Better Than Word of Mouth

Hello, dear readers. It's been...a while. I promise the blog is not dead, just sleeping for now. My 2017 New Year's resolutions include sculpting specific time out for all the sci-writing goodness. Stay tuned.

Enough maudlin overtures. Now, on to the fun!

Strem has, as any synthetic guru would attest, the highest-quality metal precursors in the biz.* Now, you could spend a weekend cracking ampoules to find out, or just open to the Supporting Information of one of Jeff Bode's recent publications in Org. Lett. Perhaps you remember this reaction - SnAP synthesis of saturated heterocycles - best from a cheeky Derek Lowe tweet:

That's in reference to the stoichiometric incorporation of tin** in the reagent, which serves as a linchpin for the eventual transmetalation to a copper species and ring closure, neatly without disturbance of the ipso heteroatomic group.

Well, much to my surprise, Prof. Bode has climbed on the recent trend of showing one's work through tactful inclusion of smartphone pics to buoy up procedure adoption. Especially with fussy transition metals, valency, contaminants, poor environment, and a whole host of other factors lead to catalyst poisoning and color changes. In the SnAP case, the litmus test seems to be formation of a correctly ligated Cu(II) ion in lutidine relative to the (probable) hexaaquo cuprate species formed as a blue heterogeneous train wreck.

The kicker? The fairly indiscreet preference for the Strem copper(II) precursor over all other suppliers. Look at the change! Night and day, and key to making these reactions work.

You couldn't buy better advertising than this....right, Strem?
Bravo, Bode group! I look forward to seeing your colorful coupling chemistry in future reads.

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*Dear Strem: please send non-sequential $50 bills to See Arr Oh at Big City Company, USA
**SnAP. Get it? [drum kit]

Molten Salt Bath, Anyone?

While paging through Organic Reactions, Vol 1 in the chemistry library*, I encountered some unusual conditions in a review of the Elbs reaction. If you're not familiar, it's a high-temperature pyrolysis** of ortho-tolyl ketones to produce polycyclic aromatic hydrocarbons (PAHs). Products produced from the reaction find use as analytical standards for oil processing, in studies of DNA intercalation, and as molecular wires.

PAH prepared by heating at 500 ^oC
Bonus: Roman numerals in older reviews? Classy, but confusing.
Source: Organic Reactions 1, p. 154

As alluded to above, the chemistry itself wasn't what caught my attention, but rather this sentence:

"The flask is charged with 152 g of the crude ketone and heated in a nitrate-nitrite bath (care!) at 430 ± 5 ^oC."

Four hundred degrees! During all my years in lab, I can't remember heating reactions past about 300, and those were with machined blocks of aluminum on an ancient Thermo hotplate.*** 

I realize that pyrolysis technologies have advanced in 70 years' time - FVP permits higher temperatures for much shorter residence times - but the concept of a molten mixture of sodium nitrate and potassium nitrite seemed both dangerous and alluring.

This is either Hawaii's Mt. Kilauea, or a molten salt bath. Or both.
Source: thelandofshadow.com

Looking through SciFinder, it seems that molten salt baths still find regular use in case-hardening and nitriding of steelwork, along with applications in cleaning organic residues off polymer extrusion dies. For extreme data-philes, the Molten Salts Research Center thoroughly analyzed a variety of salt mixture properties in a 150-page reference. Park Thermal International has published what seems to be a very conservative safety manual for nitrate-nitrite baths, and with good reason: aluminized leather aprons, tinted visors, and gauntlets help protect workers from glowing pools of salts at temperatures just below "decomposition...with extreme explosive violence."

Though I've never worked with molten salts, that doesn't mean none of my readers have. I see Milkshake has softened a 2L round-bottom flask by heating up to 380 with a graphite flake dry bath. How about you, Chemjobber?

Or are molten salt baths potential entrants in Derek's "Things I Won't Work With"?

Update (29 Nov): A commenter points out some previous Milkshake high-T campaigns.

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*Real books! Complete with yellowing pages, musty smells, and indexes full of names like Fuson, Fieser, and Bachmann.
**Can't get enough Elbs? Curious readers are directed to Name Reactions for Carbocyclic Ring Formations, 2010, Jie Jack Li and Timothy T. Curran. Review starts on p. 324.
***Obviously not counting use of a butane torch to pull pipettes, heat sieves and salts, etc.

Chemical Space Explorers

One startling omission from my Acc. Chem. Res. post? Jean-Louis Reymond's review on the vastness of his generated database GDB-17, a.k.a. The Chemical Space Project. With over 166 billion compounds  Reymond claims to have produced the largest virtual library ever assembled. The best part? It's 99.9% new-to-science compounds. As Derek has quipped, chemical space truly is "Big. Really big."

Trudging along through chemical space, using Dr. Reymond's MQN-browser.
(I realize there's no way some of these are stable - 49? 54? - but they sure do look cool!)

Of these innumerable options, how do we decide what to make next? It's like that old Wall Street saw about how "Buy low, sell high" sounds easy, but takes a lifetime to figure out. It seems straightforward to say that you've generated billions of druglike compounds in silico, but how do you find out which ones are actually drugs?

You have to start somewhere. I still recall the first "chemical space exploration" paper that truly caught my eye - a 2009 J. Med. Chem. scribed by Will Pitt and colleagues at UCB (I still keep a dog-eared copy in my file cabinet). Using machine learning, the team constructed a library (VEHICLe) containing synthetically feasible heterocyclic compounds, most of which had never been made.

Offering a partial update to Will Pitt's "Figure 6" from his 2009 J. Med. Chem. I searched SciFinder for each ring system as a substructure of reaction products, allowing for certain substitutions (say, fused phenyl in place of endocyclic olefin) and considering tautomers. By my count: 10 down, 12 to go!

Pitt issued a challenge in the introduction:

"With this work, we aim to provide fresh stimulus to creative organic chemists by highlighting a small set of apparently simple ring systems that are predicted to be tractable but are, to the best of our knowledge, unconquered."

Heady stuff. So, who will step forward to try these tantalizing targets? Someone certainly should, as Prof. Reymond seems to suggest with his own forward-leaning graphic:

GDB-17 "nearest neighbors" - closely related to known drugs, but not yet synthesized.
(I couldn't find anything similar in SciFinder, either)
Source: J-L Reymond, 2015 Acc. Chem. Res.

Do you suppose an academic candidate could make a convincing case? I'd be tickled pink if something along these lines were sent off to the NIH R01 office:

"Dear [insert funding agency] - Listen, I really want to develop novel molecules to improve human health, but I'm not collecting plants or culturing microbes, and it's too tough to compete with industry head-on. But say, there's this guy who's looked at more compounds than any other human being alive, and he says there's some structures that look really close to existing drugs that nobody's ever tried making. Mind giving me some cash for that?"

Good luck, chemical space explorers. 

USC to Acquire Scripps?

Other perspectives: The Scientist, Science, L.A. Times.

Well, that's not something you see every day.

Courtesy of U-T San Diego* - with bonus Derek Lowe quotes! - comes talk of the University of Southern California taking over gobbling up "acquiring" the Scripps Research Institute. I'm sure we'll hear much more about the motivations as events develop, but the early suggestion involves cold hard ca$h - declining NIH funding paired with expiry of major pharma partnerships on the Scripps side, billions in fundraising** on the USC side. I've been hearing about salary squabbles and shrinking department budgets at Scripps, but didn't realize things had gotten to this point.

Clouds in parking lot, 2014

I don't see the press releases on either side that U-T San Diego alludes to,
[UPDATE 6/19 - Here's the releases!]
Perhaps someone on the inside of either institution knows more? seearroh_AT_gmail

*The guys who helped break the Nicolaou to Rice saga!
** I mean, they did just get all that money from Dr. Dre...

Elemental Roll-Call

Inspired by posts from JessTheChemist and the esteemed Dr. Lowe, I've tallied mine below.
(N.B. I came up in an organometallic lab where we made many precursors from scratch...)

Hydrogen (obvious)
Helium (carrier gas)
Lithium (Li-Hal exchange)
Carbon (Darco)
Nitrogen
Oxygen (ozonolysis)
Sodium
Magnesium
Aluminum (form'n Friedel Crafts salts)
Sulfur (mercury spills)
Chlorine (oxidant)
Argon
Potassium (N-K form'n)
Manganese (reductant)
Iron (reductant)
Nickel (Ra nickel)
Copper (forming amalgams)
Zinc (organozincs, reductant)
Bromine (distilled, even...yuck!)
Palladium (hydrogenation, salts)
Silver (foil, to make salts)
Indium (reductant)
Iodine
Cerium (cross-coupling...failed)
Samarium (to make SmI2)
Platinum (hydrogenation, catalysts)
Gold (dissolve in aqua regia)
Mercury (old pressure eqpt)

So, I count 28. Pitiful against 118, but a varied lot nonetheless.

Thin Layer Consternation

Earlier today, I was involved in a minor dust-up with some commenters over at Derek's blog. A central issue concerned my (admittedly quick'n'dirty) TLC, which meant to indicate the complete consumption of the acrylate starting material for Blog Syn #002.

Well, since I was already running another entry for #003, I decided to pause and take stock of my TLC tool-box: yes, I should use a ruler, and yes, a classic TLC would have lots more info (solvent system, stain, clearer labels, etc).

So, I took a sample from my IBX oxidation of methylnaphthalene to 2-naphthaldehyde (12 h timepoint, set up in straight DMSO with 0.1 volume of H2O). Results below:

Before anyone goes crazy, that's DMSO / H2O on the baseline, and the SM at Rf ~0.8. It's stained in potassium permanganate, which forms pale yellow spots upon heating. I circled the "UV-only" spots with a pencil before staining.

I'm guessing that the tiny new spot (Rf ~0.45) represents trace aldehyde. But, as you can tell, we're still a long, long way away from completion. Sad, because it was a lot more homogeneous this time!

Readers: How's my technique? Have any more pointers?

Nitration Surprise

(File under "Learn something new every day")

Boom goes the peptide!

For some light bedtime reading, I chose Life Technologies' Molecular Probes handbook, a 1,000-page opus of how to make anything and everything biological light up in brilliant hues of Texas Red or Cascade Blue. Flipping to Chapter 1, I quickly glanced at the very first scheme in the entire catalog, and did a double-take: tyrosine nitration...by tetranitromethane!

TNM: First time's the charm!
Source: Molecular Probes Handbook

Not to tread on Derek - who has a good thing going with his "Things I Won't Work With" tales - but doesn't this look like it should be grandfathered in to his list?

"Rule of Six" violation? Check. Potentially explosive byproducts? Check Check. A brief glance at the MSDS shows some of the more exciting Hazard Codes ("H330 - Fatal if Inhaled"), and the Merck Index (#9305) ain't much better: TNM "attacks iron, copper, brass, and rubber" and "Has been proposed as [an] irritant war gas."

Fun!

But, lest I lapse into my own fit of hypocritical chemophobia, I should point out that this compound is apparently 'par for the course' for stalwart chemical biologists - it's been used since the 1920s to label proteins, and a 1966 JACS article dubs it "stable, specific, and gentle." Even PubMed brings up >600 references, so I suppose my initial gut-check was a bit unwarranted - TNM looks OK when used in dilute solutions. But, I'd still say you should think twice before considering it for routine bench work.

Chem Coach Carnival, Day Three

Chemists everywhere! It's not too late to play. Send an email along to seearroh_AT_gmail if you still want to take part.

Day 1

Day 2

Pushing ever onwards. Just after posting the round-up last night, a fresh new batch of recruits showed up! (Not that I'm complaining). Apparently, waaay more folks than I ever thought do Raman spectroscopy for a living. Today, we hear from self-acclaimed 'super-villains,' postdocs, IP counsel, Lecturers, a very familiar Fellow, and two in-silico dudes.

21. Dr. Bodwin, Prof. and Dept. Chair, "Mysterious State U. Midwest." Dr. Bodwin blogs at Everything Under the Copper Sun, Science of Cooking (hmmm...), and maintains electronic lab notebooks at Dr. Bodwin's Electronic Notebook. Call him a faculty leader, recruiter, teacher, budget-maker, just don't call him an "administrator." Dr. Bodwin's story of a grad school "mistake" led him to a whole bunch of unexpected papers...and half his thesis. 

22. Chad, physical chemistry graduate student. Chad blogs at The Collapsed Wavefunction. He claims, like many, that there's no "standard day," and his hours seem to run to grad school extremes. Chad, like many, did a two-year stint in industry before returning to grad school. He plays card games while the laser warms up. Chad recommends learning how to pronounce names of famous chemists before you have to speak them aloud at oral presentations (Good advice!).

23. Dr. Rubidium, Evil Genius / Supervillain. Dr. Rb blogs at JAYFK, Thirty-Seven, and maintains a rockin' Twitter feed. I'm fairly certain she has the henchmen claimed in the post, somewhere deep underground. Dr. Rb walks us through the convoluted world of villains: hierarchy, daily routine, and career objectives. Oh yeah, and forensic science appears in there, somehow. BWAHAHAHA!

24. Michael, grad student / blogger. He blogs at The Organometallic Reader and Cheersical Education. Michael's interests lean heavily towards pedagogy, as one can see from his fantastic organometallic lectures (online). For those who want to teach? "Start early; there's a tired old fogey out there waiting for your youth and enthusiasm." He enjoys long walks on the beach, being recognized on campus solely by voice, and anthropomorphizing chemical events.

25. Marcel, Research Prof. / Computational Chemist, University of Girona. Marcel blogs at Trends in Science. He's an "excellent scientist, performing breathtaking research." Marcel inherited a love of numbers from his accountant father, and feels his postdoc(s) taught him a lot concerning project management. Ask him about how chemistry miraculously 'cured' him of mono...

26. Derek, Research Fellow, Vertex. Derek blogs at In the Pipeline - we consider him the "blogfather" for the chemblogosphere. Derek provides a fantastic med-chem primer, touching briefly on the joys of bench work, project management, binding pockets, and what it's like to bounce around multiple companies. Some of his reactions still form sticky maroon tars; not just yours and mine. Some caveats? "Never talk yourself out of an easy experiment," and "never assume your future grad advisor won't call you in the middle of the night." ; )

27. Darren, Patent Attorney, EIP Elements. Darren blogs at The IP Alchemist (catchy!). He shows us bench types a different aspect, namely examining prior art, and how new ideas become patentable. He's fluent in Japanese; a fringe benefit of the trade (and a postdoc spent in Japan!). Darren's frequent travel to fun and exciting locales makes me dream of a career in the IP office.

28. Janet, Science Philosopher, SJSU. Janet blogs at SciAm's Doing Good Science, as well as Scientopia's Adventures in Ethics and Science. She helps people who are "scared of science" learn about where it comes from. Janet's actually a "double Doctor" - chemistry and philosophy - which you certainly don't see every day. Have a peek at her Philo 133 syllabus, quiz her about the importance of lab safety, or ask about rubbing elbows with Nobelists (twice!).

29. Mark, Applications Scientist, Rigaku Raman. Mark's full entry is published below:

Your current job: I’m working as an Applications Scientist for a portable Raman instrument company.  I’ve enjoyed spectroscopy since graduate school and this position is a good fit for my scientific interests. Because my company is a small startup, it will be a great learning opportunity to develop business skills. The company has a unique product offering for their market, and I’m confident that we’ll be successful. 

What you do in a standard work day: My current position is new, so most of my initial activities have involved training on our equipment and software, sharing insight with coworkers into the c-GMP environment, getting to know our sales force, and learning key marketing messages for the product.  I’ve also begun writing an application note and trade publication articles, as well as helping to edit the user manual.  Because I am a field based employee, I participate in a lot of teleconferences.  I’ll also travel to visit customers, help to train the sales force, and work at trade shows. My position will involve product marketing and seeking out business development opportunities.

A position like this requires soft business skills in addition to technical knowledge.  The ability to network and collaborate with project teams, organize work activity, communicate with customers and coworkers, and frequently delegate without authority are all key to succeeding.

What kind of schooling / training / experience helped you get there? I went to graduate school at a small university and earned a terminal Master’s degree in physical chemistry, specializing in FTIR and Raman spectroscopy.  I’ve held a variety of industrial and pharmaceutical R&D positions as an analytical chemist and also have prior experience as an Applications Scientist with a large analytical instrumentation company. My current position will draw upon that experience base.

I’ve learned that networking is critical career development, not only in finding a new position but also building collaborations to accomplish business goals.  Also, participation and volunteering in professional organizations, such as a local American Chemistry Society section provides opportunities to develop soft skills.

How does chemistry inform your work? I use my understanding of chemistry to help customers select the best solution for their problems or processes.

Finally, a unique, interesting, or funny anecdote about your career: I’m part of a dual chem-career couple.  My wife is a PhD chemist and is currently manager of an analytical group at a specialty chemical company.  We’ve found that geography is critical for dual chem-couples; there really needs to be enough industry where you live to support both careers.  Early in our careers, we worked at the same company.  Seeing the “writing on the wall” we found new positions and relocated before facing a dual lay-off situation.  Altogether, we’ve been really lucky with our jobs so far and work to be supportive of each other’s career growth.

30. Nathan, Computational Chemist. Nathan's full entry published below:

Your current job.

For the past 5 years I’ve led the In Silico Medicinal Chemistry research group at the Institute of Cancer Research in London. I started off as a computer scientist in my undergrad days but moved into chemistry (chemoinformatics) when I joined Prof. Peter Willett’s lab in Sheffield. I’ve had a bit of an unorthodox path to where I am today.

What do you do in a standard “work day”.

My job is now very reactive, which has changed since my time before joining the ICR when my day job was mainly programming. I support both my group and oversee support for our therapeutic projects. This involves lots of computational methods, such as: virtual library design; multi-objective prioritization; docking; pharmacophore searching; building and validating predictive models in QSAR approaches. Much of my work involves assessing the vast space of virtual compounds we could make, but we are unable to in resource-limited academia.

We are a post-graduate college of The University of London so a lot of my time is devoted to supporting our PhD students and PostDocs advising them on tools and techniques to apply in their projects. I also spend a lot of time writing papers with my colleagues, from basic computational methods right through to our teamwork on drug discovery programmes. I am also currently editing my second book, Scaffold Hopping in Medicinal Chemistry, following one that was released recently: Bioisosteres in Medicinal Chemistry.

This year we’ve also had quite a few external visitors, which has led to a few TV appearances on British television on BBC Horizon and Newsnight. You can see the programme on ‘Defeating Cancer’ here: http://www.youtube.com/watch?v=7TyB07imDug&t=42m53s

What kind of schooling / training / experience helped you get there?

I have a first degree in computer science, which was followed by a PhD from Prof. Willett’s lab in Sheffield. In my undergrad life I focused on evolutionary algorithms, particularly writing software to simulate adaptive artificial life models. It was this initial interest in ‘writing software that writes itself’ that led me to work with Peter in Sheffield. I followed this with a Marie Curie Fellowship at Avantium Technologies, Amsterdam and Prof. Johnny Gasteiger in Erlangen for two years and a Presidential Fellowship at Novartis in Basel for another three years.

I never really wanted to work in IT but wanted to use computers to answer questions in other disciplines. I think the most useful experiences I’ve had is working with colleagues from other fields. I find these interactions very rewarding, particularly if you’re unafraid to ask questions that might seem silly. An orthogonal viewpoint has put me in good stead.

Throughout my career, my academic mentors have instilled the clear importance of the scientific method. It is so important in computational sciences to ensure that we do not become beholden to our own ideas because a computer will tell you what you want to hear. At least in real chemistry Mother Nature will give you a slap and say, “No!” The computer often says, “Yes!” This can lead to what I term the ‘pretty picture’ syndrome in some computational work. I always advise my students accordingly to clearly state the hypothesis and how they’re going to test it.

How does chemistry inform your work?

I use mathematics a lot to try and explain chemical phenomena. This is not all that different to scientists in the 19th century who used mathematical representations of molecules with the advent of atomistic theory. One of my mentors referred to a chemical reaction as a context-dependent mathematical graph transform, and in the abstract this is true. I like to look back over old papers and not taken common methods for granted. It is always important to understand how different computational algorithms work: with understanding comes control and can only contribute positively to our work.

There is a famous quote from Feynman: "If it disagrees with experiment it is wrong." This should be the mantra of the computational scientist in whatever field. Our models and predictions must be reduced to practice often to both test our hypotheses but also provide a feedback loop into the system. Therefore, chemistry is fundamental to this. If I suggest a compound that does not fulfil my predicted potential, I have wasted substantially more of someone's time in the lab than in my blase prediction. Due to this, I spend a lot of time doing my best to validate my methods as often as possible.

Finally, a unique, interesting, or funny anecdote about your career.

Although I’m an in silico medicinal chemist, I have been tempted into the lab on occasion. A few years ago I spent a day in the lab working on a halogen dance rearrangement. On my way home that evening I came off my bike, breaking my arm and dislocating my shoulder. Irrationally, I blame working in the lab and that was the end of my synthetic organic chemistry career to date. I knew synthesis was dangerous, but didn’t expect this to be the result.

31. Mike, Technical Editor / Webmaster, AATCC. Mike's full entry published below:

I morphed into science writing unexpectedly, and late in my 30+ year career. I have a BS, Chemistry from the University of Virginia and an MS, Chemistry from Colorado State University, and have been an ACS member since 1980.

Someone once told me that chemists can do practically anything. I didn’t believe them then. I do now!

My loves are natural products/synthetic organic chemistry, astronomy, and meteorology. Was a research chemist primarily in health care products industry. Got swept up in the lure of computer-aided chemistry tools, especially molecular modeling. Learned Unix on my own back in the 1990s. Discovered what “gophers” were, and then, hearing about the Web, realized something big was coming. Got out of the lab and became a webmaster contracting with the National Institute of Environmental Health Sciences for two years. I then rode out the internet boom and bust, until landing my current gig as technical editor of scientific articles and webmaster for the American Association of Textile Chemists and Colorists in 2003.

Adaptability is the key to success in today’s world. I would have never guessed ten years ago that I would have enjoyed being an editor and writer. These were “hidden” talents, until the opportunity presented itself. Even more surprising was finding out that I could write for the public! I had long desired to do this, but didn’t think I had the ability. Two mentors at AATCC convinced me otherwise. As a result of their encouragement, I won a Gold Tabbie Award in 2011 for one of my newsletter articles.

I write articles for AATCC News, the association’s newsletter, relating to textile science. This includes chemistry’s intersection with the larger world of textiles: including fashion! Can you imagine: science on the runway! It’s both fun, challenging, and there is so much to learn!

Most recently, I’ve been an active proponent of social media as an engagement tool. Our Association’s LinkedIn site has become a major textile industry resource. I have little time to blog, but love microblogging (Twitter).

My advice: Do what you love, no matter what, but don’t hesitate taking opportunities to test new skills that broaden your experience. If you want to write, start on Twitter. It’s a great place to meet like-minded people and get your feet wet. Finally, be sure to keep a sense of humor about yourself and what you do-it helps when times are tough.

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32. Late Addition, just under the wire: B.R.S.M., postdoc / blogger, UK (and soon to be in the US of A!). Blogs 'eponymously' at BRSM. A true synthetic chemist, he's proud to "wear the white coat" and work at the bench. I'm jealous amazed that he's achieved so much at such a young age; blame credit the shortened British Ph.D. Seriously, though, BRSM enjoys the freedom of not being bound by grants or teaching (for now). He's prepared for a lifetime of learning...and to learn organic "in-jokes" whenever possible.

Chemistry Bumper Cars

By now, most folks on the chemblogosphere have heard the rumbles about K.C. Nicolaou's possible departure from Scripps. His landing spot looks to be Rice University, in Houston, aided by a generous multi-million dollar "golden parachute." Followup comments posted on Chemjobber and In the Pipeline saw speculation run rampant regarding other Scripps synthetic chemists, including M.G. Finn, Jin-Quan Yu, Phil Baran, and Dale Boger.

Wow. Does everyone have the moving bug?

I seem to recall Kyle over at The Chem Blog drawing us a convenient map a few years back, during another busy moving season (2005, I believe?). The past two years have proven quite busy as well, with no less than an entire ChemBark post entitled "Nocera to Harvard!" (vide infra).

Without further ado, I present my highly-researched, but definitely not-to-scale, map of synthetic faculty moves, 2011-2012.

Legend (Updated 9/20):
1.  Keith (purple) Woerpel, Irvine to NYU
2.  John (Berkeley blue) Hartwig, UIUC to Berkeley
3.  Vy (green) Dong, Toronto to Irvine
4.  Dan (crimson) Nocera, MIT to Harvard
5.  O(maroon) Yaghi, UCLA to Berkeley
6.  M.(Goldenrod) Finn, Scripps to Georgia Tech
7.  K.(Cyprus orange) Nicolaou, Scripps to Rice (confirmed!)
8.  Greg Fu(schia), MIT to Caltech
9.  (Rust)em Ismagilov, Chicago to Caltech
10. Paul (cyan) Chirik, Cornell to Princeton

I've been searching for a chemistry faculty movement metaphor. At the end of the NFL season, reporters write about the "coaching carousel," where coaches switch jobs circuitously, trapped on an employment merry-go-round. Well, that's not quite right here. Chemists usually move away for good, and there's clearly a directionality to the moves: towards more money, higher prestige, or warmer climes. Perhaps a Ferris wheel? Nah: it implies "up" or "down," a good view of the situation...and far too smooth a ride. Negative on the Gravitron, though grads and postdocs might feel like they're smashed by the pressing gravity* of an upcoming move.

I've got it: Bumper cars! Everyone starts out hesitantly, driving around in circles, hesitant to make first contact. After a few minutes, though, it's a free-for-all, everyone bouncing off each other, crashing, laughing, sparks flying off the ceiling. In the end, no one ends up where they started, and everyone has headaches. (Bear with me, it's a work in progress, doesn't yet have the oomph of a "Manifest Destiny" or "fiscal cliff.")

Faculty jostle for top spots like, well, you get it...

Credit: UK Telegraph

Are faculty moves unavoidable? It's true that the grass is always greener. But, if you're already a professor at a Top 20 institution, you likely receive the lion's share of grant monies, decent media coverage, and your pick from top-shelf graduate students. So why go? Some moves are nostalgia-driven - the Prof. wants to return home to a welcoming parade, having "done good." Some moves try to fix the two-body problem. Some happen because of missed tenure, or a feeling that it's "just time." Maybe in today's uncertain economy, it's just best to assume you won't be in any job longer than ten years...with a handful of exceptions.

Readers: Know of any more high-profile U-Hauls being loaded this academic season? If the "Chemistry Bumper Cars" trend persists, this might yet become an annual post.

P.S. Heard about a move I missed? Email me at seearroh_AT_gmail, and I'll add it here!

*I completely understand, having been involved with two moves in grad and postdoc.

Arsenic Life Wrap-Up: The Good, the 'Not-So-Good'

"Arsenic Life," a hot-button issue for much of the past year, reemerged this week with two new papers, one propitious, and one, well...not so much.

GFAJ-1 bacteria
Source: nasa.gov

As covered by Curious Wavef(n), the first paper related Prof. Rosie Redfield's well-documented efforts coaxing the GFAJ-1 strain to flourish in arsenic-rich media, which, if successful, would imply arsenate linkages in the bacterial DNA. Redfield bursts the bubble nicely, utilizing multiple tools (LC-MS, cell growth assays, gels) to cast doubt on the earlier study, even mentioning that most of the detected arsenate could be washed away with distilled water.

Well, if timing is everything, then the second #arseniclife publication really missed the boat. Last week, a commentary appeared in the open-access online journal Biomolecules, bearing the epic title From Phosphorus to Arsenic: Changing the Classic Paradigm for the Structure of Biomolecules. Heavy stuff!

This summary takes the opposite tack, casting "Dr. Wolfe-Simon's discovery" as a fighting underdog - viewed skeptically today, but enshrined and glorified by future generations much like Copernicus or Darwin (both name-dropped inside). The prose shakes the reader with thrilling, emphatic statements, lines you might find in a rousing stump speech or an action movie. A few choice selections:

"...Some have died as a result
of these discussions..."
Image Credit: Silver Lining

"It is no surprise that this work has come under what some may consider a brutal attack in the past year; the proposed repercussions almost beg of it."

"...members outside of the scientific community may view the criticisms and other events that have transpired as superfluous, vindictive, and outright scathing." 

"...the implications of [arsenic life] have the potential to shake the foundation of biology as we have known it for centuries."

 "This discovery...would be absolutely groundbreaking to all of science."

You get the point. These excesses, coupled with a few cut-and-paste sources (N.B. Don't include "page-access" dates in references) and a passing remark to Wolfe-Simon's potential scientific martyrdom, complete the commentary. Yesterday, several Twitter denizens, led by the industrious Carmen Drahl, noted a very familiar vibe to this piece. To borrow a phrase from Derek and Leonid, it sounded suspiciously like a "term paper," final reports students submit to wrap up specific college courses.

My feelings, reading Paper #2
Source: Jobbing Scriptwriter

Was it? A very strong maybe. Check out this editorial, culled from the Colorado State University Journal of Undergraduate Research  (p. 16), scribed by the lead author. Bears a rather striking homology to the Biomolecules piece, sources* and all. The second author, currently an undergraduate at Boston University, may have interacted with the CSU authors at a conference, or perhaps on a summer REU.

As corresponding author, Prof. Mark Brown (CSU) would, I'd believe, have final say over the manuscript. Did he check it against the lead author's previous work? The journal's Author Information section mentions that five external reviewers must be named, although "...the Editor will not necessarily approach them."

So, to round up this bizarre publishing escapade, we have undergraduate authors submitting previous work in an open-access, loosely-reviewed, and barely-edited online journal, all with the benediction of a faculty member? Sounds dubious...much like arsenate linkages in DNA.

*Can someone please tell me where to find Ed "Young" at Discover Blogs? : )


Update, 6.8.12 - Commenter Stuart Cantrill (Editor, Nature Chemistry) points out on Twitter that the original piece also misspelled "phosphorous" in the title. Sigh.

No Superstars? The 'Blog Nerd' Community and 'Science Pride'

Like many in the science blogging community, I try to pay homage to the chemists who've gone before me, especially those who've found their niche and momentum. These include Derek, Ash, CJ, and recently Paul over at ChemBark, who attracts a pretty diverse, passionate, and gregarious comment base.

I took issue recently with the stance of one ChemBark commenter, eugene, who stated: 

"...I sincerely hope [the "superstar mentality"] doesn’t go to any young professors’ heads in the future. Not only will you be vastly overestimating your ‘coolness factor’ with society at large, but you should focus on the science and your job please..."

Familiar scene for the "blog nerds"
Source:  U Chicago blog Science Life

A few lines before this, eugene refers to the "hype...created by the chemistry blog nerd community." (referring, no doubt, to Chemjobber's satirical piece about Dan Nocera's move to Harvard). Let's mull on that epithet: blog nerd community. I think that, by and large, we chem-bloggers enjoy this gig, which is critical because we don't really make our living here - we're all scientists by day, and writers after hours. Our online community encourages, supports, and challenges us. And sure, we're nerds . . .didn't you hear that that's cool nowadays?

But I digress. Back to eugene's comments: "...focus on the science and your job, please." I must know, what's so wrong with wanting recognition for hard work? 

Hey, it's my grad school advisor!

You've all heard the oft-repeated stigma, chemists as introverts, passing up individual glory, monastically devoted to our work until we die at our benches, pipette in hand. There's an ingrained mentality at work here, stating that the discipline is bigger than any one scientist. Chemists write all of their procedures in passive voice, deferring credit, as if the flasks and reagents had jumped up and performed the reactions themselves. I feel like eugene's comments boil down to: "Sit down, shut up, work hard, and hope it all works out."

Derek Lowe recently wrote a telling editorial, in which he explored reasons why most students shy away from work in STEM fields. Quoth the Pipeline:

"...if money and social standing are your motivating factors, you've probably ruled out the sciences for those reasons alone...I definitely did not go into science to become rich.  

There's another factor that doesn't get as much attention as it should: It takes a certain personality type to really get into this stuff. "Yes, it does," I can hear people saying, "and it's the one that we call nerdy." That can help, true, although not all of us in the labs live the stereotype"

Happiest scientist I could find!
(Although her PPE is not quite right...)
Source: 123RF

Yes. Myself, for one: I'm firmly on the ENTJ side of the Myers-Briggs, but the thought of discovering new reactions still gets me to work in the morning. So, I ask you: why can't chemists be proud of their success? Become champions for our cause, rally around research, take credit for our role in society? If judges judge, and singers sing, why can't chemists react?


Chemists: When you go to work today, before you slip on your lab coat and gloves, pause a second to think about all the time and effort you expended to be standing in front of your hood. Enjoy it - you're a superstar.