Wednesday, July 24, 2013

Sixteen Columns

Vittorio over at Labsolutely has a very clever and amusing post up re-imagining the X-Men as chemists.

So what other media genres share cross-over with our field?

The modern art form deemed the "chick flick" shares key features with tactics used to recruit students into graduate school in chemistry. Namely: (1) hopelessly romantic view of the content; (2) focus on idolizing the celebrities of the subfield (e.g. Tom Hanks, Phil Baran); and (3) careful shielding of the subject from reality of life/lab. And of course, both chick flicks and science place an emphasis on diaries.

In a salute to both, here are some chick flicks in the context of science:*

  1. How to Lose a Grant in 10 Days
  2. Unemployed Going on 30
  3. The Proposal
  4. Never Been Published
  5. 27 Postdocs
  6. What's Reproducibility Got to Do with It
  7. The Devil Wears PPE
  8. Sixteen Columns
  9. My Best Friend's Defense
  10. What PIs Want
  11. Save the Last Authorship
  12. Bridget Jones's Lab Notebook
  13. When Harry Met Sally at an ACS Regional Meeting
  14. The Lab Notebook
  15. Out of Academia
  16. Sleepless in Grant Season
  17. The English Postdoc
  18. Gloves Actually
  19. How Stella Got Her Glassware Back
  20. 10 Things I Hate About U...niversities
  21. Pride & PNAS
  22. Crazy, Stupid, Reaction Mechanisms
  23. Peggy Sue Got Funded
  24. P.S. I Love the Combiflash
  25. Flashcolumn

* Note: these are in no particular order; the author claims no expertship on relative merits of chick flicks.

Thursday, July 11, 2013

Why Steve Strauss should stop hiring English majors and hire some scientists instead

Recently, a few people I know shared this column on Facebook. Written by Steve Strauss, a lawyer/author and self-described "small business expert", the short piece from the Huffington Post makes the case that English majors are pretty much the bee's knees. Strauss prefers to hire English majors for a variety of roles, as he explains:
I love English majors. I love how smart they are. I love their intellectual curiosity. And I love their bold choice for a major. Most of all, I love to hire them. 
A recent article by the great David Brooks in the New York Times about the changing nature of the Humanities in higher education just reinforced why, when given my druthers, English majors are my employee of choice. 
And the reason is not that I am a writer; I more consider myself an entrepreneur than anything else. I run a small business and the people I hire do a variety of tasks -- SEO, project management, social media, and so forth. 
For my money (literally and figuratively), for my needs, and I suggest the needs of most small businesses, English majors are easily the top choice when it comes to getting the type of teammate who can make us all better, as they say in basketball.
Strauss goes on specify some key traits apparently endemic to the English major population. These are: (1) English majors are smart and creative independent thinkers, more so than business majors; (2) English majors are bolder risk-takers than others; (3) English majors are always better writers; and (4) English majors are easy to work with.

I suspect many scientists will disagree. I take issue with the broadness of Strauss's assertions--though he never claims to have broadly surveyed skillsets of humanities scholars, his descriptors read like mere feel-good fluff. Yes, there are English majors who have those characteristics, and many English majors are successful. But "rigor" and "difficult assignments" are not essential traits of the undergraduate English experience.  While English may allow deep thinking, it doesn't absolutely require it, and it's certainly easier to skate through an English degree than, say, one in chemical physics or organic chemistry.

You see more chemists who also know literature than you see literary analysts who know molecular orbital theory. But isn't that just because science is more specialized? Well, yes and no. Individual fields of science certainly have their own jargon, methodology, and bodies of knowledge. But the scientific process is fairly universal, and you see people switch fields in their BS/PhD and PhD/postdoc transitions.

That all sounds harsh, of course, and borders on the increasingly-prevalent-but-misguided attitude of "cut the humanities, boost only employable fields". So to clarify: I like the humanities. I really do. I've always enjoyed literature and music (both production and consumption), and I think their study is vital for making a person more culturally aware and well-rounded. I have opinions on writers and composers. I was one of those people who didn't whine about general-education requirements interfering with "real" coursework. But assigning top general employability status to English majors overlooks a key group of students who, when successful, possess all the abovementioned skills and more: science majors.

The case for hiring science majors

As previously mentioned, Strauss touted the creativity of English majors and their ability to think analytically. Creativity is essential to good science as well; skilled researchers tend to be creative people who see alternate ways to solve problems. Moreover, scientists find solutions that work, based on reality and reproducibility. This clarification is important, because "analysis" means very different things in scientific and non-scientific circles. However, scientists are quite good at two things: (1) finding information; and (2) evaluating information.

Strauss also claims English majors are superior risk-takers. But scientists are too. They have to be. Good research is always at the edge of knowledge--which means it might not work. Bench time might be wasted. A six-year PhD might produce no results and lead to no job. Ideas might get defunded and banished to obscurity. Going to grad school is a tremendous risk. So is working for an untenured professor, or starting a brand-new project. So the advantage here again goes to scientists. Additionally, scientific risk-taking is grounded in reality--helpful for businesses.

What other employable traits do scientists tend to have? Work ethic: long hours are the norm and determination over long periods of time (ca. 5 years) is required. Versatility: the scientific method is employable between variant research areas but also to management and business decisions. Technical skills: this probably goes without saying, but intimate knowledge of scientific theory and technique isn't easily gleaned from Google. Even in non-bench roles, this can be quite important. Teamwork: whereas writing English papers is a solitary venture, lab research is done in groups, and collaboration between students and labs on the experiment or project scale is commonplace. Objectivity: whereas the humanities stress the voice and identity of the individual (subjectivity), science emphasizes minimization of bias. This is useful in risk assessment, evaluation, project design, etc.

All in all, I think science majors sound pretty employable.

What we can learn from our English-wrangling colleagues

The claim about English majors being superior writers is also worth examining. Do English majors write? Yes. Do they write a lot? Most of them. Do they write well? The good ones write academic papers well, but an increased vocabulary and flowery verbiage doesn't mean good communication. Of course, many English majors are good communicators, but the degree doesn't guarantee that. And not having an English degree doesn't mean you can't write just as well as someone who has one.

It's worth noting that significant differences exist between scientific/technical and academic (non-scientific) writing. In another life, I worked closely with undergraduate writing tutors. Most were English majors, and as a lot they were very intelligent. But all of them were horrid at actually helping science students improve their communication skills. The result was a continuous stream of frustrated chemistry students with half-mangled lab reports. The writing process is fundamentally different across the humanities/science divide, which makes me skeptical that the garden-variety English major would be good at writing in a technical or scientific context (where content is highly specific, highly technical, and verbal economy is vital). Some are good at it, but it's not because of Chaucer.

That being said, scientists themselves are very commonly awful writers. Those who deny this or think it's not important are simply either ignorant or delusional. Then again, scientists are perhaps more likely to be blunt and direct, which has its appeal. Regardless, it's probably good for budding scientists to take all the writing experience they can get and to pay attention not only to the facts of what they write but the organization and presentation. Clear communication makes ideas easier to sell, cuts down on wasted time, and improves work efficiency. The ability to write well (more than just JACS communications) can be a huge selling-point when building an employment skillset, as it extends to grants, business proposals, technical reports, and intellectual property claims.

A final anecdote.

A friend of mine switched from pre-med to business during undergrad and found himself in a business database systems class. The class entailed a team-based project wherein each group of students needed to create a database system for a local business. Several of the born-and-bred business majors insisted that the class was probably the most difficult in the university. Having taken two years of pre-med coursework, my friend pointed out the difficulty and rigor in the hard sciences, especially in independent research. Oh, no way, the business majors insisted, scientific research is just following recipes.

The piece is short, so it's worth reading.  Do also peruse the comment section, which is rife with people praising Strauss's words and/or correcting each others' grammar/diction. 

Tuesday, June 25, 2013

Stop using that word: Accordance

Consider "accordance". It's a sleek, shiny word. But it's terribly misused in scientific manuscripts.

To pick on just one example, take the following text from a recent publication by Neil Kelleher's group at Northwestern (bold emphasis mine):
Our observations were in accordance with a previous study on nostocyclopeptide, where certain amino acids in the peptide sequence were found essential for the spontaneous macrocyclization of the peptidyl aldehyde intermediate into a cyclic imine.
And another example from a total synthesis of daptomycin by Xuechen Li:
The spectrum was in full accordance with those in the literature.
Not quite right.

"Accord" implies agreement. It's what writers usually mean when they use "accordance". For instance:
His dismal personal life was in accord with his excellent progress in total synthesis.
"Accordance", in contrast, implied obedience. It refers to compliance with a rule.
My one day of vacation per year is in accordance with group policy.
Examples of the correct use of "accordance" are actually hard to find. Consider this paper by Robert West at Wisconsin. An excerpt (bold emphasis mine):
In accordance with Bent’s rule, the increased R–O bond polarities of permethylated species lead to increased oxygen hybrid s-character and R–O–R bending angles in both ethers and siloxanes.
That one is arguably correct.

The difficulty is probably that "in accord with" doesn't flow quite smoothly. Perhaps a better option would be simply to say "in agreement with". Either way, reviewers probably won't catch it.

This has been a public service announcement.

Thursday, June 20, 2013

Carbenes: turns out, nature has them, too

Enzymes are like nature's little gloveboxes. It's really quite interesting what kind of chemistries are possible in aqueous, biological conditions just by manipulation of the local electronic and steric environment by the structure of enzymatic active sites.

Take carbenes. Everybody likes a carbene--it's a lone pair on carbon, but it's formally neutral, and it does interesting reactions like alkene insertion (cyclopropanation), C-H insertion, rearrangements, and the like.

One of the more interesting aspects of carbenes is their variable reactivity. They can exist in a singlet (depicted as lone-pair) or triplet (depicted as diradical) form. Depending on their electronic environment, they can react as nucleophiles (aided by a high-lying HOMO) or electrophiles (encouraged by lowering the LUMO). Their reactions can be stereospecific through concerted pathways (singlet carbenes) or non-stereospecific through stepwise mechanisms (triplet carbenes). All of this is tuned, not surprisingly, through the electronic/steric environment around the carbon in question.

Carbenes are typically highly reactive and short-lived, though examples of persistent carbenes are now well-known. N-heterocyclic carbenes (NHCs) make a prime example. The electron-rich di-adamantyl NHC shown above, for instance, was described in 1991 and can be crystallized (it melts, by the way, at 240 degrees Celsius).

Note the electronic nature of the carbene: the carbon is flanked by two nitrogens, each bearing lone pairs capable of donating electron density into the carbene's p orbital. This acts to stabilize the singlet state and imbues NHCs with admirable properties as metal ligands (electron rich sigma donors which bond quite strongly to metal centers) The most famous of these is probably Grubbs' second-generation catalyst, which bears an NHC in lieu of one of the phosphine ligands of the first-generation counterpart. Besides olefin metathesis, though, persistent carbenes (as NHCs) are quite useful ligands for tricky C-C cross-couplings. Specifically, the so-called Pd-PEPPSI complexes are useful for coupling of tetrahedral carbon centers to each other.

It turns out that nature utilizes carbenes as well. Take a look at vitamin B1--also known as thiamin. It's an essential coenzyme which, as it turns out, we can't make and must obtain in our diet. There's several forms consisting of various decorations, usually of the hydroxyl moiety. One of these is thiamin diphosphate (ThDP), which, if you didn't guess, is thiamin with diphosphate attached (it also goes by the name thiamin pyrophosphate, or TPP, which is definitely not confusing at all). ThDP is a coenzyme for pyruvate decarboxylate and pyruvate oxidase, among other enzymes.

If you look at thiamine, there's a place--right between that sulfur and its neighborly nitrogen--that seems like a nice candidate for a carbene. There's been a debate in the literature; that carbon must be deprotonated for catalytic activity, and it hasn't been clear whether the associated enzymatic reaction proceeds via a carbanion or the short-lived carbene. A recent report in Nature Chemical Biology provides evidence for the latter. The authors examined thiamin diphosphate with the enzyme pyruvate oxidase (from bacterial origins). Phosphate was employed as a mimic of the substrate (pyruvate) that would bind similarly but not form a covalent adduct--this was to see if substrate binding might correspond with the formation of a carbene.

Via circular dichroism (CD), and X-ray diffraction, the authors give evidence that although the coenzyme is C-protonated in its resting state, binding of phosphate results in accumulation of either the carbanion/carbene form. This is narrowed down to the carbene chiefly through analysis of the XRD structure. Not only was the electron density consistent, but the bond lengths and angles were similar to synthetic thiazolium carbenes previously reported. The authors mention similar results upon analysis of the ThDP/cyclohexane-1,2-dione hydrolase complex.

Essentially, under physiologically relevant equilibrium conditions, the thiamine/enzyme complex can accumulate a carbene. In water. That's quite cool.

Wednesday, May 22, 2013

Academic salaries: some numbers and graphs

The topic of academic salaries came up recently and I figured I'd look a little further. Where does chemistry stand? After all, jobs are scarce--how do academic positions pay compared to other disciplines?

Lots of resources exist for salary issues that are much more data-thorough, so take the following numbers with a grain of salt. For more in-depth info, a few resources include HigherEdJobs, The Chronicle of Higher Education, or a web search.

I took a (somewhat) random single institution (Bowling Green State University, Ohio) of medium size (ca. 15,000 undergraduates) that also offers graduate degrees (in chemistry, an M.S. in chemistry and a Ph.D in photochemical sciences are available). Ohio was chosen as an example state simply because of the ready availability of data.

Salary information (for a few years back) is available for all Ohio's higher ed institutions through the Buckeye Institute. I grabbed the 2010 info for the university and present below the averages for four standard academic ranks (lecturer/instructor, assistant professor, associate professor, and full professor) across 14 broad but somewhat arbitrarily chosen disciplines. Standard deviations aren't included and sample sizes were small in some cases, so caveat emptor and all that. (NB: click any chart for a larger view)

First, a graph of the disciplines ranked by associate professor salaries. It's quite interesting to me that chemistry is near the top--ahead of biology but also physics and geology. Moreover, associate professor salaries in chemistry rank a little short of computer science (by about $7,000) but above economics (by about $8,000). As would probably be expected, two business disciplines (management and accounting/M&IS) are way ahead. I don't know if that's endemic to the particular school or a general trend. Regardless (and probably again to no one's surprise), it looks like chemistry and the other sciences are pretty far ahead of the humanities by as much as business-related fields are ahead of science.

Ranking by full professor puts chemistry more in the middle of the pack:

Quite interestingly, though, are the salaries for assistant professor positions (typically the first 3-6 years of an academic appointment). Here the distribution is almost bimodal, with chemistry falling in a group ranging from  about $50,000 to $66,000. Then there's a $24,000 jump to the business disciplines and computer science, which compensate assistant professors on average from $89,000 up to a whopping $119,000! (For the math-challenged organic chemists, that's about double the chemistry salary for the first five years).

Why the giant divide? Market demand certainly plays a large role. Folks with graduate-level business and computer science skills are very, very employable, and generally aren't in markets plagued by the oversupply that science (and especially the humanities) face.

Lastly, check out the ranked salaries for instructors/lecturers. These are the teaching-only positions; for some disciplines this doesn't require a PhD. (For chemistry, I've seen very few lecturers without PhDs; many have postdoc or industrial experience).

Management here has the highest salary by far, but that's incidentally an n = 1 type scenario (there's only one lecturer in the management department, and they appear have an 'executive' position). Here the business gap disappears; average salaries range from $38,000 to $52,000. Interestingly, computer science ranks in at $61,000, which is probably indicative of its very high employability--you have to pay someone a lot to draw them away from an attractive industry job.

For fans of seeing-it-all, here's a ranked-by-associate graph including all four ranks.

Lastly, here's the average salaries for most of the public university chemistry departments in that particular state (Ohio) [note--data was not easily harvestable for Ohio University, Shawnee State, Central State, or Youngstown State].

This itself is somewhat interesting, as there's a wide distribution (assistant ranges from an average of $55,000 to $78,000; associate from $70,000 to $97,000; full professor from $101,000 to $131,000). Moreover, salary averages don't appear to correlate to institutional prestige (cf. Ohio State and University of Akron, for instance) nor to cost-of-living.

The ordering of schools even changes by faculty rank--Cleveland State tops out the assistant professor category, but Bowling Green wins for associate professor and University of Toledo for full professor. The only consistent element, it seems, is that Kent State pays the lowest for chemistry professors, across the board, of all the state schools shown.

Again, take all this data with a grain of salt; I just think it's interesting stuff.

Saturday, April 27, 2013

The Office and the lab

Just as the #ChemMovieCarnival drew to a close, chemistry made another appearance on national television!

In the most recent episode of The Office (a mockumentary about a paper company; it's usually hit-or-miss but still funnier than the British version*), the branch manager, Andy Bernard, was cast in a chemical safety video ("HRPDC Chemical Handling Protocol") in an attempt to break into an acting career.

The on-screen lab was pretty clearly a molecular biology or chemical biology space -- you can see microscopes, centrifuges, Pipetmans,** a cold-room, 96-well plates, and plenty of buffers; additionally, the glassware is largely Erlenmeyers, graduated cylinders, and volumetric flasks.

Unlike most featured lab spaces on TV (we're looking at you, NCIS and CSI...), it looks like the producers used an actual lab. If not an actual lab, it's a very good replica (as evidenced by the abundant bench clutter).

For the sake of the chemical community, I present a graphical abstract below.

Drying rack contains an appropriate mix of glassware.

What lab would be complete without an egregious safety violation?
(note the presence of snacks in the lower left corner)

Benchtop clutter looks about right.

Note the scientist in the far background using proper PPE.
Demonstration of eyewash station use, plus screaming.
Note that undergraduates usually have the same aversion to the eyewash station that Andy Bernard does.

And my favorite exchange of dialogue:

Director 1: Okay, stop. Why are you smiling?
Andy: I just made a character choice to be a scientist who really likes what he does and enjoys his job.
Director 2: Okay, well, maybe no smiling on this one.

* Note: some people get really upset when you say this to them. Try it!
** I love me some Pipetmans.

Wednesday, April 24, 2013

Chemical Fun from 1921

What's more fun than historical documents? Historical chemistry documents! From one such document: the following tongue-in-cheek paragraph appeared in the April edition of the briefly-published and mostly-otherwise-serious quarterly departmental (U of I) magazine The Illinois Chemist 1921, 5(3), 12.

The text (written out):

CHEMICAL FUN. Procedure (to be followed with extreme carelessness): Select several choice cut medium sized hydrogen ions from a bottle and scour until thoroughly clean. Wipe and dry carefully. Avoid handling. Lay aside. Now soak a few large chunks of metallic sodium in a beaker of distilled water and allow to stand quietly. In the meantime be collecting a pailful of cathode rays. Filter these, using suction. Beat them to a froth with two and three-quarters pounds of green radium (the red variety is highly unsuitable for this experiment). Now stir in the hydrogen ions, one at a time. Drain the sodium and put it in above mixture. Grind up with T. N. T. and put in a mortar and add all at once. Thus the mixture will become catalyzed. -- Voodoo, M. I. T.

Chemical fun, indeed. Sounds like a job for Blog Syn!