Author Archives: Neil Withers

Goodbye – and thanks

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As Stu announced about 3 months ago, I’m leaving Nature Chemistry – today!

It’s been a real privilege to be involved right from the start – when we hadn’t published any papers and the submission system was even open. The journal was a blank slate. Of course, that blank slate was pretty soon filled with papers, of which I handled my fair share. And that’s where the real privilege comes in: being the first person other than the researchers themselves to read some wonderful pieces of chemistry. The best part of this job is reading papers that make you go “Wow” – and then sharing them with the world!

One of the other highlights is going out to conferences and meeting people. I’ve been fortunate to go to some fantastic conferences, meet some chemistry heroes and visit incredible institutions. Although not quite as personal, I feel like I’ve ‘met’ lots of bloggers and tweeters through their posts and tweets, and having the ‘chore’ of reading tons of blogs so I can write blogroll every month has been extremely enjoyable.

So I’d like to thank all the authors, referees, people I’ve talked to at conferences, people who’ve entertained me in their departments, and all the bloggers and tweeters who make this job as fun as it is!

And of course, I have to thank the rest of the team, who’ve been a pleasure to work with! And that includes the people who aren’t on that webpage, our wonderful production team.

See you all over at Chemistry World!

Neil

Blogroll: Space dinosaurs!

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Highly respected organic chemist publishes a Perspective in JACS, chaos ensues.

Ronald Breslow — past president of the ACS and Priestley medallist in 1999 — is a “well-respected research lion”, in the words of SeeArOh at Just Like Cooking. Few would dispute his place in the chemistry firmament. With many achievements behind him, surely he has earned the right to close a Perspective article in JACS on the possible origin of homochirality in biological molecules with a chuckle — suggesting that humans would be better off not meeting the advanced dinosaurs, with amino acids of the opposite chirality, who may populate distant corners of the universe!

Apparently not. At least, not according to some of the dinosaur-focused bloggers/newshounds out there — such as Dinosaur Tracking or Discovery. In their defence, however, they were reacting to the press briefing that the ACS somewhat mystifyingly released. It was mystifying because it ignored the six pages of discussion about the origin of chirality of amino acids to focus on the last two ‘space dino’ sentences.

The combination of Breslow and space dinos proved tempting for some chemistry bloggers, with SeeArrOh covering the paper and its final words in the good-humoured tone in which they were surely intended. Paul Bracher, who blogs at ChemBark, has worked in the origin-of-life field, and actually discussed the scientific content of the paper — how refreshing! But Bracher certainly doesn’t mince his words giving his opinion of the ACS press office.

The final twist in the dinosaur’s tale came in the comments on Just Like Cooking and ChemBark: hasn’t Breslow written something quite similar in Tetrahedron Letters and the Israel Journal of Chemistry? The similarity is such that, at the time of writing, JACS has removed the paper from its website, citing copyright concerns.

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

Blogroll: Arnie and artemisinin

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A chemist who wants to terminate malaria and a calculation to have at your fingertips.

“Malaria. I hate this parasite. I want to kill it.” Imagine these words spoken in a voice similar to Arnold Schwarzenegger’s and you’ll understand why they nearly made Karl Collins fall off his chair, as he explained in a post at A Retrosynthetic Life. Of course, it wasn’t Arnie speaking, but Peter Seeberger of the Max Planck Institute, who discussed his efficient and cheap route to making artemisinin. Seeberger’s development means that “artemisinin factories the size of large cardboard boxes can be made for £10,000”. Overall, the cost of producing this potent antimalarial could fall to “10% of what it is today” — this might go some way to explain why Seeberger’s next appointments were with the UN and the Gates Foundation. Collins explains more about Seeberger’s career in his blogpost and you can read the Angewandte Chemie paper that reports the continuous flow synthesis via https://doi.org/c55rks.

“By the time you finish this sentence, your fingernails will have grown one nanometre.” If you read that sentence with some scepticism, you’re not alone. Zen Faulkes, who blogs at Neurodojo, asked “Is that accurate?”. To start with, his students did some guesstimations, ‘Fermi problem’ style, that showed it might be true, but like any good scientist, Faulkes wanted data. So he measured the growth rate of his fingernails using callipers accurate to 0.01 mm. After five or six measurements on ten fingers he arrived at an average fingernail growth rate of 0.92 nm per second! But wait — Faulkes went a step further and discovered it took him about 3.77 seconds to read that sentence, so his fingernails would have grown a whopping 3.47 nm. Interested readers may like to tackle the problem posed in the comments: How many moles of β-keratin are deposited onto the nail per second?

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

Your Monday answer

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On Friday, I asked “What weight could you hang from a chemical bond before it broke? How many atoms [is that]?”

Paul from ChemBark suggested “~350 pN or ~400 nanograms or so” and Ali Moeed guessed “1000+ atoms”.

To be honest, I have no idea what the right answer is! But the fun with these kind of problems is working them out, so here are two methods I used and the answers they gave. Basically, I needed to know/calculate the mechanical force required to break a bond, seamlessly convert that into a force-due-to-gravity, and then work out what mass/how many atoms would give that force (on earth). If there are any mistakes in the following, please let me know in the comments! And if you have a better way to go about it, please do so.

First method (no research): The ball-park figure for the strength of a bond in my head is 100 kJ/mol, or 2 x 10-22 J per bond. Unfortunately, that’s an energy, not a force. But energy is just force x distance, right? So let’s say the bond is broken when you’ve moved one atom 10 Å further away. The force required to do this is (2 x 10-22 J/10 x 10-10 m) = 2 x 10-11 Newtons. A mass of 0.1 kg ‘weighs’ 1 N, so the weight required to break a bond is 2 x 10-12 kg. Which is pretty small in the human-sized world, but pretty massive in the atomic world – but how many atoms? I decided to think about gold atoms, as these make pretty nice nanoparticles. Gold has an atomic weight of ~200 g/mol, or 0.2 kg/mol, so that’s 2 x 10-12 kg / 0.2 kg/mol = 10-11 mol of gold. And finally, 6 x 1023 atoms of gold/mol x 10-11 mol = 6 x 1012 atoms of gold.

Second method: Gav used popular internet-based search engine ‘Google’ to find this paper from Matyjaszewski et al in Nature, the abstract of which says “[C-C bond] strength is evident in the hardness of diamonds [etc]; on the single-molecule level, it manifests itself in the need for forces of several nanonewtons to extend and mechanically rupture one bond.” So repeating the calculations from 10-9 Newtons gives 10-10 kg, or 3 x 1014 atoms of gold.

So my two answers aren’t exactly the same, but I think they’re close enough (what’s a factor of 50 when things are between 10-12 and 1023??) to indicate that it would take a LOT of atoms – one fat ‘nano’particle – to break a bond by their weight alone. I see Paul’s answer is in a similar range, and Ali is technically right with “1000+” but that leaves quite a lot of wiggle room!

What does this teach us? Well, apart from the fact that chemical bonds are strong, perhaps just that physicsgravity is weak, chemistryelectrostatics are strong!

NOTE: As I am just about to press publish, I see John at It’s the Rheothing has tacked the problem too, but (naturally) from a polymer perspective – how long a polymer could a bond support? I won’t spoil the surprise – go and read his post!

Neil

Neil Withers (Associate Editor, Nature Chemistry)

NPG – is it for me?

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[This is a guest post from Heather Powell, a second year undergraduate student at The University of York, who has spent the week seeing what we do in the Nature Chemistry office]

After starting my degree, it didn’t take me long to realise that being trussed up in a white coat and goggles for the rest of my scientific career was not for me. And so I began to wonder what other possibilities lay beyond the end of university, because as crazy as it seems right now, there will come a day when there won’t be lectures to attend, a tutorial to hand in, or a lab script to polish off. I had always had some interest in writing, and so a week with the Nature Chemistry team seemed like the ideal opportunity to discover the ins and outs of scientific publishing.

Having expected an office bustling with briefcase-carrying, tie-adorning, earpiece-wearing commuters, it came as a welcome surprise when I saw the periodic table fighting for space on the wall with the football match schedule and tea rota. Stuart – the editor of Nature Chemistry – introduced me to the London-based team, namely Neil and Gavin, and talked me through the entire process from submitted manuscripts to printed journal. Throughout the week I got to probe the people involved in selecting the manuscripts for publication, sending them out for peer review, professionalising the images and diagrams, formatting the pages to Nature Chemistry’s specific layout, and ultimately sending the journal to the printers.

Interesting and informative though it was to talk to the team in action, the best way to get a feel for something is by doing it. And that’s exactly what I got the chance to do! I discussed some manuscripts and their suitability for Nature Chemistry, as well as researching potential referees for peer review.

Furthermore, I will have the honour of seeing my name in print in an upcoming edition of Nature Chemistry. Research Highlights are 250 word summaries of some of the most exciting papers recently published, whether in Nature itself or elsewhere, and I wrote two of them this week. The idea is to bring across the benefits of the research and why it means so much to the scientific world – but it seems often the biggest challenge in this task is choosing an appropriately witty title!

Although thoroughly enjoyable, it felt a little strange editing a News and Views piece – a 1000-word article written about a recent paper by an expert in the appropriate field. What business did I have in effectively “marking” a piece of work by a qualified scientist? The purpose is to make a paper understandable to a non-specialist scientific audience, and allow the experts to give their opinion on the subject, so the trick, as far as editing goes, is to make the article clear and logical without detracting from the author’s content. And so I suppose being a mere undergraduate was actually an advantage here – not being a specialist, I had a pretty good idea of the level of detail to be understood!

But the story doesn’t stop there. As well as the journals, you’ll also find a press team within this warren of an office – these are the guys who organise press conferences and accumulate the press coverage that Nature receives from the papers and the web. Not to mention the Nature News team who report the latest scientific developments outside the world of manuscripts, and the floor of people who work on Scientific Reports, the open access online journal of research from all areas of science. I was lucky enough to spend some time with each of these groups, experiencing the vast range of elements associated with Nature Publishing Group.

So what did I get out of the week, besides the keepsake branded pens, and possibly a wider understanding of the company than even some of the employees here!? Well, I learnt how bench results can ultimately find their way to my computer screen upon a Google search, and more importantly, that a job in scientific publishing is a highly stimulating alternative to becoming one of the white-coated professors that front our science departments.

Massive thanks to everyone who made this such an enjoyable and certainly worthwhile week!

Your weekend problem…

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A question struck me yesterday afternoon (editorial discretion prevents me revealing exactly why): what weight could you hang from a chemical bond before it broke? How many atoms?

I asked the rest of the team if they had any ideas, but got no answers I would be comfortable publishing! Still intrigued, I thought about it more while it was my turn on the tea rota.

It’s relatively easy to work out, with a little digging, but might surprise you. I’ll let you all stew on the question over the weekend – and suggest your own answers below – and return with my Fermi-style calculation on Monday!

Neil

Neil Withers (Associate Editor, Nature Chemistry)

Blogroll: Scary chemicals

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Sensational chemophobia and the problems with biofuels

‘Are you scared yet?’ This is the title of See Arr Oh’s post on Just Like Cooking but could equally serve as the unspoken subtitle of the news report he’s blogging about. First highlighted on ChemBark the investigative report from US TV channel Fox29 is about “unlocked chemistry labs and the ease with which a terrorist could steal hazardous materials”. So far, so serious. But, as ChemBark says, “the underlying point of securing labs is a valid one, but the presentation is way Way WAAAAAAY over the top”. See Arr Oh takes the presentation to task more than ChemBark, giving us some random quotes that illustrate the chemophobic sensationalism of the report, which breathlessly reveals the presence of 0.1 M HCl and ether. He counted “26 mentions of the word ‘chemical’ (or once every 14.4 seconds)” – mostly “preceded by a sensationalist adjective”. We can’t deny that lab security is an issue for serious discussion, but perhaps it deserves better reporting than it got from Fox29.

When Nobel Laureates talk, people listen — and when they write provocative editorials, people read closely. So when we spotted the editorial in Angewandte Chemie by Hartmut Michel (1988 Laureate) titled ‘The Nonsense of Biofuels‘, we sat up. And so did Ash Jogalekar at The Curious Wavefunction, where he took us through the photosynthesis expert’s arguments. First among these is the lack of efficiency of photosynthesis itself — a 4% upper limit — which is exacerbated by the energy needed to grow, harvest and transform the biomass into useful fuels. Finally, when it comes to fuelling transportation, only 20% of the energy produced by a combustion engine is used to propel the vehicle. Michel suggests that either photosynthesis needs to be improved, or photovoltaics and batteries pursued with more vigour — solar cells are around 15% efficient, and vehicles can usefully use 80% of the battery’s energy.

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

Materials Girl: Beginning of the end

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[Posted on behalf of Materials Girl]

Late last year during the fall term, YouKnowWho dropped a small bomb on my plans: I could write a dissertation using the work for my intended Master’s thesis. What?! In previous bids he had simply asked me to stay for a PhD to work on some project, whereas now there was the claim that I could finish in just another year. (I assume this means two more, bringing the total to a reasonable five years.) It was then the time for waffling. On one hand, staying would save a large amount of time and effort – no need to retake classes, create new networks, and familiarize myself with a different academic system. On the other hand, I had always planned to relocate sometime in the future to do my PhD. Also, although my search for specific jobs was coming up nil, a [very big] company had found my resume in their online bank and decided that I should work for them (after flying me in for some quick interviews) – but their tempting offer was contingent on graduating in the spring. I was conflicted.

Now that I think about it, turning down the job would feel akin to breaking up with a serious boyfriend. Would I ever get another offer or would I be reduced to a penniless, lonely miscreant forced to move into my parents’ basement while honing my skills as a barista? Was anyone else going to pick me from the sizable crowd of contenders? Did I actually possess the skill for a good position or was I deluding myself in assessing my value? The potential outcomes plagued me for months, during which time I turned down [very big company’s] offer in order to ruminate further. This should’ve been a hint that deep down I had already made up my mind, but it wasn’t until the end of winter break that I steeled myself for the long haul. I was going to stay.

So in January, I found myself on the road to oral preliminary exams in the materials science & engineering department – something mere months prior I had never dreamed of (and had gleefully ignored every term as a Master’s student). The pressure for me to pass was enormous, more so than the inherent nature of the exams. Not only did I want to avoid the mortification of retaking them, but also the required time to finish a Master’s was running dangerously low. If I spent the rest of the school year studying for the maximum two attempts at prelims, no time would be left to graduate if I failed both – thus leaving me in some horrible purgatory of no degree after three years laboring in grad school. To say the least, it was a very sobering thought and serious business.

The other major hurdle to prelims was my undergraduate background. (In)organic chemistry has distinctly different curricula from that of any engineering major. Being in materials eased the pain to a degree, although topics such as mechanical properties and diffusion were still foreign to me. Between TAing, classes, and Lab Mom duties, I stayed buried [or at least attempted to] in heavy textbooks.* Never before had I experienced such prolonged, excruciating pain in the form of studying. (Call me a bad student with no attention span, but despite sleeping through most classes I’ve learned to earn good grades after studying only days before tests. Blame the apnea?) I formed a study group with other prelim-takers from a hodgepodge of backgrounds: the physics guy knew his electrical properties beautifully, the two from chemical engineering were comfortable with thermodynamics & diffusion, the one from materials had already learned everything, etc. The group helped a bit despite our sessions being exhausting and relatively short – and sometimes spent pondering how to bribe each professor to pass us, or if it’d help to bring a bottle of vodka (or a revolver) during the actual exams. Our weekly sessions of questions, griping, and even laughter were a little reminder that I wasn’t alone in a traumatic world of stress and cramming. As it is with the rest of my grad student family, we ultimately helped each other through the blood, sweat, and tears.

*Countless thanks goes to the friends who lent me their books and support. Hopefully the cookies I’ve baked have repaid them.

To cut a long story short, after two months of studying I took prelims and PASSED. (!!!) No second attempt, no earth-shattering reprimands from professors who find me an inadequate candidate, and just about no dishonor. I am officially on the road to being Dr. MG, as well as starting to act somewhat human again. So it’s probably a good time to get back to writing those papers for YKW (which will eventually turn into the dreaded dissertation)… Gulp.

Reactions: Xingyu Jiang

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Xingyu Jiang is in the National Center for NanoSci&Tech (China), and works on using microfluidics and nanoparticles for better bio/chemical assays.

1. What made you want to be a chemist?

My mother used to teach chemistry in high school, so my family had more books on chemistry than an average Chinese family; that was the initial cause. My organic chemistry teacher Prof. Phil Eaton at the University of Chicago made organic chemistry so interesting, so I decided to stick to chemistry.

2. If you weren’t a chemist and could do any other job, what would it be – and why?

A historian for sure. I enjoy reading history. I also like maps and geography, so I might also have ended up doing some geography-related work. So maybe I’d be a geo-historian.

3. What are you working on now, and where do you hope it will lead?

We work on miniaturized methods/devices for bioassays. These methods will eventually change the way people do analysis – more point-of-care technology than large-equipment technology.

4. Which historical figure would you most like to have dinner with – and why?

The ancient Chinese king Yan Di, who personally tasted and tested many different types of plants, to find cure for diseases. He must have had a very fine and sophisticated taste. I also would like to talk to him about the experience of tasting so many different plants.

5. When was the last time you did an experiment in the lab – and what was it?

It was probably in 2007 when I showed one of my students how to print molecules onto surfaces of gold-coated glass.

6. If exiled on a desert island, what one book and one music album would you take with you?

Book: Journey to the West (a classic Chinese novel). I can survive without a music album.

7. Which chemist would you like to see interviewed on Reactions – and why?

Allen J. Bard of UT Austin. I want to know when he last did an experiment in lab.

Blogroll: Better by design

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The differences between planes and drugs, engineers and medicinal chemists … and Jimmy Stewart.

Have you ever wondered about the similarities and differences between drug design and aeroplane design? If not, don’t worry because Ashutosh Jogalekar at the Curious Wavefunction has blogged about a paper that does just that. Both of these design processes use modelling, but “compared with the aeronautical industry where modelling has been applied to airplane design for decades, why has it taken so long for modelling to catch on in the pharmaceutical industry?” Jogalekar takes us through the three reasons he sees: the complexity of biological systems compared with aeronautical ones; the natural inclination of engineers to learn programming and modelling is generally not shared by the mix of people who work in pharma; and the lack of a “comprehensive knowledge base for validating modelling techniques”. As a molecular modeller himself, Jogalekar finds the paper upbeat and hopes that “the pharmaceutical industry makes a concerted effort to test, refine, retain and discard modelling approaches to drug design at all levels”.

Derek Lowe blogged his own thoughts on the paper, noting that, in biological systems, “there are so many nonlinear effects, so many crazy little things that can add up to so much more than you’d ever think”. The “Andy Grove fallacy” — which is what Lowe calls the propensity of engineers and other outsiders to underestimate the complexity of drug discovery — is a favourite topic on In The Pipeline, so a lot of comments came from both sides of the fence — from engineers and biologists.

And finally … after pursuing exciting research on artificial photosynthesis, he left college and became a banker. A modern-day tale of the priorities of under-funded young scientists? No! It’s a scene from the Jimmy Stewart movie You Can’t Take it with You, released in 1938, which Nick Uhlig shared the clip on the Chemistry Blog.

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