He covered a lot of ground in the talk, but one of his main points was that it is “unsustainable to use people for routine operations”. Chemists train for 10 years to then stand in front of a fume hood running columns. Ley wants to develop tools that allow researchers to make better use of their time in the laboratory. Flow chemistry has many benefits over batch chemistry, one of them being that it is easy to automate.

His talk left me wondering where I’m particularly inefficient in the lab. Sample collection and recording absorption spectra are particularly time consuming. Last year I started to build an (Arduino-powered) automatic sample collector, but made it far too complicated and never finished it. Now I’ve drastically simplified it (to the design my supervisor said I should use in the first place, as he often likes to remind me) and hope to have it working by the end of next week. I reckon it could save me anywhere between 5–10 hours a week of standing around swapping vials. I’m also going to make a start on recording absorption spectra inline. Again, this will save me a few hours a week, leaving me to do something more valuable.

I completely agree with Ley about the benefits of flow chemistry, but you can’t ignore that all this equipment costs money. Ley’s group use a lot of commercially available equipment and it’s not cheap. In my group, we build a lot of apparatus ourselves because we can tailor it to our needs and it’s a lot more “hackable” (as well as cheaper).

Someone in the audience tried to make the point during questions that funding is tight, especially for those working in organic synthesis. How they meant to afford equipment like £40,000 inline infrared spectrometers? Ley didn’t really answer this question (and I’m not sure he can). He’s obviously very well funded so he can build and develop the “lab of the future“.¹ A lot of this technology might be out of the budget of the chemists who will benefit from it the most. Unfortunately they might be performing “routine operations” for some time to come.

The following experiments do not constitute rigorous peer review, but rather illustrate typical yields obtained and observations gleaned by trained synthetic chemists attempting to reproduce literature procedures…

I disagree completely. What could be more rigorous than actually trying a reaction?

So far there are three posts. The first gave a lower yield than reported. The second was “moderately reproducible”. The paper omitted details essential to the reaction’s success. The third was “difficult to reproduce” and is well worth reading—there’s a great response from one of the authors, Prof. Phil Baran.

It’s unacceptable for anyone to publish a paper without all the information necessary to replicate the results. It wastes researchers’ time and money. I’ve written before about my difficulties trying to replicate results. It’s infuriating. How do papers like this slip through peer review?

I suspect some authors don’t really know why a reaction gives a particular product, especially in nanoparticle synthesis. They manage to pull something off a few times and publish their findings, but (unknowingly) neglect parameters crucial for other researchers to be able to reproduce it. It could be something seemingly trivial, like the method used to wash the glassware. The next researcher does it differently because it’s not mentioned in the paper and gets a different result.

The only way to deal with this is for reviewers to demand thorough experimental sections. (But to do so they must have a good understanding of typical experimental procedures. This is a problem if your reviewer hasn’t been in the lab for years.)

An alternative scenario could be that the researchers, in the early stages of the work, find that doing X doesn’t work. Later they find doing Y does work. Y gets published. X stays in the laboratory notebook.

X is a negative result. On it’s own, it’s not very useful. Loads of attempted reactions don’t work. But in the context of the positive result (i.e. the paper) the negative result is actually very valuable to anyone who wants to repeat the paper. Serious consideration should be given to including them in the supplementary information.

Experimental methods are grossly oversimplified. We like things to be elegant and simple, but chemistry is complicated. There’s no excuse not to include more information because everything is published online and space constraints aren’t a problem.

Blog Syn shows that subtleties in chemistry are important. We should all acknowledge that in our own papers and demand that others do the same.

Rather than give a slide-based presentation I decided the best thing to do was give a demo. I quite like mind mapping to help me structure ideas so I made one for this. I’ve included links to web sites where appropriate. You can download a PDF of the mind map here (PDF).

It’s split into two halves: the tools that I do use, categorised into “inputs” (e.g. Twitter and RSS) and “outputs” (e.g. Google Drive), and those that I don’t with some short reasons why. If you’re interested in trying some of this out, give one or two a go and see if you find them useful. If you use something that I haven’t mentioned, let me know in the comments.

Many years ago a few people were doing some work and, to their surprise, they managed to make light come out of something that had never had light come out of it before. People were very excited about it and now lots of groups of people spend their time trying to answer questions like “how does it work?” and “how can we make it work better?”. Everyone was interested because they thought it could be used to make new things like better TVs, very small computers and different kinds of lighting. But the perhaps the most important thing it could maybe do was give us all a new way to turn light from the sun into power for not very much money.

At the moment only a few people get to see them because they are hard to make. They are hard to make for lots of reasons, but perhaps the biggest reason is that the parts you need are themselves hard to make. Everyone struggles to make enough of them exactly as they need them to be. If the parts aren’t good enough, sometimes not very much light comes out, or for only a little while, or the ones that turn light from the sun into power don’t do it very well. No one wants any of those.

It doesn’t help that the normal ways of making the parts are often only good enough for making a little at a time. If you try to make more in the same way it stops working so well. I’m part of a group of people trying to make the parts in a new way that can make lots and lots and it still be good enough. In fact, our stuff is usually better than the best stuff you can buy.

I try lots of different ways to make things. I look in books to read how other people did things to get new ideas that no one else has had before. Sometimes they don’t work, but sometimes they do and when that happens it makes me very excited and happy. Sometimes we tell everyone but sometimes we only tell a few people. We can use my new way to make the light-making and power-making things work better and for less money than ever before so everyone can have them.

What do you think?

I found course particularly interesting, so whenever I see a paper on the subject I at least read the abstract to see if anything has changed. Angewandte Chemie have recently published a paper titled Microwave Effects in Organic Synthesis—Myth or Reality? (DOI: 10.1002/anie.201204103) by C. Oliver Kappe, Bartholomäus Pieber, and Doris Dallinger.

They looked at two recently published papers that allegedly found a specific microwave effect. Both claimed microwave irradiation significantly enhanced the reaction rate or yield in a way that couldn’t be replicated by regular heating to the same temperature.

Summarising a few pages: Kappe et al. couldn’t replicate the findings and argue that the problem lies in poor temperature management. To test the existence of a specific (non-thermal) microwave effect you need to run the same reaction twice at the same temperature, one with microwaves and the other normally (e.g. with an oil bath).

However the researchers who report a microwave effect use external infrared temperature probes, which record a lower temperature than the bulk reaction mixture. Microwaves heat more efficiently than the normal heating, so the microwave reaction will give you a higher yield and both vessels are in fact not at the same temperature. Instead you must use fibre optic temperature probes placed inside the reaction vessels. Doing this eliminates any microwave specific effect. To quote:

Importantly, we firmly believe that the existence of genuine nonthermal microwave effects is a myth, as all our attempts to verify these often claimed “magical” microwave effects during the past decade have failed.

It’s a good read and, I think, a nice example of science at its best. I’m also glad I read it because a colleague and I had, for some reason, been looking at getting a microwave flow reactor—which would be completely pointless, as all the benefits of microwaves in batch chemistry (high pressures and homogeneous heating) can be readily achieved in flow using normal convective heating. If anyone could tell me why such an apparently pointless bit of kit exists, I’d like to know…

Reference: C.O. Kappe, B. Pieber and D. Dallinger, Microwave Effects in Organic Synthesis—Myth or Reality?, Angewandte Chemie International Edition, 2012. DOI: 10.1002/anie.201204103

(This raises the question of how many positive literature reports describing organic electronic devices are “correct” and not anomalous? But here I want to focus on this problem in the context of large scale device production.)

Batch-to-batch variation is bad enough with the sub-gram quantities used for small area device fabrication. Printing optimised large area devices—measured in square metres/minute rather than square centimetres/day—would be next to impossible. You need to know that this week’s batch of polymer is the same as last week’s because different molecular weight size distributions, chemical defects and impurity levels have a big effect on the required processing conditions and final device performance.

It’s quite difficult to produce organic semiconductors on the large scale required for device printing because the polymerisation reactions scale up poorly from round bottom flasks to large batch reactors. You have to re-optimise at each scale, which costs time and money.

James Bannock, who is a PhD student in the same group as me at Imperial, has been working on the use of droplet flow reactors to make poly(3-hexylthiophene) and get around the problem of batch scale up. He’s recently published his work in Advanced Functional Materials (DOI: 10.1002/adfm.201203014) and it’s open access so you can read it yourself for free.

I encourage you to take advantage of the paper being open access and have a look. There’s lots of photographs and figures. Briefly, activated monomer solution is injected into a narrow plastic tube containing a flowing stream of immiscible carrier fluid dispersed with the catalyst. Microlitre-sized droplets form, like tiny individual reaction flasks, and travel through the tubing. Because the droplets are small the chemical environment is highly homogeneous and each droplet is essentially identical. The tubing is heated in an oil bath and the polymerisation reaction (a Grignard metathesis) happens as the droplets travel through the tubing.

You can produce more material by using longer tubing and a higher flow rate. Crucially, this can be done independently of droplet size. So unlike batch reactors, nothing happens to the chemical environment and you get exactly the same polymer, with a low polydispersity index and high regioregularity. The plan is to apply this method to other organic semiconducting polymers. It provides a way to produce device-grade polymer on large scale required for large area fabrication, with minimal batch-to-batch variation, and will hopefully drive the industrial production of organic electronic devices.

Reference: J. H. Bannock, S. H. Krishnadasan, A. M. Nightingale, C. P. Yau, K. Khaw, D. Burkitt, J. J. M. Halls, M. Heeney & J. C. de Mello, Continuous Synthesis of Device-Grade Semiconducting Polymers in Droplet-Based Microreactors, Advanced Functional Materials, 2012. DOI: 10.1002/adfm.201203014

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During the session Athene Donald, who was on the panel, singled out chemists as being particularly bad at outreach and I tweeted:

.@athenedonald: Chemists are particularly bad at outreach. I suspect I’m the only chemist in the room…. #solo12jobs

— Tom Phillips (@tomwphillips) November 11, 2012

Athene later replied:

@professor_dave @tomwphillips I said some chem PIs don’t encourage students to do anything away from bench NOT chemists can’t do PE

— Athene Donald (@AtheneDonald) November 11, 2012

Obviously I don’t want to misquote anyone. All the SpotOn sessions were recorded so I listened again and at 08:28 Athene says:

The downside is, in some places, is that certain professors or lecturers or whatever, group leaders, I’ll call them, don’t encourage their students and postdocs to get out.

That there is, in some places, the attitude—personally I particularly blame the chemists, and I don’t think we’ve got any chemists [here?, audience laughter], but they don’t expect to allow their students to go and do any non-lab based work at all, be that training courses or be it outreach and I think that is appalling. And one of the things I try and do in my own university is to make sure that that gets wiped out.

I can see how my tweet looked like Athene said that the outreach chemists do is of bad quality, but what I really meant is what she said—that it’s bad that some chemists don’t do any outreach. Apologies, Athene.

I offered (at 50:38) a rather ineloquent defence, citing Exscitec and Professor Lord Robert Winston’s Reach Out lab where many chemists in my department do outreach.

Later on Athene does ask if it’s because synthetic chemistry is particularly bench-heavy and at the time I kind of mumbled some agreement, mainly that I can only work in the lab 9–6ish in case I have an accident, not leaving much time for anything else. But really that’s ridiculous and just requires effictive time management. Regardless, this all seems a bit anecdotal.

At 51:51, somebody (I think it may have been Eva Amsen) says to Athene:

I don’t think it’s a chemistry thing per se, it’s just you know the wrong chemists.

Absolutely. You get rubbish supervisors in all disciplines. Yes, it does seem that some supervisors, particularly in organic chemistry, do chain their students to the fume hood. However it’s unfair to blame all chemists for the actions of a few dinosaurs.

Update

I posted this last night then pulled it again about 10 minutes later as I thought it was too negative and unfairly critical of Athene. But Google Reader had already crawled my RSS feed and it ended up on Twitter… So I’ve reposted it and want to end it on a more positive note.

I can think of one of these dinosaur PIs at Imperial. I’m sure no one thinks their behaviour is acceptable, but they’re a “big name” chemist. They’re (superficially) good for the department and I guess the students tolerate them because they think their supervisor is good for their career—ironic considering the skills developed doing outreach might be more useful.

Departments and faculties should change the rules to require outreach and loosen the grip of these PIs on their students. In my DTC, a small amount of outreach is compulsory and more is encouraged. I think the decentralised, cross-department nature of the DTC and multiple supervisor system also makes it more difficult for bad PIs to stop their students from doing outreach.

Other students need to tell these students that it’s unacceptable for their supervisors to behave like this. Staff need to do the same.

Blimey, I made this molehill into a bit of a mountain! Twitter, eh?

Your current job.

I’m a PhD student at the Centre for Plastic Electronics at Imperial College London. I make metal nanoparticles of various shapes and sizes using flow reactors. Other researchers want them for use in organic electronic devices.

What you do in a standard “work day.”

Upon arriving at uni I immediately go for a shower because I cycle rather than take the tube. Riding my bike keeps me sane. Next thing: coffee.

After that I sit down and plan my day, most of which is spent in the lab. For my own research that involves analysing data, planning/doing reactions, ordering supplies/equipment, programming, building home-made equipment, doing electron microscopy, writing…

My work is very varied and I like it like that. I’m in a small group so everyone has to muck in and learn how to do lots of different things. Nothing is simply delegated to someone else. I think my work probably borders on chemical engineering/process chemistry.

I spent most of Friday running some preliminary tests on a new flow reactor. I also took delivery of a new optical microscope, then helped get rid of an old server rack because we’ve recently got a new optics table and need to make some space. After clearing up the mess I made in the lab I helped out our undergrad student with some MATLAB code.

I also spend one afternoon a week demonstrating for third year undergraduate physical chemistry labs. Teaching is fun, but sometimes very frustrating.

What kind of schooling/training/experience helped you get there?

I went to a comprehensive state school and sixth form before to Imperial for my undergraduate chemistry degree, where I’m now doing my PhD.

During my undergrad I did a summer placement with another group at Imperial, very generously funded by the supervisor. That confirmed for me that I wanted to do a PhD. I strongly recommend that students interested in a PhD do a summer placement.

I’ve also had a lot of non-chemistry part time jobs, mostly in bookshops. I’d like to think that’s given me a good try-anything, get-on-with-it attitude.

How does chemistry inform your work?

It doesn’t so much inform my work as form the core of it. It’s no good if I build the finest flow reactor in the world but my reaction doesn’t work.

I love running reactions, especially anything with a nice colour change. It’s so exciting when it works (and totally makes up for all the times it doesn’t). This Abstruse Goose comic sums up my feelings perfectly.

Finally, a unique, interesting, or funny anecdote about your career.

Not funny, but I’m fairly sure I’m the only person to have ever modified an Argos mini oven to make silver nanoparticles.

In the last year I’ve only been to two conferences. Unfortunately neither of them were in exotic places. The first was in York and I went with a few people from my group. As none of us are especially well-known in our field we unlike Athene had the freedom to explore York in the evenings. The second was held at Imperial and attendance was compulsory for DTC students. They were both small (no parallel talks) and lasted two days.

The speakers at both conferences, with the exception of one or two each day, were incredibly uninspiring and unenthusiastic. I remember trying to fall asleep one afternoon in York after nearly exhausting my iPhone battery reading papers. I was very disappointed as I had hoped to come back with fresh ideas but instead felt that it was a massive waste of time and money.

How can people talk so blandly about their own work? If the speaker isn’t excited by it then they most certainly can’t expect the audience to be interested. Many talks didn’t have any questions—the presentation equivalent of a death knell.

How have we ended up in this situation? I find it particularly baffling when I think about talks given by PhD students in my DTC. Recently we had a day with industry sponsors and visitors from other universities to listen to some third and final year PhD students present their work. The presentations were largely fantastic. Enthusiastic, confident, engaging, interesting… Really very good. Last month my cohort gave our MRes talks and the comments from markers were (nearly) all positive too. A world apart from the dreary, mind numbing talks I’ve sat through at my last two conferences.

Perhaps I’m overreacting, but I’ve really been put off going to anything other than something massive like the MRS conference where there will always be something related to my field and hence tolerable, even if the speaker is a bit tedious.

Does anyone else find most talks bad too? Are good talks unfortunately the exception? On the positive side, at least I’m at the beginning of my career so I can follow Athene’s advice, especially for my next trip to Italy in April:

Early career researchers, don’t kid yourself your professors enjoy themselves on such trips by seeing all the sights of the world you’ve always wanted to see yourself. Chances are, if you get to visit some far-flung place for a conference, you will enjoy your trip much more than your seniors because you live your life at a more leisurely pace. Make the most of it!

Update 2 (28th September): you can listen to the debate on Figshare and here’s a useful link to RCUK’s open access policy (PDF).

Lots of things were discussed but a couple things in particular stuck in my mind writing this on the way home.

RCUK require for CC-BY for gold, but only CC-BY-NC for green

Under the new RCUK policy researchers must either pay a fee to publish in a gold open access journal or alternatively publish in a closed access journal and then deposit the article in a repository within 6 months.¹

Gold articles must be published with a CC-BY licence. This is good as it means anyone can do what they want with the work as long as the original authors are attributed. However, green articles deposited in a repository after the embargo period are only required to have a CC-BY-NC licence, meaning that you cannot use the work for commercial purposes.

This is very disappointing. Sadly it wasn’t discussed in the debate. CC-BY-NC is, as tweeted during the debate, a licence of fear. All it says is that the authors couldn’t think of a way to make money out of the work, so they’ll be damned if anyone else does. The work might as well have never happened.

Thorley talked about open access benefiting “UK PLC”, but CC-BY-NC is at complete odds with this. CC-BY-NC stifles innovation and progress. Furthermore, if the state funded the research, then the state and the rest of society should benefit from it. Under CC-BY-NC, no one benefits.

Green is of poorer quality than gold?

A couple of people doubted the quality of papers published straight to repositories like arXiv. I’m not so convinced. Firstly, they assume the reader is stupid and can’t work out for themselves if a paper is a load of nonsense. Secondly, it assumes that peer review weeds out all the bad papers. It doesn’t. Someone suggested a kitemark to say that a particular paper in a repository is trustworthy. I hope I don’t have to explain why that’s an awful idea.

Thorley did at one point say something about gold papers being better for the lay person. Curry looked quite suprised. This is a completely different debate. Just because a paper is literally accessible to the public doesn’t mean the information contained within it is intelligible to the public. But if someone is interested enough to be reading papers I don’t think gold/green will really make that much of a difference to them—not enough to justify an APC. I wonder what percentage of papers even undergo any major revisions between submission and publication.

Concluding thoughts

CC-BY-NC for green is a real disaster. I sincerely hope RCUK revise their policy so that it’s the same as gold.

I still can’t make up my mind about green versus gold. On the one hand, I think everything should go straight into repositories like arXiv. Forget journals and use the money we save to help fund and develop repositories, (although I know this is really very unlikely to ever happen). But on the other, if we are going to pay journals to publish work, we should expect more in return. Not just PDFs, but high quality (interactive?) documents including data and code in reuseable formats and tools to help us do things like text mining. I can’t help but think there’s very little innovation in publishing, especially considering the size of their profit margins.

It’s clear a lot more will happen in the open access debate. As Thorley said, this isn’t an event, it’s a journey. Hopefully it won’t be too arduous.

Update: gold—a free market for innovation?

Having slept it on it I can see where RCUK are coming from with their preference for gold, but I think they’re overestimating what publishers actually offer at the moment. Do most journals currently add enough value for it to be worth the APC? I’m not sure. I get the feeling people tend to think that every journal produces papers as beautiful as NPG. Authors will be paying the journal to publish, therefore we should expect more in return—especially considering the tidy profit margins. At present, I don’t think gold is that much better than green in that respect.

If, as Curry said, scientists end their addiction to impact factors (increasingly likely as HEFCE will be enforcing their ban on them), gold might lead to a more free market-like situation. Scientists will look around for journals that offer the best value for money. This could really drive innovation in scientific publishing as publishers are going to be competing in terms of what they can offer scientists rather than what the journal can do for an author’s career.

(Updated on 09:02 on 27th September 2012 with additional section.)