It is tempting to call animal domestication humanity’s oldest and longest-running experiment, but professor of palaeobiology Marcelo R. Sánchez-Villagra would beg to differ. It is worth opening with a quote from The Process of Animal Domestication to set the tone: “domestication is actually pretty poor as experiments go; there are too many variables involved with little control, and no records of how things started” (p. 206). The excellent structure prevents the book from becoming an overwhelming infodump, making this a valuable synthesis of data across a large number of disciplines that will interest a wide range of researchers.

The Process of Animal Domestication, written by Marcelo R. Sánchez-Villagra, published by Princeton University Press in March 2022 (paperback, 296 pages)

Before delving in, let us consider the scope of this book. The Process of Animal Domestication focuses on genetics, evolution, development, and morphology. Such is the amount of research done on these topics that animal behaviour is barely touched on here. This would require a separate book and Sánchez-Villagra refers you to two texts published by CABI, to which I would add Grandin’s book on behavioural genetics. The bulk of the research covered here is on mammals (dogs feature prominently) and birds, with fish and insects getting two brief chapters at the end of the book.

Since many people own pets, and many more have been around pets or farm animals at some point, I am sure most of us think we understand domestication. How appropriate, then, the first chapter, that I would like to characterise as “everything you thought you knew about domestication is wrong”. Forget the notion of centres of domestication, or of it being a historic event: “Domestication is a process, a transition, without clear boundaries in place and time” (p. 25). Forego a human-centric view that sees domestication as an intentional and goal-oriented decision on our part. Consider instead the option we had no long-term vision, and that animals have agency too, some possibly choosing domestication, as Stephen Bonduriansky has argued. Forget the dichotomy between wild and domesticated, think rather of “a continuum […] of gradually intensifying relationships” (p. 1). The search for the “first” or “oldest” example is thus misguided; there are many other, more relevant questions to ask in zooarchaeology. And comparing current wild and domestic populations is fraught with difficulties: “no living population is any group’s ancestral population” (p. 14). Wild populations of now-domesticated forms are often extinct. In short, this chapter read like a sobering reality check and was the highlight of this book for me.

“Since many people own pets, most of us probably think we understand domestication. Appropriately, the first chapter could be characterised as “everything you thought you knew about domestication is wrong””

Chapters 3 to 7 form the core and cover genetics, evolution, development, and morphology. There is so much material here that I can only give you a subjective highlights reel. What is notable is that the author discusses both how domestic animals shed light on biology, and how biology sheds light on domestic animals. In other words, he discusses both studies that use domestic animals as model organisms and studies on the biology of domestication.

So, Thomas Hunt Morgan and Sewall Wright studied domestic animals to make pioneering contributions to genetics, while studying genetics has revealed how traits of domestic animals come about, e.g. the mutations underlying different head crests in pigeons. An interesting question is whether the same genes are involved in domestic phenotypes across species. The answer so far is no. Given different phylogenetic histories, different genes are responsible for producing similar phenotypes. In studies of evolutionary developmental biology or evo-devo^[1], domestic animals are model organisms in e.g. comparative embryology^[2], while evo-devo studies have revealed e.g. developmental biases during digit formation. In pigs, gene downregulation during early limb patterning means some digits do not form, while in horses they do, but increased cell death then sculpts the tissue around the remaining toes.

The chapter on ontogeny (the development from egg to adult) focuses on what studies using domestic animals have taught us about the developmental mechanisms resulting in different phenotypes. The next chapter on life history and growth focuses mostly on how domestication affects ontogeny, e.g. growth, fecundity, seasonality of reproduction, litter size, gestation length, sexual maturity, tooth eruption, and lifespan. The chapter on morphological diversification similarly shows how domestic animals have been favourite study subjects to explore the concept of morphospace (the “universe of potential phenotypes” [p. 172]) and how domestication has resulted in variation in e.g. coat colour, body size and proportion, brain size and anatomy, and size and shape of skulls and teeth.

“The core of this book covers genetics, evolution, development, and morphology and discusses both how domestic animals shed light on biology, and how biology sheds light on domestic animals”

These core chapters are followed by one rather interesting chapter on some odds and ends. Here, Sánchez-Villagra argues feralization is not just domestication in reverse. Feral animals never fully return to a wild state, and environments have usually changed in the meantime, frequently because of disturbance by humans. He discusses domestication experiments on chickens, rats, the famous long-term study on silver foxes, and the existence or not of the domestication syndrome. This is the idea that selection for tameness results in a suite of co-occurring phenotypic changes, a “package deal” that includes floppy ears, reduced aggression, and smaller brains. Sánchez-Villagra is more circumspect: though there are some generic changes across mammals, there are few universal domestic features: “domestication produces, as it happens in evolution, wonderful variation and a lack of universals” (p. viii). Finally, this chapter asks whether domestication accelerates rates of evolution. The studies discussed here had mixed outcomes and it seems that “human intervention per se does not necessarily accelerate evolutionary rates of organisms” (p. 217).

A synthesis of this calibre is obviously going to be a mile wide and an inch deep, but that is the whole point. The Process of Animal Domestication is a perfect entry point if you want to dig deeper into the biology of animal domestication, with 59 pages containing some 1500 literature references. What prevents this book from becoming an overwhelming infodump is its excellent structure. Each chapter is divided into many short, headed sections of 2–3 pages, with boxes used for asides.

“Domestication has depended on more than just animal traits; there is also a human cultural component to it. Not all people in history pursued it. “

A final point I appreciated is how outspoken Sánchez-Villagra is on topics of broader relevance. Domestication has depended on more than just animal traits; there is also a human cultural component to it. Not all people in history pursued it. Why? Because of “the different worldview or logic guiding the relations […] with other animals“. Understanding this cultural component will hopefully make us “realize the singular as opposed to universal nature of the Western world view” (p. 32). Our Western paradigm of prosperity through perpetual economic growth has stimulated the production of animal protein at the lowest cost, disregarding environmental and animal welfare issues. Selective breeding for (economically) optimal traits can cause suffering and pain. Changing this, the author argues, will require changes in consumer behaviour and economic imperatives, even embracing “the idea that limitations on industrial and population growth can make sustainable and healthy human life and environmental protection possible” (p. 167).

The Process of Animal Domestication is a fascinating book that comes highly recommended. Its synthesis of a large body of research makes it incredibly valuable to evolutionary and developmental biologists, geneticists, anthropologists, and (zoo)archaeologists. However, the writing is accessible enough that (under)graduate students wanting to read up on animal domestication can safely turn to this book as well.

1. ↑ A quick definition of evo-devo is useful, if only because Sánchez-Villagra gives such a clear one: if developmental biology studies “how a cell becomes a completely formed organism“, then evo-devo studies “how that process has changed over the course of evolution” (p. 91).

2. ↑ Domestic animals are often used out of practical considerations such as cost or ease of breeding in the laboratory. This unfortunately means we lack information on other workhorses in evolutionary biology such as cichlid fish or Anolis lizards.

Disclosure: The publisher provided a review copy of this book. The opinion expressed here is my own, however.

The Process of Animal Domestication

Other recommended books mentioned in this review:

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Every student of evolution will be familiar with the peppered moth, Biston betularia. It is right up there with the Galápagos finches as an example of evolution happening right under our noses. The story of the rapid spread of dark moths in response to the soot deposition that accompanied the Industrial Revolution, and the reversal of this pattern when air pollution abated, is iconic. Yet, as Emeritus Professor of biology Bruce S. Grant shows, there are a lot more subtleties to it than my one-liner suggests. Observing Evolution details research by himself and many others, and along the way addresses criticism—legitimate and otherwise—levelled at some of the earlier research. Eminently readable, this is a personal story of the rise, fall, and ultimate redemption of one of the most famous textbook examples of evolution in action.

Observing Evolution: Peppered Moths and the Discovery of Parallel Melanism, written by Bruce S. Grant, published by Johns Hopkins University Press in October 2021 (hardback, 306 pages)

Melanins are a group of pigments found in cells of many vertebrates and invertebrates, some of them resulting in brown or black colouration. The appearance of dark insect morphs in response to pollution by heavy industry has been dubbed industrial melanism and occurs in many species. Grant opens his book by introducing two major players in this story: J.W. Tutt, who in 1896 first explained industrial melanism in peppered moths as resulting from visual predation by birds, and Bernard Kettlewell, who became the most important worker on this from the 1950s onwards to his death in 1979. As Grant clarifies, “while [Kettlewell] did not establish the concept of industrial melanism, he certainly resurrected it” (p. 10). Grant turned his attention to this species in 1983, at that point already head-long into an academic career on genetics and evolution using both fruit flies and wasps as model systems.

The author has divided his narrative over 49 short chapters, rarely more than ten pages long, which benefits the readability tremendously. Observing Evolution is informal in tone, full of friendly wit aimed at co-workers, and richly laced with anecdotes and personal stories. Grant for instance describes his experiences as an American working in 1984 England, joining a Liverpudlian bagpipe band. The description of his 1988 research trip to Japan sprawls over 70 pages and feels somewhat like a diversion that could have been shortened, especially as it boils down to “I was looking for moths in all the wrong places at all the wrong times”. Overall, though, his personal reflections on the hard work in the laboratory and the field, normally hidden behind the data, were very recognisable and relatable. They brought back happy memories of my research on butterflies in Paul Brakefield’s group and my later fieldwork at Tvärminne Zoological Station in Finland.

“Most spectacular is Grant’s work with Denis Owen that showed the rise and fall of melanism on both sides of the Atlantic in lockstep with air quality […]”

For biologists, Grant’s accessible explanations are a superb example of science communication. Let me highlight three of the many fascinating findings discussed here. Kettlewell published results showing that light and dark morphs rest on backgrounds matching their colouration, something that neither Grant nor others have been able to replicate. Individual moths seemed to have a preference, for sure, but it was not related to their colour. Grant also examined the genetic basis behind melanism in both British and Canadian populations. Kettlewell argued for the co-selection of certain genetic modifiers promoting the expression of melanism, and, by crossing individuals from different populations where melanism was or was not present, claimed melanism broke down in the hybrids. Grant and others have attempted similar experiments, criticising his work, though these all had their own shortcomings. Most spectacular is Grant’s work with Denis Owen that showed the rise and fall of melanism on both sides of the Atlantic in lockstep with air quality as measured by sulfur dioxide concentrations (though Grant hastens to add this link is correlative, not causative). Throughout, he delivers valuable commentary on how science proceeds and is never shy to admit his own mistakes.

You will notice that the name of Kettlewell frequently comes up in the context of research that could not be replicated and this lies at the heart of the controversy around the peppered moth. This is where Observing Evolution in my opinion unfortunately falls short of realising its full potential as the definitive story on the peppered moth, even if the ingredients are all there.

First, Judith Hooper accused Kettlewell of fraud in her 2002 book Of Moths and Men, with other researchers supposedly conspiring to cover this up. Now, there is legitimate criticism to be had of Kettlewell’s research, and Grant does not hold back in doing so. For example, he points out how Kettlewell never actually confirmed his idea that moths actively select a matching background to rest on: “it was pure speculation on his part, which was promoted—without supporting evidence—by his globally influential sponsor, E.B. Ford, and consequently assimilated into the lore and literature by uncritical enthusiasts” (p. 83). Grant has worked closely with people who knew Kettlewell personally and acknowledges that all of them “regarded him as a forceful personality, full of himself and his opinions” (p. 158). But he is sure Kettlewell was not a fraud: “he might arrive at wrong conclusions through stubbornness, but not by dishonesty” (p. 159). Yet, beyond briefly mentioning Hooper’s book in the beginning, Grant does not further touch on its publication, reception^[1], and impact, even though it needlessly undermined a very well-supported model system.

“You will notice that the name of Kettlewell frequently comes up in the context of research that could not be replicated and this lies at the heart of the controversy around the peppered moth.”

Second, the flap text prominently mentions how “proponents of Creationism fomented doubts about the legitimacy of early experiments“—but you will have to wait for the epilogue to read about this^[2]. Kettlewell also did experiments that showed that birds preyed on peppered moths and preferentially picked off individuals that stood out from their background, establishing them as the agent of natural selection driving industrial melanism. There is legitimate criticism to be had of these experiments, too, but the claim that birds do not eat moths is simply false and a prime example of the deliberate distortion of facts by creationists. Michael Majerus spend six years gathering the most comprehensive dataset on bird predation of peppered moths to date, though he passed away before he could publish it. Grant and three co-authors reanalyzed Majerus’s results and published them in 2012. This is probably the most eye-catching aspect of the story—everybody wants to know who did it, after all—and is also the easiest to explain to a general audience. I was thus disappointed it is given such short shrift; its brevity contrasts painfully with the 70 pages lavished on the Japanese travelogue. Given Grant’s close involvement, I am sure that he could have written similarly lively chapters providing an insider’s perspective on this important facet of the peppered moth story.

Despite not quite hitting full marks for me, I do thoroughly recommend this book, both to evolutionary biologists and entomologists, and to a general audience only vaguely familiar with the peppered moth. Grant’s writing is accessible, his explanations of complex science easily digestible, and he is full of genuinely amusing stories. If you ever doubted the validity of this iconic example of rapid evolution, Observing Evolution will set you straight.

1. ↑ Though the mainstream press loved the book, several critical reviews were published by, amongst others, Jerry A. Coyne, Kettlewell’s colleague Bryan Clarke, historian of biology David Rudge, and Grant himself, though he does not mention the first three here.

2. ↑ A good write-up of this particular chapter in history can also be found on 3 Quarks Daily.

Disclosure: The publisher provided a review copy of this book. The opinion expressed here is my own, however.

Observing Evolution

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The reintroduction of wolves to Yellowstone National Park is one of the best-known examples of wildlife conservation. To celebrate its 25th anniversary and summarise the many lessons learned, Yellowstone Wolf Project leaders Douglas W. Smith and Daniel R. Stahler, together with wildlife ecologist Daniel R. MacNulty, bring together research from over 70 colleagues in this large, edited collection. The combination of academic content, excellent photography, guest essays, and an online bonus documentary with interviews make this the go-to reference work for anyone wanting to go beyond the headlines on this reintroduction project.

Yellowstone Wolves: Science and Discovery in the World’s First National Park, edited by Douglas W. Smith, Daniel R. Stahler, and Daniel R. MacNulty, published by the University of Chicago Press in December 2020 (hardback, 339 pages)

The first thing that struck me about Yellowstone Wolves is how well-organised the book is. Six parts contain nineteen chapters, none going beyond twenty pages, and most include a clearly signposted conclusion. To give equal airtime to so many different studies and opinions is remarkable—the six years the editors spent on this book have borne fruit. The second thing is how readable the book is. To do justice to the subtleties and complexities of real-world ecosystems means digging into scientific research. Thus, it discusses methodologies and research results and provides graphs galore, but without bogging the reader down with excessive jargon or complex statistics. Only occasionally, when the discussion turned to species interactions or ecosystem ecology, did I feel that I was reading an academic paper.

So, what have we learned from 25 years of having wolves back in Yellowstone? This book covers a wide range of topics, more than I can hope to discuss here. Sensibly, it opens with a short history of the park, wolf extermination, and the reintroduction—a dramatic story complete with last-minute lawsuits that almost scuppered the whole operation.

“The first thing that struck me about Yellowstone Wolves is how well-organised the book is. […] To give equal airtime to so many different studies and opinions is remarkable”

After some basic wolf biology, the bulk of the book discusses long-term research. This covers pathogens and parasites, the genetic studies that inform wolf pedigrees and explain why you see both black and grey wolves in the park, and, notably, the different aspects of wolf packs. How they form, how long they last, how they defend territories and compete with one another, and how they change over time. This introduces some of the legendary wolves from Rick McIntyre‘s Alpha Wolves of Yellowstone series, or the very popular female O-Six, but also reveals the value of older wolves to their pack, or the surprisingly high mortality due to intraspecific (i.e. wolf-wolf) conflict when wolves are not constantly hunted by humans.

My impression, however, is that the seven chapters across parts 4 and 5 will be the most relevant to many readers. Why? First, because the chapters on community ecology (particularly wolf-prey interactions) touch both on the concerns of the hunters and ranchers who opposed wolf reintroduction, and on the challenges faced by generations of park managers. Second, because the topic of ecosystem ecology (the effects of wolves on ecosystems) catapulted the park to internet fame.

We are going to need some history here.

Woven throughout this book is the story of how predator removal at the beginning of the 20th century saw elk populations boom, leading to concerns of too many elk overgrazing and trampling the park and surrounding farmland. From 1920 to 1968 park management and hunters culled and relocated tens of thousands of elk, leading to concerns of too few elk and, from 1969 onwards, new policies that let nature take its course. Predictably, without predators, there was a new elk boom. This is the context in which wolf reintroduction was finally put on the table.

“Of course, wolves eat elk, but the devil is in the details […] these chapters seek to correct misconceptions [as] wolves are not the ungulate killing machines some imagine”

Elk numbers have since declined again, causing—you cannot please everyone—renewed consternation. This time, though, wolves get the blame. Of course, wolves eat elk, but the devil is in the details: “what is in doubt is the size and timing of [their] contribution” (p. 187). So, these chapters seek to correct misconceptions. Though wolves are formidable pack hunters capable of taking down large prey, failure is frequent and the risk of injury high. Lacking the powerful bite and retractable claws of big cats or the muscular forelimbs of bears, wolves are not the ungulate killing machines some imagine, instead preying on young, old, and sick elk, or scavenging e.g. bison carcasses. Furthermore, elk decline started months before the wolves returned to Yellowstone in 1995. In subsequent years other predators such as cougars, bears, and coyotes also flourished, while hunters continued to shoot substantial numbers of elk just outside the park. Guest contributors weigh in here with lessons learned from other long-term wolf studies in national parks such as the island of Isle Royale, Banff, and Denali.

The other controversial topic tackled is ecosystem effects: the idea that the impact of predators on prey affects the prey’s food base, rippling down the food web and influencing a whole ecosystem. Now, such trophic cascades do occur in nature, but in Yellowstone’s case, the narrative has been hijacked by that one viral video clip, How Wolves Change Rivers. It presents a straightforward story of wolves killing elk, which reduced elk overgrazing of trees, in turn stabilising river banks and leading to the return of numerous animals. Broken ecosystem? Just add Wolves! Obviously, I am being facetious. In her contribution to Effective Conservation Science, Emma Marris examined the clip, the accusations of oversimplification, and the power of a good story. Ben Goldfarb, in his book Eager, noted that it downplays the effect of beaver reintroductions.

“the topic of ecosystem ecology […] catapulted the park to internet fame […] trophic cascades do occur in nature, but in Yellowstone’s case, the narrative has been hijacked by that one viral video clip”

Given this background, I was very curious to see how this book dealt with the matter. In one word: circumspect. The clip is only hinted at: “Some videos on the topic have garnered online audiences of millions. Although scientists have discredited some of these works as romantically simplistic […]” (p. 257). One chapter has a research group present the argument in favour of trophic cascades. They admit that indirect effects on vegetation have not been observed everywhere in the park where wolves now roam and add that players such as beavers, bison, wildfire, and disease complicate the picture. The next chapter has another research group consider more complex networks of interactions between wolves, other predators such as bears and cougars, scavengers, and herbivore prey. They open by writing that: “the preceding chapter considered […] processes in a single oversimplified food chain (i.e. wolves-elk-aspen/willow) in Yellowstone. Here, we discuss a broader set of food web relations that are too often ignored in the push to explain the links between wolves, elk, and vegetation” (p. 223). And so the discussion rumbles on.

The book ends with very relevant chapters on park management that explain the rationale behind visitor rules, celebrate dedicated wolf watchers, and hash out a framework for the perenially controversial topic of transboundary wolf management. That last one, in layman’s terms, gives recommendations for wildlife agencies on dealing with predators that cross the borders we draw on maps and come into conflict with stakeholders such as ranchers or hunters living near national parks.

As noted elsewhere, Yellowstone’s wildlife is subject to continuous change. By reintroducing wolves, scientists have had the unique opportunity to study the complexities of living, breathing ecosystems. Written by the very people who spent decades in the field doing the research, Yellowstone Wolves is a formidable achievement that presents a wide range of scientific topics in a well-organised, readable, and beautifully illustrated book.

Disclosure: The publisher provided a review copy of this book. The opinion expressed here is my own, however.

Yellowstone Wolves

Other recommended books mentioned in this review:

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The question of the tempo of evolution cuts right to the heart of evolutionary theory. Emeritus professor in evolutionary biology (and a list of other disciplines) Philip D. Gingerich here takes an empirical stab at quantifying how fast evolution happens, something which has not been done very often. The resulting Rates of Evolution is a technical monograph for an academic audience that contains thought-provoking ideas.

Rates of Evolution: A Quantitative Synthesis, written by Philip D. Gingerich, published by Cambridge University Press in May 2019 (hardback, 427 pages)

The disagreement over how quickly evolution proceeds goes right back to the days of Darwin. His idea of slow and gradual evolution has its roots in geology, specifically in uniformitarianism. Darwin’s mentor, the famous geologist Charles Lyell, was a fierce proponent of this idea, which sees geological change as slow and gradual, to the exclusion of cataclysmic explanations. Lyell heavily influenced Darwin’s thinking . One alternative to this notion of gradualism is that of punctuated equilibrium: periods of stasis punctuated by short bursts of rapid evolution. Niles Eldredge and Stephen Jay Gould coined this term in 1972, though, interestingly, the concept was not new – Gingerich here briefly documents its long history.

Now, theorising is one thing, but actually quantifying rates of evolution is something else altogether. Gingerich breaks it down into three parts: an introduction to his methods, an analysis of three groups of datasets, and an extended discussion and interpretation.

The first six chapters are vital to understanding the rest of the book. Because how, indeed, can you compare long-term rates of evolution taken from the fossil record with short-term changes observed in field studies or in the lab? How do you even compare studies that focus on radically different traits? One study might look at evolutionary rates by measuring beak size of birds over many generations. The next might look at changes in the number of fin rays and dorsal spines in fossil fish.

“Niles Eldredge and Stephen Jay Gould coined the term [punctuated equilibrium] in 1972 […] though, interestingly, the concept was not new.”

Without going into the details, Gingerich explains that it is not the trait values that matter, but the rate with which these change. Specifically, the rate of change per generation. And a rate not expressed in millimetres or number of fin rays, but in standard deviations (assuming, of course, a normal distribution of trait values). Other fun concepts introduced are random walks and Brownian diffusion, and how you can decide whether observed patterns of change in time represent stabilizing, random, or directional selection.

Yes, dear reader, prepare yourself for plenty of formulas and diagrams. I will be frank that though I read this section carefully, some of this went a bit over my head. Especially once authors start juggling with equations (“Look, I can express this term like that, and then simplify these equations by dividing by this other term, and if we now log-transform…”) my response is usually one of “I am sorry, I am just going to have to trust you on this one, because you are speaking a language that I do not comprehend”. So, if there are holes to be picked in his logic here, I am afraid I will not be the one to do it. The point is that I do understand what he is working towards, and the resulting log-log plots of change against time are elegant.

“The picture that emerges is clear, argues Gingerich: evolution is fast on a generational time scale, but once you start calculating rates over many generations most of this averages out.”

The bulk of the book is three long chapters sprawling over some 150 pages that analyse rates of phenotypic change in experimental studies, field studies, and in the fossil record. Gingerich has taken a large number of datasets from older and newer studies (including some classics) and reanalysed the data to determine rates of change. The presentation here is somewhat repetitive, especially in explanations of conventions used in figures. The upshot is that each of these studies can be consulted individually, out of order. For those who want to inspect the raw data or have a stab at analysing other studies, the author has provided datasets and R scripts online.

This deep immersion pays off big time once you make it to the discussion in the last six chapters. The results are not what you might intuitively expect! Rates of change in experimental and field studies are high, while those in the fossil record are often several orders of magnitude lower. Gingerich argues this is a sampling artefact: this dichotomy between fast and slow rates exists because we sample dichotomously. Fossil studies provide snapshots in time that hide what happened in between on the resolution of single generations, while field and experimental studies rarely continue long enough. By combining the two you can start to fill in the void in between and discern that there is a continuum. Other chapters here deal with a critical rereading of Eldredge and Gould’s ideas, the question of whether relatedness between taxa can throw a spanner in the works of quantitative comparisons, and the applications of Gingerich’s findings to genetic modelling and the idea of adaptive radiations.

“[Evolution] is only goal-directed in the sense of chasing shifting peaks in a fitness landscape […] Is this a case of “the more things change, the more they stay the same”?”

The picture that emerges is clear, argues Gingerich: evolution is fast on a generational time scale, but once you start calculating rates over many generations most of this averages out. One reason he shortly touches on is that of limits. As mentioned in , “physics is life’s silent commander”. There are limits to e.g. an animal’s size, and evolution acts rapidly enough to thoroughly explore that envelope of possibilities over the course of deep time.

The other reason is one that I feel Gingerich does not really mention, so allow me some speculation of my own here. When you say “rates of evolution”, I say “compared to what?” Surely, the answer must be “compared to rates of environmental change”. We know that evolution as a process has no ultimate goal – it is only goal-directed in the sense of chasing shifting peaks in a fitness landscape. Environments constantly fluctuate and the resulting back-and-forthing as organisms adapt means rapid change in the short term, but, on average, not much movement in any direction on the long term. Is this a case of “the more things change, the more they stay the same”?

Rates of Evolution is a technical book squarely aimed at advanced students and researchers. Though the subject matter is complex in places, I found Gingerich’s writing and argumentation clear and his discussion and interpretation thought-provoking. For any evolutionary biologist or palaeontologist interested in the question of whether evolution is fast or not and why it matters (and, let’s be honest, that should be all of us) this book is obligatory reading. It is easy to see how this monograph will be a benchmark for years to come.

Disclosure: The publisher provided a review copy of this book. The opinion expressed here is my own, however.

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“Good Enough: The Tolerance for Mediocrity in Nature and Society“, written by Daniel S. Milo, published by Harvard University Press in June 2019 (hardback, 288 pages)

First order of business to take care of is the obvious danger of misappropriation. We scientists love critical academic discussion, but are also wary of how eagerly and uncritically creationists will misappropriate and misrepresent *any* discussion of evolution: “See? See!?! I told you so, evolution is a theory in crisis!!!”. So, for all the biologists who are frantically waving at Milo to say: “Pssst, hey, don’t feed the creationists!”, do not worry, Milo takes care of that right off the bat.

Good Enough is a book in three parts. Without disrespecting Darwin’s legacy, Milo critically examines the history of evolutionary theory to explain how today’s thinking originated, offers alternative explanations, and provides sharp observations on how evolutionary thinking pervades many aspects of human society.

Darwin’s original sin, says Milo, was his obsession with domestication. Given that he was writing in the 1850s for an audience unprepared for the concepts of evolution and natural selection it is only understandable that he turned to this familiar analogy. Animal and plant breeding was something everyone understood. Next to farm animals, dog breeding was particularly popular at this time (see The Invention of the Modern Dog: Breed and Blood in Victorian Britain). So, both On the Origin of Species and the subsequent The Variation of Animals and Plants under Domestication leaned heavily on domestication as a model of evolution. This led to the idea that natural selection is as relentless as breeders are, to which Milo outlines several objections, arguing that all that matters is that organisms are good enough to reproduce and survive.

“Milo outlines several objections to the idea that natural selection is as relentless as breeders are, all that matters is that organisms are good enough to reproduce and survive”

In the process he takes aim at several icons of evolution, including the giraffe’s long neck, the Galápagos finches (see 40 Years of Evolution: Darwin’s Finches on Daphne Major Island, a true but atypical case of natural selection that should not be extrapolated to all of nature), and human brain size and complexity, which leveled off long before the advent of agriculture and the concomitant population explosion.

The second part is where Milo offers his explanation. The history of the theory of evolution has led to a near-myopic focus on natural selection. In the process, scientists often ignore anomalies or try and find adaptive explanations – biologists, it seems, just cannot resist the temptation. In a conceptual move that parallels Brandon & McShea’s Zero-Force Evolutionary Law (see my recent review of Biology’s First Law: The Tendency for Diversity & Complexity to Increase in Evolutionary Systems), Milo argues for a change in perspective. Rather than assuming function to be the default, neutrality is. A lot of traits are simply not selected for and vary randomly.

There are two noteworthy examples Milo discusses. One, the messy organisation of genetic material: many genomes are unnecessarily large and riddled with non-coding sequences. Already back in 1968, Motoo Kimura argued that most genetic variability is neutral and of no evolutionary consequence (see The Neutral Theory of Molecular Evolution and Population Genetics, Molecular Evolution, and the Neutral Theory: Selected Papers, but see also Junk DNA: A Journey Through the Dark Matter of the Genome). Two, wide ranges in phenotypic trait values. Phenotypic polymorphisms (e.g. eye colour) can easily be brushed off as irrelevant when they are equally costly. But where traits differ, sometimes dramatically, in number or size there are energetic costs to their production (e.g. sperm count, or the bizarre headgear of treehoppers, pictured right). Such variation is often taken to be the substrate for evolution to proceed by leaps and bounds. Though clearly, says Milo, such traits are not under strict natural selection themselves, they are not being optimized. And they are far too numerous to ignore.

“For traits that need to be present without needing to be optimized, excess and wastefulness are the safer options; “better to be inefficient than to be dead”

Milo patiently considers and disarms the usual adaptive explanations and then proposes several mechanisms explaining this bias towards excess. Invoking “conserved core components and processes” (widely shared and conserved features of organisms such as DNA replication, see The Plausibility of Life: Resolving Darwin’s Dilemma) and Pareto’s 80/20 rule, he argues that a small number (the proverbial 20%) of optimized traits are under strong natural selection and contribute most (the proverbial 80%) to survival. This leaves many traits that need to be present without needing to be optimized. For those, excess and wastefulness are the safer options; “better to be inefficient than to be dead”.

So far, so fascinating. I have often questioned why “no selection” is not considered more often as an explanation, so I find this argument appealing. That, of course, does not mean it is not worthwhile to look for adaptive explanations (Milo says as much). My main criticism here is that Milo might be perceived to conflate two concepts. He argues that many traits are selectively neutral and evolve randomly, something that others have done before him (see e.g. Randomness in Evolution). But he couches this in language that still sounds adaptationist. Saying that the mediocre also survive, that merely being good enough is sufficient, still implies selective pressures, albeit weaker ones.

The third part of the book is equally fascinating. Here, Milo looks at human society and offers some of his most incisive and sharp-witted observations. What sets humans apart evolutionarily is that we can perceive of a future, and with that came a seed of restlessness, of wanting to improve our lot. Through cooperation, delegation, and specialization we have created societies where we care for each other’s needs. The drive for excess led to imaginative brains that became very successful in ensuring survival for all through technology, agriculture, and health care.

“”our bored neurons crave action”. So we construct problems for ourselves to solve […] for without it “we would succumb to boredom and despair””

We have achieved this now, but the drive persists, “our bored neurons crave action”. So we construct problems for ourselves to solve, endless diversions to lose ourselves in. Politics, sports, cuisine, art, fashion, science, work – all our culture, all our questing for athletic, emotional, and spiritual goals. They are all but exercises, endless loops, to give our lives meaning. Even though we have never had it so good, we continue to compete as if our lives depend on it, for without it “we would succumb to boredom and despair”. It may sound bleak, but for all those who ever wondered what the point of it all is… Now, says Milo, contrast that with the tales we tell ourselves. Our economies are steeped in Darwinian metaphors of relentless optimization and cut-throat competition, and we continue to educate our children to excel. We have taken Darwin’s good ideas and extrapolated them to many other fields where they just do not apply.

Good Enough is nicely produced with numerous carefully designed colour illustrations. On the biological details, Milo is clearly not alone (neutral selection has been mooted by others), but his application of it to human affairs is both insightful and unsettling. His ideas are thought-provoking, no doubt controversial to some, and I look forward to pushback from evolutionary biologists. But a fun and accessible read like this is suitable for a wide audience. What a fantastic book!

Disclosure: The publisher provided a review copy of this book. The opinion expressed here is my own, however. You can support this blog using below affiliate links, as an Amazon Associate I earn from qualifying purchases:

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Other recommended books mentioned in this review:

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“Extended Heredity: A New Understanding of Inheritance and Evolution“, written by Russell Bonduriansky and Troy Day, published by Princeton University Press in April 2018 (hardback, 288 pages)

Now, to be fair, rebellious as this notion might sound, it is not entirely new. Bonduriansky & Day join a growing chorus of biologists who feel that genetic inheritance is not the whole story. Notable pioneers in this field are Eva Jablonka and Marion Lamb who have been beating this drum for a few decades now (see their books Epigenetic Inheritance and Evolution: The Lamarckian Dimension and Evolution in Four Dimensions: Genetic, Epigenetic, Behavioural, and Symbolic Variation, published in a second edition in 2014). They defined four ways by which evolution might act, while Bonduriansky & Day rather cut the pie in two and talk of genetic and non-genetic inheritance that together form the concept they christen “extended heredity”.

They also rather not raise the spirit of Jean-Baptiste Lamarck. Yes, they say, he was an influential thinker, but his ideas of inheritance of acquired characters only vaguely resemble our current understanding, and the word Lamarckian can have several meanings. So, as opposed to some others (see my review of Lamarck’s Revenge: How Epigenetics Is Revolutionizing Our Understanding of Evolution’s Past and Present), they steer clear of terms such as neo-Lamarckism. But clearly, there was a time when this kind of thinking was in vogue. How did the gene triumph?

Though this book is not a history lesson in the evolution of biological thought in the vein of Sapp’s Genesis: The Evolution of Biology, the authors nevertheless spend a few chapters examining how we got here. Obviously, there was a series of pivotal scientific discoveries: Mendel’s famous crossing experiments with peas (see Mendel’s Legacy: The Origin of Classical Genetics and Gregor Mendel: Planting the Seeds of Genetics), and the elucidation of the structure of DNA (see Watson’s DNA: The Secret of Life). But as the authors show, ideology and politics played just as big a role. There was an enormous backlash against the idea of “soft” heredity in the wake of the horrors unleashed in the communist USSR by the scientifically illiterate agronomist Trofim Lysenko (see for example Lysenko’s Ghost: Epigenetics And Russia).

“Sperm cells have long been caricatured as DNA packages with outboard motors, but carry other factors including RNA”

All this crystallised into the school of thought that became known as the Modern Synthesis (see Evolution: The Modern Synthesis) that gave rise to for example Dawkins’s famous book The Selfish Gene. Non-genetic inheritance was completely off the table, and it is remarkable, with the benefit of hindsight, to read the adamant statements from influential researchers such as Theodosius Dobzhansky or Ernst Mayr that the environment has no way of influencing DNA.

So, what are these forms of non-genetic inheritance then? Obviously, there is epigenetics in the strict sense. The authors take the treatment of the technical details of DNA methylation, histone modification, and RNA inheritance a step up from Carey’s previously reviewed book The Epigenetics Revolution: How Modern Biology is Rewriting Our Understanding of Genetics, Disease and Inheritance. There is the idea that learning and culture are a form of heredity (often put forward to explain how humans set themselves apart, see these three books for more), and there is the influence of the microbiome, which also gets passed on through the generations (see these three books for more).

“[…] the genome cannot be the whole answer for the simple reason that since life’s emergence, transmission of genetic material has happened together with the required replication machinery”

But Bondurianksy & Day offer other fascinating observations. The external morphology of single-celled organisms seems to be copied as a template in an almost mechanical fashion, including “mutilations” that were inflicted experimentally. Egg cells contain molecules and organelles, and both their nature, quantity and location, and how they are divvied up during cell division, matters. Sperm cells have long been caricatured as DNA packages with outboard motors, but carry other factors including RNA. Some of this can even originate from extracellular vesicles that travelled through the body from elsewhere and can fuse with sperm cells before fertilisation. What I didn’t even know is that after fertilisation the first few cell divisions happen under what the authors call a parentally programmed autopilot before the embryo’s genome takes over. One particularly shrewd observation the authors make is that the genome cannot be the whole answer for the simple reason that since life’s emergence, transmission of genetic material has happened together with the required replication machinery: a membrane-enclosed cell with its highly structured cytoplasm and all the material that it contains.

The remainder of Extended Heredity discusses how these ideas can be incorporated into existing evolutionary theory and why it is important. They also dedicate a chapter to deal with oft-voiced critiques and another one to speculate how outstanding puzzles in evolutionary biology could be reconsidered through fresh eyes.

Much more research, both applied and theoretical, will be required before these notions will become part of mainstream biology. In that sense, biological theories are like big ships – changing course is a slow and time-consuming process. Extended Heredity puts itself in the vanguard of this effort and is therefore by definition not the final statement on this topic. No doubt some of the things suggested here will be refuted in years to come. But the book builds a convincing case that non-genetic inheritance both exists and matters. For what is an advanced topic, its treatment could have ended up obtuse and impenetrable to outsiders. Instead, Bonduriansky & Day have written a book of great clarity, and have done so with great care. Whether you are open to the idea of non-genetic inheritance or not, this thought-provoking book deserves a close reading.

Disclosure: The publisher provided a review copy of this book. The opinion expressed here is my own, however.

Extended Heredity paperback, hardback or ebook

Other recommended books mentioned in this review:

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Some recent popular science books on culture as heredity:

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Some recent popular science books on the microbiome:

“The Epigenetics Revolution: How Modern Biology is Rewriting Our Understanding of Genetics, Disease and Inheritance“, written by Nessa Carey, published in Europe by Icon Books in March 2012 (paperback, 339 pages)

Just to make sure everyone is on the same page, a quick definition: epigenetics is the study of changes in an organism caused by changes in gene expression rather than in the genetic code itself. So, up- or down-regulation of gene activity rather than mutation. Carey starts off with a history of the first researchers that asked the right kinds of questions that led to the discovery of this field. After all, if every cell in a human (or animal) body contains all the DNA, all the genetic instructions to make a complete version of itself, then why doesn’t it? How do cells actually become so specialised to be skin cells, liver cells, or muscle cells? Do they just jettison all the genes they don’t need anymore? Or do they retain them but switch them off?

This is where epigenetics comes in. Carey introduces the various molecular mechanisms, including DNA methylation: the addition of a methyl group, or –CH₃ if you remember your chemistry classes, to DNA; and histone modification: changes to the structural protein around which DNA coils to form a larger superstructure. Her clear explanations and the many drawings included immediately answered some burning questions I had after reading Lamarck’s Revenge. DNA methylation is supposed to be quite stable, but how is it passed on during cell division when all that is duplicated is the DNA? It turns out that once you look at the biochemical details, DNA replication is a tad more complicated than that. There is a class of proteins called DNA methyltransferases dedicated to recreating methylation markers on a strand of freshly synthesized DNA.

Carey also talks about monozygotic or identical twins. In his recent book, Plomin surveyed the long-term twin studies he has been involved in (see my review of Blueprint: How DNA Makes Us Who We Are). One of his (paraphrased) take-home messages was: “Look at how identical these twins are, and how powerful a tool this has been to show that genetics is a huge determinant of behaviour.” And this is true. Yet, despite being 100% genetically identical, such twins are not *completely* identical, and differences accrue as twins age. Epigenetics offers an answer, with differences in environments experienced – starting in the uterus – leading to different epigenetic profiles or epigenomes.

“if every cell in a […] body contains all the DNA, all the genetic instructions to make a complete version of itself, then why doesn’t it?”

In subsequent chapters, Carey walks the reader through the many wonderful findings that have emerged from this field. How life experiences, such as a famine, that caused epigenetic changes can resonate down the generations and affect children and grandchildren. How epigenetic markings are wiped almost, but not quite, completely so that a sperm or egg cell, which is very specialised, can again become a completely undifferentiated cell capable of forming all the cells making up the human body. How a cell knows which chromosome came from the father, and which from the mother (and why that matters). How it can offer a mechanism explaining why traumatic childhood events leave a lasting legacy, whether physical or mental. And how understanding epigenetics can offer us a new way to understand and possibly combat diseases such as cancer.

One topic is worth highlighting in particular, as it is the subject of her second book Junk DNA: A Journey Through the Dark Matter of the Genome published three years later. We know that humans have a comparable number of genes to, say, the small soil nematode Caenorhabditis elegans, a particularly popular model organism in biological research. But what sets us apart is the amount of DNA that we have that does not code for proteins: some 98% versus 75% for C. elegans. That’s a huge difference! For every base pair in human DNA that codes for a protein, we have 49 that do not code for a protein, whereas that little worm only has three. Initially, this genetic “dark matter” was called junk DNA, but a large portion of it is actually useful, no, vital even.

“the multi-layered networks of gene regulation are a bit like that game Mousetrap: cobbled together from repurposed, multifunctional parts, and ludicrously complex”

From my review of Gene Machine: The Race to Decipher the Secrets of the Ribosome you will remember the basics of the story. DNA is read and transcribed into a single-stranded form of nucleic acid called RNA. This is then transported out of the cell nucleus to the ribosome that resides in the cytoplasm (the area of a cell outside of its core). The ribosome then translates the RNA into proteins which do all the actual work in living cells. But only 2% of DNA in humans codes for this. It turns out that in the other 98% there is also a huge amount of activity and DNA is constantly being transcribed into RNA. But this RNA never leaves the cell nucleus. It isn’t even turned into proteins! This non-coding RNA (bit of a misnomer as Carey points out) is biologically active though and is another epigenetic marker. Long stretches of non-coding RNA can latch on to DNA and suppress or stimulate gene expression. Shorter stretches can bind to the messenger RNA that is ferried from the cell nucleus to ribosomes, which offers yet another avenue for up- or down-regulation of gene expression. This is fascinating stuff that was new to me and really makes me look forward to reading Junk DNA (which I already have on order).

Early on, Carey mentions that the multi-layered networks of gene regulation are a bit like that game Mousetrap (or Rube Goldberg machines for an older generation of readers): cobbled together from repurposed, multifunctional parts, and ludicrously complex. Carey follows a clear approach in each chapter of discussing the key studies that led to certain major insights. She goes into a fair level of detail, and I wouldn’t be surprised if your eyes glaze over a bit at the alphabet soup of gene names and the details the winding, Mousetrap-esque signalling cascades. But she is quick to focus on the big picture of these experiments and provides many helpful illustrations that offer a graphical summary of the main points.

Written with much love for the field, and laced with a sense of humour and many amusing but useful analogies, Carey shows herself to be a gifted writer that can make this field accessible for readers new to the topic, while providing a level of depth and detail to satisfy an audience of fellow biologists. I have not yet read Francis’s book Epigenetics: How Environment Shapes Our Genes, published around the same time, but The Epigenetics Revolution is a superb introduction to the topic that answered many of my basic questions. The fact that it remains a useful introduction in such a fast-moving field is a huge achievement.

The Epigenetics Revolution paperback, hardback, ebook or audio CD

Other recommended books mentioned in this review:

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“Lamarck’s Revenge: How Epigenetics Is Revolutionizing Our Understanding of Evolution’s Past and Present“, written by Peter Ward, published by Bloomsbury Publishing in October 2018 (hardback, 274 pages)

Lamarck’s Revenge starts with a useful intellectual history that drives home the point that the ideas of Lamarck and Darwin were very much a product of what was intellectually fashionable at the time, and what was still unknown. So, while Darwin was heavily influenced by Lyell’s idea of uniformitarianism (introduced in my review of Cataclysms: A New Geology for the Twenty-First Century) and Malthus’s ideas on overpopulation (see my review of his An Essay on the Principle of Population: The 1803 Edition), the discovery of genetics and DNA were still many decades away. But once these had been made, they eclipsed Lamarck’s idea of the inheritance of acquired characters. Until, some now argue, epigenetics came into the picture.

Epigenetics is the study of changes in an organism caused by changes in gene expression rather than in the genetic code itself. So, up- or down-regulation of gene activity rather than mutations. Chiefly, there are three mechanisms: methylation (the addition of methyl groups to DNA), modification of histones (the proteins that give DNA its larger macrostructure, coiling its double helices around spool-like proteins), and RNA interference (the silencing of gene activity by a small piece of RNA).

These epigenetic changes are apparently heritable, though I was left with many questions as to how. Some explanation is offered for methylation but it is unclear whether we don’t know about the rest, or whether Ward assumes this known on the part of the reader. If methylation is removed from DNA when egg and sperm cells are formed, what happens to epigenetic marks during regular cell division? How, as Ward asserts, are epigenetic modifications turned into permanent changes to DNA a number of generations down the line? And what is the link or the difference between the ability of epigenetics to produce variable phenotypes and the classic mechanism of phenotypic plasticity? He mentions Carey’s The Epigenetics Revolution: How Modern Biology is Rewriting Our Understanding of Genetics, Disease and Inheritance as a landmark book summarizing basic processes from a chemical and biological viewpoint, so I have ordered this next. And a quick skim of Duncan et al’s 2014 open-access review paper in the Journal of Experimental Zoology Part B: Molecular and Developmental Evolution already provides leads to answers.

“It is ironic that Ward, having just lamented that there is so much confused usage of the term epigenetics [invokes] lateral gene transfer. Err, that’s not epigenetics.”

Having introduced epigenetics, the rest of the book addresses a variety of topics, trying to argue the importance of epigenetic inheritance for each of these. It is ironic that Ward, having just lamented that there is so much confused usage of the term epigenetics, and having established that this process by definition leaves the DNA sequence unchanged, then goes and immediately muddles the waters. He examines the origin of life and the blossoming of life after mass extinctions through an epigenetic lens by invoking lateral gene transfer. Err, that’s not epigenetics.

Now, don’t get me wrong: this large-scale exchange of chunks of DNA by viruses and bacteria is very influential (see my review of The Tangled Tree: A Radical New History of Life, and yes, lateral and horizontal gene transfer are two names for the same process). It provides a good mechanism for Stephen Jay Gould’s idea of punctuated equilibrium, the idea that evolution consists of long periods of relative stasis, punctuated by short bursts of rapid change (see Punctuated Equilibrium). And it could very well have been a driver of the rapid diversification of life after mass extinctions such as the Cambrian Explosion (see The Cambrian Explosion: The Construction of Animal Biodiversity). Ward tries to defend his choice by saying that it is not the slow-and-steady process of random mutation that Darwin proposed, therefore it is Lamarckian, therefore epigenetic. That is presenting a strict, almost caricatured interpretation of Darwin’s ideas that few evolutionary biologists still adhere to nowadays (see for example Extended Heredity: A New Understanding of Inheritance and Evolution). More importantly, this is macro-mutation, plain and simple. It is a wholesale change to a DNA sequence, and therefore by definition not epigenetic.

Ward repeats this in his final chapter on the gene-editing technology CRISPR (see also my reviews of A Crack in Creation: The New Power to Control Evolution and Modern Prometheus: Editing the Human Genome with CRISPR-Cas9). He seems intent on scaring readers with bleak scenarios of human supersoldiers and parallels to the horrors of the atomic bomb that followed the discovery of nuclear fission. Meanwhile, he ignores that, for all of CRISPR’s power and utility, many human traits are complex and polygenic (influenced by numerous genes of small effect, see for example my review of Blueprint: How DNA Makes Us Who We Are), which makes them little accessible to CRISPR editing. And again, since CRISPR allows direct alteration of the genetic code it is by definition not epigenetic.

“his idea that epigenetics coexists with classic Darwinian selection […] is attractive”

Is this just semantics? I think not. In what is supposed to be a popular science book on epigenetics this will escape the attention of many readers and leave them with the wrong ideas. Ward also misses the truly interesting bits. He briefly mentions that we have recovered signs of methylation on ancient DNA (i.e. DNA recovered from archaeological remains). Now that is revolutionary! And his idea that epigenetics coexists with classic Darwinian selection – the former operating in times of upheaval when rapid adaptation is called for, the latter in times of relative peace when mutation proceeds steadily – is attractive. It could do much to solve the conundrum of “missing links” and the lack of transitional forms in the fossil record, a favourite argument of creationists. Maybe the fossil record isn’t so incomplete after all.

The remaining chapters invoke the idea that all sorts of stresses could have played, or are playing, a role in human evolution by inducing epigenetic changes through DNA methylation. Ward poses many interesting questions. What was the epigenetic impact of experiencing the stresses of war or pandemics, or the loss of loved ones to these? What of the epigenetic impact of chemical signals released by the gut’s microbiome during periods of famine? And what of our current exposure to toxic chemicals, many of which are evolutionary completely novel? Ward here mixes research with assertion in short sections that often feel like they could have been further developed, and seems keen to quickly conclude that epigenetics must be important. His citing of both primary research and secondary sources such as blogs, TED talks or news reports seems questionable and sometimes unnecessary. Why cite news items instead of the paper being reported on?

Those familiar with epigenetics will appreciate some of the flashes of insight in this book, but the limited explanation of how epigenetic inheritance actually works, the confusion caused by prominently including non-epigenetic mechanisms, and the firm assertions when so much research is still in its infancy make it hard to recommend this book to novice readers. As my first entry into this topic I found it to be a hit-and-miss affair and will search out Carey’s book next.

Disclosure: The publisher provided a review copy of this book. The opinion expressed here is my own, however.

Lamarck’s Revenge hardback or ebook

Other recommended books mentioned in this review:

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