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?

[Read more…]

So begins my descent into madness

It’s Tuesday, the 22nd of January, and this is the first day of classes at UMM. I’m teaching the introductory biology course again (Fundamentals of Genetics, Evolution, and Development), my big core lab course in genetics, and an upper level class in science writing, and that’s enough.

As is usual for me, I tremble in a state of dread at the start of the long season of lectures and labs, but once I charge in and get started I’ll probably be surprised when I look up and notice it’s May already.

The Minnesota Science Standards are due for review

This is the time — you can give feedback on the Minnesota science standards, and you can also apply to be on the standards writing committee. Here’s where you have a chance to make a difference.

The Minnesota Department of Education is now soliciting feedback from the public on the current Science Standards via an online survey. The survey will be open until February 21, 2008.

First, review the current Science Standards on the Science Standards Web page.

Then take the Science Standards online survey.

Applications are also being accepted for individuals interested in serving on the Science Standards Revision Committee. Before applying to the committee, please read the Assumptions and the Timeline documents posted on the MDE Science Standards Web page. Serving on the committee means a commitment of at least one meeting a month, from March 2008 through February 2009. The initial 2-day meeting is scheduled for March 4-5, 2008, and is required of all committee members. Applicants who are selected for the committee will be notified on or before February 21, 2008. (Applications accepted January 8-21, 2008.)

First, read the Assumptions and the Timeline documents posted on the Science Standards Web page.

Then, apply for the Science Standards Committee.

If you have questions about the Science Standards or the revision process, please contact Clark Erickson, State Science Education Specialist, at 651-582-8753.

Please share this information with your district and school staff, particularly teachers or administrators involved in science education.

If you understand the science and want to contribute to the next set of standards for the state of Minnesota, get to work. Remember, the current standards were written under the malignant influence of Cheri Yecke, and they’re good given the difficulty of the conditions, thanks to the hard work of the previous committee. We can make these standards a shining example for the rest of the country this time.

Books for the Spring 2008 semester

The Fall semester is winding down — this is the last week of classes — so it’s time to start thinking about the Spring term.

Ugh. I don’t want to. This term has been driving me sufficiently insane as it is.

But anyway, if you’re a student thinking about all the money you’ll have to be spending on textbooks, here’s a list of what you’ll need to get if you’re taking my courses. Feel free to order them from some other source than the university bookstore. I don’t get a penny from the U bookstore, but I have to confess, the links below do tie into affiliate programs that give me a few pennies in gift certificates to the various online sources.

  • Freshman biology majors will be taking Biology 1111, Fundamentals of Genetics, Evolution, and Development (FunGenEvoDevo, for short), either in the fall or the spring term. This course is primarily a qualitative introduction to the basic concepts of the scientific method which will also give you an overview of the fields described in the title. It has three textbooks, but two of them are optional.

    • Science as a Way of Knowing: The Foundations of Modern Biology(amzn/b&n/abe/pwll), by John A. Moore. This is the primary required text for the course; you may be surprised when you read it, since it doesn’t fit the usual expectations of an introductory biology textbook. We did tell you this was a liberal arts university when you enrolled, though, didn’t we?

    • Life: The Science of Biology(amzn/b&n/abe/pwll), by David Sadava, H. Craig Heller , Gordon H. Orians, William K. Purves, David M. Hillis. This book is optional, but highly recommended, and will be used as a reference text throughout the course. You can get by using the copies in the reference section of the library, but since this book will also be used in our required biodiversity and cell biology courses, you might as well bite the expensive bullet and get a copy now. The links above are to the 8th and latest edition; it’s fine to use the 7th edition.

    • The Counter-Creationism Handbook(amzn/b&n/abe/pwll), by Mark Isaak. This book is an entirely optional resource; if you’re going to be a biologist, though, you’re going to have to argue with creationists sometime, and this text is invaluable. We will, however, only be using it for about a week, so if it breaks your budget, feel free to share another student’s copy.

  • I’ll also be teaching Genetics, Biology 4312.

    • Concepts of Genetics(amzn/b&n/abe/pwll), by William S. Klug, Michael R. Cummings, and Charlotte A Spencer. It’s a solid textbook of transmission genetics.

It all sounds so fun, doesn’t it?