Reading assignments, vol. 11

Communication of science

• Fans of ChemDraw and Pierre Morieux (who isn't??) should note that he has a second video.
• Science writing guru Khalil Cassimally provides a roundup of some useful tips for science writers.
• How accessible is your science? At Duke University, a genetics professor has proposed asking grad students to prepare a short video aimed at non-specialists to accompany their dissertations. This is a good idea, I would think; it makes science more accessible but also makes scientists work on (oft-neglected) soft skills.
• This satirical piece at The Pessimist (affiliated with Despair, Inc) about 'How to Work Like a Writer' was an enjoyable, quick read. The article gives a link to a Computerworld blog post about PowerPoint describing how to harness tactics used in writing to make presentations more effective. Though it's written for a technology/computer audience, it's worth taking to heart if you're a scientist, too.

Peer review and publication

• Neuroskeptic writes about the perhaps-sensical, perhaps-counterintuitive situation of stats quality in journals. It seems that high-impact journals (e.g. Science and especially Nature) are more likely than many low-impact journals to have insufficient statistical analysis. This may not be surprising, given the incentive for those journals to publish hyped-up work. Is there a similar trend in chemistry? I suspect that many medium-tier journals provide more solid experimental characterization and writeup than some of the flashier ones.
• Scientists unsatisfied with the status quo of journal publishing practices will find this development interesting. Biologist Michael Eisen has declared that he will publicly post each paper from his lab prior to journal submission for pre-publication, community-oriented peer review. It's a refreshing idea--hopefully others will follow suit.
• Derek Lowe points to the disappearance of the electronic-only open-access publication Journal of Advances in Developmental Research. Although he notes the relative unimportance of that particular journal, he brings up some points that open-access advocates should pay close attention to: predatory publishing and digital preservation. On a related note, Kevin Bonham writes about the premiere of a new prominent online-only journal, PeerJ.
• The story of the recent Xi Yan plagariasm endeavor (and the journal's lackluster, non-punitive response) has been written about with proper consternation by See Arr Oh. This kind of case is amazing, as it's the kind of thing routinely warned against in undergraduate writing courses and in orientation lectures at grad programs. Despite this, the plagiarists quite often win (for another plagiarist who 'won', check out Jonah Lehrer). For those with a spare half-hour, check out the Chemjobber/See Arr Oh podcast about plagiarism and peer review. Also, the comments section at the relevant In the Pipeline posting contains a discussion of the ethics of paper submission and whose fault plagiarism is (one commenter seems to think it lies with editors/reviewers and not  professors).
• In the last two weeks, two more entries came out at Blog Syn (a Pd-catalyzed site-selective C-H olefination and an IBX-mediated benzylic oxidation). Give them a read--and submit your comments if you have suggestions or questions! Blog Syn is supposed to be a discussion-oriented endeavor (and the further updated to Blog Syn #003 illustrate that, I think). On another note, despite broad support (including from more than one big-name prof), Blog Syn does have its critics. See particularly the comments section at In The Pipeline, which is brimming with vitriol (so much that Derek Lowe jumped in to defend Blog Syn).
• Science librarian Bonnie Swoger discusses common metrics of scientific publishing, such as h-index and impact factor, citing the importance of context in any comparisons. 

The job market

• Don't miss Chemjobber's Reddit Chemistry Jobs FAQ Part 1, which focuses on non-traditional jobs for chemists. As someone with a non-traditional career in mind, I found the post worthwhile and I second the recommendation of Dr. Lisa Balbes's non-traditional careers book. I found this post from the ancient literature (2011) relevant.
• Glen Ernst discusses the surplus of scientists in the job market. Accompanying his post is a graph clearly showing the recent (last ten years') trend wherein postdoctoral assignments have pulled ahead of jobs for new PhD graduates.

Research highlights

• Orac of Respectful Insolence makes a pointed criticism of anti-pharma, pro-alternative-medicine types by pointing out the aspects of alt-med hero Stanislaw Burzynski's work that would enrage his followers if Merck had done it.
• At Forbes, Steven Salzberg points out some upcoming legislation in Maryland that's being pushed by naturopaths seeking to equate 'alternative medicine' with evidence-based practices.
• Check out the always-interesting Alex Wild's public service announcement about the correct orientation of zombie ant fungus pictures. And the accompanying pictures, which are certainly cooler than anything you'll see in lab this week.
• I'm not well-versed in nutrition research, much of which gets criticized by scientists, but this piece by Scientific American intern Marissa Fessenden regarding the complicated mixtures of chemicals in food is certainly interesting. The proposal is that the complicated biochemistry of food may cause hormone-like signalling, which could lead to downstream effects. Chemophobes will be surprised to learn that food contains chemicals, of course.
• Those interested in chemophobia will find interesting this piece at Fire in the Mind which looks at the folks who oppose fluoridation of water. The phenomenon he describes--harnessing the "truthiness" of scientific studies while ignoring the real data/conclusions--is obviously not limited to fluoridation. The piece is an extension of Keith Kloor's post about how how many people simply dismiss facts.
• DNLee makes the case that a crucial way to improve STEM education is via of STEM-supportive parents and community members.
• I found two posts by Derek Lowe particularly interesting this/last week. The first was about the pharmaceutical industry and public perception--the point was that the industry doesn't need to care if people like it, as they'll still take medication. This suggests that those looking to change policies and practicis of the industry should do so by focusing on regulation and legislators, not on company-oriented protest. The second piece cast a skeptical light on an NIH claim that the causes of 4,500 diseases have been identified by research.
• It may be encouraging to science-minded folks that attendance at the Creation Museum is decreasing.
• At The Pump Handle there's a short piece about conflicts of interest, the EPA, and chromium.
• Keith Kloor writes about the tendency of the 'Freethinker' movement to shut down debate by dismissing religion as non-important. He maintains this as a problem of the 'New Atheist' movement--and I agree--since empirically, brute force never seems to be a particularly good method of conversion.
• Chad Orzel has a brief commentary on the academic cultural differences on who-teaches-what vs who-uses-what in physics and chemistry.
• Protein folding is important. NMR is important. So check out this writeup (and the original article) of a study in which temperature-controlled NMR spectroscopy was used to visualize protein folding (specifically, the folding of a DNA-binding protein from Enterococcus faecalis, a bacterium you will probably care a lot more about if you're hospitalized).
• Microbiology grad student K.D. Shives shares two opposite strategies for dealing with work-life balance in science grad school.

Reading assignments, vol. 7

No weekly link roundup last week due to the #GradMentalHealth discussion, but they resume below. Some pretty interesting stuff!

Perception of science

• Science News For Kids offers up several portraits of scientists, showcasing the importance of their work alongside their real-life interests. It's a pretty cool piece; things like this should be more common. Break stereotypes!
• For better or for worse, much of the public receives its knowledge of science through fiction, including crime dramas, medical dramas, and science fiction thrillers. That's given some false expectations. So it's interesting that the Washington Academy of Sciences has introduced a seal of approval to indicate they've thoroughly reviewed books and found the science within to be accurate. Neat concept!
• At Newscripts at CENtral Science, Sophia Cai summarizes a MIT-based web series about chemistry students. Give it a watch!
• Alex Stein has a very thorough link roundup on various sources regarding genetically-modified crops (sometimes referred to, usually biophobically, as GMOs). Included are aspects of media coverage, safety and economic research, and perspectives of scientists.
• Neuroscientist Zen Faulkes has a short but thought-provoking piece on social classes within science. It's worth considering; we see social stratification in chemistry between disciplines, within disciplines, geographically, and even between generations.
• I like writing about chemophobia, but it's important not to forget biophobia! (Is that a real term?)

Science writing

• Blog Syn is a go! This has already been covered all over the chemblogosphere, but it's worth repeating. Stay tuned as the workings and innards of Blog Syn get finalized. On a related note, Ash Jogalekar has written a post at Scientific American describing the GPCR Network as a model of open, collaborative research. It's really interesting, and one of the few examples where one could use the word "synergy" without rolling one's eyes.
• Via a carefully constructed example, Khalil Cassimally discusses scientific prose, general-public prose, and why the disconnect between the two is still relevant.
• Ben Morris argues for the obsolescence of academic journals. He puts in bullet-point format some key issues of the publishing industry discussed recently among scientists, especially in light of controversies including Elsevier's support of SOPA and the high fees ACS charges for journal access.
• It's been an interesting week as the #upgoer140 tag has abounded on Twitter. Inspired by this xkcd comic about describing technical concepts with the 1000 most common English words, numerous people have been accordingly describing their jobs (Stuart Cantrill describes being an editor; Derek Lowe describes medicinal chemistry; See Arr Oh describes organic synthesis and a lot of people participate in the comments; Chemjobber describes process chemistry; etc.). Even though it's funny to do so, I think it's also important. If you can't describe what you do thusly, do you really understand what it is you're doing or why? (If you want to give it a try, use the Up-Goer Five Text Editor).
• Science librarian Bonnie Swoger, inspired by #overlyhonestmethods, comments on those elusive journal articles that everyone cites but no one can get a copy of. Also, she highlights the importance of actually reading articles before citing them.

Research highlights

• From Quintus at Chemistry-Blog comes an account of a synthetic analogue of the ribosome. The authors (see publication in Science) used the technique to produce milligram quantities of a peptide! This was also covered in C&EN and by See Arr Oh.
• Derek Lowe gives a thoughtful perspective on an article summarizing the state of the field of "virtual screening". Worth a read for anyone interested in med-chem.
• I'm not usually a fan of reading about or listening to total syntheses, but B.R.S.M. gives a pleasant account of Shair's total synthesis of (+)-hyperforin.
• Bacterial toxins are interesting things! Check out this write-up on a PLoS Pathogens paper on toxins produced by C. difficile (nasty secondary infection common to those taking heavy loads of antibiotics). Warning to the it's-not-interesting-unless-I-can-column-it-and-solve-the-NMR-spectrum folks: the toxins in question (TcdA and TcdB) are enzymes and not small molecules. 
• Some intriguing research relating to rapid diagnostic of bacterial infections has been highlighted at Scientific American. The authors used secondary electrospray ionization mass spectrometry (SESI-MIS) to analyze breath samples for volatile organic compounds; they could correlate MS profiles to specific infections. It's an interesting idea; given the ability of bacteria to change their metabolism quite flexibly, I'd like to see how many false positives/negatives show up in actual trials.

Other

• Paul at ChemBark talks about how to get people to wear their gosh-danged goggles. He found that letting students customize their equipment led to a sense of ownership--kids saw them as their accessories rather than required/annoying items. Chemjobber shares his thoughts on the matter (and I personally find the merit badge comment amusing).
• Scientific American writer Janet D. Stemwedel writes about language regarding gun control and CDC research; she discusses the fact that many legislators want to prevent CDC/NIH research from influencing actual policy. This is relevant to areas outside gun control, of course, including chemical regulation and environmental policy. A choice quote: "legislators would rather be able to make policy unencumbered by pesky facts about how the relevant pieces of the world actually work."
• At The Worst Things For Sale, Drew points out some expensive bottled water that claims both to be "pure" and to be enhanced with fulvic acid. 
• Jean Flanagan at Sci-Ed (PLoS Blogs) has an important essay on the futility of educational research in scientific education. I found three of the presented points especially significant: (1) university and K-12 educators don't understand each others' environments, (2) practical research is looked down upon in educational academia, and (3) science education journals are most often behind paywalls, inaccessible to actual practitioners.
• From See Arr Oh comes a fun post prompting you to stop and listen to what your lab sounds like. 
• Forbes contributor Steven Salzberg (Fighting Pseudoscience) gives an important perspective on the fiscal cliff in the context of biomedical research. As it stands, the NIH is set to lose 10% of its already-stretched funding. Salzberg points out the tiny, tiny contribution of the NIH budget to the overall deficit and contrasts it to the high return-on-investment empirically shown for scientific research.
• American chemists, rejoice! The Royal Institute's Christmas Lectures are now available online.
• Artificial sweetener aspartame has been declared safe by the European Food Safety Administration after a review of the available safety data. However, since it's "synthetic" and a "chemical", what are the chances that anyone not already convinced of its safety actually reconsiders?

Reading assignments, vol. 2

Here go some interesting reads from this week:

Research policy:

• Check out this commentary by AAAS CEO Alan I. Leshner over at the Chronicle of Higher Education. He and Steven J. Fluharty bemoan the increasing cost in money and time of administrative burdens on research labs.
• Also at the Chronicle, Peter Suber (Harvard Open Access Project) and Darius Cuplinskas make the case for open access to research in order to benefit the public and spur innovation.
• At Scientific American, James M. Gentile writes about the persistent gender bias in the sciences. Most troubling is the double-blind study showing that male and female faculty members both rate female job applicants lower than male regardless of content.

Science and the public:

• I like cringe-worthy television science. See Arr Oh points some out over at Just Like Cooking
• Mark at Chemistry-Blog laments over the idiocy of chemophobia when tied with administration.

Science writing:

• Here's a Guardian/Observer column by Ian Tucker with Q&A with some prominent science writers about what makes good science writing. 
• A series of tips from Scientific American blogger Khalil A. Cassimally on how science writers can harness social media to gather information for writing purposes. 
• Matt Shipman encourages researchers to engage in public communication of science, and says funding agencies want them to as well.
• At ERV, some comments/advice on how not to be a horrible pop sci journalist. 

Other:

• On Chemistry Blog, a writeup of a K.C. Nicolaou essay just published online for Angewandte. It's a historical perspective on total synthesis. Although perhaps calling total synthesis the "flagship of chemistry" is an exaggeration.
• Chemjobber puts the fiscal cliff in perspective, and the prospects look poor (don't they always?) for grad students and postdocs.
• Drew, of webcomic Toothpaste for Dinner, issues an important and vital homonuclear warning. He also coauthors Married to the Sea which four years ago published this comic which is taped above my desk at all times. (For those still reading, Drew was previously a chemist and is also hilarious).
• At Just Like Cooking, See Arr Oh points out some scatologically unusual reaction conditions.