Archive for the 'scholarly communication' category

Defense slides

Took me a bit - I forgot to upload them to SlideShare until just now. I did pass with revisions to be approved by my advisor.

I have to tell you that it was really anticlimactic. I thought it would be a big weight off my shoulders and I would feel free and I would have minor quibbles but lots of pats on the back... but... well... I don't know.  This massive framework o' mine? The communications prof thought it was exactly the same as Shannon and Weaver (1948). Wow.

At least when I do these edits I can get on with writing up other work I've done and then prepping pieces of this for publication. So, really, no less work, but different.

I do fully intend to make this freely available with creative commons attribution and all that. The whole dissertation. I am going to do the revisions first, though, because some are pretty big.

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ACS and Just Accepted Manuscripts

A colleague posted on Chminf-l asking about the American Chemical Society's Just Accepted Manuscripts program. Most of the immediate responses were to explain the program, which is not what she asked. Here's the site's description:

"Just Accepted" manuscripts are peer-reviewed and accepted for publication. They are posted online prior to technical editing, formatting for publication and author proofing. The American Chemical Society is posting just accepted, unredacted manuscripts as a service to the research community in order to expedite the dissemination of scientific information as soon as possible after acceptance. "Just Accepted" manuscripts appear in full as PDF documents accompanied by an HTML abstract. They are accessible to all readers and citable by the Digital Object Identifier (DOI®). The manuscripts posted on the "Just Accepted" Web site are not the final scientific version of record; the ASAP (As Soon As Publishable) article (which has been technically edited and formatted) represents the final scientific article of record. The "Just Accepted" manuscript is removed from the Web site upon publication of the ASAP article, and the ASAP article has the same DOI as the "Just Accepted" manuscript. The DOI remains constant to ensure that citations to "Just Accepted" manuscripts link to the final scientific article of record when it becomes available.

The FAQ explains that this is opt-in and these copies will be removed when the ASAP and final versions are live.

Chemistry is kind of a funny field when you talk about scholarly communication and sharing (see and read everything from Theresa Velden's dissertation research on this, in particular). Journals are dominated by ACS with RSC and the other scholarly publishers following. In some areas like synthetic chemistry, there's a real reluctance to even share at meetings, no desire to post pre-prints, and tight control over data access. In more computational and analytic areas, it's a little more relaxed.

Pre-print server efforts in chemistry have been mostly unsuccessful. For one thing, the journals will not take articles posted elsewhere first. Second, there's this big tension with priority (now moving to first to file maybe will change patent things but there's still recognition issues).

With all that, there are still efforts to require self-archiving broadly across fields and to have disciplinary pre-print servers. The big publishers who are rolling in dough from the subscriptions from all the ACS accredited programs do not want to see these archives and self-archiving succeed, even though it's been shown that it doesn't harm subscriptions in physics.

Anyway, as I said on the list, this is a pretty smart move by ACS. It solves the problem of getting the science out there sooner, but still with peer review, and on the hosted platform. This version disappears and the doi points you to the official version when available so they keep the traffic in house. I'm sure the embargoes go from official publication, too, so this is more time the publisher has to disseminate the content and get attention before government funders and institutional repositories can share it.

I think it will be accepted by chemists because it is from ACS and it is after peer review. We'll see, though, if there are any typos and whatnot that offend people.


Edit to add: Thurston Miller points to a few viewpoint papers in Journal of Physical Chemistry Letters on OA (the papers themselves are not OA).

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Another dissertation on science blogs

Any readers interested in my work (and you'd probably have to be following me for a while to even know what that is), will probably be interested in that of Paige Brown Jarreau. She's a PhD Candidate at LSU and is defending any day now. She did a massive set of interviews and a survey and has shared some of her results on FigShare, on her blog, and in her Twitter stream. So far we've mostly had a glimpse of her findings - can't wait to see the rest of her dissertation (good grief the rate I'm going I guess I'll get a chance to cite it in mine :) )

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Post I wish I had time to write: Scientific meetings and motherhood

Feb 24 2015 Published by under Conferences, scholarly communication

I was reading Potnia's new post on meetings - why to go to them - and nodding my head vigorously (ouch) and connecting that to the part of the dissertation I'm writing now on tweeting meetings and the research over the years on how scientific meetings work and contribute...

and I got very sad. I'm a real extrovert and a magpie of all sorts of different kinds of research, but I can't justify spending my limited time reading articles that aren't pretty directly relevant to my job or my dissertation. When I went to bunches of meetings, I could soak a million little tidbits up, meet the people doing the work, browse lots of posters and talk to their authors. It's really a very efficient way to see what's up with a field.

and now... I haven't been to a conference since I was in my first trimester with my twins :(   Sure, I've listened in to some webinars and followed some tweets. It's not enough.

Would childcare at a venue help?  I don't know... I'd still have to get them there, I'd have to trust the childcare (what if I got there and checked them out and didn't like what I saw?), and I'm paying for childcare at home even when I go and money is super tight now with my income being the only one in our household for more than a year.  I thought about bringing my sister along and then we could see the sights together outside of hours. My work would pay my travel and my room and so I'd just have to pay her travel and everyone's food. But I can't really even swing that right now....


So yeah... at least there's twitter. The post I'd like to write actually cites references and what not.

And I'm only the 10 millionth person to have this issue this year so I  know I'm not a special snowflake but that doesn't mean I can't still bitch about it.

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Enough already with the computer-generated papers!

Feb 25 2014 Published by under publishing, scholarly communication

SIGH! Years ago there was the Sokal affair that poked fun at cultural studies. Then there was a series of efforts to create a computer program to create articles - SciGen from MIT students is a famous one. Phil Davis got a computer-generated paper accepted to Bentham. More recently there was the Bohannon AAAS "sting" operation that (unfairly) targeted only OA journals... There were also two groups that gamed Google Scholar to show more citations... And now:

Publishers withdraw more than 120 gibberish papers
Conference proceedings removed from subscription databases after scientist reveals that they were computer-generated.

Richard Van Noorden, Nature News, 24 February 2014

Ugh! At least we can't blame Cyril Labbé, the scientist in question. He didn't submit the articles, he just detected them. And in places near and dear to my heart like IEEE Xplore and Springer. These are conference papers this time. Not only did they supposedly go through peer review - but were they presented? WHAT was presented? Even if these were pranks - how funny was it if it wasn't revealed? Should the authors be banned? Should they be charged with fraud as some suggest? What a stinking mess.

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Heads Up new Science is a Special Issue on Scholarly Communication

Oct 03 2013 Published by under publishing, scholarly communication

The "sting" article that details a Sokal-Affair-type test of crap open access publishers to see if they really were crap open access publishers is getting all the attention. (do note that Hindawi and PlosONE quickly rejected the manuscript and Plos even questioned the ethical issues - hence they are not crap publishers but decent publishers).

Elsewhere in the issue that just went live at 2pm are articles on:

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The #agu12 and #agu2012 Twitter archive

I showed a graph of the agu10 archive here, and more recently the agu11/2011 archive here, and now for the agu12/2012 archive. See the 2011 post for the exact methods used to get the data and to clean it.

#agu12 and #agu2012 largest component, nodes sized by degree

#agu12 and #agu2012 largest component, nodes sized by degree

agu12 and 2012 other components no iso sized by degree n1294

#agu12 and #agu2012 other components, no isolates, nodes sized by degree

I will have to review methods to show this, but from appearances, the networks are becoming more like hairballs. In the first year, half the people were connected to theAGU and the other half were connected to NASA, but very few were connected to both. The other prominent nodes were pretty much all institutional accounts. In 2011, that started to decrease and now in 2012 you can't really see that division at all. There are the top three nodes - two the same plus a NASA robotic mission - but then there's a large second group with degrees (connections to others) around 40-80 (combined indegree and outdegree) of individual scientists.

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An image of the #agu2011, #agu11 Twitter archive

A loooong time ago, I  showed the agu10 archive as a graph, here's the same for the combination of agu11 and agu2011. I mentioned already about the upper/lower case issues (excel is oblivious but my graphing program cares) - this is all lower case (I first tried to correct but kept missing things so I just used Excel's =LOWER()). I also discussed how I got the data. I'm going to have to probably go back and do this for 2010 if I really want equivalent images because 1) I only kept the first @ (this has all the @) 2) I don't believe I did both 2010 and 10 so I probably missed some. For this image I did a little bit of correcting. One twitter name spelled wrong and quite a few people using the_agu or agu instead of theagu. I also took out things that were like @10am or @ the convention center.

I made this graph by taking my excel spreadsheet that was nicely username first@ second@ .... and copying that into Ucinet's dl editor and saving as nodelist1. Then I visualized and did basic analysis in NetDraw.

agu2011 and agu11 largest component, sized by degree

agu2011 and agu11 largest component, sized by degree

The largest component is 559 nodes of 740 and this time you don't see that breakdown where the people who tweeted @NASA didn't tweet @ theAGU. There were 119 isolates and other components with 2,3, and 10 nodes:

Other components, sized by degree (no isolates)

Other components, sized by degree (no isolates)

eta: oh yeah, one other little fix. I took out random punctuation at the end of user names like hi @cpikas! or hey @cpikas: or  well you get the idea

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Unexpected impacts of federal budget monkey business

Many government organizations are responding to the sequestration and various budget cuts by, among other things, cancelling support for conferences and cancelling all scientist and engineer travel to conferences.

Societies (like AIAA) are kvetching about their bottom lines, but this is really much more troubling than just the fiscal health of the societies given how important conferences are in keeping up in the field.

Scientists and engineers use conferences to meet potential collaboration partners and funders, to learn about new work, to maintain relationships formed at previous conferences, and to get feedback on their own work. Distance does still matter and in-person meetings are still important.*

Moreover, in some fields (**) conferences are archival and are relied upon for certification and distribution purposes. Other conferences are the first place new results are mentioned and many authors modify their work based on interactions at meetings ***.

We all complained bitterly during the previous administration about the funding of science and the suppression of some scientific results... but is this much better? How can government regulate well without being up on the science? Maybe this is temporary... but it doesn't look good.


* Olson, G. M., & Olson, J. S. (2000). Distance matters. Human-Computer Interaction, 15(2-3), 139-178. doi: 10.1207/S15327051HCI1523_4 ( there are definitely better citations for this now,... but time is limited)

** Drott, M. C. (1995). Reexamining the role of conference papers in scholarly communication. JASIS, 46(4), 299-305.

*** Garvey, W. D., Tomita, K., Lin, N., & Nelson, C. E. (1972). Research Studies in Patterns of Scientific Communication .2. Role of National Meeting in Scientific and Technical Communication. Information Storage and Retrieval, 8(4), 159-169. doi:10.1016/0020-0271(72)90001-0


note: it took me like weeks to write this because i kept (squirrel) getting distracted... hopefully it makes sense even if it's probably abbreviated from what I originally intended to write.

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Does bundling "screw libraries"?

Apr 11 2013 Published by under publishing, scholarly communication

I'm not an Elsevier apologist, really, but let's just be pragmatic here. There are lots of things to criticize them for, but I can't get as exercised about the bundling as some.

Here are my thoughts in brief:

  • What we pay for each download/view is actually pretty low
  • Our researchers have immediate access to lots of obscure things we never thought they'd need
  • Our researchers are accessing things we'd never subscribe to if offered separately
  • Even crap journals may have some good content from time to time (El Naschie not withstanding)
  • We don't have to take the bundle. We can always just subscribe to just those journals we want. Many libraries have cancelled their big deals.

Bad things:

  • Supporting some crap journals
  • Some jerk editors of crap journals advertising that we subscribe to their crap journal
  • Inflation in the cost of the big deals eating up the serials budget leaving less and less for smaller publishers or individual subscriptions.

This last thing is really bad, but it's not only the case in bundle situations. The big fancy science and technology journals are crazy expensive whether you purchase them in a bundle or individually. Our budgets are decreasing - we're cutting 5% here or 10% there when we're not facing 25% cuts - and as I said in an earlier post, 15% increases are not doable, even if new journals are added to the package.

So anyway, call me brainwashed or whatever, but I'm just trying to get the content our folks need for the money we have to spend (or, in most cases, the money our parent institution has to spend 'cause mpow is cut to the bone).

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