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Sham Skepticism: A Reality Check for Donald Prothero

DProthero.jpgAnti-ID geologist Donald Prothero is apparently no longer an active professor at Occidental College. But he's certainly making good use of his newly found free time. He's writing lots of books. In fact, this year Dr. Prothero has published at least three noteworthy titles, two of which -- Reality Check (Indiana University Press, 2013) and Abominable Science (Columbia University Press, 2013) -- attempt to position him as a guru of skepticism, rationality, and scientific objectivity. The third book will be discussed below as well -- it's his latest textbook, a new edition of Bringing Fossils to Life (Columbia University Press, 2013) -- which unashamedly promotes common ancestry using Haeckel's long-discredited embryo drawings. We'll get to that in just a moment, but for now I'd like to briefly discuss his two "skeptical" books.

Abominable Science, co-authored with Daniel Loxton, is for the most part about debunking "famous cryptids" like Bigfoot, Yeti, the Loch Ness Monster, and other mythical creatures. Not much of this is controversial, at least not in my mind. But with a foreword by Michael Shermer, Prothero's book is written in the language of "skepticism," full of odes to Carl Sagan and decrying "pseudoscience." Prothero styles himself as a hero of objective analysis, invoking "the respectability of science" over "decidedly nonscientific belief systems" such as "creationism," which he says is based upon "subterfuge." (p. 7) Though intelligent design has nothing to do with the main content of the book, he includes a superfluous rant citing the "ruse of intelligent design" which he says uses "sneakier tactics." (p. 8) Prothero thus declares: "it is typical of crackpots, fringe scientists, and pseudoscientists to make revolutionary pronouncements about the world and argue strenuously they are right." (p. 9) The irony is that in his next book, Reality Check, Prothero's dogmatic, absolutist pronouncements in favor of evolution make him sound a lot like the people he so deeply deplores. I suspect he's so self-assured about the inerrancy of his "skepticism," that he's totally oblivious to this fact.

Reality Check: How Science Deniers Threaten Our Future is even more polemical. It's intended to scare people, arousing gross disgust and hatred for anything that dissents from the consensus on evolution, global warming, and other topics. It's loaded with the jargon of "skeptics," constantly decrying the "denialists" and "pseudoscientists" who "deny scientific reality." Michael Shermer again writes the foreword, lamenting "denial or denialism," which he defines as "the automatic gainsaying of a claim regardless of the evidence for it -- and sometimes even in the face of evidence." According to Shermer, "Denialism is typically driven by ideology, politics, or religious beliefs in which the commitment to the belief takes precedence over the evidence for or against it. Belief comes first, reasons for belief follow, and those reasons are winnowed to assure that the belief is always supported." Of course you understand that neither Shermer nor Prothero would ever be guilty of putting ideology over evidence, right? For "Prothero is a skeptic. So am I," declares Shermer, and this means they "take a scientific approach to the evaluation of claims." Prothero is not just a scientist he's a "scientist's scientist" who demonstrates "agility in thinking critically about any controversy in mainstream or borderlands science." (p. xiii) According to Shermer, Prothero is "one of America's foremost experts and debunkers of pseudoscience of various stripes." (p. xii)

OK, you get the picture. Prothero is a paragon of objectivity and anyone who he disagrees with is simply in denial about the evidence. Shermer rants:

Climate denialism and creationism have a lot in common with other kinds of denialism. In each case, a well-entrenched belief system comes in conflict with scientific or historic reality, and the believers in the system decide to ignore or attack the facts that they do not want to accept. Holocaust deniers are a classic example of this. (p. 4)
So let's take a look at Prothero's "skepticism" and see if his views ever come "in conflict with scientific or historic reality."

Prothero opens Reality Check with an ominous exercise where readers are encouraged to "imagine a scenario" where an (1) "antiscientific viewpoint is extensively promoted by websites and publications of right-wing fundamentalist institutes such as Discovery Institute in Seattle, and is often plugged by Fox News," (2) "Opponents of this consensus cannot find legitimate scientists with expertise in the field who oppose the accepted science, so they beat the bushes for so-called scientists (none of whom have relevant training or research credentials) to compose a phony list of scientists who disagree on the topic," and (3) "creationists are funded not only by many rich fundamentalist churches, but also by powerful right-wing businessmen or institutes." Prothero must live in an alternate universe. Taking his points in order:

  • Regarding (1), the Darwin-loving media gives the evolution lobby a much, much larger microphone than ID proponents could ever dream of having. As we've documented here on ENV more times than I can count, the mainstream media are overwhelmingly biased against intelligent design and skepticism about Darwinian theory. The Columbia Journalism Review, a leading publication for media insiders, has explicitly and unashamedly urged that the media in covering evolution set aside journalistic norms like "balance". And yes, we've been on Fox News, that indispensable bogeyman, a couple times in the past few years, but such a handful of appearances is nothing compared to the extent to which the rest of the media promote Darwinian evolution. Any fair "skeptic" would recognize this imbalance.
  • Regarding (2), many Ph.D. biologists and other legitimate, qualified scientists are skeptics of neo-Darwinian evolution. Yet Prothero can't bring himself to acknowledge that fact, so he has to define them out of existence by calling them "so-called scientists." Who's in "denial" here, exactly?
  • Regarding (3), the Darwin lobby is lavishly funded compared to the ID movement. Prothero indulges is "poormouthing," where to obtain a rhetorical or other advantage you pretend that you're much poorer than someone else. David Klinghoffer covers this well, but my favorite example of the funding contrast is this: A few years back, the NCSE basically got over $450,000 from the government to build a website helping teachers to promote evolution. When was the last time the ID movement got $1, much less $450,000+, from the federal government to do anything? The Darwin lobby gets many tens of millions of government dollars each year for supporting pro-evolution scientific research and science education efforts, leaving a couple of small groups like Discovery Institute to privately fund both science research and ID-friendly education from a differing perspective. I think we do an amazing job with the comparatively little resources we have, a testament to the strength of the evidence for ID. But only a small dose of real skepticism is necessary to realize that the notion that somehow the ID movement is rolling in dough compared to the Darwin lobby is completely false. But I'm sure Prothero's poormouthing is great for fundraising for the NCSE.
Let's now examine some of Prothero's scientific claims in Reality Check. Does he ever "decide to ignore or attack the facts that [he does] not want to accept"? Prothero writes:
Darwin's arguments of the tree of life were made strictly on external anatomical features that scientists were documenting 150 years ago. In the late twentieth century, the most amazing confirmation of the tree of life has occurred. When the molecular sequence of biochemical in cells was determined (from RNA to DNA to any protein), they also show the same pattern of a branching pattern of similarity that the external anatomy suggests (figure 6.2). In other words, every cell in your body (and in the bodies of all organisms) proclaims the handiwork of evolution! Such discoveries make absolutely no sense unless we are all interrelated and descended from common ancestors, a reality that creationists continually deny. (Reality Check, p. 113)
But contrast Prothero's claims with what the technical literature says:
  • A 2012 paper observes that "[p]hylogenetic conflict has become a more acute problem with the advent of genome-scale data sets." According to the paper, "phylogenetic conflict is common, and frequently the norm rather than the exception." This problem pertains to both molecular and morphological data: "Incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species."1
  • An article in Trends in Ecology and Evolution concluded, "the wealth of competing morphological, as well as molecular proposals [of] the prevailing phylogenies of the mammalian orders would reduce [the mammalian tree] to an unresolved bush, the only consistent clade probably being the grouping of elephants and sea cows."2
  • A major review article in Nature reported that "disparities between molecular and morphological trees" lead to "evolution wars" because "[e]volutionary trees constructed by studying biological molecules often don't resemble those drawn up from morphology."3
  • A 2005 scientific paper, "Bushes in the Tree of Life," acknowledged that "a large fraction of single genes produce phylogenies of poor quality," observing that one study "omitted 35% of single genes from their data matrix, because those genes produced phylogenies at odds with conventional wisdom." The paper suggests that "certain critical parts of the [tree of life] may be difficult to resolve, regardless of the quantity of conventional data available." The paper even contends that "[t]he recurring discovery of persistently unresolved clades (bushes) should force a re-evaluation of several widely held assumptions of molecular systematics."4
  • The great systematist Colin Patterson stated: "As morphologists with high hopes of molecular systematics, we end this survey with our hopes dampened. Congruence between molecular phylogenies is as elusive as it is in morphology and as it is between molecules and morphology."5
He cites, "The same pattern of a branching pattern of similarity"? But the evidence shows that morphology-based trees often conflict with molecular trees. Indeed, even molecule-based trees themselves often conflict, as a 2011 paper states:
[A]s the sequences from genome projects accumulate, molecular data sets become massive and messy, with the majority of gene alignments presenting odd (patchy) taxonomic distributions and conflicting evolutionary histories.6
There are many other problems in Reality Check. For example, Prothero writes, "Genetics has also shown that a very high percentage (80-90% in many organisms) of the DNA we carry is functionally neutral and cannot be read during translation, or it is junk DNA inherited from distant ancestors, which no longer has a function and is no longer used. This would make no sense if a divine designer were composing a genome." (p. 118) Which organisms are those? Of course, a collection of papers in Nature last year suggested that the evidence is pointing in the opposite direction that, upwards of 80% of our genome shows evidence of function. Now obviously there's controversy over the exact percentage, but at the very least the jury is still out on exactly how much of the genome will turn out to be functional. For Prothero to authoritatively pronounce that 80-90% of our DNA is "junk" goes far beyond what the evidence says.

Prothero is so wedded to "junk" thinking that he says the human tailbone "no longer [has] a function." (p. 114) Really? Consider what Medscape says:

In humans, the coccyx serves important functions, including as an attachment site for various muscles, tendons, and ligaments. Physicians and patients should remember the importance of these attachments when considering surgical removal of the coccyx.

Muscles inserting on the anterior coccyx include the levator ani, which is sometimes considered as several separate muscle parts, including the coccygeus, iliococcygeus, and pubococcygeus muscles. This important muscle group supports the pelvic floor (preventing inferior sagging of the intrapelvic contents) and plays a role in maintaining fecal continence. A midline component is the anococcygeal raphe, by which the coccyx supports the position of the anus. Muscles originating on the posterior coccyx include the gluteus maximus, which is the largest of the gluteal (buttock) muscles and which functions to extend the thigh during ambulation.

Multiple important ligaments attach to the coccyx. The anterior and posterior sacrococcygeal ligaments attach the sacrum to the coccyx (similar to the functions of the anterior and posterior longitudinal ligaments spanning cervical, thoracic, and lumbosacral spinal segments). Laterally, the transverse process of the coccyx serves as an attachment site for the lateral sacrococcygeal ligaments (arising from the inferolateral sacrum), as well as for fibers from the sacrospinous ligament (arising laterally from the spine of the ischium) and the sacrotuberous ligament (connecting the sacrum with the ischial tuberosity, but with fibers attaching to the coccyx as well).

Function

The coccyx serves somewhat as a weight-bearing structure when a person is seated, thus completing the tripod of weight bearing composed of the coccyx and the bilateral ischium. The ischial weight-bearing surfaces are, more specifically, at the ischial tuberosities and inferior rami of the ischium. The coccyx bears more weight when the seated person is leaning backward; therefore, many patients with coccydynia sit leaning forward (flexing at the lumbosacral and hip regions), which shifts more of the weight to the bilateral ischium rather than the coccyx...

And then there's Prothero's claims that our eyes are "suboptimally designed" because our retinas are "beneath all the nerves and blood vessels, obscuring vision," (p. 114) even though it's not true that our vision is normally affected because of the position of the optic nerve. He also repeats the old myth that the recurrent laryngeal nerve nerve "makes no sense in the context of an intelligent designer." (p. 115)

Prothero is exactly right when he says, "The scientific method is often in direct conflict with many notions and beliefs that humans use to make decisions and guide their lives." (p. 7) Indeed, if we're honest with ourselves, science habitually compels us to discard old now refuted ideas that seem otherwise pleasing or useful.

It's noteworthy, then, that in discussing the similarity of vertebrate embryos in their early stages, he concedes the "excesses and mistakes" of "embryologists, such as Ernst Haeckel." (p. 115) In that regard, what are we to make of the fact that Prothero has repeatedly reprinted Haeckel's embryo drawings in his textbooks? I've documented this in the past, regarding his textbooks from the early 1990s, the late 1990s, and even from 2004. Earlier this year I learned Prothero was going to publish a new edition of his textbook Bringing Fossils to Life. Surely, I thought to myself, Prothero won't be including Haeckel's embryo diagrams, as he did in previous editions (documented here). But you know what? He did, as you'll see right here, on page 29, from the 2013 edition of his textbook:


There's no mention in the book that these drawings are inaccurate. The implication is that they really do show how vertebrates are "strikingly similar" in early stages of development. The caption even states the diagram is "after Haeckel," whom Prothero concedes is guilty of "excesses and mistakes" in the drawings. This tends to negate the force of Prothero's rant about the supposed dishonesty of creationists:

In fact, what is truly bizarre is that the creationists trot out the same lines of argument that they have been using since the 1960s and even earlier. No matter how many times they are debunked, they keep repeating these discredited ideas over and over. In some cases, creationist debaters (like Duane Gish) have been caught using a fallacious argument or an outright lie and were forced to retract it during debate -- but Gish went on to repeat the same falsified argument and deliberate deceptions to a different audience the following night, expecting that no one would have heard him retract it. Such dishonesty and deception is not allowed in real science, since if you make a mistake or your hypothesis is wrong, the scientific community expects you to correct it and start over; you cannot repeat arguments or data that are clearly discredited. Likewise, the fact that creationists never change their arguments or ideas, no matter how many times they've been proven wrong, also speaks to their close-mindedness and lack of scientific integrity. (Reality Check, p. 129)
This rant, typical of the skeptic-supremacist mindset of Prothero, is ironic to say the least. In reprinting Haeckel's embryo drawings, Prothero himself continues to "repeat the same falsified argument," one that he admits is wrong -- in textbook after textbook. As we've seen, many of Prothero's claims about the evidence for evolution are simply flat wrong.

Sham Skepticism

"Skeptics" like Prothero preach objectivity and regularly declare their superiority over those they disagree with. But they make and promote mistakes all the time, and sometimes don't even correct them. Thus, Donald Prothero, who Michael Shermer calls a "skeptic," a "scientist's scientist," and "one of America's foremost experts and debunkers of pseudoscience," now holds the distinction of having authored probably the most recent textbook to publish Haeckel's fraudulent embryo drawings for the purpose of promoting common ancestry. How "skeptical" is that?

References Cited:

[1.] Dávalos et al., "Understanding phylogenetic incongruence: lessons from phyllostomid bats," Biological Reviews of the Cambridge Philosophical Society, Vol. 87: 991-1024 (2012).
[2.] De Jong, "Molecules remodel the mammalian tree," Trends in Ecology and Evolution, Vol. 13: 270-274 (July 7, 1998).
[3.] Gura, "Bones, Molecules or Both?," Nature, Vol. 406: 230-233 (July 20, 2000).
[4.] Rokas & Carroll, "Bushes in the Tree of Life," PLoS Biology, Vol. 4: 1899-1904 (November, 2006) (internal citations and figures omitted).
[5.] Patterson et al., "Congruence between Molecular and Morphological Phylogenies," Annual Review of Ecology and Systematics, Vol. 24: 179 (1993).
[6.] Leigh et al., "Evaluating Phylogenetic Congruence in the Post-Genomic Era," Genome Biology and Evolution, Vol. 3: 571-587 (2011).

Photo: Donald Prothero, zooterkin/Flickr.