A co-worker mentioned to me yesterday that a colleague of his is thinking about starting an online journal club type website for scientists. The idea seems to be discussions about papers, data sets, and other web-publishable materials, from any source, in a central location. It would also have discussions about scientific culture, which made me...
It would be a place where people (students, junior faculty, etc) could learn the ropes of academia and science without the pain and misery that traditionally is required. The differences I can see from existing services is the focus on journal club-style discussions and maybe a low barrier to entry
- Shirley Wu
from twhirl
But obviously, whatever he ends up pursuing should learn from the trials and tribulations of the many related services out there (including services like FF, which is also discussion-oriented)
- Shirley Wu
from twhirl
It's easy to immediately discount any proposal that sounds like yet another facebook for scientists, but there are still some interesting and potentially good ideas out there. Unfortunately, people who aren't as familiar with the existence of these tools always think of facebook as the ideal and as a brand new idea if applied to the scientist community. Hopefully I convinced my co-worker otherwise, while still encouraging the more innovative aspects of the concept. <end rant>
- Shirley Wu
from twhirl
AcaWiki is built around a very similar concept, and John Wilbanks makes an argument for bringing journal clubs online (cf. http://ff.im/airoV ).
- Daniel Mietchen
Shirley, Besides AcaWiki (great place to have these discussions, but I'm biased! http://acawiki.org/ ) your colleague also might be interested in GradTurkey, a journal-club discussion wiki originally aimed at grad students: http://gradturkey.fastcoder.net/
- Jodi Schneider
can discussion on AcaWiki be linkable and embeddable for public like you can do on FF? If not, so why don't do journal club on FF? Can't get it
- Alexey
this topic came up during a discussion today with Mike Eisen of PLoS, re: why commenting hasn't really taken off - his thought is that people are more likely to comment if there's a central place to do it rather than individually at each journal website for each paper (how many of us access papers directly through journal websites except through PubMed anyway?). The whole time I was...
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- Shirley Wu
from twhirl
can somebody point to the platform for journal club online better then blog post? It's combine everything - presentation (ppt embedded from SlideShare or Gdocs, video embedded from YouTube/Vimeo...) presenter's opinion, discussion section under the post, embedded comments from FF, ranking of the presentation and number of views. Importantly you don't need to register or get account for commenting, it's public and linkable, moderatable . Whole world can participate. What can be better?
- Alexey
@Neil Saunders Were you thinking of JournalFire? We recently updated the site and are looking for feedback. I posted about it yesterday: http://friendfeed.com/the-lif...
- John Delacruz
"Although we would be the first to agree that PLoS ONE isn‘t perfect, neither is any journal, as Richard points out – although not until around 30 pages into the article."
- Heather Piwowar
I've skimmed most of this now. I think I agree overall with the general thrust at the end but the 30-odd pages of criticism based on a few papers seems a strange way to get there. Or maybe I'm just reading in the conclusion I want to see?
- Cameron Neylon
A lot of it feels a bit disconnected and out of date to be honest. I usually find myself nodding along with Richard's pieces even when I disagree and that wasn't the case here...
- Cameron Neylon
Sounds like skimming it is the best way to read it :-) the general thrust I think everyone get agree with, some of the arguments seem somewhat odd, indeed.
- Björn Brembs
Credit to Richard for elevating the PLoS response to a separate post, rather than leaving it languishing at the end of his long-ass essay. Also, this may be the least of his mighty works, but it does raise very important questions about peer review and pricing.
- Bill Hooker
Oh I definitely think he has some important points in there - just unconvinced about the frame he puts them in. And I do believe that costs at PLoS should come down in time - just not convinced that the attack via standards of peer review is the right one.
- Cameron Neylon
Yes, that line of reasoning bugs me too. Here are two ways to get actual data on the question: 1, what proportion of papers are published eventually? Iirc, it's around 70% -- in theory, since P.ONE will publish anything worth publishing, it should be around the same as the P.ONE acceptance rate, except to the extent that people are selectively sending their better or worse stuff there....
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- Bill Hooker
I really wish I had time and access and expertise to do the second study...
- Bill Hooker
Interesting idea, pace issues with impact factor but any other metric would also do. The figure of ~70% keeps coming up but I don't know of any good recent studies that bring that figure up to date and check across different disciplines. Second study you propose is an interesting one, if for no other reason than how would you control it properly...
- Cameron Neylon
I'm no quite sure what to make of the 42 page doc. I think I made it about halfway through, and then started really skimming. Seems like he wants it both ways. Authors should pay less money to PLoS ONE because is is just peer review lite, and it is a cash cow, but the journal should have higher quality standards and a higher rejection rate. Which way do you want it? Do you want the...
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- Joe
Joe: Sounds like you're talking median, not mean. The average (mean) could be 4+ cites per year with only one out of ten papers getting 4 or more cites. Is the median for PLoS.One paper cites available? If so, that's a much more meaningful number. (Won't comment on the Poynder thing 'cuz I haven't read it all yet.)
- Walt Crawford
You can't really use IF for any of these calculations...
- Björn Brembs
From the response: "of the 4400 articles published in PLoS ONE in 2009 around 55% of them have been cited 3 or more times (Scopus data)".
- Matt Hodgkinson
@Bjoern, that's true, I was being lazy. Eigenfactor might be better, or a simple mean/median/variance of citation numbers. @Cameron, not quite sure what you mean by "control" in this instance.
- Bill Hooker
Alas I don't, offhand. I've been doing R (badly) for years and I think there are better docs out now, somewhere. Does anyone have a recc?
- Heather Piwowar
All I know is that all our R books are always checked out. And I imagine the ebooks get pretty high use too. (Fortunately most of our licences will pay for unlimited use.)
- John Dupuis
Brian, there are a few good readings on the r-project.org website, and the whatever you do, STOP READING, and start using it. Really, pick any R tutorial, and start actually typing what they show, change it, and just use R. That's the best way to learn it. Using R is a skill, not a theory you can learn. Skills just need practice, not reading.
- Egon Willighagen
Egon, I agree. I don't retain skills I don't use on a regular basis.
- Brian Westra
pq -- "The future of scholarly publishing does look bright - just not for publishers." It even looks pretty good for publishers who aren't insanely greedy. :-)
- Bill Hooker
I wonder if they've overdone it so much, that the backlash will wipe for-profit publishing from scholarly communication entirely. IMHO they have...
- Björn Brembs
@Björn: you quote "...accompanied by an apparent decline in the quality of peer review." The lack of journal / editorial standards should not be underestimated... refereeing would have been very much better, if the editors properly trained and/or corrected them. They don't. Anyone: feel free to post a poll on who ever had his referee report rejected. One layer here is editorial...
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- Egon Willighagen
BTW, coulnd't leave this comment in your blog: STOPPED: KEY_FILES FOLDER NOT WRITABLE
- Egon Willighagen
Sorry, Egon, moved servers and haven't ironed out all the permissions yet! Thanks for the info!! Should be working now...
- Björn Brembs
"Until not so long, I thought that it was worth it. It was something that I had never questioned so far. I wanted to be a scientist since when I was five. I had done everything to become a scientist. I was a scientist in one of the top universities of the world, in one of the top five research groups on the subject. I had won a personal fellowship to fund myself. Most of my self-esteem, of my very concept of self-realization, relied on myself being a scientist. The very idea of quitting academia was a synonim of personal failure." That right there is the engine of the pyramid scheme.
- Bill Hooker
from Bookmarklet
I've heard more senior scientists dismiss this attitude as a 'typical cynical postdoc, not skilled/smart/hard working enough to make it to tenure'. These same senior scientists were junior scientists in a very different time, usually before the huge expansion of the number of available PhD candidates, where the ratio of supply to demand of graduates wasn't nearly as imbalanced. This...
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- Andrew Perry
Re: the pyramid scheme that BH and AP bring up -- I completely agree and want to add one additional point: its not just that an untenable economic situation has emerged which grad schools sweep under the rung -- its that the community itself seems to look down on those who leave academia to join industry/business or publishing or something else entirely. High rates of failure at achieving tenure at impressive school X would be ok if young students/scientists felt they had viable alternatives
- Benjamin Tseng
I agree Benjamin - I've noticed that in many academic institutions career options outside that system are rarely discussed openly, and leaving academia is considered failure (even if someone leaves to do something arguable more useful). Granting bodies usually want to encourage collaboration between industry and academia through special funding opportunities (eg, the ARC Linkage grants...
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- Andrew Perry
some more comments here: http://ff.im/ylQGj and I agree with Andrew .. thats why we should fight against even the language that is used (i.e. "quiting science")
- Pedro Beltrao
http://figshare.com/figblog... - The launch of http://figshare.com – Please test it out - “A lot of time and money is being wasted by groups around the world duplicating research that has already been carried out. We are a data sharing platform where you can add figures that would otherwise go unpublished. In doing this, other researchers will not...
"data science is more than just an opportunity to have fun and make the world a better place — it might even be how you make an honest living!"
- Deepak Singh
GSEA analysis is designed to find pathways in which differentially expressed genes are enriched. I'm looking for publications where the differential expression of a _single_ pathway gene results in altered pathway activity and phenotype. Seems mechanistically reasonable, and presumably these would escape detection by GSEA... Examples or ideas?
Very good suggestion, especially as a way to find genes to test. But short term, I'm hoping to find a published example that I can just cite. (Edited the post to clarify that.)
- Andrew Su
Heterozygous lethal mouse strains in JAX, about 50 genes, vascularization and imprinting.
- John Hogenesch
E.g. +/- Vegf mice are poorly vascularized and embryonic lethal. PMID 8602242
- John Hogenesch
'The elite journals have a rejection rate, typically, of more than 90 per cent. For no good reason, this rate is used to justify the quality of a journal and becomes a target for others to emulate. Editors have become judge, jury and, mostly, executioner.[...] Where will this end? Perhaps a journal will announce that it has achieved a rejection rate of 100 per cent - nothing by anybody is considered good enough to grace its pages.'
- Kubke
'On this issue, business schools are at the cutting edge of bad ideas. It is time for a rethink. Above all, I urge a moratorium on journal-ranking lists. Meekly accepting constraints on where we publish limits academic freedom. It means that what we research, how we do it and what methods we employ are driven by criteria at odds with what is important or interesting. Our careers are dehumanised, our scholarship damaged. This is a spectre whose haunting days should most definitely be terminated.'
- Kubke
"I can imagine few better methods of reducing intrinsic motivation, extending managerial oversight and demoralising people. It is part of the commercialisation of the academy, often justified in terms of "accountability". Such is the trajectory on which journal rankings, whatever their original intent, have placed us."
- Björn Brembs
"The most lauded journals are based in the US, and reflect the positivist and functionalist orthodoxy that dominates the discipline there. They pay relatively little attention to such problems in management theory and practice as exploitative working conditions, race or ethics. "
- Christina Pikas
…to file my Annual Performance Review. Nothing makes me shiver as much as the Dean’s email reminding us that it is time to file our Annual Performance Reviews (APRs). This year shivering does not begin to express the feeling I got upon receiving that email. What have I achieved this year? ‘Nothing’ was the first [...]
- Kubke
In the midst of various DDOS attacks, Paypal has moved to release Wikileaks' funds from it's account, after it was suspended late last week for a breach of the sites Terms of Service.
- David Bradley
Now, I would be more impressed if they acknowledged their mistake in closing an account in absence of any conviction (anywhere), and reopen the account again. It's not a bank's role to play jury and judge.
- Egon Willighagen
Exactly right Paypal. Same applies to the US agency that is shutting domains that the RIAA tells it are pirates without due legal process and before the law has actually come into force. Something similar will happen in UK soon and probably rest of EU. But, that said, P2P DNS will get around that particular problem, at least.
- David Bradley
NASA - NASA to Hold News Conference on Astrobiology Discovery <br /> <i>Science Journal Has Embargoed Details Until 11 a.m. PST On Dec. 2</i> - http://www.nasa.gov/centers...
Does one actually have an option? You need 20 years of experience to get tenure, because there is always one who does... this system sucks big time... effectively we tenure people who haven't given up, instead of the best candidates...
- Egon Willighagen
Ideally, you'd want your own lab after 1 maybe 2 postdocs - if you eventually want to get a tenured position that is. The reason: they'll ask for senior author papers and you usually don't get them as a regular postdoc.
- Björn Brembs
Sure you do... (well, perhaps I'm an exception...)
- Egon Willighagen
Sometimes you do - my thesis advisor let me have a senior authorship during my PhD thesis - but that's pretty rare, I guess...
- Björn Brembs
I have an undergrad (HHMI research scholarship recipient) who is getting first authorship on a publication, or so he claims on this resume. I haven't looked up the citation, but was impressed nonetheless.
- Mickey Schafer
~3 years into my 1st postdoc and this question is also on my mind these days. My plan is to start looking after this postdoc. I also wonder how many years one should do before moving again. Any tips ?
- Pedro Beltrao
from Android
I don't think there's any one correct answer. It so very much depends on the field, the CV, what kind of position one is looking for (e.g. "highly ranked" research U. vs. a position with more emphasis on teaching), the particular year. etc. etc.
- Mickey Kosloff
The Nobel Prize winner in economics, Joseph Stiglitz, says that his advisor in graduate student told him once, "You can't remain a promising young man forever."
- Hope Leman
I'm with Neil and Bjoern: no more than 2, preferably one. Beyond that you are being treated as a fungible data-collection unit in someone's factory, a small stone at the bottom of a large pyramid. (I did 4, though one was so abortive I try to pretend it didn't happen, over 11 years.)
- Bill Hooker
@pedro: I don't think it matters much if you spent 3 or 5 years on your first postdoc, as long as you've been productive. I'd definitely start looking for independent positions (in the widest sense) after five years, especially with your track record. They don't have to be tenure-track, but ideally they would.
- Björn Brembs
Hmm... I'm currently in an odd position in so far as that I'm coming to the end of my first PostDoc, which I got before I had done a PhD. I'm now (hopefully) going to get a PhD via the work that I've published over the last five years. I've also got ~10 years industrial experience. So does this make me a newly awarded PhD, a one-PostDoc or a washed-up drifter?!?
- Neil Swainston
from iPhone
Why, the last option, of course :-)
- Björn Brembs
It makes you uniquely qualified and uncategorizable. Bottom line no-one's going to care much beyond your publication list and any evidence of being able to bring in funding (industrial experience always looks good in the UK). To be honest in the current climate in the UK I would say all bets are off. There will be opportunities and there will be a lot of pain both institutional and personal so take a look at Deepak's post on serendipity.
- Cameron Neylon
Two is too many , unless they are very short. I general not knowing what to do and using multiple postdocs to figure things out can be regarded as a weakness. That said you can do more than two if you want to pick up a new technique or find a mentor who is worth the one additional postdoc label
- Hari
If you normalize the data, you assess the risk for the individual. That's not what they appear to have been studying. For me, it looks like they wanted to see which drug, as a whole, as the strongest effect on society, as a whole. And there, not surprisingly, it turns out that alcohol does the most damage, because it is the most widespread drug. I think that makes perfect sense and is...
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- Björn Brembs
Good point Bjørn ! However, it's the news-coverage that really sucks here, - the NPR-piece says ".....evaluated substances including alcohol, cocaine, heroin, ecstasy and marijuana, ranking them based on how destructive they are to the individual who takes them.........", which underscores the point Dr. Gunn is making on normalization.
- Nils Reinton
Interesting how they arrived at the relative weights. Anyone willing to try to assess coffee, chocolate, Döner Kebap, salted peanuts or some such on this scale?
- Daniel Mietchen
Well, they do admit their data is not 'objective' and that it also ignores positive effects the drugs may have.
- Kubke
@Daniel, I would agree, given the criteria they use, it might be interesting to see where something like 'fish 'n chips' would score in this analysis compared to some of the 'illegal drugs'.
- Kubke