Thursday, October 23, 2014

I See Berlinskis


Hey, there's a new science journal out. It's called Inference Review.

Sorry, I should have really said that it's a new "science" journal. That's because the weirdness is strong --- very strong --- with this one.

Just look at the first articles they published. One is by Michael Denton, the odd biologist who published an anti-evolution book called Evolution: A Theory in Crisis back in 1985. Needless to say, that book was filled with errors and misunderstandings. That ignorance, however, didn't prevent Denton from acquiring a big fan base among the intelligent design crowd (when does it ever?); Phillip E. Johnson and the laughable George Gilder counted themselves among Denton's fans. And Denton's new Inference Review article is touted by none other than that pathetic ID pipsqueak Casey Luskin.

Demonstrating yet another example of crank magnetism, a second Infererence Review article is by global warming skeptic William Kininmonth.

Are you beginning to get suspicious yet? Who's running the show here?

Well, we don't know. Unlike real science journals, nowhere on the website for Inference Review can one find a listing of the editorial board. I wonder why they want to hide...

A sharp-eyed commenter on a private mailing list points out, however, that the journal's twitter followers include, in addition to a few gullible science journalists, two different Berlinskis: Mischa and the eminently silly Claire Berlinski.

Hmmm. What would possess two Berlinskis to follow an obscure and mysterious "science" journal with intelligent design creationist and global warming denialist leanings?

Read some of the pages and you'll come to the same conclusion I did. That ol' poseur David Berlinski is surely involved somehow. All the signs are there: the Francophilia (why else would the grotesque caricatures be featured?), the pretension, the supercilious turns, the obsession with criticizing evolution, the solicitation for articles on mathematics topics dear to David, and the use of the word "irrefragable"; all are Berlinski hallmarks.

C'mon, David! Don't hide your light under a bushel. Come out into the open.

Monday, October 20, 2014

Most Philosophers Have Nothing Interesting to Say About The Brain


If you want to understand the brain, look to neuroscience. Most philosophers (unless they have some decent neuroscience training*) have simply nothing of interest to say. The reason why is that (a) their speculations were not tied to any physical models and (b) their claims were often so vague or incoherent they could not be verified and (c) when the claims were more precise, there was rarely an effort to prove or disprove through experimentation.

Instead, philosophers gave us time-wasters like the "Chinese room argument" (still taken seriously by some very smart people, which I find astonishing) and the silly and overblown early anti-AI claims of Hubert Dreyfus (who actually got awards for his work).

Of course, it's going to be really hard to understand how the brain works. That's because the immense complications of the brain did not arise through intelligent design -- which would have given us nice discrete subsystems that interact in controlled and efficient ways -- but rather through the rather higgledy-piggledy bricolage of billions of years of evolution.

Nevertheless, we're making some small progress in understanding the brain and the mind and the mind-body problem and perception and memory and awareness and "understanding" and consciousness and free will, and other conundrums that have baffled philosophers for thousands of years. For example, read Crick's The Astonishing Hypothesis. The tools philosophers used -- until recently -- were simply too puny to get anything reasonable done.

When you read a philosopher on the brain or the mind, look for the warning signs. Here's one: do they treat things like "consciousness" and "understanding" as a binary property -- that something either has or doesn't have? Or do they explicitly recognize that these could lie on a continuous (or at least variable) spectrum? If the former, beware.

If reading Crick is too much work, you can also show up today, at the University of Waterloo, to hear my colleague Jeff Orchard speak on "Computing Between Your Ears".

* For philosophers who really do have something to say, look at, for example, the Churchlands.

Saturday, September 27, 2014

Calling all ID Advocates: Employment Awaits


One of the points of my long paper with Elsberry was that intelligent design (ID) advocates talk a big game, but don't actually accomplish anything.

They claim their methods are revolutionary. They claim that all sorts of fields, like archeology and forensic science, use "pre-theoretic" versions of their "design detection" methodology. Yet when it comes to actually applying their methods where they would potentially be useful, what happens?

Crickets chirping...

In fact, in 2003 we published a little paper, "Eight challenges for intelligent design advocates", where we asked ID advocates to prove their silly ideas useful in practice.

Needless to say, not a single ID advocate has come forward with an answer to any of our challenges.

Well, here's another. Recently archaeologists discovered what may be evidence of the earliest sign of humans in what is now Canada.

As the article says, researchers are not completely sure yet. They may have found a stone weir constructed to catch fish, or they may have found a natural, non-human-constructed formation: "A geologist will now study the images to ensure the rocks are not a natural formation..."

Needless to say, there is no sign these researchers are basing their decision on the research oeuvre of William Dembski to decide the question.

But why not? After all, detecting design is what ID advocates say they're really, really good at. Better than all those stupid "materialist" scientists.

So have at it, ID advocates! Volunteer your massive expertise here. Do your investigations. Create your specifications, prove they're independent, tell us what the "rejection region" is, and so forth. Write a paper with your decision about these possible stone weirs. Publish it in the peer-reviewed literature --- you know, a real journal like Science or Nature, not the creationist circle-jerk that is Bio-Complexity. (Try not to be fooled the way Dembski was about the so-called "bible codes".)

What are you waiting for?

Silly Barry. Have a Cookie.


Have you ever had this experience? You're having a technical discussion and someone you don't know well is listening. Then they enter the conversation, and from the first thing they say, you realize they have absolutely no idea what's going on, but they think they do. At this point, the only thing to do is to give the poor fellow a cookie and move on.

Person 1: "So, you see, since the derived subgroup is not supplemented by a proper normal subgroup, it follows that the group is imperfect..."

Very Silly Person: "Wait a second, the rock group Brand New split off from The Rookie Lot, and they're pretty perfect."

Person 2: "Umm... yes... Here, have a cookie and go play outside."

That's why it's usually a waste of time having a discussion with intelligent design (ID) advocates. The vast majority of them have absolutely no idea what people like William Dembski claim; they just know that ID is in agreement with their religious beliefs, so they support it.

I was reminded of this when I saw the response of certified public accountant Barry Arrington to my my post pointing out his misunderstandings.

Now, maybe in some universes certified public accountants are the people to go to when you want to understand the basics of information theory. But not in the one I live in. Christians like Barry go on and on about how humble they are, but when someone takes the time to explain a basic mistake like the one Arrington made, how do they behave? With arrogance and ignorance.

I'll briefly summarize Arrington's mistakes and misrepresentations.

1. "Correction, I [Arrington] routinely ban trolls, who then claim they were banned for dissenting." A lie. All one has to do is look at this page, which has example after example of Mr. Arrington's intolerance of criticism. Then there was the famous agree with the laws of logic or be banned episode. One poster said it best: "The only firm rule at UD seems to be, Thou Shalt Not Make Barry Arrington Feel Inadequate".

2. Showing he can google a phrase just as well as the next fellow, Arrington brings in a quote from Steve Ward about pseudorandom numbers. It has pretty much nothing to do with what we are discussing, but Silly Barry doesn't understand that. Silly Barry could attend my current course CS 341, where we discuss the generation of pseudorandom numbers in Lecture 11.

3. Arrington tries to distract from his mistake by claiming "The issue is whether – as with the CD player in Ward’s illustration – it is random enough for the purposes for which it is employed." No, the issue is, was string #1 more or less random than string #2? Barry implied it was more random. I showed why he was wrong.

4. Arrington says "Shallit believes he has achieved some great triumph of argumentation by demonstrating that the first string is not truly, completely and vigorously random...". Actually, what I showed was that string #1 was actually less random than string #2.

5. "So, according to Shallit’s calculations an excerpt from Hamlet’s soliloquy is “more random” than a string of text achieved by randomly banging away on a keyboard. That is a sentence only a highly educated idiot could have written." Ahh, the traditional ploy of the scientifically illiterate: your conclusion (about evolution, global warming, the roundness of the earth, scientific theory of disease) disagrees with my preconceptions. Therefore you are the idiot! Very Silly People have used this ploy for hundreds of years. So far it's not working so well for them.

6. "The larger point – and here Shallit gives the store away – is his admission that he detected the design of the first string using rigorous statistical methods." Poor Silly Barry. I said nothing about "design" at all; the word doesn't even appear in my post. I didn't say anything about "statistical methods", either. The method I used is based on information theory, not statistics. (But Barry knows little advanced mathematics, it's clear.)

Barry, and all ID advocates, need to understand one basic point. It's one that Wesley Elsberry and I have been harping about for years. Here it is: the opposite of "random" is not "designed".

I'll say it again. Just because an event E is not "random" (more precisely, that it deviates from uniform distribution with equal probabilities) does not mean it was "designed" by some natural or supernatural agent. There are many possible explanations. It could have arisen from a uniform random process with unequal probabilities, like (in the case of string #1) a stochastic process biased towards the letters "a", "s", and "d". It could have arisen from a nonuniform random process like a Markov model. It could have arisen from some deterministic process -- basically, an algorithm -- that could have arisen naturally or with human agency. There are lots of possibilities. Silly Barry doesn't understand that.

7. "Jeffery Shallit has spent years denying the basic formulation of ID: Some patterns are best explained by the act of an intelligent agent." I'll overlook the spelling incompetence of Mr. Arrington (although it is basic politeness to spell a man's name correctly). Nobody denies human agency or the ability of scientists to detect it in many cases. What ID critics point out, though, is that those who detect human agency aren't detecting "Design" with a capital "D". They are detecting artifacts: the characteristic product of human activity. For a good look at why capital-D "Design" is basically a charade, read the fine article of Wilkins and Elsberry published in Biology and Philosophy. When Mr. Arrington gets his Very Silly views published in a philosophy journal, give me a call.

8. Yet here he is yelling from the rooftops: "That first string of text only appears to be random; I have demonstrated rigorously that it was in fact designed." This is a manufactured quote by Mr. Arrington. (Using fake quotes is a disease of ID advocates in general and Mr. Arrington in particular.) I didn't say that at all. I said string #1 was not as random as string #2 (in the sense of being more compressible), and then I guessed how it came to be constructed, a guess that is based on what I know of Mr. Arrington and keyboards and the typical behavior of certified public accountants.

9. "In ID theory the “specification” of a strnig of text, for instance, is closely related to how compressible the description of the string is. In other words, whether a given string of text is “specified” is determined by whether the description of the string can be compressed. Take the second group of text as an example. It can be compressed to “first 12 lines of Hamlet’s soliloquy.” This is simply not possible for the first string. The shortest full description of the first string is nothing less than the string itself."

Once again Barry shows he doesn't understand anything. In Dembski's original formulation, there was no requirement that the "description" of a string be compressible. (Arrington seems even more confused, in that he talks about the "description of the string" as opposed to the string itself. Does he think the specification needs to be compressible or the string? Who can tell, with such shoddy writing?) And he makes the silliest mistake of all when he says "The shortest full description of the first string is nothing less than the string itself". That hilarious misunderstanding gives away the store: Arrington has understood nothing of what I wrote. The experiment using gzip shows that string #1, just like string #2, can indeed be compressed; it shortest description is indeed shorter than itself.

Barry says that string #2 can be compressed to "first 12 lines of Hamlet's soliloquy". But of course, this is not a compression that anyone in information theory would regard as legitimate, because it does not allow one to reconstruct the string losslessly without reference to an external source: namely, a book of Shakespeare. Real compressions do not have external referents like that (except, perhaps, to the particular computational model of compression). We talk about this basic misunderstanding in my CS 462/662 course, given each year in the Winter term. Mr. Arrington is invited to attend.

Now one could consider that "design detection" takes place in a framework of "background knowledge". Then "first 12 lines of Hamlet's soliloquy" would be a specification, not a compression. But then someone raised in Mongolia would likely not have the same background knowledge. So their measure of the "specified information" or "specified complexity" of string #2 would differ from Barry's. This shows the weakness of the "background knowledge" component of ID claims, as we pointed out: quantities in mathematics and science are not supposed to differ based on who measures them.

10. And finally, here's the funniest thing of all. There are actually at least two different legitimate ways to criticize my analysis on a technical basis. I even gave a not-so-subtle hint about one of them! Yet the Uncommon Descent folks, harnessing all the power of intellectual heavyweights like Barry Arrington and Eric Anderson and Gordon Mullings, could not manage to find them. What a surprise.

Silly Barry. Have a cookie.

Thursday, September 25, 2014

Eric Anderson is Silly, Too!


I really love Uncommon Descent!

Believe it or not, they have a whole thread devoted to how horrible I am.

Here's what silly nonentity Eric Anderson says:

As I pointed out, if Shallit’s bluff were true, he would be sitting on a Nobel Prize right now and would not be revealing the secret in some college computer science class."

My supposed "bluff" is my claim that we know what produces information. But it's not a bluff. Ask any mathematician or computer scientist if they know how to produce information in the normally-understood (Kolgomorov) sense of the word, and the answer is easy.

Randomness.

Any process generating truly random bits will generate strings with high Kolmogorov information with very very high probability.

Don't expect creationists to understand this, however.

Want to know more? Attend my CS 462/662 course starting in Winter 2015.

Barry Arrington's Silly Misunderstanding


Ever since the ID creationist blog Uncommon Descent was taken over by Barry Arrington, it's been a first-class show of the irremediable arrogance and ignorance of creationists. I don't post there because Arrington routinely bans dissenters, but I do sometimes enjoy the show.

I particularly enjoyed this post because it touches on the subject of my Winter 2015 course here at the University of Waterloo. Arrington displays two strings of symbols and says "the second string is not a group of random letters because it is highly complex and also conforms to a specification". By implication he thinks the first string is a group of random letters, or at the very least, more random than the second.

Here are the two strings in question, cut-and-pasted from Arrington's post:

#1:

OipaFJPSDIOVJN;XDLVMK:DOIFHw;ZD
VZX;Vxsd;ijdgiojadoidfaf;asdfj;asdj[ije888
Sdf;dj;Zsjvo;ai;divn;vkn;dfasdo;gfijSd;fiojsa
dfviojasdgviojao’gijSd’gvijsdsd;ja;dfksdasd
XKLZVsda2398R3495687OipaFJPSDIOVJN
;XDLVMK:DOIFHw;ZDVZX;Vxsd;ijdgiojadoi
Sdf;dj;Zsjvo;ai;divn;vkn;dfasdo;gfijSd;fiojsadfvi
ojasdgviojao’gijSd’gvijssdv.kasd994834234908u
XKLZVsda2398R34956873ACKLVJD;asdkjad
Sd;fjwepuJWEPFIhfasd;asdjf;asdfj;adfjasd;ifj
;asdjaiojaijeriJADOAJSD;FLVJASD;FJASDF;
DOAD;ADFJAdkdkas;489468503-202395ui34

#2:

To be, or not to be, that is the question—
Whether ’tis Nobler in the mind to suffer
The Slings and Arrows of outrageous Fortune,
Or to take Arms against a Sea of troubles,
And by opposing, end them? To die, to sleep—
No more; and by a sleep, to say we end
The Heart-ache, and the thousand Natural shocks
That Flesh is heir to? ‘Tis a consummation
Devoutly to be wished. To die, to sleep,
To sleep, perchance to Dream; Aye, there’s the rub,
For in that sleep of death, what dreams may come,
When we have shuffled off this mortal coil,

Needless to say, Arrington -- a CPA and lawyer who apparently has no advanced training in the mathematics involved -- doesn't specify what he means by "group of random letters". I think a reasonable interpretation would be that he is imagining that each message is generated by a stochastic process where each letter is generated independently, with uniform probability, from some finite universe of symbols.

Even with just a cursory inspection of the two strings, we see that neither one of them is likely to be "random" in this sense. We immediately see this about the second string because the set of reasonable English texts is quite small among the set of all possible strings. But we also see the same thing about the first because (for example) the trigram "asd" occurs much more often than one could reasonably expect for a random string. Looking at a keyboard, it's a reasonable interpretation that somebody, probably Arrington, dragged his hands repeatedly over the keyboard in a fashion he or she thought was "random" -- but is evidently not. (It is much harder to generate random strings than most untrained people think.)

If we want to test this in a quantitative sense, we can use a lossless compression scheme such as gzip, an implementation of Lempel-Ziv. A truly random file will not be significantly compressible, with very very high probability. So a good test of randomness is simply to attempt to compress the file and see if it is roughly the same size as the original. The larger the produced file, the more random the original string was.

Here are the results. String #1 is of length 502, using the "wc" program. (This also counts characters like the carriage returns separating the lines.) String #2 is of length 545.

Using gzip on Darwin OS on my Mac, I get the following results: string #1 compresses to a file of size 308 and string #2 compresses to a file of size 367. String #2's compressed version is bigger and therefore more random than string #1: exactly the opposite of what Arrington implied!

I suppose one could argue that the right measure of "randomness" is not the size of the compressed file, but rather the difference in size between the compressed file and the original. The smaller this difference is, the more random the original string was. So let's do that test, too. I find that for string #1, this difference is 502-308 = 194, and for string #2, this difference is 545-367 = 178. Again, for string #2 this difference is smaller and hence again string #2 is more random than string #1.

Finally, one could argue that we're comparing apples and oranges because the strings aren't the same size. Maybe we should compute the percentage of compression achieved. For string #1 this percentage is 194/502, or 38.6%. For string #2 this percentage is 178/545, or 32.7%. String #2 was compressed less in terms of percentage and hence once again is more random than string #1.

Barry's implications have failed spectacularly in every measure I tried.

Ultimately, the answer is that it is completely reasonable to believe that neither of Barry's two strings is "random" in the sense of likely to have been generated randomly and uniformly from a given universe of symbols. A truly random string would be very hard to compress. (Warning: if you try to do this with gzip make sure you use the entire alphabet of symbols available to you; gzip is quite clever if your universe is smaller.)

By the way, I should point out that Barry's "conforms to a specification" is the usual ID creationist nonsense. He doesn't even understand Dembski's criterion (not surprising, since Dembski stated it so obscurely). String #2 can be said to "conform" to many, many different specifications: English text, English text written by Shakespeare, messages of length less than 545, and so forth. But the same can be said for string #1. We addressed this in detail in our long paper published in Synthese, but it seems most ID creationists haven't read it. For one thing, it's not good enough to assert just "specification"; even by Dembski's own claims, one must determine that the specification is "independent" and one must compute the size of the space of strings that conforms to the specification. For Dembski, it's not the probability of the string being generated that is of concern; it's the relative measures of the universe of strings and the strings matching the specification that matters! Most ID creationists don't understand this basic point.

Elsewhere, Arrington says he thinks string #1 is more complex than string #2 (more precisely he says the "thesis ... that the first string is less complex than the second string ... is indefensible").

Maybe Barry said the exact opposite of what he meant; his writing is so incoherent that it wouldn't surprise me. But his statement, as given, is wrong again. For mathematicians and computer scientists, complexity of a string can be measured as the size of the optimal compressed version of that string. Again, we don't have a way to determine Kolmogorov complexity, so in practice one can use a lossless compression scheme as we did above. The larger the compressed result, the more complex the original string. And the results are clear: string #1 is, as measured by gzip, somewhat less complex than string #2.

ID creationists, as I've noted previously, usually turn the notion of Kolmogorov complexity on its head, pretending that random strings are not complex at all. We made fun of this in our proposal for "specified anti-information" in the long version of our paper refuting Dembski. Oddly enough, some ID creationists have now adopted this proposal as a serious one, although of course they don't cite us.

Finally, one unrelated point: Barry talks about his disillusion when his parents lied to him about the existence of a supernatural figure --- namely, Santa Claus. But he doesn't have enough introspection to understand that the analogy he tries to draw (with "materialist metaphysics") is completely backwards. Surely the right analogy is Santa Claus to Jesus Christ. Both are mythical figures, both are celebrated by and indoctrinated in by parents, both supposedly have supernatural powers, both are depicted as wise and good, and both are comforting to small children. The list could go on and on. How un-self-aware does one have to be to miss this?

Monday, September 22, 2014

Record Coverage Fails Again


Despite the fact that Waterloo Region is the home to many scientific and technically-minded people and businesses, the coverage of science and technology by our local paper, the Record, is truly abysmal. I've written about it before.

Here's yet another example: this article about naturopathy didn't include a single skeptical voice. Couldn't the reporter have noted, for example, that homeopathy is regarded by most medical experts as a fake and worthless therapy?

Wednesday, September 17, 2014

Gelernter's Non-Response


Over the years, I've pointed out a number of times when Yale professor David Gelernter has misrepresented the truth... like the time he claimed that the US Supreme Court "outlawed prayer and Bible reading in the public schools" (they didn't; the decision he cited refers to ending teacher-led devotion and indoctrination only).

But Gelernter -- who apparently doesn't believe that academics have the duty to justify their claims and retract them when wrong -- has never replied.

Until recently, that is. My brief correction of Gelernter's wild misrepresentation of the reaction to Thomas Nagel's silly book elicited this reply from Gelernter:

Little needs saying to Jeffrey Shallit, except that I was not using "lynch mob" to suggest that Nagel’s opponents wanted him to be hanged or even gently murdered. "Nagel had some fundamental misunderstandings about science and biology" is a statement some people might possibly disagree with, especially those who care about what a person knows versus what degrees he holds. As Emerson would have said: Ph.D.’s, Mr. Shallot, are the hobgoblin of little minds.

This is preposterous in so many ways.

1. Gelernter dismisses his own misrepresentations by insinuating I interpreted "lynch mob" literally. Read my reply again, and my longer and more detailed one here. (I sent Gelernter a link.) It is clear I am objecting to Gelernter's exaggerations. Maybe Gelernter thinks describing Nagel's critics as "punks" and a "lynch mob" and "mass attack of killer hyenas" is accurate and appropriate. Does anyone else?

2. Gelernter fails to address my points, saying only "some people might possibly disagree". True enough, but does their disagreement have any rational basis?

3. Gelernter implies I am a person who doesn't "care about what a person knows versus what degrees he holds". Well, which group of people is likely to know more about evolutionary biology? Actual evolutionary biologists, who disputed Nagel's claims in detail, or Nagel and Gelernter, who have no expertise and no training in evolutionary biology? I challenge any fair-minded person to read Nagel's book (I have), Gelernter's praise of it, and the reviews by people like Orr and Elliott Sober and decide who has made the better case.

4. Finally, Gelernter can't even be bothered to spell my name correctly, even when his only task is to copy and paste it from the first line of his own reply.

All in all, it's a pretty poor performance for Professor Gelernter. But -- I am not surprised to see -- par for the course.

Monday, September 15, 2014

Meet David Gelernter, First Amendment Hypocrite


The whiny and porcine David Gelernter has a column where he makes fun of Muslim students at Yale who have objected to Ayaan Hirsi Ali speaking there.

I'm very glad that Gelernter is such a stalwart defender of the 1st Amendment of the US constitution.

But then, let's read what he says about atheists who have rightly objected to forcing nontheist schoolchildren to publicly acknowledge their belief in the Christian god: the children have a choice, Gelernter says, because they can just shut up.

Oops, I guess that 1st Amendment is just so much chin music.