Archive for the ‘Current Events’ Category

Update: First-Year Professor Craziness

Tuesday, February 4th, 2014

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

Wednesday, January 1st, 2014

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!

Suspicious Data in a JACS Paper from 2009

Thursday, November 7th, 2013

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

Tuesday, November 5th, 2013

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

Thursday, October 31st, 2013

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.

Please Vote for ACS President

Monday, October 28th, 2013

cenfc_kit_250For those of you who are members of the American Chemical Society, online voting for the national election is open and will close on November 15th. You can find your ballot instructions by searching your e-mail inbox for a message from the domain “vres.us”. Your vote is especially important—annual turnout is usually very low (~15%).

You can view the candidates’ official statements in C&EN here:

Bryan Balazs
Chuck Kolb
Diane Schmidt

The candidates’ official Web sites are here:

Balazs
Kolb
Schmidt

The candidates’ answers to ChemBark’s annual questionnaire are here:

Balazs
Kolb
Schmidt (updated 11/1)

The candidates’ answers to Chemjobber’s questionnaire on #chemjobs are here:

Balazs
Kolb
Schmidt (updated 10/31)