Life

John Brockman

• Publisher: Harper Perennial
• Year: 2016
• ISBN:
  9780062296061
• Topic: Sciences biologiques
• Subtopic: Évolution

The newest addition to John Brockman's Edge.org series explores life itself, bringing together the world's leading biologists, geneticists, and evolutionary theorists—including Richard Dawkins, Edward O. Wilson, J. Craig Venter, and Freeman Dyson.

Scientists' understanding of life is progressing more rapidly than at any point in human history, from the extraordinary decoding of DNA to the controversial emergence of biotechnology. Featuring pioneering biologists, geneticists, physicists, and science writers, Life explains just how far we've come—and takes a brilliantly educated guess at where we're heading.
Richard Dawkins and J. Craig Venter compare genes to digital information, and sketch the frontiers of genomic research.

Edward O. Wilson reveals what ants can teach us about building a superorganism—and, in turn, about how cells build an organism. Elsewhere, David Haig reports new findings on how mothers and fathers individually influence the human genome, while Kary Mullis covers cutting edge treatments for dangerous viruses. And there's much more in this fascinating volume.

We may never have all the answers. But the thinkers collected in Life are asking questions that will keep us dreaming for generations.

1

Evolvability

Richard Dawkins

[April 30, 2015]

Richard Dawkins is an evolutionary biologist and Charles Simonyi Professor of the Public Understanding of Science, Emeritus, at Oxford.

Natural selection is about the differential survival of coded information which has the power to influence its probability of being replicated, which pretty much means genes. Whenever coded information which has the power to make copies of itself—a “replicator”—comes into existence in the universe, it potentially could be the basis for some kind of Darwinian selection. And when that happens, you then have the opportunity for this extraordinary phenomenon we call “life.”

My conjecture is that if there is life elsewhere in the universe, it will be Darwinian life. I think there’s only one way for this hypercomplex phenomenon we call life to arise from the laws of physics. The laws of physics—if you throw a stone up in the air, it describes a parabola, and that’s it. But biology, without ever violating the laws of physics, does the most extraordinary things: it produces machines which can run, and walk, and fly, and dig, and swing through the trees, and think, and produce the whole of human technology, human art, human music. This all comes about because at some point in history, about 4 billion years ago, a replicating entity arose—not a gene as we would now see it, but something functionally equivalent to a gene—which, because it had the power to replicate and the power to influence its own probability of replicating, and replicated with slight errors, gave rise to the whole of life.

If you ask me what my ambition would be, it would be that everybody would understand what an extraordinary, remarkable thing it is that they exist, in a world which would otherwise just be plain physics. The key to the process is self-replication. The key to the process is that—let’s call them “genes,” because nowadays they pretty much all are genes—genes have different probabilities of surviving. The ones that survive, because they have such high-fidelity replication, are the ones we see in the world, the ones which dominate gene pools in the world. For me, the replicator—the gene, DNA—is absolutely key to the whole process of Darwinian natural selection. So when you ask the question, “What about group selection, what about higher levels of selection, what about different levels of selection?,” everything comes down to gene selection. Gene selection is fundamentally what’s really going on.

Originally, these replicating entities would have been floating free and just replicating in the primeval soup, whatever that was. But they “discovered” a technique of ganging together into huge robot vehicles we call individual organisms. An individual organism is a unit of selection in a different sense from the replicator being a unit of selection. The replicator is the unit of selection which strictly is the thing that becomes either more numerous or less numerous in the world. Nowadays we say more numerous or less numerous in the gene pool, and that’s modern post-Darwin language.

But because the individual organism is such a salient unit in which these replicators, these genes, have ganged up together, we as biologists tend to see the individual organism as the unit of action. The individual organism is the thing that has legs or wings, it has eyes, it has teeth, it has instincts. It’s the thing that actually does something. And so it’s natural for biologists to phrase their questions of purpose, of pseudopurpose, at the level of the organism. They see the organism as striving for something, working for something, struggling to achieve something.

What’s it struggling to achieve? Well, for Darwin it was struggling to achieve survival and reproduction. Nowadays we would say it’s struggling to achieve replication of the genes inside it. And this all comes about because, well, one way of putting it, and I’ve often put it like this, is to say, “Look backward at the ancestors of all modern animals,” any animals, anytime, and you can see that the individual is descended from an unbroken line of successful ancestors, an unbroken line of individuals who succeeded in surviving and reproducing. What that really means is that they succeeded in passing on the genes that built them. So we are conduits for the genes that pass through us. We are temporary survival machines.

Everything about biology can be understood in this way. Everything about biology can be understood if you say that what’s really going on is differential replicator survival—gene survival in gene pools—and the way in which they do it is by controlling phenotypes. And those phenotypes in practice are nearly all bundled up into these discrete bodies, individual organisms.

If ever there is a bundle of replicators, a bundle of genes, which passes on its genes to the next generation in a single propagule (we do that: we pass on our genes in sperms or eggs), that means that all the genes in a body—in a mammal body, in a vertebrate body, in an animal body, a normal animal with sexual reproduction—have the identical expectation of getting into future generations: namely, leaving the present body in a sperm or an egg. That means that all the genes in a body are pulling for the same end. They all have the same goal.

If they didn’t (and some of them might not: viruses, for example, have a different goal, of being sneezed out or spat out or whatever it might be), they of course are quite different, and they do not cooperate with the rest of the genes in the body. But all the genes that have the same expectation of the future, the same expectation of leaving the present body and getting into the next body, cooperate. They work together. That’s why bodies are such coherent wholes. That’s why all the limbs and all the sense organs work together. It’s simply because all the genes that built them have the same exit route to the next generation. The minority that don’t—things like viruses—have a different exit route, and they don’t cooperate, and they may kill you.

Although it’s true that the great majority of survival machines are discrete organisms, that doesn’t necessarily have to be the case, and if genes can influence phenotypes outside the body, then they will do so. This is the extended phenotype. The simplest sort of extended phenotype would be an artifact, like a bird’s nest. So a bird’s nest is an organ. It’s an organ in the same sense as a heart or a kidney is an organ, but it just happens to be outside the body and it happens to be made of grass and sticks rather than being made of the cells that contain the genes. Nevertheless, it’s a phenotype, which is produced by the animal’s nervous system working through nest-building behavior. And it does exactly the same kind of thing—namely, preserve the genes in the form of eggs and chicks, as organs of the body, like kidneys and livers and muscles.

The next kind of extended phenotype I talk about is hosts of parasites, because there are spectacular examples. For example, parasites which influence their hosts in order to get into the next host. A host body to a parasite gene is like a bird’s nest: it’s influenced by the genes. We don’t normally put it that way; we normally say that the parasite, the fluke, or whatever it is, the whole fluke influences the whole snail, to get itself passed on. But if you think at the genetic level, the genes are influencing the fluke’s phenotype, which, in turn, influences the snail’s phenotype to enhance the propagation of the fluke’s genes into the next generation. So there’s no reason to draw a line around the fluke’s body and say, “Well, outside that is no longer proper phenotype.” It is proper phenotype, it’s just that you have to think outside the box—in this case, outside the fluke—in order to get the true relationship between genes and phenotypes.

And then, generalizing further: a cuckoo in a nest influences the behavior of its host by various stimuli—by having a bright red beak and squawking in the right way and so on. And once again, just as the fluke influences the snail to get itself passed on to the next generation, the cuckoo influences the reed warbler to get itself, to get its genes, passed on to the next generation. And the change in reed warbler behavior can properly be regarded as a phenotypic expression of cuckoo genes.

My vision of life on this planet is that everything extends from replicators, which are in practice DNA molecules. The replicators reach out into the world to influence their own probability of being passed on. Mostly they don’t reach farther than the individual body in which they sit, but that’s a matter of practice, not a matter of principle. The individual organism can be defined as that set of phenotypic products which have a single route of exit of the genes into the future. That’s not true of the cuckoo / reed warbler case, but it is true of ordinary animal bodies. So the organism, the individual organism, is a deeply salient unit. It’s a unit of selection in the sense that I call a “vehicle.”

There are two kinds of unit of selection. The difference is a semantic one. They’re both units of selection, but one is the replicator, and what it does is get itself copied, so more and more copies of itself go into the world. The other kind of unit is the vehicle. It doesn’t get itself copied. What it does is work to copy the replicators which have come down to it through the generations, and which it’s going to pass on to future generations. So we have this individual/replicator dichotomy. They’re both units of selection, but in different senses. It’s important to understand that they are different senses.

Now, because the individual organism is such a salient unit, biologists after Darwin got into the habit of seeing the organism as the unit of action, and therefore they asked the question, “What is the organism maximizing?” What mathematical function is the organism maximizing? “Fitness” is the answer. So fitness was coined as a mathematical expression of that which the organism is maximizing. Of course, what fitness really is, or what it ought to be if we understand it properly, is gene survival. For a long time, fitness was equated in people’s minds with reproduction, with having a large number of children, grandchildren, great-grandchildren. Bill Hamilton and others, but mostly Bill Hamilton, realized that you had to generalize that, because if what’s really going on is working to pass on genes, then offspring—grandchildren, et cetera—are not the only ways of passing on genes. An organism can work to enhance the survival and reproduction of its siblings, its nephews, its nieces, its cousins, and so on. Hamilton worked out the mathematics of that.

It was unfortunate that Hamilton, having realized this important insight, chose to stick with the individual organism as the entity of action. He therefore coined the phrase “inclusive fitness” as the mathematical function an individual organism will maximize if what it’s really doing is maximizing its gene survival. It’s a rather complicated thing to calculate. It’s difficult to calculate in practice, and this has led to a certain amount of—not hostility, but a certain amount of skepticism about inclusive fitness as a measure, skepticism I share. But for me, the remedy for that skepticism is to say, “Well, forget about the organism and concentrate on the gene itself.” Ask yourself, as Hamilton also did, “If I were a gene, what would I do to maximize my propagation into the future?” Hamilton did that, but he also later took a sort of false trail (it’s strictly correct but not helpful) by asking, “If I’m an individual, what would I do to maximize my gene survival?” Both ways of phrasing it are correct—they’re both correct if you can get the calculation right—but one of them is rather harder to do. If you’re trying to do intuitive Darwinism, if you’re trying to work out what you would expect to happen in the world, I think it’s better to ask the question, “What would I do if I were a gene?,” rather than, “What would I do if I were an elephant?”

In both cases this is a personification. Nobody really thinks that either genes or elephants scratch their heads and think, “What would I do?” But it’s a useful trick, a useful dodge when you’re trying to get the right answer as a field biologist in the Serengeti. It’s a useful trick to say what would I do if I was a [blank] and you could fill in the end of that sentence by saying either “if I was a gene” or “if I was an elephant.” And you’ll get the right answer if in the gene case you concentrate on self-replication and if in the elephant case you concentrate on passing on genes. So we have these two logically equivalent ways of expressing what’s going on in Darwinism. Both of them Hamilton used. I think some of the opposition to Hamilton, which has recently surfaced, is because people have realized that inclusive fitness is not a practical way of doing things. It’s a difficult thing to calculate. And my suggestion would be—and I said this to Hamilton—to abandon inclusive fitness and concentrate instead on personification of the gene, and then you’ll get the right answer.

George C. Williams in 1966 wrote a brilliant book, Adaptation and Natural Selection, roughly at the same time as Hamilton was working, and they both tumbled to the same truth, which is that what’s really going on in natural selection is survival of genes. Williams was eloquent on this. Williams said things like, Socrates may have had any number of children, we don’t know that, but what Socrates really passed on, if he passed on anything, was genes. It’s genes that pass through the generations. And so whenever you’re talking about teleonomy, whenever you’re talking about pseudopurpose, which is what we see in life—what’s it for, what’s the adaptation for, who benefits, cui bono—whenever you ask that question, you should be looking at the level of the gene. Williams realized that; Hamilton realized that.

In The Blind Watchmaker, I wanted to get across the idea that cumulative selection can give rise to immense complexity and dramatic changes. So I wrote a computer program for the Macintosh, which presented on the screen a range of phenotypes built by an algorithm I called its embryology, which was actually a tree-growing algorithm. And the shape of the tree was governed by genes. There were nine genes, I think, in the first version, and so what the user saw on the screen was a “parent,” as I called them, in the middle, and fourteen other biomorphs around it were the offspring. They were built by genes, which were nine numbers. The genes could mutate by either having a small amount added to their value or a small amount subtracted from their value. So all the nine biomorphs looked a bit different—obviously descended from the same parent but they were a little bit different. And you could choose with a mouse which one to breed from; it glided to the center of the screen, produced fourteen offspring and so on. It went on and on through generation after generation. You could breed anything you liked. It was a most extraordinary experience, to breed massively different shapes from the original by gradual degrees, and they came out looking like insects, and flowers, and all sorts of things.

I’m pleased to note that although I’d thought I’d lost these biomorphs—because modern Macs don’t run the software that old Macs do—a wonderful man called Alan Canon in Kentucky wrote to me and said he wanted to revive them. So I sent him all my old Pascal code, which would no longer run, and he’s now hard at work producing phoenix from the ashes—my old programs—and I’m simply delighted by this.

I then went to the Artificial Life Conference organized by Chris Langton, and I gave a talk called “The Evolution of Evolvability,” which I think was the first time the phrase had ever been used, and it’s being used quite a lot.

The original biomorph program had nine genes. I later enlarged it to sixteen genes. I added genes that did things like segmentation, that had biomorphs arranged serially along the body, like a centipede, which has lots of different segments, or a lobster, which has lots of segments but each segment can be a little bit different. I had genes that had symmetries of various kinds. So the repertoire of biomorphs that became possible to breed then dramatically increased. It was still limited, but nevertheless it increased. And it occurred to me that this was a good metaphor for radical changes in embryology that happened at certain important times in evolution. For example, I just mentioned segmentation. The very first segmented animal had some kind of major mutation which gave it two segments instead of one, I’m guessing. It may have been three. It can’t have had just one and a half segments; there must have been at least two. It duplicated everything about the body. If you look at the body of an earthworm or a centipede, it’s like a train, like a truck. Each truck is similar to the neighboring trucks and may be identical.

Before the origin of segmentation in the ancestors of earthworms or centipedes, the ancestors of vertebrates, animals must have evolved as one single segment, and they would have evolved in the same sort of way as my biomorphs did when they had only nine genes. Then the first segmented animal was born. It must have been radically different from its parents. This must have been a major mutation. And as soon as the first segmented animal was born with two segments—the same as each other, probably—it wasn’t a difficult thing to do in one sense, because all the embryological machinery to make one segment was already there. To double it would have been a major step; nevertheless all the machinery is there. It’s not like inventing a whole new organ, like an eye. That cannot happen. It’s got to happen by gradual cumulative selection, which is the main message of The Blind Watchmaker. But once you’ve got the machinery to make an eye, or to make a vertebra, or to make a heart or anything like that, you could make two, because the machinery is already there. That’s what segmentation is.

And so when segmentation was invented by some kind of macromutation, a whole new flowering of evolution became possible, and vertebrates, arthropods, annelids, all exploit this new embryological trick of segmentation. I illustrated this with my biomorphs, because when I added the segmentation gene for the macromutation, which I had to program in, a whole new flowering of morphology could appear on the screen. You could evolve much more exciting animals because segmentation was there. Similarly with the genes for symmetry. I had genes doing kind of mirror-image morphology in two different planes. And immediately I started being able to breed things like flowers, butterflies, beautiful creatures.

The evolution of evolvability, then, is an evolutionary change which makes a radical alteration in embryology and opens up f...