Emergence in biology

The beautiful behaviour of this flock of starlings is an example of a class of phenomena variously known as emergent, collective or more-is-different behaviour. The point is that a single starling, or two starlings cannot show this striking phenomenon, you need hundreds or thousands of starlings, to see it. A liquid is a less obviously exciting example of an emergent phenomenon. One or two water molecules aren’t a liquid, you need at least about a hundred to make even a tiny water droplet.

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Biologists arguing over liquids

Balsamoil Protean

Chemical engineers, chemists, physicists and food scientists have been studying coexisting liquids like the (black) balsamic vinegar and (yellow) olive oil above, for over a hundred years. Cell biologists have been busy with other things over this time. But over the last few years at least some cell biologists seem to not only be studying coexisting liquids but arguing over them.

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Scaling down someone else’s idea

UntitledWhen you have as few genuinely original ideas as I do, one way to make progress is to borrow (with appropriate attribution) other people’s ideas. I have been wondering about how a virus such as the corona virus (shown on the left as the knobbly object*) gets through the mucus (pale blue) that lines the inside of nose and throat, to attack the cells (pink) underneath this mucus. Viruses need to get inside our cells to take them over and allow the virus to reproduce.

One of the functions of mucus may be to trap or somehow to provide a barrier to the viruses. After some Googling it occurs to me that this problem of blocking movement of a virus is more-or-less the same as the problem water companies have, although the scales are very different.

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Viruses in motion

SARS-CoV-2 without background A lot of my research looks at how to move particles around, particles about 100 nanometres across. For example when we made stratified coatings we did this with a mixture of particles of sizes 60 and 400 nanometres. The corona virus (see above) is about 100 nanometres across. Viruses are barely alive. They have no metabolism themselves, no more than the inert colloidal particles my colleagues and I study. The virus above has the genetic material in the centre, surrounded by a protein coat. The red things are its spike proteins, that help it enter and infect a cell. The colours above are false, I think it is reconstructed from electron (not light) microscopy.

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Only one in a billion hits

Paracetamol acetaminophen 500 mg pillsYesterday I attended a seminar by a speaker from a big pharmaceutical company. She talked about techniques to look at drug molecules in single cells. This is very very hard, which is why it is very much a work in progress. Each one of our cells is tiny, a fraction of a tenth of a millimetre across, and so invisible to the naked eye. But this is still large enough to be home to billions of protein molecules, of thousands of different types. Most drug molecules work by targeting a particular one type of protein molecule.

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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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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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Moving to where the energy is

ATPanionChemDrawThe human body is a colony of about 30 trillion cooperating cells, each of which needs to burn energy to survive. Within the cells, a lot of the energy is carried around in the form of a molecule called ATP. A single one of our cells may have ten billion or more molecules of ATP, and these molecules are very dynamic. A single ATP molecule may be used to release its energy, then regenerated only a second later. So, there are huge ATP currents and gradients inside cells. And ATP is a big molecule, its structure is above. From left to right, there are three charged phosphate groups (each with a P = phosphorous), a sugar in the middle, and at the part at the top right is also found in one of the bases in DNA.

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Politely disagreeing with the BBC and a teacher

Artists at All City Coffee 25I am currently teaching biological physics to third-year physics undergraduates. As part of this I teach about how living organisms acquire food molecules, oxygen etc, and how large living organisms, such as ourselves, transport these food molecules, oxygen, etc around our bodies. A fundamental point that I make, is that diffusion is only fast enough to support the demands of life when the movement is over very small distances, around 1 mm or less. Over distances more than very roughly 1 mm, some sort of flow is required to move molecules around. Over distances of centimetres, metres and above, diffusion is very very slow.

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Eating for ten trillion

Adults are recommended to eat about 2000 kilocalories per day. As this is an energy divided by a time it is a power consumption, and in the proper units, it is about 100 Watts. The power consumption of our bodies is a pretty basic feature of how our bodies work, but there is not much known about why a 80 kg guy like me needs 100 W, not 10 or 1000 W. We know* our brain needs of order 10 W, and our heart about 1 W, but for example we have only a poor idea of why our brain burns through 10 Joules every second.

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