Monthly Archives: January 2011

Blogroll: Taking the P

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[As mentioned in this post, we’re posting the monthly blogroll column here on the Sceptical Chymist. This is a longer version of February’s article.]

The publication of a paper revealing an arsenic-loving bacterium sent the blogosphere into overdrive.

It started quietly enough. NASA announced a forthcoming press conference “to discuss an astrobiology finding that will impact the search for evidence of extraterrestrial life” that was due to published in Science. Some people put two and two together and made about 57: Jason Kottke, for example, suggested that NASA had “discovered arsenic on Titan and maybe even detected chemical evidence of bacteria utilizing it for photosynthesis”. When the paper came out you could almost feel the hype deflating, but plenty of people still found the “Bacterium That Can Grow by Using Arsenic Instead of Phosphorus” interesting. The column inches in the press and blogs mounted up, but meanwhile people had got hold of the paper, read it carefully and critically. Really quite critically. To take just one fairly prominent example, blogging (micro)biologist Rosie Redfield, whose bottom line on RRResearch was basically “Lots of flim-flam, but very little reliable information”.

With people starting to notice the blogosphere’s reaction, science writer Carl Zimmer contacted 13 experts, all of whom gave the paper a bit of a thumbs-down in an article for Slate. With the juggernaut of scepticism gathering pace, the first author on the paper, Felisa Wolf-Simon, issued a statement that they “welcome lively debate” but that they “invite others to read the paper and submit any responses to Science for review so that we can officially respond”. Indeed, the backlash against the backlash was supported by Dr Isis, who forthrightly told those critical of the work to ‘Put your experiment where your mouth is! […] The language of those discussions needs to be data’.

For a take on the more chemical aspects of all this, Blogroll’s usual suspects, including In the Pipeline, ChemBark and the Curious Wavefunction, all weighed in and added their thoughts.

The whole episode caused many to question the roles of peer-review, press conferences, public engagement and blogging – so many we couldn’t even just list them. For a good round-up, check out Ed Yong’s ‘post-mortem’ post on Not Exactly Rocket Science.

And finally…if you’re worried about the future of peer-review after this, why not read some of Environmental Biology’s funniest reviewers’ quotes. There are gems like this one: “The biggest problem with this manuscript, which has nearly sucked the will to live out of me, is the terrible writing style.”

[This longer version includes a few bits (paragraphs 3 & 4) that we had to cut to fit the physical column. There is obviously a lot more out there on the arsenic bacteria story, but hopefully this will serve as a useful starting point for anyone who has missed all the fun!]

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Back to the future (of chemistry)

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As I’m sure many of the readers of this blog will know, 2011 is the International Year of Chemistry. This has chemists looking to both the past and the future of our subject.

When we launched Nature Chemistry back in 2009, our first issue included a feature called ‘The future of chemistry’ where we asked eight leaders in the field to share their vision for how their own fields might (and/or should) develop in the coming years.

If you missed it at the time, we invite you to go and have a look at what they had to say. This (and everything else published in the April 2009 issue) is completely free to access, no registration required.

Ryoji Noyori in Synthesizing our future — Ideally, we should aim at synthesizing target compounds with a 100% yield and 100% selectivity and avoid the production of waste. This process must be economical, safe, resource-efficient, energy-efficient and environmentally benign.

Harry B. Gray in Powering the planet with solar fuel — Some time in the future we will be able to put three components of our atmosphere — carbon dioxide, nitrogen and oxygen — along with sea water into solar reactors to make not only fuels, electricity and pure water, but polymers, food and almost everything else we need.

Mark A. Johnson in Experiment and theory in harmony — With the overall perspective of contributing accurate, experimentally vetted, molecular-level pictures of reactive pathways and relevant structures, physical chemists are in an excellent position to engage chemistry in all of its complexity.

Barbara Imperiali in Interrogating biology with a chemical lexicon — . . . most good things take time and we must remind the community that chemistry, like a fine wine, may take many years to mature.

Gary M. Hieftje in Weighing up the future of scientific tools — Modern science, indeed much of the future, will be driven and enabled by the scientific instruments that are just now emerging.

James H. Clark in Chemistry goes green — The challenge for green chemistry is not just to replace undesirable chemicals . . . but also to make sure that, wherever possible, the substitutes and the chemistry used to manufacture them are green and sustainable.

Achim Müller in Predicting a structured future — . . . chemists should always have their eyes open for interesting but unexpected phenomena that could open new avenues of research.

J. Fraser Stoddart in Thither supramolecular chemistry? — . . . we need to forsake embracing routine projects that we know will yield results and lead to answers that are largely expected, so as to face challenges that are function-oriented and applications-driven . . .

We hope you enjoy travelling back in time just a little to consider what the future may hold!

Stuart

Stuart Cantrill (Chief Editor, Nature Chemistry)

Materials Girl: Great Expectations

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[Posted on behalf of Materials Girl]

From an undergrad point of view, grad students primarily existed as TAs and nameless faces roaming through campus doing “research” and being “busy” (and consuming large amounts of alcohol). Even while applying to graduate school and pondering my future, the life and expectations for a graduate were just horror stories channeled by PHDcomics. I read them all, laughed, shared a few on Facebook, and continued on in vague disbelief.

I’m not sure if new students know or are expected to know what’s ahead in the grand journey of grad school. Some come expecting excitement and research, others foresee only classroom activities and a prestigious degree, and a few are there solely to escape the job market. My own expectations were of toil and mild masochism, as told by an older grad, but I really had no clue what was required – other than the department’s obligatory coursework, writing a thesis, etc. Somewhere along the line, it was implied that there would be scientific research galore.

From the other direction, I wonder what is expected of your average grad student in science/engineering. Personally, I’ve experienced an insurmountable flood of research, classes, teaching, friends, seminars, networking, papers, students, presentations, emails, administrative finagling, ever more research, and all else. Not to sound too negative, but it appears that no amount of work can fulfill the wishes of any PI – hence the term “insurmountable”. I’ve settled on temporarily appeasing mine, as his approval may only come upon producing 26-hour days and publishing numerous Nature papers. However, that is simply my own perspective as deep breath one of only two grad students working full-time for a young Assistant Professor who never runs out of random ideas and is on the verge of applying for tenure in a small engineering department at a large research university. This is a very special position, I have discovered over the last year. I am putting the experience under my belt as “personal development”, in addition to a distinctly varied skill set for a mere Master’s minion.

From what I’ve heard otherwise, any graduate experience consists of sweat, sleep deprivation, and suffering in varying degrees. Most complain, but keep working. A select few love everything about it. The specifics, I cannot tell, although numerous books have been published on the subject. (We just don’t have time to read any; this one has adorned my apartment’s bookshelf since I bought it.)

My own days are full and good, at least if YouKnowWho* is not feeling too cantankerous. Still, despite my loyalties, I wonder if my choice of advisor would change had I known anything significant/specific about grad school and professors beforehand. Whose advice should I have sought, and what words of wisdom did I miss? You might say that I was unprepared; the bulk of my undergraduate years were spent in class, studying, and doing homework. (As we all know now, those are nonexistent activities to grads after a year or two.) Academic skills? Passable. Networking? Mediocre. Sanity? Intact – a sure indication of lacking experience. Research? Decent, but unrelated to half of my graduate projects. If all students planned on graduate school, I would suggest mandatory research from undergrads. “Expect this and much, much more”, or something along those lines.

Before this post turns in a treatise (and falls under the “too long; didn’t read” category), I’d like to ask what our readers think about the issue. Were I still the undergrad version of MG, what would you tell me to prepare in advance? What did YOU expect from grad school, and did it turn out to be realistic? How or could you have changed it? As it is, I still have a PhD and new university ahead – I welcome everyone’s wisdom.

*This particular nickname for our “beloved supervisor” has generated quite a few Harry Potter jokes, despite the lack of original intention.

The greatest chemist of all time?

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Disclaimer: this was a bit of Twitter-related fun and while it does throw up some interesting observations, this is in no way a properly executed comprehensive survey of ‘the greatest chemist of all time’…

It’s not an easy question, and probably not a fair one either. What do we mean by ‘greatest’ and, for that matter, what do we mean by ‘chemist’? We’re probably only on safe ground with ‘all time’!

This all started over lunch a couple of days ago when the London-based members of the NChem team (myself, Gav and Neil) were having lunch at NPG towers with, amongst others, the chief editor of Nature Nanotechnology (@drpeterrodgers). After the usual football banter had come to an end, somehow we got on to the topic of iconic figures in physics and chemistry.

If you ask physicists to name the greatest of all time in their field, many will choose Einstein or Newton — see this Physics World story (free registration required) and this BBC piece. Of course there are many other great physicists, but ask for just one name and it usually boils down to one of those two. In chemistry, however, we came to the conclusion that there aren’t just one or two names that stand out from the crowd — there’s just a crowd.

To put this to the test, we decided to conduct a wholly arbitrary and definitely unscientific poll on Twitter, asking the simple question — who is the greatest chemist of all time? No qualifiers and no guidelines, other than you can only pick one name. No ranking of multiple individuals and no shared glory. No debate (at this stage) of whether someone would have been classified more as a physicist than a chemist in their time. And the results don’t include retweets of suggestions, unless they specifically indicated that they were additional votes for, rather than just RTs of stuff people found interesting. Many thanks to everyone who responded.

And so, here are the results:

We had 86 votes in total, with a whopping 36 different suggestions of who is the greatest chemist.

The top four places go to: Linus Pauling (16 votes), Dmitri Mendeleev (11), Antoine Lavoisier (7) and Marie Curie (6 votes).

Then we have Robert Burns Woodward (4), Michael Faraday (4) and Gilbert Lewis (3).

Everyone else just got one or two votes — and they are (in no particular order): Amedeo Avogadro (2), Fritz Haber (2), Friedrich Wöhler (1), Alfred Werner (1), Henry Moseley (1), Paul Walden (1), Robert Robinson (1), Ludwig Boltzmann (1), Jacobus Henricus van ’t Hoff (1), Jābir ibn Hayyān (2), E. J. Corey (2), August Kekulé (2), Robert Boyle (1), Walther Nernst (1), Svante Arrhenius (1), Shigeru Terabe (1), James Joule (1), Victor Grignard (1), William Perkin (1), Stanislao Cannizzaro (1), Wallace Carothers (1), Emil Fischer (1), Wilhelm Ostwald (1), Niels Bohr (2), Ryōji Noyori (1), Paracelsus (1), Mother Nature (1), Louis Pasteur (1), Humphry Davy (1).

There are some notable names not mentioned, including Gibbs, Dalton and Priestley.

What does this mean? We’ll consider this more thoroughly in an upcoming editorial, but for now it is clear that even in this small sample size, there are many different chemistry heroes. Sure, Pauling and Mendeleev got a few more votes than the others, but they’re not streaking ahead — and there is a long tail here.

Is this a problem for chemistry — not having a unifying iconic figurehead that we can point to? Maybe, maybe not. But in a year when our subject is being celebrated on the global stage and we take stock of its wider appeal in the world, it’s something to consider (not that we can really do much about it though!). The International Year of Chemistry is rightly celebrating Marie Curie and her contributions to chemistry, and she does well in our little poll, but is one of many names.

Perhaps we should be proud that there are so many names mentioned in response to the question of who is the greatest, it must reflect — in some measure — the diversity and depth of our subject.

Returning again to the question itself — it is not an easy one, because how do you compare the likes of Woodward and Mendeleev, or Pauling and Wöhler. The answers to the question we pose are wholly subjective, but it’s more the whole exercise and breadth of responses that are more enlightening.

We really hope you join the discussion in the comments to this blog post — and please do add your votes for who you think is the greatest chemist of all time.

Stuart

Stuart Cantrill (Chief Editor, Nature Chemistry)

International Year of Chemistry – bumper Nature issue

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Well, 2011 brings us the International Year of Chemistry and Nature has kicked things off with an issue bursting at the seams with chemistry news, opinions, features, research letters – even the Futures science fiction on the back page!

The issue starts off with an editorial on ‘Chemistry’s understated majesty‘. The editorial starts off with an Adam Sandler joke, but don’t let that put you off; it goes on to discuss the International Year of Chemistry and how chemistry and chemists should seize every opportunity this year to “to bring to light [its] hidden contributions to science and society at large […] when chemistry is good, it is very, very good. It deserves its celebration.” Amen to that!

The chemistry continues with a rather personal column from David Nichols, whose work on “drugs to improve memory and cognition in patients who have schizophrenia” has been used by people less concerned by ethics to make so-called ‘legal high’ drugs.

There are two news Features: one by Richard Van Noorden on the problems facing the commercialisation of the nanoforms of carbon (fullerenes, carbon nanotubes and graphene). The other is by Katharine Sanderson (former blogger at this parish) on green chemistry.

And now come the opinions. George Whitesides and John Deutch take a long hard look at the state of chemistry, as it is “at the end of a century of expansion”. They don’t pull many punches: “chemistry must be braver in its research choices and in how it organizes them”, for example. Fortunately, Whitesides and Deutch offer some “real-world solutions”: Rewrite the social contract; Do away with the old disciplinary structures; Focus on chemistry’s strengths; Teach students, rather than use them.

Next up, ten leading chemists share their priorities for the future and which scientists have inspired them. Can you guess who Kit Cummins and Martyn Poliakoff take inspiration from? Or Laura Kiessling and Paul Alivisatos?

(Hmm, this is turning into a much longer blogpost than I envisioned, but it really is a great issue!)

The chemical bond is one of the few (only?) things that is common to all branches of chemistry, so surprise that something so fundamental is so often debated should be tempered by the knowledge that, with so many people interested in it, it’s bound to be prodded and poked endlessly. Science writer Philip Ball (who recently wrote about Pauling’s classic The Nature of the Chemical Bond) looks ‘Beyond the bond’: what is a chemical bond? This is also the focus of the latest Nature podcast.

Following on from Phil Ball’s retrospective look at Pauling’s book, there’s another retrospective review in this issue, and it’s of a book whose title might remind you of a certain blog. No prizes for guessing, it’s Boyle‘s The Sceptical Chymist! The 1661 book is put in context by Lawrence Principe, and it may surprise you to learn that Boyle does not usher in modern chemistry and slate alchemy. Slightly more up to date, there’s also a review of Lauren Redniss’ Radioactive: Marie and Pierre Curie, A Tale of Love and Fallout by Giovanni Frazzetto.

The original research takes in the supramolecular (a 12-porphyrin nanoring built by Vernier templating), the organic (sensing the anomeric effect in a solvent-free environment) and the biochemical (taxadiene synthase structure and evolution of modular architecture in terpene biosynthesis)

And finally…the Futures article raises a glass to ‘The last laboratory’.

Phew. Glad you stuck with me this far, rather than just going to the page that collects them all IYC2011 content from across the Nature journals together. I should note that some of the content is behind the Nature paywall, but I’m pretty sure the editorial and news Features are freely available.

It’s a fantastic collection of articles and a great start to IYC2011!

Neil

Neil Withers (Associate Editor, Nature Chemistry)