The word “epigenetics” once meant simply “development”—that is, the way the genome worked itself into an organism through the production and regulation of proteins and absorption of food and materials from the outside, and the turning of some genes on and others off in different tissues. Now, however, the term means roughly “forms of inheritance that rest on modification of the DNA sequence,” and by “DNA sequence” I mean the sequence of four bases (A, G, C, and T) that constitutes the DNA code.
We now realize, though, that some DNA bases can be modified, and in an inherited way, in a manner that can affect the development, behavior, or structure of an organism. Such modification often takes place via DNA methylation, in which some of those four bases acquire methyl groups, thereby changing how the DNA functions.
Such methylation, as you’ll see by reading the Wikipedia link above, is important in organismal development—something we’ve realized only in recent decades. For example, there is differential “imprinting” of DNA via differential methylation in male versus female parents, and this results in the DNA in the zygote doing different things depending on whether it came from mother or father (organisms have paired chromosomes, getting one from each parent). This has led to speculations about the evolution of differential imprinting resulting from different interests of mother and father in how and which zygotes develop.
Methylation is also important in silencing the X chromosomes of female mammals that have two X chromosomes. This silencing equalizes the gene dosage between XX females and XY males (Y chromosomes barely have any genes), so normal development usually means keeping the dose of X-linked genes (and hence the amount of proteins they make) the same in both sexes.
Anyway, that kind of epigenetics is itself based on the DNA code. That is, the A, C, T and G sequences, and the environment in they find themselves, are “programmed” by natural selection to add or remove methyl groups from other parts of the DNA. Such adaptive epigenetic programming must perforce rest on the sequence of DNA bases, because methylation of the DNA is not inherited in a stable way. In imprinting, for instance, those bases that are methylated differently between the sexes are “reset” in the offspring: the methylation vanishes and is re-constituted before reproduction by whatever sex the embryo happens to be. That reconstitution is programmed in the DNA code itself. Methylated bases in DNA don’t usually get passed on from one generation to the next. There are two important points to add.
First, as I said, if methylation is itself an adaptation produced by natural selection, it ultimately must rest on changes in the sequence of unmethylated A, C, T, and G bases in the DNA. Only unmethylated bases are stably inherited, and evolution demands stable inheritance. There must be something about the DNA sequence that controls its own methylation. (Note that some methylations can last for several generations, though that’s not common.) For a population to change over time and acquire adaptations (or features that evolve through nonadaptive processes like genetic drift), whatever types of replicators that are inherited must remain unchanged, with of course the exception of mutations in the DNA code. But if the DNA code changed unpredictably back and forth each generation, natural selection and evolution wouldn’t work.
Second, there are also epigenetic changes that are induced not by the DNA sequence but by the environment. Temperature, starvation, and other environmental factors can cause methylation of the DNA as well. The thing is, though, that such changes, because they’re rarely passed on to future generations, cannot serve as the basis of evolutionary change. Such changes constitute true Lamarckian inheritance, i.e., the inheritance of acquired characteristics.
And lots of studies show us that Lamarckian inheritance doesn’t operate. Changes that are induced by the environment, or the organism’s “striving,” can’t somehow get incorported into the DNA. An athlete, for example, doesn’t produce kids with bigger muscles. And after millennia of circumcision, Jewish boys are still obstinately born with foreskins, giving my readers plenty to argue about.
Further, genetic analysis of adaptations that have arisen in evolution (like differences between closely related species of stickleback fish), invariably shows that they rest in changes in the base sequence of DNA (if that kind of genetic resolution is possible). Those changes can be in either “coding” sequences (that moiety of DNA that makes proteins), or “regulatory” sequences (those bits of DNA that regulate the expression of coding genes). There is, frankly, not a scintilla of evidence that adaptations of organisms rests on epigenetic DNA changes produced solely by the environment.
My conclusion: if epigenetic changes are involved in an evolutionary adaptation, they must be coded for in the DNA rather than acquired from the environment alone.
Nevertheless, there is a vocal subset of biologists who see the “Lamarckian” form of epigenetics as of great importance in evolution: a neglected area that is truly non-neo-Darwinian. This claim rests solely on a few studies showing that epigenetic change in DNA induced by the environment can sometimes be passed on for several generations. But there’s no evidence that this has produced any adaptive features of organisms. The subset of biologists that trumpet “nongenetic” epigenetics as an important but neglected part of evolution—evidence that the modern theory of evolution is wrong or woefully incomplete—are latter-day Kuhnians who seek to forge a new paradigm, a paradigm that rests on shaky pillars.
After all, you don’t get famous in biology by showing once again that neo-Darwinism is right (even though it happens to be!). Epigenetic-mongers of the “Lamarckian” stripe (there’s also a sub-breed involving a process called “genetic assimilation,” which can occur but for which there’s little evidence in nature) are wannabee Heisenbergs. (The Wikipedia article on “genetic assimilation”, at the link above, is a very good explanation of the process, and must have been written by an expert. But note that it adds that “It has not been proven that genetic assimilation occurs in natural evolution, but it is difficult to rule it out from having at least a minor role, and research continues into the question.”)
I write about epigenetics at length because I think we need to understand the claim that discoveries in epigenetics show that modern evolutionary theory is either wrong or incomplete. This claim, which is wrong, often rests on a confusion between the adaptive methylation of DNA that is itself coded for by the DNA, and evolved by natural selection, and the nonadaptive methylation of DNA that occurs by effects of the environment. Adaptive, genetically based epigenesis is a relatively new finding—and an important one, but it’s a finding that fits comfortably within the existing evolutionary paradigm. Only “Lamarckian” epigenesis, in which environmental changes somehow become permanent and inherited adaptations, would pose a severe challenge to neo-Darwinism. And we have no examples of that.
Yet this very possibility is touted in a new Nature News piece by Sujata Gupta, “Epigenetics posited as important for evolutionary success.” The claim in this piece is that recent work on invasive species shows that epigenetic modification is not only helping species invade new habitats, but also in a “Lamarckian” manner:
“There are a lot of different ways for invasive species to do well in novel environments and I think epigenetics is one of those ways,” says Christina Richards, an evolutionary ecologist at the University of South Florida in Tampa.
Although biomedical researchers have been investigating the links between epigenetics and human health for some time, evolutionary biologists are just beginning to take up the subject. Richards, who helped to organize a special symposium on ecological epigenetics at a meeting of the Society for Integrative and Comparative Biology (SICB) in San Francisco this month, says that the field has the potential to revolutionize the study of evolutionary biology.
Well, a lot of far-fetched stuff has the theoretical potential to revolutionize the study of evolutionary biology, including the possibility that the DNA of any species is transcribed only when there’s a plant within 100 miles. What’s important is whether there are data to support that revolutionizing. And in this case, there don’t seem to be. Gupta cites two examples of things that supposedly portend a revolution, one of them suggesting a Lamarckian role in epigenetic evolution. Here’s the first data:
Even so, there are hints that epigenetic diversity could be helping invasive species to thrive. For instance, Andrea Liebl, a fifth-year doctoral candidate at the University of South Florida, studies house sparrows (Passer domesticus) in Kenya, which, as descendants from a single group, have very little genetic diversity. But when Liebl combed the genomes of the birds to look for parts that had methyl groups attached — a key epigenetic marker — she found a high level of variability across populations.
Now this is a meeting report, and apparently hasn’t been published, but what is presented here gives me no confidence that epigenetics plays any role in invasion, nor has anything to do with any feature of these sparrows. This seems to be—the description is unclear—simply a correlation of population differences with DNA methylation differences, not a demonstration that methylation caused the population differences or is somehow involved in “invasibility”. The methylation differences could be produced by the different environments of different populations, and have nothing to do with adaptation—or anything else.
Further, it’s erroneous to imply that only a few invading individuals make the descendant population immune to evolution because it lacks genetic variability. A single fertilized female, for example, carries fully half of the heritable genetic variation of the population from which she came. That fertilized female carries fewer forms of genes than does her population, but those variants that are present are there in high frequencies (this is because a single fertilized female has four genomes, so each variant gene has a frequency of at least 25% in the next generation.) Thus, showing that a group was founded by a few individuals does not mean that it couldn’t subsequently evolve, or that environmentally-acquired methylation must have been important.
Further, even if a group was genetically homogeneous—a group of clones—it could still invade if it’s simply a better competitor than the species already there. Competitive success isn’t always based on evolution after invasion, but simply—as in the cane toad in Australia and Hawaii—on features of the invader that evolved before it invaded, and on evolved features of the residents that make them susceptible to the invader. That’s all well known ecological dogma, and the accepted explanation for why species on isolated islands are often displaced by invaders. I suspect that if all cane toads were genetically identical, they’d still have been successful invaders in Hawaii and Australia. The local fauna simply isn’t used to them! And they’re poisonous!
Here’s the second bit of evidence that Gupta uses to make the case for an important revision of evolutionary theory:
Similarly, in the invasive plant Japanese knotweed (Fallopia japonica), Richards found that genetically identical plants — knotweed reproduces clonally — have different leaf shapes and grow to different heights depending on where they live. Like the sparrows, the knotweeds exhibited high epigenetic diversity. Cristina Ledón-Rettig, a molecular biologist at North Carolina State University in Raleigh, who also helped organize the symposium, says that mapping the level of epigenetic modification may reveal “whether a population is going to tank or survive”.
Here we have a clonal population showing different methylation patterns in different habitats. They also have different phenotypes in different habitats. There is no evidence cited by Gupta that the former causes the latter. Thus such a correlation shows very little.
We’ve long known that clonal plants can assume different growth patterns in different habitats. That may often be because of evolved and adaptive plasticity (if you’re a plant near a tree, start climbing it to get support and sunlight). Alternatively, the patterns may simply reflect nonadaptive developmental responses to the environment. There is no evidence from Gupta’s summary statement that a). the invading knotweed was genetically homogeneous (the study described could have been an experimental one using clones); b). the methylation had anything to do with the different phenotypes in different environments; or c). the epigenetic differences can be inherited from one generation to the next—a prerequisite for “non-Darwinian” epigenetic evolution. Note that the emphasis on clonality, and on genetic homogeneity in the sparrows, is supposed to suggest that the supposedly adaptive methylation patterns were not evolved via changes in the DNA sequence, but produced by the environment and somehow inherited. It’s as if the authors see a necessity for Lamarckian epigenesis because there’s not much variation in the organisms’ DNA sequences.
Gupta talked to me for an hour the other day, and I explained the problems with this idea as best I could, including the many experiments showing that adaptations are based on changes in DNA sequence. She ignored all that. The only caveat that appeared in her piece was this:
Some critics aren’t ready to accept the links between epigenetics and invasive species. Jerry Coyne, an evolutionary geneticist at the University of Chicago in Illinois, says their success can be explained by well-established evolutionary theories. Sometimes a species moves into an unoccupied niche, and sometimes a small amount of genetic diversity goes a long way. “It doesn’t have to have a lot of variation to evolve,” he says. “We have perfectly good other reasons, which are based on more solid premises, on why invasive species succeed.”
Well, there I am again as a cranky old defender of neo-Darwinism. I thought my counterarguments, most of which were omitted, were convincing, or at least worth mentioning, but do you think that Gupta is going to let go of an exciting “non-Darwinian” idea just because of a grumpy biologist like me? No way! She concludes her piece on a revolutionary and upbeat note: Darwinism revolutionized! Much of what we know is wrong!
But with the cost of gene sequencing dropping, symposium organizers predict that research into ecological epigenetics is poised to take off. There could be several powerful studies coming out that show “how gene expression changes if the environment changes”, says Aaron Schrey, a population geneticist at Armstrong Atlantic State University in Savannah, Georgia.
It’s as if I said nothing at all: that adding my critique was merely a journalistic ploy to give a formal nod to the “other side.” Well, maybe ecological epigenetics is poised to take off, but I doubt that, with the data presented, it will revolutionize the field. There are formidable theoretical and empirical problems with the idea that acquired epigenetic markers are important features in adaptation. But of course I’ll keep my mind open in case some are found.
As I said, evolved epigenetic changes based on evolution of the DNA sequence may well play important roles in evolution—roles that we don’t yet appreciate. But I would bet a lot of dosh that we won’t find Lamarckian epigenetics, or even genetic assimilation, playing large roles. The enthusiasm expressed by Gupta and the researchers seems largely unjustified.
I emphasize again that I didn’t go to this meeting, and I don’t think the relevant work has yet been published, so Gupta may not have properly represented the results. But she certainly misrepresented, or at least failed to explain, the underlying biology and theory. Either way, it’s a gross failure of scientific journalism.
Science journalists love new findings that promise to overthrow existing paradigms (we don’t see headlines saying “Still another case of natural selection described!”), but they often fail as real journalists in such breathless pieces. It’s often because they don’t understand the science, or have to leave out important details. Either way, Gupta’s article, if read by people who don’t know about epigenetics, does the field a disservice.
This wouldn’t bother me so much if it wasn’t another of those tiresome claims that modern evolutionary theory is drastically wrong or incomplete because of some recently-discovered phenomenon. I heard the same claims when evo-devo surfaced, and while that area has found some exciting stuff, like the conservatism of Hox genes, it hasn’t changed our underlying view of how evolution works. I predict that in the coming few years we’re also going to hear similar Kuhnian claims about epigenetics. And I predict that findings in that area will also fit comfortably within modern evolutionary theory.
Although I’m a skeptic, and seen as a diehard supporter of neo-Darwinism, I think that an objective observer would agree that that that current paradigm is working pretty well. I haven’t yet heard the guns and shouts of revolutionaries on the horizon.