Are the liquid droplets in cells spandrels?

Spedale degli Innocenti (detail)Forty years ago Stephen Jay Gould and Richard Lewontin introduced what they called spandrels, to the field of evolutionary biology. My impression is that this idea has been controversial in evolutionary biology ever since. Spandrels in the original sense of the word are illustrated above. The word spandrel comes from architecture, and basically it refers to the parts of the arches above which have the blue discs with a relief person in them. They are the spaces between the arch and the roof. The point that inspired Gould and Lewontin, is that arches are directly functional parts of archtecture, they hold up the roof. But by their very nature arches leave gaps, that is unavoidable but not directly functional. These gaps can be filled in by spandrels, which themselves are not directly functional — the ceiling will not collapse if they are removed.

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The “exemplary statistical safety record” and the fireball visible 60 km away

Deepwater Horizon offshore drilling unit on fire 2010I am revising a numerical physics course for the forthcoming semester, in particular the bits about data analysis. So I have been reading a couple of books to both learn from them, and to see if they could be useful to the students. One compact but good summary is The Data Loom by Stephen Few. It is quite introductory and short, so I am thinking that it could be good to recommend to the students. It covers a lot of ground and I like the author’s practical, sceptical tone. It is also has some excellent examples.

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Self-destructing droplets


Olive oil with Balsamic Vinegar
Above are droplets of balsamic vinegar (mainly water, but tastier of course) in olive oil. Water and oil phase separate, hence the droplets. The droplets above are maybe a few millimetres across, and they won’t move unless you stir the oil. This blog post is about much smaller droplets, too small to be seen with the eye, so the picture above of much larger droplets, will have to do. Smaller droplets can move. And two scientists working in Darmstadt in Germany, Hajian and Hardt, have seen small droplets move, which is not so surprising. But what is surprising is that they then dissolved.

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Reacting droplets

The movie shows a system that starts to separate into two liquids (yellow and purple), just as oil and water do, but is then kept as a dynamic system of droplets that split, evaporate and form again, by a chemical reaction. This chemical reaction converts yellow molecules to purple, and then back to purple again, and this cycle drives the droplet breakup seen in the last two-thirds of the movie. This simulation is of a very bad model of liquid droplets in living cells, there is a movie here of real droplets in real living cells, from the work of Cliff Brangwynne and co-workers.

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Capturing sunlight in droplets

RubiscoLife on Earth, including ourselves, relies totally on photosynthesis. Photosynthesis pulls carbon from carbon dioxide in the air to make the molecules of which plants are made of. Then we eat these plants, and, if we are not vegan, the products of animals that eat these plants. Photosynthesis, like everything else in biology, is the product of evolution. Very simply speaking there are two schools of thought on evolution. The first is that it is an incredible process that has produced marvels such as a soaring eagle with eyesight keen enough to see a rabbit a kilometre away. The second is that it is a blind process that gradually cobbles together just-about-working solutions to the problem of living and reproducing.

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Statisticians for machine learning

I am starting to sort out my Python teaching for the coming semester; the course contains some introductory data analysis. As part of this, I have just read a relatively old (2001) but I think influential article that compares and contrasts two schools of data analysis. Roughly speaking these are:

  • School A): fit a simple-as-possible model function to the data, for example a straight-line or exponential fit, to try and understand what is going on.
  • School B): use a machine learning algorithm such as a neural net, or a support vector machine, to obtain the best possible predictions.

The author is Leo Breiman, a statistician, who was encouraging his fellow statisticians to give School B a try. He thought many statisticians were sticking too rigidly to School A, and this inspired him to write this article, which argues for School B.

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My code crashes a lot but at least I didn’t leave a 10,000 ton cruiser stranded

Starboard bow view of USS Yorktown (CG-48) underway in Caribbean c1985Over the summer I am teaching myself a bit of the Lattice Boltzmann simulation method, and rewriting my second-year computing teaching, to be in Python and use Jupyter notebooks. As always with my coding, I am getting problems with numbers that should be positive (such as  a density) being zero or negative, which fatal consequences for that run. In parallel, I am doing a bit of trawling the web to see, and learn from, what other people do, when they teach computational physics using Python and Jupyter notebooks.

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Summertime droplets

I am having a busy summer. I have the usual research paper to finish, and course to update by autumn. Last week I both co-ran a course for the 12 PhD students who are part of the EU RAMP network I and they are part of, and caught up with graduating students and their families, at the summer graduation ceremony. But I do have a bit of time to teach myself something new.

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Mixing it up

Schwarz-weiß-Melange (spiralförmig)The picture shows what happens when you stir together two viscous (= like honey) liquids together, the liquids fold into each other to form swirls. Here the swirls are visible because the two viscous liquids are white and black paints. It is a nice illustration of the necessity of diffusion (random motion) of molecules, to mixing. The liquids are very viscous, which suppresses diffusion, and so mixing. If the liquids were more like water, which is not viscous, diffusion would blur the white and black swirls into a uniform grey — this is what happens when you mix milk into tea, you start with a pale milky swirl surrounded by the darker black tea surrounding it, before the milk and initially black tea blur into each other.

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Seventeen top-ten universities

The 2020 Guardian University League Tables are out, and Saturday’s print edition ran with the headline “Oxford falls to third place in university rankings”. As someone who teaches data analysis that seemed to be quite a definite statement to me — there is no obvious caveat to indicate how confident they are of this statement. This omission concerns me, but to be fair to The Guardian, they have the 2020 league table data available for download as a spreadsheet. It looks like a fair number of the data values are missing, so I turned to the 2019 league table data. This data set looks complete, and is of the same form. Each university has nine data values, and in each case the analysis assumes that it is the bigger the better, i.e., large values of each number indicate a good university, or good teaching, somehow*.

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