A list

Possibly useful for a number of reasons (especially if you are convening a conference):

http://sites.google.com/site/scienceprofsuk/the-list

Things that I noticed while compiling (note this is based only on RAE-18 returned departments):

There are 36 female Chemistry professors/180 total female academics (unless I miscounted/mistyped [Ed 19/04/11: I had - I'd managed to miss Liverpool, now corected]). UCL does the best with 5 of these.

23 hold research fellowships, mostly Royal Society, EPSRC or Dorothy Hodgkin.  There are 2 FRS’s.

York does really well on total representation.  I had heard good things about their activities with Athena Swan too.

Alison is a popular first name, as is Christine.

Crystallography and solid state inorganic chemistry seem fairly popular, as is computational chemistry.

Some university websites are diabolical if you want to find the staff pages, and there are interesting things departments have done to look like they had more staff.  Others were very easy to navigate – these tend to have followed a standard format and have probably bought a package from an outside provider (as they were quite similar).

I’m sure there is a lot more analysis that could be done, but I really need to procrastinate less.

[Ed 19/04/11]: Also, let me know if there are any additional corrections, and if you want to generate an extended list – then I can link to it from here.

BBC Chemical Historian – Grade C

Way back in the distant past, when I was a fresh-faced young academic ready to inflict new and exciting things on undergraduates, I developed a scenario-based problem for use in our final year.  Having found it years later, I now realise it was an early attempt at a Problem-based learning (PBL) scenario, before this method of teaching had really received much exposure in Higher Education in the UK.  PBL essentially gives students an open-ended problem space to explore and develop.  Properly run, “facilitators” guide students through the process of thinking through a problem (mostly by doing the two-year-old trick of repeatedly asking “Why?” to every undergraduate response/question, but in a slightly more sophisticated fashion).  Students then proceed along a natural investigation path to solve the problem, or at least come up with a really good go at it (as there may be no actual solution in the traditional sense).

Fairly quickly in my career, I ended up meeting Tina Overton, who is an excellent practitioner of this method, and I can highly recommend to anyone teaching undergraduate chemistry, especially analytical chemistry, many of her PBL resources.  They are well thought through, and evaluated for success with students.  In a future post, I will hopefully describe our adaptation of the scenario “New Drugs for Old” for the local climate: “Dragon’s Den”.  As part of our first year programme, the course containing this scenario has been so successful and popular that we have had to cap our entry numbers!

But for now, and for those who are interested, I figured I should make available my original work for adaptation for those who are interested.  Please take it with the caveat that it was developed many years ago …

Students are given a variety of materials to start with.  This includes:

• An advertisement for BBC Chemical Historian
• An email from the director of Chemical Archeology
• A news clipping from the local paper
• A hand-written letter from Chris Ewans (the Hero of the piece) to his wife, describing the plague in more graphic detail, including the key facts that it attacks bone (jellifying its victims) and causes skin lesions.  Unfortunately, I’ve lost the original, but it’s a good place to start an adaption if you want to use the material.

The overall scenario is then presented to students is as follows:

“You and two/three friends have just taken up positions as chemical historians working for BBC television.  Your aim: To do some detective work and discover how Chris Ewans saved his crew in 2006.  You have all the information that you need to create the TV show – to be historically accurate may be a little more difficult.  Your boss wants you to produce a small preliminary show that details how Chris worked out what sort of drug was required, how he would have gone about firstly designing it and synthesising it (this should include a moderately detailed synthetic scheme, but be careful to try and be as chemically accurate as possible – other scientists will be watching your show), a few descriptors on chemical technology of the time that Chris may have used, including some diagrams/schematics of apparatus, and finally discuss how he might have tested his compound.

Remember that you only have sketchy information.  You need to make a story that is plausible that others will understand, is consistent with the facts, and fits your supervisors requirements.

You will have to present your groups findings to a group of other teams working in the area for comment.”

I had prepared a guide for facilitators/coordinators, but it is very brief.

I’d be interested if anyone finds this material useful and especially if you adapt it for your own purposes.

Xaim – getting it working on 64 bit Ubuntu

While at MIT last year on sabbatical, I was introduced to AIM calculations.  The exact nature of the chemical bond is highly controversial and always has attracted debate and interest, as highlighted recently in Nature in the article “Beyond the bond“.  AIM stands for Atoms in Molecules, an approach developed by Richard Bader at MacMaster university, and is another way of approaching an understanding of what we call a ‘bond’ that has seemed surprisingly effective.  I had heard of this approach before and had been intrigued, but not found the time to explore any further.  Thus, on sabbatical, I was blessed with some time to try out AIM, and, even better, an enthusiastic graduate student who had been learning about AIM and was happy to tell me everything he knew.  He lent me his book “Atoms in Molecules: An Introduction“, by Paul Popelier at Manchester, which I can highly recommend as presenting a clear and readable guide to starting out with AIM. (I’d met Paul once to discuss Ionic liquids (an area of our research) and he was immensely helpful and nice, another reason to recommend this book :)

One of the programmes used for AIM analysis at MIT is XAim.   It is linux-based and produces nice diagrams that can describe key features of the wave-function from Gaussian and ADF wfn outputs, such as the electronic density rho and the laplacian of the density.  These features are used to interpret ‘bonding’ characteristics in a molecule and can provide surprising results, relative to what may be expected from classical valence bond theory.  Wfn output files are generated in Gaussian using the output=wfn keyword in the route card (the part that starts with # and defines the parameters of the calculation), along with a filename for the wfn file at the end of the geometry description, separated by a single line.  A fuller description is available on Gaussian’s website.

However, arriving back in the UK meant getting my own copy of Xaim.  Xaim is available only as binaries and unfortunately, on Ubuntu 10 I soon discovered it wasn’t working with the error:

/usr/local/XAIM/bin/Xaim: No such file or directory.

This was a rather obscure error, since it didn’t really hint at which file or directory was missing and the program had been properly installed with the correct permissions.  Online searching also got me nowhere, except to realise a couple of other people had had the same issue.  I had a sneaking suspicion that it might be to do with libraries, but where to start?

Well, since it was a boring sunday afternoon and I was procrastinating on a number of other projects (ok, I was running stuff in the background), I finally got around to sorting this out.  It took me about 4 hours of trawling through usegroups, so hopefully these instructions are useful to someone to save them a stack of time:

First thing I tried was to look for the missing libraries using ldd.  Unfortunately ldd gave me the following error:

$ ldd Xaim
not a dynamic executable

I solved this from the following forum post: http://ubuntuforums.org/archive/index.php/t-1041476.html by downloading the ia32 libraries:

sudo apt-get install ia32-libs

Running XAim again now gave the following error:

./Xaim: error while loading shared libraries: libXm.so.3: cannot open shared object file: No such file or directory

with ldd of Xaim now working and affording the following response:

$ ldd Xaim
linux-gate.so.1 =>  (0xf77bb000)
libm.so.6 => /lib32/libm.so.6 (0xf777a000)
libXm.so.3 => not found
libXt.so.6 => /usr/lib32/libXt.so.6 (0xf7726000)
libX11.so.6 => /usr/lib32/libX11.so.6 (0xf7609000)
libc.so.6 => /lib32/libc.so.6 (0xf74af000)
/lib/ld-linux.so.2 (0xf77bc000)
libSM.so.6 => /usr/lib32/libSM.so.6 (0xf74a6000)
libICE.so.6 => /usr/lib32/libICE.so.6 (0xf748c000)
libxcb.so.1 => /usr/lib32/libxcb.so.1 (0xf7472000)
libdl.so.2 => /lib32/libdl.so.2 (0xf746e000)
libuuid.so.1 => /lib32/libuuid.so.1 (0xf7469000)
libXau.so.6 => /usr/lib32/libXau.so.6 (0xf7465000)
libXdmcp.so.6 => /usr/lib32/libXdmcp.so.6 (0xf745e000)

A forum post at http://ubuntuforums.org/showthread.php?t=39556 suggested that libmotif3 needed to be installed.  I tried this:

sudo apt-get install libmotif3

but still got the same ldd response, even though /usr/lib/libXm.so.3 was now present.  Linking it to /lib32 or /usr/lib32 also did not help, the reason being that it was a 64-bit library.

$ ldconfig -p |grep -i libXm.so.3
libXm.so.3 (libc6,x86-64) => /usr/lib/libXm.so.3

confirmed by

$ ./Xaim
./Xaim: error while loading shared libraries: libXm.so.3: wrong ELF class: ELFCLASS64

This therefore required a manual install of the 32 bit libraries to override.  These were downloaded from ftp://ftp.uni-hannover.de/pub/mirror/linux/ubuntu/pool/multiverse/o/openmotif/libmotif3_2.2.3-2_i386.deb

and installed using:

sudo dpkg -i –force-architecture libmotif3_2.2.3-2_i386.deb

(which gave a number of warnings).

[edit: a better method for installing the 32-bit library is as follows:

mkdir libmotif
sudo dpkg -X libmotif3_2.2.3-2_i386.deb libmotif
cd libmotif/usr/lib
sudo cp libXm.so.3.0.2 /usr/lib32/
cd /usr/lib32
sudo ln -s libXm.so.3.0.2 libXm.so.3

this installs the correct library in the correct place and stops ubuntu automatically upgrading you to the 64-bit version, then rendering Xaim unworkable again.]

ldconfig now told me that all the locations were the correct 32bit architecture:

$ ldconfig -p |grep -i libXm.so.3
libXm.so.3 (libc6) => /lib32/libXm.so.3
libXm.so.3 (libc6) => /usr/lib/libXm.so.3
libXm.so.3 (libc6) => /usr/lib32/libXm.so.3

Although ld was now giving issues:

$ ld /usr/local/XAIM/bin/Xaim
ld: i386 architecture of input file `/usr/local/XAIM/bin/Xaim’ is incompatible with i386:x86-64 output

but now running Xaim worked (provided it was run through X by first invoking xhost + and then using ssh -X option).  Hurrah!

So hopefully you can look forward to some lovely maps produced by XAim in our future papers.

Whither the academy

I was just reading an interesting comment by Anne Peattie about her experiences with non-open access literature.  She raises the point that, out of a direct academic circle, she is unable to access most literature, especially that which is deemed as “high impact” (read: Nature and Science).  This reminded me of something I have been thinking of for quite a while in the context of what does a University now a days provide for an academic, in these days of increasing corporatisation.  That is, what makes Universities attractive and competitive employers for the best minds?  Many of us joined so that we could apply our talents to interesting and difficult long-term research problems, and to communicate our love of science to the inspired next generation.  Many now find they spend increasing time filling in pointless administrative forms, dealing with ‘customers’ and facing increasing managerial pressure to behave as if we were in business (but of course for around 1/3 the salary we could potentially earn in the “real world”). I think we are soon approaching a tipping point.

So what ties disgruntled researchers to the University sector, where other opportunities clearly seem better?  Why bother having to earn grants to pay your salary via the university if you could just do it directly?

Some idea of flexible working still holds, although this is gradually being eroded by requirements to have one’s wherabouts traced continually.  Other employment at this level has reasonable flexibility. And certainly self-employment allows as much flexibility as you can manage.

Partially the requirement for large equipment is limiting, but nowadays contract agreements with a local centre or analytical lab can often be more cost effective than the University-run operations (and often more reliable).  This is down to often ineffective use of the University’s economy of scale.  Lab space is likely (I haven’t costed it though) to be cheaper to rent than the university space charging models. And if you are doing computational chemistry, then services such as Amazon’s AWS can provide cheap access to Petaflops.  This may be adequate for a majority of researchers, especially those not at the largest national institutes.

The two big drivers that therefore hold the whole thing together, from my point of view are these:

1. Letterhead.  The University letterhead still allows access to grants, ability to be taken seriously by journal editors and credibility.  With the rise of open access publishing through blogs and alternative online resources the necessity for journals become less of an issue, especially as these are becoming vehicles for esteem factors driven by University rankings, rather than outlets for scientific discourse.  Getting grants, however, is still likely to be restricted to the anointed few.  A shame, because, as highlighted above, grant agencies may find that freelance researchers give them greater value for money.  However, the intrepid freelancer may be able to find alternative private sponsors.

2. Literature.  This is the biggest hold.  Access to up to date articles to keep up with the best science is still a significant requirement and this access is denied (as highlighted in Anne’s article) one the University setting is left.  However, there is an interesting trend to smaller Universities significantly downsizing their libraries anyway (see links in “zero-sum publishing game”).  Unless you are at a big institution (and even if you are) you are likely to be missing some critical literature that is hard to come by.  More and more is accessible from central resources, such as the British Library, although for a price.  However, as we get access to more open-source journals of good quality, the need to go through the university for access to restricted hallows of information lessens.

All this points to science as a hobby becoming back in vogue in the not-too-distant future, as options for this are emerging, alongside a vibrant diy-science community.  There will be less control by Universities, meaning they will have to push their brand harder.  The upcoming battle will be interesting to watch …

A short idea on traceability

More and more, the unique identity of researchers is an issue that various agencies are trying to resolve.  This includes resolution through commercial servers, such as Thompson-Reuters Researcher ID, or through [soon to be running] not-for-profit organisations such as the ORCID service (see article here).  Ad-hoc services can also serve to help, including the more ‘social’-networking approach of academia.edu.

However, one thing that is missing from many of these efforts is a unique researcher email.  Whenever a paper is published, the corresponding author must include their email address for replies and requests (for example for extra data, clarifications or preprints).  With the mobility of today’s researchers then, this can be an issue in both tracing material, and in identifying uniqueness.  To solve this, a researcher email server should be initiated alongside the other identification techniques – any time a research goes to publish, they should thus be required to utilise this central contact point.  It would be relatively straight forward for journals to request this, and should help tracking down researchers as they move from institution to institution.

 

<addendum>  Further comments and ideas at Friendfeed.

Service Learning – The Sessions

In a previous post, I described my plans for a short service-learning project to be run with third-year undergraduate students.

The session went mainly as planned, although, as with many first time sessions there could have been some improvements.  The teaching room was far from ideal – being a large computing room, so students were spread out and it was difficult for them to get into groups to discuss things, as I had conceived.  The first question of the session revolved around perceptions of science by the general public.  Students were asked to come up with a list and discuss in pairs, and then their ideas were collated. The results were interesting, although I wonder how much the answers were skewed towards their perception of what they thought I wanted to hear, especially given the title of the session had been given as Science, ethics and the public.

Students responded as follows regarding the public view of science and scientists:

• Unethical
• People think you are smart and “geeky”
• People confuse science with “bad science”
• All scientists are Mad Scientists (ed: it was noted that the only one we know of who fits the stereotype is Martyn Poliakoff)
• Science is Heresy (ie religion vs science)
• “Nuclear is bad”
• Some people find science interesting (but not cool)
• Many people think science is useful
• Science is a window to a brighter world (but may be tinged with cynicism)
• Chemists always in a lab ‘playing’ with chemicals  (ie not relevant)
• Caused all the world’s problems or solved all the world’s problems (depending on who you talk to)

I was quite disappointed that many were quite negative.  They also seemed to reflect the views the students had of themselves in part, ie a little embarrassed to be doing science (inferred through the eg ‘not cool’ addendum and the use of geeky as derogative).  Our battle for science marketing still has a ways to go in the UK, it seems.

Students then proposed methods to engage people in science:

• Science video blogs
• More in-depth education (the example given was science TV for kids in the Czech republic)
• Better/more press releases
• Science Festivals
• Nobel Prizes (topical as they had been announced that week)
• More popular science TV – especially comedy like Big Bang Theory
• A broader science curriculum (which is in-line with the usual government proposals)
• Science Museums
• Improvements in Science Journalism (driven by blogs)
• Better simplification of complex topics

Interesting here I thought was the inclusion of video and blogs as media – these are clearly on student radar.  Two of the students did engage me in a counter argument though: they perceived all these measures as only being of interest to those already interested in science. They identified the people that needed the most science input as those who classically don’t engage in science, and therefore would not be part of the target audience for the above activities.  The problem here is that if they are parents, they might also avoid (deliberately or passively) engaging their children – and this is where an interest in science is critical.  I agree with the students that this is certainly where we need to look at innovative ways to engage this segment of the population, not covered by the standard approaches. [note post-post: also highlighted today in the guardian http://www.guardian.co.uk/science/blog/2010/oct/26/skeptics-pub-stephen-fry]

The rest of the session was devoted to coming up with ideas that the students could enact to engage the wider community.  These were presented, collated and voted upon to generate a short-list.  Finally three projects were selected by the students to carry out:

• Bottle rockets
• Cake
• Food Science Experiments Youtube channel

There were some good ideas that didn’t get the popular vote, or were impractical.  One suggestion was to work with a multi-national fast food outlet to add science-factoids (perhaps about the food you are eating) to napkins or wrappers.  I think this would be excellent in practice, but was a bit out of our league for a short project.  Next time perhaps … Similarly, a science column in the local student paper was also an excellent idea, but there were too few takers.  There were also a couple of sillier ideas, such as developing a chemistry-themed crime fighting organisation.

In retrospect, I’m reticent about having allowed too much freedom in this part; it would have been nicer for students to interact with a range of community partners, some of whom they might not have considered as beneficiaries of chemistry and their skills.  The increased freedom was primarily down to the short notice, meaning no time to organise formal community partners.  The lack of time to organise a block of funding (as this must be procured externally) also made this less than ideal.  Next time, we will hopefully have a larger lead time (ie > 1 week + other teaching commitments) to enhance the outcomes.

On the upside, because the students have selected their own project, the level of contribution should be enhanced.  The second session involved more detailed planning, with feasibility forms (much like grant-request forms) and peer review by the other teams.  Most of the flaws were easily spotted, and revised forms completed.  Next post … how did it all go (for Team Bottle Rocket!).

Service Learning – bringing science to the community

This afternoon we will be trying an experiment in “service learning” – a concept introduced to me over the summer by Susan Sutheimer from Green Mountain College in Vermont, one of the top US colleges for undergraduate education in environmental and sustainable practices.  Service learning is a method of teaching that they have used successfully in their Green Chemistry programme, and involves engaging students actively in projects that directly benefit the community.  One of her more elegant examples (in my opinion) was the natural dying of romper suits (known in the US as ‘onesies‘) that were later donated to a local charity.  You can read more about Susan’s approach to Service learning and the developments they have made in J. Chem. Ed., 85 (2), 231-233, 2008.

Our plan today is to do a more general science and society session as part of the final year research skills module.  Why include this in research skills?  The reason is we think it is extremely important for our students to be able to interact with the community to share their enthusiasm about science (that which hasn’t been beaten out of them by three years of modern university education), especially if they are going on to apply their skills to research.  It will allow them to develop an appreciation for how their science and research can be applied to wider problems of society, or at least start to get them to think in this context.  However, in our session we do not just plan to discuss what science can do for the community, but what the community can do for science.  This is little touched on in conventional academia, which is filled with Impact statements and the like, imposed by research councils to demonstrate value for money for the tax-payer.  Often academics feel under seige in the constant need to justify the utility of their work, especially when the goals/questions are much broader in a specific attempt to generate unforseen impacts.

The role that the community can play is becoming significant.  As scientific data is becoming more complex and relying more on sampling of larger and larger populations, data collection and processing is often becoming the limiting step.  Often, computing programmes are not yet sophisticated enough to deal with the classification methodology required; or physical data collection is more than one research team can handle.  The use of the community to help now has its own term: “Citizen Science” and has been helped enormously to come to fruition by the advent of general access to the internet.

Citizen Science aims to help optimise processing bottle-necks, for which a sophisticated analysis (easy for humans but difficult for computers) is required, and also help to engage the public in science.  Initial examples, such as SETI@home involved public computers, but in a passive way.  Recently there have been a couple of stand-out examples requiring active participation of the citizen scientist:

• Galaxy Zoo
• Fold-It!

Galaxy Zoo recruits the general population to analyse galaxy structures – an example of too much data that is too complex yet to be sorted by computers.  This approach could potentially lend itself to other complex datasets, such as (protein) electron microscopy (EM) data, where snapshots of thousands of molecules need to be grouped and classified to generate a 3D image.

Fold-It harnesses the ability of humans to identify improved strategies for energy minimisation of protein structures, over the current algorithms used computationally.  This approach has already been successful in generating experimentally unknown structures that are much better suited to applications such as drug design.

A summary of these approaches was published in the journal Nature as one of their news features.

Organisations such as the BBC and the Guardian are also actively engaging in involving the public in science and related journalism.  Sucess has been had over many years with the bird-watch survey, publicised through Radio 4, that gets people to report in birds that they see in their local area.  This is an example of how the broad geographical location of citizens can aid in getting simultaneous observational data that would be extremely difficult with only a small team of scientists, even aided by specialised equipment.

As part of our session, we will hopefully develop awareness in our future scientists of how they might engage the public with their science in an active fashion.

Of course this is not all one way, and the major outcome of the session will be for the students to contribute to the local community with their current science.  My approach will be to break them into groups to discuss ideas of what they might contribute, come up with a list of suggestions, get a vote for some of the most popular ones and then spend time this week and next week organising to make it happen.  For me, I am quite excited to see what these students come up with – this particular group were exposed to problem-based learning as part of one of our newly developed first-year modules, and some of the groups excelled in their creativity and attention to detail.  The ‘service learning’ approach is along similar lines, but now it will be for real.  How they cope two years later with more experience will be exciting to see and I have high hopes.

We have already brainstormed some ideas for what they could contribute:

• Setting up information sheets on nutrition for the local farm vegtable box scheme
• Food education stand at the local food fair
• Taking out a primary school group to do an activity like water-sampling, or going out and doing a chemistry show
• Having a science bake-sale (with appropriate information to the public) and donation to a charity – this idea was inspired by the excellent ‘Not so humble pie’ science cookie roundup and the periodic table cupcakes.
• Painting a science/chemistry mural on our local building site fence (we have made enquiries and have preliminary permissions :).  This has the advantage of being up for more than a year, fully exposed to the entire public of Bangor.  We might also get local artists involved in this, as I have some contacts. [may need to combine the above bake sale to raise money for paint though!]

The real science content may vary, but we hope the students primarily have fun and get some engagement with the public.  Wish me luck for this afternoon!