Element of (last) month: A pinch of sodium

In the midst of the blog relaunch, a trip to China last December (which I plan on telling you about in a future post), and the end-of-year holiday period followed by a start-of-year busy period, I didn’t get the chance to write about our December in your element article. This is the first competition winning essay that we’ve published — I think I did mention last year’s essay competition a couple of times.

Margit Muller – PhD student in pharmacology at the University of Copenhagen – highlights how sodium is far from being as mundane as it may seem. Wise daughters from old fairy tales who tell their royal father they love him as much as sodium chloride (they might have said “salt” in the original version) know this, but let’s take a look at the chemistry arguments.

Since its discovery in 1807 by Sir Humphry Davy – who was on a rather impressive element-discovering spree – sodium has amazed chemists. Reports dating back to the 1850s already describe its spectacular reactivity, including its reaction with water that contributes to entice generations of (mischievous) school kids to chemistry according to some Reactions pieces. Among other applications, it is also what makes for pretty yellow flames in fireworks.

Read the article (subscription required) to find out just how crucial sodium is in biological processes, and how essential it is to maintain a good balance of sodium outside and within the cells. Membrane proteins are in charge of controlling specific sodium channels, which let Na+ ions in and out of cell as required and regulate all sorts of processes related to pretty much everything we do, from muscle contraction to neurotransmission. You have been warned, disturbing this sodium influx can have pretty serious consequences! For example, this is just what makes tetrodotoxin from pufferfish (or fugu) — one of the most toxic substances on earth — poisonous…

Anne

 

Anne Pichon (Associate Editor, Nature Chemistry)

Blogroll: Better by design

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]

Reactions: Arthur Suits

Arthur Suits is in the Department of Chemistry at Wayne State University, and works on chemical reaction dynamics and astrochemistry.

1. What made you want to be a chemist?

When I was 10 I got the ingredients for gunpowder for Christmas after much pleading. I’ve always been fascinated by the magic of chemistry, whether it is exploding rockets or quantum mysteries. I would probably be locked away in Guantanamo nowadays for the things we did back then.

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

Novelist/filmmaker. Our world seems rather finite to me some times, and the freedom to create new worlds and new characters is very appealing.

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

In collaboration with Bob Field’s group at MIT we are developing a new instrument, inspired by the chirped-pulse microwave technique invented by Brooks Pate, that we hope will merge the fields of spectroscopy and dynamics and yield a very powerful new tool with which to study a broad range of chemical phenomena. We are grateful to NSF for generous support for this effort.

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

Jesus perhaps, I would like to be included in that famous painting.

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

I was in the lab briefly yesterday with my students, although I was not running it myself. We are studying the photodissociation of ozone in the presence of a strong nonresonant laser field.

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

The Complete Works of Shakespeare and “Live Evil” by Miles Davis.

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

Margaret Murnane at JILA. Although technically a laser physicist, her work is broad in scope and is having a profound impact on the understanding of electron dynamics in molecules at the shortest timescales.

In praise of posters

Can you imagine scientific meetings without poster sessions?

The busiest — and loudest — areas of any conference are most likely to be the poster sessions. This is surely testament to the power of the humble poster: they are the places to see the newest science and talk to the people who actually do the work in the lab. The Nature Chemistry editors are frequently to be found inspecting and discussing posters (with or without a beer in hand…) that catch their eye at the conferences they attend throughout the year.

But once upon a time there must have been meetings without posters. So when was the first poster and who came up with the idea? Sadly, it looks as though history has not recorded the exact moment for us to celebrate. As far as we can tell, however, the idea originated in Europe before spreading to North America in 1974 at the Biochemistry/Biophysics Meeting in Minneapolis. The American Chemical Society then introduced poster sessions for the fall national meeting, in Chicago in 1975, a move that was seen as a ‘trail blazer’.

Since those early days of poster pioneers, the rise of personal computing alongside desktop publishing and graphical design software has further driven the evolution and development of posters. Of course, having the right tools to hand does not guarantee that the perfect poster will be produced every time.

So what makes a good poster? Fortunately for the more graphically challenged presenter, there are books, websites, blogs and even a Flickr photo group devoted to academic posters. From the combined experience of the Nature Chemistry team (which includes one first and two third prizes from our student days), we can also offer some advice. Clarity and content are key. Can all the text be read from a reasonable distance? Imagine that your poster is the highlight of the session: your ideal collaborator (or an interested editor) could be struggling to make out your conclusions at the back of the adoring crowd!

As with any presentation meant for an external audience, considering who makes up that audience and suitably tailoring your poster is critical. The amount of background material needed for a small subject-specific meeting will be very different from that needed for an ACS meeting with many thousands of attendees. When presenting your poster to other delegates, finding out what level of background knowledge they have will mean you pitch it at the right level and gives you the chance to create a dialogue.

As mentioned in the first paragraph, one of the key attractions of most poster sessions is the opportunity to talk to the people — typically graduate students or postdocs — who have actually performed the experiments. Getting the inside track on how the project really developed in the lab, rather than how it is presented in the finished research article, can often be fascinating. As networking events, poster sessions are unequalled at most scientific meetings: relaxed and full of opportunities to bump into people who might make the ideal advisor for that post-doctoral position you were looking for — and vice versa.

Posters are often a scientist’s first presentation or even publication, and can represent the first step on their journey to public scrutiny, feedback and peer review. This alone should be enough to raise them in people’s estimation, and not be treated as an afterthought by conference organisers or attendees.

[This post is an abridged version of the editorial in the February 2012 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.]

Neil

Neil Withers (Associate Editor, Nature Chemistry)

PS This editorial was inspired by a conversation I had with Steve Koch at ICBIC last year

Reactions: Su-Yuan Xie

Su-Yuan Xie is in State Key Laboratory of Physical Chemistry of Solid Surfaces & Department of Chemistry at Xiamen University, China, and he works on carbon-based materials – especially fullerenes.

1. What made you want to be a chemist?

The term of “elements” is translated as “Yuan Su” in Chinese. Almost certainly because my first name (Su-Yuan) is simply the reverse form of “Yuan Su”, my classmates gave me the nickname of “chemical elements” since I was a little boy. To some extent, this chemistry-related nickname pushed me to study chemistry.

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

I might have become a doctor, because I admire the people who cure disease and take care of patients. It is really excited to bring health and happiness to someone.

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

I am working on synthesis of carbon-related materials, especially the fullerenes, a class of carbon cages with promising properties (such as electron acceptor) for photovoltaic application. Among various dreams, I hope that my work would bring more and more new structures of fullerene into the reality, and help people to find new electron acceptor materials used in future solar cells.

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

I admire Sir Isaac Newton very much. He is the greatest physicist for his seminal discovery about Law of Gravity. I am wondering how he could discover the Law of Gravity from such an inappreciable fact with an apple dropping onto the ground.

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

My last experience to perform experiment was in 2005 when I spent sabbatical year in Clemson University. The experiment was about the functionalization of boron nitride nanotubes.

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

I would take the Fortress Besieged by Chung-Shu Chien, and a piano music album by Richard Clayderman.

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

Lawrence T Scott at Boston College, for his systematic research on chemical synthesis of bowl-shaped hydrocarbons that are so beautiful and in principle useful.

Materials Girl: Secret professor tunnels

[Posted on behalf of Materials Girl]

Many moons ago, Stu mentioned the following to me via email: “…the last paragraph of this post is (a) quite funny – ‘secret professor tunnels’ and (b) I thought it might inspire a blog post about seeing professors out of context from the viewpoint of an undergrad.” Disregarding the fact that I am no longer an undergrad, I’ve had several notable run-ins with professors outside of the classroom.

My most surprising out-of-classroom experience took place at a small Japanese grocery store, which I visited infrequently since it required a cumbersome bus ride from campus. On this day, I was happily minding my own business of sniffing unfamiliar pastries and reading strange labels (UFO brand ramen? collagen sheets?). While I was thus employed in a cramped aisle, a bothersome individual decided to block my way out. Imagine my surprise upon looking up to see my very European organic lab instructor from year one! Never before had I seen him outside the chemistry building, answering a mountain of emails in his office or running between labs to identify mystery compounds in students’ beakers and curtail impending explosions (courtesy of those who failed to properly vent their glassware). He chuckled and in his thick accent asked what I was “up to” – a question that I directed right back to him, being apparently out of his element in the market… Turns out, our overworked, exacting, talkative, lovably cantankerous*, and irreplaceable prof got hitched to a nice Asian lady from so and so. Who’da thunk.
*Other students may vehemently disagree with me on this point, considering the heavy workload and strict grading in his mandatory classes.

The most amusing meeting occurred last year outside a certain campus eatery around lunchtime, as I passed by one of my senior year inorganic profs. He caught my eye, paused for a microsecond of recollection, then exclaimed, “Shouldn’t you have graduated by now?!” Having been just one in a sea of faces for a single term, I was rather surprised that he remembered me. However I quickly procured a grin (with less impishness than his) and explained that I’d defected to the MSE department for grad school. My memory fails here, but I expect that he gave me slight admonition for the departure from chemistry.

Perhaps this incident is less amusing than the aforementioned professor himself. This is someone who brought pizza to our final and promised extra points to all who turned in papers that were free from grease stains. (Of course, this resulted in 30 or 40 chem majors munching on cold pies after finishing the exam.) The first problem on the final made reference to duck excrement, in context of projectile length and standard deviation… While I am not an advocate of the theme, having recently forbidden one of my students to use “poop” in the title of his term paper, I appreciated the reflection on his great sense of humor – a quality I’ve found in very few educators. On top of that, he was a fantastic -if not snarky- teacher and a source of anything from sound academic advice to genuine encouragement. My hat goes off this venerable professor. I hope he knows how much we still love him and recollect stories from his class.

This last story technically didn’t occur outside of the classroom, but I can’t resist a quick deviation to quote an o-chem prof’s explanation of backside attack: “If you kick my butt, my arms fly up!” And with that quote for the ages, dear readers, I leave you to contemplate your own stories of professorial glee – I’d love to hear them!

Element of the month: Oxygen origins

Oxygen is everywhere. Really, few elements are more abundant in the universe — in fact just two, hydrogen and helium. It combines with most other elements from the periodic table to form an incredibly wide range of compounds which serve an incredibly wide range of purposes. Just looking at the Earth: oxygen-bearing compounds are found in the mantle, crust, oceans and seas, atmosphere and living organisms, not to mention natural and man-made materials such as silica, zeolites, textiles, ceramics and drugs. Oh, and oxygen also takes part in energy production, as well as a variety of processes that range from metabolic to geological.

Oxygen is most frequently encountered in the form of isotope 16O, much more stable than 18O and 17O — this is because 16O boasts 8 protons and 8 neutrons, a ‘magic number’ in the atomic world that confers special stability. In this month’s ‘in your element’ article (subscription required), Mark Thiemens from the University of California, San Diego, explains how determining the ratio of oxygen isotopes has greatly contributed to our understanding of the evolution of natural processes and life on Earth. For example, the ratio of 18O to 16O is different in the atmosphere and in oceans (this is called the Dole effect). This difference arises from the photosynthesis and respiration of land-based or marine organisms, which means it can be used to deduce the evolution of terrestrial and marine activities.

Yet, the role of oxygen in the formation of the solar system remains unclear. Some meteorites that are known to be among the oldest objects in the solar systems have an unexpected oxygen isotopic distribution. Despite progress in the field, described by Thiemens in his article (they involve measurements on solar wind samples!), this distribution still remains unaccounted for, and exactly how the current celestial objects were formed remains unsolved for now.

Anne

 

Anne Pichon (Associate Editor, Nature Chemistry)

Blogroll – A hot topic

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

Looking closely at pepper spray and an explosive mouthful.

People may think that blogs — even those about chemistry — only cover what the blogger had for breakfast and the occasional picture of cute kittens. Hopefully this column has dispelled some of those thoughts in the past few years, but if anyone still needs persuading, Deborah Blum’s post About Pepper Spray should do the trick. Written shortly after a “shocking incident involving peacefully protesting students at the University of California-Davis”, Blum took her readers through the chemistry behind the innocuously named weapon. For those familiar with the Scoville scale, pepper spray is about 1,000 times hotter than jalapeños and up to 25 times hotter than habaneros. But if you think that the effect is similar to the stinging eyes you may have experiences after not being careful in the kitchen, Blum warns “we’re not talking about cookery but a potent blast of chemistry”. Capsaicins, the compounds that confer heat on both chillies and pepper spray, “inflame the airways, causing swelling and restriction” making it particularly dangerous “to people with asthma and other respiratory conditions”. So dangerous, in fact, that it has been linked to around 75 deaths.

Blum’s post about such a newsworthy topic gathered so much attention it’s been re-posted in many venues, including Scientific American where it was the most popular item on the site for days. She even appeared on the Rachel Maddow show on MSNBC to discuss pepper spray (the segment can be found via this link).

On a less controversial, although slightly more explosive, topic, Derek Lowe treated us to another thing he won’t work with, hexanitrohexaazaisowurtzitane. Hiding behind that mouthful are six nitrogen atoms, each bonded to one of six nitro groups. If you dare to even imagine making it, Lowe suggests that you “picture a bunch of guys wheeling around drums of fuming nitric acid while singing the Anvil Chorus from Il Trovatore”.

Reactions – Paul Dauenhauer

Paul J. Dauenhauer is in the Department of Chemical Engineering at the University of Massachusetts Amherst, and he works on high temperature chemistries of biopolymer/biomass conversion to fuel and chemical feedstocks.

1. What made you want to be a chemist?

Like many people on this blog, chemistry classes in high school were an enlightening and engaging experience. The synthesis and study of chemicals has a creative aspect that is much like playing with childhood toys such as Legos. At the same time the study of chemical processes is quantitative, and solving the mysteries of how chemical bonds break and form is similar to putting together the clues of a Sherlock Holmes story. So I guess my interest in chemistry comes partly from my childhood interests of creative toys and great novels.

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

If I was capable, I would become a professional musician. My personal hobbies are playing the trombone and banjo, and it is interesting to think about a career spent performing or producing new and original music.

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

We are currently working on understanding the high temperature (>400 °C) thermolysis chemistry of biopolymers such as cellulose and lignin. These are the largest volume polymers on the planet, and they can be thermally deconstructed through gasification or pyrolysis to fuel precursor mixtures that will lead to renewable biofuels. Our specific work focuses on understanding the different glycosidic cleavage pathways of cellulose as it thermally decomposes to an array of anhydrosugars, furans, and volatile oxygenates such as glycolaldehyde. We have recently discovered some of the key reaction mechanisms of furan formation which we hope will lead to a complete kinetic description of cellulose pyrolysis.

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

I would very much enjoy having dinner with President Jimmy Carter. In retrospect, his energy policies focusing on renewable energy and efficiency seem visionary! When reading his energy proposals or watching his speeches from the White House (on YouTube), he was advocating many of the policies and technologies that are currently adopted by major corporations. At the time of his presidency, he had the courage to push America toward the future. I would be interested to hear his opinions on how we could continue to improve our energy economy in a way that is sustainable for America and the World.

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

This past summer, I worked with a graduate student to characterize the carbohydrate dimers in aerosols produced from pyrolysis of cellulose. It turns out that cellulose liquefies at high temperature and spontaneously ejects little droplets of liquid by a mechanism called ‘reactive boiling ejection’. We sampled the particles and determined their composition to demonstrate that they come directly from molten cellulose as opposed to an alternative nucleation/condensation mechanism.

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

I would select, “Dave Brubeck Trio & Gerry Mulligan, Live at the Berlin Philharmonie.” This live concert is probably the best performance of Dave Brubeck, and the solos by both Mulligan have amazing energy. The crowd is also really involved in the show which produces an engaging musical experience. I would also select Patrick O’Brian’s Master and Commander book series. While this is technically a 21- part nautical adventure series, it is one continuous story that is sufficiently complex that it could be read multiple times, which would be useful if I only had one book. Additionally, the series has so much information about ships, hulls, sails, etc. that I could probably use it to escape the island!

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

I would like to hear from Professor James Dumesic at the University of Wisconsin Madison. His scientific presentations have a unique sense of humor, and I’m sure his blog answers would be equally entertaining.

Reactions – Shutao Wang

Shutao Wang is in the Institute of Chemistry, Chinese Academy of Sciences, and his research is focused on bio-inspired interfacial chemistry — in particular materials and developing artificial biointerface with controllable adhesion.

1. What made you want to be a chemist?

I have to mention my chemistry teacher in high school. In his special humorous style, he managed to catch everyone’s attention with one piece of chalk and show us a colorful world of chemistry. I enjoyed the fact that that molecules can talk to each other, and at times come up with new phenomena to shake the rules of modern physics. Now, I love chemistry because, as in the words of IUPAC on the occasion of the International Year of Chemistry, “Chemistry — our life, our future.”

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

If so, I would like to try to be a cook and perhaps I could be a good cook because I am curious about tastes. There is a lot of similarity between cooking and chemistry; they are the art of mixing but more than mixing. I believe that I can make some creative and appetizing food you may never have tried (my 3-year-old kid always likes whatever I cook!).

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

We are working on the design and synthesis of bio-inspired interfaces with controllable adhesive properties. To achieve this major property, there are several steps — from discovering specific adhesive phenomena in natural or biological systems, to revealing what chemical and physical mechanism are behind them, to designing and synthesizing functional molecules, and to integrating these molecules within multiscaled structures to form an artificial interface/surface with controllable adhesion.

Adhesion is one of basic properties at solid surfaces, but remains a significant challenge in surface chemistry and related applications such as marine antifouling coatings, anti-adhesive artificial blood vessels, and selective cell adhesion. For example, how can we capture a few circulating tumor cells from billions of blood cell? This is a great technical challenge for the common approaches like immuno-beads separating method based on antibody-antigen molecular interactions.

Facing this challenge, learning molecular and structural recognition from nature, we are trying to develop artificial multi-scaled biointerfaces with specific recognition and adhesion for disease diagnosis (e.g. rare cell capture for early cancer detection and fetal diagnosis). We hope to discover some new principles on adhesion from biology, and use chemical approaches to solve one or two of important adhesion-related challenges in our daily life and industrial applications.

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

I would like to have dinner with Albert Einstein if I can travel through time because I like what he said and did – “Imagination is more important than knowledge… while imagination embraces the entire world, and all there ever will be to know and understand”!

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

It was last Friday, my graduate student and I carried out measurement of the adhesive force between pollen and stigma of wild chrysanthemum. It will help us to understand the specific recognition and adhesive property between pollen to its corresponding chapiter and design novel adhesive interface.

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

If exiled on a desert island, I would like to take Wikipedia, the free encyclopedia that anyone can edit, and the music of “I’m on My Way” from the Shreck soundtrack.

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

Akira Fujishima is a Japanese chemist, professor emeritus at the University of Tokyo. He is well-known for significant contributions to the discovery and research of photocatalytic and superhydrophilic properties of titanium dioxide (TiO2). He simplified the photo-electron conversion in the photosynthesis system of plant to a photo-induced electron-hole separation in TiO2. This is the way to learn from nature and go beyond nature, my favorite field!