Photograph by Arthur Rosen.
Alces alces – moose, Denali National Park, Alaska.
I’ve learned that leave has been granted for acceptance of the amicus briefs from the Dennis family and NCSE. The briefs in the case are now complete (see NCSE’s compilation). I’m told that Freshwater requested an expedited hearing, meaning that only the initially submitted briefs–plaintiff’s, defendant’s, and the two amicus briefs–will be in play. The case has been submitted to the appeals court where it will be heard by a three judge panel. They may or may not schedule oral arguments. If they do, I’ll try to be there.
]]>Since January 10, 2012, I’ve been unable to connect to my email or any of the web applications serving Antievolution.org, Austringer.net, and TalkDesign.org from my Verizon FIOS residential internet service account. The servers hosting those are on a Verizon FIOS Business service account.
This isn’t a problem with the servers. I’m able to access everything fine via my smartphone or from other ISPs.
This isn’t a problem just at my house. My parents’ ISP is Verizon FIOS, and they’ve been unable to access the Austringer blog since January 10th, too.
This limits my efficiency on dealing with things if my home internet doesn’t actually get me to the sites I do system administration on and the email where various lists are handled. I’m using AnonymoX just to be able to hit various sites in my browser, which is a real pain.
The favor: If you have Verizon FIOS, try pulling up the Austringer blog. If you have the same problem, your browser will timeout rather than display anything. Please leave a comment saying whether you were successful or unsuccessful in getting the blog. If you are unsuccessful, I’d really appreciate it if you could enter a ticket with Verizon technical support. Reference ticket numbers TXP08R8CY and FLCP08R8EN if you put in your own ticket. I’ve had tickets in since January 10th, but no solution has turned up, and a high-level Verizon network person tonight seemed to be on the verge of cancelling the tickets that are currently active without fixing the problem.
]]>Science Foundation Arizona is sponsoring a postdoctoral scholar program at Arizona State University that offers a really sweet deal:
Bisgrove Scholars will receive an annual stipend of $60,000, benefits and an additional $20,000 per year for research expenses. The Bisgrove appointment is renewable on a year-to-year basis for a maximum initial term of two years, contingent upon the availability of funds.
This program is only open to individuals who have no prior post-doctoral experience and obtain a PhD prior to appointment, i.e. doctoral students in their last year of studies. So while you may be now eating ramen every night in the lab while trying to finish up the last experiment you need to graduate, this time next year, you could be eating ramen sprinkled with gold dust and angel tears, while trying to finish up the last experiment you need for a grant proposal. (Did I mention that rent is cheap here?)
Another qualification is that your research has to fit with the Science Foundation Arizona’s mission: “Areas include, diagnosis and prevention of disease, sustainable energy and the environment, and information and communications technologies at the human interface.”
You will also need to specify possible mentors for your research project. (Hey, I’m available!)
For instructions on how to apply, see http://graduate.asu.edu/bisgrove.
Applications due Feb 15th.
]]>The governor of Kentucky plans budget cuts of $350 million over two years, including $50 million from public education and substantial cuts to higher education – but has managed to find $11 million to build an interchange to a phantasmical Ark Park, according to LEO Weekly, a Louisville alternative newspaper. Presumably the interchange, which will connect to a 1-mile road between Interstate 75 and a town of 3500, will go to roughly the same place as the Bridge to Nowhere or one of its brethren.
The governor, Steve Beshear, reportedly understands that his state “struggles due to the lack of an educated labor force” and admits that his proposed budget “is inadequate for the future needs of our people.” Maybe he should read a recent editorial in Science magazine and ponder whether the poor performance of US students in science and mathematics can be traced to politicians who cut education budgets and pander to anti-scientific crackpots.
]]>Photograph by Arthur Rosen.
Alces alces – moose, Denali National Park, Alaska.
Press release: Genetic data expert to bolster ASU’s high-throughput DNA analytics
Unfortunately, they forgot to mention my collaborator, Prof. Steve Steve.
PS, we are still looking for a postdoc and students.
]]>
Nest of bushtit – Psaltriparus minimus – Walden Ponds, Boulder, Colorado. The nest to the upper right may be an oriole’s nest. Identifications courtesy of Wild Bird Center, Boulder.
Do you know of any graduating or recently graduated baccalaurate students who are considering graduate school? Do they come from disadvantaged backgrounds or belong to underrepresented groups in biomedical sciences? If so, then ASU has a program built for them: ASU PREP.
PREP scholars spend 75% of their time working as technicians on a research project under the direction of an experienced ASU faculty mentor, in a laboratory with PhD graduate students and/or postdoctoral fellows. The program director and faculty advisory committee help scholars identify the research area and mentor that best matches the interests and goals of each scholar. Scholars receive a salary of $21,000 per year. Scholars participate in a one to two year program, dependent on each individualized development plan.
Applicants must be U.S. citizens or permanent residents that have completed their undergraduate degree from an accredited U.S. college or university within the last three years. Applicants must intend to apply to a Ph.D. graduate program within two years. Individuals who contribute to the diversity of the graduate student community and to the biomedical or behavioral sciences, at ASU and nationally, are strongly encouraged to apply.
Application deadline is March 30, 2012
See http://graduate.asu.edu/prep for full details and application instructions.
]]>Update: The Dennis family’s amicus brief is now up on NCSE.com.
The two main briefs in John Freshwater’s appeal of the Knox County Court of Common Pleas’ decision to uphold Freshwater’s termination by the Mt. Vernon Board of Education are now up on NCSE’s site. The two amicus briefs, from NCSE and the Dennis family, have not yet been accepted by the court. NCSE’s brief is on the site linked above; the Dennis’ brief is not yet available online, though I’ve read a copy.
I’ll briefly (!) summarize what I see as the core arguments of the briefs here, and go into more detail below the fold.
Freshwater’s appeal brief: Basically argues that (a) Freshwater only taught “alternative scientific theories”, (b) there are good pedagogical reasons to do so, and (c) he has free speech and academic freedom rights to do so. Also argues that the moves against Freshwater are motivated by religious animus, though it’s silent about specifically who feels that animus.
Board’s response brief: Argues that because student attendance is required and the public school has an interest in protecting itself against the consequences of illegal actions by teachers, Freshwater, as an agent and employee of the public school, does not have unfettered free speech or academic freedom rights. Also argues that the Common Pleas court did not abuse its discretion when it elected to not hold public hearings in view of the extensive record generated by the administrative hearing.
NCSE amicus brief: Puts Freshwater’s behavior in the context of the history of attempts to teach creationism in the public schools, and argues that his teaching was both pedagogically and scientifically unsound.
Dennis family brief: Reviews Freshwater’s impermissible injection of religion into his teaching, and disputes his de-emphasis of the Tesla coil incident, pointing out the inconsistencies in Freshwater’s stories about the incident.
The case is not yet scheduled for oral arguments. I’m told that Freshwater requested an expedited hearing, which I understand means that there will be no back-and-forth, no rebuttals and rejoinders, in the paperwork. What’s there now is what the appeals court will use to make its decision.
Some remarks and elaborations below the fold
]]>Freshwater’s brief claims that teaching about “alternative scientific theories” is pedagogically appropriate and he has free speech and academic freedom rights to do so. As I wrote earlier,
Throughout this argument, the brief refers to multiple “theories”-it refers to “popular alternative theories” (p. v); “various alternative theories” (p. 10); “competing theories” (twice on p. 10); “alternative theories” (p. 12, p. 14); “alternative origins of life theories” (p. 14); and “widely-accepted theories on the origins of life” (referred to as consistent with “the views of multiple world religions” on p. 14). All the references are attempts to represent Freshwater’s presentation of creationist materials as “a permissible and valuable pedagogical exercise” (p. 15) in a [public] middle school science classroom.
Of course, Freshwater did not in fact teach about “alternative scientific theories,” and no evidence was ever introduced to suggest that he did. His handouts, videos, and remarks were from creationist web sites, and were not evidence in support of “alternative scientific theories” but rather embodied the traditional creationist “two models” approach pioneered by the Institute for Creation Research and now most strongly advocated by Answers in Genesis. Knock down evolution and creationism wins by default.
Freshwater’s brief argues that he is permitted to teach about alternative scientific theories in public schools, and the brief claims that’s all Freshwater did. This is a new claim in the Freshwater saga: previously in both public statements and sworn testimony Freshwater has denied teaching creationism or intelligent design. (See also here for a summary of an interview of Freshwater on Fox News; the original clip is apparently no longer available on the web.) So like Freshwater’s mutually contradictory stories about whether he used the Tesla coil to make an “X” on Zach Dennis’ arm or no mark at all (summarized here), Freshwater’s story has…erm…evolved. Apparently he (or more likely, his Rutherford Institute handlers) have implicitly conceded that they cannot rebut the testimony and evidence about Freshwater’s use of creationist handouts and videos and are now attempting to alter the interpretation of that behavior.
This new Freshwater claim made its first appearance to my knowledge in a recent radio interview Freshwater did with David Barton, the notorious quote faker, where Freshwater claimed that he taught “robust evolution.” By that, Freshwater explained, he meant that
I showed what was the evidence for evolution, I showed evidence that was opposed to evolution. I showed all sides. … You need to study it all, especially in a public school. You need to see all the evidence. And there’s some great evidence for, and there’s some great evidence that goes against it. And I think the kids need to see all evidence rather than indoctrinating them only on one side or the other.
He taught the evidence for evolution? One wonders how much comparative genomics and molecular genetics Freshwater, with his Associate’s degree in Wildlife and Recreation and his Bachelor’s degree in education, taught in his 8th grade class. Did he mention the phylogenetics of pseudogenes or that of endogenous retroviruses? I’m fully aware that undergraduate degrees are not the sole determinant of one’s knowledge, but Freshwater has given us no evidence at all that he actually knows much about the evidence for evolution or that he’s competent to assess what “great evidence” is.
Freshwater further argued in his appeals court brief that he has a First Amendment free speech right to teach those alternative theories. This is again a new claim for Freshwater, and reflects the current generation of creationist tactics in state legislatures (see here for an early (1999) account of that tactic, and here for the Disco ‘Tute’s “Free Speech on Evolution Campaign.”)
Board’s response brief
As noted above, Freshwater’s brief claims that he was only teaching “alternative scientific theories.” That, of course, is knee-deep horse manure: Freshwater used a range of creationist materials in an attempt to cast doubt on various scientific findings and science’s strongly corroborated theories–common descent, evolution by natural selection, the reliability of physics in radiometric dating, the reliability of geology in its finding of an old earth, and so on. Further, he argued that he had both the free speech right and the academic freedom to do so.
The Board’s brief rebuts both the free speech and academic freedom claims, citing case law to show that the courts, including the Supreme Court, have consistently ruled that when public school teachers are operating in their role as teachers they do not have the right to teach any damn fool notion they please. The Board’s brief argues that the school has a clear interest in what speech teachers utter in their classrooms, and that the Board can regulate that speech so as to not bring the Board into legal jeopardy. The brief argues that “The Board’s decision [to terminate Freshwater] was appropriately affirmed by the trial court because it has a right to control its own speech. The Board exercised control of its speech by preventing [Freshwater] from continuing to improperly teach religion in class.” The argument is that a teacher is an agent of the Board, and that improper behavior–e.g. impermissible speech–by a teacher exposes the Board to legal jeopardy. It therefore has the right to govern that speech. Freshwater’s injection of creationism into his class was “…made pursuant to his duties as an employee,” and was not made in his capacity as a private individual, which would be protected speech. The Board “…took legitimate and appropriate steps to ensure that one of its teachers did not distort its teaching of science to impressionable eight graders by endorsing Christian religious beliefs” (p. 13).
Further, the Board’s brief argues that the Court of Common Pleas did not abuse its discretion when it denied Freshwater’s request for a public hearing in that court, arguing that the extensive administrative hearing record (38 days of hearings, more than 80 witnesses generating 6,344 pages of transcript, and 350 exhibits) was sufficient basis for the Common Pleas judge to choose not to hold additional hearings and make his decision on the basis of his review of that record.
NCSE’s amicus brief puts Freshwater’s approach into the context of the history of attempts to attack the teaching of evolution. NCSE’s brief reviews the history of creationist attempts to subvert the teaching of science, and identifies Freshwater’s approach as being in the “third generation” of such attempts, the two-prong ‘teach the controversy and push intelligent design’ generation. The entire brief is well worth reading for its succinct review of the history of the issue.
Dennis family’s amicus brief reviews the evidence bearing on Freshwater’s injection of religion into his classroom and his teaching of science, and argues that the minimization of the Tesla coil incident in his appeals brief is inappropriate. It also points out the inconsistencies in Freshwater’s sworn statements about that incident, which are similar to his inconsistency in his statements about whether he taught creationism, sometimes denying it (e.g. in sworn testimony in the administrative hearing) and sometimes affirming it (e.g., in his radio interview on Nov 30, 2011). As noted above, the same sort of inconsistencies are found in his varying claims about whether he taught creationism and intelligent design.
]]>My high school, Athens Academy in Athens, GA, is currently offering an Evolutionary Genetics course to 11th graders (16–17 year olds). They are mostly using an curriculum from the University of Georgia funded through a grant for K-12 evolutionary education development.
Take that creationists.
]]>The other night our local PBS station re-aired a NOVA two-hour special, What Darwin Never Knew. It was pretty cool stuff, and incidentally featured Sean Carroll of UW Madison. I mention that because I want to digress for a moment. I live in Madison and since July of 2009 have been organizing Madison Science Pub. Every month I invite a different UW science professor to come to Brocach Irish Pub on the downtown square and talk about their field to a very interested, attentive, and inquisitive audience. I have an open invitation to Dr. Carroll to come talk, but he always seems to be too busy or something. Yes, yes, I know he runs a lab, and is Vice President for Science Education at the Howard Hughes Medical Institute, teaches, publishes, has a family, etc., etc., but come on, Sean… free beer! There. I’ve said my piece, back to the matter at hand.
]]>The show was full of great stuff, but I had an authentic “oh wow!” moment about halfway through the program. The scene switched to a lake in British Columbia populated by fish called sticklebacks. Species of sticklebacks in the ocean have “a pair of fins on its belly that are like spikes. They are for defense. The spikes make the stickleback hard to eat,” but the lake sticklebacks have lost them.
Researchers David Kingsley and Dolph Schluter wanted to find out how the lake sticklebacks lost their spikes, and went digging through the fish’s DNA. “We know these genetic switches exist. But they’re still very hard to find,” Kingsley said. “We don’t have a genetic code that lets us read along the DNA sequence and say, ‘There’s a switch,’ to turn a gene on in a particular place.”
(In the show transcript Kingsley is identified with the HHMI. Hey, Kingsley, next time you see Carroll getting something out of the vending machine in the hall, remind him about Science Pub.)
Eventually Kingsley and colleagues found the switch, and sure enough it was mutated and no longer turns on the gene that makes spikes. They believe that this has implications for other more distantly related species and might even explain why manatees lost their legs when they left land for water. (I’ve developed this habit whenever I hear something like this to immediately wonder what Answers in Genesis has to say on the matter. Keep reading to find out.)
Additionally, the sticklebacks teased the researchers with a tantalizing clue. From the show, “the lake stickleback may have lost its spikes, but evolution has left behind some tiny remnants: the traces of bones. And they are lopsided, bigger on the left than on the right.”
“Wouldn’t it be amazing if, in fact,” Kingsley said, “this classic unevenness is the signature of using the same gene to control hind-limb-loss in incredibly different animals?” Well, the evidence continued to mount, because Kingsley and team then examined “boxes” of manatee bones and found the same left-right lopsided pattern. Manatees have left pelvic bones bigger than their right.
After the show I plugged “sticklebacks manatees limb loss” into Google and started clicking links. The most laydude friendly post I found, unsurprisingly, was on one of my favorite sites, sciencedaily.com, published on June 4, 2009. It’s an interesting piece and I highly recommend you read it, but I’ll touch on a few points here.
Mike Shapiro, first author on the paper cited in the Science Daily post, said, “We knew that in many cases of evolution, the same gene has been used over and over again - even in different species - to give the same anatomy.” But here the story gets more complicated, because, at least according to this post, different genes may be responsible for the spike loss in different species of stickleback. “This is very surprising because these species are fairly closely related,” said Shapiro.
What’s noted in this piece that was absent from the PBS show is the actual gene responsible for the sticklebacks spikes: Pitx1. Interestingly, in the last paragraph of the post we read, “While the new study shows different genes can control the same trait in two closely related species of sticklebacks, researchers already knew that in some cases, the same gene can control similar traits in distantly related species. Pitx1 controls loss of the pelvis in threespine sticklebacks and is tied to club foot in humans.”
In fact, it looks like Pitx1 was suspected even further back then the NOVA show, or the 2009 Science Daily post, because I also found this paper from the April 2004 issue of Nature. Shapiro and his co-authors closed the paper saying, “Many other populations show the same left-right asymmetry that is a characteristic feature of Pitx1-linked pelvic reduction in mice … Mutations in or closely linked to the Pitx1 locus may contribute to many other examples of evolutionary reduction of pelvic structures in natural populations, a possibility that can now be tested by further genetic studies and direct analysis of Pitx1 structure and regulation in multiple populations, species and genera.”
So it looks like a pretty compelling case for Pitx1, and regulatory switches related to its expression, being responsible for limb loss in many different species, including manatees. What’s interesting after reading up a bit on a topic like this is to search for it on the Answers in Genesis site. The sheer breadth of topics AiG manages to cover is pretty impressive, until you realize that the depth with which they cover them is, well, very unimpressive.
Plugging Pitx1 into AiG’s search engine finds an article called “How Manatees Lost Their Legs?” by Dr. Georgia Purdom. After recapping the basics of the research, she states that “[t]he changes in the regulatory region of the gene are thought to be quite ‘young’ (10,000-20,000 years ago).” Wait, what? I thought that the world was only about 6000 years old! But it’s okay; she’s just reporting what scientists think. She then adds, “[f]rom a creationist standpoint, this change may have happened as a post-Flood event [after about 2304 BC, that is] when rapid speciation occurred as a result of the drastic changes in environment and predator-prey interactions.”
Now prepare yourself for some weapons-grade irony, folks. In the very next section, under the heading “Where’s the Evidence,” Purdom faults the research for extrapolating the possibility that manatees lost their hind limbs through the same mutation and mechanisms that sticklebacks have in the wild, that have caused club feet in humans, that have caused reduced limbs in lab mice (more in the 2004 Nature paper), because the actual genes in manatees have not yet been sequenced to show the mutations.
There is more research to do, no doubt, but it’s more than reasonable after the work the researchers have done so far to think about Pitx1 in other species, including manatees. But for Purdom to make this the central point of her objection to the research after proposing spikeless sticklebacks the result of “a post-Flood event when rapid speciation occurred” is hilarious. If only AiG were held to the same standard for evidence as actual scientists!
If Purdom’s main problem with the research is that Shapiro “has not examined the Pitx1 gene in manatees yet,” wouldn’t this be a golden opportunity for Dr. Purdom, who has a PhD in molecular genetics, to ask Ken Ham for a budget to do the research and show that there is no correlation between Pitx1 and limb loss or reduce pelvis size in manatees? (This is yet another project for the list of unfunded creationist research that I started assembling in my previous post, of course.) I’m sure that Shapiro, Kingsley and a lot of other scientists, would welcome the opportunity to review her published results as she has done theirs.
(This piece is cross-posted to ScienceDenial.com.)
]]>The Cartwright Lab at Arizona State University is seeking Postdoctoral Research Associates in the area of Computational Evolutionary Genetics (broadly defined). The Cartwright Lab is part of The Center for Evolutionary Medicine and Informatics (CEMI), one of 10 research centers in the Arizona State University’s Biodesign Institute.
Research in the Cartwright Lab covers many different questions in population genetics and molecular evolution, at the interface of biology, statistics, and computer science. A majority of our research involves developing, implementing, and applying novel methodologies to study genomic datasets. Potential research topics for postdoctoral research associates include
For more information see http://scit.us/ or http://labs.biodesign.asu.edu/cartwright/.
To apply, forward one document that includes a cover letter, detailed CV, and 3 references to [Enable javascript to see this email address.]. Please put the job title in the subject line of the letter. The initial closing date is January 31, 2012, Applications will continue to be accepted and considered until the job is filled/closed. A background check is required for employment. ASU is an EO/AA employer and is committed to excellence through diversity.
See full ad at http://www.biodesign.asu.edu/jobs/p[…]-12-15-11-54
Contact Dr. Cartwright at [Enable javascript to see this email address.] or 480-965-9949 for more information.
]]>Photograph by David Young.
Bear Lake, Rocky Mountain National Park. Yes, this really is Bear Lake.
Charles Darwin in 1816. Detail of a painting by Ellen Sharples. Public domain.
And the Center for Inquiry provides a short list of resources for campus organizations or anyone else who wants to sponsor an event. In particular, you may contact their speakers bureau to find speakers on evolution, creationism, and intelligent-design creationism (it is a complete mystery why hardly anyone from Panda’s Thumb is on that list, but we will not go into that now). Additionally, Center for Inquiry directs you to the International Darwin Day Foundation, where you may find a list of activities near you, and, of course, the National Center for Science Education.
CFI recommends that you try to teach someone about evolution or other scientific principles and notes that the Public Broadcasting System has a wealth of material on evolution, science, and Darwin. The Understanding Evolution Web page is likewise an excellent resource.
Finally, not mentioned by CFI, the Clergy Letter Project lists 400-odd religious congregations that plan Evolution Weekend activities, February 10-12. Indeed, it may be of interest to some that Science can help church keep its young folk.
]]>As I reported a month ago, the Rutherford Institute, acting on behalf of John Freshwater, appealed Judge Otho Eyster’s decision in the Court of Common Pleas to the Ohio 5th District Court of Appeals. Eyster ruled that the Mt. Vernon Board of Education’s termination of Freshwater was justified on the evidence of the administrative hearing.
Now additional documents are becoming available. The first to be publicly available is NCSE’s amicus brief (pdf). Yet to come are an amicus brief being filed by the Dennis family and the school board’s brief. The deadline for filing is today, January 13, and I expect that final copies will be publicly available soon. When they are I’ll write a longer post summarizing them after I have a chance to read them all.
The case is not yet scheduled for oral arguments before the Court of Appeals. The Court’s schedule is published through February, 2012.
]]>