At 19:20 this afternoon, someone found their way to Science After Sunclipse by searching for the query, avoid girlfriend attachment. I’m the second hit. Of 312,000.
For my post, “Preferential Attachment in Python.”
Continue reading Google WTF
Neuro-Journalism Mill
The Neuro-Journalism Mill is a website (with a slightly different organization than your average blag) which is dedicated to sorting good journalism from bad, where the brain is concerned. The former is labeled wheat, while the latter is sorted into the chaff. The Mill carries the sponsorship of the James S. McDonnell Foundation, which seems to have a brain-heavy focus, naturally making me wonder if there are analogous places one could get paid to critique the journalism of physics. (Perhaps the JSMF would give me money for writing about “complex systems”?)
Questions of my own financial gain aside, I’m glad to see people providing this kind of critique. Getting anybody to listen is, of course, the next step, and given the stakes involved, it’s a step we should devote serious effort to taking. I’ve opined before — and I’m not the only one — that our advancing knowledge of the brain will become an increasingly hostile front in the struggle against anti-science. What is happening with evolution today will happen with cognitive science in ten years, and so learning how the people are informed — and, often, misinformed — is vitally important.
(Link via Mind Hacks and Brain Waves.)
“Framing” in the Funny Pages
OK, I know I said I wouldn’t write anything more about “framing science.” I mean, when Chris Mooney and Matt Nisbet used Lakoff’s concept of “frames” to say that Richard Dawkins was doing wrong, and when Sean Carroll used the public-policy notion of the “Overton Window” to argue that Richard Dawkins was doing right. . . “Windows”? “Frames”? I think it’s time for a beer. Or more.
Despite all that, I think I need to say just one more thing. I’ve discovered why scientists are apt to hate the terminology of “framing,” no matter what they think of the challenges involved in communicating science. And, believe it or not, I made this discovery thanks to Doonesbury.
Psychedelic Bibliographies
Advances in the History of Psychology, a blog operated out of York University, has posted annotated bibliographies of psychedelic research, both on general psychological research and on studies focusing specifically on LSD.
(Hah! And you thought I was just trying to make a strange juxtaposition in my title.)
The AHP folks note something which I find interesting but not wholly unexpected: while plenty of papers have been written about LSD and marijuana, the academic literature doesn’t appear to have histories dedicated to the two-carbon phenethylamines like 2C-B or other significant drugs like DMT, DOM or mescaline. These remarkable little molecules sometimes get mentioned in general discussions or in studies of other drugs, but they don’t appear to have peer-reviewed literature of their own. PiHKAL (1991) and TiHKAL (1997) seem to be the end of the line.
One unfortunate consequence of this lack is our inability to judge the universality of neurological reactions to chemical stimuli. In this context, I’d like to bring up the paper by Bressloff, Cowan, Golubitsky and Thomas in Neural Computation (2002), “What geometric visual hallucinations tell us about the visual cortex.”
Continue reading Psychedelic Bibliographies
Scraping the Bottom of the Garden
Last Thursday night, while a bunch of us were eating sushi, we realized that something had to be done about our excessive indulgence in nerd humor. It was consequently declared, “Every time you tell a geek joke, God kills a fairy. Thus, you must after each such joke clap your hands and proclaim, ‘I believe in fairies! I believe in fairies!'”
For example, suppose I asked, “How do Communist electrical engineers study capacitors?”
“I don’t know, Blake, how do Communist electrical engineers study capacitors. . . Sigh. . .”
Continue reading Scraping the Bottom of the Garden
What Shalizi Doesn’t Know
Cosma Shalizi writes of a discovery — an unexpected appearance of Borges’ “Tlön, Uqbar, Orbis Tertius.”
An edition of the old translation of this story, illustrated by an artist signing themselves only as “Rikki”, and published in 1983 by a press called the Porcupine’s Quill in Erin, Ontario. (Found, presumably mis-filed, in the cultural studies section of one of the two decent used book stores I’ve found in Pittsburgh.) The illustrations are dedicated to Carl Sagan, among others, and are nicely weird, menacing and suggestive. The map of Uqbar is also well done. I know nothing about the artist but would like to learn more.
Re-reading, I am struck by the terrific economy with which Borges tells the story of an elaborate, centuries-spanning conspiracy to take over the world. It is only too easy to imagine how much more space any contemporary author would take to tell this story, without adding anything to the effect. For that matter, why not a summer action movie version? (It’s hardly a greater stretch than what they do to Philip K. Dick.)
Either Shalizi doesn’t know or he was prevented from saying that Borges was the uncredited original author of Fight Club (1999). Don’t believe me? Just read this excerpt from a review Borges published of Dr. Jekyll and Mr. Hyde (1941).
Continue reading What Shalizi Doesn’t Know
Dawkins in The Sunday Times
Peter Millar writes for the Times Online about Richard Dawkins and his latest antics.
Even modern global oil corporations have used dowsers to search for deposits. But now Richard Dawkins, the man who told you that God was not only dead but had all along been a bogeyman invented by bogeymen, has levelled his sights at the whole new age caravanserai, including astrologers, spirit mediums, faith healers and homeopathic medicine. Is it high noon for the Age of Aquarius? It is the believers in Aquarius (and Leo and Taurus and Pisces) who attract the first body blow in Dawkins’s new Channel 4 series The Enemies of Reason, which begins next week.
Dawkins is horrified that 25% of the British public has some belief in astrology — more than in any one established religion — and that more newspaper column inches are devoted to horoscopes than to science. Leaning back on a sofa in the faded gothic splendour of Oxford’s 14th century New College he sighs with something approaching despair: “It belittles our universe. To have astrologers demeaning astronomy by tapping into the spine-tingling wonder of the universe is . . .†he struggles briefly for a word, then finds one and pronounces it with a keen awareness of the irony: “Sacrilegious!â€
Channel 4 commissioned The Enemies of Reason as a follow-up to The Root of All Evil? (2006). The first broadcast is scheduled for 13 August 2007, with the second installment broadcast one week later.
Behe on The Colbert Report
Last night, Michael Behe was Stephen Colbert’s guest on The Colbert Report. It was, shall we say, educational.
BEHE: Nobody was searching for the limits of Newton’s theory when Newton first proposed it. He thought that he had solved all of physics. But then when —
COLBERT: You mean about how — how apples fall?
BEHE: Apples fall, cannonballs go. But then —
COLBERT: Mm-hmmm.
BEHE: But then when —
COLBERT: He invented the cannonball? He invented the dive — the cannonball?
[audience laughs]
BEHE: Cannonballs fly.
Oh, yes. It’s nice to know that nobody checked to see if Newton was right, or if “universal gravitation” was really universal.
Wait. You say that it was Edmund Halley who used Newton’s laws to predict that comets travel in elliptical orbits, and that the comet seen in 1456, 1531, 1607 and 1682 would return in 1758? How could Halley say such a thing, after Newton had made his view clear that all comets travel in parabolic paths? It’s in the Principia, for Heaven’s sake! And you say that Halley was the one who realized that the stars are not fixed to a “celestial firmament” but instead move through space? How dare you imply that the views of one person are not the entirety of science! Sir, how dare you have the temerity to insist that people did not take Newton at his word but instead used his theories to make predictions about the world which they could then compare to observations to — I can hardly even articulate such a heretical notion — see if Newton was wrong.
What! Are you telling me it was the French, those wine-swilling, toad-munching surrender monkeys, who had the audacity to test Newton’s prediction that the Earth is an oblate spheroid? Sir, you could tell me all you want about the 1735 expeditions to Peru and Lapland under Charles-Marie de La Condamine and Pierre-Louis Moreau de Maupertuis respectively — the former of which incidentally brought back the first rubber and curare Europe had ever seen — but the mere suggestion that Newton’s word was not good enough is so repugnant I refuse to consider the matter further.
It gets better:
Continue reading Behe on The Colbert Report
Change My Name to Springer
Dear academic publishing industry: play nice, and we won’t crush you under our advancing wall of ice.
Google Scholar’s publisher policies insist that people searching journal articles through Google “must be offered at least a complete abstract.” Content which is restricted to subscribers can only be included “as long as you can show a complete abstract (or more) to all users who arrive from Google and Google Scholar.”
So why do all my Google Scholar searches retrieve SpringerLink and IngentaConnect pages which purport to be PDF files — even including text from the paper body in the Google summary — but upon clicking the link turn out to be generic portal pages asking for money? Whether I even get the paper’s abstract or not depends upon the IP address from which I surf.
Look, I don’t expect to get online content for free. (I certainly deserve it, but that’s a different story.) Nevertheless, a little bit of forthright behavior and a willingness to play by the rules already written down would make everybody who uses the Web for academic purposes a whole lot happier.
SEE ALSO:
- John Baez, “Web Spamming by Academic Publishers” (31 July 2007), The n-Category Café.
- Pierre Far, “Academic Publishers as Spammers” (2 August 2007), BlogSci.
Dendritic Evo-Devo
Remember way back, when I mentioned genetic algorithms in the course of criticizing Michael Egnor? I described, conceptually, a way of using the mechanisms of mutation and selection to discover the structure of DNA, given X-ray crystallography data.
Let a “gene†in the computer’s memory be the spatial locations of molecular units: sugars, phosphates, purines, pyrimidines — the small molecules which Franklin, Pauling et al. knew were the constituents of DNA. We create a “gene pool” of random variations, and then we iterate the genetic algorithm (GA), using as fitness function a comparison between a calculated X-ray diffraction pattern and the X-ray images taken experimentally.
Imagine tossing out a thousand random guesses about what DNA looks like. For each guess, we could calculate what the X-ray diffraction pattern would look like given that particular molecular structure. Most of the time, it won’t look anything like the X-ray pictures we take in the laboratory, but a few of them will by happy accident look a little more like the real thing. This slight preference becomes the starting point for selection. We let our ideas breed, giving favor to those which perform best. The irresistible logic of Darwin goes to work.
(This is a bit of a perspective shift. Instead of thinking like sane people do about DNA carrying genes, we’re considering an abstract sort of gene which defines the shape of a hypothetical DNA structure.)
If we’d invented fast and cheap computers before we knew about DNA — say, in some parallel Sliders world or steampunk fantasy where computers happened five decades sooner — this might well be how scientists would have tried to solve DNA. It requires much less cleverness, and correspondingly more computer time. As I mentioned before, people have applied this method to figuring out molecule shapes, although to my knowledge nobody has tried to “re-solve” DNA this way.
An interesting point: if our “genes” are molecular positions and our “phenotypes” are X-ray diffraction images, then it looks like we’ve got a non-trivial “morphology” between the two. Some “development” has to take place, although it rather happens “all at once.” It might be interesting to look at a GA in which structures are generated by a really non-trivial development process.
How about, say, the growth of neurons?
Continue reading Dendritic Evo-Devo
Late Enough at Night
Late enough at night, category diagrams start looking like adinkras and network motifs.
Categories and Surreals: Disordered Thoughts
I’ve been going through André Joyal’s category-theoretic construction of the surreal numbers, futzing around to see how restricting the construction to yield only the real numbers affects things. (See my earlier remarks on this and/or Mark Chu-Carroll’s discussion for background information.) If I were an actual mathematician, I’d probably be done by now. Instead, I have a headful of half-baked notions, which I’d like to spill out into the Intertubes (mixing my metaphors as necessary).
Why would a physics person even care about the surreal numbers? Well, ultimately, my friends and I were going through Baez and Dolan’s “From Finite Sets to Feynman Diagrams” (2000), which touches upon the issue that subtraction can be a real pain to interpret categorically. If you interpret the natural numbers as the decategorification of FinSet, then addition is easy: you’re just talking about a coproduct. But subtraction and negation — oh, la!
Continue reading Categories and Surreals: Disordered Thoughts
Brief Vacation-but-not-really
Posting will be light this week. With luck, I’ll get a rerun of some old material I wrote at another site up here Wednesday or Thursday. In the meantime, here’s a lengthy discussion at Russell Blackford’s place about emergent properties and consciousness.
When you’re sated on that, check out Mark Liberman’s “Thou shalt not report odds ratios.” See, this is why the denizens of the science-blogging community should include Language Log in their travels: problems like bad math reporting in science journalism affect us all.
QUICK UPDATE: Isabel has more on the bad math in journalism issue at God Plays Dice.
Lolkats and Lolkets
I’m actually surprised I haven’t seen this yet: a LOL-Krazy Kat.
The next step, of course, is a “LOL-ket,” done in Dirac bra-ket notation. You know, “In ur Hillburt spase, evolvin ur statez.”
New Sidebar Whoosywhatsits
I souped up the “Reader Favorites” list on the sidebar. Instead of being a fixed list, it now plucks a random half-dozen from the Favorites category.
The icon takes the scarlet A from The Out Campaign and John Pieret‘s pensée flower from here.
Book Shelving as Social Commentary
Back in the days when postmodernism was almost new and you could still get a good riot at a political party convention, Jorge Luis Borges wrote, “In a modest, silent way, by arranging books on shelves, we ply the critic’s art.” Today, we have all the same literary experiences that previous generations enjoyed, but we do them harder, faster and longer — and perhaps with less silence and modesty, to boot. Most obviously, we “shelve” music and video with the same ease that Borges’ contemporaries arranged books. In our immodest, noisy way, we’ve all been music critics since about 1999.
Even before Napster and the MP3, we made mix tapes; long before multi-gigabyte hard drives, we had the drawer full of VHS cassettes. It’s just gotten easier, more global and more slick. More now, and less TwenCen.
Concomitant with all this has been another change. When, in the early years of the Barnes-and-Borders-a-Million, idle teenagers would move William S. Burroughs’ Naked Lunch (1959) to the “summer reading” section — because there was nothing else to do in Huntsville, Alabama — we (I mean, they) didn’t put up weblogs about the experience.
Continue reading Book Shelving as Social Commentary