Look my way

Posted on 30 Sep 2008 by Catherine Goodman

I’ve been chatting with some friends these last couple of days, and we’ve developed a new* theory that could generally be applied to chemistry/chemists, so I thought I’d share. The idea is that there are two kinds of people in the world: those who know things and those who look things up. The first category also includes the subgroup ‘people who don’t know anything but pretend that they do’ (which is a topic for another day).

It’s obvious that, in the modern age, it’s becoming increasingly easier to look things up. It used to be that you had to go to college or a library (or perhaps to someone’s house who had a set of encyclopedias) to learn about the Diels-Alder reaction or the physical properties of mercury. But now you just use a book you have handy, or the internet, or even your phone to find out almost anything instantly. I assume this is why I’ve never been asked to memorize the periodic table (aaaaah! Chemistry sacrilege!!). Anyway, this inspires a few questions:

1. Given the extent of information that is now available, is it even possible to be a person who knows things anymore, or are we all just people who look things up, with some people looking up less things than others?

2. Does it matter if we don’t know things, and just look things up? What information is worth knowing?

3. Do we specifically know less because it’s easier to look things up? Meaning, do our minds subconsciously say “what’s the point in really learning the preferred ionization state of Iridium if you can get the information in 3 seconds and instead use those neurons to remember what time your favorite TV show is on?” And if that’s the case, can we reverse that? Do we want to?

I don’t have the answers to these questions. It is obvious that it’s hard to know where to look some things up if you never learned them in the first place, or at least how to use that information once you have it if you never had a place for it in your overall world view. … Anyway, I’m curious to know what you guys think.

Catherine (associate editor, Nature Chemical Biology)

OK, you probably have all already thought of this. But, that should mean that your comments are even more thoughtful and inspired??

Where’s my Nobel fix?

Posted on 30 Sep 2008 by Stuart Cantrill

It’s getting to be that time of year again…

With no odds (or anything else for that matter) posted on ChemBark and Thomson seemingly not making any predictions this year, where do I go for my Nobel Prize gossip?

Well, it seems as though medGadget has come to the rescue, and is running a ‘Guess-A-Nobel’ contest’ – just leave a comment on their blog post with your picks for who will win the Chemistry (or Physics or Physiology/Medicine) prize and you could win an iPod nano (or two or three).

Amongst the guesses for the chemistry prize, Whitesides is getting some attention, with two votes, and Tsien also has two votes (along with others for using fluorescent tags to monitor proteins). Ken Houk – one of my former UCLA colleagues – also gets a mention.

One of the suggested winners is a bit of a long shot if you ask me – not only has John Pople already won the Nobel Prize in Chemistry for his development of computational methods (and winning two Nobels is rare – Curie, Pauling, Sanger and Bardeen are the only individuals to achieve this feat), but he died in 2004, which is the bigger handicap, because Nobel Prizes aren’t handed out posthumously.

So, go along to medGadget and leave your picks – and while you’re at it, leave us a comment here to let us know who you think will win – no iPods up for grabs, but the respect of the Sceptical Chymist audience awaits…

UPDATE: Thomson must have put up their picks today… – they weren’t there yesterday when I checked. They’ve gone for Lieber or Matyjaszewski or Tsien (doesn’t seem fair that they get three picks).

Stuart

Stuart Cantrill (Chief Editor, Nature Chemistry)

Chemiotics: Auditing P-Chem

Posted on 30 Sep 2008 by Stuart Cantrill

Posted on behalf of Retread

Why would an ex-organic chemist, retired MD do that? The P-chem you need for organic chemistry is pretty simple. You can look at most reactions and figure the overall entropy and enthalpy, and we get pretty good at figuring out delta-deltaG and manipulating it to get reactions to go the way we want.

Well, the answer is because nearly all the really interesting questions in cellular biology involve physical chemistry. Look back at the post of 20 March where throwing a growth factor at a cell resulted in a two fold change in phosphorylation in 924 of 6,600 phosphorylatable sites in 2,244 different proteins. We have some 478 enzymes (called kinases) to accomplish this reaction. Why so many? Because most kinases have a limited number of substrates. Studying the phosphorylation reaction itself (e.g. the classic chemistry) tells you very little. What determines which kinase associates with which substrate? That’s exactly where physical chemistry comes in. The association of one protein with another doesn’t involve covalent (or even ionic) bonds. It’s mostly van der Waals and hydrogen bonding, along with solvent effects. Pure P-Chem.

Non(classical chemical) bonding protein association is crucial in the normal life of the cell (and sometimes in its death). Consider the mediator complex. It is required for the molecular machines which transcribe DNA into RNA (the three RNA polymerases) to actually do their work. Depending on the organism, the mediator complex has between 20 and 30 proteins and a mass of 1-2 megaDaltons. Also, RNA polymerase II itself isn’t just one protein, but 12 (in yeast) with a mass of 500 kiloDaltons — again held together by noncovalent interactions.

A personal reason for studying P-Chem is the protein folding problem, where nary a covalent bond is formed. I’d certainly like to get up to speed to read the literature and find out if the ‘potential energy funnel’ is more than a fancy way to say that (biologic) proteins fold into their final shape quickly. As docs, we do this all the time. Consider the diagnosis of idiopathic thrombocytopenic purpura. Impressive, n’est-ce pas? However, all it means is that you are bleeding because you don’t have enough platelets (a type of blood component) and we don’t know why.

We’ve already been through the 3 laws of thermodynamics, the second introduced by Carnot’s brilliant analysis of the changes in state of an ideal gas as it went around his cycle, and his discovery (better construction) of the concept of entropy. Even after nearly 200 years, the power of his thought is impressive. I doubt that most of you have the time, but you will be similarly impressed with the stunning power of Darwin’s mind if you read “The Origin of Species”. All of you have more background (just by inhaling the zeitgeist) than he did. If you really have a lot of time, read “Darwin’s Ghost” by Steve Jones along with Darwin. Jones updates "The Origin .. " to 2000 chapter by chapter. Although Jones is an excellent writer, Darwin wins each chapter hands down.

Finally, the course is being given at the local state university. It’s very gratifying to see that state universities continue to function as the giant engines of social mobility that they were for my parents’ generation, educating immigrants and the children of immigrants. The present crop of students isn’t predominantly from eastern and southern Europe as my father’s class was at Rutgers 80 years ago. But immigrants they are, and 3 of the students I’ve spoken to were born in Nigeria, Haiti and Poland.

NChem Research Highlights: Ultracapacitors, nitrogen cleavage and applied asymmetric catalysis

Posted on 29 Sep 2008 by Stephen Davey

This week both Neil and Gavin are away, although this time they are both working! Neil is attending the 6th International conference on Inorganic Materials in Dresden, and Gav is yet to return from China, having been at TACC 2008 (computational chemistry) and is combining his trip with some visits to labs close by.

So down to business with this weeks research highlights – Tim is first up writing about the an energy storage device that utilizes the special properties of graphene.

Gav writes about computational investigations into a catalyst that cleaves the immensely strong triple bond in dinitrogen – very topical given the conference he has been attending.

And…me, I’m covering a total synthesis that provides a tough test for no less than three pieces of synthetic methodology.

Finally a mention has to go to the cover of this week’s Nature, with its special feature on the US election (see the story in The Times). To get the full benefit of this cover though you’ll need a print copy (open it right out so you can see the front and back covers side by side – a truly fantastic accident).

Steve

Stephen Davey (Associate Editor, Nature Chemistry)

Reactions: Saiful Islam

Posted on 26 Sep 2008 by Neil Withers

1. What made you want to be a chemist?

I remember when about 15 years old being excited about a project on growing crystals and also going to the Royal Institution (London) to hear an inspiring lecture on photochemistry given by the late Professor George (Lord) Porter. Until then I hadn’t realised that you could do chemistry as a full-time job.

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

Dream job: footballer (soccer player) down the left-wing. Other job: get more involved in politics (also on the left). Sadly the distribution of wealth/power in the world is still very unequal. Most positive democratic change in the 19th and 20th centuries would not have happened without people getting involved in progressive struggle.

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

(a) Probably most/all chemists already contribute by advancing knowledge. Chemistry underpins so much of current science. Some obvious wider contributions to be made are: sustainable energy, solutions to disease (e.g. HIV, malaria, cancer), clean water and reducing pollution. In my field, fundamental materials chemistry is key to future breakthroughs in clean energy conversion and storage.

(b) Engage with the public (and popular media), promoting the importance of evidence/reason over superstition. To some, the word ‘chemical’ has become synonymous with poison. But Joe (and Josephine) Public should know that all matter, animal, vegetable or mineral, is made up of chemicals. They should imagine what it would be like without chemicals: no food or medicines; no TV or computers; no plastics or sex hormones. The list is endless. Indeed, without chemicals there would be no life!

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

Charles Darwin – to find out how he got his big, powerful idea (of evolution by natural selection), and how he dealt with religious challengers. Outside science, Mahatma Gandhi – a remarkable man in the successful struggle against British imperial rule. Around the second world war, he was asked by a journalist what he thought of western civilisation. He replied: “I think it would be a good idea”.

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

Not sure if this counts, but since my research is largely computational chemistry, I still dabble in some simulations. I wasn’t very good at practical organic chemistry during my undergrad days at UCL (in the early 80’s). Last experiment in the lab: solid-state synthesis of spinel oxides (NiMn₂O₄) during my PhD.

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

Fiction: the rich, dazzling “One Hundred Years of Solitude” by Gabriel Garcia Marques. And a collection of 20th century poetry (W.B. Yeats, W.H. Auden, P. Neruda etc).

Non-fiction: “Unweaving the Rainbow” by Richard Dawkins; essential reading for conveying the beauty, wonder and excitement of science.

CD: The Smiths “The Queen is Dead” with the Morrissey/Marr classic track “There is a Light that Never Goes Out”. I can play it really loud and not disturb the neighbours! To make me laugh, I would also like the CD of Monty Python’s “Life of Brian”, which ends appropriately with the song “Always Look on the Bright Side of Life”.

Saiful Islam is in the Department of Chemistry at the University of Bath, and works on aspects of solid-state materials chemistry with emphasis on atomic-scale modelling of new materials for fuel cells and lithium ion batteries.

Materials Girl: Living with chemists

Posted on 25 Sep 2008 by Stuart Cantrill

Posted on behalf of Materials Girl

The past summer was a highlight for me, not only because of the research I did during my internship at a Large Company, but also due to the people I met there. In addition to co-workers being friendly and helpful (and the building wonderfully air conditioned in the 100+ degree weather), my fellow interns were exceptionally bright, scientifically minded (not just intelligent), sociable and interesting. Rarely have I lived or worked with students who could just as easily and happily talk about synthesis and characterization as they could sports and movies.

While attempting to strain pasta without a sieve, one [male] intern bemoaned the difficulty of the task and called for a desiccator. Any nerdy shirt that I wore would be appreciated, as opposed to causing strange looks to be cast in my direction. We could tie-break a card game by whoever most quickly stated the atomic mass of element ‘X’… And despite all that, we could be considered normal by the general public – we were musicians, collegiate athletes, cooks, a frat boy, and presidents of clubs unrelated to science. We attended midnight showings of movies, showed up for work half-asleep and visited tourist traps on the weekends. One of the guys drove well over 2000 miles in a truck, just to bring his plasma TV and Xbox.

I like to think that we dispelled the stereotype of chemists being smelly, wild-haired nuts in stained lab coats, or under-fed nerds living in library study lounges. Brilliance is hiding under the guise of normalcy, between talking about the awesomeness of molecular imaging and of playing Halo.

It’s now nearing the beginning of my fall quarter. I am once again one of the 1000+ students living in my particular residence hall. My roommate is a second-year music major, and we get along splendidly; lately we’ve united in griping about how obnoxiously loud the freshmen have been late at night – do they really need to “party” in the dorm room next door? Soon I shall be balancing senior year coursework and deciding whether to apply to grad schools asap (and what to study), or to take a year off and work…

Ernest Eliel

Posted on 24 Sep 2008 by Stuart Cantrill

It is with some sadness that I note the passing of Ernest Eliel – a stereochemistry giant in my eyes – and many others I presume. His book – Stereochemistry of Organic Compounds – (later editions written with Wilen and Mandel) was, along with March and Vogel, one of the essential chemical bibles to be found in the lab during my PhD work. My copy is, even now, sitting on the shelf behind me here in the Nature offices… and it still has the price tag on the back – £29.95 apparently, which is peanuts compared with today’s prices!

I leave you with a quote about Eliel from Fraser Stoddart – whose only book (to date) is on the stereochemistry of carbohydrates – who shared the following sentiment with me in an e-mail late last night:

He was one of my heroes. At his best in the 70s, it was an awesome experience to listen to him in full flight. Above all, he was a very nice person unlike a lot of the insufferable barons who were around at that time.

Stuart

Stuart Cantrill (Chief Editor, Nature Chemistry)

RSC Roadmap

Posted on 23 Sep 2008 by Neil Withers

As you’re reading this, I bet you’ve also read some of our Reactions interviews. In amongst the ‘Desert Island Discs’/lifestyle questions is number 3: How can chemists best contribute to the world at large? The answers to this weighty question are always fascinating and quite wide ranging.

Now, the Royal Society of Chemistry (the UK’s professional body and learned society for chemists – yes, they did just try to rename the LHC) is trying to put together a roadmap to answer the question – or at least how they prioritise their output to help achieve such a goal. The process has been going on since March, and is now in its second online consultation period.

Anyone – not just RSC members, but any chemistry stakeholder – can register at the website and get their thoughts taken on board.

The thing that strikes me is that the level of detail is pretty impressive. Each of the seven main themes (such as energy, water, public engagement and trust) is further broken down into subthemes, which are then taken down to the nitty-gritty. For instance, picking the first option each time: Energy:Biofuels:Additives to maximise biofuel efficiency group.

After another round of online consultation in November, the final report will be submitted to the RSC General Assembly before the roadmap is launched in December and implementation begins. It looks as if the RSC is going to a serious amount of effort to make sure it’s going in the right direction – I’ll be interested to see what the outcomes are in December. (Although hopefully in a very condensed form – the ‘summary report’ of the first phase is 90 pages!)

Neil

Neil Withers (Associate Editor, Nature Chemistry)

NChem Research Highlights: Organo-photo-catalysis, funny fullerenes and anti-freeze proteins

Posted on 22 Sep 2008 by Neil Withers

Here are this week’s pick of the (chemistry) pops: Research Highlights

In a smooth (and completely serendipitous) link to big Nature‘s insight on small molecule catalysis, we feature a new step in catalysis: merging the features of organocatalysis with photocatalysis. The paper’s by David MacMillan, who also has a commentary in the insight here.

Next up, we all know that C₆₀ is a wonderfully symmetrical molecule, shaped like a football/soccer ball, right? Well, that’s only one of 1812 possible isomers of C₆₀, and two of the less symmetrical ones have now been made. They’re not as pretty as buckminsterfullerene, but you can functionalise them in more specific places.

Here in the northern hemisphere, leaves are starting to change colour, but it feels a long time until we’ll need to dig out the anti-freeze. Some animals survive sub-zero temperature thanks to anti-freeze proteins, but how they work hasn’t really been well understood. Now molecular dynamics simulations have shown that it’s the ordering of the water molecules around the protein that disrupts the crystallisation.

And finally…want to build a space elevator? Carbon nanotubes to the rescue! Is there anything they can’t do…?

Neil

Neil Withers (Associate Editor, Nature Chemistry)

Taking solace in synthesis?

Posted on 19 Sep 2008 by Stephen Davey

Reading my newspaper on the way to work this morning, I was surprised to discover that Jonny Wilkinson – England rugby hero for those that don’t know – likes a bit of quantum physics. Apparently, he was always full of self-doubt until he discovered Schrödinger’s cat!

I subscribe to the theory that if you claim to fully understand quantum physics then you’ve missed the point, so quite what he means by this you’ll have to find out in his new book, but it set me to thinking: does anyone take solace in chemistry? Personally, I like a good total synthesis, but it’s more likely to make me wonder if I could ever have come up with that particularly clever rearrangement or new methodology, than to solve any thoughts of inadequacy.

Do you have a favourite piece of chemistry to think about when you need a bit of reassurance? How about some chemical reaction dynamics (Gav?), or perhaps you enjoy a good crystallography table (Neil?). We’d love to hear from you.