Friday, October 9, 2009
Evolution to and fro
In the last bit of tidying up after our trip, Holly asked us to comment on a recent paper in Nature (An epistatic ratchet constrains the direction of glucocorticoid receptor evolution, Bridgham et al., 461, 515-519, 24 September 2009), related to the question of whether evolution can, or does, ever go backwards. This is a long-standing question among evolutionary theorists; indeed, in 1890, Belgian paleontologist Louis Dollo addressed it by proposing what is now known as Dollo's Law: "An organism is unable to return, even partially, to a previous stage already realized in the ranks of its ancestors."
But, what does it mean to ask whether evolution can reverse itself? As Bridgham et al. themselves point out, there are many ways to make a given trait, not all genetically equivalent. So, is evolutionary reversal the replication of an older form, which wouldn't necessarily have to involve the same genes as the original iteration? Or, does it mean replication of the same form, produced by the same genes? The first, reproduction of an ancestral form in a novel way, is much more plausible than the second, given the apparent strength of contingency and cooperation in development; what gets made next depends on what's here now, and that depends on what was just here. Thus, to reproduce an ancestral form would require that each step in the evolution of a protein be reversed, along with each step in the evolution of the proteins with which it works. And, because, say, a receptor cooperates with a ligand, although imprecise receptor/ligand binding often works, neither can change too drastically too quickly, lest the signal telling the cell what to do next won't get sent. So, reversal of form and DNA sequences would require reversal of each of the co-evolutionary steps that led to the modern form, which seems highly implausible.
In addition, reversal to a previous form, via the same genes or not, would require the return of the environment in which that form was once successful, and that makes it that much more implausible, since environments are always changing. As Bridgham et al. say, "The past is difficult to recover because it was built on the foundation of its own history, one irrevocably different from that of the present and its many possible futures." So, because of so much that is known about biology, we would a priori agree with Dollo's Law.
All that said, Bridgham et al. actually put the question to a test. They engineered a hormone receptor protein to mimic its ancestral state and the steps it took to become the modern receptor it is, and evaluated its function along the way. In its ancestral state, the receptor was 'promiscuous', able to bind with different classes of hormones, but over 40 million years, and with an estimated 37 different amino acid changes, it lost that ability and became specific to a single class of hormone. The authors found that only 2 amino acid changes were necessary for the receptor's evolved specificity but that subsequent amino acid changes that "optimized the new specificity of the glucocorticoid receptor, also destabilized elements of the protein structure that were required to support the ancestral conformation." Thus, building in just the 2 original changes wasn't sufficient to allow them to resurrect the receptor's ancestral function. They conclude that too many changes are required for successful reversal of the receptor to its ancestral function. Does this prove that evolutionary reversal is impossible? No, but it does suggest that contingency and cooperation are indeed foundational principles in development and evolution, and are important reasons why reversal is unlikely.
How unlikely?
Perhaps the points can be more clearly and immediately seen if we ask how probable rather than plausible they are. A mutation replacing an A with a T in DNA can be reversed, the T being replaced with an A--changes that do occur. But because in general mutation is very improbable at any given spot in DNA, the same specific mutation is even less probable. And even if that chance were, say, 1/1000 (much much greater than is actually the case), if 100 of these reversals were needed, the chance would be 1/1000 to the hundredth power, infinitessimally small. And this doesn't take account of the order, viability of intermediate stages in the reversal process, etc. So while most things like this might be possible, they are too unlikely to take seriously if we're thinking about anything at all complicated.
And we can seal the 'no' deal in two other ways. First, we already know that things can reverse. People who have a certain height can have shorter children but their children could again be taller. Much of the time this will be due to different genotypes.
And many mutations involve deletions of DNA, sometimes of chunks many nucleotides long. It would take a fairy godmother to wave a wand to reverse this and somehow conjure up the exact chunk to be re-inserted some time later.
Darwinism as natural law
Here's another way to think of it. Evolutionary theory, since Darwin, has attempted to be a natural science based on natural law. Darwin was very Newtonian in this, suggesting that natural selection was a kind of 'force', rhetoric often used today even though we have a strong sense of probabilism (including both mendelian sampling of genes from parent to offspring, and genetic drift in which the frequency of genetic variants changes in a population strictly by chance).
In a perfectly Newtonian world, nature is predictable and retrodictable. If you know the state today you can predict tomorrow, or tomorrow you can predict today (e.g., by changing the sign of the equation from plus to minus, so to speak). This was an ideal until the 20th century, roughly speaking, when disturbances such as quantum theory showed that things were not so uniformly homogeneous in time.
Largely stimulated by Darwinian thinking, even physicists began to realize that time had a direction. If change is probabilistic, we can go from today to some state tomorrow, but tomorrow we can't tell what today's state had been.
In principle, if we compare DNA sequences between species, we see that evolution diverges forward in time, as mutational changes occur in different descendant copies of a gene from generation to generation, producing a branching or tree-like structure of sequence relationships. These are presumably related to traits, like fingers and leaves, and natural selection (and drift) produce differentiated, adaptive organisms over evolutionary time.
In a sense, this would not seem to be reversible. Once you can make a limb (on a tree or on your body), it is so complex a process that you can destroy it but you can't go back to the state before it was a limb.
However, if you just look at the nucleotides, as we said above, traits of organisms involve many different genes, and the probability of everything being exactly reversed is trivially small, even if mathematically possible.
If you want to be a stickler for exactness then you have the answer: reversal is technically possible but in practice impossible. But if you look at traits or function, then evolution certainly reverses itself. That's what happened in the evolution of flightless birds. Different lineages of insects have repeatedly evolved, or de-evolved, similar states related to the number of ocelli (small central eyes), and different lineages of amphibians have gained or lost tadpole stages in their development. Some of these may involve reverse mutations in the same genes, but there are undoubtedly different genetic pathways 'forward' as well as 'backward' in this phenotypic sense.
As so often is the case, the answer depends on the question. Dollo's principle seems reasonable (if not a 'law' in the cosmic sense) in regard to complex adaptive traits. Different versions of what seem to be the 'same' trait usually have at least some genetic differences. In that purist sense, you really can't go home again.
-Ken and Anne
Wednesday, October 7, 2009
Selecting people
In the Rival del Garda meeting we were happy to see Luca Cavalli-Sforza for the first time in many years. Luca, a towering figure in human genetics in the last third of the 20th century, was one of the most important conceptual leaders in uniting population (evolutionary) genetics, along with culture and language, in accounting for current human diversity. Luca, long at Stanford but who retired back home in Italy a few years ago, is well into his '80s, but still spry enough and intellectually lively. Ken had interacted with him extensively in the past, including a mid-70s sabbatical in his lab at Stanford, and subsequently in the attempt to organize a global human genome diversity project (HGDP).
Luca gave a talk at the meeting on natural selection in humans. We wondered whether, at his age and removal from Stanford he could really be up to date with the huge, rapidly emerging literature on searches of the human genome for signatures of selection. Intense, highly technical genomewide comparison of variation between humans and other primates, but especially among human continental groups, has been undertaken by many investigators using HGDP-like samples and the genetic variation in the HapMap project.
There, the idea is to find genes or genome regions in which variation is reduced in ways suggesting that specific selection has taken place--such as to produce lighter or darker skin color in various continents and/or climates, or the ability of humans to resist malaria, or of adults to digest milk (these are the classic examples).
Such searches are for classically Darwinian effects. That is, they're about who in a population has higher 'fitness'--net reproductive success because they survive better or simply have higher fertility. The search is difficult and only a few specific instances have been found, for reasons too much to go into in this post. But there is at least widespread belief that there's been quite a lot of such selection since we spread out from our African ancestral home to become a globally distributed species: how could we inhabit the globe's diversity of environments without this being the result of natural selection?
Well, Luca surprised us. His point was about culture rather than genes per se. He quite correctly noted that our having culture helped us adapt quickly to diverse environments (clothing and fire, rather than fur, to protect against cold, for example, or language to communicate among coordinated hunters or gatherers).
Non-Darwinian group selection
Luca's evidence was thus entirely unrelated to the current genomewide statistical searches, but instead related to our rapid global expansion that could not be explained by genes--except by our species' shared genes related to thinking ability, that made us capable of culture.
Humans have clearly expanded rapidly at the expense of other species. We have invaded every environment, and displaced other species where needed, advancing some such as cattle or wheat for our own use instead. Our numbers have increased in a few thousand years from a few thousand to a few billion. Nothing could be clearer as proof of natural selection in humans.
However, this is not Darwinian selection in the usual sense! Instead it is a kind of group selection, the favoring of our group vis-a-vis groups of other species that we displaced. It is closer to the version of selection and evolution proffered by Alfred Wallace (who came to his ideas independently of Darwin). Wallace gave more stress to group competition and group struggle against environments, while Darwin clearly and strongly stressed competition among individuals within groups.
The two are not incompatible at all, and both processes can be occurring at any or every time. But it's not what people have in mind these days, in their frenetic hunt for good and bad genes. So Luca may or may not be up to date in that area of work, but he certainly pointed out what is, for our species, clearly and by far the most important aspect of selection involving humans! Far more important than the rather minor kinds of selection we know about at the specific gene level--even including malaria and skin color effects.
Politically correct, if scientifically incorrect
However, in stressing this view, Luca went on to argue that because selection in humans was culture-based, there was little evidence for racial differences that could be attributed to selection. Race differences (here, let's ignore the problems with the term 'race'), he said, are superficial only. They don't reflect natural selection beyond such traits as skin color. The argument is one Luca has been making for decades, as he has been perhaps by far the leader in trying to relate human genetics to human culture, such as correlating language with geography with genetic variation. But his argument unfortunately reflected a quite out-dated view, that in some ways can even be said to be politically correct, if scientifically incorrect. To see why, let's look at the case that was made.
Luca has long pointed out that, to a considerable degree, human genetic differences are correlated with geography. The farther apart geographically that two people are (here, we refer to 'indigenous' people rather than recent intercontinental migrants), the more different they are genetically. This is called 'isolation by distance.' There is quibbling about the details, but the idea is basically accurate: French and Swedish people are genetically more like each other than French and Koreans are. This, Luca argued, shows that there cannot be much due to natural selection, because selection is related to local environmental conditions, which can be very different in nearby regions, or very similar in distant regions, would not leave such a generic pattern of differences.
But there's a subtle fallacy here. Selection of a given trait affects only the genes that produce that trait, not the whole genome. Even if selection is affecting all genes at all times, each gene is affected by different environmental conditions. And selection works not with global variation, but only with variation present in any local area. Thus, even with selection, we see isolation by distance effects.
More importantly, isolation by distance is studied by using genomewide variation. There is often a deliberate choice of genetic variants that are thought not to be involved in functionally important traits (so-called selectively neutral parts of the genome), and hence variants that are not involved in selection. Isolation by distance in the genome overall, especially at such neutral regions, is perfectly compatible with all sorts of selection going on at individual genes, but differently in different world regions.
We can see this easily in another way. Two people can have a trait, like blue eyes, diabetes, or color blindness for the same genetic reason. As a rule, the same genetic variant found in two people are descendant copies of a single original mutation that occurred sometime in the past. In that sense, they are close relatives at that particular gene. But if you look at genomewide variants, they will have no particular relationship relative to other people in the population.
So, whatever you think about the pervasiveness or importance of natural selection in the history of different human 'races', the isolation by distance argument is basically irrelevant.
Thus, while the massive global expansion of humans is overwhelming and persuasive evidence for culture-based group selection favoring humans, the global human expansion is perfectly compatible with all sorts of local selection taking place. How much of that has actually happened is a separate question requiring its own kind of evidence; and so far, that evidence has been very hard to come by.
Tuesday, September 22, 2009
My brain is no bigger than a caveman’s
Many people, including myself, consider Richard Dawkins to be well above average when it comes to intelligence.
The point here is not to bark about Dawkins potentially misspeaking. He may wish he had said things differently here, and
- Holly Dunsworth, guest blogger
Further
Race is a Four-Letter Word: The genesis of the concept by C. Loring Brace (2005)
Wednesday, September 9, 2009
What problem was Darwin trying to solve....and did he actually solve it?
At the meeting Ken attended in Brazil last week, he got involved in a discussion with the distinguished ecologist Doug Futuyma of SUNY/Stony Brook. Ken had asserted that despite the title of his book, Darwin had not, in fact, solved the 'species' problem. First, beyond individuals, species are the nearest we have to objective categories in nature. Usually, we define species as populations that cannot interbreed to produce fertile offspring. But even there our definitions are often vague or imprecise.
Variation, even genomewide variation, can exist without speciation (it does among individuals within every species!). Widespread adaptive variation can exist without leading to speciation (humans are variable worldwide for presumably adaptive reasons--e.g., skin color, yet we're one species). And mating barriers can arise without adaptation in the usual sense (e.g., hybrid sterility genes).
In that sense Darwin did not solve the species problem he named his book after. Doug Futuyma suggested, however, that Darwin's main objective was not speciation per se, but the process that leads to it. Indeed, Darwin wanted 'natural selection' in the title of his book, because that was the process he was invoking as an extension of artificial selection by breeders, to explain long-term biological change and the origin of adaptive structures.
But was 'species' an incidental interest or a primary one? We think the answer is that species was indeed a central objective, and yet it is not separable today, nor in Darwin's mind, from the ultimate result of the process which is speciation. This seems clear in the way Darwin's book was written, in the materials presented to the Linnaean Society, and also in letters he wrote around the time of the book and earlier, around 1844, when he drafted a private sketch of his ideas.
The process was an extension of agricultural and hobby breeding, that clearly led to variation. But Darwin was also determined to show that species--natural 'types'--were not the result of specific acts of creation. The nature of 'transmutation' as it was often called at the time, was hotly debated and of course then, as now, centrally involved religious explanations of the world. Darwin was convinced that 'varieties' and 'species' arose gradually through natural processes.
So, while he did not solve the species problem per se (which is not a 'neat' problem in any case), he provided brilliant insight as to the nature of the processes that, in various ways, are involved in natural divergence that leads to the origin of species.
Friday, June 12, 2009
Karl Marx Stares Down Herbert Spencer

When we were there, a few others were gathered round to reflect upon the historically influential man's tomb. A British woman was singing the Internationale while her friend took her photo. A young American, wearing an old hippie-style US Army jacket, walked up and complimented her on her singing. He asked her if she would take his photo as he stood by the monument. She said yes, if he'd also sing the Internationale. He protested that he could only sing the American version, but as his new friend aimed the camera

But there is a rather great irony in this tomb. Marx had originally been buried 200 M away from his current location. The original site, a rather plain one, was not on a major walkway through the cemetery, and as Marx grew in fame, it along with the surrounding burials were being trampled by tourists. So after a fund was made available for the large new monument, the Marx family remains were moved. But just opposite the new location was the site of one of the other most noteworthy former Londoners who are interred in Highgate: Herbert Spencer.
The irony is that Marx was a strong advocate for both the potential for human improvement, and the eventual evolution of egalitarian human society, while Spencer was the advocate of what became called 'social Darwinism' and the person who coined the term 'survival of the fittest', the exact opposite of Marx's view about human nature--and who justified social inequality as Nature's way that society would

The two may or may not have met--they were born at the same time (1818 and 1820) but Marx died in '83 while Spencer lived until 1903. Spencer was English and of the middle class while Marx was an immigrant living largely in poverty and so on, often relying on the help of the politically left but wealthy mercantile class. Did those who chose the new burial site for Marx know of this juxtaposition? Wikipedia says not, but we don't know if that's accurate or not.
The difference of views, between darwinian and marxist social evolution could hardly be more marked, even though both were historical materialists, saying that evolution of organisms, and society, respectively, were the result of historical processes.
We don't know what Spencer thought of Marx, or even if they referred to each other (that must be well-known to historians and should be easy to determine). But it's worth reflecting that both views were prominent and expressed at the same time, in the same place, and with the same facts at hand. It's not at all unusual for opposing or opposite views to be held by contemporaries who use the same facts, sometimes selectively, to advance their views. In this case, Marx and Spencer were both working in the 'Newtonian' era in which it was believed that there were Laws of Nature that, if understood, could be used to the betterment of human society. This grew out of the so-called Enlightenment period, and tensions were greatly increased by the French Revolution which, until it unraveled, threatened the world's existing non-egalitarian order. How could both authors, and others who allied with them or who expressed similar views, both claim to be empirical and scientific and yet disagree so profoundly--and does this have any lessons for us today?
The answer to the latter question is that we'll never know until tomorrow, when someone can look back in retrospect and see how competing ideas worked out. But it is at least almost always true that there are such ideas. Even when a theory is widely or universally accepted, such as evolution, there are always debates about aspects of the theory on the edge of current understanding.
Darwin rested his case on short-term observations of current adaptations, comparative biology, artificial breeding experience, biogeography and geology, and extrapolation of these things into the deep past. He provided convincing evidence for the fact of common historical origins of life forms, and natural selection was a mechanism that would work in principle even if its long-term effects could not be directly observed. For Darwin. evolution had no direction, value, or ending point, but was a continuing process (except in industrial societies, which he thought in many ways had finally suspended the role of natural selection).
Marx also used comparative methods (with Engels, for example, using anthropological observations on world cultures, especially the 'primitive' pre-industrial ones that colonialists had observed around the world), and detailed analysis of the current economic system (capitalism). He predicted that social evolution would resolve class conflicts, and his views were taken to mean that the desired endpoint wasn't far way. For those dedicated to the theory, like Lenin, the endpoint was just a revolution away! Society would then, in a sense, suspend the inherent conflicts between ideas and their antitheses. For Marx, social evolution did have a direction, one that was inevitable because it was due to a natural Law, and it also had an end point.
Whether or not the juxtaposition of these great men's tombs was inadvertent, it certainly set up interesting contrasts that the cemetery presented to us on a drizzly walk.
Wednesday, June 3, 2009
Singing along
This is interesting, because there is so much stereotyping in popular culture, guidebooks, and the like, that describes what 'the' so-and-so bird does. But over time, for all sorts of animals, domestic and wild, local speech dialects have been detected, so the story here is not a great surprise. The idea here is that in each city, birds become more distinct over time, so that they no longer recognize each other's songs.
The discussion then took a rather predictable evolutionary turn. If these birds continued to have locally differing dialects, then birds from different areas could no longer communicate to mate, and this would lead to the evolution of new species. Partly, this is simply a matter of our own--the scientists'--definition of what a species is. There, there's not really a difference (that one can test) between 'don't mate' and 'can't mate', and in either case we declare the two groups to be different species.
This is classic, but rather superficial Darwinism, one of the issues we write and think a lot about. There is nothing wrong with the logic itself. Long-term isolation is likely eventually to lead to the accumulation of so much genetic difference that members of each area could no longer mate successfully.
But how long does this take? Probably hundreds, or thousands of generations (or more). Think about that in this context. How stable are urban areas in a place like Britain, relative to such long times? For birds, that would mean centuries or millennia (or more). Given the rapid change of urban landscapes, transportation, and environmental changes, the odds that simple local dialects, which have been observed to develop in a short period of time, would persist or remain sufficiently isolated for such lengths of time seem remote, even if certainly not impossible in principle.
Species can remain mating-compatible even after hundreds of thousands or even millions of years of separation. Humans (who have dialects if any species do!) inhabit the entire terrestrial globe, and at the end points (the tips of South America and Africa) have been isolated for around 100,000 years (5,000 generations at least), and are still fully mating-compatible.
Oversimplified evolutionary explanations are pat, often irrefutable because untestable, and the problem is that they cover over some of the more interesting questions about how things actually happen (one of the issues we raise in The Mermaid's Tale). Speciation may be due to the accumulation of large amounts of small genetic differences due to local adaptation (behavioral, such as by mating calls, or otherwise); that was certainly Darwin's idea of what happened. But this need not be so. Small genetic changes in chromosomal compatibility can also lead to mating isolation (some of these are called hybrid sterility mutations), without any of the usual kinds of adaptations due to natural selection. And what happens over eons of time is unlikely in most or at least many cases to be easily extrapolated from what is observed in just a couple of generations.
It's for this reason that we caution against such simplifications. They give a semblance of understanding according to a widely, if often uncritically, accepted theory. But they are a reflection of scientific impatience that can obscure the facts that may be important for a deeper understanding.