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

A few novel excuses for priestly child abuse

The Catholic Church is getting desperate. All this evidence is turning up of priests physically and sexually abusing young people in their care, and of the church administration being more concerned with protecting pedophile priests and the reputation of their organization than protecting children, so someone has to be blamed. How about the damn dirty hippies and those pesky reporters?

“The so-called sexual revolution, in which some especially progressive moral critics supported the legalisation of sexual contact between adults and children, is certainly not innocent,” he said, adding that the media was also at fault.

That was the excuse of a Catholic bishop to the ongoing discovery of a history of child abuse in Germany. The similar pattern of child abuse in Ireland prompted the Pope to dig up some excuses…in this case, because priests weren’t devout enough.

The pontiff also noted “the more general crisis of faith affecting the Church,” the statement said, adding Pope Benedict “also pointed to the more general crisis of faith affecting the Church and he linked that to the lack of respect for the human person and how the weakening of faith has been a significant contributing factor in the phenomenon of the sexual abuse of minors”.

Who knew the whole Catholic church was infested with free-lovin’ hippies and godless agnostics and atheists?

The way he’ll fix the problem is by calling for “a deeper theological reflection” on child buggery. I really don’t think it takes much deep thought to see that causing harm to children trusted to your care is a bad idea.

By the way, in an interesting side issue, the papal nuncio was asked to appear before an Irish committee on foreign affairs to talk about this problem. He haughtily replied that it was “not the practice of the Holy See that Apostolic Nuncios appear before Parliamentary Commissions”, which is rather interesting. The Vatican has a rather interesting status as a sovereign, independent state with membership in the UN, and pretends to be a participating nation in the world community of states. But apparently they also feel that they are not bound by secular obligations.

The Templeton Foundation plays some more games

It’s just sad. The arguments the apologists for religion make seem to be getting more and more pathetic, and more and more unconvincing. There is going to be a lecture, announced in the Times Higher Education supplement, by someone trying to reconcile science and religion in the history of the Royal Society. How is he going to do it? By arguing that members of the society in 1663 were religious. Woo hoo. They also wore funny powdered wigs, treated syphilis with mercury, and argued that there had to be precisely seven planets because it was a number sacred to geometers, but I doubt that he’ll be resurrecting those old ideas.

While an early memorandum of the Royal Society declared that fellows would avoid “meddling with divinity, metaphysics, morals”, its 1663 charter stated that its activities would be devoted “to the glory of God the creator, and the advantage of the human race”.

Officers were even required to swear an oath on “the holy Gospels of God”.

In reality, Professor Harrison said, “almost without exception, early modern natural philosophers cherished religious convictions, although these were not invariably orthodox. Some – but by no means all – made the point that they were motivated to pursue scientific inquiry on account of these religious commitments.”

Far from being militant atheists, they “believed that the disinterested study of the structures of living things could offer independent support for the truth of the Christian religion, and refute atheism”.

Yes, so? They were wrong.

Believers have been trying for centuries to find objective evidence for the truth of Christian mythology. The fact that they’ve been searching is not in itself evidence for their superstitions. The fact that they have not come up with such evidence, though, and haven’t even made any progress in coming up with a convincing argument, does suggest that they’ve failed. It’s simply meaningless to declare that people 350 years ago felt that their religion motivated their pursuit of science; it does not support the validity of the religious part. They might as well argue that the people who built Stonehenge 5000 years ago were motivated by their pagan beliefs to study astronomy — the astronomy is cool, but animism is not hallowed by its antiquity.

It’s an unpersuasive mess. It’s also tainted by association; the lecture is sponsored by the Faraday Institute, which is just a mouthpiece for the Templeton Foundation. Ho hum. Get some new arguments, guys.

Coordinating an atheist dinner in Melbourne

I think I’m the main course. Anyway, Bride of Shrek is trying to organize the seating for the dinner in Melbourne on the 13th of March, and the plan is for the Pharyngula horde to sit together (I think it is so our uprising and assault will be more effective), and in order to do that, the she needs you to send her your conference booking confirmation number, which should be on your ticket or receipt. Then she’ll get that information to the conference organizers, and they’ll put you at the same table with me. I think.

Send the magic number to Bride of Shrek soon.

If you aren’t going to the conference but are going to be in Melbourne on Friday afternoon, she’s also organizing something for you, too.

Exorcism is a booming business

Hard to believe, but this medieval nonsense is still going on. Poland has more than 100 professional exorcists, and they recently met in a conference.

Congress participants argued that demonology lessons should be treated more seriously in seminaries and that ordinary people, too, would benefit from knowing more about exorcisms. During the congress, the priests discussed the main causes of possession by demons such as occult, esoteric beliefs like magic, eastern meditation and homeopathy.

Oooh, demonology lessons. Those should be good. Don’t forget to take them seriously when some geezer tells you that your wicked thoughts about Scarlett Johansson are the work of the minor demon Booglebegonzapootie.

I do appreciate that they’re updating the list of demons to include the ones drawn to homeopathy. I wonder if you get rid of them with a fully succussed 100C dilution of holy water?

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.

Sal Cordova is a slimy little sewer goblin

Without hesitation, I can tell you who the most contemptible, repulsive creationist I know is: he tops even Ray Comfort and Ken Ham in the pantheon of creationist liars for Jesus. It’s the otherwise negligible Sal Cordova, a whiny little nobody with no talent and no reputation other than his ability to cobble up some of the most disgusting innuendo. His latest achievement is to tie the murders by Amy Bishop to evolution; he’s found that Bishop is named in the list of supporters of the Clergy Letter Project, which means he gets to sneer a bit.

Amy Bishop was charged in the murder of several people recently. Now, there are some very fine Darwinists like Francis Collins, and I don’t mean to say Amy Bishop is representative of all Darwinists. But I’d recommend that if the Clergy Letter Project wishes to put on a good face for Darwinism, they might consider disassociating themselves from Amy Bishop.

They may not want to promote “survival of the fittest” in their sermons today. That would be kind of poor taste in light of the fact a presumed societal degenerate (Bishop) is the “fittest” survivor while 3 (possibly 4) innocent victims are the “unfit” dead.

As if the preachers were going to endorse Bishop’s actions from the pulpit; as if evolutionary biologists anywhere promote the kind of simplistic ruthless extermination that Cordova fantasizes over as the only possible fitness strategy. All we learn from his nasty little dig at evolution is that he doesn’t understand it — he does have some competition from Ray Comfort in the stupidity department — and that he’s willing to capitalize on a tragedy to make a fallacious argument against science.

And, as usual, he loves to make the out-of-context quote from Charles Darwin, in this case, the phrase “How I did enjoy shooting,” taken from
The Autobiography of Charles Darwin. As if Charles liked to open fire on his rivals and climb to eminence on the corpses of his competitors. Here, by the way, is the full quote in context; he was an enthusiastic sportsman who liked hunting game, and would have been sick with disgust at the thought of shooting people.

I kept an exact record of every bird which I shot throughout the whole season. One day when shooting at Woodhouse with Captain Owen, the eldest son, and Major Hill, his cousin, afterwards Lord Berwick, both of whom I liked very much, I thought myself shamefully used, for every time after I had fired and thought that I had killed a bird, one of the two acted as if loading his gun, and cried out, “You must not count that bird, for I fired at the same time,” and the gamekeeper, perceiving the joke, backed them up. After some hours they told me the joke, but it was no joke to me, for I had shot a large number of birds, but did not know how many, and could not add them to my list, which I used to do by making a knot in a piece of string tied to a button-hole. This my wicked friends had perceived.

How I did enjoy shooting! But I think that I must have been half-consciously ashamed of my zeal, for I tried to persuade myself that shooting was almost an intellectual employment; it required so much skill to judge where to find most game and to hunt the dogs well.

Slimy Sal repels me, so I’ll leave it to Allen MacNeill to take his post apart.

Sal, what precisely is the point of this post? It seems to me you are making the following assertions:

A1) Amy Bishop is a member of the consultant group for the Clergy Letter Project

A2) Amy Bishop is alleged to have murdered three of her colleagues and seriously injured three others by shooting them

A3) Charles Darwin indicated that he enjoyed shooting (target unspecified)

There appears to be considerable evidence in support of these assertions. However, it is also clear that your intention in making these assertions is the following:

I1) Amy Bishop is an evolutionary biologist

I2) Evolutionary biologists enjoy shooting

I3) Some evolutionary biologists enjoy shooting their colleagues to death

And from this you appear to be strongly suggesting the following conclusion:

C1) The practice of the science of evolutionary biology predisposes people to commit murder by shooting their colleagues to death.

It is a matter of simple historical record that many of the regular commentators at this website agree with something very similar to C1. Indeed, they waste no opportunity to state it as an incontrovertible fact, and cite this “fact” as a reason to reject the methodology, conclusions, and (by implication) the character of the practitioners of evolutionary biology, and especially Charles Darwin.

Let me therefore construct an exactly equivalent line of “reasoning”:

A4) Andrea Yates was a member of a Christian worship group led by the itinerant Christian preacher, Michael Peter Woroniecki

A5) Andrea Yates was convicted of murdering her five children by drowning them in a bathtub

A6) John the Baptist indicated that he enjoyed submerging sinners in water

Again, there appears to be considerable evidence in support of these assertions. Using the line of reasoning you seem to be promoting here, it would be equally “reasonable” to make the following inferences:

I3) Andrea Yates is a Christian

I4) Christians enjoy submerging people in water

I5) Some Christians enjoy murdering their children by drowning them

You should therefore be very willing to accept the following conclusion:

C2) Christianity predisposes people to murder their children by drowning them.

Please correct me if I have somehow misconstrued your intentions here. Also, please explain how your training in science and scientific reasoning leads you to make arguments of this form.

And,while you’re at it, please let me know how you can look at your own reflection in the mirror after making arguments like this.

We can always play the guilt by association game…in this case, the nastiest person I know is Sal Cordova, a creationist, therefore creationists are all people with no sense of common decency.

Australia 1, New Zealand 0

Next month, I’m going to be attending the Global Atheist Convention in Melbourne, and originally, I had planned to make this a grand tour and was even thinking about a side trip to New Zealand. Plans have changed — one of the consequences of my long journey to California and Ireland, lovely as it was, is that too much travel at once, with all the confinement and awkwardness, is that I’ve wracked up my back rather severely — I’m trying to get some mobility and quiet the shrieking agony right now so I can cope again, but I’m just afraid that another string of non-stop pinioning to airplane seats will end with me in even worse shape.

So I had to squelch the New Zealand detour. Sorry, gang, I’ll try again some other time, and give you my full attention.

Anyway, so here’s the current, greatly reduced and I hope survivable plan. I’ll be in Melbourne from 11-14th of March (or maybe a day or two longer). I’m going to be in Canberra 19-20th of March, where I’ll be getting together with some notorious luminaries of the Australian anti-creationism movement, John Wilkins, Chris Nedin, Jim Foley, and Ian Musgrave. I’ve got some flexibility in my schedule, obviously, but I’m going to moderate my travel…which means I’m going to stay around the southeast part of the country (sorry, Perth and Darwin and Alice Springs). If anyone wants to draft me to give a talk somewhere in that week in that general neighborhood, get in touch with me. I can easily give a bit of talk with amusing anecdotes about those crazy American creationists, like Ken Ham and Ray Comfort.

But be gentle. I’ve got knives in my spine right now, and so I’m not going to go too wild with long distance excursions once I get there.