Update: First-Year Professor Craziness

ChemBark Moving to St. LouisHello, friends.

Apologies for the continued radio silence, especially in light of the fact that several instances of data manipulation have recently been exposed through “corrections” published in a variety of journals. The beautiful thing about having a blog is that you can update it whenever you want. Sometimes, life happens and blogging takes a back seat…

I continue to fly by the seat of my pants as a first-year assistant professor. One of the main differences about moving on from life as a grad student and postdoc to life as a professor is the tremendous weight of responsibility involved. If you put something off as a grad student or postdoc, you are usually just inconveniencing yourself. But when you fall short in your duties as a professor, the problem is compounded by the multitude of students who are affected. While a variety of to-dos may arise, it is simply untenable to show up to lecture unprepared, because you’re not just wasting your time, you’re wasting the time of 30+ students. And when you delay getting something set up in the lab, you are letting your group down. I imagine the feeling of being a new professor is similar in many respects to being a new parent—there is so much to do and so little time, but if you don’t get all of your work done, bad things will happen (not to you, but to innocent young’uns for whom you care deeply).

I’m teaching Organic Chemistry II this semester, which is proving to be enjoyable. Once again, it is somewhat stressful to have to create a brand new lecture every 48 hours, but I’ve got a great group of students to keep me going. In lab, my research group is growing and things are continuing to take flight. Outside of lab, I got married a month ago and that was splendid. As luck would have it, a few days after we returned to St. Louis, our high-rise apartment building experienced a massive flood because some genius left his window open over the winter break and the sprinkler lines in his room froze. The water damaged seven floors and knocked out all of the elevators in the building. Unfortunately, my wife and I live on the 11th floor. It is also unfortunate that I have a spinal cord injury that makes it difficult for me to climb stairs. So, since January 7th, I’ve been practically homeless. Some nights I sleep in my office, some nights I sleep in a hotel, some nights I invest the 90 minutes it takes for me to crawl up the 10 flights of stairs. My wife and our dog have been real troopers in this ordeal, and it sounds like one elevator might be working by the end of the week—though after four weeks of this crap, I am not holding my breath.

I hope to return to blogging more regularly soon. In parting, please enjoy a scan of a letter from my property management company to the tenants of our building. I want to vomit every time I read it.

 

clb_burst_pipe_letter



Some Fantastic Christmas Presents

Bethany Halford and the crew at C&EN‘s Newscripts blog run an annual holiday gift guide with some cool gift ideas for chemists, but sometimes it’s more exciting to be surprised by the creativity of your family.

I got a few great chemistry presents for Christmas. The first was a Periodic Table of Magnets that I’ll put on my office door. Next, from one of my new brothers-in-law, I received a fail button in the colors of SLU that plays the sad trombone sound. I’m not sure if all of my students will appreciate this gift, so maybe I’ll keep it in an inconspicuous location. My orgo lab instructor at NYU used to have a bullseye taped to his wall captioned “hit head here”. He would point to it when students realized a silly mistake they made on a exam. I thought the sign was hilarious, but some of my classmates thought it was obnoxious.

From my other new brother-in-law, I received a copy of “How to Live Longer and Feel Better” signed by Linus Pauling. Very, very cool. Apparently, signed chemistry texts by Pauling command a much higher price tag, but I would much rather have something signed relating to Pauling’s medical quackery than chemical bonding or crystallography.

Finally, from my lovely fiancée wife, I received this:

stuffed_animal_chembark_ed

That, my friends, is total victory: a stuffed animal version of ChemBark’s mascot, Ed the Dog. I am a very lucky boy.

That’s it for the chemistry presents, but I got a bunch of other great gifts and had a wonderful wedding three days later (that will be the subject of another post). I hope everyone had as good a holiday break as I did, and best wishes for a happy and productive 2014!



The Pauper Professor’s Orgo Library

chembarkfc_kit_200Well, it looks like I’ve been ignoring the blog again. Sorry about that.

We are in finals week here at SLU, and the end-of-the-semester crunch has definitely crunched me (with a lot of help from lab stuff, two chemistry “business” trips within the last month, and the fact that I will be getting married in two weeks (!).

I’m teaching Organic 1 this semester, and it has consumed an inordinate amount of time. But the experience has also been a lot of fun and a good training ground for figuring out how to run a class efficiently.

Like many orgo teachers, I began the year by insisting to the students that the best way to do well in the class is to work practice problems (and lots of them). When I was a wee lad taking orgo at NYU, I walked uptown to the fantastic Barnes & Noble at 5th and 18th and bought copies of Vollhardt and Streitwieser to supplement the problems in Jones. My weekly routine was to read through the Jones chapter in two nights while also making index cards that cataloged each reaction along the way. The rest of my week would be spent doing all the problems in Jones, then as many in Streitwieser and Vollhardt as I could stomach.

But textbooks aren’t cheap, and I feel icky about asking students to shell out extra money for supplemental problems after they’ve already forked over $260 (!) for the class’s required textbook. Of course, the used-book market is flooded with cheap, old editions of organic textbooks.

Over the course of this semester, I undertook a mini-project that involved scouring half.com for deals and assembling a small library of textbooks and solutions manuals as a resource for my sophomore organic students. The last volume arrived two weeks ago, and now my collection occupies almost an entire bookshelf in my office:

cheap_orgo_textbook_library

There are 16 books there: 8 sets of texts and solutions manuals. Here’s what I paid for each book + manual:

Bruice: $3.43 + $0.75
Carey: $3.26 + $0.75
Heathcock/Kosower/Streitwieser: $1.05 + $1.18
Jones: $0.75 + $0.75
Loudon: $4.07 +$4.12
Smith: $0.00 + $0.00 (this is the one SLU uses)
Vollhardt/Schore: $1.05 + $0.75
Wade: $2.22 + $0.75

Those costs are steals compared to the prices listed on Amazon. The shipping on each item ranged from $1.89 to $3.99 and was always more than the cost of each book. In total, my little collection set me back $74.14. The plan for next semester is to cart them over to the main library where they can be kept on short-circulation reserve. Students can check out the books for a day at a time—long enough to work or copy the problems in a chapter, but not long enough to hog the resource. Anyway, with eight texts as options, I’m hoping the market for orgo practice problems at SLU is now saturated. I should never again hear wailing about there not being enough practice problems available.

Anyway, the final exam for my class is this Friday—the 13th. I expect the only students who will encounter bad luck are those who haven’t been working enough practice problems.



Organic Chemistry Exam Show-and-Tell

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.



How JACS Treated the Anonymous Tip of the Rodriguez–Marks Paper

ChemBark InvestigatesBy the time the chemist who noticed the suspicious data published in the Rodriguez–Marks paper had contacted ChemBark, the chemist had already anonymously notified the Journal of the American Chemical Society with the concerns. A member of the staff at the journal responded to this initial message with the following:

To Whom It May Concern:

Thank you for your message regarding J. Am. Chem. Soc. 2009, 131 (16), pp 5902–5919. Indeed JACS takes ethics quite seriously. We would be pleased to investigate your concerns. Before proceeding, however, we ask that you reveal your identity.

Sincerely,
(REDACTED)

The implication of the official response from the journal was troubling. It implied that for the investigation to proceed, the whistleblower would need to reveal his/her identity.

Surely a journal that grants anonymity to referees would appreciate why a reader who was calling attention to possible misconduct by a well-known, powerful chemist would want to remain anonymous. Furthermore, JACS is a member of the Committee on Publication Ethics (COPE), and the source reports he reminded the journal that “COPE supports a whistleblower’s right to remain anonymous”. Beyond COPE, Ivan Oransky (co-editor of the blog Retraction Watch) has also summarized why editors shouldn’t ignore anonymous tips.

To its credit, the journal responded favorably to the source’s gentle reminder about COPE’s policy, and the investigation was allowed to proceed.

After the paper in question was retracted, ChemBark asked JACS Editor-in-Chief Peter Stang by e-mail:

When the source initially contacted the journal in August with these concerns, the journal office responded to him/her “We would be pleased to investigate your concerns. Before proceeding, however, we ask that you reveal your identity.”

As you know, the source refused to identify himself/herself and defended his/her right to anonymity in the process. While the journal eventually relented and proceeded with the review, the initial implication was that the source would need to identify himself/herself for an investigation to proceed. Was the request and wording of the initial response from the journal “standard procedure”? Is the journal worried that such a response could have a chilling effect on the identification of suspicious or irreproducible data? Why would the identity of the source matter if the concerns are reasonable?

Dr. Stang’s response included the paragraph:

I will say, however that the request for the individual to identify themselves was unnecessary. The  identity of the “whistleblower” was immaterial to the issues raised and did not  prevent JACS from considering the allegation and taking action. All ACS  Journals take all cases of alleged research improprieties very seriously and have established procedures for reviewing and taking appropriate actions, where warranted, to preserve the integrity of the scientific record. Institutions and funding agencies  also have established departments, policies and procedures for handling  allegations of data fabrication by researchers. Upholding the scientific record requires the vigilance of all participants in the research community.

All credible reports of suspicious data should be thoughtfully considered by the corresponding journal, whether reported anonymously or not. Journals should be grateful to anyone who attempts to correct the scientific record and understanding of why a tipster might want to remain anonymous. While JACS‘s initial response was troubling and “unnecessary”, it would appear as though the editors have taken steps to correct how they handle anonymous tips.

That is an encouraging outcome.



Suspicious Data in a JACS Paper from 2009

Covers of JACSOn Tuesday, the Journal of the American Chemical Society published a retraction notice for a paper titled “Bimetallic Effects for Enhanced Polar Comonomer Enchainment Selectivity in Catalytic Ethylene Polymerization” by Brandon A. Rodriguez, Massimiliano Delferro, and Tobin J. Marks (J. Am. Chem. Soc. 2009, 131, 5902−5919).

The retraction notice reads:

The authors have been unable to reproduce the synthesis and spectroscopic characterization of the ethylene/acrylate copolymer described in this article. Accordingly, the authors are retracting this publication due to concerns over the validity of the aforementioned data. The authors regret any confusion that may have been created by publication of this work.

A casual reader might encounter this notice and think this is exactly how the system should work: a scientist told of a problem with his published procedure went back, attempted to repeat the work, found he couldn’t, and published a notice to inform the community.

But a closer inspection reveals that there is more to this story that the retraction notice would indicate.

ChemBark was alerted to problems with this paper in August by an astute chemist who wishes to remain anonymous. One day earlier, the source had contacted Peter Stang, the editor-in-chief of JACS, to alert the journal to abnormalities with data in the paper. ChemBark respected the wishes of the source and allowed a traditional editorial review of the paper to be completed before reporting the matter on the blog. With the publication of the retraction notice yesterday, the authors have publicized that their work is problematic. It would appear that an initial review of the paper is complete.

The authors’ wording of the retraction does not indicate specifically what was wrong with the paper, but a brief inspection of the data (including those in the Supporting Information) reveals the following abnormalities:

Figure 3: The baselines of these spectra are peculiar in that they are thick but very straight. The thicknesses and shapes of the peaks are also peculiar. Some of the tall peaks lack the wide bases you would expect of them. Finally, some of the peaks appear to have a different background (i.e., noise) and line thickness (as if they originated from a different source).

marks_retraction_figure_3

Figure 6: The baselines (i.e., noise) of the two NMR spectra appear to be identical. The peaks look irregular—like solid lines.

Figure 7: Again, some of the peaks have lines that are much thicker than the rest of the spectrum. They look unnatural.

Figure S19 (in the SI): The NMR spectra taken at various temperatures have identical noise in their baselines, which would be very, very unusual. The peaks of interest appear irregular and have different line shapes.

marks_retraction_figure_s19

Figure S21: The background of the peaks appears different from the background of the rest of the spectrum, as if the peaks were cut-and-pasted into the spectrum.

Figure S22: Same as above. The spectrum in Figure S21 and the bottom spectrum of Figure S22 appear to have the same baseline noise even though these spectra are reported to be of two entirely different compounds.

marks_retraction_figure_s22

That’s not everything that looks peculiar, but do not simply take my word for it. Go to the paper, have a look, and judge for yourself (paper, SI). ChemBark does not know why these data look the way they do, but they do look unnatural.

On Tuesday, ChemBark contacted Professors Tobin Marks (the corresponding author on the retracted paper) and Peter Stang (the Editor-in-Chief of JACS) by e-mail for comment.

A response was received on Wednesday from Alan K. Cubbage, the chief communications officer for Northwestern University. In the interest of fairness, we are reporting this e-mail its entirety:

Mr. Bracher, your inquiry to a Northwestern University professor, Tobin Marks, was referred to me, as I am the chief communications officer for Northwestern.

As you note in your email, two Northwestern University faculty members and a former Ph.D. student have retracted a publication that appeared several years ago in the Journal of the American Chemical Society. The authors are Brandon A. Rodriguez, who received a Ph.D. from Northwestern in 2009, Tobin Marks, a professor of chemistry, and Massimiliano Delferro, a research assistant professor of chemistry. The article was retracted because the authors were unable to reproduce a portion of the data described in the article.

Northwestern University has established processes and procedures for reviewing issues relating to research integrity.  If concerns were to be raised regarding the data that was the subject of the retraction, the University would use those procedures in its review.  Part of those procedures, which follow the steps mandated by the federal government, is that any review remains confidential.

Thank you for your interest in Northwestern.

Best wishes,

Alan Cubbage

ChemBark also received an e-mail response from Peter J. Stang, the Editor-in-Chief of JACS. In addition to asking about the possibility of fabrication and the specific concerns listed above, we asked for his thoughts on Paul Weiss’s recent editorial in ACS Nano. Dr. Stang’s message is also copied below in its entirety, with the exception of one paragraph (that will be communicated in the next post on the blog, a follow-up to this story):

Dear Dr. Bracher:

Thank you for your communication regarding  Bimetallic Effects for Enhanced Polar Comonomer Enchainment Selectivity in Catalytic Ethylene Polymerization   authored by Brandon A. Rodriguez, Massimiliano Delferro, and Tobin J. Marks [http://dx.doi.org/10.1021/ja900257k] that has been retracted {10.1021/ja409590r] from the Journal of the American Chemical Society (JACS).

As you know, concerns with this paper were brought to my attention in late August by an anonymous source.  Apparently this source also communicated the same concerns to you.  I am disappointed that you felt obligated to  not communicate these concerns  to JACS directly  at that time and deferred to your source to do so. Please know that JACS takes all allegations regarding the validity of  data reported in published articles very seriously.

These concerns were shared with the author and a  thorough editorial review of the article and accompanying information was conducted by JACS. The authors have retracted the article – it would not be proper to speculate on some of the questions you have posed.

(Omitted paragraph — to be discussed in next post)

ACS and its Editors adhere to the principle that the observance and practice of high ethical standards is vital to the entire scientific enterprise.  Toward that end, guidelines for a course of conduct by those engaged in the publication of chemical research, specifically, editors, authors, and manuscript reviewers are set forth in ACS Ethical Guidelines to Publication of Chemical Research -http://pubs.acs.org/userimages/ContentEditor/1218054468605/ethics.pdf.

ACS Publications  is a member of the Committee on Publication Ethics (COPE). ACS Editors adhere to  a process established by COPE to review suspicious/fabricated data -http://publicationethics.org/files/u7140/Flowchart%20Fabricated%20B%20revised.pdf

With regard to the editorial in ACS Nano, I believe that it is well-reasoned and articulated. Public speculation and  finger-pointing before all of the facts are gathered, assessed and decided upon is, in my opinion, counterproductive.  A confidential rigorous review of allegations based on the COPE  prescribed process is the best means to determine an appropriate action in response to those allegations.  As you know, outcomes of these reviews may very well have a lasting impact on the researcher(s) involved and we need to let the facts dictate those outcomes.

Thank you for advising that ChemBark will post a story on the retractionhttp://pubs.acs.org/doi/abs/10.1021/ja409590r. I offer my assistance in reviewing a draft and through cc have alerted  Dr. Tobin, the corresponding author.

Peter J. Stang

 

ChemBark could not locate an e-mail address for Dr. Brandon Rodriguez, the first author on the paper, but did send him a message seeking comment through Facebook. We received no reply. We will publish any comments from Dr. Rodriguez as soon as possible after they are received, and we note that he (and everyone) is welcome to post comments in the discussion thread below. We also note that the community owes a debt of gratitude to the chemist who brought these concerns to light in a professional and considerate manner.

So…here we have a case where a suspicious paper from a very high-profile group was allowed to go through the “traditional” private review process espoused by scientists like the editor-in-chief of ACS Nano rather than public review on a blog. ChemBark did nothing to interfere with the investigation or the actions of the editors at JACS.

Is this how the system should work?

 

Editor’s Notes: Neither Dr. Stang nor anyone at Northwestern were allowed to view an early draft of this story. The spectra used to construct the images above were taken from figures in J. Am. Chem. Soc. 2009, 131, 5902−5919 (paper, SI). The next post on ChemBark will deal with how the journal handled a specific aspect of this review.