Sunday, January 31, 2010

Portrait of a Jihadist

Andrea Elliott in the New York Times has this troubling story about Omar Hammami, a college boy turned Muslim extremist. It's definitely worth reading.

Clearly the path that took Hammami from Alabama, where he was raised, to Somalia, where he leads a rebel movement, is complicated and formed from multiple incidents in his life. But it is interesting to see the role played by religion, and in particular, Christianity.

Raised by a Christian mother and a Muslim father in the deep South, Hammami clearly felt conflicted. But, according to the story, he was indoctrinated in "Perdido Baptist Church, a tiny congregation whose preacher warned of hellfire and damnation" and induced to attend Bible camp. He found it hard to reconcile the claims of fundamentalist religion with science: he wrote “Sometimes I get confused because the Bible says one thing and our textbooks and Darwin say another" in his journal at age 12. Well, of course, if you feed your child religious lies, they're going to be confused when they learn about science.

We can see in the article the corrosive influence of the particular brand of Islam that Hammami adopted. After his conversion, he swore at a former teacher, "assailing her for being Jewish". He dropped out of studying computers because he couldn't tolerate the presence of women. "He began subscribing to conspiracy theories about 9/11", the article explains.

Now he participates and leads troops in an extremist Somali movement that does things like publicly stoning to death a 13-year-old girl accursed of adultery. How did his mind get so warped?

Part of the answer, it seems to me, is the credulity induced by his religious upbringing and his failure to regard religious and other kinds of claims skeptically. There is a direct path from the claims of fundamentalist Christianity to the claims of 9/11 truthers and the claims of radical Islam. All spin an elaborate tale with no evidentiary justification.

We don't serve our children's or society's best interest by indoctrinating them with these kinds of claims at an early age. We need to teach kids to think more skeptically and give them the tools to analyze and decide between conflicting claims. And somehow we need to make sure kids aren't threatened with hellfire if they don't adopt the views of their minister. That's just a form of psychological terrorism, which in this case led to tragic consequences.

Sunday, January 24, 2010

Sign in the Harvard Museum

Here's a sign in the Harvard Museum of Natural History.

Wouldn't it be better to say that supernatural explanations for biological diversity were once considered and later discarded?

Why do you think it says "many scientists and religious leaders do not perceive an inherent conflict between religion and the scientific theory of evolution"? Wouldn't it be more honest to also mention that many scientists and religious leaders do perceive that religion and evolution are in conflict?

Wednesday, January 20, 2010

The Meyer-Atkins "Debate"

Take a listen to this "debate" between Stephen Meyer and Peter Atkins. The interviewer is Justin Brierley, and creationist Mark Haville, who is bringing the film Expelled to the UK, also joins them.

Some comments: Meyer was polished and smooth, but quite rude. Atkins stumbled a bit and didn't always make his points effectively.

Meyer repeats his claim that

2:01 "If you're trying to explain an event in the remote past, you should be looking for causes that are known to produce the effect in question."

He omits a very important point. You don't look for arbitrary causes; you look for causes that you have reason to believe existed at the time. Humans can make mountains, but that doesn't mean when we examine Cambrian orogeny that we should seriously consider humans as a cause.

The burden is on intelligent design advocates to show that an "intelligence" existed in the distant past before they can invoke it as a cause.

2:30 "What we know from experience, from our uniform and repeated experience, which is the basis of all scientific reasoning, is that information comes from an intelligent source ... whenever we trace information back to its source, we always come to a mind, not material process..."

This is completely false, as I have shown. Atkins should have given an example, like weather, to show that this is false.

4:15 "Instead of responding to arguments that we're making ... we get this kind of name-calling, creationists in cheap tuxedos, religion masquerading as science..."

This is completely bogus. Even though they consider intelligent design to be nonsense, many scientists have taken their valuable time to explain, in detail, why the arguments are wrong. The problem is, this has no effect on committed creationists like Meyer. It doesn't matter to Meyer that the arguments in his BSW paper have been debunked; you won't see any retraction by Meyer of his bogus claims or any acknowledgment that his arguments were wrong.

Meyer knows perfectly well about books like Why Intelligent Design Fails: A Scientific Critique of the New Creationism and Mark Perakh's Unintelligent Design. And he knows perfectly well that these books do respond to the arguments of intelligent design creationists.

As for name-calling, Meyer would have more credibility if it weren't for the incessant name-calling emanating from his side. Those who support evolution are repeatedly denigrated by intelligent design creationists, who routinely compare evolutionary biologists to Nazis, Soviets, and the Taliban. Meyer himself has compared Ken Miller to a Nazi.

6:39 Meyer rambles on without letting Atkins making his point.

7:13 Atkins correctly says Meyer is wrong about information, but gives as his examples of information "structures emerging without an agent actually generating the structure, and information ... is a kind of structure". Meyer mentions "a vortex emerging in a bathtub" - Atkins says this is information.

9:15 Atkins says the Universe as a whole is becoming more chaotic, more disorganized. There are local abatements of chaos - these constitute information.

10:30 Meyer: "Spontaneous order is not the same thing as information."
Atkins: "Yes it is".
Meyer: "There is a distinction between order and information."

Later, Meyer: "... Specified complexity".
Atkins: "What do you mean by specified complexity?"

This was a good point by Atkins, but it should have been hammered home. Atkins should have asked Meyers to say what units specified complexity is measured in. He should have then asked, what is the specified complexity of a mountain? A tornado? A book? He should not have allowed Meyer to pretend that "specified complexity" is a well-defined measure that is used or accepted by anyone except intelligent design advocates.

Meyer: "The chemical bonds that allow for the structure of the molecule as a whole do not determine the sequence of the bases in the DNA molecule."
Atkins: "No, evolution determines that."
Meyer: "That is just an assertion. That's what remains to be proven."
Atkins: "What do mean, just an assertion?"
Meyer: "You have to point to a physical process that is capable of doing the work of sequencing the bases."

Meyer is being moronic or disingenuous here. He knows perfectly well that mutation followed by selection, as well as other processes like genetic drift, is the physical process that biologists believe "sequenc[es] the bases". Atkins should have called him on this.

12:05 Meyer conflates origin of life ("chemical evolution") with evolution.

Mark Haville at 13:30:
"When Prof. Atkins asks a question like, 'Has evolution taken place, yes or no?', that's rather like me saying to you, have you stopped beating your wife? Because I'm guiding you to a yes or no answer."
Atkins: "What's wrong with yes or no answers?"
Mark: "The reason is, you have to define what kind of evolution you're talking about."
Atkins: "OK, evolution that has taken us from inorganic matter to our current biosphere."
Mark: "So you're talking about not cosmic, not chemical, not stellar or planetary, but organic. But then, when you're talking about organic, are you talking about macro or micro?"
Meyers: "Are you talking about directed or undirected? The term is fraught with ambiguity."
Atkins: "OK, then, I'll clarify then: undirected."
Meyers: "Undirected. And chemical evolution, is there a an accepted theory of chemical evolution that accounts for the origin of life?"

Here Atkins is letting himself get beaten up from two sides, and of course the interviewer did not intervene. Instead of letting Haville distract by talking about "cosmic" and "stellar" and "planetary" evolution, Atkins should have said, "Don't play games here by bringing in extraneous concepts. You know perfectly well what we're talking about because I just said it: evolution that has taken us from inorganic matter to our current biosphere. Do you accept it or not?"

15:10 Justin Brierley, talking about Expelled "The film starts out with the case of one particular scientist who lost his job at the Smithsonian Institute. This was Richard Sternberg, and he published a paper of yours in a peer-reviewed journal and lost his job for it."

Of course, this is blatantly false. Sternberg did not lose his job (and he was at the Smithsonian Institution, not the "Smithsonian Institute"). Couldn't the inteviewer do the basic homework needed to understand what happened?

15:54 Meyer: "He didn't lose his job. He had his office taken away, his access to scientific samples, his keys, his friendly colleagues were interrogated as to his religious and political beliefs and affiliations, he was transferrred underneath the supervision of a fellow scientist who was known to be hostile to him and then he was ultimately demoted."

This is, as I have remarked before, an inaccurate and misleading summary of what happened. You can read Ed Brayton's article to learn the true story.

20:15 Atkins: "I will make a concession to you, Stephen, which is that you do ask interesting questions. You ask, how does the eye develop. You ask, how does information emerge in the cell, things like that, and these are, in my view, valid questions."

This was a bad rhetorical tactic. Atkins should have also explained that the questions that Meyer asks are nothing new. Futhermore, they have been or are being answered. Maybe not in the detail that Meyers demands, but the answers are being found. There was a day-long symposium on the evolution of the eye at MIT just two months ago. And we know how information "emerges": from the processes of mutation and natural selection.

22:00 Meyer: "If you're look at the Rosetta stone, you can look in vain if you limit yourself to materialistic explanations of wind and erosion and the like and don't open yourself to the possibility that mind played a role in the organization and sequencing of those characters."

This is a typical misdirection by intelligent design creationists, and Atkins should have hammered him hard on it. "Materialists" have no problem taking into account human actions; what do you think archaeologists do? But there is a huge difference between saying that the Rosetta stone was written by an Egyptian, and saying that it was written by some unknown "intelligence" whose properties and motivations we know nothing about.

33:10 Julian: "Julian Baggini, for example, who is an atheist philosopher here, said when I got in touch with him, "The Discovery lot are thoroughly disreputable." I mean, what's causing this particular kind of backlash against your organization, Stephen?"
Meyer: "Well, you're talking to people who have a strong precommitment to materialism or atheism.
Julian: "Why would they say you are disreputable? What have you been doing or saying that makes you disreputable?"
Meyer: "I guess that you'd have to let them answer that question. But I think what's actually disreputable is that we're challenging the rules of science - rather self-serving and arbitrary rules of science - which they have been using to shut down the debate."

Meyer knows perfectly well why his Discovery Institute is derided as "disreputable". It's because the spokespeople for the Discovery Institute utter untruth after untruth.

As for "shut[ting] down debate", where has this been done? Creationists raise their loud and ignorant voices in books, magazines, and on the Internet. Who has censored them? What they don't get to do is label their religious claptrap as "science" and force it down the throats of public school kids; Judge Jones put a stop to that.

34:27 Q. "Why won't you let Stephen publish his paper then, on the issue, if it's such an interesting issue?"
Atkins: "Because it's outside the mode of standard scientific procedure."

A terrible answer. Atkins should have said, "You're being ridiculous. Meyer's paper was published, and I had no say about whether or not it should have been. The problem is, the ideas in his paper were by turns, trivial and wrong, and the paper got published anyway. Lots of junk gets published, you know. If he wants his ideas to be taken seriously, he has to make a good case for them. We can evaluate what the scientific community thought about his ideas by looking at how many papers have cited his. Virtually no one has. The verdict is in: Meyer's ideas are simply not of interest to the scientific community."

There's more similar nonsense - listen for yourself. I think Atkins was at a bit of a disadvantage because his rhetorical style was too polite; he let Meyer and Haville walk over him. But he also didn't always produce effective responses to Meyer's bogus claims.

Tuesday, January 19, 2010

A Neat Problem on Card Arrangements

Here's a neat problem on card arrangements. I learned about it on reddit. Here's the easiest way to state it:

Given a deck of 52 cards shuffled randomly -- a deal -- what is the probability that, somewhere in the deck, there is an Ace adjacent to a King?

Try to figure it out before looking at the analysis below.

At first glance, it doesn't seem so easy. For example, if we fix the positions of the Kings, then the Aces could appear on either side of a King, giving (it seems) 8 possibilities for an Ace to appear. This suggests that the number of deals where an Ace fails to be adjacent to a King is

(52 choose 4) : choose positions where the Kings are
* (4!) : choose the relative order of the 4 Kings
* (40 choose 4) : choose the positions for the Aces: not where the Kings are, or on either side of them
* (4!) : choose the relative order of the Aces
* (44!) : choose the positions of the remaining 44 cards.

This gives a probability of no Ace adjacent to a King of 9139/19458, or about 0.4697.

Unfortunately, this naive analysis is wrong. Why? If we're trying to compute the number of deals where an Ace fails to be adjacent to a King, we didn't consider the fact that in many deals, there will be two or more Kings adjacent to each other, thus increasing the number of places where Aces could go. Similarly, Kings could appear at the beginning or end of the deck. So the real probability of no Ace adjacent to a King should be somewhat higher than we computed.

Of course, we could go through all the possibilities of how many adjacent spots there are. But that is an awful calculation. I asked Ian Goulden, a professor in the Combinatorics & Optimization department at Waterloo, and he came up with this lovely argument - which I've modified slightly:

We start by choosing all the cards that are neither Kings nor Aces. There are 44 other cards, and so there are 44! ways of arranging them. Now we're going to insert the Aces. But to do so, we'll first figure out how the Aces are arranged by breaking them up into contiguous nonempty blocks. For example, you might have three Aces in a row, and then a 4th Ace somewhere later on. There can be 1, 2, 3, or 4 contiguous blocks; let the number of blocks be k (and we'll have to sum on k from 1 to 4).

Once we have the number of blocks, we need to assign the number of Aces in each block. It's not hard to see that this can be done in (3 choose k-1) ways. For example, for k = 1, there is only one way: put all 4 Aces in a single block. For k = 2 we can have the first block with 1 Ace, and the second with 3; or the first with 2 and the second with 2; or the first with 3 and the second with 1, etc. Finally, we can put the Aces themselves into these blocks in 4! ways. Now that we have the Aces in the blocks, we need to insert them into the 44 cards. There are 45 gaps between these 44 cards where we can insert the k blocks (including a gap to the left of each card and one at the right end), so that gives (45 choose k) ways of doing this.

We now have 48 cards laid out, and it remains to insert the 4 Kings. We'll do this in order: the King of Hearts first, the King of Spades next, then Diamonds, then Clubs. When we insert the first King, we can't put it immediately to the left of each block (there are k places); nor can we put it to the right of each Ace. So there are 49 positions, of which (4+k) are ruled out. So there are only 45-k places to put the King of Hearts. Then there are 46-k places to put the King of Spades, 47-k places for the King of Diamonds, and 48-k places for the King of Clubs.

Thus, the total number of deals where no King is adjacent to an Ace is
(44!) * Σk=14 (3 choose k-1)(4!)(45 choose k)(45-k)(46-k)(47-k)(48-k) =
41435794890014187172891516774574832972049361890932487618560000000000. Dividing this by 52! we get 300684703/585307450, or about 0.5137, as the probability that no King is adjacent to an Ace. So the probability that in a random deal there will be a King adjacent to an Ace is 284622747/585307450, or about .4863.

As a check, this agrees with a paper of David Singmaster entitled "The probability of finding an adjacent pair in a deck", Mathematical Gazette 75 (1991), 293-299. Goulden's formula is much simpler and more elegant than Singmaster's.

Generalizing the ideas above, Ian Goulden considered the more general situation where you have N cards, C cards in the first group, D cards in a second disjoint set, with C ≤ D. Then the probability that no card in the first group is adjacent to a card in the second in a random deal of N cards is given by

Σk=1C (C-1 choose k-1)*(N-C-k choose D)*(N-C-D+1 choose k)/( (N-D choose C)*(N choose D)).

Thanks to Ian Goulden for letting me post his beautiful solution.

Dembski: Prayer Can Change the Past

If you have time to waste, listen to this podcast of Bill Dembski being interviewed about his latest book.

I haven't read the book, but apparently one of his claims is that all evil - even natural evil like typhoons and earthquakes - is ultimately due to human sin. For Dembski, human sin is so corrosive that it has the magical power to have causation backwards in time. While Christians claim to be humble, this seems to be one of the most megalomaniac religious claims of all time: that the ancient physical history of the Universe, which developed over billions of years, is dependent in part on the "sin" of humans today and in the recent past. Earthquakes may have occurred millions of years ago, but they're still our fault.

Another of his ideas seems to be - I kid you not - that the effect of prayer could go backward in time. He cites as an example this story told by Helen Roseveare. When working as a medical missionary, she needed a hot water bottle to keep a premature baby warm. Lacking one, a child at the mission prayed that one would arrive - and that same afternoon, one did. A miracle, obviously, and an answered prayer. Even more miraculously, the parcel had been sent 5 months earlier -- so if the prayer were really effective, its effects would have had to go backward in time.

What do you think of Roseveare's story? If it really happened as recounted (which I doubt, since stories like these are notoriously exaggerated - witness the claims of "leg lengthening" at faith-healing ceremonies - and get more and more elaborate with each telling), then was it really a miracle? Surely people send packages to medical missionaries all the time, and it is not a stretch to think that people would include all sorts of objects that might be useful, including a hot water bottle. And even if it was a miracle, wouldn't it have been easier for their god to simply arrange for the baby to arrive at the usual time, instead of being premature? And how about all the millions of people who have prayed sincerely without relief? Why did Mike Turner die, trapped by a boulder in Wyoming, while his prayers went unanswered?

It's extremely hard, seeing all the suffering in Haiti, to maintain that the Christian god is a loving one. So Christians are forced to develop an elaborate edifice to justify suffering. A more honest and realistic view is that, if a single god really exists, then he's a nasty son-of-a-bitch. I once asked a famous Catholic theologian if anyone had ever tried to develop a theology about the characteristics of a god based on what we actually see in the world: suffering, pain, natural catastrophes, etc. He seemed very surprised by the question, thought about it for a bit, and answered, "no".

Although Dembski thinks prayer might change the past, he also seems to think that once we know that an event has occurred, then there's no point praying about it. But why couldn't his god then change everyone's memory of the past, too, so that no one knew the event occurred, and then change the event itself? The rules for Bill's god seem completely arbitrary.

Along the way, we learn other aspects of Dembski's "thought". He is an old-earth creationist and he also subscribes to the "vaccines cause autism" woo. He believes in a literal Adam and Eve, specially created by his god, but he also thinks that evolutionary biology is compatible with this: biology, according to Dembski, speaks of "breakaway populations" and "genetic evidence" that there was an "initial pair" starting a new population. (This, of course, is not true. Founder effects occur with a small population, not necessarily an "initial pair". And while the genetic evidence points to a "Mitochondrial Eve" and a "Y-Chromosomal Adam", these two people did not live at the same time.)

What do theologians make of his book? No surprise: they lap it up. J. P. Moreland says, "I have read very few books with its deep of insight, breadth of scholarly interaction, and significance. From now on, no one who is working on a Christian treatment of the problem of evil can afford to neglect this book." It seems no idea is too silly for credulous theists to take seriously.

Sunday, January 17, 2010

More Mind-Boggling Stupidity from O'Leary

Denyse O'Leary, the World's Worst Journalist™, is at it again.

Here she fulminates against Richard Dawkins in her inimitable mangled syntax, quoted exactly as written:

[About time someone said the obvious. Darwinism does not work, Never has, never will. Kept alive by a taxpayer-funded, court-supported Darwin industry that is nearly a century old.[A shame and a scandal, and a waste of tax money. For the moment, I will set aside the completely ridiculous quasi-religious obsequies paid to Darwin. It got so bad that Darwin was compared to Lincoln. And while we are here, Dawkins claims he cannot produce an original statement of his big no-design theory - though professionals associated with the goals of this site reconstructed it - and it doesn't work.

Translation for those who don't speak Denysish:

"taxpayer-funded, court-supported Darwin industry" = evolutionary biologists who have forgotten more science than Denyse ever knew. Denyse's fulminations against academia remind me of this quote from Gordon Allport: "College professors are suspect because whenever emotion is in control, anti-intellectualism prevails."

"Dawkins claims he cannot produce an original statement of his big no-design theory" = intelligent design crackpots making a big deal out of the fact that Dawkins no longer has his original BASIC program for his famous "Methinks it is like a weasel" example of how natural selection can do hill-climbing. Never mind the fact that any idiot can produce a functionally equivalent program in a few minutes. Well, maybe not any idiot.

"professionals associated with the goals of this site reconstructed it - and it doesn't work" = pure hogwash. The idea works, and is used all the time in industry.

And she calls herself a journalist!

Note added January 19: O'Leary has now edited her page to remove one (but not all) of the syntax errors. The original version is preserved above for posterity.

Friday, January 15, 2010

Creationists Lie To Kids

Take a look at this science poster hanging in a school classroom, claiming to provide evidence that the earth is young.

It lies and lies and lies and lies:

- the eruption of Mt. St. Helens made canyons like the Grand Canyon: debunked here

- a "plesiosaur" that washed up on a beach shows dinosaurs are still alive: almost certainly a basking shark carcass, like the one discussed here

- "polystrate" fossils: explained here

And that's just from the first two photos.

Fundamentalist "education" rots your mind.

Thursday, January 14, 2010

More on Signature in the Cell

Yesterday, I showed how the treatment of information in Stephen Meyer's book, Signature in the Cell, contains many misunderstandings and unjustified claims.

Today, I want to focus on what I call the "dishonesty factor" of the book: claims that are misleading or just plain false. The philosopher Thomas Nagel has stated that "Meyer’s book seems to me to be written in good faith." Perhaps, after reading these examples, he might reconsider his assessment.

pp. 1-2: Meyer gives a very misleading account of the events surrounding the dubious publication of his shoddy article in the Proceedings of the Biological Society of Washington (footnotes omitted):

First, in August 2004, a technical journal housed at the Smithsonian Institution in Washington, D.C., called the Proceedings of the Biological Society of Washington published the first peer-reviewed article explicitly advancing the theory of intelligent design in a mainstream scientific periodical. After the publication of the article, the Smithsonian's Museum of Natural History erupted in internal controversy, as scientists angry with the editor -- an evolutionary biologist with two earned Ph.D.'s -- questioned his editorial judgment and demanded his censure. Soon the controversy spilled over into the scientific press as news stories about the article and editor's decision appeared in Science, Nature, The Scientist, and the Chronicle of Higher Education.

The media exposure fueled further embarrassment at the Smithsonian, resulting in a second wave of recriminations. The editor, Richard Sternberg, lost his office and his access to scientific samples and was later transferred to a hostile supervisor. After Sternberg's case was investigated by the U.S. Office of Special Counsel, a government watchdog organization, and by the U.S. House Committee on Government Reform, a congressional committee, other questionable actions came to light. Both investigations bound that senior administrators at the museum had interrogated Sternberg's colleagues about Sternberg's religious and political beliefs and fomented a misinformation campaign designed to damage his scientific reputation and encourage his resignation. Sternberg did not resign his research appointment, but he was eventually demoted.

This account is misleading in almost every respect. For the true story, you can consult Ed Brayton's fine article in The Skeptic. Here are some facts that Meyer saw fit to omit:

1. Sternberg arguably engaged in misconduct in publishing the article. The council of the Biological Society of Washington, publishers of the journal, issued a statement saying that "the associate editors would have deemed the paper inappropriate for the pages of the Proceedings because the subject matter represents such a significant departure from the nearly purely systematic content for which this journal has been known throughout its 122-year history" and "Contrary to typical editorial practices, the paper was published without review by any associate editor; Sternberg handled the entire review process." As Brayton argues, "Sternberg’s decision to publish the paper without the normal peer-review process is a flagrant breach of professional ethics that brought disrepute to the Smithsonian."

2. Meyer's claims about retaliation against Sternberg are bogus. Before the controversy and before the article was published, Sternberg (who only held a courtesy appointment at the Smithsonian and was not employed by them) and others were informed about a reorganization of the department that would require a change of offices. Sternberg later was moved again because he requested the move. It is a falsehood to claim he lost his office as a result of retaliation.

3. There was no campaign against Sternberg. His misconduct in publishing the article was discussed - as it should have been - but ultimately no action was taken. No one was "interrogated".

Let's go on to see other misrepresentations in Signature in the Cell:

p. 5: Meyer overstates the impact of Dembski's work by calling it "groundbreaking". Falsely claims Dembski "established a scientific method for distinguishing the effects of intelligence from the effects of undirected natural processes. His work established rigorous indicators of intelligent design..."

This is in line with the usual tactic of creationists: credential inflation. Dembski's work has received a minuscule number of citations in the scientific literature, while truly important work typically receives hundreds or thousands of citations. So in what sense can Dembski's work fairly be considered "groundbreaking"?

Similar credential inflation can be found on pages 178-9, where Meyer says of one of Dembski's articles that it "broke important new ground in understanding pattern recognition." Yet the pattern recognition literature has somehow ignored this "important new ground".

p. 36: Victorian scientists viewed cells as " "homogeneous and structureless globules of protoplasm," amorphous sacs of chemical jelly, not intricate structures of manifesting the appearance of design."

This claim has been repeated again and again by creationists, but it is not true. Fergodsake, the nucleus was discovered in 1833. Here are more detailed rebuttals by Afarensis and Wesley Elsberry.

p. 120: [About the movie Expelled] "When the producers came to our offices to plan interviews, the told us they wanted to find a way to represent what DNA does visually, so that a genera audience could follow the scientific discussion they planned to incorporate into the film. They commissioned a visually stunning three-dimensional animation of DNA and the inner workings of the cell and retained a team of molecular biologists to work closely with the animators."

Somehow Meyer manages to leave out the inconvenient fact that their "visually stunning" animation of the "inner workings of the cell" was ripped off from XVIVO's Inner Life of the Cell.

I could cite even more examples, but this is enough to give the general idea. Whether it's about the technical details of information theory, or the more prosaic details of controversies, Meyer's accounts simply cannot be relied upon.

Wednesday, January 13, 2010

The Essential Larry McMurtry

Larry McMurtry has made a career writing novels featuring eccentric characters who don't really know what they want. I like his characters, but they are pretty mysterious to me. In particular, the women he writes about are like no women I know.

I really enjoyed his early novels, such as All My Friends are Going to Be Strangers and The Last Picture Show, but haven't enjoyed much since Lonesome Dove.

His latest novel, Rhino Ranch, seems to be more or less in the mold of the last 20 years. I wouldn't say it's a good novel -- but there are some very enjoyable passages, such as this one, which seems to me to be quintessential McMurtry:

"You won't rebel," Annie said firmly, putting a rosy Texas grapefruit before him. Though nearing thirty, Annie looked about sixteen. Duane was charmed by her, as he had been more or less since the moment they met.

"You can always have all the fruit you want," she reminded him. "Your problems lie in the nonfruit areas."

Nonfruit areas! That's classic McMurtry.

Stephen Meyer's Bogus Information Theory

A couple of months ago, I finished a first reading of Stephen Meyer's new book, Signature in the Cell. It was very slow going because there is so much wrong with it, and I tried to take notes on everything that struck me.

Two things struck me as I read it: first, its essential dishonesty, and second, Meyer's significant misunderstandings of information theory. I'll devote a post to the book's many mispresentations another day, and concentrate on information theory today. I'm not a biologist, so I'll leave a detailed discussion of what's wrong with his biology to others.

In Signature in the Cell, Meyer talks about three different kinds of information: Shannon information, Kolmogorov information, and a third kind that has been invented by ID creationists and has no coherent definition. I'll call the third kind "creationist information".

Shannon's theory is a probabilistic theory. Shannon equated information with a reduction in uncertainty. He measured this by computing the reduction in entropy, where entropy is given by -log2 p and p is a probability. For example, if I flip two coins behind my back, you don't know how either of them turned out, so your information about the results is 0. If I now show you one coin, then I have reduced your uncertainty about the results by -log2 1/2 = 1 bit. If I show you both, I have reduced your uncertainty by -log2 1/4 = 2 bits. Shannon's theory is completely dependent on probability; without a well-defined probability distribution on the objects being discussed, one cannot compute Shannon information. If one cannot realistically estimate the probabilities, any discussion of the relevant information is likely to be bogus.

In contrast, Kolmogorov's theory of information makes no reference to probability distributions at all. It measures the information in a string relative to some universal computing model. Roughly speaking, the Kolmogorov information in (or complexity of) a string x of symbols is the length of the shortest program P and input I such that P outputs x on input I. For example, the Kolmogorov complexity of a bit string of length n that starts 01101010001..., where bit i is 1 if i is a prime and 0 otherwise, is bounded above by log2 n + C, where C is a constant that takes into account the size of the program needed to test primality.

Neither Shannon's nor Kolmogorov's theory has anything to do with meaning. For example, a message can be very meaningful to humans, and yet have little Kolmogorov information (such as the answer "yes" to a marriage proposal), and have little meaning to humans, yet have much Kolmogorov information (such as most strings obtained by 1000 flips of a fair coin).

Both Shannon's and Kolmogorov's theories are well-grounded mathematically, and there are thousands of papers explaining them and their consequences. Shannon and Kolmogorov information obey certain well-understood laws, and the proofs are not in doubt.

Creationist information, as discussed by Meyer, is an incoherent mess. One version of it has been introduced by William Dembski, and criticized in detail by Mark Perakh, Richard Wein, and many others (including me). Intelligent design creationists love to call it "specified information" or "specified complexity" and imply that it is widely accepted by the scientific community, but this is not the case. There is no paper in the scientific literature that gives a rigorous and coherent definition of creationist information; nor is it used in scientific or mathematical investigations.

Meyer doesn't define it rigorously either, but he rejects the well-established measures of Shannon and Kolmogorov, and wants to use a common-sense definition of information instead. On page 86 he approvingly quotes the following definition of information: "an arrangement or string of characters, specifically one that accomplishes a particular outcome or performs a communication function". For Meyer, a string of symbols contains creationist information only if it communicates or carries out some function. However, he doesn't say explicitly how much creationist information such a string has. Sometimes he seems to suggest the amount of creationist information is the length of the string, and sometime he suggests it is the negative logarithm of the probability. But probability with respect to what? Its causal history, or with respect to a uniform distribution of strings? Dembski's definition has the same flaws, but Meyer's vague definition introduces even more problems. Here are just a few.

Problem 1: there is no univeral way to communicate, so Meyer's definition is completely subjective. If I receive a string of symbols that says "Uazekele?", I might be tempted to ignore it as gibberish, but a Lingala speaker would recognize it immediately and reply "Mbote". Quantities in mathematics and science are not supposed to depend on who is measuring them.

Problem 2: If we measure creationist information solely by the length of the string, then we can wildly overestimate the information contained in a string by padding. For example, consider a computer program P that carries out some function, and the identical program P', except n no-op instructions have been added. If he uses the length measure, then Meyer would have to claim that P' has something like n more bits of creationist information than P. (In the Kolmogorov theory, by contrast, P' would have only at most order log n more bits of information.)

Problem 3: If we measure creationist information with respect to the uniform distribution on strings, then Meyer's claim (see below) that only intelligence can create creationist information is incorrect. For example, any transformation that maps a string to the same string duplicated 1000 times creates a string that, with respect to the uniform distribution, is wildly improbable; yet it can easily be produced mechanically.

Problem 4: If we measure creationist information with respect to the causal history of the object in question, then we are forced to estimate these probabilities. But since Meyer is interested in applying his method to phenomena that are currently poorly understood, such as the origin of life, all he's really doing (since his creationist information is sometimes the negative log of the probability) is estimating the probability of these events -- something we can't reasonably do, precisely because we don't know that causal history. In this case, all the talk about "information" is a red herring; he might as well say "Improbable - therefore designed!" and be done with it.

Problem 5: All Meyer seems interested in is whether the string communicates something or has a function. But some strings communicate more than others, despite being the same length, and some functions are more useful than others. Meyer's measure doesn't take this into account. A string like "It will rain tomorrow" and "Tomorrow: 2.5 cm rain" have the same length, but clearly one is more useful than the other. Meyer, it seems to me, would claim they have the same amount of creationist information.

Problem 6: For Meyer, information in a computational context could refer to, for example, a computer program that carries out a function. The longer the program, the more creationist information. Now consider a very long program
that has a one-letter syntax error, so that the program will not compile. Such a program does not carry out any function, so for Meyer it has no information at all! Now a single "point mutation" will magically create lots more creationist information, something Meyer says is impossible.

Even if we accept Meyer's informal definition of information with all its flaws, his claims about information are simply wrong. For example, he repeats the following bogus claim over and over:

p. 16: "What humans recognize as information certainly originates from thought - from conscious or intelligent human activity... Our experience of the world shows that what we recognize as information invariably reflects the prior activity of conscious and intelligent persons."

p. 291: "Either way, information in a computational context does not magically arise without the assistance of the computer scientist."

p. 341: "It follows that mind -- conscious, rational intelligent agency -- what philosophers call "agent causation," now stands as the only cause known to be capable of generating large amounts of specified information starting from a nonliving state."

p. 343: "Experience shows that large amounts of specified complexity or information (especially codes and languages) invariably originate from an intelligent source -- from a mind or personal agent."

p. 343: "...both common experience and experimental evidence affirms intelligent design as a necessary condition (and cause)
of information..."

p. 376: "We are not ignorant of how information arises. We know from experience that conscious intelligent agents can create informational sequences and systems."

p. 376: "Experience teaches that whenever large amounts of specified complexity or information are present in an artifact or entity whose causal story is known, invariably creative intelligence -- intelligent design -- played a role in the origin of that entity."

p. 396: "As noted previously, as I present the evidence for intelligent design, critics do not typically try to dispute my specific empirical claims. They do not dispute that DNA contains specified information, or that this type of information always comes from a mind..."

I have a simple counterexample to all these claims: weather prediction. Meteorologists collect huge amounts of data from the natural world: temperature, pressure, wind speed, wind direction, etc., and process this data to produce accurate weather forecasts. So the information they collect is "specified" (in that it tells us whether to bring an umbrella in the morning), and clearly hundreds, if not thousands, of these bits of information are needed to make an accurate prediction. But these bits of information do not come from a mind - unless Meyer wants to claim that some intelligent being (let's say Zeus) is controlling the weather. Perhaps intelligent design creationism is just Greek polytheism in disguise!

Claims about information are central to Meyer's book, but, as we have seen, many of these claims are flawed. There are lots and lots of other problems with Meyer's book. Here are just a few; I could have listed dozens more.

p. 66 "If the capacity for building these structures and traits was something like a signal, then a molecule that simply repeated the same signal (e.g., ATCG) over and over again could not get the job done. At best, such a molecule could produce only one trait."

That's not clear at all. The number of repetitions also constitutes information, and indeed, we routinely find that different numbers of repetitions result in different functions. For example, Huntington's disease has been linked to different numbers of repetitions of CAG.

p. 91: "For this reason, information scientists often say that Shannon's theory measures the "information-carrying capacity," as opposed to the functionally specified information or "information content," of a sequence of characters or symbols.

Meyer seems quite confused here. The term "information-carrying capacity" in Shannon's theory refers to a channel, not a sequence of characters or symbols. Information scientists don't talk about "functionally specified information" at all, and they don't equate it with "information content".

p. 106: (he contrasts two different telephone numbers, one randomly chosen, and one that reaches someone) "Thus, Smith's number contains specified information or functional information, whereas Jones's does not; Smith's number has information content, whereas Jones' number has only information-carrying capacity (or Shannon information)."

This is pure gibberish. Information scientists do not speak about "specified information" or "functional information", and as I have pointed out, "information-carrying capacity" refers to a channel, not a string of digits.

p. 106: "The opposite of a complex sequence is a highly ordered sequence like ABCABCABCABC, in which the characters or constituents repeat over and over due to some underlying rule, algorithm, or general law."

This is a common misconception about complexity. While it is true that in a string with low Kolmogorov complexity, there is an underlying rule behind it, it is not true that the "characters or constituents" must "repeat over and over". For example, the string of length n giving a 1 or 0 depending on whether i is a prime number (for i from 1 to n) has low Kolmogorov complexity, but does not "repeat over and over".

p. 201 "Building a living cell not only requires specified information; it requires a vast amount of it -- and the probability of this amount of specified information arising by chance is "vanishingly small."

Pure assertion. "Specified information" is not rigorously defined. How much specified information is there in a tornado? A rock? The arrangement of the planets?

p. 258 "If a process is orderly enough to be described by a law, it does not, by definition, produce events complex enough to convey information."

False. We speak all the time about statistical laws, such as the "law of large numbers". Processes with a random component, such as mutation+selection, can indeed generate complex outcomes and information.

p. 293: "Here's my version of the law of conservation of information: "In a nonbiological context, the amount of specified information initially present in a system Si, will generally equal or exceed the specified information content of the final system, Sf." This rule admits only two exceptions. First, the information content of the final state may exceed that of the initial state, Si, if intelligent agents have elected to actualize certain potential states while excluding others, thus increasing the specified information content of the system. Second, the information content of the final system may exceed that of the initial system if random processes, have, by chance, increased the specified information content of the system. In this latter case, the potential increase in the information content of the system is limited by the
"probabilistic resources" available to the system."

Utterly laughable. The weasel word "generally" means that he can dismiss exceptions when they are presented. And what does "in a nonbiological context" mean? How does biology magically manage to violate this "law"? If people are intelligent agents, they are also assemblages of matter and energy. How do they magically manage to increase information?

p. 337 "Neither computers by themselves nor the processes of selection and mutation that computer algorithms simulate can produce large amounts of novel information, at least not unless a large initial complement of information is provided."

Pure assertion. "Novel information" is not defined. Meyer completely ignores the large research area of artificial life, which routinely accomplishes what he claim is impossible. The names John Koza, Thomas Ray, Karl Sims, and the term "artificial life" appear nowhere in the book's index.

p. 357: "Dembski devised a test to distinguish between these two types of patterns. If observers can recognize, construct, identify, or describe apttern without observing the event that exemplifies it, then the pattern qualifies as independent from the event. If, however, the observer cannot recognize (or has no knowledge of) the pattern apart from observing the event, then the event does not qualify as independent."

And Dembski's claim to have given a meaningful definition of "independence" is false, as shown in detail in my paper with Elsberry -- not referenced by Meyer.

p. 396: "As noted previously, as I present the evidence for intelligent design, critics do not typically try to dispute my specific empirical claims. They do not dispute that DNA contains specified information, or that this type of information always comes from a mind..."

Critics know that "specified information" is a charade, a term chosen to sound important, with no rigorous coherent definition or agreed-upon way to measure it. Critics know that information routinely comes from other sources, such as random processes. Mutation and selection do just fine.

In summary, Meyer's claims about information are incoherent in places and wildly wrong in others. The people who have endorsed this book, from Thomas Nagel to Philip Skell to J. Scott Turner, uncritically accepting Meyer's claims about information and not even hinting that he might be wrong, should be ashamed.

Tuesday, January 12, 2010

When is a Request Inappropriate?

I get a lot of requests in e-mail from people in theoretical CS: requests to write letters of recommendation, to serve on thesis committees, to referee papers, to serve on grant evaluation committees, to read a paper that someone wrote and let them know what I think of it, etc. In this I am not unusual - probably many of my colleagues get even more requests than I do.

Occasionally, however, I get requests that I find inappropriate. One of them arrived today. A student from a developing country asked me to send him an electronic copy of a paper by Ginsburg and Spanier that appeared in SIAM Journal on Control in the 1960's.

Here's what I wrote back:

Let me explain to you - hopefully gently - why your request for me to provide you with a copy of an article that I cited in my book is an inappropriate one.

First, your university library probably has this journal.

Second, if they do not, academic libraries participate in something called "interlibrary loan" where they can get copies (usually for free) of articles in journals they do not have. You should try this next.

Third, although it's reasonable to contact an author and ask them for a copy of a paper they wrote, it's usually not reasonable to write to person A to get a copy of person B's paper. The exceptions might be 1) if person A and person B are co-authors; 2) if the paper appeared in an extremely obscure venue and is basically impossible to get. In that case, it might be a reasonable request, /but/ you would need to acknowledge that you would be wasting the other person's time and apologize in advance for doing so. Neither 1) nor 2) apply here.

Fourth, think about what would happen to me if everyone who read one of my books asked me to provide them with an article I cited. I would never get any work done!

I thank you again for your interest in my book, and I apologize for not being able to help you.

Was I wrong? Should I have spent the 10 minutes it would have taken to log on to the Waterloo library system, locate the article, download it, and send it to him?

Monday, January 11, 2010

Bumper Sticker Fail

The bumper sticker reads: "Welcome to America / Now Speak English".

The license plate reads "THREDZ".

Do I need to say more?

Maybe I do. My grandfather came to the US in 1912. For many years he spoke only Yiddish and very broken English. Despite this, he managed to start a business and raise a family.

There's no requirement that immigrants to the US speak English fluently. The vast majority of them will learn English because it is in their economic self-interest. And their children will almost certainly speak English - probably better than the owner of this car, who can't seem to spell "threads".

[Yes, I know, it's the name of his business. There you can find other logically and/or grammatically suspect utterances, such as "Experts in embroidery, screen-printing and sourcing products with creative distinction are just a few of the things that set Thredz Unlimited apart from others."]

Saturday, January 09, 2010

Richard Wiseman at Boston Skeptics

Great time at the Boston Skeptics meeting in Harvard Square last night. Richard Wiseman delivered a very funny 1-hour presentation about magic, science, skepticism, and mass media.

He showed a couple of videos. Here's one called "The Amazing Colour-Changing Card Trick":

And here's another called "Corkology". Stop the video before he shows you how it's done and try to figure it out.

And who was that mysterious man in black in attendance? Why, none other than the mysterious Blake Stacey.

Thursday, January 07, 2010

New Pi Computation

Here's an interesting item: Fabrice Bellard has computed 2,699,999,990,000 decimal digits of π on a single desktop computer, beating records previously held by supercomputers.

The computation took about 131 days, and beats the previous record of 2,576,980,370,000 decimal digits.

Speaking of π, this interesting page lets you search for patterns in the first 200 million digits of π. For example, 00000000 appears for the first time at "position 172,330,850 counting from the first digit after the decimal point".

Wednesday, January 06, 2010

Weirdest Request to Work With Me

I get a lot of requests from students who want to work with me - often Indian students who want to do "summer internships". But here is the weirdest one I've gotten so far:

I, A****** P*****, am a fourth year undergraduate student enrolled for the Dual Degree Course (5 year B.Tech + M.Tech) in the Department of Civil Engineering, Indian Institute of Technology, Kharagpur, the leading engineering university of the country.

I am currently in pursuit of an internship/project for a period of 8 weeks during May 2010 to July 2010, which would be of help to me in gaining experience and required knowledge in the field of structural engineering.I have been regularly following your articles in the journal of Finite Elements in Analysis and Design. I have gone through your article Finite element formulation for geometric and material nonlinear analysis of beams prestressed with external slipping tendons which was intellectually very stimulating. I then checked your website and am happy to be genuinely excited about any fortunate opportunities of working under your esteemed guidance. I am very interested in the field of structural engineering and am in the idea of pursuing my doctoral degree in the same field.

Needless to say, I don't work in "structural engineering", and I never have published in Finite Elements in Analysis and Design.

Tuesday, January 05, 2010

Discovery Institute Busted

It seems the clowns at the Discovery Institute just can't stand being criticized - so much so that they issued a bogus DMCA takedown notice on a youtube video. The DI says it's all about the unauthorized use of their logo, and they say they don't "contest right [sic] of this user to publish satire, parody, or criticism", but that's about as believable as their other claims.

Monday, January 04, 2010

Somerville and Schuklenk on Dignity

Margaret Somerville weighs in on "dignity" here.

Udo Schuklenk takes apart the concept of "dignity" here.

Who do you think has made a better case?

Sunday, January 03, 2010

Who's the President of Physics?

From xkcd, with a hat tip to Adrian Petrescu.

Saturday, January 02, 2010

The Mascot

My wife recently gave me a copy of The Mascot: Unraveling the Mystery of My Jewish Father's Nazi Boyhood, by Mark Kurzem. The book, which came out in 2007, is the story of Alex Kurzem, a man who, at the age of 5, watched his family being murdered by a death squad in Koidanov (now Dziarzynsk, Belarus) during World War II, then escaped to the woods where he was "adopted" by Latvian SS soldiers. The soldiers treated him as a "mascot", made him a child-sized SS uniform, and featured him in propaganda videos -- all without apparently realizing that he was Jewish. Alex kept his past hidden from his family for 50 years until he revealed it to his son, the author of the book (who tragically passed away quite recently). Eventually Alex tracks down what was probably his family and learns his true name.

Since some other recent Holocaust memoirs, such as Binjamin Wilkomirski's Fragments: Memories of a Wartime Childhood, Herman Rosenblat's Angel at the Fence, and Misha Defonseca's Misha: A Mémoire of the Holocaust Years, have proven to be false in part or in full, it is not surprising that Kurzem's amazing story would be greeted with some skepticism. And indeed, I was initially skeptical. After all, part of the story is based on a 70-year-old man's recollection of events when he was 5 years old. But the documentation provided, including photographs, convinces me that the main lines of the story are genuine, although some minor details may be incorrect.

The book depicts Latvian fascists in a rather unflattering light, so it is not surprising that some far right and Latvian groups want to cast doubt on Kurzem's story. For example, 60 Minutes did a segment on Kurzem, and some of the comments are nasty and anti-Semitic:

Jerzy Ulicki-Rek, for example, says "As 56 years old sane man who studies "holo-history" and "holo-miracles" since over 20 years I do not believe in yours crazy story", while an anonymous commenter writes "Z.O.G. is at it again." (Z.O.G., in case you didn't know, is a neo-Nazi abbreviation for "Zionist Occupation Government", the supposed control of the government by Jews.)

Edith S. Kubicek on amazon writes "For the past year grave doubts have been raised concerning the veracity of this compelling tale. The doubts were first initiated by the Latvian community in Australia and a number of U.S. researchers now agree that this book may be a complete hoax." But she does not mention any of these "U.S. researchers" by name, and the book is so well-documented it seems difficult to doubt large parts of the story.

The book is well-written, almost like a mystery. I'd definitely recommend this surprising and unsettling book to anyone interested in World War II or Holocaust history.

Friday, January 01, 2010

Free Will Being Challenged

I have thought for a long time that "free will" is an incoherent philosophical concept. I'm not sure one can define it in any reasonable way. It is not simply the capacity for choice, because a machine flipping a coin would achieve the same result. So what is it? For the present, I will assume it refers to our feeling of being "in control".

We all have the sensation of being "in control", but how do we decide whether a biological organism other than us possesses free will? Does a bonobo have it? A dolphin? A cockroach? A bacterium? Can philosophy alone offer any guidance? I don't think so. Samuel Johnson once remarked, "All theory is against the freedom of the will; all experience for it." But we know that our common-sense experience doesn't always match up to the physical world, as in our strange system for perceiving color and how it can be fooled. So simply feeling that we have free will doesn't mean we actually do. Maybe we don't.

I think it quite possible that we lack free will in any reasonable sense - that, in fact, our actions are essentially deterministic. Despite this, I also think that our feeling that we are "in control" has a plausible basis -- I guess this makes me a "compatibilist", like Daniel Dennett. But I have a slightly different take on why, which is probably not original, but which I've never seen discussed in philosophy texts, although someone has probably done so. Namely, I'd guess that our computational hardware and software is so complex that it is not easy to predict the outcome of any situation with high probability - and in particular, we cannot even know how we ourselves will react in any given situation. We probably can do a simulation in principle, but in practice such a simulation would take too much time. So although we don't have free will in actual fact, the unpredictability of our actions makes it appear we do to beings with limited computational resources, such as ourselves. I'm hopeful that the theory of computational complexity may eventually play a role in a generally-accepted solution to the conundrum that has baffled philosophers for centuries.

The experiments of Benjamin Libet and co-authors cast doubt on our perception of being "in control". Libet found that subjects had activity in their brains about 300 milliseconds before they were aware of their volition to press a button. A more recent study found brain activity as much as 10 seconds before subjects were aware of their own conscious decisions. This popular article in Wired addresses it; for more technical details, see the article in Nature Neuroscience.

I was motivated to mention this by a recent solicitation to give money by my alma mater that mentions a freshman seminar devoted to these topics. I think it's great that cutting-edge research (the Nature Neuroscience article is from 2008) makes it so quickly to undergrad classes. And as we understand the science of decision-making better, more philosophers will be able to base their age-old speculations on some actual data instead of armchair thoughts.