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.

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.

linklog 060420

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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.”
  • – 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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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.

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.

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.

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,
On the wall?
Spine like beads
Strung on a wire,
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.

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.

weekly verse

Still can’t stick to Fridays, but I’m trying to post some verse every week.

Catharanthus roseus
Vinca, myrtle,
sorcerer’s violet,
my mother’s favourite
of dull corners,


world travellers,
in native dress—
bright little faces
in odd places.