Archive for the ‘Scientific Literature’ Category

Papers That Got Off to a Good Start

Thursday, August 6th, 2015

This week, an interesting discussion on Twitter was sparked by the publication of this paper in JACS:



That’s a great first sentence to a paper, and soon people chimed in with other memorable examples.


Tehshik Yoon pointed out this review on C-H activation as his favorite:



…which Nicolas Fanget countered with a microbiology paper from 2000 that begins with a quote from Monty Python’s Flying Circus:



My personal favorite belongs to the man himself, R.B. Woodward, who began a 1963 paper with the simple exclamation, “Strychnine!”:



Are there any other chemistry papers out there with memorable openings?

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.

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).


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.


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.


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 [] 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 -

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 -

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 retraction 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.

Response to ACS Nano Editorial on Reporting Misconduct

Wednesday, October 23rd, 2013

ChemBark's Jackie Jaws, the Jaded JACS RefereeYesterday, the entire editorial board of ACS Nano published an editorial on how scientific misconduct should be reported and dealt with. The piece took square aim at chemistry blogs, and I’ve decided to publish my thoughts as an open letter to Paul Weiss, the Editor-in-Chief of the journal:

Dear Professor Weiss,

Yesterday, I read your editorial titled “Be Critical but Fair”, within which you and the other editors of ACS Nano outline an official policy that calls on those who discover suspicious data to report their findings directly to the journal (where they can be scrutinized privately) as opposed to blogs and social media (where the findings will be scrutinized in the open). It is with candid disdain that I write this (public) blog post to explain why I believe your policy is misguided, and ultimately, damaging to the institution it seeks to protect.

Before going further, I want to thank you for the job that you and the rest of the board perform as editors. You are the primary stewards of the chemical literature, and the gravity of this responsibility is immeasurable. I imagine there are times when the extra salary you receive as editors does not adequately compensate you for the hassles of the job. I have no taste for this stress, but I am glad there are scientists among us willing to step up to the plate. Thank you for your service.

It is because of the immense responsibility of your job as a steward of the chemical literature that the community has an interest in analyzing your actions and holding you accountable for them. Everyone makes mistakes—from lowly chemistry bloggers to exalted editors-in-chief of ACS journals—but the true tragedy of any mistake is when we fail to learn from it. Recently, the process of peer review at your journal failed in a most spectacular manner. Similar high-profile cases recently occurred at your sister journals (e.g., Nano Letters and Organic Letters), and these cases of suspected misconduct are slowly working their way through the process of editorial review.

One common vein to this recent rash of suspicious papers is that they were brought to light on chemistry blogs. As you may already know, I am the editor of one of these blogs, ChemBark. I read with particular interest the comments you directed at those who discuss misconduct on blogs and Twitter:

In science, we face a similar problem: the numbers of blogs, twitter messages, etc. in which individuals accuse others of academic fraud are steadily rising. Although one might think that this trend is generally beneficial for the purity of science, there are also obvious risks involved. Thus, in this Editorial, we outline some general behavior guidelines that we believe should be followed in such cases. In general, we need to respect our law, in dubio pro reo, which tells us not to condemn anyone before wrongdoing has been proven. It is easy to tweet a message like “X committed fraud and manipulated data”, but how do we know that this is, in fact, true, and that instead, it was perhaps person Y who sent the tweet who just wanted to damage an unwanted competitor? We are convinced that it is important to “clean” the scientific literature from manipulated data, incorrect statements, plagiarism, etc. However, when these issues arise, they need to be investigated with good scientific conduct. In other words, be critical but fair.

The implication of your last statement is that the coverage of scientific misconduct by ChemBark was unfair, and I take great offense to this postulate. I use this word because you have not cited a single shred of specific evidence in support of your statement. When has a chemistry blogger ever raised serious suspicions about the validity of data in a paper only to be later proven incorrect? If a researcher submitted a manuscript to ACS Nano that did not include even one specific piece of data in support of his conclusions, the journal would reject the manuscript immediately. It is a shame that the editors do not hold their own writing to a similar standard.

You said on Twitter that the journal has a policy never to cite blogs or tweets, as if this represents a valid defense of why you couldn’t provide specific facts in support of your ideas. First, your tweet was absolute rubbish. Stuart Cantrill, chief editor of Nature Chemistry, immediately pointed out you wrote a previous editorial that cited the Retraction Watch blog. Second, why on Earth would you have a blanket policy not to cite blogs or tweets? Is ACS Nano so recalcitrant to changes in the publishing industry that it feels ideas voiced online can be ignored or reapportioned in print without credit? I hope not.

The true reason that your editorial did not cite a single instance of a blogger’s leveling false accusations of scientific misconduct in chemistry is that no such instance exists. To imply otherwise is dishonest sophistry that does not befit the editors of a major chemistry journal. In the very rare instances where commenters make weak accusations in the discussion thread of a blog post, the comments are ignored or ridiculed. Despite the fact that the majority of popular chemistry blogs serve as places for civil and thoughtful analysis, your editorial treats blogs as shady underground operations where anonymous bloggers are free to wreak havoc on innocent scientists. Again, I challenge you to find one anonymous chemistry blogger who has broken a story of possible misconduct. I use my real name on ChemBark, and Mitch Garcia blogs under his real name at Chemistry-Blog. Your editorial could have easily cited our work in reporting suspicious papers, but of course, doing so would not have fed into your desired narrative.

Returning to your statement above, you note that “we need to respect our law, in dubio pro reo, which tells us not to condemn anyone before wrongdoing has been proven.” First off, your translation isn’t even correct. A more accurate translation is “when in doubt, favor the accused.” This tenet is why our legal system requires proof “beyond a reasonable doubt”, and the idea has nothing to do with trying cases in public versus private. The fact that you drew on our legal system—which is famous for holding trials that are televised or open to members of the public—to support your policy is ridiculous.

While bloggers who report cases of possible misconduct are indeed accountable to the law, that law is not “in dubio pro reo”. Rather, bloggers are accountable to defamation law. If any chemistry blogger were to raise baseless accusations of misconduct against a scientist, the blogger would open himself to (i) financial ruin from an adverse finding in a civil claim, and (ii) professional ruin in the court of community opinion. Bloggers need to be careful about what papers they choose to highlight regarding scientific misconduct, but this is no different from how newspapers and magazines need to be careful about how they handle their coverage of crime in everyday life. Do we want newspapers to abstain from reporting major crimes until a trial by jury has concluded? No, that’s crazy. There is a public interest served in covering these stories, and news outlets play a valuable role in gathering, distilling, and reporting this information. As both a chemistry blogger and a human being, I need to make sure that the facts I report regarding possible scientific misconduct are accurate and the opinions I voice are rooted in reason. That’s the bottom line, and I am accountable to the very intelligent readership of the blog and to our legal system (should someone have a problem with my coverage). No blogger can expect to level spurious claims of misconduct and get away with it.

Your editorial continues with a statement that peer review is “the best way to avoid potential academic fraud” and correctly notes that the system sometimes fails. When it does, you implore readers who find evidence of misconduct to report it directly to you so you can conduct an investigation in private. You note:

The difference between this formalized accusation investigation and reports in blogs or on Twitter is that, during the investigation, the authors of the article under dispute have a fair chance to explain, and the decisions are made by known experts in the field. After we have made our decision, all are welcome to comment on it in any blog, even if they have different opinions; this is their privilege. We strongly suggest that such comments be made without the cloak of anonymity, using real names and affiliations, so that direct and open discussion of the work can be understood by others.

I hope you can appreciate the irony of how you begin by extolling the virtues of (anonymous) peer review and conclude by haranguing bloggers and commenters to register their opinions “without the cloak of anonymity.” It takes a lot of gall to make those statements in the same line of thought.

Furthermore, the idea that the public should not be free to point out deficiencies of a (publicly) published paper without first receiving clearance from the editorial board of ACS Nano is preposterous. The notion is antithetical to the freedom of inquiry espoused by the academic community and the freedom of speech held sacred by American society. Unless I am mistaken, the “A” in ACS Nano stands for American. In America, it is not a “privilege” to comment publicly on a subject; it is a right.

Your assertion that commenting on papers is a “privilege” smacks of the elitist, opaque, closed-door, Old-Boys’-Club approach that many lament has become standard operating procedure in too many areas of chemistry. Many young chemists decry that success in our field is not so much about what you do, but whom you know. Blogs are helping to level the playing field by putting users on equal terms and democratizing the flow of information. In order for any self-governing and self-policing body to operate effectively, members of the community must stay informed about important issues they face. There can be nothing more important to chemistry than the integrity of our data; it is the foundation on which our knowledge is built. Private systems of dealing with misconduct do so in a darkness where—even if an investigation takes place on the level—those outside will always have their doubts. The open system afforded by blogs shines a light on problems so all can see, participate, and judge for themselves. While private peer review of papers may make sense to eliminate errors before they’ve been published, once a paper is out in the open, it should be fair game for comment. There is no point in dragging problems back inside only to leave a trail of blood and a multitude of questions behind.

I would like to think that the private system you espouse could also function efficiently, but recent history has proven otherwise. Despite the importance of maintaining the integrity of the scientific record, the chemical community has been routinely kept in the dark about cases of scientific misconduct. Journals, universities, and governments seem to share as little as possible about their investigations. Just look what happened with the Sezen–Sames retractions. The case involved a shocking rampage of deceit and was probably the worst scandal to hit organic chemistry of all-time, but it took a FOIA request from me and C&EN to release the details of the case to the community. How can chemists be expected to learn from and prevent scandals without knowing any of the specific details? It’s ridiculous! Do you pledge to release all of the specific details of your investigations that result in adverse findings against an author?

Journalism—including that provided on chemistry blogs—is one way to address this vacuum of information. The Founding Fathers of the United States protected the freedom of the press in our Bill of Rights because they knew that an informed electorate was essential to the efficient operation of our government and the prevention of tyranny. A (small) part of what I’ve tried to do with ChemBark is to shed light on cases of scientific misconduct in our field such that these cases can be discussed and analyzed by the wider chemical community. It is unfortunate that there exists a need for bloggers to invest some of their time in this effort, but experience has repeatedly shown that chemists cannot rely alone on journals, universities, and governments to keep them informed.

Regardless of how persistent you are in your attempt to intimidate the blog community into keeping silent, bloggers will continue raising these issues. The health of our science is at stake, and the importance of its protection far exceeds the cost of however you and your colleagues decide to punish us for openly analyzing important issues in our field.

In summary, I believe your editorial is unfair and completely misguided. I am dismayed that it represents not only your personal opinion, but the professional opinion of every member of your editorial board (who signed it). You all have perverted an embarrassing, spectacular failure of peer review at your journal into a condemnation of the community that exposed and prevented the proliferation of your error. Chemists should be outraged at your editorial, and I hope they see through this shameless attack on those of us who use blogs and social media to analyze articles rather than the traditional method of grumbling in solitude. In the future, I suggest your effort will be better spent listening to the constructive feedback bloggers and their readers provide rather than attacking them for conducting their analysis in a public forum. Finally, on Twitter yesterday, you mentioned a willingness to engage further in a discussion of the merits of open vs. closed review of problematic published papers. I do not hold grudges and would be happy to participate in whatever forum you deem appropriate. Please keep me informed if you remain interested in hosting such a symposium.

Yours in chemistry,