Author: Joshua Howgego

Philosophical advice on ‘magic crystals’ and talking back to psuedoscience

“So Beth had this amazing thing, where she went to this guy who sorted her back out,” my mum is saying, “he uses crystals and everything.”

flickr photo by inskora

My wife and I are in attendance at a lonely Suffolk pub for our annual Christmas get together with both sets of parents. Conversation focuses on the back problems of middle age, the latest tale of woe about my very elderly grandma and the lives of my old school friends who never left to go to university.

I look sceptical. “Crystals?” I say, raising an eyebrow.

A few tables away a well-dressed lady and a man in wellington boots grasping a pint are stroking a dog lying by the bar.

Mum fixes me with one of her looks. “Josh, what you don’t know is, the guy could roll the crystals around on her back and tell immediately where her back hurt without even asking”.

I’m loosing it, but so as not to cause a scene in front of all the middle class people, I mutter something under my breath about what sort of person honestly believes in magical crystals.

 

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The student voice in the debate over UK Doctoral Training Centres

In the academic year 2011-12 the EPSRC, a UK science funding council, pulled funding for about a third of the physical science PhD project studentships the organisation had previously funded. Academia was feeling the first fruits of the council’s decision to scrap project studentships completely and, perhaps understandably, many greeted the news with dismay. The move was part of the EPSRC’s shaping capability strategy - the council’s plan to change the way it funds UK science during the recession. The goal is to ensure UK research remains top quality, but also contibutes profit-making innovations to the economy (some academics are really quite angry about this latter part).

So traditional PhD projects – where a student is assigned a supervisor in a specific subject, and then basically just gets on with their research for three years, emerging as an expert on the other side – are beginning to disappear in the UK. In their place a new way of training PhD students is emerging: the Centre for Doctoral Training (or CDT) [1].

There are several differences between a CDT and a traditional project studentship PhD. For one thing, CDT students generally spend their first year doing ‘research broadening sabaticals’ in several different labs, rather than jumping straight into one project. This means the PhD lasts four years instead of the traditional three and that the students, in theory, have a broader knowledge of their subject. They also receive specially tailored training in ‘transferable skills’, and generally “more attention from academics” (as we’ll hear in a moment).

Unfortunately, all this comes at a price. Each CDT student accounts for about 60% more cash per year than an equivalent project studentship. Perhaps because of this, CDTs polarise academic opinion. One told me that the ”soft skills” the candidates would develop were “an appalling waste of young scientists’ talent and an utter waste of tax revenue”. Other academics remain in favour of CDTs, arguing that multidisciplinary scientists are an absolute prerequisite for the kind of complex science that goes on in the 21st century.

So who is right – are CDTs the way forward, or a dangerous detour? I co-authored this article on the subject, where I noted down some of the complicated issues surrounding this debate. But I felt like the voice of the students was missing; one criticism of the CDTs is that they create a two-tier atmosphere, where the remaining project studentship guys are left feeling like second class citizens in the presence of their trained-up, super charged CDT peers. But is that actually true – do the students really feel like that? I decided it would be a good idea to ask them. So - equipped with bad coffee from the library canteen – I sat down to have a chat with Tom, Jazz and Freddie, three students from Imperial College London’s Department of Materials. Allow me to introduce them:

One thing I uncovered in my research into this topic were fears that tensions would develop between CDT students and project studentship students. With all that extra money and special training being bestowed on those in the CDT, would ‘outsiders’ feel a bit jealous?  Here’s another extract from our conversation:

So maybe there is a little inter-PhD course tension! But of course each CDT is different. I had already spoken to Adrian Sutton, the founder of the CDT that Tom and Jazz are part of, and he told me it was very much his mission to have the benefits that the CDT brought to his department “spill over” into the rest of the school’s research too. An independent mid-term review [2] of the EPSRC’s CDTs seemed to agree that this could happen, saying that CDTs could ‘act as a nucleation site[s] to focus a range of research and training activities.’ But this has to be driven by the management team, it doesn’t just happen automatically.

I asked the students what they thought about the staff managing their CDT. It sounds like a best practice from the CDT is shared accross the department, so how important were the staff in shaping this experience?

Lastly we turned to the issue of multidisciplinary science. Almost the whole point of CDTs is that they are multidisciplinary. But perhaps some types of science don’t fit neatly into that mould – do CDTs suit some types of science better than others?

Interestingly the students agreed that some subjects are inherently multidisciplinary, and so that suits the CDT model quite well. But, according to Freddie, it’s not that people who do project studentship PhDs are somehow incapable of working in multidisciplinary environments, it’s just that CDTs have that idea specifically in mind.

It was good to talk to the students – I feel like now I have a much fuller picture of the debate. Having said that it won’t, of course, make any difference; CDTs seem to be here to stay.

Not all academics are completely happy with that. Recently the House of Lords Select Committee on Science and Technology asked a range of expert witnesses about whether PhD training in the UK is on the right track (as part of a wider report on higher education in STEM subjects). The Engineering Professors Council (EPC) said (pdf, see p. 169) that some of their members would contend that “a PhD is a journey of scientific discovery; some training along the way may be helpful but it is not the main point.” So clearly some still see all the extra training the CDT students get as a dilution.

The consensus seems to be that CDTs are good, as long as they are done well. But perhaps we shouldn’t assume a PhD training monopoly for the CDTs would be a good thing.  The EPC put this quite nicely, so let’s give them the final word:

“We would see advantage in having several [PhD training] models working side by side, to give flexibility and the best capture of excellent candidates. DTCs fit within this, but should not be the only model”. (p. 171).

Notes

1. Confusingly, people sometimes refer to these as ‘Doctoral Training Centres’, so on occasions the acronym becomes DTC instead of CDT.

2. The word ‘independent’ might be slightly misleading here. The pannel of reviewers included academics from Oxford University and Newcastle University, both of which host EPSRC funded CDTs. So, by ‘independent’ the EPSRC obviously don’t mean that the reviewers had no professional connection with CDTs.

IMAGES: Flickr, CIMMYT

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The geekiest practical joke ever?

I was once asked to pick my ‘ultimate chemistry hero’ for a series on great scientists. It was a hard decision – there are a lot of great chemists out there – so in the end I ducked the question and turned it into a sort of joke. The perfect light entertainment to revisit just before Christmas, I thought.

I picked Melvin Calvin as my hero. But it was only because of an amusing story I was told by the legendary John Kilcoyne  that I began to take serious notice of Calvin’s work. That said, Calvin is a man worthy of standing alongside some of the other giants of the chemical sciences. Most scientists will instantly associate Calvin with the famous biochemical cycle, named in his honour, which he elucidated. In the 1950s, when Calvin carried out his work, little was known about the details of photosynthesis and the idea that carbon dioxide was the feedstock for making plants’ sugary foodstuffs wasn’t widely accepted.

Calvin set about conducting torturously complex experiments to assess the impact of everything from light, pH, carbon dioxide and oxygen on photosynthesis. All this needed an elaborate array of instruments and Calvin’s 1955 paper in the Journal of the American Chemical Society has a figure showing one such set up. It looks like exactly the sort of thing a stereotypical mad scientist would dream up and was undoubtedly exacting both to set up and use on a daily basis.

Here’s the diagram – can you spot anything unusual about it yet?

I wasn’t lucky enough to ever meet Calvin (he died in 1997), but according to Kilcoyne he was a serious man with little patience for jokes or pleasantries. This contrasted starkly with his graduate student, A. T. Wilson, who was, it would seem, a bit of a practical joker. Wilson reputedly made a wager with his departmental secretary that he could sneak in a picture of a man fishing into one of the diagrams in a forthcoming paper without his supervisor noticing. He won his bet and the fishing man is still in the diagram today. Calvin never found out.

There he is!

Silly stories aside, Calvin’s work was immensely important and he received the 1961 Nobel Prize in Chemistry for it. The mechanisms of photosynthesis which he helped work out still seem magical to us today; that a plant can take literally thin air and turn it into energy-storing organic compounds is quite incredible. But interestingly we face an analogous challenge today in the shape of the seemingly impossible task of generating cheap, clean energy. It seems clear we need more chemistry heroes of at least the same calibre as Calvin to address this problem. And what with the hard work it will inevitably take, a sense of humour would probably help too.

This is an edited version of a story that was originally published on the Chemistry World blog.


Josh Howgego spent the last four years peering into round bottomed flasks, working on a chemistry PhD. Now he has turned his hand to writing about science, and is currently studying science communication at Imperial College London. Follow on Twitter: @jdhowgego

 

 

 

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Automatic chemistry

PLOS is pleased to relaunch its Student Blog with this post from Joshua Howgego, a chemistry grad currently in the Science Communications program of Imperial College, London. Please come back to hear more from Josh and other promising writers who will share opinions and experiences while studying a scientific discipline or the communication of science.

Many of the criticisms of science boil down to the fact that the people who do science are only human – they make mistakes, head down blind alleys, look out for their career and hedge their bets. But what if we could make science automatic? It would take all of that unattractive partiality out of the endeavour. But would that be a good thing? Chemistry, perhaps more than any other science, is already becoming automated, and in this post I’ll explore what that looks like and what it could mean.

The most obvious example of how automation is influencing chemistry comes in the shape of Chematica, a map of organic chemistry, published by Bartosz Gryzbroswski earlier this year [1]. The map comprises a series of nodes – actually around 7 million of them – each representing an organic molecule, connected by links representing chemical reactions that can be used to transform one molecule into another. Gryzbroswski’s team have spent years working out the structure of the network.

This is not just any map. It has been called an ‘internet for organic chemistry,’ but (perhaps because I have just moved to London) I prefer the analogy of the London Tube Map. The important thing about this map is that it is a schematic – and that’s exactly what Chematica is. The emphasis is on connections, not necessarily on ‘relatedness’ in the real world. On the tube map stations can look miles apart, but on the surface, they are often much closer to one another than you would think. For chemists it is the habits and traditions of their discipline that sometimes make the connections between chemicals hard to spot. Chematica reveals them.

Because of this, one intriguing use for the map is to identify new routes to medicinally important molecules. For example, if new reaction sequences can be identified which all share the same solvent, they can be performed in tandem, without having to purify the material between steps. On an industrial scale innovations like this could save huge amounts of time, money and effort. Grybrowski reports that Chematica has found new routes to some of the substances that his spin-out company Prochimica makes, offering savings of up 45% on their target molecules.

It sounds impressive, and the reports have certainly made headlines among the chemical community (for example, see this piece by Phillip Ball). But it would be easy to imagine some of the more crusty members of the chemical academe grumbling that the map will take the art out of organic synthesis. Many practitioners of the discipline think of making complex molecules as a bit like chess: planning an attack on a compound takes scientific understanding, sure, but also skill and creative thinking (the final few steps of the challenging organic syntheses are even known among chemists as the ‘endgame’, in chess parlance).

Prostaglandin E2 is a complex molecule with quite a few medicinal uses. There have been numerous inventive syntheses of this compound over the years; one very recently [2].

But some think that automating the process could actually mean chemists have more time to be creative. That is what Craig Butts of the University of Bristol is hoping, anyway. Butts is director of Nuclear Magnetic Resonance (NMR) spectroscopy in the chemistry department at the university. This technique is the the key weapon organic chemists have when trying to work out what the chemicals are that they make in their round-bottomed flasks. The process of acquiring the data is no mean feat, and interpreting it to elucidate the structures of molecules requires expertise. But Butts has been designing a program that will one day, he hopes, make the elucidation of molecular structure by NMR an automatic process.

“Philosophically, I think a lot of chemistry could be automated”, he says. “And I’ve always felt that people shouldn’t spend a lot of time doing something that a computer or automation process can do for them faster, and hopefully better”.

“Even just using automated procedures to confirm that the structure of a compound that you’ve just received from a supplier is indeed what it says on the bottle – these sorts of things are really big in [the chemical] industry at the moment – because they want to minimise the amount of person time it takes to establish a simple fact.” So the theory is that, with fewer mundane fact-finding tasks to grapple with, chemists should have room for more creativity.

And if chemical techniques become easier to use via automation, it should also mean that non-experts will be able to try them out for size. Varinder Aggarwal, a respected synthetic organic chemist, also at the University of Bristol, is working on ways of doing full-blown chemical synthesis which he hopes will one day be so simple to use, that any intelligent person can have a go. He is designing reactions that have inherently predictable outcomes. In a video produced for the university’s new website, he’s candid about why that might be useful:

“Ultimately, if we can automate [our process], it means that people outside of the discipline of organic synthesis will be able to create their own molecules. It won’t just be really hard-core organic chemists who can do that; it’ll be a much broader pool of scientists […] and they’ll be able to include their own creativity, and create something that’s much bigger than what we have at the moment.”

Critics of Chematica might like to imagine a dystopian future where all art is removed from science, and our drugs and plastics are designed by machines. But, in the short term at least, the opposite seems more likely to be true. We are free to choose how we use automation, and – if we make the right choices – its widespread application in chemistry may eventually herald in a new era of creativity.

1. C. M. Gothard et al, Angew. Chem. Int. Ed., 2012, 51, 7922. (DOI: 10.1002/anie.201202155)

2. G. Coulthard et al, Nature, 2012, 489, 278 (DOI: 10.1038/nature11411)

 

Josh Howgego spent the last four years peering into round bottomed flasks, working on a chemistry PhD. Now he has turned his hand to writing about science, and is currently studying science communication at Imperial College London. Follow on Twitter: @jdhowgego

 

 

 

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