Friday, June 28, 2019

The bloody delusions of silicon valley medicine

On a recent flight, I watched the HBO documentary The Inventor: Out for Blood in Silicon Valley. It chronicles the dramatic rise and fall of Elizabeth Holmes, founder of a start-up, Theranos, that claimed to have revolutionised blood testing.



There is a good article in the New Republic
What the Theranos Documentary Misses
Instead of examining Elizabeth Holmes’s personality, look at the people and systems that aided the company’s rise.

In spite of the weaknesses described in that article, the documentary made me think about a range of issues at the interface of science, technology, philosophy, and social justice.

The story underscores Kauzmann's maxim, ``people will often believe what they want to believe rather than what the evidence before them suggests they should believe.''

Truth matters. Eventually, we all bounce up against reality: scientific, technological, economic, legal, ...  It does not matter how much hype and BS one can get away, eventually, it will all come crashing down. It is just amazing that some people seem to get away with it for so long...
This is why transparency is so important. A bane of modern life is the proliferation of Non-Disclosure Agreements. Although, I concede they have a limited role is certain commercial situations, they seem to be now used to avoid transparency and accountability for all sorts of dubious practises in diverse social contexts.

The transition from scientific knowledge to a new technology is far from simple. A new commercial device needs to be scalable, reliable, affordable, and safe. For medicine, the bar is a lot higher than a phone app! 

Theranos had a board featuring ``big'' names in politics, business, and military, such as Henry Kissinger, George Shulz, Daniel Mattis,.. All these old men were besotted with Holmes and more than happy to take large commissions for sitting on the board. Chemistry, engineering, and medical expertise were sorely lacking. However, even the old man with relevant knowledge Channing Robertson was a true believer until the very end.

Holmes styled herself on Steve Jobs and many wanted to believe that she would revolutionise blood testing. However, the analogy is flawed. Jobs basically took existing robust technology and repackaged and marketed it in clever ways. Holmes claimed to have invented a totally new technology. What she was trying to do was a bit like trying to build a Macintosh computer in the 1960s.

Wednesday, June 12, 2019

Macroscopic manifestations of crystal symmetry

In my view, the central question that Condensed Matter Physics (CMP) seeks to answer is:
How do the properties of a distinct phase in a material emerge from the interactions between the atoms of which the material is composed? 
CMP aims to find a connection between the microscopic properties and macroscopic properties of a material. This requires determining three things: what the microscopic properties are, what the macroscopic properties are, and how the two are related. None of the three is particularly straightforward. Historically, the order of discovery is usually: macroscopic, microscopic, connection. Making the connection between microscopic and macroscopic can take decades, as exemplified in the BCS theory of superconductivity.

Arguably, the central concept to describe the macroscopic properties is broken symmetry, which can be quantified in terms of an order parameter. Connecting this microscopics is not obvious. For example, with superconductivity, the sequence of discovery was experiment, Ginzburg-Landau theory, BCS theory, and then Gorkov connected BCS and Ginzburg-Landau.

When we discuss (and teach about) crystals and their symmetry we tend to start with the microscopic, particularly with the mathematics of translational symmetry, Bravais lattices, crystal point groups, ...
Perhaps this is the best strategy from a pedagogical point of view in a physics course.
However, historically this is not the way our understanding developed.
Perhaps if I want to write a coherent introduction to CMP for a popular audience I should follow the historical trajectory. This can illustrate some of the key ideas and challenges of CMP.

So let's start with macroscopic crystals. One can find beautiful specimens that have very clean faces (facets).


Based on studies of quartz, Nicolas Steno in 1669 proposed that ``the angles between corresponding faces on crystals are the same for all specimens of the same mineral".  This is nicely illustrated in the figure below which looks at different cross-sections of a quartz crystal. The 120-degree angle suggests an underlying six-fold symmetry. This constancy of angles was formulated as a law by Romé de l'Isle in 1772.


Rene Just Hauy then observed that when he smashed crystals of calcite that the fragments always had the same form (types of facets) as the original crystal. This suggested some type of translational symmetry, i.e. that crystals were composed of some type of polyhedral unit. In other words, crystals involve a repeating pattern.

The mathematics of repeating units was then worked out by Bravais, Schoenflies, and others in the second half of the nineteenth century. In particular, they showed that if you combined translational symmetries and point group symmetries (rotations, reflections, inversion) that there were only a discrete number of possible repeat structures.

Given that at the beginning of the twentieth century, the atomic hypothesis was largely accepted, particularly by chemists, it was also considered reasonable that crystals were periodic arrays of atoms and molecules. However, we often forget that there was no definitive evidence for the actual existence of atoms. Some scientists such as Mach considered them a convenient fiction. This changed with Einstein's theory of Brownian motion (1905) and the associated experiments of Jean Perrin (1908). X-ray crystallography started in 1912 with Laue's experiment. Then there was no doubt that crystals were periodic arrays of atoms or molecules.

Finally, I want to mention two other macroscopic manifestations of crystal symmetry (or broken symmetry): chirality and distinct sound modes (elastic constants).

Louis Pasteur made two important related observations in 1848. All the crystals of sodium ammonium tartrate that he made could be divided into two classes: one class was the mirror image of the other class. Furthermore, when polarised light traveled through these two classes, the polarisation was rotated in opposite directions. This is chirality (left-handed versus right-handed) and means that reflection symmetry is broken in the crystals. The mirror image of one crystal cannot be superimposed on the original crystal image. The corresponding (trigonal) crystals for quartz are illustrated below.


Aside. Molecular chirality is very important in the pharmaceutical industry because most drugs are chiral and usually only one of the chiralities (enantiomers) is active.

Sound modes (and elasticity theory) for a crystal are also macroscopic manifestations of the breaking of translational and rotational symmetries. In an isotropic fluid, there are two distinct elastic constants and as a result, two distinct sound modes. Longitudinal and transverse sound have different speeds. In a cubic crystal, there are three distinct elastic constants and three distinct sound modes. In a triclinic crystal (which has no point group symmetry) there are 21 distinct elastic constants. Hence, if one measures all of the distinct sound modes in a crystal, one can gain significant information about which of the 32 crystal classes that crystal belongs too. (See Table A.8 here).

Aside: the acoustic modes in a crystal are the Goldstone bosons that result from the breaking of the symmetry of continuous and rotational translations of the liquid.

This post draws on material from the first chapter of Crystallography: A Very Short Introduction, by A.M. Glazer.

Friday, May 31, 2019

Max Weber on the evolution of institutions

Max Weber is one of the founders of sociology. This post is about two separate and interesting things I recently learned about him.

A while ago I discussed Different phases of growth and change in human organisations, based on a classic article from Harvard Business Review. [Which had no references or data!]
My friend Charles Ringma recently brought to my attention somewhat related ideas from Max Weber.
According to Wikipedia

Weber distinguished three ideal types of political leadership (alternatively referred to as three types of domination, legitimisation or authority):[52][111]
  1. charismatic domination (familial and religious),
  2. traditional domination (patriarchspatrimonialismfeudalism) and
  3. legal domination (modern law and state, bureaucracy).[112]
In his view, every historical relation between rulers and ruled contained such elements and they can be analysed on the basis of this tripartite distinction.[113] He notes that the instability of charismatic authority forces it to "routinise" into a more structured form of authority.[79]

I also learnt that Weber had a long history of mental health problems. According to Wikipedia

In 1897 Max Weber Sr. died two months after a severe quarrel with his son that was never resolved.[7][37] After this, Weber became increasingly prone to depression, nervousness and insomnia, making it difficult for him to fulfill his duties as a professor.[17][26] His condition forced him to reduce his teaching and eventually leave his course unfinished in the autumn of 1899. After spending months in a sanatorium during the summer and autumn of 1900, Weber and his wife travelled to Italy at the end of the year and did not return to Heidelberg until April 1902. He would again withdraw from teaching in 1903 and not return to it till 1919. Weber's ordeal with mental illness was carefully described in a personal chronology that was destroyed by his wife. This chronicle was supposedly destroyed because Marianne Weber feared that Max Weber's work would be discredited by the Nazis if his experience with mental illness were widely known.[7][38]

This puts Weber in a similar class to many other distinguished scholars who had significant mental health problems: Boltzmann, John Nash, Drude, Michel Foucault, ...

Tuesday, May 28, 2019

Spin-crossover in geophysics

Most of my posts on spin-crossover materials have been concerned with organometallic compounds. However, this phenomena can also occur in inorganic materials. Furthermore, it may be particularly relevant in geophysics. A previous post discussed how strong electron correlations may play a role in geomagnetism and DMFT calculations have given some insight.

A nice short overview and introduction is
Electronic spin transition of iron in the Earth's deep mantle 
Jung‐Fu Lin Steven D. Jacobsen Renata M. Wentzcovitch

[It contains the figure below]
The main material of interest is magnesiowüstite, an alloy of magnesium and iron oxide,
(Mg1xFex)O




Experimental studies and DFT calculations suggest that as the pressure increases the iron ions undergo a transition from high spin to low spin. The basic physics is that the pressure reduces the Fe-O bond lengths which increases the crystal field splitting.
In geophysics, the pressure increases as one goes further underground.

DFT+U calculations are reported in
Spin Transition in Magnesiowüstite in Earth’s Lower Mantle 
Taku Tsuchiya, Renata M. Wentzcovitch, Cesar R. S. da Silva, and Stefano de Gironcoli

The main result is summarised in the figure below.
There is a smooth crossover from high spin to slow spin, as is observed experimentally. However, it should be pointed out that this smoothness (versus a first-order phase transition with hysteresis) is built into the calculation (i.e. assumed) since the low spin fraction n is calculated using a single site model.  On the other hand, the interaction between spins may be weak because this is a relatively dilute alloy of iron (x=0.1875).
Also, the vibrational entropy change associated with the transition is not included. In organometallics, this can have a significant quantitative effect on the transition.

The elastic constants undergo a significant change with the transition. This is important for geophysics because these changes affect phenomena such as the transmission of earthquakes.

Abnormal Elasticity of Single-Crystal Magnesiosiderite across the Spin Transition in Earth’s Lower Mantle 
Suyu Fu, Jing Yang, and Jung-Fu Lin


A previous post considered changes in the elasticity and phonons in organometallic spin-crossover. Unfortunately, that work did not have the ability to resolve different elastic constants.

Friday, May 24, 2019

Is this an enlightened use of metrics?

Alternative title: An exciting alternative career for Ph.Ds in condensed matter theory!

There is a fascinating long article in The New York Times Magazine
How Data (and Some Breathtaking Soccer) Brought Liverpool to the Cusp of Glory 
The club is finishing a phenomenal season — thanks in part to an unrivaled reliance on analytics.

This is in the tradition of Moneyball. Most of the data analytics team at Liverpool have physics Ph.Ds. It is led by Ian Graham who completed a Ph.D. on polymer theory at Cambridge.

On the one hand, I loved the article because my son and I are big Liverpool fans. We watch all the games, some in the middle of the night. On the other hand, I was a bit surprised that I liked the article since I am a strong critic of the use of metrics in most contexts, especially in the evaluation of scientists and institutions. However, I came to realise that, in many ways, what Liverpool is doing is not the blind use of metrics but rather using data as just one factor in making decisions.
Here are some of the reasons why this is so different from what now happens in universities.

1. The football manager (Jurgen Klopp, who has played and managed) is making the decisions, not someone who has never played or has had limited success with playing and managing (a board member or owner).

2. The data is just one factor in hiring decisions. For example, Klopp often spends a whole day with a possible new player to see what their personal chemistry is. Furthermore, he has watched them play (the equivalent of actually reading the papers of a scientist?).

3. A single metric (cf. goals scored, h-index, impact factor) is not being used to make a decision on who to recruit. Rather, many metrics are being used, to develop a complete picture. Furthermore, a major emphasis of the Moneyball approach is finding ``diamonds in the rough'', i.e. players who have unseen potential, because their unique gifts are being overlooked (because they are currently undervalued because they score poorly with conventional metrics) or they would be a potent combination with other current plays. The latter was a decision is recruiting Salah; the data suggested he would be a particularly powerful partner to Firmino. On the former, the article discusses in detail the analysis that led to Liverpool recruiting the Ghanian midfield,  Naby Keita.
Keita’s pass completion rate tends to be lower than that of some other elite midfielders. Graham’s figures, however, showed that Keita often tried passes that, if completed, would get the ball to a teammate in a position where he had a better than average chance of scoring. What scouts saw when they watched Keita was a versatile midfielder. What Graham saw on his laptop was a phenomenon. Here was someone continually working to move the ball into more advantageous positions, something even an attentive spectator probably wouldn’t notice unless told to look for it. Beginning in 2016, Graham recommended that Liverpool try to get him.


What might be an analogue of this approach in science?
A person who does not attract a lot of attention but has a record of writing papers that stimulate or are foundational to significant papers of better-known scientists?
A person who does very good science even though they have few resources?
A person who is particularly good at putting together collaborations?

Other suggestions?

Tuesday, May 21, 2019

Public talk on emergence

Every year in Australia there is a week of science outreach events in pubs, Pint of Science. I am giving a talk  tomorrow night, Emergence: from physics to sociology.
Here are the slides.

In the past, when explaining emergence I have liked to use the example of geometry. However, one can argue that a limitation of that case is there are not necessary many interacting components to the system. Hence, I think the example of language, discussed by Michael Polanyi is better.



Saturday, May 18, 2019

Phonons in organic molecular crystals.

In any crystal the elementary excitations of the lattice are phonons. The dispersion relation for these quasi-particles relates their energy and momentum. This dispersion relation determines thermodynamic properties such as the temperature dependence of the specific heat and plays a significant role in electron-phonon scattering and superconductivity in elemental superconductors. A nice introduction is in chapter 13 of Marder's excellent text. [The first two figures below are taken from there].

The dispersion relation is usually determined in at least one of three different ways.

1. The classical mechanics of balls and harmonic springs, representing atoms and chemical bonds, respectively. One introduces empirical parameters for the strengths of the bonds (spring constants).

2. First-principles electronic structure calculations, often based on density functional theory (DFT). This actually just determines the spring constants in the classical model.

3. Inelastic neutron scattering.

The figure below shows the dispersion relations for a diamond lattice using parameters relevant to silicon, using method 1. I find it impressive that this complexity is produced with only two parameters.

Furthermore, it produces most of the details seen in the dispersion determined by method 3. (Squares in the figure below.) which compare nicely with method 2. (solid lines below).

What about organic molecular crystals?
The following paper may be a benchmark.

Phonon dispersion in d8-naphthalene crystal at 6K 
I Natkaniec, E L Bokhenkov, B Dorner, J Kalus, G A Mackenzie, G S Pawley, U Schmelzer and E F Sheka

The authors note that method 3. is particulary challenging for three reasons.
  • The difficulties in growing suitable single-crystal samples. 
  • The high energy resolution necessary to observe the large number of dispersion curves (in principle there are 3NM modes, where N is the number of atoms per molecule and M is the number of molecules per unit cell). 
  • The high momentum resolution necessary to investigate the small Brillouin zone (due to the large dimensions of the unit cell).
The figure below shows their experimental data for the dispersions. The solid lines are just guides to the eye.

The authors also compare their results to method 1. However, the results are not that impressive, partly because it is much harder to parameterise the intermolecular forces, which are a mixture of van der Waals and pi-pi stacking interactions. Hence, crystal structure prediction is a major challenge.

A recent paper uses method 2. and compares the results of three different DFT exchange-correlation functionals to the neutron scattering data above.
Ab initio phonon dispersion in crystalline naphthalene using van der Waals density functionals
Florian Brown-Altvater, Tonatiuh Rangel, and Jeffrey B. Neaton


What I would really like to see is calculations and data for spin-crossover compounds.