natural selection

Defining evolution

PNRJ Logic of Kindness, tribal paradigm , , , , , , , , ,

Feb 2 JDN 2460709

In the last post I said I’d explain the basics of evolution, then went into a bunch of detail about genetics. Why all this stuff about DNA? Weren’t we supposed to be talking about evolution? Yes—but it’s impossible to truly understand evolution without understanding DNA. This unity between genetics and evolution is called the Modern Synthesis, and it is the unified field theory of the life sciences. It’s quite different from what Darwin invented in 1859, but the fundamental insights were his; the Modern Synthesis is a body of flesh over the skeleton of Darwinian evolution. Now that I have explained the basics of DNA, it is time to discuss evolution itself.

The fundamental unit of evolution is the gene. (Darwin, among others, insisted that the fundamental unit of evolution is the organism, because it is organisms that are born and die. There is some truth to this, but given the presence of phenomena like kin selection and genetic drift, we also need to consider genes themselves. Richard Dawkins makes a distinction between “replicators” (genes) and “vehicles” (organisms) that makes a great deal of sense to me—both are necessary parts of the same system, and it’s a little silly to ask which is “more fundamental”.) The fundamental unit of evolution is not the population or the species; it is populations that evolve, but they evolve by natural selection acting upon individuals and genes. Natural selection is not sensitive to “the good of the species”; it is only sensitive to the good of the organism and the good of the gene.

A gene is a section of DNA that, when processed by the appropriate proteins, produces a particular protein. Most DNA is not in the form of genes. The majority of DNA has no effect—you can change it without affecting the organism—and most of the rest is involved in regulating the genes, not in producing proteins. Yet, genes are the recipes by which we are made. Human beings have genes for hemoglobin that oxygenates our blood, genes for melanin that pigments our skin, genes for serotonin that transmits signals in our brains, genes for keratin that makes up our hair, and about 46,000 other genes that produce other proteins (the Human Genome Project is still working on the exact number). An allele is a particular variant of a gene which produces a particular variant of the resulting protein. Alleles in melanin genes give different people different colors of skin; a particular allele in a hemoglobin gene gives some people sickle-cell anaemia.

When the distribution of alleles in a population changes, that is evolution. Yes, that’s all “evolution” means: Changes of distribution in alleles in a population. When a baby is born, that’s evolution. When a person dies, that’s evolution. This is what we mean when we say that evolution is a fact; it is a fact that alleles do change distribution in populations. Individuals do not evolve, populations evolve. You will never see a dog turn into a cat, nor an ape to a human. You could see, if you were watching for millions of years, a population of animals that started very dog-like and got increasingly cat-like with each generation, or a population of animals that started very ape-like and got increasingly human-like with each generation. Even these latter are not necessary occurrences; under different environmental circumstances, the same genes can evolve in completely different directions.

Fitness is the expected number of copies that an allele is likely to produce in the next generation.(There are a few subtly different ways of defining fitness; the one I prefer is the expected value of the number of copies of a given allele in the next generation. The fitness f of an allele a at generation t is given by the expectation of the number n of copies of that allele in that population at generation t+1: f(a,t) = E[n(a,t+1)]This is an \inclusive fitness measure, which accounts for kin selection better than exclusive fitness measures like “predicted grandchildren” or “expected number of reproductively-viable offspring”. In practical terms these generally give the same results; but when they don’t, the inclusive measure is to be preferred.)

Fitness is a probabilistic notion—alleles with high fitness are likely to be passed on, but this is not guaranteed. “Survival of the fittest” ultimately just means that genes that are likely to make many copies are likely to have many copies. It has been said that this is a tautology, and indeed it is; but so is the Pythagorean Theorem. Some tautologies are useful, and all tautologies are undeniably true.

What causes evolution? Organisms are born, reproduce, and die. Any time this happens, it changes the distribution of alleles in the population—it is evolution. If there was a reason why the ones who lived lived and the ones who died died, then the actual number of copies of each allele in the population will reflect the fitness of those alleles; this is called natural selection. On the other hand, if it just happened by chance, then the distribution of alleles won’t match the fitness; this is called genetic drift. Examples of each: Trees are tall, giraffes eat leaves, so giraffes with longer necks get more food and live longer—that’s natural selection. A flood rips through the savannah and kills half of the giraffes, and it just happens that more long-necked than short-necked giraffes die—that’s genetic drift. The difference can be subtle, since sometimes we don’t know what the reasons are; if it turned out that there was some reason why floods are more likely to kill long-necked giraffes (they can’t swim as well?), then in fact what we thought was genetic drift was really natural selection. But notice: Natural selection is not chance. Natural selection is the opposite of chance. If evolution happens by chance, that’s genetic drift. Natural selection is evolution that happens for a reason.

Natural selection changes populations, but what causes them to separate into distinct species? Well, a species is really a breeding population—it is a group of organisms that regularly interbreeds within the group and does not regularly interbreed outside the group. In most cases, breeding between species is actually impossible; but in many cases it is simply rare. Indeed, there is a particularly interesting case called a ring species, in which interbreeding possibilities rest on a continuum rather than being sharply delineated. In a ring species, there are several distinct populations for which some can interbreed easily, others can interbreed with difficulty, and others can’t inbreed at all. A classic case is the Ensatina salamanders who live in the Central Valley in California. There are nineteen populations, and each can interbreed with its adjacent populations—but the two populations at the far ends cannot interbreed. Ensatina eschscholtzii eschscholtzii can interbreed with E.e. croceater, which can interbreed with E.e. oregonensis, and so on all the way to E.e. klauberi—but E.e. eschscholzii on one end can’t interbreed with E.e. klauberi on the other end. Are they different “species”? It’s difficult to say. If all the intermediates died out, we would call them different species, Ensatina escholzii and Ensatina klauberi; but in fact genes do sometimes pass between them, because they can both interbreed with the intermediates. Really, the concept “species” fails to capture the true complexity of the situation.

This is not a problem for evolutionary theory—it is a prediction of evolutionary theory. We should expect to see new species occasionally forming, and while they are in the process of forming there should be many intermediates that aren’t yet distinct species. Evolution predicts gradual divergence, and sometimes we are lucky enough to see that divergence in process.

Natural selection can only act upon alleles that already exist; it chooses the best out of what’s available, not the best that could possibly exist. This is why dolphins breathe air instead of water; breathing water would be much better for their lifestyle, but no dolphin has yet been born who can breathe water. The alleles aren’t there, so natural selection cannot act upon them. If a mutant dolphin is someday born who can breathe water, as long as they don’t suffer from other problems as a result of their mutation, they are likely to live a long time and have lots of offspring; in a hundred generations perhaps water-breathing dolphins would form a new species, or even replace air-breathing dolphins. And notice how short a time that is: 100 generations of dolphins is only about 1000 years. We could watch this happening in historical time. If it had happened a million years ago, the fossil record would probably never show the intermediate forms. This is why we don’t see transitional forms between closely-related species; because the differences are so subtle, the necessary changes can occur very rapidly, in too few generations to ensure fossilization.

Indeed, monogenic traits—those that can be changed by a single mutation—never produce transitional forms. There is a single gene for sickle-cell anaemia in humans; we should not expect to see people with “30\% sickle-cell anaemia”, because there are only three options: you either have no copies of the sickle-cell allele (normal), you have one copy (sickle-cell trait), or you have two copies (sickle-cell anaemia). In fact, in this particular case, the one-copy variant isn’t even mild anaemia; it is a generally healthy non-anaemic state that offers protection against malaria. There is a single gene for six fingers in humans. Two copies gives you six fingers; one copy doesn’t do anything. Even if we had access to every individual organism that ever lived, we still wouldn’t see transitional forms for monogenic traits. Given that we actually have fossils of less than one in ten billion organisms that ever lived, it’s not surprising that most evolutionary changes leave no mark in the fossil record.

Furthermore, it’s important to understand that natural selection, even when there is plenty of variation to act on, does not produce perfectly-adapted organisms. It only produces organisms that are good enough to survive and pass on their alleles. In fact, there can be multiple fit alleles of the same gene in a population—all different, perhaps even some better than others, but each good enough to keep on surviving.

Indeed, the fitness of one allele can increase the fitness of another allele, in a number of different ways. The most morally-relevant ones only make sense in terms of game theory, so I will wait until later posts to get into them, but there are a few worth mentioning here. The first is co-evolution. Organisms evolve to suit their environments—but part of an organism’s environment consists of other organisms. Bees would not function if there were no flowers—but nor would flowers function without bees. So which came first, the bee or the flower? Neither. Ancient ancestors of each evolved together, co-evolved, the proto-flowers growing more flower-like as the proto-bees grew more bee-like, until finally an equilibrium was reached at the bees and flowers we see today.

Another way that organisms can affect the evolution of other organisms is through frequency-dependent selection, in which the fitness of a given allele depends upon the distribution of other alleles of the same gene. The most important case of frequency-dependent selection is in sex dimorphism, the differences between sexes within a species. If there are more males than females, the fitness of females goes up—it pays to be female; you’ll get your choice of males. Conversely, if there are more females than males, it pays to be male. Hence, over time, sex distributions reach an equilibrium at 50% male and 50% female, which has happened in almost every species (eusocial insects are the only major exception, and it’s due to their weird genetics). There are other cases of frequency-dependent selection as well; for instance, in stag beetles (Lucanidae), there are three kinds of males, called “alpha”, “beta”, and “gamma”. Alpha males have large horns and fight heavily with other alpha males; they risk being killed in the process, but if they win the fight, they get all the best females. Beta males have short horns and only fight other beta males; this limits their mating pool, but prevents them from being killed by alpha males. Finally, gamma males look just like females and will occasionally sneak past an alpha male and mate with his females. This is frequency-dependent selection because the success of each strategy depends on the other strategies in a fashion similar to rock-paper-scissors. If gamma males become very common, beta males will become more successful, because they won’t get cheated the way alpha males do. If beta males become common, alpha males will become more successful, because they can beat beta males in fights. If alpha males become common, gamma males will become more successful, because they can cheat alpha males. In the long run, the system settles into an equilibrium with a certain fraction of all three types.

A third way alleles affect other alleles is in sexual selection; in sexual selection, the alleles of one sex affect the alleles of the other sex, because sexual compatibility has obvious advantages. For instance, when there are lots of alleles in peahens that make them attracted to big, colorful tails, there is a fitness advantage to being a peacock with a big, colorful tail. Hence, alleles for big, colorful tails in peacocks will be selected. But then, if all the males have big, colorful tails, there is a fitness advantage to being a female who prefers big, colorful tails, and so a positive feedback loop forms; the end result is peacocks with ridiculously huge, ridiculously colorful tails and peahens who love them for it.

Everything above is very technical and scientific, and I imagine it is not very controversial or offensive to anyone. In future posts, I’ll get into the stuff that really upsets people, the true source of controversy on evolution.

Nature via Nurture

PNRJ cognitive science, core principles , , , , , , , , , , , , , , , , , , , , , , , ,

JDN 2457222 EDT 16:33.

One of the most common “deep questions” human beings have asked ourselves over the centuries is also one of the most misguided, the question of “nature versus nurture”: Is it genetics or environment that makes us what we are?

Humans are probably the single entity in the universe for which this question makes least sense. Artificial constructs have no prior existence, so they are “all nurture”, made what we choose to make them. Most other organisms on Earth behave accordingly to fixed instinctual programming, acting out a specific series of responses that have been honed over millions of years, doing only one thing, but doing it exceedingly well. They are in this sense “all nature”. As the saying goes, the fox knows many things, but the hedgehog knows one very big thing. Most organisms on Earth are in this sense hedgehogs, but we Homo sapiens are the ultimate foxes. (Ironically, hedgehogs are not actually “hedgehogs” in this sense: Being mammals, they have an advanced brain capable of flexibly responding to environmental circumstances. Foxes are a good deal more intelligent still, however.)

But human beings are by far the most flexible, adaptable organism on Earth. We live on literally every continent; despite being savannah apes we even live deep underwater and in outer space. Unlike most other species, we do not fit into a well-defined ecological niche; instead, we carve our own. This certainly has downsides; human beings are ourselves a mass extinction event.

Does this mean, therefore, that we are tabula rasa, blank slates upon which anything can be written?

Hardly. We’re more like word processors. Staring (as I of course presently am) at the blinking cursor of a word processor on a computer screen, seeing that wide, open space where a virtual infinity of possible texts could be written, depending entirely upon a sequence of miniscule key vibrations, you could be forgiven for thinking that you are looking at a blank slate. But in fact you are looking at the pinnacle of thousands of years of technological advancement, a machine so advanced, so precisely engineered, that its individual components are one ten-thousandth the width of a human hair (Intel just announced that we can now do even better than that). At peak performance, it is capable of over 100 billion calculations per second. Its random-access memory stores as much information as all the books on a stacks floor of the Hatcher Graduate Library, and its hard drive stores as much as all the books in the US Library of Congress. (Of course, both libraries contain digital media as well, exceeding anything my humble hard drive could hold by a factor of a thousand.)

All of this, simply to process text? Of course not; word processing is an afterthought for a processor that is specifically designed for dealing with high-resolution 3D images. (Of course, nowadays even a low-end netbook that is designed only for word processing and web browsing can typically handle a billion calculations per second.) But there the analogy with humans is quite accurate as well: Written language is about 10,000 years old, while the human visual mind is at least 100,000. We were 3D image analyzers long before we were word processors. This may be why we say “a picture is worth a thousand words”; we process each with about as much effort, even though the image necessarily contains thousands of times as many bits.

Why is the computer capable of so many different things? Why is the human mind capable of so many more? Not because they are simple and impinged upon by their environments, but because they are complex and precision-engineered to nonlinearly amplify tiny inputs into vast outputs—but only certain tiny inputs.

That is, it is because of our nature that we are capable of being nurtured. It is precisely the millions of years of genetic programming that have optimized the human brain that allow us to learn and adapt so flexibly to new environments and form a vast multitude of languages and cultures. It is precisely the genetically-programmed humanity we all share that makes our environmentally-acquired diversity possible.

In fact, causality also runs the other direction. Indeed, when I said other organisms were “all nature” that wasn’t right either; for even tightly-programmed instincts are evolved through millions of years of environmental pressure. Human beings have even been involved in cultural interactions long enough that it has begun to affect our genetic evolution; the reason I can digest lactose is that my ancestors about 10,000 years ago raised goats. We have our nature because of our ancestors’ nurture.

And then of course there’s the fact that we need a certain minimum level of environmental enrichment even to develop normally; a genetically-normal human raised into a deficient environment will suffer a kind of mental atrophy, as when children raised feral lose their ability to speak.

Thus, the question “nature or nurture?” seems a bit beside the point: We are extremely flexible and responsive to our environment, because of innate genetic hardware and software, which requires a certain environment to express itself, and which arose because of thousands of years of culture and millions of years of the struggle for survival—we are nurture because nature because nurture.

But perhaps we didn’t actually mean to ask about human traits in general; perhaps we meant to ask about some specific trait, like spatial intelligence, or eye color, or gender identity. This at least can be structured as a coherent question: How heritable is the trait? What proportion of the variance in this population is caused by genetic variation? Heritability analysis is a well-established methodology in behavioral genetics.
Yet, that isn’t the same question at all. For while height is extremely heritable within a given population (usually about 80%), human height worldwide has been increasing dramatically over time due to environmental influences and can actually be used as a measure of a nation’s economic development. (Look at what happened to the height of men in Japan.) How heritable is height? You have to be very careful what you mean.

Meanwhile, the heritability of neurofibromatosis is actually quite low—as many people acquire the disease by new mutations as inherit it from their parents—but we know for a fact it is a genetic disorder, because we can point to the specific genes that mutate to cause the disease.

Heritability also depends on the population under consideration; speaking English is more heritable within the United States than it is across the world as a whole, because there are a larger proportion of non-native English speakers in other countries. In general, a more diverse environment will lead to lower heritability, because there are simply more environmental influences that could affect the trait.

As children get older, their behavior gets more heritable—a result which probably seems completely baffling, until you understand what heritability really means. Your genes become a more important factor in your behavior as you grow up, because you become separated from the environment of your birth and immersed into the general environment of your whole society. Lower environmental diversity means higher heritability, by definition. There’s also an effect of choosing your own environment; people who are intelligent and conscientious are likely to choose to go to college, where they will be further trained in knowledge and self-control. This latter effect is called niche-picking.

This is why saying something like “intelligence is 80% genetic” is basically meaningless, and “intelligence is 80% heritable” isn’t much better until you specify the reference population. The heritability of intelligence depends very much on what you mean by “intelligence” and what population you’re looking at for heritability. But even if you do find a high heritability (as we do for, say, Spearman’s g within the United States), this doesn’t mean that intelligence is fixed at birth; it simply means that parents with high intelligence are likely to have children with high intelligence. In evolutionary terms that’s all that matters—natural selection doesn’t care where you got your traits, only that you have them and pass them to your offspring—but many people do care, and IQ being heritable because rich, educated parents raise rich, educated children is very different from IQ being heritable because innately intelligent parents give birth to innately intelligent children. If genetic variation is systematically related to environmental variation, you can measure a high heritability even though the genes are not directly causing the outcome.

We do use twin studies to try to sort this out, but because identical twins raised apart are exceedingly rare, two very serious problems emerge: One, there usually isn’t a large enough sample size to say anything useful; and more importantly, this is actually an inaccurate measure in terms of natural selection. The evolutionary pressure is based on the correlation with the genes—it actually doesn’t matter whether the genes are directly causal. All that matters is that organisms with allele X survive and organisms with allele Y do not. Usually that’s because allele X does something useful, but even if it’s simply because people with allele X happen to mostly come from a culture that makes better guns, that will work just as well.

We can see this quite directly: White skin spread across the world not because it was useful (it’s actually terrible in any latitude other than subarctic), but because the cultures that conquered the world happened to be comprised mostly of people with White skin. In the 15th century you’d find a very high heritability of “using gunpowder weapons”, and there was definitely a selection pressure in favor of that trait—but it obviously doesn’t take special genes to use a gun.

The kind of heritability you get from twin studies is answering a totally different, nonsensical question, something like: “If we reassigned all offspring to parents randomly, how much of the variation in this trait in the new population would be correlated with genetic variation?” And honestly, I think the only reason people think that this is the question to ask is precisely because even biologists don’t fully grasp the way that nature and nurture are fundamentally entwined. They are trying to answer the intuitive question, “How much of this trait is genetic?” rather than the biologically meaningful “How strongly could a selection pressure for this trait evolve this gene?”

And if right now you’re thinking, “I don’t care how strongly a selection pressure for the trait could evolve some particular gene”, that’s fine; there are plenty of meaningful scientific questions that I don’t find particularly interesting and are probably not particularly important. (I hesitate to provide a rigid ranking, but I think it’s safe to say that “How does consciousness arise?” is a more important question than “Why are male platypuses venomous?” and “How can poverty be eradicated?” is a more important question than “How did the aircraft manufacturing duopoly emerge?”) But that’s really the most meaningful question we can construct from the ill-formed question “How much of this trait is genetic?” The next step is to think about why you thought that you were asking something important.

What did you really mean to ask?

For a bald question like, “Is being gay genetic?” there is no meaningful answer. We could try to reformulate it as a meaningful biological question, like “What is the heritability of homosexual behavior among males in the United States?” or “Can we find genetic markers strongly linked to self-identification as ‘gay’?” but I don’t think those are the questions we really meant to ask. I think actually the question we meant to ask was more fundamental than that: Is it legitimate to discriminate against gay people? And here the answer is unequivocal: No, it isn’t. It is a grave mistake to think that this moral question has anything to do with genetics; discrimination is wrong even against traits that are totally environmental (like religion, for example), and there are morally legitimate actions to take based entirely on a person’s genes (the obvious examples all coming from medicine—you don’t treat someone for cystic fibrosis if they don’t actually have it).

Similarly, when we ask the question “Is intelligence genetic?” I don’t think most people are actually interested in the heritability of spatial working memory among young American males. I think the real question they want to ask is about equality of opportunity, and what it would look like if we had it. If success were entirely determined by intelligence and intelligence were entirely determined by genetics, then even a society with equality of opportunity would show significant inequality inherited across generations. Thus, inherited inequality is not necessarily evidence against equality of opportunity. But this is in fact a deeply disingenuous argument, used by people like Charles Murray to excuse systemic racism, sexism, and concentration of wealth.

We didn’t have to say that inherited inequality is necessarily or undeniably evidence against equality of opportunity—merely that it is, in fact, evidence of inequality of opportunity. Moreover, it is far from the only evidence against equality of opportunity; we also can observe the fact that college-educated Black people are no more likely to be employed than White people who didn’t even finish high school, for example, or the fact that otherwise identical resumes with predominantly Black names (like “Jamal”) are less likely to receive callbacks compared to predominantly White names (like “Greg”). We can observe that the same is true for resumes with obviously female names (like “Sarah”) versus obviously male names (like “David”), even when the hiring is done by social scientists. We can directly observe that one-third of the 400 richest Americans inherited their wealth (and if you look closer into the other two-thirds, all of them had some very unusual opportunities, usually due to their family connections—“self-made” is invariably a great exaggeration). The evidence for inequality of opportunity in our society is legion, regardless of how genetics and intelligence are related. In fact, I think that the high observed heritability of intelligence is largely due to the fact that educational opportunities are distributed in a genetically-biased fashion, but I could be wrong about that; maybe there really is a large genetic influence on human intelligence. Even so, that does not justify widespread and directly-measured discrimination. It does not justify a handful of billionaires luxuriating in almost unimaginable wealth as millions of people languish in poverty. Intelligence can be as heritable as you like and it is still wrong for Donald Trump to have billions of dollars while millions of children starve.

This is what I think we need to do when people try to bring up a “nature versus nurture” question. We can certainly talk about the real complexity of the relationship between genetics and environment, which I think are best summarized as “nature via nurture”; but in fact usually we should think about why we are asking that question, and try to find the real question we actually meant to ask.