Godawful academic mess

Several people have asked me to dig into this and post something on Pharyngula, but I really don’t want to — the more I look at it, the more I recoil in baffled disgust. Cedarville University, one of those bizarre Christian colleges that just makes me want to gag in the first place, has terminated the contracts of two tenured faculty, David Hoffeditz and David Mappes, in their biblical studies department. Right away, I oppose the action of the university on general principles: short of engaging in some kind of criminal behavior, it’s a key part of academic freedom that tenure means the freedom to explore any intellectual path, no matter how weird. I even support Michael Behe’s tenure at Lehigh, and you all know how looney I think he is.

So what did Hoffeditz and Mappes do to earn revocation of tenure? Rob a bank, seduce a student, make death threats to Howard Stern? None of the above: they chose sides in an extremely abstract and utterly useless theological debate.

A theological impasse dividing Cedarville’s campus has also played a role in the controversy. Known as the “truth and certainty debate,” the dispute involves a somewhat rarefied but hotly contested question of faith: Can Christians enjoy certainty of Biblical truth, or do they merely have the assurance of their faith that the Bible is factual?

It is a question that folds into a still larger debate over how much Christianity should reconcile with the intellectual context of postmodernity. Those who hold to a belief in certainty, Mr. Hoffeditz and Mr. Mappes among them, tend to consider themselves more theologically conservative.

Those theological themes figured prominently in the open letter written this January to the faculty, administration, and trustees of Cedarville by a group of 14 current and emeritus Cedarville faculty members–a group calling itself the “Coalition of the Concerned.”

That letter refers to Mr. Mappes and Mr. Hoffeditz–and also to three other professors who either resigned or were denied tenure in the 2006-7 academic year–as “theologically conservative” members of the Bible department. “There is fear that other theologically conservative members within the department and the general faculty may be terminated,” the letter says.

It’s like watching two groups of clowns arguing over the brand of cream pie filling they should use, only less substantial. It just confirms my opinion that any parent who sends a child to Cedarville is doing them a criminal disservice — please send them to a real college, OK?

However, it also looks like Cedarville doesn’t really have academic freedom — the point of academic freedom is that you don’t get to fire professors for holding views that you find objectionable, and that’s exactly what is going on here. On top of all that, the American Association of University Professors is investigating the case, and they’ve said flat out that it’s problematic because church-related institutions have “explicit limitations on academic freedom” … which is to my mind grounds for denying them the privilege of being called an institution of higher education in the first place.

Evolution 2008 is for teachers

Teachers, come to Minneapolis this summer! Not for the Republican convention, but for the other great big important meeting that will be taking place: Evolution 2008.

Teachers in particular get a really good deal: a special workshop is planned, specifically on the teaching of evolutionary biology in the schools. We’ve got some good speakers (and me) lined up, and the registration cost of a mere $20 not only gets you into the workshop, but into the regular meetings as well. Here are the details:

Evolution 101 Workshop for K-12 Educators
Friday, June 20, 2008
Bell Museum of Natural History
University of Minnesota
.625 CEUs

One $20 registration also gives K-12 teachers access to sessions and symposia by the sponsoring scientific organizations, as well as social events and keynote speakers for the full conference, June 20-24.

The EVOLUTION 101 workshop provides K-12 educators with information to effectively teach evolutionary biology in public and private school science classrooms. The workshop provides teachers the opportunity to interact with professional scientists who are eager to encourage evolutionary pedagogy. With one registration, K-12 teachers will also have access to presentations by the professional organizations, as well as keynote speakers for the full conference, June 20-24.

Registration: $20 non-refundable

A certificate of completion and .625 Continuing Education Units will be awarded for attendance at this workshop.

For more information about this workshop and to register on-line, please visit:
http://www.cce.umn.edu/conferences/evolution/evolution_101.html

The workshop is sponsored by the Society for the Study of Evolution (SSE), Minnesota Citizens for Science Education (MnCSE), and the Bell Museum of Natural History, with the generous financial support of the ADC Foundation.

The University of Minnesota is an equal opportunity educator and employer.
© 2008 Regents of the University of Minnesota. All rights reserved

Are our high schools teaching evolution?

Blogging on Peer-Reviewed Research

The Ecological Society of America has just published an article that surveys the state of science teaching in the US. Some of the results are somewhat reassuring — the majority of our college-bound high school students are at least getting exposed to evolution to some degree — but they’re also getting taught creationism to an unfortunate degree. Here’s the abstract to give you the gist of the story.

How frequently and in what manner are evolution, creationism, and intelligent design taught in public high
schools? Here, I analyze the answer to this question, as given by nearly 600 students from major public universities nationwide in a survey conducted during the spring of 2006. Although almost all recent public high-school graduate respondents reported receiving evolution instruction, only about three-quarters perceived that
evolution was taught as a “credible scientific theory”. Creationism and intelligent design were reportedly presented almost one-third and one-fifth of the time, respectively, though respondents recalled that both concepts
were presented as lacking scientific credibility much more often than not. The survey results are presented in
composite form and also disaggregated with respect to the strength of evolution-related state standards, red
state-blue state divisions, and the regional location of states within the country.

You can also hear the author discussing the methodology and results in a podcast, which I think is a wonderful idea. (Maybe every paper should be accompanied by a 15 minute podcast in which the author explains the work to a general audience…).

Here’s the good news/bad news data.

i-e964a4c7747b7e9f698a455ed2d71f36-inst_freq.jpg
(Click for larger image)

The good news: look at that, 92% are getting taught about evolution to varying degrees. I also think it’s good news that 26% say they’re getting “in depth” instruction, although, of course, this is self-reported by students who probably don’t know how much depth there is. At least this tells me that a solid majority of teachers are trying, and are not silenced by pressure from the public.

The bad news: 30% are getting taught about creationism, and 20% are learning about intelligent design. That’s a waste of time and resources, and it’s an indicator that the urgings of creationists for a false “fairness” might be having some effect.

Now, of course, maybe they’re learning about creationism in high school because the teacher is slamming it as bogus nonsense, as I do in my university classes. There’s a little good news there, too: over 70% of the time, evolution is taught as credible theory, but as for creationism…

Additionally, when intelligent design is taught, it is
perceived to be presented as a credible scientific theory at
a rate higher (34%) than that for creationism (18%).
This confirms one of the few narrow points of agreement
between intelligent design’s proponents and critics: intelligent design is intended to look more “like science” and
less “like religion” — and to these recent public high-school graduates, it does.

So we can say that the majority of the time creationism is taught, it is disparaged to some degree and is not taught as a credible scientific theory. That’s reassuring. Of course, we could take a glass-half-empty view and note that in those cases where ID is taught, it’s taught as a credible theory an appalling third of the time, and it’s also a successful strategy for boosting the reputation of creationism.

The situation isn’t quite as bad as I feared, although there is a significant minority that are getting taught creationism uncritically in the public schools. What I’m missing is a couple of things. This is information taken from a select population of college bound students, and those students are more likely to have had exposure to science, and are also more likely to be attentive. I’d like to know what impressions other students have of their science instruction.

This is also a collection of exactly that, student impressions. I’d like to see a complement to this study that surveys actual curricula and faculty attitudes. I know how tuned out students can be, so I can’t say that I entirely trust student reports.

Bowman KL (2008) The evolution battles in high-school science classes: who is teaching what? Front Ecol Environ 6(2):69-74.

We have an image problem

RPM has put up an amusing bestiary of typical science seminar attendees — it’s all true, I’ve seen all of those people.

But you know what the problem is? It’s a collection of pedants and old people! Where are the celebrities misbehaving in our talks? Maybe we’d get more attention for science if we had a Paris Hilton vamping around, or a Britney Spears breaking down and flashing her anatomy, or a Mel Gibson getting drunk and haranguing the speaker about his Jewish background, followed by a Chris Crocker histrionic shrieking at everyon to leave the speaker alone.

Scientists are a pretty dry and sedate lot, I’m afraid. I’ve never seen anyone like that at a seminar.

Full-Time, One-Year Faculty Position at UMM Biology

Full-Time, One-Year Faculty Position in Biology
University of Minnesota, Morris

The University of Minnesota, Morris seeks an individual committed to excellence in undergraduate education, to fill a full-time, one-year position in biology beginning August 18, 2008. Responsibilities include: teaching undergraduate biology courses including an introductory level survey of organismal biology (with lab) and a core ecology course (with lab); advising undergraduates; and sharing in the governance and advancement of the biology program as well as the campus at-large.

Candidates must be at least A.B.D. in ecology, organismal biology or a closely related field. One year experience teaching undergraduate biology is required. (Graduate TA experience is acceptable.)

The University of Minnesota, Morris (UMM) is a nationally-recognized, small, selective, residential, undergraduate liberal arts campus of the University of Minnesota. It has an enrollment of about 1650 students with 120 faculty members. The campus is located in west-central Minnesota, 160 miles from Minneapolis, in a rural community of 5000 people. The college is organized into four academic divisions, of which Science and Mathematics is one. Disciplines represented in the division are Biology, Chemistry, Computer Science, Geology, Mathematics, Physics, and Statistics. The college attracts excellent students many of whom go on to graduate or professional studies. Visit www.morris.umn.edu/positions/ to learn about other open positions at UMM.

Excellent fringe benefits and a collegial atmosphere accompany the position. Appointment will be at the Assistant Professor level for those having the Ph.D. in hand and at the Instructor level for others. The standard teaching load is twenty credit hours per year.

Applications must include a letter of application, resume, transcripts, a teaching statement (in which teaching goals and methods are discussed), and three letters of reference. Send applications to:

Biology Search Committee Chair
Division of Science and Mathematics
University of Minnesota, Morris
600 East 4th Street
Morris, MN 56267-2128

Applications will be accepted until the position is filled. Screening begins March 14, 2008. Inquiries can be made to Ann Kolden, Executive Office and Administrative Specialist, at (320) 589-6301 or koldenal@morris.umn.edu.

The University of Minnesota is committed to the policy that all persons shall have equal access to its programs, facilities, and employment without regard to race, color, creed, religion, national origin, sex, age, marital status, disability, public assistance status, veteran status, or sexual orientation.

A most unsatisfying resolution

The Warda and Han paper has been officially retracted, and the editor has made an official statement, as reported in the Chronicle of Higher Ed.

The paper has drawn a blizzard of criticism in the blogosphere about the peer-review process at the journal, Proteomics. The editor of the journal, Michael J. Dunn, a professor at University College Dublin’s Conway Institute of Biomolecular and Biomedical Research, told The Chronicle last week that the paper had passed peer review.

Today’s announcement says that the two authors of the article, who are scientists at Inje University, in South Korea, agreed to the retraction. Initially only one of the authors had asked for a retraction.

In the news announcement, Mr. Dunn said: “Clearly human error has caused a misstep in the normally rigorous peer review that is standard practice for Proteomics and should prevent such issues arising.”

The plagiarism is bad all right, but my main concern was that such a blatantly goofy paper made it through peer review. How? All Dunn is saying is that it did pass review, which suggests that somehow, someone read it and didn’t pull the alarm, and even approved it. Was it a lazy reviewer? Or was it some other kind of hole in the process? “Human error” is an awfully vague label.

We may not ever get an answer, but you know everyone will be scrutinizing Proteomics papers critically. Other journals, too, of course — a reader just sent me another freaky paper that I’ll describe tomorrow.

One author responds

I’ve received email from one of the authors of that bafflingly bizarre paper on mitochondria. I’m still confused.

Dear Dr. Myers

First of all, I am very sorry for that trouble for you.
I found the serious mistakes in the paper during the process of edits, which I confused between the early drafts and the latest versions: I did not check the use of the sentences in the references (more than 200 references). Finally I made serious error to make the final version.
In order to rectify an error, I requested to retract the paper to the editorial office of Proteomics.
Thank you very much for indicating this carelessness.
Based on this good experience, I will study science and prepare a manuscript with caution.
Again, I am very sorry for that trouble for you.

With best regards,

Jin Han

The author is clearly not a native speaker of English, but I can’t criticize that — his English is far better than my Korean. The explanation that this was just a confusion of an early draft simply doesn’t work. We are talking about a peculiar title and a specific, grammatically correct assertion made in the abstract that is not supported in the text, except by a claim of a “mighty creator”. Where did that come from? One of the authors? Someone who assisted them in polishing the language? The instance of plagiarism are also left dangling.

It also doesn’t address the other concern here. If we accept the idea that Warda and Han made a clumsy mistake and submitted the wrong draft, one that was full of errors, we’re still left with the question of how that mess made it through peer review to the stage just prior to publication. Something broke somewhere, and one unfortunate consequence of the retraction of the paper by the authors is that we may not find out what.

The authors don’t need to apologize, especially not to me. All I’m interested in is tracking down how a paper that is so thick with warning signs could get so far through the review process.

Is that David Horowitz I smell?

The beautiful state of Washington, my native home and still home to many of my family members, has some people ready to enact some major legislative stupidity. David Horowitz was a right-wing nut who was making noise a few years ago with his witch hunt for evil leftists (Hi, Michael!) and his promotion of an Academic Bill of Rights, which was basically a ham-handed attempt to force academia to grant special privileges to intellectually bankrupt ideas, all under the guise of “fairness”. The Washington bill reeks of that familiar stench.

This bill aims to impose the ideological biases of ignorant politicians on the curricula of the state’s universities. It claims to be about “intellectual diversity,” but it’s really about stripping intellectual responsibility from the hands of professors. You can read the whole thing, but as an example of the kind of superficial promises the bill wants to make, but which do little more than corrupt the integrity of the classroom, look at this clause:

Develop a procedure in which a student may present his or her objection to a classroom assignment due to its opposition with the student’s conscience.

What, exactly, is a student’s conscience here? Well, if a UW biology professor tries to demand her students understand the mechanisms of evolution, a creationist student could formally demand accommodation for his beliefs. A chauvinist in a feminist history class could demand a better grade for his paper claiming that women have been oppressing him because they keep turning down his demands for dates. Basically, it throws the doors wide open and allows students to turn their subjective, poorly formulated, or even falsified “objections” into legitimate excuses to subvert the classroom…which is exactly the intent of deranged ideologues like Horowitz.

I know some Washington state residents read this blog. Get on the phone or email to your representatives and tell them that SB 6893 is a disaster in the making and that they better not support it. In particular, if your rep is on the Committee on Higher Education (which contains two of the sponsoring senators, unfortunately — Shin and Delvin) make sure to voice your displeasure and let them know that anyone who supports this abomination of a bill is no friend to higher ed.

A baffling failure of peer review

A dismaying update: the paper in question contains a significant amount of outright plagiarism, and large chunks of text are taken literally from Butterfield et al. 2006, “Oxidative stress in
Alzheimer’s disease brain: New insights from
redox proteomics,” European Journal of
Pharmacology 545: 39-50. I hope we hear from Han and Warda sometime; they’ve got a lot of ‘splaining to do.

Mitochondria are fascinating organelles. They are the “powerhouses of the cell” (that phrase is required to be used in any discussion of their function) that generate small, energy rich molecules like ATP that are used in many cellular chemical reactions, but they also have important roles in cell signaling and cell death. They also have a peculiar evolutionary history, arising as endosymbionts; their ancestors were independent organisms that took up residence inside eukaryotic cells in a mutually happy and long-lasting relationship. They exhibit some interesting relics of that prior history, as mitochondria have their own private strand of DNA which encodes some of the genes needed for the chemical processes they execute. Other genes for those functions have migrated over evolutionary time into the nuclear genome, which means the mix of gene products operating in the organelle are from two sources, the mitochondrial and nuclear genome. It’s a good subject for studies in proteomics.

Right now, there is a paper that is available as an Epub ahead of print in the journal Proteomics. It is not promising. In fact, all you have to do is read the title to make you wonder what the authors, Warda and Han, were smoking: “Mitochondria, the missing link between body and soul: Proteomic prospective evidence.”

Attila Csordas asks, “Can you tell a good article from a bad based on the abstract and the title alone?”, and I’m inclined to say yes. Sometimes you get pleasant surprises in the full paper that were not well described in the abstract, but when the abstract and title contain hints that the bridge is out and that somebody has switched the train to the wrong tracks, you can predict that there will be a train wreck if you read further. Here’s the abstract. I’ve highlighted one provocative statement.

Mitochondria are the gatekeepers of the life and death of most cells that regulate signaling, metabolism, and energy production needed for cellular function. Therefore, unraveling of the genuine mitochondrial proteome, as the dynamic determinant of structural-functional integrity to the cellular framework, affords a better understanding of many still-hidden secrets of life behind the already known static genome. Given the critical mitochondrial role under different stress conditions, the aim of the current review is to merge the available scientific data related to mitochondrial proteomes and frame them into a reliable new agreement extending beyond the limited already accepted endosymbiotic hypothesis into broader fundamental mechanisms orchestrating cellular outcome on behalf of cell survival. The focus of this work is to cover first the mitochondrial proteome/genome interplay that is currently believed to be implicated in a range of human diseases. The mechanochemical coupling between mitochondria and different cytoskeleton proteins and the impact of the mitoskeleton on mitochondrial structure and function are then addressed. Further crosstalk between mitochondria and other cellular organelles, e.g., the ER and the nucleus is then discussed. Additionally, the role of mitochondria in apoptosis and the mitochondrial contribution in intercellular communication mediated by gap junctions are also described. These data are presented with other novel proteomics evidence to disprove the endosymbiotic hypothesis of mitochondrial evolution that is replaced in this work by a more realistic alternative. Furthermore, the role of mitochondria in development of oxidative stress-based diseases, e.g., neurodegenerative and cardiovascular diseases is pointed out together with the prospective proteomics view as an alternative prognostic and diagnostic tool for interpreting many mitochondria-related anomalies. The insights generated by recent proteomic research that provide a rational impact on possible mitochondrial-targeted therapeutic interventions are also discussed.

My blog makes a career out of describing train wrecks, so how could I not continue on and read the paper?

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