ChemBark

My friend Roger was searching for—well, I don’t know what he was searching for, but this is what he found:

That is from the Web site for the Biochemical Journal, which the editors have decided to call “BJ Central”. There’s also “BJ Mobile” among a group of other specialized BJ sites. I particularly enjoy the menu option labeled “Submit to BJ”.

This set of abbreviations is much less subtle than the two previous front-runners on the puerility scale, PNAS and Anal. Chem. Are the editors really that oblivious?

First they ignore you,
then they laugh at you,
then they fight you,
then they join you,
then everybody wins.

Mahatma Gandhi posted that piece of advice on his blog shortly before his death in 1948, and it still holds true today.

After admitting that chemistry faculty typically roll their eyes at blogs and that he personally doesn’t have time for them, Phil Baran—or, more precisely, the Baran Lab at Scripps—has established the newest chemistry blog on the Internet. Baran and his lab are at the top of the game of organic synthesis, so this is a major development for academic chemistry. Their participation can do nothing but lend legitimacy to an activity that has been robustly and repeatedly poo-pooed by the respected Old School of our field.

The establishment of the Baran Lab’s blog fell out of the ongoing post-publication review of IBX-promoted benzylic oxidation at Blog Syn, a relatively new site that focuses on checking synthetic procedures in the vein of Organic Syntheses. Post-publication peer review is something familiar to the chemical blogopshere. Previous examples include the questioning of the science in the “Arsenic Life” paper, the exposure of duplication by Breslow in the “Space Dinosaur” saga, and the experimental investigation into the oxidation-by-NaH paper in JACS. Blog Syn takes post-publication review of synthetic procedures to the next level by coordinating replication of the procedures among a group of bloggers who compile and compare their results for all to see and discuss.

Last month, Blog Syn decided to examine a method for IBX-promoted benzylic oxidation published as part of Baran’s graduate work in K.C. Nicolaou’s lab. What started as a straightforward effort to test the (questioned) reproducibility of the reaction quickly evolved into a vigorous and thoughtful discussion of both the merits of anonymous bloggers’ questioning peer-reviewed research and of the reaction itself. Baran and the first author of the paper have participated actively in the generation of data and its analysis, and the most recent development appears to be improved mechanistic insight as to how the reaction might work.

Those interested in this specific reaction can check out the discussion for themselves, but all chemists can appreciate the value that blogs and other Web 2.0 venues offer in terms of advancing scientific knowledge and enriching our understanding of chemistry. While blogs may often engage in journalism that is a little rough at the edges, the ease of online publishing has helped to provide open venues for meaningful discussion, to give voice to important ideas, and to democratize power in a field where many grumble that power is overly centralized. What Blog Syn has started is a great service to the field of organic chemistry, and I look forward to the wealth of material that the Baran Lab can bring to the table in its own addition to the blogosphere.

Great stuff!

Edit to add: This great post by Rich Apodaca at Depth First places Blog Syn in historical context among similar experiment-based efforts in the chemical blogosphere. The post also offers an interesting analysis of the role that blogger anonymity plays.

Edit: Another (similar) great analysis and comment thread in this post by DrFreddy at C&EN‘s blog.

Here’s one more piquant paper for the file.

I got into a discussion yesterday about chemistry in PNAS and what important papers had been published in the journal. The best I could do off the top of my head was Lewis and Nocera’s review on powering the planet in 2006. After getting dinged from Science and Nature, most chemists seem to turn to Nature Chemistry, JACS, or Angewandte instead of PNAS.

Figuring there had to be something better, I dropped the question on the Twitter feed, and @josarc came through with this gem—a paper by Fred Sanger on DNA sequencing cited a whopping 64,989 times according to Web of Knowledge.

To put that number in perspective, it is almost 1.4 times the total sum of citations for papers by K.C. Nicolaou over his entire career (47,585).

Hot damn. This has got to be the record for chemistry, right?

A kind reader of the blog brought my attention to a piece of commentary in Advanced Synthesis & Catalysis titled “Ethical Conduct in Chemical Research and Publishing”. The lead author of the piece is none other than Ryoji Noyori, who won a share of the 2001 Nobel Prize in Chemistry for his work in asymmetric catalysis. Noyori is the Chairman of the Editorial Board of the journal, while the second author is the Editor of the journal.

I agree with a lot of what Noyori has to say, because a lot of it is obvious:

The research supervisor – group leader, principal investigator (PI), however he or she is called – is the main person to pass on the tradition of science to the next generation. Senior scientists have an obligation to instill strong ethical and moral values in their progeny…However, the education of graduate students should not be the sole responsibility of the research supervisor; each department should have a collective responsibility for the education of its students and for the activities of its professors. It is regrettable to see that in many departments the professors each form their individual kingdoms with a minimum of departmental cohesion.

also:

Fraud is hard to detect in a manuscript and is usually discovered only after publication, if at all. This should lead to retraction of the article.

Yep. The majority of the six-page article is full of statements like the above, which are pretty hard to argue against. But every now and again, Noyori makes some statements that strike me as mostly right, but a little odd:

When the careers of students depend entirely on the relationship to their professor, and only successful results count, then there is a large temptation for abuse on both sides.

I’ll agree that this relationship is very important, but to the point of using the word “entirely”? That’s not an assertion I would make.

It is hard to understand the logic behind committing fraud in spite of the apparent short-term gains. Scientific progress is achieved on the basis of previously published results. Fraudulent results cannot obtain a place of significance in the advancement of science, because they are not reproducible. Therefore, scientific fraud is a suicidal act for the career of the perpetrator. Integrity is an essential requirement for conducting scientific research.

This statement strikes me as naive. I think I understand many of the reasons why people commit fraud, just as I can understand why someone would murder someone else. In both cases, these reasons do not justify the crime, but there is still reasoning and logic at play.

Now, on to two passages that greatly interested me:

Another form of self-plagiarism is to cut and paste large segments of text from previous publications. The case of the Breslow publications offers important insights into the question of self-plagiarism. Ronald Breslow is one of the most highly respected chemists alive, and has made an enormous contribution to chemistry in his distinguished career of over 50 years. He published three personal review articles on the origins of homochirality. Many people are irritated by attacks on Breslow, since it is the right of every scientist to repeat their own ideas in different contexts, especially in talks or review articles. Indeed Breslow was unaware of any misconduct, since he has specifically made changes so as not to infringe on copyright laws. Nevertheless, the invited Perspective in JACS was withdrawn “at the request of the author due to similarity to his previously published reviews..” This is a difficult matter. “Self-plagiarism” can in fact be highly beneficial to the community. Eminent scientists travel worldwide and present almost the same lecture to many audiences; the goal is to have the largest possible dissemination of the ideas and results. The bottom line in publishing similar overviews should be whether it serves the advancement of science by reaching different and larger audiences. Copyright law needs to be respected, but other solutions in the interest of science should be sought to facilitate the widest dissemination of seminal reports. In conclusion, the repetition of a sentence or parts of a sentence is not considered plagiarism or self-plagiarism.

I cannot believe that the top editors of a journal are going to the mat for Breslow’s duplicate publication. I think most editors view the case as a classic example of self-plagiarism that is wholly unacceptable. “Self-plagiarism” is not simply restating your own ideas; it is lifting identical or minimally-altered pieces of writing for re-publication in a new article without clearly indicating that this material was published previously. The reasons self-plagiarism is unethical are: (i) it wastes resources, like the financial resources of the second journal and the time of those scientists assigned to referee material that has already been refereed once before, (ii) it traps the second journal in an adverse legal position with respect to copyright law, and (iii) it uses deception to “game” a system where publications are viewed as the principal metric of accomplishment in research.

And there is a huge difference between giving scientific talks and publishing scientific papers. Justin Bieber can perform “Baby” to audiences in Ottawa, Newark, and Richmond, but he can’t get away with publishing the song over-and-over on subsequent albums under different labels. Noyori’s opinion here is nothing short of bizarre.

If Noyori truly feels that “self-plagiarism can…be highly beneficial to the community”, I suggest that everyone submit self-plagiarized material for duplicate publication in Adv. Synth. Catal. I think he and the other editors will quickly change their tune.

Finally, here is the editors’ requisite thumbing-of-the-nose to blogs:

The Internet has become a major medium of communication in research and is contributing to the democratization of the global science community. Society is conditioned to consider that the printed word is valid; unfortunately, this trust cannot be extended to the Internet. Scientific results put onto the Internet without peer review have a serious problem with credibility. The American Chemical Society guidelines contain a section on publishing outside the scientific literature, but more comprehensive ethical guidelines are needed for publishing in the social media. More harmful is the publishing of irresponsible criticism and slander, even in the blogs of highly respected journals (see the Comments to the C&EN article on Breslow, cited below). Ethical guidelines condemn personal criticism and yet one often sees unscientific accusations, rumor or innuendo in the Internet. The mass media tend towards sensationalism and are not considered scientific, but irresponsible personal accusations on the Internet in an alleged scientific context are damaging to the individuals and to the entire image of science.

What a surprise: the editors of an expensive peer-reviewed journal denouncing the prospect of publishing scientific research for free on the Internet. Also, I love how they criticize “irresponsible criticism” on blogs without specifically citing what they find wrong. They only drop a numbered reference to the web page for the Breslow duplication story at C&EN, which has a comments thread that is heavily moderated by the editors. Someone please identify the slanderous comments that Noyori thinks are so irresponsible. Is this the best he could do?

Earlier this week, I sent a questionnaire to the two current candidates for ACS President-Elect. The first candidate to respond is Tom Barton, Distinguished Professor Emeritus of Chemistry at Iowa State University. I have posted his responses below, in full.

Thank you, Professor Barton, for responding and engaging the online community of chemists on these matters of great importance to the society!

Response of Prof. Tom Barton, Candidate for ACS President-Elect

Hi Paul,

Thanks for giving me an opportunity to take a shot at these important questions.  You will see in my responses that I don’t have the complete picture on any of them.  If elected I would plan on spending a significant portion of the first year getting that picture and probing membership on their views on these and other concerns.

Tom

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

For those who are not up to date on this case, as I wasn’t when first asked about it, there is an excellent summary by Marianna Bettman, an Ohio law professor to be found at http://www.legallyspeakingohio.com/2012/09/merit-decision-am-chem-soc-v-leadscope-thumbs-up-on-unfair-competition-claim-thumbs-down-on-defamation-claim/.  I found it to be an excellent discussion.  As only a candidate, I do not know the intimate details of how and why ACS got into this, nor of the situation that they face at the moment.   Thus, I must reply with the general statement that I have always believed and always have acted on the principle that openness is the best policy.  In my lifetime, the most dramatic examples of the dangers of secretiveness were perhaps in the behavior of the Atomic Energy Commission, who wrongly believed and operated under the premise of “the public doesn’t need to know”, when in fact the public had a desperate need to know.  There are many more examples where secretive behavior by parts of government ultimately created situations far worse than complete openness would have produced.  Thus, as ACS president I would want to see all the history and strive to make all that was pertinent and not legally encumbered available to the entire ACS membership.  Yes, that includes legal fees.

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

I have received a number of enquiries as to my views in this arena, and conclude that a lot of people feel rather strongly about this issue.   In tracking down the actual numbers I found different ones in different sources but they are all awe-inspiring.  It is important to remember that executive compensation operates within a market.  If your compensation is not competitive, there is real risk that you can lose the type of talent that you need for the organization to succeed.  That said, the membership of ACS has every right to request and get an explanation for the magnitude of these salaries.  There is an annual process by which the salaries are set and thus, the ACS can provide the rationale(s) involved and report to membership (via C&EN) why the salaries are what they are.  Said report should provide examples from similar societies, keeping in mind that ACS is not only the world’s largest scientific society, but certainly the most complex (and D.C. is hardly the least expensive place to live).  I would support a policy that in the future, salary histories of all employees making over some minimal level would be annually reported to the membership in C&EN.  Again, this is a simple matter of openness.  If one is not prepared to justify how one is spending someone else’s money, one should not spend it in that fashion.

I would add that where I have worked for the past 45 years, Iowa State University, all faculty and staff salaries are published annually in the newspaper (now on paper’s website).  The only time this has bothered me is when I was not included because my salary did not reach the minimum!

Lastly I would note that I do not see the logic in giving everyone a bonus every year.  The only reasonable justification for a bonus is that the employee exceeded your expectations.  If you are giving bonuses every year, you need to rethink your expectations.  Once again, if there are good reasons, all that is needed is to inform membership of them

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

I don’t have the data to take a reasoned stance on this at this time.  I’ll have to get it, however, as I have had a couple of interesting emails about this in the past few days, which have caused me to have some potential concerns.  It is hardly unreasonable for users to be concerned about the costs of necessary materials, and ACS needs to be sensitive to the real fiscal constraints in the budgets of their members/subscribers.  Using profits resulting from ACS publications to fund other parts of the operations, considered to be of significant value, up to a point seems reasonable to me.  I can see no reason not to inform membership of the details, specifics and magnitudes, and then try to get feedback via the local sections.  Once again it is a simple matter of openness.  If you are not proud to tell people what you are doing with the money, you need to rethink what you are doing with the money.  Actually I imagine that ACS has an admirable story to tell here.  As I said, I don’t have enough information to provide a detailed answer at this time, and that is largely because such information is difficult to obtain.  There clearly is considerable concern about pricing out there (e.g. www.attemptingelegance.com and www.insidehighered.com/news/2010/12/02/acs ) but “tiered pricing”, “value-based pricing” and confidential negotiations with individual institutions have made it difficult to see a clearly defined pricing picture.  One group truly stands out as having serious problems and that is small liberal-arts colleges with quite small chemistry departments, who have to pay what to them are very large sums of money to subscribe to the number of credible chemistry journals required for ACS accreditation.  With the fiscal situations of these institutions being often dire, it has become difficult if not impossible for them to comply.  I strongly believe that we need to work on a solution to this problem.  I also believe that there must be solutions, as our reason for existence is to serve our members.

A question I have, and have not yet found an answer, is has there been an accounting of the actual costs of publication now versus the pre”technology-revolutionized” costs.  Surely the costs have been lowered by electronic publishing, and one might have expected that to be reflected in subscription costs.  Maybe it has been, or perhaps the loss of revenue from individual subscriptions has more than offset any savings.  I don’t know, and I’m sure many members would like to see a C&EN article addressing this situation.

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

I would prepare a series of profound video vignettes of the great successes of chemistry which have benefitted the world (and the U.S. economy) to be shown via every possible media outlet, and to be used for workshops for Congressional legislative staffs.   The purpose is to help the general public, and quite importantly, lawmakers understand that support of chemistry is an investment with a long history of success.  This is of course not a new idea, but is the best one of which I know.  A key will be how to find affordable ways to get the message out.  Purchasing commercial broadcast time is very expensive, so leveraging new media like social media and the blogosphere would have to part of the answer.  While I don’t consider the public’s perception of chemistry to be quite the problem that once was the case, this effort to get the word out that ours is an enabling science will always be with us.

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

I realize that it is comforting to hope that there is one silver bullet or some magic pill that will make everything alright again, but it just isn’t going to happen.  In recent months I have spoken and written about my belief that it is entrepreneurship which has the best chance of building a new employment base for chemistry in America.  However, for this narrowly focused question I would try to address the issues that have caused and are still causing our jobs to depart our country.  Although I am usually loath to address a problem with a meeting, I would propose a summit meeting of the industrial leaders of chemistry to develop a list of factors that make leaving America attractive; kiss off the ones we really can’t deal with (e.g. lower wages elsewhere) and get to work on the ones we can.  Understand that lower labor costs are not the only issues in this game.  As I discussed a bit on my website, there is no surer route to moving jobs out of America than to impose unreasonable regulations on American industry.  This may be an unpopular subject to raise, and I am sure will engender some cries of anguish, but if there is anything within the bounds of ethical behavior that can be done to produce and protect jobs for American chemists, we must do it.  The health of the American chemical industry is of utmost importance to us and we must not forget this.

6. What is your favorite element and why? 

Hey! I thought the softball question is supposed to come at the beginning of an interview.  That having been said, I’ll answer it.  Silicon.  Why?  Because it is so close to carbon, yet so far away in its behavior.  I am particularly enchanted by the richness of its thermochemistry as compared to that of carbon.  For example, the isomerization of the carbene analog, R₂Si:, to a silene analog of an olefin, RHSi=C<_, is essentially isothermal!  Or that SiH₄ thermally decomposes to H₂  +  :SiH₂  in a single concerted step.  Compare these observations with the drastically different cases in organic chemistry.

Note: Any response provided by Prof. Barton’s opponent in this election, Prof. Luis Echegoyen, will be posted within a day of its receipt.

Derek Lowe just called attention to this item in today’s Chronicle of Higher Education. Here’s the snippet that reeled me in:

“The built-in inequity in the pricing model that ACS has come up with makes it very difficult to act in collegial, supportive ways while we look out for our own interest,” she said.

According to Ms. Rogers, she’s not alone in her gloomy assessment of the situation. “I may be saying this publicly, but there’s a lot of people saying it quietly,” she told The Chronicle.

(Observers, including some commenters on Ms. Rogers’s call-to-action blog post, have noted a potential conflict of interest for the chemical society, which serves as an accreditor of chemistry programs as well as a publisher of chemistry journals. A certain number of high-quality journals is required for accreditation. They don’t necessarily have to be ACS journals, though, and losing accreditation as a result of canceling ACS subscriptions does not appear to be a worry for SUNY-Potsdam’s chemistry program.)

A spokesman for the American Chemical Society said that the group would not offer a response to Ms. Rogers’s blog post or the conversation that’s sprung up around it. “We find little constructive dialogue can be had on blogs and other listservs where logic, balance, and common courtesy are not practiced and observed,” Glenn S. Ruskin, the group’s director of public affairs, said in an e-mail message. “As a matter of practice, ACS finds that direct engagement via telephone or face-to-face with individuals expressing concern over pricing or other related matters is the most productive means to finding common ground and resolution.”

Wow. I’ve got too much to do to comment now, but you’d better believe I’ll have more later.

Edit: I received the following e-mail message from Glenn Ruskin at 1:00PM (PDT):

Paul:

Good afternoon.  We have not yet met, but I hope to do so at some point in the future.

I noted your ChemBark posting regarding my comment in the Chronicle of Higher Education (CHE) and I wanted to provide a bit more context.

It was not my intention, nor the intention of ACS, to denigrate blogs or users/contributors of blogs.   My comment was directed toward the blog that was the subject of the CHE story.  Unfortunately, CHE did not use the totality of my comment as I think it would have been clear that I was speaking specifically to the blog that was the point of the story.  Here is the totality of my statement (bolded section was omitted by CHE):

“We find little constructive dialogue can be had on blogs and other listservs where logic, balance and common courtesy are not practiced and observed.  As a matter of practice, ACS finds that direct engagement via telephone or face-to-face with individuals expressing concern over pricing or other related matters is the most productive means to finding common ground and resolution.  Therefore, we will not be offering any response  to this blog posting or the conversation that has ensued.

I respect and appreciate responsible bloggers, those that thoughtfully engage on those blogs as well as those that utilize listservs.  No insult was intended, and apologies to those that interpreted the comment that way.  These outlets provide important avenues to further dialogue and collaboration and are valuable assets in the ever evolving digital age.

The individual responsible for the above cited blog certainly has the right to her opinion, but that does not excuse rude behavior or her use of profanity and vulgarity in addressing ACS or its employees. While not evident in the most recent postings, I won’t repeat what she has posted in the past.  But I think you would agree that vulgarity and profanity postings do not lend themselves to meaningful, productive and civil discourse, thus our decision not to engage any further with her on this topic.

Glenn Ruskin

So, it would appear that the absence of a comma after the word “listservs” in the original statement was intentional, such that the subsequent clause of the sentence was restrictive (consult Strunk & White, rule #3). I am not that familiar with the blog in question, so I cannot speak to the blogger’s rudeness, but I sincerely hope that the ACS does engage in a public dialogue about the pricing of its journals. I am outraged, as a chemist and a human being, that there are some schools that are being forced to encourage their students to curtail their exploration of the chemical literature because the ACS is charging enough “per click” to bust these schools’ budgets.