Archive for the ‘research’ Category

Words, words, words…

February 8, 2017 Leave a comment

I have the good fortune of having three PhD theses on my desk at present, two where I am the external examiner and one where I am the internal. They are all on interesting topics, one very related to my own work and the other two a little more obliquely related. While reading theses for examination is a chore – you need to make lots of notes and make sure you have sensible questions to probe the student on, it is also a really good way to concentrate on a specific subject and hopefully learn something along the way.

Having picked up the first one to read my heart sank a little as it became clear that there were going to be lots of rather strangled grammar. If you are an aspiring or current PhD student, you need to know that the quality of your science is what will take you through in the end, but your viva is likely to be a hell of a lot easier if the examiner does not need to stop every paragraph to note how you have deviated from the norms of good English.

My strong advice: throughout your PhD, write as much as you can and get feedback on your work. This can be from your supervisor, lab mates or friends or through courses that I imagine all Universities (certainly in the UK) offer on academic writing. Or maybe by writing a blog. Also try, and this can be hard, to thoroughly proofread your final thesis, and get others to do so too. This will make your examiner’s job so much easier, and so much more enjoyable, allowing them to focus on what you have done. Words your means of delivering your message. Make sure they are your friends.

Buildings and Bodies

Sir Andre Geim, discoverer of graphene is quoted in the Times today (£), speaking at the Hay Festival, about the new £60M Graphene Centre based at The University of Manchester. It says, “…of the £60 million of public funds invested in the centre, just £9 million had been spent on equipment and nothing on staff.” He also comments on the fact that the building has taken 5 years to build and in this time other countries have streaked ahead of the UK in graphene research.

I can’t comment on the later point, not being a graphene expert, but on the former, there is clearly a delicate balancing act to be made between supporting infrastructure and funding people to actually do the work. What else might £60M have gotten us? Well, conservatively you could have funded (perhaps not at one institution), £10m of equipment, and then invested the other £50M in 5 year research professorships, say 50, with six figure investments into support packages for each. In the short term this would give a much bigger bang for your buck in research terms than a new building. Longer term, I’d assess the same would be true – but the costs would have to be found at institutions to support these new staff, and they would have to be winning competitive external awards to support their research. I’m sure the new centre will ultimately do well, but I can’t help feeling that to jump on new and innovative research directions it is not buildings that are needed.

There is clearly a need for new buildings at times, but I am not convinced we are well served by these types of investments (this is essentially, if I understand correctly, a directly funded Government initiative (£38M from Government, £23M through ERDF). We have an ample University estate, and graphene research in the UK would probably have been much better served by distributed funding, with the focus on bodies and basic research and not buildings.

Summer Studentship Dilemma

We have been lucky enough to have been awarded two summer studentships through the Institute of Physics Top50 placement scheme this year. This has meant that we have had a large number of applications for summer studentships from outside the University, whereas normally, most of our summer students tend to be pretty local. We have had twenty eight applications for our posts and having read through them all it looks like it is going to be a tough decision.

This got me to thinking: what is the purpose of a summer studentship? If this were a PhD position, or postdoc, or permanent staff member I’d be looking for the very best applicant, who shows the most potential, but reading through the CVs made me wonder, if an 8-week studentship, which is clearly not a job in any sense, should be judged in the same way? It is clear from the CVs there there a bunch of talented, motivated and above all experienced undergraduate students out there – they have undertaken previous research projects and tick the boxes in terms of writing a decent CV; they have things to talk about. But equally there a bunch of students who I started to worry about – they are clearly bright, with good grades and I am sure would do a good job over the summer, but they have little experience. Some have little experience of anything with patchy evidence of summer jobs or part time jobs, others can show that they have worked in a shop, but little else. I worry that many of these students, when it comes to getting real jobs after graduation, will struggle, based on their CVs. I know some of this is self-imposed, but equally I know many students simply can’t either find, or can’t afford to do, shiny research placements. There are many restrictions on finding such roles. I also know that when I was in a similar position my CV was somewhat thin – I’ve always been fairly reserved and wasn’t so good at putting myself ‘out there’. Unfortunately, now more than ever, it’s what you do in your holidays that marks you out for employers, especially when there are so many graduates with 1sts and 2.1s.

And so I wonder – is the purpose of my summer studentships to offer the opportunity to students who have never had it, or to propel on even further their more experienced peers – do I want to help improve some of the those CVs, offer some training and mentoring and the chance for something different to those who might not have had it before, or just go for the best qualified? Bear in mind that the students are unlikely to do anything earth shattering in 8 weeks, so I can genuinely offer these placements without worrying if the student is going to be absolutely brilliant – I’m mainly looking for application and a genuine interest in the topic area of biophotonics. I could also look at getting the best students in with a view to PhD places next year – but the less experienced could be just as good as the experienced if given a chance. I am still mulling over how best to approach this task.

[Also, 29% of applicants are female, 71% male, so still a bit of a hill to climb to get to any sense of equality in the physical sciences. In fact this is a decent ratio compared to other application processes for more senior posts that I have seen].

A different way

Like many physicists, I suspect, I grew up gripped by the developments in quantum mechanics that happened at the start of the 20th century. This is often portrayed as the work of lone geniuses: Einstein, Bohr, Schrodinger, Heisenberg and the rest. That this work was carried out in isolation is to some extent true, but there was a surprising amount of collaboration and certainly discussion between the big hitters of the time. This work, and related studies in areas such as radioactivity, ultimately led to one of the biggest scientific collaborations that had ever existed – the Manhattan Project. This was an altogether different beast: one goal, build a bomb. Many of the brightest minds, engineers, physicists and chemists came together to work out how to achieve what they viewed as something that could help to win the war.

In modern times we have our own parallels of such large scale collaborations, CERN being the most obvious example. These mainly occur because of the huge scale and expense of the projects under consideration. I do often wonder though if we wouldn’t be much better placed to carried out nearly all scientific research through such large ‘crowdsourced’ efforts.

I have a small research group, too small to easily carry out the various ideas that I might have, too small to have the resources to fund all the experiments I’d like to try. It may be that I can persuade a funding council to give me money for these ideas, but the odds are against me. I can then wait and see if we can do them on the fly somehow, or find, depressingly, that someone beaten us to it, a few years after my original thought. I suspect nearly every scientist has similar thoughts about work that just never gets done.

But there are lots of groups out there, lots of talented people, lots of equipment going spare – lots of slack at certain times within any research group, big or small – why don’t I just publicly lists all my ideas and hope someone else runs with it and sees if it’ll work or not? It doesn’t work like that of course. We are precious with our ideas as they define our careers, the funding that we do get, which in turn allows us to build our groups and justify the continued need to employ us. Even collaborations, which are a way to help realise ideas that often we can’t do ourselves can be difficult, time consuming and often not quite what you need if you team up with the wrong group.

This does, I suspect, also have the problem of massively slowing down progress. We all want to win the prize, get the plaudits, get the pay rise, and this stems from doing the work and having your name in the right place on the author list. In this day and age of open access publishing, open data and near instantaneous access to all knowledge it does seem that if the end goal, the experiments, the finding things out is what we want to achieve , that our current way of ‘doing’ science seems increasingly outdated.

Could we do things differently? Would it be possible simply to fund research teams that can then respond to new ideas – take the very best ideas and see them through – have secure funding for staffing and equipment at certain Universities and then let academics the world over provide them with the ideas? This would provide much greater focus and possibly much greater efficiency in how we spend research money. An example would be, say, a centre for optical microscopy in the life sciences, based, for arguments sake at Dundee. We fill it with 100 staff and then throw open to the world the idea to present us with the most pressing problems in the area. It may be that these ideas receive some peer review to set priorities and then we task the centre with solving the problems. The originator of the idea gets appropriate credit, and the centre works collaboratively with the research community to help it make progress. We set up these little ‘Manhattan Projects’ with stability for staff, enhanced training for students, and better opportunities to exploit the research through critical mass. In a sense it centralises the experimental skills and distributes the ideas. It is a model that appears to work for very large scale experimental work, but would it be more efficient than our current massive distribution of experimental skills?

As it happens I am reading J. Craig Venter’s most recent book ‘Life at the speed of light‘ which in a way promotes this idea – a highly skilled, well funded lab pushing for a clear and ambitious research goal. Admittedly he was (and is) in competition with other groups, but if that funding was more concentrated and the initial thinking open and free for wider input and discussion to happen, could things have gone even more quickly? Do we want to see the results and the progress and quickly as we can or keep all the glory for ourselves?

The answer is that I am not sure – the model would seem to work in some cases, but clearly has problems, and would more than likely have to be globally accepted to work in the way I think it could. But with new paradigms appearing in the field of ‘open’ academia very rapidly, maybe there is a different way that we could do science, and actually see more of the collective ideas of the research community come to light and bear fruit.

Media Interactions

This week I have a “News and Views” article published in Nature, which is a discussion of a research paper published in Physical Review Letters outlining an experiment in which a a mirror made from colloidal particles was trapped using laser beams. The idea is that this could be extended to much larger scale devices suitable for making space mirrors, for things like telescopes. Interestingly this article that I wrote about in Nature was then picked up by Physics Todayin a sort of degrees of separation from the original work game. I’m not quite sure what this tells me, other than the media is a bit different from academia – it’s rather faster paced, it scavenges material from where it can, and that I have the utmost respect for media people who can write quality material over a vast range of subjects with rapid turnaround times. I like writing stuff, but quick and accurate is not always my strong point (note the length of time since my last blogpost), but the communication of what we, scientists, do is really important. I’m glad that it is not always down to those at the coalface do that communication.

Note if you have comments on my article you can leave them at the bottom of the Nature page.

The Droplet Laser

A laser is a fairly simple thing at heart. You need a couple of mirrors a chunk of material with the appropriate atomic characteristics and an energy source to get it all started. When teaching lasers to my undergraduates I often flippantly remark that “if you hit it hard enough, pretty much anything will lase,” [1] meaning that if you can get enough pump energy in the material requirement of the laser material don’t matter too much. While this isn’t quite true, it didn’t stop some of the original laser pioneers trying to make an ‘edible‘ laser out of jelly (or Jello-o for American viewers). In this they didn’t quite succeed, but they were able to get gelatin doped with fluorescein dye to lase and this could then be eaten, as the dye “was almost non-toxic”.

In some recent work (Optics Letters 38 1669 (2013), behind a paywall, sorry) work between my group and Alper Kiraz‘s at Koc University in Istanbul we have had a shot at making both slightly unusual and potentially edible substances lase, namely a microscopic droplet of water. This too is based on using the water droplet as a host medium for the lasing material (Rhodamine-B – which is likely a carcinogen, so you might not want to digest it) and a bit of glycerol for stability. Our work is based on using optical tweezers to trap the droplet in mid-air using an infra-red laser and then we illuminate it with a second pulsed, high energy, (green) laser. The droplets (water aerosols) are around 10 microns, so 10 millionths of a meter, in diameter. Pretty small! The nice thing about water droplets is that they tend to form very nice spheres, and this gives us a very simple way to form an optical cavity. Normally we would use mirrors to form the cavity, for example in a Helium-Neon laser, but here like that gets into the droplet can undergo total internal reflection and can get trapped inside. This enables a large optical field to build up and gets us above the energy threshold needed to see any laser action. This effect is called a whispering gallery resonance, and is the same effect as seen (or heard) in cathedral domes, like the ‘Whispering Gallery‘ in St. Paul’s Cathedral in London. Here, if you stand on one side of the gallery and whisper into the wall, the sound is able to creep around so that your friend on the opposite side of the dome can hear you clearly.

In the figure below you can see the output from the laser – these are in the form of cavity ‘modes’, which are the little spikes in the diagrams. The top two figures show the outputs below the laser threshold, while the third shows a higher pump energy and laser action. The inset shows the trapped laser droplet.

Droplet Laser Modes

The figure shows the outputs of the cavity formed by the water droplet – the peaks indicate the ‘modes’ of the cavity, where a whole number of wavelengths fit round the droplet circumference. The top two figures show the output below the laser threshold, while the lower figure shows ‘laser modes’.

Our laser is not the first to make use of water droplets as the lasing host – there has been work on bigger droplets trapped using ultrasound and on surfaces but ours is the first to make use of optical tweezers to hold the laser. This should enable us to look at very small droplets, explore tuning of the laser through controlled heating, and it gives us significant control over the movement and placement of the droplets.

So what could you do with a droplet laser? Well there is quite a lot of work on using whispering gallery modes in solid spheres as sensors, and one could imagine extending this to liquid spheres. As we can easily place things within the droplets we could also use them as more general probes – the idea would be that perturbation of the laser in some way would allow us to probe the contents of the droplet. It might also allow us to sensitively probe the shape and dynamics of the droplet, which is very hard to do otherwise due to the very strong surface tension. We are only just starting to think about the possibilities.

On a personal note, this is an experiment that I thought up many years ago, and which we started to do when I worked in St. Andrews. We got some preliminary results showing droplet fluorescence but then the PhD student working on it had to write up and finish and we never quite got back to it. So it’s very satisfying to have finally done it, with a little help from my friends, and also that no-one else has done it in the meantime!

[1] Turns out this was a phrase used by Art Schawlow (see here, well worth a read), which means either great minds think alike, or I pinched it from him. I’ll stick with the former.

Physics and Life Sciences/Biophotonics Initiative

It seems appropriate that as EPSRC starts up its ‘Understanding the Physics of Life‘ network (also discussed by Athene Donald on Occam’s Razor) that we in Dundee are also starting up a new collaborative project between Life Sciences and Physics. The College of Life Sciences in Dundee is a world leading centre of research in a range of biological topics and in many ways is the dominant research centre in Dundee. Physics plays a rather more modest role in the life of the University, but in recent years we have been gathering significant momentum, and a range of pilot projects between physics and life sciences have now started to deliver results.

We have had some grant success recently as well, playing a part in an MRC Optical Microscopy proposal funded through Life Sciences and we have also just been awarded an Innovative Doctoral Programme ITN based at Dundee to help train a number of early career researchers in fully interdisciplinary projects. This should become active next year and lead to a significant boost in the number of projects we run between our two departments.

To try and cement these relationships further we have also established a trial project to host a space within Life Sciences that can be used by physicists to develop new techniques and tools side by side with the biologists. Our initial goals are to look at the development of new light sheet microscopy devices as well as test out in-house developed lasers for suitability as multiphoton imaging sources. We have a one year postdoctoral position advertised at present to work on these topics and also try and act as an interface point for staff looking to try out new pilot projects – including some of my own on intracellular optical manipulation. So if you are looking for a new interdisciplinary biophotonics role or know someone who is, please apply at the link above (you can contact me for more info).

We are also expanding our staff in biophysics – we have just welcomed Dr Ulrich Zachariae to the Division, who will work on computational biophysics problems, and hopefully will form close ties to the Drug Discovery Unit here, and will be welcoming a further biophotonics staff member next month. We have also been very lucky in our recruitment process for ‘Dundee Fellows’ and we’ll be adding another computational biophysicist later in the year, and hopefully to other biophysics areas depending on if offers are accepted.

Our goal in all this is to try and tackle new and bigger scientific problems by working together and we have exciting plans to try and make this area grow further at Dundee. So I am hopeful that we can make a big mark in the ever expanding research world at the physics and life sciences interface.