Tag: biology

Evolution and Cognition

(This month’s post features a photo of Stentor coeruleus by Jasper Nance on Flickr. Under a microscope, this little guy looks translucent white, with green and brown bubbles trapped inside of it. It’s roughly cone shaped, rooted to some debris at its narrow base, bent at a ninety degree angle as its wide, cilia-lined mouth quests about for food)

Sometimes I like to talk about all sorts of living things as “intelligent,” even ones that are very simple and reflexive in their behaviors. That’s because I tend to think of the process of evolution itself, and everything it creates, as intelligent. In some sense, I feel like the simplest of creatures are particularly intelligent in their design, because they don’t waste any effort on “thinking” or complexity when they don’t have to. But this isn’t how most people use the word “intelligent,” which is a problem. It’s not a particularly well defined word, either, so I think my view deserves some clarification. How are evolution and cognition related to each other? That’s something I’ve been thinking about a lot lately.

Perhaps it’s best to start with some of the simplest life on the planet: bacteria. They are basically just little robots, controlled by a simple “computer” made out of proteins and genes (here’s a great book on the subject). They certainly don’t “think” like we do, but they do perceive their environment and respond to it appropriately. They seem to have a model of their tiny selves, and their relationship with their environment, that lets them make good decisions from moment to moment, to survive in a hostile world with intermittent food, and many poisons and predators about. They aren’t particularly creative, but their evolved programming can handle a very wide range of contingencies, responding in appropriate ways to just about anything that their ancestors have encountered in the past.

Even very simple computer programs can learn. It’s just a matter of observing when two experiences tend to go together, and recording that association for later. This is all that “AI” is doing, and it can be shockingly effective. There’s no reason that a “computer” made of proteins and genes couldn’t do the same thing. But simple cells like bacteria don’t need to do this. They reproduce so quickly, they can simply evolve instead. The difference is surprisingly subtle. Bacteria use a relatively fixed “program” for themselves. Unlike a mind, it isn’t made to reorganize itself to conform with experiences in the world, it just does what it does. However, this “fixed” program is constantly being subjected to random edits (mutations), so it does change. The main difference is that genes accommodate to the environment by death and survival, rather than learning within a lifetime. Bacteria are incredibly prolific. E. coli can easily fill a single square millimeter with over 10 billion cells, and a population can double in twenty minutes. As long as some of the random edits are good, and they spread quickly, bacteria can adapt in real time to their changing environment, without learning.

What’s interesting is that more complex cells do seem to learn. Animals like you and me are built out of vast numbers of eukaryotic cells, but our ancestors were actually single-celled eukaryotes, and there are still plenty of those thriving out in the wild today. These cells are much larger and more complex than bacteria. In the past, they actually swallowed up other cells, that went on living inside of them. So, they’re actually like little clusters of several cells in one, working together as a team. Thanks to one of these symbiotic partners, mitochondria, eukaryote cells have a much larger energy budget than bacteria. Their genomes also have much more complex structure and regulatory mechanisms. They can actually re-write the instructions in their genes after reading them, using a process called splicing. We’re still not completely sure that these single cells do what we’d call “learning,” because we only recently thought to look for that, and it’s rather difficult to prove definitively. But there’s good reason to suspect they can.

There’s a single-celled eukaryote called Stentor coeruleus that is shaped like a tiny trumpet. It’s actually considered to be huge for a single cell, at a whopping two millimeters long. That may not seem like much, but it’s 1,000 times bigger than an E. coli bacterium. This little guy is very sensitive to vibrations, which it uses to detect predators. When it feels threatened, it contracts into a tiny ball to make itself harder to catch. What’s interesting, though, is that when it feels the same vibration over and over again and doesn’t get eaten, it learns to ignore vibrations at that frequency (but not other frequencies). That learning is flexible, because if the vibrations get stronger (as if the predator were getting closer, perhaps), it can change its mind and go back to treating them as a threat. This sort of behavior is pretty simple, but I would consider it “intelligent” in a minimal sense. It has a non-trivial model of the world that it updates in real time without having to evolve to do it.

As organisms get larger and more complex, they also become slower. They move more slowly and they reproduce more slowly. They also tend to have larger, more complex genomes which are much harder to successfully edit with random mutations. As this happens, life needs to find ways to keep responding quickly, and one solution is to invest more in cognition. Even single celled organisms like Stentor seem to do this. Larger organisms like plants have even more complex cognition. Plants may not seem very intelligent, but they can learn, behave strategically, and even communicate. They interpret clues over a season to guess when it’s safe to grow, they maneuver around obstacles and each other to get access to light, and warn each other when pests show up. This isn’t thoughtful, exactly, but neither is it simply hard-wired. There’s flexibility, context sensitivity, memory. Real, non-trivial computation. More complex organisms, like animals, have even evolved their own specialized “computers” built out of cells: brains. They are much more intelligent than plants, in one sense, because their behavior is so much more flexible and dynamic. They really can think, which for most people seems to be the gold standard for intelligence.

The powerful thing about investing in cognition is that it makes evolution easier. An intelligent organism doesn’t need to evolve exactly the right behavior for a situation, it just needs to be “close enough” from birth that learning can take it the rest of the way. For instance, most animals have to learn how to walk. That means when an animal is born a little different, say with legs that are shorter than usual, it can figure out how to work with that. In fact, if having short legs turns out to be useful, they might do better than their peers, even if they have a body type never seen before in their family history. If a species has to re-learn the same behavior in every generation in order to survive, then natural selection will favor individuals that learn that skill more easily and reliably. For instance, baby deer learn to walk very quickly, seemingly because they are born with some innate clues for how to do this, and an urgent desire to do so. In this way, behaviors that were at first creative solutions to novel problems can slowly become reliable programs encoded in the genes. This sort of dynamic is sometimes called “genetic assimilation” or “the Baldwin Effect,” and it’s one of the key ways that life uses its evolved intelligence to shape the process of evolution to make it more efficient.

This is why I like to think of evolution and cognition as continuous with one another. They are different things, but they are both kinds of learning, just happening on different time scales, and there is flow between them. Flexible cognition can make evolution much easier, and evolution can generate new opportunities for cognition to work with. You might say that organisms like bacteria, which are little more than fully-automated evolved mechanisms, aren’t intelligent because their behaviors are rigid and can’t adapt without evolution. But perhaps an evolving population of bacteria is intelligent? It can be quite flexible and dynamic, adapting to dramatic changes in the environment in minutes. This is why they can be so difficult to control, and often very challenging for our immune system (which is very intelligent and flexible) to keep up with.

Organisms like plants rely a lot on evolved mechanisms, but they also have some minimal real-time learning and flexible behavior, so I would consider even a single plant to be intelligent. Animal species like insects, reptiles, and mammals shift the balance even further toward real-time cognition. In a sense, every organism is precisely as smart as it needs to be to live its lifestyle. If it can be successful and thrive without expensive, complicated, biological computation that can learn in real time, that’s a good “design.” I consider that to be intelligent, even if the organism itself doesn’t seem so intelligent. Every organism evolved from a single common ancestor, and has had just as much time to adapt. Some have become extremely good at being extremely simple, with precisely honed, fully automatic routines controlled by genetics that have stayed stable for hundreds of millions of years. Others have less refined innate behaviors, and make up for it with flexible learning and cognition. Neither option is better, and evolution explores the full range of that spectrum, finding a huge variety of strategies to survive and thrive in a complex world!

Building Bodies

(The image for this post is a human embryo after six days of development: a blastula. The structure needed to construct a body is just starting to take form. Before this point, it’s mostly just a lump of undifferentiated cells. Image credit: Jenny Nichols)

Humans live in the macroscopic world. We’re used to interacting with other people and animals that are about the same size as us. Of course, everything we see as an “individual” is actually made up of unimaginably vast numbers of cells and molecules in constant churning motion, but to us they just look like solid, physical objects. This is normal to us, but it’s a totally alien experience to our most primitive ancestors. We are descended from individual cells that lived fully autonomous lives in a microscopic world. It’s truly extraordinary and weird to think that they would band together by the trillions to form human bodies, and yet that’s what they do. How did that come to be?

Our ancient ancestors were protists, single cells with complex lives. Each one had to find food, shelter, and resources. Just as we do, they continuously decided how to live, trying to survive and thrive in a chaotic world, and to set their children up for success. Sometimes they lived in communities and ecosystems, building networks of mutually supportive relationships. They’d form vast colonies of closely related cells, generally working together, communicating, maybe even specializing and subdividing tasks. And yet, each cell was still responsible for its own well-being. There was no top-down coordination. Each individual decided for themselves what to do. Cooperation would naturally arise when it was useful, and break down again the moment incentives changed.

As we now know, cells can do extraordinary things when they work together on a shared plan. In today’s animals, each cell has an established role to play. Collectively they build complex, macroscopic bodies that observe, think, move, and reshape the world at a vastly larger scale. But try telling that to a single cell! For two billion years, they were honed by evolution to fight tenaciously for their own survival as free-living individuals, and to prioritize their well-being and their offspring. Collectively, the cells of a macroscopic individual may fare better than they would alone, but not all of them. Think of the cells that line your stomach, whose life’s purpose is to get dissolved by acid so that other cells don’t have to. How does evolution convince a cell to do that voluntarily?

More importantly, most animal cells are evolutionary dead-ends. We have specialized sex cells whose only job is to produce children. Every other cell in the body is denied that privilege. Many of those cells still divide occasionally, but all their offspring will die out when the body does. They have no way to influence the next generation of their species. This is a huge contradiction, because those cells evolved for reproduction. For billions of years, the cells who contributed the most to the next generation were favored. Perhaps the most fundamental fact about life is that it proliferates, rapidly filling up every corner of the planet. How do you reverse this core instinctual drive in every living cell?

It’s quite likely that multicellularity evolved and fell apart many times. Discovering this trick is very hard, for the reasons outlined above and more. What’s even harder, though, is holding onto this innovation once it’s found. In order to maintain an animal body, every cell must compromise its well-being for the good of the whole, for a lifetime. If any cell decided to cheat—to live as a rebel among conformists, and selfishly exploit the body environment—it would have a distinct and powerful advantage. It would outperform the others, undermine their hard work, proliferate much faster, maybe even start a whole new successful family line as single cells, feasting on the remnants of the would-be body. Mutations that broke multicellularity must have been common!

Yet, today we live in a multicellular world. How did we make that work? There’s an interesting theory to explain this, and it explains something else strange, too: every single multicellular organism has sex. Some reproduce asexually, too, but the mechanism of sexual reproduction is universal. This is not at all the case for single cells. They exchange genetic material with other cells, but they don’t depend on others to reproduce. They do that entirely on their own, using whatever genes they have at the time. So, perhaps sex and multicellularity are linked? Perhaps sex came first, and is part of what made multicellularity possible? There are a few good reasons to think this, but for me the most compelling is that sexual reproduction creates mothers, and puts them in control.

Generally speaking, the process of building an animal body is decentralized. There is a sort of top-down coordination, using patterns of hormones and bio-electricity to shape a coherent whole, but this has to be generated by the cells themselves. Every cell autonomously figures out where to be and what role to play, via coordination with its neighbors—but not at first! At the very beginning of the process, the embryo’s genes are switched off and the mother’s genes direct the first stages of growth. In an egg or a womb, the mother also has full control over the environment in which development happens, which further shapes the process even once the embryo takes over. This gives Mom the power to set things up just right such that multicellularity is the only viable outcome.

The single cells of an early embryo aren’t a body yet. They default to the independent lifestyle they had for two billion years before the advent of multicellularity. The cells have to work together to build an organism with unified awareness and agency, but that means at first there isn’t one. There’s nobody to coordinate the cells, and no “greater good” to serve. Why should they work together? That’s where the mother comes in. She takes full control and forces the cells into the right starting configuration. She shapes the growing embryo and assigns roles to each cell by tweaking their gene expression. The child cells only get to take over once the general layout of the embryo is established, and the growth process is already underway. Once an individual emerges from the collective behavior of those cells, it can carry on the rest of the work of building a body.

From that point on, there’s very little temptation to cheat. The clockwork of the body has been set into motion. Each cell’s needs are provided for, and their freedom is restrained by the bonds they’ve already formed with their neighbors. The reproductive cells have already been isolated, making it impossible for rogue cells to influence the next generation. They could still rebel and do their own thing. That’s what cancer is. But it’s much harder than playing along, and carries serious risks. The immune system actively hunts for rebellious cells, and kills them on sight! It’s also a futile exercise. A cancer may grow and thrive and proliferate for years, but this is self defeating. When the cancer cells undermine the host body, they destroy their own environment and drive themselves to extinction.

Once cells are locked into this multicellular arrangement, something interesting happens to the selective forces that shape their evolution. As always, the reproductive cells carry subtle genetic differences from their parent, tiny mutations that serve as evolutionary experiments. Changes in an egg cell’s genes affect the behavior of every cell that follows, and thus the body and behavior of the child as a whole. But a new selective filter has been established. Only variations that are beneficial to both the cells and the individual are allowed through. Mutations that damage either level of the system produce unfit individuals who often won’t even develop to maturity. This creates a pressure for cells to become more cooperative building blocks, and for bodies to become more supportive homes for cells.

The takeaway here is that each living cell is a creative, intelligent, and autonomous survival machine. That makes multicellularity a tricky balancing act that’s hard to discover, and even harder to maintain. It seems likely that sexual reproduction and motherhood were essential ingredients to make this possible. In a sense, multicellularity isn’t passed on genetically, it’s passed on physically; each multicellular organism has to assemble the next generation from individual cells before that child can carry on building itself. The cells don’t know how to do it on their own, and they don’t care to. Yet, once a mother forces them into the shape of a growing embryo, it’s in each cell’s best interest to play along. For about 1.5 billion years, evolution has worked hard to maintain this tenuous arrangement by aligning incentives between cells and bodies. Both systems coevolve to complement each other, to ensure the multicellular compromise is the wise choice going forward, for everyone involved.

This is a speculative story, but well supported by evidence. It’s largely inspired by The Evolution of Individuality by Leo Buss, a very technical book about cellular and developmental biology, which goes into vastly more depth and detail than I did here about the complex lives of single cells and the struggle to align incentives across multiple scales. In particular, that book explores the very different ways plants and fungi have overcome the challenges of building macroscopic bodies. It’s a fantastic reminder that what animals do is not “normal,” it’s just what we’re used to. We’re actually quite strange and exceptional, as life goes. Most living things are single cells, and even when it comes to bodies, our way of doing it is just one of many. It’s a brilliant and eye-opening book, but a challenging read, so I wanted to write a more accessible summary, to share these ideas more broadly.

The Universe Evolves

(This month’s featured image is a photo of the Carina Nebula taken by NASA’s James Webb telescope. It’s a vast cloud of gas and dust, slowly condensing, with hundreds of stars visible in the background behind it. The colorized image almost looks like orange mountains with a blue mist rising from them, set on a black background with bright, six-sided starbursts.)

Normally, when we talk about evolution, we mean what life does. It’s Darwin’s magic formula. You need reproduction. You need to pass on a copy of your genes, with a little variation, so things don’t just stay the same. Natural selection will weed out the less fit individuals, so they have fewer kids. The more fit individuals become more prevalent and, over time, life as a whole evolves to be more fit. Yet, this isn’t a very satisfying story. For one thing, how did it begin? Did life just start evolving out of the blue? I think story is more compelling if we think about evolution a bit more abstractly. In a sense, the physical universe itself evolves. It doesn’t have reproduction and inheritance, but it sure does have variation and selection, and this has caused it to change dramatically over the course of history.

For the first 370,000 years or so, all of space was filled with a boring, homogeneous cloud of energy and plasma. That universe is now extinct, and for one simple reason: it was unstable. In our universe, stability is the ultimate definition of “fitness.” What persists, exists. Patterns of matter and energy that get generated more often and stick around longer become more prevalent. Those that are rare and fragile exist only fleetingly. The plasma universe is gone because gravity causes matter to clump together. It was like a pencil, balanced on its tip. As soon as it became just a little unbalanced, it rapidly fell farther and farther away from that delicate equilibrium. Plasma condensed into molecules, gas clouds, and stars.

Of course, evolution needs variation to work. To find what’s better, you need to weed out what’s worse. For life, reproduction is the engine of variation, but that isn’t necessary if you have unimaginably vast scale. The universe started out with very little variation, but it steadily increased as matter interacted with itself. Gravity caused hydrogen molecules to group together in uneven clumps, and held them there. They sat around for millions of years, slowly growing bigger, until the force of their own weight ignited a fusion reaction. The gas clouds became stars, and in their cores new elements were born. The universe’s population gradually became more diverse.

That’s the counterintuitive thing about stability: it can generate diversity. When patterns become more numerous, and they stick around for longer, chaos starts to kick in. Every star and every planet is a little different. They have unique histories and influences and opportunities. They might be richer in this element or that one, bigger or smaller, hotter or colder, more or less affected by collisions. This diversity only compounds over time, as these objects smash together and interact in complex ways. The longer they stick around, the more they change, recombine, and become more elaborate.

So, for 13 billion years, the universe evolved. Its population became stranger and more complicated. Today we have about a hundred “naturally occurring” elements that didn’t exist at first, but had to evolve through multiple generations of stars fusing atoms, exploding violently, and gradually reforming. We have many kinds of stars, planets, solar systems, and galaxies, that support an astonishing variety of chemical processes that have had a very, very long time to develop. They produce “primordial soups,” pocket environments full of useful molecules for life, a steady energy source, and self-perpetuating chemical reactions. We think this happened at least once to seed all life on Earth, but it may in fact be very common.

I think this story is an essential foundation for understanding evolution as life does it. Because life didn’t start this process. The universe provides energy and raw materials in vast amounts. It provides the chaos and entropy that drives seemingly random variation, and the slow, continual breaking down that causes natural selection to prefer stable, commonly made forms. The laws of physics cause the universe to evolve towards stability, diversity, and complexity, at least for a while, until it starts to wind down again and settle into entropy. Life merely constrains that process, making it more efficient and productive, for the simple reason that matter that does so becomes more prevalent.

In these primordial soups, some chemical systems evolved to enclose themselves in bubbles, protecting delicate reactions from the outside world. These self-made “individuals” evolved regular cycles of reproduction, explicitly making copies of themselves rather than waiting for the right reactants to come together again by chance. They evolved DNA to constrain these copies, and make them more precise reproductions of the original. They evolved sophisticated error checking, which made the copies more robust and reliable. But this also gave life the power to manage variation across generations, and thus shape its own evolution. Life evolved sex to further manage variation, accelerating innovation by sharing genetic recipes across lineages. Life evolved an astonishing variety of sexual and reproductive practices, allowing it to evolve in different ways, with different patterns of variation and selection, each suited to a different range of environments and lifestyles.

The physical Universe evolves—in the most primitive way imaginable, but it still produces stability and complexity in a vast number of diverse forms. It generates the seeds of life, without any guidance or direction. Life evolves differently, because it constrains this process, making it discrete, digital, and managed. This started very simply, just discovering chemical reactions that isolate and maintain themselves. But perhaps this is the origin of what we think of as “intelligence” or “agency”? Without noticing, matter became “opinionated,” preferring certain forms and acting explicitly to promote them. From there, life’s “opinions” about itself only became more demanding and elaborate.

We often present evolution as one simple story, but there are many ways to evolve. Evolution is more like a general principle than a specific algorithm. Even just life as we know it, all based on the DNA molecule, has invented an astonishing variety of different and complex ways of evolving. Bacteria, fungi, plants, and animals use DNA differently. They grow, behave, and reproduce in completely different ways. How many other ways might there be to do it? When we present evolution as a single, constant thing, we limit our imagination. Evolution evolves, and it takes as many diverse forms as it makes.