Friday, December 9, 2016

Metric madness: McNamara and the military

Previously, I posted about a historical precedent for managing by metrics: economic planning in Stalinist Russia.

I recently learnt of a capitalist analogue, starting with Ford motor company in the USA.
I found the following account illuminating and loved the (tragic) quotes from Colin Powell about the Vietnam war.
Robert McNamara was the brightest of a group of ten military analysts who worked together in Air Force Statistical Control during World War II and who were hired en masse by Henry Ford II in 1946. They became a strategic planning unit within Ford, initially dubbed the Quiz Kids because of their seemingly endless questions and youth, but eventually renamed the Whiz Kids, thanks in no small part to the efforts of McNamara. 
There were ‘four McNamara steps to changing the thinking of any organisation’: state an objective, work out how to get there, apply costings, and systematically monitor progress against the plan. In the 1960s, appointed by J.F. Kennedy as Secretary of Defense after just a week as Chair of Ford, McNamara created another Strategic Planning Unit in the Department of Defense, also called the Whiz Kids, with a similar ethos of formal analysis. McNamara spelled out his approach to defence strategy: ‘We first determine what our foreign policy is to be, formulate a military strategy to carry out that policy, then build the military forces to conduct that strategy.’ 
Obsessed with the ‘formal and the analytical’ to select and order data, McNamara and his team famously developed a statistical strategy for winning the Vietnam War. ‘In essence, McNamara had taken the management concepts from his experiences at the Ford Motor Company, where he worked in a variety of positions for 15 years, eventually becoming president in 1960, and applied them to his management of the Department of Defense.’ 
But the gap between the ideal and the reality was stark. Colin Powell describes his experience on the ground in Vietnam in his biography: 
Secretary McNamara...made a visit to South Vietnam. Every quantitative measurement, he concluded, after forty-eight hours there, shows that we are winning the war. Measure it and it has meaning. Measure it and it is real. Yet, nothing I had witnessed . . . indicated we were beating the Viet Cong. Beating them? Most of the time we could not even find them. 
McNamara’s slide-rule commandos had devised precise indices to measure the immeasurable. This conspiracy of illusion would reach full flower in the years ahead, as we added to the secure-hamlet nonsense, the search-and-sweep nonsense, the body-count nonsense, all of which we knew was nonsense, even as we did it. 
McNamara then used the same principles to transform the World Bank’s systems and operations. Sonja Amadae, a historian of rational choice theory, suggests that, ‘over time . . . the objective, cost-benefit strategy of policy formation would become the universal status quo in development economics—a position it still holds today.’ Towards the end of his life, McNamara himself started to acknowledge that, ‘Amid all the objective-setting and evaluating, the careful counting and the cost-benefit analysis, stood ordinary human beings [who] behaved unpredictably.’
Ben Ramalingam,  Aid on the Edge of Chaos, Oxford University Press, 2013. pp. 45-46.
Aside: I am working on posting a review of the book soon.

Given all this dubious history, why are people trying to manage science by metrics?

Wednesday, December 7, 2016

Pseudo-spin lattice models for hydrogen-bonded ferroelectrics and ice

The challenge of understanding phase transitions and proton ordering in hydrogen-bonded ferroelectrics (such as KDP, squaric acid, croconic acid) and different crystal phases of ice has been a rich source of lattice models for statistical physics.
Models include ice-type models (six-vertex model, Slater's KDP model), transverse field Ising model, and some gauge theories. Some of the classical (quantum) models are exactly soluble in two (one) dimensions.

An important question that seems to be skimmed over is the following: under what assumptions can one actually "derive" these models starting from the actual crystal structure and electronic and vibrational properties of a specific material?

That quantum effects, particularly tunnelling of protons, are important in some of the materials is indicated by the large shifts (of the order of 100 percent) seen in the transition temperatures upon H/D isotope substitution.

In 1963 de Gennes argued that the transverse field Ising model should describe the collective excitations of protons tunnelling between different molecular units in an H-bonded ferroelectric. Some of this is discussed in detail in an extensive review by Blinc and Zeks.
An important issue is whether the phase transition is an "order-disorder" transition or a "displacive" transition. I think what this means is the following. In the former case, the transition is driven by the pseudo-spin variables and there is no soft lattice mode associated with the transition.
Perhaps, in different language, is it appropriate to "integrate out" the vibrational degrees of freedom?
[Aside: this reminds me of some issues that I looked at in a Holstein model about 20 years ago].

There are a lot of papers that make quantitative comparisons between experimental properties and the predictions of a transverse field Ising model (usually treated in the mean-field approximation).
One example (which also highlights the role of isotope effects) is

Quantum phase transition in K3D1−xHx(SO4)2 
Y. Moritomo, Y. Tokura, N. Nagaosa, T. Suzuki, and K. Kumagai

One problem I am puzzling over is that the model parameters that they (and others) extract are different from what I would expect from knowing the actual bond lengths, vibrational frequencies, in the system and the energetics of different H-bond states. I can only "derive" pseudo-spin models with quite restrictive assumptions.

A recent paper that looks some of rich physics associated with collective quantum effects is
Classical and quantum theories of proton disorder in hexagonal water ice 
Owen Benton, Olga Sikora, and Nic Shannon

Monday, December 5, 2016

Hydrogen bonding at Berkeley

On Friday I am giving a talk in the Chemistry Department at Berkeley.
Here is the current version of the slides.

There is some interesting local background history I will briefly mention in the talk. One of the first people to document correlations between different properties (e.g. bond lengths and vibrational frequencies) of diverse classes of H-bond complexes was George Pimentel. 
Many correlations were summarised in a classic book, "The Hydrogen Bond" published in 1960.
He also promoted the idea of a 4-electron, 3 orbital bond which has similarities to the diabatic state picture I am promoting.
There is even a lecture theatre on campus named after him!

Friday, December 2, 2016

A central result of non-equilibrium statistical physics

Here is a helpful quote from William Bialek. It is a footnote in a nice article, Perspectives on theory at the interface of physics and biology.
The Boltzmann distribution is the maximum entropy distribution consistent with knowing the mean energy, and this sometimes leads to confusion about maximum entropy methods as being equivalent to some sort of equilibrium assumption (which would be obviously wrong). But we can build maximum entropy models that hold many different expectation values fixed, and it is only when we fix the expectation value of the Hamiltonian that we are describing thermal equilibrium. What is useful is that maximum entropy models are equivalent to the Boltzmann distribution for some hypothetical system, and often this is a source of both intuition and calculational tools.
This type of approach features in the statistical mechanics of income distributions.

Examples where Bialek has applied this includes voting patterns of the USA Supreme Court, flocking of birds, and antibody diversity.

For a gentler introduction to this profound idea [which I still struggle with] see
*James Sethna's textbook, Entropy, Order parameters, and Complexity.
* review articles on large deviation theory by Hugo Touchette, such as this and this.
I thank David Limmer for bringing the latter to my attention.

Wednesday, November 30, 2016

Photosynthesis is incoherent

Beginning in 2007 luxury journals published some experimental papers making claims that quantum coherence was essential to photosynthesis. This was followed by a lot of theoretical papers claiming support. I was skeptical about these claims and in the first few years of this blog wrote several posts highlighting problems with the experiments, theory, interpretation, and hype.

Here is a recent paper that repeats one of the first experiments.

Nature does not rely on long-lived electronic quantum coherence for photosynthetic energy transfer Hong-Guang Duan, Valentyn I. Prokhorenko, Richard Cogdell, Khuram Ashraf, Amy L. Stevens, Michael Thorwart, R. J. Dwayne Miller
During the first steps of photosynthesis, the energy of impinging solar photons is transformed into electronic excitation energy of the light-harvesting biomolecular complexes. The subsequent energy transfer to the reaction center is understood in terms of exciton quasiparticles which move on a grid of biomolecular sites on typical time scales less than 100 femtoseconds (fs). Since the early days of quantum mechanics, this energy transfer is described as an incoherent Forster hopping with classical site occupation probabilities, but with quantum mechanically determined rate constants. This orthodox picture has been challenged by ultrafast optical spectroscopy experiments with the Fenna-Matthews-Olson protein in which interference oscillatory signals up to 1.5 picoseconds were reported and interpreted as direct evidence of exceptionally long-lived electronic quantum coherence. Here, we show that the optical 2D photon echo spectra of this complex at ambient temperature in aqueous solution do not provide evidence of any long-lived electronic quantum coherence, but confirm the orthodox view of rapidly decaying electronic quantum coherence on a time scale of 60 fs. Our results give no hint that electronic quantum coherence plays any biofunctional role in real photoactive biomolecular complexes. Since this natural energy transfer complex is rather small and has a structurally well defined protein with the distances between bacteriochlorophylls being comparable to other light-harvesting complexes, we anticipate that this finding is general and directly applies to even larger photoactive biomolecular complexes.
I do not find the 60 fsec timescale surprising. In 2008, Joel Gilmore and I published a review of experiment and theory on a wide range of biomolecules (in a warm wet environment) that suggested that tens of femtoseconds is the relevant time scale for decoherence.

I found the following section of the paper (page 7) interesting and troubling.
The results shown in Figs. 3 (a) and (b) prove that any electronic coherence vanishes within a dephasing time window of 60 fs. It is important to emphasize that the dephasing time determined like this is consistent with the dephasing time of Ď„hom = 60 fs independently derived from the experiment (see above). It is important to realize that this cross-check constitutes the simplest and most direct test for the electronic dephasing time in 2D spectra. In fact, the only unique observable in 2D pho- ton echo spectroscopy is the homogeneous lineshape. The use of rephasing processes in echo spectroscopies removes the inhomogeneous broadening and this can be directly inferred by the projection of the spectrum on the antidiagonal that shows the correlation between the excitation and probe fields. This check of self-consistency has not been made earlier and is in complete contradiction to the assertion made in earlier works. Moreover, our direct observation of the homogeneous line width is in agreement with independent FMO data of Ref. 12. This study finds an ∼ 100 cm−1 homogeneous line width estimated from the low-temperature data taken at 77 K, which corresponds to an electronic coherence time of ∼ 110 fs, in line with our result given the difference in temperature. In fact, if any long lived electronic coherences were operating on the 1 ps timescale as claimed previously (1), the antidiagonal line width would have to be on the order of 10 cm−1, and would appear as an extremely sharp ridge in the 2D inhomogeneously broadened spectrum (see Supplementary Materials). The lack of this feature conspicuously points to the misassignment of the long lived features to long lived electronic coherences where as now established in the present work is due to weak vibrational coherences. The frequencies of these oscillations, their lifetimes, and amplitudes all match those expected for molecular modes (41, 42) and not long-lived electronic coherences.

Monday, November 28, 2016

Polanyi and Emergence before "More is Different"

The common narrative in physics is that the limitations of reductionism, the importance of emergence, and the stratification of scientific fields and concepts were first highlighted in 1972,  by P.W. Anderson in a classic article, "More is Different" published in Science. Anderson nicely used broken symmetry as an example of an organising principle that occurs at one strata and as a result of the thermodynamic limit.

The article was based on lectures Anderson gave in 1967.
The article actually does not seem to contain the word "emergence". He talks about new properties "arising".

I recently learned how similar ideas about emergence and the stratification of fields was enunciated earlier by Michael Polanyi, in The Tacit Dimension, published in 1966, based on his 1962 Terry Lectures at Yale.
The book contains a chapter entitled "Emergence".

Here is a quote:
you cannot derive a vocabulary from phonetics; you cannot derive the grammar of language from its vocabulary; a correct use of grammar does not account for good style; and a good style does not provide the content of a piece of prose. ... it is impossible to represent the organizing principles of a higher level by the laws governing its isolated particulars.
Much of the chapter focuses on biology and the inadequacy of genetic reductionism. These ideas were expanded in a paper, "Life's irreducible structure," published in Science in 1968.

I recently learned about Polanyi's contribution from
The concept of emergence in social sciences: its history and importance 
G.M. Hodgson

Here is a bit of random background.

Before turning to philosophy, Polanyi worked very successfully in Physical Chemistry. Some readers will know him for his contributions to reaction rate theory, the transition state, a diabatic state description of proton transfer, the LEPS potential energy surface based on valence bond theory, ...

Polanyi was the Ph.D. advisor of Eugene Wigner. Melvin Calvin, a postdoc with Polanyi, and his son, John Polanyi, went on to win Nobel Prizes in Chemistry.

Google Scholar lists "The Tacit Dimension" with almost 25,000 citations.
The book was recently republished with a new foreword by Amartya Sen, Nobel Laureate in Economics.

Friday, November 25, 2016

Should you quit social media?

The New York Times has an interesting Op-ed. piece Quit Social Media. Your Career May Depend on It, by Cal Newport, a faculty member in computer science at Georgetown University.

When I saw the headline I thought the point was going to be an important one that has been made many times before; people sometimes post stupid stuff on social media and get fired as a result. Don't do it!
However, that is not his point.
Rather, he says social media is bad for two reasons:

1. It is a distraction that prevents deep thinking and sustained  "deep" work. Because you are constantly looking at your phone, tablet, or laptop or posting on it, you don't have the long periods of "quiet" time that are needed for substantial achievement.

2. Real substantial contributions will get noticed and recognised without you constantly "tweeting" or posting about what you are doing or have done. Cut back on the self-promotion.

Overall, I agree.

When I discussed this and my post about 13 hour days with two young scientists at an elite institution they said: "you really have no idea how much time some people are wasting on social media while in the lab." Ph.D students and postdocs may be physically present but not necessarily mentally or meaningfully engaged.

A similar argument for restraint, but with different motivations, is being advocated by Sherry Turkle, a psychologist at MIT. Here is a recent interview.

I welcome discussion.