Tiny Victories from Bloggy Activism

The chemblogosphere has certainly taken an activist turn in the past few years. Remember feeling the excitement of Paul's 2009 NaH oxidant live-blog? The ensuing four years saw chem blogs "cantrilling" space dinosaurs, uncovering IBX's secrets, investigating suspicious TEM images, and even weighing in on Nobel Prize selection. Heavy stuff!

Long-time readers understand that I've been in something of a self-imposed exile in the past few months, owing to a lengthy job search. But I couldn't resist writing about a mini-Christmas-miracle that arrived on 12/26. Seems that Dr. Brian Myers, the current ACS Division of Organic Chemistry webmaster, had acted upon my June post investigating the strange DOC logo:

"As a result of this posting, the ACS Organic Division has reverted to using the older version of the logo where the "D" is more prominent. It turns out the logo was "updated" in about 2007 while trying to make a high-resolution graphic for posters, NOS bags, and such. At that time, the leadership was unaware of the fact that the molecule was supposed to spell out DOC.  

As one senior DOC executive committee member recently wrote: 'I assumed it was a truncated steroid, which made historical sense. However it isn't because the ethyl and methyl aren't attached to the right places of what would be the CD rings.'"

Presto, Change-o!

Huzzah! The corrected logo now proudly adorns the DOC main page, and I even got a shout-out in their FAQs. I'm not gonna lie - I felt a small twinge of pride seeing this tiny change I helped effect.

But how did we get the logo in the first place?

Challenge: Dr Myers wants to know if anyone out there can remember the initial DOC logo designer:

"As far as I can tell, the first appearance of the logo was in 1985 on the NOS Program book; however, I would love to know the history of this including the name of the person who designed the original logo"

Anyone with insider info should leave a comment or email me at seearroh_AT_gmail. Let's put this chemistry "cold case" to bed!


A belated Merry Christmas to all, and hopes for a very Happy New Year
See Arr Oh

A Tasty New Development

Hey there, readers! You may have seen the chatter this morning, or perhaps you've seen Carmen's or Andy Revkin's write-ups?

It's time to hear it from the dog's mouth: I'm now part of the Food Matters family over at Scientific American!

Now, this doesn't mean I'm closing up shop here at Just Like Cooking; far from it. Following Ash's example, I'll write about my love of food chemistry over there, and my love of [everything else] over here. Sound good?

Have a peek at Bora's intro post to learn more about all the new faces, and check out all the smart things my co-authors have written over the years.

Looking forward to this exciting new adventure. Thanks again to everyone who made it happen, and for all of you here at JLC for reading.

Link Farm: Chemistry Communication

Blogs, like any medium, shift, change, and grow over time. At first, I devoted my humble corner of the internet to food chemistry. After a while, it became a tool to root out misconceptions about chemistry in popular culture.

Well, to borrow a phrase from Click and Clack, I've come around for the "third half of the show" - figuring out how to bridge the gap between the growing public desire for accessible, informative, entertaining science content and chemistry's approach to that communication. A lot of terms have swirled around this issue: "punching down," #BogusChem, "Inside Baseball," 'in-reach' not outreach, #chemophobia, and "dumbing down," to name just a few.

Thanks for the tip about the magnets, Andre!
(P.S. Yes, I know "D" isn't an element)

This post will serve as a (growing) collection of pieces dedicated to thoughtful chemistry outreach.
Readers: Have a favorite post I haven't included? Send it along in the comments.

Janet Stemwedel, Doing Good Science: "When we target chemophobia, are we punching down?"

Chad Jones, The Collapsed Wavefunction: "Punching down? I don't remember swinging at all."

Ash Jogalekar, The Curious Wavefunction: "Where's the chemistry lobby? On why we need a National Center for Chemical Education."

See Arr Oh, Just Like Cooking: "The Chemistry Popularity Conundrum"

Michelle Francl, Slate: "Don't Take Medical Advice from the NY Times Magazine"; Nature Chemistry: "How to counteract chemophobia";

Paul Bracher, ChemBark: "Combatting Chemophobia"

Rebecca Guenard, Atomic-O-Licious: "Chemistry Isn't Just About Chemicals"

Science 2.0: "Chemophobia - The Unnatural Fixation of Activists"

Chemjobber, Dr. Rubidium, See Arr Oh, Chemjobber: "Chemistry Avengers" (podcast)

Marc Leger, Atoms and Numbers: "Consider the audience when addressing chemophobia"

Chris Clarke, Pharyngula: "Did you know douchebags are full of dihydrogen monoxide?"

Andrew Bissette, Behind NMR Lines: "In defense of #chemophobia"

More to come...

Slow Down, Bob

An open letter to R.B. Woodward (RIP):
(Playfully adapted from Dr. Freddy's post)

Dear Bob,

Listen, I know you can't hear me right now, but I feel like this post may be overdue. Back in your day, the closest thing to "blogs" were the Editorial pages of the newspaper and (actual, cork) bulletin boards. Thus, I'll ask on behalf of all struggling grads and bench chemists: could you please stop being so darn productive?

Someone recently pointed me in the direction of your dual MIT theses. That doctoral title, what chutzpah!

I know, I know, things were different back then. You didn't have a single NMR in your dissertation; after all, it wasn't invented yet! Ditto mass spec or HPLC traces. You characterize everything by mp, bp, and elemental, and yet I can't believe you finished your Ph.D. in a year. 

Dissertation Stats: 64 (typewritten) pages, 23 (hand-drawn) structures, 27 references

Of course, we all know what happened next. You postdoc'd at Illinois for maybe two weeks, and jumped over to Harvard for a 40-year stint. You (almost) single-handedly applied UV and IR to molecular characterization, you made strychnine, chlorophyll, and B12, and you won a single-scientist Nobel at the ripe old age of 48. Some folks even thought you might have deserved (at least) one more! 

Your personality still towers over us today - legends of blue suits, chain smoking, and three-hour lectures abound in roughly 58.8%* of recent blog posts. Even your fashion sense is back in vogue, (perhaps) influenced** by your invisible hand.

While you were making quinine and cortisone in your 30s, we're now just trying to find good, stable jobs. So Bob, please enjoy your well-earned rest, and stop reminding us of how life could have been a few generations ago. We just can't bear the comparison.

*Studies show that roughly 95% of statistics are made up on the spot

**And Mad Men

Chem Coach Carnival, Day Five

The sun's slowly setting on another great (US) National Chemistry Week. It's been a blast hanging out with so many different flavors of chemists this week, and I hope to stay in touch with all of you through the magic of online social media. Best of luck to all involved.

45. Piper, inorganic grad student, UC Berkeley. Piper blogs at Berkeley Science Review, Science Exchange, and maintains a really replete website which I'm sure will one day garner her a high profile science + media job! She says Twitter and Facebook help her plan "conference submissions" (that's what I'll tell my boss). Piper relies on to-do lists as tools to help maximize daily efficiency. Her lab buddies include a guy best known for Veritaserum and bezoars.

46. Mystery postdoc, MedChemBlog. This scientist knows that two things make work easier: coffee (huzzah!) and switching between lab and desk work to reduce monotony. MCB came into synthetic chemistry via pharmacy, which seems to be a common corridor I've overlooked. Remember how high you jumped the first time you heard an LN2 tank vent?

47. Doctor Galactic, postdoc, UK. Doc blogs at Doctor Galactic and the Lab Coat Cowboy. He has great fun doing bench chemistry, and blames "two Scots" for instilling his love for science. Somehow, he manages to tie Gollum and "brain madness" into his post. Doc doesn't recommend trying to finish a Ph.D. in just three years...

48. David, Synthetic Chemist, RTI International. David blogs at Chemical Space. He stresses the importance of networking; his current job came from a slew of former contacts: "being bold with contacting people got me here." Adaptation and flexibility are David's secrets to an enjoyable career. And a story about exploding Grignards? Always good for a laugh.

49. Rich, Chemist / Software Developer, Metamolecular. Rich blogs at Metamolecular and Depth-First. He owns a small business, and has yet to rely on government funding - no small feat in today's economy! Rich's post, like much of his writing, wins the #ChemCoach Pragmatism Prize: "How to Get a Job Like Mine." He's working on getting o-chem into your iPad in app-form, no small feat for a former med-chemist-turned-programmer. One of his major goals? "...Making life easier for those who work in labs." A noble calling.

50. Phillip, Science Correspondent, Chemistry World (He blogs at their eponymous site). His witty title might win the #ChemCoach "Pure Pith" award. Holy cow, he's also decorated blogger Tot Syn's former flat mate! (small world, this chemistry community). A simple collection of 'gerunds' from his post shows you all he gets wrapped up in: hunting, picking, writing, ticking, meeting, researching, specialising, editing, teaching, training, oxidising, clearing, alkylating, everything, anything! Want to know what it's like to move a truckload of chemicals cross-country? Phil's your guy.

51. Chris "Ziggy" Zeigler, Editorial Associate, ACS Undergrad Office. "Ziggy" blogs at Reactions. Chris apparently "partitions" himself professionally: 1/4 salesman, 0.25 customer service, a dash of editor, part admin. He plans National Meeting activities - including the always-popular demos - and maintains the Office's Twitter and Facebook presence. He almost became a pastor (really!). Chris worked with a former Bills linebacker...installing chromatography equipment.

52. Ash, Molecular Modeler / blogger, small biotech startup. Ash blogs at two different versions of the popular Curious Wavefunction: one at FoS, and one at SciAm. He loves models, organic chemistry, and can tell you anything about R.B. Woodward. Ash points out (correctly) that everyone "from the intern to the CEO" hears your views in a small outfit, and you end up filling many roles. Ash strikes me as well-versed in just about everything, a view shored up by references to Greek philosophy, French verbs, and complex algorithms. 

53. LabMonkey4Hire, Lab Monkey / Process Chemist. LM4H = also the name of his eponymous blog. A pharma guy, he knows how to move bench -> pilot -> kilo, and how to make data come alive: "No one wants to see 200 HPLCs in a presentation!" The main goal, LM explains, is to simulate reactor conditions on much smaller scale, and tweak variables accordingly. He compares full PPE for lab decon to "...being in a bizarre '90s rave video." 

54. Organometallica, grad student. OM blogs at Colorblind Chemistry. I've published his full entry below:

Your current job

I am presently a PhD student (not yet candidate, but soon!) at the University of Illinois at Urbana-Champaign. I am an organic chemist presently working under the supervision of an inorganic chemist, meaning that my training is about as organometallic as one could hope to engineer into their degree program, I suppose.

What you do in a standard “work day”

By this point, I'm completely done taking classes, and so the largest devotion of my time is to research, which often keeps me up to the wee hours of the morning. My research is very young (I am my advisor's first and currently only student) and so in a broad sense I am trying to prove the idea that first row transition metals are not condemned to single electron chemistry with the ultimate goal of both emulating and superseding palladium using iron catalysts.

What I didn't appreciate when I applied to graduate school is how much time each day (in the early years at least) is devoted to things outside of research. Twice a week, I teach a graduate level advanced inorganic chemistry class, which comes with its own share of outside responsibilities. I also have to give seminars and am required to attend them, too. On top of all this, I supervise three undergraduate students in the laboratory, meaning that no two days are the same and that I spend large expanses of time discussing chemistry with scientists of all sorts of levels of experience. It's somewhat gymnastic in how often I have to think-and rethink-all of my ideas and reiterate them in pursuit of a larger goal.

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

I hold a BSci in Chemistry, and that's the extent of the schooling that I had. Interspersed with this, I held three jobs in pharmaceuticals in the years leading up to graduate school. I became interested in organometallics as an undergraduate in Tobias Ritter's lab, where I got a taste of practical catalysis. After a winding first year at UIUC, I decided that my skills were best suited to fundamental research identifying and elucidating new modes of reactivity, the training for which was largely physical chemistry and was primarily self-taught.

How does chemistry inform your work?

Obviously chemistry pervades my research, but I find that general principles of chemistry have been most useful in my teaching assignments. Often in the research lab we get absorbed in technical details, but one of my favorite things to do is quiz undergraduates informally about why HCl, AcOH, and Cl2 share very similar smells, or why adding salt to an aquarium doesn't change the pH. Seeing the light bulb go on when they realize that a simple chemistry principle applies to their day-to-day life is one of the most rewarding parts of my job.

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

My (short) career has been littered with various fires, explosions and similar ilk that are probably not worth discussing here, but one interaction with a biologist strikes me here.

When I worked at a small, now defunct, biotech where I was the only lab chemist. Tasked with setting up synthesis facilities, I went about ordering chemicals. My first solvent order was turned down and I was promptly called into the big boss's office. He, a biologist, pointed out a 4L bottle of ether and exclaimed, "this is what they used to use to anesthetize mice, is this an absolutely necessary risk?" 

55. Dr. LC Square. LC's full entry published below:

Your current job.

Associate Principal Scientist, Process Chemistry, Merck. I currently work in a group which interfaces Discovery Chemistry with Process Chemistry. This assignment has broadened my view of pharma beyond “typical” process chemistry. Gaining experience collaborating with discovery teams and a keen understanding of the interplay between medicinal chemistry SAR processes and various preclinical study designs. Before that I focused on development, scale-up and application of chemical processes for the synthesis of Active Pharmaceutical Ingredient (API); A more “typical” process chemistry role, supporting kilo-scale deliveries under Good Manufacturing Practice (GMP).

What you do in a standard "work day."

Currently my typical day is a ~50/50 mix of lab-work and various administrative responsibilities. These could include on any given day:

- discovery core team meetings

- larger therapeutic area presentations/meetings

- coordinating external (outsourced) projects

- meeting with reports to assign & discuss projects

In the lab, I typically work from mg to 500g scale with most reaction performed on multi-gram scale.  We have the odd larger batch but for the most part we define routes to API for the first pre-clinical studies or key intermediates for Med Chem, developing key SAR diversification-point reactions and then scale-up. Big enough to want to be as efficient as possible, but small enough to resort to chromatography and sub-optimal processes if need be. It’s all about finding the good enough line! Though I still take pride in developing crystallizations to extract a nice white solid from dark brown goo!

During a typical day I almost always collaborate (phone, email, or physically meet) with people in other functions (MedChem, Pharm Sci, Safety, Biology and DMPK for example).  This assignment also includes playing the role of connector between the discovery and development phases of development ranging from lead-ID to First-In-Human clinical trials.

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

I did my undergraduate studies in Biopharmaceutical Sciences (Medicinal Chemistry Option), a multi-disciplinary program which included 2-3 years of biology and biochemistry.  Though I didn’t realize the potential at the time, my understanding of biochemical processes has served me well. Many chemists end up there because they didn’t care for bio… I’m glad I stuck with it.

I obtained my Ph. D. in organic chemistry specializing in transition metal catalysis. More specifically, I had the great opportunity to work on Direct Arylation (also known as C-H Activation, though I hate that term) with Keith Fagnou, just when the field was taking off (2003-2007).  This made it a very exciting time to be a graduate student.  Though my graduate training in organic chemistry is at the core of what I do as an applicant of organic chemistry in my day to day activities, I find that I learned a plethora of other vital skills I leverage every day. Here’s an example:

Keith always believed that establishing a collaborative research environment was more important than work hours and expected us to be productive during “regular” work hours. He never demanded anybody work late at night and weekend hours were optional.  If you were in the lab late or on a weekend, it’s because you wanted to be. We were all expected to support each other and help each other succeed.  This ultimately led to a group culture where the success of the team was more important than individual success.  From this incubator that was the “Fagnou Factory” I learned and developed:

1)   Teamwork

2)   Leadership & Mentoring

3)   Giving & Receiving Feedback

4)   Motivation Through Autonomy & Ownership

All of these things are essential for drug discovery & development. One of my mentors at Merck on told me “these halls are filled with great scientists, but science alone is not enough” for drug discovery & development program to succeed.

How does chemistry inform your work?

It’s at the foundation of it. I see the world through chemists’ goggles. It also affects my perception as an experimentalist. In chemistry, you can have an idea in the morning, test it in the afternoon and get your answer in the morning. That type of “just try it” attitude is how process chemists innovate. My personal rule is that if you have less than 3 steps to get to test your hypothesis, you HAVE to try. You can’t be afraid of failure.

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

In grad-school, my friends and I were notorious for pulling the best pranks for April fools. My contribution to this went as follows: We placed an ad in the Saturday edition of the paper listing Keith’s relatively new Saturn for sale for “$1999 or best offer. Must sell fast!” Giving only his office # to call back, he returned Monday to 83 phone messages with the phone ringing about the car every 1-2 minutes all morning. Surprisingly, it took him most of the day to figure out we were to blame, as we were able to deflect his accusations convincingly. Finally after, eliminating his father-in-law or other faculty members, he broke one of us and we all had a good laugh at his expense over beers that night!

----------

*Honorable Mention Section*

Thanks to Deborah Blum, Science Writer / Author, University of Wisconsin-Madison. Deb writes amazing stuff like The Poisoner's Handbook and blogs at Discover's Elemental and PLoS's Speakeasy Science. Deb featured our little blog effort on Knight Science Journalism Tracker earlier today. Thanks!

Not to be outdone, champion Editor Rachel Pepling, she of the C&EN blog community (and a chemist-by-proxy), featured us on Grand CENtral. Most appreciated.

Stay tuned for a roundup post later this weekend...or whenever I get on it. (Zzzzz...)

Trending Up

I've been pleased to see blog traffic picking up in the past few months (Thanks!).

For those unfamiliar, most blog toolkits show graphical representations of hits against time, so you can tell when certain posts gain readership by distinct "blips" on the trendline. The chemblogosphere has coined several punny, tongue-in-cheek epithets for increases that result from specific sites. Here's a few I've heard bandied about:

Reader Submission: Found Chemistry,
Hendersonville, NC

The "Lowe Lift"
The "ChemBark Crush"
The "Chemjobber Jump"
The "Slate Slam"
The "Reddit Rise"
The "Bora Bump"
The "Zimmer Zing"

With my pithy phrasing cap on, may I suggest a few more?

The "Wavefunction Wobble"
The "B.R.S.M. Blast"
The "CENtral Science Cuddle"
The "TotSyn Trifle"

Readers, have I missed any?

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.