Monday, February 27, 2012

This might explain conservative reality denial

I read with great interest, and a bit of dread, this essay by Chris Mooney, "The Republican Brain: Why Even Educated Conservatives Deny Science - and Reality," Saturday 25 February 2012. It was a preview of his forthcoming book of the same name.

I was favorably impressed with Mooney's 2005 book, The Republican War on Science New York: Basic Press. And will probably read this next one. But, if his premise is correct, that conservatives cannot learn, I'll be a bit depressed.

PS: the Kuhn paper is almost done, and I'll be back to blogging. Really!

Tuesday, February 21, 2012

More Speciation- but they are still just bacteria

The single-celled Bacteria and Archaea constitute the largest, and most successful forms of life on Earth. And, they have been for at least 3.5 billion years. For those inclined to read this sort of thing;

Hinsby Cadillo-Quiroz, Xavier Didelot, Nicole L. Held, Alfa Herrera1, Aaron Darling, Michael L. Reno, David J. Krause, Rachel J. Whitaker

Patterns of Gene Flow Define Species of Thermophilic Archaea

PLoS Biol 10(2): e1001265. doi:10.1371/journal.pbio.1001265

The paper has relevance to origin of life studies, and speciation mechanisms.

PS: The paper rebutting creationist Joe the Surgeon is progressing. I'll submit it directly to the Baylor University Medical Center Proceedings before posting more here at Stones and Bones.

Sunday, February 12, 2012

Other critiques of Joe the Surgeon

Joe Kuhn, MD wrote an extended bit of creatocrap that I have been debunking- bit by bit. They are; Part 1, and Part 2. I still hope to have Part 3 (of five) ready today.
This is more like Part 2.1

The Baylor University Medical Center Proceedings had invited Charles Stewart Roberts, MD, to provide a pro-science commentary published in the same edition.

Since then, Baylor UMC Proceedings has also presented a pre-print rebuttal by Gregory G. Dimijian, MD. I find it rather significant that the Baylor folks have already linked this from their current issue's Table of Contents.

Two other critiques are on-line, one by Jerry Coyne, and one by "Afarensis."

I think there is much more to say.

One question that I really have no idea of how to answer is "Why?" Why would any editor allow this crap to run in their journal?

One possibility is that they wanted to expose Joe Kuhn as an idiot.

Friday, February 10, 2012

Parallel Universe: bibliolatry v. reality

A few months ago I wrote a short item about Mail-oder Theology Degrees. My friend Richard Hope left a comment,
It's like there's a parallel universe in which it's the title that counts, regardless of its provenance. Pure Kent Hovindry. Hey--"Hovindry" as a term for it. That's more succinct than my previous term, inflationary credentialism.

As it happens, the notion that creationists live in an alternate (if not exactly 'parallel universe' since I think they are skewed) has some other promoters. Karl Giberson, and Randall Stephens wrote an OpEd for the New York Times last October 17th, which mentioned
"... many evangelicals created what amounts to a “parallel culture,” nurtured by church, Sunday school, summer camps and colleges, as well as publishing houses, broadcasting networks, music festivals and counseling groups. Among evangelical leaders, Ken Ham, David Barton and James C. Dobson have been particularly effective orchestrators — and beneficiaries — of this subculture. "The Evangelical Rejection of Reason," (The New York Times, October 17, 2011).

We have to award priority to Giberson, and Stephens, if only by one day.

It is no surprise that Giberson and Stephens are attacked in the fundy press, or that one attack comes from creationist historian, Discotute Richard Weikart "Should We Believe the Intellectuals?"

I hope to attend to that over the weekend, as well as Joseph Kuhn: Part 3.

Tuesday, February 07, 2012

Joseph A. Kuhn, MD. Part 2.

I am fraking “Dissecting Darwinism” by Joseph A. Kuhn, MD, published in Baylor University Medical Center Proceedings (BUMC Proceedings).

Kuhn makes various errors of fact and logic throughout his introductory pages. Mostly the result of sloppy thinking, and ignorance. For example, Kuhn said that ‘neo-Darwinism’ “reflected knowledge of reproduction and recombination, leading to potentially greater shifts in species.” What it reflected was a rejection of Lamarckian ideas of heritable acquired characteristics. Kuhn wrote that the “modern synthesis” was “proposed in 1950 to incorporate the knowledge of genetics, systematics, paleontology, and other fields.” Actually, the modern synthesis was proposed mathematically in the 1930s to merge genetic and evolutionary theory. Prior to this, genetics was promoted by antievolutionists as an alternative explanation to the diversity of species. The modern synthesis is built on the realization that the unit of evolution is an inter-reproductive population, taxonomically equivalent with “subspecies.” The term itself was introduced in a 1942 book by Julian Huxley titled, “Evolution: The Modern Synthesis.” (I have highlighted below the earlier papers by the most influential contributors). Major contributors were; R.A. Fisher, The Genetical Theory of Natural Selection (1930), J.B.S. Haldane; ten papers between 1924 and 1934 collectively known as “A Mathematical Theory of Natural and Artificial Selection,” see also, “Possible Worlds and Other Essays” (1928), Wright, Sewall (1932). "The roles of mutation, inbreeding, crossbreeding and selection in evolution" Proc. 6th Int. Cong. Genet 1: 356–366.

Reading these authorities, and other contemporaries, one learns that the field of paleontology is nearly ignored by evolutionary theorists at the time. The resulting revolution in systematics, or taxonomy really waited until the 1970s. This brings up Kuhn’s next error (at least big enough to irritate me). He wrote, “These mutations can occur gradually or rapidly via a term called saltation or punctuated evolution (sic).”

What is first irritating is that ‘terms’ don’t cause mutations. Second, there is nothing outside the fevered minds of creationists called “punctuated evolution.” The idea of ‘punctuated equilibria’ was introduced very dramatically by "Punctuated equilibria: an alternative to phyletic gradualism" (1972) pp 82-115 in "Models in paleobiology", edited by Schopf, TJM Freeman, Cooper & Co, San Francisco. Steve Gould, and Dick Lewontin in their 1979 paper, “The spandrels of San Marco and the Panglossion paradigm: a critique of the adaptationist programme.” (Proc R Soc Lond B 205 (1161): 581–598) extended the idea to argue that their punctuated equilibria idea could accommodate apparently non-adaptive mutation. Then “saltation” is not at all related to “punctuated” anything, it is derived from the Latin for “leap” is the notion of single-step speciation. This actually is known to happen, particularly common in speciation by plant hybrids. For example, de Vries (1905) found an unusual variant among his plants. O. lamarckiana has a chromosome number of 2N = 14. The variant had a chromosome number of 2N = 28. He found that he was unable to breed this variant with O. lamarckiana. He named this new species O. gigas. (I have dozens of other examples of observed emergence of new species on this link).

I am tired, and the weather sux. So there is sadly much more time to spend tomorrow on “Joseph A. Kuhn, MD. Part 3.”

Freaking Weird Stupid Shit

I posted a reply to a twit creationist a few weeks ago. It was entitled "A British creationist asked." I used a public domain photo of some guys from Papua New Guinea to reply to the question, "Why do we wear clothes?" What I particularly liked was that this family was waiting to greet the next batch of Christian missionaries to their village.

There has been a steady stream of perverts using Google images searching for "Naked little boys," "Naked family," "Naked Africans," "Naked men," and so on.

Yo' stupid!

Dey aint neked!

Oh goody: Bruce R. Booker's Degrees and Affiliations

So, a few days ago I received an email from Rabbi(?) Booker. It seems he had been trying to get in contact to let me know he was unhappy with my two paragraph review of his education, and that he had composed a stunning (29 page) refutation, "Bruce R. Booker's Degrees and Affiliations." Most of it is a cut-n-paste job, and I cannot help but wonder if this follows a pattern of Booker's early scholarship. I have no idea. If one of my students passed this in for credit, I would have flunked them.

Some weeks ago, I posted a short comment about Mail order theology degrees. The focus was on the educational qualifications of a creationist pastor, Graham Lovelady, of Ogden Utah. I wondered at what sort of education this genius must have received to be able to reject the work of thousands of dedicated scientists, and millions of pages of scientific results. I found that Lovelady had his "graduate degree" from a mail-order house called "Biblical Life College and Seminary." It turned out that the Biblical Life gang has their own in-house psychotherapy, which made it all the more interesting.

In my post, I reviewed the qualifications of some of the faculty members of Biblical Life College, based on their website vita. One of these was Bruce R. Booker.

Here is what the mail-order house has to say about "dr" Bruce R. Booker, Associate Professor of Hebraic Heritage Studies (retrieved Feb. 7, 2012):
B.B.S.—Biblical Life College & Seminary | M.A.—Columbia Pacific University | Ph.D.—Columbia Pacific University | Th.D. - Biblical Life College & Seminary.

Dr. Booker received s’micha (ordination) as a Messianic Rabbi through United Messianic Jewish Alliance. He currently serves as the Messianic Rabbi of Beth Yeshua Messianic Fellowship, Priest River, Idaho. Bruce has led several Messianic fellowships and congregations since 1989, including Beth Shalom Messianic Congregation, Sandpoint, Idaho, and Beth Shalom Messianic Congregation, formerly of Colton, CA - currently in Rancho Cucamonga, CA.

He is the author of several books including: THE LIE Exposing the Satanic Plot Behind Anti-Semitism, A Merciful Severity - A Study of Christian Anti-Semitism through the Centuries, God, Give me Patience NOW!, A Call to Holiness, and What If?

So, what do have here?

Four degrees from unaccredited mail-order schools, two of them supposedly "doctorates." As I wrote earlier;

Colombia Pacific University (CPU) was closed by court order in 2000, but the court did not review degrees awarded between 1978 and mid-1997. The first implementation of the 1989 Private Postsecondary and Vocational Education Reform Act was in 1991. Columbia Pacific University was given a provisional "grandfather" status until its degree programs, and faculty qualifications were reviewed. When this was done in 1996, this so-called school was found to fail minimal standards for a degree-granting institution.

So, “Doctor” Booker has quite a distinguished academic pedigree, one degree from an unaccredited correspondence school, two more from another unaccredited correspondence school that was ordered to cease and desist by the State of California for unethical, and unprofessional practices (i.e. awarding fake degrees), then back to the first correspondence “college” for another ‘doctorate,’ and then joining the faculty of his unaccredited alma mater.

There really is nothing to add. Rabbi(?) Booker's 29 page screed adopted the view that my post was all about himself, and not "pastor" Lovelady, or so-called "teleios therapy." For some additional fun, you might look over Booker's C.V.

Monday, February 06, 2012

Joseph A. Kuhn, MD. Part 1.

Some creatocrap was smeared on the Internet today. (Yes, what a surprise). The bit I examined was from the Discotute touting “peer reviewed” papers supporting ID creationism. Most of the papers the Discotutes promote as “supporting intelligent design” creationism don’t really do such a thing. So, I started reading the paper at the top of their list, “Dissecting Darwinism” by Joseph A. Kuhn, MD, published in Baylor University Medical Center Proceedings (BUMC Proceedings).

I didn’t get very far before I read, “John Hunter proposed a gradual formation of species through mutation 70 years before Charles Darwin published his observations in On the Origin of the Species. Therefore, history reveals that surgeons are uniquely capable of gathering information, making observations, and reaching conclusions about scientific discoveries.” (The secondary reference is eventually found to a popular press book).

Needless to say really, but Dr. Kuhn is a surgeon, and so by his logic also “uniquely capable” because over 200 years ago, John Hunter was an accomplished scientist and surgeon. What should we then conclude about the career of Josef Rudolf Mengele? When I was a professor of medicine in psychiatry, we often marveled how surgeons imagined they were “uniquely capable” in all aspects of life. Kuhn goes on to brag that physicians are the “the brightest minds, based on competitive test scores and undergraduate performance.” Since his audience are most likely physicians, I am sure this claim is accepted as sage wisdom. Kuhn does provide one early chuckle when he writes, "In fact, the physician represents the penultimate expert on applied molecular pathways as they relate to human conditions." The "penultimate" anything is the "next to last." Of course this egotist thinks it meant the 'most superior,' but that will always be the actual scientist who did the actual research that physicains learn to apply clinically.

Kuhn does do the full bore creationist dance, which I'll return to in Part 2.

I was more curious that Darwin never mentioned John Hunter. In all the later editions of “Origin of Species,” Darwin began with a “Historical Sketch” of evolutionary thinking. His remarks on the speculations of Buffon regarding the species question explain why he was less impressed with Hunter as well. Darwin wrote it was unnecessary to go into details with Buffon because he did not, “enter on the causes or means of the transformation of species.” It was this which Darwin's theory addressed.

The collected papers from John Hunter (1728-1793) mentioned by Kuhn were published in 1861, edited, and augmented by Richard Owen. “Essays and observations on natural history, anatomy, physiology, psychology, and geology, Volumes 1, 2” John Hunter, and Richard Owen. London: J. van Voorst, 1861. In his “Introduction to Natural History,” Hunter makes the observation at the beginning of a section titled, “On the Origin of Species,” that “Are we not led on to the wolf by the gradual affinity of the different varieties in the dog? Could we not trace out the gradation of the cat, horse, cow, sheep, fowl, etc. in a like manner?”

This section is very brief, merely two paragraphs. In the second, Hunter approached a point similar to Darwin when he speculated that the East Indian cattle were probably the more primitive, as they had fewer varieties, and were “… more likely to go through varieties in new countries [i.e. under new external influences] than in its original country.” Owen is often portrayed as an opponent of Darwin’s, so I was surprised that in a footnote to this section, he remarked “The best attempt to answer this supreme question in zoology is has been made by Charles Darwin in his work entitled “On the Origin of Species by Natural Selection” 1859. (Footnote 2, Page 37).

I read nothing in the rest of the 399 pages of Volume 1 that Kuhn could have confused with mutation, or heritable variation, natural selection (or any other selection than agricultural). Since Kuhn's assertion apparently relied on a secondary reference, and even that rather vague, I decided to plow on through the entire ~1000 pages.

The second volume of “Essays and observations on natural history” is a 491 page text on comparative anatomy, and a number of Appendixes. Hunter in his opening essay urged that only those well versed in human anatomy should under take comparative studies. I personally went in the opposite direction, dissecting fish by the hundreds before I studied much human material, and I should add that my interest was nearly entirely on bones. Hunter and I would agree on this latter focus, as he wrote on page 2 of his comparative anatomy regarding the skeleton. On the same page, Hunter wrote, "... I dare say that the different manner of living gives rise to the different formation of the viscera." He later added that an animal's 'external matter,' "... relate to the way of life that each animal is adapted to..." To this, Owen added a footnote saying, "A question still under controversy. The advocates of the 'Transmutation' or 'Natural Selection' hypothesis may take Hunter's words in their literal sense, and claim him as of their party." (Footnote 1, Page 2).

Hunter did not finish 3 pages before his examination of humans took a powerfully racist turn. He wrote that “white” men were “the most perfect of that genus” as we have the largest hands, and heads. These were the features he felt indicated “perfection” in humans, and he asserted that “The negro from Africa has both a small head, and very small hands and feet.” Even so, these obviously false statements compare well against the notorious modern “scientific” racist J. Philippe Rushton. Rushton claims to have “proven” that a large penis results in low intelligence and criminality, and thus Africans are stupid criminals due to big penises. Compare these beliefs with Charles Darwin, who wrote in "The Descent of Man, and Selection in Relation to Sex" (John Murray, London, 1871), "It may be doubted whether any character can be named which is distinctive of a race and is constant." Also, "By the way, a Negro lived in Edinburgh, who had traveled with Waterton and gained his livelihood by stuffing birds, which he did excellently; he gave me lessons for payment, and I used often to sit with him, for he was a very pleasant and intelligent man." -- Charles Darwin, Autobiography of Charles Darwin 1809-1882 (restored edition)(1958), Nora Barlow editor, p.51., Or, "I do not see that an orthognathous face would cost more than a prognathous face; or a good morale than a bad one." (LETTER 412. TO FRANCIS GALTON. Down, January 4th, 1873).

However, there was nothing that I read which justified Kuhn's claim that Hunter, "proposed a gradual formation of species through mutation." Maybe if Kuhn knew how to provide a proper citation, we could learn what he referred to in his paper. In psychiatry, we called it "making shit up."

There was one feature of particular interest to any student of the relationship between scientific advancement, and religious bias. In 1855, Richard Owen gave a lecture to the Royal College of Surgeons as part of his appointment as the Hunterian Professor of Anatomy. The talk was examining a yet unpublished manuscript by Hunter, “On Extraneous Fossils,” written from Hunter’s address on fossils given in 1793 to the Royal Society of London. In the latter paper, Hunter described his results from treating various recent bones, and shells and similar fossil specimens with different acids. Hunter was particularly interested in what he called “the animal substance.” From his descriptions, I suspected this “animal substance” is mostly collagen, and osteocalcin, and this seems to be confirmed in Hunter’s essay “Of the Preparation of Bones,” when compared with "Chemical Technology and Analysis of Oils, Fats, and Waxes" (Kowitsch, 1895).

The address in 1793 was never published. Owen explained that the the Society editors objected to Hunter's conclusion that the the Earth was very ancient. Variation in the degree of fossilization among the thousands of specimens Hunter examined had clearly led him to conclude that this was the result of processes across “many thousand centuries.” A Major Rennell wrote to Hunter on behalf of the Royal Society requesting that the time frame be altered to “many thousand years” so as to not alienate young earth creationists. Instead, Hunter withdrew the paper from publication only months before his death on October 16, 1793. This early example of how creationism impedes scientific understanding of Nature was new to me.

I will say that refuting creatocrap can occupy the days I am not fishing.

Here is a link to Part 2.