A Cell’s Eye View of Evolution, Part 1
(This month’s image is a photo I took of the full-scale model of Babbage’s Difference Engine at the Mountain View Computer History Museum. This is one of the first examples of a programmable digital computer. It’s a completely mechanical device, operated by hand crank.)
This is part one of a three-part series. For an overview, check out the introduction.
In the traditional story of evolution, each organism lives a single lifestyle, and the forces of nature select which ones are fit enough to reproduce. From that perspective, evolution is something that happens to life. But this story fails to explain something very strange and important: cells are not single-purpose machines. Although they only live one lifestyle at a time, they have the capacity to live an infinite variety of lifestyles, depending on their DNA programming. That requires an enormous amount of complexity and effort that doesn’t directly contribute to a life well lived. In fact, being programmable doesn’t help at all in a single lifetime if the program never changes. So why does life work this way?
To make sense of this, let’s look at a parallel example in computer technology. Consider an ATM. It’s a highly specialized kind of machine, but these days if you look under the hood you’ll often find a Windows PC that’s programmed to be an ATM. That seems like an odd choice at first. ATMs do things most PCs don’t (like dispensing cash), and Windows supports things that you don’t want in an ATM (like running random programs off the internet). You could make a better, safer, more efficient ATM if you designed a custom machine for that purpose, but nobody does that, because it’s harder. Digital computers are so versatile and easy to reprogram that they show up everywhere. As they get used in new applications, their range of capabilities expands, enabling new use cases and further innovation.
Cells are very similar. Being programmable doesn’t help with any one lifestyle, but it makes it possible to explore new lifestyles relatively quickly and easily. Each individual operates in a complex, roundabout way that only uses a fraction of the cell’s potential. That seems like a bad thing, but the adaptability makes it worthwhile. The world is in constant flux, especially once organisms started actively changing things and competing with one another. Very few evolved lifestyles withstand the test of time. For this reason, nature doesn’t just select “the best lifestyles” for life. Life invested in a general purpose platform to make the search for new lifestyles more efficient.
Let’s take a closer look at how the platform works. A cell can be thought of as a kind of microscopic robot. The “programming” for that robot is stored in DNA, which is surrounded by a complex mechanism that reads that data and uses it to produce the form and behavior of the organism. Each cell has a very limited capacity for intelligence, but they’re very good at working together. Like a sort of “autonomous smart matter,” they collaborate by the trillions, which is how every form of intelligence on this planet is made. There’s no reason to think there’s an upper limit to what can be built in this way.
What makes this possible is the protein-synthesis engine at the core of every cell. The nucleus of a cell is a bit like the brain of a human, in that it’s a specialized sort of computer that’s “in control” of the cell. It’s surrounded by the cell’s body, which serves as the interface between the program in its nucleus and the outside world. This is where the similarity ends, though, because the nucleus and the brain are very different kinds of computing devices.
The nucleus works by continuously handling requests, looking up protein recipes, and sending those recipes back out to the cell for construction. A cell can make an astonishing variety of complex molecules this way. These proteins are what make up the cell, its inner workings, and outward behaviors. They serve as building material, messages, tools, or even nano-robots that move about within the cell, manipulating other molecules, and doing useful work all on their own. Sometimes a single protein can serve all of these roles, depending on context. They interact with each other in a vast complex network of activity that keeps the cell alive.
These cellular mechanisms continuously send messages back to the nucleus, reporting on the cell’s health, situation, and needs. The nucleus uses this information to figure out what proteins to make next, adapting the cell’s makeup and behavior to fit the circumstances. For instance, E. coli bacteria normally feed on glucose sugar, but they can eat lactose instead, if that’s what’s available. When that happens, the cell reports to the nucleus that it’s running low on energy and what molecules are around. The nucleus then decides to switch some genes on and off, which instructs the cell to make different enzymes, which results in different cascades of chemical reactions, in order to digest and use the lactose. By reading the DNA differently, the nucleus shifts the whole cell from one lifestyle to another, in response to a changing environment.
Another way to think of the nucleus is as the engine of the cell. The proteins it makes drive all the chemical reactions that keep the cell alive. Ultimately, everything the cell does is about collecting the energy and raw materials to feed that engine and keep it running. This is the cell’s metabolism. When the engine runs faster, the organism becomes more active, moving, “thinking,” and reacting with speed and vigor, but quickly burning through its energy stores. When it runs slowly, the cell becomes sluggish and conserves its energy. If it ever comes to a full stop, the cell dies, or, in special cases, enters suspended animation. In other words: cells live to make proteins, and making proteins is what makes cells alive.
DNA is where the cell keeps all these protein recipes, but the DNA molecule itself is completely inert. It just carries information, like a computer memory card. It can’t do anything by itself, and certainly can’t make a body from scratch. To build an organism, you need a cell to interpret the gene sequence and do the construction. This is why cells always reproduce by splitting in two. The daughter cell is basically just half of the parent cell, full of the same soup of proteins and organelles, in a fully operational state. The only part that’s really “new” are the DNA molecules in the nucleus, freshly copied from the parent(s). Any changes in that DNA program will only manifest when the daughter cell sends a message to the nucleus and gets a different response back than its parent would have seen.
That means that every cell has the crucial responsibility of reading and writing those DNA programs. They contain every useful protein recipe life has discovered, and must be actively maintained over generations or those recipes will be lost. But what does life actually record in the DNA? Geneticists say DNA is made of four amino acid base pairs (A, G, T, C), which are grouped into triplets called “codons” that serve as instructions for protein synthesis. That makes it seem “natural,” as if that were the only way to do it. The truth is, the code is totally arbitrary. Life made it up. By trial and error, life invented a coding scheme. It gave meaning to those molecules and all the ways they can be combined. The programming language of life was invented by life. It wasn’t the beginning, but a tool that cells made to manage their behaviors, learn new ones, and pass knowledge to future generations.
Let’s put that all together. A cell is a programmable micro-robot (in technical jargon, a “universal automaton”), capable of making virtually any protein and living virtually any lifestyle. In a sense, a cell is not just one organism, but potentially an infinite variety of organisms, depending on the programming in its nucleus. But how does the program get written? Life had to do all the work itself, without a programmer in the traditional sense. A cell has no mind with which to analyze its DNA and understand what it means. It cannot imagine the consequences of any changes to its programming, or test them out to make sure they are safe. And yet, somehow life invented a programming language and used it to write countless programs and build the full diversity of organisms we see on Earth.
We’ll delve into the details of how this happened in the next two blog posts. At a high level, though, there are two main parts of the story:
- Life is self-made. Each cell is relatively simple and mindless, but working together in huge populations over long stretches of time, they develop their own programming. How they do it is quite different from how a human programmer would, but from a collective perspective, there are also some surprising similarities.
- Life influences future generations. Organisms don’t just worry about their own survival, they put an enormous amount of time and energy into influencing the next generation for the better. Science is only beginning to understand this, but it offers the tantalizing possibility that, in some limited sense, life might steer its own evolution.
More on that next month.
What do you think? Did reading this make you think of life, cells, or evolution any differently? Any new ideas? Does anything I said sound wrong or misleading? Do you have other ways of looking at it? This post is more speculative than usual, and represents some of the ideas I hope to pursue in my PhD research, so I’m very interested in criticism and feedback. If you have any thoughts, please let me know in the comments!
Thinking with Nate 