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John Dupuis posted an entry on Confessions of a Science Librarian
E-Science, Science 2.0, Open Science
Wednesday at 1:40 pm - Link
Good post. - jokrausdu
err e-science = science + grid, science 2.0 = science + web 2.0, open science = science + open access. Almost. I would say e-science is a bit bigger than just grid and data, to me it encompasses all of the issues of computer-enhanced science. - Richard Akerman
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Of course, only librarians (and people working in libraries ;-) would get all worked up about definitions. Like I said, I can live with escience being the all-encompassing term. On the other hand, data+grid is sufficiently different from sci+w2 that it would be nice to have separate terms. I wish I could draw a Venn diagram in FF! - John Dupuis
I'd say open science = science + openNESS -- the application of free-as-in-speech and free-as-in-beer to the entire enterprise of science. At the, well, radical end is JCB's Open Notebook Science -- "no insider information". I'd put the other end of the spectrum at Open Access -- that's where Open Science begins, for me. - Bill Hooker
One more try from me: Open Science = Open Source (software) + Open Access (publishing) + Open Data (full release after OA publication, at minimum) + Open Standards (metadata/semantic web to make sense, and full use, of all the Open info) + Open Licencing (legal protection where needed, Public Domain otherwise). - Bill Hooker
Bill, that's perfect. Open Science is a kind of overlay on different aspects of science. - John Dupuis
I think I came closer to defining the minimal goal of Open Science yesterday in discussion with Gavin Bell at NPG: 'Improving science communication by making more of the material that supports the claims made in peer reviewed papers publically available, accessible, and re-useable' - it has the advantage of actually leaving the 'open' word out altogether and scares people less because it sounds incremental - Cameron Neylon
e-Science means different things to different people I think. The e-Science program in the UK was very much about Grid computing so people associate those together. e-Science and Science 2.0 are necessary tools for achieving the goals of Open Science. So I almost see e-Science as technical tools and Science 2.0 as social tools - Cameron Neylon
@Cameron: I like your version (defining minimal aims) better than mine (an attempt at an overall definition -- probably always doomed). One quibble: "improving" and especially "more" both leave too much wiggle room. "Optimising" and "all"? I think it's better to be clear than to try not to scare people. - Bill Hooker
Thanks, Cameron. I agree with Bill that it's a very good way of defining the various terms. It's more or less what I was trying to get at (rather unsuccessfully, I guess) in my original post. - John Dupuis
I don't think you were unsuccessful, John; I think what we have here is people thinking this through for themselves, spurred by your post. Not a bad thing! - Dorothea Salo
Absolutele Dorothea - and it's an importat discussion to have. Bill, the wiggle room is quite deliberate. This is about getting something on the table that people can actually do today - as we move forward we aim to remove the qualifications. So as worded it is todays standard, as you would word it, it is tomorrow's standard. - Cameron Neylon
Google Reader
Maxine shared an item on Google Reader
American Dream
yesterday at 3:05 pm - Link
"the [vacant] doe-eyed daughter eager to throw open her [legs] arms to any inbred redneck" -- what a class act that Henry Gee is. I can see why Nature is proud to be associated with him. - Bill Hooker
#politics #culturewars - Richard Akerman
I wonder if they've read it! - Maxine
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Matt Pfefferle posted a message on Twitter
delicious
Michael Nielsen bookmarked a page on delicious
Mark Newman: The first-mover advantage in scientific publication
Thursday at 4:12 pm - Link
"Mathematical models of the scientific citation process predict a strong "first-mover" effect under which the first papers in a field will, essentially regardless of content, receive citations at a rate enormously higher than papers published later. Moreover papers are expected to retain this advantage in perpetuity - they should receive more citations indefinitely, no matter how many other papers are published after them. We test this conjecture against data from a selection of fields and in several cases find a first-mover effect of a magnitude similar to that predicted by the theory. Were we wearing our cynical hat today, we might say that the scientist who wants to become famous is better off -- by a wide margin -- writing a modest paper in next year's hottest field than an outstanding paper in this year's. On the other hand, there are some papers...that buck the trend and attract significantly more citations than theory predicts despite having relatively late publication dates..." (via Dave Bacon) - Michael Nielsen
Glad to see this finally studied. The comment in the middle is wrong, though: "we might say that the scientist who wants to become famous is better off -- by a wide margin -- writing a modest paper in next year's hottest field than an outstanding paper in this year's" It enormously undervalues being able to figure out what the important questions are that everyone else _should_ be working on, and will be in one year. - Michael Nielsen
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haven't read the article yet - but the only catch seems to be betting on the right horse. Sort of like playing the market - you'd have to know what was going to be hot next *or* convince people what you're doing is hot. - Christina
I don't think it has to have anything to do with thinking about what's fashionable, or marketing your work, or whatever. You can do this by figuring out ahead of everyone else what is important and tractable, and working on that, rather than going with what is fashionable. - Michael Nielsen
This might be considered supportive of a publish-early-publish-often, use preprint servers, Open Science type approach. - Bill Hooker
Right on, Bill. The people who want to be famous should write the first paper in next year's hot field. The people who want to understand something will be the ones who write outstanding papers in today's hot fields. - Mr. Gunn
@Mr G: I see your point, but actually I was thinking something different. If you publish "as you go", using preprint servers and not faffing about trying to get things into Nature et al, you may just find that you've written the seminal paper for next year's hot field. - Bill Hooker
Bill - you can still go to Nature - just drop it in Nature Precedings first - Jean-Claude Bradley
I was wondering how this relates to the citation advantage that preprints seem to confer, which is often suggested to be related to "early access" in addition to a quality bias: http://eprints.ecs.soton.ac.uk... - Hilary
We're in vogorous agreement, Bill! Liberal use of preprint servers can help the slow, thorough work compete with the forward-thinking but more shallow work in today's novelty obsessed research culture. - Mr. Gunn
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Neil Saunders posted a message on Twitter
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The Life Scientists: Mitchell J Stanton-Cook posted a message
“Feeling depressed as writing a document to become a confirmed PhD student. Keep thinking "how much is a PhD student really worth?" Money is broght in by work that leads to grants for the PI, money from publications... I'm beginning to think the AU20K is really harsh when you can make that on welfare”
Tuesday at 7:40 pm - Link
if you think about it though, it's not just work that you're providing but also training/education that you're receiving. in addition, it might filter out those really interested in science.. (don't expect me to be this understanding of the powers that be once i start next month ;) - laura
Just make sure you enjoy what you are doing. Money isn't everything after all. - imabonehead
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I'm not a money person (if I was I would be doing something I'm not passionate about) but it would be nice to be paid on the correct side of the poverty line. I just feel a little bit ripped off by the government with their lack of respect and understanding. Rent doubled in 5 years, petrol prices almost doubled in the same time frame, food prices.... - Mitchell J Stanton-Cook
I've been told today by a PI that science is worlds second oldest profession. And IMHO it _IS_ better than the oldest one;) - marcin
$AU20k does sound a bit low to me (I assume that's Australian). It was $14k in my day and that is going back a bit now. But I think it is important to remember its a stipend, not a salary. And that you are also paying the penalty for the proportion of students who don't make a contribution and suck up resources. I guess the stipend is still set by government though in Oz or is there a market? When I left it looked like there was going to be a bidding war for the best students. - Cameron Neylon
There's always Poland where you could get $5000 a year and gas is $2.4 per liter (ca. $9-10 per gallon, all are US dollars). :) But little more seriously (but not really serious), you should start getting used to feeling of being underpaid. I'm yet to meet a scientists that is getting paid what he/she is worth :) - Pawel Szczesny
Cameron: There is a thing called an APA-I ... where an industry partner contributes some "top-up" money (usually just AU $5K/pa). There doesn't seem to be many APA-I scholarships negotiated in the biosciences (at least where I am), although engineering students seem to get them. I think PIs / students avoid them because the hassle of the IP issues (including sometimes 'sealed' thesis chapters) is not worth $5K/pa. Maybe if it was easier to quantify the value we generate .... - Andrew Perry
Compare it to your undergrad times: education isn't free. And this time you are getting paid for learning. Just make sure you really like what you are doing, because you are not in it for the money. Never will be. - dekay
Agree with Laura - it's a prequalifier for serious scientists. Yes is an expensive choice, like all education, but doing a PhD 20 years ago really helped my career in the pharma industry and it was well paid compared with doing a Post Doc. I decided to take the pain early for the gain later. - Sally Church
I didn't mind my PhD fellowship at all. First time I had ever earned anything, so it wasn't that bad, plus I didn't have to pay any tuition fees. As others have pointed it, it makes sure you're committed. Now once you have a PhD and get paid a pittance, that I have a serious problem with. - Deepak
What Deepak said. A few years of frugal living is no big deal, it's when you come out the other end of the meatgrinder and your real, after-tax income goes *down* instead of up that's a problem. Bear in mind also that the opportunity cost of a PhD is unrecoverable: you'll never catch up the lost earnings even if you calculate them at minimum wage. Only do this if you really, really have a jones for research, because otherwise it Will Not Be Worth It. - Bill Hooker
Also, Sally and Laura, I strenously object to the idea that you can only be a "serious scientist" if you have a PhD. I doubt that's exactly what you meant, but it's a common and absurd and offensive trope. A PhD is an endurance test, nothing more. It's not especially good training most of the time -- very dependent on supervisor, most suck -- and it's certainly not any kind of quality control, just look at the many morons who get PhDs by some witches' brew of politics, asskissery and blind perseverence. - Bill Hooker
@Bill: I absolutely didn't mean to say you need a PhD to be a 'serious scientist'. Doing a PhD for little money when one could be making big bucks in some other sector might, just might, show some commitment to science (or let's say it should...). Not doing a PhD does not imply lack of commitment or interest. Regarding the quality of training and being happy with what little stipend you may get, I prefer sticking to my idealistic assumptions for now, as I'll be starting next week. - laura
@laura: I say (and believe) that "most suck" but that doesn't mean they all do, and in particular if you are aware in advance of how the system works (and fails) then you are in a good position to make it work for you. Just the fact that you are on FF means you are *vastly* better informed than, say, I was when I started my PhD. So let me try to offset my negative tone above and say: welcome to the community, good luck, and let me know if there's any way I can help you. - Bill Hooker
Bill, my apologies. You're right, didn't mean it in that way at all, more as an indication of commitment. Like Deepak, I enjoyed mine, worked hard and didn't mind 3 years of frugal living in London. We had a lot of fun and good supervisors/facilities, so it can be done. - Sally Church
Only three years.... I always forget that it's so short in the UK. I just started year seven of my PhD this week. I'll be done in a few months, but *still*. And my lab mate is in her 8th year, and another one did a MSc in 5 years. There need to be better rules in North America about when you can *stop*. - Eva
it is rarely actually three years - the UK system does encourage finishing but it does so by creating a situation where you spend 6-9 months working with no money whatsoever. The US situation there is usually some money but no sense of a strict deadline as I understand it - is that fair? - Cameron Neylon
I think in general, we could do better at teaching PhD students time management. The basic strategy seems to be: thrash wildly for X years, then write up whatever you have. Start with 3 months of planning with a timeline at the end of it - even if you don't follow it to the letter. - Neil Saunders
I think at UQ they are changing this now. There is no need to write up a thesis. graduation depends on papers not how well you write your magnum opus which if you're lucky more than your supervisor and the reviewers will read. - Colin Archer
Don't know what it's like in Aus now but when I went through ('98) the average for a full-time PhD was close to 5 years -- and the stipends were 3 years with a hard-to-get 6 month extension. I finished my final 18-24 months (took nearly 5.5 yrs) on $12K that I borrowed from my parents (v lucky to have that opportunity, too). - Bill Hooker
Google Reader
Cameron Neylon shared an item on Google Reader
OKF launches an open science mailing list
yesterday at 6:26 am - Link
The Open Knowledge Foundation has set up a mailing list which will aim to become a low volume general announcement list for the Open Science community. In many ways the last thing we need is another mailing list but this is probably the best way of getting the widest involvement. - Cameron Neylon
Ugh. Are you on any of the OA lists? Signal:noise is terrible. I much, much, much prefer blogs and FF as a way of communicating. - Bill Hooker
Blog
Deepak posted an entry on business|bytes|genes|molecules
The independent research institute will drive biomedical innovation
Thursday at 11:33 pm - Link
I think we could face the issue of too many research units if there would be no change in the way science is communicated. Typical "research" page of scientific institutes tells me nothing about what they actually are doing. - Pawel Szczesny
I've seen innovative things come out of all of the types of organizations you mention. I think it's great that there more choices now, not just straight academia vs industry. People will be able to discover what kind of context clicks for them and hopefully will be happier and more productive as a result. - Sutee Dee
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If I had the choice, I'd work in a snazzy, well-funded institute over a uni any day. As you say in the post, it's up to unis to figure out how best to collaborate off-campus; otherwise, their research future is bleak. - Neil Saunders
I think there are also risks here of concentrating more of the available money in fewer places in the hands of fewer people. The big institutes tend to lead to centralisation and attract people who get money out of the government systems as well (at least in the UK). Not saying it's all bad but we also need mechanisms for many small amounts of money to be widely distributed IMO - Cameron Neylon
Ditto Cameron... - Andrew Su
Completely agree. We need that continuum and diversity. The difference is that you aren't necessarily (not all institutes work that way) worrying about your next grant. In the end it's all about execution. Research institutes aren't ideal for all kinds of projects, but for certain kinds I think they are by far the best way to get brains together and get them focussed. - Deepak
Of course, there is another aspect, the virtual institute, which adds another layer of possibilities - Deepak
As an insider (I spend about half my time at the Broad) I have to say the living is easy. In the sense that, unlike my previous gig at an allegedly research-intensive dept in a decent uni, people are not only interested in research, but in the types of experiments you can't get funded traditionally. The Broadacious view is that if it isn't impossible, it's not that interesting. - Chris Cotsapas
The basic mechanism is: take clever people from many areas, give them effectively unlimited resources (core facilities, easy access to funds etc) and a mandate to transform biology, and sit back and watch the fireworks. - Chris Cotsapas
ditto Pawel: if the way science is done doesn't change, everything else we try to do is a band-aid on a sucking chest wound. - Bill Hooker
Chris echoed my Utopian view. It's not centralization per se. It's a case of, what happens when you put a bunch of smart people in the same building. That said, I have seen institutes that are just universities without the teaching requirements - Deepak
Agree with Deepak. But the whole point of the Broad is to avoid precisely that. So far, with some success. At the announcement, Eric Lander pointed out that so far we've averaged a paper every three days over four years. So something must be working :-) - Chris Cotsapas
It's a hard balance, because someone does need to be there to do the actual construction once the groundbreaking work is finished. Universities are a pretty good place for this, then it's back to private enterprise to actually make something commercial out of the work. - Mr. Gunn
Blog
Björn Brembs posted an entry on bjoern.brembs.blog : a neuroscientist's blog
JoVE is diversifying
Thursday at 9:13 am - Link
also see http://jove-blog.blogspot.com/... - Graham Steel
Do you think anybody would be interested in providing/accessing Science 2.0 (open science, open access, post-publication assessment, etc.) content to JoVE? Discussions, software reviews, online journal feature comparisons, anything like that? - Björn Brembs
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Bjorn, you mean something like feeding Bioscreencast to JoVE? - Pawel Szczesny
As I discussed with JC I would like to see the introductory videos for the instruemnts at ISIS (http://www.isis.rl.ac.uk) done as papers for JoVE - Cameron Neylon
@Pawel: Indeed! That would be exactly the kind of content we would like to try and see if people are interested in it. We are thinking of a number of such features and this sort of screencasts is one of them. Another are lectures/talks and posters. - Björn Brembs
Cameron: I think this would make fantastic content! - Björn Brembs
Bjorn - it would be great, and useful for us, plus it gets over the argument with the instrument scientists (who are busy people) as to why it is worth doing...'because you get a paper' is a good carrot - Cameron Neylon
Cameron: I'll talk to the higher-ups about that. I personally find it highly interesting! - Björn Brembs
Have you ever embedded a video from e.g. Jove or SciVee into FriendFeed or your blog or website? - Judson Dunham
This blog post embedded a JoVE video http://bjoern.brembs.net/comme... and this one a SciVee video:http://bjoern.brembs.net/comme... - Björn Brembs
A lot of conferences film the talks, esp. the keynote, often just so that they can be watched on a screen by those who couldn't fit into the auditorium. JoVE could publish whole conferences -- that would sure beat waiting for the "proceedings" issue of whatever journal, when there even is such a thing. - Bill Hooker
Similarly, the "visiting speaker" thing gives scientists a chance to get really good at a particular presentation -- e.g. Jean-Claude's talk on ONS or Michael Nielsen's talk on the future of science -- maybe JoVE could have a "visiting speakers" section like a virtual research department. - Bill Hooker
Bill, those are great suggestions! Basically, almost everything that goes on your CV would be good to have in some permanent form. I mean, the listed posters, talks, etc. only exist on my CV after the event is over... It'll be interesting to see if the founders share my enthusiasm about this and which of these ideas will actually be implemented. There is so much potential! - Björn Brembs
FriendFeed
The Life Scientists: Andrew Perry posted a message
“Job Ad: Grimwade Research Fellow (5 year term), Department of Biochemistry and Molecular Biology, University of Melbourne.”
Job Ad: Grimwade Research Fellow (5 year term), Department of Biochemistry and Molecular Biology, University of Melbourne.
Thursday at 5:05 pm - Link
This position has just been advertised in the Department I work in. It's a pretty good deal for any senior Postdoc ready to make the transition to PI. - Andrew Perry
Andrew, how do you think your dept would view Open Science? - Bill Hooker
My feeling is that the Department wouldn't have any problem with Open Science per se, however the usual currency of high impact peer reviewed publications and acquiring grants still would apply, like most places. Those who are publishing well and bringing in grants to fund their research tend to be more highly regarded and do less teaching ... I can't imagine the Department really cares either way about the 'details' of how this type of success is achieved (Open vs. the status quo). - Andrew Perry
Thinking of applying Bill? - Neil Saunders
Sorta... it's a bit out of my league I think, plus I did just spend 6 years and tens upon tens of thousands of dollars to get the US to allow me to stay here... I dunno. - Bill Hooker
Blog
Björn Brembs posted an entry on bjoern.brembs.blog : a neuroscientist's blog
Why are open access supporters defending the impact factor?
Wednesday at 12:27 pm - Link
This issue drives me absolutely bugfuck insane. How do the "you're right but there's nothing we can do" people think anything ever gets changed? - Bill Hooker
What matters is that people accept PLoS ONE as peer reviewed. For that I would argue it is worth trying to get an IF because it means that Thomson accept that the pone approach is peer review. But I absolutely agree with Bjorn that fatalism is not helpful. Are people just too scared to stand up and speak their mind in appointment panels? - Cameron Neylon
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i think it has to do with maintaining the status quo. People want change but don't want to be the shaker. Too worried about how they are perceived. Bjorn is right, entirely fatalistic. - Kevin Z
TS must be having a ball... But what is ridiculous is the fact that OUR committees need numbers to judge scientific value and merit - by pointing a finger at TS, three more are pointing at us... - Karl Kraus
I have to say, my views are a lot like the comments in the original post. But, it seems that IF as a 'metric' is not going away until members from this community (or other like minded people) get on the hiring and tenure committees. How many people out here are on such a committee? So you can complain all you want - but just talking and writing is probably not going to change things soon. Got to get into the 'system' and change it from inside - Rajarshi Guha
Indeed. I repeat again, the system needs to change and someone has to do the changing. My hope is that people interested in changing the system are going to be in a position to do so soon enough - Deepak
Does anyone have any idea of what to say to these people to convince them without offending them? - Björn Brembs
It seems that the value and reasoning is quite clear -that's what I got from the comments on your post. What is going to have to happen to persuade the 'old guard' is explain what's in it for them - and that's going to be tricky! Seriously, it appears that the whole process is stuck in a vicious circle. For IF to fade out you're going to need a community that does not depend on it but the current community, it appears (I may be wrong) does not have the power to actually effect that change - Rajarshi Guha
@Rajarshi: that's what kills me, the community *does* have that power -- they just won't exercise it. If researchers would ignore Thomson and publish only in OA (green or gold) journals, within a few years we would see the overblown concept of a "prestige journal" reigned in and citation statistics could be collected at the level of the individual paper and aggregated as needed (job interview? aggregate the candidate's papers; institutional review? aggregate over the whole school; etc). - Bill Hooker
I think the idea that IF is a bad measure is a strong one in a scientific sense. It is bizarre to me that scientists who worry greatly about measuring stuff insist on measuring something multidimensional with a tool that is known to be poor. I wonder if a candidate could sue for being excluded based on IF as it is a demonstrably poor measure? - Cameron Neylon
Rajarshi - I've sat on appointment panels but not yet at tenure/professor level. But I am starting to ask these questions. FWIW when _I_ look at a CV the important criterion is relevance to the needs of the post; number of papers and where they are come a distant second and third respectively (how important I think the papers are is more relevant) - Cameron Neylon
@Cameron: I definitely think the case is strong enough that you could sue if the IF can be shown to have played a major role in the decision! - Björn Brembs
@Cameron - it's great to see that at least one person doesn't obsess over paper count and papers in Nature :) I can only hope more people will follow this path - Rajarshi Guha
@Bill, while I agree that *this* community does have that power, it's important to remember that members of this community are also members of other communities, viz., their academic departments and in those communities IF, paper count etc are still king. So they might get kudos from this community, but not necessarily from their (possibly) more important community (the one that gives them tenure, say) - Rajarshi Guha
FriendFeed
The Life Scientists: Bill Hooker posted a link
twidox: a free, user generated online library... publish, distribute, share, and discover
Wednesday at 9:18 pm - Link
"Documents on twidox are accessible to everyone online and will allow people to share their knowledge and help others with their work, learning, teaching and research. The focus of the website is on: * professional and industry specific documents * research material * academic papers and articles * coursework and dissertations * data and statistics" - Bill Hooker
Currently in "private beta"; might be a useful preprint/presentation server. via Peter Suber http://www.earlham.edu/~peters... - Bill Hooker
I'm not quite sure what this is supposed to be... - Björn Brembs
I signed up for the "private beta" but have yet to get my account info. I'll post more when I have a chance to tinker with it. - Bill Hooker
FriendFeed
The Life Scientists: dekay posted a message
“Does anyone have a theory why exactly scientist are so "under"paid vs other disciplines?”
Wednesday at 11:34 pm - Link
As Fox Mulder once said, I have plenty of theories :) - Neil Saunders
I love Fox Mulder. He had his priorities right - Deepak
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One theory: skills, experience, education are irrelevant. Contribution to "the economy" determines salary. It's hard to measure how scientists in academia contribute to GDP. Let's face it, many of them don't. - Neil Saunders
Because scientists are so much passionate that you can have them work even at very low salaries... so why pay them more? (basic supply and demand stuff...) - Enro
In addition to what Neil said, funding is wasted on the same experiments over and over again. It's not only about five groups working on the same problem today, but also about wasting resources on repeating experiments that were done 10 years ago. As far as I heard, money wasting is included in the science budgets, but that doesn't make measuring impact of science on GDP any easier. - Pawel Szczesny
It's not just scientists. Software Engineers (read MS in Computer Science) are pain $10-20K less that they might make if they were working in industry. They are doing the same kind of work AND getting appreciated much less. You have to really like scientific research to want to enable it in that kind of environment - Deepak
What Enro and Pawel said... - Björn Brembs
Supply and demand? Even now, with the relatively low salary, there are too many scientists (compared to the number of tenured positions). - Michael Kuhn
Pretty much just an echo here. Society doesn't value research appropriately because it's difficult to measure its value -- you need to think and look over long timescales, decades or longer, which people aren't used to doing and political cycles actively discourage our "leaders" (ha!) from doing. The NIH puts out a feeble little pamphlet "why fund science?" every so often, but I don't know of any concerted effort to make a strong business case for research. - Bill Hooker
There is a common belief that science is a noble profession. Society considers those who work in science to be privileged. The privilege conferred on those who can do science is supposed to compensate for lower salaries. - Jack H. Pincus
Jack, unfortunately, I don't see too much privilege given to scientists either these days (at least in the US). - Deepak
You're not in an income-generating field. You're also not generally employed to do something that management wants to get done so they can create a product: you're there because you've got the research bug. - Chris Cotsapas
Interesting to see how people are reading "scientists" as "scientists in academia" ;) Thanks to Chris & Bill for a different perspective… - dekay
It's because academic scientists are the ones that are the most underpaid, dekay. Industrial scientists are still underpaid relative to their education level, but nowhere near as bad as academic scientists. - Mr. Gunn
one of my theory that it happen because society & government can not estimate value (impact) of scientific products. It's not electronics or software or food... scientists produce papers!!! No doubt some of them will be translated and find application in medicine or other technologies but most of them not. So income (money that government or other foundations invest to academic science) much more then outcome - benefits for society and highly expected products. - Alexey
People are rewarded ('paid') based on how much 'obvious' (or relevant) contribution or product they make for their society. Scientists are not paid well because their contribution to the society is not really obvious. Their work can be presented in an important way (e.g. fight cancer) - and I think that's how scientists manage to get some money - but the problem is that for what they do, 99% of them do not generally have (or care) about an answer that is of beneficial to the society. Only 1% do. - JWS
FriendFeed
The Life Scientists: Chris Lasher posted a message
“Should I bold important descriptive statistics (e.g., total number of genes, percent of total with one condition) in the results section of my poster that are not included in a table? Is this distracting or helpful?”
Thursday at 9:13 am - Link
$0.02 from me: distracting. I'd prefer the section be structured so as to emphasize whatever you want me to take away from reading it, rather than be confronted with RANDOM SHOUTING in the middle of the text. :-) - Bill Hooker
I second Bill's opinion - Lars Juhl Jensen
Thanks guys. This was my intuition. KISS, right? - Chris Lasher
I am with Bill in this. Less text, less tables, more graphics. KISS - PauloNuin
I think you should bold them. The usability/readability of a poster is a lot like a website -- the vast majority of people quickly browse for something that catches their eye. See useit.com for more details. - Donnie Berkholz
supplementary data as handout? published on the web? ;) - dekay
Google Reader
Lars Juhl Jensen shared an item on Google Reader
Big data: How do your data grow?
Wednesday at 3:29 pm - Link
Liking now I managed to get to them; is it just me who has problems resolving Nature DOIs? - Neil Saunders
Nope, I got an error too. - Bill Hooker
FriendFeed
The Life Scientists: hubfeed posted a link
Recommended journals and their preprint policies
Wednesday at 10:02 am - Link
"Given some text, JANE will recommend journals in which to publish, and ROMEO will tell you whether each journal publisher accepts papers that have been published as preprints." - hubfeed
Still has some bugs... - hubfeed
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double like! :-) - Björn Brembs
Thanks! Now all we need is a "send document to journal" button ;) - Hilary
Awesome. - Bill Hooker
Having done several tests on it, it has certainly suggested some bizarre journals to me. I have heard several people say that it can be useful for suggesting peer-reviewers, however. - Maxine
I want the 'write paper and submit to journal button' along with the 'referee paper/grant' button :-) - Cameron Neylon
JANE suggested perfectly when my co-workers tested with unpublished abstracts. Quite impressive. - Anders Norgaard
delicious
Michael Nielsen bookmarked a page on delicious
LiveScience: Era of Scientific Secrecy Near End
Tuesday at 10:11 am - Link
An article on open science for a general audience. - Michael Nielsen
Cameron Neylon, Jean-Claude Bradley and Sabine Hossenfelder all get extensively quoted. Nice to see! - Michael Nielsen
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indeed - thanks for bookmarking Michael - Jean-Claude Bradley
The exciting news to me is that the "public" is interested in this. The article is being, clipped, dug, etc. - Nice Fish Films
Most excellent -- one quibble, I'd like to see "no insider information" credited to Jean-Claude. - Bill Hooker
well thanks Bill - the author removed it after some reformatting of the original paragraph :) I didn't ask for it to be removed - I have no problem with that paragraph - Jean-Claude Bradley
so you think that private company will always permits to their scientist to share data with the rest of the world? - Piero Giacomelli
@Piero: some will, some won't. The hypothesis is that the sharing model will prove more efficient, so early adopters will realize an advantage and eventually the mainstream will adopt their methods. There are no guarantees but I think it's worth testing the hypothesis. - Bill Hooker
Depends on the information. Pharma companies are already sharing pre-competitive information. Stuff that they would need to repeat in the absence of any data availability. With things like GWAS, it might be impossible to do for a company, so they will collaborate with universities and make the raw data public (e.g. Novartis) - Deepak
Expression data (eQTL) too. See Rosetta/Merck. - Chris Cotsapas
@Chris, oops. Should have included that one esp cause I have used that in talks :) (I was at Rosetta Biosoftware) - Deepak
Google Reader
Deepak shared an item on Google Reader
Buried Alive
Tuesday at 10:33 am - Link
For the record, I *would* be up in arms if the women had "merely been censured" or whatever the phrase was, but I hardly think it a moral failing to be *more* outraged by what actually happened. - Bill Hooker
I think the point that Amit was trying to make was (and it's very cultural) is that in South Asia, we only get outraged about these things when they hit the absurd, while the "censure" part happens all the time - Deepak
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Yeah, I rather missed the point I'm afraid: the piece was aimed at a readership from a different culture than mine. If I'd paid attention to the masthead I'd have realized that and not made my earlier comment. - Bill Hooker
:) 'tis OK. One reason I keep my linking to such stories limited. Most people won't necessarily get the back story - Deepak
Isn't this post sort of related to the discussion that religious beliefs are exempt from criticism? For some people, century-old traditions (which includes most religions) have been exempt from criticism. You can almost believe whatever crazy stuff you want, as long as you say it's your religion, the people who criticize you for it are the ones who need to defend themselves. - Björn Brembs
Similar concept. In places like India, tradition and religion are so intertwined, it's difficult to separate them sometimes - Deepak
getting amit's point i think. this may be more horrible than merely censuring, but it doesn't mean that censuring would be okay. it happens in western culture too though, even if on a much much smaller scale, so one can (try to) extrapolate. re religion: if it's a matter of blessing eggs, bread and salt on easter sunday you may have no right to criticise the ridicule. if it's a matter of human lives, i think it's a different story. - laura
Blog
Graham Steel posted an entry on McBlawg
...and this is Planet Earth
Tuesday at 5:53 am - Link
You should also have a look at this video http://www.youtube.com/watch?v... - Pierre
nice one Pierre, thanks. - Graham Steel
Of course, this is what came into my mind: http://www.youtube.com/watch?v... - Bill Hooker
YouTube
Pawel Szczesny published a video on YouTube
iPlots and Bioinformatics Career Survey
iPlots and Bioinformatics Career Survey
Tuesday at 5:38 am - Link
wonderful - Deepak
Thanks Deepak. I wasn't sure if that actually provides some insight into data, or just is looks fancy. - Pawel Szczesny
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The only thing missing is context to a degree. Some overlays/labels along the timeline would be great - Deepak
Except for the tendency, nothing more/else could be concluded. Any ways to improve the presentation? I'd be happy to learn anything out of it. :) - Marcin
It does me good to see this: data collected openly, shared openly, and re-used openly. A glimpse of a less competitive scientific future. - Bill Hooker
Great work Pawel - Michael Barton
Thanks Michael. iPlots is a brilliant piece of software, isn't it? :) - Pawel Szczesny
delicious
Sally Church bookmarked a page on delicious
Scientists may have cured cancer last week - more on DCA
September 1 at 1:52 pm - Link
There are two sides to every story and the data on DCA is not yet mature - animal data does not always translate to humans - Sally Church
Every positive article on it says it's a universal cure but not marketed because there's no money in it. That requires at least two highly improbable things to be simultaneously true. - Mr. Gunn
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Sally, unfortunately even less then one third of protocols which work in vitro and in vivo work in human when clinical trial started. In some areas (such as gene therapy for instance) - even less. thousands compounds and biological agents were tested and never show efficacy in clinic after trials started. So as far as it not on trial yet and human study results didn't publish there is no reason for excitement - Alexey
People grasp at straws all the time. A non-profit or alternative medicine company could easily develop it if it's as good as they think it is. The reality is indeed that without patent protection, no pharma or biotech company is going to touch it with a barge pole. - Sally Church
Alexey: I'm not excited about this compound at all, quite the opposite in fact but I get emails all the time about it from lay people reading about DCA, so decided to do some more in depth research and bookmark some of the links for reading before writing a broader blog post about my findings. - Sally Church
i meant author of blog post seem like got exited about it - Alexey
"without patent protection, no pharma or biotech company is going to touch it" -- I disagree. If it works half as well in humans as it's claimed to work in vitro and in mice, the pharma/biotech sector will be falling all over themselves to make derivatives with unaltered or enhanced activity so that they can patent those and make all kinds of absurd claims about "their" "new" drug. - Bill Hooker
Alexey: yes, most of the blogs and articles on it are very gung ho indeed - Sally Church
Bill: Last time this came up I spoke with several friends in the pharma industry who are responsible for licensing and the lack of IP protection was the reason they all used for not being interested. Perhaps if a modified form (eg pegylated) could be developed, then maybe. Then again, the trial data I've seen on DCA so far has been mixed. - Sally Church
delicious
Michael Nielsen bookmarked a page on delicious
Michael Nielsen » Six Rules for Rewriting
August 20 at 2:11 pm - Link
This shows up twice in my friendfeed, because I bookmarked it at del.icio.us (useful for tracking purposes). This is a minor irriation of FriendFeed. - Michael Nielsen
I also bookmarked it in del.icio.us but optioned to make it private. It's a function that I wish was available for all my FF aggregations. For example I've become very sparing about flagging a track as loved on last.fm because I find it can appear superfluous. I like the functionality but wish I had more editorial control over the content. - Garret McMahon
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Garrett - I don't want to make it private, because that prevents it from appearing in certain other contexts I'd like it to appear - in this case, my del.icio.us network. It'd be nice to make it private for FF, and public to my del.icio.us network. That doesn't seem to be possible at the moment. - Michael Nielsen
Maybe FF could suppress anything that has "[noff]" anywhere in the title or description. Okay, that's gross. But if the same user posts the same URL on several different services (including potentially FF itself), it should somehow collapse or combine them. - ⓞnor
@nor - it occurs to me that FF could filter your del.icio.us stream so that only things tagged with ff were displayed in your friendfeed. An alternate system in the same vein: if noff were a tag, an item would be supressed. - Michael Nielsen
FF could offer such a filtered thread if you fed it the RSS feed for the tag you chose, instead of your straight-up delicious feed. - Dorothea Salo
Dorothea - yeah, that'd be ideal. - Michael Nielsen
I think Simpy and Diigo both allow you to set up RSS feeds of specific tags or combinations of tags. - Bill Hooker
Silly question - why don't you just delete the duplicate from Friendfeed? Yes, it requires manual intervention, but then again, so would adding tags like "noff" to the title. - Hilary
Hilary - del.icio.us stuff tends to show up pretty randomly on friendfeed, often hours or days after tagging it on delicious. So I could do that, but it'd be deleted at a random interval after first appearing. I guess it's a minor thing. -