Editorial: Beyond the printed page

[‘Cross-posted’ from issue 3, this is our editorial that explains some of the innovations in the HTML versions of our articles. We’d really like as much feedback as possible, so comment away! Apologies for any formatting weirdness]

The publication of scientific discoveries remained tied to ink and paper for over 300 years, but the rise of the internet over the past few decades has transformed scholarly communication. Just how far this revolution can go depends not just on publishers, but on authors and readers too.

Although much has changed since 1665, when the first issue of The Philosophical Transactions of the Royal Society was published, the basic unit of scientific communication is not all that different. The role of an editor at Nature Chemistry is one that Henry Oldenburg, the first editor of Phil. Trans., would probably recognise. But now that most people read journal articles that they have downloaded from the web, rather than pulled down from a shelf, the article itself — not just its delivery — is on the verge of major changes. Some of these are linked to the vision of Tim Berners-Lee and others for the future of the internet — the semantic web[1, 2]. In this concept, information is labelled in such a way that computers can understand what it is, rather than just humans, as is generally the case at the moment.

Rather than the HTML version of the article being a narrow reflection of the printed page, it can offer enhancements beyond clicking to bring up figures or references — which simply mimics how people can flick through hardcopies anyway. Enhancements that further enrich articles are already being offered by other publishers, including the Royal Society of Chemistry with Project Prospect3. Among other services, this highlights words that are terms in the IUPAC Gold Book and links to their definitions. Beyond simply being an educational tool, this also means that papers on similar concepts are linked together. Apart from the fledgling ChemSpider Journal of Chemistry4, there are few other publishers exploiting the full potential of their online articles. Although the American Chemical Society are testing several interesting and useful innovations on the JACS-beta website5, such as downloadable PowerPoint and ChemDraw files, none of these so far enriches the text of the articles.

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Reactions – Erin Carlson

Erin Carlson is in the Department of Chemistry at Indiana University, and works on the development and application of advanced chemical biology and systems biology technologies to both define the mechanisms of bacterial development and pathogenesis and identify potential therapeutic agents.

1. What made you want to be a chemist?

My dad is a bioorganic chemist, so my interest in the field isn’t surprising. When I was in elementary school, we bought one of those crystal growing kits from the science museum and grew them in a beaker in his lab. I still have that beaker in my home office. I started work in his laboratory at 14 and have never looked back.

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

I would be a photographer for National Geographic. This job would encompass several of my favorite activities; travel, learning about other cultures and photography.

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

Very broadly, we are working to define biochemical pathways associated with disease. Although it’s probably not practical to expect that we will be able to directly find the cure for a major disease, I hope that we will make fundamental contributions that will ultimately enable the development of new treatments.

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

Mahatma Gandhi. Although I have long been intrigued by Gandhi and his philosophies, a recent trip to India intensified my interest and has spurred a great deal of reading and learning about this incredible man.

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

I was in lab just over a week ago synthesizing a molecule for an assay that one of my students is performing.

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

The book I’ve been enjoying that most lately is At the Helm: A Laboratory Navigator by Kathy Barker. I have found it to be invaluable as I start my career as a new faculty member. But I suppose if I were on a deserted island, I wouldn’t really have the opportunity to be running a research lab so I might have to rethink this selection…

I can’t possibly decide on one album since music is such an integral part of my life. At the moment, I would select For Emma, Forever Ago by Bon Iver and The Flying Club Cup by Beirut.

Materials Girl: Expectations

Posted on behalf of Materials Girl

In discussions with various professors, I’ve noticed that researchers seek out an interesting range of qualities for their minions – aka: grad students. One absolutely required creativity and out-of-the-box thinking. The next expected independence and strategizing, while insisting that he himself was not the greatest of researchers (he’s amazing and brilliant).

Another said that inherent intelligence and academic background were irrelevant – he just wanted his students to work hard. (This was not too concerning. That is, until I was told that the HR lady received complaints from a different prof who was displeased that his students didn’t come in every weekend… Uhh…) My own advisor never asked for my experience or qualifications, being seemingly content with the fact that I was excited to be in the lab and willing to try anything.

So then, what other characteristics are required? Which are the most important, and to what branches of study?

Reactions – Eugenio Coronado

Eugenio Coronado is in the Institute for Molecular Science at the University of Valencia, and works on molecular magnetism, in the design, study and processing of new magnetic molecules and materials exhibiting multifunctional properties.

1. What made you want to be a chemist?

One initial reason was the central position of chemistry, in between physics and biology. Another more recent reason was related with the structure of matter, its beauty, and the unique possibility offered by chemistry for manipulating these structures to create new compounds exhibiting new properties.

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

A painter or a cartoonist, as these artistic activities also involve a significant amount of research and a lot of creativity.

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

I am starting to work on molecular spintronics. The main hopes in this new area of nanomagnetism are to show that chemistry can provide new magnetic molecules and materials, which conveniently designed and nanostructured, should lead to useful spintronic heterostructures and to new opportunities in nanospintronics and quantum computing.

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

Leonardo da Vinci. For me this figure represents the perfect combination of scientist and artist.

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

My last chemical experiment was done at Georgetown University, USA, in July 1987 in the lab of Prof. Louis Baker. I was preparing a cobalt magnetic cluster encapsulated by a polyoxometalate. It resulted to be the first polyoxometalate molecule exhibiting ferromagnetic exchange interactions. In physics I performed more recent experiments at the ILL in 1991 to study the magnetic excitations in this kind of clusters.

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

Apart from a survival guide, I would take Homer’s Odyssey. As music, I would take Vivaldi music (and a Spanish guitar).

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

I would like to see interviewed relevant scientists (not chemists) having seminal contributions in chemistry (for example, Nobel prizes in chemistry coming from other fields). Aaron Klug (physicist interested in biochemistry) should be an excellent choice.

The RSC and ChemSpider

As announced by the RSC Press Office and the ChemSpider blog, the Royal Society of Chemistry has acquired ChemSpider, the structure-based database.

Gosh. Reaction from the blogosphere has been positive and congratulatory (see the comments on Tony’s blog post and Peter Murray-Rust’s post).

Richard Kidd, head of the RSC’s Informatics department (formerly Production) has also blogged about it on the Chemistry World blog. He says “The ChemSpider service will continue to be free to access on the web” – answering the question that I was planning to ask in this post! Phew.

So that means that ChemSpider’s future – previously a tad shaky if Tony had fallen foul of his backyard snakes or his basement flooded – is pretty secure.

It’s going to be interesting to see how this develops: ChemSpider has been the new kid on the block (compared to the venerable Beilstein, Gmelin, Chemical Abstracts etc), but now it has the equally venerable RSC backing it up. I imagine adding the RSC’s extensive archive (dating from 1841, nearly 1.5 million pages) would add a hefty chunk of data.

[And not a single bad spider-related joke spun out of this post…]

Neil

Neil Withers (Associate Editor, Nature Chemistry)

Materials Girl: Readjusting

Posted on behalf of Materials Girl

It occurred to me that all this time I’ve had a mistaken notion/approach about my undergraduate education… First year was newly discovered distress in the form of higher standards, 10+ page papers, and relatively detailed lab experiments that didn’t go as well as planned. (98% yield on the first time doing a distillation? Why doesn’t my unknown ether smell like roses?! Hah!) I swore that after surviving such troubles from o-chem, nothing else would be difficult – even if I loved the subject.

The next fall, I realized that organic actually isn’t that difficult – physics was infinitely worse for me. Also, to my chagrin, bombing one final could mean getting one crappy grade that permanently tanked a good GPA. I looked forward to the day I returned to the realm of ~3.8.

During third year, after changing my major, I was introduced to the world of materials engineering, research, and more upper division classes. I wondered how half of my undergrad education was already over and why school was still so traumatic at times. If only I could just get another A and earn Latin Honors, all my troubles would dissipate… Now, with over two-thirds of my final year finished, I’ve almost convinced myself to believe that grades aren’t THAT important. It’s all about experience and adaptation!

The “moral” is, I’ve come to recognize, that there will be hardship at every stage of education – and life. Sometimes it’s unbelievably mind-blowing, depression-causing, head-banging-on-desk, extreme hardship. The difficulties just come in different forms, and once you get used to something, situations change. So it’s not about looking forward to when something unpleasant is over, but figuring out how to make it bearable. Enjoyable, even.

Perhaps I’m reiterating obvious truths, but it should be about the journey. I shouldn’t have the mindset of only looking forward to when my GPA goes back up or when graduation rolls around. You have to stop and smell the roses, right? Just make sure that the whiffing doesn’t make you pass out…

Reactions – Ross Kelly

Ross Kelly is in the Department of Chemistry at Boston College, and works on the synthesis of natural products and molecular devices (motors, brakes, etc.).

1. What made you want to be a chemist?

When I was growing up in the 1950s, chemistry sets still contained good stuff (like powdered magnesium) and even a twelve-year old could get the ingredients of gunpowder (sulfur, powdered charcoal and saltpeter) at the drug store no questions asked. Not surprisingly, rockets, bombs and homemade fireworks first hooked me on chemistry. While the inability to easily lay one’s hands on “dangerous” chemicals may make childhood safer these days, I fear that without the allure of “bangs and stinks” to grab them when they are young, fewer people will go into chemistry in the future.

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

I like designing and making things and I have spent my career designing and making molecules. But I expect I would have enjoyed designing and making other things instead. Being a mechanical engineer or a mechanic or machinist or maybe even a furniture maker (I design and build furniture as a hobby) appeal to me.

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

I answer this question at the risk of inflicting lame duck status on myself, since one is most commonly known by his research program. For the past five years or so I have been winding down my research effort. Fortunately, I did that when I had a choice, rather than now when the current funding crisis might have forced it on me. I will continue to teach organic chemistry to undergraduates, which I enjoy and seem to be good at.

A word to the (un?)wise: lecture demonstrations have fallen out of favor in organic chemistry, but the students really like them and they liven up the class. I do something nearly every class. “Demonstrations” don’t have to be a lot of work: projecting the lists of ingredients from various foods, drug store products, etc., or passing around samples of familiar odiferous chemicals are easy ways to connect with the real world.

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

Leonardo da Vinci and Linus Pauling are two that come to mind. Not even taking into account his art, Leonardo was phenomenally creative, and I find his engineering ideas fascinating. Pauling was amazingly smart and figured out so many things. I would like to hear him explain how he missed the structure of the double helix – he got so many other things right.

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

Most of us who end up in academia do so because we were unusually good in lab as grad students and postdocs. One of the ironies is that most of us then have to forsake what we enjoyed and what got us here. It has been a long time since I have done anything in lab except to occasionally show a technique to a student.

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

I like to read, so I would prefer to bring a bookcase (or a Kindle) full of books, but if I could only bring one book, it might be Dostoyevsky’s classic Crime and Punishment, but for a strange reason. Several times in my life I have started Crime and Punishment, but never gotten into it. If it were the only book on the island, I expect I would finally finish it.

I don’t spend all that much time listening to music, so I would much prefer bringing a radio-controlled model airplane to fly. Many people won’t understand, but I would find that more relaxing than listening to music.

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

That is a hard question. The ones that I would be most interested in (viz Emil Fischer) are dead, which makes for a tough interview.

Reactions – Kristopher McNeill

Kristopher McNeill is in the Department of Chemistry at the University of Minnesota, and works on the environmental chemistry of aquatic systems.

1. What made you want to be a chemist?

I had a crush on a girl in high school and she told me I looked good in a lab coat during a chemistry lab. I wish I were kidding. Prior to that, I had a strong, yet nebulous, interest in all things science-y, especially space travel.

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

It’s a sad fact that I am not that good at anything else, but I do enjoy (listening to) music and (engaging in amateur) graphic design. Maybe I would be a music blogger with a swank website and live off ad revenue! I could interview musicians and post their interviews on my blog. Hmm, this is starting to sound a lot like your job.

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

My research group is focussed on chemical reactions that occur in aquatic systems. Right now we have projects on the fate of wastewater-derived pharmaceuticals in surface waters (with Prof. Bill Arnold), how sunlight participates in the breakdown of natural organic compounds in estuaries (with Prof. Jim Cotner), remediation of groundwater polluted with chlorinated solvents using metal-based reactions, the environmental chemistry of carbon nanotubes (with Prof. Chris Cramer), and sunlight-mediated inactivation of pathogenic viruses and bacteria (with. Profs. Kara Nelson, Ali Boehm, and Tamar Kohn), among other things! As you can see, we like to collaborate with other research groups. I would argue that most problems in environmental science are just too big for any one research group or one research discipline to tackle — you have to collaborate to make headway. Plus, we have a lot of fun interacting with folks with different expertise.

I’ll tell you about one ongoing project that has captured my interest lately. It involves triclosan, the active ingredient in anti-bacterial handsoap. In the US and Canada, our use of anti-bacterial products results in something like three milligrams of triclosan per person per day being washed down the drain. So, at a wastewater treatment plant that serves a million people, about a metric ton (1000 kg) of triclosan comes to the plant every year. About 10% makes it through the plant as either the parent compound or chlorinated derivatives. Prof. Bill Arnold and I have had a few students over the years looking at what happens when triclosan and the chlorinated triclosan derivatives in the wastewater effluent are exposed to sunlight. Our focus has been on one particular set of troubling reaction products, which are chlorinated dioxins. What we have been working on lately is trying to determine the extent to which triclosan is a significant (or insignificant) source of chlorinated dioxins to the aquatic environment. The work is ongoing, so you will have to check back to see what we find!

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

Rachel Carson. She is arguably the single most important figure in launching the modern environmental movement and my field of study, environmental chemistry. Most people think of her interest in birds, which comes through so strongly in Silent Spring, but her real love was aquatic systems, which is mine as well. I understand that she was not much of a conversationalist, so dinner might be a bad venue. I think I would pack a lunch and arrange for a hike along the coast.

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

Last summer, with help from some graduate students, I attempted to measure differences in the steady-state concentration of singlet oxygen in filtered and unfiltered Lake Superior water by following the disappearance of furfuryl alcohol. I didn’t see any differences. The more interesting part of the story is that the experiment was conducted on the top deck of the R/V Blue Heron on a beautiful sunny day in the middle of Lake Superior. Field work is one of the few opportunities that I take advantage of to get my hands dirty doing science. The last molecule that I made by myself from setup to cleanup was probably bis-(trimethylphosphine)zirconocene back when I was a graduate student.

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

Radiohead’s OK Computer comes to mind as an album that I could stand listening to again and again and again. It is good for intent listening, casual listening, waking, sleeping, running, and setting the mood for my island cocktail parties. Borges’ Labyrinths is the book I would take. It is a collection of his short works that is so dense and so endlessly interesting, it might take being exiled on a desert island to ever really figure it out.

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

Oliver Sacks always has something interesting to say. He is not a practicing chemist, but he definitely is has a chemist’s soul. I have always enjoyed talking with Carolyn Bertozzi, but realize now that I do not know her music and literature tastes!