Pinky Pinky, Hanky Panky

That pink regions in the pic show the self-plagiarzed portions in just two pages (pages 4 and 5) of a paper published recently in the Journal of the American Chemical Society (JACS) by Ron Breslow, an ex-President of ACS.

The picture is from Stuart Cantrill, who has posted two more: Page 1 and Page 2 and 3.

Nature News Blog has a good summary of this fiasco, which has led to calls for the paper's retraction. [See also Rahul's post].

JACS has temporarily removed the paper from its website "due to possible copyright concerns"; the notice at the paper's web URL adds, "The Journal’s Editor is following established procedure to determine whether a violation of ACS Ethical Guidelines to Publication of Chemical Research has occurred.”

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Breslow is also a co-author of two JACS papers (published in 1989 and 1990) that were so sloppy and so riddled with basic errors that they cried out for retraction or correction. Two brave souls tried, through independent efforts, to get JACS editors to publish their Scientific Comment on the two papers. Read their tale in Nature (1992) [paywalled, unfortunately].

Breslow became President of ACS in 1996.

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Thanks to Pradeepkumar for the e-mail alert with links to the Nature News Blog and the 1992 paper.

Public Discussions of Problematic Publications

Oh! Indian Intellectualism is the blog of GnaanaMaargi (GM) who appears to be an academic at an Indian institution. Please go and say hi to him (or is it her? I don't know; I'll go with 'he' until I'm corrected).

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In his second post, GM urges Indian academics to boldly enter the public sphere: "speak up and speak out, in public". But he follows it up by taking a curious turn in his latest post in which he seems to argue that there was something illegitimate about the recent newspaper revelations of problematic publications from high profile scientists -- specifically, Prof. C.N.R. Rao and Prof. Ashutosh Sharma.

Here's what I think is the main reason for his complaint:

Going to the media if one does not get due justice in the appropriate scientific fora may be understandable, but doing so otherwise is simply not appropriate. And, it does a dis-service not just to the accused but to the entire scientific community, whose image is tarnished.

This concern for procedural correctness is misplaced. Consider the Rao case. After being alerted about the problems in his paper, Prof. Rao even offered to retract the paper, but eventually settled the issue by publishing an apology. The news stories appeared over two months later (without interfering with GM's preferred sequence), primarily because of who he is. Or, take the Sharma case; in what I consider a very brave act, The Student confronted Prof. Sharma about the problems in his paper. The news story (which appeared over 100 days after The Student's first e-mail) has this to say about Sharma's response:

[The Student] ... noticed the similarities in December 2011 and sent an email query to the paper’s first author ... and senior author Ashutosh Sharma ...

... scientists say that emails exchanged between the student and the IIT faculty members suggest that the faculty members tried to badger her into silence in December 2011 and offered to issue an erratum only after an anonymous email raked up the issue earlier this month.

In other words, The Student did all she could, before backing off (or, was forced to back off). The situation stayed there until "an anonymous email raked up the issue" last month; it was only the (threat of) news coverage that eventually forced Sharma into doing the right thing [see Footnote 2, below]. If this is not an argument for public discussions of problematic papers, I don't know what is.

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Another reason for GM's disgust with the news stories appears to be his concern about the cost to personal reputations of the scientists concerned. Here's how he frames the issue about CNR's apology:

Whoever ... took that resolution of an independent scientific journal to the media had very little business doing so -- it seems like an obvious case of vendetta or one-up-man-ship.

Leaving aside GM's evidence-free speculation about the whistleblower's motives, he is still barking up the wrong tree here: the primary cause of the scientists's PR problems is not the whistlblowing, but their own prior acts of omission and commission. More importantly, this sort of personality-oriented analysis obscures the real issue, which is this: "When shit happens, how does one deal with it?" [see Footnote 3] In other words, among the many ways of reacting to adverse news, which one did these top scientists choose? (And, is that newsworthy?)

Consider just for a minute a what-if scenario in which Prof. Rao, on being alerted about the plagiarism in his Advanced Materials paper (sometime in late 2011), took the help of someone to investigate and identify the source of the problem. This step might have made him aware of other papers that were similarly tainted (instead of seeing them revealed in blog comments), and allowed him to take corrective steps on all the problematic papers -- well before presspersons started mobbing him in February of 2012. In this scenario, there might still have been some news stories, but they would have sounded a lot more positive than they did -- some might even have praised him for his actions.

In real life, though, that's not how Prof. Rao responded [see Footnote 1] -- and that made the story even more newsworthy.

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In his focus on procedural correctness, reputational consequences, or whistleblowers' motives, GM misses what I think is the most important question: have the news stories been good for science? The answer is, "Yes, absolutely." Consider:

1. The news stories allowed a discussion of students' writing skills as a source of weakness in the chain that connects an interesting research question to the eventual publication of its answer. This could lead to creating and implementing remedial measures at our academic institutions.

2. A lot of people (including scientists) now have an enhanced awareness about ethics in science. The news stories, and the subsequent discussions in blogs, offer some guidance on how (not) to deal with problematic papers especially when the problems are not of one's own making, as well as on how to avoid them in the first place.

3. Only the possibility of newspaper coverage spurred Prof. Sharma into thinking about issuing an erratum [see Footnote 2].

IMHO, these are all good, positive things.

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Footnote 1: Prof. Rao's initial response included disowning his coauthors after underplaying the problem by saying, "This should not be really considered as plagiarism, but an instance of copying of a few sentences in the text." [By the way, does this gel with other reports that said he offered to withdraw the paper?] When problems in a few other papers came to light, his response was revealing: "... I don’t know who is trying to do this damage to me."

Footnote 2: Rahul has the most apt comment:

Somehow [the news of Prof. Sharma issuing an erratum] reminds me of Churchill’s comment about Americans, that they “can always be counted on to do the right thing, after exhausting all other possibilities.”

Footnote 3: This is a variation of a formulation was articulated by Prof. N. Raghuram at the Workshop on Academic Ethics last July:

That research misconduct happens (every once in a while) should not be shocking. What is truly shocking is the lack of a coherent, fair response to the discovery of misconduct [perhaps not his exact words; I'm quoting from memory].

Indian Higher Ed Links

These news items seem significant, but I haven't seen a focused discussion of what led to these decisions and what they might mean on the ground. Let me park them here for the moment:

1. Aarthi Dhar in The Hindu: Doctors pursuing higher studies in the US to sign return bond.

2. Linah Baliga in ToI: Govt bans use of live animals for education, research.

Blood and Gore in Book Reviews

John Sutherland has a terrific piece in The Guardian: Which book reviewer will win the 'hatchet job of the year' award? Not only does he have links to some of the juiciest of them, he even links to a review that demolished one of his own books!

I should make full use of this opportunity to link to demolition jobs that are pure fun: Matt Taibbi and Mihir Sharma. But they reviewed non-fiction, while Sutherland's piece is about reviews of fiction, poetry, anthologies, and the like.

Some excerpts:

Give someone a hatchet and, quite likely, they'll get bored of clearing the literary undergrowth and sink it in some luckless writer's skull. More so in a hothouse literary world like London's. And it's fun to watch, so long as the hatchet isn't descending on your own cranium. Every sport benefits from a bit of blood. Personally I stop reading reviews at the first mention of words such as "splendid", "magisterial", or "meticulous". Gore beats puff every time. [...]

I've published some 28 books ("Splendid", all of them), over what some unfriendly reviewers have recently been implying is an overlong career (notably that young stripe Sam Leith, damn him, who I see is one of the hatchet judges). Most reviews of my books have been friendly. But there's always been a couple of stinkers. And those are, inevitably, the ones you can – 40 years later – still recite by heart. More so as, when time passes, you begin to suspect your assailant may have got some things right.

My most recent effort, Lives of the Novelists: A History of Fiction in 294 Lives, has received the kinds of review that would please my mother in the Spectator, the Times, the Financial Times, the Independent, the Evening Standard. But it got the loo read of the year award in Time Out ("top of the world, Ma!").

It also got a review of such savagery in the Telegraph that, if I were a betting man, I'd go down to Paddy Power and put a tenner on Jonathan Bate walking away with the 2012 hatchet of the year award, still dripping with my warm blood and brains. (That's the one link you clicked on, isn't it? Point proved). Forget loo read of the year. As far as Bate is concerned my luckless volume wouldn't even qualify as toilet paper.

Prof. Ashutosh Sharma Issues an Erratum

Here it is: Biomimicked Superhydrophobic Polymeric and Carbon Surfaces (April 2012), DOI: 10.1021/ie300772p.

This erratum presents an addition to the original article. Two schematic figures (Figures 1 and 2) and some text of the experimental protocol on the preparation of negative PDMS replica of leaf in the Experimental Section were inadvertently published in almost-identical form (but with different preparation conditions) to that in a thesis by [The Student] (1) The authors also inadvertently omitted the citation to this work. The authors sincerely apologize to the editors, reviewers, and readers of the journal, and to the thesis author for this oversight. [Bold emphasis added].

[This text is followed by a reference to The Student's MTech thesisi].

Here's the front page article in The Telegraph that started it all; hers's my first post on this case (and more; and much more at Rahul's post and its comments section). In a post on the problems in Prof. Sharma's paper, I said:

The Student's thesis deserved a citation [in Prof. Sharma's paper] for (a) having achieved much of what the authors of I&EC paper achieved, but three years ahead of them, (b) developing the protocol for making negative and positive replicas, and (c) reporting a set of results that ought to have been compared and contrasted with those reported in the paper.

In acknowledging the plagiarism committed by the authors, the erratum addresses (a) and (b), but indirectly. By its very nature, an erratum is probably not a good place for (c). Finally, the authors have done the right thing by apologizing to The Student.

Steven Weinberg on the Future of Big (Experimental) Science

LHC may have been built successfully, but according to Weinberg, it may very well be the last of its breed, because it's going to be almost impossible to get the kind of funding needed for the next (and much more powerful) accelerator or observatory. He comes to this conclusion based on his experience with physicists' failure in the 1990s to get adequate funding for their dream machine -- the Superconducting SuperCollider (SSC); the project was abandoned after spending some 2 billion dollars on it.

How about a funding model based on international cooperation and collaboration? He's pessimistic about this as well; he says, "We saw recently how a project to build a laboratory for the development of controlled thermonuclear power, ITER, was nearly killed by the competition between France and Japan to be the laboratory’s site."

All in all, not a good prognosis for Big Science. Here's an extract on how a combination of political rivals as well as scientific rivals (scientists who argued that the money is better spent on Small Science) helped kill the SSC project:

So in the next decade, physicists are probably going to ask their governments for support for whatever new and more powerful accelerator we then think will be needed. ...

That is going to be a very hard sell. My pessimism comes partly from my experience in the 1980s and 1990s in trying to get funding for another large accelerator.

[... snip, snip...]

What does motivate legislators is the immediate economic interests of their constituents. Big laboratories bring jobs and money into their neighborhood, so they attract the active support of legislators from that state, and apathy or hostility from many other members of Congress. Before the Texas site was chosen, a senator told me that at that time there were a hundred senators in favor of the SSC, but that once the site was chosen the number would drop to two. He wasn’t far wrong. We saw several members of Congress change their stand on the SSC after their states were eliminated as possible sites.

Another problem that bedeviled the SSC was competition for funds among scientists. Working scientists in all fields generally agreed that good science would be done at the SSC, but some felt that the money would be better spent on other fields of science, such as their own. It didn’t help that the SSC was opposed by the president-elect of the American Physical Society, a solid-state physicist who thought the funds for the SSC would be better used in, say, solid-state physics. I took little pleasure from the observation that none of the funds saved by canceling the SSC went to other areas of science.

Hilarious Take on Fairness Creams

Triggered in part by a recent (viral) video ad that shows "[a] married girl thinking about those shame-shame areas of her body, that too while having coffee with her husband!", Suchi Govindarajan has penned a hilarious commentary in Himal South Asian about fairness creams and the video ads for them. Fabulous stuff -- go read it now!

Among the things Govindarajan mocks is "technology behind the bleach and fairness creams." Which reminded me of the infamous Challenge of the Month that launched a crowdsourcing experiment put together jointly by DST and P&G [by the way, the experiment appears to have died after two "Challenges"].

Here's a quick taste of what Govindarajan dishes out:

I am hearing there is lot of technology behind bleach and fairness cream. Are you knowing that some creams is coming direct from smart scientists at research institutes? First of all, these creams are all acting at a cellular level, not like our rose powder. Some ions are being released by the cream, and it is going into the underside of skin and just burning all the melanin into hot air (this melanin is useless compound anyway). At the same time, the ions are going outside and building big shield like Karna had in Mahabharata TV show. This shield is preventing bad things like sunlight, dust, common sense, etc. I am also reading on how the cream is improving IQ. It seems our brain is like a cauliflower. Fairness creams are having some hi-fi technology, namely Nano OzoNe Sensitiser agents. This NONSens agents is going into brain and like cement, it is sitting between the cauliflower gaps and that is how it is increasing IQ. I am really amazing about this every time.

An Early Example of a Patent Troll

Written by Gary L. Reback almost ten years ago, this article -- Patently Absurd -- describes the drivers behind the horrible degeneration of the patent system in the US. The entire article is worth reading, but this description of an early patent troll is just fantastic:

My own introduction to the realities of the patent system came in the 1980s, when my client, Sun Microsystems--then a small company--was accused by IBM of patent infringement. Threatening a massive lawsuit, IBM demanded a meeting to present its claims. Fourteen IBM lawyers and their assistants, all clad in the requisite dark blue suits, crowded into the largest conference room Sun had.

The chief blue suit orchestrated the presentation of the seven patents IBM claimed were infringed, the most prominent of which was IBM's notorious "fat lines" patent: To turn a thin line on a computer screen into a broad line, you go up and down an equal distance from the ends of the thin line and then connect the four points. You probably learned this technique for turning a line into a rectangle in seventh-grade geometry, and, doubtless, you believe it was devised by Euclid or some such 3,000-year-old thinker. Not according to the examiners of the USPTO, who awarded IBM a patent on the process.

After IBM's presentation, our turn came. As the Big Blue crew looked on (without a flicker of emotion), my colleagues--all of whom had both engineering and law degrees--took to the whiteboard with markers, methodically illustrating, dissecting, and demolishing IBM's claims. We used phrases like: "You must be kidding," and "You ought to be ashamed." But the IBM team showed no emotion, save outright indifference. Confidently, we proclaimed our conclusion: Only one of the seven IBM patents would be deemed valid by a court, and no rational court would find that Sun's technology infringed even that one.

An awkward silence ensued. The blue suits did not even confer among themselves. They just sat there, stonelike. Finally, the chief suit responded. "OK," he said, "maybe you don't infringe these seven patents. But we have 10,000 U.S. patents. Do you really want us to go back to Armonk [IBM headquarters in New York] and find seven patents you do infringe? Or do you want to make this easy and just pay us $20 million?"

After a modest bit of negotiation, Sun cut IBM a check, and the blue suits went to the next company on their hit list.

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I had read this article long ago, and even remember unsuccessfully googling for it sometime ago; I'm glad I found it via Brad DeLong's link-post.

Congratulations ...

... to Prof. K. VijayRaghavan (Director, National Centre for Biological Sciences, Banaglore) and Prof. M. Vidyasagar (who is currently with the University of Texas - Dallas, after decade-long stints each at the Centre for Artificial Intelligence and Robotics, Bangalore, and TCS, Hyderabad) who have just been elected to the Fellowship of the Royal Society. [News via Subhra Priyadarshini at Indigenus].

Awesome!

Prof. Partho Sarothi Ray's Interview

On NDTV, aired on the day he was released on bail (two days ago). [Link via Rahul]

Partho strikes just the right note in the interview, expressing his concern that six of his fellow activists are still in jail, his outrage that fighting for the rights of slum dwellers gets the State to respond with such fury, his anguish that the current government -- one whose election he appears to have supported -- is repeating the mistakes of the earlier one.

Annals of Unusual Awards

I'm sure the people who created this award mean well, but why insist on the nominees being already dead at the time of nomination? [link via DrugMonkey].

For one thing, it makes this part of the FAQ sound rather spooky:

Who does SfN contact when a decision has been made?

SfN will contact nominators to notify them that a decision has been made. SfN will only contact nominees if they have been selected to receive an award.

1982: Imagining the Intelligent Encyclopedia

Bob Stein has posted a bunch of wonderful pictures of imagined scenarios in which people use the intelligent encyclopedia. Pretty amazing how much those futurists got right.

Check out his post: Back to the Future -- In honor of Encyclopedia Britannica giving up its print edition:

These drawings date from 1982 (thirty years ago). Alan Kay had just become the Chief Scientist at Atari and he asked me to work with him to continue the work I started at Encyclopedia Britannica on the idea of an Intelligent Encyclopedia. We came up with these scenarios of how the (future) encyclopedia might be used and commissioned Glenn Keane, a well-known Disney animator to render them. The captions also date from 1982.

Links

1. Tony Cookson: How similar are the markets for textbooks and drugs?

2. Charlie Stross: What Amazon's E-Book Strategy Means.

3. Mihir Sharma: Our Creamy Layer.

   India is the most elitist, exclusive, unequal and stratified country in the world, and we don’t even know it. The Indian elite – which smugly calls itself the “middle class”, since it alone benchmarks itself globally – has constructed walls of privilege for itself that are all the more powerful for being invisible to many eyes. And if not invisible, then concealed behind other words — “culture” and “merit”, for example.

4. Data on suicides in IITs, IIMs and NITs for the years 2009-12 [via Satyanarayan's tweet].

Awesome Abstract of the Day

Via the guys with an uncanny eye for hilarity -- aka Retraction Watch -- here's the abstract, in full:

In this study, a computer application was used to solve a mathematical problem

Published in 2010, the paper (which a commenter recommends for its utter hilarity) with this awesome abstract was retracted by the journal recently "as the article contains no scientific content and was accepted because of an administrative error."

Read all about it at Retraction Watch.

Prof. Dibyendu Nandi's Appeal to Scientists

Update [9:30 p.m.]: Dr. Partho Sarothi Ray has been granted bail -- he should be out sometime in the morning tomorrow. Some good news, coming as it does on the 10th day of Partho's detention.

* * *

Rahul has already posted the text of a letter from Prof. Dibyendu Nandi, an astrophysicist and Prof. Partho Sarothi Ray's colleague at IISER-Kolkata.

Prof. Nandi sent his letter by e-mail to quite a few people, and at his suggestion, I'm also posting it here -- the idea being that the call for justice for Prof. Ray should reach as many people as possible:

Fellow Scientists,

I am writing to you as an individual and in my personal capacity of having known you. You are perhaps, by now, aware of the plight of Partho Sarothi Ray -- a faculty at IISER Kolkata, whom I consider to be one of our most talented scientists. Partho was picked up by the police for a peaceful demonstration against the eviction of slum dwellers in Kolkata and is still in judicial custody. I would like to bring to your attention that a website detailing the case of Partho has been set up by some of us and is available at:

https://sites.google.com/site/appealforjusticeforpartho/

Personally for me, it has been difficult to come to terms with this case; however, I have come to realize that whether we completely support Partho's activities beyond academics, or not, is not the point. What is important is that there has been a miscarriage of justice to one of our fellow scientists; somebody who has never compromised on his science and his teaching at our Institute.

I encourage you to peruse the material in the website, including the many news stories and testimonials about Partho that are in the public domain and make an independent assessment. Based on this, I also request you to consider giving Partho's case and this website wide publicity within your Institutes, Scientific Organizations, Academies and beyond and join the appeal for justice. If you would like to give a testimonial on behalf of Partho and are willing to have it hosted in a public domain, write to us at: forpartho@gmail.com .