Physics: the view from the bath

The View from the Bath

2008-01-04T03:20:22Z

If anyone is reading this and is also a subscriber to Physics World from the Institute of Physics, then you may have seen my latest effort at writing on topics in physics at the back of the January 2008 issue. It's in the "Lateral Thoughts" section, entitled "Post-modern Physics - bathtub style". The original title was "Post-modern Physics: the view from the bath", but that was too long for the magazine.

The view from the bath is a reflection on the fact that most of my best ideas come from meditating in the bath. To that end, we have just had a nice new soaker tub installed!

I will be adding a few more articles of this type to this blog as time permits. I will mostly be commenting on things that crop up in Physics Education, as opposed to Physics Research. Topics such as "What should we be teaching?" and "How should we be teaching?" are the order of the day. As I am teaching two courses of first year physics this term, my time might be a bit limited. As both of these courses are quite large (165 and 90 students respectively), teaching them requires extra attention and some different techniques to small classes. I'll try and mention my ideas.

Andrew Robinson, Physics and Engineering Physics

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The Masters of Uncertainty

2008-01-04T03:44:36Z

Some time ago, I was acting as the exam invigilator in one of our large first year Physics final exams. We were sharing the grim Saturday morning experience of a three hour examination with other classes in Economics and Sociology. Now in Canadian exams, the students tend to ask more questions than I was brought up to expect , coming from the British exam system, where nobody dares ask a question! This makes the invigilation a bit more stimulating, but only just. Confirming the worst prejudices of most physicists when it comes to sociology, all of the sociology students had left after 90 minutes, leaving the grim faced physics and economics students to sweat it out to the bitter end.

In a moment of boredom, I glanced at the rubric on the front of an abandoned Sociology paper. It was a multiple choice exam, and the instructions stated “Pick the answer which is most nearly right”. I made the comment to a fellow-Physicist that our students would hate that. First year students want “The Answer”, of which there is only one possible. But wait a minute, we are physicists. We understand the difference between accuracy and precision, we understand statistical fluctuations, we know that the Truth, the Whole Truth and nothing but the Truth has to have error bars appended, we quantify uncertainly and we wear our underpants outside our trousers. Sorry, got carried away there. So why do we have this variation between what we actually do, which is assign a certain uncertainty to every result, and what the general public, including first year students, think we do, which is to provide “The Answer”?

We can see this in recent debates and opinions in our local newspaper, the Saskatoon Star Phoenix, where there have been debates on global warming (which is an international socialist conspiracy, apparently), too much salt in the diet and energy saving light bulbs are a bad idea because of the mercury which they contain. Inevitably, the nay-sayers mention to a single article written by a scientist that dissents from the majority view and say, “Look there! A Scientist says this, so it must be correct”. This of course ignores the many other scientific articles which take the opposite viewpoint. As practising scientists we are used to weighing up the evidence, which may come from multiple sources, with a wide variation in credibility and conclusions, so that we can sum up our final position. Actually, non-scientists have to do exactly the same thing in real life too – a similar process goes on when you make a decision to buy a new car, for example. So why does the public think that we approach problems any differently? I think part of the problem comes from the science taught in schools. There are very few examples of problems set which have large quantities of data from different data sets, some of dubious quality or relevance, which then require critical examination. Obtaining “The Answer” for this type of problem may be difficult, if not impossible. Being able to do this sort of problem is very useful in many walks of life such as management, intelligence officers, child rearing, to name but a few. So why don’t we teach people how to do it?
When I came to mark the physics exam, I came across an answer to a problem which I had set on Young’s double slit experiment, where I gave a certain amount of information and required the distance between the two slits to be calculated. A classic example of a problem with “An Answer”! The periphery of the page was covered in a set of hieroglyphics which even Thomas Young himself, a noted translator of ancient languages, would have been hard put to translate. The only thing resembling an answer was near the middle of the page, where the phrase “Pretty close” was visible. Imagine my dilemma. Do I give marks, for what is essentially a true statement, or am I looking for the “Answer”. Fortunately, I was spared this tough decision; in the rubric for my exam, there was the instruction “No credit will be given for a correct answer without supporting working”. Some things are certain, even for the masters of uncertainty.

Who is this Andrew Robinson anyway?

2008-01-08T22:21:02Z

It is a sad fact that Andrew Robinson is a rather common name in the English speaking world. Robinson is supposed to be the fourth most common surname after Smith, Jones and Brown. While I was a student at Bath University, the top rugby player at the local club (and an England International) was Andy Robinson. When I worked at BNFL for a while, the chief chemist was called, you've guessed it, Andrew Robinson. Now I am writing about physics, there is a very good author of biographies of famous scientists called, Andrew Robinson. His website is http://www.andrew-robinson.org/,

A quick look through Google also reveals other Andrew or Andy Robinson's associated with physics in various capacities:

Andy Robinson, Semiconductor Physics Group, Cavendish Laboratory and Andrew Robinson at the Dept. of Physics, Rochester Institute of Technology.

Finally, there is also Andrew J Robinson, an actor who player Garak on Star Trek Deep Space Nine (a tenuous link to physics)

If I've forgotten anyone, then as one Andrew Robinson to another, I'm sorry. Please let me know and I'll add you to the hall of fame.

If you need to contact me then please do so by e-mail at

andrew DOT robinson AT usask DOT ca

My website is http://physics.usask.ca/~andrew/robinson.html

But Is It Really Physics?

2008-01-09T02:17:23Z

The motivation for writing this article has its origins in a design study project for final year undergraduate Engineering Physics students at the University of Saskatchewan, which I devised and supervised during the academic year 2005-6. Our students form design teams of 3 or 4 people and then tackle a design project over the whole of their final year which can be of any particular theme. These projects are devised either by faculty members or by collaborating scientists and engineers from outside research organizations, such as the Canadian Light Source, or the Saskatchewan Research Council. Some projects incorporate a considerable mechanical or electrical design component, others involve development of electronics systems and some are software development projects, usually aimed at solving a particular scientific or engineering project. The projects which were offered in 2005-6 included: a microcontroller based grain-dryer, software for calculating the optimum position for wind turbines for power generation, developing hardware based optical alignment systems for the Canadian Light Source and my own offering, development of a hardware accelerated search system for identifying proteins from mass spectrometry data. We find that these projects are extremely valuable in teaching our students a formal design process, project management and presentation skills, both oral and written.
My own offering for the project fell squarely in the area of proteomics [1]. The problem to be solved is to take a sample, of biological origin, and identify the proteins within it. The presence or absence of particular proteins is significant as indicators of disease, or other characteristics of the organism, such as drought resistance in plants. Proteins are large molecules, consisting of chains of amino acids which are not readily analysed easily, so the preferred method of protein identification is to use a chemical reaction to break up the protein into smaller fragments, known as peptides. Typically each peptide contains between 4 and 20 amino acid residues. We can then use an analytical technique known as tandem mass spectrometry to identify the constituent amino acids within the peptide and the order in which they appear in the peptide. This amino acid sequence in the peptide is usually a unique indicator of which protein the peptide originated from. There are 20 naturally occurring amino acids, each one of which can be represented by a single letter of the alphabet. The problem in essence is one of text searching for a small sub-string (the peptide) from a large number of very long strings (the protein sequence) . One solution to the problem the use of an electronic device known as a Field Programmable Gate Array (FPGA) system [2], which can be thought of as lots of logic circuits which can be configured as many parallel processors to carry out simple and repetitive tasks [3]. This is widely used as a digital signal processing device in the communications industry, particularly in cable television applications. This type of programmable electronic device falls in the computer science field for programming the device and developing the algorithms and electrical engineering for a detailed knowledge of the workings of the FPGA and many of the applications.
As you will have noticed, although protein identification is an important scientific problem in the life sciences, the directly relevant subject disciplines are anything but physics, hence the title of this article. However, it quickly became apparent (as I had hoped) that the skill sets required to solve this type of problem are ones possessed by final year undergraduate physics students.

]]> In this article I will to explore how the physics profession enables interdisciplinary research either directly applying our knowledge of physics or by using the skills acquired by having formal training in physics. I will discuss the ramifications of these things to the content and design of undergraduate degrees, to the planning of graduate degree programs where such research is undertaken, post-doctoral and other research and to how such research is perceived within a Physics department. I will also touch upon such vital matters as getting academic tenure and finding research funding for such projects. I hope that these opinions based on my own experiences and my observations of other people’s experiences, will be of use to those readers who are going to choose physics as a career, those who are thinking of studying physics at university and those in academic positions who are responsible for physics teaching and research. It is intended to provoke a discussion, not provide a prescription for the future. Many of the points raised may have already been addressed in the policies of some post-secondary institutions and I look forward to comments from others in the physics profession.
There are many areas where physics has been or is becoming increasing important in other traditional subject areas of scientific research, as well as in new emerging fields.
I will draw on personal experience in one field of interdisciplinary studies: that of surface science [4]. This is a highly interdisciplinary research field, which is concerned with the properties and behaviour of surfaces of materials, atoms or molecules adsorbed onto those surfaces, chemical reactions on surface and growth of layers of ultra-thin films on surfaces. Practitioners of surface science may be found in Physics, Chemistry, Materials Science and Engineering Departments. My particular research interests lie in the structure of atomic adsorbates on metal surfaces. So how did I end up interested in proteomics problems?
The answer is quite simple: I married a Canadian Physicist! My wife, Katie, who is also a surface scientist, wanted to carry out post-doctoral research on metal oxide surfaces at Oxford University, so I needed to find gainful employment in the Oxford area.
It is instructive to note that Katie, having graduated from Queens’ University, Kingston, Ontario with a doctorate in Physics, went to do research in the Inorganic Chemistry department at Oxford, because that was where much of the surface science research was done. This mobility between academic disciplines is typical in surface science.
I was fortunate to secure a job with a proteomics company in the Oxford area, Oxford Glycosciences (OGS), sadly now defunct owing to a corporate takeover. OGS were looking for a scientist who understood mass spectrometry and could program computers to help them in their quest to automate protein identification using high-throughput mass spectrometry. My physics based skill-set matched rather well with their requirements, even though my biological knowledge was severely lacking, and so I got the job, as the only physicist working with a team of biologist, chemists and information technology specialists. I quickly realized that the most valuable skill stemming from a physics background was the ability to reduce a given problem to its bare essentials and construct a simple model and hence provide a solution [5]. As the human genome project was just coming to fruition [6], this was an intensely vibrant and lively time within the life sciences field and I spent four enjoyable years working on these problems [7].
I have touched on two areas of science where physics skills are essential. There are many other examples of this. Surface Science is moving towards biology, with a great interest in biological surfaces [8] and also towards astronomy, with initiatives to study surface reactions of molecules at surfaces of grains of material in space [9]. One of the hot research topics in condensed matter physics is in the area of “soft condensed matter”, the study of colloids, gels, liquid crystals, and biologically important systems such as cell membranes [10]. No discussion of “hot topics” in physics at present would be complete without a reference to nanoscale physics [11], where physics based experimental techniques are essential, as is a detailed understanding of quantum effects.
We should also not forget that biology itself, and particularly the great advances made in molecular biology [12] benefited greatly from the influx of physicists after World War Two. The names of Francis Crick and Maurice Wilkins [13], two of the co-discoverers of the structure of DNA spring immediately to mind, but there are many others too. Most of these scientists were trained as physicists, but then chose to apply their knowledge in the biological area. It is interesting to note that Wilkins worked in the newly established Biophysics laboratory at King’s College London. This was an early attempt to emphasize the overlap of physical and life sciences.
As physics merges with other subject areas, we now have to ask ourselves, what makes a physicist useful in these emerging fields? We would hope that training in physics would lead to a skilled professional who is able to analyze a problem and dissect it down to a basic and simplified model [5]. Of course, part of the professional skill of the physicist is to know when the model is too simple to be useful. The “model” for the problem will include a mathematical description, so we also require skills in devising and solving the mathematical framework. The model must be tested against known data either by experiment or by some form of modeling and simulation. We also require some basic ethics in the training too, models, experiments and results must be described honestly. Finally, and this is often the most neglected element in physics training, the physicist has to be able to communicate the ideas to others, not only within physics, but to non-physicists as well. It may be that the specialist knowledge of traditional areas of physics, such as quantum mechanics, classical mechanics or thermodynamics are less important than the skills learnt while mastering those subjects.
Now we need to analyze the training opportunities at various different levels in the physics academic community. I will confine myself to the teaching, training and practice of physics within the post-secondary (University) system in this article; many of the skills required in industry will be similar, but that is an article in itself.

Undergraduate Level Physics

In some ways, training physicists with useful skills in other disciplines is easiest to visualize at the undergraduate level. We need to ensure that the Bachelors degree in Physics has sufficient core physics courses in it to ensure that the skill set developed is has all of the elements which I mentioned above. Then we come to the thorny problem of what extra elements to add to the basic curriculum. As physics has natural interfaces with the geological sciences, biological sciences and chemical sciences, it is not difficult to recommend that our undergraduate student takes some “out of physics” scientific courses.
Students thinking about taking a degree in physics should look carefully at the curriculum at their institute of choice. Does it provide a narrow or a wider training? Don’t forget that study in areas not directly related to physics, such as economics, English or foreign languages may also be useful to you later in life. As a personal example, I took three years of German at school, and found it invaluable later on when I was a post-doctoral physicist in Berlin. My decision to go to Berlin was partly based on the fact that I did know a smattering of German.
An interesting exercise is to look at the faculty in your chosen department. What are their research interests? Do they have backgrounds or research collaborations with non-physics partnerships? To foster an environment of multi-disciplinary scientific endeavor, faculty in the department need to appreciate the strengths and weaknesses of each discipline. In my first year I had a physics lecturer (who shall remain nameless) who referred to chemistry as “Oh, it’s just quantum electrodynamics”. Bad impression! Contrast this with my second year lecturer on the Physics of Atoms and Molecules, Bob Evans (Professor R Evans, FRS). He actually recommended “Physical Chemistry” by Atkins as one of the course textbooks. Recommendations like this would be heresy in some physics departments! Even after all this time, I still cherish his comment at this, “Don’t be put off by the word ‘chemistry’ in the title, there is a lot of good physics in there”. Right on!
The survey carried out by the Canadian Association of Physicists in1997 on highly qualified personnel [14] shows that of the respondents with a BSc., 34% use their physics knowledge directly in their work and 57% use the skills/modes of thought stemming from their physics background. Obviously our training at the undergraduate level already provides a great deal of useful vocational training for our students. As university level teachers, we should always be aware that the majority of our students will not be going into academic jobs, and we should strive to ensure that an appropriate skill set is taught for those who will be employed outside of the academic environment. This might include more emphasis on written and oral communication skills and team working skills. These can often be developed through student participation into mini-research projects, such as our design project.

Graduate Level Physics

The area of graduate studies presents some of the most difficult problems for interdisciplinary research. This section is intended to promote discussion by faculty supervising interdisciplinary research projects and faculty overseeing the administration of graduate courses. We actually have two classes of students entering these academic programs, those from a physics background, and those from another discipline, who are perfectly suitable for graduate training, and may actually be more suitable for the proposed research, but lack the detailed background knowledge in physics.
The first group is relatively easy to handle, they need a set of graduate level classes which give them more formal training in physics, to hone their skills in problem solving, and they need courses in the subject area of their eventual research topic. These have to be provided by their supervisor or other faculty, or by taking classes in other departments.
The difficulty comes with the students who come from a different scientific background moving into a physics department. For example, in surface science, it would be natural to recruit graduate students with a first degree in chemistry. Can these students be trained in physics skills by taking the same set of graduate courses as those with a first degree in Physics? Throwing them in at the deep end, straight into graduate level physics classes may be unfair. However, if we make them take “catch up” classes in physics first, and then take the physics graduate classes then their graduate degree program looks unattractive, with an onerous course load and less time to carry out research. Potential graduate students are well advised to carefully examine their proposed course of study in the context of their entrance qualifications.
If a Physics department has a very rigid set of guidelines as to what a graduate student is expected to do in terms of course work, then this policy will actually prevent an interdisciplinary research group within the physics department from recruiting potentially able graduate students from outside physics. This poses a complex set of challenges to both supervisors in interdisciplinary research areas and those who run the graduate programs. This is a dilemma faced by many physics departments in their graduate programs. There are some fairly cumbersome administrative workarounds, such as joint supervision with faculty in another department or giving faculty in physics some official status in another department. We should not lose sight of the fact that this may mean that we lose a graduate student from the physics tally, even though they may do all their research within the physics department. I do not pretend to have all of the answers to this problem, but it seems to me that a class of graduate degrees which allow multidisciplinary studies would be an attractive option. Perhaps an MSc. or PhD in “Physics and ….” would be appropriate. This would allow more flexibility in choosing appropriate course of study. The key word here is flexibility, on the part of both the physics department and at the university level. I would note here that the title of the higher degree should include some idea of the subject area; this is primarily to aid the holder of the degree when applying for jobs; an MSc. in Interdisciplinary Studies will impress potential employers far less than, for example, an MSc. in Physics and Bioinformatics.
Recruiting post-doctoral researchers into a Physics department is one of the least problematic areas of interdisciplinary research work. One area of difficulty may be in assigning teaching duties. Many researchers want to gain teaching experience. Finding a suitable niche within a physics department for, say, a physical biochemist who wants to teach physics students might prove to be a little challenging.

Faculty Positions

Recruitment of staff intending to pursue interdisciplinary research into faculty positions is bound to provoke the “Is it Physics?” question, given the shortage of such positions. The attitude of the department is crucial. Do they see themselves as traditional physicists who don’t stray into other subject areas, or have they embraced multidisciplinary research? Do they view their department as a place to do physics or do they view the department as a place with a large number of trained personnel able to attack a wide variety of interesting scientific problems? Are they willing merely to be the providers of skilled scientific workers to other subject areas, or do they want to do that research in-house?
There are several legitimate questions which have to be asked when making an appointment. Is the appointee going to be able to teach physics courses? Where does the research funding come from? Is research done by this person going to impress any national accreditation bodies?

Interdisciplinary Research

Now I examine the problems of doing research in a physics department on a non-physics topic. Is it Physics? There are two related issues here. One is the credibility of the research within the department. Is it judged as “good science” even if it is not physics, for the purpose of salary review, support for tenure and allocation of departmental resources? The other issue is how to obtain financial support for such a project. In Canada, the natural route within a Physics department would be to apply to the Natural Sciences and Engineering Research Council (NSERC) for funding. However, suppose the research also falls within the remit of other funding organizations, such as the Canadian Institutes of Health Research (CIHR) or Genome Canada? It is quite possible that each organization will consider another as being a more suitable funding agency. NSERC has taken steps to avoid this conundrum, by appointing an interdisciplinary research grant selection committee. Similar considerations will no doubt apply to funding agencies in other countries too. Collaborative applications are probably the best way to go here, as this can emphasize the multidisciplinary scope of the project.

Conclusions

Physics as a discipline produces a well trained and highly employable work force. The strict definition of physics research has been blurred in recent years by the application of physics principles to other disciplines. This has resulted in many exciting discoveries and will lead to innovative research, both pure and applied, well into the next century. As a profession, we should always be reviewing how we deliver high quality research in all areas of physics and how we continue to provide a high quality educational experience for our students as we train the next generation of physicists. I strongly urge any students considering a career in physics to look at the advantages of a sound training in the physical sciences and to plan flexibly for their future careers. I hope that this article will provoke some discussion on interdisciplinary teaching and research.

Acknowledgements

Firstly I must thank my EP495 design team, Ryan Ziegler, Chad Phipps, Paul Kulyk and J. Scott Woods for their contribution. They turned in an outstanding design project and impressed everyone with their ability to quickly get to grips with areas of science and technology, such as mass spectrometry, with which they had little formal experience or training. As role models for well trained graduate physicists, they are second to none. Secondly, I would like to thank Tony Kusalik, of the Department of Computer Science for spotting the possibilities for working with FPGA technology and getting all interested parties together. Thirdly, the Proteomics and Bioinformatics team at the NRC Plant Biotechnology Institute, Andrew Ross, Doug Olsen and Jacek Nowak for all their efforts in this project. Fourthly, I must thank Scott Davis of VCom, who generously provided a computer to put the FPGA board in, and Xilinx Corporation for donating the FPGA development board and software. I also would like to thank the Physics and Engineering Physics Department at the University of Saskatchewan for their support of these interdisciplinary research projects. Finally, I must thank my wife Katie, without whom this article would not have been written.

References

[1] M J. Dunn (ed.), Proteomics Reviews 2001, Wiley-VCH, Germany, 2001.
ISBN 3-527-30314-6
A very impressive animated overview of the proteomics process from the Children’s Hospital, Boston, USA is available online at:

http://www.childrenshospital.org/cfapps/research/data_admin/Site602/mainpageS602P0.html

[2] T. Oliver, B. Schmidt, D. Nathan, R. Clemens and D. Maskell
Bioinformatics Applications Note, 21(16), 3431-3432 (2005)

A. Alex, M. Dumontier, J. S Rose and C.W. V. Hogue
Rapid Communications in Mass Spectrometry 19, 833-837 (2005)

[3] C. Small, “User programmable gate arrays”
Electronic Design News, 34(9),1989

[4] A website describing surface chemistry suitable for undergraduate level scientists is provided by Roger Nix from the department of Chemistry, Queen Mary College, UK:
http://www.chem.qmul.ac.uk/surfaces/scc/

[5] A review of how an experienced physicist approaches a scientific problem is given in
A. Van Heuvelen, Am. J. Phys 59 (10), 891-897, (1991)

[6] T.G. Wolfsberg, J. McEntyre and G.D. Schuler, “Guide to the draft human genome” Nature 409, 824-826 (2001)

[7] S.J. McGowan et al, “Annotation of the Human Genome by High-Throughput Sequence Analysis of Naturally Occurring Proteins.”
Current Proteomics, 1(1), 41-48 (2004)

[8] B. Kasemo, Surface Science, 500, 656-677 (2002)

[9] D.A. Williams and T.W. Hartquist, Acc. Chem. Res. 32, 334-341 (1999)

See also the University College London Centre for Cosmic Chemistry and Physics website for a simple overview of the subject and useful links:

http://www.chem.ucl.ac.uk/cosmicdust/surfacescience.html

[10] R.A.L. Jones, Soft Condensed Matter, Oxford University Press, 2002
ISBN-10: 0-19-850590-6, ISBN-13: 978-0-19-850590-7

[11] M.A. Ratner and D. Ratner, Nanotechnology: A gentle introduction to the next big idea, Prentice Hall PTR, 2003
ISBN 0-13-101400-5

[12] A web-based teaching resource on molecular biology, suitable for high school students and teachers is available from the Rothamstead Research Centre of the Biotechnology and Biological Sciences Research Council (BBSRC) in the UK.

http://www.rothamsted.bbsrc.ac.uk/notebook/index.html

[13] M. Wilkins. “The Third Man of the Double Helix: The Autobiography of Maurice Wilkins”. New York: Oxford University Press, 2003

[14] B. Robertson and M. Steinitz, “Review Of Canadian Academic Physics: Highly Qualified Personnel Study”, Canadian Association of Physics, 1997

Available online at: http://www.phys.uregina.ca/ugrad/hqp.html