Tag Archives: biology

Living Stars: What is Bioluminescence?

Recently something unusual happened: I had an idea that was illustrated and published in Wired. They have a gallery of hybrid animals up, including drawings made by students in the CSU Monterey Bay Science Illustration Program, and my contribution was bioluminescent starlings. I personally think that watching a murmuration of glowing starlings flocking would be amazing. But how does bioluminescence work exactly?

Bioluminescence is light emission from a living creature. How does that happen? Remember that light is a form of energy, and if a particle undergoes a transition from one energy level to another, the difference in energy has to go somewhere and may be emitted as light. Much of the light we get from the sun comes from atomic energy level transitions that happen inside it. But the same thing can also occur in more complex chemical reactions: excess energy can be used to create a new compound, or heat up the reactants, but it may also be emitted as light. (Whether or not this happens depends on the mechanism of the chemical reactions and, as usual, on energy minimization.)

So bioluminescence occurs when a chemical reaction happens, inside a living organism, that emits light. It’s actually relatively common in deep-sea creatures, who don’t have much other light around. But it’s also seen closer to shore in bioluminescent algae, and on dry land with fireflies. What these creatures have in common is that they produce luciferin, a class of pigments that can be oxidized to produce light, and luciferase, an enzyme that catalyzes the reaction. These creatures can then use the bioluminescence to communicate with other creatures, for camouflage, luring prey, or attracting mates.

Some plants show bioluminescence too, though there are many competing theories on whether they gain some evolutionary advantage from it or not. But there are also many researchers working to introduce bioluminescence into plants and animals, by adding the genes that create luciferin and luciferase, or by adjusting their expression. Self-lighting could help with imaging, but making more things bioluminescent has both a practical and an aesthetic appeal.

Advertisements

Entropy and Life

Entropy is a measure of how many configurations could yield the same macrostate, and thus how probable the macrostate is. It can be a measure of information, or a measure of disorder in a physical system. But what about the entropy of biological systems?

Relatively few configurations yield life, compared to the many that don’t. Life is highly ordered, so living organisms should have much lower entropy than their non-living constituents. In fact, using energy to create and maintain order is one of the key signatures of life! One implication of life having low entropy is that life is improbable, which so far seems to be true based on the limited observations we have of other planets. But another implication is that living things act to reduce entropy locally, in the organism, there must be a corresponding increase in entropy somewhere else to offset that reduction. This is required because of the second law of thermodynamics, which says that by far the most statistically probable outcome is an entropy increase. But the second law applies to ‘closed systems’, which means a system that cannot exchange heat or energy with its surroundings. An organism that can interact with its surroundings can expel entropy via heat, to gain local order and reduce local entropy. Global disorder still increases, but for that organism, the ability to locally reduce entropy is literally a matter of life and death.

An obvious example of this principle is humans. Our human bodies are very highly ordered compared to inanimate things like air and water. Even compared to dirt, which has a whole ecosystem of microbiota and larger organisms like worms, a human represents many times more order. But this doesn’t contradict the second law, because the way we maintain life is to take in food and expel very disordered waste products. Humans can extract the chemical energy in the food and use it to maintain or decrease local entropy levels, and thus stay alive. Obviously other animals do this too, though they may eat different things than we do or digest them in different ways. And actually, the plants that we and other animals eat have done something similar, except that instead of getting chemical energy from combustion they are able to extract it directly from the sun’s light. Plants maintain their low entropy by releasing heat and high-entropy waste products, and anything that eats plants (or that eats something that eats plants) is converting solar energy into local order as well as expelled heat.

If you’re really feeling clever, you might ask, what about the planet Earth? If we’re receiving all this sunlight, and making life from it, shouldn’t there be a corresponding buildup of entropy on the planet, in the form of waste heat or some other disordering? Isn’t the Earth a closed system, isolated in space, whose order is constantly increasing?

But if a closed system is one which exchanges no heat with its surroundings, then the Earth doesn’t qualify because it is obviously exchanging heat with the Sun! The Earth receives a massive number of photons from the sun, which is where plants, and by extension the rest of us, get energy to create order. But in addition, the Earth is also radiating energy and heat into space, as all objects do. The incident energy from the sun is directional, high-energy, and highly ordered, but the energy the Earth radiates into space is in all directions, low-energy, and very disordered. That’s where the excess entropy is going!

Thus, life on our dear planet is not a violation of the second law of thermodynamics at all, because living organisms and even huge ecosystems are not closed systems. What’s more, the creation of order from chaos actually requires a net increase in entropy: it requires a reconfiguration of atoms and microstates, and the most likely outcome of any reconfiguration is an increase in entropy.  Many of chemical reactions necessary for life are entropically driven, where the outcome has many more available states than the inputs so the reaction is statistically favored to occur. Organisms that do work to create order must also create entropy, and the organisms most likely to survive are often those with the most clever control of entropy generation. So the proliferation of life is not threatened by entropy, as in the popular conception, but actually depends on entropy generation!

Electronics: The Bigger Picture

In our exploration of electronics, we started at the atomic level with the fundamental properties of subatomic particles. We looked at emergent properties of collections of atoms, like the origins of chemical bonding and electronic behavior of materials. Recently we have started to move up in scale, seeing that individual circuit components affect the flow and storage of electrons in different ways. At this point I think it is worthwhile to take a step back and look at the larger picture. While individual electrons are governed by local interactions that minimize energy, we can figure out global rules for a circuit component that tell us how collections of electrons are affected by a resistor or some other building block, creating the macroscopic quantity we call current. From there we can create collections of circuit components that perform various operations on the current passing through them. These operations can again be combined, and where we may have started with a simple switch, we can end up with a computer or a display or a control circuit.

One way to picture it is like a complex canal system for water: we have a resource whose movement we want to manipulate, to extract physical work and perhaps perform calculations. At a small scale, we can inject dye into a bit of water and watch its progress through the system as it responds to local forces. But we can look at water currents at a larger scale by adding up the behavior of many small amounts of water. In fact, scale is a type of context, a lens through which a system can look quite different! Electrical engineers who design complex circuits for a living tend to work at a much higher level of abstraction than do scientists working on experimental electronic devices. The electrical engineers have to be able to imagine and simulate the function of impressive numbers of transistors, resistors, and other components, as shown below. Whereas a device physicist focuses on the detailed physics in a single circuit component, to learn what its best use might be. They are each working with the same system, but in different and complementary ways.

When I first started writing here, I talked about science as a lens through which we can view the world: a set of perspectives that let us see the things around us in a different way than we are used to. But there are lots of different worldviews and perspectives within science, depending on scale as well as other contexts. A discussion of electrical current, for example, could be handled quite differently depending on whether electrons are moving through a polar solvent like water, or synapses in the brain, or a metal wire connecting a capacitor to an inductor. Scientists who have trained in different fields like physics, chemistry, or biology can imagine very different contexts for discussions of the same phenomenon, so that even when the fundamental science is the same, the narrative and implications may change between contexts.

But in the end, whether you are a scientist or just interested in science, it helps to know not only that an electron is a tiny charged particle, but also how it behaves in electronic circuits, in chemical bonds between atoms, and in biological systems. And to know that it’s possible to build computers out of gears, billiard balls, or even crabs! But the size and properties of electronic computers have led them to dominate, at least for now.