Michael Nielsen
Open notebook quantum information - http://michaelnielsen.org/blog...
Another open notebook! This one is from Tobias Osborne, and is focused on quantum information. Link: http://tjoresearchnotes.wordpress.com/ - Michael Nielsen
It's interesting - I still struggle with the idea of what an open notebook looks like for a theoretical scientist. But then I don't have a clear idea of what a notebook, or a working space, looks like for a theoretical scientist. When I think I don't tend to write stuff down until I have at least some version in my head basically. - Cameron Neylon
Cameron - As with labs, I think the key concept is being "more open"; completely open is an ideal that will probably never quite be achieved. Tobias is taking steps in that direction, trying to blog ideas soon after he has them. I've suggested to him setting up a delicious stream so that people can see papers he's reading, as well; adding FriendFeed on top would provide a nice layer of commentary and interaction. - Michael Nielsen
I think that a notebook is perhaps the wrong model for a theorist and that, as Michael suggests, just being more open is the key. "Open Brain-Dump", "Open Discussion" or "Open Collaboration" would possibly be a better terms for what this means to a theorist. I actually prefer "Brain-Dump" because it includes things that are not explicitly collaborative, such as Garrett Lisi's work. - Matt Leifer
As with Cameron I'm not sure how well the Open Notebook concept maps onto theoretical fields. If you take a look at the definitions and categories: http://en.wikipedia.org/wiki... I think what Tobias is trying to do is not ONS - it sounds more like a research blog - commenting on papers he reads - Jean-Claude Bradley
The term "Open Notebook" refers to a mandatory sharing of all experimental data for a given project. If you didn't find entries for the past 30 days in a true ON you can infer that no experiments were performed during that time. There is a category in the Wikipedia page on ONS referring to Partial/Pseudo ONS. This would include all attempts at being more open in sharing research without strict adherence to all the implications of ONS. - Jean-Claude Bradley
Jean-Claude's comments are fascinating. Hmm, the term "Partial/Pseudo ONS." sounds pejorative. This is interesting, "...is not ONS - it sounds more like a research blog - commenting on papers he reads." - Hope Leman
Jean-Claude - taking that definition literally, it's not possible for a theorist to do open notebook science. Of course, many theorists keep notebooks, and it's certainly possible for them to be made open; it would seem strange (at least to me) not to call that open notebook science, despite the lack of data. - Michael Nielsen
A clarification: Tobias' blog contains, so far as I can see, mainly research ideas and background to those ideas. It doesn't (yet) have much commenting on papers he reads. It would certainly be nice for it to be more systematically open, though, with things like auto-generated lists of what he's reading, and so on. - Michael Nielsen
@hleman It isn't meant to be pejorative - just accurate based on the accepted meaning of ONS. See the Wikipedia discussion and references there to see the source of PONS http://en.wikipedia.org/wiki... - Jean-Claude Bradley
@Michael - people might have used the term "Open Notebook Science" to mean any number of things but until Sept 26, 2006 it had not yet been indexed on Google. By using the term consistently, it avoided the confusion that had evolved around terms like "Open Source Science' or even "Open Science". Having a definition that anyone can look up makes it much easier to talk about things http://drexel-coas-elearning.b... - Jean-Claude Bradley
Jean-Claude - terms changing can be a good thing (not always, of course). I think your definition of ONS was a great step, but that any definition which completely excludes theory is incomplete, and needs elucidation. - Michael Nielsen
How to define ONS for theory seems like an interesting challenge. Ideally, I think, a researcher would share as much as possible - all the ideas, partial results, dead ends, reading, conversations, calculations, drafts in progress, and so on - of what goes into theoretical work, preferably in an integrated, standardized and machine readable format. - Michael Nielsen
@Michael - the reason it is called Open Notebook is that a notebook has an extremely well defined meaning in experimental sciences. If you work at Merck I don't think they will let you redefine what a chemistry notebook is and does. The term notebook has a strong history in the experimental sciences - so that everyone knows what an ELN mean - theoretical investigations don't map on the Wikipedia definition of that: http://en.wikipedia.org/wiki... - Jean-Claude Bradley
@Michael - can't you use the term Open Journal to fit your purpose for theoretical investigations? That way we can avoid the profound ambiguity that developed over the term Open Source Science. - Jean-Claude Bradley
I think Jean-Claude's explanatory phrase "no insider information" suggests a better way to look at the issue than strict definitions, against which some edge case or other can always be set. Whether you're doing experiments or not, if it takes more than a day or so for everything you know to appear on the web, then whatever record you're keeping is not an Open Notebook. Conversely, if the world knows everything you know, in as close to real time as possible, then you are keeping an Open Notebook. - Bill Hooker
Hi, all. I am new to this subject and am greatly benefiting from the above discussion. As a newcomer to this discussion of nomenclature, I agree with Jen-Claude’s comments to Michael that Open Notebook Science should be used to refer to projects in the basic sciences and/or that fit the model of the electronic lab notebook. I would like to ask both Michael and Jean-Claude to ask what would fall under the rubric of “Open Journal,” in that case. To wit, elsewhere on FriendFeed, Jean-Claude used the term, “research blog.” Could you use, perhaps, Steve Koch’s and your own various blogging endeavors as examples? And where would Michael’s own blog fit in? It is basically a blog proper, right? And where does the word “wiki” come in given that many of these projects as probably more wiki-like than blog-like. And Open Journal sounds like a fancy name for a blog—would it be somehow different in format from a blog? That is, would it feature more data and perhaps not be open to comments, as blogs usually are? - Hope Leman
@hleman The reason I used the term "research blogging" is that it has come to mean blogging about peer-reviewed work after publication, mainly due to the success of http://researchblogging.org/ Without consistent use of the term it really could mean anything. "Science blogging" is a general term that covers all of the examples we discussed here. "Open Science" is also a very general term that could apply without problem to what we are discussing. - Jean-Claude Bradley
@Bill yes "no insider information" is the idea -and we are lucky in the experimental sciences to have a formal way of keeping track. If you did an experiment and you didn't make it completely public - it isn't ONS. Ironically it is probably the requirements of patent law that have placed the greatest pressure on the mandatory maintenance of lab notebooks in a timely and rigorous format. From what I understand Michael is saying there is no such culture in the non-experimental sciences. - Jean-Claude Bradley
It seems reasonable to me to use the term "Open Notebook Science" to mean no insider information in the context of both theory and experiment. It's true that the theoretical examples I'm aware of all fall well short of that ideal at present. - Michael Nielsen
@Bill's comment about writing down "everything you know": I understand and agree with the spirit of this, but for many practices it's just not possible to write it down. Good lab technique is learned by doing. Being clear about these aspects might lessen our normal resistance to new practices. - Bill Anderson from twhirl
"it's just not possible to write it down" -- I didn't say write it down, I said put it on the web. Cue Moshe from JoVE... :-) - Bill Hooker
OK, I sit corrected. Nonetheless, can everything be "put on the web"? What new practices are we developing for open science? (And what about those Openistas?) - Bill Anderson from twhirl
What I'm gathering from this conversation (and the wikipedia article) is that ONS has a specific meaning, and that it is an electronic version of an "ordinary" lab notebook that is freely accessible to anyone in the entire world (via the internet). Accompanying this is also the requirement for posting "all raw and processed data, and any associated material." As Jean-Claude pointed out, this is heavily influenced by patent law, and I think presumably in a drug discovery / chemistry kind of setting. The wikipedia article calls this "the logical extreme of transparent approaches to research," but I after reading this comment thread, I think I disagree with that. I think it's the logical extreme of making everything that has been TRADITIONALLY recorded available to everyone. So it seems the definition of ONS is tied to a popular definition of a standard experimental lab notebook. What I mean is there are many things missing that could be new forms of shared material. - Steve Koch
A simple example is the JoVE mentioned above. Or an idea that occurred to me today: it would be very useful to store screenshots of what I'm working on on my machine while writing code and processing data. You could easily include automated screenshots in your open notebook, but this is not required for ONS as defined now. You could also record video of everything you do and that is not required. So I don't think it's the logical extreme of transparency. That said, I don't think having a specific definition of ONS in this way is a bad thing. Extreme transparancy would probably creep out a huge fraction of people, while ONS might not. ONS can be a clearly defined and reasonable goal as part of the "wider Open Science movement" as mentioned in the wikipedia ONS article. http://en.wikipedia.org/wiki... - Steve Koch
An idea that I can't seem to form well is this: A really good motto for a scientist who wants to be open could be this: "Be as open as I personally want to be." This is very different than "be as open as possible." What I am specifically thinking is that young scientists (i.e., not yet beaten-down) seem to usually have very natural tendencies towards open science. But the overall level of natural talent for openness may vary enough that "open notebook science" may just not be the best method of openness for some people. But everyone can strive to "be as open as they want to be", and resist pressure to be closed coming from outside (fear of scooping; lack of technical means; resistance from colleagues). In contrast to these external pressures, I think it may be legitimate for someone to want to be open, but also maintain some privacy so they can get a personal reward of doing something all by themselves, for example. Perhaps posting all of their electronic notes 6 months or a year down the line. - Steve Koch
That wouldn't be ONS, but a version of openness that would be helpful and admirable. - Steve Koch
Steve's got an interesting point there. If you look at what JC does which is perhaps more closely tied to the concept of a traditional notebook you would see that it is more complete than my notebooks are. I think perhaps I've been focussed more on trying to expand the range of stuff we_can_ get onto the web. - Cameron Neylon
I need to get back in touch with Harry Collins at Cardiff Uni who gave a good talk on the limits of what knowledge can be transferred (and to some extent the relationship between that and the media through which it is being transferred) http://pirsa.org/08090033/ for the talk and http://friendfeed.com/e... for commentary - Cameron Neylon
@Steve -Nobody is saying that ONS is the only - or even the best way - to share. It completely depends on the researcher's objectives, their collaborators, where they intend to publish, etc. That's why there is a PONS section on the Wikipedia articles describing alternatives to ONS like putting in a delay, selectively sharing some experiments, etc. - Jean-Claude Bradley
The usefulness of ONS is that it explicitly allows one to assume that if it is not in the notebook it has not been DONE. One can also assume that ALL experiments in that project are reported. This allows anyone to analyze exactly how experimental science is actually done - how many failures to successes, how many errors get corrected, how a protocol evolves, how science in a field actually gets reported, etc. ONS is not a moral judgment or even a recommendation - it is just a well defined term - Jean-Claude Bradley
Hi, Jean-Claude. But can you indeed assume that, "if it is not in the notebook it has not been DONE?" After all, the notebooks are voluntary projects and not heavily regulated, right? What if a shrewd member of a team spots potential blockbuster commercial applications of a finding? Would she be under any legal (as opposed to moral) obligation to report that finding in an open notebook? - Hope Leman
@Hope - IP and scooping are the usual fears of doing ONS - and these are detailed in the Wikipedia entry. From a legal/patent perspective the ON is a publication and you should absolutely not do it if you are chasing after IP. All collaborators in an ONS project need to be very clear on that. Of course you give up your interests in IP when you publish in a regular journal - you are just doing it earlier here. - Jean-Claude Bradley
@Hope. There is no legal requirement to tell the truth. You can lie about all kinds of things on your blog or wiki but is it worth it for your reputation? I would expect that if someone had started out doing ONS and realized that it was not working out they would announce that they are scaling back to a PONS system or just stop sharing completely. - Jean-Claude Bradley
@Jean-Claude (4 and 5 posts up): I did not feel like you were making moral judgments or any kind of pressure. And I do think that your goal for a well defined ONS has a lot of value. I am, though, struggling with how moral compasses should be set in regards to ONS. My thoughts are muddled. - Steve Koch
This just occurred to me. There is a parallel with wikipedia here. Wikipedia has very specifically defined standards for articles. These standards are very much derived from the traditional old-school encylopedias. Sometimes casually, I can think "who cares?" But wikipedia editors stuck to those principles and succeeded fantastically. This is similar (in my mind) to what Jean-Claude is telling us about ONS. A rigorous definition was probably a key for wikipedia's success. - Steve Koch
When things arose that did not fit this model, but were useful, they didn't change the wikipedia model, but created new pieces to the open information project. Similarly, as Jean-Claude tells us, ONS is only one piece of the open science puzzle. Having a specific, easily understood, historically-modeled definition for ONS may be critical to maximizing its effectiveness as a puzzle piece. - Steve Koch
@Steve - yes ONS is a very small piece of the Open Science puzzle. The vast majority of researchers will not want to do this - and it probably should not be their first choice to experiment with OS. In fact, at the Southampton OS conference that Cameron organized last summer, we came to the conclusion that the PONS variant of just making available your lab notebook pages and/or raw data AFTER peer-reviewed publication is a concrete step that is much more realistic for most. - Jean-Claude Bradley
Hi, all. This continues to be a fascinating discussion. I have just tweeted Steve’s superb rumination, “Personal Open Science Challenges” http://tinyurl.com/bxphvw in the hope that it will become widely read, as it so cogently addresses so many of these matters. I found this passage particularly interesting, “I do worry about being scooped, but I have already concluded that being open does not increase the chances of being scooped. I believe being open decreases the chances of being accidentally scooped substantially. Furthermore, I even believe that being completely open would reduce the chances of being purposefully scooped. This is because the published track record would make it easier to shame the person who did the scooping.” I was surprised by Jean-Claude’s comment here, “Of course you give up your interests in IP when you publish in a regular journal.” Really? I didn’t know that. Does the simple act of publishing at any stage result in the surrender of intellectual property rights? - Hope Leman
@Hope - yes when you publish - and it does not have to be in a peer-reviewed journal - your ideas and work you forfeit your ability to submit international patent filings. You have a year in the US but without the international rights a lot of value is lost. In the US you can file a provisional patent when you publish and that buys you one year to submit a full patent. - Jean-Claude Bradley
Hi, Jean-Claude and D0r0th34. Thank you so much--I didn't know what Jean-Claude mentions and it shocking that what D0r0th34 says is still the case. All the more reason in the latter case so be pro-open access. You are both very kind to take the time to tutor me in such matters. - Hope Leman
IP is a whole other confusing issue. I'm fundamentally in favor of patents. Commercialization of ideas helps the world. I took a fantastic entrepreneurship course in graduate school, and came to realize that patents are essential for obtaining venture capital. Patents are a form of openness, but you have to be careful about disclosures. That's annoying and difficult for me to deal with. It would be great if you could have one year to retain international rights as well. - Steve Koch
I am not sure patents are the be all and end all of innovation, and the current patent regime leaves a lot to be desired. Personally, I think core science should not be patentable and only implementations of core science merit IP protection. But yes, you do have to make up your mind up front about how open you want to be in a case where you are discovering compounds etc, but I still think that's doable - Deepak Singh
@Steve I have to disagree with you that "patents are a form of openness" - and it would be interesting to take a poll in our immediate community here to see how many would agree. Having been through the process a few times - you have to come up with claims as broad as will be accepted by the reviewer. Claims are statements about experiments that you have not done to prevent other people from benefiting from similar work. Patents are legal instruments - not scientific documents - and certainly not open. - Jean-Claude Bradley
I would say patents are a form of publication - and if we are targetting the opening of notebooks upon publication as a viable goal then patents could legitimately be included amongst that. I have very little time for the current patent system as it works in practice but the principles it was founded on were of encouraging innovation by requiring disclosure before granting legal protection of the right to exploit. So disclosure is at the heart of what it is supposed to be about - Cameron Neylon
Cameron said what I was thinking. I'm not informed enough for a debate, but I'll participate in your poll :) I feel in my gut that protecting valuable IP will both speed-up and maximize the impact of a new technology we invent (if we're lucky enough to do so). I'd love if one of my students wanted to start a company someday and our IP was used to obtain venture capital. I don't think patents are inherently evil. I plan on submitting disclosures when we can, and not worrying about international rights.. - Steve Koch
Steve - I think it would be worthwhile discussing your strategy with your IP office. I don't think the people I worked with over the years when I was getting patents would have agreed to file without the possibility of international rights. It is just too expensive for the institution to invest without the expectation of proper international protection. I don't think you can pursue ONS and IP at the same time - not about being evil - just about value priority. I would be curious to hear what they say. - Jean-Claude Bradley
JC -- the people in our IP office here are quite good. I've been keeping them posted about my blogging etc., and they have been supportive and interested in helping us with our IP. They educate me on the repercussions of actions, but aren't trying to coerce me one way or another. In regards to international specifically, they did not seem as worried as your IP people. I got this same impression as a graduate student at Cornell. That doesn't make sense to me, but it's what they said, I think. - Steve Koch
Steve - every place is different - I'm glad you're in communication with them and it should be interesting to see how it plays out. - Jean-Claude Bradley