Month: February 2025

Naive moral Darwinism

PNRJ ethics, tribal paradigm , , , , , ,

Feb 23 JDN 2460730

Impressed by the incredible usefulness of evolutionary theory in explaining the natural world, many people have tried to apply it to ethical claims as well. The basic idea is that morality evolves; morality is an adaptation just like any other, a trait which has evolved by mutation and natural selection.

Unfortunately the statement “morality evolves” is ambiguous; it could mean a number of different things. This ambiguity has allowed abuses of evolutionary thinking in morality.

Two that are particularly harmful are evolutionary eugenics and laissez-faire Darwinism, both of which fall under an umbrella I’ll call ‘naive moral Darwinism’.

They are both terrible; it saddens me that many people propound them. Creationists will often try to defend their doubts about evolution on empirical grounds, but they really can’t, and I think even they realize this. Their real objection to evolution is not that it is unscientific, but that it is immoral; the concern is that studying evolution will make us callous and selfish. And unfortunately, there is a grain of truth here: A shallow understanding of evolution can indeed lead to a callous and selfish mindset, as people try to shoehorn evolutionary theory onto moral and political systems without a deep understanding of either.

The first option is usually known as “Social Darwinism”, but I think a better term is “evolutionary eugenics”. (“Social Darwinism” is a pejorative, not a self-description.) This philosophy, if we even credit it with the term, is especially ridiculous; indeed, it is evil. It doesn’t make any sense, either as ethics or as evolution, and it has led to some of the most terrible atrocities in history, from forced sterilization to mass murder. Darwin adamantly disagreed with it, and it rests upon a variety of deep confusions about evolutionary science.

First, in practice at least, eugenicists presumed that traits like intelligence, health, and even wealth are almost entirely genetic—when it’s obvious that they are very heavily affected by the environment. There certainly are genetic factors involved, but the presumption that these traits are entirely genetic is absurd. Indeed, the fact that the wealth of parents is strongly correlated with that of their children has an obvious explanation completely unrelated to genetics: Inheritance. Wealthy parents can also give their children many advantages in life that lead to higher earnings later. Controlling for inherited environment, there is still some heritability of wealth, but it’s quite weak; it’s probably due to personality traits like conscientiousness, ambition, and in fact narcissism which are beneficial in a capitalist economy. Hence breeding the wealthy may make more people who are similar to the wealthy; but there’s no reason to think it will actually make the world wealthier.

Moreover, eugenics rests upon a confusion between fitness in the evolutionary sense of expected number of allele copies, and the notion of being “fit” in some other sense, like physical health (as in “fitness club”), socially conformity (as in “misfits”) or mental sanity (as in “unfit to serve trial”). Strong people are not necessarily higher in genetic fitness, nor are smart people, nor are people of any particular race or ethnicity. Fitness entails the probability of one’s genes being passed on in a given environment—without reference to a specific environment, it says basically nothing. Given the reference environment “majority of the Earth’s land surface”, humans are very fit organisms, but so are rats and cockroaches. Given the reference environment “deep ocean”, sharks fare far better than we ever will, and better even than our cousins the cetaceans who live there. Moreover, there is no reason to think that intelligence in the sense of Einstein or Darwin is particularly fit. The intelligence of an ordinary person is definitely fit—that’s why we have it—but beyond that point, it may in fact be counterproductive. (Consider Isaac Newton and Alan Turing, both of whom were geniuses and neither of whom ever married or had children.)

There is milder form of this that is still quite harmful; I’ll call it “laissez-faire Darwinism”. It says that because natural selection automatically perpetuates the fit at the expense of the unfit, it ultimately leads to the best overall outcome. Under laissez-faire Darwinism, we should simply let evolution happen as it is going to happen. This theory is not as crazy as evolutionary eugenics—nor would its consequences be as dire—but it’s still quite confused. Natural selection is a law of nature, not a moral principle. It says what will happen, not what should happen. Indeed, like any law of nature, natural selection is inevitable. No matter what you do, natural selection will act upon you. The genes that work will survive, the genes that fail will die. The specifics of the environmental circumstances will decide which genes are the ones that survive, and there are random deviations due to genetic drift; but natural selection always applies.

Typically laissez-faire Darwinists argue that we should eliminate all government welfare, health care, and famine relief, because they oppose natural selection; but this would be like tearing down all skyscrapers because they oppose gravity, or, as Benjamin Franklin was once asked to do, to cease installing lightning rods because they oppose God’s holy smiting. Natural selection is a law of nature, a fundamental truth; but through wise engineering we can work with it instead of against it, just as we do with gravity and electricity. We would ignore laws of nature at our own peril—an engineer who failed to take gravity into account would not make very good buildings!—but we can work with them and around them to achieve our goals. This is no less true with natural selection than with any law of nature, whether gravity, electricity, quantum mechanics, or anything else. As a laser uses quantum mechanics and a light bulb uses electricity, so wise social policy can use natural selection to serve human ends. Indeed, welfare, health care, and famine relief are precisely the sort of things that can modulate the fitness of our entire species to make us all better off.

There are however important ways in which evolution can influence our ethical reasoning, which I’ll talk about in later posts.

The real source of the evolution debate, part 2

PNRJ Logic of Kindness , , , , , , , , , , , ,

As I discussed in my last post, the propositions that people really object to are not evolution per se. They are distinct but conceptually related ideas, such as adaptationism, common descent, animalism, abiogenesis, and atheism.

In my last post I dealt with adaptationism and common descent; now its time for animalism, abiogenesis, and atheism.

Animalism

Next we must consider animalism, the proposition that humans are not “special”, that we are animals like any other. I’d like to distinguish two forms of animalism which are quite different but often confused; I will call them weak animalism and strong animalism. The former is definitely true, but the latter doesn’t make any sense. Weak animalism is the observation that human beings have the same biological structure as other animals, and share a common ancestry and many common traits—in short, that humans are in fact animals. We are all born, we all die; we all breathe, we all eat, we all sleep; we all love, we all suffer. This seems to me a completely unassailable observation; of course these things are true, they are essential to human nature, and they are a direct consequence of our kinship with the rest of the animal domain. Humans are not rocks or plants or empty space; humans are animals.

On the other hand, strong animalism is the claim that because humans are animals, we may (or should) “act like animals”, stealing, raping, murdering, and so on. It is true that all these behaviors, or very close analogues, can be observed in the animal domain; but at the same time, so can friendship (e.g. in chimpanzees), affection (e.g. in penguins), monogamy (e.g. in gerbils), and many other behaviors. The diversity of behaviors in the animal domain is mind-bogglingly huge. There are animals that can sever and regrow limbs and animals that can infest and control other animals’ minds.

In the only sense in which we are “just animals”, the fact justifies no moral claims about our behavior. This matter is not a trivial quibble, but a major factor in the evolution debate: Intelligent Design proponents made a similar complaint when they objected to Bloodhound Gang’s song “The Bad Touch” which includes the line, “You and me baby we ain’t nothin’ but mammals // So let’s do it like they do on the Discovery Channel”. This may make for entertaining music (and I’ve no objection to sex or even promiscuity and seduction per se), but it is highly fallacious reasoning, and it’s clearly hurting the public understanding of science. If you insist on saying that humans are “just animals”, you should be very clear about what this means; I much prefer to remove the condescending “just” and say “humans are animals”. For to say humans are just animals would be like saying the Earth is just a planet, or love is just a chemical reaction. If all you mean is that the example is an instance of a category, you don’t need the “just”; by saying “just”, you clearly are trying to assert some sort of equivalence between members of the category, one that would deflate the status of the particular example. Yet if you have to say it, it probably isn’t true; no one would point at a random rock and say “this is just a rock”—instead you point to the Earth and say “this is just a rock”, when in fact it is a very special rock. Humans are a very special animals, the Earth is a very special planet, and love is a very special chemical reaction (closely tied to that most mysterious of chemical reactions, consciousness). We are members of one vast animal family—indeed, one vast family of life—but we are most definitely the wisest and most powerful member.

I’m honestly not sure what I would do if I tried to “act like an animal”; I suppose I would be born, breathe, eat, sleep, love, suffer and die—but I was going to do these things anyway, whether I wanted to or not. Indeed, by weak animalism, humans are animals, and so by acting like human beings we are in fact acting like animals—the animal Homo sapiens.

Abiogenesis

Next comes abiogenesis, the proposition that living things came from nonliving things. Well, where else would they come from? The only way to deny this proposition is to say that living things always existed. (If God made life, he would have done so by being a living thing that always existed.) The problem with this idea is that it doesn’t really explain where life comes from, it only pushes its origin back into the infinite past. Scientists are making progress in using nonliving chemicals to produce replicating entities that are very similar to life, and inn 2010 scientists created the first all-synthetic bacterium, but to do it they had to use pre-existing bacteria to set up the reactions. This lends credibility to the idea that life came from nonlife, but in fact even this wouldn’t conclusively demonstrate abiogenesis; it would prove that life can arise from nonlife, but that doesn’t mean it did originally. The truth is, we really don’t understand much about the origin of life, and even less about the origin of the universe; but this does nothing to undermine evolution or even common descent. No one doubts the existence of gravity simply because we don’t know what caused the Big Bang!

Atheism

Finally, and most controversially, there is atheism. Theism is belief in a superhuman being that responds to prayers and performs miracles; atheism is the negation of theism. This is all atheism means; if you think it means something more than this—absolute knowledge that there cannot be a creator being, or no ultimate foundation for morality, or no meaning to existence, or whatever else—that isn’t atheism. An atheist is someone who doesn’t believe in a personal divinity, someone who says that there are no superhuman beings that intervene in our lives. This is a fairly strong claim in itself, since if correct, atheism implies that religion as we know it—prayer, rituals, miracles, holy books—is utterly false. Deep philosophical religion, like that practiced by Einstein or Kant, remains intact; but the religion of churches, mosques and temples is completely undermined.

Evolution doesn’t imply atheism, but it does support it, in the following sense: Evolution answers the question of “Where did we come from?” without requiring God. Even before we knew about evolution, religion wasn’t a very convincing answer to that question; but we didn’t really have a better one—and now we do.

Yet atheism is clearly correct. This is something we can infer directly from a large body of scientific evidence. I’ve already addressed this topic in previous posts, so I’ll be brief this time around.

Maybe there is a kind of religion that could be reconciled with science; but it’s not a theistic religion. Perhaps there is a God who made the whole of the universe, set it running in perfect harmony to achieve some divine plan. This is called deism, and it’s a scientifically respectable position. But then, it is senseless to pray, since God isn’t going to change the divine plan on behalf of tiny creatures on a backwater planet of a backwater star in a backwater galaxy. It is plainly wrong to call such a being “he” or even “He”, since no being so vast and powerful could ever be properly described in the petty terms of a biological male—it would be like saying that gravity has testicles, energy conservation has a beard, or causality has a Y chromosome. I’m not sure we can even fairly say that God is a conscious being, for consciousness as we know it seems too vulgar a trait to assign to an entity of such vastness. In fact, the theologian Paul Tillich thought even existence a concept insufficient to describe the divine. It is foolish to look to ancient books to understand God, for its work is written from horizon to horizon in the fabric of the universe, and these ancient books are but pale shadows of its grandeur. It is naive to suppose that we are special beings created in God’s image, for God has made many millions of species on this planet, and probably countless more on other distant planets; furthermore, God’s process of production favors insects and bacteria and requires massive systematic death and suffering.

And even once we have removed everything we knew of religion, even this truncated theology suffers from an egregious flaw: Such a creator offers us no evidence of its existence. A deistic God is indistinguishable from the universe itself, definitely in practice and perhaps even in principle. I don’t really see the point in using the word “God” when the word “nature” captures what we mean much better. Saying “God is vaster than we can imagine, and of course by `God’ I mean the universe” strikes me as like saying “The Sun is powered by magical unicorn love, and of course by `magical unicorn love’ I mean nuclear fusion.”

And theism, religion as we know it, is philosophically and scientifically bankrupt. Imagine an airline pilot who lets go of the controls and prays to God to fly the plane; imagine a surgeon who puts down the scalpel and prays to God for the patients to be healed. That’s the sort of thing we would do if theism were true. It would make sense to do these things—it would be rational to do these things—under the presumption that there is a God who answers our prayers. You can’t escape this; if it makes sense to pray for your sick grandmother, then it doesn’t make sense for her to take medicine—because if God is in control, then chemistry isn’t. The fact that hardly anyone really would resort to prayer when an obvious and effective scientific alternative is available (and the fact that people who do are considered fanatical or even insane) clearly shows that theism is bankrupt, and that hardly anyone believes it confidently enough to actually live by it. No one except the craziest fanatics believes in God the way they believe in gravity.

I’m sure this book will be perceived as yet another “angry atheist” “attacking” “religious people”; on the contrary, I am a respectful and reflective atheist criticizing theistic religion. I respect religious people; I do not respect theistic religion. Indeed, I respect religious people too much to let them go on believing such ridiculous things. What glorious powers of human reason are wasted on such nonsense! If you believe in the subtle, abstract, inscrutable God of Einstein or Spinoza, very well. We disagree only about the most abstract matters, almost at the level of semantics (what you call “God” I prefer to call “nature”). Our beliefs and values are not only reconcilable but nearly identical.

On the other hand if you believe in a magical personal God, a God who writes books and answers prayers, then my criticism is indeed directed at your beliefs; I think you are mistaken, gravely, dangerously mistaken.

Atheism is a scientific fact.

Conclusion

Evolution is a fact. The Modern Synthesis of genetics and natural selection is among the most certain scientific theories ever devised; it is the unified field theory of life on Earth. The following claims may be controversial in our society, but they are also scientific facts: Living things are adapted to their environment by natural selection; all life on Earth is descended from a common ancestor; humans are animals; life arose by natural processes; and theistic religion is false. You can accept these facts, or else you can live in denial.

Yes, in principle evolution is a theory that can be doubted, but in principle everything in science is a theory that can be doubted. If you want certain, undeniable truths, you will need to stay with logic and mathematics—and even then, you’ll need to be careful about your axioms. Otherwise, you must always be open to a thin sliver of uncertainty, a sliver that should be no larger for evolution than for gravity or photosynthesis. (Of the three, gravity is by far the least-understood.)

The convergence of scientific evidence in favor of evolution, a 4.5-billion-year-old Earth, genetics, natural selection, common descent, adaptationism, weak animalism, and yes, even atheism, is so incredibly massive that we’d have to give up half of science to abandon these things. Any revisions we do make in the future will necessarily be minor, leaving the core of truth intact.

To doubt that rubidium decays into strontium at the same rate now it did a million years ago, you must explain how the fundamental laws of nuclear physics that we have verified to twelve decimal places are incorrect.

To doubt that cetaceans evolved from land mammals, you must explain why they breathe air instead of water and swim vertically rather than horizontally, unlike nearly everything else in the sea.

To believe in microevolution but not macroevolution, you must think that there is some mysterious force that prevents what has happened 100 times from happening an additional 100,000 times for the same reasons—for, if repeated many times, a 0.01% systematic change per century, a darwin of evolution (lowercase for a unit of measure, like the newton of force or the weber of magnetic flux), is more than enough to account for the transition from archaea to eukaryotes over 3 billion years, and vastly more than is needed to account for the transition from apes to humans over 5 million years. In fact, observed rates of evolution in the short term have reached the level of kilodarwins, thousands of darwins.

To doubt that life on Earth has changed and diverged over time you must ignore the most obvious facts about a remarkably rich and well-organized fossil record. There are no rabbits in Precambrian layers. There are no trilobites in Mesozoic layers. There are no primates in the Jurassic, and no sauropods in the Tertiary. There have never been a human fossil and a dinosaur fossil found in the same rock. Creationists like to claim that the fossil record sorted itself by size and lifestyle (as here), but in fact there are large and small, land and sea, in pretty much every layer of the fossil record—just not the same ones, because the organisms in lower layers died off and were replaced by the organisms in higher layers. Pterodactyls look a lot like a birds, come in roughly the same size ranges as birds, and seemed to live similar lifestyles, but you’ll never find the two buried together. Looking at the fossils, you can’t help but infer evolution; if God made the fossils, he must have wanted us to believe in evolution.

The real source of the evolution debate, part 1

PNRJ Logic of Kindness , , , , , , , , , , ,

Feb 9 JDN 2460716

The last few posts have been about evolution; but everything I’ve said in them has been very technical and scientific, and I imagine it is not very controversial or offensive to anyone. In fact, I would guess that anyone who believes in Creationism, upon reading my definition of evolution as “change in allele distribution in a population”, was thinking, “Of course we believe in that. But that’s not evolution.” Actually it is; evolution is change in allele distribution in a population. What people are objecting to isn’t really evolution.

There are however several propositions that people do object to, which are conceptually related, but not strictly implied by evolution. They are adaptationism, common descent, animalism, abiogenesis, and atheism respectively. They are all true—and in what follows I will offer a defense of each—but they are not necessarily entailed by evolution or the Modern Synthesis, and so they should be considered separately on their own merits. This post will deal with adaptationism and common descent, and I’ll save the others for a later post.

Adaptationism

Adaptationism is the principle that living organisms have the traits they do because these traits are adaptive, that is, that they are beneficial to fitness. It’s obvious that this isn’t completely true in every case; whales have hipbones despite having no apparent use for them, and the human appendix seems mostly useful for collecting toxins and occasionally exploding. There are also limits to how much an organism can change given its current structure; the emerging field of developmental evolutionary biology, or evo-devo, seeks to characterize these limits more precisely.

But in general, adaptationism is an incredibly powerful principle, one which makes sense of the diversity and complexity of life on Earth in a way no other theory can. Natural selection predicts that organisms will become more and more adapted over time; adaptationism is based on the fact that we have had plenty of time to adapt really, really well. In fact, it can be argued that adaptationism is really what evolutionary theory is about, that all this business about changes in allele distributions is useful but not really the point of the enterprise.

When we look at the world, we see that living things are extremely complex and well-suited to their environments; theologians used to say (in fact some still do) that this was evidence that living things were designed by a perfect God.

The problem with this argument was exposed almost immediately by David Hume: If complex things need designers, aren’t designers even more complex than what they design? But then, the designer needs a designer-designer, and the designer-designer needs a designer-designer-designer, and so on into an infinite regress! Another problem with this sort of Intelligent Design thinking is that it cannot explain the cases when adaptationism fails—in particular, why do so many species go extinct? Recently a theory of “Intelligent Recall” was proposed for this purpose; but this forces us to think of our designer as no more intelligent than a financial analyst or an automobile engineer! What kind of God would make mistakes in design?

And now we know better: The remarkable complexity and fitness of living organisms can be entirely explained by adaptationism. When we ask why dolphins have fins, why birds have wings, why centipedes have so many legs, why snakes are so long, or why humans have such enormous brains, adaptationism gives us the answer: organisms have these traits because having these traits benefited their ancestors. In some cases it’s pretty obvious how this would work (having fins lets dolphins swim faster, swimming faster has obvious benefits in catching fish and escaping sharks, so dolphin ancestors with more fin-like limbs survived better); in others we’re still working on the specifics (there is as yet no consensus on how humans got so incredibly smart compared to other animals); but in general adaptationism has explained a huge body of data that we couldn’t account for any other way.

Common descent

Common descent is the proposition that all living organisms on Earth are descended from a common ancestor. This implies, in particular, that human beings share a common ancestor with other animals. The former is strictly stronger, and not quite as certain; at least in principle it could be that some broad classes of organism do not share a common ancestor, but nonetheless it would still be quite clear that humans share a common ancestor with chimpanzees. In practice nearly all biologists agree with the strongest form of common descent, that all living organisms on Earth share a common ancestor. Recently the biochemist Douglas Theobald mathematically compared this strongest form of common descent (universal common descent) with several other models of phylogenetic history, finding that universal common descent was the most probable result by a factor of at least 102000—a 2001-digit number. That is, scientists are 99.999,999,999,999,999,999… (on with 1,980 more nines!) percent sure that universal common descent is right. This is not hyperbole; it is mathematically precise. At this point any sliver of uncertainty left in universal common descent needs to apply to all of our fundamental knowledge of physics and chemistry; in order to be wrong about this, we’d need to be wrong about everything.

How are we so sure? Nature presents us with a very consistent pattern of observations that simply make no sense any other way. Traits in living things (and, we are increasingly finding, genes) have distinct patterns, structural similarities that exist between species irrespective of their lifestyle; we call these similiarities homologues. (Similarities that are due to lifestyle—e.g., both dolphins and fish have fins—are called analogues.) Dolphin skeletons are more like dog skeletons than they are like fish skeletons, even though dolphins live more like fish. Bat skin is more like human skin than like bird skin, even though bats live more like birds. The most parsimonious explanation is that these traits were passed on from some common ancestor—that dolphins and dogs have similar skeletons because dolphins and dogs are actually genetically related somehow, and they differ from fish because they are more distantly related.

Once we began to understand DNA, we became able to detect even more compelling homologues. Many kinds of mutation are completely ineffectual; some involve a change to DNA that doesn’t do anything, others swap out two amino acids that are essentially the same; in fact because of the way genes code for amino acids, it’s possible to have a change in a gene that isn’t reflected in the resulting protein at all. All of these changes have no effect on the organism, but they are still passed on to offspring. When you find two organisms that have the same trait (e.g. bats and birds both have wings), if that trait does something important (lets you fly), then maybe it’s just a similarity in lifestyle; if that happens we call it convergent evolution. But when we’re looking at a DNA sequence that doesn’t do anything, lifestyle can’t be the reason—it must be either common ancestry or pure coincidence. Statistical analysis can rule out pure coincidence, and then we are left with only one possibility: common descent. A third option often proposed by Creationists simply doesn’t work: A common designer of sharks and dolphins would not give one a cartilaginous skeleton and gills and the other a bony mammalian skeleton and lungs. There is no reason for dolphin skeletons to be more like dog skeletons than shark skeletons—except that dogs and dolphins share closer common ancestry to each other than they do to sharks.

There are thousands of traits and genes that we can use to assess these relationships. When we do this, we find a remarkably consistent organizational structure, a pattern of a few common ancestors diversifying into a wide variety of descendants—it looks a bit like a tree, so we call it a phylogenetic tree. In some cases there is ambiguity about which species are more closely related, and we need to gather more evidence. This is a normal part of evolutionary biology research.

One thing is not disputed: Humans share a common ancestor with apes. This is simply too obvious from the morphological and genetic homologues. Human and chimp DNA coincides 95-98\%, depending on how you count insertions and deletions.

A standard measure of genetic distance is the Nei distance; a larger Nei distance implies more genetic differences, which in turn suggests that the common ancestor was further in the past. (Exactly how it’s calculated is a bit too technical for this post.)

Humans and chimps have a Nei distance of 0.45. This similarity between humans and chimps represents a closer similarity than that between dogs and foxes, who differ by a Nei distance of 1.1. Almost anyone can see that dogs and foxes are related animals; so why is it so hard to believe that humans and chimps are related too?

Creationists often claim that we never find the transitional forms predicted by evolutionary theory, but this is simply not true. We do in fact see many transitional forms; feathered dinosaurs mark the transition from reptiles to birds, ambulocetids mark the transition from land mammals to cetaceans, therapsids mark the transition from reptiles to mammals, and a huge variety of hominids marks the transition from apes to humans. It’s important to understand what this means: transitional forms are not bizarre combinations of their descendant organisms, but fully-functional lifeforms in their own right that have descendants very different from one another. Just as your grandparents are not a combination of half of you and half of your first cousin, common ancestors are not simply half-and-half combinations of their descendant organisms. Ambulocetids are not half-deer/half-dolphin, they are somewhat deer-like yet somewhat dolphin-like mammals whose ancestors were on average slightly more deer-like and whose descendants were on average slightly more dolphin-like. Different traits changed at different times, generations apart: Ambulocetids began to swim before they lost their legs, and even modern dolphins haven’t lost their lungs or hipbones.


This is such a deep, marvelous truth that Creationists are missing out on: All life on Earth is part of one family. We are kin with the dogs and the cats and the elephants, with the snakes and the lizards and the birds, with the beetles and the flies and the bees, even with the flowers and the bushes and the trees.

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.