 |
|
| FriendFeed is the easiest way to share online. Learn more » |
Cameron Neylon › Comments
Worried, with @aswarren, that Google Wave is too complicated to be "email... invented today".
Yann Abraham, Cameron Neylon, Mary Canady and Neil Saunders liked this
No contemporary communication paradigms function really well on it. And that's a Bad Thing. Sure it's "like" email, sure it's "like" IM, sure it's "like" Google Docs, but as the combination of all of those, none of those ways of thinking about it work effectively. I can't imagine it appealing to anybody but a very small portion of people on the net. And that's a Really Bad Thing.
- Chris Lasher
Agree, I don't think it's anything like what email would be like "if invented today". My feeling is that it's usefulness will be determined by the number + quality of robots/gadgets/whatever they are. Another thought: the best software does one thing well.
- Neil Saunders
Dan Hagon made a good point which was to think about where the pain points are in today's processes and find the cases where Wave deals well with those. Or to put it another way, what are the use cases where the ability to collaborate are most effective. The most interesting demos will be the ones where people don't know they are using Wave though I suspect.
- Cameron Neylon
Though there is another point - Wave is exactly like email in the way that people have extremely different ideas about what it is for and how to use it. Half of this discussion is people talking past each other.
- Cameron Neylon
You've got a point there, Cameron. Much of the criticism I hear about Wave is really just criticism of the knocked-together client. Not much interesting is going to happen with Wave until the serious developers start playing around with it and putting some really good stuff together. Whether or not that'll happen is yet unknown, but Wave is a pretty cool tech from a protocol standpoint....
more...
- Mr. Gunn
Christopher Granade liked this
Yes, usually it appears as a flashing minimized window at top left
- Cameron Neylon
Thanks, Cam.
- Graham Steel
British Library's Bitter Digital Milestone - http://opendotdotdot.blogspot.com/2009...
Daniel Mietchen, Allyson Lister, Anders Norgaard and 3 other people liked this
ouch
- Richard Akerman
well, "like" may not be the right word... :)
- Allyson Lister
No, but it is a bit much...
- Cameron Neylon
*sigh* it's a depressing but understandable development. rare-materials collections have been making spare cash off selling stuff (including digital stuff) for quite a while now, as support from Teh Taxpayer has been dwindling. it's fairly natural to think in terms of perceived sustainability rather than mission. regrettable, but natural.
- D0r0th34
Fwd: The need for clear data licenses :: High Earth Orbit - http://highearthorbit.com/the-nee... (via http://friendfeed.com/cavlec)
Daniel Mietchen liked this
Via D0r0th34
- Cameron Neylon
Nature Communications Q&A - http://blog.openwetware.org/science...
Mr. Gunn, Pedro Beltrao, Claudia Koltzenburg and 5 other people liked this
NPG responds to a series of questions about the new journal Nature Communications. Some interesting responses but nothing terribly earth shattering.
- Cameron Neylon
Waveboard is a Google Wave client for Mac and iPhone. Does notifications so that you don't have to call before sending. http://www.getwaveboard.com/
Michael Kuhn, Björn Brembs and Richard Akerman liked this
I haven't tried it myself, but some dissatisfaction from my colleagues when they did. Safari on the iPod touch seems to do a reasonable job with Wave (ignore the warnings and click through), but lacks notification of course.
- AJCann
Google Wave on the iPhone is really slow, even over WiFi. Waveboard for the Mac solves a small but important problem: it is tricky to get the ID of a Wave from the browser. You need the ID for linking. Expect many more Wave applications 6-12 months from now.
- Martin Fenner
Am waiting for Wave to speed up on android as well. You'd think with Wave and Android both being from the Google stable it'd be quicker, but no...
- Jan Aerts
This week seems to haveagain seen a significant increase in Wave users. I can now reach a lot if not most Science 2.0 people via Wave. I have a few Wave invites left, please drop me a note if you still need one.
- Martin Fenner
Ditto - have a full batch of second round invites at the moment
- Cameron Neylon
Scientists still not joining social networks -- Scholarly Kitchen -- http://scholarlykitchen.sspnet.org/2009...
'Mummi' Thorisson, Mike Chelen, Joe.... and 13 other people liked this
Personally, am not convinced of some of the assumptions, e.g. "...Both are unfortunate, but are parts of the current culture [reference to sharing early lab results]. Any network that hopes to succeed must adapt to the culture of the community, rather than trying to rewrite it." First, though likely rare, I think there are instances where culture gets "re-written" -- another perspective is that this form of communication provides an alternative to established routes. That is, does not replace them but adds to the diversity of communication means.
- Mickey Schafer
The only thing I really disagree with here is that I think there will be a shift towards more open approaches as more examples of success show up. Then everyone will go over the edge like lemmings and there will be a backlash again but by then the funders will be piling in with conditions to push things forward.
- Cameron Neylon
<cynical>It doesn't matter what the scientists think. What matters is what the funders demand of them.</cynical> Open science doesn't really depend on "[online] social networks" and never has. It's true that most open-science sorts are active social networkers, but when the rubber hits the road, I don't care who's on FriendFeed -- I care who's sharing data. If the funders demand the latter and not the former, good on 'em. Behavior will shift accordingly.
- D0r0th34
But the funders are the scientists in most cases - so a mixture of pushing from within the community - as well as top down mandates will get us there. The question is how to get the funders into a position where they feel bound to impose mandates _and_ provide the infrastructure that makes it possible to observe them...?
- Cameron Neylon
Mmm, I'm not sure I agree. Funding infrastructure relies on a fair amount of scientist labor, yes -- but it's not career scientists who have been calling the funder shots; it's been top-level administrators (some of whom are ex-scientists, admittedly) looking at bottom lines. The Wellcome Trust mandate didn't come from scientists. Neither did the NIH policy. <cynical>One can't rely on scientists for effective science policy.</cynical>
- D0r0th34
Fair enough. UK Research Councils case is more nuanced. Even Wellcome Trust policy was driven to a certain extent by the fundees or at least not in the face of belligerent opposition from them. But comparing the independent funders like Wellcome to the Research Councils (run more by councils of academics) is instructive.
- Cameron Neylon
I thought the spin on your lovely shout out for Medeley on ch 4 news was interesting, Cameron (nice monitors btw!). 'government backing for innovators to meet and share' was the message. Have you had any responses to that yet? Maybe systems like Mendeley will be the things that start to crack the nut of social networking for scientists? I'm not sure it's a killer app, more the thin end of the wedge...
- Jo Badge
Shorter DC: I don't like social networks or spend any time on them, so they must be useless.
- Bill Hooker
I'm afraid they're not my monitors but those for the control room for one of the instruments (not incidentally the one that got filmed in the piece - but at least there was no blue liquid!) But they are in fact necessary to keep the instrument running and processing data efficiently.
- Cameron Neylon
Bill, I am afraid your DC is heads on :-)
- Claudia Koltzenburg
I can imagine a report from 1670, a full five years after the creation of academic journals, concluding that virtually no scientists were using academic journals as a matter of course, and thus they are useless. (Technological progress has sped up a lot since 1670, of course. But social change isn't all that much faster, in my opinion. And this is fundamentally a social change.)
- Michael Nielsen
Michael++
- D0r0th34
I think we also tend to forget the granddaddy social software: email. In some fields there are tremendously active listservs that have been around for over a decade especially at research universities where faculty got email before it really caught on in the wider world. What evidence would convince a scientist that Facebook, LinkedIn or Twitter offer better communication opportunities than an archived listserv?
- Jenny Reiswig
Well, aren't most scientists using email as "communication opportunities" and nothing else? (social network, listserv etc)?
- Maxine
were observations limited to sites specifically designed for scientists? perhaps to the exclusion of other significant mainstream platforms like facebook or twitter
- Mike Chelen
Jenny: it might be better to gauge usage based either on features such as address book management or by traffic metrics such as size of audience
- Mike Chelen
When “good enough” just doesn’t cut it - http://mndoci.com/2009...
Ruchira S. Datta, suelibrarian, Daniel Mietchen and 6 other people liked this
Is this a symptom of writing software for publication and then moving on?
- Michael Barton
It's a symptom surely of what the measured endpoint is - getting the data out for the paper - not producing something that has real utility. It's the good enough _for what_ bit that is the problem here surely?
- Cameron Neylon
It's all of those things. Worth remembering that in many cases, academic researchers who write software are not professional software developers. I think in the past and to some extent now, many people would answer "yes, good enough is just fine". I'm encouraged to see a new generation of computational biologists who clearly have been trained in software development and care about things like re-usability, reproducibility, testing, version control, distribution and so on. It is getting better.
- Neil Saunders
That's fair - constant suprise to me that I seem to know more about software development best practice than the academic researchers I talk to. I blame Greg Wilson of course...need to get Software Carpentry or similar course made compulsory for all science undergraduates :-)
- Cameron Neylon
And to those who don't get why this is important: we should spell out the cost (both financial and in time) to a research project, every time a new person starts on a project and has to clean up the mess of files and code left by their predecessors. I've seen this time and time again.
- Neil Saunders
Or write it into the grant conditions. That spells out it out pretty clearly...
- Cameron Neylon
Neil, I agree with you. I think that's going to change, as more and more software developers enter the life sciences, folks who care about maintenance, quality, etc. But the PIs are still a problem. Of course, this is not just academic research though. I've seen it in companies and perhaps that's the difference between between someone who stays middle of the road and someone (someone could be an entity) who excels
- Deepak Singh
couple of off topic things: I think your RSS is not working, or you might have changed it. It doesn't show up on my GReader. Also your Fork Me link to GitHub is not pointing to your account.
- Paulo Nuin
Paulo, the feed seems to be OK at this end. and yep, do need to fix that Fork Me link. Thanks
- Deepak Singh
Survival of the fittest will show how good things are. In the (free) open source world quality/time_to_invest will show, and for commercial world the quality/price will do the same.
- joergkurtwegner
Joerg, I think that's beginning to happen, especially with open source alternatives pushing purchasing behavior. Plus expectations have changed. No one is going to use an internal search engine with a several millisecond response time, when you are used to Google
- Deepak Singh
Perhaps I'm the pessimist, but if all scientific software were merely 'good enough' I'd be in heaven. Good enough would at least imply that it compiles/runs/etc.
- Paul J. Davis
I think "good enough" in software is favored when an individual needs to get something done and faces limitations in terms of time or financial resources in accomplishing the task. Within those constraints, "good enough" is the best way of making progress rather than waiting 'til someone writes the best possible code. It shouldn't remain that way, but if its cutting edge research, a clear market demand may not have been established as an incentive for some one to create a particular piece of software.
- Jill O'Neill
Jill, I've seen enough evidence where that's not the case. PI's tend to lose interest when they have papers published, or if a grad student or postdoc leaves. In the case of commercial entities, it's a cultural thing. Constraints can lead to phenomenal code.
- Deepak Singh
Isn't it similar to the evolutionary selection, with academics having a set of "pressures" different from those needed to develop #1-type software? Once the paper gets published, there is no pressure for researcher to improve the code, and things remain "good enough". While in a commercial setting there is always strong pressure from the side of the customer/competition, which drives the development further. I.e. to solve the problem one needs to bring some kind of pressure element to the academic setting.
- Yaroslav Nikolaev
Daniel Mietchen to Daniel's feed, Science 2.0, Science in the long run, Research Funding 2.0, Young scientists, The Life Scientists
Fwd: Research grants: Let’s end this shared madness by Wellcome Trust director Mark Walport, Times Higher Education - http://www.timeshighereducation.co.uk/story... (via http://friendfeed.com/dullhun...)
Ian Simpson, Ruchira S. Datta, Richard Akerman and 14 other people liked this
"So what are we proposing? We will phase out project and programme grants and instead, extend the model of fellowship support to researchers who are salaried by their university or research institute. "
- Daniel Mietchen
"We look to the scientific community to bring us their best ideas." - looks like an invite for another round of Fantasy Science Funding (this time from the perspective of the Wellcome Trust).
- Daniel Mietchen
Having been a Wellcome Trust International Travelling Fellow I've appreciated Wellcome's visionary approach to funding, and applaud their initiative here. This isn't a fantasy, this is Wellcome, and it will happen...
- Richard Badge
I agree, I don't think this is fantasy. They will do what they say. Few, the light is finally dawning.
- Jo Badge
For background on Fantasy Science Funding, see http://ways.org/en... . This piece shall also serve as a basis for an upcoming post on "What would research funding look like if it were invented today?" ( http://ff.im/9SvED ) which is intended to contain a general analysis of the funding situation, combined with some specific examples....
more...
- Daniel Mietchen
this looks bit but I don't really understand what it means in practice. You apply for a fellowship but does that not mean that you still are asking for the resources for a defined programme of work? If slightly less tightly defined? Will be interested to see what this means in detailed terms.
- Cameron Neylon
Critique: An inward-looking scheme which must eventually collapse due to failure to recruit new talent (and lack of a proper career structure will speed that up). Bye bye UK science.
- AJCann
I would suggest to them to do a significant part of the review process in the open, and to abandon it for some control group that meets basic eligibility criteria.
- Daniel Mietchen
@ajcann cynic ;-) what do you propose instead then? At least they are trying to acknowledge that science is done by good people with good ideas, giving them the freedom to follow those ideas to their logical conclusions and not to a pre-determined end point that you can only guess at.
- Jo Badge
But this strategy cannot be successful in the long term as it is anti-innovative and will inevitably degenerate into an old boys club.
- AJCann
@ AJCann: It has already gone much of that way, and I interpret Walport's piece as a sign of consciousness of the matter and an invitation for constructive criticism, albeit he seems to be very concerned about the opinions of other funders.
- Daniel Mietchen
The Wellcome trust is certainly one of the organizations that are most upfront (and sometimes brutal) in saying what they want and being forceful in maximizing their return on investment. I would certainly give them the benefit of the doubt to some extent on this one. But there is also something of a perception that it is something of a closed club. Partly this is down to a conscious...
more...
- Cameron Neylon
Yes, but not a viable strategy for UK science overall. It works for Wellcome as long as they can cannibalize the fresh talent funded by someone else. It won't work over the longer term is all (or most) agencies go down this route.
- AJCann
Well at least junior researchers can apply for an EPSRC grant.
- AJCann
Alan, let me ask the tough question - _is_ there a viable strategy for UK science overall? As in a strategy that views UK science in isolation? Having just got back from China I've got to say it certainly feels like we're toast unless we build our personnel and physical infrastructure in a bigger framework.
- Cameron Neylon
Probably not at the present/proposed levels of funding and considering what is being asked. Developing economies regard fundamental research as a route to prosperity. Decaying economies seems to regard science funding as a drain. It would be possible to fund selected areas, e.g. sustainable technologies, healthcare, and focus limited funding, but in this proposal inadequate funding is...
more...
- AJCann
It's interesting how explicit that is in the China case. The spending of money to speed development as well as to bring people back to support this. Building a new campus expected to house 20,000 scientists in a five year timeframe just doesn't seem to bother them. At the same time the heirachical and top down nature of the society and organization of their science doesn't seem to support radical developments. Will be very interesting to watch though.
- Cameron Neylon
Biotechniques.com: "The NIH's $12.2M Facebook for researchers" http://www.biotechniques.com/news...
Björn Brembs, 'Mummi' Thorisson, Neil Saunders and Chris Lasher liked this
I'm liking this for Cameron Neylon's spot-on warnings to curb their enthusiasm. Best "come back to reality" quote: "'Scientists have little or no interest in sharing useful information. Indeed, our whole reward and communication system is based on limiting access to valuable information,' he added."
- Chris Lasher
Yes, I'm liking it for sceptical reasons too. "VIVO will be in good company"? Hardly. The "fb4sci" tag fires the imagination and makes me want to know more? Quite the opposite, actually.
- Neil Saunders
Agreed - the fact that they think it fires the imagination is the thing I find most deeply worrying. It means that they don't have much awareness of the online discussion in this space over the past 12 months (full disclosure - I consulted on another bid into this call that wasn't successful)
- Cameron Neylon
Aw, everybody is so cynical nowadays...
- Euan
Its true :-) What worries me is that the PIs don't seem aware that everyone is cynical...
- Cameron Neylon
I need some feedback/career advice.
Bora Zivkovic, TheIndustryStandard, Meryn Stol and 23 other people liked this
Many of you know I've been working with Mendeley as a sort of ambassador/community liaison. I started this because I've always felt a little shut out from contributing to open science/open access/open data because I don't work for a publisher, don't really write code, and wasn't in a job where I could openly share data. This was a way to influence how things develop by promoting the people who "get it".
- Mr. Gunn
I had to quit for the "real job" a little while back and found not only that I had more time to work for Mendeley, but that I started getting other offers/opportunities also.
- Mr. Gunn
Now I've got a newborn daughter and am liking the time I can spend at home with her, which raises the following conundrum: Can I do more of this community liaison work for companies that support/promote open access and put my research career on hold, or is there not any future in this?
- Mr. Gunn
Can I trust the friends and colleagues I've met on here to be able to have a real discussion with me, keep me honest, and tell me if I'm backing the wrong horse as I take on more clients, or would I be considered a sell-out? Would people believe that my opinions still come from me and my experiences, or would people just think "You're only saying/supporting that because they're paying...
more...
- Mr. Gunn
Do you think there's room to grow in this kind of role or am I just wishfully thinking that I can make my own job in this tough economy and get to spend time with my daughter too?
- Mr. Gunn
I really believe this is a way I can contribute to changing how science is being done, opening up the process, disintermediating scientific discovery, and all those noble sounding things, but do you buy it, or do you think I'll not only become corrupted by money but lose my relevance because I'm not really doing science anymore?
- Mr. Gunn
Can I help companies that don't quite get it to improve and become better and more responsive to their community of users or will I lose touch?
- Mr. Gunn
I will be saying nothing works better than inspiring people by setting examples, I will not go with holding my research career even it is not working well as long as I have passion for discovering something. But there are certain realities and money is one of them. Ambassador/community liaisoning is other way to contribute back to the science, but it will be too early to give up your...
more...
- Abhishek Tiwari
Mr. Gunn. You can absolutely do so, but as you note, you cannot do this with one client. It will have to be a consulting/pundit role (you should probably have a chat with Paul Miller at some point http://cloudofdata.com). The life science industry will be challenging given the limited opportunities, and in this economy, this will not be a walk in the park. As to whether you have to be...
more...
- Deepak Singh
And we'll tell you if you're being an idiot. It also depends on what you really want to earn. You're not going to get rich doing this, at least not quickly.
- Deepak Singh
Abhishek, I could cite all the times when I've recommended Papers or Zotero instead because it really was better for what the person was looking for as evidence that I don't always have to say what the official line is, but that wouldn't illustrate all the discussions I've had where the company point of view _became_ my point of view. This is exactly the kind of discussion I want to be...
more...
- Mr. Gunn
Thanks Deepak. I know you will, and I'm not looking to get rich. I'm looking to do work for people I believe it, be a force for good, and at least for the moment, spend more time at home with my daughter.
- Mr. Gunn
Mr. Gunn, it will only taint it if you let it, although there will people who'll always be skeptical. As long as you are honest and present your point of view rationally, you'll be fine
- Deepak Singh
I'd like to think that being open and transparent online helps illustrate my biases, too.
- Mr. Gunn
Way outside my area of expertise, but I would think the "consulting/pundit" thing that Deepak mentions would involve lots of travel, especially to start. Not sure how conducive that is to spending more time at home...
- Andrew Su
Andrew, missed that bit. There would be a fair bit of travel
- Deepak Singh
from iPhone
Tough call MrG. I'm not concerned about you selling out, plus I will call you out if I think you are sliding into that trap (as, I'm sure, will the rest of the FF posse). My larger concern would be whether you can make a living that way. Is there a more regular (but part-time) gig that you could get to buffer the difficulties of forging a new path? For instance, do you write easily and...
more...
- Bill Hooker
Having a part-time gig would allow you more freedom to take risks and experiment, and could be phased out as and when your liaison/consulting work grew.
- Bill Hooker
Bill, that's a really great idea. My current commitments are only part-time, so having something more steady would both help the bottom line and insulate me from selling-out criticism - "I don't need to do this." Please, put me in touch.
- Mr. Gunn
the ultimate evidence for or against bias is behavior, would such a position restrict or inhibit assuming a critical perspective?
- Mike Chelen
What fun would that be, Mike? I just wanted to do a sanity check against my friends and colleagues here to make sure that at least some of them would promise to call me out if I started to not make any sense or drift away from the principles of openness this community takes as a fundamental principle.
- Mr. Gunn
Interesting situation! My take is that people who have no history of interaction with you, will not spend a lot of time looking you up online. As soon as they know you're being paid to do this, you'll be a sales rep - which means there isn't even any need to look you up, they already know who/what you are. Thus, IMHO, no online history will get you out of the sales rep box.
- Björn Brembs
I agree with Bill's suggestion, and also his non-worry about bias. Or rather, we're all biased, but you don't come across as a sell-out company mouthpiece to those who know you, so you can let that slide. Bjorn isn't tender, but he's right. Either way, you won't change it by adding on more opportunities to be a facilitator. And forging your own path to be more with your family - having been there, I would say you won't regret it later. One always has career regrets, but that's because we only have one life.
- Heather
Mr. Gunn. A full time liaison for a company will effectively make you sort of a sales rep. I have been a sales rep myself - which was a valuable learning experience, but I suspect, like me, not one you would fit comfortable into for a longer period of time (several years). When I left university, my friends and colleagues told me that I had a time-limit of 1-2 years to get back into...
more...
- Nils Reinton
Thanks, Nils, Heather, Björn. My intent is not to work full-time for a specific company, and I'm not doing that now. My intent is also to talk more about ideas and trends and less about specific products. Although I do spend a fair amount of time recommending Mendeley, I think Zotero shares their mission and I just personally prefer Mendeley. I used Zotero to write my first paper and it came down to me just wanting a desktop, full-screen app instead of their browser add on.
- Mr. Gunn
Björn - We all have our various reasons to believe what we do and say what we do. In my role, I'm not being paid to say anything or to have a certain opinion. In fact, I think where I disagree with the Mendeley guys is more valuable to them than where I agree, because what they're basically paying me for is my insights as a scientist who knows the field and keeps current with...
more...
- Mr. Gunn
I know I can't speak for anyone, and I'm not appointing myself spokesperson, but if I spend a lot of time listening to, talking about, and synthesizing ideas, and I can also effectively market those ideas to people who need to hear them (that is, companies who want to listen and adapt), isn't that a win? Couldn't that be my way to make a positive contribution to open access and linked data and personalized medicine and these causes that I already believe passionately in?
- Mr. Gunn
"Couldn't that be my way to make a positive contribution to open access and linked data and personalized medicine and these causes that I already believe passionately in?" YES, absolutely, you are already doing this very well. If you can make a living out of it, I salute you :-)
- Nils Reinton
Perhaps consider not just consultancy for companies, but also undertake work for public sector agencies (major libraries or funders), charities or not-for-profit companies.
- Frank Norman
Mr. Gunn - sure I think such a person would definitely be worthwhile to us! I was referring to people who do not know you: if you approach them and tell them you work for company X, my bet is that most of them will think "ah, he's a failed scientist trying to get me to use their products". Of course, this doesn't stop people from using company X's products (or sales reps would die out...
more...
- Björn Brembs
this is a great thread, Mr. Gunn, cheers for starting it, very interesting points, everyone; I would like to second Nils and Frank, and I think that some journals might also be interested in your advice (and community liaison work) and that this would certainly be a great service for anyone near to being an OA and linked data addict - isn't this a pretty wide range of users? we might create a list of arguments that you might wish to choose from when talking to journal publishers - test them on me ;-)
- Claudia Koltzenburg
Mr Gunn...you might know me from the ChemSpider system. For almost 3 years ChemSpider was run as a "for the community" project at my cost. i.e. My wife and kids lost a lot of access to me, despite the fact that I worked from home. It did NOT pay any bills...it just about covered costs. No, I was a consultant for a number of companies and worked hard for them, traveled a lot and used my...
more...
- Antony Williams
OT b/c it's blog not job related *but* I would cite this FF thread at some stage in this one. http://ff.im/YB4p from Feb '09.
- Graham Steel
Nils, thanks! Frank - that's a great idea. Can anyone put me in touch with someone at one of those agencies/companies? Björn - I see what you mean. Online rep doesn't translate offline automatically. Claudia - I've got a series of arguments, gleaned over the years from participation here and elsewhere. Can I send you an email? Antony - yes, I'm familiar with your work, and I have a...
more...
- Mr. Gunn
Mr. Gunn, one thing I've noticed in recent conversation with doctors (not academic MDs) is that most do not know much at all about OA, aren't sure what to make of a statistics-rich, data-driven science environment (or how to connect that data to actual human patients), and are leery about packages being hawked to them. Many are similar to me in age, meaning they didn't grow up in a...
more...
- Mickey Schafer
Well, I see myself being able to help in explaining these issues, but I don't think I'd get too far hawking products. I'm just not that kind of person.
- Mr. Gunn
Even products you truly believed were worthwhile?
- Jack (a.k.a. Jeber)
Yeah, I just don't think I'm the salesman type. I think I'm more effective developing ideas than products.
- Mr. Gunn
You don't have to be a salesman to develop products. Product development requires a better understanding of customer needs than anything else out there. Being a product manager was one of the most satisfying jobs of my life
- Deepak Singh
from IM
Mr. Gunn -- I wasn't suggesting that you represent product -- actually, I was thinking more in terms of a "knowledge broker" -- the slow adoption of some technologies (whatever they may be) is often b/c the persons needing the tools don't know how to evaluate them -- sometimes, they may not know how to evaluate their own needs. Having an expert who can help someone understand the landscape, help them make choices based on needs (as opposed to sales pitches) is a very valuable resource. Just a thought!
- Mickey Schafer
Another area that is worth looking at, though probably represents a short term play, is that there are lots of people out there putting out calls for tenders to do small research projects in the Social Media/Publishing/Data/Science space. Again its patchy, and not regular but with some reliable money coming in from e.g. editing and writing this kind of work could do two things, firstly...
more...
- Cameron Neylon
MrG, did you get my email? I sent it to a gmail address that I have listed for you in my address book.
- Bill Hooker
Yes, I got the one you sent and I really appreciate it. I do plan to follow up when I get back into town.
- Mr. Gunn
? any author here who uses, e.g., WebCite http://www.webcitation.org/, for sustainable references of multimedia files?
Jean-Claude Bradley, Peter Miller, 'Mummi' Thorisson and 2 other people liked this
I am planning to use WebCite for my thesis.
- 'Mummi' Thorisson
I use WebCite, but it caused considerable confusion the one time I did so in a formal publication. I sent a letter to the editor at Haematologica, and after several rounds of cluelessness I simply gave up. Part of the cluelessness was that they clearly did not understand WebCite, and wanted me to "verify the date on which I accessed the cited web resources" or some such. Dinosaurs.
- Bill Hooker
I 'm afraid there is so many Dinosaurs in our world of Science , especially in medical community ..:(
- Ana Ivkovic
I've got some webcite used in a paper coming soon in a PLoS Journal near you - unfortunately they caught my slightly sneaking citations and pushed them into the main text body rather than the references but nonetheless it is a useful service.
- Cameron Neylon
thank you, none of my tests has given any positive results for multimedia files, though, did this work out for yours?
- Claudia Koltzenburg
No I didn't try with multimedia - as I've not got it to work in the past. Webcite just archives an html copy as I understand it, so multimedia wouldn't be expected to work. Its a problem.
- Cameron Neylon
Claudia - as you've just seen http://ff.im/aW3GI we did archive Excel files - I would imagine multimedia files such as m4v might work too - although you would need to supply the viewer
- Jean-Claude Bradley
this sounds like a splendid idea, Jean-Claude, has anyone tried this out yet - supplying the viewer? would this actually be done during the archiving procedure on the WebCite server?
- Claudia Koltzenburg
not that I know of Claudia
- Jean-Claude Bradley
Call for proposals ESOF2010 - http://www.health.mafservizi.it/c10_001...
Claudia Koltzenburg, OpenSci Info, Mike Chelen and 5 other people liked this
I am inclined to submit a proposal for a session on Open Science. If any of you plan to go there or wish to contribute to the session, let me know.
- Daniel Mietchen
from Bookmarklet
Update (a few months later): The main deadline for session proposals is gone, but Eurodoc ( http://www.eurodoc.net/ ) are planning to submit a session for the "young scientists" part, for which the deadline is Sep 30 (next Wednesday). Preliminary title (possibly familiar to some of you): "What would science look like if it were invented today?" Would any of you be available to join the...
more...
- Daniel Mietchen
People from the Oxford Internet Institute put in something on Science and the internet - can't remember the exact details but could put you in touch.
- Cameron Neylon
from twhirl
Yes, Cameron, please do. But participation in our session would not be limited to pre-selected themes or people - we plan to do it as open as possible.
- Daniel Mietchen
Absolutely. Just a case of demonstrating that the thinking is connected up :-)
- Cameron Neylon
The current draft of the proposal is at http://etherpad.com/What-wo... .
- Daniel Mietchen
Seems to me that a session on Open Science could fit well within theme #10 ("Policy - what follows?") of the http://www.esof2010.org/themes... : "European science, research and innovation policies; the role of EU and national institutions; European science policy in a global context; international S&T cooperation policies; the changing landscape of European...
more...
- François Dongier
The deadline for the Scientific Programme (and also the "Policy what follows" theme) has already passed, it will be submitted in the Career Programme. So as Daniel wrote, it should be for young scientists to inform them about developements and also to involve them in a debate on new developments. For now, it is most urgent find people for the list of speakers which will be connected online to talk about Science 2.0.
- weppens
session accepted: http://ff.im/bi8Mb .
- Daniel Mietchen
Well done.
- François Dongier
Still, if any of you would like to join the session remotely (or perhaps even physically), please let us know.
- Daniel Mietchen
The bioinformatic-journal/software hydrid - http://boscoh.com/protein...
Joe Dunckley, Christopher Ing, Chris Miller and 18 other people liked this
Yes, yes. Very much like.
- Neil Saunders
Bosco, this is a superb idea. Along with starting up a new journal/software hybrid, it will be great if existing journals insist users to submit source code, executable or VM of a bioinformatics software / database / server to a centralized repository like 'biohub.org'.
- Khader Shameer
This is a good idea.
- Michael Barton
While not linked to an actual repository (but rather, provides a snapshot of the s/w and data for the article), Journal of Statistical Software, does pretty much this
- Rajarshi Guha
@Frank, this makes sense, since otherwise the paper would be static and refer to old versions. But then this assumes that as the s/w is updated, so is the paper
- Rajarshi Guha
me likey too
- Deepak Singh
The more I think about it, the more I think some big-wig bioinformaticians should do a deal with Google Code to edit a journal. That might even align with Google Scholar.
- Bosco Ho
@Frank, in that case, why bother with a VCS? Why not just put a tarball with the source code for the version that goes with the paper?
- Rajarshi Guha
Great idea, but I can't see it working for data sets. Yes data sets evolve and should track provenance somehow, but having been in and around standards groups for some time now, this is an impossible task for a publishing group to take care of, especially considering the nature of big-data bioinformatics. Plus if goes against best practices for software source control (use factories, don't store your database...)
- delagoya
There are some interesting and non-trivial questions around this kind of idea as to what peer review should look like. Should such a journal provide virtualisation environments so that the code can be run? Example data should be a requirement presumably? Are peer reviewers expected to evaluate code "quality". Anyone thoughts on this would be extremely useful...and help guide a project like this into reality.
- Cameron Neylon
My answers to Cameron's points: (1) no, (2) yes, sample data would probably be used to run tests which should pass, (3) quality is somewhat subjective - minimum requirement should be that code runs and generates output as expected - but reviewers could certainly suggest code improvement where appropriate.
- Neil Saunders
So if the answer to 1) is no, does that mean that you can't necessarily expect referees to actually run the code? Or compile it? Or just that you pick referees appropriately? Or conversely that "refereeing" becomes a process of building up enough positive comments or karma points in the repository...? It seems to me that you want to bring the best of versioning systems and best practice...
more...
- Cameron Neylon
Referees should certainly be able to run code - I'm just not sure that virtualisation through the web interface is the way to do it. Seems like an additional layer of complexity that might get in the way of making this idea work.
- Neil Saunders
@Cameron & Neil: If it could be figured out how to to handle the virtualization (or having remote access to machines), I think that'd be a highly valuable addition to peer review. Easy for me to say (not knowing how to implement it), but I think it's a great goal to strive for. It doesn't seem too crazy to have the journal have a bunch of machines on hand so the authors can remotely upload / install code and referees could then remotely log in to look at and try out code.
- Steve Koch
I can't figure out where to jump into this thread. Personally, I think we just need a place to publish locations, i.e. the code is here, data is there and this is the version we used, etc. That must be maintained and being able to maintain that should become part of the funding process. Since funding agencies are the ones who are funding this research they need to include the ability to...
more...
- Deepak Singh
My feeling is that being able to run the programs somewhere on a server without downloading them is important - but that is very much a user's perspective. I often look at useful things that are made available and just have no clue how to actually make them work. A good range of downloadable executables would probably do the job for me though. Additional question: what are the standards for web services?
- Cameron Neylon
Which is why VM's and cloud services are such a big deal for demo's and provenance now. You can package up a VM with the exact stack that you want and make it available, either as a service or a VM you can launch yourself. It's too easy not to do it
- Deepak Singh
@Deepak : Cloud + VM is an an interesting combination, but should have an accessible pricing that is affordable to a larger research community
- Khader Shameer
I think there should be strict guidelines while reviewing bioinformatics software / database / servers to test the resource. I had a recent experience : a reviewer wrote extensive list of points to reject a server that we developed with out trying what exactly it is doing or to know how does it differs from other existing resources. I strongly support the hybrid journal model, also it...
more...
- Khader Shameer
Let's talk specifics. VM images are great, but you are tying your release to a particular release of a particular platform. A better approach is to start from a base OS (like a linus distro ISO) and have a set of build instructions for system set up and application building. My favorite of the moment would be Chef.
- delagoya
Second, academics love to solve a problem with a novel algorithm and then move on. In fact it is in their best interest to move on after milking a project for all it's worth, publication wise. Maintenance, or even robust testing (couch... Tophat ... cough ... Bowtie .. cough ) is not even on the radar. Frankly I am not so sure it should be. Maintenance requirements may slow the pace of...
more...
- delagoya
@delagoya, good point. If I have made significant improvements, why update the old paper? better to try for a new paper!
- Rajarshi Guha
delagoya, chef's fine too. Find a common medium/mechanism that works for the community. The resources are certainly there. It's a matter of trying things out. As someone I know says, start simple, and iterate
- Deepak Singh
Khader, that's where the funding agencies come in. They need to provide mechanisms for sustainable funding here.
- Deepak Singh
The nice thing about a hybrid journal is that it might be possible to have new dois/database entries for "significant" updates. Not perhaps just place holding papers as is the case sometimes in the NAR database issue but when something has changed significantly you can get a new paper without needing a new algorithm or service. I like the idea of funding to support "orphan" code and services as well. Make it worth money and people will do it.
- Cameron Neylon
Delagoya - as a naive user I disagree. I really don't want to have to build, I want to use in the lowest stress way possible and a hosted VM seems like a good way to enable that - as well as allow for longer term preservation. We may not be able to run linux on future hardware but will probably be able to handle VMs for longer (actually having written that I'm not sure its true - would be interested in more expert perspectives)
- Cameron Neylon
I almost missed this discussion. I really like the idea but I wonder how discovery type projects fit in. I mostly use code to look for trends. If anything I might make some predictor to enhance existing data. For these reasons most of what I do is one off scripts around perl and R. Maybe this sort of project does not belong in a bioinformatics journal at all.
- Pedro Beltrao
Pedro, great question. Personally, if we included all glue code, small scripts, etc this would be unsustainable and defeat the purpose of peer review as well
- Deepak Singh
@Pedro, I don't see a journal/software hybrid as replacing all bioinformatics journals. I think there's a place for journals that discuss pure algorithms and ideas. These would do exploratory type programming. Normal journals service these papers quite well. For me, a hybrid model targets specifically those papers that describe a program that is meant to be used by other people. In that...
more...
- Bosco Ho
Bosco, you're thinking along the lines of a communications journal aren't you. And then people can go to work on the code if it is on github or something
- Deepak Singh
@Deepak. Yep. The disconnect I see is that pragmatically, it's the open-source project that counts. The article in the bioinformatics journal is so that we can get a place-holder to collect citations that contribute to our academic CV. The journal/software hybrid provides the most efficient way to this goal.
- Bosco Ho
Very nicely summary of the problem. Really, the whole concept of a journal article about software is stupid. What does an academic article do? Alert people to a new finding/discovery. But in the case of software - well, the software is the finding. And people are "alerted" by finding it on the web, downloading it and using it. As Bosco says, the sole role of an article here is a CV tick - hence the hybrid approach. Non-academic programmers must find all of this very odd.
- Neil Saunders
What's the best way to embed a pdb crystal structure into a wikipedia article? Is there a gadget that allows reader to rotate & zoom? Or is static png the way to go?
Jane Breezler, Paul Bacchus, Konrad Förstner and 4 other people liked this
How about an animated gif rotating it?
- Ruchira S. Datta
I agree that's better. I didn't know how to do it easily, so just put a snapshot in. It's my new stub article on Tus: http://en.wikipedia.org/wiki...
- Steve Koch
I realized what I actually want: A widget that will display a molecular dynamics trajectory of the system, while allowing user to rotate, zoom, pull on atoms, etc. ... Comp. people get to work :)
- Steve Koch
One of the web widgets they offer at the PDB might work in the context of Wikipedia but I would guess this is one to have a wider conversation about? Andrew Su and Tony Williams would have an idea of the logistics at least.
- Cameron Neylon
The Jmol community has been trying for a long time now to get it available in Wikipedia... you could ask on jmol-users@ ...
- Egon Willighagen
For small molecules, Noel's TwirlyMol looks nice http://baoilleach.blogspot.com/2009... , as it doesn't require plugins. But it doesn't seem to scale well for proteins.
- Pawel Szczesny
Steve, try asking on http://sciencestack.com.
- Jane Breezler
There's a long and tangentially relevant discussion here http://en.wikipedia.org/wiki.... As Egon alludes to, there is an effort to get the Jmol extension installed, but I don't see much activity http://en.wikipedia.org/wiki.... Proteopedia has Jmol: http://www.proteopedia.org.
- Andrew Su
As part of the Gene Wiki effort, we uploaded ~66k thumbnail images created by the EBI to wikicommons, and categorized them by SCOP. http://commons.wikimedia.org/wiki... Of course, they are auto-generated so they probably don't illustrate what you'd want to illustrate.. (and certainly not an MD trajectory...)
- Andrew Su
Thanks! Oh, and BTW, I was kidding about the MD trajectory, including the ability for the reader to pull on atoms in a real-time MD simulation. :)
- Steve Koch
Jmol has been up for discussion for a long time. I am not aware of any movement to support it at present. You might want to put the crystal structure hosted in Jmol elsewhere and make a link to it from the Wikipedia page rather than having it in the Wikipedia article itself.
- Antony Williams
Glatiramer Acetate Cheminformatics Problem and Fifth ChemInfo Retrieval Class - http://usefulchem.blogspot.com/2009...
 |
Abhishek Tiwari, Antony Williams, Egon Willighagen and Cameron Neylon liked this
Polymers are where the problem with assuming that chemistry is structure centric come home to roost of course. Nico Adams has been looking at developing ways of describing polymers effectively and it really isn't straightforward. The whole notion of substance, chemical, and structure get very very messy.
- Cameron Neylon
What is distressing is that someone added that initial obviously incorrect SMILES and it propagated easily to all those databases. As Tony has said many times curation is a big challenge in chemical databases.
- Jean-Claude Bradley
I'd say the cause of everyone blindly copying data, is that they are happy enough to be able to copy data at all... it all starts with Open Data and the right to fix things, and share those fixes...
- Egon Willighagen
+1 Egon
- Cameron Neylon
I'm not sure that the reason people are copying data are because it's Open. PubChem continues to proliferate yet it is NOT Open. We've had this exchange before..PubChem is NOT Open data but I "judge" it gets copied because people treat it as an authority. It is not a good idea to treat PubCHem as an authority as it is a repository...non-curated and with no efforts underway to curate it...
more...
- Antony Williams
I agree that PubChem should not be treated as authoritative, but the big advantage it has over ChemSpider is that it can be downloaded and re-used.
- Michael Kuhn
I agree that people copying PubChem is indeed not because it is Open... that one is copied merely because it is free and confuse that with Open. That said, I love to see the day that there was a court ruling on that state of the PubChem data, which is at some places claimed to be Public Domain, something refering to the copyright being with the providers, while at other places... a bullet proof statement would be *very* useful indeed.
- Egon Willighagen
Michael - there is every intention to provide access to the ChemSpider structure collection in the near future. This will not include all associated information in a record as the associated information has mixed licensing but free to use.
- Antony Williams
ChemSpider and Wikipedia have the advantage that errors can be corrected. Are there mechanisms in place to correct errors in DrugBank, PubChem and the many other derivative databases?
- Jean-Claude Bradley
DrugBank: yes, David Wishart is said to be quite responsive to comments. Same for KEGG. PubChem: NO. They just aggregate tons of source databases, and you would have to hunt down the source and hope it makes it way downstream... Thus ChemSpider's annotation efforts are invaluable, and I would love to be able to re-use them
- Michael Kuhn
Michael...drop me an email at antonyDOTwilliamsATchemspiderDOTcom and let's discuss how you want to use information and what you need to get at and it might be an issue of simply pointing you to the right web services. Lots of people are using ChemSPider through web services at present. We'd love to help you
- Antony Williams
thanks Michael
- Jean-Claude Bradley
There is also a curated KEGG: http://biometa.cmbi.ru.nl/
- Egon Willighagen
Biometa appears to be static since 2007. The SDF file mostly contains R groups. Seems weird
- Antony Williams
Martin Ott moved to Sheffield... (http://www.lhasalimited.org/index...) I'll try to ping Vriend about the future of BioMeta... or the code behind it.
- Egon Willighagen
Webel - a web service based python library for chemical information - http://baoilleach.blogspot.com/2009...
Deepak Singh, Rajarshi Guha and Peter Miller liked this
Potentially a nice simple library for implementing in AppEngine based web services and/or Wave robots. Simple text search, MW, SMILES etc. Or I could finish wrapping the ChemSpider API properly...
- Cameron Neylon
Reflections on Science 2.0 from a distance - Part II - http://blog.openwetware.org/science...
Allyson Lister, Jan Schmirmund, Steve Koch and 6 other people liked this
I like your description about linking between different ontologies derived (and utilised) within different contexts. IMO shoehorning standards to fit leads to dogma, not innovation.
- Ant Beck
how easy is it to reconstruct your lab work if it used a just-in-time or transient ontology?
- Alec
I don't know - and there isn't really anything to compare it to either in terms of ease. There are many things that make it hard to use our lab records and we need to work on all of them.
- Cameron Neylon
FYI, I just drank 10 billion trillion atoms of deuterium.
Cameron Neylon liked this
Is now a good time to mention the myth about how D2O can cause neurological disorders. Its very popular amongst the neutron scattering community because we swim in the stuff.
- Cameron Neylon
Sure! I haven't come across that myth yet. And not trying to be careless with my posts, I am just amused / intrigued by how much deuterium is in regular water.
- Steve Koch
I think I dreamt this week about a study that showed that deuterium was actually important in a few biological processes :)
- Egon Willighagen
Don't even get me started on the deuterium dreams I've been having lately :)
- Steve Koch
Cheated!
If you present data from another paper, you should at the very least acknowledge the author(s). Right or wrong? (Some of my data has recently been published in another paper)
- Jan Wessnitzer
Shocking.
- Jo Young
???
- Björn Brembs
You should reference and cite the data. Whether via citing a paper or a dataset I don't mind, but citation is key.
- Cameron Neylon
Google Code Blog: Introducing Closure Tools - http://googlecode.blogspot.com/2009...
Fergus Gallagher, Anders Norgaard, Euan and 2 other people liked this
Google open-source a bunch of Java Script tooling
- Cameron Neylon
One for the language geeks. What's the plural of lingua franca?
Matthew Todd and Michael Kuhn liked this
if we're being snobbishly latinate, linguae francae.
- D0r0th34
Hah! I guessed right then...reckon I'll be snob :-)
- Cameron Neylon
I think 'oxymoron' might get close ;)
- Pete
UK PubMed Central: Interview with Phil Vaughan - http://network.nature.com/people...
Duncan Hull, Richard Akerman, Graham Steel and Cameron Neylon liked this
Capturing 90% of recently published UK biomedical literature? Really? I'd love to believe it but I'm struggling here.
- Cameron Neylon
That is quite a % step up from the last set of figures in Sept (09) which reported a 35% compliance rate http://www.scribd.com/doc...
- Graham Steel
Do the eight UK PubMed Central funders fund 90% of life sciences research in the UK? In that case 90% is the potential, the 35% compliance mentioned by Graham (up from 15% in November 2006) is the current reality.
- Martin Fenner
Hhmm. I'll seek clarification 'bout this.
- Graham Steel
Martin I'd believe that 90% figure. But not submissions to UKPMC. I have given up trying to submit stuff because the need to link it to a specific grant is such a pain.
- Cameron Neylon
Influence a National Service – In 140 Characters - http://ukwebfocus.wordpress.com/2009...
Cameron Neylon liked this
Nice example of responsiveness that twitter and similar services can provide if people are there and willing to engage constructively
- Cameron Neylon
Reflections on Science 2.0 from a distance - Part I - http://blog.openwetware.org/science...
Mr. Gunn, Benjamin Tseng, Steve Koch and 6 other people liked this
Interesting point - could only track down Jon's tweet via Friendfeed. Possibly an argument for piping mine back in - or perhaps setting up a secondary account for archiving...
- Cameron Neylon
a secondary acct for archiving is a good idea.We tend to pull the RSS from tags on the day of any event and stick them in FF or google reader. Having an RSS feed of your own tweets into GR could work too. Tweetstream is definitely pretty transient these days.
- Jo Badge
I use FF as a searchable repository of my tweets, at least for now.
- Bora Zivkovic
The third para of that post was delightful. I also use FF exactly as Bora does, and to search for the tweets of some others. In fact I've toyed with setting up 'imaginary friends' of people / corporate tweets which don't have an FF account for this purpose but haven't got round to it yet. I really don't use FF enough!
- Jo Brodie
Love it: "...the natural unit of science research is the blog post".
- Bill Hooker
Next-gen PhDs fail to find Web 2.0's 'on-switch' - http://www.timeshighereducation.co.uk/story...
Nic, Jo Young, Cesar Sanchez and 13 other people liked this
Why am I not suprised...?
- Cameron Neylon
saw the press release for the original piece of work behind that yesterday here: http://www.rin.ac.uk/our-wor...
- Jo Badge
Like as in "I share your...concern? Despair?"
- Neil Saunders
Ah I missed that - also interesting in the context of the NIH grants - anyone tracked any more information on those projects?
- Cameron Neylon
I don't really despair but assuming that group culture and practice will change because some young people come in isn't suprising. Search happens with a single person, so they will use those tools, but social bookmarking requires groups acting together. This means that you at least need critical mass within the group, or more likely, active encouragement from the top.
- Cameron Neylon
Change is happening, But ... very ... slowly.
- AJCann
hmm, just skimming the report (from Brisith library) says that librarians need to reconnect with scientists - errr, when were they connected?
- Jo Badge
I'll set the librarians on you.
- AJCann
and here we are. what? oh, well, it's a given that people contact their friends first before the librarian - that's been found in our literature for probably close to 100 years. i'm thinking that search engines probably are above friends now... .what's really great is if you're friends with a ton of your scientists and engineers so even if they don't call "the library" they say, "well I'll just call Christina" (I get that a lot)
- Christina Pikas
but about the article - I'm happy to see this because it supports the findings of the first wave of articles on the uptake of ICTs in science from the 90s. 1)it's not just a matter of time, 2) it isn't necessarily a matter of age (not all youngsters want to try or know how to use all new technologies), etc.3) usage across areas of science will differ
- Christina Pikas
*bays at the moon* *sniffs* *catches a whiff of scientist* AROOOOOOOO! *chases*
- D0r0th34
From Jo's comment, an outside observer would have to ask: Is it that science librarians make no effort to connect with researchers (which, given people like John D. and Christina P., I find VERY hard to believe) or that researchers show no interest in a connection? "You can lead a horse to water" and all that... but what do I know, being neither a scientist nor a librarian?
- Walt Crawford
I think another aspect of this is the plain old fashioned 24 hour day. My students -- and yes, they are undergrads -- are absorbing so much content information that they MUST learn or they fail, and doing so much volunteer/shadowing that they MUST do or they cannot get into grad school, and even those doing research are so busy learning western blots and how not to screw things up that...
more...
- Mickey Schafer
I'm wondering what our generation is going to say the one after us is failing to adopt. Seems to me like there's an unspoken assumption behind the question - either there has to be mass uptake for it to be useful or something along the lines of "What's the business model?" These questions invariably seem to come as people are trying to justify the use of web20 tools to themselves or...
more...
- Mr. Gunn
Distributed Science, Part 2 - http://scienceblogs.com/commonk...
'Mummi' Thorisson and Graham Steel liked this
John Wilbanks nails it - no surprises there then :-)
- Cameron Neylon
Tomorrow’s Giants 1 – Big Data - http://semanticscience.wordpress.com/2009...
Cameron Neylon liked this
"We need to develop mechanisms and infrast[r]ucture for the small “long-tail” laboratory scientists…the big data guys have this figured out anyway."
- Rich Apodaca
its ok. Current uk policy is to do everything possible to eliminate those troublesome long tail scientists. We only do world leading science here [...sigh]
- Cameron Neylon
from fftogo
Daniel Mietchen, Claudia Koltzenburg, 'Mummi' Thorisson and 3 other people liked this
interesting, thanks. Some questions and a comment: Why place journal articles in 'physical' only? there are excellent e-only journals and hence e-only articles. Also, the traditional concept of an 'article' is changing, so, given interactive elements and all, I guess what you call an 'article' may come in a new shape (just consider, e.g., OAI-ORE) and might well move towards what you mark as central affairs of 'Research 2.0'
- Claudia Koltzenburg
nice. I would place Wikipedia further towards formal myself and on a trajectory heading further in that direction. Peer review on WP can be as rigorous and infuriating as any journal. Not always of course but sometimes and becoming more so.
- Cameron Neylon
from fftogo
Thanks for the fast feedback. I am working on blog posts to put the two diagrams into more context. The lines between online/informal/UGC and print/formal/traditional are certainly blurred more than the diagram highlights. It is my hope that by situating items in their traditional orientations on these scales, I can better demonstrate the blurring of those lines to a general audience. I will take all feedback into consideration when preparing a second version.
- Michael Habib
What did you have in mind when you put private sharing as "more formal" than public sharing?
- Mr. Gunn
Not sure now that I look again. I don't think I would put private sharing there anymore
- Michael Habib
Naturally occurring deuterium is essential for the normal growth rate of cells... [FEBS Lett. 1993] - PubMed result - http://www.ncbi.nlm.nih.gov.li...
Ian Holmes, Dan Hagon and Jean-Claude Bradley liked this
The role of naturally occurring D in living organisms has been examined by using deuterium-depleted water (30-40 ppm D) instead of water containing the natural abundance of D (150 ppm). The deuterium-depleted water significantly decreased the growth rate of the L929 fibroblast cell line, and also inhibited the tumor growth in xenotransplanted mice. Eighty days after transplantation in 10 (59%) out of 17 tumorous mice the tumor, after having grown, regressed and then disappeared. We suggest that the naturally occurring D has a central role in signal transduction involved in cell cycle regulation.
- Steve Koch
This is one of those papers you have to read (and while you're reading it, I'm patenting my deuterium-depletion filter for home use and sending the press release to the daily mail, national enquirer, and Oprah).
- Mr. Gunn
I haven't read it yet. Are you hinting that it's good or bad?
- Steve Koch
Haven't read it yet either
- Mr. Gunn
Not having read it, it could be that whatever they're doing to deplete the deuterium is leaving some harmful stuff in the water, and that certainly sounds more likely, but one would think the editorial process would weed out such obvious mistakes, but mistakes do happen and I've seen some crazy stuff come out of eastern european labs and the related articles are also all kinda obscure, but prions and transposons were once thought to be crazy fringe ideas too...
- Mr. Gunn
Well, you may be onto something. In methods, they say, "Deuterium-depleted water (30-40 ppm D) was obtained from tap water (150 ppm) by electrolysis," ... Seems a bit sketchy to use tap water, even in 1993. ... All that aside, I've been a quite surprised this weekend at how drastically D versus H can change the chemistry of things. I'd been inappropriately biased towards thinking the...
more...
- Steve Koch
Steve, could you give an example of a case where D versus H is known to change the chemistry? I, too, had (have) the bias you mention.
- mkz
@mkz, there're some general examples at wikipedia "kinetic isotope effect" http://en.wikipedia.org/wiki... ... There are also reports that heavy water tastes differently than H2O (can't find link now), which would most likely be chemistry (right?). The strong toxicity of heavy water to eukaryotic cells also argues for chemical effects. I guess I don't know the best example.
- Steve Koch
A grad student in our lab, Andy Maloney, did a kinesin motility assay in heavy water on Friday and saw an amazing array of cool effects (http://openwetware.org/wiki...) ... At this point, is tough to figure out the science, but it's nevertheless very exciting. One thing we want to try is to compare D2O to...
more...
- Steve Koch
Wow, I didn't know heavy water was toxic. I figured the vibrational spectra would change when you change the isotope, and guessed minor changes in molecular structure could similarly occur, but it seems the effects are much more pronounced than that.
- mkz
Those experiments look interesting! (Not that I know much about the field.) D2O versus H2(O18) sounds like an interesting experiment, too, hopefully we'll be able to follow the results here.
- mkz
I know, amazing, huh? (heavy water toxicity) The funny thing is I was thinking D2O would be a simpler way of probing water activity, compared with osmotic stress. Ha!
- Steve Koch
As for the experiments, Andy is an Open Notebook Science (ONS) practitioner, so all his results (as of now) will be available. It's actually been a conundrum for me this weekend as to whether or not to advertise his results. A good case study in ONS--on the one hand, I'm super-excited. On the other hand, we don't know what's going on, and I feel like he may prefer some time to figure some things out. Who knows? Glad you liked his experiments!
- Steve Koch
@mkz, I put some thoughts on Andy's notebook's "talk" page here: http://openwetware.org/wiki... I was amazed to find out they actually use D2O to stabilize proteins in vaccines.
- Steve Koch
It is indeed a good case study in ONS, I'm happy to hear the results will be available, but I'd understand if you guys changed your minds. I'm not sure how open I could bring myself to be when I make a discovery, waiting to be explained/utilized. Good luck with the project.
- mkz
Just looked at your comments, reading that page was fun (and heavy water ice sinks in water?--nice).
- mkz
Going to bed now, thanks for your comments.
- mkz
Good night, and thanks for your thoughts!
- Steve Koch
Steve the videos on Andy's page you link to look awesome but I'm not sure I understand exactly what was done - is there a section with the experimental details or is that what you guys are debating whether or not to release?
- Jean-Claude Bradley
@Jean-Claude: What specifics would you like to know? I'm still in the process of making my experimental procedure available on OWW of which I will link to in my notebook. So, I apologize if things are still in disarray when it comes to the specifics of how I do things.
- Andy Maloney
There's no debate on releasing anything--all info is desired to be public. In fact, there's no debate at all except in my own mind--as to whether to specifically invite people to look at the results (which I did above) via a blog post or other. @Andy, I think what Jean-Claude is saying is that it's very much not evident what your experimental methods are, mostly because of the...
more...
- Steve Koch
Andy - I was looking for which materials and in what amounts were added at what times to understand the videos and the effect of the deuterium. I'm intrigued by the effect of isotopes in chemical processes and I think your experiments could yield valuable insight. We've also very briefly looked at the effect of deuteration on smell http://usefulchem.wikispaces.com/Exp218 because of the putative detection of molecular vibration in receptors
- Jean-Claude Bradley
It's worth noting that most commercial D2O is pretty filthy from a colloid chemistry perspective. Strictly speaking ultrafiltration or reverse osmosis is required to get to the kind of water quality one routinely expects these days for the normal stuff. But it's way too expensive to blow 10 L of D2O on getting a water purifier fully exchanged...
- Cameron Neylon
Jean-Claude: Yep, this is going to take a while to clean up and do what you ask. I'm really motivated right now to start an experiment so, I will have to come back to this later tonight. I'll let you know when I have a draft for a materials and procedure page.
- Andy Maloney
from a completely different perspective, then it wouldn't be a good idea to use a D20 moisture mist? The latest thing in cosmetics: http://snipurl.com/t0vih
- Mickey Schafer
@Jean-Claude, cool smell experiment! (Is row 2A mislabeled, or am I misreading?) I've been wanting to try some kind of isotopic smell thing ever since reading the Turin book.
- Steve Koch
@Cameron thanks for that tip. We're keeping it in mind now that the results could be attributable to contaminants. Question: It's definitely too expensive for us to think of doing that. But wouldn't Sigma be able to afford doing so?
- Steve Koch
@Mickey: good find!
- Steve Koch
Steve - thanks yest that was a mislabeling and it is fixed now - although note that (as indicated in the conclusion) the results in the table are not meaningful. Designing a statistically valid test like this is harder than it might seem and would require many more samples. The best I would hope from this experiment is to motivate a few more researchers to take a few minutes and sniff -...
more...
- Jean-Claude Bradley
Thanks Andy - I'm not asking to write a full report. It is probably enough to just post the experimental notes. In our lab that would correspond to the "log" section, whereas the full well formatted report is the "procedure" section to be written later. (e.g. http://onschallenge.wikispaces.com/Exp130 ). If that isn't how you keep track of experiments could you let me know what...
more...
- Jean-Claude Bradley
Hey Jean-Claude, Interesting smell reference in a review I'm reading: "2.5.1. Olfaction in fish. Hara [40] investigated the ability of the whitefish, Coregonus clupeaformis, to distinguish between the odor of glycine (Gly) and fully deuterated glycine (Gly-ds). Over the concentration range of 10^-8 to 10^-4 M, these fish avoided solutions of Gly-ds and preferred solutions of Gly." From:...
more...
- Steve Koch
Other ways to read this feed:
