Blogroll: Fast cars and guitars

[As mentioned in this post, we’re going to post the monthly blogroll column here on the Sceptical Chymist. This is January’s article.]

Looking back at the C&EN archives and pondering science’s more subtle influences.

To launch the online archive of Chemical & Engineering News, reaching back to the first issue in 1923, Editor-in-Chief Rudy Baum blogged about his recent attempt to track down ‘Silence, Miss Carson’, a 1962 review of Rachel Carson’s highly influential book Silent Spring. In those pre-archive days, he had to use a fair amount of “laborious (though pleasurable) effort to find [it]”, but now it’s a few clicks away. Others in the chemical blogosphere used some clicks to find their mentors in the newly digitized pages. Paul Bracher on ChemBark found a 1969 cover story about his post-doc advisor Harry Gray, who is pictured strumming his guitar. Inside, Gray is described as talking “in a breezy vernacular more often associated with locker rooms than with chemistry labs” and owning two fast cars. Unfortunately for Sam at Everyday Scientist, the coverage of his advisor, W. E. Moerner, is less in depth/lifestyle-focused but he does unearth some choice pictures of other Stanford chemists.

Who are “the Velvet Undergounds of science”? This question was posed by Chad Orzel of Uncertain Principles, and echoed by The Curious Wavefunction. For those less au fait with the influential but commercially unsuccessful New York band, Orzel defines this as “somebody whose work was only read by a tiny number of people, but ended up being incredibly influential on those people and subsequent generations”. Orzel nominates Sadi Carnot, whose book about heat in the 1820s laid “the foundations for essentially all of thermodynamics”, but which “basically nobody read until after his death”. Wavefunction suggests, among others, Josiah Willard Gibbs “for thermodynamics: He published his founding contributions in an obscure Connecticut journal.” Both are excellent nominations (there are more in the comments on both posts), but it does beg the question ’What is it with thermodynamics?

Pacifichem 2010: Dispersion corrections and gelation

This morning I went to some physical chemistry sessions on computational quantum chemistry. I won’t attempt to summarize the various interesting points raised by the speakers as well as the members of the audience, but I’d like to highlight one conclusion from Stefan Grimme’s presentation: he showed that dispersion corrections should really be used routinely – rather than occasionally – in density functional theory (DFT) methods. Pavel Hobza, who next took the stage, wholeheartedly agreed, saying in particular that these corrections play an extremely important role when it comes to biomolecules.

After another few talks in that session – including a very engaging presentation from Mark Gordon about his favourite molecule, water – I nearly didn’t make it to the sessions held in a different hotel because the roads were getting flooded… [well, yes, after I mentioned the lovely weather and warm temperatures it’s only fair to let you know that we did have a lot of rain today]. But all went well and I managed to see some anion coordination chemistry, including a photo of beautiful crystals growing in a supramolecular gel, from Jon Steed’s lab (photo that appeared recently in a certain chemistry journal). Steed’s group first form a supramolecular bis(urea) gel for which the gelation can be reversed by adding an anion. They then use the gel as a matrix for the crystallisation of organic compounds, and subsequently remove it (by anion addition) to collect the crystals. Gels are often mentioned as promising host matrices for drugs, and this approach could serve for pharmaceutical polymorph screening.

The last talks of the conference will be held tomorrow morning — and this also marks the end of Chemistry Week, as December 15-20 had been officially proclaimed by the Governor and Lieutenant Governor of the State of Hawai’i.

It has certainly been a great meeting, with engaging presentations and discussions as well as very enjoyable evenings – for example, we were treated to some traditional chanting and dancing not only from Hawaii but also from the other Polynesian countries. And this is how I got to see a real New Zealand Haka (well known to those who like to watch international rugby), a little before a ‘fire dance’ accompanied by fireworks on Waikiki beach…

The only thing is that I missed a few speakers that I really wanted to go and listen to – I may just have to come back in five years time!

Anne

Anne Pichon, Associate Editor (Nature Chemistry )

Pacifichem 2010: Variety is the spice of life

This past couple of days I have been attending more traditional, ‘core’ areas of chemistry at the inorganic, macromolecular and organic sessions. I first went to “the new age of advanced materials” symposium, and although I was fighting a little bit of jet lag and sleep deprivation (not a good combination) it made for a very interesting morning. Among exciting endeavours on helicity, supramolecular chirality, and controlled assembly and organization, Sam Stupp from Northwestern University showed interesting bioapplications with his supramolecular polymers, such as some neurotherapy studies that look promising against Parkinson’s disease.

In the inorganic sessions, I indulged in some metal–organic frameworks (MOFs) chemistry — these relatively young hybrid materials seem to be acquiring some maturity, rapidly moving to a new level of complexity and functionality. For example, Seth Cohen from University of California, San Diego, wishes that they could soon(ish) be used as scaffolds, in which just the right functional groups would be held in just the right place and orientation to mimic a metallo-protein active centre. Talking about bio-inspired applications, I particularly liked this comment from Ivan Huc that “mimicking isn’t copying”: scientist do get inspiration from nature – who controls activity, accessibility, or selectivity with remarkable precision – but rather than trying to reproduce the same functions they will then look to construct systems that do what nature cannot.

This morning I headed over to a ‘redox redux’ session on non-innocent ligands from an inorganic and an organometallic perspectives. Although as Cortlandt Pierpont reminded us they have been alluded to as far back as 1966, and described clearly in 1978, the role of these redox-active ligands had then not been mentioned much. They have recently been attracting attention, and I was happy to see elegant compounds and reactivities, including a combination of redox and acidic activities in Thomas Rauchfuss’ talk, or some unusual oxidation states [such as Pd and Pt(III), Ag(II), or Ni(III)] from Martin Schröder’s lab. Over on the organic side of things, a symposium dedicated to Bob Moss was also packed with intermediates and unusual molecules, and we saw in particular some pretty versatile reactivity from carbenes and nitrenes.

I’d like to borrow the (nearly) last thought for today from Eugenio Coronado at the University of Valencia, who showed some interesting studies in which monolayers – rather than molecules – serve as building blocks to prepare functional materials. He highlighted that this work requires a combination of inorganic, organic, coordination, supramolecular and surface chemistries, which fits nicely in the spirit of such a broad conference.

And finally… for those of you who haven’t finished their Christmas shopping, check out the Periodic Quest! Featuring two board games and about 4 or 5 card games – all centred about the elements, as the name suggests – this might just be the perfect present to keep busy with (chemistry-friendly) family and friends during those long winter nights (those what?)

Anne

Anne Pichon, Associate Editor (Nature Chemistry)

Pacifichem 2010: Warm welcome

I am now – for the first time – in Hawaii, attending the Pacifichem meeting [officially the International Chemical Congress of Pacific Basin Societies] (I resisted the urge to start this post by “Aloha”, a word I’ve heard a lot in the past day or so). The meeting is huge: 275 symposia, more than 1,000 papers, 12,000 delegates! This is a ‘self-assembled’ conference, in which the symposia are organized ‘from the bottom up’ — each symposium is submitted by a group of organizers, from at least 3 countries from the Pacific rim (Canada – host country this year – the US, Japan, New Zealand, Australia, Korea and China). This makes for a very diverse meeting. The only thing is that it is a little hard to pick which sessions to go to, with speakers that overlap. Also, should I go to topics I’m familiar with, such as the inorganic or macromolecular sessions, or plunge into the much less familiar?

According to our chairman, this year Pacifichem encouraged symposia at the interface between chemistry and other topics, such as health, environment and alternate technologies, where chemistry plays a leading role. In this spirit, today I attended parts of the sessions on analytical and environmental chemistry in human health; generation of hydrogen from water; and nanoparticle-based materials – and really enjoyed this variety. In the nanoparticle-based materials session, for example, we heard interesting approaches on how inorganic synthesis could be harnessed to control the properties, and pattern, particles. One talk that stood out for me was that of Terry Bigioni, from the University of Toledo. Usually, with nano-clusters, obtaining a uniform morphology and narrow size distribution is what matters — as Bigioni said, no-one is going to notice if you are missing about a hundred atoms. Today, however, he talked about magic (close-shell) clusters, in which every atom counts. These particularly stable sizes have been identified for gold [see for example this cluster reported in Science by Kornberg and co-workers], but much less is known about silver. Bigioni showed that, under wet chemical syntheses, silver clusters also form discrete clusters of specific sizes. These seem to share some of the stability rules of the gold clusters, but only to some extent, suggesting that there is more to the story than an extension of the gold clusters’ reactivity…

I also very much enjoyed the opening ceremony in the evening, at which Paul Corkum gave a wonderful talk that made physical chemistry very exciting, and even approachable. We can normally look at either the dynamics (femtochemistry) or structure (X-ray diffraction) of a particular system. In his lecture, Corkum talked about how new laser-based ways to image matter might soon make it possible to ‘film’ orbital changes during a chemical reaction, and perhaps make a 3D molecular movie. In the same way as the first film (‘The Horse in Motion’) made the cover of Scientific American in 1878, Corkum predicts the first ‘molecular movie’ will be on the cover again by 2018… Only eight years left! Exciting times.

Overall, a warm welcome from Pacifichem — and I’m not just talking about the temperature. I certainly look forward to the rest of the week, including some inorganic and macromolecular sessions.

Anne

Anne Pichon, Associate Editor (Nature Chemistry )

Chemistry’s year

[This post is based on the editorial in the January 2011 issue — the full text can be accessed here, available for free to all registered users. We welcome feedback on our editorials in the comments section below.]

The United Nations has proclaimed 2011 to be the International Year of Chemistry. Under this banner, chemists should seize the opportunity to highlight the rich history and successes of our subject to a much broader audience — and explain how it can help to solve the global challenges we face today and in the future.

Many subjects have been the basis of ‘International Year’ designations by the United Nations and 2011 is chemistry’s year. This provides chemists the opportunity to not only celebrate specific past glories, but also to champion its role in addressing critical challenges in modern society. These global issues include sustainable energy, climate change, and the provision of clean food and water — as prominently featured in the United Nations’ Resolution and also on the International Year of Chemistry (IYC) website.

One historical aspect being brought to the fore is that 2011 is the one-hundredth anniversary of the award of the Nobel Prize in Chemistry to Marie Curie for the discovery and study of polonium and radium. Her scientific achievements are all the more extraordinary because they are set in the context of a very male-dominated era.

Undoubtedly there are now fewer barriers and less bias faced by women in science compared with Curie’s day, but nevertheless, since the inception of the Nobel Prizes in 1901, only one other woman has been awarded the physics prize and only three other women have received the chemistry prize (one of whom is Marie Curie’s daughter, Irène Joliot-Curie). So although Marie Curie’s contributions to chemistry should be celebrated in their own right, it is also a chance to reflect on how far gender equality has come in science — and how much further it needs to go to ensure a level playing field for women and men.

In addition to marking this significant anniversary, two other stated goals of the IYC are to get young people more interested in chemistry and generate more enthusiasm for its creative aspects. Both of these aims are obviously tied up with the future of our subject — chemistry is far from finished as an intellectual discipline (despite what may be written about it elsewhere). There are undoubtedly many discoveries yet to be made and new generations of enquiring young minds will be required to make them.

Two important areas of chemical research highlighted by the IYC prospectus are molecular medicine and advanced materials. Developments in these areas are crucial to modern life and yet they are not always recognized as being fundamentally chemical at their core. Here is an opportunity for chemists to clearly articulate to a wider audience just how much of contemporary science, medicine and technology is underpinned by chemistry.

Take materials as just one example; we need to get the message across that many of the materials intrinsic to our everyday lives would not exist without advances in chemistry — consider how many synthetic organic polymers or designer inorganic ceramics you rely on in a typical day, and imagine what life would be like without them.

The IYC provides a focal point for the past successes of our subject to be celebrated and its future potential to be emphasized — but we should be wary of simply preaching to the choir. As chemists, we have a pretty good grasp of how important our subject is and where it sits in the grand scheme of science itself. The biggest impact of the IYC should not be on chemists, but those who are not (or not yet) chemists.

The IYC provides a framework through which chemistry should be clearly and enthusiastically communicated with the wider public, highlighting how crucial it is in everyday life and why it is vital for our future.

Blogroll: We don’t like blogs…

[As mentioned in this post, we’re going to post the monthly blogroll column here on the Sceptical Chymist. This is December’s article.]

…we love them — but not everyone shares our opinion.

In a post on Everyday Scientist titled ‘caveat grumptor’, Sam alerted the blogosphere to an editorial in Analytical Chemistry and lit a fire that burned long and wide. Royce Murray, the journal’s editor, “casts science blogging in a very unfair light” according to Paul Bracher on ChemBark when Murray “believe[s] that the current phenomenon of ‘bloggers’ should be of serious concern to scientists”. Derek Lowe agrees on In the Pipeline that there “is indeed a lot of inaccurate nonsense on the internet”, but points out that it exists in newspapers, magazines and “in the peer-reviewed literature, too”. Lowe also takes issue with the notion that bloggers are unqualified: “the most widely read ones are all written by chemists”, and suggests that the editorial itself might have benefited from some of the fact-checking or peer-reviewing that Murray is worried is missing from blogs.

David Kroll, at the ACS’s own CENtral Science Terra Sigillata, also responds — he is concerned “that not enough scientists are bloggers” and “that a scientist of [Murray’s] stature and influence holds negative views of science blogs”. Kroll stands up for blogs, as they allow scientists to “communicate effectively to the public”. The final word goes to the commenter on Kroll’s post, identified only as ‘J’, who pointed out that Murray is “a sort of blogger and he doesn’t know it […] The difference is that his ‘blog’ is monthly, has appeared mostly in print until the past few years and there is no place for others to comment.”

Ever shaken your head at some of the more ingenious examples of table-of-contents graphics? Now you can see some choice examples and suggest your own at TOC ROFL — we must admit that a couple of Nature Chemistry’s own graphics have made the list.

Blogroll – the column

Instead of blogging about our plans to update the list of links this page carries (updated today you’ll be pleased to know), I’m talking about Blogroll, the column that goes in the monthly issue of Nature Chemistry.

This short, 300-word, column is basically intended to provide a snapshot of the interesting, funny, wacky, serious, contentious writing and issues that we read every month on chemistry blogs. This column has been on our wish-list right from our first meeting to discuss what sections we wanted in the journal. As our most recent Blogroll says ‘We don’t like blogs…we love them’! One of the things we’re aiming for is widening the audience of the blogosphere to those (perhaps more senior) chemists who don’t read blogs.

Which is why we couldn’t fail to cover the reaction to Royce Murray’s editorial in Analytical Chemistry for our latest issue. We were pleased to get some positive comments about it on Twitter, but also noted @biochembelle muttering about the irony of a column about blogs being behind a paywall.

Now, whether Blogroll should be in the journal or on the blog has been discussed in the team a few times this year, particularly as the Research Highlights pages might be changed a little next year. The main points in favour of keeping it in the journal are that this (hopefully) gets it under the noses of the non-blog-reading chemistry public, whereas to our blog readers, it’d be old news. But fear not, blogateers, for blogroll will remain in the journal! But fear not, non-subscribers, for we’re going to post it on the blog too! December’s column will be posted soon.

Looking back at the past two years’ worth of Blogroll, we’ve covered some 43 different blogs/magazines, with a few (16) getting repeat visits. For those who like meaningless lists, in the lead is the Chemistry Blog with 9 mentions, closely followed by C&EN (magazine, rather than blog) on 7, In the Pipeline with 5, then Everyday Scientist and Wavefunction level-pegging on 4.

Pulling together and writing Blogroll is one of my favourite tasks of the month, so thanks to all the bloggers we’ve covered so far – keep up the good work!

Neil

Neil Withers (Associate Editor, Nature Chemistry)

Revision notes

[This post is based on the editorial in the December issue — the full text can be accessed here, available for free to all registered users. We welcome feedback on our editorials in the comments section below.]

Revising a manuscript in response to the comments of referees should not be about doing the bare minimum to get a paper published. Addressing criticisms that are genuine and constructive can lead to much more compelling research articles.

An e-mail arrives in your inbox from the journal to which you sent your last research paper and it has a subject title that begins ‘Decision on manuscript xxx’. Your heart leaps as you quickly find the phrase ‘we are pleased to inform you’ in the first paragraph, but then it sinks as you scroll down through the referee reports…and keep scrolling…and keep scrolling…and keep scrolling. You finally reach the end of the e-mail and it seems as though, to answer all of the referees’ queries, you’ll need another three years, two more post-docs and a fresh pot of grant money.

This situation is not uncommon and the process of revising a manuscript has the potential to be a frustrating one — but if authors and referees are prepared to engage in a constructive dialogue (mediated by the editor), then it can be a rewarding experience that results in a much improved paper.

Peer review can — and should — play a significant role in improving not only the presentation, but also the rigour and quality of research reported in articles. A fresh pair of eyes looking over a research paper is likely to spot holes in logic or data that, if filled on revision, could significantly strengthen the conclusions drawn from a study. Aside from flaws, referees can also ask questions or make suggestions that help guide the future direction of a research project.

Armed with a list of suggestions from referees, an author must revise their manuscript and then convince the referees and editor that it is now ready for publication. To help those involved judge the changes made during revision, Nature Chemistry ask that authors go through them point-by-point in a letter written specifically for the referees. Trying to discuss all of the changes in a long-winded essay style can make it more difficult for the editor and referees to follow.

The editors understand that some referees may have unrealistic expectations as to what extra work is required before publication and also that sometimes there are genuinely no right or wrong answers — merely progressive scientific debate. The editors also appreciate that busy authors would prefer to make as few changes as possible, and even though carrying out all of the referees’ suggestions may not be required for publication, all authors are expected to take each technical and scientific concern seriously.

Those authors who choose not to carry out extra experimental work or data analysis as suggested by a referee must provide a compelling argument for why that is the case, convincing the reviewers that their conclusions are fully supported without the additional work. In cases where authors and referees disagree on the revisions required, it is the editor who is responsible for making the final decision.

As a closing comment it is worthwhile remarking that the ‘honesty’ involved in peer-review can sometimes be abrasive and hard to ignore as an author, but we very much advise both authors and referees not to personalise the process. Remaining polite and professional throughout, even if others involved are not, is unquestionably the best option and enables the review process to remain focused on the science.