Friday, May 6, 2016

Postdoc Required? Check the Job Ads!

Both the New York Times and C&EN have written pithy pieces today referencing the recent Science survey about factors influencing postdoctoral study. 

The tone of all three comes across as confused, painting Ph.D. students as ill-informed, directionless lambs who take on postdoctoral appointments as, in the words of the Science authors, "default...holding patterns" because they "...don't know what they want to do with their lives." (NYT).

Well, for those of us, like me, who postdoc'd with the intention of going into industry, why did I "waste my time in a post-doc" (Science) for seemingly no reason? Here's some telling quotes, highlighting from me:

From Science: "...career goals are quite diverse even among these postdoc-planning students...[t]his may be surprising, given that the postdoc is not typically considered a stepping-stone toward nonacademic careers"

From C&EN: "Many students don’t have a sense of how many jobs are available or what background they require, Doyle says. Chemistry students think they need a postdoc for some high-level industry jobs in the pharmaceutical industry, for example."

From NYT"[in 2013]...the most common reason students gave for doing a postdoc was that they thought it would increase the chances of getting the job they wanted."

These sound bites sound aloof at best, slightly pandering at worst. Here's my question: Did anyone quoted for this story, or the authors of the Science study themselves, actually read the job ads for the industrial positions in question? Maybe students' fears are well-justified, because the ads I'm seeing from multiple companies read like this:

GSK, API Chemistry Automation Team Member

Pfizer, Sr. Scientist - Obesity + Eating Disorders

Amgen, Scientist, Immuno-Oncology

Genentech, Sr Scientific Researcher, Discovery Ophthamology

In case you missed it, all recommend postdoctoral research. I didn't have to go digging for these, either - simply typing "chemistry" along with "postdoctoral" or "post-doc" into the Career search engine on any corporate site will reveal roles like these. I find it rather ironic that the last quote from the Science lead author reads: "We don’t know enough about the industry labor market” (C&EN write-up). That seems to be the only part of this whole situation I completely agree with. 

OK, grumpiness aside, how can this situation be fixed? I actually appreciate the incentive strategy advanced in the paper, which neither news outlet captured well. Here's most of the penultimate paragraph from Science, highlighting again mine:
"Whereas the recent National Academies report recommends that students make career plans early in the Ph.D. program, we argue that they should consider labor market conditions and career options before starting a Ph.D. program. Doing so may avoid escalating commitment to a research career and may prevent individuals from entering a postdoc holding pattern. Graduate schools could encourage career planning by requiring that applicants analyze different career options and justify why a Ph.D. is the most promising path forward. Funding agencies could implement similar requirements, especially in conjunction with moving a larger share of funding from research grants to training grants and individual fellowships."
Amen. One thing I believe saved me from five years of postdoc purgatory was walking in "eyes open," understanding exactly what jobs I'd qualify for and where I needed to end up to pay back all my student loans. I also realized it would be no cakewalk: I began applying for jobs in my second year of study, and never looked back. 

Grad students: If you're confused about your options, feel free to drop me an email at seearroh_AT_gmail. Confidentiality guaranteed.


Thursday, May 5, 2016

Two Billion Compounds?

I've been cracking my skull against a peculiar problem this week:
How many unique molecules compounds have ever been made?*

I'm referring to those produced by humankind, over the past 250 years - give or take a decade - of formal chemistry effort. CAS claims 100 million molecules in their collection, and predict, at the current rate of registration, another 650 million over the next 50 years.

Berries by the side of the road, 2016.
Not counted in billions.
Certainly other databases exist, a well-curated larger example being ChemSpider (34 million), but I'm sure the Venn diagram for that against CAS overlaps quite a bit. Ditto PubChem, which according to ChemConnector had over 37 million structures in 2009, but lots of errors, duplicates, and isotopomers, to hear him tell it. Outside the med-chem arena, there are exciting new collections such as the Aspuru-Guzik lab's Clean Energy Project, to identify photovoltaic materials. Surely the assembled collection of privately-held corporate data from all chemistry, pharma, biotech, and engineering firms must include another windfall; ~200 million compounds?

So, let's try a thought exercise - say we limit the set of what we call "made," or synthesized. We won't consider polymers, whether natural (DNA, polysaccharides) or artificial (Teflon, urethanes). Screening collections, libraries, and combinatorics; unless someone produced >1 mg, I'm leaving it out. Metal complexes and salts are in, since most of the time inorganic and formulations colleagues still produce quantities you can hold and measure (and get a melting point on!).

Granted, by referring explicitly to the public and private chemistry databases, I'm not including dark reactions, those failed experiments or perhaps non-optimal yields that never make it to publication. Based on my lab career (and that of my hood-mates), I'd say there's a comfortable 5-10 molecules made for every 1 that gets reported somewhere. Of course, since many of those are literature preps or repeat reactions, I don't think it inflates the count that much; truly, novel molecules tend to creep into papers and patents somehow.

Chemical space gurus, I apologize - I only want to count things that have been bottled, columned, purified, and analyzed. Large computational data sets of billions - unless they've been made and characterized - aren't up for consideration. Neither are metabolites isolated from plants or microbes; no fair counting what we relied on other organisms to make. S'posing this means we also leave out decomposition products and geological materials.

So them's the rules: 1 mg produced and characterized, non-polymeric, must have been made or produced with human hands. Salts and metals are in, along with isotopomers and stereoisomers.

What do readers and commenters think? My guess is in the title of this post.

--

*On the Twitter, Peter Kenny points out that I should, in truth, be asking after compounds, not molecules. Fair enough.
** Another reader points out that ZINC15, the database of "stuff you can buy now," only includes ~10M at present.

Sunday, May 1, 2016

X-Files' Freezing Catalyst: Digging Deeper

A random Friday afternoon link at Chemjobber's place clued me into Mitch's post, about a random NMR encountered in an old episode of '90s sci-fi classic The X-Files. By some odd coincidence I, too, was watching the episode sometime in early April, though I didn't get my notes and pictures together in time. Alas.

(Before we get too hung up on the episode's premise - that in 1996 computational chemists at MIT were performing in silico calculations on a "catalyst" intended for rapid body freezing - let's also remember that this episode shows us protagonist Lisa, a wunderkind doctor / chemist / radiologist, strutting out of her lab sans questioning after her patient spontaneously combusts!)

Now, to the structure of "Compound X" - I took a close-up of the computer terminal Lisa's working on, right around 17:00. Yes, folks, that's 1,2-dichloro-1,1,2,2-tetrahelio-ethane. Carbon-helium bonds can't exist, shout the skeptics? Well, 1993 marked production of the first He@C60 clathrate (story here), and friend of the blog Henry Rzepa had a theoretical paper in 2010 discussing charge-shift C-He bonding. True, isolable heliocarbons are still at large, for anyone seeking a high-risk, high-reward tenure project [ducks].

Molecular modeling has always looked best on Macs. There, I said it.
Fox Broadcasting Corp.

In his post, Mitch calls attention to the NMR, though I found the second analytical spectrum more entertaining, since it has an actual reference printed across the top. Turns out the producers did their homework for this one - this spectrum is an example of spectral linear combination to quantify small amounts of metabolites in blood plasma - good call!

Real science! In a sci-fi show! Who knew?
Fox Broadcasting Corp.

Back to the (flimsy) plot: certain details are over-the-top cheesy, like the "hand scanner" Jason uses to access his facility - it looks like it was built from an old dot-matrix calculator screen screwed into a subway post:

State-of-the-art security for the "MIT Biomedical Research Facility"
Alternate caption: I spent a weekend building this prop, and they used it for 4 seconds of footage.
Fox Broadcasting Corp.

The writers have also presaged the warm-liquid-goo-phase meme from Austin Powers, as the antidote to the freezing catalyst seems to be epinephrine, DMSO, electroshock...and complete-body immersion in a human-sized deep fryer:

Warm liquid goo phase - Complete!
Fox Broadcasting Corp.

Spoiler alert - the concluding scene, a conflagration in the "MIT computer mainframe," would likely have set the Schrock and Buchwald groups back quite a number of years.


Finally, I'll leave you with a silly futuristic quote: "The technology to engineer [Compound X] is still 5, 10 years away..." Sorry, Dr. Lisa - it's been 23 years since this episode aired, and to my knowledge, we're still not making per-heliated small molecules. Maybe check back in another three decades.

--
If you enjoyed this post, try some of the others in the Chemistry Movie Carnival from 2013.

Sunday, April 24, 2016

Feng Zhang's CRISPR "Miami Moment"

I've spent a bit of time this week trying to grok the ever-expanding frontier where biology meets chemistry. RNA therapeutics, chemical probes, synthetic biology, protein engineering...I could go on and on. Of course, this list would be woefully incomplete without the new cool kid: CRISPR.

If you've read a few of the stories surrounding this field's origins, you'll recognize the names Doudna, Charpentier, and Zhang. An interesting story arc emerges in the countless biographies surrounding Feng Zhang, now at MIT / Broad. Here, it's retold through the lens of WIRED author Amy Maxmen:
"Soon after starting [at the Broad], he heard a speaker at a scientific advisory board meeting mention Crispr. 'I was bored,' Zhang says, 'so as the researcher spoke, I just Googled it.' Then he went to Miami for an epigenetics conference, but he hardly left his hotel room. Instead, Zhang spent his time reading papers on Crispr and filling his notebook with sketches on ways to get Crispr and Cas9 into the human genome. “That was an extremely exciting weekend,” he says, smiling."
Have you ever had a point in your life like this?  Perhaps Zhang truly found the conference boring, and researching CRISPR was his best escape. However, since this story crops up so often, I'd like to think it's an attempt to capture the "flow" state as it applies to crystallization of a new field of research or career direction. Hopefully you recognize the feeling - total immersion, loss of time, tuning out all external concerns while your brain opens up to the vast possibilities of something truly new.

Clearly, a computer algorithm with a scientific sense of humor printed this lotto ticket. 

From my own experience, I can remember a handful of flow moments that I sustained for longer than a few hours. In the first, I spent two or three days reading everything I could about a competitor's catalysis research - hoping not to get scooped - and encountering multiple exciting ideas about monodentate ligand binding left unexplored. In another, I tried to track the entire Vinca metabolism from Tryp to the few hundred polycyclic alkaloids like vincristine and ajmaline. Plant metabolism turns out to be much more complex than I'd ever imagined.

Readers, I'm certainly not alone...can you recall when you've experienced a version of Feng's Miami moment? What was it like?

Wednesday, April 6, 2016

WWWTP? Math Non-profit Edition

Saw this "promoted Tweet" go by on the Twitterz earlier this evening.
But something just didn't add up.

Can you spot the problem?

Sunday, February 21, 2016

WWWTP? Slate "slate" Edition

A slate on Slate, a frustrated man next to a frustrated organic structure. The title?
"Teaching the Teachers."

Judging by his chemical acumen - yes, this man needs teaching. Desperately.

 How did he manage to make the western 1,4 diene without it slipping into conjugation?
Inquiring minds want to know.

Saturday, February 20, 2016

What's that Crud in My NMR Sample?

Scene:

The reaction finished in 20 minutes by TLC. You grabbed a quick aliquot for LCMS; one peak! Quickly, you quenched, extracted, perhaps pushed through a silica plug for good measure. After concentration, a gorgeous white powder formed, so you pulled high vac for 20 minutes and rushed down to "get your proton on." But, darn it! Still wet with traces of, well, something...

Friends, has this ever happened to you? Trace impurities in otherwise perfect spectra lead to much head-scratching and SI docs labeled "final product_spectrum 5." 

The three papers linked to this post should help.

The new chart offers recommendations (colored arrows) based on Chem21 assessments of environmental impact, safety, and toxicity. Shown above are chemical shift tables (1H) in deuterated chloroform, acetone, and dimethyl sulfoxide.

If I were joining a synthetic lab this year, or starting an internship / work-study, I'd download 'em all and thumbtack liberally to the back of my bench. Guaranteed utility.