Tag Archives: flagella

Flagella and Philosophy

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Most bacteria, including E. Coli bacteria, which cause food poisoning, move around by using flagella. Under the microscope, flagella look like kinked up hairs sticking out of the cell and undulating rapidly. If you remember high school biology you might already know, or think you know all about flagella. They’re those hairl-like  things that cells whip back and forth to move forward right?

Not exactly. There are basically two kinds of flagella, the ones that bacteria have, and the ones that eukaryotic cells have. The eukaryotic ones do in fact whip back and forth. The bacterial ones, however, actually propel the cells they’re attached to by corkscrewing through the fluid. As I went over in a previous post, the situation bacteria are presented with isn’t the same as a submarine in a ocean. It’s more like a submarine in a large silo filled with vibrating pebbles. Drag is a huge deal. Bacteria need a powerful technique to move around and a corkscrew type action works rather well.

When you use a corkscrew on a wine bottle you basically turn it around in a circle as it progresses into the cork. So here’s a question: how does a bacterium do that? The flagellum has to be attached to the cell with a buttload of strength to pull the cell along, but at the same time it has to be able spin around like a drill bit. If you look at all the different components of the flagellum (pictured below) you can see that the structure is pretty complicated. WTF? Aren’t bacteria supposed to be primitive organisms?

Well, yes and no. You see, the thing that’s easy to forget about evolution is that every thing that’s around has been evolving for just as long as everything else. It’s just that while our cells were busy trying to figure out how to differentiate and work together to get to places where there was better food and water and such, bacteria were hunkering down and learning to live in the environments they found themselves in. They’re just as good at being bacteria as our cells are at being part of a larger organism. Still, the flagellum is so mind-bogglingly complicated and yet robust in its implementation, that it has from time to time been used to prove or disprove the non-existence of God.

The argument runs something like this: “We and the organisms of Earth have to have been created by a God,” say creationists, “because the bacterial flagella is so complicated that it could not possibly have been formed by chance, any more than a hurricane could blow through a ship yard and create an aircraft carrier.”

“But,” say non-creationists, “each protein that makes up the structure of a flagellum looks similar to proteins used in other, less complicated bacterial structures. Furthermore the flagellum of E. coli is only one variant of many, indicating that one Doesn’t it make sense that flagella might have come from mutations that put the proteins together in ways that were somewhat beneficial? If even one bacterium survived a trying situation better than its neighbors, it would quickly begin to dominate. And evolution of bacteria has been directly observed in nature and in the lab. At the very least that seems more plausible than everything getting poofed into existence through some unknown process by a magical man in the sky.”

You can probably tell which side I favor.

Something that you start to notice if you study biology is how complicated and diverse proteins are. Proteins aren’t just little specks that bump into each other in random ways. Each protein has a different shape and different areas that have different properties that interact with other proteins in different ways depending on environmental factors. It’s an imperfect analogy, but you could almost say proteins have personalities. Almost like people, proteins will work together, compete with each other, and even find things in their environment and use them to accomplish a “goal.” A protein may be stuck in a bad position, for example, and it may come into contact with another protein that likes to pry things apart, and then they will help each other out.

So it’s not exactly the same situation as a hurricane picking up a bunch of aircraft carrier parts and arranging them into a complete aircraft carrier. Its more like a bunch of people who don’t know how to make an aircraft carrier getting a steady supply of parts and enough time and resources to try things out. Eventually, given enough time, people in that situation will eventually make something like an aircraft carrier. Though they’d probably start out making houses, cars, and a number of other things out of the parts before hand. In fact you could look at the current real-life production of an aircraft carrier as an example of evolution. Evolution is simply the effect of variation subjected to some environmental pressure. There were many different types of ship before the aircraft carrier came about. For one thing, there had to be aircrafts in order for there to be any use for one. Humans wanted a place to put planes on the ocean and the aircraft carrier fulfilled that purpose

In a similar way, proteins just want to be in equilibrium, and so they will often use things like enzymes to make equilibrium easier to achieve.

If you are doubtful of any of this, you need only see a video of how a flagellum is formed in a bacteria. The formation of a flagellum is a marvelous and awe-inspiring dance and it happens hundreds of times a second in a single organism ALL THE TIME. You don’t need religion for miracles. You just have to look around.

Size is Everything

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Innerspace is a Steven Spielberg movie that came out in 1987 starring Dennis Quaid, Martin Short, and Meg Ryan. It’s a sort of remake/homage/rip off of a movie that came out in the sixties called Fantastic Voyage, which Isaac Asimov wrote a novelization for. Both movies center on the idea of shrinking people to microscopic sizes and then injecting them into other people to go through the body and fix diseases. This is a really neat idea, and there are some scientists who are finding ways to use microscopic robots to take the place of the humans in the movies and accomplish some of the same things. However, there are two reasons why the scientists are using robots and not Dennis Quaid. First, shrinking people is probably impossible, and second, even if it were possible people wouldn’t be able to do anything once shrunken.

I can show the how true the first point is with common sense for the most part. If humans are made up of cells, how could it be possible to shrink a human to a size smaller than a cell?

Now you could come back with “well, the cells just get smaller!” But cells have to be the size they are. Otherwise they wouldn’t be large enough to hold all the organelles that keep the cell alive and functioning the way it needs to. The organelles themselves are made up of proteins that are in specialized arrangements. A cell has to constantly maintain the numbers of ions it has inside it for example. The cell can use an organelle called an ion channel to do this, but the channel has to be a specific shape. If it is too large it will let all sorts of ions in or out and the cell won’t be able to maintain the right mix of ions. Too small and the channel won’t let anything in, and it might as well not be there. If these channels were shrunk by even five percent, they would no longer function the way they need to. If ion channels don’t work for cells, they die. If all of a person’s cells die, they die too. If a shrink ray shrinks everything equally, a person shrunk even a foot smaller would most likely die within a few moments.

And of course there’s the problem of how it could happen in the first place. In the movie Honey I Shrunk the Kids, the Rick Moranis character says that we are made up of mostly empty space and his shrink ray gets rid of that empty space. First off this idea is based off of the Bohr model of the atom, which has an electron whizzing around a nucleus like a planet orbits around a sun. This isn’t how things are. There isn’t any empty space as such. The more current electron cloud model fits better. The exact location/momentum of an electron cannot be precisely determined and so we can think of it as a sort of cloud around the nucleus. Okay but at any moment we can still say that the atom is mostly empty right? And if we could take out this empty part you could maybe shrink something?  To be fair, there is a real world situation in which this does happen. It’s called the Sun. It’s a lot more bright and ‘splody than what we see in the movie.

To be more precise, and less smart alecky, the reason why the electron is so far away from the nucleus of an atom, is due to its energy. In order to get closer to the nucleus, an electron has to lose energy. When an electron loses energy, it releases a photon. The more energy an electron loses the more energetic the photon is. Photons with a lot of energy, such as X-rays or Gamma rays, are a form of harmful radiation. Never mind that this hypothetical magic device would most likely rip someone apart rather than truly shrink them, the energy released from “removing the space” in all the atoms would be huge, and would likely kill quite a few people.

The second reason why we’ll never have a manned mission to someone’s colon is something called the Rydberg constant. The Rydberg constant is a number you get when you divide inertial forces (momentum, or how long you keep going after you stop trying to move in a direction) by drag forces (friction and viscosity, or how hard you have work to move forward in the first place). The higher the Rydberg constant, the more you are concerned about momentum and the lower, the more drag forces dominate. Generally speaking, the larger you are, higher your Rydberg constant.

We live in a world with a pretty high Rydberg constant.  We can roller skate and ride a bike, coasting almost half the time. When we swim, we pull the water back with our hands and we’re carried forward enough that we can get our hands back into position for another stroke without moving back to our previous position.  These are all situations where the Rydberg constant is high.

We can create low Rydberg constant situations for ourselves if we want though. Imagine a swimming pull full of Jello. If you try to swim in that, you are going to have some problems. For small animals though, they live in this low Rydberg constant situation all the time. An ant that wants to get a drink of water has to be very careful not to get stuck in it.

Even something as large as a cat, experiences a lower Rydberg constant. A cat can fall from many stories up and still suffer only a few broken legs due to the drag forces that act on it as it falls. The cat, being small, has a larger surface area in relation to its mass, and so drag forces come into play more quickly.

For a bacterium, or a hypothetical impossibly shrunken human, the Rydberg constant would be so low, it would be like that swimming pool full of Jello, only worse. You might imagine a vat of gravel that’s shaken up continuously while you’re inside it. Bacteria typically have some sort of flagellum that corkscrews through the stuff they’re in so they can move forward. Why don’t they just use turbines like a submarine would? Well one reason might be that they never developed such a structure in their evolutionary history. The more applicable reason is that in order to combat the drag from the surroundings, a turbine on a bacteria-sized machine would have to be so large, that the drag of the turbine itself would affect the machine’s movement. Imagine trying to use a submarine in a vat of gravel. Or even more ridiculous, an airplane. It’s just not going to work. So you’d have to have a differently shaped vehicle than in the movies. And you can just forget about leaving the vehicle.  You wouldn’t be able to swim around any more than a feather can dictate economic policy.

It often seems like size is just an arbitrary attribute. There are so many stories about shrinking and growing larger because on some level it seems possible. There are a lot of complications hidden under the surface however. An elephant is a very large animal, but it’s bones are thicker in proportion to its size to make up for that. If you shrunk an elephant down to the size of a cat, it wouldn’t be able to move it’s limbs around. If you blew up a cat to the size of an elephant, it would suffocate under its own weight.  Every time you decrease or increase size by a factor of ten, you enter a different world.

Size is everything.