Archive for the ‘Education’ Category

Organic Chemistry Exam Show-and-Tell

Wednesday, November 13th, 2013

ChemBark's Orgo BunnyWhen I was in college, there was a professor who was notorious among the grad students for stopping them to show off his organic chemistry exam questions. Unlucky TAs on their way to the bog would get tied up for what seemed like hours going through drafts of exams in the hallway.

But now I think I know how he felt. There’s a certain degree of satisfaction associated with writing a problem that makes students integrate their knowledge of multiple subjects within a given set of consecutive chapters in whatever textbook you’re using.

Instead of stopping TAs in the hallway at work, I figured I could move the practice into the 21st century by using the blog. I’ll post any gems I’m proud of in this thread. Feel free to share your favorites as well.

To start…

Exam 1, Problem 3-2. (8 points) Draw the most (Brønsted–Lowry) acidic, optically-active isomer of C6H10.

Click here for the answer. The chapters for this exam included acids and bases, isomerism, functional groups, alkanes, and stereochemistry.

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.

–Paul

Waking Up to a Dream Job

Wednesday, September 25th, 2013

ed_academic_bigLast month, I started as an assistant professor of chemistry at Saint Louis University. I’ve wanted to be a chemist ever since I was 15 and enraptured by Dr. Liebermann’s three-year chemistry sequence at my high school. My wonderful experience as an undergrad at NYU cemented these plans and the goal of a career in academia.  Almost every academic decision I’ve made since high school has been directed toward being able to teach chemistry and conduct research.

I feel very fortunate to have successfully navigated the job market, and I wish all the best to those of you going out for jobs now. I could never make sense of everything I saw when my colleagues and I applied for jobs. It was an incredibly tough experience, made all the more frustrating by the opaque nature of the process. You never know exactly what’s important, what schools are looking for, or if they’ve even received your application. So little information is shared that when it finally trickles in from second- and third-hand sources, you treat it like valuable military intelligence—dispatches from the front lines of battle. Some people win, but many don’t and must endure a long wait until the next application cycle opens.

Despite the elation—and relief—of getting the job I’ve always wanted, I haven’t really had the opportunity to savor the moment. The hectic experience of moving halfway across the country blended with the hectic experience of setting up the lab at SLU. Two weeks later, classes started and my head has been spinning ever since. SLU definitely values teaching more than your typical Ph.D. chemistry department, and I am teaching two classes this fall: (i) sophomore organic chemistry for majors and (ii) an introduction to the chemical literature + scientific presentations.

The semester hit me like a freight train. The volume of work is unbelievable. I give four lectures a week, and because it’s my first time teaching, these lectures all have to be created from scratch. The joy of being finished with a lecture is quickly superseded by the crushing realization I have to prepare and deliver another whole lecture in 47 hours. On Mondays, I give two lectures, so weekends are particularly filled with fun. Aside from preparing lectures from scratch, there is the other nasty detail that I’ve never written exams before so I can’t distribute old ones as practice tests. So, instead of writing one new exam per unit, I have to write three. And as it turns out, writing thoughtful exams also takes a lot of time. I suppose I could give my colleagues’ old exams,  but everyone emphasizes different things and I feel that the practice exams I give students should reflect what they’ll see on my exams.

In many ways I feel like a new parent. I’ve gone through life as a kid saying, “when I grow up, I’m going to do it this way.” Now is my chance to correct all of the problems I experienced as a student. One of the things I disliked about taking organic chemistry was that no one took the time to explain things in answer keys. Answer keys are a wonderful opportunity to teach; just dropping an answer on students is frustrating to them. Of course, writing detailed answer keys takes a lot of time, but I’m making it a point to do so. Here was the key from my last practice exam. Let’s see how long I can keep it up.

Outside of lecture preparation, there’s a whole bunch of grading to do and many, many meetings with students and advisees. When I was a grad student and postdoc, I could keep my calendar on a small index card. Now, I have so many meetings every week, I finally surrendered and registered for Google Calendar. I get multiple text messages every day reminding me whom I’m supposed to meet with, when, and where. On top of that, students and colleagues stop by my office regularly, which is great. I live for these interactions, but they are another investment of time. Basically, the only time I can get work done is at home, which is yet another weird/counter-intuitive realization I’ve made in the past month.

Despite the fact that I always feel I’m doing something, I am still amazed how quickly work piles up. Up to 50 new e-mails a day land in my inbox, and some of them I just can’t get to. Unfortunately, friends and blog stuff are the ones that typically get pushed to the back burner, so my deepest apologies if you’re waiting on a reply about something. Also, while I have yet to submit a research paper from SLU, referee requests have already found their way into my SLU inbox.

So, the last five weeks have been crazy, but enjoyable. I really like working with students and I have a fantastic group of colleagues. I hope to update the blog more often, but it’s one of those things that is easily pushed to the back burner. I’m looking forward to the time when I will teach a class for the second time and I’ll already have the material ready to go, but sadly, that is at least a year away. In the meantime, I’m just hoping to keep my head above water…

Review: ChemDraw for iPad

Thursday, August 22nd, 2013

chemdraw_squareA long time ago, the people at Perkin-Elmer gave me a free download of their not-yet-released ChemDraw app for the iPad. The product eventually launched and I never got around to reviewing it because I was tied up with other things.

I did play around some after downloading it, but my big question was always, “Why bother?” That is, why would I bother drawing structures with a bare-bones version of ChemDraw on a tablet when I could just use a souped-up version of the program on my laptop? Drawing structures with your fingers is kind of hard, the screen is limited in size, and you have to e-mail the structures to yourself for use elsewhere. So, at first, I was not impressed.

Fast forward to the second week of July when Tara and I took a trip to St. Louis to pick out an apartment and meet with prospective grad students. I had a free morning one day, so I came to campus early and sat in on an organic class taught by my colleague Mike.

What was one of the things Mike was doing? You guessed it: using ChemDraw for iPad.

I had only thought about the uses of ChemDraw to research chemists, but it’s actually a really neat tool for teaching. First, the iPad can be connected to the projection system in our lecture rooms, so you can jot reactions down on the tablet instead of using chalk. One of the advantages of this approach is that you can save screenshots and post them online afterwards, so students needn’t worry about copying everything from the board.

That’s not a big deal by any means—chalk is fine—but what is much cooler is how the app can be used as a tool for studying stereochemical assignments. There is a feature in the app that automatically labels carbon stereocenters as R or S and alkenes as E or Z. Thus, making a practice problem for yourself is as easy as toggling the setting off, drawing a molecule, trying your hand at making the assignments, then toggling the setting on to check your answers. Very neat:

chemdraw_ipad_stereochem_practice

On top of that, students can draw nice, clean structures to pose questions about reactions and mechanisms to their classmates or teachers. That’s not bad at all for $10, especially when you consider that a single copy of ChemDraw Standard costs $170. (And our textbook costs $240.)

And, of course, there are things for both students and researchers to appreciate. You can use the tablet to draw a structure and have the app spit out its formula, mass, and mass-by-atom percentages. This feature should be handy for students in orgo labs. You can even use these functions to (improperly) handle solvates when you are desperately trying to get your elemental analyses to pass.

If there is one thing that is especially annoying/limiting about the ChemDraw app, it’s that there’s no tool that lets you draw text or formulae directly onto the screen. I’m hoping Perkin-Elmer fixes that in the next version, but overall, it’s worth the $10.

Disclosure: ChemBark was given the application for free (a $9.99 value).

Other reviews: In the Pipeline, Chemjobber, Chemistry World, Andre the Chemist, Macs in Chemistry, Chemistry and Computers

Edited to add (7 Sept 2013): The latest edition adds a bunch of new features, including text boxes (see below).

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?

Nothing.

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.