Going beyond the data?

In a 2007 Nature paper Engel et al. reported the data below showing the amplitude of an optical signal versus time.

The lower curve is the Fourier transform [using a new numerical method they developed explicitly for this paper] of the upper data.
They interpreted this data as evidence for quantum coherence between the excited states of different chromophores in a photosynthetic protein, since an oscillatory signal is a signature of quantum interference (Rabi oscillations). Engel et al. went on to claim that this coherence enabled the biomolecule to function in a highly efficient manner because:

…the system is essentially performing a single quantum computation, sensing many states simultaneously and selecting the correct answer, as indicated by the efficiency of the energy transfer. In the presence of quantum coherence transfer, such an operation is analogous to Grover's algorithm, …such a scheme can provide efficiency beyond that of a classical search algorithm.

This Nature paper greatly excited many in the quantum information community and has led to a host of theoretical papers about "quantum biology". The paper has already been cited hundreds of times.

But is this enthusiasm and hyperactivity justified? Given the noisy data and the absence of any concrete measurements of entanglement (e.g., violation of Bell inequalities) are the conclusions and claims really justified? I do not think so, as I have expressed several times in previous blog posts.

There is an interesting new preprint A critical view on transport and entanglement in models of photosynthesis by Tiersch, Popescu, and Briegel which has the abstract:

Quantum effects in biological light-harvesting molecules, such as quantum coherence of excitonic states and entanglement have recently gained much attention. We observe a certain discrepancy between the original experimental work and several theoretical treatments of coherent excitation transport in light-harvesting molecules. Contrary to what is generally stated, we argue that entanglement in such molecules is generally not equivalent to the presence of coherence but mostly introduced by initial assumptions underlying the models, and that entanglement, as opposite to coherence, seems to play no role in the transport efficiency.

Preparing good talks is hard work

Almost anyone can cobble together some powerpoint slides.
But, actually preparing a good talk is very hard work.
This is on my mind because this week I am working on a colloquium I am giving this friday.
Why is it hard work, even for the experienced?
Because you have to decide what material to leave out!

A dubious argument for quantum biology

Over the past decade there has been an amazing set of experiments performed which involve seeing quantum interference associated with the wave nature of very large molecules. The figure below is taken from a nice review article by Markus Arndt and Klaus Hornberger. It shows some of molecules, including as many as one hundred atoms and of the order of one thousands of elementary particles (protons, neutrons, and electrons).

The figure below shows some of the interference fringes seen.

Occasionally I hear these incredible experiments used as a "proof of principle" to justify the possible role of significant quantum effects in biology. However, I think this a fanciful view because of the following significant constraints in the experiments:

• They involve single molecules
• They are performed in vacuum.
• The quantum interference is associated with the centre of mass degree of freedom. By, definition this does not couple to all the internal degrees of freedom.

This is a very long way from a biological cell where the molecules are packed close to one another and interact strongly with their surrounding environment of water.

I cannot deny this

This week the UQ Physics Colloquium was given by John Cook on Communicating Climate Science and Countering Disinformation. He is a UQ physics graduate and now writes an influential blog Skeptical Science which aims to present peer-reviewed climate science in an accessible fashion that answers climate change skeptics. He has also developed a popular Phone application which answers 10 common used arguments of climate change skeptics. He recently published a book Climate Change Denial.

Here is my summary of some of the main points.

97 out 100 climate scientists believe that humans are causing carbon dioxide levels to rise.
Why?  There are many different lines of evidence.
In contrast, only 58% of the general public believe this. This is because the mainstream media gives the impression of a 50/50 debate.

Several references were made to a book Merchants of Doubt"  by Naomi Oreskes and Erik Conway which documents how vested financial interests have funded disinformation campaigns to undermine public debate about issues on which the scientific evidence is clear.

John summarised a paper Denialism: what is it and how should scientists respond?
which argued that there are 5 characteristics common to other denials as well. e.g., dangers of cigarette smoking, HIV causes AIDS, young earth creationism,
[I think this also applies to some proponents of quantum biology!]

1. Cherry picking of data
e.g. glacier mass balance. there are a few glaciers that are indeed growing. But the vast majority are shrinking.
Human carbon dioxide emission is only a small fraction of total emission from the planet. This ignores that natural processes balance out absorption and emission.

2. Promoting the views of fake experts
e.g. The petition project - 31,000 "scientists" have signed it.

3. Impossible expectations
Always demanding more evidence and complete certainty.

4. Logical fallacies
Climate changed has happened before

5. Conspiracy theories
e.g. climategate. But, 8 independent investigations have found no evidence of conspiracy

In contrast, to denialism genuine skepticism considers all the evidence and weighs it. I would add a sixth common feature of denialsm: a lack of humility to acknowledge that their lack of relevant scientific expertise, experience, and knowledge may just possibly mean that their opinion is not valid.

John answered one question I have had for a while. Why do weather fluctuations increase with increasing global temperatures?
This is due to the water cycle because higher temperatures lead to more evaporation, more drought, more water in atmosphere.

There is one complex and subtle issue which was not addressed and I do not understand. That is the views of and role played by distinguished physicists such as Freeman Dyson, Bob Austin, William Happer, and Bob Laughlin. They are not climate scientists but on some level are "skeptics". Indeed, some of them unsuccessfully petitioned the American Physical Society to change its policy on climate change. Why do they believe what they do? Perhaps it is just a mixture of physics hubris and political sympathies...

Overall, I thought this was a great colloquium. It generated a lot of good questions and discussions.

How much money should I ask for?

As little as possible! What?
Occasionally when I review grant proposals I am dismayed by the large amount of money that some people, especially junior people, ask for. I wonder who, if anyone, is advising them to do this. A few things to consider when you prepare your proposed budget:

• The greater the requested budget the greater the scrutiny of the application.
• If your budget is 2 or 3 times the budget of competing applications the funding agency will almost always think that it is better to fund 2 or 3 groups rather than just one.
• Getting some money is always better than getting none, especially if you are starting out.
• The kudos of actually getting the grant is fairly weakly dependent of how much money you actually get.
• The maximum possible allowed budget is not a good guide as to how much you should ask for. A better guide is the average size of grants previously given to applicants of comparable stature and experience to you.

And if you do get the grant, but the budget is trimmed substantially, don't whine. There are plenty of unsuccessful applicants who would happily take the money.

Singing superlatives of superconductivity

I recently gave two lectures on superconductivity to a fourth year undergraduate Condensed Matter Physics course. In hindsight, there are few points that I did not discuss but should have included:

• the relevance of BCS theory and Cooper pairing to nuclear physics and neutron stars
• how the Meissner effect can be viewed as a photon obtaining mass and that this idea is key to electro-weak theory and to the Higgs boson

These issues are nicely discussed in an article Superconductivity's Smorgasbord of Insights: A Movable Feast by Adrian Cho which appeared in Science last month to celebrate the Centenary of Kamerlingh Onnes discovery. It contains the figure below.

The complex nature of the self energy

I am trying to understand under exactly what conditions it is (or is not) meaningful to use a self energy to describe and understand experiments on a strongly correlated metal which may be (at least in some sense) a non-Fermi liquid. This is particularly motivated by a recent paper on the overdoped cuprates.

Below are some statements which I am trying to ascertain the truth of and relationship between them. I believe
1. and 2. are always true.
3. and 4. are equivalent but are not always true.
5. is true.
I am not sure about 6.

1. The one-electron Greens function G(k,E) is an analytic function of energy E.

2. One can always define a self energy by Dyson's equation

where G0 is the non-interacting Greens function. This self energy will be an analytical function of E.

3. If E is treated as a complex variable G(k,E) has isolated simple poles in the complex plane. These poles correspond to quasiparticles. One can then write down a Boltzmann transport equation for these quasiparticles.

4. The self energy can be written as a convergent perturbation expansion. This ensures adiabatic continuity and the existence of quasi-particles.

5. If G(k,E) has a non-integer power law dependence on E there will be a branch cut in the complex plane. This means a description in terms of quasi-particle poles is inadequate.
[This is what happens in one dimension with Luttinger liquids].

6. Branch cuts in the plane may mess up the Kramers-Kronig relation which relates the real and imaginary parts of the self energy.

So, I welcome thoughts about the above claims.
Is there somewhere that this is all written down and discussed clearly?
I have gleaned the above from my subconscious memory of a diverse range of sources.

The figure is from Piers Coleman.