Archive for the ‘Scientific Publishing’ Category

Textbooks Make Me Feel Dirty

Monday, August 3rd, 2015

ChemBark Ed on Dollar BillWe’re three weeks away from the start of the semester at SLU, and this time of year always brings the first wave of e-mails from the next class of students. While these messages vary in length and tone, they can generally be distilled to one question: “Professor, what do I really need to buy for your course?”

Can I use the previous edition of the text? Do I really need a model kit? Do I really need the model kit on sale in the bookstore? Can I share my model kit with a friend? Do I have to buy the subscription for the online homework?

Whenever I read these e-mails, a part of me dies inside. I feel their pain. They’ve just paid their bills for thousands of dollars in tuition, with two more years of it to go. And now, after absorbing that massive hit, they’ve got to scrounge up another $375 dollars for my coursepack. It’s a slap in the face.

The cost of these materials makes me sick, and the prices are rising at an astounding rate. For my college organic text, I paid less than half of what students are asked to pay today. Are today’s books really worth double my book, which remains a valued reference on my office bookcase? Has our understanding of introductory organic chemistry really changed that significantly in the last 15 years? No.

I’ll be teaching Organic Chemistry I for Majors again and using the same coursepack we did when I arrived at SLU.  It contains: (i) the textbook, (ii) the solutions manual, (iii) a plastic model kit, and (iv) a subscription to the online homework assignments. That all costs about $375 when purchased together.

Three hundred and seventy-five American dollars!

While I could easily point the finger at the publishing companies as the villains that they are, ultimately, they are not the problem—I am. After all, I’m the one who assigns the books for my course. And for that, I’m truly sorry, but allow me to explain:

While there are a dozen good organic texts, I think we can all agree that it makes sense for a class to adopt a single textbook. As a teacher, I literally want everyone on the same page, with a precise understanding of what information everyone is responsible for. In the absence of a strong external force, inertia will govern this decision. It makes sense for an instructor or department to stick with the book it used the previous year, because the switching costs of an instructor having to rework the syllabus, slides, and order of practice problems can introduce a lot of unnecessary work. And there are benefits to students when we use the same book as the year before, because they can buy a used version. Furthermore, they can get something out of borrowing their friends’ old notes and exams.

Now, here’s where the publishing industry appears and sinks in its fangs. The used-book market poses a serious threat to their revenue stream, because they only make money by selling new copies. It’s the bookstores and old students who make money from the used-book market. So, what do the publishers do? Release a new edition! By releasing a new edition, the publishers can (i) find professors to drive orders of new books and (ii) stop printing the old edition so colleges can’t find enough used copies of it, forcing adoption of the new edition.

These new editions usually contain few or no substantive changes relative to the previous edition. It can be as silly as shuffling content between chapters, renumbering the practice problems, and adding a few new photos. Case in point is the 4th edition of the text I use now. Anyone with the 3rd edition would have no problem following my class, because hardly anything changed.

Another thing that burns me up is that by the 4th edition of a text, you’d expect all of the errors would have been ferreted out and corrected by now. Have they? No. I maintain a list of errata in the text on my webpage and use it to show my students that organic chemistry must be hard—not even the textbook’s author can get it right.

Textbook publishers erode the used-book market to drive the sale of expensive new editions, but professors are complicit in maintaining this skewed market. Why? Because we are the ones that assign these textbooks as required course materials. And you know why professors don’t especially care? Because we get our textbooks for free. The publishers will just give away a $250 text to us because they want us to force 200 students to buy it. They’ll even sweeten the deal by giving us free lecture slides that correspond to the text. The sales technique is brilliant: make life as easy as possible for the professors and give them free stuff so that they will force their students to buy your product. While it’s not exactly a kickback, it’s not terribly far from it.

So, the textbook market is not a fair one as far as students are concerned. Students can’t shop around for the highest quality book at the best price; they are essentially required to buy whatever textbook their professor decides at whatever price the publisher is charging. And as if that wasn’t enough to make you sick, publishers send instructors e-mails like the one I received a month ago:

From: <Textbook Publisher>
Subject: When it’s required, they’re prepared required_advert_450Disgustingly shameless. I feel gross just reading it.

Hey, instructor buddy! You want your students to learn? Well, then you need to *require* them to purchase our expensive online add-on! And don’t worry—we’ll give instructors free access to the system, of course!

Don’t get me wrong. I recognize that authors and publishers perform a valuable service. While our understanding of first-year organic chemistry hasn’t changed in 30 years, our ability to make instructive figures has certainly improved to the point that no one would choose a text from the 1980s over those offered today. So yeah, publishers should be compensated for the materials they produce. But at the same time, there is a limit to what is reasonable. Issuing a ‘new’ edition every three years at $375 a pop is ridiculous.

So, students, please forgive me. I know the system is unfair, but there really isn’t a good alternative at the moment. I would much rather you spend $375 on a nice iPad and download the coursepack for free. Unfortunately, the free organic texts in existence pale in comparison to the expensive texts out there, and the time required for a professor to produce all of the necessary materials for a class is too much to do in one shot. I hope you will believe me when I say that I’m working on it, but it’s going to take some time. Every year I produce a little more material and build towards the goal of obviating the need for an expensive text. Give me 20 years and that should become reality. I hope someone else beats me to it.

C&EN is Cutting Staff

Thursday, July 30th, 2015

CEN Fake Cover of Paul BracherYesterday brought the alarming report that Chemical & Engineering News (C&EN) is cutting eight members of its staff. It appears that these cuts are rooted in the continued sag in advertisements and other sources of revenue at the magazine.

If I recall correctly, C&EN had a similar cutback when the economy tanked, and it is alarming to see a new round of cuts. I think C&EN serves an important and underappreciated role as the major—sometimes, only—means by which many ACS members keep track of chemical news, major advances, and society business. For any large democratic organization to operate efficiently, good journalism is required to keep the electorate informed.

Based on grumbling in comment threads, I think many people are skeptical whether C&EN fulfills this role, but the magazine is really the only publication that comes close (as far as the ACS is concerned). It is more than distressing to see these cuts and think what they mean for the coverage the magazine will be able to provide. Will there still be resources to send reporters to courtrooms (as with the Patrick Harran case)? Will the magazine pursue misconduct cases with the same vigor it has in the recent past?

I know that C&EN recently underwent major changes in its editorial staff, and I hope that means they will be reevaluating their approach to ‘new media’. There is revenue there, along with the chance to engage a wider audience. Given the latest round of cuts, it’s obvious that staying the course and relying on a traditional model is not working. When one looks at the direction of major news outlets like the New York Times and Washington Post, it is bizarre to see that C&EN shuttered its CENtral Science blog network. The blog platform never got the resources it deserved. There was never a full-time blogger who could throw herself into the system and innovate, rather than juggling a responsibility to pump out stories for the print edition.

I’ve got to wonder whether anyone there ever considered the obvious move of hiring Derek Lowe, the godfather of the chemical blogosphere. Given Lowe’s problems ‘under the hood’ at Corante and his impending move to Science Translational Medicine, I have to imagine C&EN could have made a competitive offer. His blog would have represented a strong foundation at C&EN on which to build.

But that ship has sailed. I hope the magazine’s future efforts experience fair winds, because the chemical community needs and deserves good journalism. Fortunately, the staff at the magazine is a great group of people. I hope the Society gives them the resources and editorial latitude they need and deserve to keep the membership well informed.

Editor Discusses F—ing in Nature

Sunday, February 8th, 2015

nchemfc_kit_250Stu Cantrill, editor of Nature Chemistry, has performed a profoundly beneficial service for our field: he has tracked the use of the word “fuck” (and its variations) throughout the 146-year history of the esteemed journal Nature.

Stu’s interest in the subject was piqued after seeing bollocks in a recent edition of the journal. He traced the first pair of ‘bollocks’ back to 1998.

Stu was able to find two innocent ‘Fuck’s in 1937 and 1985—they were proper nouns—before the first virulent ‘fuck’ appeared in 1989. This stuff is fascinating; check it out.

Stu takes a look at many other dirty words, and his analysis includes the expected reference to the infamous copper nanotube (CuNT) paper in ChemComm. Albeit unintentional, there is no better example of how ridiculous the acronym scene has become in science. I had several conversations in grad school excoriating some of the more creative acronyms devised by labmates.

And finally, this is an excellent opportunity to boast that I hold the honor of being the first person to write the F-word in Nature Chemistry, if you don’t count the hundreds of times fourth-year graduate students have scrawled it in the margin of papers after getting scooped.

That’s an accomplishment sure to impress the tenure committee.

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

Monday, November 11th, 2013

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

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.