Reactions – Duncan Bruce

1. What made you want to be a chemist?

My inspiration was the man who taught me for four years at Trinity School, Carlisle – Mike Fossey. He showed me the beauty, breadth and logic that underpins chemistry and made me realise what an exciting subject it is. It was a real thrill some years later to send him a paper published with another of his ex-pupils who carried out an undergraduate project with me in Sheffield.

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

Ancient history always fascinated me – an academic career in that direction would be a possible alternative.

3. How can chemists best contribute to the world at large?

This list is long, as chemistry has a unique ability to permeate so many aspects of our lives. However, perhaps the biggest challenges that the world faces at present relate to energy. We need new and renewable sources, we need to use it more efficiently, and we need to find viable ways to store it and also to store newer fuel sources such as hydrogen. Chemists are central to these issues and their creativity can make a real impact.

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

Nelson Mandela. To endure the imprisonment and then to come out and lead with such wisdom, taking such a major place on the world stage and in the hearts of so many people, means for me that there would be so much to learn from him. And from what I have seen through the media, he would be terrifically good company.

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

I am in the lab quite often working with members of my group on the identification of liquid crystal phases by optical microscopy. However, in terms of ‘rolling up my sleeves’ and doing a reaction, the answer is ‘rather recently’. Listened to a visiting seminar speaker and went to the lab the same afternoon to make something prompted by one of his slides. Simple reaction – acidify to dissolve the base in water and then co-precipitate. Now all we need to do is get it pure, find out what it does and get a crystal structure…

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

I tend to read contemporary authors such as Ian McEwan, Sebastian Faulks, Louis de Bernières and Peter Carey. However while it is something that I have read only recently, I would take Suite Française by Irène Némirovsky. So much has been written about this book, yet its sheer humanity and observation of the human condition would bear reading over and over again. Music is much more difficult. My tastes are diverse from baroque through romantics and Shostakovich to 60s/70s rock and the present day. However, for its ability to move and stir emotion, Beethoven’s 9th Symphony would probably be my choice with his Violin Concerto (which reminds me of the English Lake District) a close second. However, any CD would have to be homemade, as I’d need Debussy’s Deux Arabesques No. 1 played by Pascal Rogé and Stairway to Heaven, too.

Duncan Bruce is in the Department of Chemistry at the University of York and works on various aspects of materials chemistry, with a strong emphasis on liquid crystals.

Focusing in on mass spectrometry

Almost every chemist has used mass spectrometry at some point at some point in his or her scientific life, but did you know about all of its cool applications in the study of proteomics? This field has been growing by leaps and bounds as more and more biologists discover the power of mass spectrometry. Check out Nature Methods’ special Focus issue on mass spectrometry in proteomics applications.

Allison Doerr (Associate Editor, Nature Methods)

Sugar Daddy: Looking both ways

[Editor’s note: another guest blogger has joined our team…]


Posted on behalf of Sugar Daddy:

I guess Sugar Daddy is a somewhat ironic nickname, as I am a graduate student, and my friends make anywhere from 2- to 5-fold more money than I do in the so-called “real world,” which I hope (for their sake) is nothing like the MTV reality TV show of the same name. But I do work with carbohydrates, so maybe we should just roll with it.

Anyway, I am in my fourth year of a PhD program working in a chemical biology lab. My research involves the proverbial “little bit of synthesis, little bit of biology,” and things have been going well. I guess you could say I’m living the chemical biology dream: synthesize a molecule, show that it has biological activity in cells, and then take it all the way to a living organism.

This week, I’ve been simultaneously thinking about the past and the future. It is recruiting season in our department, and therefore many wide-eyed first-year students are showing up asking to be told about the research projects in my lab. As I describe my work, which I can more or less do on autopilot, I start to reminisce about what it was like to be a first-year student – how random all the decisions I made then seem in hindsight. Did I choose my school because I “had a better gut feeling” about it? No, I tell myself, it was because I liked the students and professors I had met, and of course the research interested me the most as compared to other schools. And why did I pick this lab? Did I pick my project or was I gently nudged toward it? No complaints, but how much did I really know about what I was getting myself into at any stage of the game? Was I delusional, thinking that I had complete control over my scientific destiny, at least on the five-year timescale? As the saying goes, a little knowledge is a dangerous thing.

And speaking of “as sayings go,” the whole autopilot experience (of describing my project without really having to think too hard about what to say) reminds me of a moment in high school (where we really were naïve, that’s for sure), and specifically in English class. My teacher had us read “Politics and the English Language,” a 1946 essay by George Orwell about how the English language had deteriorated to the point that people merely strung together short familiar fragments rather than construct novel phrases and ideas. I think this essay should be required reading for every scientist, or at least those that will ever have to write a paper, book, or grant proposal. Okay, for the next first-year that shows up, I’m going to describe my project in a completely novel, illuminating way. Ugh, that certainly feels like it’ll be an endothermic process.

So, that was the thinking about the past. How about the future? A post-doc is on the horizon. (There, by the way, is Orwell’s thesis in action.) More on that next time. With all this thought about the past and the future, I suppose that doesn’t leave much time for the present. Guess I’ll wait until tomorrow to HPLC that compound…

Imaging is dino-mite!

My continued search into the literature revealed this interesting contribution, which focuses on the development of imaging agents that target hydroxyapatite (a calcium salt related to bone growth and calcium deposition in general). The overall idea is that if we had near-infrared contrast agents that were targeted to microcalcifications (which also usually consist of hydroxyapatite), we could better detect the early stages of breast cancer because the agents would be easy to visualize in live subjects. Bisphosphonates are known to bind hydroxyapatite, but making these compounds hasn’t been easy, either because of poor solubility, or the poor yields or harsh conditions of known reactions. John Frangioni and his colleagues now report both a new, facile method for the synthesis of these compounds and concomitant conjugation to a known NIR contrast agent, and also their application to imaging in pigs. It seems pretty interesting, in particular as I’ve never made any C-P bonds myself.

The other aspect of the paper which intrigued me is the use of ‘large animals’ in the title. While I don’t think anyone would argue that pigs are large animals (and P.S.: love the graphical abstract), I found myself wondering: how large of an animal can these compounds really be applied to? People? Horses? Bears? Even… dinosaurs? (which, as I still like to nurture my third-grade self, seems about the biggest animal you could ever imagine. Sorry, blue whale). It made me further think that maybe we’re missing an opportunity to have more nerdy science lingo: similar to the generic ‘gazillion’ to mean a very large number, maybe we could use the prefix ‘dino’ to indicate a very large size of something? Then, as kind of the antithesis of ‘nano’, we could have dinotechnology (although maybe we’ve already had this one?), dinorobots, dinomachines… In more common usage, you could say someone has a dinohouse (instead of a mansion), a dinohead (for someone really egotistical), or a dinocollection of … well, whatever you have a lot of. What do you think? Will it catch on? Will it be, dare I ask, a dinophenomenon?

Catherine (associate editor, Nature Chemical Biology)

Someday we’ll all be free

I’ve been searching the literature today, and came across this interesting paper about platensimycin. This antibiotic was only initially reported last year, but there are already a bunch of total and partial syntheses of it. So why do we need yet another synthesis of it? Because we always need more ways to synthesize molecules. Duh. This one, however, it particularly fun because it reports the synthesis of a key intermediate for platensimycin without using protecting groups (in 8 steps; ~10% yield compared to 10-16 steps and ~5-11% yield) and in a much more scale-up friendly manner (several steps are quantitative and require no purification). It makes me wonder if this protecting group-free idea (recently also reported by Baran et al.) is catching on, or if Tiefenbacher and Mulzer just have their eye on the prize (in terms of thinking about the chemical engineering side of making the molecule). What do you guys think? And is it even possible to dissect those two motivations?

The other fun thing about this paper is that it’s one of those syntheses where I want to get out my molecular model kit to see how all these 3D transformations occur.

Finally, another interesting thing I discovered in looking deeper into this story is that the molecule was only initially reported (in the literature) on May 18th, 2006, and the first total synthesis of the molecule was submitted for publication September 21st of that same year. Clearly, someone either has magic hands or had advance knowledge of the structure. For those of you in the synthetic field, how critical is it to get inside information on new structures that are found? And what’s the source in general – a friend who does this research, a talk at a conference, your own culture of bacteria? And what’s the price of this knowledge, or is it, like this synthesis, free?

Catherine (associate editor, Nature Chemical Biology)

Reactions – Milo Shaffer

1. What made you want to be a chemist?

I think I get my scientific leaning from my father, presumably a mix of genetics and his infuriating tendency, when I was young, to answer any question either with a ‘what do you think?’ or a demand for a numerical estimate. That I ended up in chemistry rather than another science, probably reflects the great mix of real world problems with opportunities for creativity.

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

I’m occasionally tempted to continue a family tradition of giving up science/engineering in favour of art; however, my early teen plan to become an architect would be a more grounded choice, and one that might provide me more satisfaction – though, I would probably try to squeeze in as many textures, shadows, and angles, as possible, using dynamic effects that change with time or conditions.

3. How can chemists best contribute to the world at large?

Clearly there are many problems facing society that require technical solutions, particularly relating to sustainability and energy; the alternative is effectively a return to the dark ages or worse. Chemists have a pivotal role in developing the enabling molecules/materials and understanding. At the same time, it is important to recognize that directing research too tightly may not be the best strategy; pure, open-ended research is needed to create dramatic breakthroughs.

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

Aristotle, the father of natural philosophy, an eloquent speaker, an enquiring mind, not to mention a rich source of political and cultural perspective on our own world. I’m not sure about his cooking, however – perhaps Auguste Escoffier would be a better choice.

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

About a month ago, looking at electrochemical impedance spectroscopy of what we call ‘structural supercapacitors’ – an invention based on multifunctional materials that simultaneously store energy and provide mechanical strength and rigidity.

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

If I’m allowed to transfer two battered tapes of live performances of my uncle, John Bell, to CD, his songs would cheer me up immensely during any lonely moments. For my book I might take Heller’s Catch 22 – a favourite that improves with rereading – but I’d probably settle for a good ‘Learn Mandarin’ textbook. It would certainly keep me busy, and I love learning new things; the kanji would provide aesthetic pleasure, and Chinese might even be the world language by the time I get off the island.

Milo Shaffer is in the Department of Chemistry at Imperial College and works on the synthesis, modification, and application of nanotubes and nanorods.

Six degrees of Stuart Schreiber

Finally, another way to inject some Hollywood into science: an adaptation of the ‘six degrees of Kevin Bacon’ game, or if you prefer, just ‘six degrees of separation’ in general. This one references Stuart Schreiber partially because he’s obviously a great scientist in the field of chemical biology, but mostly because the alliteration is nice. If you fall into the California chemical biology contingent, you could play ‘Six degrees of Schultz’; whichever floats your boat.

While knowing how I’m connected to Schreiber (me to Vince Rotello, to Harry Wasserman, to Gayle Schulte (then at Yale), to Schreiber; 4 degrees of separation) and Schultz (me to Scott Singleton, to Peter Dervan, to Schultz; 3 degrees of separation) is fun, the non-specific one seems more pervasive amongst conference attendees or just any scientists who are meeting and finding out, yet again, how small the world of science truly is (as when I randomly discovered my current coworker’s undergraduate TA was one of my good friends in my postdoc lab). Even amongst people you already know, it’s fun to find out how interconnected you are (for example, Nina Goodey, my undergraduate study partner (just moved to Montclair State), connects to me through Steve Benkovic (her postdoc advisor) who was also Singleton’s postdoc advisor; perhaps we should rename the game ‘Six degrees of Scott Singleton’? Also nice alliteration).

Are there any rules that would need to be changed to adapt this game to the wide world of science? Does someone have to work for someone else, or can just being at the same university at the same time (and presumably knowing each other) count? What about collaborating with someone? Can you count the person who hosted your visit to a university, or invited you to give a talk? These last two are certainly less easy to know about or verify, so perhaps a rule would be that there has to be evidence of the connection in the literature? (in which case, perhaps my connection to Schreiber would be more appropriately recapped as JACS 2001, 123, 7626; JOC 1989, 54, 2785; JOC 1992, 57, 2641; JACS 1987, 109, 4718). What do you guys think? And how do you connect?

While you think about that, I’ve got to go see if I can convince someone to make it six degrees warmer in here…

Catherine (associate editor, Nature Chemical Biology)

Time, time, time

This year is speeding by, as evidenced by the fact that our October issue has gone live. This one is a focus on ‘molecular metrics’, which deals with all the different ways that cells and biological systems count and measure both physical objects and states (such as changing times or other conditions). The pieces range from discussions of how flipping a single amide bond can control a host of downstream processes to how the length of limbs (and zebrafish fins in particular) and telomeres are controlled or functionally deciphered, with many stops in between. The cover also features some cells gearing up for an architectural career, so check it out!

My perception that this year is just completely getting away from me makes a nice parallel with thinking about how individual cells and brains and proteins measure time. I’m sure my feeling that it really should be, oh, May or so, is part of a cellular defense mechanism, because if we tried to store memories of what happened every day, our brains would quickly explode or just get full. However, it is a bit disconcerting to feel so out of whack with the continually advancing calendar. My solution? I’m hoping that we do develop Pensieves, and then I can store my memories in there, leaving room to keep the recent weeks and months in my brain. In that case, it’d be nice to look back once in a while and, as Paul Simon so eloquently said, see what’s become of me.

Catherine (associate editor, Nature Chemical Biology)

Structurally unsound

Are chemists anally retentive when it comes to chemical structures? Making sure that structures are error-free is certainly vital for a chemistry paper (and for an editor, one of the biggest headaches of the job). Just one wedge bond displayed as a hash could completely confuse the take-home message of a paper.

So imagine how annoying it would be if you saw a structure being repeatedly published with errors in it, and in lots of different places. This is just what has happened to Ian Fleming.

Back in 1967, he published a paper in Nature that finally nailed the absolute configuration of the structure of chlorophyll (Nature subscribers can see the paper here – it’s well worth a look). Yet he reckons that since then, whenever he has seen the structure reproduced, there is a 50:50 chance that the stereochemistry will be wrong.

Over the years, he’s tried to correct this where possible, including, on one occasion, an incorrect structure on a book cover. But it still happens. Out of curiosity, I had a look at the structure on Wikipedia – and sure enough, it was wrong (see for yourself, but be quick; I’ll contact them shortly to get it corrected). The actual structure can be found here at PubChem.

Who knows how often this happens? But then again, if a structure appears somewhere that isn’t necessarily directed at chemists (such as in the Wikipedia entry), does it really matter? Is it just the chemist’s equivalent of getting upset about the incorrect use of an apostrophe? I think it does matter – especially in sources on the web, which are increasingly being mined for technical information. But if you think I should just take a cold shower and calm down, by all means let me know.

Andy

Andrew Mitchinson (Associate editor, Nature).

Reactions – Marcus Weck

1. What made you want to be a chemist?

You have to blame my high school chemistry teachers. Chemistry and biology were the only two topics in high school that came naturally. Math, languages, etc., were always way too much work for me. Combine this with fun hands-on experiments and unexpected explosions during chemistry classes… what kid can ask for more?

I have to admit that my first 2-3 years as an undergrad in Germany nearly ‘eliminated’ any love towards chemistry. My professors were stuck 50 years in the past (science and age wise) and the lectures they gave were somewhere between boring to non-existent (one just has to love the German university system). I was very close to switching majors and decided that I would leave chemistry when I failed my first course. Only after the ‘vordiplom’ did things get interesting and I have to credit my first advisor, Helmut Ringsdorf, for bringing back my love for science.

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

No question, I would be a music conductor. I love classical music, the one great passion (but for my family and friends) besides chemistry. The only times I can ‘let go’ of chemistry and not think of it is during an opera or symphony performance.

3. How can chemists best contribute to the world at large?

I do not want to repeat what all the other scientists below pointed out. Clearly, chemists have to make major (or the key) contributions to very important scientific problems and challenges in our society ranging from the environment to health. All of us work on scientific problems related to these challenges.

One issue we as scientists are not addressing (or at least not doing a good job at) is educating the general public about science. The lack of understanding of the basic principles of science of the general public including our societal ‘leaders’ (politicians, etc.) results directly into some very dangerous and problematic decisions (or the lack of decisions to address problems), i.e., we as scientists knew 20-30 years ago that carbon dioxide emissions are not good for the environment. However, we were not able to relate the importance of this to the general public and to our governments.

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

That’s a tough one. If it’s just me and one person, I would go for Mozart. This will be for sure an entertaining dinner.

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

To be honest, my last time doing an experiment in lab is some time ago, I guess approx. 6 years (my second year as an assistant professor). I still help group members out now and then, but do not have my ‘own’ project or run my own reactions. Most likely my group would kick me out (or leave the room) if I went back into the lab.

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

These are always the toughest questions. I think I would bring the ‘Ring der Nibelungen’ (can I take all 14 CDs instead of just one since they count as ‘one opera cycle’?) from Richard Wagner (The poor animals on the island. They have to endure Wagner all the time. They might send me back to civilization). The book is tougher. I think I would either go with Tolkien’s Lord of the Rings or Gogol’s Dead Souls.

Marcus Weck is in the Department of Chemistry at New York University and works on organic materials with emphases in supramolecular polymers, biomaterials, optical materials and catalysis.