JACS comment section? Back to the future

It's been a very interesting couple of weeks in the realm of Blog Syn (the beginning of Blog Syn #003A has a roundup for anyone who hasn't been following). People across a number of blogs have noted the importance (or at the very least, usefulness) of chemists participating in social media and rapid web communication (indeed, even Phil Baran's lab has started a blog, despite hegemonic bias against blogging in the field of organic synthesis). 

How can chemists use social media to the greater benefit? Take, for instance, the first comment in Chemjobber's reply to the IBX+water conclusion. Polychem says (bold emphasis mine):

This work makes me think that every paper published on pubs.acs.org deserves its own comment section. I can imagine it being abused, but there may be some good insights by having essentially a wider peer review where you don't have to pay to print your rebuttal.
Good job Blog Syn people!

 Hmm... a comment section at JACS? Check out this 1996 editorial from the journal! For those stuck outside the paywall, an excerpt:

There is no question that digital computers have had a large impact on the publication of scientific research. JACS uses computers in the management of the journal data base and in production of the journal. Most manuscripts are now submitted in final form as floppy disks, and e-mail is often used for correspondence with authors and reviewers. Recently, especially with the wide accessibility and usage of the World Wide Web (WWW), interest has turned to electronic publishing, i.e., to the posting of manuscripts on the web rather than, or in addition to, producing a hard copy (print) journal. The advantages of electronic publishing include the faster appearance of a paper at a presumed lower cost than printing (with the attendant possibility of wider distribution) as well as the ability to provide materials, like computer programs, movies, color figures, and large amounts of experimental data, not available in the hard copy. Concerns about electronic publishing include the maintenance of the quality and integrity of the published literature, providing for the long-term archiving of papers, and assuring that financial support is available to carry out the needed peer review and maintenance of the archive. These points are discussed in a booklet available from ACS Publications: Will Science Publishing Perish?

Interesting that the ACS proposed lower cost and wider distribution--I wonder if that worked out that way? The last section of the editorial is also a fun read:

JACS Web Page -- An Experiment. The JACS web page (accessible via the ACS publications page at http://pubs.acs.org) displays instructions for authors, links to supporting information, and the table of contents for the latest issue of the journal. As an experiment we will also try out a section for selected correspondence and comments. Readers can submit, by way of a form available on the web page, scientific comments pertaining to recently published JACS papers. Authors will be asked to reply. Posting of comments will not be automatic. Comments for posting will be selected by the editors and they will not be sent out for review. There will be no appeals for comments not selected. Comments will not be published in hard copy or CD versions of the journal nor will they be archived. We hope these comments will generate interesting discussions and help amplify and clarify ideas and results published in JACS papers. They are not meant to discuss priorities or present still unpublished ideas or results. Additions and corrections will still be published in the printed version of JACS. We hope the level of discussion on the JACS page will be significantly higher than the average WWW newsgroup! This experiment will be terminated if the community feels it is not useful (or if it becomes too burdensome for the editors). At this time we cannot accept manuscripts submitted electronically for review; however, we are investigating the possibility of doing this in the future. As stated at the outset, the science publication field is evolving rapidly. The new possibilities are intriguing, but the community will best be served by an orderly evolution that involves the best features of both the print and electronic media.

It's quite revealing to see the difference between scientific publishing just 17 years ago (oh wow, 1996 was 17 years ago??) and now--after all, electronic submission is de rigueur not only for SI but for main text and for correspondence with reviewers.

More interesting, though: there was a comment section on JACS before the journal even started putting the manuscripts themselves online. Seems like unusually progressive thinking by the ACS!

But if you go to the JACS website now, there's no comment section. What happened to it? A search of editorials from the journal gives no relevant hits and a 2002 editorial discussing other web-based aspects of JACS makes no mention of it. Did it die a quick, fiery death?

Indeed, there's a lot of room for publishers to include the community in scientific discourse. Some do a little: Nature Chemistry, for instance, has a good metrics section that indexes blogs (but no comment section). The ACS journals don't have comments, nor do Taylor & Francis, the RSC journals, Elsevier, or PNAS.

Does anyone do comments?

Yes! Take a look at PLoS One (example article): they have comment section built in to a very slick web interface.

It'll be interesting to see how the face of scientific communication changes over the next few years.

Reading assignments, vol. 9

This week's stuff is pretty heavily communication-themed; a lot of that is going around with the ScienceOnline 2013 deal having gone down. Anywhere, here's some general science enjoyment:

Chemophobia

• Chemophobia has been a major topic of the social-media-dom recently due to the ScienceOnline 2013 conference. In particular, Saturday marked the chemophobia-specific portion of the conference (Session 8A), which included a contemporaneous Twitter discussion via the hashtag #chemophobia. For those who had to work this Saturday (woo, columns, woo) the session notes have been posted online, and there's a quite impressive wiki entry containing an abundance of relevant and interesting chemophobia-related links and discussions.
• Michelle at The Culture of Chemistry has a thoughtful analysis of a recent chemophobia-rife New York Times story; she points to language and how it affects perception of concepts.
• Paul at ChemBark shares his tips and proposed strategies for how to combat chemophobia. It's a good read that sums up the origins and dangers of chemophobia pretty well. The recommendations are good, too: ACS should be doing its part (come on, guys!) but graduate students and faculty need to take it upon themselves to do outreach, regardless of the perceived waste of time. (That being said, the hostile intellectual atmosphere and the rough job market make spending any time on outreach seem unappealing to those trying to get as many ninth-author Tet. Lett. papers as possible published before graduating).
• Don't miss this latest Chemjobber podcast, wherein he discusses chemophobia and chemical communication with freelance writer/chemist Rebecca Guenard. 

Science communication

• See Arr Oh pokes fun at general features of chemistry blog entries.
• I found this guest post by Frank Swain both insightful and heartening. He writes of his UK-based BenchPress Project, which seeks, among other things, to have volunteer scientists give guest lectures to journalism students. The goal is to increase science and math (maths) literacy among journalists. I think it's a pretty important effort; even if scientists themselves try to do outreach and writing, journalists have the broadest audience and the means to reach them. Changes in science communication have to come from within both sectors!
• David Rubenson argues that despite a growing need for science communication, the quality of science communication has been in decline. He points to several symptoms (e.g. cluttered slides) and causative agents (e.g. overstretched researchers). I found significant his reference to two Nobelists who published infrequently (also, it reminded me of Daniel Day-Lewis).
• Always-interesting and often-controversial, Keith Kloor discusses the relative importance of general science literacy and news literacy. He argues for the importance of the latter (while not neglecting the former); in particular, he calls for news literacy to have a place in education. It shouldn't be an unfamiliar concept to scientists, who (should) be experienced at evaluating credibility of sources.
• UIUC anthropologist and science blogger Kate Clancy has an interesting piece (relevant to anyone who uses social media, especially those who write) about the pros and cons of filling out your online presence with your real identity.

Pseudoscience and denialism

• Notorious TV doctor Dr. Oz has received some negative limelight this week. Derek Lowe, for instance, responds to a recent New Yorker profile by commenting quite frankly (and accurately) on the gross degree of subjectivity and religiosity purveyed by Oz. Lowe is probably preaching to the choir, but he makes a very strong argument by pointing out that the institution of medicine, which is responsible for Oz's success, was decided not a post-modernist, choose-your-own-facts endeavor. Orac is not pleased, not surprisingly, and criticizes Dr. Oz's recent endorsement of homeopathy. In the vein of homeopathy, this video is relevant and amusing. Lastly, see this quick list of some downright wrong beliefs peddled by the good doctor.
• Moving from medicine to sports, read a brief account of some pseudoscientific nonsense from athletes.
• Amazingly, the teaching of evolution is still threatened by denialists the world over. It's a big problem in Turkey, for instance, where the Scientific and Technical Research Council of Turkey has stopped publishing books that support the theory of evolution. Evolution has been in Turkey's crosshairs for a while. Meanwhile, here in the United States, we have Missouri House Bill 291 (titled the "Missouri Science Standard Act"). Read P.Z. Myers' breakdown of the legislation (which is in limbo). The bill is pretty frightening, pretty blantantly pro-creationism, and also terribly hypocritical. Also, Greg Laden points out a new anti-science bill in Arizona and the contrasting opposition to an anti-science bill in Montana.

Other

• This week Brandon Findlay has been running a series of posts about column chromatography. It's a good introduction or a good refresher, so give them a read.
• Derek Lowe has an interesting take on drug names (and how they've changed!).
• Neuroscientist Jessica Carilli makes the case for grad school in light of recent discussions of the unhealthy aspects of graduate study as well as the abysmal scientific job market.
• It's not infrequent to hear people complain about the uselessness of certain research programs, or at least to insist that they're too expensive (if the financial benefits aren't immediately obvious). Pete Etchells comments on NASA and the Curiosity rover, arguing against these viewpoints and giving some examples of how NASA technology has been repurposed for wide benefit.
• Maryn McKenna explores the poultry industry: specifically, how lack of transparency leads to unsustainable antibiotic use practices that contribute to widespread antibiotic resistance.

[Edit: I forgot Brandon Findlay's columns week! Urp!]

Reading assignments, vol. 6

First week of 2013 has rolled in. Some news from the week:

Public health

• Lead has received its due this week. In light of a MotherJones article by Kevin Drum correlating lead exposure with violent crime, Chemjobber has posted his questions and comments on the matter. Meanwhile, Deborah Blum writes an engaging account of the interplay between industry, science, and public health workers over the century in regards to lead exposure and toxicity. Of course, crazy-blog Age of Autism has found a way to turn this into chemophobic shrill regarding vaccines (it's like how everything turns into a Hitler argument on the Internet). 
• Maybe not exactly public health, but close: A lot of people suffer from celiac disease, an autoimmune disorder resulting in intolerance to gluten. It's an inherited disorder and has significant consequences for dietary choices. I thought this report in C&EN was interesting; researchers have engineered bacteria to display peptides randomly, then selected for peptides which bound hitherto-unknown antibodies in celiac patients. Read about it in the original article!
• This article at ScientificAmerican highlights an interesting find related to drug resistance.

Social media and science

• In what I call "Blog Syn" (after "Org Syn", aka Organic Syntheses, the journal that ensures procedures are reproducible before publication), the blogging/Twitter community has engaged in a sort of post-publication peer review of a recent JACS article. The original paper, which describes the deceptively simple use of Fe-S clusters in the synthesis of heterocycles, is currently an ASAP in JACS. See Arr Oh drew attention to the paper; subsequently, another chemist tried the procedure, giving only traces of the desired product. After a JACS editor noticed, See Arr Oh contacted the authors, and as of the time of this writing, no response was given. All this before the article was assigned a page number! This is closely reminiscent of the NaH oxidation post-publication headscratching a few years ago. It'll be interesting to watch; this kind of stuff has important implications for modern publication and peer review.
• Razib Khan, of Discover's Gene Expression, opines that the blogroll is dead and/or useless, having been functionally supplanted by readily available RSS readers. Meanwhile, at Collide-a-Scape, Keith Kloor highlights a revealing finding, published in Science, that readers of science writing are increasingly influenced as much by article comment sections as by article content. Concerning, given the number of crazies who like to troll the science. Note that the intro to the Science paper reads like it was written in 1994. 
• Not exactly science, but still interesting: Scott Huler notes the increasing use of Twitter and other social media outlets in disaster relief efforts and emergency scenarios.
• In a New York Times piece, Mary Ann Giordano notes that scientific topics have recently been popular on scientific media. This is probably due in part to excellent outreach efforts by NASA and other groups. Good news for scientists, and encouraging: outreach is worth it.

Public perception of science

• Genetically-modified crops are controversial in the public eye. William Connolley responds to what he sees as some besides-the-point or obvious questions posed last week by anti-GMO activists. The GMO dialogue never really seems to change (much like the autisim/vaccine dialogue). Meanwhile, Keith Kloor weighs in on the public misinformation about GMOs.
• Keith Kloor writes of a surprising similarity between the Republican Party and environmentalists: a lack of diversity. This obviously hurts public perception of the environmental movement, which is often seen as a mouthpiece of the well-off who don't understand the needs of the impoverished people who depend on natural resources (i.e. Appalachia, much of Africa, etc.).
• Both Keith Kloor and Derek Lowe discuss the recent turnabout of prominent environmentalist Mark Lynas, who for a long time fought GM technologies in agriculture but now is in favor of them.
• This excellent Q&A between Keith Kloor (a lot of him this week) and Daniel Sarewitz touches on a key issue in the science/politics/culture intersection. Sarewitz urges that while scientists should participate in political processes, transparency on clearly political issues is vital. 
• A Guardian column by Dean Burnett discusses the negative reaction by many to a childrens' TV show that portrayed vaccines as the safe and necessary public health measures they are. It's a really entertaining (and frustrating!) read.
• See this guide (as described by Justin Gillis) to the current state of climate change science. Useful for scientists to have; inevitably you'll have the climate change talk with a non-scientist friend.

Academia

• A recent commentary on Forbes describing being a professor as the least stressful job has drawn criticism. The article is pretty myopic, honestly. But it's refreshing that the author, upon receiving numerous contrarian comments, posted an addendum. However, there's still been a sustained social media response, including this detailed "real look" as well as this excellent analysis. Additionally, a list adapted by HuffingtonPost from CareerCast describes what they say are the least stressful jobs. This illustrates a cultural stereotype of professors that probably stems from the humanities.
• Interestingly, Bengu Sezen (who will be described in research ethics courses for decades as a shining example of what not to do) has secured a university position. What.
• Over at ScientificAmerican, Hada Shema discusses the numerous problems with using citation analysis and related metrics in evaluating influence of researchers. Of course, this doesn't stop meaningless lists such as this from being published. Citation analysis will probably remain quite popular, because it's easy.
• This still counts as academia (just not university): last week I mentioned Indiana Senator Dennis Kruse's push to allow creationism in Indiana schools. Now he's pushing to make recitation of the Lord's Prayer a part of the school day.

Other

• Everyone stay tuned; this week Chemjobber and I will be having a dialogue exploring whether or not graduate school in chemistry is bad for your mental health. It starts tomorrow (Monday) over at Chemjobber. 
• Derek Lowe discusses a recent paper on the nature of high-throughput screening collections. Not surprisingly, HTS collections are often narrow and biased; is this just because of synthetic tractability or is it also peacocking by the suppliers? Not surprising; HTS can be controversial, as some people think it hasn't nearly lived up to its promise, but others say it's vital. 
• This is cool for the art-inclined: some surrealist illustrations from 1970s textbooks by artist Karl Nicholason. Biochemistry figures still look like that.
• See Arr Oh points out some delightful chemophobia you can buy at Target
• Photographer and scientist Alex Wild points out why photographers shouldn't pretend to be biologists (click through!).  It's facepalm-worthy here, but also concerning: so much research is denounced publicly as "obvious" because people are willing to assume they know things based on "common sense". This kind of illustrates the concept.

Reading assignments, vol. 1

A very short list of some new and old links of note this week:

This week:

• Bonny Swoger at Scientific American discusses information skills we should incorporate into science education.
• Chemjobber notes the attrition rate in PhD programs. The comments below are discouraging, including a comparison of PhD vs MD lifetime earnings.
• Read these comments by scicurious about the relevance of getting a PhD to science writers.
• I found Derek Lowe's commentary on a PLoS One article about human factors in selection of compounds for biological screening interesting.
• On CENtral Science and NorthJersey (source), an account of a 29-year-old chemist poisoning a coworker.

Old links rediscovered:

• Webcomic artist/blogger Drew points out the idiocy of caffeinated soap at The Worst Things for Sale.