Thursday, March 28, 2013

Stipends: A waste of funding?

A little while ago the subject of teaching assignments came up among some colleagues (as it is wont to do).  Specifically, we were discussing which PIs had habits of sticking their students on repeated teaching assignments and which PIs didn't have their students teach unless they really wanted to.

I was a little surprised that one of the very well-funded synthesis groups here had an abundance of TAs. One of the students (him/herself a TA) explained it thus: "We don't like to waste money on paying people." The point was that they viewed grant money as primarily for supplies and fancy instrumentation. For instance, they'd shelled out quite a bit of cash recently for some fancy chromatography and microscopy equipment.

It was an interesting perspective, and I'm not sure what to think of the philosophy.

I've seen PIs before who tended to put students on TA quite frequently -- for their entire PhD, in many cases. But those have typically been groups with little-to-no funding, where available grant money wouldn't even cover a meager grad student stipend.

I've also seen well-funded PIs who limit their students to two semesters of teaching (or whatever the departmental requirement happened to be), regardless of external fellowships available to the individuals in their lab. In those cases, a large portion of the available grant money is devoted to stipend/tuition expenses.

So a lab that has plenty of cash that it needs to burn and decides to burn it by buying valuable (but not essential) upgrades--that's different.

It might be a subdiscipline thing. I suspect that "hard" synthesis groups -- methodology and total synthesis -- tend to rely more on a TA culture (perhaps the funding situation is less predictable here?). In contrast, most biologically-oriented organic groups seem to find the funding (from training grants and other sources) to keep their lab RA-based. Additionally, some grants have specifications.

Even so--can personnel costs be considered a "waste"? The word I would suggest is "investment." But it might be because I think a well-trained, happy chemist with decent instrumentation/supplies is more valuable than a slightly nicer MPLC.

Monday, March 18, 2013

Singers and musicians, apocryphal quotes, and chemists

Recently, I saw the following quote get shared widely among my acquaintances on a particular social media outlet:
Singers and Musicians are some of the most driven, courageous people on the face of the earth. They deal with more day-to-day rejection in one year than most people do in a lifetime. Every day, they face the financial challenge of living a freelance lifestyle, the disrespect of people who think they should get real jobs, and their own fear that they’ll never work again. Every day, they have to ignore the possibility that the vision they have dedicated their lives to is a pipe dream. With every note, they stretch themselves, emotionally and physically, risking criticism and judgment. With every passing year, many of them watch as the other people their age achieve the predictable milestones of normal life - the car, the family, the house, the nest egg. Why? Because musicians and singers are willing to give their entire lives to a moment - to that melody, that lyric, that chord, or that interpretation that will stir the audience’s soul. Singers and Musicians are beings who have tasted life’s nectar in that crystal moment when they poured out their creative spirit and touched another’s heart. In that instant, they were as close to magic, God, and perfection as anyone could ever be. And in their own hearts, they know that to dedicate oneself to that moment is worth a thousand lifetimes.
-David Ackert, LA Times
I kind of hate to reproduce it--not because it's pandering and indulgent*, necessarily, but because I can't find the original source, and as a scientist, that bothers me. It's attributed to David Ackert of the LA Times. No one seems to mention that the LA Times website doesn't even mention a David Ackert, much less this quote. So the authenticity/origin is dubious (that doesn't seem to matter to those who push it along). 

A quick search of the internet reveals several modifications of the quote, wherein people have substituted 'actors' and 'artists' for 'singers and musicians'. So, I figured: why not 'chemists'? (We do use instruments). Let's try.
[Chemists] are some of the most driven, courageous people on the face of the earth. They deal with more day-to-day rejection in one [group meeting] than most people do in a lifetime. Every day, they face the financial challenge of living a [STEM] lifestyle, the disrespect of people who think they should get real jobs, and their own fear that they’ll never work again. Every day, they have to ignore the possibility that the vision they have dedicated their lives to is a pipe dream. With every [column], they stretch themselves, emotionally and physically, risking criticism and judgment. With every passing year, many of them watch as the other people their age achieve the predictable milestones of normal life - the car, the family, the house, the nest egg. Why? Because [chemists] are willing to give their entire lives to a [synthesis] - to that [ring], that [stereocenter], that [functional group], or that [weird perfluorinated tail] that will [get them into JACS, or Org. Lett., or heck, Tet. Lett., it's gonna get ignored anyway]. [Chemists] are beings who have tasted life’s nectar in that crystal moment when they poured out their [organic layer by mistake] and [broke] another’s [favorite sep. funnel]. In that instant, they were as close to [unemployment] as anyone could ever be. And in their own hearts, they know that to dedicate oneself to that moment is worth a thousand lifetimes [...PSYCH! Hahahahahahaahahaah. Heh.].
-David Ackert, LA Times
Seems to fit.

Update: 11:05 PM. Re: source of original, for those interested (thanks to Chemjobber for the legwork). According to David Ackert:

* Caveat: I've done a lot of music stuff myself; I'm not hating on musicians here. Just saying.

Monday, March 4, 2013

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.

Sunday, February 24, 2013

Reading assignments, vol. 11

Communication of science


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


Research highlights

Thursday, February 14, 2013

A rose by any other IUPAC name...

Today is Valentine's Day, and what's more quintessentially appropriate than roses? If you're enjoying the scent of flowers today, you have chemicals (*gasp*) to thank!

Here's a few of those chemicals found naturally in the scent of various rose cultivars:


Enjoy your terpenes, everyone!

References (further reading for the brave)
  1. Flament, I., Debonneville, C., and Furrer, A. (1993). Volatile constituents of roses: Characterization of cultivars based on the headspace analysis of living flower emissions. In Bioactive Volatile Compounds from Plants, R. Teranishi, R.G. Buttery, and H. Sugisawa, eds (Washington, DC: American Chemical Society), pp. 269–281. DOI: 10.1021/bk-1993-0525.ch019
  2. Charles S. Sell. (2003). A fragrant introduction to terpenoid chemistry. Cambridge: RSC, Royal Society of Chemistry. pp. 256–257. ISBN 978-0-85404-681-2.

Tuesday, February 12, 2013

Stop using that word: Facile

Certain words tend to catch on in the scientific literature, such as "novel", which increased exponentially in usage starting in the 1980s. One of those catchy words is one that I previously* used like candy: facile.

Chemists like to describe reactions as "facile." By that, they usually mean easily-performed, smooth, or simple. You know, not much fuss involved. And indeed, that's one of the definitions (from the OED):
adj. (1) a. That can be achieved with little effort; straightforward, easy. In later used freq. in disparaging sense: contemptibly easy. b. Of instructions, a device, etc.: easy to understand or make use of; simple. c. Of a course of action, a method, etc.: presenting few difficulties.
That is the original, historical meaning. Another (more modern) definition carries a different implication (from the Oxford Pocket Dictionary):
adj. (1) ignoring the true complexities of an issue; superficial; or (2) (of a person) having a superficial or simplistic knowledge or approach
And if you type "facile" into Google, you get this immediately:
adj. (esp. of a theory or argument) Appearing neat and comprehensive only by ignoring the true complexities of an issue; superficial
Essentially, "facile" in modern usage (last century or so) has a negative connotation. And take a look at the synonyms for facile (Oxford again):
simplistic, superficial, oversimple, oversimplified, schematic, black and white; shallow, pat, glib, slick, jejune, naive
It's interesting to note that wiktionary has a chemistry-specific entry for "facile":
(chemistry) Of a reaction or other process, taking place readily.
Of course, language is defined by usage, so maybe I'm being picky here. But why not describe procedures as "straightforward", "robust", "easily performed", or any number of other, less ambiguous descriptors? (My intuition says those terms sound too common/"blue-collar" to many academics)

When did "facile" catch on? Well, from a crude PubMed search, it looks like the late 1990s was the tipping point (incidentally, PubMed makes it way easier than SciFinder to get data on this kind of thing. Sorry, CAS). Additionally, most of these references are (not surprisingly) from synthetic organic chemistry papers. See also this description of the two meanings of the word and their historical context.

The shrouded meaning of facile adds overlooked complication when authors start to invent words (after all, organic chemists are wont to derivatize things). There's a handful of examples from the literature that use "nonfacile" (which isn't even a word; go ahead, check the OED or Merriam-Webster).

Take this example from an otherwise-good trifluoroborate-preparation paper (Lennox, A.J.J., Lloyd-Jones, G.C. Angew. Chem. Int. Ed. 2012, 51(37), 9385-9388. doi: 10.1002/anie.201203930):
Replacing MeOH with diethyl ether led to co-precipitation of 2a with other potassium salts (KF/RCO2K etc.), thus making isolation of pure 2a nonfacile. Switching to MeCN kept trifluoroborate 2a in solution, but an excess of carboxylic acid (e.g. acetic or ortho-iodobenzoic acid) was still required (Scheme 2).
So if "facile" means "contemptibly easy" or "appearing neat and comprehensive only by ignoring the true complexities of an issue", what does "nonfacile" mean? Was isolation of 2a not contemptibly easy (just acceptably easy?). Did isolation merely appear difficult while really, under the surface, it was simple?

Stop using that word.

* i.e. before a reviewer pointed out the proper definition.

Sunday, February 10, 2013

Reading assignments, vol. 10

Here's the link roundup for the week:

Science communication

Denialism, chemophobia, and fraud

Chemical education & academia

Public policy

Other