Archive for the ‘Lab Management’ Category

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 The joy of being finished with a lecture is quickly superseded by the crushing realization I have to prepare and deliver another whole lecture in 47 hours.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…

Chemistry World and Others on Dodgy Data

Thursday, September 5th, 2013

ed_baseballcap_150Hello, friends. Pardon the radio silence of late. My first semester of teaching just started at SLU and my head is already spinning. I’ll have a full post on that subject soon, but I wanted to weigh in on a few recent pieces regarding the cases of suspicious data that were reported here and elsewhere.

Reporter Patrick Walter wrote a story earlier this week for Chemistry World that examined whether blogs are appropriate venues for policing the chemical literature for misconduct. I was interviewed for—and quoted in—the story, which I feel is thorough, is balanced, and represented my positions accurately. As you might imagine, I argue that blogs are indeed appropriate venues to report suspicious data and to analyze how the community should respond to misconduct.

There are plenty of people who disagree with me—to varying extents—and the article raises their concerns as well. That is fantastic, because this is a discussion that we need to have. I am happy to engage in thoughtful debate on the subject (see posts here and here) in hopes that we, as a community, can arrive at a more efficient system for removing manipulated data from the literature and preventing their publication in the future.

Mitch André Garcia, who runs both Chemistry-Blog and the chemistry subgroup of Reddit, is one of the people who took exception to my post on the manipulated spectra in Organic Letters. Here is what he wrote on Twitter:

I’m left scratching my head here. How do the nanochopsticks he reported qualify as “acceptable to cover” for being “egregiously manipulated and…in a high impact journal” but not the erased impurities in the Anxionnat/Cossy spectra reported here? Seems pretty hypocritical. And if we can’t agree on whether these cases meet his standard for “egregiously manipulated” and “high impact”, how are we supposed to agree on anything?

My view on the matter is that anyone who wants to raise concerns publicly about data may do so, with the full realization that they are putting themselves on the line. If I raise concerns about the integrity of data in a paper, I am accountable to defamation law and the high intelligence and ethical standards of the readership here. I can only bring information to people’s attention. If that information is wrong or doesn’t support my opinions, I will be excoriated in the comments and lose credibility. If what I publish is defamatory, I will probably also be sued. The root cause of the outrage among chemists about these papers cannot be attributed to blogs; the data speak for themselves.

A few days ago, John at the blog It’s the Rheo Thing posted some cautionary advice to “activist [bloggers] that are confronting examples of fraud, plagiarism and other publishing infractions in the technical literature”:

What goes around, comes around. Many are pleased to bring the axe down hard on someone’s head, and hold as many people responsible as possible (from ALL the authors to the principal investigator and maybe even beyond that), but we need to keep in mind that publishing scientific research is a human effort and as such, will be imperfect at times even when no harm, deceit or other nefarious activity is intended. Many of the commentators screaming for blood are young professionals you have yet to run a large, established research group, but who think that they will be able to do so flawlessly in the future. Of course that won’t happen. You will have failings and shortcomings and things will go wrong despite your most fervent intent to prevent it. Most people do not have a problem with that.

Most people. But there will be plenty of others wanting your head on the same chopping block and with an added level of glee since you were responsible for bringing so many down yourself. It’s human nature. We can’t change it, this perverse desire to bring down the people bringing down others. Worse yet, these efforts to trap you may be entirely without merit. That won’t matter. “A lie can travel halfway around the world while the truth is still putting on its shoes” (Mark Twain). Your name and reputation can be placed in the same trash heap as those truly deserving it far more easily than you can ever imagine. Despite your noble intents and purity of heart.

User “juicebokz” on Reddit called John’s post “a letter to ChemBark”, and I feel compelled to weigh in with the following points:

Do you seriously think that the responsibilities of running a modestly popular blog don’t weigh on me? Do you think that I don’t consider whether I am treating the subjects of these sorts of posts fairly? These posts are not aimed at destroying scientists; they are aimed at protecting science. I do not take joy in the downfall of others, but I am not going to let a miscreant’s potential downfall prevent me from discussing a topic that I feel is important. Should any researchers be “brought down” for data fabrication, I will not be the person responsible for bringing them down. They will have been the people responsible for their own downfall.

And I am by no means a perfect person. Everyone makes mistakes and does things of which they are not proud. The point is that you have to pay for your mistakes, then dust yourself off and go about living a productive life. Should anyone gather the motivation to search through my past, or present, they’re going to find stuff that will embarrass me…but they are not going to find any fabrication of data.

As for drawing attention to co-authors who very likely did not actively participate in the fabrication of data, I still stand by the position that authors must share the responsibility for the content of their papers. “Share” does not mean “share equally”, but all authors should at least read through their papers and keep an eye out for things that are obviously wrong. When you are a corresponding author, ensuring the integrity of the data in your papers must be one of your priorities. If you think I’m alone in this view, please go back and read Smith’s editorial in Organic Letters. Any punishment doled out regarding fabricated data in a paper should be proportional to (i) one’s active involvement in the fabrication and (ii) one’s responsibilities as a conscientious scientist and/or manager. These responsibilities should be the subject of more discussion among chemists.

Finally, does anyone really think I am helping my career by reporting on scientific misconduct? Do you have any idea how uncomfortable it is to send e-mails to the editor-in-chief of a high-impact journal in my field asking for comment about how he’s going to deal with manipulated data in a paper written by one of his associate editors? Was it lost on people that Smith’s response to my inquiry was addressed “Dear Bracher”? It’s certainly not the most cordial of salutations. I asked a follow-up question by e-mail and was not given the courtesy of a reply.

I don’t like these sorts of awkward interactions, but asking hard questions is part of doing a thorough job of reporting, so I’ll just bite the bullet. I can only hope these interactions don’t come back to hurt me down the road, but that’s a possibility. At the end of the day, I would love not to have to write about scientific misconduct because (i) chemists have stopped doing it or (ii) universities, journals, and government have created a good system for dealing with it.

Now, how do we make that happen?

Organic Letters on the Lookout for Data Manipulation

Friday, June 7th, 2013

Photograph of Bengu Sezen, Columbia University, ChemistryAmos Smith, the editor-in-chief of Organic Letters, just published an editorial to alert the community that the journal has hired a data analyst and that the editors are inspecting the data in papers (including the Supporting Information) for evidence of manipulation:

I write to alert the organic chemistry community to a serious problem related to the integrity of data being submitted for review and publication by Organic Letters and to outline steps that the Journal is taking to address this concern. Recently, with the addition of a Data Analyst to our staff, Organic Letters has begun checking the submitted Supporting Information more closely. As a result of this increased scrutiny, we have discovered several instances where reported spectra had been edited to remove evidence of impurities.Such acts of data manipulation are unacceptable. Even if the experimental yields and conclusions of a study are not affected, ANY manipulation of research data casts doubts on the overall integrity and validity of the work reported.

Smith went on to state that the corresponding authors of manuscripts would be held responsible and punished by the journal for any manipulation of data, although no specifics were given for what sort of punishment would be doled out:

In some of the cases that we have investigated further, the Corresponding Author asserted that a student had edited the spectra without the Corresponding Author’s knowledge. This is not an acceptable excuse! The Corresponding Author (who is typically also the research supervisor of the work performed) is ultimately responsible for warranting the integrity of the content of the submitted manuscript.

The responsibility to foster a research environment where all involved can confidently present their results, even if they are not optimal, resides with each research supervisor and Corresponding Author. At times, the inherent power of a research advisor’s position can create an atmosphere that leads some to embellish results.

I have noted before that professors (i.e., corresponding authors) often seem to receive the lion’s share of credit  (e.g., prizes, invitations, fame) for great papers, but students receive most of the blame when misconduct is unearthed. I am glad that Smith is holding corresponding authors accountable for the work that is published by their labs. Professors, as managers, have a responsibility to control the quality of their lab’s output. Famous and/or scary PIs should not be surprised that when they badger and yell at students for higher yields and cleaner baselines, some students are going to resort to inflating yields and manipulating spectra. I am not at all saying this is right; I’m just saying it happens, and part of the reason it happens is because some PIs reward it.

Smith’s editorial also makes me think back to our original reporting regarding the Sames-Sezen retractions and how Columbia University completely erased the following section from their policy on research misconduct:
In modern collaborative research, the implications of academic misconduct or fraud go far beyond the individual; they also affect collaborators whose own work has been committed to objective search for truth. The specter of guilt by association may lurk in the background for many years to come. Therefore, joint authorship requires joint responsibility; each author claiming credit for the entire work must also be aware of joint discredit. Investigators in collaborative research projects each must make reasonable and periodic inquiry as to the integrity of and processes involved in gathering and evaluating data. It should be understood that overall responsibility for the integrity of collaborative research rests with the principal investigator. Senior investigators cannot be allowed to escape the consequences of the discovery of misconduct or fraud committed under their supervision.

Yes, they deleted that section DURING their investigation. Of course, Sames is still a professor at Columbia while Sezen has had her Ph.D. revoked. The way Columbia dealt with that case was a travesty—a complete disgrace.

I hope Smith sticks to his guns.

H/T: Excimer
More discussion: Just Like Cooking, Chemjobber, r/chemistry

Lab Manuals

Thursday, May 16th, 2013

ChemBark's Orby the InsectI’m always interested to come across instructional documents on chemistry professors’ Web sites. These documents can be great resources, because they often contain very practical advice about safety, direction on how to maintain instruments, and guidance on experimental technique from experts in the field. Taking the time to commit this information to writing also helps prevent “institutional” loss of memory when senior members of the lab graduate without having properly trained the next generation of students.

Unfortunately, you don’t come across that many lab manuals online. Perhaps this is because some of them are distributed in hard copy only. Perhaps, some professors don’t want to explicitly write procedures and safety guidelines in fear they might be used against them in court. My guess, however, is that most people can’t find the time to sit down and write out this information—or they don’t see the value in doing so.

Jim Tour’s “Guidelines for Research” is among my favorite documents. He gets very specific about some of the advice he doles out. For instance, all nitrogen bubblers left on overnight should have a flow rate of one bubble per second or less. Tour provides guidance on how he likes notebooks to be kept, and he also provides expectations about work ethic and vacations. Finally, there is the passage on personal hygiene:

Personal Hygiene: Although not customary in all countries, Americans generally bathe at least several times per week. As a result, many Americans are offended by the infrequent bathing habits of others (whether Americans or internationals). Thus, you may be leaving a negative impression of yourself without ever knowing it. Unfortunately, bad impressions are often difficult to overcome. Likewise, be sure to use an underarm deodorant since most Americans find body odor to be most offensive. I have seen people causing themselves to be ostracized by others simply because of poor personal hygiene habits.

It might seem trifling or overbearing to provide advice on this level, but the info is correct and I wish more people heeded Tour’s advice.

While the idea of writing a manual all at once seems daunting, I think that doing it in pieces seems quite reasonable. In fact, I think you can assemble some really good tidbits of advice from material that is already posted online. These documents are almost like official memoranda to members of professors’ labs. For instance:

The famous “How to Write a Scientific Paper” article in Advanced Materials had its beginnings as a type-written memo from George Whitesides to his lab.

There’s also Ken Suslick’s cool presentation on how to give a talk.

And I like how some professors provide specific instructions on how to ask them for letters of recommendation.

Anyway, before I go writing similar stuff in the future, I wanted to know if you all had come across any great lab manuals or memos. Leave them in the comments, and I’ll compile a list below.

Lab Manuals

Jim Tour’s “Guidelines for Research
Melanie Sanford’s “Group Welcome Kit
Dave Collum’s site
Bart Bartlett’s “Standard Operating Procedures
Turro Group’s site
Watson Group Manual
Tolman Lab’s “Standard Operating Procedures
Armen Zakarian’s site

 

Starting Up a Chemistry Lab: Advice & Bargains

Tuesday, April 9th, 2013

ed_academic_bigBefore I go and do anything stupid, I wanted to ask everyone for advice about starting up a university chemistry lab from scratch. While it looks like I’ll be inheriting some glassware and chemicals in my assigned lab space, I’ll basically need just about everything you can think of. I know that places like Sigma-Aldrich salivate at the prospect of reeling in people like me, and I’ll definitely take my wish list to them and their obvious competitors for quotes, but I’d love to use this thread as a resource for crowdsourcing wisdom about how to get the most bang for your start-up buck. I see no sense in wasting money.

I’ll begin:

– I am routinely appalled at how much the safety glasses in chemistry catalogs cost (e.g., $11 for a run-of-the-mill pair from Aldrich). I love the style variation and price offered by Northern Safety (e.g., $4 or lower for a better pair). I know $7 is not a huge deal, but it adds up when you’re buying enough to outfit a bunch of people. Also, with decent safety glasses as low as $2, there is no excuse for not carpetbombing your lab with eye protection (for large groups of visitors, etc.) and tossing out nasty, old, scratched-up glasses.

– The cost of balances, especially in scientific catalogs, is unbelievably high. I like the deals offered at Affordable Scales. I think my plan will be to purchase one nice analytical balance to be used only when necessary, then a bunch of “precision” balances for routine lab work. For most things, it doesn’t matter if you make your buffer with 15.1 g of salt versus 15.005 g. In my experience, grad students and postdocs abuse balances. I’d rather have them abuse less-sensitive units than nice ones.

– Stirring hot plates also seem to cost way more than they should. That said, I am leaning towards splurging for IKA models, because I have had bad experiences with other brands. Anyone out there have a favorite hot plate or know where to get a good deal?

If you’d rather send me your advice by e-mail, feel free. I’ll protect your super-secret identity and post it to the thread myself. And if you’re a magnate of industry and have unwanted equipment you want to donate to charity (i.e., me/SLU), let me know. ;)

Thanks!

Long Weekend, Big Plans

Friday, August 31st, 2012

My plans for Labor Day weekend are all set thanks to a nice discovery during a group clean-up yesterday:

Plenty of gloves? Check. Multiple boxes of FIXANAL? Check.

Who would name a brand of buffer concentrates “FIX ANAL” and shape the container like a…well…errrr?

Germans. That’s who. I guess you can just add this to the list of cross-cultural marketing blunders, though I am not certain that there wasn’t someone who did this on purpose. Who else sells buffer mix in an odd tube like that?