Luo went on to do precisely what Woodmorappe ... and Johnson ... and Berlinski (and all the rest of the antievolutionary set) have not. He related the anatomical data to the full animal, and its attendant lifestyle. After all, even cynodonts had to eat.

Because important changes in feeding mechanisms are reflected by the temporomandibular joint and lower jaw at the transition to mammals, clear-cut differences in the apomorphies in these critical areas between the two competing hypotheses would lead to different understandings of the evolution of the masticatory apparatus. The tritheledontid-mammal hypothesis differs significantly in a posteriori predictions regarding the functional evolution of the mammalian feeding mechanism.[51]

Here is where the utility of parsimony analysis comes into its own, as Luo described the different implications of the competing relationships. The tritheledontid path (which Luo favors) focuses attention on the distinctive mammalian jaw: "an increasingly stronger temporomandibular articulation, a more flexible symphysis (which permitted fine control of the mandibular movement), and increasingly precise matching of the opposing post-canines leading to the differentiation of wear facets for shearing. All these occurred without any major disruption of the basic adaptation to carnivory and/or insectivory."

By contrast, in "the framework of the tritylodontid-mammal hypothesis, interpretation of the evolution of feeding function is enormously complicated."This is because the carnivorous/insectivorous adaptation and herbivory would had to have arisen repeatedly "among major clades," a scenario less consistent with how animal anatomy and behavior function in the real world.

What uncertainty there may be to mammal origins in this specialized instance turns on the fine detail of which adaptations were driving the overall process, not that the anatomical data were so diverse that evolutionists were plucking relationships out of a hat.

So, where does all this leave us?

Given that (1) Woodmorappe's "cladistic analysis" wasn't a cladistic analysis.

And that (2) all three of his pivotal supporting tables contained readily detectable mathematical and categorical mistakes.

And that (3) his underlying creationist approach to the forensic data and their relation to biological reality was simply to ignore them.

We may legitimately return to the core question that mathematician Berlinski thought to evade in his March 2003 caveat about not prejudicing an article by its source. How could anybody in their right mind rely on the apologetic arguments of anyone who thinks the world is only a few thousand years old? Or think at least that you could take isolated bits of their output seriously, far beyond any jurisdiction of their expertise, if only you didn't bother with checking out their general reliability first?

This is a scholarly issue, plain and simple.

4. Corroborating evidence: the Malhotra Case, or why no one ought to be taking Woodmorappe seriously

Had plotting Woodmorappe's position on the epistemological landscape been a daunting task, fair to shrivel the brain stem of all but the most stout of heart, one might have forgiven Johnson or Berlinski this lapse on account of excessive timidity or a short attention span. But the fact is that documenting Woodmorappe's special skills in information management required no more than a quick scan of the internet for some of his published oeuvre, and a willingness to take the plunge and look up some of his sources.

The first thing you might learn is that "John Woodmorappe" is actually the nom de guerre of a certain Jan Peczkis. Woodmorappe/Peczkis operates with feet in both the creationist and evolutionist camps, but because he writes under different names in each, he has been able to indulge in one of the stranger Jekyll & Hyde episodes in the long tradition of distorted creationist scholarship. Wearing a feigned evolutionist hat, Peczkis has suggested in The Science Teacher (1993) how adaptive change could be illustrated to students by classroom exercises and disported in the Journal of Vertebrate Paleontology (1994) on dinosaur body mass. Benign enough, it would seem ... until you checked out one of his online papers (at the YEC "Revolution Against Evolution" site) in which "Woodmorappe" brazenly held up his own 1993 Peczkis piece as an example of "A Hands-on Science Activity that Demonstrates the Atheism and Nihilism of Evolution."[52]

It would be as if one were to discover that Richard Dawkins were really Phillip Johnson in disguise.

But even muffling all these unsettling tactical alarm bells going off around Woodmorappe, there would still remain the fact that Woodmorappe has no reputation for sound technical scholarship to tarnish.[53]

A particularly useful example of this that I uncovered independently concerns how random mutations in the mitochondrial fuel stations in our cells tick away like clocks to measure at least roughly how many millions of years separate the common ancestry of the living forms that possess those specific mtDNA configurations.  But as Woodmorappe's worldview cannot accept all those millions of years, the mitochondrial evidence has to be brought "in line with the biblical time frame" of only a few thousand years. As part of this effort, Woodmorappe asserted:

Contrary to conventional evolutionary wisdom, some earlier evidence indicated that mtDNA is not subject only to neutral mutations (Fos et. al. 1990, MacRae and Anderson 19880. However, much of this evidence was ignored because it did not fit the reigning evolutionary belief in the primacy of neutral mutations (Malhotra and Thorpe 1994, p. 37).

The new field evidence indicates, however, that mtDNA is subject to natural selection. Malhotra and Thorpe (1994) studied the sequence of mtDNA among certain lizards in islands of the Caribbean Sea. They found morphological (i.e. anatomical) variation in these lizards. following moisture gradients on the islands: the animals' coloration, number of scales, and body proportions varied with local ecological conditions.[54]

All this sounds well mannered, doesn't it? Direct assertions are accompanied by specific citations from perfectly legitimate journals. And if one were reading such a statement in Science or Nature you could be reasonably confident that there would indeed be some correspondence between the two.

But that's not the venue, is it? We're reading the arguments of someone prone to arrange the data set to arrive at a theologically necessary conclusion. Under that impetus, scratch the surface and we discover Woodmorappe's documentation isn't at all that he's making it out to be.

Like Phillip Johnson's parsing of his own source material on the mammals in Darwin on Trial, Woodmorappe had to overlook the part of MacRae & Anderson where they had explicitly cautioned against the very conclusion to which he was so anxious to jump:

Uneven evolutionary rates among mtDNAs or even within an mtDNA molecule, although important to document, will not invalidate use of the clock. The mtDNA clock would still be valid under many circumstances, because its rate is an average taken over time, much as it is for molecular clocks associated with nuclear genes.[55]

Just as he had with Luo et al. on mammal paleontology, Woodmorappe also failed to report what it was that MacRae & Anderson had actually found out. This was not a case of mutational differences between the mtDNA originating because of natural selection (as he tactically implied), but rather the distribution of specific variant mitochondria ("haplotypes") within the hybrid zone of a population. Thus selection could nudge an "AAB" distribution into an "ABB" one ... more Bs, not changes in either A or B (which is what would have affected the neutral ticking of the mitochondrial clock in the way Woodmorappe wanted his readers to think).[56]

Apart from intimating that Malhotra & Thorpe were claiming "much of this evidence was ignored because it did not fit the reigning evolutionary belief in the primacy of neutral mutations," Woodmorappe didn't go into details about which evolutionary scientists were supposedly doing this ignoring. It certainly couldn't have been the many authors who have cited the MacRae and Fos papers over the years -- or the other researchers who have contributed parallel findings without suffering any evident neglect.[57]

But it turns out Malhotra & Thorpe hadn't even made the claim Woodmorappe attributed to them.

Far from asserting that the work of MacRae and Fos had been "ignored" by any evolutionists, Malhotra & Thorpe started off by documenting the contrary: several groups of researchers had been actively trying to test the early artificial selection findings of MacRae, Fos and others, but without success. The point of Malhotra & Thorpe's new paper was to contribute a useful field example that might help resolve the continuing dispute over whether natural selection could affect mitochondrial haplotype frequencies -- and if so, under what circumstances.[58]

5. Implications: Forbidden topics and a serious lack of antievolutionary curiosity

The wonderful irony of the Malhotra episode concerns what Johnson or Berlinski might have stumbled upon had they descended from lofty Olympus to take a peek at the undercarriage of this Woodmorappe vehicle. In that unlikely event, they could have slid straight into a whole pile of science that has definitely been "ignored." But not by evolutionists ... it is creationists who have been ignoring this research.

Perhaps the most obvious area is the question of why there are mitochondria in our cells for Woodmorappe to refer to in the first place.

It is well recognized today that biologist Lynn Margulis (once married to archetypal skeptic Carl Sagan, by the way) was correct when she popularized earlier theories that cellular organelles like mitochondria and chloroplasts are the remnants of formerly free-living organisms that were joined in an "endosymbiotic" relationship with nucleated cells. Following these episodes of bacterial indigestion some billion-odd years ago, a few of these ancient endosymbionts eventually evolved into higher metazoans ... among them Woodmorappe, Johnson and Berlinski.[59]

Thus to even bring up the subject of mtDNA is either to reject the solid body of observation on which their endosymbiotic origin is based ... or implicitly accept the common descent of all organisms possessing them. Trying to invoke mtDNA without tackling the accepted evidence for endosymbiosis is yet another example of creationist reluctance to grapple with data that buffets their rigid worldview. Examples again span the antievolutionary gamut: from overt creationists like the ICR's legal consultant Wendell Bird twenty years ago, through to the Intelligent Design cadre at the Discovery Institute busily sandbagging the Wedge trenches today.[60]

Still another area of antievolutionary data avoidance that Malhotra & Thorpe's work impacts is the voluminous literature of "biogeography" which concerns the distribution of life, living and fossil.[61]

From the start, biogeography has provided a powerful link in the chain of evolutionary evidence, and for good reason. It is no coincidence that both Charles Darwin and Alfred Wallace came independently to their view of speciation by natural selection after encountering firsthand what things were alive (and not) around the world, especially on isolated islands. There is a distinct pattern to the distribution of life (no big vertebrates on sizable real estate like Hawaii, for instance, even though the place is capacious enough to sustain them ecologically).

One possibility is that the Intelligent Designer capriciously avoided plopping down new "types" in any of these instances, perhaps in order to placate evolutionists. But the simpler alternative is that the absence of such "Darwin-busting" examples is due to everything coming to be where and what it is solely by the natural process of descent with modification that evolutionists have so carefully documented over the last hundred-odd years.

That evolutionary theory alone has been able to account for this circumstance is further supported by the abject silence of creationists on it. It is a bald fact of documentary scholarship that biogeography is one of the great verboten subjects of antievolutionism, ignored with monotonous regularity though the whole body of anti-Darwinian literature (including once again, Phillip Johnson).[62]

And we're still not yet done tracing the dire evolutionary connections embedded in Malhotra & Thorpe's work. Consider this recent comment by Ogden & Thorpe: "Rapid morphological differentiation and adaptation to local environments is a well-documented phenomenon that has been previously demonstrated in a number of Anolis lizards."[63]

This represents one end of the microevolutionary process that eventually cascades into how species differentiation can be driven by ecological factors, an area further overlooked again by (you guessed it) Phillip Johnson.

The trail here is especially revealing, as it offers further clues about how Johnson approaches information he dislikes as opposed to the congenial sort proffered by chaps like Woodmorappe.

Invoking paleontologist Niles Eldredge as an authority to dismiss (of all things) the fossil evidence for macroevolution in Eldredge's own field of specialty, Johnson confidently claimed: "The non-occurence [sic] of Darwinian change is particularly evident where fossils are most plentiful -- in marine invertebrates, for example. There it's all variation within the type, with no substantial evolution. Thus Eldredge, a trilobite specialist, tells stories about hominids when he wants to lecture about evolution."[64]

Which was about as true as Woodmorappe's tight filtration of mitochondrial haplotypes.

First we may note that Johnson's idea that Eldredge fell back on "hominid stories" instead of trilobites appears to have turned on the one time Eldredge debated with Johnson. Because of the venue (a Christian college where that particular issue was of more than passing concern to the audience), Eldredge opted to use human evolution as his prime example.[65]

Like Berlinski with Nilsson & Pelger's Figure 3, though, Johnson then jumped to the conclusion that Eldredge had been using hominids as a general rule. But the fact was, as one might have expected, invertebrate trilobites supplied the centerpiece of Eldredge's many books and articles on evolution. Had Johnson not been showing the same sort of attentiveness to distracting detail as he did with Woodmorappe, he might even have caught this 1981 Eldredge statement "From my own work I can cite the trilobite genera (from the Lower Devonian of Bolivia): Kozlowskiaspis -- Metacryphaeus -- Malvinella -- Vogesina, which are connected by a compelling array of intermediates."[66]

When he repeated his claims about static invertebrates in his 1997 book, Defeating Darwinism, Johnson referenced Eldredge's own 1995 entry, Reinventing Darwin. Since that book was not trying to beat dead horses, Eldredge hadn't explicitly discussed the transitional trilobite evidence he'd mentioned elsewhere. Which reminds us of the general scholarly principle that when trying to draw conclusions on matters of substance, it is often prudent to be familiar with more than just a single source.

Johnson's "scholarship" has consistently failed that test.

But again like Woodmorappe with Malhotra & Thorpe, Johnson compounded his own difficulty by failing to appreciate that in this 1995 book Eldredge had moved on to another subject.[67]

Indeed, as I discovered when comparing a wheel-spinning e-mail exchange I had with Johnson in 1997 with the contents of Reinventing Darwin, Johnson was getting the point of it backwards. Like a seemingly innocuous equation that spawns a host of momentous conclusions once it is applied to specific instances, it was Eldredge's contention that uniting Darwin's concept of natural selection with modern population genetics squares with the pattern of speciation bursts amid stasis found so routinely in the fossil record. So Johnson was trying to invoke Eldredge's idea of fossil stasis to refute the Darwinian mechanism, when it was the whole point of Reinventing Darwin that the Darwinian mechanism inevitably and neatly explained that fossil stasis!

One of the main themes of Reinventing Darwin was that a species is more than a homogenous block of individuals -- it also represents a competing mixture of breeding populations ("demes") and ecological groupings ("avatars") that can affect how natural selection and speciation play out in particular cases. And as it turns out, the lizard research of Malhotra, Thorpe and their colleagues bears directly on that fascinating topic.[68]

Quite a body of connecting links in the evolutionary chain to step over, isn't it? But then, maneuvering around evidence has been the standard procedure among antievolutionists, which is why they have yet to legitimately earn the right to take a place at the High Table of serious debate. And why my reading Berlinski (shunted by "the indefatigable" Johnson) trying to invoke Woodmorappe on a topic about which neither has even the slightest proficiency struck me as so characteristically funny.

6. Conclusion: How the Woodmorappe Affair fits into a larger pattern of antievolutionary behavior, and what it tells about Discovery Institute "scholarship" (Johnson and Berlinski style).

Berlinski is the equivalent of the unskilled hunter, taking random potshots at the neighbor's cow instead of the elk that was his putative target. But Johnson has feigned far greater familiarity with the issues, having devoted whole books to the controversy: Darwin on Trial, Reason in the Balance, Defeating Darwinism, and The Wedge of Truth. Yet apart from one sloppy treatment of a science citation in Darwin on Trial (intimating that paleontologist Philip Gingerich didn't know his business when he detected the vestigial legs on some early whale fossils) Johnson has not shown any urge to familiarize himself with the body of available scientific literature.[69]

But we do know he does pay attention to the output of Answers in Genesis, don't we?

Just how long (or assiduously) he has been doing this is unclear, but in The Wedge of Truth he explicitly cited the "Australian creationist organization" for several apologetic bits. He commented on a 1997 AiG video interview with the bête noire Richard Dawkins, in which the British evolutionist was nonplussed at being challenged to provide evidence of natural selection creating new genetic information.[70]

Johnson also alluded to a 1990 quote book by Young Earth creationist geologist Andrew Snelling supporting the propriety of the antievolutionary cottage industry of tactical authority quoting. Though not quite so surreal as Woodmorappe/Peczkis, non-creationist geologist Alex Ritchie has noted a similarly compartmentalized double scholarly life for Snelling. While one Janus face publishes uncontroversial papers in his discipline that accept the conventional dating framework, Snelling's AiG religious persona absolutely rejects that chronology in favor of unadulterated Flood geology.[71]

Which brings us full circle, for Snelling and Woodmorappe/Peczkis are ironically appropriate resources for Phillip Johnson, who has similarly cordoned off his more public Wedge apologetics from his own Sunday preaching and hobnobbing with Young Earth creationists.[72]

Johnson is of course in good apologetic company when it comes to drawing on Answers in Genesis, since these days they supply a lot of the ammunition used by contemporary creationists. A case in point would be the discussion chatter at AOL concerning an informal June 2003 poll of their membership on "Do you believe humans evolved from apes?" Half of the hundred thousand respondents answered, "No, God created humans separately from animals." But when it came to marshalling what the "scientific evidence" for this position was, several posters readily recommended readers consult the AiG (and even Kent Hovind's "Dr. Dino" website) to learn about the incendiary facts that evolutionists are supposedly afraid to let anyone hear.[73]

Thus Johnson's parlay of Woodmorappe falls squarely into a larger cultural context in which a sizable number of Americans are sufficiently scientifically illiterate to actually believe that organizations like Answers in Genesis purveys information reliably. Or at least are singularly unwilling to look close enough to detect the frequency of when they're not.

In turn, Berlinski's huffing that Darwinists shouldn't be looking "to the fossil record with perfect equanimity" because of anything Woodmorappe had written represents the purest of scholarly farce. It reminds me of how creationist Clifford Wilson approached the nasty "E" word some years ago. Early in the 1960s Max Flindt authored a pamphlet, "On Tiptoe Beyond Darwin," which argued spacemen had engineered Hybrid Man (us) for their earth colony (apparently as rather absentee landlords, judging from the infrequency of their calling), and fellow UFO buff Otto Binder popularized it. When it came to their version of antievolutionism, Wilson blithely followed Flindt and Binder right off the cliff:

Until writings such as these began to be prominent in recent times, most of the forthright opposition to the Darwin-based theory of evolution came from Christians who saw it as opposing the Bible. Now many ufologists reject Darwin on biological and other grounds. Many of their arguments were valid, but to insist that man has therefore resulted from a space-earth sexual union is conjectural. There is still no better explanation than that of Divine creation.[74]

Well, now that UFO believers (or Answers in Genesis) have written off Darwin, no need to bother consulting scientists who might actually have some expertise in the area. In Wilson's world at least, Flindt and Binder were just as adequately "prominent" for him as Woodmorappe evidently is for the paleontologically challenged Fellows at the Discovery Institute.

If we're looking for a methodological moral to this extraordinary "Tale of Two Citations" one may paraphrase a venerable saying ... by their sources shall ye know them.

[49] Luo (1994, 101) tabulated a dozen apomorphies shared by mammals and tritheledontids, and a complementary set of ten for the tritylodontids. The paroccipital process relates to how great an extension there was to a small segment of the quadrate bone, Luo (1994, 105), while Luo (1994, 115-117) examined the implications of the tooth replacement mode in Sinoconodon.

[50] Luo (1994, 111). Figure 6.8 on the following page illustrated the six cladograms (with the Treelength values for the permutations ranging from 183-188 for the Tritheledontidae model, and 185-194 for the Tritylodontidae model). Luo (1994, 112) summarized: "a tritheledontid-mammal group is consistently favored over the tritylodontid-mammal group by a small difference, regardless of various permutations in the arrangement of more distantly related cynodonts."

[51] Luo (1994, 113).

[52] Peczkis (1993; 1994), with the online paper New Educational Activities for Home Schooling Science: A Hands-on Science Activity that Demonstrates the Atheism and Nihilism of Evolution. Recall also Woodmorappe's fiery response to Glenn Morton (note [27] above).

[53] Woodmorappe has been criticized mostly on the turf of radiometric dating (which Flood believers have to dispose of in order to salvage their compressed Genesis geochronology). Woodmorappe's Byzantine use of the literature has been noted by many of his critics. There's Glenn Morton's take with reply by Woodmorappe. There's Kevin Henke's piece, and Steven Schimmrich has links to Woodmorappe's rejoinder and Schimmrich's further commentary.

[54] Woodmorappe's "Upsetting Pet Theories: Surprising New Evidence that Molecular Clocks Can Run Very Fast" was obtained from the Young Earth creationist website "Revolution Against Evolution". These pieces apparently originally appeared in the Bible-Science Association's Creation Moments (evidently a radio broadcast, though none of Woodmorappe's items appear to have been archived among the transcripts at Creation Moments). Note also the geocentric connection of the BSA (per note [3] above).

[55] MacRae & Anderson (1988, 485). Apparently less aware of the dire implications of their own work that Woodmorappe seems to think, Malhotra & Thorpe have continued to apply the lessons of genetic clocks in evaluating the evolutionary relationships of species, as indicated by their part in Stenson et al. (2002).

[56] Haplotype shifts can be rapid indeed, as Pergams et al. (2003) indicate with a study of the mtDNA in mice museum specimens caught around Chicago since 1855. Since we have many mitochondria copies in each of our cells, and thus whole populations within each organism, let alone when compared to an entire population within a species, the maintenance of variant mtDNA (heteroplasmy) understandably relates to a host of factors. This runs from the influence of the nuclear genome itself, Farge et al. (2002), to the effect of the difference in recombination rates between nuclear and mitochondrial DNA, Weinreich & Rand (2000). There's even the need to consider the tendency for cytosine to fall off the DNA molecule, Chatterjee & Singh (2001). Ohta (2002) summarizes ongoing refinements to the "nearly neutral theory" contending "that the interaction of drift and selection is important and occurs at various levels, including synonymous and nonsynonymous substitutions in protein coding regions and sequence turnover of regulatory elements." See Birky (2001), Gerber et al. (2001), Rand (2001) and Allen (2003) for further reviews, and Contamine & Picard (2000) for details on yeast (most studied in part due to its technical accessibility). Moreover, although mtDNA is usually inherited maternally, occasionally the paternal copies can barge in to shift the observed balance -- see Schwartz & Vissing (2002) or Städler & Delph (2002) for recent examples, and Bromham et al. (2003) for perspective.

[57] Recent citations of MacRae & Anderson (1988) and Fos et al. (1990) would include García-Martínez et al. (1998), Kann et al. (1998), Babcock & Asmussen (1998), Nielsen & Weinreich (1999), Rand et al. (2001), Hattori et al. (2002) and Orive & Barton (2002). See also the chain from Yoneda et al. (1992) and Dunbar et al. (1995) to Mambo et al. (2003) and Taylor et al. (2002) on shifts in mtDNA proportions due to replicative advantage and selection.

[58] Among the contrary papers cited by Malhotra & Thorpe (1994, 37) in their opening paragraph were Nigro & Prout (1990) and Kambhampati et al. (1992). Malhotra & Thorpe (1994, 37) concluded this paragraph with: "In general, the debate has been largely confined to theory and is seldom explicitly tested against real data at the microevolutionary level." This "largely confined to theory" summary is still a far cry from Woodmorappe's general accusation of evolutionists ignoring the evidence on account of the "reigning evolutionary belief."

[59] A survey of the progress of the biological acceptance of the endosymbiotic theory may contrast Gamlin & Vines (1986, 156-158) with a listing of microbiology milestones in Tortora et al. (1995, 9) honoring Margulis under the year 1981 apropos the endosymbiotic "Origin of eucaryotic cells." See also de Duve (1995, 162-166; 1996), Stansfield et al. (1996, 361-365), Dawkins (1998, 225-231), Kurland & Andersson (2000), Mayr (2001, 45-48), Zimmer (2001, 111-115), Ryan (2002), and Palenik (2002) re Martin et al. (2002). Cyanobacteria appear also to have lent plants cellulose synthase, Nobles et al. (2001), and Gupta (1998), Martin & Müller (1998), Maynard Smith & Szathmáry (1999, 59-78), Margulis et al. (2000) and Hartman & Fedorov (2002) explore the contenders for the endosymbiotic origin of eukaryotes.

[60] Behe (1996, 189) kept endosymbiosis at arm's length with this brief comment: "Symbiosis theory may have important points to make about the development of life on earth, but it cannot explain the ultimate origin of complex systems." Both Behe (1996, 26, 278n) and Johnson (1998, 101-107; 2000, 72) have preferred to selectively invoke Margulis as an authority figure for her criticism of Dawkins-style Neo-Darwinism, drawing on Mann (1991) and Brockman (1995). Fellow ID biologist Jonathan Wells (2000a) managed to miss the subject altogether. Farther afield, while Gordon Mills (1998) gymnastically mentioned mitochondria minus endosymbiosis, mathematician Dembski (1999, 176; 2002, 319) continues to dub symbiosis "speculative" without reference to any of its concrete examples, like mitochondria. The compartmentalized narrative in Bird (1989, Vol. 1, 100, 210) fielded both evasions, including a critical authority quote by Philip Whitfield -- ironic given his impending agreement with the theory, Whitfield (1993, 28-29).

[61] For example, Malhotra & Thorpe's papers figure in R. P. Filson's "Island Biogeography and Evolution" for students working out the evolutionary relationships of the Canary Island Gallotia lizards. Cf. Malhotra & Thorpe (2000) offering the pros and cons of local volcanic activity playing a role in the divergence of Anole lizards in the Dominican islands over the last 30 thousand years (time frames utterly meaningless in the context of Woodmorappe's YEC worldview).

[62] Cracraft (1983, 183-184), Strahler (1987, 365-366) and Ecker (1990, 42-43) have noted the glaring absence of biogeography on the Creation Science "things to think about" list -- and Peterson (2002, 18) has spotted the same lacunae in the more recent Intelligent Design mutation. Denton (1985, 33-34) skirted closest to the precipice in Evolution: A Theory in Crisis, which has been highly influential in the ID movement (drawn on most notably by Phillip Johnson and Michael Behe). Although acknowledging the import of the evidence in cases like the Galápagos, Denton did not ponder just how much of the data set could be accounted for by such means, or whether such patterns showed up just as regularly in the fossil record. While Johnson (1991, 151) relegated biogeography to a passing sentence, Morris & Morris (1996, 237) played coy: "For some reason, the geographical distribution of animals and plants is often cited (and has been, since before Darwin's time) as an evidence of evolution."

[63] Ogden & Thorpe (2002, 13615), citing Malhotra & Thorpe (1991), Losos et al. (1997) and Thompson (1998).

[64] This passage concluded his Letter 6 (December 6, 1996) in a PBS-sponsored exchange with Ken Miller (with a plethora of links on the net, as at TalkOrigins). Each contributed a quartet of letters, starting off with Miller on November 14, 1996, and ending with Johnson's December 9, 1996 entry. The characterization of the debate by Johnson (1997, 123-124) dated the exchange to "early 1997" and dismissed Miller's substantive points as "stock arguments" without actually discussing any of them.

[65] Eldredge (2000, 134, 191n) recounted his side of the debate.

[66] Eldredge (1981, 19). See also Eldredge (1982, 118), reprised in Eldredge (2000, 122) on why creationists are so off the mark on the matter of trilobites as merely "variation within a kind."

[67] While Johnson (1997, 59-61) drew on Eldredge (1995, 95) for a seemingly incriminating claim that evolution "never seems to happen" in the fossil record (Eldredge was referring to the comparative rarity of preserved intermediate examples at the species level), he did not otherwise address any of Eldredge's main argument.

[68] See Thorpe & Richard (2001) on the ecological association of ultraviolet markings, and Schluter (2001) for a survey of comparable literature. Eldredge (1995, 174-197) and Gould (2002, 602-606, 644-652, 701-709, 881-885) discuss the evolutionary theorists and their conclusions relating to the new terminology of demes and avatars, and Wakeley (2000) illustrates a technical application.

[69] Gingerich et al. (1990), cited by Johnson (1991, 178). Johnson's Research Note citation mistakenly dated the Gingerich paper to "July 15." But that typo was less momentous than Johnson (1991, 178-179) secondarily drawing a quote by quirky 1930s British creationist Douglas Dewar via Denton (1985, 216-218) describing the absurdity of whales evolving from a land form. In 1935 Dewar helped found the "Evolution Protest Movement" in Britain with a group of like-minded British eccentrics to combat Darwinism's purported goals of moral degradation (promoted by psychoanalysis), human extinction (via birth control), and political revolution (through communism), Numbers (1992, 145-152). Not all that dissimilar panic buttons from those being pressed by Phillip Johnson three score years hence. But the irony is that by the mid-1990s paleontologists were digging up the very intermediate "whales with legs" that Dewar's critique had demanded (and which Denton and Johnson had quoted). See Gould (1994), Gingerich (1994) or Zimmer (1998) for surveys, and Thewissen & Hussain (1993), Gingerich et al. (1994; 2001), Thewissen et al. (1994; 1996; 1998; 2001), Thewissen & Madar (1999), Luo (2000), Thewissen & Bajpal (2001) and Spoor et al.(2002) for relevant technical info. Incidentally, Don Batten's "A Whale of a Tale? (Ambulocetus)" spun the Answers in Genesis view of snippets of these data in much the same way Phillip Johnson had Gingerich's 1990 paper (impugning the technical expertise of the paleontologists). Although prompted by Ken Miller in his PBS letter exchange with Johnson, and again at the 1997 Firing Line debate, Johnson has assiduously avoided thinking about these new fossils. Out of sight, out of mind. Indeed, his sole comment on the new whale fossils in Johnson (1997, 59-60) offers a laundry list of things he doesn't investigate: "I've long been fascinated by the conflicting messages Darwinists provide concerning the fossil evidence. On the one hand, they proudly point to a small number of fossil finds that supposedly confirm the theory. These include the venerable bird/reptile Archaeopteryx, the ‘whale with feet' called Ambulocetus, the therapsids that supposedly link reptiles to mammals, and especially the hominids or ape-men, like the famous Lucy. These examples, all from vertebrate animals, are pressed very insistently on me in debates as proof of the 'fact' of evolution and even of the Darwinian mechanism." Johnson then went on to field his Eldredge invertebrate argument recounted above.

[70] Johnson (2000, 39-40, 177n, 180n) directed the reader to the jabs pro and con at Answers in Genesis and Australian skeptics' rival "No Answers in Genesis" website, which included Dawkins' response. Dawkins suspected an ulterior creationist motive to the question because of the odd way it was put. Natural selection doesn't do (or need to do) any "creating" on its own, for new genetic information comes about by the perfectly natural processes of variation during genetic replication. Selection of course would be perfectly capable of preserving the changes in the individual, and potentially spreading them through a whole population.

[71] Alex Ritchie's critique at "No Answers in Genesis" sparked a rejoinder by Snelling.

[72] None of Johnson's published books or articles have alluded to his many interactions with the creationist community. For example, he addressed the 1999 installment of Rev. D. James Kennedy's "Reclaiming America for Christ" conferences, where he mentioned his lay sermonizing. What Johnson has avoided at all opportunities is any investigation of Kennedy's long-standing advocacy of literal Flood Geology (as well as the preposterous belief that the constellations of the Zodiac were placed in the heavens to illustrate Christian doctrine). Johnson has also been a congenial guest on Hank Hanegraaff's "Bible Answer Man" call-in show on conservative Christian radio -- as has Bill Dembski (cf. note [2] above). Although the Bible Answer Man doesn't go out of his way to call attention to his own Young Earth beliefs, either, he does consider Johnson the premiere philosopher of the new creed. And Johnson's laudatory "Forward" to Hanegraaff (1998, xi-xiv) repaid the compliment: "He exposes the specific wrong answers and provides lots of references to other literature." As indeed he had, citing among other error-laden YEC authorities, Morris & Parker (1987), Sunderland (1988) and Gish (1995). Farther afield, Johnson even supplied a cheery back cover recommendation for Hare Krishna creationists Cremo & Thompson (1993), whose worldview slides off the cosmological map. Forbidden Archaeology was published by the Bhaktivedanta Institute, and dedicated to Hare Krishna’s founder, "His Divine Grace A. C. Bhaktivedanta Swami Prabhupãda." The "Hare Krishna News Network" site dedicated to Prabhupãda's teachings includes the claim that NASA faked all the Apollo moon landings. Part of their argument rested on secular Apollo deniers-a crowd who got a publicity boost in February 2001 via a special on the Fox network (whose "documentary" telecasts have seldom been burdened by either editorial discretion or taste) … followed by a punch in the nose by Buzz Aldrin in 2002. See Plait (2002, 155-173) or the Fake Moon Landings website for field guides to this surreal area-cf. also the rationalist attitude of Smith (2000, 16) and warnings of Oberg (2003). Of relevance is how Prabhupãda's reasoning turned on scriptural authority, precisely like Henry Morris on the Genesis Flood. In "Man On the Moon-A Colossal Hoax that Cost Billions of Dollars," Prabhupãda (who died in 1977) declared that "The Vedic account of our planetary system is already researched, concluded, and perfect. The Vedas state that the moon is 800,000 miles farther from the earth than the sun. Therefore, even if we accept the modern calculation of 93 million miles as the distance from the earth to the sun, how could the 'astronauts' have traveled to the moon-a distance of almost 94 million miles-in only 91 hours (the alleged elapsed time of the Apollo moon trip)? This would require an average speed of more than one million miles per hour for the spacecraft, a patently impossible feat by even the space scientists' calculations." So much for those fuddy-duddy astronomers who reasoned centuries ago that the moon couldn't possibly be farther away than the sun and still cause solar eclipses. Judging by Rowley (1971, 117), Hare Krishna literature has considered space travel a waste of effort for some time, recommending instead that visitations to the planets be accomplished via Krishna Consciousness.

[73] A random but typical online example of the sort of daisy chain apologetics that fuels contemporary creationism would be Jason Gastrich's "Jesus Christ Saves Ministries." A section titled "Sound Teachers" explained how he had "learned awesome things from" a band of "godly people" that included ministers John Ankerberg, Jerry Falwell, Billy Graham and David Jeremiah, but also apologists like Dave Hunt, Tim LaHaye, Josh McDowell, Chuck Missler and John Weldon. As for antievolutionism, the deck was stacked with Young Earth ideologues: Duane Gish, Ken Ham, Hank Hanegraaff, Kent Hovind, Henry Morris, Jonathan Sarfati, and John Woodmorappe. And, oh yes, Phillip Johnson.

[74] Clifford Wilson (1974, 191). Just as Wilson was writing his UFO book, Flindt & Binder (1974) collaborated on Mankind -- Child of the Stars, whose screwball aspects are noted by Kossy (2001, 19-21). For some irony, Wilson (1972; 1976) had been extremely critical of Erich von Däniken for his mangling of archaeology (which Wilson relied on to prove the veracity of the Bible). So it was curious to read the former hotel manager turned Ancient Astronaut sage penning a laudatory foreword to Flindt & Binder (1974, 12) that concluded: "I know of no work since Darwin that deserves as much attention with regard to the evolution of man."Given von Däniken's own scholarly myopia, this was probably true. For a tidy refutation of the alien intervention theory, see J. Richard Greenwell, "Tiptoeing Beyond Darwin: An Examination of Some Unconventional Theories on the Origin of Man," in Story (1980, 153-166). And just to complete a pithy chain of citation: in 1978 Wilson co-authored a book with Ankerberg's other half John Weldon (see note [25] above) opining on demonic UFOs. And Wilson & Weldon (1978) ended up being the sole citation representing creationist thoughts on probability assessments of the origin of life in, of all places, Dembski (1998, 55-56, 59-60). Small world, isn't it?

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