Calling All "Open Notebook" Wackaloons
June 27, 2008
Are there any experimental scientists out there advocating for and using open notebooks? Not navel-gazing theoreticians that sit around drinking coffee and making shit up, but actual real scientists: people fucking with shit in a laboratory. Because frankly, “Open Notebook” sounds like the kind of batshit wackaloonery that people who don’t even know what a real lab notebook looks like would be propounding.
DrugMonkey 
June 27, 2008 at 11:23 am
Young hip Web2.0 era scientists: ohhhh wikinotebook!
PP: Get off my lawn!
PP- stop being so old !
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June 27, 2008 at 11:28 am
Hey, I’m a navel-gazing theorist who just finished drinking her coffee but I know what a lab notebook looks like! Anyway, I still don’t think open notebook sounds like a good idea. (but, whatever, people can spend their time how they like)
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June 27, 2008 at 11:31 am
PP, Please define “actual real scientist” and “real working scientist”.
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June 27, 2008 at 11:32 am
Since this whole Kristin Roovers/OHRI thing went down, it might be cool to have somewhere you can see a person’s raw data in its entirety for verification/clarification reasons. Might have to put it up *after* the work has been published, though.
A new person picking up someone else’s project might want to pore over existing notes to avoid re-running completed experiments and take note of established dead ends.
Just playing devil’s advocate. 🙂 I think biomed is a little too competitive to make full use of stuff like Open Notebook.
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June 27, 2008 at 11:36 am
Yes.
P.S. Thanks once again for elevating and progressing the discourse.
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June 27, 2008 at 11:57 am
Open notebooks are kinda useless, but access to raw data (in spreadsheet format) might be useful when we come across those papers with poor statistics. I for one would reanalyze someone else’s data properly just for my own satisfaction (and then post it on the web – AHAhahahaha!).
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June 27, 2008 at 12:08 pm
Rectoractician,
It is difficult to define an actual, real scientist, but I am sure that PP is one.
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June 27, 2008 at 1:08 pm
Nature Precedings has put up an interesting presentation (pdf/ppt formats) about Open Notebook Science. The comments section of the page is worth a look, too.
http://precedings.nature.com/documents/39/version/1
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June 27, 2008 at 1:47 pm
@ S. Rivlin- So PP is like pornography?
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June 27, 2008 at 3:41 pm
I don’t mean to get all rational here, but my main objection to the Open Notebook movement is the premature disclosure of intellectual property. I know that Jean-Claude Bradley has made the point that he only puts up work on his lab’s malaria projects with compounds in the public domain. My concerns are that you may never know what work may become patentable.
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June 27, 2008 at 3:53 pm
Yeah, what’s your fucking problem? LOLZ!
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June 27, 2008 at 4:58 pm
I like the idea of submitting ACTUAL unpolished data as supplementary information, like crystal coordinates and NMR spectra and un-edited western blot scans and mass spec datasets. It would improve the transparency and accountability a lot for reproducing stuff or tackling controversial issues.
People’s true open notebooks would just be embarrassing–I think of all the times I half-assed something and barely wrote any of it down because I didn’t really think it would work, or wrote things like “oops I f’ed up and spilled it” with a frowny face.
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June 27, 2008 at 5:08 pm
You should see the notations in PhysioProf’s old notebooks detailing experimental failures. HAHAHAHAHAH!!!!
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June 27, 2008 at 5:13 pm
OK, I am more than 40 years past doctoral research, and 30 years into business-type IP. But certainly back in the day, computer analysis of perfectly legitimate data did not find its way into notebooks. (I was working at the time for a now well-known NASA institute, for a now well-known NASA employee).
I suppose that now it is different, but at that time word processors did not exist in the grad student world.
Actually the present-day standard, such as it is, would be welcome because my final data, on 9-track tape, got written over, and some casual printouts became the definitive record. I remain pissed as hell.
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June 27, 2008 at 7:05 pm
Becca, you’ve got it, babe, that’s what PP stands for. 😉
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June 27, 2008 at 9:19 pm
My concerns are that you may never know what work may become patentable.
1. Who gives a rat’s? I’m a scientist not a moneygrub. (Pre-emptive: usual rejoinder is that drugs won’t get developed if Big Pharm can’t make its usual obscene profits; bullshit. Ask any Brazilian with HIV.)
2. Doesn’t the same argument count against ever publishing anything, since you can’t publish first and patent second?
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June 27, 2008 at 9:36 pm
@PP: don’t confuse advocating with proselytizing. You keep flailing away at the same strawman, the idea that we ONWs are claiming that all science everywhere should be Open in real time. We’re not.
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June 27, 2008 at 9:40 pm
If it’s curated, edited, or analyzed, then it ain’t a fucking Lab Notebook, and it’s stupidly misleading to call it one.
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June 27, 2008 at 9:51 pm
Dude, you don’t get to decide what words mean. There’s plenty of room in “notebook” for the way you keep notes and the way I keep notes and the way Jean-Claude keeps notes.
Also, you never “curate, edit or analyze” stuff in your notebooks? Weird.
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June 27, 2008 at 10:00 pm
Notebooks are just supposed to be “here’s what happened” for someone else (or you later) to keep a record for reproducing or proving when something first happened. In grad school I used to get really irritated at my undergrad mentees when they would take notes on scrap paper messily and then recopy a polished version into their “actual” lab notebook later (a common British practice). If you do that, and don’t keep the REAL record of what you REALLY DID, and you don’t have a perfect memory of where you put your hands when, you totally lose any information about what went wrong (or right about what you did wrong–extremely important to be able to track back to).
Also, intellectual property protection is a lot more complex than people being moneygrubs. It serves as a mark of who first conceived of an idea, and as an academic you SHOULD care about protecting yours even more, because if any company ot wind of something they could make money from out of your work and you didn’t have it protected, they wouldn’t hesitate for a heartbeat to screw you as far as they could out of any credit for your creativity.
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June 27, 2008 at 10:11 pm
Of course I don’t get to “decide” what “notebook” means. If people wanna distort the commonly understood meaning of the term “notebook”, which incorporates the idea that the contents are contemporaneously recorded, rich with ephemera, and later converted into something of lasting value, they are certainly free to do so. But it’s stupid and counterproductive to use a word with a commonly understood meaning to refer to something different.
To the extent people are talking about openly posting edited, curated, analyzed datasets on the Internet, they should call it Open Data or whatever. I can see how that kind of thing would have some utility. Calling it “Open Notebook” is just a shitty analogy.
To the extent people are talking about openly posting real lab notebooks on the Internet, it’s fucking stupid.
There you go: no more strawman.
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June 27, 2008 at 11:05 pm
i agree with PP. semantics or not, “open notebook,” doesn’t really have a real purpose or service. yes, keeping a notebook is important. yes, it is documentation of your work. yes, it is open to whomever wants to look at it. we’ve got nothing to hide. but what is the real purpose? to check someone’s math? to re-analyze data? to see their thought processes? do you guys ever look at your own lab members’ notebooks THAT OFTEN? give me a frickin break.
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June 28, 2008 at 1:44 am
The concept of an open notebook is absurd and I think it would ultimately result in more confusion than clarity. Furthermore, looking through someone else’s notebook blows. I’ll do it if I have to, but finding what I want is usually accompanied by a large amount of irritation.
I’m using notebook in the traditional sense. 😉
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June 28, 2008 at 8:08 am
Abel – I think you must have misunderstood because I never said that I only discuss compounds in the public domain. If we selectively put up information I would not call it Open Notebook Science.
A laboratory notebook is at minimum a record of what was observed and done, without discrimination. We put that information in the log section of the experiment at the end of the page. We put our raw data in the Results section and over time fill out the discussion and conclusion sections. For those of you saying that is not a standard lab notebook you’ve apparently had a different training than me.
This page is an example:
http://usefulchem.wikispaces.com/Exp150
No lab notebook is meant to be read as a journal. It should mainly be of interest to researchers trying to repeat experiments or understand if our experiments failed in the same way that theirs did. For higher level discussions I use a blog to summarize information that I can back up with links to the notebook.
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June 28, 2008 at 8:28 am
And I continue to remain surprised by how close-minded scientists are, how little they understand about some relatively simple concepts, and how “science” has somehow become secondary to all kinds of other issues.
ONS is a model. Is it for everyone? No. Should it be practiced by everyone? No. Is it a perfectly viable model. Absolutely. You go into it fully understanding the pros and cons. You know … choice and all that.
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June 28, 2008 at 2:50 pm
I suspect your blog would be empty if not for the people you try to irritate with your … creative style of arguing. Here is a challenge for you. For the next half a year start posting constructive blog posts where you give ideas to improve something (it can be cooking for all I care) without insulting anyone in the process. Lets see how your blog audience holds up.
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June 28, 2008 at 3:18 pm
Holy shit! That’s fucking brilliant!
If you hadn’t issued this amazing challenge, it never would have occurred to me in a million years to publish posts designed to help biomedical scientists improve their grantwriting, overall grant-seeking strategies, running of their labs, strategizing research programs, successful interviewing for faculty positions, giving scientific presentations, mentoring students and post-docs, making the most of scientific conferences, responding to peer reviewer comments on submitted manuscripts, or dealing with journal editors. This is because my single-minded devotion to insulting people has taken up all my time and attention, such that I never even realized that anyone would ever possibly want to read about any of that stuff.
But now with your insightful challenge, that so cleverly and penetratingly pierces right to the sad ineffectual insult-laden heart of this blog, I have seen the light, and will get right the fuck on it!
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June 28, 2008 at 4:25 pm
Now that I have actually read some of your other blog posts I take back my last comment. I’ll rephrase, stick to the useful stuff, or ask whoever wrote those blogs posts to write all of your blog. Based on the few insult laden blog posts that I had seen before I never though you were actually capable of providing with useful information. If there was a way to exclude blog posts like this one from your feed I would even subscribe to it.
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June 28, 2008 at 4:48 pm
Here you go, an RSS feed of your blog after rinsing (link). Now I can read your blog.
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June 28, 2008 at 5:09 pm
Dude, what the fuck have you been smoking?
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June 28, 2008 at 5:45 pm
There is something kind of amusing about somebody who I think is championing ‘open science’ rinsing a blog.
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June 28, 2008 at 6:10 pm
pinus,
Admittedly, I find PP’s language disturbing and I have commented directly to him about it. For some reason he thinks it is cool to interject the “f,” the “s” and the “mf” words as often as he can into almost any post and response of his. I am not sure exactly why he has chosen to do so, but in my humble opinion, it absolutely diminishes his message, whatever it is.
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June 28, 2008 at 8:15 pm
S.Rivlin, go start your own PG-13 blog!
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June 28, 2008 at 9:46 pm
your not so humble opinion,
Wow, PP, PG-13! This is brilliant. I guess you consider your own blog ratings to be triple X – for mature scientists only.
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June 28, 2008 at 11:22 pm
It serves as a mark of who first conceived of an idea, and as an academic you SHOULD care about protecting yours even more, because if any company ot wind of something they could make money from out of your work and you didn’t have it protected, they wouldn’t hesitate for a heartbeat to screw you as far as they could out of any credit for your creativity.
But if that’s your concern, public disclosure in an open notebook is a perfectly adequate way to assert your priority, and certainly every bit as good as a private notebook. Disclosure is only a problem if you’re planning to file your own patents, not for attacking someone else’s.
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June 29, 2008 at 6:43 pm
My concerns are that you may never know what work may become patentable.
Good point, considering that scientists don’t always get to decide what may be patentable-sometimes it’s the university or research institution that decides, and keeps patent attorneys on staff for just this purpose. I’m by no means a moneygrub, and my one patent is for “intellectual property”/techniques, rather than an instrument or a drug. I had no idea that it would be patentable, and I felt rather like an unwilling pawn for the institution, my boss (who wanted tenure), and the attorneys to use in a patent game.
The relative timing of published methods, grant applications, and notes/photos/other crap in my lab notebooks seemed to be critical in this process, and the Open Notebook concept would add yet another concern. I’m not dismissing it, or claiming that it’s wrong or inappropriate – rather, just supporting Abel’s point that the release of data may be an issue down the road. I’d check with the intellectual property/tech transfer wonks at my university first.
Of course the Open Notebook platform is a choice, just as reading ScienceBlogs is a choice- which ones, how frequently, etc. Perhaps one reason that the language at this one (which doesn’t bother me in the slightest- PhysioProf is like the uncensored Gordon Ramsay of ScienceBloggers) gets up the noses of some readers is that there really isn’t another blog here that routinely has similar post topics. If you want endless links to YouTube clips or rants about creationists and religious wackjobs, you’re spoiled for choice…but where else (at ScienceBlogs) are you going to get detailed posts about writing R01 proposals or lab management strategies? Has to be someone(s) who has federal funding, runs a research lab, publishes regularly (absolutely required to get/keep federal funding), reviews manuscripts, sits on study sections, knows the system. Why would I pay attention to Obi Wan Nopubsi?
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June 30, 2008 at 8:50 am
Barn Owl,
Are you saying that since there is no other scienceblog that deals with this blog’s topics, you will hold your nose and read it? Or that the colorful language here makes its posts more comprehensible?
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June 30, 2008 at 4:02 pm
Are you saying that since there is no other scienceblog that deals with this blog’s topics, you will hold your nose and read it? Or that the colorful language here makes its posts more comprehensible?
Neither. I *thought* I wrote rather clearly that the language doesn’t bother me, so no need to hold my nose…errrr…beak. Bigotry, whether racial, ethnic, or regional, puts me right off a blog, as do sexism and homophobia-I haven’t seen any of that here at DrugMonkey. I can understand, however, that the swearing might upset other readers, and my point was that there aren’t any other blogs in this particular “stable” that offer the same types of posts about writing R01s and lab management.
I don’t think the “colorful” language makes the posts any more or less comprehensible.
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June 30, 2008 at 6:25 pm
I specifically like the swearing part. For serious.
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June 30, 2008 at 10:21 pm
agree with arlenna.
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July 9, 2008 at 6:26 pm
re: patents. @bill: I think there’s some debate as to whether publishing on the internet precludes patenting. In the US you get a one year grace period after publishing (however publishing is defined) to file for a patent: http://library.findlaw.com/2004/Sep/27/133585.html
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