A Ph.D without scholarship?

An interesting and controversial question for Ph.D's in science and engineering is too what extent students should be expected to have become "scholars." This issue also came in an earlier post about whether being able to write should be a necessary requirement for getting a Ph.D.

To me, some key characteristics of scholarship are the ability to frame and answer questions, ability to put a problem in the context of a discipline, a knowledge of and critical appreciation for earlier work in the field, and the ability to communicate about the topic.

On the other hand, a really important Ph.D will probably involve some highly technical (and specialised) achievement whether it is making a new molecule, developing a new computer algorithm, deriving or solving an equation, fabricating a new electronic device, or developing a new experimental technique, ....

Scholarship and technical achievement may be almost orthogonal to each other.

At UQ after one year of enrollment in the Ph.D program students must write a ten page report which defines their project, gives a literature survey, and sets goals and a timeline for finishing their Ph.D. I am on the committee which reviews each student. I increasingly struggle with the lack of scholarship and the highly technical focus of the student reports. I have tried to come up with a list of what I would like a student to be able to do at this stage. Here is a rough attempt which will hopefully generate some discussion. (The numbers are extremely rough).

State three big scientific questions in this field.

State a specific scientific question that your project will answer.

What are five key concepts in this field?

What are five landmark papers in the field from the last century? For each paper write several sentences saying why it is so important.

Which three papers from the last 5 years are most relevant to your project?

Evolution does not optimise everything

When discussing biological molecules performing some function I often read statements by physicists and chemists along the lines, "evolution over billions of years has optimised this physical property so the molecule can perform its function."

My understanding of evolutionary biology is limited. However, I think these statements present a mis-understanding.

Evolutionary pressures lead to changes that will increase the chances of survival, or perhaps more correctly over time the biomolecular systems which can survive best in their environment survive....

But the crucial point is that the "fitness function" of a biomolecule depends on many variables. The optimum fitness function will not optimise all variables.

Consider the specific example of light-harvesting complexes for photosynthesis. The fittest will not necessarily be those which transport energy the fastest. There are many other variables such as robustness to UV light, sensitivity to changes in pH, matching the solar spectrum, .....

A similar issue arises with photovoltaic cells. Everyone is trying to achieve a greater efficiency and there are often statements such as "if we can make organic cells operating at 12 per cent (or some other number) we will save the planet". But there are many other key variables: cost, durability, stability, scarcity of materials, .....

If someone found a way to make 2 per cent solar cells that were made of naturally occuring materials, cost 1 cent/square metre to manufacture, and were completely reliable for 30 years, ..... well I think we would be done....

Please correct my mis-understandings....

Postdoc available

Subject to final administrative approval, I am about to advertise a two year postdoc to work on the theory of interlayer magnetoresistance in strongly correlated electron materials. Previous posts on magnetoresistance give the flavour of the relevant science.

I will post a link to the official advert when it is approved.

What determines the colour of an organic dye?

This week I read most of chapter 4 of the book, Colour and Constitution of Organic Molecules by John Griffiths. I think it is a must-read for anyone working on dye molecules. It is at an elementary level and so accessible to both chemists and physicists, experimentalists and theorists. I fear much of the content has been forgotten or is unknown to many working on these materials, whether quantum chemists or biologists trying to find new molecules for fluorescent marker or people working on dye-sensitised solar cells.

Griffiths gives a nice discussion of resonance theory and then discusses its "failures", stating:

The apparent failure of resonance theory in these systems arises from the assumption that only low energy resonance forms need to be considered as contributing to the ground and first excited states.

Indeed, work by Seth Olsen and I (mostly Seth) shows for methine dyes (including flourescent proteins) how to do this in a systematic manner.

Beware of curve fitting

In a comment on a previous post about charge transport in organic materials Doug Natelson brought to my attention a recent preprint. It is a really nice paper and is a cautionary tale about drawing conclusions from curve fitting.

In a Nature Materials paper last year, Alan Heeger's group at UCSB considered the electric field and temperature dependence of the current in an organic field effect transistor. They fitted the observed dependence to that for a theory which describes slightly dirty long one dimensional conducting wires with strong electronic correlations (Tomonaga-Luttinger liquid theory). This theory gives a good description of charge transport in single carbon nanotubes. However, it is not clear if there is a physical reason to expect the TLL theory to be relevant to "dirty" crystals of small organic molecules.

However, Worne, Anthony, and Natelson show that for their data on similar devices the curve fitting to the TLL theory is problematic. In particular, the apparent "scaling collapse" is fortuitous. They state:

decreasing T moves subsequent temperature data sets up and to the right on the graph, even if the data themselves do not change with temperature at all. In fact, any weakly temperature dependent dataset that resembles a power-law can be made to fit onto a single line if plotted in this way with an appropriate choice of α. Data collapse with this plotting procedure is not sufficient to demonstrate TLL physics.

There is another reason why I am skeptical about any claim of "metalllic" behavior in these systems. Their mobility is much less than than the "minimum mobility"of 1 cm^2/Vsec that is necessary for the coherent transport associated with delocalised electrons and band structure.

Examples of inhomogeneous mixed valence

In contrast, to homogeneous mixed-valence the inhomogeneous mixed-valence case involves a mixture of different integer valence ions which occupy inequivalent lattice sites in a static charge-ordered array. Examples of this are provided by Fe3O4, Eu3O4 and Eu3S4.

The following material and figure is copied from the chemexplore web site

Magnetite (Fe3O4) has the AM₂X₄ spinel structure, of the "inverse" type :

Magnetite has the empirical formula Fe₃O₄, or Fe²⁺(Fe³⁺O₂)₂, “ferrous ferrite”. Its formula as a spinel would be Fe³⁺_tetFe²⁺_octFe³⁺_octO₄ , where "tet" and "oct" stand for tetrahedral and octahedral coordinations by the oxide anions. In the above model, the blue spheres represent the tetrahedral iron(III) cations , and the red spheres are the octahedrally coordinated iron(II) and (III) cations. The oxide anions are shown as the green spheres. Because of the fortuitous inverse nature of the magnetite structure, ferrous and ferric cations are both in the similar octahedral coordination by oxides. In "normal" spinels, such as the mineral spinel itself (magnesium aluminate), the A cation is tetrahedral and the M cations are both octahedral:

However, this inverse-spinel charge ordering has recently been challenged in favour of the normal spinel charge structure where the Fe3+ ions exclusively occupy all the octahedral sites while the Fe2+ ions reside in the tetrahedral sites.

What happens in higher order oxides of cerium is not so simple, as discussed here.

Sell your science not your hyper-activity

One of the most important sections in grant applications in Australia is where applicants have half a page to described their "significant contributions to the field".

Such material is also important in CV's and job applications.

Many people seem to write things like:

-I published a paper in a high impact journal and it has been cited and I got invited to speak on it at a conference.

-I worked on topic XYZ where I learnt how to use technique ABC and then I got offered a job at the prestigious University of Mediocrity.

-I have used state-of-the art software to calculate such and such a property of this exotic material which is a really hot topic right now.

-I previously got a grant. Therefore you should give me another one.

These are all activities not contributions to scientific knowledge.
Grants are inputs not outputs.

Instead you should write something like:

I developed a new technique to measure the position of atoms in crystals to a resolution that was an order of magnitude better than existing techniques. With collaborators from Austria, we were able to show that the actual structure of blah-blah materials was different from that predicted by the standard theoretical model....

This led theoretical chemists to develop a new model which shows that entropic effects are actually important in determining the most stable crystal structure at room temperature.....

Research is all about knowledge creation, not about busyness, metrics, or points scoring.