Posted on behalf of the Prospective Professor

After months and months of grueling travel, crazy cab drivers, late night practice talks and waking up wondering what city I was in, I thought the worst of it was over. Little did I know that the fun had just begun. I am happy to say that I was able to find a job, and not just any job, but what seems to be the “perfect” fit for me. But after a few weeks of celebration and relaxation, that little voice started up again, “what have you gotten yourself into?!” I’m about to start a job for which I have never been trained!

Certainly my feelings aren’t unique. I’ve had conversations with countless people over the years discussing this very issue. Most of us will have spent at least 7 years pursuing our doctoral degree and doing postdoctoral research. And during this time, we may teach a few lab sections, write a quiz or two and hopefully compose a fellowship application. But never during this time do most of us get training in lab managements skills, mentoring techniques or budgeting (time or money). In essence, every step of my training has prepared me to be a bench scientist. And lets face it, after so many years of schooling I’m lucky if I can budget my monthly groceries let alone supplies for an entire lab, as well as funds to make sure my students can hardly afford their groceries!

Everyone tells me that I will learn with time. I just hate to think of the disasters that will happen in the meantime: Exams with an average score of 17%, a student crying after groups meeting or a lab left empty on the weekends (horror of horrors!). I will start my new position filled with nervous excitement and ready to learn many new lessons. The first question on my mind is, how do I attract students to my lab? I keep having flashbacks to junior high dances where we all waited at the side of the gym desperately hoping that someone would ask us to dance and wondering, “will anybody like me??”

Posted by Catherine Goodman at 02:52 PM | Permalink | Comments (0) | TrackBacks (0)

1. What made you want to be a chemist?

When I was a junior high school student, I was charmed by the periodic table. I have never lost interest in it because of its beauty. I needed to understand the nature of all atoms. Now, there is a big Japanese poster of "A periodic table for a family" produced by the Japan Foundation of Public Communication on Science and Technology in my office, so I can always see it.

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

A painter or a farmer. One of my grandfathers was a painter. He painted beautiful pictures of plants or animals on Japanese traditional cloth. My other grandfather was a rice farmer. He grew Koshihikari, the very popular and most expensive variety of rice in Japan. My family considered me to be the most likely successor in either event.

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

Education. People tend to keep chemistry at a distance. A product that originates from natural resources is highly thought of by people, in other words, they tend to be afraid of "a chemically synthesized compound". For example, vanilline extracted from vanilla beans and chemically synthesized vanilline are virtually the same compound, but they will choose the former even if it’s three hundred times more expensive than the synthetic one. It's crazy! I think the goal of chemists is to produce people who have high scientific or chemical literacy by using our chemical knowledge.

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

Prof. Adolf Butenandt, Nobel Prize winner, and also the person to discover the first insect pheromone, bombykol. I am interested in bio-regulators such as insect or microbe pheromones and hormones. I would like to hear his private lecture about his historical work on the isolation of bombykol.

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

Yesterday. I am active in our lab. My teacher and master, Professor Kenji Mori (now 73 years old), is still active in his lab! So I can't retire.

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

I like movies, especially Science Fiction movies. So, I would take the soundtrack of Star Wars and explore the island with the music in the background during the day. And I will go on reading Crime and Punishment by Fyodor Dostoevsky at night.

Arata Yajima is in the Department of Fermentation Science at the Tokyo University of Agriculture and works on the synthesis of natural products and biosynthetic intermediates interest at the interface of chemistry with biology particularly the microbe pheromones and rice phytoalexins.

Posted by Alison Stoddart at 05:22 AM | Permalink | Comments (1) | TrackBacks (0)

Another Friday, another batch of Research Highlights for you all to enjoy.

Steve's is about a pretty clever hydrogel. Hydrogels are potential carriers for drugs, but how do you get them to release their cargo in the right place? Aptamers are the answer...

Gav has written about some work by Richard Zare's group that looks at how viruses might 'break in' to cells. They used surface plasmon resonance to study a model virus attaching itself to a model cell.

And finally...oligoamide foldamers are strings of amides or amino acids that...well, fold up. A bit like proteins or DNA do. But if you can get them to fold AROUND something, you can use them to trap molecules. Jane tells us more about work done to this end in France and China.

Hope you enjoy this crop - if you have any feedback or comments, please let us know!

Neil

Neil Withers (Associate Editor, Nature Chemistry)

Posted by Neil Withers at 04:42 AM | Permalink | Comments (0) | TrackBacks (0)

Hi everyone,

This week the Nature Chemistry team have been thinking about how we display our wonderful papers (when we finally open the doors and eventually publish a paper, anyway).

We’d really like to see what everyone else thinks about some of the things we discussed after looking at what other journals have to offer.

So, the things we’re interested in:

(1) HTML vs PDF: does anyone read the HTML articles? Do you read the PDF on-screen or print it out?

(2) Big vs little graphics: what does everyone else think about the tiny size of the graphics in ACS html articles?

(3) Tagging/’semantic web’: what do you think about the toys on the RSC’s Project Prospect? What kind of things would you like to see tagged/linked to other content in Nature Chemistry? For instance, Steve would love to do something with named reactions.

(4) 3D molecular structures: do these help your understanding of a paper?

(5) How useful to you are InChIs and SMILES?

(6) Forward linking: the RSC and Elsevier/Science Direct offer this – do you use it? Would you use an RSS feed that alerted you to new citations of a particular paper.

(7) Would you actually comment on papers if there was a comments box at the end?

(8) We really like the Biochemical Society’s HTML article style (sample one here) – do you?

If we could get a deluge of posts about this one, we’d be overjoyed! And this is your chance to voice your opinion on what a Nature Chemistry paper should look like.

Neil

Neil Withers (Associate Editor, Nature Chemistry)

Posted by Neil Withers at 06:13 AM | Permalink | Comments (12) | TrackBacks (0)

Posted on behalf of Retread

Back in the 80s when artificial intelligence (AI) was going to make humans obsolete, LISP was the programming language of choice for AI. As a neurologist I was interested in intelligence in any form (machine or otherwise) so I tried to learn it. Most programs looked like gibberish. There was a great quote in a book "Let's Talk LISP" after a particularly convoluted piece of code — "Relax you, never understand anything, you just get used to it".

I think the same thing has happened with our understanding of biologically relevant proteins. We've just become used to the fact that biological proteins have a dominant shape. However, we also know that other polymers don't. DNA and RNA certainly don't have a single shape.

So why do biologically meaningful proteins have one? Consider enzymes. The amino acid side chains comprising the active site are found all over the protein rather than next to each other in the sequence. Chymotrypsin, one of the best studied enzymes, has a catalytic triad made from histidine #57, aspartic acid #102 and serine #195. To function, they must be brought near to each other and held there fixed (and in the proper orientation to boot). The same holds for structural proteins that make up muscle and the cytoskeleton.

Yet only 10 kcal/mole — 2 hydrogen bonds — is enough to denature them. Not much of an activation energy — not even close to a covalent bond. Once denatured, Anfinsen showed that ribonuclease found its way back to the original shape, implying that there were no other conformations of similarly low energy available to it.

It is remarkable that we only have 20,000 or so protein coding genes when you consider just how large possible protein space is. In this regard, proteins are like English words. There are very few of them when you calculate how many there could be. Sonnet #18 — "Shall I compare thee to a summer's day?" contains 114 words of which 17 are 7 or more letters long. The Oxford English dictionary contains 600,000 or so words of all lengths. There are 8 x 10^9 strings of 7 letters. Few of them have meaning.

Words are a lot shorter than proteins. There are 8 times as many strings of 4 amino acids (20^4 = 160,000) than we have proteins. My guess is that this isn't an accident, because I doubt that most strings of amino acids have a dominant shape (e.g., biological meaning), and even if they did, they couldn't find it quickly enough (the Levinthal paradox again).

How would you prove me wrong? Is the question even meaningful scientifically? I (of course) think it is quite meaningful in a philosophic sense, since it bears on just how probable or improbable life is. The next post will discuss some gedanken experiments which could settle the question (or show that it is unanswerable).

Posted by Stuart Cantrill at 05:03 AM | Permalink | Comments (0) | TrackBacks (0)

Happy Friday everyone, and welcome to this week's batch of research highlights.

Fullerenes:
Buckyballs act just like giant atoms, complete with s, p and d orbitals that are bound to the sphere's hollow centre

Antitumour agents:
Hiding a potent, but insoluble, anticancer drug inside a cage complex represents a new approach to the use of inorganic chemotherapeutics

Self-assembly:
Discrete complexes comprising stacks of up to nine aromatic molecules can be assembled in one step from a few simple building blocks

As for last week, anyone can read the articles for free, but you need to sign up for a free account first.

Neil

Neil Withers (Associate Editor, Nature Chemistry)

Posted by Neil Withers at 05:08 AM | Permalink | Comments (0) | TrackBacks (0)

1. What made you want to be a chemist?

I enjoyed chemistry in high school and continued to enjoy chemistry at MIT. When I made a polymer in an advanced organic chemistry lab, I was hooked and then pursued my PhD in polymer science and engineering at UMass, Amherst.

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

After graduating from MIT, I was accepted to both graduate school and medical school. If I wasn't a chemist, I would probably have been a medical doctor (not sure what type though).

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

We can advance knowledge. We can take advantage of these advancements in knowledge to influence policy and create better products for the future. I'm particularly interested in tissue engineering/regenerative medicine where we can design polymers for use in tissue regeneration and delivery of drugs/therapeutics.

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

Both Ralph Waldo Emerson and Abraham Lincoln are revered in our family (our sons are named after them, in part) - they were both great thinkers and great leaders. This would be an interesting experience.

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

When I was on sabbatical, I learned how to obtain primary neurons in Drs. Freda Miller and David Kaplan's labs - this was in 2003. The initial "sabbatical" became the basis for a PhD project, which Laura Yu completed (4 years later). I also recently did a demonstration for my son's grade one class last week (April 2008) on dissolving an egg shell in vinegar - but this probably doesn't count as an experiment!

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

I would take the book on "How to get off a desert island" and bring a solar-powered iPod.

Molly Shoichet is in the Department of Chemical Engineering and Applied Chemistry at the University of Toronto and works on tissue engineering strategies to promote regeneration after traumatic injury in the central nervous system and targeted delivery in cancer.

Posted by Alison Stoddart at 05:05 AM | Permalink | Comments (0) | TrackBacks (0)

We've just received a press release letting us know that the Diamond Light Source ('the UK's world-class synchrotron facility') has just had its first users on its new test beamline (B16 for all you big facility junkies out there!). This is only the 8th of the 40 planned beamlines.

The lucky scientists are from Royal Holloway, University of London, and they're developing high-res XRD techniques to map crystal imperfections. Moreton Moore (who Google reveals is also a Councillor on Runymede Borough Council) has spent a large part of his career studying...diamonds. Not just a girl's best friend, industrial diamonds can contain tiny inclusions of metal that could cause failure. So being able to separate out the elements within the metal using the hard X-rays from Diamond could lead to better industrial diamonds.

The new test beamline's job is to allow researchers (academic and industrial) to test their optical components. Kawal Sawhney, Principal Beamline Scientist, said 'It enables us to push our capabilities and advance the technology that is available to users, without interrupting the schedule of the other beamlines, ultimately resulting in better, cutting-edge science.'

Having used the neutron source at ISIS (on GEM and HRPD) and the old synchrotron source at Daresbury (9.1) in my PhD, I tend to get a bit green-eyed over this sparkling new facility. Daresbury especially was a source of mild dread to us all, probably because of the prospect of running an experiment over 48 hours, in which you need to change the image plate every 20 minutes. This required two of us to stay up until 4am before the other two team members took over. The unfortunate thing is that the furnace broke at around 9am, thus slightly ruining everything. That's to say nothing of the rubber bands and sticky tape that seemed to be holding everything together – or the infamous canteen!

Neil

Neil Withers (Associate Editor, Nature Chemistry)

Posted by Neil Withers at 10:54 AM | Permalink | Comments (1) | TrackBacks (0)

Hi everyone, I'm Neil, one the new associate editors on Nature Chemistry, and this is my first post here at the Sceptical Chymist. The eagle-eyed chemistry publishing blog aficionados among you may just remember some of my posts over on the Chemistry World blog, about such crucial topics as t-shirts, food and even science.

Today’s topic is inspired by a rather sad story...I found out around Christmas time that my first ever science teacher at my village middle school recently died at a fairly young age of motor neurone disease. So this post is dedicated to the memory of Mr Challinor – Gareth, I believe.

I vividly remember some of his first lessons back when I was a 9 year old, 20 years ago. The school buildings were quite new (10 or so years old at the time), so the little lab was pretty well kitted out. But he really instilled in us the fact that science wasn't about Bunsen burners or any of the other complicated apparatus we were all seeing for the first time. A scientist's most important tools, he said, were his or her eyes, to observe what was happening.

One of the first experiments I remember him showing us was incredibly simple, but also incredibly powerful. He'd told us about atoms, and how burning material was essentially just adding oxygen to it. To prove that things do get heavier once you’ve burned them, he carefully weighed some magnesium foil in a crucible, then set fire to it. After the bright white flame died away, he re-weighed the crucible and guess what? The weight had indeed increased.

As well as teaching us about atoms and combustion, something else he did in that experiment also stands out. He got one of the class (Jamie Preece, since you asked) to watch over his shoulder as he did the weighing (we couldn’t all fit around the balance). This was just to show that he wasn’t making it all up, that we shouldn’t believe him 'just because he said so', but to show what he said had happened actually did. That's a pretty important first lesson in science for anyone, but especially a 9 year old: don’t just take someone's word for it, see for yourself.

So, if anyone else would like to share their first ever experiment with the world, please let us know in the comments below!

Neil

Neil Withers (Associate Editor, Nature Chemistry)

Posted by Neil Withers at 06:36 AM | Permalink | Comments (5) | TrackBacks (0)