Biomedical science has never been more exciting or productive. Research tools have become increasingly powerful, and progress continues to accelerate. Yet, these are stressful times for many biomedical scientists, because competition for grant support, jobs, and publishing in the most prestigious journals is also accelerating. The stress associated with publishing experimental results--a process that can take as long as obtaining the results in the first place--can drain much of the joy from practicing science. - Duncan Hull
I'm not paying $10 to read a letter to a GlamorMag. - Bill Hooker
"Both editors and referees could help. Referees need to be more thoughtful when recommending additional experiments and to make sure that these experiments are truly needed to justify publication. Editors should insist that reviewers rigorously justify each new experiment that they request. They should also ask reviewers to estimate how much time and effort the experiment might require. With this information in hand, editors can more easily override referees'excessive demands. This requires confident, knowledgeable, and experienced editors, and it risks alienating referees, who are often hard to come by. Nonetheless, editors should be encouraged and empowered to perform this crucial task." - Duncan Hull
"A more radical solution, which is already used by some journals, is to have editors and their relevant editorial board members triage papers so that only those that meet the criteria of interest, novelty, and importance appropriate for the journal are sent out for formal review. This will save reviewers' time. In addition, papers that clear this initial hurdle can then be reviewed solely for scientific accuracy, appropriateness of controls, clear writing, and justification of the conclusions." - Duncan Hull
Science Progress is amazing. I subscribe to only the best posts via AideRSS, which I can't recommend highly enough for those of us without enough time: http://www.aiderss.com/rss/gre... - Donnie Berkholz
"Like" as in "I like that someone noticed this and is still pushing the issue". - Andrew Perry
Well, if it's tre that the odds of someone getting a tenure track position by 35 are only 7%, there's only one solution: make PhD programs a mandatory two decade ordeal! That should get most people past 35! - Todd Harris via twhirl
"In 2007, two hundred scientists received six or more NIH grants, and a single investigator won 32 grants, while many others got close to ten." This sounds ridiculous. It is clear that this investigator cannot be coordinating closely all those projects. - Pedro Beltrao
It's a classic catch-22. Increasingly, funding consists of large grants to established researchers with stellar track records. However, to become established and build a track record, you need funding - which you can't get. I'd actually like to see postdocs desert academia en masse; let's see where the big bosses would be without their slave labour. - Neil Saunders
I've always wondered how science would work with a more active 'union' for PhD students and/or PostDocs .... if they went on strike how would things pan out ... it's not like public transport employees or a big building project with tight deadlines ... the 'general public' probably wouldn't notice for years. Hence the level of exploitation that occurs (not saying every student/postdoc is exploited, but many are, and I think the lack of any power in a stop-work is a large part of it). - Andrew Perry
I still get a little bugged by the assumption that PhD = career in academia - Deepak
Yeah, I've often wondered how long it would take for anyone to notice if academic researchers went on strike :) - Neil Saunders
Thing is, the rules are different in academia. Basically, if you're not independently-funded, you don't count and are not free to pursue your own agenda. So we end up working for successful group leaders and furthering their careers, rather than our own. I personally think it's wrong that senior researchers get credit for minimal input, solely because they hold the grant, but that's how it is. - Neil Saunders
Neil ... one of the many reasons I wasn't interested in academia. In a good company, you get recognized (as does your manager) when you do well. In academia, it seems like the managers (PIs) get undue credit ... nothing wrong with academic science. I quite envy the freedom from time to time, but there's a lot more - Deepak
@Neil: don't disagree with you, but just to play DA: it's brutal to get and hold onto a lab as a PI, and once you're there it takes all your time and energy just to hang on. (Unless you're one of the silver-spoon Big Shots, but there are a lot more small, struggling labs than big fat ones.) So there's a PI catch-22 as well: you have to take credit for what your lab does, or you get no credit at all. I keep wondering whether Pawel and his freelancing ideas might not be a viable alternative model... - Bill Hooker
@Bill - don't disagree with you either. In theory, a PI is rewarded for their previous hard work, skills in organisation, directing research, mentoring and so on. Sometimes, it even works out like that :) However, I do think we've entered an era where the system actively favours established researchers and actively discriminates against young, early-career scientists. I think it's untenable and would like to see it proved so by people voting with their feet and getting out. - Neil Saunders
I think there's definitely a "rich-get-richer" thing going on. I also think that competition has reached the point -- 7%! -- where we might as well draw names out of a hat. (Sneaky self link: http://3quarksdaily.blogs.com/...) There's not much correlation any more between smarts+hard work and success. Something's gotta give. - Bill Hooker
@deepak: One problem is that academic training is done by academics. That's all they know. They aren't prepared to train people for careers in other environments. And as for grad students striking, it's been done, and doesn't really work for reasons mentioned below. Besides, aren't we all in it for the love of discovery? Are you really going to go on strike when your killer experiment you've spent a year setting up is coming to fruition, your bunnies need a bleed, or you need to read galleys? - Todd Harris via twhirl
Todd, I wouldn't disagree with that, but there are more than enough PhDs who move on to industry, where quite frankly I enjoyed the science I did. I think the stike that Neil refers to is people choosing industry over academia - Deepak
That is indeed the action I meant. The whole notion of striking PhDs/postdocs is ridiculous! If your job (any job) is really making you so unhappy, then look elsewhere. I'm acutely aware of "whinging postdoc" syndrome when we explore these issues. I have no time for those "life is so hard in academia" style of blogs. It really isn't. - Neil Saunders
Well, the strike I was referring to was a real strike, not a shift out of academia, but for reasons Todd (and I) have already stated, it wouldn't work, it would have to be a pretty bad situation before things came to that, and despite problems overall most junior scientists do love their work to much to do it. Because of this, it's one less bargaining chip that they have to improve their situation, unlike some other industries. So in reality, I guess a move to industry is a good alternative to a strike ... - Andrew Perry
Especially since it's often a pretty good alternative, and you get to build stuff and often, esp in a small company, get to do some very interesting research - Deepak
I came to this discussion late (ironically because I'm writing yet another grant) but thought I add anyway. I train people in my lab for academics or industry. Most have gone on to industry as it turns out. Since I've worked in both settings its easy for me to make the training fit either option. I try to give the person the chops for either and then let them pick. - Maureen
Since we are talking about alternative career paths it could be worth mentioning that scientific publishing is still growing at a strong pace. I think if I was not happy with research in academia publishing would be the place I would look for an alternative. - Pedro Beltrao
Postdocs: A 1960s invention because they didn't have enough professorships. Lame. Lame. Lame. - Mitchell Tsai
Comments came back today for a .au funding round. A comment directed at a senior researcher with 10 000+ citations was "very good track record but very no recent first author papers". Also last year the Platypus was not exciting, this year the reviewers are so excited they are creaming their pants. Two questions. Who are the idiots who review these grants (I hope it isn’t those who hold 10+ grants)? Are the only things that get funded something that's been big in the media? It appears very short-term hype focused vs long term vision - Mitchell J Stanton-Cook
This is the logical outcome of poorly synchronized boom-bust cycles in funding, training and the availability of scientific careers in any given place. On top of this, since science is now a transnational career possibility, problems are being exacerbated by even more short-sighted policies in other countries. Some interesting comments here: http://bigpicture.typepad.com/... - Heather
Reading this has rather put me off continuing in academia. I like doing research, but I'm not sure if I fancy spending most of my time writing grants if I become successful. Success in research = do less research ? - Michael Barton
Michael, I do think that to an extent it's a choice. I know a few PIs who still write their own code. Even in industry you can choose your track (technical vs. management). Most of my friends are still in the technical track and at least managing large projects if not right in the middle of them. - Deepak
"Success in research = do less research?" Depends in part on the field. A few years ago I started going to occasional math and philosophy meetings (I'm a physicist). I noticed the senior mathematicians and philosophers were a much more interesting and happy bunch than the senior physicists, on average. My eventual theory was that the relatively low level of funding in mathematics and philosophy was actually a boon for these people. Most senior physicists are machines for turning coffee into grants. - Michael Nielsen
@Pedro – yep, I can recommend publishing :-) BTW, we (=Mol Syst Biol) are still looking for a second editor... - Thomas Lemberger
@pedro re: one investigator with 32 grants - I think I read in a follow-up article in Science or Nature a few months ago that they didn't distinguish between types of grants, so that individual actually had a slew of conference grants and not research grants (he is the main organizer for a major series of conferences), so he was an outlier. Still, there are a distinct minority with the majority of research grants, so I don't disagree that the system needs to change.. - Shirley Wu
Nature had that article (Pubmed ID#: 18354436): 32 grants to Andy Robertson, Chief Scientific Officer of the Keystone Symposia; those 32 grants averaged $15,312 a piece. - dsbreak
"In addition, much of the dynamic network behavior may not yet have been surveyed, given that the bulk of the data reported in Isalan et al. were collected in rich media" ... A lot of it is buried in supplementary materials but we tried several experimental conditions. - Pedro Beltrao
That's a cracking paper, went down well as a paper talk in our lab meetings! And yes we noticed a certain name on the author list ;) - Daniel Swan
"At LIFESTYLE PETS, we are particularly concerned about animal and bioethics, and continually study and discuss these issues both internally and with leading experts". .....OK...that's reassuring, ....not ! - SciPhu
Sorry to ruin your fun, Ntino, but come on...the guy registered the site under his real name. - Mr. Gunn
Rafael says he would like some feedback on what we most dislike about Sciencedirect, Scopus, etc. Let me be the first to mention the 255+ character URLs in science direct(which breaks Connotea's bookmarking) and the lack of a "this article's entry on pubmed" link on the article pages. Anything else? - Mr. Gunn
William, thanks for the feedback. Based on your post, I would be interested to find out scientific community's views about accessing ScienceDirect via web services and developing applications that can be shared/used by other subscribers. - Rafael Sidi
Rafael, I'll send you a note on that one offline. You can guess what my view is on this. SD etc are treasure troves of information. By thinking about it as a service, Elsevier can really help the community and hopefully there will be people who will develop some killer apps - Deepak
Maybe SD should change the final name of the PDF that is generated for saving. Sometimes it is fine to edit it by hand before saving, but sometimes something different than sdarticle.pdf would be easier. - PauloNuin
Rafael, CISTI is always keen on using web services - I emailed you with more info. - Richard Akerman
There's another provider that provides "fulltext.pdf" - forget which one. I don't care too much since my PDFs go straight to CiteULike and are renamed, but if they didn't, I'd be annoyed. - Neil Saunders
Elsevier gives the fulltext.pdf, Oxford gives the number of the first page. BMC is the best. - PauloNuin
Improvement for ScienceDirect's PDF naming is on the way. - Rafael Sidi
That's awesome, Rafael. What about rewriting/shortening the URLs and adding links from the sciencedirect page to the article's entry on Pubmed, CiteULike, etc? - Mr. Gunn
William, we'll look into shortening the URL and other links too. Currently we are linking from article page to www.scopus.com and www.2collab.com (yes, they are both Elsevier products) - Rafael Sidi
Why do we need a closed science search? I can't access it unless my clients use it so tend to stick with PubMed and Scholar. I can find science blogs on Google Blogs search. Disease information on Kosmix. What's the extra value in paying for something? - Sally Church
That's exactly what I'm talking about, Rafael. I see that and think, "Oh, they're just linking to their own sites. That's what I would expect from a big corporation." You can't use the "crowd" for your advantage. You have to be a part of it, first, and small startups tend to understand this better, which leads to them innovating more rapidly, which leads to people who spent time creating the content in the first place getting more value from it. - Mr. Gunn
I know Elsevier has lots of competent engineers and more money to throw at this than a little startup, but unless you start with the right ideas first, you'll get nowhere. Elsevier needs something like Yahoo Berkeley http://www.yahooresearchberkel... - Mr. Gunn
i don't like in all of life science search engines absence of citations links: who cited this paper (who, how many times and when...) - it's should be incorporate in the search and freely available - Alexey
Hi Deepak, nice post, when it comes to a more distributed and less centralised annotations of genomic databases, you have to mention DAS / BioDAS http://www.biomedcentral.com/1... - Duncan Hull
Duncan, good point. At some point, I need to compile all the resources and figure out which ones are actually any use. Any other recommendations? - Deepak
Don't forget that NCBI has quite a reasonable API: eutils (http://www.ncbi.nlm.nih.gov/en...). It gets a lot of use in programming libraries (e.g. Bioperl) but for some reason, doesn't get much publicity or usage in web applications, mashups etc. - Neil Saunders
@Duncan I wondered if there is a recent paper using Biodas ? On my side, I've been trying to use the one from UCSC/Genome-Browser but the results where unuseable (not enough verbose, information missing, etc...) and I then went back to their anonymous mysql server. - Pierre
I like your comparison with Wikipedia. I guess Wikipedia works because it scales well by distributing curation of information across many users. Would be nice if NCBI/EBI could do this. My impression though is that many scientists would initially look down their nose at this, and would need a good use case to demonstrate the potential. - Michael Barton
I wonder if there is any usability/adoption data on the effect of introducing a common RSS logo/button, which was a similar initiative. Will a universal "Edit" button actually encourage more people to edit wiki's ... and is this always a good thing ...? (ie. if the button was *too* successful it could trigger something like Usenets "Eternal September", where the influx of AOL users was blamed on the"degradation of standards of discourse". I doubt that would happen though, since there is no IE support ... yet). - Andrew Perry
Doesn't work on OpenWetWare yet ... I think they need to install the UniversalEditButton MediaWiki Extension. - Andrew Perry
When it comes to writing a PhD, Latex is the daddy. - Duncan Hull
Interestingly, LaTeX submissions of scientific papers are slowly being accepted, but almost nobody accepts Word 2007 files :) Here's PLoS statement: "Manuscripts prepared in LaTeX may be submitted in PDF format for use during the review process. Post acceptance, however, these authors will be asked to submit their .tex files and formatting information as a zipped file. Please consult our LaTeX Guidelines for a list of what will be required.
Please note: At this time we cannot accept for review or revision any documents created in Microsoft Office 2007, even if 'saved down' to the 2003 version. " - Pawel Szczesny
Thats a pain in the ass, you have to use something like latex2rtf http://latex2rtf.sourceforge.n... on final submission, but it screws up a lot of stuff. Unfortunately, MS Word seems a better option for collaborative authoring, but Latex and Bibtex come into their own when you're writing a PhD :) - Duncan Hull
Duncan, as far as I know, for some journals conversion to rtf is not necessary anymore (but it looks like a recent thing). PLoS and Bioinformatics (two journals I've checked) allow final submissions in LaTeX given all the files are packed into a single zip archive. On the other hand I must agree on the Word being better option for collaborative editing, but I recall seeing somewhere online TeX editor (aka Google Docs for LaTeX). - Pawel Szczesny
Please, add [[Category:Biogang_members]] at the bottom of your user profile on OWW, so we can be found. - Pierre
Pawel .... do you have any thoughts. Anyone else. Perhaps we can have the following sections. 1. Discussions 2. Projects Anytime someone decides to run with an idea or discussion it can be promoted into a project. Not sure if that's too complication or not. One can also have independent pages, e.g. for information and events, etc - Deepak
Thanks Pierre; it's going to be good having a mediawiki expert on board - Neil Saunders
Deepak, looks good for me. So it would be: 1. About/Information etc. (single page) 2. Discussions (list of pages) 3. Projects (list of pages) 4. Events (single page)? - Pawel Szczesny
Sounds right for now. Let's keep it relatively low overhead at this point. I should get a chance at some point today to get things moving - Deepak
Pawel, thanks for pointing out the RSS issue with "dewikified" version of the page. We'll have a look into it. - Ricardo Vidal
I've started the move. The markup doesn't transfer automatically, so might require tweaking. - Deepak
OK ... basic move has been done, including structure 1. Main Page (equivalent to About) 2. Discussion (talk to your hearts content, create new pages) 3. Projects (formal projects) and 4. Events (two events there right now). More tomorrow. Back to code now - Deepak
I've added a template to make navigation easier. Feel free to change the logo and layout - I made something quick, but it shouldn't be the final look. - Pawel Szczesny
"But having been through a startup myself, I think there's much more you can do in the other direction: decreasing economic inequality. People love starting companies. You get to be your own boss, work on something you love, do something new and exciting, and get lots of attention. As Daniel Brook points out in The Trap, 28% of Americans have considered starting their own business. And yet only 7% actually do.
What holds them back? The lack of a social safety net. A friend of mine, a brilliant young technologist who's been featured everywhere from PBS to Salon, stayed in academia and the corporate world while all of her friends were starting companies and getting rich. Why? Because she couldn't afford to lose her health insurance. Between skyrocketing prices and preexisting condition exclusions, it's almost impossible for anyone who isn't in perfect health to quit their job. (I only managed because I was on a government plan.)
Anyone with children is also straight out. Startup founders tend to be quite y" - Attila Csordas
maybe explains why Obama has such a strong showing in silicon valley? Other than the fact that it's full of smart people who get it? - Mr. Gunn
Get your head out of the clouds! Oh wait, I mean, keep your head in the cloud :) Best of luck! BTW, as I've said here at FF numerous times, I'm a big fan of Nick Carr's book. - Mike Reynolds
sounds like a very interesting move! - Daniel Swan
I wasn't aware that you were changing jobs. I wish you the best of luck! Congratulations! - Ricardo Vidal
Nice! They are lucky to get you - I look forward to your reports behind these new trenches - Jean-Claude Bradley
Paulo ... am I glad I have a full feed. Hopefully that works for you - Deepak
Congrats! Excellent. Excellent. Excellent. - Matt Wood
Too cool. Looking forward to hearing all about it. - Neil Saunders
Congrats. Looking forward to science clouds. - Richard Akerman
Good luck Deepak, and welcome to the wonderful world of Web Services on the cloud :) Will you be working with Werner Vogels at all? http://www.acmqueue.com/module... - Duncan Hull
Thanks folks. This is gong to be interesting for sure. A world where I wont be talking to science types every day. Duncan, I am too low down the food chain :). - Deepak
So, basically I can say now "I know someone at Amazon" or "my friend at Amazon" ... Congrats and hope to hear more from you there. - PauloNuin
Just occurred to me how much fun you'll have editing your profile at all the social networks :) - Neil Saunders
Luckily for most of them I use my personal info. As long as I changed LinkedIn I am probably in good shape :) - Deepak
Belated congratulations. I bet AWS will be a really cool place to work, all the stuff they do seems really fun and webby. - Michael Barton
Any of you familiar with Yubnub .. it's also very cool - Deepak
Yeh, YubNub is great .. I need to get into the habit of using it more. I made a PDB search command for it a while back ... try "pdb 1ZU2" (or some less egotystical PDB ID). Maybe I should make a bash frontend that launches a new browser tab of a YubNub command ... - Andrew Perry
Eric: yes, functionally goosh isn't all that different to bookmark keywords, apart from the snazzy 'terminal' interface. As far as I understand YubNub is a little more 'programmable' (eg ifThen), although the bulk of it's commands are just equivalent to something that could be done with a bookmark keyword. - Andrew Perry
