April 2006 ArchiveSunday, 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: Not the least of T.S. Eliot's
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
Powered by Simpy and Feed2JS; the archive, aka my Simpy account, is here. 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
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:
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 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: 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 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
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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.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.)
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.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).
<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.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:
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.
Thursday, 20 April
linklog 060420
Powered by Simpy and Feed2JS; the archive, aka my Simpy account, is here. Wednesday, 19 April
linklog 060419
Powered by Simpy and Feed2JS; the archive, aka my Simpy account, is here. 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!"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.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
Those are all available online via the poet's own site, and all are from her new book, Hapax, as is the author photograph. 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.(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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