Poem on Your Blog Day

It’s Poem On Your Blog Day, to mark the end of National Poetry Month. The original idea was to post about your favourite poem and link to a bio and/or other work by the same poet. I don’t have a favourite poem, and for the rest I’m pressed for time as always so I’ll just point to this post about AE Stallings, my favourite contemporary poet.
But I feel bad not posting any verse at all, so here’s one I’ve been meaning to put up:

The Love-Song of Vice-Chancellor Prufrock; or, Prufrock Among The Students

Not the least of T.S. Eliot’s
contributions to literature is
the opportunity for gratuitious
parody afforded by ‘Prufrock‘.
Senza tema d’infamia…

Let us go, then, you and I,
When the campus is spread out beneath the sky
Like a student stupefied by a timetable;
Let us pass by certain half-deserted rooms
Wherein, one just assumes,
Some course on T.S. Eliot drones on;
Pass by the roses, ornaments and ponds,
The fountains, gardens and the sculptured hedges
(Where, along the edges,
Poorer students have been known to make their homes)—
The grounds this time of year are just exquisite;
Let us go and make our visit.
Through the windows student faces peer,
Desperate for passing-grades and beer.
The greasy smog that drips from eaves
And eats away the drains…
The greasy smog that settles down and leaves
My Beemer stained…
And indeed there will be time
For the yellow smoke that oozes from the labs,
Etching black streaks down the sandstone walls,
For all the corpses on the med-school slabs
And all the corpses in the Admin. halls;
Time for Law, and Arts, and time
Especially for Engineering
(A million dollar grant this year,
From MIM and Hastings-Deering);
Time to put on gowns and meet the press,
Then let some junior Dean assume the mess—
(Pause here; observe the humble stance
Of department heads who overspent their grants)—
In a minute there is time
For conclusions and exclusions which my secretary signs.
Through the windows student faces peer,
Desperate for passing-grades and beer.
And indeed there will be time
To wonder whence the funds next year will come;
Time yet to rouse the dragon from its slumbers,
To further raise the numbers
Of full-fee-paying students from overseas—
(They will say: “He doesn’t care about our own!”)
It is impossible to please!
I’d like to do more, Heaven knows,
But how could I let the Staff Club close?
For I have known them all already, known them all,
Known every meeting and the people in it,
I have measured out my life with transcribed Minutes;
I know Departments dying with a quiet moan,
So how can I go on?
And how should I begin?
With wild demands and waving hands,
Like students sitting-in?
Or shall I make requests through all the proper channels?
Approach each Government Department mandarin
With humble mien and careful creases in my flannels?
Do I dare to make a speech?
I shall turn the voice-mail on, and take off for the beach!
I should have been four furry little paws,
Scuttling across the floors of silent refectories.
And would it have been worth it, after all,
After all the heads brought in on platters,
After graduations and initiations,
And the gossip, and the post-exam-week chatter?
Would it, after all, have been worth while
To have brought the Student Union to its knees,
Assured each valued colleague of their tenure,
To sit, proud puppet-king, among these
Trophies—and smile as janitors smile?
Is any thing worth while?
I grow old… I grow tired…
How long before the Trustees have me fired?
I have been feathering my own nest all along,
Without regard or pause for right or wrong.
I have heard the students laughing, singing songs;
I suspect what they were laughing at, was me.
We have lingered in our chambers, half-asleep
On pillows made of crumpled formal gowns;
What student’s voice would dare to wake us now?

A question for my tens of readers.

I know a few people are reading the linklogs, so I thought I’d ask: would you prefer it as a sidebar? I could convert to a three-column layout, with the existing columns much as they are (just a bit thinner) and a third, probably central, column that would contain just the linklogs.
Also, I’ve been doing them as blog posts so that I could send trackback pings and people could comment on them — but trackback fails as often as it works (MT, I’m looking at you), no one is commenting on the link posts, and converting from my Simpy/Feed2JS setup is a bit of a hassle. So, should I just leave it as a feed? You can see what that would look like here.

linklog 060426

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Science blogging continued: more about scooping.

In something of an aside to his reply to Abel’s musings about a medical wikipedia, Orac makes a couple of good points about publishing hypotheses on blogs and the “scooping” issue:

[…]most cases of scooping aren’t nearly as blatant as the one [PZ Myers described]. Most are a lot more subtle, and the vast majority don’t involve any chicanery at all. Indeed, in my experience, most cases involve multiple labs working on the same question. In such cases, one of these groups will inevitably succeed at publishing their results first, and the rest will be “scooped,” no dishonesty or using ideas or experimental protocols without appropriate attribution necessary. […] (In fact, I wouldn’t even call it getting “scooped.”)

The Grey Area Problem, yes. (As an aside: I quite agree, being beaten to publication by legitimate methods is not the same thing as “being scooped” as I mean the term, though of course “scooped” is used both ways. Perhaps we need a better term for the despicable version.) My main point about grey areas is that their inevitability is not a dealbreaker: we have the tools and infrastructure to deal with them. Orac goes on to say:

In an ideal world, Bill Hooker’s concept would be the way things should work and any hint that labs might be scooping each other would result in offers of collaboration, but that isn’t always how things actually work.

The gentle implication of naivete is, of course, perfectly reasonable, and the realpolitik of the science tribe is already forcing me away from any strong position I might have started staking out (see, e.g., this).
Nonetheless, I think there’s a place for the naive position, and I’d like to keep it around, even if only to mark a boundary — “OK, fine, that’s too much trust, but how close to that can we get?”. Here’s the thing: that’s the way it does work with me. I won’t ever steal an idea from you, and if we are interested in the same questions I’d much rather share the work and the credit between us than turn science into some bullshit macho game. If you want to be famous, go ahead and be the guy on TV if our work is important enough to get coverage — I don’t give a rat’s. I just want to do science without running out of funds every year or two, and I don’t see why I should have to claw my way past my colleagues into one of the increasingly scarce tenure track positions to do it.

More on Net Neutrality

Again via David, there’s another campaign to get Congress to protect the net: Don’t Mess With The Net. They have a blog to keep you up-to-date on developments and campaign efforts, the obligatory letter to Congress, and if you have a blog yourself you can join their list of supporters.
Further update: I couldn’t find the text of the COPE act because it’s still in commitee; in comments below, Ralf points to the Benton Foundation; they have their own summary and what seems to be a pdf of the bill (scroll to bottom of page). I don’t know anything about the Benton Foundation, so caveat lector.

Of course, none of my open science ideas matter much if greedy bastards kill the internets.

David Weinberger has a post up about the importance of internet neutrality and links to Save The Internet; Free Press also has a Net Freedom Now campaign. You can visit these sites to find out what net neutrality is (STI, NFN) and why it’s under threat (STI, NFN).

  • Net neutrality is the principle that all bits are equal: that all users have equal access to the network, and service providers are not allowed to discriminate between users by means of different levels of service.
  • It’s under threat because the greedy bastards in the cable/phone companies want to be able to decide which sites will load at what speed, so that they can privilege their own services and content and block their competitors’. Do you really want an internet on which you cannot send mail saying “AT&T sucks”? Don’t think it can’t happen. To make matters worse, those greedy bastards have bought some of these greedy bastards, and according to STI:

    Congress is now considering a major overhaul of the Telecommunications Act. The primary bill in the House is called the “Communications Opportunity, Promotion, and Enhancement Act of 2006”

    Unfortunately, I cannot find the text of this or any related bill on Thomas or by scanning House votes. If anyone can point me to the actual legislation in question I’d appreciate it. (I did manage to find S.2360, the Internet Non-Discrimination Act introduced by Ron Wyden and designed to protect net neutrality.)

  • This matters to you because, to paraphrase David:
    • innovation and creativity: will suffer if your bank balance makes more difference than your brain power to what you can do on, and with, the web
    • monopoly: loss of net neutrality will create a breeding ground for anticompetitive practices; another Bell, anyone?
    • freedom of speech: this one ought to be self-explanatory
    • democracy: the web has been a great leveler of political playing fields (thank you, Dr Dean!) and promises to be a powerful way for ordinary people to have their voices heard — unless it becomes just another tool of the wealthy
  • What you can do: for starters, send a letter to your Congresscritters here and sign MoveOn’s petition here. Include a note like mine:

    Keep the media conglomerates’ greedy hands off our internet! A neutral internet is a powerful engine of creativity, innovation, free speech, free markets and democracy. It must not be placed in the hands of a few wealthy campaign donors by greedy and short-sighted political opportunists. Please support Sen Wyden’s Internet Non-Discrimination Act (S.2360) and oppose the Barton/Rush COPE Act.

OK, I’ll play

So film critic Roger Ebert has come up with a list of “102 movies you should have seen if you want to have a serious discussion about film“, and all the cool kids are playing. Well, I’m enough of an artwanker to enjoy the occasional serious discussion about film, so here goes; the ones I’ve seen are in bold:
“2001: A Space Odyssey” (1968) Stanley Kubrick
“The 400 Blows” (1959) Francois Truffaut
“8 1/2” (1963) Federico Fellini
“Aguirre, the Wrath of God” (1972) Werner Herzog
“Alien” (1979) Ridley Scott
“All About Eve” (1950) Joseph L. Mankiewicz
“Annie Hall” (1977) Woody Allen
“Apocalypse Now” (1979) Francis Ford Coppola
“Bambi” (1942) Disney
“The Battleship Potemkin” (1925) Sergei Eisenstein
“The Best Years of Our Lives” (1946) William Wyler
“The Big Red One” (1980) Samuel Fuller
“The Bicycle Thief” (1949) Vittorio De Sica
“The Big Sleep” (1946) Howard Hawks
“Blade Runner” (1982) Ridley Scott
“Blowup” (1966) Michelangelo Antonioni
“Blue Velvet” (1986) David Lynch
“Bonnie and Clyde” (1967) Arthur Penn
“Breathless” (1959 Jean-Luc Godard
“Bringing Up Baby” (1938) Howard Hawks
“Carrie” (1975) Brian DePalma
“Casablanca” (1942) Michael Curtiz
“Un Chien Andalou” (1928) Luis Bunuel & Salvador Dali
“Children of Paradise” / “Les Enfants du Paradis” (1945) Marcel Carne
“Chinatown” (1974) Roman Polanski
“Citizen Kane” (1941) Orson Welles
“A Clockwork Orange” (1971) Stanley Kubrick
“The Crying Game” (1992) Neil Jordan
“The Day the Earth Stood Still” (1951) Robert Wise
“Days of Heaven” (1978) Terence Malick
“Dirty Harry” (1971) Don Siegel
“The Discreet Charm of the Bourgeoisie” (1972) Luis Bunuel
“Do the Right Thing” (1989 Spike Lee
“La Dolce Vita” (1960) Federico Fellini
“Double Indemnity” (1944) Billy Wilder
“Dr. Strangelove” (1964) Stanley Kubrick
“Duck Soup” (1933) Leo McCarey
“E.T. — The Extra-Terrestrial” (1982) Steven Spielberg
“Easy Rider” (1969) Dennis Hopper
“The Empire Strikes Back” (1980) Irvin Kershner
“The Exorcist” (1973) William Friedkin
“Fargo” (1995) Joel & Ethan Coen
“Fight Club” (1999) David Fincher
“Frankenstein” (1931) James Whale
“The General” (1927) Buster Keaton & Clyde Bruckman
“The Godfather,” “The Godfather, Part II” (1972, 1974) Francis Ford Coppola
“Gone With the Wind” (1939) Victor Fleming
“GoodFellas” (1990) Martin Scorsese
“The Graduate” (1967) Mike Nichols
“Halloween” (1978) John Carpenter
“A Hard Day’s Night” (1964) Richard Lester
“Intolerance” (1916) D.W. Griffith
“It’s a Gift” (1934) Norman Z. McLeod
“It’s a Wonderful Life” (1946) Frank Capra
“Jaws” (1975) Steven Spielberg
“The Lady Eve” (1941) Preston Sturges
“Lawrence of Arabia” (1962) David Lean
“M” (1931) Fritz Lang
“Mad Max 2” / “The Road Warrior” (1981) George Miller
“The Maltese Falcon” (1941) John Huston
“The Manchurian Candidate” (1962) John Frankenheimer
“Metropolis” (1926) Fritz Lang
“Modern Times” (1936) Charles Chaplin
“Monty Python and the Holy Grail” (1975) Terry Jones & Terry Gilliam
“Nashville” (1975) Robert Altman
“The Night of the Hunter” (1955) Charles Laughton
“Night of the Living Dead” (1968) George Romero
“North by Northwest” (1959) Alfred Hitchcock
“Nosferatu” (1922) F.W. Murnau
“On the Waterfront” (1954) Elia Kazan
“Once Upon a Time in the West” (1968) Sergio Leone
“Out of the Past” (1947) Jacques Tournier
“Persona” (1966) Ingmar Bergman
“Pink Flamingos” (1972) John Waters
“Psycho” (1960) Alfred Hitchcock
“Pulp Fiction” (1994) Quentin Tarantino
“Rashomon” (1950) Akira Kurosawa
“Rear Window” (1954) Alfred Hitchcock
“Rebel Without a Cause” (1955) Nicholas Ray
“Red River” (1948) Howard Hawks
“Repulsion” (1965) Roman Polanski
“The Rules of the Game” (1939) Jean Renoir
“Scarface” (1932) Howard Hawks
“The Scarlet Empress” (1934) Josef von Sternberg
“Schindler’s List” (1993) Steven Spielberg
“The Searchers” (1956) John Ford
“The Seven Samurai” (1954) Akira Kurosawa
“Singin’ in the Rain” (1952) Stanley Donen & Gene Kelly
“Some Like It Hot” (1959) Billy Wilder
“A Star Is Born” (1954) George Cukor
“A Streetcar Named Desire” (1951) Elia Kazan
“Sunset Boulevard” (1950) Billy Wilder
“Taxi Driver” (1976) Martin Scorsese
“The Third Man” (1949) Carol Reed
“Tokyo Story” (1953) Yasujiro Ozu
“Touch of Evil” (1958) Orson Welles
“The Treasure of the Sierra Madre” (1948) John Huston
“Trouble in Paradise” (1932) Ernst Lubitsch
“Vertigo” (1958) Alfred Hitchcock
“West Side Story” (1961) Jerome Robbins/Robert Wise
“The Wild Bunch” (1969) Sam Peckinpah
“The Wizard of Oz” (1939) Victor Fleming

Twenty-four. Meh. Got me some catchin’ up to do.

Finger length and aggression, or, the kind of thing I do for a living: Part 1.

A while back, there was some buzz about a study showing that, to quote the media reports, “Finger length predicts physically aggressive personalities”. Like everyone else, I wondered what my finger length said about me.
You can get a pdf from here. The authors found that mean index finger:ring finger ratios were 0.947 (M) and 0.965 (F). Here’s their method:

Scanning was conducted prior to examining or analyzing questionnaire scores. A Hewlett Packard Scan-jet 5400C was used to scan participants’ hands. Before scanning, small marks were drawn on the basal creases of the index and ring fingers using a ballpoint pen by the first author. This was done to increase accuracy because it was difficult to see the creases clearly on the scans. Both of the participants’ hands were scanned at the same time, palms down. Participants’ index (2D) and ring (4D) fingers were measured from the hand scans using the GNU Image Manipulation Program (GIMP). The total length of each digit in units of pixels, from the middle of the basal crease to the tip of the finger, was determined using the GIMP “measure” tool. The first author took all of the measurements. Ratios were calculated by dividing the length, in pixels, of the second digit (index finger) by the length, in pixels, of the fourth digit (ring finger) for both hands. This technique provides good reliability (r = 0.98, d.f. = 8, P <0.01 blind test-retest of 10 individuals each scanned twice, with one week between the two scans).

I found that it wasn’t at all difficult to see the creases on a scan (Epson Stylus CX7800, 300dpi), but choosing which crease to call the baseline is not entirely straightforward. I only scanned my right hand, as the authors found stronger sexual dimorphism on the right than on the left hand, and this is consistent with earlier literature:


Here’s a closeup of the base of the fingers (ring on the left, index on the right):

See what I mean? Even if you draw a line with a pen, where do you draw it? You have to decide by eye: if you try folding the fingers towards the palm in an attempt to use the fold to direct the pen tip in some sort of objective manner, the skin is too loose to get a consistent result. Next, I drew lines on the crease closest my palm using the line tool in Photoshop, and delineated the end of each finger using the freehand lasso tool to identify the far edge:

So as to be readily visible on the web, that image shows a 2-pixel line, thinner than you could get with most pens, but for the actual measurements I used a 1-pixel line. I rotated the image until the finger axis was as nearly horizontal and the crease as nearly vertical as possible, then cropped from crease to end of finger; according to this method my ring finger is 885 pixels long and my index finger 902 pixels, giving me a ring:index an index:ring ratio of 0.981 1.02, higher than even the female average.
Or is it? The averages I quoted are from just one study, and even my brief attempt at a home-made replication shows that there could be significant measurement issues here. Further, whether or not my measurements and those averages are accurate, what does it all mean? How strongly does this particular morphological measurement correlate with, say, aggression; what’s the proposed mechanism behind the correlation, and what other correlations might that predict?
Tune in next time (it’s Sunday and I’ve been on the damn computer all day!) to watch one scientist (me) apply general principles of scientific reasoning to questions outside his own experience but (I hope) within his competence.

linklog 060422

  • qwer.us
    Free online to-do list management.
  • Kite Aerial Photography by Scott Haefner | Panoramas How-to
    Awesome: 360-degree panoramas! “Only two images are needed to create these panoramas. I take one looking straight down from the kite using a simple rig, and a second looking straight up from the ground. Both images are shot with a circular fisheye lens that has a 180 degree view (Nikon FC-E9). You can think of it as if each image contains a “hemisphere” of information” Via.
  • Future of Computing: Web focus : Nature
    Nature web focus Special: “In the last two decades advances in computing technology, from processing speed to network capacity and the internet, have revolutionized the way scientists work. From sequencing genomes to monitoring the Earth’s climate, many recent scientific advances would not have been possible without a parallel increase in computing power – and with revolutionary technologies such as the quantum computer edging towards reality, what will the relationship between computing and science bring us over the next 15 years?”
  • Browse Blogs – postgenomic.com
    Together with Bora’s roundup, a compendium of science related blogs. Also, eatonweb. Q: canonical list on a wiki somewhere?
  • O’Reilly Radar > Supernova 2005: Attention
    “Continuous partial attention. Dan Gould: “I quit every social network I was on so I could have dinner with people.” The next aphrodisiac is committed full-attention focus. In this new area, experiencing this engaged attention is to feel alive. Trusted filters, trusted protectors, trusted concierge, human or technical, removing distractions and managing boundaries, filtering signal from noise, enabling meaningful connections, that make us feel secure, are the opportunity for the next generation.” There really is a Next Big Thing in these ideas, I’m convinced. Via Selva.
  • Home Page of Dr. Eitan Bachmat
    “I am the world’s worst storage systems researcher. This is not surprising given the fact that I don’t know anything about operating systems and file systems in particular. Instead of doing experiments I perform thought experiments. I can’t program. I like working with models from the 60’s even though they are regarded by nearly the entire community as being completely useless. I myself admit that they are completely inaccurate. I am also probably the only researcher who insists on considering serial workloads in which only a single I/O is sent at a given time, preferably with ample time between them. I also like to consider performance related problems which I know in advance to have no application. I have come to be a systems researcher because I was a terrible mathematician. To summarize my relations with mathematics, I love mathematics, it does not love me back. Given this situation I had to leave this relationship at some point. As revenge, I am exploiting mathematics in my new role as a systems researcher. This has not added to my popularity in the systems world.” Something tells me Dr Bachmat is actually pretty good at what he does. Via.
  • Adventures in Ethics and Science: Hierarchies of misconduct.
    Scientific misconduct = FFP: Fabrication (making shit up), Falsification (not a la Popper, but altering data) and Plagiarism. Is the latter a lesser offence? I say no.
  • Rhosgobel: the Iraq Index
    Radagast points to the Iraq Index as a source of data on that beleaguered country. I don’t know anything about the Brookings Inst.
  • Aetiology: Bikinis make macho men stupid
    Macho men are stupid long before any bikinis enter the equation.
  • Terra Sigillata: Formerly proprietary natural products research database released in web version
    This is excellent news: Professor Norman R. Farnsworth of the University of Illinois at Chicago will release his group’s NAPRALERT database this week to open access.

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some scienceblogging tools

1. A comment on Pedro’s post about Bora’s post about scienceblogging led me to Stew, and reminded me about Postgenomic, which is Stew’s creation. PG is a feed aggregator, but it’s a feed aggregator with big ideas:

Postgenomic aggregates the feeds from life science blogs in order to do useful and interesting things with them. It’s kind of like Technorati crossed with a really big hot papers meeting.

Its main uses – hopefully – are to:

  • List the current top life science news stories and the hottest recent papers (or the papers most often cited by bloggers, anyway)
  • Store and index reviews of papers
  • Store and collate reports from conferences
  • Help bloggers to share their expertise and, flipside of the same coin, to find useful papers on a given topic

Hopefully, as the site develops and the database grows the fourth point can be accomplished by organizing the papers by topic (perhaps using MeSH terms, or keywords, or the Technorati tags from the posts containing links to them). If you’re looking for papers on, say, Bayesian networks in molecular biology but don’t know where to start then you could fire up your browser, click on the appropriate tag in the Postgenomic index and be presented with a list of relevant papers and the blog posts that talk about them.

This is a great idea, and dovetails nicely with the current scienceblogconversation about what scienceblogging is, and what it might be good for. (You can add your blog to the postgenomic index by emailing Stew, and here are some ways to make sure the indexing goes smoothly.)
2. In the comment that sparked this post, Stew pointed to WebCite:

WebCite is an archiving system for webreferences (cited webpages and websites), which can be used by authors, editors, and publishers of scholarly papers and books, to ensure that cited webmaterial will remain available to readers in the future. If cited webreferences in journal articles, books etc. are not archived, future readers may encounter a “404 File Not Found” error when clicking on a cited URL.
A WebCite reference is an archived webcitation, and rather than linking to the live website (which can and probably will disappear in the future), authors of scholarly works will link to the archived WebCite copy on webcitation.org.

This not only provides a solution to the dead links problem,it also provides external timestamp authentication (which, as discussed elsewhere, is an issue when using blog posts to stake out academic/intellectual territory and avoid being scooped).
3. Stew found WebCite via Alf of HubLog. Alf discusses various solutions to the dead links/timestamp problem, including using Spurl (which is how I backup my Simpy archive) and his own cite bookmarklet. The bookmarklet allows you to grab a timestamped blockquote from another page, like so:

<blockquote cite=”http://hublog.hubmed.org/archives/001243.html” title=”HubLog: Creating a citable archive of a web page on Sat Apr 22 2006 15:59:48 GMT-0700 (Pacific Standard Time)>Academic papers or weblog posts often need to refer to external web pages; generally, you want people to see the external pages as they were when you wrote about them.
The simplest way to do this is a standard hyperlink, combined with a quote of the appropriate section of the text. If you’re referencing long pages though, lots of lengthy quotes could get out of hand.</blockquote><cite><a href=”http://hublog.hubmed.org/archives/001243.html”>HubLog: Creating a citable archive of a web page</a></cite>.

Note: the original text included a link, which the bookmarklet doesn’t preserve, but it’s no big deal to add those back in (you could use “view selection source” if there were lots of links).