Saturday, August 27, 2011

I am so easily distracted by fishing

I really appologise to anyone frustrated by my somewhat inconsistent follow-up on some posts.

I have an excuse!!!!111!!!

This was a very tasty, if small, bluefin tuna I caught fishing ~150 miles SW of San Diego, California. We were aboard the New Lo-An out from Point Loma. It was a good 1.5 day trip- good boat, good crew, and hungry fish. I returned home with about 50lbs of meat. Since fresh bluefin is selling retail for ~$27 a pound, I made better than retail on a $450 trip.

Next week I'll leave on the Pacific Queen for another shot at the tuna. One day will be my last off-shore trip, and then I'll be more diligent at writing.

Tuesday, August 23, 2011

Baleen whale evolution and creationists

A rather obnoxious oral surgeon, Don Moeller DDS MD MA, recently posted a challenge to the effect of “where any mutation of the amelogenin gene or any other enamel protein has resulted in anything but a detrimental effect,” and, “explain to me how no less than twenty enamel subtypes appear in the fossil record with NO pathological enamel and no precursors,” and, “let me know why there is NO oral pathology ( eruption sequence, postion variation, developmental cysts, tumors etc) in ANY fossil.”

As for the later, I have seen fossils with tooth pathology, and osteopathies of the mandible and maxilla including impaction. Bone erosion, and tooth loss to bacterial infections are of course common. So there.

As it happens, I have been collecting articles on whale evolution for several years as a hobby. I indulge my hobbies, as they have often resulted in money making career paths, and work is more fun when it doesn’t seem like working. This also gives me the opportunity to educate Dr. Dr. Moeller, MA. However, I doubt he will be able to take advantage since the poor man is a creationist.

First, the general problem that creationists like Moeller present to Christian theology is that any gap, or open question in science is where they try to justify their belief in God. Here are a few hints that this is a stupid, and anti-scriptural effort; 1 Timothy 1: 3, 2 Corinthians 3: 5, Titus 3:9. In plain words, “Tis a dangerous thing to engage the authority of scripture in disputes about the natural world in opposition to reason; lest time, which brings all things to light, should discover that to be evidently false which we had made scripture assert.” Telluris theoria sacra (1684 English edition, “The Sacred Theory of the Earth” Preface, pg. 10), Reverend Thomas Burnett (1635?-1715).

For more recent books, I suggest;

Miller, Keith B. (editor)
2003 “Perspectives on an Evolving Creation” Grand Rapids: Eerdmans Publishing

Hyers, Conrad
1984 “The Meaning of Creation: Genesis and Modern Science” Atlanta: John Knox Press (Conrad Hyers has served as Professor of the History of Religion and Chair of the Department of Religion at both Beloit College and at Gustavus Adolphus College. He is also an ordained Presbyterian minister)

Haught, John F.
2001 “Responses to 101 Questions on God and Evolution” New York: Paulist Press Haught is a Catholic theologian who testified as a plaintiff expert in the Dover, Pa “Intelligent Design” trial.

Frye, Roland Mushat (editor)
1983 "Is God a Creationist?: The Religious Case Against Creation-Science" New York: Charles Scribner's Sons, Inc.

Rabbi Natan Slifkin gives a very interesting Orthodox Jewish perspective in “The Challenge of Creation: Judaism’s Encounter with Science, Cosmology and Evolution” (2008 New York: Zoo Torah and Yashar Books).

Every time a creationist’s demand for more evidence from science is met, their god argument grows weaker. This is the ultimate doom of all such "god of the gaps" theologies. And it is in fact an unnecessary argument. But, Dr. Moeller picked the fight, and here is the 1-2-3-4-5 “yer-out.” For now, I’ll just post the relevant articles, their abstracts, and a link to each. The hard part for me was making links to free texts.

Erich M.G Fitzgerald
2006 “A bizarre new toothed mysticete (Cetacea) from Australia and the early evolution of baleen whales” Proc. R. Soc. B 7 December 2006 vol. 273 no. 1604 2955-2963

Extant baleen whales (Cetacea, Mysticeti) are all large filter-feeding marine mammals that lack teeth as adults, instead possessing baleen, and feed on small marine animals in bulk. The early evolution of these superlative mammals, and their unique feeding method, has hitherto remained enigmatic. Here, I report a new toothed mysticete from the Late Oligocene of Australia that is more archaic than any previously described. Unlike all other mysticetes, this new whale was small, had enormous eyes and lacked derived adaptations for bulk filter-feeding. Several morphological features suggest that this mysticete was a macrophagous predator, being convergent on some Mesozoic marine reptiles and the extant leopard seal (Hydrurga leptonyx). It thus refutes the notions that all stem mysticetes were filter-feeders, and that the origins and initial radiation of mysticetes was linked to the evolution of filter-feeding. Mysticetes evidently radiated into a variety of disparate forms and feeding ecologies before the evolution of baleen or filter-feeding. The phylogenetic context of the new whale indicates that basal mysticetes were macrophagous predators that did not employ filter-feeding or echolocation, and that the evolution of characters associated with bulk filter-feeding was gradual.

Thomas A. DEMERE, Michael R. MCGOWEN, Annalisa BERTA, John GATESY
2008 “Morphological and Molecular Evidence for a Stepwise Evolutionary Transition from Teeth to Baleen in Mysticete Whales” Systematic biology, vol. 57, no1, pp. 15-37

-The origin of baleen in mysticete whales represents a major transition in the phylogenetic history of Cetacea. This key specialization, a keratinous sieve that enables filter-feeding, permitted exploitation of a new ecological niche and heralded the evolution of modern baleen-bearing whales, the largest animals on Earth. To date, all formally described mysticete fossils conform to two types: toothed species from Oligocene-age rocks (~24 to 34 million years old) and toothless species that presumably utilized baleen to feed (Recent to ~30 million years old). Here, we show that several Oligocene toothed mysticetes have nutrient foramina and associated sulci on the lateral portions of their palates, homologous structures in extant mysticetes house vessels that nourish baleen. The simultaneous occurrence of teeth and nutrient foramina implies that both teeth and baleen were present in these early mysticetes. Phylogenetic analyses of a supermatrix that includes extinct taxa and new data for 11 nuclear genes consistently resolve relationships at the base of Mysticeti. The combined data set of 27,340 characters supports a stepwise transition from a toothed ancestor, to a mosaic intermediate with both teeth and baleen, to modern baleen whales that lack an adult dentition but retain developmental and genetic evidence of their ancestral toothed heritage. Comparative sequence data for ENAM (enamelin) and AMBN (ameloblastin) indicate that enamel-specific loci are present in Mysticeti but have degraded to pseudogenes in this group. The dramatic transformation in mysticete feeding anatomy documents an apparently rare, stepwise mode of evolution in which a composite phenotype bridged the gap between primitive and derived morphologies; a combination of fossil and molecular evidence provides a multifaceted record of this macroevolutionary pattern.

Toshiyuki Kimura* and Yoshikazu Hasegawa
2010 “A New Baleen Whale (Mysticeti: Cetotheriidae) from the Earliest Late Miocene of Japan and a Reconsideration of the Phylogeny of Cetotheres” Journal of Vertebrate Paleontology 30(2):577-591.

A new, well-preserved mysticete fossil is described and diagnosed here as Joumocetus shimizui, gen. et sp. nov. The holotype specimen was recovered from the earliest Late Miocene, Haraichi Formation, Annaka Group, Gunma Prefecture, Japan. Although many cetotheres have been found from the Pacific realm, the Cetotheriidae sensu stricto is relatively rare in terms of taxonomic diversity and also abundance of specimens. Joumocetus will be the fourth genus of the Cetotheriidae sensu stricto from the Pacific and the geologically earliest and most archaic Cetotheriidae sensu stricto yet reported. Joumocetus retains a number of primitive characteristics, and our phylogenetic analysis indicates that Joumocetus is placed basally among the Cetotheriidae sensu stricto. Our analysis clearly indicates a monophyly of the Cetotheriidae sensu stricto and of a clade that consists of Balaenopteridae, Eschrichtiidae, and cetotheres. The results also indicate the monophyly of the following two groups: cetotheres not belong to Cetotheriidae sensu stricto (= Isanacetus-group) and Cetotheriidae sensu lato (= Isanacetus-group + Cetotheriidae sensu stricto); however, the monophylies of these groups are not well supported by bootstrap analysis. Consequently, the relationships and definition of these mysticete taxa remain unclear. Based on the present study and a review of previous studies, we suggest that the Isanacetus-group is a paraphyletic taxon that includes the ancestors of two clades, Balaenopteridae + Eschrichtiidae and the Cetotheriidae sensu stricto.

Robert W. Meredith, John Gatesy, Joyce Cheng and Mark S. Springer
2011 “Pseudogenization of the tooth gene enamelysin (MMP20) in the common ancestor of extant baleen whales” Proc. R. Soc. B 7 April vol. 278 no. 1708: 993-1002

Whales in the suborder Mysticeti are filter feeders that use baleen to sift zooplankton and small fish from ocean waters. Adult mysticetes lack teeth, although tooth buds are present in foetal stages. Cladistic analyses suggest that functional teeth were lost in the common ancestor of crown-group Mysticeti. DNA sequences for the tooth-specific genes, ameloblastin (AMBN), enamelin (ENAM) and amelogenin (AMEL), have frameshift mutations and/or stop codons in this taxon, but none of these molecular cavities are shared by all extant mysticetes. Here, we provide the first evidence for pseudogenization of a tooth gene, enamelysin (MMP20), in the common ancestor of living baleen whales. Specifically, pseudogenization resulted from the insertion of a CHR-2 SINE retroposon in exon 2 of MMP20. Genomic and palaeontological data now provide congruent support for the loss of enamel-capped teeth on the common ancestral branch of crown-group mysticetes. The new data for MMP20 also document a polymorphic stop codon in exon 2 of the pygmy sperm whale (Kogia breviceps), which has enamel-less teeth. These results, in conjunction with the evidence for pseudogenization of MMP20 in Hoffmann's two-toed sloth (Choloepus hoffmanni), another enamel-less species, support the hypothesis that the only unique, non-overlapping function of the MMP20 gene is in enamel formation.

J. A. Jackson, C. S. Baker, M. Vant, D. J. Steel, L. Medrano-González and S. R. Palumbi
2011 “Big and Slow: Phylogenetic Estimates of Molecular Evolution in Baleen Whales (Suborder Mysticeti)” Mol Biol Evol (2009) 26 (11): 2427-2440.

Baleen whales are the largest animals that have ever lived. To develop an improved estimation of substitution rate for nuclear and mitochondrial DNA for this taxon, we implemented a relaxed-clock phylogenetic approach using three fossil calibration dates: the divergence between odontocetes and mysticetes ~34 million years ago (Ma), between the balaenids and balaenopterids ~28 Ma, and the time to most recent common ancestor within the Balaenopteridae ~12 Ma. We examined seven mitochondrial genomes, a large number of mitochondrial control region sequences (219 haplotypes for 465 bp) and nine nuclear introns representing five species of whales, within which multiple species-specific alleles were sequenced to account for within-species diversity (1–15 for each locus). The total data set represents >1.65 Mbp of mitogenome and nuclear genomic sequence. The estimated substitution rate for the humpback whale control region (3.9%/million years, My) was higher than previous estimates for baleen whales but slow relative to other mammal species with similar generation times (e.g., human–chimp mean rate > 20%/My). The mitogenomic third codon position rate was also slow relative to other mammals (mean estimate 1%/My compared with a mammalian average of 9.8%/My for the cytochrome b gene). The mean nuclear genomic substitution rate (0.05%/My) was substantially slower than average synonymous estimates for other mammals (0.21–0.37%/My across a range of studies). The nuclear and mitogenome rate estimates for baleen whales were thus roughly consistent with an 8- to 10-fold slowing due to a combination of large body size and long generation times. Surprisingly, despite the large data set of nuclear intron sequences, there was only weak and conflicting support for alternate hypotheses about the phylogeny of balaenopterid whales, suggesting that interspecies introgressions or a rapid radiation has obscured species relationships in the nuclear genome.

Note: As it happens, I live and work in an area particularly well suited for Miocene whale fossils. There is indeed a number of unpublished fossils, sitting in the warehouse of the museum I was formerly a director of, which physically support the “rapid radiation” of baleen whale evolution.

Edited to as a related citation;
Zhe Wang, Lihong Yuan, Stephen J. Rossiter, Xueguo Zuo, Binghua Ru, Hui Zhong, Naijian Han, Gareth Jones, Paul D. Jepson and Shuyi Zhang. 2009. Adaptive Evolution of 5′HoxD Genes in the Origin and Diversification of the Cetacean Flipper. Mol Biol Evol (2009) 26(3): 613-622 (

Sunday, August 21, 2011

A qualified, partial victory in Capistrano

The Ninth Circuit Court of Appeals has just published their decision that Capistrano Unified School District’s high school teacher, James Corbett, was not vulnerable to the claim that his classroom statements violated the First Amendment rights of a former student, Chad Farnan. The suit was filed by his parents in 2009 while Chad was still a minor. The case has attracted considerable press attention, locally and nationally. It is also the topic of a number of online discussions, for example, "Lost Opportunity in San Juan Capistrano." In the original, and amended plaintiff complaints (all court documents are available on-line through the National Center for Science Education), there were a dozen or so statements Farnan claimed to have secretly recorded during Corbett’s classes. During the trial, several were found to have been so severely edited, and redacted by Farnan that their meaning had been totally altered.

Following the trial Judge’s decision, only a single statement made by Corbett, as alleged by Farnan, was found to be questionable.

“At that point, I stood up and said, “I’ll tell you what. I will sign a statement giving you — you do not have to defend me, but I will not leave John [Peloza] alone to propagandize kids with this religious, superstitious nonsense... John wanted to talk about creation as a science and all that stuff, but you get involved in that argument, you just lose because it’s just nonsense. . . .”

The original law suit made a common error of equating creationism with Christianity. This is nonsense. Unfortunately, Corbett's legal team never challenged this error, and instead argued he had a First Amendment right that allowed him to be critical of creationism/religion. If Crobett, acting as a public employee, were to say as part of his public job that "Christianity is rubbish," or "Islam is rubbish," he would have been in violation of the Constitution, and his contract. To state that young earth creationism is rubbish is merely stating a fact that in no way attacks Christianity, or Islam, or any other religious sect. Where is the Church of Creationism? What are their sacraments? How do I know who is a member of the Church of Creationism?

There are Jewish, and Muslim creationists who maintain the same absurd, and false claims opposing the sciences of biology, geology, and astronomy directly, and even chemistry and physics indirectly, as do the garden variety Christian creationists. There are Neo-pagan, and Animist creationists. There are Native American creationists who insist that all sciences, especially archaeology, were invented merely to suppress Native Americans. There are Hindu creationists who insist that the Earth is infinitely old. So, Corbett's remarks regarding CTREATIONISM cannot be said to be "anti-Christian," and in fact there are thousands of Christian Clergy who reject creationist foolishness as well. Google "Clergy Letter Project."

Non-the-less, Corbett's remarks re: creationism were not directed against any religion in particular. In fact, Intelligent Design creationists try to pretend (unsuccessfully) they are free of any religious motivations.

To say that fear of black cats, or Friday the Thirteenth is superstitious nonsense is merely the truth. So to is saying that creationism is superstitious nonsense merely the truth. Creationism is not a religion. Creationism is not protected any more than fear of black cats, or Friday the Thirteenth, or fear of vaccinations.

At the same time, there is no creationist dogma that is not ultimately reducible to a religious doctrine held by the proponent of creationism. For this reason, creationism is not eligible to be taught in government sponsored, public schools. Creationism is used as a tool by the proponent to advance their personal religion through the coercive power of the State.