A Cell Is a Dumb Machine

When I was a kid, I watched Once Upon A Time…Life, a great TV show about the body, with a particular focus on the immune system. A highly accurate show, it explained a great deal to my child’s mind, but left me with a subtle mistake: it anthropomorphized every aspect of the immune response. All cells were people, hormones were little robots, viruses were bad people, etc. It was magical. Which is wrong.

There’s nothing magical about a cell; there is only complexity. My first of many combined “ahah” and “duh” moments recently was realizing how it all works on a molecular level. So let me give a quick tour of the cell as a machine. That’s different from explaining what each part of a cell does; I don’t know, and it depends on the type of cell. This is strictly about the conceptual functioning of a cell.

I do take a few things for granted:

  • You’re familiar with the concept of molecules.
  • You know that molecules have different shapes.
  • You’re comfortable with the idea that molecules move around randomly.

Signals and Responses

You’ve probably seen one of these before:

giphy
Source; presumed in public domain.

It’s a water mill. The big wheel is connected to a wheel inside, and so the water makes the wheel outside turn the wheel inside, which grates against a flat stone.

Do you know what the mill doesn’t do? It doesn’t grind wheat—where would it get the wheat from? If wheat happens to be there, it also grinds the wheat into flour, but the machine itself only turns a stone grating against another stone. I know this seems obvious and picky, but it’s important to distinguish what things do by configuration from what they do incidentally. By configuration, a mill turns a big stone against another big stone. Incidentally, it grinds grain that is put between the stones.

You can think of the water as a signal and the grating of the stones as a response. Cut off the water, and the stones stop grating. Bring it back, and the mill starts anew. Cells are basically extremely complex networks of signals and responses. There is an entire field dedicated to figuring out what the networks look like called signal transduction, but what matters is understanding that fundamentally, all that cells do, all day long, is respond to signals.

Molecules and Ions

“Fair. But what are those signals? And what does a ‘response’ look like?”

Alright, time to talk about cell structure. Nothing too fancy; simply this: a cell has an inside and an outside (technical terms). Separating them is a membrane. On this membrane are receptors; when they are activated by something outside, they trigger a response inside. And what are those receptors? What triggers them? What do they trigger?

The answer is the same for all three questions: molecules and ions. I’m going to talk about molecules, but ions are equally important, primarily as signals.

“Molecules” is a deceptive term, because molecules can go from trivially simple things like oxygen gas (two atoms of oxygen) to proteins, which consist of thousands or tens of thousands of atoms, to DNA, which consists of billions. But the molecules we’re interested in have interesting properties:

  • They can change shape when they touch another molecule.
  • They can go back to their original shape when the other molecule is removed.

Turns out, with these two properties you can make all sorts of ridiculously complicated systems. Here’s a (fake) example. Imagine a system with two big molecules, I and II. Now add two smaller molecules, A and B, to the mix:

  • Molecule A can combine with Molecule I.
  • Molecule B can combine with Molecule II.

When either combination happens, the big molecule changes shape. The first shape is “closed” and it forms a cage; the second shape is “open” and the cage is, well, open.

With me? Ok, now the magic happens if:

  • When Molecule I is Closed, it traps some of Molecule B. When it is Open, it releases it.
  • When Molecule II is Closed, it traps some other molecule, call it Molecule C. When it is Open, it releases it.

Then you can see that if Molecule A touches Molecule I, it releases Molecule B. If the newly released Molecule B touches Molecule II, it releases Molecule C in turn. And that is how a cell can receive a signal to die if, say, Molecule C is toxic.

Randomness

“Wait, how does Molecule A ever touch Molecule I? And even assuming that happens, why would Molecule B then ever find Molecule II?”

Let’s not worry about Molecule A touching Molecule I yet; that’s better left for a post about the blood stream, which is fascinating in and of itself. The second part, Molecule B finding Molecule II was the second big “ahah” moment that I had thinking about cells. It all happens at random. And yet it happens consistently.

This can come about several different ways. One way is for Molecule I to release a lot of Molecule B; then there is so much that sooner or later, one Molecule B floating around in the cell is bound to find a Molecule II floating around as well; the more Molecule B there is, the sooner it will happen. Another way is for there to be a lot of Molecule IIs in the cell; same principle: even if there are few Molecule Bs, one of the Molecule IIs is going to find them, and the next step in the link continues. Yet another way is for the Molecule II to have a fixed spot very close to Molecule I, so that when the latter releases Molecule B, it’s very close to its target.

The point is that if you have enough molecules inside a cell, sooner or later they will meet and the reaction will happen. You can change several things to make it sooner rather than later, and depending on how quick the reaction time needs to be, each reaction has its own parameters. If it’s important that the cell die RIGHT NOW when it comes across Molecule A (for instance, Molecule A is only around if the cell itself is infected), the concentrations of Molecule B and II might be very high. For less urgent situations, it might take a lot longer.

Complexity

“That sounds too simple. Cells do all sorts of things, like divide, or process energy, or send neural signals along.”

Cells have many signaling pathways that have many different functions, all enabled by every molecular behavior you can imagine. There are molecules that play dual roles as receptors and signals; there are molecules that block molecules from being triggered; there are ions that serve as signals for many different receptors; there are molecules that accelerate the interaction of certain receptors and certain signals; there are molecules that impede those interactions; there are molecules that trigger cell division; there are molecules that trigger cell death; there are molecules that prevent cell death; there are molecules that trigger ingestion of other cells. Molecules and ions control every aspect of how a cell works—because there’s nothing else that could.

So whence the complex behavior we observe? Back to the mill. Remember how I said the mill doesn’t grind grain? Every cell in the body is highly specialized and does its own thing, yet, isolated, it is as useless as a mill with no grain to grind. It will respond exactly as designed to the right signal, but it is only the combination of cell responses from multiple signals that we will recognize as behavior. Something must provide the grain; something must take out the flour.

If you want a different kind of metaphor, you need less than ten basic constructs to do everything a computer can do. From showing you this blog post to playing your favorite algorithms-as-traditional-European-dances video (what, you don’t have one?), it can all be represented with those ten constructs. So is it surprising that cells, with endless possible molecules to draw from, can carry out miracles?

I’m going to discuss this in a lot more detail in future posts, but if you take nothing else from this one, take this: it’s molecules all the way down. The complex behavior of human bodies is built up, molecule by molecule, out of dumb machines responding completely predictably to stimuli. That we don’t know all the details, that we don’t see all the paths, doesn’t distract from this very simple chemical reality.

 

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