Coyne was quoted in this article on homeschooling, which brought in an unexpected surge of email, including some rather nasty words from the Christians. This doesn’t surprise me at all; criticizing religion, especially the more far-out beliefs that are clearly unsupportable and in contradiction to all of the evidence, is always a reliable trigger to start some kooks spewing.

Homeschooling is another trigger. People care very much about their kids, and so telling them that they’re wrecking their children’s future by giving them a substandard education poisoned with a falsified ideology is not the kind of thing that will get you pleasant nods of approval…even if it is true. I’m one of those people who thinks we ought to be consistent and require everyone to attend an accredited school, public or private, and that private schools ought also to be required to meet certain secular standards, such as that their science education ought to address the evidence reasonably. You want to send your kids to a school that teaches them all about Jesus? Fine. But it doesn’t count as a legitimate education unless it also teaches the basics of science, math, history, English, etc. in a way that meets state education standards.

It’s the same principle that warrants requiring vaccinations for all children: for the defense of our society.

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.

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

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.