April 2006 Archive



Sunday, 30 April
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?



Wednesday, 26 April
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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Tuesday, 25 April
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.



Monday, 24 April
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).

Briefly:

  • 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.



Sunday, 23 April
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:
hand1.JPG

Here's a closeup of the base of the fingers (ring on the left, index on the right):
closeupRI.jpg

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:
hand2.JPG

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.



Saturday, 22 April
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.

Powered by Simpy and Feed2JS; the archive, aka my Simpy account, is here.

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).

New to the blogroll: more meta-science

In comments below, Pedro Beltrao of Public Ramblings says:

What I disagree with is that we should go ahead and try to change things starting with the assumption of good faith. There is a percentage of people with bad intentions, this is clear, so we should plan for this. Open systems like wikipedia and digg are having problems and are taking steps to solve them. I suggest we keep an eye on these pioneering online social systems and see what solutions they come up with.
He's right, and it's an important point. When I said we should assume good faith, I wasn't clear. I didn't mean we should naively pretend there are no assholes in science. What I meant to convey was that, in addition to the sorts of measures we can learn from systems like wikipedia, we should do two things: 1, change the emphasis of the culture of science from suspicion to trust; and 2, have more faith in our ability to identify and deal with cases of bad faith as they arise. In other words, relax.

I think that we have good reason to approach fellow researchers as potential collaborators rather than potential scoopers (see below), and that when bad actors try to take advantage of that approach we also have, as a community and as individuals, the means to deal with them. When I say "the means to deal with them", I mean to include the sorts of checks and balances that Pedro is talking about.

Plentiful though they are, stories of scooping and other assholery are vastly outnumbered by the stories you don't hear, precisely because they are the stuff of every day:

  • the PI who lent you her unsubmitted grant so you could copy the format for your own
  • the postdoc who spent half a day digging through the -80 freezer to find the plasmid you wanted
  • the NIH staff scientist who sent you transgenic fibroblasts in response to an out-of-the-blue email
  • the paper you're an author on even though all you did was teach someone a technique they didn't end up needing1 ("we said you'd be an author, so you're an author")
and so on and on. Those are all true examples from my own experience, and I'd like to invite readers to add their own in comments. It would be nice to hear about the up side of the scientific community for a change.


1 I should clarify: an acknowledgement "for technical assistance" would have been more appropriate, and these days I would insist on that. At the time, I gave in and took the free ride. Mea culpa. I included the example just to point out that researchers are often generous even with that most precious commodity, publication credit.



Friday, 21 April
Quick followup on science blogging.

There's a lot of great discussion going on at the moment about science blogging, the community of science, publishing and so on. I don't have time for a comprehensive roundup (though Bora's updates here cover most of it), but I want to quickly follow up on a comment that Abel Pharmboy made:

Bill Hooker was most vocal in Bora's comments and in a separate post at his own Open Reading Frame on how "scoopers" should be shunned by the scientific community.
(This was sort of tangential to the main point of his post, which is why I'm doing this here instead of in his comments.)

The point I want to make is this: for all my talk of shunning, and for all that I'm absolutely serious about increasing the risk associated with "anti-collegial behaviour" like scooping, I'm aware that we don't want to start a program of witch hunts. There will be grey areas, hard-to-prove cases, and we'll just have to err on the side of trust -- be scrupulous about "innocent until proven guilty". Better ten scoopers get away with it than one innocent be labelled a scooper. We don't have to catch 'em all, just associate a greater cost with the activity.

Further, it's not so much about punishing wrongdoers as altering community attitudes. Scientists now tend to shrug and say, "that's how the game is played" or some such -- as though that's how it HAD to be. Worse, people are not inclined to speak up and say, "Hey, I thought of that some time ago", because the response will be along the lines of "too bad, I published it so it's MINE ALL MINE bwahahaha!". If someone says to me, "Hey look, here's a blog post of mine outlining the central theme of your paper six months before you submitted it", I'm not going to say "tough luck". At the very least, I'm going to invite that person to work with me on questions we're both interested in, so we can publish together in future -- and more, I'd be happy to have my published work updated to give credit for their independent discovery. For one thing, how does it hurt me to admit that someone else also came up with "my" ideas? It amounts to a "note added in proof" if there are independent data involved, and a pretty ordinary courtesy if it's just about the concepts. Further, I don't WANT credit for something I didn't do, only for things I did do (and I don't even care so much about that, so long as interesting questions keep getting answered1). If someone else came up with an idea or a result before I did, I want that known -- I'd feel like a fraud otherwise, if the community thought I was first but I knew otherwise.

In closing, let me just deal with one common objection to this idea of a more open system: that the world is full of assholes. Whenever I discuss openness, be it publishing data on blogs or being willing to share credit or listing one's bioreagents on BioRoot, I meet with a reaction that boils down to "what if someone takes advantage of me?". What if someone scoops me, what if someone fakes a blog post to get me to acknowledge them in a paper, what if someone keeps asking me for reagents and never gives any out? Well, to begin with it's a lot healthier (and, I'd argue, more productive in the long term) to start with an assumption of good faith than with the idea that everyone is out to cheat you. It's perfectly true that there will be assholes trying to take advantage, but here's the thing: they're doing that now, and the system we have is not hindering them much. In a more open system predicated on good faith interactions, assholery becomes harder to hide and get away with. As far as dealing with assholes as they appear, I return to a point from my last post: we're scientists, we present and evaluate evidence for a living. So if I'm going to accuse someone of scooping, for instance, I know -- it's my job to know -- what kind of evidence I need and how to get and present it. If I'm answering charges of assholery, I know what kind of evidence to demand, or to present in my defense. Give it a chance, I say: there aren't as many assholes as you think, and we already know how to cope with them.




1 To the extent that I do care, it's a job security issue: my ability to win funding and get or keep jobs in science is largely dependent on getting credit for my discoveries. That (job security) is a common lament among researchers, and it's a function of the career structure/hierarchy, which is another problem for the community to deal with; for instance, there's an interesting discussion here. For now, let me just point out that a system in which everyone gets the credit they've earned, because everyone is willing to give it (as in my personal thought-experiment above), seems to me to offer more security than a dog-eat-dog system.



Thursday, 20 April
linklog 060420

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Wednesday, 19 April
linklog 060419
  • University of Evansville: Richard Wilbur Award
    I'd like to have all of these eventually, at least if the standard is even close to Stalling's Archaic Smile.

  • Science and Politics: what's that PhD good for?
    Not much, according to many biomed researchers. See also recent threads at YoungFemaleScientist. Why is it that people who solve problems for a living are, apparently, not bringing their tools and expertise to bear on their own life/career problems?

  • Warnock's Dilemma - Wikipedia, the free encyclopedia
    Reason #1 is, of course, why no one ever comments on my blog.

  • Zoho - Affordable software for individuals, small & medium business
    Free online apps: word processor, spreadsheet, personal planner, chat and html editor. Via.

  • PLOrk: Princeton Laptop Orchestra
    "The Princeton Laptop Orchestra (PLOrk) is a newly established ensemble of computer-based musical meta-instruments. Each instrument consists of a laptop, a multi-channel hemispherical speaker, and a variety of control devices (keyboards, graphics tablets, sensors, etc...). The students who make up the ensemble act as performers, researchers, composers, and software developers. The challenges are many: what kinds of sounds can we create? how can we physically control these sounds? how do we compose with these sounds? There are also social questions with musical and technical ramifications: how do we organize a dozen players in this context? with a conductor? via a wireless network?"

  • One Bag (all about packing, luggage, and travelling light)
    I'm pretty good at this already, but it never hurts to have more ideas.

  • feh-muh-nist: But, you're not fat!
    "There's a short circuit in the brain that says someone we love cannot be fat which we hate, so we conclude that the person we love must not actually be fat. When someone says that they do not see a fat person as fat, they mean to be kind and complimentary. They mean something like, "I see you as like me" or "I don't see you the way I see other fat people." The problem with this is that aligns fat with something undesirable, offensive, and bad. "Other" fat people are sloppy, lazy, and bent on self-destruction, but not you! You, the fat friend, are different. You, despite your size, keep a tidy house, dress neatly, exercise, eat well, and are, in all other respects, like them."

  • Open Access News: What OA will make possible
    The indispensable Peter Suber and the annoying but valuable Stevan Harnad. Note to self: read this.

  • Minimum Security: Bill Napoli is a douchebag
    I don't usually approve of privacy invasions, even of the privacy of assholes, but in the case of Bill "raped and sodomized as bad as you can make it, plus she had to be a virgin to start with" Napoli, I'll make an exception.

  • AlterNet: WireTap: Tipping in America
    This article seems about right to me -- I'd like to know what people working in service jobs think of it. Also, the average tip is ~19%? Is that among those who tip, or averaged across all diners? I suspect the former, but don't have data.

  • Informed Comment: Americana in Arabic
    Juan Cole: "Long-time readers know that as a result of the September 11, 2001, attacks and subsequent events, I decided a couple of years ago that something had to be done about the woeful lack of understanding between the United States and the Muslim world. There will always be differences, but there need not be differences based on ignorance or fantasy. The Arab world alone has a population of 300 million and a combined economy of some 1 trillion dollars a year.

    My response has been to found, with some colleagues, the Global Americana Institute, which aims, initially, at getting central works of American thought and history into Arabic. I think we also have to try to endow a chair at an Arabic-speaking university, but more on that later. It has taken a long time to get all the state and Federal permissions, but we are finally done. The Global Americana Institute is a fully recognized 501(c)3 charity, and donations are tax deductible. I am coming to the public with a plea to support us. We will, of course, also be approaching foundations and other funders, but I am hoping that this project is something that can garner grassroots support."

  • - - - the essence of rabbit - - -
    Bunny Mandala: 1500 bunnies from 500 artists. Via.

  • Pink Tentacle
    Luminous squid! Pretty!

  • Early Christian Writings: Introduction
    "The purpose of this web site is to set out all of the Christian writings that are believed to have been written in the first and second centuries, as well as a few selected from the early third. I have also included non-Christian documents that may have special bearing on the study of early Christianity in order to make this web site a comprehensive sourcebook. I have provided links to English translations for all of these documents. When available, the work has also been provided in the original language, usually Greek. I have also provided information and scholarly opinion regarding the background, authorship, dating, and provenance of these documents."

  • LiveScience.com - Poll: Everybody Else is Fat
    In a survey of 2,250 adults by the Pew Research Center, 90 percent of respondents say "most other Americans" are overweight. But only 39 percent see themselves as overweight, and only 70 percent said the people they know are overweight.

  • Inhabitat
    Sweeeeeet: "a house that engineer, Paul Pedini, built with the design expertise of John Hong from Single Speed Design in Cambridge, Massachusetts. At a final cost of $150 per square foot, most of the materials for the house were free, minus the expenses to ship the materials (formerly I-93 off-ramps from the heart of the transportation artery through Boston,unofficially known as the "Big Dig") to Lexington, MA"

  • Uncertain Principles: Every Day I Write (in) the (Lab) Book
    Chad posts an excerpt from his lab notes. I'm always interested to see how other people keep theirs.

  • Guardian Unlimited Books | By genre | Stuart Jeffries talks to leading feminist Catharine MacKinnon
    "This has been MacKinnon's feminist approach to porn for a quarter of a century: the victims of porn need to be empowered by law to seek remedies for harm they suffered, existing male-framed laws being inadequate to the challenge." MacKinnon's ideas, as presented briefly in this review, make a lot of sense to me. Note to self: read the book.

  • Easily Distracted » Blog Archive » Societal?
    I also dislike the word, but other commenters make a decent case for a definition that's usefully non-redundant with "social".

  • Lichen
    Mostly ambient/minimalist electronica. Like a melodic PanSonic, sorta.

  • |_|_|_|_|_|_|_|_|_|_|_|_|
    "arrangements of binary data into stimulating audio and visual formats... All pretty minimal, anonymous and anti-authorial by design"Snippets of electronica, braincandy, mmm. Via Rob; see also lichen.


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Tuesday, 18 April
Science blogging: what's it all about? Part 1 of an ongoing series.

I've been posting pretty much nothing but verse, photos and linkdumps for a while now, partly because I've been exceedingly busy and, if I'm honest, mostly because serious original posts are a lot of work. The main reason, however, for the blog name change and the switch to my real name was that I want to start using this blog for talking about, thinking about, and even doing science, and recent posts by several other bloggers have prodded me into action.

I want to come back to issues and ideas raised by YoungFemaleScientist, Chad and Dr Free-Ride, but for today I'll mostly just point to Science and Politics.

Bora recently posted an elegant, scholarly, professional level discussion of Chossat's Effect in humans, complete with preliminary data, an hypothesis and an explicit request that the post be cited as a scientific communication; I noted this in a linklog and said he was helping to "usher in a new era of scientific publishing", and I wasn't kidding. I got online in about 1993, before there were blogs as we know them now, and my immediate reaction to this new medium was two-fold: "my people!" and "eee, publishing revolution!" I was right on the first count (even met the spousal unit online), and it's been slower than I'd have liked but I still think I was right on the second count as well. I'm not the first to observe that blogs are conversations, and conversations between scientists are where a lot of the creative action is; collaboration is a fun and powerful way to extend one's intellectual and practical reach. What better way to keep up with what's happening on relevant benches around the world than a well-connected network of lab weblogs (lablogs)?

Today, Bora has gone further with this idea. By way of answering the question "what are science blogs doing now?", he sets out a pretty comprehensive taxonomy of the current community. The category that interests me right now is "hypotheses and data", and I agree with Bora that there are two kinds of blog post in this category:

A) "This is my hypothesis and I am staking the territory here. I intend to test this hypothesis in the near future and you BETTER NOT try to scoop me!"
B) "This is my hypothesis, but I have no intention to follow it up with actual research. However, I'd love to see it tested. Please someone test it! And if you do, you will have to cite me in the list of references as your source for this hypothesis"
I would rewrite (A) to read: "This is my hypothesis and I plan to test it; if you can contribute, with ideas I haven't had or reagents I don't have or whatever it might be, great: let's collaborate. There's no need to steal when you can share."

Here we run into a personal bete noir of mine: "scooping". This means what it sounds like: taking advantage of someone else's work, to which the Scooper had advance (pre-publication) access by way of a conference presentation, visiting lecture, conversation, manuscript review, blog post or whatever, in order to slam a rapid publication into press ahead of the Scoopee, the person who actually had the idea. In Bora's comments, PZ Myers provides a personal example:

I got burned several years ago. I had a complete description of the protocols we were using in a teratology study, with some preliminary pictures of some of the results, all on the web. A few months later, my students found a paper published describing similar results in a fairly big name journal, and the protocols, which they had worked out by trial and error, were identical right down to the fraction of a percent of various reagents. It was damned obvious that they'd found our description and literally copied every step of our experiment...and there wasn't so much as an acknowledgment. The authors hadn't even bothered to contact us.

It was particularly galling to go to meetings afterwards and have people ask me, "Oh, so you're doing experiments like so-and-so?"

I've said elsewhere, I said in Bora's comments, and I'll say again: those assholes should be shunned. To do that to another researcher should basically mean the end of your career, by way of community opprobrium if not active sanction. I asked PZM what he did about his scoopage, and I'll be interested to hear his response. What typically happens is nothing: the scoopee shrugs and says something like "I couldn't prove they didn't think of it themselves, and it's too much trouble, and I don't want to rock the boat".

NNNNNNNGGGGGGGGHHHHHH!!! That galls me nearly as much as the initial assholery!

Of course, you don't want to smear "SCOOPER" all over an innocent researcher's reputation, and of course there will be grey areas and cases that are difficult to prove. But we are scientists, ferfucksake: we evaluate evidence for a living. It's what we do. Case in point: PZ lays out good-looking evidence of guilt in his comment, and as I said in reply:

As Bora points out, a blog post is a timestamped piece of evidence, a well-pissed-on territorial tree. It shouldn't take more than an hour or two with the lab books from the suspect lab to tell whether or not they stole your protocols -- unless they made up very careful fakes, which frankly would be more work than doing the damn experiments and not nearly as interesting.
You don't have to go screaming over to the offender's lab, punch him in the face and carve "SCUMBAG" into his forehead with a rusty scalpel. Simply contact the apparent scooper and lay out your evidence in a calm, straightforward manner. Frame it as an enquiry: my work shows considerable similarity to yours, how about we work together on some of these questions? If he blows you off, take it to the senior editor of the journal he published in; the journal has a vested interest in evaluating your claims, because they need a reputation for impartiality. While you're at it, cc: the apparent scooper's boss/es (dept head, dean of school, whatever). If you're wrong, that should become clear pretty damn fast -- and you haven't carved anything into anyone's face, so a sincere apology is all that's required. (Speaking for myself, if I were the innocent apparent scooper, at this point I'd be happy to talk about future collaborations, and possibly adding an acknowledgement about independent prior art to the paper in question.) If you're right, you may or may not get active satisfaction in terms of having the paper rescinded, or your name added to it, but you will have taken a stand against an unacceptable but all-too-common practice and, in doing so, nailed a big stanky turd to the scooper's reputation. Science, like all human endeavours, runs to a certain extent on reputation, so the mechanism is already in place to deal with this problem. The risk associated with scooping is currently very low; if you're willing to do it, you can probably get away with it. And there are always assholes in every field, so there will always be someone willing to do it. The good news is that collaborations are already CV fodder, in many cases regarded even more highly than individual efforts when it comes to promotions, grants and so on. We therefore do not need to raise the risk associated with scooping very high -- we can be absolutely scrupulous about proof, and about avoiding witch hunts -- before sharing becomes a more attractive option than stealing.



Monday, 17 April
weekly verse: AE Stallings

StallingsAE.jpg Another week went by without any verse on this blog, and April is National Poetry Month, and my favourite living poet AE Stallings has a new book out -- so without further ado, enjoy:


Variations on an old standard


Come let us kiss. This cannot last—
Too late is on its way too soon—
And we are going nowhere fast.

Already it is after noon,
That momentary palindrome.
The mid-day hours start to swoon—

Around the corner lurks the gloam.
The sun flies at half-mast, and flags.
The color guard of bees heads home,

Whizzing by in zigs and zags,
Weighed down by the dusty gold
They've hoarded in their saddlebags,

All the summer they can hold.
It is too late to be too shy:
The Present tenses, starts to scold—

Tomorrow has no alibi,
And hides its far side like the moon.
The bats inebriate the sky,

And now mosquitoes start to tune
Their tiny violins. I see,
Rising like a grey balloon,

The head that does not look at me,
And in its face, the shadow cast,
The Sea they call Tranquility—

Dry and desolate and vast,
Where all passions flow at last.
Come let us kiss. It's after noon,
And we are going nowhere fast.


Noir


Late at night,
One of us sometimes has said,
Watching a movie in black and white,
Of the vivid figures quick upon the screen,
"Surely by now all of them are dead"—
The yapping, wire-haired terrier, of course—
And the patient horse
Soaked in an illusion of London rain,
The Scotland Yard inspector at the scene,
The extras—faces in the crowd, the sailors;
The bungling blackmailers,
The kidnapped girl's parents, reunited again
With their one and only joy, lisping in tones antique
As that style of pouting Cupid's bow
Or those plucked eyebrows, arched to the height of chic.

Ignorant of so many things we know,
How they seem innocent, and yet they too
Possess a knowledge that they cannot give,
The grainy screen a kind of sieve
That holds some things, but lets some things slip through
With the current's rush and swirl.
We wonder briefly only about the girl—
How old—seven, twelve—it isn't clear—
Perhaps she's still alive
Watching this somewhere at eighty-five,
The only one who knows, though we might guess,
What the kidnapper whispers in her ear,
Or the color of her dress.


Ultrasound


What butterfly—
Brain, soul, or both—
Unfurls here, pallid
As a moth?

(Listen, here's
Another ticker,
Counting under
Mine, and quicker.)

In this cave
What flickers fall,
Adumbrated
On the wall?

Spine like beads
Strung on a wire,
Abacus
Of our desire,

Moon-face where
Two shadows rhyme,
Two moving hands
That tell the time.

I am the room
The future owns,
The darkness where
It grows its bones.


Those are all available online via the poet's own site, and all are from her new book, Hapax, as is the author photograph.

logolepsy | Bill Hooker | 17 Apr, 2006 | | [Trackbacks](0)


Tuesday, 11 April
linklog 040613

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Whup. Ass.

Apropos the last entry, via Atrios: Alisa Valdes-Rodriguez got some monkeymail and replied in much better style than her idiot correspondent deserved:

MICHAEL SAYS: 3. They do not register for selective service and do not serve in the military - forcing legal Americans to defend them.

ALISA SAYS: Sigh. According the U.S. government, all male immigrants -- legal and otherwise -- are required by U.S. law to register for selective service.

According to the National Center for Immigration Law, one in ten U.S. soliders who have DIED in Iraq have been immigrants. Five percent of those serving in our military are illegal immigrants.

The first soldier to die for the United States in the current war in Iraq was Marine Lance Cpl. Jose Gutierrez, an illegal immigrant from Guatemala.

(Emphasis mine.) Good enough to die, not good enough to vote. I had no idea.

That's just a sample, too -- you should read the whole thing. By reading one blog post you can be better informed about the current immigration debate than anyone in the mainstream media.



Monday, 10 April
Somos trabajadores, no terroristas: Portland 060410.

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