At some point, such heritable regulatory changes will be created in a test animal in the laboratory, generating a trait intentionally drawing on various conserved processes. At that point, doubters [of organic evolution] would have to admit that if humans can generate phenotypic variation in the laboratory in a manner consistent with known evolutionary changes, perhaps it is plausible that facilitated variation has generated change in nature.

Gerhart, C. and Kirschner Marc W. The Plausibility of Life: Resolving Darwin’s Dilemma. New Haven: Yale University Press; 2005; p. 237, emphasis added.

Our basic claim is that biological thinking about heredity and evolution is undergoing a revolutionary change. What is emerging is a new synthesis, which challenges the gene-centered version of neo-Darwinism that has dominated biological tought for the last fifty years. The conceptual changes that are taking place are based on knowledge from almost all branches of biology, but our focus in this book will be on heredity. We will be arguing that

• there is more to heredity than genes;
• some hereditary variations are nonrandom in origin;
• some acquired information is inherited;
• evolutionary change can result from instruction as well as selection.

These statements may sound heretical to anyone who has been taught the usual version of Darwin’s theory of evolution, which is that adaptation occurs through natural selection of chance genetic variations. Nevertheless, they are firmly grounded on new data as well as on new ideas. (Jablonka, Eva. Evolution in Four Dimensions (Life and Mind: Philosophical Issues in Biology and Psychology) (p. 1). The MIT Press. Kindle Edition.)

Putting Humpty Dumpty Together Again 

Imagine an entangled bank, clothed with many plants of many kinds, with birds singing in the bushes, with various insects flitting about, with worms crawling through the damp earth, and a square-jawed nineteenth-century naturalist contemplating the scene. What would a modern-day evolutionary biologist have to say about this image—about the plants, the insects, the worms, the singing birds, and the nineteenth-century naturalist deep in thought? What would she say about the evolutionary processes that shaped the scene? (Jablonka 2014, 235)

Undoubtedly the first thing she would say is that the tangled bank image is very familiar, because we borrowed it from the closing paragraph of On the Origin of Species. The nineteenth-century naturalist who is contemplating the scene is obviously Charles Darwin. The famous last paragraph is constantly being quoted, the biologist would tell us, because in it Darwin summarized his theory of evolution. He suggested that over vast spans of time natural selection of heritable variations had produced all the elaborate and interdependent forms in the entangled bank. (Jablonka 2014, 235)

Our modern-day evolutionary biologist would almost certainly go on to say that she thinks Darwin’s theory is basically correct. However, she would also point out that Darwin’s seemingly simple suggestion hides enormous complications because there are several types of heritable variation, they are transmitted in different ways, and selection operates simultaneously on different traits and at different levels of biological organization. Moreover, the conditions that bring about selection—those aspects of the world that make a difference to the reproductive success of a plant or animal—are neither constant nor passive. In the entangled bank, the plants, the singing birds, the bushes, the flitting insects, the worms, the damp earth, and the naturalist observing and experimenting with them form a complex web of ever-changing interactions. The plants and the insects are part of each other’s environment, and both are parts of the birds’ environment and vice versa. The worms help to determine the conditions of life for the plants and birds, and the plants and birds influence the worms’ conditions. Everything interacts. The difficulty for our evolutionary biologist is unraveling how changes occur in the patterns of interactions within the community and within each species. (Jablonka 2014, 235-236)

Take something seemingly simple, like where a plant-eating insect chooses to lay its eggs. Often it will show a strong preference for one particular type of plant. Is this preference determined by its genes, or by its own experiences, or by the experiences of its mother? The answer is that sometimes the insect’s genetic endowment is sufficient to explain the preference, but often behavioral imprinting is involved. Darwin discussed this in the case of cabbage butterflies. If a female butterfly lays her eggs on cabbage, and cabbage is the food of the hatching caterpillars, then when they metamorphose into butterflies her offspring will choose to lay their eggs on cabbage rather than on a related plant. In this way the preference for cabbage is transmitted to descendants by nongenetic means. There are therefore at least two ways of inheriting a preference—genetic and behavioral. An evolutionary biologist would naturally ask whether and how these two are related. Can the experience-dependent preference evolve to become an inbuilt response that no longer depends on experience? Conversely, can an inbuilt preference evolve to become more flexible, so that food preferences are determined by local conditions? (Jablonka 2014, 236)

Similar questions can be asked about the plants on the entangled bank. The most obvious effects of the insects’ behavior are on the survival and reproduction of the plants. Being the preferred food of an insect species may be an advantage to some of them, because it means that their flowers are more readily and efficiently pollinated. If so, those plants that the insects find tasty may become more abundant. Any variation, be it genetic or epigenetic, that makes a plant even more attractive to the insects, or that makes its imprinting effects more effective or reliable, will be selected. Conversely, if the insects’ food preference damages the plants, variations that make it less attractive or more resistant to insect attack will be favored. For example, plants often produce toxic compounds that are protective because insects cannot tolerate them. The ability to produce such toxins will be selected. In some species toxin production is an induced response, brought about by insect attack, but in others it is a permanent part of the plant’s makeup. Once again, an evolutionary biologist would want to know whether there is any significance in this. When there is an induced response, presumably involving changes in gene activities, does this affect the likelihood or nature of changes in the plant’s DNA sequence? Do epigenetic variations bias the rate or the direction of genetic changes? Are the genetic and epigenetic responses related in any way? (Jablonka 2014, 236-237)

How would an evolutionary biologist think about the worms that feature in Darwin’s entangled bank? Earthworms must have been one of Darwin’s favorite animals, because he devoted the whole of his last book to them. Visitors to Down House, his home for many years, can still see vestiges of his worm experiments in the garden there. Earthworms are a good example of something that is true for many animals and plants: they help to construct their own environment. Darwin realized that as earthworms burrow through the soil, mixing it, passing it through their guts, and leaving casts on the surface, they change the soil’s properties. The environment constructed by the earthworms’ activities is the one in which they and their descendants will grow, develop, and be selected. An evolutionary biologist therefore wants to know how the species’ ability to change its environment and pass on the newly constructed environment to its descendants influences its evolution. How important is such niche construction? (Jablonka, Eva. Evolution in Four Dimensions (Jablonka 2014, 237)

Very wisely, Darwin avoided mentioning human beings when he summarized his “laws” of evolution in the final paragraph of The Origin. He realized that suggesting that humans had evolved from apelike ancestors would land him in very deep trouble, and he was going to be in enough trouble as it was. Although he knew full well that his own species is also a product of natural selection, he left discussing it to a later book. He did devote a lot of space in The Origin to humans, however. In particular, he described how, through selection, they had changed plants and animals during domestication. Darwin would have been well aware that the naturalist observing the entangled bank was potentially the most powerful evolutionary influence acting on it. Humans could divert a stream, so that the bank dries out and many of the organisms inhabiting it die; or they might introduce new plants or animals, thereby altering the whole web of interactions in the bank. Without doubt, humans are the major selective agents on our planet, and have carried out the most dramatic reconstruction (usually destruction) of environments. Today, in addition to changing plants and animals by artificial selection, humans can alter the genetic, epigenetic, and behavioral state of organisms by direct genetic, physiological, and behavioral manipulations. We are only at the beginning of this man-made evolutionary revolution, which will affect our own species as well as others. Our ability to manipulate evolution in this way is derived from the human capacity to think and communicate in symbols. Through the symbolic system, we have the power of planning and foresight. As the evolutionary biologist knows, this has had and will continue to have effects on all biological evolution. (Jablonka 2014, 237-240)

As she looks at the entangled bank, a modern-day evolutionary biologist would know that explaining how natural selection has produced the complex, interacting living forms she sees is a formidable task. She could recruit the help of specialists, who might enable her to explain bits of the scene: the geneticists could look at the genetic variants in the plant and animal populations, and see how they influence survival and reproductive success; the physiologists, biochemists, and developmental biologists could look at the adaptive capacity of individuals; the ethologists and psychologists could tell her about the animals’ behavior, and how it is shaped by and shapes conditions; the sociologists and historians would tell her what role humans have had in developing the bank; the ecologists would investigate the interactions between the plants, animals, and their physical environment. Each of the specialists would probably be convinced that their own findings and interpretations are the most significant for understanding the whole picture, and that the other parts of the study are of marginal significance. This is what usually happens when people look at the isolated parts of a system. A lot of knowledge can be gained from this approach, but eventually it is necessary to reassemble the bits—to put Humpty Dumpty together again. How do the genetic, epigenetic, behavioral, and cultural dimensions of heredity and evolution fit together? What influence have they had on each other? (Jablonka 2014, 240)

[Now, Jablonka, begins the interesting part of the story, putting Humpty Dumpty back together again, the unfinished synthesis, still in progress, the re-synthesis of evolutionary theory which includes development, epigenetics, and ongoing revelations that few can even keep pace with.]