Peptides publishes a clunker

I’ve got my hands on a strange paper by D Kanduc: “Protein information content resides in rare peptide segments”. Here’s the abstract.

Discovering the informational rule(s) underlying structure-function relationships in the protein language is at the core of biology. Current theories have proven inadequate to explain the origins of biological information such as that found in nucleotide and amino acid sequences; an ‘intelligent design’ is now a popular way to explain the information produced in biological systems. Here, we demonstrate that the information content of an amino acid motif correlates with the motif rarity. A structured analysis of the scientific literature supports the theory that rare pentapeptide words have higher significance than more common pentapeptides in biological cell ‘talk’. This study expands on our previous research showing that the immunological information contained in an amino acid sequence is inversely related to the sequence frequency in the host proteome.

What? This is an intelligent design paper? How interesting. Unfortunately, the abstract is wrong, and ‘intelligent design’ is not a popular way to explain information in biological systems, and I read through the whole thing, and missed the part where it actually supports ID.

Here’s what the paper actually does: it dissects a sample protein and asks about the frequency of its components in the proteome. It looks specifically at calmodulin (CaM), an important and highly conserved protein that is involved in all kinds of developmental and physiological interactions. The rather arbitrary unit the protein is broken down into is 5 amino acid chunks, or pentapeptides, and each pentapeptide sequence is searched for in genes other than CaM. If this is the initial sequence of CaM,

MADQLTEE…

Then what Kanduc does is search the proteome for MADQL, ADQLT, DQLTE, etc., and count the number of times each appears. Rare pentapeptides are equated with high information content, and common ones are assigned low information content. Some pentapeptides, in his analysis, are found only in CaM, while others are found multiple times, with an average of 12 occurrences. This is supposed to be significant.

It’s also where he loses me. If you search a completely random string of amino acids for an arbitrary pentapeptide, it should turn up, on average, once in every 3,200,000 amino acids. If you search a long enough chunk of amino acid sequence, one that’s long enough to generate on average 12 hits, what you’d expect to see is a bell-shaped distribution — some pentapeptides may appear only once, while others appear dozens of times, just by chance. And that is what Kanduc sees. That some pentapeptides are unique to CaM is perhaps not too surprising, especially when you consider that the proteome is not a random sequence at all, but the product of frequent gene duplications and is also refined by selection.

So far, this idea that some pentapeptides will be rare and others common, is utterly uninteresting and unsurprising. I would have liked to have seen some consideration of the null hypothesis, that the distribution is due to chance alone, but that seems to be totally lacking. If I’d been reviewing the paper, I would have sent it back with a request for revisions to consider that possibility.

However, Kanduc does propose something that actually is interesting: that the rare pentapeptide sequences in specific genes also correlate with regions that have important functional roles.

Using the CaM features, attributes and annotations reported at www.uniprot.org/uniprot/P62158, we find that modification sites, structural beta strand motifs, functional domains, and epitopic determinants are confined primarily to areas of low similarity with the human proteome.

Now that’s kind of cool, if true. It’s also a bit unsurprising. He does examine the length of the CaM protein and show that rare pentapeptide regions are also sites for for acetylation, ubiquitylation, and phosphorylation, and also at the calcium binding site, for instance; but these are functional regions of the protein where one would expect some selection for specific properties. We get a different analysis, in which naturally occurring pentapeptide fragments that are known to have significant biological activity are searched for in the human proteome, and found to be fairly rare. Again, this might be an expected result explained by selection — after all, a sequence that can trigger apoptosis might be expected to be confined by selection to a limited range of sites — and don’t seem to me to require postulating an intelligent designer.

As a paper that hints at some possible functional correlations in the proteome, it’s mildly diverting. It’s weak in that it doesn’t address the null hypothesis very well — I get the impression the author is more interested in fishing for correlations than in actually testing his hypothesis. Where it starts triggering alarm bells, though, is the shoutout to creationists. Kanduc says this about CaM:

…the CaM sequence is characterised by both specificity and complexity (what information theorists call ‘specified complexity’); in other words, it has ‘information content’.

Uh-oh. “Specified complexity” is a meaningless phrase; the creationists have not defined how to measure “specification”. In this case, Kanduc hasn’t either, and his criterion for calling it “specified complexity” is that CaM has various functional domains, which is kind of expected for a protein that has functions. I find it interesting, too, that he doesn’t provide a citation for his claim — Dembski doesn’t get an acknowledgment. Probably because it would be a too-obvious hint about where in looney-land this idea is coming from, and because Dembski doesn’t bother to explain how to calculate “specified complexity” either.

Also, there’s something suspicious about the phrasing there — it seems to be straight out of Meyer 2000:

Systems that are characterized by both specificity and complexity
(what information theorists call “specified complexity”) have
“information content”.

Hmmmmm. (Thanks to Blake Stacey for picking up on that identity.)

Another problem with the paper is the conclusion, which is some unholy amalgam of a dog’s breakfast and a word salad, and either way is grossly unappetizing.

Researchers in the fields of biology and immunology need to define objective informational entities and reductionist basic laws that are valid everywhere and for everything. As new objects and scientific laws are absorbed into experimental protocols and reports, abstract terms such as “sense”, “edit”, and “attack” as well as old dogmas such as the self/non-self dichotomy will become obsolete in favour of more intelligible and concrete theories and biological activities. This process will enable the effective translational application of science to medicine.

What the heck does that mean? What does it have to do with the rest of the paper? Again, if I’d been reviewing it, that would have gone back with a recommendation to delete the gobbledygook and write a conclusion that actually makes sense in the light of the rest of the paper.

What we have here is yet another case of poor reviewing and editing. There is a germ of an interesting observation in the work that the author fails to examine critically and convincingly, but the main intent seems to be to inject the words “intelligent design” into a reviewed scientific paper (while failing to justify why that is a useful hypothesis) and for the author to ride some obscure immunological hobbyhorse which is also not addressed by any of the data. It’s remarkably sloppy work that should have been sent back for extensive revision, rather than being published as is.

I do notice that it was received at Peptides on 20 January, and then bounced back and accepted after what must have been only minor revisions only two weeks later. The journal is commendably fast in its turnaround, but this looks like a case where haste just churned up the garbage a bit more.

Kanduc D. Protein information content resides in rare peptide segments, Peptides (2008), doi:10.1016/j.peptides.2010.02.003

Melissa Hussain committed Thought Crime!

And she may be fired for it.

Hussain is an eighth grade science teacher in North Carolina who was getting harrassed by bible-thumping students in her classroom — harrassment that was apparently encouraged by their red-necked ignorant parents. The kids were giving her Bibles and Jesus postcards and reading Bibles instead of doing their classwork, and seemed to have enjoyed flaunting their dumb-ass religiosity at her. So she vented on Facebook. The parents got indignant that she would dare to express her unhappiness with their darling little children, and are pressing to have her fired — but the curious thing is that the only comments they quote all seem reasonable and moderate.

Hussain wrote on the social-networking site that it was a “hate crime” that students anonymously left a Bible on her desk, and she told how she “was able to shame” her students over the incident. Her Facebook page included comments from friends about “ignorant Southern rednecks,” and one commenter suggested Hussain retaliate by bringing a Dale Earnhardt Jr. poster to class with a swastika drawn on the NASCAR driver’s forehead.

Notice that other people are making rude comments about the Bible-thumpers (and I feel the same way), not the teacher. That was the worst they could find? That she rejects religious harrassment and shamed her students to get them to stop doing it?

Here are some more atrocities from her Facebook page.

Parents said the situation escalated after a student put a postcard of Jesus on Hussain’s desk that the teacher threw in the trash. Parents also said Hussain sent to the office students who, during a lesson about evolution, asked about the role of God in creation.

On her Facebook page, Hussain wrote about students spreading rumors that she was a Jesus hater. She complained about her students wearing Jesus T-shirts and singing “Jesus Loves Me.” She objected to students reading the Bible instead of doing class work.

But Annette Balint, whose daughter is in Hussain’s class, said the students have the right to wear those shirts and sing “Jesus Loves Me,” a long-time Sunday School staple. She said the students were reading the Bible during free time in class.

“She doesn’t have to be a professing Christian to be in the classroom,” Balint said. “But she can’t go the other way and not allow God to be mentioned.”

I think teachers have a right to complain when their students and their students’ parents spread rumors and are disruptive in class. And yes, singing “Jesus Loves Me” during science class is inappropriate, a waste of time, and a transparent attempt to taunt the teacher. I also doubt that there is such a thing as “free time” in a science class: more likely, they’re given time to work as individuals or groups on classwork, and reading their Bible is not getting their work done. Eighth grade science class is not Sunday School, although I guess some retrograde retard might understandably confuse the two.

And of course Hussain is getting no support.

Thomas and Jennifer Lanane, president of the Wake County chapter of the North Carolina Association of Educators, said she wasn’t aware of the details of the Hussain case, but said that teachers need to be careful about information they put online.

“We are public figures,” Lanane said. “We are held to a higher standard.”

Quit your jobs, Lananes. You should be ashamed. Stand up for the educators you supposedly represent; I do hold teachers to a higher standard, a standard that involves honesty and integrity and service to their discipline. The Lananes know nothing about this case, but are willing to throw a teacher who struggled with a classroom of militant morons to the wolves. Idiots who confuse “held to a higher standard” with refusing to challenge their students or bowing to community pressure, instead of to being forthright and outspoken, are the peril here.

I support Melissa Hussain. She sounds like a fine teacher who made entirely appropriate responses in a difficult situation, and I want more teachers who are willing to oppose the willful stupidity of communities full of science-hating throwbacks who want to impose Sunday School ‘rigor’ on science education.

Tragedy at the University of Alabama Huntsville

Tenure reviews are extremely stressful: imagine a job evaluation in which you may be told that you’ve been doing a fine job, you’re doing interesting work, but you aren’t quite as dazzling as your employer would like…so you’re fired. And then, because academic jobs in your specialty are scattered very thin on the ground, you get to spend a year struggling to find a new position (with the same horror show finale possible), and pack up and move to a completely different part of the country, uprooting all your connections that you may have built up over the last 5 or 6 years. What makes it even worse is how much you lose, since if your tenure committee approves you, you get a secure job for the rest of your life.

The stresses do not excuse Amy Bishop, however, who attended her tenure review meeting and when it did not return a favorable result, pulled out a gun and murdered and wounded her colleagues. Three are hospitalized with injuries, one is in critical condition; these three are dead.

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Gopi Podila
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Maria Davis
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Adriel Johnson

I’m horrified. Good people with years of training and years of productivity ahead of them, with families and loved ones left behind, all wiped out in a flash of insanity, and leaving a body of students who are going to be scarred by this one awful event.

I’m also dismayed — I’ve been at meetings like that many times, where we walk in with trust in our colleagues that the worst we will face is a bitter intellectual argument. I’ve sat at tables with my fellow faculty lined up around them, and never before thought how easy we’d be as targets for one mad person to fire upon. The ease of access to handguns is a great social evil, one that too easily simplifies the conversion of disagreement into lethal combat.

Express your anger and grief here, or on Drugmonkey’s open thread.

Abel has more on her academic status — she seems to have had active grants and a foothold in industry.

And holy crap — Bishop shot and killed her brother in a shotgun accident in 1986! Or maybe not so much an accident — some reports say it was during an argument.

You can’t even trust ELCA

There are a lot of small four year colleges around, and the competition is tough. We feel it at my university, the University of Minnesota Morris, and it’s difficult because we can’t honestly say that all those other colleges are bad — they’re actually very good because they value the same advantages that we do — small class sizes, personal attention to every student, a curriculum that emphasizes breadth of knowledge and the integration of ideas. So it’s always good to see some place where we, as a secular and public liberal arts university, have a clear advantage.

Concordia College is one of our peer institutions, and they certainly do offer a good education. But like many of the small private colleges around, they are affiliated with a religion, in this case the Evangelical Lutheran Church of America. Like most of these colleges, though, they’re not dogmatic about their faith, and you can attend no matter what your religion, or lack of it (colleges that demand adherence to one faith are not our peers at all — they tend to be crap colleges anyway). However, sometimes the board of trustees, or whatever organization is managing the place, will meddle. Such meddling has occurred at Concordia.

The college denied the formation of the student organization Concordia Atheists-Secular Students at Concordia College on the basis that atheism is not in compliance with “college standards,” despite the support it received from the Campus Ministry Office.

What “college standards” do atheists not meet? Are we not equal members of the Concordia community? Do we not share the same rights to express our religious views as those that participate in Sunday Night at East or in Tabernacle?

According to the most recent Concordia College Factbook published for the 2008-2009 academic year, upwards of 16 percent of the school population reports no religious affiliation. The group already has 60 members on Facebook, which, just as an example, is 37 more members than the Campus Republicans (a recognized organization) can claim. How can a school deny the recognition of such a sizable minority of its students?

How can they do it? Easy. The college is founded and run by blinkered faith-heads — liberal ones, but still a group with peculiar, irrational biases, and sometimes those biases will flare up and slap students in the face.

The solution is easy, though. If you’re thinking of going to college, or have children who will be going to college, you should look into small liberal arts colleges — they really are phenomenal places for learning. But you should also emphasize that you want to attend a secular, public liberal arts college; one that doesn’t give a damn about your religion. Like (shameless plug) UMM.

We also welcome transfer students.

California crazy

Two distressing news stories out of that wealthy western state:

  • Berkeley High School has a serious problem: it’s a good, relatively well-funded school, but black and latino students aren’t doing as well as white students. Their solution: kill those expensive science labs and redirect the money to remedial classes. Science classes with no labs? Inconceivable! That’s what a body of earnest, well-meaning, and apparently scientifically illiterate parents and teachers have decided to do.

    You cannot learn about science without doing science. It’s like deciding to continue to teach theater and music, but without that troubling and time-consuming business of performing. Or like having a football program that never plays any games (I know, that one is pure fantasy…discontinuing a football team is much, much harder than simply shutting down teaching labs).

    I’m also surprised at the casual bigotry in the proposal. Demolishing their science program won’t hurt black and Latino students? Right. When I taught at Temple University, the biology labs were full of ambitious black students scrambling to pick up those essential, basic lab skills that they needed to be doctors and nurses someday…skills that were not taught in the impoverished urban schools of North Philadelphia. Is Berkeley training their minority students to be part of the cutting edge of science and technology and medicine, or are they more interested in turning out service workers for Taco Bell?

  • Here’s another tricky situation: the California Science Center is being sued for turning away the showing of an intelligent design creationism movie. It’s a tough case, because public institutions should be interested in presenting arguments for issues in science — even if it is a controversial story, the answer to abuses of free speech is more free speech.

    However, there are other parts of this story that mean I can’t just jerk the ol’ free speech knee. One key point is that what the movie was presenting was not a scientific controversy at all—seriously, any movie that tries to present the Cambrian as a serious problem that makes evolution impossible is celluloid trash. Because the venue can be leased should not imply that the CSC is open to anyone showing home movies, or to the latest porn impresario from the San Fernando Valley using it for the premiere of his latest flick. I would think a science center would have a vested interest in protecting its reputation for showing science.

    And of course, the creationists know about that reputation. That’s why they try to book prestigious places of science, like the Smithsonian, your local museum, or as we see all the time at the University of Minnesota, the physics auditorium, to show off their bogosity in the reflected luster of science. The reverse is also true: scientists don’t rush to unveil their latest discovery at the nearby church.

    The science center also had clear grounds for canceling the showing: the creationists tried to imply in promotions that the movie showing was a Smithsonian-endorsed event, which it was not — they were merely a gang of bozos who had the cash to lease the room. The center also had a clause in their agreement to prevent that kind of credibility-theft, requiring promotional materials to be screened before release.

    It’s all part of a growing problem: creationists know that their institutions have no scientific credibility at all, and they desperately want to borrow some authority for their lies from real science.

Teaching Your Inner Fish

Next Fall, I’ll be back in the classroom teaching introductory biology again. One thing I’m planning to do is to use Shubin’s Your Inner Fish for that course…and just look what the good man has done just for me: all the figures from the book have been released as powerpoint slides.

OK, he probably didn’t think about me at all, and he’s releasing them for everyone to use, but still…it’s awfully serendipitous.

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Grab ’em all, teachers! These are tools for getting more evolution into the biology classroom!

The University of Minnesota has failed to enshrine racism in its policies!

Katherine Kersten is Minnesota’s own version of Glenn Beck. She’s a ‘columnist’ (literally true, since she is given a regular column to fill with right-wing nonsense) for the Star Tribune, and is a regular embarrassment. She recently aimed her smear-gun at the University of Minnesota, in a deranged tirade that has been picked up by Wing Nut Daily and Hot Air (read the comments at that site for a glimpse of how insane the right wing has become).

What made her so angry? The UM has a program in the college of education called the Teacher Education Redesign Initiative, or TERI. It’s a reasonably routine effort; the college is reevaluating their program, trying to set up appropriate priorities for teacher education, and is churning out documents as various groups wrestle with decisions about what’s important in their programs. Like I say, it’s routine — I’ve had to read lots of this kind of thing as part of the general output of a university bureaucracy — and it’s also a good thing, that university divisions exhibit at least a little introspection and flexibility.

Kersten does not think this is a good thing. She has her own strange view of what the effort is all about.

In a report compiled last summer, the Race, Culture, Class and Gender Task Group at the U’s College of Education and Human Development recommended that aspiring teachers there must repudiate the notion of “the American Dream” in order to obtain the recommendation for licensure required by the Minnesota Board of Teaching. Instead, teacher candidates must embrace — and be prepared to teach our state’s kids — the task force’s own vision of America as an oppressive hellhole: racist, sexist and homophobic.

Except…the report says nothing of the kind. You can read it yourself, if you want, although you probably don’t — it’s written in lumbering, repetitive, earnest Academese, which is a dialect of Bureaucratese, and it isn’t pretty. I get this stuff in my mailbox and it makes me want to claw my eyes out, so it took some masochistic discipline to dig into it voluntarily, but Kersten misrepresents the thing from top to bottom.

There is a grain of truth to what she says: the report does say that we need more emphasis on recognizing and appreciating diversity, and that we need more equitable representation of American culture in the teacher workforce. It does not say that America is an “oppressive hellhole”; that’s her own weird interpretation. She should have looked deeper. Doesn’t the fact that we’re training teachers at all imply that America must be a pit of ignorance and stupidity that needs correcting?

She’s basically taking the blinkered and customary wingnut position that any discussion of how we can improve the country implies that we are currently in a less than sublime state of perfection, which makes any constructive suggestion an unpatriotic act of treason.

This has set the wingnuts on fire. They are complaining bitterly about the goals of the UM college of education.

In an October 28, 2009, proposal to the Minnesota-based Bush Foundation, the college promises that it will revise its curriculum toward the “development of cultural competence.” The college’s full articulation of this vague concept at present is just what the Race, Culture, Class, and Gender Task Group has determined it to be.

Not only that, however, the college in its proposal promises to start screening its applicants to make sure they have the proper “commitments” and “dispositions”:

Develop admission procedures to assess professional commitments.

We recognize that both academic preparation and particular dispositions or professional commitments are needed for effective teaching. [Emphasis in original.]

The college promises that it will begin using “predictive criteria” to make sure that future teachers will be able to develop an acceptable level of “cultural competence”-apparently, those who do not pass the political litmus test and seem too set in their beliefs will never get admitted. This is far worse than what Columbia Teachers College does with its own “dispositions” requirement, and far in excess of what the National Council for the Accreditation of Teacher Education (NCATE) has ever mandated.

Never trust a kook to quote anything. When you see one line extracted from a document, and then spun out into a fable of planned oppression of a political point of view, you know there’s got to be something more that they’re leaving out. In fact, in this case you might be wondering what political views this ‘litmus test’ is intended to exclude…like, no Republicans will ever be allowed to teach again?

Nope. Here’s what they mean by ‘dispositions and commitments’.

Develop admission procedures to assess professional commitments.

We recognize that both academic preparation and particular dispositions or professional commitments are needed for effective teaching. Our school-based partners have told us that they would like to hire beginning teachers who demonstrate the commitment to focus relentlessly on student learning and take responsibility for the learning of all students without seeking excuses in the community, family, and culture of the students. They want teachers who can communicate and collaborate with each other and with the families and communities of their students. In response to our school partners, we will develop admission procedures that identify candidates with the potential to demonstrate these commitments as teachers.

Note the part I put in boldface. That’s what has Kersten incensed, and that is fueling the fear of right-wing reactionaries. They’re saying they want teachers who want to teach, and who do not sit around blaming the failure of students on their race or ethnicity. That’s it. It isn’t a political litmus test at all — it’s saying that bigots who won’t try to teach all of their students equally do not make good teachers.

That’s the sentiment that Kersten, Hot Air, and the Wing Nut Daily find horribly objectionable.

Fundamentally, it’s yet another admission that that (R) after politician’s name has become shorthand for (Racist). Conservative politics has become so tainted with lunatic anti-immigrant, anti-diversity, anti-human policies that a college can’t even say that tolerance and encouragement of the non-white portion of our populations is a good goal to work towards without being accused of being unpatriotic.

It’s not surprising. These are the same people who think Lou Dobbs would make a good president, and who dream of a Beck/Palin candidacy in 2012.

Our secret power…EXPOSED!

Professor Thomas Tang of Middle Tennessee State University has broken the code of silence and revealed one of the vast powers which are conferred upon us when we land an academic job. It’s true, professors can send you to hell.

Frustrated over cheating allegations, one professor at Middle Tennessee State University took the idea of a traditional honor code in a controversial direction.

Suspecting that one of his MBA candidates had just cheated on an exam, Professor Thomas Tang had each of them sign a pledge that said if they had cheated, they’d be condemned to an eternity in Hell.

The pledge went on to say if the student cheated they will “be sorry for the rest of [their] life and go to Hell.”

Don’t worry, though, I only use it sparingly — on students whose cell phones go off in class, on the ones who raise their hands and ask, “Will this be on the test,” and on the ones who write “YAY JESUS” on the class evaluation forms at the end of the term.

Oh, and just a hint: don’t cut off college professors in traffic.

That’s not an unfair question!

This story strikes a little close to home, because I’ve faced exactly the same kinds of complaints from some of my students — except that these are Religious Studies students. They are very upset because they consider one of the questions on a standard exam to be “unfair”. Here’s the question:

Question four on Islam, worth 20 marks, gave candidates a quotation referring to the Qur’an and the prophet Muhammad. Then it asked candidates: “With reference to the quotation, analyse the role played by the revelation through the Prophet in the life of Muslims.”

It sounds reasonable to me. They’re students of religion — I’m sure they’ve discussed the idea of revelation often enough, they’re supposed to be able to interpret texts, they’ve been given a quote, now all they have to do is spin out a nice line of blather, which again, is almost certainly a skill students of religion are expected to know.

But no. These students make some familiar complaints.

One student identified only as Clare said: “When we reached section three I think most students in the state had a communal heart attack as we discovered obscure and obtuse questions which were from absolutely no part of the otherwise very straightforward syllabus.

“I just lost 20 marks from a paper I studied very hard for.”

As a number of schools called for an explanation, Newington College student Nick Grogin said he was stunned by one question.

“I had never seen anything like that in the syllabus,” he said. “Nothing about it related to what I had studied and been taught.”

There was nothing about Islam in their studies? That would be deplorable. Or there was nothing about revelation, or about interpretation in their studies? That would be even more shocking.

These are students who don’t get it. I’ve had a few of them in biology classes, too. Some students think that if the answer to a question wasn’t plainly spelled out in lecture or in their texts so that they can just “study” (a verb that in some vocabularies means “memorize”) and spit back that very same answer, the question is unfair. Wrong.

Clare and Nick, you fail. And you deserve to fail. And not just because you’re wasting your time in Religion Studies.

A good test also examines a student’s ability to think, to come up with good answers to brand new problems. When a student is so limited in their intellectual ability that they are incapable of generalizing from principles they learned in the context of Christianity to Islam (or, as I’ve sometimes discovered, when they are flummoxed by a problem in Mendelian genetics in zebrafish rather than flies), they’ve flunked the thinking part of the exam.