# Category Archives: Good Science

## Book Review – The Gene

Following the March Meeting, I took a vacation for a couple weeks, returning home to Bangkok, Thailand. During my holiday, I was able to get a hold of and read Siddhartha Mukherjee’s new book entitled The Gene: An Intimate History.

I have to preface any commentary by saying that prior to reading the book, my knowledge of biology embarrassingly languished at the middle-school level. With that confession aside, The Gene was probably one of the best (and for me, most enlightening) popular science books I have ever read. This is definitely aided by Mukherjee’s fluid and beautiful writing style from which scientists in all fields can learn a few lessons about scientific communication. The Gene is also touched with a humanity that is not usually associated with the popular science genre, which is usually rather dry in recounting scientific and intellectual endeavors. This humanity is the book’s most powerful feature.

Since there are many glowing reviews of the book published elsewhere, I will just list here a few nuggets I took away from The Gene, which hopefully will serve to entice rather than spoil the book for you:

• Mukherjee compares the gene to an atom or a bit, evolution’s “indivisible” particle. Obviously, the gene is physically divisible in the sense that it is made of atoms, but what he means here is that the lower levels can be abstracted away and the gene is the relevant level at which geneticists work.
• It is worth thinking of what the parallel carriers of information are in condensed matter problems — my hunch is that most condensed matter physicists would contend that these are the quasiparticles in the relevant phase of matter.
• Gregor Mendel, whose work nowadays is recognized as giving birth to the entire field of genetics, was not recognized for his work while he was alive. It took another 40-50 years for scientists to rediscover his experiments and to see that he had localized, in those pea plants, the indivisible gene. One gets the feeling that his work was not celebrated while he was alive because his work was far ahead of its time.
• The history of genetics is harrowing and ugly. While the second World War was probably the pinnacle of obscene crimes committed in the name of genetics, humans seem unable to shake off ideas associated with eugenics even into the modern day.
• Through a large part of its history, the field of genetics has had to deal with a range of ethical questions. There is no sign of this trend abating in light of the recent discovery of CRISPR/Cas-9 technology. If you’re interested in learning more about this, RadioLab has a pretty good podcast about it.
• Schrodinger’s book What is Life? has inspired so much follow-up work that it is hard to overestimate the influence it has had on a generation of physicists that transitioned to studying biology in the middle of the twentieth century, including both Watson and Crick.

While I could go on and on with this list, I’ll stop ruining the book for you. I would just like to say that at the end of the book I got the feeling that humans are still just starting to scratch the surface of understanding what’s going on in a cell. There is much more to learn, and that’s an exciting feeling in any field of science.

Aside: In case you missed March Meeting, the APS has posted the lectures from the Kavli Symposium on YouTube, which includes lectures from Duncan Haldane and Michael Kosterlitz among others.

## Discovery vs. Q&A Experiments

When one looks through the history of condensed matter experiment, it is strange to see how many times discoveries were made in a serendipitous fashion (see here for instance). I would argue that most groundbreaking findings were unanticipated. The discoveries of superconductivity by Onnes, the Meissner effect, superfluidity in He-4, cuprate (and high temperature) superconductivity, the quantum Hall effect and the fractional quantum Hall effect were all unforeseen by the very experimentalists that were conducting the experiments! Theorists also did not anticipate these results. Of course, a whole slew of phases and effects were theoretically predicted and then experimentally observed as well, such as Bose-Einstein condensation, the Kosterlitz-Thouless transition, superfluidity in He-3 and the discovery of topological insulators, not to diminish the role of prediction.

For the condensed matter experimentalist, though, this presents a rather strange paradigm.  Naively (and I would say that the general public by and large shares this view), science is perceived as working within a question and answer framework. You pose a concrete question, and then conduct and experiment to try to answer said question. In condensed matter physics, this often not the case, or at least only loosely the case. There are of course experiments that have been conducted to answer concrete questions — and when they are conducted, they usually end up being beautiful experiments (see here for example). But these kinds of experiments can only be conducted when a field reaches a point where concrete questions can be formulated. For exploratory studies, the questions are often not even clear. I would, therefore, consider these kinds of Q&A experiments to be the exception to the rule rather than the norm.

More often then not, discoveries are made by exploring uncharted territory, entering a space others have not explored before, and tempting fate. Questions are often not concrete but posed in the form, “What if I do this…?”. I know that this makes condensed matter physics sound like it lacks organization, clarity and structure. But this is not totally untrue. Most progress in the history of science did not proceed in a straight line like textbooks make it seem. When weird particles were popping up all over the place in particle physics in the 1930s and 40s, it was hard to see any organizing principles. Experimentalists were discovering new particles at a rate with which theory could not keep up. Only after a large number of particles had been discovered did Gell-Mann come up with his “Eightfold Way”, which ultimately led to the Standard Model.

This is all to say that scientific progress is tortuous, thought processes of scientists are highly nonlinear, and there is a lot of intuition required in deciding what problems to solve or what space is worth exploring. In condensed matter experiment, it is therefore important to keep pushing boundaries of what has been done before, explore, and do something unique in hope of finding something new!

Exposure to a wide variety of observations and methods is required to choose what boundaries to push and where to spend one’s time exploring. This is what makes diversity and avoiding “herd thinking” important to the scientific endeavor. Exploratory science without concrete questions makes some (especially younger graduate students) feel uncomfortable, since there is always the fear of finding nothing! This means that condensed matter physics, despite its tremendous progress over the last few decades, where certain general organizing principles have been identified, is still somewhat of a “wild west” in terms of science. But it is precisely this lack of structure that makes it particularly exciting — there are still plenty of rocks that need overturning, and it’s hard to foresee what is going to be found underneath them.

In experimental science, questions are important to formulate — but the adventure towards the answer usually ends up being more important than the answer itself.

## Citizen First, Scientist Second

I have written previously in praise of the scientific community becoming more diverse over time. I emphasized its importance because people with different cultural backgrounds often synthesize ideas that are sometimes not juxtaposed in other cultures. It is almost unquestionable that the US scientific enterprise has benefited greatly from the inclusion of scientists from around the world. Because the scientific community has become more diverse in the past few decades, it has also meant that science (at least in the academic sense) has become more open and international. As a member of the international community myself (I am a Thai citizen), recent events have been tough to watch as a scientist, immigrant and person.

This past week has seen some, I would consider, unsavory events affecting the scientific and higher education communities in the US. There was a temporary ban put in place by the US government barring citizens from seven Middle Eastern and African countries from entering the US. Some students are stranded outside the US, unable to return before the spring semester starts.

Day to day, science requires enormous attention to detail, patience doing precise theoretical or experimental work, and time to work without distractions. It is easy to get wrapped up in one’s own work, forgetting to pick one’s head up to look at what is going on around you. If events are not directly affecting you or someone close to you, it is easy to forget that these things are even happening.

In this spirit, I encourage you to attend (or organize!) department town hall meetings and speak up in support of your international colleagues. There is a planned Scientists’ March being arranged, and I urge you to attend if there is a gathering near you. To be perfectly honest (like most scientists), I am a person of thought rather than a person of action, but it is always necessary to be a citizen first and a scientist second.

## An Interesting Research Avenue, an Update, and a Joke

An Interesting Research Avenue: A couple months ago, Stephane Mangin of the Insitut Jean Lamour gave a talk on all-optical helicity-dependent magnetic switching (what a mouthful!) at Argonne, which was fascinating. I was reminded of the talk yesterday when a review article on the topic appeared on the arXiv. The basic phenomenon is that in certain materials, one is able to send in a femtosecond laser pulse onto a magnetic material and switch the direction of magnetization using circularly polarized light. This effect is reversible (in the sense that circularly polarized light in the opposite direction will result in a magnetization in the opposite direction) and is reproducible. During the talk, Mangin was able to show us some remarkable videos of the phenomenon, which unfortunately, I wasn’t able to find online.

The initial study that sparked a lot of this work was this paper by Beaurepaire et al., which showed ultrafast demagnetization in nickel films in 1996, a whole 20 years ago! The more recent study that triggered most of the current work was this paper by Stanciu et al. in which it was shown that the magnetization direction could be switched with a circularly polarized 40-femtosecond laser pulse on ferromagnetic film alloys of GdFeCo. For a while, it was thought that this effect was specific to the GdFeCo material class, but it has since been shown that all-optical helicity-dependent magnetic switching is actually a more general phenomenon and has been observed now in many materials (see this paper by Mangin and co-workers for example). It will be interesting to see how this research plays out with respect to the magnetic storage industry. The ability to read and write on the femtosecond to picosecond timescale is definitely something to watch out for.

Update: After my post on the Gibbs paradox last week, a few readers pointed out that there exists some controversy over the textbook explanation that I presented. I am grateful that they provided links to some articles discussing the subtleties involved in the paradox. Although one commenter suggested Appendix D of E. Atlee Jackson’s textbook, I was not able to get a hold of this. It looks like a promising textbook, so I may end up just buying it, however!

The links that I found helpful about the Gibbs paradox were Jaynes’ article (pdf!) and this article by R. Swendsen. In particular, I found Jaynes’ discussion of Whifnium and Whoofnium interesting in the role that ignorance and knowledge plays our ability to extract work from a partitioned gases. Swendsen’s tries to redefine entropy classically (what he calls Boltzmann’s definition of entropy), which I have to think about a little more. But at the moment, I don’t think I buy his argument that this resolves the Gibbs paradox completely.

A Joke:

Q: What did Mrs. Cow say to Mr. Cow?

A: Hubby, could you please mooo the lawn?

Q: What did Mr. Cow say back to Mrs. Cow?

A: But, sweetheart, then what am I going to eat?

## Coupled and Synchronized Metronomes

A couple years ago, I saw P. Littlewood give a colloquium on exciton-polariton condensation. To introduce the idea, he performed a little experiment, a variation of an experiment first performed and published by Christiaan Huygens. Although he performed it with only two metronomes, below is a video of the same experiment performed with 32 metronomes.

A very important ingredient in getting this to work is the suspended foam underneath the metronomes. In effect, the foam is a field that couples the oscillators.

## Data Representation and Trust

Though popular media often portrays science as purely objective, there are many subjective sides to it as well. One of these is that there is a certain amount of trust we have in our peers that they are telling the truth.

For instance, in most experimental papers, one can only present an illustrative portion of all the data taken because of the sheer volume of data usually acquired. What is presented is supposed to be to a representative sample. However, as readers, we are never sure this is actually the case. We trust that our experimental colleagues have presented the data in a way that is honest, illustrative of all the data taken, and is reproducible under similar conditions. It is increasingly becoming a trend to publish the remaining data in the supplemental section — but the utter amount of data taken can easily overwhelm this section as well.

When writing a paper, an experimentalist also has to make certain choices about how to represent the data. Increasingly, the amount of data at the experimentalist’s disposal means that they often choose to show the data using some sort of color scheme in a contour or color density plot. Just take a flip through Nature Physics, for example, to see how popular this style of data representation has become. Almost every cover of Nature Physics is supplied by this kind of data.

However, there are some dangers that come with color schemes if the colors are not chosen appropriately. There is a great post at medvis.org talking about the ills of using, e.g. the rainbow color scheme, and how misleading it can be in certain circumstances. Make sure to also take a look at the articles cited therein to get a flavor of what these schemes can do. In particular, there is a paper called “Rainbow Map (Still) Considered Harmful”, which has several noteworthy comparisons of different color schemes including ones that are and are not perceptually linear. Take a look at the plots below and compare the different color schemes chosen to represent the same data set (taken from the “Rainbow Map (Still) Considered Harmful” paper):

The rainbow scheme appears to show more drastic gradients in comparison to the other color schemes. My point, though, is that by choosing certain color schemes, an experimentalist can artificially enhance an effect or obscure one he/she does not want the reader to notice.

In fact, the experimentalist makes many choices when publishing a paper — the size of an image, the bounds of the axes, the scale of the axes (e.g. linear vs. log), the outliers omitted, etc.– all of which can have profound effects on the message of the paper. This is why there is an underlying issue of trust that lurks in within the community. We trust that experimentalists choose to exhibit data in an attempt to be as honest as they can be. Of course, there are always subconscious biases lurking when these choices are made. But my hope is that experimentalists are mindful and introspective when representing data, doubting themselves to a healthy extent before publishing results.

To be a part of the scientific community means that, among other things, you are accepted for your honesty and that your work is (hopefully) trustworthy. A breach of this implicit contract is seen as a grave offence and is why cases of misconduct are taken so seriously.

## Ruminations on Raman

The Raman effect concerns the inelastic scattering of light from molecules, liquids, or solids. Brian has written a post about it previously, and it is worth reading. Its use today is so commonplace, that one almost forgets that it was discovered back in the 1920s. As the story goes (whether it is apocryphal or not I do not know), C.V. Raman became entranced by the question of why the ocean appeared blue while on a ship back from London to India in 1921. He apparently was not convinced by Rayleigh’s explanation that it was just the reflection of the sky.

When Raman got back to Calcutta, he began studying light scattering from liquids almost exclusively. Raman experiments are nowadays pretty much always undertaken with the use of a laser. Obviously, Raman did not initially do this (the laser was invented in 1960). Well, you must be thinking, he must have therefore conducted his experiments with a mercury lamp (or something similar). In fact, this is not correct either. Initially, Raman had actually used sunlight!

If you have ever conducted a Raman experiment, you’ll know how difficult it can be to obtain a spectrum, even with a laser. Only about one in a million of the incident photons (and sometimes much fewer) actually gets scattered with a change in wavelength! So for Raman to have originally conducted his experiments with sunlight is really a remarkable achievement. It required patience, exactitude and a great deal of technical ingenuity to focus the sunlight.

Ultimately, Raman wrote his results up and submitted them to Nature magazine in 1928. Although these results were based on sunlight, he had just obtained his first mercury lamp to start his more quantitative studies by then. The article made big news because it was a major result confirming the new “quantum theory”, but Raman immediately recognized the capability of this effect in the study of matter as well. After many years of studying the effect, he came to realize that the reason that water is blue is basically the same as why the sky is blue — Rayleigh scattering goes as $1/\lambda^4$.

Readers of this blog will actually notice that I have written about Raman scattering in several different contexts on this site, for instance, in measuring the Damon-Eschbach mode and the Higgs amplitude mode in superconductorsilluminating the nature of LO-TO splitting polar insulators and measuring unusual collective modes in Kondo insulators demonstrating its power as probe of condensed matter even in the present time.

On this blog, one of the major themes I’ve tried to highlight is the technical ingenuity of experimentalists to observe certain phenomena. I find it quite amazing that the Raman effect had its rather meager origins in the use of sunlight!