Mickey Kosloff › Likes

Jonathan Eisen
Am still waiting for Nature to fix genome paper access so am posting some PDFs of papers; here is Vibrio cholerae paper from 2000 #opengate
You could also preemptively post them to the References Wanted group :) - Egon Willighagen
Iddo Friedberg
Our ISME J paper on protist diversity in Antarctic lakes is out. #fb #microbialecology http://www.nature.com/ismej...
Bill Hooker
Open and Shut?: PLoS ONE, Open Access, and the Future of Scholarly Publishing - http://poynder.blogspot.com/2011...
This will generate some heat. - Bill Hooker from Bookmarklet
"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A lot of it feels a bit disconnected and out of date to be honest.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.... more... - 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... more... - 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
@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
This article is also discussed at http://blog.the-scientist.com/2011... - Joe
Marking os I remember to look at this later today when back in my office (wish there was a bookmark this for later feature) - Hedgehog
Björn Brembs
Jonathan Eisen
Still frustrated that Nature hasn't fixed free availability of some genome papers: so here is 2002 Plasmodium falciparum paper #opengate
Can't you put them on Nature Preceedings? - Egon Willighagen
interesting idea - not sure - Jonathan Eisen
seems that this would not work from reading their guidelines, http://precedings.nature.com/site... but it would be funny to do ... - Jonathan Eisen
What Jon has done here is perfectly legitimate. As he knows the licence is CC-NC he can share the pdf in any way that he wishes for non-commercial purposes... - Cameron Neylon
Jonathan, the limiting factor for NaturePreceedings is not having copyright anymore, I guess? - Egon Willighagen
Deepak Singh
Michael Nielsen
The Technium: Computational X - http://www.kk.org/thetech...
A useful generative template. - Michael Nielsen
Martin Fenner
The Trouble with Bibliographies - http://blogs.plos.org/mfenner...
good to see this spelled out, Martin :-) "What you want is at least a direct link to the cited work using the DOI (if available), and a lot of journals do that. You don’t want to have a link to PubMed using the PubMed ID as the only option (as in PubMed Central), as this requires a few more mouseclicks to get to the fulltext article. And you don’t want to go to an extra page, then use a link to search the PubMed database, and then use a few more mouseclicks to get to the fulltext article..." - Claudia Koltzenburg
Jennifer Mackenzie Jones
Truthy visualises memes on twitter on a realtime basis. - Jennifer Mackenzie Jones
Jonathan Eisen
Please help keep the pressure on Nature Publishing Group to restore free access to genome papers #opengate - http://phylogenomics.blogspot.com/2011...
Please help keep the pressure on Nature Publishing Group to restore free access to genome papers #opengate
This seems like a job for Twitter, so I re-tweeted. If we all do that surely it will get noticed and passed on. (Someone could get in touch directly but I wouldn't know who to contact.) - Bill Hooker
Pedro Beltrao
Egon Willighagen
still puzzled why #acs meeting abstracts end op in #webofscience and book chapters do not... the latter actually get cited :(
Jean-Claude Bradley
By displaying the combination of a comics and of a periodic table poster on the wall of your kids’ room, you are giving them a chance to get familiar with the building blocks of the universe in a fun way. Once they will see the periodic table poster at school, they will relate to it as if it were a toy. http://www.periodictableforkids.com/
Egon Willighagen
#google reports about 167 retractions on the #nature website http://www.google.se/search...
Mmm... Science made it difficult to use this approach :( - Egon Willighagen
Cameron Neylon
Jonathan Eisen
If inclined to believe recent J. of Cosmology paper on meteor microbes, try reading some other JC papers; #awful #painful #crap - http://journalofcosmology.com/Pansper...
Heather Piwowar
Do you know the media relations person for your department? If not, why not? #makeyoursciencematter
Make your science matter -- why and how to engage with media and policy makers. Awesome book. http://amzn.to/chKLNc - Heather Piwowar
What media relations person? - maʀtha
It is a person who helps investigators write up press releases for general-interest or high-profile studies, and helps media find experts in a university for their stories. For example at UBC: http://bit.ly/aCdWdu at Pitt: http://www.news.pitt.edu/media-c... - Heather Piwowar
aka "media/press officer" as mentioned by PLoS ONE: http://blogs.plos.org/everyon... - Heather Piwowar
I do, but the only time I needed her, I could reach her - Ramy Karam Aziz
I do, but mainly because he has the office next door and catches the same bus as I do... - Cameron Neylon
I do. The office actually works quite closely with us academics. - Kubke
Big Joe Silenced
Ridiculously awesome pic of Discovery and the ISS taken from the ground! | Bad Astronomy | Discover Magazine - http://blogs.discovermagazine.com/badastr...
Ridiculously awesome pic of Discovery and the ISS taken from the ground! | Bad Astronomy | Discover Magazine
"I think I remember that scene from Star Wars! This remarkable picture was taken by Rob Bullen on Saturday February 26 from the UK, using an 8.5″ telescope. I’ll note that’s relatively small as telescopes go! But the ISS is now over 100 meters long, and if it’s directly overhead (that is, the closest it can be to an observer on the ground) it appears large enough to easily look elongated in binoculars — in fact, it would be big enough to look elongated to someone with good eyesight and no aid at all*! Still, images like this are difficult to obtain even with a carefully guided telescope equipped with a video camera. Oh — did I mention that Rob hand-guided his telescope for this shot? Yeah. Wow." - Big Joe Silenced from Bookmarklet
looks like a shot from some crazy 50s saucer men B flick. only it's real. - Big Joe Silenced
Ami Iida
Gallery: 10 Stunning Science Visualizations http://www.wired.com/wiredsc...
Iddo Friedberg
Björn Brembs
Egon Willighagen
So how hard is it to get a Tenure Track job in Academia? - http://www.science3point0.com/sociald...
"This translates roughly to a 4:1 ratio, which is similar to the Benderly and the AFT ratios. This is far better than 300:1 but still of concern." - Egon Willighagen
I thought 300:1 was rather high but 4:1 seems rather low to me...I would have thought around10-20:1 would be the right number. - Cameron Neylon
I have been guessing 10:1 for a while in the US, based on some figures I saw (sorry, can't think where) that showed 20,000 new postdocs produced each year but only 2,000 tt jobs coming onto the market. Three hundred seems high even for applicants per position (unless at MIT/similar). - Bill Hooker
Bill, 200-300 (or higher) applicants per position is often quoted in many places, see my comments in that thread: http://friendfeed.com/brembs... Given it's not limited to these few top universities, it either tells a bit about science jobs market, or shows how many institutions are as good as MIT ;). - Pawel Szczesny
The thing about US "ivy league" schools is that they are not about education (though you can probably get a decent education at some of them) -- they are there as a filter, and their primary product is imprimatur. You may learn the same info and skills at Buttlick College, Arizona, but the job is going to go to the guy with the Harvard degree every time. In the US, at least. This is how the economic elite got the upper hand in the first place, and how they mean to keep it. - Bill Hooker
That's a bit tangential -- my point is that I would expect more applicants to a high-prestige school because of prestige, not necessarily because of real quality. Though there is a circular effect, whereby it might actually be better to be on staff at a prestige school, since they use their prestige to attact good teachers and researchers -- i.e. more fun colleagues. - Bill Hooker
The 300 figure, at least for me personally, is a rough average over the US positions I applied for and where I was told the number. In Germany, there are ~24,000 professors and every year ~25,000 PhD's graduate (all subjects). This means, if no. of positions is constant and assuming an average career of a professor of 30 years, one out of 30 PhDs in Germany has a shot at a professorship. However, the number of applicants for each professorship in our field is ~60... - Björn Brembs from iPhone
@Bill... Cambridge UK PhD research is not that much different from good NL universities... however, the funding is much higher, allowing Cambridge to buy more advanced equipment... moreover, students are more prestigious, making them ask more and better questions, which makes teachers better... - Egon Willighagen
I note that tenure track is a US phenomenon. Many junior lecturers (Assis. Prof. in US terms) are on contracts that simply terminate after X years, usually without any official means of extending them. (Correct me if wrong...) - Noel O'Boyle
Jonathan Eisen
Thanks to @ryneches (PhD student in my lab) for finding this: Disappearingspoons.com - http://www.disappearingspoons.com/
Bill Hooker
Fun to browse for ideas. Concrete foam, stainless steel yarn, low-temperature thermoresins, microtooling, etc etc etc. - Bill Hooker from Bookmarklet
Heather Piwowar
Just submitted minor revisions to PLoS ONE for publication of my dissertation results. w00t :)
The paper still reads a bit like a dissertation chapter, but I've decided this is a good thing. Useful to see gory details of analysis methods sometimes, to remember what that looks like. - Heather Piwowar
Though the lit review is a bit stale by now. oh well! At least it won't get any staler by publisher delay since PLoS ONE is so fast. - Heather Piwowar
A shout-out thank you to the reviewers. The paper is better because of their comments. - Heather Piwowar
YAY for open review. Several useful conversations and collaborations have resulted, without awkwardness of blind reviews. - Heather Piwowar
And finally, YAY for the PLoS no-hassle fee waiver. The reported work was unfunded. $0 for OA pub. PLoS wants it anyway. - Heather Piwowar
Good question. It felt different, because when I submitted my first paper PLoS ONE hadn't published anything yet, it was just getting going. Documentation, etc more clear now. And the submission software is a bit slicker I think. Maybe the reviews took a bit longer to get back this time? But overall, very similar. - Heather Piwowar
Bill Hooker
Experimental Error: Most Likely to Secede - Science Careers - Biotech, Pharmaceutical, Faculty, Postdoc jobs on Science Careers - http://sciencecareers.sciencemag.org/career_...
Depressing. - Bill Hooker from Bookmarklet
Well, depressing and funny at the same time... - Björn Brembs
I suppose my equivalent of moving small bits of liquid from one place to another would be schlepping files around because I've run out of disk space. The latter still sounds like more fun. Small favors. - Ruchira S. Datta
@Ruchira, as someone who does both - yes, maybe ;-) - Mickey Kosloff
Bill Hooker
Deepak Singh
USA Inc.: Red, White, and Very Blue - BusinessWeek - http://www.businessweek.com/print...
Mr. Gunn
Goodbye academia, I get a life. – blog.devicerandom - http://blog.devicerandom.org/2011...
I really dislike the term "quiting science" ... its very rarely really about quiting science. Many people that get a job outside the academic track after PhDs continue doing science or managing projects in companies. We need to get this out of our vocabulary. We are not quitting if we get a job somewhere else. There are so few jobs that its really pure luck these days to get to manage a lab in an university or research institute. Its not failure and the stigma only favors the perpetuation of this problem. - Pedro Beltrao
Pedro, I agree! - kendrak
Agreed. We need to get rid of the concept of academic research vs. everything else. - Mr. Gunn from YouFeed
I agree Pedro! Science is way of life. - Sandra
That whole science = academia mindset just drives me batty - Deepak Singh from iPhone
it is why I got out and went into comic books, much simpler without all the attitude. - Comics Forge
Agreed.<Academia> isAProperSubsetOf <Scientific Practice>. - Dan Hagon from Android
Maybe it's one of the weird quirks of transportation engineering, is that Academia is recognized as part of the larger research community, so leaving it doesn't have the same stigma. Really, we need to look at how funding models sustain the divide. - kendrak from Android
Linking to the other thread here: http://ff.im/yl8tB . I've sometimes been given the impression that for some fields of engineering leaving industry to become an academic is considered failure, rather than the other way around (along the lines of "those that can do, those that can't teach"). Is this a commonly held belief or is my sample size just too small ? - Andrew Perry
Andrew, I think the general attitude academics had with industry has changed quite a bit over the years, particularly in departments that benefit from such collaborations (biotech, chem, engineering, CS, etc). Lots of that going on here at U of I. Not sure how it is going the other way (industry to academia), but I think the perception there would be based on how your job performance was in industry. A number of profs here are from industry and are well-regarded in their fields. - Christopher Fields
Cameron Neylon
Is this the same person? -- http://www.ncbi.nlm.nih.gov/pubmed... -- I always like to know whether the person telling me how to do my job can in fact do it themselves. - Bill Hooker
I'm pretty sure that is not the same Grant R, Bill. If you look at his (abandoned) NN profile, you will find a completely different list of papers. http://network.nature.com/profile... - Lars Juhl Jensen
No is the is the simple answer to that. More structural stuff. His written a lot more at F1000 and the Scientist recently if you want examples (not papers obviously). I'd certainly rate him as one of the better and definitely more flexible writers I know. He ran courses on this for students in Sydney I think. - Cameron Neylon
My comment there: "Maybe that’s not what you’re saying, but I’d guess that enthusiastic writing will not be the same as scientific writing. In other words, could it be that the kind of writing you’d like to see does not belong in scientific papers? Exaggeration often helps to make the point: “I did a PCR and we got this totally awesome band at 500kb, while in the control it was at... more... - Björn Brembs
@Bill, your comments freaks me out a bit -- my whole job entails teaching people (mostly in the med sciences) how to write then publish...while I've published once in trade, I've yet to publish in an academic journal. But I've helped lots and lots of folks over the years develop papers into publishable units (and write essays that got huge fellowships, and once even, a letter that got a child a visa to leave China after 2 failed attempts by the parents). So, am I qualified? - Mickey Schafer
In response to the post itself, I have recently found that I pass along editorials and letters written by the editors of journals for the kind of things they have to deal with -- then reverse engineer for students what that means for writing. Interestingly, while mechanics are still an issue, most of the problems have to do with making sense, not making style. Not everyone can write with style; but I will contend with my last dying breath that anyone can learn to write competent prose:-). - Mickey Schafer
@Mickey, I was mostly responding to the tone of the piece, which got up my nose. I don't write papers with editors in mind, I write for readers -- as you say, the point is to make sense; style is rather beside the point imo. (On the other hand, I haven't written a real paper in years, so I'm not one to be throwing stones here.) - Bill Hooker
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