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.



ACS Expanding Open Access

Covers of JACSIn an interesting move last week, ACS Publications announced plans to expand the number of papers it offers through open (free) access. The centerpiece of these plans is the birth of a new multidisciplinary journal, ACS Central Science, that will be 100% open access. The society has also generously agreed to open access to 365 articles of the 40,000 it publishes per year. Hooray.

It will be interesting to see how the new publication is received, because the Society already has a journal dedicated to multidisciplinary coverage of chemistry: JACS. JACS is easily the flagship of all of the Society’s journals, and one is right to question whether the new addition could hurt the JACS brand. Will ACS Central Science rise to—or exceed—the same level of prestige as JACS, or will Central Science be considered a lower-tier journal? Will the new journal siphon off quality papers from JACS, or might it become a dumping ground for manuscripts first denied publication by her sister journal?

Time will tell. It’s also worth noting that ACS Publications lifted the name of the journal from the blog network at C&EN, so perhaps some rebranding is in order over there.

In the wake of the open-access announcement, a quick Google search allowed Stu Cantrill to find a “proprietary and confidential” set of PowerPoint slides from the ACS Publications Division. In the presentation, division president Brian Crawford identifies “open access mandates” as a “challenge” to the division. Crawford goes on to outline a goal to “accommodate [the] need for authors to comply with OA mandates while maintaining the Society’s economic hold on copyright in a ‘mixed economy’.” The new journal and (very minor) expansion of open access to the rest of the journals would seem to be the Society’s answer to the problem.

And the ACS should be applauded for inching closer towards embracing wider access of the material it publishes, but these are baby steps in an industry that is evolving by leaps and bounds. In my view, the problem is not that journals charge subscription fees for access to their publications, but rather how obscene some of these fees have become. Demanding open-access to papers rubs me the wrong way, because the journals perform a valuable service for which they should be compensated. The problem is that the ACS—a nonprofit society ostensibly dedicated to the advancement of chemistry and the chemical enterprise—is acting like a capitalist publishing corporation trying to milk every last dime out of the market for scientific journals.

I feel bad for the people at ACS, because they are really headed down the river fast. The revenue from the publications division is what fuels the massive bureaucracy of the ACS, and the society is almost out of ideas to stay afloat. Instead of embracing the new direction of publishing, the ACS has fought tooth and nail to protect its old standing through ruthless management of its subscription business. They have leveraged the quality of their journals against those who employ the researchers responsible for creating this quality. Eventually, as print revenue goes down and schools start standing up to exorbitant access fees, the Society is going to have to enact deep cuts to its lavish spending on Sixteenth Street. Leadership should focus on making these cuts now instead of plunging their hands deeper into the pockets of our nation’s schools and businesses for the few remaining pennies.



Questionnaire Answers from Dr. Diane Schmidt, Candidate for ACS President-Elect

Earlier this month, ChemBark sent a questionnaire to the three current candidates for ACS President-Elect. The set of questions was similar to the set distributed last year that Tom Barton was kind enough to answer.

ChemBark is publishing each candidate’s response—complete and unedited—in dedicated posts. Dr. Chuck Kolb’s answers and Dr. Bryan Balazs answers ran in previous posts. The next candidate to respond is Dr. Diane Schmidt (whose response was delayed due to jury duty). Her answers appear below.

Don’t forget to vote in the ACS national elections!

 

Response of Dr. Diane Schmidt, Candidate for ACS President-Elect

1. What are your thoughts about the historically low voter turnout (~15%) typical of ACS national elections?

Apathy is difficult to cure. One suggestion would be to have greater publicity in C&EN (perhaps a cover article) to raise the profile and awareness of the national elections. The option to vote electronically does not appear to have had the impact of  greater participation in the national elections that was expected.

2. What is your stance regarding the fees that ACS Publications charges companies and universities to access journals?

Journal pricing is complex and is probably best understood by dealing in specifics for specific schools and companies rather than generalities.  When I get these questions, I always refer people to Pubs.  In many cases there are custom solutions that can be crafted for individual circumstances.

My view is that ACS journals offer high value and high impact at competitive pricing. The quality and the value of the trusted, peer reviewed information provided by ACS journals is a very good value vs. other publishers.

3. What is your stance on the ACS’s executive compensation packages?

Full transparency is important. Perhaps a C&EN comment on the process that is used would help get everyone on the same page as to what is actually in place and the process that is used to determine compensation.

You may remember that the Board held a town meeting on Executive Compensation after Council in Fall, 2005, and perhaps a refresher is in order via a C&EN comment. C&EN calls attention to the ACS Form 990 filing each year and tells readers how to access that document on acs.org. Here’s the link to the 990 notice on page 6 of C&EN.

http://www.cendigital.org/cendigital/20121210??pg=8&search term=990&doc id=-1&search term=990#pg8 

4. What are your thoughts on the recent ACS vs. Leadscope case? Do you believe that society records pertaining to the lawsuit—including legal fees—should be made public?

Full transparency is important.

The background as I recall is that all public reports on Leadscope in the early days were modulated by the fact that it was active litigation.  The events relating to the litigation go back to 1998. For a long time, virtually nothing happened, then there was the trial.

For nearly a year after the settlement in 2012, an extensive Q&A was advertised on the front page of the ACS website. It can still be found at:

http://www.acs.org/content/acs/en/about/aboutacs/acs-v-leadscope-questions-and-answers.html

One of the difficulties I think with this case is it spanned quite a number of years perhaps making it difficult to follow. My impression is there were regular updates in C&EN over the course of the legal proceedings as the case unfolded, reports in Council of the case status by the Chair of the Board, as well as updates in the Councilor Bulletin. Perhaps a summary in C&EN tying all of the bits and pieces together that were published over time as the case unfolded would be helpful with links to the publically available information. My understanding is that the Chair of the Board reports which include Leadscope are posted on the ACS website.

The most recent report on Leadscope and the financial impact on ACS was by the Chair of the Board  and was presented in Council last Spring. I believe his remarks are posted on the ACS web.

My understanding is that the proceedings of this case are in the public record. To read a summary of the case prepared by the Supreme Court of Ohio’s Office of Public Information, click here: http://www.courtnewsohio.gov/cases/2012/SCO/0918/101335.asp

5. What one specific item would you, as ACS President, make your first priority to improve the public perception of chemistry?

Outreach. Chemistry improves the lives of all. Communicating specific examples such as chemistry’s role in clean water, food safety, medicinal improvements, diagnostic techniques, etc.  that the general public experiences daily, but does not identify as chemistry. This would help make the connection between the role of chemistry and the improvements the general public experiences in daily life because of the contributions of chemists and chemistry. The ACS Landmarks Program does this to some degree. During the International Year of Chemistry, many examples of how chemistry improves life daily were posted on the ACS website. There is an opportunity to go the next step and more broadly communicate these.

6. What one specific item would you, as ACS President, make your first priority to improve the employment situation for chemists?

Ensure that all members and all chemists know of and have access to the many ACS employment tools and services already in place. Work with staff and members to further enhance, expand and improve these tools.

7. What is your favorite chemical compound with respect to color or smell?

My favorite chemical compound is caffeine, especially delivered in chocolate. It was my first total synthesis as an undergraduate.