Stop using that word: Accordance

Consider "accordance". It's a sleek, shiny word. But it's terribly misused in scientific manuscripts.

To pick on just one example, take the following text from a recent publication by Neil Kelleher's group at Northwestern (bold emphasis mine):

Our observations were in accordance with a previous study on nostocyclopeptide, where certain amino acids in the peptide sequence were found essential for the spontaneous macrocyclization of the peptidyl aldehyde intermediate into a cyclic imine.

And another example from a total synthesis of daptomycin by Xuechen Li:

The spectrum was in full accordance with those in the literature.

Not quite right.

"Accord" implies agreement. It's what writers usually mean when they use "accordance". For instance:

His dismal personal life was in accord with his excellent progress in total synthesis.

"Accordance", in contrast, implied obedience. It refers to compliance with a rule.

My one day of vacation per year is in accordance with group policy.

Examples of the correct use of "accordance" are actually hard to find. Consider this paper by Robert West at Wisconsin. An excerpt (bold emphasis mine):

In accordance with Bent’s rule, the increased R–O bond polarities of permethylated species lead to increased oxygen hybrid s-character and R–O–R bending angles in both ethers and siloxanes.

That one is arguably correct.

The difficulty is probably that "in accord with" doesn't flow quite smoothly. Perhaps a better option would be simply to say "in agreement with". Either way, reviewers probably won't catch it.

This has been a public service announcement.

Plagiarism and the role of publishers

Anyone who reads Just Like Cooking or Chemjobber is by now probably aware of the freshly-discovered plagiarism case wherein a 2013 Chem. Eur. J. article by Professor Xi Yan lifts, verbatim or nearly so, entire portions of a three-years-prior (2009) JACS paper by Professor Valérie Pierre. Reading the commentary, the plagiarism is pretty egregious. Additionally, comments and a further blog post by See Arr Oh have brought up more instances of plagiarism like this.

Of course, #spacedino is immediately brought to mind (for the uninitiated, that particular hashtag refers to the 2012 controversy where esteemed chemist Breslow, of Columbia University, was found to have submitted what amounted to essentially the same publication to multiple journals; it was only really caught because biologists took his lame ending joke seriously). After lengthy conversation on various media and social media outlets, the offending papers were retracted at Breslow's (and others') request (though initially he denied wrongdoing).

While the Breslow violation was aggravating and arguably wrong, the Yan violation is worse. I don't think that's a very controversial point to make, but it's an important one to recognize. The Breslow affair fell into what some categorized as an ethical grey zone; the Yan violation is in clear things-they-tell-you-from-day-one-in-university territory.

Rapid retraction is vital, I'd wager; thought many retracted papers still get heavily cited or believed, early correction is probably the best way to prevent such propagation. Once an article has been believed as true for a substantial period of time and gets included in dissertation of paper-introduction citation-vomits, less care is taken to check the original source and see the glaring retraction notice. Better to stop the train before it leaves the station.

I think this highlights the role of open and quick dialogue among scientists, along the same lines as Blog Syn. The ability to rapidly disseminate these issues when they are discovered can, ultimately, improve the quality of scientific communication. In a pre-social-media era, it was certainly easier to just assume a paper would slip by unnoticed. Not so much anymore; via Twitter, for instance, a wide audience can be quickly reached. See Arr Oh wrote that he has notified the two publishers (Wiley and ACS); it will be very interesting to see what action occurs.

Of course, a point could be made that such post-publication watchdog action shouldn't be necessary. Aren't these things peer reviewed? Alas, I think anyone with a healthy dose of realism is aware that a good bulk of reviewers put in the minimum conceivable effort in reviewing (consider the sheer quantity of bad Supplementary Information files). Usually, this is justified by a variety of factors, namely that reviewers are (1) busy and (2) unpaid. (And they aren't held accountable if the article is later retracted).

But hey, you know who are paid? Publisher staff. I'm a bit surprised that more journal editors haven't made a practice of submitting manuscripts to plagiarism detection software. There's many available; universities often have TAs use them to check undergraduate papers. One comment on Chemjobber's blog points out that Elsevier provides access to one such service, iThenticate, to its reviewers. One readily available service, eTBLAST, compares blocks of text to databases of scientific papers using the BLAST algorithms commonly employed in bioinformatics for sequence alignment. In short, many tools exist for plagiarism detection. So what's the deal, journals? A common claim of open-access opponents is that paywall publishers "add value" to papers by the publication process.

So why aren't all papers routinely submitted to these checks after peer review and before publication? Ideally, reviewers should do a thorough job vetting submitted articles and should be supplied with tools to do so. But publishers share that responsibility. If you can Cantrill an article, it shouldn't slip by.

(One caveat: I'm not sure about the journal coverage of many of the anti-plagiarism packages. eTBLAST, for instance, appears to have access to Medline and PMC, but doesn't seem to have many of the synthetic journals in full-text. That's from an initial assessment; I may be wrong. CrossCheck, the service powered by iThenticate, has a very wide list of included content, but interestingly, I don't immediately see ACS on the list). Is it possible that some of these illustrated issues just don't get picked up by the software?

Lastly, something that would be very interesting: how much scientific plagiarism occurred in the pre-software-detection era? That is, how prevalent were issues of plagiarism in the 1960s? If one took journals from the 1960s, for instance, and ran them through this software--what would they find? Is it more prevalent now? Is it less prevalent? When did scientific plagiarism mature? I suspect the issue is a very old one.

Reading assignments, vol. 7

No weekly link roundup last week due to the #GradMentalHealth discussion, but they resume below. Some pretty interesting stuff!

Perception of science

• Science News For Kids offers up several portraits of scientists, showcasing the importance of their work alongside their real-life interests. It's a pretty cool piece; things like this should be more common. Break stereotypes!
• For better or for worse, much of the public receives its knowledge of science through fiction, including crime dramas, medical dramas, and science fiction thrillers. That's given some false expectations. So it's interesting that the Washington Academy of Sciences has introduced a seal of approval to indicate they've thoroughly reviewed books and found the science within to be accurate. Neat concept!
• At Newscripts at CENtral Science, Sophia Cai summarizes a MIT-based web series about chemistry students. Give it a watch!
• Alex Stein has a very thorough link roundup on various sources regarding genetically-modified crops (sometimes referred to, usually biophobically, as GMOs). Included are aspects of media coverage, safety and economic research, and perspectives of scientists.
• Neuroscientist Zen Faulkes has a short but thought-provoking piece on social classes within science. It's worth considering; we see social stratification in chemistry between disciplines, within disciplines, geographically, and even between generations.
• I like writing about chemophobia, but it's important not to forget biophobia! (Is that a real term?)

Science writing

• Blog Syn is a go! This has already been covered all over the chemblogosphere, but it's worth repeating. Stay tuned as the workings and innards of Blog Syn get finalized. On a related note, Ash Jogalekar has written a post at Scientific American describing the GPCR Network as a model of open, collaborative research. It's really interesting, and one of the few examples where one could use the word "synergy" without rolling one's eyes.
• Via a carefully constructed example, Khalil Cassimally discusses scientific prose, general-public prose, and why the disconnect between the two is still relevant.
• Ben Morris argues for the obsolescence of academic journals. He puts in bullet-point format some key issues of the publishing industry discussed recently among scientists, especially in light of controversies including Elsevier's support of SOPA and the high fees ACS charges for journal access.
• It's been an interesting week as the #upgoer140 tag has abounded on Twitter. Inspired by this xkcd comic about describing technical concepts with the 1000 most common English words, numerous people have been accordingly describing their jobs (Stuart Cantrill describes being an editor; Derek Lowe describes medicinal chemistry; See Arr Oh describes organic synthesis and a lot of people participate in the comments; Chemjobber describes process chemistry; etc.). Even though it's funny to do so, I think it's also important. If you can't describe what you do thusly, do you really understand what it is you're doing or why? (If you want to give it a try, use the Up-Goer Five Text Editor).
• Science librarian Bonnie Swoger, inspired by #overlyhonestmethods, comments on those elusive journal articles that everyone cites but no one can get a copy of. Also, she highlights the importance of actually reading articles before citing them.

Research highlights

• From Quintus at Chemistry-Blog comes an account of a synthetic analogue of the ribosome. The authors (see publication in Science) used the technique to produce milligram quantities of a peptide! This was also covered in C&EN and by See Arr Oh.
• Derek Lowe gives a thoughtful perspective on an article summarizing the state of the field of "virtual screening". Worth a read for anyone interested in med-chem.
• I'm not usually a fan of reading about or listening to total syntheses, but B.R.S.M. gives a pleasant account of Shair's total synthesis of (+)-hyperforin.
• Bacterial toxins are interesting things! Check out this write-up on a PLoS Pathogens paper on toxins produced by C. difficile (nasty secondary infection common to those taking heavy loads of antibiotics). Warning to the it's-not-interesting-unless-I-can-column-it-and-solve-the-NMR-spectrum folks: the toxins in question (TcdA and TcdB) are enzymes and not small molecules. 
• Some intriguing research relating to rapid diagnostic of bacterial infections has been highlighted at Scientific American. The authors used secondary electrospray ionization mass spectrometry (SESI-MIS) to analyze breath samples for volatile organic compounds; they could correlate MS profiles to specific infections. It's an interesting idea; given the ability of bacteria to change their metabolism quite flexibly, I'd like to see how many false positives/negatives show up in actual trials.

Other

• Paul at ChemBark talks about how to get people to wear their gosh-danged goggles. He found that letting students customize their equipment led to a sense of ownership--kids saw them as their accessories rather than required/annoying items. Chemjobber shares his thoughts on the matter (and I personally find the merit badge comment amusing).
• Scientific American writer Janet D. Stemwedel writes about language regarding gun control and CDC research; she discusses the fact that many legislators want to prevent CDC/NIH research from influencing actual policy. This is relevant to areas outside gun control, of course, including chemical regulation and environmental policy. A choice quote: "legislators would rather be able to make policy unencumbered by pesky facts about how the relevant pieces of the world actually work."
• At The Worst Things For Sale, Drew points out some expensive bottled water that claims both to be "pure" and to be enhanced with fulvic acid. 
• Jean Flanagan at Sci-Ed (PLoS Blogs) has an important essay on the futility of educational research in scientific education. I found three of the presented points especially significant: (1) university and K-12 educators don't understand each others' environments, (2) practical research is looked down upon in educational academia, and (3) science education journals are most often behind paywalls, inaccessible to actual practitioners.
• From See Arr Oh comes a fun post prompting you to stop and listen to what your lab sounds like. 
• Forbes contributor Steven Salzberg (Fighting Pseudoscience) gives an important perspective on the fiscal cliff in the context of biomedical research. As it stands, the NIH is set to lose 10% of its already-stretched funding. Salzberg points out the tiny, tiny contribution of the NIH budget to the overall deficit and contrasts it to the high return-on-investment empirically shown for scientific research.
• American chemists, rejoice! The Royal Institute's Christmas Lectures are now available online.
• Artificial sweetener aspartame has been declared safe by the European Food Safety Administration after a review of the available safety data. However, since it's "synthetic" and a "chemical", what are the chances that anyone not already convinced of its safety actually reconsiders?

Reading assignments, vol. 4

The following are some interesting topics and posts from the last week or so. A lot of links, but they're pretty good.

Online education (i.e. MOOCs)

• At the Chronicle of Higher Education, George Washington University Dean Doug Guthrie criticizes Coursera, a for-profit company that partners with universities to offer massive online open courses (MOOCs). Guthrie insists that Coursera is a fad; "thoughtful interactions" do not occur; and educators are frequently creating a crowd, not a community. It's a valid point; online education has promise but very often falls short, even with the best of intentions. See also this other criticism/analysis of MOOCs.   While we're at it, if you really want to read more about MOOCs check out this year-in-review about MOOCs.
• In the midst of the recent surge in MOOC popularity, the University of Illinois at Urbana-Champaign is running an online Intermediate Organic Chemistry course, taught by educational specialist Michael Evans and Dr. Jeff Moore.
• Dayna Catropa and Margaret Andrews compare MOOCs to MOCCs (midsized online closed courses), predicting that MOCCs will replace MOOCs, as they provide an opportunity to monetize the online experience and deliver it to smaller groups.

Public health

• Antibiotic resistance is a serious public health concern, but a potential new class of antibiotics that take advantage of the dependence of certain pathogens on the thioredoxin system is displaying promise against MRSA, drug-resistant TB, etc. Malaria is also notoriously drug-resistant, and this press release details a surprisingly simple whole-plant antimalarial strategy that may be effective and cost-effecient. This stands in contrast to the widespread practice of synthetic, pure drugs.
• While we're on the subject of antibiotics, Katherine Harmon at ScientificAmerican writes on recent findings that amoxicillin is not only overprescribed but is ineffective compared to a placebo for most of its common applications. Add another one to the "no, seriously, stop giving out antibiotics like candy" file.
• Antibiotic use in agriculture is controversial, and Maryn McKenna at WiredScience writes on the FDA's reluctance to compel companies to disclose farm antibiotic use. On a related note, The Pump Handle criticizes a recent USDA decision to "modernize" poultry inspection; the author says that the new guidelines, which aim to speed up the inspection process, would threaten food safety.
• Personalized medicine has gotten a lot of recent attention as a strategy for fighting disease (particularly cancer). The general strategy is to target therapeutics based on a patient's genome. However, personalized medicine has its skeptics, and a commentary by Sharon Begley examines recent evidence that this approach may never be effective.

Scientific communication

• Terminology and jargon is integral to scientific communication and has traditionally been an obstacle to deaf and hearing-impaired people. Douglas Quenqua writes about crowdsourcing-oriented efforts at creating a sign language scientific lexicon.
• Both Chemjobber and Derek Lowe comment on a perplexing press release about Parabon's drug delivery technology that sounds more like a Michael Crichton novel. The press release's author has responded, as well, with a degree of consternation at the press release's negative reception. I think this exchange really highlights some concerning issues about scientific communication to a broad audience.
• University librarian Barbara Fister comments on how undergraduates struggle to learn how to do literature-based research. She posits that how we frame/present the task influences a student's perception of their own ability to complete it (just call it Finding Stuff Out). It's an interesting read; the philosophy is familiar to me from when I tutored writing. I think we can draw some parallels to how we teach scientific thinking and how the public perceives scientific writing.
• At ScientificAmerican, Khalil Cassimally lists some good practical guides for developing science journalists. There's about 11 of them listed; read and bookmark them! On a related note, see this post by Khalil about how science writers keep their notes organized.
• Chemist Phil Davis has listed his 17-years-deceased PhD adviser as a co-author on a paper. While it's good to give credit where it's due, don't all authors have to consent to publish? This just generally seems weird given the elapsed time.

The F word (funding)

• At the Chronicle of Higher Education, Indiana University president Michael A. McRobbie warns that the fiscal cliff may spell out serious damage to research universities. He makes the case that this would be perilous to the economy, as research drives innovation in engineering/manufacturing.
• The United States is not the only place where scientists are feeling the squeeze of a scant funding environment. Nature gives an account of Spanish scientists who protested their government's reductions in science funding (39% drop since 2009).

Scientific philosophy

• On HuffingtonPost, Dr. Rupert Sheldrake writes a commentary on the arrogance of modern science, criticizing materialism and insisting that dogmatic thinking is "crippling" modern science. I disagree with most of what he says; it's overly dramatic, simplistic, and feels like it's pandering to the pseudoscientist crowd (as well as an advertisement for the author's new book). But it's worth reading; is this a pervasive viewpoint?
• For the philosophically inclined, read this. (tl;dr = is science tool-driven or idea-driven??).

Other

• B.R.S.M. has a good post examining a recent essay by Kappe in Angewandte regarding "non-thermal microwave effects" (spoiler: they probably don't exist). See also a simultaneous piece by Tom W. Phillips over at A Chemical Education.
• A criticism on reaction norm about feeble efforts by departments to insist they're preparing students for "alternative careers". The author states that departments and faculty are not in touch with or interested in actually preparing students for non-traditional careers.
• P.Z. Myers gives an account of a saddening (and infuriating) case of a biologist illegally baiting and killing an aging jaguar, then covering it up.
• Really cool guest post at Scicurious about the basics and history of X-ray crystallography.
• STEM education has gotten a lot of attention and advocacy recently, but Gwenn Schurgin O'Keeffe touts the arts as essential to fueling creativity and cross-fertilizing other skillsets.
• Deirde Lockwood, a chemical oceanography graduate student discusses the increasing time-to-degree for chemists at CENtral Science. She thinks four years is too short, and limiting programs to shorter periods of time would breed easier projects and softer chemists.
• Ronald Breslow dancing to Gangnam Style? Yes, please.

Blind to colorblindness

Since venturing into the more biology-oriented side of organic chemistry, I've noticed something in chemical biology and biochemistry papers that really isn't a problem in synthetic journals. Color. Biologists/chemical biologists love using color. And that makes sense; the meaning of a figure can be more easily conveyed by dyanamic coloration. Consider the following micrograph from an ACS Chemical Biology article (DOI: 10.1021/cb300171p). The figure depicts measurement of zinc levels in mitochondria in different cell types. It's a nice looking figure, and reasonably clear.

But then you go to print the articles (some of us do that) on your black and white printer and the figures become incomprehensible.

Of course, the obvious question: so what? Why not use a color printer? Or simply view things on the computer or a tablet? Content is delivered overwhelmingly by the web now; isn't it natural that figures reflect the most common viewing medium?

Well, yes. But it's still a problem for a sizeable minority (not many women, but as many as 10% of men) of the population who experience colorblindness. "Colorblindness" is a blanket term to refer to any disorder resulting in loss of color perception. Completely grayscale colorblindness is very rare, but difficulty telling red and green apart is relatively common. Variability is seen in the degree of impairment; many people are simply "red-green weak", whereas others cannot tell the two apart.  Blue and yellow are also indistinguishable to some people, though this is less common.

The previously mentioned figure would look like this to someone with protanopia, a form of red-green colorblindness (note that colorblind images were simulated using Photoshop and the Vischeck plugin).

An important thing to note is that what appears illegible in grayscale is not necessarily illegible for colorblindness; a comparative example is shown below  Thus, it's possible to use colors effectively and still accommodate the colorblind population. Take this example from a Merck drug discovery paper (DOI: 10.1021/cb2003225). The quality of the original image (left) is not significantly damaged for a person with red-green colorblindness (center), even though the figure is indiscernable when rendered grayscale (right).

Web developers take colorblindness into account. It's an important topic in website design; professional web designers must ensure their content renders to readers who can't see, can't hear, can't see well, use Apple products, or other disabilities. As such, guidelines have been set up to ensure accessibility, including recommendations for color and contrast. The W3C standards, for example, "help make the Web accessible to people with disabilities including auditory, cognitive, neurological, physical, speech, and visual disabilities" (read more here if you're interested). Validation tools are commonly employed to ensure websites meet these standards.

So why haven't some journals gotten the message?

Consider the following examples, shown in the original form on the top/left with simulated protanopia beneath/right. Both of the example figures are from a 2008 JACS article (DOI: 10.1021/ja807872s). In this first example,  the graph is illustrating the fluorescence response of a bisboronic acid rhodamine derivative to various peptide substrates in order to demonstrate its selectivity. First off, this figure is difficult to read in the first place. But in the original full color image, peptides 1 and 10 are clearly the top symbols. In the colorblind-simulation image, it's tougher to tell. Is it 10 or 6 or 4? Is it 1 or 7? 9 kind of looks close, too. There's the little lines behind the markers, but those are confusing themselves. While the text clarifies this figure further, the figure label does not.

The next example is even worse. The results of labeling studies are shown. In their original color (left) they're quite striking. But the labels are red and green. Hence, under red-green colorblindness, the pictures are meaningless.

This should be unacceptable; all modern fluorescence imaging programs have the option of changing the display color of a particular fluorescent channel; hence, it is trivial to simply recolor the red or green channel to another color (i.e. blue). Take the following figure from a Nature Methods article (DOI: 10.1038/nmeth735) by Alice Ting. Here, the authors have false-colored the fluorescent dyes (Alexa-568 is in reality red and has been colored orange; CFP is cyan-fluorescent protein and is usually cyan anyway but has been adjusted). As shown from comparing the original figure (left) and the colorblind-simulated image (right), very little detail is lost and the figure is clear.

What do the publishers say about color accessibility? Not much. Consider ACS's policy from its Author Guidelines for JACS:

Color. The use of color to enhance the clarity of complex structures, figures, spectra, schemes, etc. is encouraged. Color reproduction of graphics will be provided at no cost to the author. Color graphics should be submitted in CYMK, not RGB, color mode. Graphics intended to appear in black and white or grayscale should not be submitted in color.

Okay. No mention of accessibility. And JACS is fairly broad, and most of its TOC images even contain color. Let's also briefly consider the color policies of a few other journals: ACS Chemical Biology, Cell, Nature Chemistry, Science, PNAS, and PLoS One. There's not much point in reproducing the individual journal guidelines here, but ACS Chem. Bio., Cell, Nature Chemistry, PNAS, and PLos One all say essentially the same thing as JACS, with no mention of handicap accessibility.

The figure preparation guidelines for Science condense colorblindness to one concise sentence:

Avoid using combinations of red and green together.

Some journals are aware; the author guidelines for Nature Chemical Biology, for instance, make some recommendations (interestingly, Nature's formatting guide doesn't mention them, nor does Nature Chemistry):

Authors are encouraged to consider the needs of colorblind readers (a substantial minority of the male population) when choosing colors for figures. Many colorblind readers cannot interpret visuals that rely on discrimination of green and red, for example. Thus, we ask authors to recolor green-and-red heatmaps, graphs and schematics for which colors are chosen arbitrarily. Recoloring primary data, such as fluorescence or rainbow pseudo-colored images, to color-safe combinations such as green and magenta, turquoise and red, yellow and blue or other accessible color palettes is strongly encouraged.

Granted, for some applications, color is unavoidable; take fluorescent microscopy for example. But the ease of making color figures/graphs/charts/schemes has outpaced some journals' awareness of accessibility standards.

In practice, I think the Nature publishing group does a pretty good job with this. And it's possible these things are perhaps checked in the review process even if not mentioned in the author submission guidelines. But I don't think it would hurt to provide this information upfront.