Archive for the ‘Grad School’ Category

Orgo Thursdays

Monday, August 10th, 2015

ed_academic_bigOne of the nice things about being a professor is that you have the agency necessary to successfully garner support for causes you feel are worthwhile. Earlier this year, I brought to SLU something that I had sorely missed from my time as an undergrad at NYU: organic division problem sessions. These were held once a month during the school year and worked as follows:

Each organic group took turns hosting the sessions. The hosts would be responsible for bringing pizza, beer, and 3 or 4 hard, graduate-level organic problems. The organic students and faculty would gather at 6 pm, eat, drink, and work the problems. Volunteers would put up their answers, the audience would nitpick and argue, the faculty would weigh in with suggestions, and if no one could figure them out, the people who brought the problems would set us straight.

The attendance of organic graduate students was expected, and undergraduates were welcome to attend. In something of a paradoxical twist, I think these sessions were instrumental in both (i) making me appreciate that organic chemistry is hard and (ii) making me feel like organic chemistry was something I could do.

At Harvard, I attended Christina White’s monthly organometallic sessions, even though I was the dumbest participant by far. Each person was responsible for bringing one slide that summarized a recent paper from the literature. While these weren’t problems, there was a fair amount of arguing over mechanisms. The White Lab’s departure to Illinois marked the end of these sessions for me. It’s kind of unfortunate that Harvard had nothing else—that I know of—considering the rich history of late-night organic chemistry seminars at Harvard led by Woodward.

Earlier this year, I decided to champion these blasts from the past and start one at SLU.

On the third Thursday of every month, I host a voluntary organic problem session. I bring pizza and three graduate-level problems, and the students work them over, present ideas, and face my ridicule—or occasionally, approbation. Usually I steal problems from texts, but if I’m feeling saucy, I’ll write them based on interesting papers I’ve come across and stashed away.

While attendance at Orgo Thursdays is completely voluntary—except for my grad students, for whom the session replaces group meeting that week—we’ve averaged 12 participants over the first seven sessions. That’s makes the sessions just a shade smaller than those at NYU, and isn’t too shabby given the size of our department.

Now that I’ve seen these sessions from both sides of the table, I am convinced of their value in a number of areas:

1. For any skill, if you don’t use it, you lose it. The problems keep students and me thinking about fundamental course material long after final grades are in the books. The continued practice is going to help our grad students become better teachers and perform better on their comprehensive exams, which are taken in the summer between their second and third year.

2. There is something to be said for placing students in uncomfortable situations where they have to think on their feet and be brave. This is a life skill that classes often don’t focus on developing.

3. These sessions are a great opportunity for everyone to interact with people from other research groups. I believe strongly that departments should actively foster wide collegiality, where students and faculty have meaningful interactions not only with their labmates, but with people in other labs. Such an environment is so much more enjoyable and supportive than when each group is an island.

4. These sessions help me get to know our students better. It’s never a good situation when a professor has to write a ‘third’ rec-letter for a student he hasn’t talked to since a class four years ago.

5. The problem sessions give undergrad students an opportunity to stay involved in organic chemistry after their sophomore classes in the subject are done. Undergrads also get a taste for what graduate school is like, given they are working graduate-level problems alongside our graduate students. When I was an undergrad, it was empowering to participate in these sessions.

My plan is to keep hosting Orgo Thursdays until I run out of problems or money to buy pizza. So long as people keep coming, I assume they see value in the activity too.

Thesis Acknowledgments

Thursday, March 19th, 2015

ed_academic_bigChemjobber has a post up asking readers what information they put in the acknowledgments sections of their dissertations.

I have always been fascinated by whom grad students choose to acknowledge. As a first-year, I used to pull old theses off the shelves of our group room and read the acknowledgments sections from front-to-back. Some were long; some were incredibly terse. Some were over-effusive in praise; some had cutting zingers. But every acknowledgments section was interesting and, I felt, gave me some sense of the personality of the student whose research had helped lead the group to where it was.

About once a year, I would go to the chemistry library and similarly indulge my curiosity on a grander scale. I would climb the stairs to the balcony where old theses were kept and hunt for interesting names: Nobel laureates, current professors, recent friends who’d graduated, and grad students present at remarkable events (e.g., when Corey won the Nobel, when various professors had moved labs, and when Jason Altom took his life). I’d flip through their work, admire the figures, and always finish by reading the entirety of their acknowledgments. It was fascinating, and I cherished the glimpse of what each scientist was feeling at my point in their career.

People often joke that your acknowledgments are the only part of your thesis anyone will read carefully, including the professors on your committee. But that isn’t a joke—it’s the truth. When I was writing my thesis, I viewed writing the acknowledgments section as a wonderful opportunity to thank everyone from my educational career, past and present. It was six-and-a-half pages of joy to write.

And since the dissertation guidelines at my school allowed students to include epigraphs, I twisted a line of a famous poem such that it would serve, in my estimation, as a sufficiently veiled comment on my sentiments at the time.

To this day, I keep a copy of my dissertation on my iPad and I read the acknowledgments section every four months or so. Yes, I’ve almost memorized it by now, but reading it again always brings back a flood of happy, sad, and funny memories.

Sometimes, you need that.

UCLA Professor Patrick Harran Strikes Deal with Prosecutors

Sunday, June 22nd, 2014

BulldoodyPatrick Harran, the UCLA professor who faced four felony counts in connection with the death of Sheri Sangji in a laboratory fire, has struck a deal with prosecutors that allows him to avoid charges in exchange for a $10,000 fine, 800 hours of community service, and running a lab free of safety violations. So long as Harran completes his end of the terms of the agreement, he will avoid trial and have an untarnished criminal record.

What a relief!

As an assistant professor in charge of a research lab, I could not be happier with this outcome. I have a lot of stuff to worry about, and ensuring the safety of my students cannot be allowed to get in the way of important things like finding consulting gigs, collecting awards, traveling to international conferences, and stealing ideas for grants. All of those OSHA rules are meant for industry, not academia. The bar for what passes as safe in academic labs is clear, and people who want to work under moderately safe conditions know better than to go to graduate school. The government simply can’t expect me to be responsible for what happens in my lab, which is well over 50 feet from my office and not even the same direction as the restroom. I’m happy to buy enough safety goggles and almost enough lab coats to outfit my students, but the rest is up to them. If Aldrich has written a technical note on their hazardous experiment, my students know not to bother me.

The most important aspect of the Harran deal is how it extends the long, proud tradition of excusing PIs of any professional responsibility for their work. Society recognizes that professors are only supposed to have good things happen to them. We get the lion’s share of credit for papers, not the students or postdocs. We get the big salaries, not the students or postdocs. We get the awards, not the students or postdocs. On the flip side, professors must be protected from negative consequences at all costs. If an accident happens in one of our labs, that’s the students’ fault. If multiple papers from one of our labs contain fabricated data, that’s the students’ fault as well. Clearly, professors are not responsible for supervising their groups for integrity or safety. We know this because Dalibor Sames and Patrick Harran are still in charge of their labs. I applaud Columbia and UCLA for recognizing that you can’t discriminate against professors for trivial things like irresponsibility and incompetence. Anyway, it’s the competent professors you need to watch—lightning never strikes twice, right?

Of course, I realize that there should be some consequences when something truly horrible happens. In these situations, professors must arrange for perfunctory punishments that allow all of the parties charged with oversight to save face. That’s what we saw here: UCLA threw some money at a scholarship in the victim’s name and at establishing a safety program it should have had in the first place. Personally, Harran was forced to donate money to the hospital where his student died. Incidentally, I think $10,000 was way too much; the man only earns $301,000 a year. How is he going to make ends meet with just $291,000? At least Harran’s lawyers were clever in how they disguised the 800 hours of community service as a major inconvenience instead of court-mandated preparation for the Broader Impacts section of Harran’s next NSF proposal. Killing two birds with one stone is exactly why good lawyers get paid the big bucks.

In all seriousness, I think the deal agreed to by prosecutors is a grave injustice, but one that comes as no surprise in today’s legal system. Without any changes to the material facts of the case, how does the DA go from charging someone with four felony counts to striking a deal that allows Harran to have a spotless record with a payment, community service, and actually doing his job of running a lab free of safety violations? Note that this was not a plea bargain; Harran pleaded guilty to nothing—not a misdemeanor, or even an infraction.

The game plan of Harran’s legal defense was quite effective: delay, delay, and delay. They gummed up the works with continuance after continuance and motion after motion. In the end, it appeared the prosecutors were willing to do anything just to clear the case. I mean, was this deal what the prosecutors were holding out for all of these years? What makes it all the more worse is that the original deal called for 400 rather than 800 hours of community service. The judge had to step in and double it.

My heart goes out to Sheri’s family for their loss. While I think our legal system has denied them justice, my hope is that the field of chemistry does not forget what happened to her. I hope UCLA’s reported new-and-improved safety culture persists, and I hope the rest of the world of academic chemistry also strives to do a much better job regarding safety than it has in the past. At the very least, I can guarantee you that Sheri’s death has had an indelible, positive effect my approach to safety and how I manage my lab and students.


For more coverage: C&EN’s Jyllian Kemsley and Michael Torrice have done a fantastic service for the community in covering the case, and Chemjobber has been curating links to coverage on his site.

Doctor? No.

Wednesday, October 16th, 2013

bracher_office_doorI generally like to be respectful of people. Toward this end, I try my best to address people properly. You’ll find that I’m pretty liberal in using “Dr.” when addressing letters and e-mails, because you never know when someone is going to get upset at being called “Mister”. In contrast, few people seem to get upset at being called a doctor when they are not. When I was applying for faculty positions last year, I am certain I conferred Ph.D. degrees on a multitude of unsuspecting departmental staffers whose job it was to assemble the applicants’ files.

On the flip side, I have a personal aversion to signing anything as “Dr.” I always check “Mr.” when filling out forms, and I cannot bear to end an e-mail with “Dr. Bracher.” As I am now a teacher, this has established a weird dynamic where students address their e-mails to “Dr. Bracher” and I return them by signing “Paul.” I know this has got to weird the students out because I remember fretting over how to address professors when I was in college. Do you call them “Professor”, “Doctor”, or by their first name? I am pretty sure I always opted for “Professor.”

In my undergrad research lab, it was always a big deal for students when the boss started signing his e-mails to you by his first name. It was an unmistakable signal that you had made it and was regarded as a rite of passage in the lab. In contrast, my graduate and postdoc advisors were pretty much known exclusively in the lab by their first names. Of course, the undergrad-professor dynamic is much different from the dynamic with grad students and postdocs, but it’s always interesting to see how these differences manifest themselves.

Some students attempt to solve the e-mail problem by using the non-direct “Hi,” “Hey,” or “Hello there” salutation. Of course, in trying to avoid any awkwardness, this device mostly just draws attention to it. Would you walk up to a professor and address her as “Hey”? Some of my colleagues sign their e-mails to students as “Dr. D” (or similar), which is an interesting compromise between formal and informal. At the same time, it makes me question what I should address these professors when we are in front of students. Can I say “John” (as I normally would), or should I say “Dr. Doe”?

While I don’t especially care what people call me and would never be offended by any of the standard choices, I prefer “Paul”. But after two months in St. Louis, it seems as if I’m going to be “Dr. Bracher” to the vast majority of students. To friends, colleagues, and those online, I will still be “Paul”, while to family at home, I have always been “P.J.” All are fine with me.

Yesterday, I found myself reconsidering whether to sign my e-mails to students as “Dr. Bracher” to make them feel more comfortable. My conclusion was not to change—signing “Dr. Bracher” would probably make me feel just as weird as if they were to address their e-mails to “Paul”. Anyway, the decision of what to call myself has got to be one of the few privileges to which I am entitled in this new job.


Andrew Myers and Harvard Sued by Former PhD Student

Sunday, June 30th, 2013

ChemBark InvestigatesDr. Mark Charest, a chemistry PhD student who graduated from Harvard in 2004, is suing the university and Andrew Myers, his PhD advisor, over the royalties associated with a patent covering intellectual property developed during Charest’s graduate work.

In 2005, the Myers Lab published this paper in Science that described a new synthetic route to 6-deoxytetracycline antibiotics. Charest was the first author on the paper, and the work was patented by Harvard’s Office of Technology Development (prior to submission for publication). A company, Tetraphase Pharmaceuticals, was started to commercialize the work by licensing the tetracycline patent from the university.

According to Charest’s complaint:

  • Harvard’s policy is to distribute royalties equally among all of the inventors on a patent unless the inventors agree to a different distribution.
  • Harvard OTD asked Charest and his former labmates to voluntarily accept a distribution of 50% to Myers, 15% to Charest, 15% to Dionicio Siegel, 15% to Christian Lerner, and 5% to Jason Brubaker (the five co-authors of the paper).
  • The four co-authors besides Myers agreed amongst themselves to a distribution of 18.75% to Charest, 11.25% to Siegel, 10% to Lerner, and 10% to Brubaker. Myers would not participate in this discussion and his 50% share was not open to discussion.
  • When Charest later spoke to Myers, Myers told Charest to “tread lightly”, “be careful”, and “think about [his] career”. Charest interpreted these statements as threats.
  • Charest initially refused to accept an unequal distribution of the royalties, and then engaged in a series of exchanges where Harvard’s representative threatened to directly cut Charest’s share of the royalties or to shift the distribution of licensing payments to a second patent on which Charest was not listed as an inventor. Fearful of this threat, Charest signed an agreement to accept 18.75% of the royalties for the first patent (presumably, the distribution arranged by the four postdocs/students).
  • The second patent never materialized, and Charest believes it was a ruse fabricated to force his hand to volunteer to let Myers get a 50% cut of the royalties.
  • Later, Charest describes a second act in which Harvard’s OTD did shift royalties away from Charest’s patent.
  • Myers refused to serve as a reference when Charest applied for a position at a venture capital firm, and Myers would not return phone calls when a potential employer directly contacted Myers regarding Charest.

Charest appealed to an internal review board at Harvard, but his case was unsuccessful. His lawsuit filed on Friday seeks reallocation of the royalties, punitive damages, and a bunch of other stuff that is outside my complete comprehension. Read the document for yourself.

It will be interesting to see how this story plays out, but it would seem to be yet another cautionary tale that when you are a graduate student, you are in a position of incredible weakness. As is said, your advisor holds your paycheck in one hand and your letter of recommendation in the other. And in case you are naive, the chains don’t get unshackled just because you’ve graduated. You’re still going to need that letter of recommendation for future jobs, so if your old boss wants to take 50% of the royalties, what’s to stop him?


Disclosure: I went to Harvard for my graduate work and regularly came into contact with Myers, Charest, and Brubaker, as my desk was right next to the Myers Lab. I know Mark Charest and had several conversations with him over the course of my graduate career. I think I saw him one or two times after he graduated, and I’ve had no interaction with him since I graduated from Harvard.

H/T to A.D. for tipping off ChemBark

Elsewhere: Universal Hub, Chemjobber (analysis of prof-student/postdoc fiduciary relationship), Chemistry Reddit, Chemical & Engineering News, In The Pipeline, The Harvard Crimson.