January 2011 Archives

Libellula lydia


Photograph by Kurt Andreas.

Photography contest, Honorable Mention.


Libellula lydia – common whitetail dragonfly, New Paltz, New York, spring, 2009.

I’ve had the good fortune of having some papers published recently, and my intention is to eventually summarize all of them for our readers. The first paper that I’m going to discuss is a methodology paper concerning a way of extracting phylogenetic information from regions of multiple sequence alignments that are full of indels (insertions and deletions) and difficult to align:

PICS-Ord: unlimited coding of ambiguous regions by pairwise identity and cost scores ordination. (link)
Robert Lücking, Brendan P Hodkinson, Alexandros Stamatakis and Reed A Cartwright
BMC Bioinformatics 2011, 12:10 doi:10.1186/1471-2105-12-10

Background We present a novel method to encode ambiguously aligned regions in fixed multiple sequence alignments by ‘Pairwise Identity and Cost Scores Ordination’ (PICS-Ord). The method works via ordination of sequence identity or cost scores matrices by means of Principal Coordinates Analysis (PCoA). After identification of ambiguous regions, the method computes pairwise distances as sequence identities or cost scores, ordinates the resulting distance matrix by means of PCoA, and encodes the principal coordinates as ordered integers. Three biological and 100 simulated datasets were used to assess the performance of the new method.

Results Including ambiguous regions coded by means of PICS-Ord increased topological accuracy, resolution, and bootstrap support in real biological and simulated datasets compared to the alternative of excluding such regions from the analysis a priori. In terms of accuracy, PICS-Ord performs equal to or better than previously available methods of ambiguous region coding (e.g., INAASE), with the advantage of a practically unlimited alignment size and increased analytical speed and the possibility of PICS-Ord scores to be analyzed together with DNA data in a partitioned maximum likelihood model.

Conclusions Advantages of PICS-Ord over step matrix-based ambiguous region coding with INAASE include a practically unlimited number of OTUs and seamless integration of PICS-Ord codes into phylogenetic datasets, as well as the increased speed of phylogenetic analysis. Contrary to word- and frequency-based methods, PICS-Ord maintains the advantage of pairwise sequence alignment to derive distances, and the method is flexible with respect to the calculation of distance scores. In addition to distance and maximum parsimony, PICS-Ord codes can be analyzed in a Bayesian or maximum likelihood framework. RAxML (version 7.2.6 or higher that was developed for this study) allows up to 32-state ordered or unordered characters. A GTR, MK, or ORDERED model can be applied to analyse the PICS-Ord codes partition, with GTR performing slightly better than MK and ORDERED.

Availability An implementation of the PICS-Ord algorithm is available from http://scit.us/projects/ngila/wiki/PICS-Ord. It requires both the statistical software, R http://www.r-project.org and the alignment software Ngila http://scit.us/projects/ngila.

My co-author, Brendan Hodkinson, has already covered it on his blog, and the software can be downloaded from my website.

In phylogenetic analysis, regions of sequences that contain a lot of overlapping indels are difficult to align, and whatever alignment that is produced is considered to have a low signal-to-noise ratio. Typically these regions are removed from any phylogenetic analysis, but we propose a method to convert the information they contain into mutli-state characters.

Those are two of the questions that Michael Berkman and Eric Plutzer ask in their new book Evolution, Creationism, and the Battle to Control America’s Classrooms. Their answers are not entirely comforting. The authors, who discussed some of their findings in Science the other day, analyze a number of well-known polls and also their own poll of biology teachers, which they conducted in 2007. They conclude that a substantial majority of Americans want creationism taught in public schools – not necessarily creationism alone, but creationism nonetheless. They also note that the number of citizens who support evolution alone is increasing at the expense of those who want both taught but not, presumably, those who want creationism alone taught. A myriad of court decisions, however, has ruled out teaching of creationism in any form. The nation is divided, as they put it, by religion, education, and place.

In a response to publication of the Cheng, et al paper in PNAS which demonstrated an evolutionary pathway to the antifreeze gene that protects fish from freezing in Antarctic water (see also my post on it), Casey Luskin, attack gerbil of the Disco ‘Tute, invokes Stephen Jay Gould’s infamous “just so” phrase. Luskin then kindly outlines the three steps in constructing a “just so” story to account for biological phenomena. Here I’ll walk through Casey’s steps for a parallel case to show just how specious his claim is. The parallel case is accounting for how a particular boulder, indicated below by the red arrow, got to where it was in a landslide (image used by permission of Air-and-Space Museum).


Casey Luskin takes note of the Elsberry and Shallit essay in Synthese 2011/01 in this way:

I would have hoped that if Weber, a biochemist, was going to refute intelligent design, he would have provided more detail. Weber might protest that such an argument would be more appropriate to make in a scientific journal rather than a philosophy journal. What are we to make, then, of the fact that Wesley Elsberry and Jeffrey Shallit have a technical and scientific response to William Dembski in the issue of Synthese?

It turns out that Elsberry and Shallit have a sophisticated but extremely out-of-date contribution in the issue which seems based upon their old 2003 article, “Information Theory, Evolutionary Computation, and Dembski’s Complex Specified Information.” In fact, their piece in Synthese has exactly the same title as that old piece. This out-of-date paper has only one citation post 2004, and it isn’t to a paper that deals with the work of Dembski. In terms of their citations to Dembski’s work, their latest citation is 2004, despite the fact that Dembski has published multiple peer-reviewed papers in recent years studying the origin of information.

We submitted our essay to Synthese on 2009/03/23. It was released online by 2009/04/20. It appears in print in the January 2011 issue. In general, authors can only respond to papers that are published before the date of publication.

So let’s look at the list of “peer-reviewed papers in recent years” that Casey says shows that we weren’t keeping up with Dembski. I’ve scraped these from the linked page and added dates and elapsed time values from our essay submission date.

Bernoulli’s Principle of Insufficient Reason and Conservation of Information in Computer Search
William A. Dembski and Robert J. Marks II
Published 2009/10, 6 months after our submission

Conservation of Information in Search: Measuring the Cost of Success
William A. Dembski and Robert J. Marks II
Published 2009/09, 6 months after our submission

LIFE’S CONSERVATION LAW: Why Darwinian Evolution Cannot Create Biological Information
William A. Dembski and Robert J. Marks II
Published 2009/06/16, 2.5 months after our submission

The Search for a Search: Measuring the Information Cost of Higher Level Search
William A. Dembski and Robert J. Marks II
Published 2010/04/01, 12 months after our submission

Efficient Per Query Information Extraction from a Hamming Oracle [with Erratum]
Winston Ewert, George Montañez, William A. Dembski, Robert J. Marks II
Conference held 2010/03/07-09, 11 months after our submission

Evolutionary Synthesis of Nand Logic: Dissecting a Digital Organism
Winston Ewert, William A. Dembski and Robert J. Marks II
Published 2009/10, 6 months after our submission

A Vivisection of the ev Computer Organism: Identifying Sources of Active Information
George Montañez, Winston Ewert, William A. Dembski, Robert J. Marks II
Published 2010, at least 8 months after our submission

Not a one of the linked papers Casey referred to was published prior to our essay’s submission. Casey obviously expects critics either to shut up entirely or to be clairvoyant.

It should also be noted that the papers Casey erroneously cites aren’t delivering modifications of Dembski’s “complex specified information” concept. Nor do they set aside any of the concerns we raised about Dembski’s earlier outings in critiquing evolutionary computation. Quite the contrary, Dembski has elaborated his “probability amplifier” tosh into what he now calls “active information”. If Casey believes that an argument of ours would be significantly affected by something presented in those papers, he is welcome to be specific: identify which argument of ours he thinks is affected, and which part of the very recent papers bears upon it, and how it actually relates to our argument.

In any case, trying to claim that an essay should cite papers published after its submission is simply the level of argument we’ve come to expect from Casey Luskin. Coming unstuck in time may happen to Casey, but the rest of us have to experience things sequentially as they happen.

(Original post at the Austringer.)

Darwin Week

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If any of our readers or contributors are taking part in Darwin Week activities, I’d like to invite them to announce those activities here. The International Darwin Day Foundation lists the better part of 100 activities here, most but not all between February 9 and 12. But if anyone has any pet activities to publicize, please go at it in the comments.

I will start: One of my colleagues tells me that the Iowa City event on February 11 and 12 will feature two talks by Frans de Waal, one technical, and one general. The general talk is entitled “Morality before Religion: Empathy, Reciprocity and Fairness in our Fellow Primates.” You may find the entire schedule and location at the link directly above.

The Secular Students and Skeptics Society at the University of Colorado is sponsoring a weeklong event, February 7-11. On Wednesday, February 9, I will discuss my contention that our sense of morality is an evolved trait; by a not entirely surprising coincidence, de Waal’s work figures into my talk. The no doubt sassy students will also show the movie “Creation” on Monday, February 7, followed by a discussion led by philosophy professor Carol Cleland. Again, you may find the entire schedule and locations at the link.

All I have so far. I invite anyone else who wants to publicize a specific event to do so in the comments.

Update, January 26: Please see below the fold for an update by Michael Zimmerman of the Huffington Post.

Rhyothemis variegata


Photograph by Buddhini Samarasinghe.

Photography contest, Honorable Mention.


Rhyothemis variegata – common picture wing or variegated flutterer, Sri Lanka.

Denisovans and the species problem


A few weeks ago I blogged on the Denisovans, a new group of human relatives discovered through genetic analysis of two bones from Denisova in Siberia (Reich et al. 2010, Nature 468:1053). Fascinatingly, the Denisovans seem to have made about a 5% contribution to the genome of living Melanesians.

I mentioned that this new discovery did not seem compatible with a young-earth creationist framework, and awaited with interest a creationist explanation of the findings. Answers In Genesis (AIG) has now commented on the Denisovans. No explanation, merely a one-sentence handwaving solution:

Answers in Genesis Wrote:

But the most interesting twist (from the evolutionary perspective) is that modern humans from New Guinea have Denisovan DNA. While an evolutionary perspective interprets this as meaning that Guineans’ ancestors “interbred” with Denisovans, a biblical perspective interprets this as simply meaning that the descendants of one of the people groups leaving Babel eventually settled in what is now New Guinea.

It’s not clear what this even means. After all, their ‘biblical perspective’ had exactly the same interpretation (that the descendants of a group leaving Babel settled in New Guinea) even before we knew about the Denisovan genetic contribution. This ‘explanation’ fails to address a key point: how did the Denisovan genes get into Melanesians, if not by interbreeding with Denisovans?

And the above scenario doesn’t resolve any of the other problems with a young-earth framework.

Child abuse indeed


Georgia Purdom is a functionary–a “scientist”–at Ken Ham’s Answers in Genesis. She has a Ph.D. in molecular genetics from the Ohio State University and was for a time on the faculty at Mt. Vernon Nazarene University in Ohio. (Interestingly, she left MVNU after 6 years, about the time when tenure decisions are made in most institutions. I know nothing specific, but it’s always fun to speculate.) In a recent blog post commenting on the Freshwater affair she wrote this:

I teach Sunday school for first through third grade, and over the next few weeks we’ll be discussing dinosaurs, radiometric dating methods, natural selection, and mutations. I teach them that what they learn in public school in regard to historical science concerning these ideas is not the truth.

That’s child abuse of a very high order, worse even than Freshwater’s because the children are so much younger. Those kids are screwed.

The “intelligent design” creationists over at the Discovery Institute have long maintained a hypocritical stance. For public consumption, they say that they favor “teaching the controversy”. However, almost any time they control the forum, they pretty ruthlessly make it impossible for one to hear anything but their own spin on a topic. Now, they are asking for comments.

Cloud iridescence


Cloud iridescence. The brightest example of cloud iridescence I have ever seen – visible without polarizer or sunglasses for around an hour. The photograph is not enhanced in any way. The sky, alas, is underexposed and appears black; enough to make a person long for Kodachrome.

A Horoscope I’d like to see


(This follows on from my article on the recent Astrology kerfuffle and was written (but not used) in 2005 for Australian Sky and Space. The positions are correct for 2005, but Mars has obviously moved by now)

Even though the Sun passes through the classical constellation Ophiuchus, it is not included in the astrological zodiac. Also Cetus, where several planets can spend some time, is excluded (most recently Mars was briefly in Cetus). As well, Pluto wanders a bit further from the Zodiac than the others due to its high eccentricity, but the constellations it wanders into are excluded from the astrological zodiac. And what about asteroids, Kuiper belt objects and Plutinos? Astrologers are divided over whether to include them in charts, and although you can find astrological predictions on the internet that do include these objects, your average horoscopes exclude them. And what about space probes? Size and mass is no obstacle to astrological relevance, surely these messengers of human curiosity and hope should be included? Sadly, they are not.

I think it is a great shame that these constellations and objects are excluded from western horoscopes, they would be far more colourful than the wishy-washy current versions that suggest that Mars may be making you a little more aggressive. So I have written the kind of horoscope I would like to see.

A Storm in a Zodiacal Teacup


The Sun in the constellation Ophiuchus on December 12, contary to coomets of some astrologers.

A recent article by astronomer Parke Kunkle has had the twitterverse and astrologers in an uproar by pointing out that Sun no longer enters the constellations associated with the zodiac due to precession of the equinoxes.

Now, readers of the Panda’s Thumb might wonder why a kerfuffle about a pseudoscience like astrology warrants attention on a blog devoted to evolution. However, there is a parallel between how astrologers respond to criticism and how anti-evolutionists respond to criticism. So you might find it interesting (oh, and yes, astrology is rubbish).

Changes to AP biology test?


An article in last week’s Education Life supplement to the New York Times reports that the College Board is working on a “wholesale revamping of A.P. biology,” a revision which will substantially reduce memorization and will also provide a model curriculum. The new curriculum will rely more on laboratory experiments and hypothesis testing, and less on memorization. The goal, according to the Times, is to allow the students to “focus on bigger concepts and stimulate more analytic thinking.” The changes will take effect beginning with the 2012-13 school year. The Times notes that the changes are important because “critical thinking skills” are necessary for advanced college courses and jobs.

I read this fascinating book while I was on a freighter island-hopping in the Marquesas Islands in French Polynesia. Vermeij explained clearly, for example, why islands have less biological diversity than continents, why some islands are characterized by giant tortoises or giant flightless birds, why the tropics have so many nasty poisonous creatures that you do not want to step on when you go snorkeling. I could probably tell you much more, but “island” is oddly not in the index.

The subtitle of the book is “How adaptation explains everything from seashells to civilization.” But I saw the book as more a description of nature from a systems point of view - how everything interacts with everything else, how causes are rarely simple but rather are multifaceted. The book is not, as you might have guessed, a defense of the primacy of adaptation against genetic drift (one entry in the index, page 6), and sociobiology or evolutionary psychology is barely mentioned (page 18). The book tells you how adaptation explains seashells (Vermeij’s specialty), but not civilization; not really.

Tenacious DNA


Some pretty amazing video. A few inaccuracies, an elision or two, but an impressive 12 minutes or so nonetheless.

Via Mano Singham.

Gene duplication enables a novel function to evolve

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The Sensuous Curmudgeon calls our attention to a new study by researchers at the University of Illnois and the Chinese Academy of Sciences that traces the evolution of a new function via gene duplication. Since I’m not a molecular guy, I’ll very briefly describe it and refer you to the news release and published paper (behind the PNAS paywall). Very briefly, the Antarctic eelpout has a gene that codes for an antifreeze protein, a member of a protein family called AFP III, that enables the eelpout to survive the freezing temperatures in Antarctic waters. It has been hypothesized on genetic homology grounds that the antifreeze gene evolved via duplication of a gene that codes for sialic acid synthase, a cellular enzyme, and subsequent selection for the antifreeze function in one of the duplicates via an escape from adaptive conflict process. From the linked news release:

“This is the first clear demonstration - with strong supporting molecular and functional evidence - of escape from adaptive conflict as the underlying process of gene duplication and the creation of a completely new function in one of the daughter copies,” Cheng said. “This has not been documented before in the field of molecular evolution.”

And from the Abstract:

We report here clear experimental evidence for EAC-driven evolution of type III antifreeze protein gene from an old sialic acid synthase (SAS) gene in an Antarctic zoarcid fish. We found that an SAS gene, having both sialic acid synthase and rudimentary ice-binding activities, became duplicated. In one duplicate, the N-terminal SAS domain was deleted and replaced with a nascent signal peptide, removing pleiotropic structural conflict between SAS and ice-binding functions and allowing rapid optimization of the C-terminal domain to become a secreted protein capable of noncolligative freezing-point depression. This study reveals how minor functionalities in an old gene can be transformed into a distinct survival protein and provides insights into how gene duplicates facing presumed identical selection and mutation pressures at birth could take divergent evolutionary paths.

As the Curmudgeon points out, this is precisely the kind of evidence that Disco ‘Tute attack mouse Casey Luskin asked for a year ago:

Many scientific papers purporting to show the evolution of “new genetic information” do little more than identify molecular similarities and differences between existing genes and then tell evolutionary just-so stories of duplication, rearrangement, and subsequent divergence based upon vague appeals to “positive selection” that purport to explain how the gene arose. But exactly how the gene arose is never explained. In particular, whether chance mutations and unguided natural selection are sufficient to produce the relevant genetic changes is almost never assessed.

There it is, Casey.

Freshwater: The termination resolution


This is the full text of the termination resolution adopted by the Mt. Vernon City Schools Board of Education on January 10, 2011. Turns out the mover didn’t read the whole thing.



WHEREAS, John Freshwater (“Mr. Freshwater”) is currently employed by the Board as an eighth grade science teacher as Mount Vernon Middle School; WHEREAS, as a result of his position with the Board, Mr. Freshwater is a member of the bargaining unit represented by the Mount Vernon Education Association (“MVEA”) and is governed by the terms and conditions of employment set forth in the collective bargaining agreement between MVEA and the Board (the “Agreement”);

WHEREAS, the Board has promulgated reasonable policies, rules and standards for the management and control of its workforce and for the safe and efficient governance of its employees, in compliance with State and Federal law;

WHEREAS, the Board not only expects, but requires, its employees to adhere to the reasonable policies, rules and standards promulgated by the Board, as well as State and Federal law;

WHEREAS, Mr. Freshwater is an employee and charged with and compensated for not only his performance while at work but also for his knowledge of and adherence to the aforementioned Board policies, rules and standards, as well as State and Federal law;

WHEREAS, Ohio Revised Code §3319.16 sets forth that a teacher employed by the Board of Education may be terminated for “good and just cause;”

WHEREAS, under the Agreement and the statutory law of Ohio, Mr. Freshwater is subject to R.C. §3319.16 and may be terminated for “good and just cause;”

WHEREAS, under Section 3319.16, Mr. Freshwater was provided notice, signed by the Treasurer, of the Board’s intention to consider the termination of his teaching contract(s);

WHEREAS, Mr. Freshwater filed a written statement with the Treasurer on June 30, 2008, requesting a public hearing before the Board;

WHEREAS, the Board requested that a Referee preside over the hearing, as appointed by the State of Ohio Superintendent of Public Instruction, pursuant to Section 3319.16 of the Revised Code;

WHEREAS, a Referee conducted a public hearing, commencing October 2, 2008 and extending through June 22, 2010, with testimony and evidence offered by Mr. Freshwater and the Board;

WHEREAS, the Referee issued a Report on Friday, January 7, 2011, recommending “the Board of Education of the Mount Vernon City School District … terminate John Freshwater’s contract(s) for “good and just cause;”

WHEREAS the Board adopts the Referee’s Report, finding the following conduct as “good and just cause” under Revised Code Section 3319.16 for the termination of Mr. Freshwater’s teaching contract(s):

§ Mr. Freshwater injected his personal religious beliefs into his plan and pattern of instructing his students. In doing so, he exceeded the bounds of all the pertinent Bylaws/Policies of the Mount Vernon City School District;

§ In 2003, Mr. Freshwater unsuccessfully petitioned the Board to allow him “to critically examine the evidence both for and against evolution.” Despite the Board’s rejection of this proposal, Mr. Freshwater undertook the instruction of his eighth grade science students, as if the suggested policy had been implemented;

§ On more than one occasion, Mr. Freshwater was reminded by his superiors that he must abide by the Bylaws & Policies, as they related to religion in the curriculum;

§ Mr. Freshwater’s “evidence” against evolution was based, in large part, upon the Christian religious principals of Creationism and Intelligent Design;

§ Mr. Freshwater’s use of “against evolution” materials ran afoul of the District’s Bylaws/Policies;

§ Mr. Freshwater used unauthorized handouts to challenge evolution, based in large part upon the Christian religious principals of Creationism and Intelligent Design;

§ Mr. Freshwater used motion pictures (Expelled; No Intelligence Allowed) and videos (the Watchmaker) to challenge evolution, which were based in large part upon the Christian religious principals of Creationism and Intelligent Design;

§ Mr. Freshwater taught his students to use the code word “here” when teaching students to question printed materials from science textbooks, which were approved and provided by the Board;

§ Mr. Freshwater taught his eighth grade students that homosexuality is a sin, so anyone who chooses to be a homosexual is a sinner. Mr. Freshwater also taught his students that science and scientists can be wrong when they declare that there is a genetic predisposition to homosexuality;

§ Mr. Freshwater not only injected his subjective, biased, Christian religion based, non-scientific opinion into the instruction of eighth grade science students but also gave those students reason to doubt the accuracy and or veracity of scientists, science textbooks, and/or science in general;

· Mr. Freshwater acted in defiance of direct instructions and orders of the administrators (Insubordination);

§ Mr. Freshwater was directed to remove or discontinue the display of all religious articles in his classroom, including all posters of a religious nature, and whereas, Mr. Freshwater has failed to comply with that directive and, further, has brought additional religious articles into his classroom, in a direct act of insubordination;

WHEREAS, the Referee’s Report has determined that the multiple incidents described above, in total, represent a sufficient bases/grounds for termination; the Board further determines that each individual action independently constitutes “good and just cause” for the termination of Mr. Freshwater’s teaching contract(s), whether considered individually or jointly;

NOW THEREFORE BE IT RESOLVED, that the Board terminates any and all employment contracts of Mr. Freshwater with the Mount Vernon City School District Board of Education. The Treasurer shall furnish Mr. Freshwater with written notice, denoting the Board’s termination of his employment contract “for other good and just cause,” in accordance with Ohio Revised Code §3319.16 and the collective bargaining agreement.

BE IT FURTHER RESOLVED, that Mr. Freshwater’s termination shall take effect at 11:59 p.m. on January 10, 2011.

BE IT FURTHER RESOLVED, that it is hereby found and determined that all formal actions of the Board of Education concerning and relating to the adoption of this Resolution were adopted in an open meeting of the Board, and that all deliberations of the Board and any of its committees that resulted in such formal action were open to the public when required by law, in full compliance with the law.


Mrs. Paula Barone: Yea

Mrs. Jody Goetzman: Yea

Mrs. Sharon Slane-Fair: Yea

Mr. Steve Thompson: Nay

Dr. Margie Bennett: Yea

The foregoing is a true and correct excerpt from the minutes of a meeting of the Board of Education of the Mount Vernon City School District conducted on January 10, 2011.

Freshwater: Terminated


After a nearly two-hour executive session, the Board of Education of the Mount Vernon (Ohio) City School District tonight voted by a 4-1 margin to terminate the teaching contract of John Freshwater. I’ll have a copy of the resolution of termination later, but it was very short. It was read by the mover, Paula Barone, in so soft a voice that my digital recorder didn’t pick it up.

There was essentially no public discussion by the Board after the executive session and little before it. What little discussion there was before the executive session was generated by Steve Thompson, Board member and public Freshwater supporter. Thompson said that he had recused himself from deliberations on the federal litigation (though not from administrative hearing deliberations) on advice from attorneys David Millstone and Sarah Moore (as had Barone), and he wanted to know what was different that allowed Barone to withdraw her self-recusal regarding administrative hearing matters. Thompson said “I find a tremendous amount of hypocrisy in that decision.” The President of the Board, Dr. Margie Bennett, noted that in her letter of recusal Barone had said that various legal advisers, including those from the Ohio School Boards Association, had told her she had no ethical issue with participating in the matter, and Bennett affirmed that Barone had the right to withdraw her recusal. Barone said it was her right and her responsibility to participate in the deliberations.

With that the Board went into executive session, to emerge an hour and forty-five minutes later and adopt the termination resolution. Unless Freshwater elects to appeal to the Knox County Court of Common Pleas, the first step on the state court ladder, that ends this sorry affair.



Photograph by Ken Lord.

Photography contest, Honorable Mention.


Waxing crescent moon, February 2, 2010, Pitt Meadows, B.C. Mr. Lord assures us, “It’s the moon, it’s cosmological! The picture was captured with a Canon T1i DSLR camera at prime focus on a 10-in Meade SN-10AT telescope from my back yard. 1/800 s, ISO 400. 5 exposures of the full view of the moon were stacked together (not a mosaic) in Registax to reduce noise and distortions, producing a sharper final image.”

Freshwater (Updated): Summary of the referee’s recommendation


Update: PDF of the recommendation at NCSE and NCSE’s article on it.

I obtained a copy of the referee’s recommendation (not from any of the principals in the case or their legal representatives) concerning John Freshwater’s termination and summarize it here with heavy quoting. I expect that the full document will be available on NCSE’s site soon, where “soon” is probably Monday.

The Board’s Amended Motion to Consider Termination adopted in June 2008 cited four grounds for the action. The referee addressed all four in his recommendation. They were (summarized briefly):

1. Using the tesla coil to mark the shape of a cross on students’ arms.

2. Failure to adhere to the established curriculum.

3. Participation in (rather than passive monitoring of) Fellowship of Christian Athletes activities.

4. Disobedience of Orders (insubordination).

More below the fold

Freshwater: Referee recommends termination


Knoxpages.com is reporting this morning that R. Lee Shepherd, the referee in the administrative hearing on the termination of John Freshwater as a middle school science teacher in Mt. Vernon, Ohio, has recommended that Freshwater be terminated. I don’t have the referee’s report yet, and will post more when I do. Meanwhile see Adam Taylor’s story at the linked site.

The 1981 Miller-Morris Debate


In 1981 Kenneth Miller and YEC Henry Morris (founder of the Institute for Creation Research) debated whether “… the theory of evolution is superior to the theory of special creation as an explanation for all the scientific evidence related to origins.” Greg Laden has videos of it, as does NCSE’s Youtube channel (audio is from a tape of the debate with visuals added by NCSE staffer Steve Newton), and now NCSE has posted a transcript of the audio here.

Question for commenters: What arguments, if any, do contemporary ID proponents offer that Morris does not? (When commenting on specifics from the debate please give a video number (of four) and an approximate time in the video or transcript so others can locate it,)

Rayleigh scattering


Photograph by Marilyn Susek.

Photography contest, Honorable Mention.

Susek - SunPower.jpg

Rayleigh scattering at sunset, near Ravenfield, UK. The sun is near the horizon, and its rays travel a long distance through the atmosphere, which filters blue light as a result of Rayleigh scattering. The clouds are therefore illuminated by red light and appear red. In this picture the sun is somewhat overexposed and incorrectly appears yellow.

NABT Molecular Insights videos available online


Via the recent Carnival of Evolution, NCSE notes that a series of four videos collectively titled “Molecular Insights into Classical Examples of Evolution” that were presented at the recent Conference of the National Association of Biology Teachers are now available online. They feature Edmund D. Brodie on predator/prey arms races, Allen G. Rodrigo on rapidly evolving viruses, Hopi E. Hoekstra on the genetics of color adaptation, and Sean Carroll on genetic switches and the evolution of form.

Are they fossils of Ediacaran metazoa?


In Ediacaran roots extend deeper in time? Joe Meert described enigmatic fossil impressions that could be interpreted as Ediacaran metazoa (multi-celled animals) from strata some 100 million years older than previously known. Now Chris Nedin, a palaeontologist who has worked with Ediacaran and early Cambrian material, has a comprehensive post on his blog Ediacaran titled “770Ma Ediacara (?) Fossils from Kazakhstan (sadly no)”:

Two questions to be asked then. Are these deposits c. 770 million years old? Are these specimens examples of Ediacaran fossils?

I think the answer to the first question is yes, and the answer to the second question is no. I’ll explain below.

Leave comments here or there; Joe has already commented there.

Jars to Stars


NASA photo.

This article is so far off task that I thought of defining a new category, Way the Hell Off Topic, to complement Slightly Off Topic. But I want to alert anyone who may be interested in the publication of a new book, From Jars to the Stars, by Todd Neff, a book about Ball Aerospace and how they came to shoot a projectile at a comet – and hit it.

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