Thursday, June 24, 2021

The science and politics of the origins of covid-19

I want to begin by stating some hypotheses. Some may be obvious. Others may be contentious. I will number them so that people can easily make comments about specific ones. The underlying issues are illustrated in recent debates about the possible origins of covid-19.

1. Systematic critical thinking is essential to scientific progress and public policy. Healthy doses of skepticism can be valuable.

2. Science progresses well by making multiple hypotheses and examining carefully what evidence is consistent with each of the hypotheses. This is something that Murray Gell-Mann wished someone had told him when he was twenty years old.

3. Transparency is essential to science. People need to share data, including primary data. The more that such data is publicly available the better. This is what open science advocates. 

4. Science is built on ethical conduct, both implicit and explicit. It is important that declarations of conflicts of interest are not just a box-ticking exercise.

5. Scientists cannot have allegiance to some greater authority than truth and integrity. Problematic allegiances include to a company, a family, an institution, a political party, or to a nation. An example is the case of the recent change to the charter of Fudan University, indicative of the stranglehold that the Chinese Communist Party has over Chinese universities.

6. Given these issues about integrity and conflicts of interest luxury journals are problematic because there is a conflict of interest between the commercial success of the publisher in the short term (achieved by promoting hype, i.e. newsworthy sexy scientific breakthroughs, even if they are wrong) and the boring work of doing careful painstaking science.

7. One approach to solving some of these problems is self-regulation of scientific communities. However, when sub-communities (e.g. virologists, string theorists) self-regulate this may be impeded by conflicts of interest.

8. Given the issues above, science journalists need to be more critical and skeptical. Too often they seem in awe of scientists and want to promote hype as it sells. Journalists need to ask more hard questions about conflicts of interest, weak reasoning, claimed "breakthroughs", hype, proposed great technological applications, and the "science as saviour" narrative.

9. There is a fear among scientists about publically speaking about scientific uncertainty and ambiguity. This fear is understandably driven by the experience of "skeptics" latching onto uncertain statements to promote climate change denialism, young-earth creationism, and anti-vaccines. Thus, a great challenge in public engagement is to educate about the role of uncertainty in science.

10. Science always occurs in a political context whether it is in Australia, Romania, or China. The context will always have some influence, but it should not be determinative.

11. The greater the stakes (whether potential Nobel Prizes, company profits, government scandal, a disaster) in play, the greater the likelihood will be for mistakes, corruption, deception, and cover-up. Consequently, the level of scientific diligence and regulation needs to be proportionate to the possible benefits and risks. Extraordinary claims require extraordinary evidence.

12. Beware of the argument from authority. A hypothesis should be accepted or rejected based on the quality of the reasoning and evidence provided, not on the scientific prestige (or lack thereof) of the proponent.

All of the claims above I see played out recently in debates about the origins of covid-19. Two distinct hypotheses are dissected in a helpful and long article recently published in the Bulletin of Atomic Scientists.

The origin of COVID: Did people or nature open Pandora’s box at Wuhan?  Nicholas Wade 

Hypothesis 1. The virus spread from a wet market in Wuhan. The virus was zoonotic, i.e. as a result of evolution it crossed the species barrier from bats to humans.

Hypothesis 2. The virus spread from the Wuhan Institute of Virology where a research group was investigating bat viruses and doing "gain of function" research to see how the bat viruses might be modified genetically into a form that could infect humans. 

The article is worth reading because it carefully lays out the science while also raised many of the issues I mention above. A few things that I learned follow.

There is significant evidence that the MERS, SARS1, Ebola viruses are zoonotic. The evidence consists of finding intermediate genetic forms in intermediate species. Often this evidence was found within months of the disease outbreak. In contrast, after 18 months there is still no evidence of intermediate forms for SARS2.

The "gain of function" research in Wuhan was being funded by the USA National Institutes of Health, via a grant to the EcoHealth Alliance of New York, led by Peter Daszak. Wade writes

"We stand together to strongly condemn conspiracy theories suggesting that COVID-19 does not have a natural origin,” a group of virologists and others wrote in the Lancet on February 19, 2020, when it was really far too soon for anyone to be sure what had happened. Scientists “overwhelmingly conclude that this coronavirus originated in wildlife,” they said, with a stirring rallying call for readers to stand with Chinese colleagues on the frontline of fighting the disease.

Contrary to the letter writers’ assertion, the idea that the virus might have escaped from a lab invoked accident, not conspiracy. It surely needed to be explored, not rejected out of hand. A defining mark of good scientists is that they go to great pains to distinguish between what they know and what they don’t know. 

It later turned out that the Lancet letter had been organized and drafted by Peter Daszak, ... This acute conflict of interest was not declared to the Lancet’s readers. To the contrary, the letter concluded, “We declare no competing interests.”

Wade points out that there is no direct evidence for either of the two hypotheses (which he calls theories).

He also talks quite a bit about "who is to blame" and claims that we need to know the answer as to which hypothesis is correct in order to know how to prevent the next pandemic. However, I disagree. Based on the evidence we already have we can conclude the following.

A. New deadly viruses can be zoonotic. The best way to reduce their likelihood is to close wet markets and reduce environmental destruction.

B. Even if SARS2 did not spread from the "gain of function" research in Wuhan it is completely plausible that it could have. Thus, given such risks that research should be stopped until a case is made that the possible benefits outweigh the risks and that it is done with much greater transparency and regulation than currently.

For balance I include an extract from Wikipedia

In May 2021, Wade published an article which advanced the claim that COVID-19 likely originated from a leak at the Wuhan Institute of Virology.[12][13] Wade's article generated significant controversy,[14] and has become one of the most-cited pieces in support of the lab leak hypothesis.[15] This claim is at odds with the prevailing view among scientists that the virus most likely has a zoonotic origin.[16][17][18][19] Some experts have supported taking the lab leak possibility seriously, while the majority consider it very unlikely, calling it "speculative and unsupported".[20][21] Others noted the explosive and implausible nature of Wade's allegations about virologists conspiring to avoid blame for causing the pandemic,[22] with Science-Based Medicine among those calling Wade's argument a conspiracy theory.[23]

Another article worth reading (recommended by a commenter on this blog) is

Beijing’s useful idiots: Science journals have encouraged and enforced a false Covid narrative by Ian Birrell.

Thursday, June 17, 2021

What materials have a transition from a metal to a band insulator?

 A metal and a band insulator are distinct states of matter. 

A suitable order parameter is the Drude weight, defined as the integral over frequency of the frequency-dependent conductivity at zero temperature.

How might a single material undergo a transition between a band insulator and a metal? 

The schematic below (from Kittel) illustrates three distinct possibilities for the band structure and band fillings.


(a) Band insulator. The bands do not overlap and the lower band is full. This occurs if there is an integer number of electrons per primitive cell in the crystal. 

(b) Metal I. The bands overlap and the system is a metal regardless of the number density of electrons.

(c) Metal II. The bands do not overlap. There is a non-integer number of electrons per primitive cell.

Suppose the number of electrons is fixed, (i.e. there is no chemical doping).
How can a metal-insulator transition occur when some physical parameter (such as pressure) changes?

Scenario A.
There is no structural phase transition associated with the metal-insulator transition.
A transition between (a) and (b) can occur. This means that at the transition the volume of the Fermi surface will be zero.
This may be an example of a Lifshitz transition (where there is a change in the topology of the Fermi surface), based on this 1959 paper by I.M. Lifshitz.

[Aside: I find this nomenclature confusing because there is also a Lifshitz point, where there is a phase transition between commensurate ordering (such as Neel antiferromagnet) and incommensurate ordering (such as a spiral antiferromagnet).
This is E.M. Lifshitz, co-author with Landau of A Course in Theoretical Physics, and I.M.'s brother.]

Scenario B.
The transition is accompanied by a structural phase transition, such as the doubling of the size of the primitive cell in the crystal.
One example of the latter is the Peierls transition in a one-dimensional metal with one electron per lattice site. Dimerising the lattice produces an energy gap at the Fermi wavevector leading to an insulator.
Another example is the transition from graphite to diamond that occurs at about 15 kbar of a pressure. The crystal structure changes and consequently there is a transition from a semi-metal to an insulator.

I have a few questions for readers. The discussion above involves basic solid state physics but I have not seen it clearly set out before. 

1. Do I have the physics correct?

2. Do you know somewhere this is discussed?

3. For scenario A, are the metallic and insulating states adiabatically connected?

4. Do you know of any specific materials where scenario A. actually occurs?

Thursday, June 10, 2021

Universities are not a business, but ...

 It is no surprise to most readers that I do not believe that "the university is a (billion-dollar) business and so should be run accordingly." I reject the "entrepreneurial model" and think this has been a disaster, particularly for Australian and UK universities. Universities are not a business. Universities are also not a family, a finishing school for wealthy children, a community service organisation, a job training school, or a government department, ... Universities are universities. They are about thinking.

Previously, I have posted that management is not leadership, and how the "full economic cost model" in the UK has been a disaster.

But, having said that it might surprise some readers that it is not unusual for me to look at "business" literature on leadership, project management, and managing employees. The Harvard Business Review (HBR) is a particularly good source of helpful and stimulating ideas. Previously, I have mentioned articles relevant to the evolution of organisations, the role of humility in leadership, and managing people (great managers play chess not checkers).

Articles and ideas about business cannot be applied blindly to university contexts. Ideas presented may not be relevant or need to be adapted.

I have wondered why the "business" literature such as HBR is useful and I don't go elsewhere. There are very few helpful articles I am aware of that specifically address university contexts. I think this is because business is really "big business", i.e. there is an incredibly large market for books, ideas, articles, university degrees, ... about management. Hence, the best material such as HBR articles, are well-researched, well-written, and very accessible. 

The latest article I read carefully may be relevant and helpful to several specific situations in universities that readers may encounter. (Currently, I am interested in similar issues in an NGO context).

1. When a senior professor is running a large research group with many students and postdocs it can be very helpful (for all concerned) if there is a more junior scientist (e.g. a research assistant professor) who takes responsibility for many day-to-day operations, especially when the professor is absent. For particularly large groups the professor may also have a PA/secretary/administrator.

2. Most large research institutes will have something like an operations manager who takes responsibility for administrative matters such as finance, reporting, personnel, organising meetings, and interacting with other administrators.

3. Most university departments now have a department manager or deputy chair who takes responsibility for administrative matters. They report to the department chair.

How do these two people best work together? What are their relative roles and responsibilities? In particular, what are lines of reporting, decision-making authority, and future career options for the second person? 

These are important questions because when these two people work well together it can be a great blessing to all concerned. And, when they go bad, it can be a disaster...

The best analog in business may be the relationship between a CEO and a COO (Chief Operating Officer). There are similarities and differences. The article I found helpful is 

Second in Command: The Misunderstood Role of the Chief Operating Officer

by Nathan Bennett and Stephen A. Miles

There are seven basic reasons why companies decide to hire a COO... This tremendous variation implies that there is no standard set of great COO attributes... Still, certain common success factors came up consistently in the interviews, the most important being building a high level of trust between CEO and COO. Trust comes from meeting obligations on both sides: The COO must truly support the CEO’s vision; keep ego in check; and exhibit strong execution, coaching, and coordination skills. The CEO must communicate faithfully, grant real authority and decision rights, and not stymie the COO’s career.

What do you think? Feel free to share any relevant experiences from the university context. 

Thursday, June 3, 2021

A Myth about Condensed Matter Physics?

What is condensed matter physics about? 

In his beautiful book, The Problems of Physics (originally published in 1987), Leggett has a nice chapter about condensed matter physics, Physics on a human scale. The abstract begins:

This chapter argues that the widespread notion that the discipline of condensed matter physics is devoted to deriving the properties of complex many-body systems from that of their atomic-level components is a myth, and that the analogy of map-making is much more appropriate.

Here are some quotes that clarify Leggett's argument.

a number of cases, particularly in the traditional areas of the physics of gases and crystalline solids, in which a model which treats the behaviour of the whole as essentially just the sum of that of its parts (atoms or electrons) has been quite successful; and a few more in which, even if a ‘one- particle’ picture fails, a description in terms of pairs of particles interacting in a way which is not particularly sensitive to the environment gives good results. But these cases, despite the fact that they totally dominate the presentation of the subject in most elementary textbooks, are actually the exception rather than the rule. 

In virtually all the frontier areas of modern condensed-matter physics, the relationship between our understanding of the behaviour of matter at the microscopic level of single atoms and electrons, and at the macroscopic level of (say) liquids and solids, is actually a good deal more complicated than this.

If the activity just described is not what condensed-matter physics is all about, then what is it about? I would claim that the most important advances in this area come about by the emergence of qualitatively new concepts at the intermediate or macroscopic levels—concepts which, one hopes, will be compatible with one's information about the microscopic constituents, but which are in no sense logically dependent on it. 

... [these new concepts] provide a new way of classifying a seemingly intractable mass of information, of selecting the important variables from the innumerable possible variables which one can identify in a macroscopic system;

All this is not to deny that an important role is played in condensed-matter physics by attempts to relate the macroscopic behaviour of bulk matter to our knowledge concerning its constituent atoms and electrons. Indeed, the theoretical literature on the subject is full of papers which at first sight seem to be claiming to ‘derive’ the former from the latter—that is, to do exactly what I have just said condensed-matter physicists do not do. 

It is precisely this compelling need to isolate, from a vast and initially undifferentiated mass of information, the features which are relevant to the questions one wishes to ask, which distinguishes condensed-matter physics qualitatively from areas such as atomic or particle physics...

In this situation I believe that it is sensible to reorient our view of the kinds of questions that we are really asking in condensed-matter physics. Rather than chasing after the almost certainly chimerical goal of deducing the behaviour of macroscopic bodies rigorously from postulates regarding the microscopic level, it may be better to view the main point of the discipline as, first, the building of autonomous concepts or models at various levels, ranging all the way from the level of atomic and subatomic physics to that of thermodynamics; and, second, the demonstration that the relation between these models at various levels is one not of deducibility but of consistency—that is, that there are indeed ‘physical approximations’ we can make which make the models at various levels mutually compatible.

In different words, condensed matter physics is all about emergence! [Although, I know Leggett does not like the way the word is used]. 

The centrality of intermediate scales was also emphasised by Tom McLeish in Soft Matter: A Very Short Introduction.

When I recently read Leggett's chapter I was concerned that this might be in conflict with my draft manuscript of Condensed Matter Physics: A Very Short Introduction.  In the first chapter, I wrote the following.

The central question of Condensed Matter Physics

Generally, condensed matter physicists grapple with one question. Because it is so important I state the question in three different ways.

How do macroscopic properties emerge from microscopic properties? 

How do the properties of a state of matter emerge from the properties of the atoms in the material and the interactions between the atoms?

How do the many atoms in a material interact with one another to collectively produce a particular property of the material? 

I think this is consistent with Leggett's perspective, particularly because I do later emphasise emergence and intermediate scales. On the other hand, I may not have the same emphasis (or strong language) that Leggett does. 

Leggett's view is particularly pertinent today because a quarter of a century later there are probably a lot more people who would say that they are condensed matter physicists but would subscribe to the "myth". This is because of the rise of computational materials science due to massive increases in computational power and better computational methods such as those based on Density Functional Theory (DFT), using "better" functionals and DMFT (Dynamical Mean-Field Theory).

What do you think?