Birth of a legend?

First of all, I hope you’ll all excuse the somewhat overreaching title of this post – the coincidental timing of this and the previous post, however, seemed to merit some comparison.

Second of all (and the point of this post): The National Academy of Science has elected 72 new members and 18 foreign associates (which is the maximum that can be elected in any given year, apparently), of which a pleasantly surprising number are chemists (such as Frances Arnold, Steven Boxer, Steven Buchwald, Ken Dill, Michael Grunstein, Eric Jacobsen, and Tim Swager). Go chemists! It is perhaps worth noting, however, that only a small number of these folks have mustaches (which bodes well for Ken Dill; to be explained later).

The NAS site also tells us that ‘election is considered one of the highest honors that can be accorded a scientist or engineer’. What do you guys think? Are you more impressed by someone who is in the HHMI? Or someone who’s won a Cope Award, the Priestley Medal, or the Nakanishi Prize? How do you think the Kavli Prize will stack up (to be awarded for the first time in May)? Do you think NAS membership (or, in fact, most of these awards) would be more or less impressive if the rationale for who was picked was more transparent? Or do you find that the people doing great work come to be well-known and well-respected regardless of these external trappings?

In any case, it’s clear that chemists are doing some moving and shaking (and shaving) these days. Congratulations to the new NAS members.

Catherine (associate editor, Nature Chemical Biology)

Sex and the chemist

What is it that chemists really have on the brain? To answer the question, try clicking on this link to a book review in the New York Times, and have a look at the molecular structure to see if anything leaps out at you.

So what did you see? If you’re anything like the chemist that wrote in to the New York Times to complain, you’ll have spotted that some of the carbon atoms appear to have formed five bonds. Fair enough. But did you notice that the molecule is actually spelling out the word ‘sex’?

Credit goes to the Newsmakers section of Science for telling this story of a chemist who was prepared to admit that he missed the point. I have to say, I think I’d have missed the point of the graphic too…

Andy

Andrew Mitchinson (Associate Editor, Nature)

Reactions – Donald Tomalia

1. What made you want to be a chemist?

My curiosity! Born with a strong dose of curiosity, I found early in life that this drive addicted me to chemistry. I found that no matter how many problems were solved, their solutions led to so many more new questions. That feature alone has made chemistry an insatiably exciting hobby, my “best friend”, and a lifetime career.

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

Probably a landscape architect. Firstly, I enjoy performing physical work. Secondly, I intuitively enjoy thinking about the unique function, dynamics and possible benefits that architecture contributes to structure at the pico-, nano- and micro-scale level. I believe one should expect to find similar issues at the macroscopic level. Undoubtedly, that is why I enjoy horticulture/gardening so much as a hobby.

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

Chemistry is so pervasive in life; the environment, our health, society and even our presence in the universe. As practitioners of such a ubiquitous discipline it is our responsibility to be certain that our efforts are positive and for the good of all these issues.

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

Undoubtedly, John Dalton, Manchester, England (1766- 1844). I have always admired his courage, vision and commitment that led to his “New System of Chemical Philosophy” (1808). His vision and efforts launched our traditional chemistry platform from which all chemists have enjoyed, enhanced and derived benefits. I toast to Dalton on each of my birthdays since we share the same birthday (September 5), however, 172 years apart.

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

I conducted a dendrimer synthesis and a photochemical experiment within the past six months. I was curiosity driven by why a particular nanoscale dendrimer we had synthesized exhibited extraordinary fluorescence properties yet possessed no traditional fluorescent chromophores. At this time, these fluorescent properties have been confirmed; however, I still do not have a complete answer as to why they exhibit fluorescence.

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

My favorite book is The Notebooks of Leonardo da Vinci. I never cease to be amazed by his extraordinary discipline, articulation and keen observations on all aspects of life. My favorite CD would contain all the compositions/works of Wolfgang Mozart. I always seem to find fresh inspirations, excitement, new ideas and fulfillment in the presence of his unique notes, scales, musical patterns and sounds.

Donald A. Tomalia is Director of The National Dendrimer & Nanotechnology Center and Distinguished Research Scientist/Professor at Central Michigan University. He is engaged in research with a focus on nanomaterial synthesis (i.e., dendrimers, metal nanoclusters, etc.), their nano-stoichiometries, nano-sterics and the identification of nanoperiodic reactivity and assembly patterns associated with these well defined nanomaterials to produce higher complexity.

Nature Chemistry research highlights

Each Friday, the Nature Chemistry website will be updated with three new research highlights about interesting work that has caught the attention of the editors, here is this week’s line up:

Heterogeneous catalysis:

Scanning transmission electron tomography is used to create 3D images of active sites in nanoscale catalysts

Surface chemistry:

Subsurface carbon and hydrogen have an important role in selective palladium-catalysed alkyne hydrogenation

Alkaloid biogenesis:

Indole alkaloids extracted from closely related fungi lead to questions about how their biochemical pathways have evolved

The highlights are free to access, but you need to have a (free) nature.com account.

Stuart

Stuart Cantrill (Chief Editor, Nature Chemistry)

Journal journeys: Day 84, Team Chemistry

Apologies for not posting in Journal journeys as much as I would have hoped – the one overwhelming feature of setting up a new journal is that it leaves very little time to blog…

I did want to take 10 minutes, however, to let you know that Nature Chemistry now has an editorial team – although it’s not complete just yet (we’re also looking for someone to be based in the Tokyo office). Brief editor bios (and their stunning headshots) can be found here on the new Nature Chemistry website. Each editor will also write their own Reactions piece in the coming weeks, so that you’ll get to know them a little better – and perhaps I’ll even get around to writing one myself sometime soon.

As part of the new website, we’ll also be publishing three new research highlights each Friday*, covering what we think are important papers appearing in the literature. These will be freely available on the Nature Chemistry website (although you may have to register for a nature.com account to access them).

*The first batch go live – with the new website – on a Thursday, not a Friday, because as I have learned, never push a new product live on a Friday… it doesn’t give you too much room for error before the weekend hits…

Stuart

Stuart Cantrill (Chief Editor, Nature Chemistry)

I’d like to teach the world to do a perfect TLC…

In case you weren’t aware, today is ‘World Laboratory Day’. This website tells us that “World Laboratory Day celebrates the place where great discoveries, inventions, and medical cures are born. It’s also where mad scientists dwell.” I was actually going to go in a completely different direction upon hearing the name of the holiday – something more to do with celebrating your international collaborators, thanking that company 3,000 miles away for making the small molecule you want to do assays with, or sharing the candy that someone brought back from a recent conference overseas… I also have to take issue with the poor grammar of the sentence (gosh, I really have become a nerd!), which suggests to me that mad scientists dwell in World Laboratory Day, which seems a bit unusual (unless World Laboratory Day is frozen in time like Brigadoon, perhaps? Ok, enough randomness.).

Although a lot of screen time is given to mad scientists in movies, TV shows, and even the news (nothing says ‘Watch the 11:00 news’ like a scientist raving about time machines or cloning him/herself), I don’t see a lot of true scientific content devoted to these beloved figures. For example, a friend of mine suggested there could be a journal just for research from mad scientists (plots to take over the world, new kinds of poisons, etc., which would have the side benefit of making it extremely easy to fight terrorism (by arresting all the corresponding authors)), but there could also be conference sessions or entire conferences devoted to ‘Ways to create living matter using a corpse’s brain’ or ‘How to accidentally change the size of your family members so that they get lost in your back yard and hilarity ensues’. What about special grants programs for people working on cloning dinosaurs into frog eggs, or switching faces back and forth? Really, I think this is a whole section of the science community we’ve been ignoring for too long. Unfortunately, most of these ideas don’t really tie in to chemistry very well… perhaps we chemists are just too normal for all that silliness?

Anyway, I’m off to see if I can find some nice European chocolate. Hooray for globalization!

Catherine (associate editor, Nature Chemical Biology)

Chemiotics: Why should a protein have one shape?

Posted on behalf of Retread

Well of course they don’t, but the proteins we know the most about (because they can be crystallized and their structure determined by X-ray diffraction) do have a shape. Sperm whale myoglobin, the first protein to have its 3-dimensional structure determined, showed that this couldn’t be the whole story. Sperm whales (air breathing mammals after all) use their myoglobin to carry oxygen during their hour-long dives down to 1000 meters. Kendrew and Perutz’s crystal structure showed no way for oxygen to find its way in to the embedded porphyrin ring. Amazingly, the 153 amino acids of myoglobin must themselves breathe to let the oxygen in.

All it takes to denature (seriously change its tertiary structure so it is no longer functional) a protein of 100 amino acids is 10 kcal/mole (Voet & Voet – Biochemistry 3rd Edition p. 258). That’s two hydrogen bonds – not much.

Sight your eye at the alpha carbon of one of the amino acids of this protein, looking toward the carbonyl carbon. There are three conformational energy minima the carbonyl can adopt. That’s potentially 3^99 = 10^48 conformations (clearly an overestimate because of self intersection, but still, a huge number). Yet to be crystallizable, this protein must choose just one of them, and it must be lower in energy by 2 hydrogen bonds than all the rest.

In addition, to get to this single structure, the protein can’t possibly sample all the conformations available to it. The rotation barrier of ethane is 12 kJ/mole and a barrier of 73 kJ/mole allows a rotation rate of 1 per second, and every 6 kJ changes the barrier by a factor of 10 at 25 deg C (Clayden et al. Organic Chemistry pp. 450-1). So the maximum rate of rotation of ethane is 10^11 per second (at a body temperature of around 37 deg C) rather than 10^10 at 25 deg C. This is clearly an upper bound on the rotation rate as the mass attached to the alpha carbons of a protein will make the rotation far slower, but let it pass (that’s why I chose ethane in the first place). That’s 10^37 seconds to sample the conformations available, far longer than the age of the universe. This is the Levinthal paradox.

So for the crystallizable proteins (all of biological interest so far) one conformation out of all those available must be more stable (but only by two hydrogen bonds) than all the rest, and the particular conformation must be findable quickly (or we’d all be dead).

How likely is this for a ‘random’ sequence of amino acids. We’ll probably never know (but we might if we’re lucky). This is the subject of the next post…

ChemPod 5

The new chemistry podcast from Nature is now live! – and can be found here.

In this episode of Chempod, we get caught up in catalysis, discover drawbacks to some Alzheimer’s drug candidates, and bring you a round up of the best of the American Chemical Society meeting in New Orleans.

(…and I make my podcasting debut – please be gentle…)

Enjoy!

Stuart

Stuart Cantrill (Chief Editor, Nature Chemistry)

Here comes the judge

Hey everyone, our May issue is now online. Check it out!

In the review in this issue about reactive oxygen species, Christine Winterbourn makes an interesting comment. She says:

“The early days [in free radical research] were notable for healthy and at times vigorous debate on how free radical chemistry could be rationalized with biological observations. Such debate is still needed today.”

This comment made me think about something I read a couple of months ago in a plane magazine*, which was an interview with Gary Taubes. In describing his new book, he says:

“If I had my druthers, I’d have the public health authorities institute something more akin to the legal system to decide what we know is so and what we don’t. They’d get a jury made up of 12 exceedingly good scientists, none of whom have worked in the fields of nutrition, obesity and chronic disease. Teams of competing experts would present the evidence for or against a particular belief – say, the healthfulness of low-fat diets, or whether salt causes hypertension. The jury would be able to cross-examine witnesses – i.e., those researchers who believed their studies provided some useful evidence. And then maybe the jury would deliberate for as long as it took to give an answer. If they didn’t believe some particular piece of advice was justified, but they couldn’t say it wasn’t, they’d suggest what experiments had to be done to know for sure.”

It’s an interesting idea – that of whether enough debate is occurring in general and how specifically ‘debates’ might occur to be most productive. I feel like I don’t see a lot of debate occurring… I wonder if scientists are less willing to voice their opinions (outside of more regulated talks) than a generation ago, or if there are fewer topics that we feel completely adrift about? Or are there instead more topics that, as we continue to learn, we feel more adrift about, and so it’s less easy to set forth a specific hypothesis (which then makes it difficult to argue for that hypothesis)? What do you guys think? Going back to Gary Taubes’ idea, it seems like there are many biological or medical questions that are unresolved, perhaps at least partially since there are so many different ways of conducting clinical trials or dosing mice, etc. However, if you could assemble a chemistry jury, what topics would you set before the court?

Catherine (associate editor, Nature Chemical Biology)

*Sadly, I don’t remember the airline, so can’t reference this properly. Feel free to tell me!