# Don’t Make Baby Gauss Cry

Because this is, of course, what everyone ought to do with a computational paper, we’ve put our code online, so you can check our calculations, or use these methods on your own data, without having to implement them from scratch. I trust that I will no longer have to referee papers where people use GnuPlot to draw lines on log-log graphs, as though that meant something, and that in five to ten years even science journalists and editors of Wired will begin to get the message.

Mark Liberman is not optimistic (we’ve got a long way to go).

Among several important take-home points, I found the following particularly amusing:
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# Power-law Distributions in Empirical Data

Throughout many fields of science, one finds quantities which behave (or are claimed to behave) according to a power-law distribution. That is, one quantity of interest, y, scales as another number x raised to some exponent:

$$y \propto x^{-\alpha}.$$

Power-law distributions made it big in complex systems when it was discovered (or rather re-discovered) that a simple procedure for growing a network, called “preferential attachment,” yields networks in which the probability of finding a node with exactly k other nodes connected to it falls off as k to some exponent:

$$p(k) \propto k^{-\gamma}.$$

The constant γ is typically found to be between 2 and 3. Now, from my parenthetical remarks, the Gentle Reader may have gathered that the story is not quite a simple one. There are, indeed, many complications and subtleties, one of which is an issue which might sound straightforward: how do we know a power-law distribution when we see one? Can we just plot our data on a log-log graph and see if it falls on a straight line? Well, as Eric and I are fond of saying, “You can hide a multitude of sins on a log-log graph.”

Via Dave Bacon comes word of a review article on this very subject. Clauset, Shalizi and Newman offer us “Power-law distributions in empirical data” (7 June 2007), whose abstract reads as follows:
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# Oh No, Not Again

Dammit, Warren, we don’t need you spreading pseudoscience along with everybody else. The Heim theory “spacedrive” is a total crock. Remember, this is the nonsense which John Baez called “a run-of-the-mill crackpot theory” and of which Sean Carroll said,

Just so nobody gets too excited â€” this paper is complete nonsense, not worth spending a minuteâ€™s time on. If I find the energy I might post on it, but this is no better than the other hundred crackpot preprints I get in the mail every year.

For details, you can start here and here. It looks like I might have to dig that post out of my “drafts” pile after all. . . .

New Scientist has a lot to answer for.

# Quick Post: Voices on the Net

Whoo! The Powers That Be keep inventing deadlines for me, so I will feed the blagobeast with a quick, quote-heavy post. Mark Chu-Carroll’s review of Behe’s The Edge of Evolution has attracted the attention of some creationist trolls, and some of the responses have been both memorable and pithy.

A mysterious being known only as Xanthir, FCD said the following:

As Mark implied, the distinction between micro- and macro-evolution is artificial and false. It amounts to drawing a line in the sand and saying, “Evolution can change things this much, but no further.” It says this without any reason why evolution wouldn’t be able to go past that point, and what’s more flies directly in the face of reams of actual data. It’s basically akin to splitting math into micro- and macro-arithmetic, and saying that numbers greater than a billion are part of macro-arithmetic and don’t occur through natural counting processes, and thus things that involve numbers past that line must have been created whole rather than building up from smaller quantities. The problem with that, of course, is that you can always add 1. Same thing here — you can always add one more mutation.

If you prefer the point made by early-1990s music video, see my earlier post, “Square One on Infinity” (and don’t say I didn’t warn you).

For the standard TalkOrigins critiques of the creationist micro/macro ploy, see here and here.

# 1 / 3 = 30%

OK, there’s so much to pick on in the Creation “Museum” that it constitutes a classic “target-rich environment,” but one of Media Czech’s photos is just too good to pass up:

First, I think rounding off to one significant figure represents a great advance for creationist mathematics. Dividing 1 by 3 to get 30% is a big improvement over their other, ahem, arithmetic issues (insisting on 6,000 when the actual figure is 13.7 billion, for example). Second. . . .
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# Behe’s Bad Arithmetic and Worse Science

I would like to celebrate the official release date of Michael Behe’s new book, The Edge of Evolution, by pointing out a grotesque factual error in its very heart.

A major theme, if not the major theme, of Behe’s diatribe is the disease known as malaria. He wants to prove that evolution by natural means of any but the most trivial features of living things is completely impossible, and he uses the parasites which cause malaria as his test case. Unfortunately for him, but happily for the decades of scientific discovery which he tries to condemn, the mistakes in his argument tear it asunder.

Since Behe’s argument is built upon malaria, and in particular the evolution of the parasite Plasmodium falciparum to be resistant to the drug chloroquine, we should look at what modern biology has learned about how chloroquine resistance evolved. As chloroquine was “the best and most affordable antimalarial drug” in the history of antimalarial drugs, the evolution of resistance to it — and the spread of that resistance throughout the world — poses a real problem, which scientists are naturally eager to investigate.

# CEO Kills 250 Million Americans

My day job, about which I am Not Yet At Liberty To Speak in detail, brings me into contact with people I didn’t expect to meet when I graduated MIT with a physics degree. I could understand rubbing elbows with software developers, but healthcare policy professionals were a whole ‘nother world. I mean, I managed to meet and mingle with a set technician for The Truman Show, not to mention Mary Prankster. (A friend of mine spent a year in Los Angeles, driving around with a Dresden Dolls bumper sticker. One day, a guy stopped her in a parking lot and exclaimed in wonder and joy, “You like the Dresden Dolls?” To which she replied, “I know the Dresden Dolls.” She assures me that I’ve met them too, at a party somewhere in this town, but it must have been an absolutely smashing party because I have no recollection of it whatsoever.) But corporate executives?

So, it is with considerable surprise that I find myself equipped to tell the tale of the CEO who killed 250 million Americans.
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# All ur hogs R belong 2 us

(Because the memes of yesteryear are ever so sweet, even ‘pon the jaded palates of today.)

I was distressed to see Cecilia fall for the giant hog story. The pictures, supposedly of an 11-year-old boy posing with the carcass of a giant pig he killed near Delta, Alabama, are almost certainly fakes. They bear all the earmarks of forced perspective illusions, and in some cases suggest Photoshop trickery as well.

Why can’t the Boston Globe, Yahoo News or CNN look at the lousy focus and say the pictures are clumsy forgeries? Are news organizations now obligated to run uncritical coverage of every tall tale that gets a little attention? (I once caught a fish this big. . .) Facts matter, people!

I am quite frustrated at my inability to find words spiteful enough to capture the distaste I feel for this bunkum. Fortunately, the idioms of the Internet are there to rescue me:
Continue reading All ur hogs R belong 2 us

# Chu-Carroll on Behe’s The Edge of Evolution

Dear Gentle Readers: At the bottom of this essay, I’m collecting links to reviews of Behe’s book The Edge of Evolution, replies to reviews and so forth.

Well, now the burden is off me, and I can devote my book-reviewing time to good books, like the works of Hector Avalos. Mark Chu-Carroll has reviewed Michael Behe’s new book, The Edge of Evolution. In short, it’s as bad as I thought it would be. When I first heard about it, the only information available was the flap copy: the publisherâ€™s blurb and four laudatory quotes. I found that with a trivial amount of Web-searching, each laudator was revealed to be a creationist sympathizer â€” which didn’t bode well for the contents of the book itself. What, they couldnâ€™t get even one serious biologist to say something good about it?

My prediction, although in principle falsifiable, was not falsified but instead borne out by further investigation. Don’t you love it when that happens?

Behe’s new book comes at an interesting time in the ongoing struggle against arrogant ignorance. Once upon a time, the law mandated that Genesis be taught in science classrooms; then came “equal time” for science and mystical anti-science, followed by “creationism” and “creation science” which then became “Intelligent Design,” about which we had to “teach the controversy.” (Of course, like a linear portrayal of biological evolution, this little “X followed by Y” story focuses only on one path, on a single twig of a ceaselessly diversifying bush. Just as there are still living descendants of the dinosaurs, there are still Old Earth Creationists, ideological descendants occupying their own branch of the phylomemetic tree.) After the thumping “Intelligent Design” got at Dover, many of us wondered how the opposition to reason would reinvent itself. One strategy, embraced by at least one twig, is to rebrand the very word evolution:
Continue reading Chu-Carroll on Behe’s The Edge of Evolution

# Lou Dobbs’ Bad Math on Leprosy

Carl Zimmer’s The Loom occupies a prominent place in my RSS reader, and right now, he and his readers are chatting it up about how Web 2.0 (or perhaps Web 3.1, Web 95 or Web ME) can help the cause of science journalism. Go and contribute! (My own thoughts run along a slightly different track: what are the shortcomings of Web 2.0 which we can address while improving the communication of science?)

And now that we’re thinking about journalism, I’d like to call the Gentle Readers’ attention to Dean Starkman’s piece in the Columbia Journalism Review blag discussing Lou Dobbs and leprosy. The short version is this: Dobbs said that 7,000 new cases of leprosy have occurred in the United States during the past three years. That’s not true. The real number is 431. Dobbs went uncorrected by NPR and 60 Minutes, and was not called out until today’s New York Times. As David Leonhardt writes in that publication,

When Lesley Stahl of â€œ60 Minutesâ€ sat down to interview Mr. Dobbs on camera, she mentioned the report and told him that there didnâ€™t seem to be much evidence for it.

â€œWell, I can tell you this,â€ he replied. â€œIf we reported it, itâ€™s a fact.â€

Unfortunately for Dobbs, numbers are not so pliable. (For example, reporting that the number of Iraqi WMDs was greater than zero did not make that assessment a fact.) To understand this situation, we should backtrack to the source.

# Unintended Consequences

I don’t think this is the outcome which the Discovery Institute wanted.

Background information from PZ Myers:

Oh, dear. John West of the Disco Institute is in a furious snit because, after refusing to grant tenure to Guillermo Gonzalez, Iowa State University did promote Hector Avalos, of the Religious Studies department, to full professor. You can just tell that West is spitting mad that Iowa would dare to keep Avalos around, and thinks it a grave injustice that one scholar would be accepted, while their pet astronomer gets the axe. So now they’re going to do a hatchet job on Avalos.

After reading about Avalos’s books Fighting Words (2005) and the forthcoming The End of Biblical Studies (2007), I decided to buy both of them. The former should arrive on the twenty-fifth and the latter a few days into June.

Being the amateur hack that I am, I’ll write up my impressions here after I’ve read what Avalos has to offer. Until then, I’ll be finishing John Allen Paulos‘s A Mathematician Reads the Newspaper (1995). Short take on it, so far: it has its good points, but it’s not as solid as Innumeracy (1989, new edition 2001) and Beyond Numeracy (1991).

# Dark Energy Weirdness

OK, has anybody here heard of Tori Amos? She’s apparently a friend of Neil Gaiman, which is cool, but her Wikipedia article doesn’t cite enough sources for me to figure out what she’s about. Apparently, she’s releasing a music album entitled American Doll Posse; I’d tell you more, but her website requires “the latest flash player.” I did manage to find out that for this album, Amos created five alter egos, four of which are based on Greek goddesses with the fifth being Amos herself. (For the record, the goddesses are Artemis, Persephone, Athena and Aphrodite.) Eris, the patron goddess of the Internet, inspired somebody to write the following on Wikipedia:

On March 23, 2007, toriamos.com released an audio clip from Amos, stating that each of the characters from American Doll Posse has her own online blog. She urged fans to find them, saying “Happy hunting.”

Well, I know where at least one of them is. Pip (Athena) maintains a LiveJournal, on which she writes (this being the point of my odd little story),

# Recycled Rant: the Quantum Mind

This is a topic which seems to come up with depressing regularity, so I figure I should put my stance on the record. The bulk of this post is recycled from a Memoirs of a Skepchick comment thread.

For various reasons, I am extremely skeptical of the notion that consciousness could be rooted in quantum phenomena. Of course, the entire world is quantum, in a sense: itâ€™s the principles of quantum mechanics which determine the properties of materials out of which the world is made. Like Democritus of Abdera said twenty-five hundred years ago, â€œNothing exists save atoms and the voidâ€, and quantum physics constitutes the rules by which atoms play.

The challenge, then, is not to say â€œall is quantumâ€ (a statement with no more content, by itself, than saying â€œall is loveâ€). In what way do the strange and esoteric mathematical descriptions of the atomic and sub-atomic world build up the everyday stuff with which we are so familiar? This is a deep problem, one with many mysteries left to resolve, and physicists spend lots of time worrying about it. One thing which we do know is that when you put a lot of quantum particles together, at a certain point they stop acting in the quantum way and become better approximated by Newtonâ€™s laws of classical mechanics. This is odd, because if you put a pile of classical pieces together, you get a bigger classical object! Newtonâ€™s laws reproduce themselves at higher scales, but the quantum laws do not.

Itâ€™s a bit like discovering that all the ordinary houses on your ordinary street are made of bricks from Faerie.
Continue reading Recycled Rant: the Quantum Mind

# Newsweek on Sex-Ed and Statistics

Via the Knight Science Journalism Tracker comes Sharon Begley’s story in Newsweek entitled “Sorting Out Good Science From Bad” (7 May issue, strangely enough). It runs under the sub-heading, “Just Say No — To Bad Science.” The content shouldn’t surprise anyone who grew up with Darrell Huff’s fascinating little book, How To Lie With Statistics (1954, reissued 1993). In a chatty two pages, Begley’s piece looks at one particular trick: selection bias.
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# I Guess It’s a Deuteron

Seed has just offered the world a “Cribsheet” on string theory. It looks pretty slick, although their portrayal of a “hydrogen atom” seems to have an extra nucleon (as Wolfgang notes in the Cosmic Variance thread). I’m inclined to forgive the multiple electron orbits, since they only show one actual electron — and besides, ellipses aren’t that great a way of drawing orbitals anyway.

(Incidentally, if you want to see orbitals in video, check out episode 51 of The Mechanical Universe, available for free online via Annenberg Media.)

They do cite Barton Zwiebach’s First Course in String Theory (2004), which gives me a slight tinge of pride. I mean, somebody had to work the problems in the last five chapters to see if they were solvable by students and not just professors.

The portion of this post below the fold is a rough draft of several different rants, developed in embryonic form and smushed together. Read only if you’re exceptionally curious.
Continue reading I Guess It’s a Deuteron