Wednesday, May 4, 2016

[Scene: Jules and Vincent, in a diner, post-seminar]

Credit: YouTube
Vincent: Yeah, but what did you think about the presenter calling that synthetic step 'clever'? He even put it in his slides.

Jules: I wouldn't go so far as to call that synthetic step clever, but it definitely worked. I don't think it was "clever", that reaction was "straightforward". "Straightforward" goes a long way in a presentation.

Vincent: So a reaction needs to be more innovative than straightforward to be a "clever" synthetic step. Is that true?

Jules: Well we'd have to be talkin' about one clever motherf*****n' synthetic step. I mean it'd have to be five times more clever than that Woodward total synthesis of reserpine, you know what I'm sayin'?

Warning Letter of the Week: Lost safety glasses edition

Looks like Polydrug Laboratories got a tough 483 from the FDA recently:
Our investigator observed specific deviations during the inspection, including, but not limited to, the following.

1.    Failure to record and investigate all quality-related customer complaints according to an established procedure.

During the inspection our investigator found a torn sheet of paper titled “Product Quality Complaints” on the floor of your warehouse. We compared it to your firm’sofficial complaint log and discovered that only 2 of the 17 customer complaints on the torn sheet were recorded in your firm’s official complaint log. Further, your firm indicated that there may be additional unlogged and/or uninvestigated complaints, but did not provide further explanation. Your firm had not investigated the complaints we found on the torn sheet. These uninvestigated complaints reported API that were either sub-potent or contained filth, including the following problems:
  • low assay value for [redacted] API
  • particles and hairs in [redacted] API
  • an insect and dirt in [redacted] API
  • safety goggles in [redacted] API
  • [redacted] scoop in [redacted] API
I'm a little surprised about the lost safety goggles and scoop - I am under the impression (that like surgical suites and the dreaded sponge count) items need to be logged in and out of final product packaging areas. 

What is the price of HPLC acetonitrile?: 5/4/16 edition

Something that bothers me about spending on lab consumables is that it is very difficult to track the price of certain supplies. The amount of transparency is quite low; with that in mind, I plan to track the price of a 4X4L case of HPLC-grade acetonitrile weekly indefinitely as a public service.

I initially plan to look three places: the Sigma-Aldrich website, EMD-Millipore's site and also P212121, a site of Sean Seaver, a chemblogosphere stalwart. I have also added an unnamed lab supply house:

Sigma-Aldrich (4X4L, HPLC grade, ≥99.9%, 34851-4X4L): $1,150
Unnamed Very Large Supplier (4X4L, HPLC grade, 99.8% min (GC assay)): $190-230
EMD-Millipore (1X4L, HPLC grade, 99.8% min (GC assay), AX0145-1): $288.00*
P212121 (4X4L, HPLC grade, Purity >99.9%, PA-30000HPLCCS4L): $135.00**

*I know that EMD-Millpore offers 4X4L cases, but I can't find them on their public websites.
**There's a minimum of 5 cases. 

Also, there is a University of Wisconsin-Madison datum that shows HPLC MeCN at $46.50 for 4L (thanks, Anon!)

Tuesday, May 3, 2016

The scientist's Kobayashi Maru

"Prayer, Mr. Saavik. Thesis committees don't take prisoners."
Credit: unwinnable
I have recently been enthralled by Hope Jahren's "Lab Girl." Professor Jahren is a geobiologist at the University of Hawaii; she has written a blog for a long while, and recently published her book, which is mostly memoir, interspersed with comments about botany. She is an exceptional narrator - upon reading this sentence, I burst out loud in laughter and knowledge that I would never write so well: 
I have become proficient at producing a rare species of prose capable of distilling ten years of work by five people into six published pages, written in a language that very few people can read and that no one ever speaks. This writing relates the details of my work with the precision of a laser scalpel, but its streamlined beauty is a type of artifice, a size-zero mannequin designed to showcase the glory of a dress that would be much less perfect on any real person. 
 Readers of this blog will enjoy this sentence:
"You may have heard that America doesn't have enough scientists and is in danger of "falling behind" whatever that means) because of it. Tell this to an academic scientist and watch her laugh." 
The book is getting wide and deserved praise, so it is with some trepidation that I express my discomfort with this passage that I have excerpted. Preceding the passage, Professor Jahren relates the time that she went to Ireland, collected many samples at significant personal cost and then was forced to throw them away at the airport since she did not have the proper permits:
Bill would forever after refer to that trip as "the Wake," whereas I dubbed it "the Honeymoon," and we took to reenacting its climax at least once a year. Whenever we got a new recruit to the lab, his or her first task was to label empty vials, hundreds of them. We'd explain that this was a necessary preparation for a large-scale collection we had scheduled and give directions for a long and complicated alphanumeric code, rich with Greek letters and nonsequential numbers, to be inscribed on each vial in pen, along with the order of production.  
After a day of steady labor on the part of the newbie, we'd hold a summit and either Bill or I would play Good Cop and the other would play Bad Cop (we traded off). The meeting would start out with our asking the newbie how he or she had liked the task and whether this sort of work was tolerable. It would then slowly morph into a discussion of the upcoming sample collection and the rationale behind its purpose.  
Little by little, Bad Cop would become more and more pessimistic as to whether the proposed collection would test the hypothesis after all. Good Cop would resist this logic at first, urging Bad Cop to consider the fact that the newbie had put so many long hours into the preparation. Even so, Bad Cop just couldn't let go of the nagging realization that this approach wasn't going to yield an answer, and finally Good Cop had no recourse but to agree that starting over was as unavoidable as it was necessary. At this point, Bad Cop soberly gathered up the vials and dumped them en mass into a lab waste receptacle. The Cops exchanged a knowing look, and Bad Cop trudged off without satisfaction, leaving Good Cop to observe the newbie's reaction.  
Any sign that the newbie regarded his or her time as of any value whatsoever was a bad omen, and the loss of so many hours' work was a telling trial of this principle. As a corollary, any recognition of futility was perhaps worse. There are two ways to deal with a major setback: one is to pause, take a deep breath, clear your mind and go home, distract yourself for the evening, and come back fresh the next day to start over. The other is to immediately resubmerge, put your head under and dive to the bottom, work an hour longer than you did last night, and stay in the moment of what went wrong. While the first way is a good path toward adequacy, it is the second way that leads to important discoveries.  
One year I played Bad Cop but forgot my reading glasses and so returned early to the melee. Our newbie, named Josh, was busily digging his vials out of the refuse bin, separating each one carefully from the used gloves and other trash. I asked him what he was doing and he said, "I just feel bad that I wasted all these vials and stuff. I thought I could unscrew the caps and save them, and they could be extras or something." As he continued with his task, I caught Bill's eye and we smiled at each other, knowing that we'd identified yet another sure winner. 
I agree that science requires such dedication, and yes, while a trip home may attempt to preserve your sanity, facing your problems and fixing them right then and there will certainly lead to faster answers immediately. Having the fortitude to face such a failure and go right back to problem-solving is indeed the sign of a passionate scientist.

However, is there a point to such an artificial test of character? Are there other tests of character that don't involve wasting hours of mind-numbing work for an undergraduate? (Isn't there enough mind-numbing work already without coming up with a fake test?)

There is so much artificiality to job interviews and training scenarios that perhaps something like this is really not too far out of the norm. That said, if I were Josh and I found out this was a fake situation, I would be royally irritated.

Readers, what do you think? Is this indeed the ultimate test of character for a scientist? Do you believe in the no-win scenario? Are there better tests that are less artificial? 

Ivory Filter Flask: 5/3/16 edition

A few of the academic positions posted recently at C&EN Jobs:

Moscow, ID: The University of Idaho, looking for an assistant professor of inorganic chemistry; $59,000-$65,000 offered.

Milledgeville, GA: Georgia College & State University is looking for an organic chemistry lecturer.

Possibly the best or worst title of the year: "NMR Spectroscopy Expert with NMR Facility Manager Responsibility", Montana State, Bozeman, MT.

Isn't that just "NMR Facility Manager"? or maybe "assistant professor of chemistry (specialty in NMR)"? I dunno. $65-80k offered.

Philadelphia, PA: Two postdocs? staff scientist? positions at the University of Pennsylvania, one in peptide synthesis and the other in mass spectrometry.

Waco, TX: Postdoctoral position in boron complex research at Baylor.

St. Louis, MO: Synthetic postdoctoral position at St. Louis University.

Oxford, MS: Synthetic postdoctoral position at the University of Mississippi School of Pharmacy.

Bellingham, WA: Western Washington University is searching for a visiting assistant professor in analytical chemistry.

Collegeville, PA: Ursinus College is looking for a visiting assistant professor of chemistry. 

Monday, May 2, 2016

Department of Move Along, Nothing to See Here

The preliminary conclusion of the UC Center for Laboratory Safety is that the University of Hawaii - Mānoa needs a major overhaul of its safety systems, and it is promptly publishing the results of its self-critique and lessons learned.

Just keeeeeeeeeeeeeeding!!! Via Jyllian Kemsley, Hawaii-Manoa's press release:
In its preliminary investigation, the UC Center for Laboratory Safety, considered a national leader in laboratory safety, determined that the explosion was an isolated incident and not the result of a systemic problem. The UC Laboratory Safety Team was on the Mānoa campus the week of March 28.
Also, in the comments over the weekend, Dr. Kemsley notes:
U Hawaii Manoa Environmental Health & Safety Director Roy Takekawa said at a March 17 press conference that the lab had been inspected in January and "passed all requirements." 
 Nope, sounds like an isolated incident to me. 

RIP Harry Kroto

Oddly, it's not on the newswires yet, but C&EN tweeted yesterday (and there was also a blogpost) that Harry Kroto has passed away. Condolences to his family and friends.

UPDATE: Bethany Halford's C&EN article on his passing. Also, Curious Wavefunction's thoughts on Professor Kroto.

18 patent brokers?!?!

Also in this week's C&EN, an article by Frank Hersey about moves in China's research enterprise to move faster towards commercialization: 
...In light of the increasing push to transfer technology to industry, Tianjin University in 2013 opened China’s first national center for patent and intellectual property. The Tianjin University Technology Transfer Center now has 18 full-time patent brokers who work on moving technology from the university to industry. 
Removing the need for central approval for the sale of intellectual property will, in turn, grant China’s universities and institutes greater autonomy in what they research. 
“Passing greater autonomy to universities and cutting the red tape on the reporting for grants involving science and technology is a very big thing because, in general, funds have been very controlled. So if we see policies that allow for more entrepreneurial ventures within the university—your degree programs, new directions for research—that the university can control, then we get bottom-up control. This will have a big impact on research in general, and chemistry is poised to benefit enormously,” Siegel says. 
Or, as Yu summarizes, China’s new policies “will encourage chemists to get involved in ‘useful’ research.”
I still haven't really figured out how Chinese granting agencies work and what power and funds are pooled in Beijing. That said, is anyone else weirded out about the push to commercialize work from universities? Hard to know what will be better for China...  

This week's C&EN

A few of the articles from this week's C&EN:

Friday, April 29, 2016

Are you a chemist and over 50? Write in!

A phenomenal request from Logan's Run:
I would be much more interested to read "how chemists keep their jobs past 50," but I think that getting enough anecdotes to write a story would be challenging. 
Are you a chemist, still a chemist, not a "boss of bosses" and over 50? I would love to publish your story. Please write in to, and I would be happy to publish your story. Anonymous or not, that's up to you.

(My father, whom I love, spent the last ~15 years or so of his engineering career basically working his heart out, running completely scared of being laid off from his employer before he could reach retirement age. He woke up every day determined to be a great asset to his company, thinking about his job pretty much every waking moment that he was not thinking about his family or his other (few) responsibilities. I'm not sure that's attainable for most folks.) 

Job posting: B.S. chemist, Plain City, OH

From the inbox, a position at Quanta BioDesign in Plain City, OH:
The successful candidate will be an essential part of our QC/QA team providing analytical support in characterizing our dPEG® products for both catalog sales and products in clinical trials. Will support company scientists in acquiring and interpreting QC data as well as assist customers who have QC-related questions about our products. Will be a vital link in the development of the dPEG® technology. Excellent communication, problem solving, and time management skills are critical aspects of this position.
Best wishes to those interested.

Thursday, April 28, 2016

So which one of you is it?

John Bohannon is an interesting character who always seems to get a good story. Here he is in Science, having somehow gotten SciHub's Alexandra Elbakyan to give him all of SciHub's downloading data. You gotta read this article, and then come on back here for my weird question: 
...The intense Sci-Hub activity in East Lansing reveals yet another motivation for using the site. Most of the downloads seem to be the work of a few or even just one person running a “scraping” program over the December 2015 holidays, downloading papers at superhuman speeds. I asked Elbakyan whether those download requests came from MSU's IP addresses, and she confirmed that they did. The papers are all from chemistry journals, most of them published by the American Chemical Society. So the apparent goal is to build a massive private repository of chemical literature. But why? 
Bill Hart-Davidson, MSU's associate dean for graduate education, suggests that the likely answer is “text-mining,” the use of computer programs to analyze large collections of documents to generate data. When I called Hart-Davidson, I suggested that the East Lansing Sci-Hub scraper might be someone from his own research team. But he laughed and said that he had no idea who it was. But he understands why the scraper goes to Sci-Hub even though MSU subscribes to the downloaded journals. For his own research on the linguistic structure of scientific discourse, Hart-Davidson obtained more than 100 years of biology papers the hard way—legally with the help of the publishers. “It took an entire year just to get permission,” says Thomas Padilla, the MSU librarian who did the negotiating. And once the hard drive full of papers arrived, it came with strict rules of use. At the end of each day of running computer programs on it from an offline computer, Padilla had to walk the resulting data across campus on a thumb drive for analysis with Hart-Davidson.
All right, which one of you is downloading all of ACS' articles? 

Ask CJ: who are your favorite pharma/biotech analysts/writers?

Great question from the inbox, and one that I'd love to get an opinion on myself: 
Dear CJ and friends, 
As a relatively new chemistry hire in Pharma, I've been looking to broaden my perspective on the industry. In a world where everyone and their pet gerbil is a SeekingAlpha writer who spews out the shallowest of hot hot takes on the latest company press releases, I would like to know which analysts you and your readers think are worth the time and clicks.  
I'm not just looking for industry news, I want people with strong, but thoughtful opinions: particularly those who write from a business perspective, but show a passable understanding of the science behind it. One such person who comes to mind, for instance, is Adam Feuerstein. 
I'm wondering if your readers could list a few of their favorite industry analysts and writers, 
With eternal gratitude,
My two answers that come off the top of my head? Matt Herper at Forbes and Lisa Jarvis at C&EN. 

What happens to assistant professors who go into industry?

Professor Carolyn Bertozzi is the editor-in-chief of ACS Central Science, one of ACS's newer journals and the first that is entirely open-access. She has written a number of opening columns, and they're all worth reading and considering (how often do I get hear the internal thoughts of someone who is a heck of a lot closer to a trip to Stockholm than I ever will be?). Here's an interesting aside from her most recent column, which is about the dearth of senior women chemistry faculty: 
With autonomy comes responsibility, of course, and many people will count on you to keep the ship afloat and headed in the right direction. Occasionally women articulate to me that such responsibility looms large in their mind, that their aversion to academia is rooted in a fear of judgment and failure. In response, I share with them what my dad said to me when I once admitted these feelings. First, he reminded me of the first time he handed me the keys to the car, and I peeled out of the driveway without concern for the depth of my qualification. Then the conversation went like this:
Dad: “You got your own lab? Go for it. What do you have to lose?”
Me: “What if I can’t get grants funded?”
Dad: “So what, as long as you still get paid. Try again.”
Me: “What if I don’t get tenure?”
Dad: “So what, it is still a good starter job that builds skills for many other (higher paying) jobs.” 
He was right about that. My friends who didn’t get that coveted promotion jumped into high-level industrial positions they could never have acquired had they started their career in that same company. You see, after six years running a lab in academia, they had project and budget management experience. They had done HR, PR, and built a valuable network of colleagues and collaborators. No age-matched bench chemist in industry could develop that portfolio of skills at the same pace.
It is the last sentence that I would like to examine. Is this actually true? Far be it from me to doubt Professor Bertozzi's superior years of experience to mine own, but I find this to be a tiny bit skepticism-inducing. I suspect that it depends on the definition of "my friends" and "high-level". Also, is it really true that "no age-matched bench chemist in industry could develop that portfolio of skills?" I think there's plenty of argument to be made that industry is just as good at academia at forcing collaboration, and growing project and budget management experience.

(This draws me to another aside, and another CJ-like complaint about the lack of solid data about job cohorts: what happens to untenured assistant professors of chemistry? Where do they go? What do they end up doing? Do they actually go straight to "group leader" or "director" in industry? Rather than relying on the opinions of prominent chemical biologists or random bloggers, wouldn't it be great if we just knew, i.e. had a database somewhere?)

Readers, your thoughts? Is there enough anecdata out there to support this? 

Wednesday, April 27, 2016

Ask CJ: what to do when there are layoffs of rumors at your company?

Readers, a question from the inbox for which I have relatively little experience: when rumors of layoffs start at your company: what should you do?
A. Nothing. Plan a little, brush up your CV, that's about it.
B. Work on plans for career changes, think about going back to school.
C. Get out ASAP.
D. Other
Please don't take the above choices as the only one.  

The funniest paper you will read today

Credit: Ma et al., Angew. Chem. Int. Ed.
Thanks to Free Radical, I note a paper in Angewandte Chemie from a Chinese team [1] where they coated gloves with tannic acid and found that it greatly improved the ability of the gloves to catch fish.

I kinda love this idea; sure, catching fish in your hands is awesome (you can really imagine a version of these gloves being sneaked into a noodling championship in Mississippi), but who knows what uses this invention will be used for?

1. Ma, S., Lee, H., Liang, Y. and Zhou, F. (2016), "Astringent Mouthfeel as a Consequence of Lubrication Failure." Angew. Chem. Int. Ed.. doi:10.1002/anie.201601667

Tuesday, April 26, 2016

"Nucleotides are not permitted in organic products."

Via Twitter user @mem_somerville, a lawsuit from the Organic Consumers Association against two formula manufacturers.

If you'd like to read some high-test chemophobia, these lawsuits (PDFs) are a great place to start. 

Postdoc: biochemistry postdoc, University of South Florida

From the inbox:
We have an opening for a joint position in the labs of Professor Michael White (Department of Global Health) and Professor Jim Leahy (Department of Chemistry) at the University of South Florida.  This is a post-doctoral position to join a drug discovery project focused on identifying new treatments for malaria.  The successful applicant will establish new methodology for assaying kinases that are difficult to express and develop protocols using the new assays to screen small compound libraries.  Candidates with biochemical experience are preferred.  Interested candidates should contact Jim Leahy ( 
Best wishes to those interested.  

Job posting: NIH postdoctoral position in chemistry

From the inbox:
A postdoctoral position is immediately available in the laboratory of Daniel Appella, Senior Investigator in the Intramural Research Program at NIDDK, NIH. The objective of our research is to use chemically designed Peptide Nucleic Acids (PNAs) to uncover novel facets of biology (for background, see: Nature Communications, 2014, 5, 5079 and J. Am. Chem. Soc. 2014, 136, 12296). In this position, training will be provided on synthetic preparation and purification of PNA as well as the application of PNA to multivalent scaffolds and RNA detection. Candidates must have a Ph.D. in Organic Chemistry (or a closely related discipline) and possess a strong desire to work at the interface of chemistry and biology.  Interested candidates should send a C.V. (listing three references) and cover letter to Daniel Appella ( no later than June 1, 2016.
Best wishes to those interested.