Whose fault is plagiarism?

The controversy about the plagiarised Ph.D of the President of Hungary, Pal Schmitt, is making for "interesting" reading. In 1992 he received a Ph.D for a 200 page thesis that contains 17 pages directly translated from a German book. The rest seems to largely be a translation of work by a Bulgarian sports writer. A committee from the university reviewed the case and wrote a 1100+ page report (!) and concluded that he should keep his degree. The supervisors and examiners were to blame! However, following widespread criticism, the university just announced that they would revoke the degree.

Following the resignation of the German Defence minister for another plagiarised doctorate it seems that the academic backgrounds of prominent politicians are getting more scrutiny. This raises an interesting question. Which of the following is more likely to be true?

• there has been a lot of plagiarism in the social sciences and humanities but it is only being detected in the case of these politicians because of the increased scrutiny
• leading politicians are often ambitious individuals who "cut corners" and so are more prone to commit plagiarism

Unfortunately, the leadership of Australian universities is not immune from this problem. A decade ago the Vice Chancellor of Monash University, David Robinson, was forced to resign because of plagiarism.

A simple model for non-classical magnetoresistance

Previously I have posted about a diverse set of layered strongly correlated electron materials which exhibit a non-classical magnetoresistance. Specifically, the magnetoresistance can be largest (smallest) when the current and magnetic field are parallel (perpendicular).
Michael Smith has just published a nice paper Anomalous interlayer magnetoresistance in bilayer crystals which considers a simple concrete model that exhibits such behaviour. The key physics is that in alternating layers the conducting chains are perpendicular to each other. This does occur in some organic charge transfer salts, as mentioned in footnote 1 of the paper.

Should you work with a young turk or an old fart?

Picking an advisor/supervisor is one of the most important decisions that budding young science students must make at the final year undergraduate and Ph.D level. You should pick the advisor rather than the topic. A colleague once said to me, "Students are very good at picking bad supervisors."

An important aspect to the choice is whether is better to work with an energetic young faculty member (lecturer/Assistant Professor) (a "young turk") or a well established faculty member (Professor) (an "old fart").

Here are a few random thoughts on the relative merits of each. Bear in mind these are just generalisations and ultimately you will be working with (or for) an individual human being not some abstract concept or social classification. There are always exceptions.

Young turks offer you energy and enthusiasm. They have a lot riding on your success and may have significant time to invest in you. They may be working in some exciting new area or technique. Because they are closer to you in age they may be easier to build a strong personal and working relationship. On the down side they lack experience at picking research projects, particularly ones suitable to the average student, and lack experience at supervision. They may be so desperate to succeed (survive) they may want to take more credit than they deserve for your work. If they don't have tenure they may leave in the middle of your Ph.D. Will they take you with them if they move to a different institution? You want your supervisor to help you get a job or a place in a good Ph.D program. A junior scientist may not have the necessary contacts and reputation necessary for this.

In contrast, old farts may offer you wisdom, experience, and stability. Hopefully, they have learnt from the mistakes they made when they were a young turk and are now more effective at picking good research topics, particularly ones suitable for students, and will produce publishable results in a reasonable time. They may also be able to quickly see dead ends and save you a lot of time. On the other hand, they may be stuck in a rut in an old research field and be getting distant from nuts and bolts technical details. Worse, they may have lost interest in science and just be concerned about getting grants or an invited talk in some exotic locale...
They may be so busy with travel and/or administration that you will never see them. [But there are exceptions, e.g, Glenn T. Seaborg]. They don't have much riding on your success. They have already successfully graduated students. They don't need to get tenure or get promoted. If you aren't successful or bomb, it will be more likely that you will be blamed than them. But, a positive letter of reference from them may carry great weight to their extensive international network of senior colleagues and help land your next position.

On balance, I think the ideal situation is to have both a junior and senior person involved in your research. Two possible ways this might work.
i) A junior person is your main advisor, but you regularly talk informally to a senior person for feedback on what you are doing. This requires permission from your advisor.
ii) A senior person is your main advisor, but you work closely with a junior colleague in their research group, e.g., a senior postdoc.

Again, I stress these are just broad generalisations. There will always be exceptions. e.g., junior faculty who won't invest significant time in students, and old farts who won't give appropriate credit to their students. Senior people also take jobs elsewhere and may leave you behind...

I welcome comments. Who do you think might be the best option?

Quantum chemical justification for an empirical correlation

A challenge to quantum chemistry is to describe many of the empirical correlations that experimentalists have painstakingly catalogued. For example, an earlier post discusses a correlation between the rate of a photoisomerisation reaction and the electron withdrawing ability of a substitutent. An important empirical rule for organic dye molecules is the Dewar-Knott rule which relates the frequency (wavelength) of maximum light absorption [the colour of the dye] to the electron withdrawing (or donating) ability of a substituent.

Seth Olsen recently published a nice paper which gives a high level quantum chemistry justification of the Dewar-Knott rule for a family of diarylmethane dyes, including Michler's hydrol blue. The graph below shows how the excitation energy varies with a parameter characterising the composition of the ground state many-body wavefunction, and which varies with the substituent X.

Getting nervous at the biomolecular dance

Enzymes are amazing.
Today I went to an interesting chemistry seminar today by Ian Dance,
Nitrogenase reduces N2 to NH3 and CO to hydrocarbons. What chemistry is used?
It was also a David Craig lecture and was a model seminar for a general audience.

A major industrial process is the fixation of nitrogen to from ammonia.
N2 + 3H2 -> 2 NH3.
This is done via the Haber-Bosch process and requires pressures of 1000 atm and high temperatures of 450 degrees C with iron or ruthenium as catalysts.

However, nature does this at room temperature and pressure via nitrogenase enzymes. A surprising recent discovery was that vanadium nitrogenase can also reduce carbon monoxide to small hydrocarbons.

Dance used an interesting dance (!) metaphor during the talk. You need a stage [key part of the enzyme], centre stage [the active sites], dancers [the intermediate states], and a choreography [reaction mechanisms].

The stage for nitrogenase is shown below. the FeMo-co, which can be viewed as two  cubes [one is Fe4S3 and one Fe3MoS3] that have been fused together at a N vertex. Only very recently was the N atom seen in the enzyme structure.

Previously it was thought that the Mo atom on the bottom was the active site but now it is believed to be a pair of the Fe ions in the upper cube.

Something I thought were particularly interesting:
To obtain a good supply of protons to the active site one possible mean is a chain of hydrogen bonded water molecules [see the orange circles below].

A few things in the talk made me nervous.
All the calculations are based on some version of DFT. There was no mention of what functional was used, basis sets, convergence tests, or benchmarking.
Dance is using his own personal method for finding transition states.
It is not clear that he has a ground state with the correct spin, S=3/2.
There are tens of "molecular orbitals" [presumably actually Kohn-Sham orbitals] within about 1 eV of the so-called "HOMO" and "LUMO".
All the calculations are done in gas phase without implicit or explicit solvent (water + protein).
Many of the calculated activation energies are in the range 2-20 kcal/mol [0.1-1 eV for the physicists]. Is DFT really very reliable on this scale for such large molecules, particularly including 8 transition metal atoms?
Because the calculation gives too large an activation energy compared to experiment it was suggested that proton tunneling may occur below the barrier. [Apparently, it is not possible to test this hypothesis experimentally with isotope substitution.] [My experience with proton tunneling in enzymes is that this is subtle and murky issue].

Much of the material in the talk is in a summary paper

At what temperature are quasi-particles destroyed?

An interesting question [which has featured in many of my blog posts] concerns defining the coherence temperature at which quasi-particles in a Fermi liquid are "destroyed". There are several possible experimental signatures of this:

• absence of a sharp dispersing peak in the one electron spectral density (as seen in ARPES)
• collapse of the Drude peak in the optical conductivity
• collapse of the linear in T term in the specific heat capacity
• a peak in the thermopower versus temperature
• deviations of the resistivity temperature dependence from T^2
• the resistivity becoming larger than the Mott-Ioffe-Regel limit.

I tended to think that these would all occur at the approximately the same temperature.
(A Nature paper also makes a similar assumption.)
However, Jure Kokalj pointed out to me that DMFT gives quite different temperatures for the different signatures above. For example, in this PRB the thermopower and specific heat have a peak at a temperature at which there is still a Drude peak.

A PRL I recently blogged about contains the "throw away" line that got my attention:

the Fermi liquid behavior in two-particle properties is more fragile than in single-particle ones. Indeed, in the well-known Kondo problem the Kondo resonance persists at temperatures up to 2T_K while the magnetic susceptibility saturates to a Pauli form only below T=0.2T_K.

That is an order of magnitude difference in temperature scales!

This point can be seen in this nice paper by Costi, Hewson, and Zlatic. For example, compare Figures 2, 7, and 16, which show the specific heat, spectral density, and thermopower, respectively.

It would be nice to have a simple physical picture of the origin of these disparate temperature scales. Perhaps it is something as mundane as different convolutions and moments of the Fermi-Dirac distribution.

A case study in getting published

I was pleased to learn this week that my paper on hydrogen bonding has been accepted for publication in Chemical Physics Letters. I believe this may be one of the most significant papers I have written. Time will tell...

The paper has an "interesting" history. Six months ago I sent the paper with the title Unified description of hydrogen bonding and proton transfer by a two-state effective Hamiltonian to Physical Review Letters. I chose PRL because I thought the paper was significant and it approached the problem from a physicist's point of view, putting simplicity and physical insight before chemical detail. However, based on one brief referee report, an Adjunct Associate Editor rejected the paper. I wrote a rebuttal and resubmitted it. You may find the rebuttal interesting reading as it highlights what I consider to be some fundamental issues about what is good and novel science, particularly of complex chemical systems.

I was optimistic because I thought my rebuttal was persuasive [what do you think?] and I have a long track record of publishing in PRL. A few times with PRL I have received two negative reports, rebutted them, and eventually got the paper into PRL. However, the Adjunct Associate Editor would not give the paper further consideration. I found this rather disappointing.

I then gave the paper the more modest, specific, and technical title A diabatic state model for donor-hydrogen vibrational frequency shifts in hydrogen bonded complexes and sent it to Chemical Physics Letters. It received two detailed, helpful, and positive referee reports. Although one of referees still thought along the lines of "this is so simple surely someone must have done it before."