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Science Careers Blog

April 14, 2010

Scientists Discuss Openness on FriendFeed

Many of the Open Science advocates I talked to for last week's story, Scientists Embrace Openness, pointed me to their active community on FriendFeed. In particular, Steve Koch of the University of New Mexico suggested that I start a discussion there after the story came out. I did, and the result (pasted below, lightly edited) was a fascinating, wide-ranging conversation on topics related to Open Science, some of which we hadn't had space to cover in the original story. Highlights include discussions about Open Notebook Science tools (OpenWetWare, Google Docs, BenchFly), the opinions of "mainstream" and young scientists about Open Science, and the obstacles to doing medical research in an open way. We even compared notes on getting "scooped" in science and journalism.

If you'd like to leave your own comments, you can do so on this blog or in the original FriendFeed thread.

Chelsea Wald to Chelsea's feed, Science Commons, Open Notebook Science Solubility Project, Science 2.0
Hi, everyone! Today I'm here discussing my ScienceCareers story, "Scientists Embrace Openness," about the career implications of Open Notebook Science, Open Data, and general science openness: http://sciencecareers.sciencemag.org/career_.... Let me know what you want to talk about...
April 9 
Michael R. Bernstein, Paul Bacchus, Mike Chelen and 31 other people liked this

Hi Chelsea, great article, what led you to write it? - Andrew Lang

Thanks, Andrew! Jim Austin [@SciCareerEditor on Twitter], the editor of ScienceCareers, assigned me this article. (There are two main ways to get work as a freelance writer: pitch or get assignments.) I'm not sure what exactly led him to the topic, but I know that a conversation with Brian Krueger played a role. I knew very little about the topic, but Jim intuited that it would be a good fit for me as a writer. It turned out to be a really fun story to report and write. - Chelsea Wald

Anthony Salvagno asked me in an email: "How long did it take from first concept to publishing?" I sent my first email interview request on Feb 11, so the story took me about two months to write. (This, of course, doesn't count the time Jim spent coming up with the idea.) I wasn't working on the story full-time, though. Depending on my other projects, some weeks I worked intensively; others, hardly at all. It helped that the Pacific Northwest Science Commons Symposium took place soon after I got this assignment; I attended virtually (when the video stream was working) and got something of a crash course. - Chelsea Wald

HI, Chelsea. I very much enjoyed the article and will be adding it to my ONS delicious tag arsenal! What I appreciated about the read was its focus on practitioners -- in the class where I discuss ONS as a practice (I am not a scientist, but train young scientists to write), there is always at least one student who writes an elegantly argued, pro-ONS piece, and having an essay that is about people rather than focusing on the ideal itself works nicely to help that student feel less isolated. - Mickey Schafer

Hi, Mickey. Yes, I was tasked with writing an article on the practical challenges associated with openness, especially for early-career scientists. I quickly came to appreciate that ONS practitioners have to go to fairly heroic lengths in order to make their notebooks open, and I wanted to emphasize that. I also came to appreciate that those same ONS practitioners realize that it's simply not practical for most scientists to do the same -- at least with the current state of technology (not to mention the standard measures of academic success). I don't know why, but I expected a more rigid ideological stance, and I was totally wrong. By the way, it's really cool that you're discussing ONS in a scientific writing class. I bet others here (and I) would be interested in hearing more about it. Do a lot of students write essays arguing against it? - Chelsea Wald

Mickey - what you are doing with your class sounds very interesting - are your students willing to share some of their essays? - Jean-Claude Bradley

Hi folks. Thought I would join in here and say that I started developing an interest in Open Science perhaps 6 months ago. I've been monitoring it, but not too closely, since then. A couple of Twitter posts, perhaps channeled from FriendFeed, got me off my butt and made me decide it was time. Though I don't remember what it said, one of those posts was from Brian Krueger. I contacted him and he got me started. I handed this off to Chelsea and she took it from there, very skillfully. - Jim Austin

Jim - thanks for the feedback on how it came about - I hope your interest in Open Science continues! - Jean-Claude Bradley

I'll definitely continue to keep an eye on it. I think it connects to a couple of other big issues right now -- importantly, data sharing and trying to achieve a more integrative science, especially medical science. There's a lot riding on that, it seems to me, and a lot of people these days are talking about, and working on, integrating research resources. - Jim Austin

Hi Chelsea, thanks for referring me to this discussion! I think the Koch and Bradley labs are great examples of the younger generation of scientists embracing available technologies and trying to improve the research process by taking a new approach, which should be applauded. I really like Jean-Claude's idea of trying an open project out on the side to get started- it's a nice way for people to test the waters with minimal risk. I think it's essential that open access resources extend beyond notebooks to training materials as well, which was my goal in starting BenchFly- allowing people to document and share how they perform techniques in their labs. Technology affords us a tremendous opportunity to democratize science by providing expert instruction to anyone with an internet connection. - Alan Marnett

Mickey - do you see any trends in your students' opinion of ONS? Is it generally for or against? Any year-to-year trends? - Alan Marnett

Hey Chelsea and Jim and everyone, sorry I'm getting to the party late. Yesterday you mentioned a conversation between you and Koch about parallels between Journalism and ONS. Could you go into more detail? I would like to hear your take on it and figure out if there are any ways the we (the ONS community) could help you attain more openness. Of course, like JCB says, starting small is a great way to get involved. - Anthony Salvagno

Hi, Anthony. The party's going on all day. It's more like an open house, I guess. The back story is this: When I was reporting this story, Steve suggested that I ask his students (including you) questions about working in an open lab. We tossed around the idea of doing it on FriendFeed, so that others could listen in and participate. I liked this idea but became concerned that it could tip off other (read: competitor) journalists who could then scoop me. Sound familiar? I didn't get around to asking Jim for his take on it because soon after that I had my first, pretty painful experience with a "scooping." (In this case, it doesn't mean that someone stole my idea, just that she got around to publishing a story about it first -- in this case, she beat me by about a week. This happens often in journalism, as in science.) Still smarting from that, I decided to go for a more traditional, closed approach. (more coming) - Chelsea Wald

Do you think you might experiment with live reporting? By this I mean you "publish" information as you receive it in an informal method. Scientists can preprint articles in something like Nature Precedings and get early feedback. Then you could publish your formal written report when it is all done using the information you had previously compiled. - Anthony Salvagno

Also, how likely would it be for journalists to collaborate on a project? Maybe have more names attached to one article like we do for journal articles. - Anthony Salvagno

Because I was reporting the ONS story at the same time, I a) became more sympathetic to the concerns of scientists with respect to being open, and b) began to wonder whether there was a place in journalism for an "open notebook" approach. What would it look like? Would sources agree to participate in it? Would editors agree to it? Would it help establish a priority so that scooping would be less likely, or would it make it much more likely? I know I'm not the first person to ask these questions, but I haven't yet heard a serious discussion of it in the journalism world (not that there hasn't been one; I just haven't heard it yet). - Chelsea Wald

Gosh, this is getting (even more) interesting. Keep it going !! - Graham Steel

Anthony, here's an example of a rough-draft article that has left some journalists mystified recently: http://www.scientificamerican.com/article.... (Note that the writer is a Science Careers contributor.) I have not discussed this project with anyone in the know. - Chelsea Wald

As for collaboration, it happens sometimes within news organizations, but it would be hard to see how that would work across organizations. In science, if you find out that someone at another institution is working on the same thing, one response is to turn your competitor into a collaborator and publish together. But could that work in journalism? Doubtful. The usual response is to try to get to print as fast as you can. - Chelsea Wald

Chelsea, Thanks for pointing out Beryl's article. Beryl is, as Chelsea notes, a long-time contributor to Science Careers. She has written a monthly column for -- not sure -- maybe 5 years? And she writes on many of those same topics for us. As you may know, Scientific American is now owned by Brits -- the publishers of Nature -- so I suppose that represents a kind of sharing. ;-) - Jim Austin

Hi, Chelsea. I also really enjoyed the human element your article brought to the process, across all levels from tenured to faculty down to graduate students. I'm also intrigued by your parallels in the journalism world. While ONS has led me to new collaborations, it's often been something I've had to approach very cautiously with most collaborators. How do others address this? - Carl Boettiger

There are some really important differences between journalism and science -- but there are also some parallels. As may of you are probably aware, there's a parallel discussion going on about journalism, openness, and business models. - Jim Austin

Hi, Carl! Glad you found this. Many people told me that they had to close off projects due to collaborators. That, or drop the project altogether. Maybe others will weigh in on specific examples. - Chelsea Wald

Yes, Jim's right that we shouldn't forget about major differences between journalism and science. In the article, Jonathan says: "Given that taxpayers are paying for our work, I think that the default should be to be open unless you can prove that it's a bad idea." Taxpayers are NOT paying for my work. Journalism is a public service, but it also has to make money. - Chelsea Wald

I will just add to Chelsea's comment: Non-profit models of journalism exist, but even they need revenue -- which means inventing new ways to ensure objectivity. What happens to National Public Radio when there's a Republican Congress? (A: They lose funding.) So you can see that there are interesting parallels and differences. It's all research, even if the methods, and the nature of the knowledge, are different. - Jim Austin

But in journalism, value typically equates to exclusivity, especially today. If you want to generate revenue, you have to be able to offer something that people can't get for free. I think that's a major difference. - Jim Austin

Now, I'd like to ask a question of the scientists here. One of my preoccupations these days is with translational research -- trying to accelerate the rate at which basic-science breakthroughs become real-world therapies. If you're not biomedical, then consider the obvious parallels, like materials for electronics. Does running an open lab take you completely out of that game? Is an open laboratory only for the non-applied? - Jim Austin

Hi Chelsea. As I said on Jon Eisen's thread http://ff.im/iJeZZ yesterday, I was very impressed with this article. As a patient advocate and non scientist (very interested in science) as I blogged about here http://mcblawg.blogspot.com/2008... , I personally would like to work more openly and am of the view that your article and this discussion has had a positive effect/impact, so thank you !! - Graham Steel

Thanks, Graham. You bring up some interesting questions about tools in your post. I use google docs all the time, and my understanding is that many ONS researchers do, too. Does anyone care to discuss collaboration/ONS tools? - Chelsea Wald

Chelsea, ask Bora Zivkovic about "Open Notebook" journalism: http://scienceblogs.com/clock... - Martin Fenner

@ Chelsea, Jean-Claude, -- sorry for the late reply -- I am on a grading frenzy and wasn't supposed to be checking in at FF at all until next week! The essays in questions are blog posts replying to Michael Neilson's "Future of Science" essay and an HHMI article titled something like "So you wanted a revolution" (both can be found linked here: http://web.clas.ufl.edu/users...): that blog has remained private according to student wishes. This year, one student wrote a passionately worded and rather elegant post about ONS (she's on her way to med school). She gave me permission to make it public, but I don't know how to make a single blog post public and keep the rest private. If/when I get my blog started, her post will find its way there. - Mickey Schafer

@ Alan -- same apology as above! I have only held this discussion 2 times, so there are no trends to report. Last year, there was more open skepticism, but there were also more argumentative personalities who knew each other well. It will be interesting to watch over time. This year, a couple of students remarked it might have been better to have this conversation before they had finished their research. No student has yet ever heard of it, so also did not know any practitioners. - Mickey Schafer

Thanks for checking back in, Mickey! - Chelsea Wald

@Jim -- "What happens to National Public Radio when there's a Republican Congress? (A: They lose funding.)" -- this is about the scariest thing I've heard in a while. I live and breathe NPR. They had an interesting discussion last week, I think it was, about the fate of CNN. Given the importance of "branding" to attract a particular audience, CNN is losing ground to Fox and MSNBC alike. They quipped the same could be true of NPR -- at least NPR has public supporters paying out of their pockets. - Mickey Schafer

@Mickey, I didn't mean they would be totally unfunded, NPR is notable for having a relatively stable revenue base, and an independent news apparatus. I was thinking of 2005 when, accused of having a liberal bias, their funding -- about $400 million at the time from the CPB (including both NPR and PBS) -- came under threat from Congress. NPR works hard and successfully (as far as I can tell) to divorce editorial decisions from private-sector (including nonprofit private-sector) contributions. It's a good model. - Jim Austin

Hi, Martin. Thanks for pointing me to that post (I'm familiar with Bora and his work, but I hadn't seen this). I'm noticing, however, that "traditional media" don't get mentioned until step 4 of his model. I suppose that means it wouldn't work if someone gets assigned a story, as I did in this case; unless, of course, the publication agreed to it. - Chelsea Wald

@Chelsea: "...unless of course the publication agreed to it." I would welcome an intelligent proposal, as long as it was on topic (that is, about Science Careers). I'm always eager to try new things. - Jim Austin

Wow, cool! You all heard it here first! - Chelsea Wald

Very interesting. I let Bora respond to that. - Martin Fenner

Talk about coming to the party late... This is a really good discussion. I thought the article gave a good perspective on the topic. In your research, did you get a feel for how mainstream researchers feel about the topic, Chelsea? I know my quote came off as quite skeptical, but in my work with LabSpaces, I've found most researchers to be unwilling to talk openly and publically about their current research secrets. When I first launched the site, the University of Iowa legal department contacted me and told me to put a disclaimer on there that any public dissemination of ideas/data could make obtaining patents nearly impossible. - Brian Krueger - LabSpaces

Its a common sentiment Brian expresses, but I think it is becoming less common. When everyone holds their cards to their chest, they don't learn as fast that their great idea was tried and rejected by 4 people before they happened upon it. Most of the secrets are really neither that secret nor patentable. This is one of the areas I'm most hopeful open science will illuminate. - Mr. Gunn

Hi, Brian. You were here in spirit. ;) My sense is that most researchers would say that Open Notebook Science is fine...for other scientists. You know, everyone I talked to was pretty realistic and probably wouldn't disagree with you: The entire scientific enterprise is not suddenly going to go open. By the way, I'm fascinated by your interaction with the legal department. Any of the scientists here have similar experiences? - Chelsea Wald

Jim, I recently wrote about some of the obstacles of doing medical research online here: http://blogs.nature.com/mfenner... Some issues are patient privacy, recruitment and reporting bias when clinical trial results would be openly available in an ongoing study, and commercial interests of pharma companies that sponsor trials. - Martin Fenner

Drug companies are starting to be more open as well: Is open innovation the way forward for big pharma? http://dx.doi.org/10... - Martin Fenner

For this story, I emailed with Sriram Kosuri of OpenWetWare. His comments didn't make it into the story, so I thought I'd add them here (a luxury I don't normally have!): Q: How many users does OWW have? Of those, how many are actually posting bona fide Open Notebooks, as opposed to, say, just hosting lab websites? If you don't have exact numbers, can you estimate? What kind of growth are you seeing? Are there any other Open Science/Open Notebook Science trends that you're seeing that might be of interest to our readers? A. You can get a feel for the general statistics here: http://openwetware.org/wiki... (7423 registered users: which is a gross overestimate of the actual every day users, as is any site like this) and here, which gives a better view of daily activity as well as notebooks specific activities: http://openwetware.org/wiki... Another good place to look to see what people are editing at any given time is here: http://openwetware.org/wiki... Q. Many Open Notebook scientists are telling me that OWW is a good (and even necessary) place to start with an Open Notebook, but that it's not sufficient. They're also using, for example, google spreadsheets. Are you planning to roll out any features in the near future (say, the next year or so) that will make OWW a more comprehensive solution for ONS? Is that even a goal for OWW? A. We have been trying to be pretty responsive to the needs of the ON contingent on OWW. We think that people using such notebooks tend to contribute to more knowledge available to the public related to the actual process of doing science, both indirectly by people being exposed to those notebooks, and directly by having more users directly contributing to OWW. I think the biggest notebook user group comes from the iGEM competition that is held every year. Since these teams are mostly composed of undergraduates for a mostly friendly competition, they don't mind having their stuff up in public, and secondly, need online collaboration tools to keep a team together to work towards a shared goal. By being a part of the community, especially a group that is learning about biology, they sometimes have a better incentive to contribute to protocols and other information on the site so that it is easier to find and digest. In terms of actual tools that will help, I think there are a lot coming from the outside that we are thinking of incorporating, but we don't have a massive team, and we are mostly at the mercy of our volunteer community. So we help where we can (setting up the lab notebook feature for example was something requested by the community, and most of the revisions were spearheaded by folks using the service). Q. Any other thoughts about OWW and ONS? A.I think on our front, we are engaging many in the ONS community that have been really pioneering stuff by providing them with as many tools as we can. I think in terms of thought leaders, Cameron Neylon really helped us along the way, though I have a feeling you've already have been engaging him. - Chelsea Wald

Sorry for the lousy formatting there. Any help on how to make it better? - Chelsea Wald

That's the longest comment I've ever seen on FF. Formatting aside, how did you manage to do this ?? Cool !! - Graham Steel

Haha! I didn't know it wasn't supposed to be possible. Cut and paste, baby! - Chelsea Wald

Dang and thanks again !! Right. I need to lie down so off to watch http://en.wikipedia.org/wiki... Apparently, it's meant to be rather good. Next? - Graham Steel

@Martin, Thanks for the links to your posts. I will read them with interest. - Jim Austin

@Chelsea, I don't know if you've spoken to Koch about this, but we have a patent for our optical tweezer technique. I don't know all the specifics of it because I'm just a slave in the lab (just kidding) but I know we are open and we have this (as an example of people other than medical sciences). - Anthony Salvagno

As for tools I'm really big into Google Docs. My notebook is on OWW and I hate making tables in html and css and starting using google docs as soon as I discovered they existed. I also use Evernote to quickly get pictures from my pc on the web. Because of friendfeed's ability to add rss feeds (among other things) I can create groups here that contain possible related posts from all my web work. I can then simply link or frame that group into my OWW if I need to gather information from various places. I also just got a droid and have been using apps to help me control everything. - Anthony Salvagno

Examples of what I'm talking about: http://openwetware.org/wiki... and http://openwetware.org/wiki... and http://openwetware.org/wiki.... - Anthony Salvagno

I'm providing a bunch of links of pages in my notebook that have integration from different sources. I also have protocol pages not in my notebook and upload video protocols to youtube and embed them in right on the page with the protocol (see here: http://openwetware.org/wiki...). I've been meaning to switch to BenchFly but I ran into a snafu. Alan has been working on the issues very diligently trying to fix the problem and we've found a workaround for now (thanks Alan!). - Anthony Salvagno

Also if you'll note posting lots of comments could be another way for you to format one really long comment. Sorry if I pissed anyone off. - Anthony Salvagno

One more note... this thread kicks ass! It's so awesome I want to curse more, but I'll hold back. - Anthony Salvagno

@Mickey would it be possible to send me the student essay that hasn't been posted? I could post it on my blog and give you and said student full credit. Another alternative would be to post the essay here on ff as a series of comments with the thread being the title of the essay. What do you think? - Anthony Salvagno

Thanks for these contributions, Anthony. I'm sure people will find it useful to see the tools of ONS in practice. I also have to say that I use google spreadsheets for my personal and business finances, and it's reassuring to know that scientists trust them enough to keep their precious data safe! - Chelsea Wald

Anthony, I enjoy seeing how you embed google spreadsheets into your notebook; I've been frustrated by formatting tables in html and this looks very promising! I've been using OWW's rss reader (http://openwetware.org/wiki...) to display articles I've recently added to my library in my notebook, would be interested to see more about how you're using both rss and other apps. - Carl Boettiger

@Carl I really have no good way for handling RSS as I don't use them that much. I don't like how OWW handles RSS. I've actually been trying to figure out a good way to port my notebook as an RSS feed so it goes to friendfeed or yahoo's program that I haven't been able to use yet. The few feeds I do link to get funneled into friendfeed. As for other apps... I've been using Picasa (Google) to upload images or Flikr, I've also been working with Jack Zerby from Flavors.me to get better acquainted with handling RSS feeds for scientific use. Flavors is a nice website that contains a bunch of web sources (youtube, blogger, etc), but doesn't have much for RSS sorting. I use Youtube, Google Docs, I tried to get Google Calendar for the lab but no one uses it, Blogger, Friendfeed. I'm sure I'm forgetting stuff too. Ever since I discovered how to iframe things I've been able to embed just about anything on the internet into my notebook which has been super useful. You could email me if you wanna talk more about all this. - Anthony Salvagno

One more note about RSS feed from wiki (OWW): I learned recently that there is a mediawiki extension that enables you to export your work as an RSS (see http://openwetware.org/wiki...). I've emailed Bill asking to implement it but I think he's disappeared. Sorry for digressing off topic. - Anthony Salvagno

Excellent article! And great thread here. Don't know if you saw the video from this panel on Open Science at Columbia about a year ago: http://scienceblogs.com/clock... As for open journalism - that is tough, but definitely worth a thought. Some newspapeprs (famously Greensboro News & Record as a very early adopter of the practice) now put their article drafts online first, open up for comments, edit according to corrections/suggestions from the readers, and then publish the improved version in the paper edition. Carrboro Citizen has an interesting model - they have a student site (UNC students of a particular journalism class) called Carrboro Commons from which the Citizen editors pick most interesting articles, edit them and publish in the paper: http://scienceblogs.com/clock... - Bora Zivkovic

I know I'm very late to the party here (inconvenient time zones) but the question Chelsea raises about translational research is a very interesting one. For me its all about asking the question "how do we most efficiently maximise return on investment, in this research, for the investor?". Where the investor is the public and its not directly patentable stuff the answer is clear. Where something is directly patentable and the investor is a private citizen or company it might be the case that keeping it private is better (especially in a very large company with good internal communications). But for instance if you are doing early stage exploratory drug development with public money, today, you probably should keep it under wraps because if you don't and can't patent then in the current environment no-one will be prepared to run with it into clinical trials. Maybe (hopefully) this will change in the future and I bet there are cases where it isn't true. What would be really interesting would be good case studies that really show where the edges are...both legal, financial, and social - Cameron Neylon

Jim and Chelsea, it would be great if discussions like this were linked from the article. Either by allowing comments (as in the PLoS journals and now Nature), or by showing links to blogs, Friendfeed, etc. that talk about the article. - Martin Fenner

+1 Martin. - Graham Steel

@Bora Thanks for the ideas on open journalism. I guess I might try an experiment in the near future here. - Chelsea Wald

@Cameron Thanks for joining! You bring up some great points. Does anyone paying attention to this thread know of some case studies that could help shed light on those "edges"? - Chelsea Wald

Martin and Graham: I agree. I don't know whether something like that is in the works, but I'll make sure that the suggestion gets passed on. - Chelsea Wald

There is a Research Information Network funded study going on in the UK at the moment that is looking at researcher perceptions in this space but I don't know of any solid social science studies of outcomes (as opposed to opinions and perceptions) at the moment. The example I give isn't hypothetical tho - I am involved in a research consortium seeking funding to do such development. If we get it I'll look at the situation but it seems likely that my part of the project won't be able to be open for the reasons I describe. No point doing this if we prevent it going into human trials because we can't patent. - Cameron Neylon

Great discussion! Concerning embedded Google spreadsheets, my students do use them in our notebooks but I try to discourage their use in general - or at least make sure that there is a link to the spreadsheet nearby in the page. The problem is that when we create an archive of the notebook and all associated data files, embedded content still appears live in the archived version while links to Spreadsheets get converted to links to frozen Excel sheets. You also can't view the formula and web services called directly from embedded Google Spreadsheets, which is critical for data provenance. For more details see: http://usefulchem.blogspot.com/2010... - Jean-Claude Bradley

On Open journalism, two quotes from http://scienceblogs.com/bioephe... : (1) "The Nieman Lab's Josh Benton noted that this "cult of rewriting" is grossly inefficient: what added value do journalists bring to the table when all they're doing is rewriting one another's work? Such journalists are at best aggregators and curators, much like bloggers: only a few traditional media hubs have the resources to do original reporting, and they often end up coming back to blogs as sources." (2) "The result is a constant reshuffling and repackaging of content, with very few assurances that it's accurate - just as in 18th century New York." --> What if we developed a habit of linking to the raw data? Yet the problems start earlier - journalists all too often "forget" to link to the appropriate source. Case in point: http://scienceblogs.com/clock... . - Daniel Mietchen

The previous comment (and this one too) was submitted from http://openwetware.org/wiki... - will try embedding FF threads into OWW as another way of archiving. Jean-Claude's comments above on Google Docs may apply, though. - Daniel Mietchen

@Anthony -- yes, I think either sending to you or posting here would be possible. The teacher-y side of me wants her to be protected, as an undergrad with all that status or lack thereof implies -- I have students getting butts kicked by PIs who've just decided after 2 years to take an interest in their work, 3 weeks before graduating -- turns out there is a strong prejudice against the premeds in many labs that I didn't know about -- very disturbing to me. - Mickey Schafer
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