The Sceptical Chymist nature.com homepage The Sceptical Chymist is a blog by the editors of Nature and the Research journals - and a forum for our readers, authors and the entire chemical community. We'll discuss what's new and exciting in chemistry and chemical biology, be it in our journals or elsewhere. We hope for spirited conversation! To contact the editors directly with confidential questions or feedback, please email 'thescepticalchymist at boston.nature.com'. Reactions - Julie MacPherson 1. What made you want to be a chemist?From an early age I was always really interested in my surroundings, what made things work they way they do, why was the sky blue, that sort of thing, so it was no surprise to me or my parents that I really took to studying the sciences at school — especially after having to have my bedroom carpet replaced after getting burning hot solder on the surface whilst attempting to make a very crude electronic organ! I knew I would end up doing something that revolved around science, but it wasn't until I was doing my PhD that I actually thought that I would be good enough to be an academic. I actually had a tough time deciding whether to study physics and chemistry at university (as I really enjoyed them both) but as it turns out, even though I opted for chemistry with research crossing many boundaries, these days I actually dabble a fair bit in both physics and biology, which really suits me. 2. If you weren't a chemist and could do any other job, what would it be - and why?I think I would like to do something that engages the more artistic side of my personality. I am a very visual person and creative art can be very powerful, emotive and engaging, so a photographic career has always appealed to me. On the days I really let my imagination run wild I would have loved to try my hand at sculpture. A long time ago I started writing a non-scientific novel but never got the time to see it to completion so I will never know if a literary career was for me! 3. How can chemists best contribute to the world at large?I think there are many ways — one of my main roles I believe is as an educator to instill the drive for knowledge and learning in the next generation of students and show them how to think creatively and importantly how to research. Obviously, of equal importance is the research we do, which is crucial and can have a tremendous impact on current issues — for example the production of medicines for the diseases that blight our society, finding new materials that will offer alternative solutions to the energy crisis. 4. Which historical figure would you most like to have dinner with - and why?I suppose I should be expected to suggest a scientist but actually the person I would like to meet most is Auguste Rodin. His sculptures are truly amazing they convey so much emotion in the human form. I often find with art that the more you know about the person that created the work the more you truly understand and appreciate as so much of themselves is embodied in the created object. That statement is probably also true of most scientists.5. When was the last time you did an experiment in the lab - and what was it?I try and go into the laboratory most days as this is the part of the job I most enjoy, seeing the experiments in action, discussing the results with the students. However, I haven't done my own experiment (from start to finish) for a few years now, but I am no stranger to getting my hands dirty and the students will often find me fixing a piece of equipment or helping them out with an experiment. I always tell them doing a PhD is one of the best times of your scientific career as you get to focus on one thing with no distractions 6. If exiled on a desert island, what one book and one CD would you take with you?I think the book I would take is Dante Alighieri's Divine Comedy — I remember first reading this when I was in my early twenties and never got past the "Inferno" as they were so many messages within messages that it took me ages to work out all the hidden meanings and symbolism, so I was left with Dante and Virgil waiting to enter purgatory. On a desert island with the time allowed hopefully I would be able to pass through purgatory to paradise to finally meet Dante's Beatrice. The CD is a bit trickier as I have a really wide musical tastes, so I could take a number, but Moby's Play might keep my spirits uplifted.Julie Macpherson is in the Department of Chemistry at the University of Warwick, and works on the development and application of new imaging techniques and carbon-based materials for sensing applications. Posted by Neil Withers at 06:42 AM | Permalink | Comments (0) | TrackBacks (0) Reactions - Luisa De Cola 1. What made you want to be a chemist?I was always a very curious child and I liked science in general. I guess my first choice would not have been chemistry but biology or medicine and indeed I studied biology for one year before realizing that chemistry was my preferred discipline.2. If you weren't a chemist and could do any other job, what would it be - and why?I like many very different things. Perhaps a medical doctor, a neurologist, or a musician or perhaps a film director.3. How can chemists best contribute to the world at large?Chemists make our world! Everything we eat, drink, any clothes we wear, anything we touch is chemistry! The challenge now is surely to solve the energy crisis, the water problem and to improve early diagnosis of illness.4. Which historical figure would you most like to have dinner with - and why?I would love to have dinner with Albert Einstein. I had since I was very young a special admiration for him as a scientist but in some respect also for his turbulent life.5. When was the last time you did an experiment in the lab - and what was it?I must confess that I am often in the lab, even just to look at my student showing me something... The last time I did manually something myself was about 3 years ago showing one of my student how to separate an iridium complex using an alumina column.6. If exiled on a desert island, what one book and one CD would you take with you?This is a very difficult question... perhaps the book would be One Hundred Years of Solitude by Gabriel García Márquez. The CD I alternate jazz and classical music but I also love pop music. I guess would probably be Bill Evans or Keith Jarrett the Köln concert.Luisa De Cola is Professor in Physics and Chemistry at the Universities of Münster (Germany) and Twente (The Netherlands). Her main interest is luminescent and electroluminescent molecules and nanomaterials. Posted by Neil Withers at 06:56 AM | Permalink | Comments (0) | TrackBacks (0) Materials Girl: The bell curve doth toll Posted on behalf of Materials GirlFinals are, at last, over and winter break has begun! ‘Tis the season for living at home, sleeping in, catching up on blogging, and checking grades online obsessively! (More precisely, I am procrastinating on studying for the GRE. Ugh. The vocabulary words I’m familiar with nowadays are on par with trimethylxanthine, eigenfunction, and nanorod, not termagant, eleemosynary, and nadir).As far as grading goes, some form of curving seems standard among non-humanities classes. My science professors tend to aim for “nice” exam averages of 60-80, then curve results so that the wretched students scoring 50% get C's instead of F's. The brilliant engineering profs think everything is completely straightforward and write “easy” exams. Hah!From a student’s perspective, I generally don’t have problems with curving. It’s nice to not worry about getting +90% on everything and risk having a few arithmetical errors or forgotten arrows kill perceived performance. However, if someone achieves those high scores and stays well above average, an A still isn’t guaranteed. And, that really sucks. It seems to boil down to two choices: battling tests & grading rubrics to score some set percentage, or battling classmates to be at the top of the pack. At the end of the day, it’s just a matter of a little luck and how well you fight (and get back up when beaten down) – regardless of the opponent.Everyone says to not worry about GPAs, but it can’t be completely written off – especially since some schools give out A’s more easily than others. Experience and recommendations aside, how much do grad schools and companies really factor in what university an applicant comes from? At career fairs, recruiters always, always begin by looking for the GPA on my resume. It does make sense, since a 5-10 minute conversation can’t really tell them how qualified or knowledgeable I might be. But, what if I had a B in a class because my peers were a little bit better that time around, and I could’ve taken the same class the next term and gotten an A? I don’t think the 4.0 from community college will be of much help... Posted by Stuart Cantrill at 11:39 AM | Permalink | Comments (5) | TrackBacks (0) NChem Research Highlights: Biosensing dyes, strong biomimics and levitating beads So here it is...Research Highlights, everybody's having fun. But before we all disappear for Christmas, here are the final RHs of the year.I covered a pretty smart idea for a class of biosensors. Reducing cynanine dyes means they don't fluoresce, until they come into contact with the nasty reactive oxygen species that mess around with cells. Even cleverer, the reduced forms can slip in and out cells willy-nilly, whereas the fluorescing ones are trapped inside the cells, showing you where the problem is.You might well have seen this one elsewhere, but now you can read Tim's take on the biomimetic material that's thin and strong - it's all about the ice templating, you know.Last, but by no means whatsoever least, it's a nifty idea for what could become 'TLC for solid-supported synthesis'. And it involves magnetically levitating beads!And finally...unlike the BMJ we haven't got a load of spurious research to make it into the news-light festive season newspapers - watch out for next year though - and we're a week before the RSC releases the same story about hangover cures for the 3rd or 4th year running, so I'll leave you with some mathematical clues to help you wrap presents better!See you all in the New Year - thanks for all the comments in 2008!NeilNeil Withers (Associate Editor, Nature Chemistry) Posted by Neil Withers at 05:32 AM | Permalink | Comments (0) | TrackBacks (0) Reactions - Ivan Dmochowski 1. What made you want to be a chemist?For almost as long as I can remember, I’ve loved math and applying math to understanding the physical world. I grew up near Woods Hole, MA, which meant that there were high-quality local science fairs and “real scientists” as judges. My experiences of designing and performing independent science projects whet my appetite for science research. My interest in chemistry started in high school, where I had two very good chemistry teachers. However, I didn’t know many chemists, and I never really considered a career in chemistry.As an undergraduate at Harvard, I gravitated towards the chemistry major, somewhat through a process of elimination. In my Junior year, I worked in the labs of Prof. George Whitesides, and was amazed at the breadth of interesting projects going on in his lab, and the range of activities in which he was involved. This was my first real exposure to university research chemistry, and I was hooked! The idea of being able to solve difficult and interesting real-world problems using a scientific discipline — chemistry — appealed to me very much. It also appealed to me to “spend the rest of my life in school” and to have opportunities to travel widely, and to make friends and pursue scientific collaborations around the world. And, even as a college student, it seemed great to be able to pursue problems of one’s choosing, and to have very little oversight in the form of a boss. I had so much fun doing chemistry research in college that it became clear to me that I should continue. I applied to chemistry graduate school and found a great mentor in Prof. Harry Gray at Caltech, who inspired me to pursue a career in chemistry.2. If you weren’t a chemist and could do any other job, what would it be - and why?I would love to try many different careers, but one of my first loves was baseball. I think it would be fun to be a Major League baseball pitcher. I played Little League as a kid, and always particularly looked forward to game days when I was pitching. The pitcher has the opportunity to control the outcome of the game, and time slows down when you’re on the mound. I love the feeling of needing to make every pitch count, and all of the mental challenges of trying to compete and win. In the off-season, baseball players also have the opportunity to do a lot of good in their communities.3. How can chemists best contribute to the world at large?That’s a great question. One of the things I love most about a career in chemistry is how many different doors it opens. Indeed, chemistry is great training for many undertakings. The general public forgets, I think, that science can be a wealth- and health-creating enterprise. Chemists have improved the lives of millions of people by developing new drugs, and chemists have created many thriving companies. Chemists are also great educators--of students in the classroom and citizens at large. Many university presidents are chemists, perhaps due to the administrative aspects of running a lab. Collectively, chemists can do a lot of good by designing new drugs, new materials, and new processes that will make the world a cleaner, healthier, and more sustainable place, and in the process employ millions of people. But, the world also desperately needs chemistry representatives to go into politics, and fill positions at the highest levels of government. The planet is facing major challenges in energy and healthcare, and chemists must take the lead in addressing these problems, both individually and collectively.4. Which historical figure would you most like to have dinner with - and why?I love studying history, particularly the history of science. I think it would be wonderful to have dinner with Albert Einstein, and get some insight into how he observed the world and solved problems. It also seems like he had a great sense of humor, and I suspect the dinner would be very entertaining.5. When was the last time you did an experiment in the lab - and what was it?I occasionally perform experiments using my lab’s confocal microscope. For example, I’ve done some experiments recently that involve developing a fluorescent probe to study how anesthetics work. Research is great fun, but I find that it can be frustrating when I don’t have much time to devote to it. I generally have more fun these days watching my graduate students and postdocs conduct experiments in lab. When things go well, I get to see lots of good data!6. If exiled on a desert island, what one book and one CD would you take with you?Assuming I didn’t need to learn a new language or unusual skills to survive, I would probably take a copy of Shakespeare’s complete works, as there would be a play for every occasion — sad, funny, historical, or strange. It’s unlikely that I would bring a CD. When I’m alone, I usually enjoy the peace and quiet. If I were in exile, it’s likely I would try to keep doing whatever it was that had led to my exile!Ivan Dmochowski is in the Department of Chemistry at The University of Pennsylvania and works on developing chemical tools for addressing long-standing problems in biology and materials science. Posted by Neil Withers at 06:36 AM | Permalink | Comments (2) | TrackBacks (0) Top 10 Research Highlights of 2008 So, with 2008 drawing to a close, we thought we'd select our favourites from the chemistry we've covered this year. The five of us editors had two picks each, so here's our top 10 (in no particular order):GavIon transport: Testing the waterEigen complexes, Zundel complexes, Grotthuss mechanism: there’s some great terminology related to water structure but we still don’t fully understand it! This paper was a good example of how fancy spectroscopic techniques can be used to understand just what is going on with the seriously speedy diffusion of hydroxide ions in water.Catalytic hydrogenation: Guided by theory The importance of heterogeneous catalysis to the chemical industry really can’t be overstated, so one of my favourites this year was this theoretical paper by Jens Nørskov and friends. They use computational methods to seek out the best (and economically viable) alternatives to expensive industry-standard hydrogenation catalysts. Watch out for a review in this area next year!StuNobel Prize 2008: Green fluorescent proteinOver the past few years GFP has been a favourite pick in the numerous 'what will win the Nobel Prize in Chemistry this year' lists. And now it has — and deservingly so. The question is, what will be the consensus pick for the next few years?Coordination polymers: Ringing the changesA research highlight that combines two of my favourite things — beer and football...no wait, I mean coordination polymers and Borromean rings.SteveOrganocatalysis: Making light work of itMost organocatalytic reactions involve typical polar reactions between one nucleophilic and one electrophilic partner. Not only is this approach radical, solving a long-standing problem in asymmetric synthesis, it was also the easiest headline I wrote all year.Enzyme catalysis: Enantioselectivity evolvedEveryone knows that enzymes are good catalysts, but the search for the right enzyme can be a long one. I love the idea of training an enzyme to do what you want – and biasing evolution by using a clever reaction design is probably the ultimate way of achieving this.AnneChirality: Handed overChirality can be a somewhat tricky property to introduce in materials. Here, the chirality of organic linkers is preserved and passed on to the bulk of an organosilicate material directly during the synthesis — a very elegant chirality transfer.Molecular network: Random order Check out these molecules that, when adsorbed onto a surface, form hexagonal ‘holes’ in a regular array regardless of how they arrange themselves. This leads to an ordered — yet aperiodic — molecular network. NeilProtein chemistry: Handy crystallizationThe combination of painstaking chemical synthesis of both forms of the protein, followed by the conceptual leap to crystallise both of them in order to get the X-ray structure, made these two papers extremely impressive. And when you add the cool application – antifreeze proteins to help preserve donated organs — it adds up to work that made me say ‘I wish we’d published it!’Superconductivity: The good samariumIt's solid state inorganic chemistry, it's superconductivity — I love it. This is just a sample of the 'gold rush' of work that was triggered by the pnictide superconductors.And slightly less seriously, here are our top 10 Research Highlight headlines of the year:Come on sileneThe magnificent sevenCage closedThe good samariumHeterogeneous chemistry on MarsAll features great and smallKnot your usual moleculesSupersize sandwichThe 39 stepsCaught in a trapAnd many thanks to Jane for copy-editing and Dipti for publishing everything for us all year!NeilNeil Withers (Associate Editor, Nature Chemistry) Posted by Neil Withers at 11:46 AM | Permalink | Comments (0) | TrackBacks (0) All I want from Santa... One year in high school I was a 'secret Santa', where I was anonymously responsible for getting presents for another person. Last year in the NPG office we had a gift exchange where people randomly got silly things and then we played an elaborate game to decide who got what. There are many kinds of these little holiday adventures, yet none to do with science. Why not? I could imagine a lab surprising another lab by cleaning all their glassware, or the delivery of a big drum of silica with a red bow on top. What about people getting each other gilded, monogrammed pipettes? Or making up those paper coupons that are alternately endearing and/or scream out 'I didn't know what to get you' that are good for one hour of literature searching, or one extraction, or the use of the last unbroken, unscratched 50 mL RBF (if there is even such a precious, precious thing)? Perhaps graduate students could arrive to find tiny presents in their lab coat pockets from the science Santa? Maybe that only works if you leave them by the hood...Anyway, I was thinking recently about what science presents I wanted for the holidays, and suddenly realized "What could be better than the January issue of Nature Chemical Biology?!?" We've got not one, but now two pages of research highlights. We've got 10 crystal structures, 8 protein blobs, and 2 mice on our table of contents. We've got single amino acids, peptides both short and long, and proteins doing all kinds of cool stuff. Not only is the issue full of goodies, but we give you a couple of other things to look forward to in the year to come. With all this inspiration, I think it's time to look for packages of reagents that will fit on a sleigh... Catherine (associate editor, Nature Chemical Biology) Posted by Catherine Goodman at 01:54 PM | Permalink | Comments (1) | TrackBacks (0) They'd none of them be missed – why 20 amino acids and not 15? Posted on behalf of RetreadMaking DNA is metabolically expensive. 4 ATPs are consumed making adenine (and that's even when you start with 5 phosphoribosyl alpha pyrophosphate – PPRP). This is why parasites living inside cells have such small genomes. As soon as they figure out a way to get the host to do their metabolic work, they jettison the (now redundant) DNA. The leprosy organism which lives inside cells sheathing nerve processes has only two-thirds the DNA of its cousin, the tuberculosis organism. There are many similar examples and not all are bacterial. As you know, 'the' genetic code is made of nucleotides which come in four varieties (abbreviated A, T, G, C). There are 16 possible combinations when nucleotides are taken 2 at a time, 64 combinations taken 3 at a time. 64 combinations is clearly is overkill for just 20 amino acids. So most amino acids have multiple combinations of 3 nucleotides (called codons) which code for them – these are the synonymous codons. Two amino acids (leucine, arginine) have 6 synonymous codons, 2 have none (e.g., just one codon – methionine and tryptophan), the rest fall inbetween. If proteins contained only 15 amino acids, you could cut genome size by one-third – that's 4 billion or so ATPs/cell if the 3 other nucleotides are as expensive to make as adenine. As the late senator Dirksen used to say – a billion here, a billion there, pretty soon you're talking real money (this was in a older, happier pre-bailout time). Why 15 and not 16 amino acids? Because you need a codon to tell the machinery when to stop – such codons were known as 'nonsense', back in the day when all the genome was thought to do was code for protein. Look at the side chains of the 20 amino acids with your chemist's eye. Some are so similar as to be redundant. Glutamic acid and aspartic acid are chemically the same, differing only by a methylene group – get rid of one. Glutamine and asparagine are just the amides of the two acids (why they aren't called glutamide and asparamide is beyond me). Get rid of one of them. Similarly threonine and serine differ only by an extra methyl group. Not only that but the several hundred different enzymes which add phosphate to them (inappropriately called kinases) don't bother to tell them apart – get rid of one. Do we really need 4 different hydrocarbon side chains (methyl, isopropyl, sec-butyl, isobutyl)? Maddeningly sec-butyl belongs to isoleucine, and isobutyl belongs to leucine. Get rid of two of them – probably a long one and a short one. Other chemists might choose different amino acids to let go.Removing these 5 amino acids from the total cuts the DNA required to code for them down by one-third, saving all that synthetic ATP. Of course, synonymous codons disappear in the process. Nonetheless, we should be able to build pretty decent proteins from the 15 amino acids we have left. No chemical functionality present in the original 20 has been lost. Clearly this hasn't happened in the real world. Just why not is probably a matter of history, and an endless source of armchair speculation (like this post). Could there be a reason for all this coding redundancy, or at least could there be mechanisms to keep it in place? I think such mechanisms exist, but you'll have to give up the protein-centric notion that all DNA does is code for protein. Even better, there is excellent recent hard experimental data to back this up. But that's the subject of the next post. Posted by Stuart Cantrill at 07:42 AM | Permalink | Comments (4) | TrackBacks (0) Crosspost: What element do you want for Christmas? Pop over to the Big Nature news blog The Great Beyond to see what element people want for Christmas...there's a video too.Personally, I'd like some helium, to keep everyone entertained with squeaky voices while we're waiting for the turkey to cook. Posted by Neil Withers at 09:39 AM | Permalink | Comments (2) | TrackBacks (0) NChem Research Highlights: Chiral alcohols, entrapment and nanotube motors I'm dreaming of...Research Highlights.Making tertiary alcohols (ones without any hydrogen atoms attached to the carbon) with controlled chirality is a lot trickier than making other chiral species like secondary alcohols — those methods often rely on the difference in size between hydrogen and the other substituent. But now, using a simple method allows the choice of two achiral reagents to control which enantiomer is formed. And don't forget to check out the News and Views article that Andy sold his soul so you can read it for FREE (for a week).Germanium is an element in the no-man's land of semi-metals between metallic and non-metallic elements, but it's still not really a metal. And non-metals have rarely been observed as dications without a lot of accompanying ligands. But now dicationic germanium has been trapped inside a cryptand cage and caught with no clothes on. Which is a great amount of effort to go to in order to let Gav use the headline Caught in a trap.And my prayers have been answered: a paper with supplementary info movies that show what's going on. So, go and read Tim's highlight about nanocapsules shuttling up and down inside carbon nanotubes, then watch the videos.And finally...even though we haven't published any issues yet, and won't have an impact factor until about 2011, when we're out and about we still get asked what we think Nature Chemistry's magic number will be. Who knows?? Perhaps by then Thompson ISI will be using the corrected impact factor, as suggested by our heroes over at PHD comics.NeilNeil Withers (Associate Editor, Nature Chemistry) Posted by Neil Withers at 05:11 AM | Permalink | Comments (0) | TrackBacks (0) Search this blog: Subscribe Subscribe to this blog's feeds: Blog PostsBlog Posts with Comments [What is this?] Author Andrew Mitchinson Catherine Goodman Gavin Armstrong Joshua Finkelstein Katharine Sanderson Neil Withers Other Authors Stephen Davey Stuart Cantrill Features Chemiotics Conference reports Confessions of a former chemist Journal Club Journal journeys Materials Girl NChem research highlights Other Columns Prospective Professor Reactions Rookie Rocky Sugar Daddy Reactions - Julie MacPherson Reactions - Luisa De Cola Materials Girl: The bell curve doth toll NChem Research Highlights: Biosensing dyes, strong biomimics and levitating beads Reactions - Ivan Dmochowski Top 10 Research Highlights of 2008 All I want from Santa... They'd none of them be missed – why 20 amino acids and not 15? Crosspost: What element do you want for Christmas? NChem Research Highlights: Chiral alcohols, entrapment and nanotube motors Out of 923 total comments, the most recent were: TCO on CFCs: Confessions of a former chemist TCO on Materials Girl: The bell curve doth toll MG on Materials Girl: The bell curve doth toll Heather Etchevers on The Sceptical Twitterer? 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