Fossils are our prime source of information about life in the past. As I delve deeper into palaeontology and earth sciences, the process of fossilisation increasingly fascinates me. How does dead biological tissue fossilise? What information is lost, what is added, and what is distorted in the process? And, ultimately, how true or filtered a picture of past life does the fossil record provide? The edited book Fossilization brings together scientists from a range of disciplines working on cutting-edge topics. The result is a well-written if somewhat eclectic collection of chapters that addressed some of my queries and also answered questions I did not even know I had.
Fossilization: Understanding the Material Nature of Ancient Plants and Animals, edited by Carole T. Gee, Victoria E. McCoy, and P. Martin Sander, published by Johns Hopkins University Press in May 2021 (hardback, 290 pages)
This book needs some context. Despite the single-word title, Fossilization is not a textbook that will introduce you to taphonomy, the process of fossilisation. (I might be overlooking something, but my impression is that there is no good recent textbook and I would need to refer readers to older books such as Life History of a Fossil or Taphonomy.) Nor does this edited collection strive to be an as-broad and as-inclusive overview as possible. No, essentially Fossilization is a showcase of the research being done at DFG Research Unit FOR 2685 at the University of Bonn in Germany. Funded by the Deutsche Forschungsgemeinschaft (the German Research Foundation), this is a consortium of nine research projects under a program titled “The Limits of the Fossil Record: Analytical and Experimental Approaches to Fossilization”.
What these projects are, however, is interdisciplinary. As two of the editors clarify in their introduction, the focus of this research unit is the small: evidence at the histological, cytological, and molecular level. This is where palaeontology starts touching on neighbouring disciplines and progress requires the know-how and input from e.g. microbiologists, organic chemists, mineralogists, geochemists, pharmacists, and petrologists. Furthermore, “fossilisation” is much more than just bones turning to stone. It is an umbrella term for several geochemical processes that vary with both tissue chemistry and the environment, encompassing processes such as silicification (of wood), pyritization (of arthropods), permineralization (of bones), and others.
“[…] there are two preservation pathways [in amber] with radically different outcomes: either decay with loss of all soft tissue so that only an arthropod-shaped void remains or, spectacularly, complete preservation.”
Next to an introductory and a concluding chapter, Fossilization contains eight chapters that break down into four chapters on palaeobotany, two on fossil animals, one on amber preservation, and one on Raman spectroscopy, all of which clock in at between 20–40 pages. Throughout, attention is paid to the many modern variations of microscopy, spectroscopy, and spectrometry that can be brought to bear on fossil material. What stood out is how readable these chapters are. I am not much of an expert in any of the above disciplines, yet found that I could follow along with most chapters just fine. And some of this material is outright fascinating.
Thus, there is a chapter on soft-tissue preservation at the microscopic level, think cells or blood vessels, in dinosaur and other tetrapod bones. Is this original material or biofilm produced by bone-degrading bacteria? I remember this discussion making news headlines a few years ago. A review of studies so far concludes that the evidence points towards the former. Another chapter looks at the fossilisation of reproduction-related tissues and structures in avian dinosaurs and birds, and what analytical methods you could use to detect them. So far we have found evidence of e.g. ovarian follicles, shell membranes, eggshell pigmentation, and medullary bone (this is incidentally the same study that Lomax referenced in Locked in Time).
Two chapters stood out in particular. Chapter 5 looks at soft-tissue preservation of arthropods trapped in amber. The authors argue that there are two preservation pathways with radically different outcomes: either decay with loss of all soft tissue so that only an arthropod-shaped void remains or, spectacularly, complete preservation. They then discuss what factors might be responsible for this dual pathway. Chapter 8 draws heavily on the work of one of the authors, Conrad C. Labandeira, and reviews fossil evidence for insect-plant interactions, looking both at traces of insect damage, but also at structural and chemical defences in plants. We know that insects and plants coevolved but these authors propose a model of four phases during the last 400 million years of arthropod herbivory expanding and, in response, plant defences developing. This is a fascinating idea that is crying out for a popular treatment, and if I had to point a university press towards an idea for a new book, this chapter is it.
“Given the book’s somewhat eclectic selection of topics and relatively high price tag, who is this for? [individuals] might wish to only consult a few chapters. I would thus argue that this book is particularly suitable for academic and institutional libraries.”
More technical chapters give an introduction to Raman spectroscopy and how it can be used in palaeontology, and the structure and chemistry of silica in mineralized wood. Fossil wood also features in a chapter on experimental silicification of wood in the laboratory with comparisons to the fossil record. This chapter mentions the interesting phenomenon of in vivo mineralization where living trees in certain environments, for example Yellowstone National Park, are already fossilising during their lifetime. Finally, there is a chapter on colour in the palaeobotanical record which gives a thorough introduction to colour in living plants and then asks whether the colours we see in fossil plants result from original material, their degradation products, or from later diagenetic processes. A colour plate section, relevant especially to the last chapter, is included.
Given the book’s somewhat eclectic selection of topics and relatively high price tag, who is this for? Depending on your interests and background, your mileage may vary and you might wish to only consult a few chapters. I would thus argue that this book is particularly suitable for academic and institutional libraries. For them, it is a worthwhile investment as edited collections of this kind are often picked up by the likes of Springer or Elsevier who publish print-on-demand books with production values not nearly half as nice as Fossilization at double the price.
Disclosure: The publisher provided a review copy of this book. The opinion expressed here is my own, however.
Other recommended books mentioned in this review:
__________________________________________________________________
]]>
History will forever associate Charles Darwin with the theory of evolution, but the idea was in the air. Had not Darwin published his famous book, someone else would have likely snatched the prize. Husband-and-wife duo John and Mary Gribbin here examine the wider milieu in which Darwin operated and the many thinkers who preceded him. Given their previous collaborations, the first two parts of On the Origin of Evolution read like a well-oiled machine, but the book falters when they turn their eyes to the legacy of Darwin’s ideas.
On the Origin of Evolution: Tracing ‘Darwin’s Dangerous Idea’ from Aristotle to DNA, written by John Gribbin and Mary Gribbin, published in Europe by William Collins (a HarperCollins imprint) in November 2020 (hardback, 288 pages)
When you study the history of science, it seems there is just no way around Aristotle. In the context of this book, his legacy is the idea of the great chain of being: the notion that life can be ordered from simple to complex forms, with humans at the top as creation’s crowning glory. It was readily adopted by Christian thinkers and hamstrung evolutionary thinking for millennia.
Still, as the first third of this book shows, some people did ponder both man’s place in nature and the relationships between living beings. Liberally quoting from their writings, the authors introduce you to notable characters and their brilliant early flashes of insight. For example, Thomas Aquinas, writing in the 13th century, allowed for species to develop in their striving for perfection but rejected the idea of new ones arising after God’s act of creation. Fossils were long misunderstood, neither recognized as ancient nor as the remains of extinct creatures. I was therefore particularly fascinated by 17th-century British polymath Robert Hooke who may well have been one of the first to recognize fossils for what they were. His ideas on species formation and extinction seem prescient. In the 1770s, Lord Monboddo already argued that humans descended from apes. And yet, the dots were not connected into a bigger picture. Particular sticking points were extinction and the age of the Earth, a puzzle to which James Hutton and other geologists would later contribute much.
When the book gets to Darwin, the tempo slows right down and the middle third of the book examines Darwin’s life and simultaneous developments around him. The Gribbins sketch how Darwin, ever careful, worked on his ideas for decades, also because he felt that, as a geologist, one could not “examine the question of species who has not minutely described many” (p. 134). Something he subsequently spent years on. The history of how Alfred Russel Wallace later came to similar conclusions and ran them past Darwin in a letter, and how Charles Lyell and Joseph Hooker presented both their work at a meeting of the Linnean Society, is well-known. What the Gribbins here clarify is that, if it seems strange to us now that Wallace’s letter was publicly presented by a third party without his consent, this was the custom of the time. Communications of scientific interest were expected to be made public as quickly as possible. Various quotes from Wallace indeed show nothing but a man who was very chuffed to have his work mentioned alongside Darwin’s.
“[…] the first two parts of On the Origin of Evolution read like a well-oiled machine, [numerous] details left me with the impression that the authors have been meticulous […]”
The Gribbins also pay attention to Erasmus Darwin (Charles’s grandfather) and relevant contemporaries such as Jean-Baptiste de Lamarck and Georges Cuvier. They give Lamarck his due and note the irony of him accepting evolution but denying extinction, and Cuvier denying evolution but accepting extinction. If the two had not ended up bitter enemies they might have put two and two together. Another lesser-known figure who came tantalisingly close, and virtually coined the term natural selection, was arborist Patrick Matthew who buried his thoughts in the appendix to a book on naval timber. Darwin was unaware of his work despite Matthew’s later public charges, the Gribbins write. Other notable details are a public admission to a change of heart over whether a letter from Darwin to Wallace was intended to warn Wallace off. The Gribbins used to think so, but are now persuaded it was not. They also clarify the oft-repeated factoid of On the Origin of Species selling out on the day of publication: “this is only true in the sense that all the copies had been bought up by the bookshops, ready to sell on to their customers” (p. 166). An observation that, working for a bookseller myself, rings true. These and other details left me with the impression that the authors have been meticulous up to this point. (I admit this is a risky thing to say; whole academic careers have been built on studying Wallace and Darwin’s lives, so cue people more knowledgeable than myself pointing out errors next).
On the Origin of Evolution competes for your attention with Rebecca Stott’s 2012 book Darwin’s Ghosts, which similarly traced Darwin’s intellectual forebears. That book ended with the above-mentioned presentation at the Linnean Society, so the Gribbins have the opportunity to set themselves apart with the last third of their book, which examines the development of Darwin’s ideas by later scientists. Although I enjoyed the book up to this point, the last part is where it fell a bit flat for me.
The Gribbins weave their narrative through the work of Gregor Mendel and its triple rediscovery decades later; the discovery of the structure of DNA, honouring the long course described in Unravelling the Double Helix; and the discovery of how DNA codes for amino acids. It touches on horizontal gene transfer, epigenetics, and twin studies and the discovery of polygenic traits. All important topics for sure, but they omit so many others as to make this part of their history rather haphazard.
“[…] the last third of their book, which examines the development of Darwin’s ideas by later scientists. […] omits so many [topics] as to make this part of their history rather haphazard.”
Two oversights stand out. They discuss how extinction ultimately became accepted but leave out the next chapter: the mass-extinction debates, which was a conflict between uniformitarianism and catastrophism. Similarly, they recognize Wallace as the grandfather of biogeography but leave out how the long-resisted idea of plate tectonics explained palaeobiogeographic patterns. Basically, they completely ignore the rise of palaeobiology and its contributions to evolution. Beyond these, they mention horizontal gene transfer, but not Carl Woese and his proposal of a Last Universal Common Ancestor. They feature Thomas Hunt Morgan’s research on Drosophila, but not the emergence of evolutionary developmental biology. They profile Barbara McClintock’s struggle to get her discovery of mobile genetic elements accepted but not Lynn Margulis‘s struggle to get endosymbiosis recognized. And although the Sources and Further Reading section lists other major thinkers, there is no discussion of, say, Ernst Mayr and the problem with species definitions, the work of Stephen Jay Gould, or the debate on levels of selection. Sexual selection and phylogenetics are completely absent.
They cram this last part in a mere 70 pages while repeatedly mentioning not being able to go deeper. I am not sure why. At 253 pages of text, the book is not particularly long. Had they spent another 50 or even 100 pages, I feel they could have done it more justice. I will be the first to concur that writing such an overview is challenging. Part of the problem, I think, is that the authors (John a science journalist with a PhD in astrophysics, Mary a teacher) do not have a thorough background in (molecular) biology and reach into unfamiliar territory, as evidenced by some elementary mistakes. On p. 218 they mention DNA contains three purines and one pyrimidine, and correct themselves two sentences later (there are two of each). They mix up the DNA base pairs on p. 226 (CT and AG pairs) but get it right on p. 227. And on p. 244 they mention the human genome consists of 6 billion base pairs which is double the actual number. Anyone who has had to study Alberts’s brick will have had these facts drummed into them, but their acknowledgements are silent on whether fellow biologists provided feedback on the manuscript. Now, I do not want to blow a few factual errors out of proportion, but together with the brevity of the material included, and the many other topics not covered, this last part left me less than satisfied.
Overall then, this book is an excellent introduction to the history of evolution before and up to Darwin that retains important detail despite being relatively brief. I was less impressed with the coverage on the developments since Darwin, which would benefit from supplementary reading. I hope a future review of The Black Box of Biology will fill in some of the blanks regarding molecular biology.
Disclosure: The publisher provided a review copy of this book. The opinion expressed here is my own, however.
Other recommended books mentioned in this review:
__________________________________________________________________
__________________________________________________________________
__________________________________________________________________
__________________________________________________________________
__________________________________________________________________
__________________________________________________________________
__________________________________________________________________
__________________________________________________________________
__________________________________________________________________
After three previous books in this format on fossils, rocks, and dinosaurs, geologist and palaeontologist Donald R. Prothero here tackles the story of evolution in 25 notable discoveries. More so than the previous trio, this book tries to be a servant to two masters, resulting in a mixed bag.
The Story of Evolution in 25 Discoveries: The Evidence and the People Who Found It, written by Donald R. Prothero, published by Columbia University Press in December 2020 (hardback, 360 pages)
Prothero has organised The Story of Evolution in 25 Discoveries in a logical fashion. After convincing the reader that the universe and our planet are, indeed, really old, he considers some of Darwin’s lines of evidence for evolution, followed by several great transitions in evolution as revealed by the fossil record, more recent evidence from genetics and molecular biology, and, of course, evidence for the evolution of humans.
As in his previous books, Prothero manages to dig up some remarkable stories. For example, Darwin initially mistook the finches on the Galápagos for wrens, blackbirds, and other species. Only when he handed them to the famous ornithologist John Gould for a second opinion did it become clear that these were all finch species adapted to local conditions on the different islands. It later fell to others such as Peter and Rosemary Grant to do the long-term studies that elevated them to the icon of evolution they have become. Meanwhile, Othniel Charles Marsh’s monograph on primitive birds that still had teeth was unexpectedly branded a waste of taxpayer’s money when US congress was looking for excuses to cut funding to the US Geological Survey in the 1890s.
In many places, Prothero is careful and balanced in his coverage. He highlights the contribution of the historically overlooked Alfred Russel Wallace who independently hit on the idea of natural selection after Darwin had already been labouring on it for decades. And while Ernst Haeckel was accused of fraud over his famous drawings showing the embryonic development of different vertebrates, Prothero explains how there is a kernel of truth to Haeckel’s claim that ontogeny recapitulates phylogeny, even if “he may have been a bit overzealous in his drawings” (p. 69). On Jean-Baptiste de Lamarck and his ideas, Prothero clarifies how there was much more to him than the caricature of the “guy who got evolution wrong” (p. 198) that he became.
“In many places, Prothero is careful and balanced in his coverage […] he clarifies how there was much more to Jean-Baptiste de Lamarck […] than the caricature of the “guy who got evolution wrong””
There are classic topics such as convergent evolution, the evolution of the eye, and Lynn Margulis and her theory of endosymbiosis. The relatively young branch of evolutionary developmental biology and the discovery of Hox genes showed that, actually, yes, nature does make leaps and does not always result in slow and gradual changes. Throughout, Prothero repeatedly reminds you that the evolutionary relationships between organisms are like a bush, and not a linear progression from primitive to more advanced creatures. He explains that evolution does not always result in perfect adaptations—they only have to be good enough to help in producing the next generation. And he points out that natural selection can only ever work with the material at hand, resulting in many jury-rigged contrivances, including in humans.
Now, Prothero is also a noted sceptic. A good deal of this book has the secondary aim of showing that creationism is an utterly flawed idea and that the evidence for evolution reveals no traces of intelligent design whatsoever. The thing is, he already did this exercise in Evolution: What the Fossils Say and Why It Matters, so does it need repeating? He spends no fewer than seven chapters here on examples of transitional fossils that provide a detailed picture of fish leaving the water, whales returning to it, birds evolving from dinosaurs, giraffes evolving longer necks and elephants longer trunks, horses losing their toes and snakes their legs, and turtles acquiring shells. You almost get the feeling that he just cannot help himself.
I have few gripes with the topics that Prothero chose to include here, but I felt somewhat disappointed by all the topics he left out as a consequence of this secondary mission. Two notable omissions are the process of domestication, even though Darwin used numerous examples of it in On the Origin of Species and then wrote a separate book about it. The same is true for Darwin’s other big idea: there is no mention of sexual selection, sperm competition, or mate choice.
“[…] this book has the secondary aim of showing that creationism is an utterly flawed idea […] but I felt somewhat disappointed by all the topics he left out as a consequence […]”
Beyond these, there is little on speciation and biodiversity, the formation of higher taxa, or the difficulty with species concepts. Epigenetics is mentioned, but not by name. The textbook example of the peppered moth is included, but there is no further discussion on camouflage, mimicry, or warning signals. Richard Dawkins has to make do with two brief mentions, but there is nothing about the different levels of selection, whether selfish genes or group selection. And I am sure Prothero could have beautifully explained the difference between the modern and extended syntheses.
The focus on convincing the reader of the evidence against design raises the question of who this book is written for. For evolutionary biologists like myself, Prothero is preaching to the choir, while creationists are unlikely to pick this book up. The best this might achieve is to remind biologists of the evidence for evolution if we ever find ourselves debating creationists.
Prothero is a fantastic science communicator, and I really enjoy this format of 25 vignettes by which to examine the many facets of a topic. The material that he did choose to include is written with verve and balance. In my opinion, however, the dual motive underlying The Story of Evolution in 25 Discoveries means that he left out many relevant topics and has written a book of narrower focus than the title might suggest.
Disclosure: The publisher provided a review copy of this book. The opinion expressed here is my own, however.
Other recommended books mentioned in this review:
__________________________________________________________________
__________________________________________________________________
__________________________________________________________________
__________________________________________________________________
__________________________________________________________________
__________________________________________________________________
__________________________________________________________________
__________________________________________________________________
__________________________________________________________________
__________________________________________________________________
]]>
The Genesis Quest is one of those books that quickly makes a good case for its own existence. It takes the reader through the century-long research endeavour on the origin of life, providing a big-picture overview of who’s who and how their ideas have waxed and waned. Such an overview requires an outsider’s perspective on the whole show, which is exactly what science writer Michael Marshall achieves in my opinion. A superb starting point if you want to read more on this subject, this is the book I wish I had read earlier.
The Genesis Quest: The Geniuses and Eccentrics on a Journey to Uncover the Origin of Life on Earth, written by Michael Marshall, published in the US by the University of Chicago Press in October 2020 (hardback, 360 pages)
Judging by the long history of creation myths, the question of our origin has always fascinated us. But creation myths, contends Marshall, are not an answer. The scientific question of how life originated from non-living matter, a process known as abiogenesis, needed the theory of evolution and a conception of the age of the Earth before it was conceived of. (On a side-note, this seems to harken back to the now obsolete idea of spontaneous generation; the two are similar, but not the same.) What The Genesis Quest shows is a research community that started out unified, then splintered into competing fields, and is only recently showing signs of a reunification.
Marshall takes the 1920s as his starting point, which is when the Russian scientist Alexander Ivanovich Oparin and the British biologist J.B.S. Haldane independently theorised that life could have arisen from non-living chemicals in a step-wise fashion in Earth’s primitive oceans. Experimental support for the Oparin–Haldane hypothesis was delivered by chemists Harold Urey and Stanley Miller in the famous Miller–Urey experiment. In a laboratory setup simulating early Earth conditions, they created organic molecules such as amino acids from simple precursors. Though iconic and launching the field of prebiotic chemistry, their findings quickly became obsolete as criticism mounted. Earth’s early atmosphere was probably unlike their simulation, nor were the chemical steps observed necessarily realistic.
During the ’70s and ’80s, disagreements arose over which of life’s essential functions came first, which basic molecules came first, where on the planet this happened, and which organisms held the clues to the questions. Consequently, the field gradually splintered into four competing schools of thought that Marshall discusses in turn.
“Though each school has advanced the field, none of them have provided a complete and satisfactory solution to life’s origin”
The proteins-first school argues amino acids can spontaneously form complex proteins and even proteinoid microspheres (a sort of protocells), but it receded with the death of Sidney Walter Fox. The compartmentalisation-first school argues that life needs a container if it is not to fall apart immediately. Experiments by key figures such as David Deamer, William Hargreaves, and Pier Luigi Luisi showed how precursors can spontaneously form lipids which can then form protocells, and how they can be coaxed to divide or pick up molecules relevant to life’s biochemistry.
The other two are arguably the more widely known ideas. The replication-first school has become synonymous with the RNA World hypothesis and got boosted by discovering that RNA can have enzymatic activity (so-called ribozymes) and that it sits at the heart of ribosomes. Lastly, the metabolism-first school argues that energy underlies everything, for without a constant input to counter the second law of thermodynamics, entropy wins and life falls to pieces. This idea was boosted by the discovery of deep-sea hydrothermal vents, argued to be ideal biochemical reactors by Jack Corliss. Mike Russell predicted the existence of alkaline vents in the ’80s based on geological formations and was vindicated by the discovery of the Lost City hydrothermal field in 2000. These would provide a gentler environment and, from reviewing Alien Oceans, it is clear that alkaline vents still have currency.
Though each school has advanced the field, none of them have provided a complete and satisfactory solution to life’s origin. Experiments often fall short or have doubtful real-world relevance. This is the part of the book where Marshall finally plays his own hand and clarifies which scenario he favours based on the evidence so far. Along the way he throws out some fascinating ideas. He charts how some people have changed their minds and a new school is emerging that argues that “the essence of life is the interaction of all three” (p. 250), i.e. genes, metabolism, and a membrane-bound cell. Experiments by Jack Szostak, initially an RNA-world devotee, have partially succeeded in creating a model system with genes copying themselves inside membrane-bound protocells, though they still lack metabolism. Arguably, the boundaries between life and non-life become fuzzy once you start looking at such self-sustaining networks of chemical reactions, which is the domain of systems chemistry “The first life was so intimately bound up with its surroundings that it is difficult to tell what should count as organism and what as surroundings” (p. 272). He also highlights Harold Morowitz‘s argument that life should be considered at the level of ecosystems, or, in Marshall’s words “The first cell was not alone: it belonged to an instant community” (p. 270).
“Arguably, the boundaries between life and non-life become fuzzy once you start looking at […] self-sustaining networks of chemical reactions.”
Some people are now focusing on where such protocells would get their chemicals from, and e.g. Deamer, initially a compartmentalisation-first devotee, favours terrestrial tide pools undergoing wet-dry cycles as the best place for this. Marshall does not put much faith in hydrothermal and alkaline vents, though he does entertain the option that life might have arisen in more than one way, which opens “the possibility that several kinds of life arose in different places, and either merged or competed” (p. 278).
Marshall discusses many more researchers who made important contributions than I have space to mention here (the chapter on Graham Cairn-Smith and his notion of replicating crystals in clay stands out). This overview is arguably the book’s strongest point, but I have two additional observations. First is his eye for subtlety and detail. For example, he clarifies how speaking of the “Oparin–Haldane hypothesis” obscures the fact that their ideas differed subtly, and he explains the difference between hard and soft versions of the RNA-world thesis. Second, his version of the story of how the structure of DNA and the ribosome were discovered matches what I have read in other books.
Based on these observations I feel reasonably confident to claim that Marshall knows his stuff, even though he is “only” a science writer. I use inverted commas as I feel science journalism has a sometimes undeserved bad reputation. Here, however, having an outsider without allegiance to any research group is an advantage. The acknowledgements mention his close reporting on origin-of-life research for over a decade and 46 pages of references to journal articles back up the ideas he presents here. Clearly, Marshall has done his homework.
“This overview [of the different schools of thought] is arguably the book’s strongest point […] having an outsider without allegiance to any research group [reporting on it] is an advantage.”
Despite the serious intention, the book is very readable. He provides just the right amount of biographical information without losing focus on people’s ideas. There is the occasional footnote with nerdy pop-culture references, which is amusing when used in moderation. And he can be refreshingly brusque and honest. When introducing Haldane, he cracked me up by remarking that “Ronald Clark’s biography J.B.S. is essentially one long stream of outrageous anecdotes punctuated by occasional outbreaks of science” (p. 44) which matches the picture I got from Haldane after reviewing a more recent biography. Criticism of some of Walter Fox’s work on proteinoid microspheres is summarised as “nice experiment, but would it happen in the real world?” (p. 142). And an older Stanley Miller is described as being “very much in the ‘criticise anyone who challenges me’ phase of his career” (p. 194).
This is not the first book to give a history of this field, nor the first one written by a science journalist. Though I have not read those books, a quick comparison suggests they spend more time surveying thinking in Antiquity, which is something Marshall only briefly surveys in his first chapter. Given that I have recently been reading a fair bit about astrobiology and the origin of life, this is the book I wish I had read first. If you have any interest in delving deeper into origin-of-life research, The Genesis Quest makes a fantastic starting point that will give you the lay of the land. It gets my unreserved recommendation.
Disclosure: The publisher provided a review copy of this book. The opinion expressed here is my own, however.
Other recommended books mentioned in this review:
__________________________________________________________________
__________________________________________________________________
__________________________________________________________________
__________________________________________________________________
]]>
Advances in medical research mean we have come to grips with numerous diseases and health conditions over the decades. But, like a game of whack-a-mole, you solve one set of problems to only have other, often more complex problems take their place. There is valid criticism to be had of medicine and its reductionist approach and What Is Health? sees neurobiologist Peter Sterling offer a critique grounded in physiology.
What Is Health?: Allostasis and the Evolution of Human Design, written by Peter Sterling, published by MIT Press in December 2019 (paperback, 257 pages)
Much medical thinking and education, writes Sterling, revolves around homeostasis: self-correcting negative feedback loops, comparable to the thermostat in your house. These allow the body to regulate physiological processes, e.g. blood pressure, without involving the brain. However, he found that many endocrine cells, those that release hormones, do have nerve endings terminating on them. Homeostasis is part of the story, but “error-correcting feedback offers no basis for a full model of human design” (p. xxx*). Together with Joseph Eyer, he coined the term allostasis in the 1980s: the brain is involved by predicting the body’s needs and mobilising resources to meet expected demand, temporarily up- or downregulating processes when an organism’s environment changes. In simple terms, homeostasis corrects, allostasis predicts. This also gives us Sterling’s definition of what health is: “the capacity to respond optimally to fluctuations in demand” (p. 154).
This idea has been criticised from various sides as resulting from too narrow a reading of homeostasis, “a travesty that has taken root in textbooks and is widely taught to students as the only kind of control system“, that is not offering anything “that was not already apparent, or at least readily derivable, from an accurate reading of the original concept of homeostasis“. I am receptive to such criticism. Though I was not trained as a physiologist, my layman biologist understanding of it is that e.g. a healthy blood pressure already falls between a range of values and that what is considered optimal depends on whether you are at rest or exercising. Do we really need allostasis as a separate concept? Especially Carpenter is fierce in his criticism: “there is a need to reassert the unitary nature of homeostasis and the variety of forms it can take, so that we are not obliged to reinvent what was common knowledge even 30 years ago, nor to introduce artificial distinctions and boundaries within a field that is in truth perfectly unified.“
“In simple terms, homeostasis corrects, allostasis predicts. But do we really need a separate concept? I am not sure that disagreements over definitions make much difference to Sterling’s point that modern life can break this physiological control system.”
Having read the rest of this book, however, I am not sure that disagreements over definitions make much difference to Sterling’s argument that modern life can break this physiological control system. Before getting to that discussion, though, he spends the first four chapters on a deep evolutionary history tour to trace the origins of the components of allostasis. This tour encompasses the molecular details of the genetic code, protein functionality, and ATP synthesis and hydrolysis to store and release energy at a cellular level. It encompasses the evolution of multicellularity and what we inherited from our worm-like ancestor in the way of cellular clocks, early brains, and feedback regulation between the different parts. (Side note, this is likely where dopamine was introduced as the brain’s reward signal for useful behaviour, enabling learning.) It encompasses the evolution of endothermy and the respiratory and cardiovascular adaptations enabling it. And, finally, it encompasses the evolution of Homo sapiens when it left Africa some 150,000 years ago. Sterling argues that changes to our brain allowed us to oust our Neanderthal cousins. Summarising from his book Principles of Neural Design, he gives a bird’s-eye-view of how the brain is organised for optimal functioning, what we inherited from our primate ancestors, and what we changed.
Overall, these chapters are well written and full of fascinating information, though I am not sure all of it is necessary to understand allostasis. Also, there are a few minor points I take issue with. I understand that phrases such as “a reptile evolved two new features and came out as a mammal” (p. xxv) and “At the pinnacle of life’s energy-driven complexity, perches—precariously—Homo sapiens” (p. 1) are shorthand. However, they could be mistaken for outdated linear thinking about evolution, even if Sterling’s writing in the rest of the book suggests no such thing. We did not evolve from reptiles. We share a common ancestor with them but they have been on an equally long evolutionary journey. Furthermore, Sterling strongly argues that evolution has produced optimal structures or, where tradeoffs make something seem suboptimal, optimal trade-offs. His endnotes explain that e.g. our appendix and the seemingly backwards design of our retina are actually functional, and he concludes that “[…] clear examples of suboptimality are scarce, if they exist at all” (p. 9). I am not sure I agree. The circuitous loop taken by the recurrent laryngeal nerve or the design of our throat that puts us at constant risk of choking are but two of many examples that Nathan Lents discussed in his book Human Errors. We know that evolution cannot simply start from scratch and that it reuses, repurposes, and rejiggles existing structures for new functions. Furthermore, Daniel S. Milo’s Good Enough criticized adaptationist storytelling and made an interesting argument for the persistence of the mediocre. Perhaps these are just issues of semantics and, seeing they do not really bear on his central argument, I will not dwell on them further.
“the simple pleasures of life were sources of regular small pulses of dopamine. These eroded, first gradually with the advent of agriculture, then rapidly with the Industrial Revolution, leading to our modern, dopamine-deprived lifestyle.”
Having taken the deep evolutionary tour, chapters 5 and 6 are where Sterling finally drops the payload and delivers the goods. The mechanism of allostasis breaks down when demand is excessively high for sustained periods. The body responds by shifting its operating range upwards and what used to be exceptional becomes the new normal. In the example of blood pressure you end up with chronic hypertension. Something similar happens with our reward circuits. We evolved as socially living hunter-gatherers that had regular physical exercise, where children of different ages played together unsupervised, where we learned and perfected skills such as hunting over decades, and where the elderly contributed to care of the young. Call them the simple pleasures of life but that is the whole point, they were sources of regular small pulses of dopamine. Sterling argues that instead we now try to get our dopamine hit from alcohol, nicotine, drugs, food, gambling, pornography, or shopping. And many of these activities deliver greater surges, with allostasis adapting us to take such surges as the new normal, fostering addiction. By his reasoning, the Western epidemic of hypertension, obesity, depression, suicide, alcoholism, and addiction to drugs and gambling are all a consequence of our modern, dopamine-deprived lifestyle. He will even throw in climate change, resulting as it does from excessive consumption of goods, meat, and (air) travel.
There is no shortage of recent books arguing that we are the victim of an evolutionary mismatch with instinctive brain circuits that cause us to e.g. overeat; that we have become unfit for purpose and our hunter-gatherer origins mean that we are poorly adapted to modern life. Sterling puts neurological flesh on the bones of that argument. More importantly, he pleads with us not to blame our evolutionary heritage. This reward circuit “inherited from worms […] works exactly as it is supposed to—just not for what it was intended. This has been termed a “mismatch” […] but that euphemism avoids facing squarely that “how we live now” is intolerable to a large fraction of our population” (p. 138). The tragedy is that medical practitioners try to combat this epidemic of apparently intractable chronic illnesses with pharmacotherapy—a pill here, a beta-blocker there—in a vain attempt to correct specific physiological parameters without recognizing that “the underlying biochemical and neural circuits are not actually broken” (p. 165).
“contrasting our hunter-gatherer lifestyle with “how we live now” raises the question: what of the intervening [time]? […] did we suffer the same epidemic of lifestyle diseases that we see now?”
By and large, I am on board with Sterling’s line of reasoning. We did indeed live as hunter-gatherers for the vast majority of our evolutionary history, and the argument of our current dopamine-deprived lifestyle is attractive.
However.
I am always a bit wary of single-cause, killer hypotheses that seek to explain a wide range of topics with one causative agent. Some claims here do seem rather sweeping, and to write, for example, that “it is sobering to notice that the growth of smartphones and Facebook parallels the growth of mass shootings” (p. 132) risks conflating correlation and causation. But more importantly, contrasting our hunter-gatherer lifestyle with “how we live now” raises the question: what of the intervening ten to fifteen thousand years that Sterling skips over? He limits himself to writing that our drip-feed of regular, small dopamine pulses eroded, first gradually with the advent of agriculture, then rapidly with the Industrial Revolution that “accelerated the process and exaggerated it grotesquely” (p. 131). Archaeology and palaeopathology tell us that the shift from foraging to agriculture was a Faustian bargain that initially took a heavy toll on our health. Our stature diminished and especially our teeth recorded the effects of this dietary change. But did we suffer the same epidemic of lifestyle diseases that we see now? Or was it the Industrial Revolution and especially the Great Acceleration that pushed us over the edge? In the latter case, it would seem there are more ways than the hunter-gatherer lifestyle to live a fulfilling life.
Are there solutions? Fortunately, Sterling does not advocate we head back to the caves and draws attention to the, I think, underappreciated argument that history has acted as a ratchet: “higher population densities gradually disallowed any return to the wild” (p. 128). One option is to work with the body’s mechanism of allostasis, not against it, through what he dubs “system therapy”, which is basically what rehab is for drug addicts. It is hard and slow, but the only way to resensitize our body’s reward circuit to more modest dopamine pulses. Preventative strategies would involve changes to modern life to restore physical and mental challenges, lifelong learning, and social relationships between the generations. These suggestions are, to my taste, rather generic and I would have loved for him to develop this part of the book fuller.
Given that neurobiology can be a technical topic, Sterling writes accessibly and makes good use of numerous illustrations to clarify principles further. I found the detour into deep evolutionary history particularly interesting, even if not all of it was relevant to the central argument. Though I am on the fence regarding some of the material here, What Is Health? is overall a cogently argued book that provides both reason for concern and food for thought.
* Have I forgotten to insert a page number here? No, this quote is taken from the first 32 Roman-numeral-numbered pages of prefatory material.
Disclosure: The publisher provided a review copy of this book. The opinion expressed here is my own, however.
Other recommended books mentioned in this review:
__________________________________________________________________
__________________________________________________________________
__________________________________________________________________
__________________________________________________________________
]]>
A pandemic is probably a good moment to understand how vaccines are developed and how they work. This short and educational primer offers relevant background information on viruses and the immune system, and goes into much more detail on vaccines than other recent introductory books. How to Make a Vaccine is written by immunologist John Rhodes who brings to the table both his background in academic research on vaccines and his experience working for GlaxoSmithKline from 2001 to 2007. His narrative approach of choice is to tell the story of viruses, immunology, and vaccines through the history of scientific discovery.
How to Make a Vaccine: An Essential Guide for COVID-19 & Beyond, written by John Rhodes, published by the University of Chicago Press in March 2021 (paperback, 184 pages)
Some of these historical episodes were by now familiar to me. For example, Charles Maitland’s first variolation experiments on prisoners, Edward Jenner’s use of cowpox vaccine to combat smallpox, and the 1950s race for a polio vaccine between Jonas Salk and Albert Sabin. Or the bizarre history of the 19th-century maritime expeditions to distribute the first vaccines around the world, keeping them alive on the long journeys through a carefully orchestrated living chain of infection. Other episodes were new to me. For example that Jenner was not the first to experiment with cowpox vaccination. How Wendell Stanley first visualized viruses under an electron microscope in 1935, and how June Almeida first visualized coronaviruses in 1968.
The only place where I felt this historical approach broke down a bit was when it came to the immune system, which is a complicated topic. The components of our byzantine immune system were not necessarily discovered in a logical order, and I would have loved some illustrations here. Instead, there is a useful table on page 22 summarising the different B and T-cells and their myriad tasks. Nevertheless, I found Rhodes’s explanations of how the different components of the immune system function the clearest I have come across so far. For example, I keep confusing antibodies and antigens (I know, as a biologist I should be ashamed for having to admit this). However, when Rhodes writes “the fragments of germs (pathogens) […] soon became known as antigens” (p. 16) it finally activated a mnemonic in my head.
“[…] I found Rhodes’s explanations of how the different components of the immune system function the clearest I have come across so far.”
Chapters four and five are, to me, the core of this book and obligatory reading. I found them exceedingly useful. The first explains the six steps in vaccine development: exploratory, preclinical, phase I, II, and III trials, and regulatory review. This strict procedure ensures vaccines are safe. In part, it is a product of past errors, such as the 1955 Cutter Incident when a particular batch of polio vaccines had not been properly prepared. The only question I felt Rhodes could have asked and answered more explicitly is how COVID-19 vaccines could be developed so quickly. Many people worry that they have been rushed and might not be safe. You have to read between the lines a bit, but the answers are there. For instance, existing vaccine platforms that can quickly be repurposed, technological advances in genetic sequencing and engineering, rapid dissemination of new findings through open publishing platforms and preprint servers, and financial investment such as Operation Warp Speed in the US. Importantly, a large fraction of your population is exposed to the disease during a pandemic, which allows you to rapidly see what fraction of vaccinated people still fall ill, i.e. how effective your vaccine is. Normally, gathering enough data to draw statistically robust conclusions takes a long time, and an epidemic might burn itself out before you get a chance to do so. As a result of all this, there were 232 (!) candidate vaccines when this book went to print.
The second chapter walks you through the six established types of vaccines. All vaccines rely on exposing your immune system to an antigen to activate an immune response, but there are different approaches. Rhodes provides much more detail and for each type also gives examples of COVID-19 vaccines that are being developed. But, briefly, one way of categorising them is the non-living versus living vaccines. The former use dead viruses, parts of viruses (protein subunits), or virus-like particles, but typically need an additive, a so-called adjuvant, to elicit a sufficiently strong immune response. The latter are more potent and rely on living but weakened viruses or use a replicating or non-replicating carrier, a so-called vector, that is modified to contain fragments of a particular virus.
“Chapters four and five are, to me, the core of this book and obligatory reading. I found them exceedingly useful. The first explains the six steps in vaccine development […] The second chapter walks you through the six established types of vaccines.”
And then there are the new kids on the block, DNA and RNA vaccines, which differ in that they get straight to the heart of the matter. After all, the sole purpose of a virus is to deliver its DNA or RNA to a host cell and commandeer its machinery to produce more viruses. These vaccines achieve the same by directly administering engineered pieces of DNA or RNA that code for viral proteins. As Rhodes highlights, especially RNA vaccines hold great promise as they do not replicate, do not integrate into the host’s DNA, interact directly with the cell’s machinery without intermediate steps, and, like other RNA fragments, after a while are naturally broken down by resident housekeeping enzymes. Both the Pfizer and Moderna vaccines that are currently being rolled out to combat COVID-19 are RNA vaccines.
Finding and testing vaccines are only the first steps to getting a virus under control, so I was very pleased to get an immunologist’s perspective on the additional hurdles. This concerns practical logistical problems such as mass-producing billions of syringes and glass vials, figuring out who should be vaccinated first, and the problem of nations competing rather than collaborating to get their hands on vaccines.
“[…] I was very pleased to get an immunologist’s perspective on the additional hurdles. This concerns practical logistical problems [but] more importantly […]the vexing problem of what he understatedly calls vaccine hesitancy.”
More importantly, however, Rhodes addresses the vexing problem of what he understatedly calls vaccine hesitancy. I found his approach here admirably balanced. He gives the background to a few infamous vaccine scare stories (e.g. the Wakefield affair) while explaining some of the actual problems that can sometimes arise, and how lessons have been learned from this to design safer vaccines. Nor does he trivialize the anti-vaccination movement entirely: “Is it right to attribute all issues of vaccine refusal to superstitions, conspiracy theories, and irrationality? Of course not.” (p. 114), while highlighting more subtle reasons. At the same time, he makes the sharp observation that we need to rebalance “perceptions of individual liberty versus collective responsibility and the good of the community” (p. 116). This, I would add, is true of several other public health measures over which some vocal minority groups have been making a right kerfuffle.
How to Make a Vaccine joins several recent pocket-sized paperbacks that offer brief overviews, whether it is of viruses in general, SARS-CoV-2 in particular, or the botched response of governments. It is an especially nice complement to Chakraborty’s and Shaw’s Viruses, Pandemics, and Immunity that focused more on the immune system and only briefly covered vaccines. Helpfully, the further reading section at the back breaks down references per chapter into general and technical literature.
At a time when online searches for books on vaccines are more likely to turn up misinformation than reliable literature, How to Make a Vaccine is a required primer that demystifies concepts and gives an informative overview of how vaccines are developed and how they work. An essential guide indeed.
Disclosure: The publisher provided a review copy of this book. The opinion expressed here is my own, however.
Other recommended books mentioned in this review:
__________________________________________________________________
__________________________________________________________________
]]>
Last year August, science writer Ed Yong put it very nicely: “you see, the immune system is very complicated“. Yet, understanding it is important to understanding how the COVID-19 pandemic might evolve, why we are faced with certain public health measures, and how we can hope to combat the pandemic with tests and vaccines. In this brief book, physics and chemistry professor Arup K. Chakraborty and immunologist Andrey S. Shaw offer a general introduction to how our immune system reacts to viruses, and how our medical inventions help out.
Viruses, Pandemics, and Immunity, written by Arup P. Chakraborty and Andrey S. Shaw, published by MIT Press in February 2021 (paperback, 206 pages)
I was particularly looking forward to this book. Amidst the growing crop of books on COVID-19, the immunological details have been somewhat neglected. Kucharski’s The Rules of Contagion looked at the epidemiology of disease outbreaks but was written just before the pandemic materialised (the paperback addresses this to some extent), while Rabadan’s Understanding Coronavirus does what it says on the tin, focusing on the virus, SARS-CoV-2, and the disease, COVID-19.
Viruses, Pandemics, and Immunity is nicely balanced in the way it treats all the relevant elements to understand this topic. You get two chapters with history, introducing you to early procedures and to important scientists such as Edward Jenner, Robert Koch, and Louis Pasteur. By the end of it, you will understand the difference between variolation and the vaccine methods of respectively Jenner and Pasteur. This is followed by three chapters with the scientific nuts and bolts, looking at viruses, the immune system, and epidemiology, and two final chapters looking at the medical countermeasures of antiviral therapies and vaccines. In all of these chapters, details and findings on SARS-CoV-2 and COVID-19 are highlighted.
“Viruses, Pandemics, and Immunity is nicely balanced in the way it treats all the relevant elements to understand this topic, [highlighting] details and findings on SARS-CoV-2 and COVID-19.”
I admit that I found the middle three chapters a bit hit and miss. The one on viruses is, I think, great, explaining how viruses work by taking over the host cell’s replication machinery, how DNA and RNA viruses differ, why COVID-19 went global while SARS and MERS—also caused by coronaviruses—did not, and how SARS-CoV-2 differs from other RNA viruses that we understand better, such as influenza and HIV.
In light of what I said earlier about the immune system, it is not surprising that the chapter on immunity is the longest. It introduces the two components of our immune system, innate and adaptive, and how both function when the body detects an intruder. The innate immune system is, relatively speaking, the simpler of the two, responding to infection immediately by recognizing general characteristics of bacteria, viruses, and fungi. The authors can describe this in five pages, including details on Toll-like receptors and cytokines. The adaptive immune system needs more time to gear up, 5–10 days in humans, and is the more complex of the two. In some 20 pages, the authors here introduce the byzantine arrangement of B lymphocytes that combat viruses directly, and T lymphocytes that destroy infected cells in the body, as well as the memory cells that both types contribute. But rather than discuss the innate and adaptive immune system in the order in which they get activated, the authors discuss them in reverse order, which I found a bit counterintuitive. Given the complicated nature of the beast, the level of detail might challenge readers not well-versed in biology, though a helpful “putting it all together” section runs you through it all again at the end of the chapter.
“Given the complicated nature of the [immune system], the level of detail might challenge readers not well-versed in biology, though a helpful “putting it all together” section runs you through it all again […]”
Similarly, the chapter on epidemiology explains the relevant concepts: the basic reproductive number R0, epidemiological models, the effects of public health measures (“flattening the curve”), and herd immunity. The authors also highlight why different countries have been less or more successful in addressing the pandemic, something that will be explored in-depth in Fighting the First Wave. But here, too, the writing sometimes gets a bit complex. The authors spend three pages on a convoluted explanation with numerical examples to tell you that the more infectious a virus is, the higher the fraction of your population that needs to be immune before herd immunity kicks in. Furthermore, they exclusively discuss social distancing and different strategies to achieve herd immunity, from intermittent lockdowns to simply “weathering the storm”. But the two other pillars of public health measures, hand washing and face masks, are not even mentioned, even though they make important contributions to reducing R0.
The last two chapters are spot on again, focusing on the two main weapons in our medical arsenal. Antiviral therapies block one or more steps (entry, replication, assembly, and release) in the viral lifecycle and there is a brief discussion of existing antiviral therapies such as remdesivir and dexamethasone that have been repurposed for use against SARS-CoV-2. Vaccines, then, stimulate our immune system and this is where the immunological details come in again. How to Make a Vaccine covers all these topics in more detail, but there is a good introduction here to the different types of vaccines, clinical trials, and vaccine development, as well as the logistical challenges of the currently required large-scale production and a brief note on why vaccines are safe and certainly preferable over the alternative. Unavoidably, when discussing promising vaccine candidates against COVID-19, some information is already dated. The Moderna vaccine was undergoing trials when this book was written, while the AstraZeneca and Pfizer ones were in the developmental stages. All three are now being rolled out.
“[…] the book is livened up with cartoony illustrations [though] the decision to not include figure captions limits their utility.”
Throughout, the book is livened up with cartoony illustrations by Philip J. Stork, a senior scientist at Oregon Health & Science University. However, the decision to not include figure captions limits their utility in my opinion. Despite annotations in the figures, some are quite cryptic by themselves. Captions could have formed the perfect bridge and condensed the sometimes complex details found in the body of the text.
Viruses, Pandemics, and Immunity bundles introductions to a number of relevant topics, effectively replacing the need to e.g. get several Very Short Introductions. By highlighting what we know about COVID-19 and SARS-CoV-2 for each of these topics, this welcome book plugs a gap, especially where the immune system is concerned. General readers will want to heed Yong’s warning though, because, you see, the immune system is very complicated.
Disclosure: The publisher provided a review copy of this book. The opinion expressed here is my own, however.
Other recommended books mentioned in this review:
__________________________________________________________________
__________________________________________________________________
__________________________________________________________________
]]>
Convergent evolution was the subject of the first book I reviewed on this blog and is a topic I keep returning to. MIT Press recently published two further books on it, Convergent Evolution on Earth in 2019 and Contingency and Convergence in 2020. I felt the time was ripe to finally read their 2011 book Convergent Evolution that I bought some years ago. All three of these are part of The Vienna Series in Theoretical Biology, a series I hold in high regard. This, then, is the first of a three-part dive into what I consider one of evolutionary biology’s most exciting topics.
Convergent Evolution: Limited Forms Most Beautiful, written by George R McGhee, Jr., published by MIT Press in December 2011 (hardback, 322 pages)
George McGhee is a Professor of Palaeobiology at Rutgers University and a member of the Konrad Lorenz Institute for Evolution and Cognition Research in Austria. The latter can be considered the alma mater of this series, as its three editors work here. The book’s subtitle, Limited Forms Most Beautiful, is a play on Darwin’s triumphant conclusion to On the Origin of Species where he wrote that “endless forms most beautiful […] are being evolved“.
For those needing a refresher, convergent evolution refers to the ubiquitous pattern of evolution repeatedly hitting on the same or similar solutions to a problem in different organisms. One commonly cited example, shown on the book’s cover, is that of wings. Birds, bats, and pterosaurs all modified their forelimbs into appendages used to generate lift. This is where I feel Convergent Evolution does not get off to its strongest possible start. Together with definitions, it immediately dives into a discussion on the subtle distinction between parallel and convergent evolution before deciding that the former is but one type of the latter. However, do not let this put you off, as the book is very accessibly written throughout.
Despite not planning to be an “Encyclopedia of Convergent Evolution”, the bulk of the book falls into the listicle category, with five of its eight chapters providing numerous tables with examples of convergent evolution. Two chapters tackle convergent structures in animals and plants, for example the eyes and ears involved in prey detection and reproductive structures such as plant seeds. Next to many remarkable examples, what stands out is how some adaptations are so common that you would forget they evolved convergently numerous times. Take viviparity, which is neither unique to terrestrial animals nor even to vertebrates; live birth also repeatedly evolved in marine animals and invertebrates.
“[…] some adaptations are so common that you would forget they evolved convergently numerous times.”
More interesting even for evolutionary biologists are the subsequent three chapters where McGhee considers molecules, minds, and ecosystems. Molecules makes sense, as there are many examples of repeated evolution of DNA sequences coding for, say, a light-sensitive protein in eyes. Or of different amino acid sequences evolving to produce functionally and geometrically very similar proteins, such as antifreeze proteins in cold-water fish species. Convergent evolution of minds here means the repeated evolution of behaviours such as tool use or social hunting. But ecosystems? McGhee makes the convincing argument that whole assemblages of organisms, all with their specialised roles, have evolved repeatedly.
Where the book gets really interesting, and the theoretical biology part comes to the fore, are the last two chapters. One reason for convergent evolution is constraints imposed by physics—Cockell memorably summarised this with the phrase “physics is life’s silent commander”. The other is developmental constraints. Some biological forms that evolve are non-functional and lethal, these are the freaks of nature, the animal anomalies.
These two meet each other in the concept of theoretical morphology, which can be thought of as the less whimsical version of speculative zoology: an exercise in mapping all the possible forms, existent and non-existent, an organism could take, with the aim of answering why some morphologies evolved but others did not. The total set of all possibilities forms a hyperdimensional morphospace. McGhee wrote more about this in his 2007 book The Geometry of Evolution where he applies it to the concept of the adaptive landscape to explain why evolution favours certain solutions over others (in short, because not all solutions are equally good). I realise that if you are not well versed in evolutionary biology this might all sound rather abstract. I thoroughly recommend Andreas Wagner’s brilliant books Arrival of the Fittest and Life Finds a Way as introductions to the idea of evolution as life endlessly probing the hyperdimensional space of all possible options (whether morphologies or DNA and protein sequences).
“[…] physical and developmental constraints form a Venn diagram in morphospace. All life forms, extinct and extant, are found [here]”
McGhee here shows how physical and developmental constraints form a Venn diagram in morphospace. All life forms, extinct and extant, are found in the space where the two constraints overlap: these are the forms that are both functional and viable. Lethal mutants are those that are allowed by physics but not by developmental constraints. Those that are developmentally but not physically allowed are of particular interest to astrobiology. “Not physically allowed” comes with an asterisk that reads: not on Earth. But what of other planets? Could silicon-based life forms exist on planets with extremely high or low temperatures? Peter Ward thought so, but Charles Cockell makes a case for the universality of carbon-based lifeforms. This leaves a vast set of possibilities not accessible to life due to the constraints imposed by both development and physics.
The other big question touched on is the predictability of evolution with McGhee juxtaposing the two dominant schools of thought. There is Stephen Jay Gould’s view of evolution as being dominated by contingency (i.e. chance events) and therefore being unpredictable if it was to be repeated. The second is the view of Simon Conway Morris and others who argue that evolution is predictable and its outcomes inevitable. In McGhee’s eyes, the latter is the clear winner and his argumentation why is worth reading.
There are some points of criticism that McGhee does not tackle here. Are we cherry-picking examples when arguing for convergent evolution? Are we even seeing patterns where there are none? To return to the example of the wings on the book’s cover: though all involve modification of forelimbs, the details differ. And is shared genetic ancestry predisposing organisms to converging on similar solutions? Losos tackled these questions in a very balanced manner in his brilliant book Improbable Destinies.
McGhee delivers a fascinating tour through convergent evolution with this book and I am especially intrigued by the subtitle of his 2019 book which promises to apply this further to astrobiology, and which I review next.
Disclosure: The publisher provided a review copy of this book. The opinion expressed here is my own, however.
Other recommended books mentioned in this review:
__________________________________________________________________
__________________________________________________________________
__________________________________________________________________
__________________________________________________________________
__________________________________________________________________
]]>
Did life arise merely by accident? Many scientists feel uncomfortable with talk of goal-directedness and greater plans, as it reeks more of religion and theology than rational explanation. And with creationists lurking, the risk of “smuggling God in through the back door” under scientific pretences (as Richard Dawkins put it) is something to be wary of. Without descending into this territory, Universe in Creation might skirt dangerously close to it for some. In turns lyrical, unsettling, and, yes, speculative, this book argues that life may be written into the most basic laws of nature.
Universe in Creation: A New Understanding of the Big Bang and the Emergence of Life, written by Roy R. Gould, published by Harvard University Press in May 2018 (hardback, 273 pages)
Roy R. Gould, a Principal Investigator and Education Analyst at the Harvard-Smithsonian Center for Astrophysics, here takes a two-pronged approach to examine the emergence of life. He follows the cosmological story from the Big Bang forward, and, since life’s origin somewhere in the middle remains impenetrable, he also follows the story of evolution today back in time.
The first part was the more unfamiliar territory for me as it put forward some ideas that I had never heard of. Not being well-versed in cosmology, it is hard to be sure how widely accepted they are. Gould starts with observations by Hubble (the astronomer, not the telescope) that every galaxy in the universe is moving away from us. An expanding universe seems odd, as “gravity should attract, not repel“, writes Gould. Similarly, if the universe started with a cosmic explosion, its light should have sped off into space and be long gone. Instead, astronomers discovered that cosmic microwave background radiation, a leftover from the Big Bang, is coming at us from all directions. So, we need a new idea, and things will get more speculative going forward: “We will put aside our observations about the universe, take a deep breath, and dive into the world of ideas” (p. 42).
See, writes Gould, the terms “Big Bang” and “expanding universe” are somewhat misleading metaphors. Rather than expanding outwards into something, the universe expands inwards. How? Einstein’s model of gravity predicts that: “the universe is continuously creating more space [because] the scale of length is shrinking [with time]” (p. 61). Space is continuously welling up between the galaxies. The universe is fractalizing. This was one of those interesting and, for me, novel ideas. Gould traces its history through the 18th-century discussions between Isaac Newton and Gottfried Leibniz (is the universe the same scale everywhere?). Through the mathematician Bernhard Riemann’s questioning of a cornerstone of geometry (is the length of a line independent of its position?). And, of course, through Albert Einstein who argued that mass distorts space and time, an idea that was confirmed with the recent discovery of gravitational waves by the LIGO detector. A logical follow-up question is what happened in the beginning, allowing Gould to recount how the Big Bang theory was conceived.
“Rather than expanding outwards into something, the universe expands inwards. How? […] the universe is continuously creating more space [because] the scale of length is shrinking [with time].”
Where it gets more speculative, and for some readers perhaps questionable, is when Gould asserts that the universe has a building plan. He refers to the universe’s infrastructure: the elementary particles making up atoms, and the forces that animate them (gravity, electromagnetism, and the strong and weak nuclear forces). He marvels at the exact proportions in which these forces work: “nature’s specifications guarantee the stability of atoms” (p. 86), and remarks how slight tweaks of these values would have precluded the formation of even hydrogen atoms, and with it life.
“Why is the infrastructure of the universe so hospitable to life?“, asks Gould (p. 88), noting that this is known as the fine-tuning problem. One scientific perspective says this is a leading question and there is no reason: “nature does not “intend” to produce either atoms or life” (p. 88). A more speculative idea is that of the multiverse: “a vast landscape of universes, almost all of which would be stillborn” (p. 89). Our universe is the lucky exception where life flourished. But there is another perspective.
In 1983, physicist John Archibald Wheeler asked a question that Gould revisits throughout this book. In short: Is the universe set up such that intelligent life is guaranteed to arise? Gould thinks yes, and explores several highlights in the universe’s evolution in support. In its infancy, the universe was not completely uniform, it was just the right kind of lumpy for matter to coalesce into stars and galaxies. Had starting parameters been different this would not have happened, so “the universe was built from the start with a clever set of plans” (p. 109). Of the chemical elements forged in large stars that are scattered when stars explode, Gould writes: “it is truly marvellous that they are created in the abundances needed to form planets and to nurture life” (p. 118).
“Gould’s injection of meaning into events does not sit comfortably with me. Is the cosmos miraculously fine-tuned for life, or is life miraculously fine-tuned to the cosmos?”
This is where I found the book at its most unsettling. Gould’s injection of meaning into events does not sit comfortably with me. Is the cosmos miraculously fine-tuned for life, or is life miraculously fine-tuned to the cosmos? There is a subtle difference. Plus, we have no record of all the times life tried to take off and failed. This is a bit reminiscent of the bias that can arise when you exclude zeros and missing values during the statistical analysis of data sets.
The other half of the book looks at evolution today and works backwards. Without resorting to a veiled attempt at scientific creationism, Gould makes two arguments that life arises naturally from the laws of nature and is not just a happy coincidence. One, life’s ability to replicate depends on the molecular properties of its machinery (DNA and RNA) that are ultimately dictated by the fundamental properties of matter (what Gould earlier called the universe’s infrastructure).
Two, chance has a role to play, but random does not mean unpredictable. You can have a system with randomly behaving components that, as a whole, is still predictable. The molecular machinery of life has random behaviours (e.g. mutation and recombination) with a predictable outcome: genetic diversity. “Chance is the engine of diversity, and with enough diversity anything seems to be possible” (p. 183). This touches on some of the hottest topics in evolutionary biology such as convergent evolution, the predictability of evolution, and the origin of evolutionary innovations.
“Gould makes two [evolutionary] arguments that life arises naturally from the laws of nature and is not just a happy coincidence”
That last question touches on one of my favourite books: Andreas Wagner’s Arrival of the Fittest. Elsewhere, I rather verbosely summarised its central thesis as “evolution probing multidimensional spaces of possible protein sequences to rapidly come up with innovative solutions to life’s problems” (one day I will review that book properly, I promise). Gould, the science poet, outdoes me: “The landscape of evolutionary success appears to be very broad; there are many pathways of mutation that preserve function. Nature is wonderfully redundant.” (p. 201)
Compared to the cosmological argument in the first half of the book, I thought Gould makes a more appealing and sound argument here. Also as I consider it an example of life being fine-tuned to the cosmos rather than vice-versa. A final trio of chapters deals with senses and sensations, an exploration of the Mandelbrot set as an example of design without a designer, and the recent discovery of large numbers of exoplanets that might finally start offering resolutions to the Drake equation and the Fermi paradox. I was already savouring the taste of an argument well made at this point, so these chapters were like a dessert to me.
Gould is an enthusiastic and, at times, lyrical guide, and Universe in Creation is not hard to follow. It elicited contrasting responses, both fascinating and discomfiting me. That, surely, is the hallmark of an intellectually engaging book.
Disclosure: The publisher provided a review copy of this book. The opinion expressed here is my own, however.
Other recommended books mentioned in this review:
Schilling’s Ripples in Spacetime paperback
, __________________________________________________________________
]]>
Goldsmith’s Exoplanets hardback
, 
Vakoch & Dowd’s The Drake Equation hardback
or The history of life is punctuated by major transitions and inventions: fish that moved onto land, reptiles that turned into birds. But how did these happen? In Some Assembly Required, Professor of Organismal Biology and Anatomy Neil Shubin provides an up-to-date and utterly engrossing account of the latest thinking on the great transformations in evolution. And he has one clue for you: nothing ever begins when you think it does…
Some Assembly Required: Decoding Four Billion Years of Life, from Ancient Fossils to DNA, written by Neil Shubin, published in Europe by Oneworld Publications in March 2020 (hardback, 271 pages)
When Charles Darwin formulated his ideas, he was candid about weaknesses and gaps in his thinking. Shubin opens the book with one vocal critic, St. George Jackson Mivart, who thought Darwin’s ideas were flawed. If evolution is a process of gradual changes via mutation and natural selection, then how are major transitions supposed to arise? It sounds like a sensible question and to this day creationists like to trot out this argument. Darwin had five words for Mivart (and I am not building up to an obscenity-laden punchline here): by a change of function. Shubin beautifully clarifies this on page 27: “innovations never come about during the great transitions they are associated with”. I am just going to step back while you read that sentence again.
What Shubin gets at is that evolution takes shortcuts. Rather than inventing new traits from scratch, it repurposes existing ones. Examples Shubin gives are air-breathing in fish, which was repurposed to make lungs in land animals, and feathers on dinosaurs that originally evolved in a different context, but were repurposed for flight. Shubin has spent a research career working on our fishy ancestor, Tiktaalik rosaea, which was the subject of his previous book.
This is but one of the many ways in which evolution can achieve rapid and major transitions. Subtle changes during embryonic development can have large impacts later in life. Shubin introduces German naturalists Karl Ernst von Baer, who observed that early-stage embryos of different species looked very similar, and Ernst Haeckel, who took that idea too far with his motto “ontogeny recapitulates phylogeny” and took some liberties with his famous embryo drawings.
The real kicker here? Walter Garstang and the sea squirt.
“innovations never come about during the great transitions they are associated with. I am just going to step back while you read that sentence again.”
Sea squirts hatch as free-swimming tadpoles, complete with nerve cord, gill slits, and a connective tissue rod, a sort of proto-backbone. Adult sea squirts lose all this when they metamorphose. Garstang proposed that the ancestor of all vertebrates resulted from the freezing of larval traits during sea squirt development. I came across this before when reviewing the rather technical Across the Bridge, where Henry Gee mentions it almost off-handedly on page 167: “Paedomorphosis produced the ancestor of vertebrates”. You would be forgiven for missing the significance of that sentence. Shubin’s talent lies in turning this observation from a “What…?” into an “Oh my god!” moment.
Or take Félix Vicq D’Azyr’s realisation that some body parts are copies of each other. Ray Lankester’s observation that species can evolve by losing traits. (The evolution of limbs repeatedly involves the loss or fusion of bones, always in the reverse order in which they are formed, a sort of last in first out principle: last formed first lost). Stephen Jay Gould’s thought experiment of “replaying the tape of life” and the question of how repeatable evolution is. (The answer: quite.) Lynn Margulis’s idea of endosymbiosis. Or Nicole King’s work on choanoflagellates: the single-celled creatures you have never heard of that can form colonies and are the closest living relative to multicellular life forms.
Time and again, Shubin shows how evolution can reuse, repurpose, or rejiggle already existing structures and processes. I don’t know about you, but these kinds of spine-tingling revelations were what drew me to study biology.
“Time and again, Shubin shows how evolution can reuse, repurpose, or rejiggle already existing structures and processes.”
Another powerhouse of innovation is DNA, and genetics can tell us much about evolution. These sections are a giddy ride where Shubin highlights one after another stupendous concept. Take the huge similarity between e.g. chimps and humans: genome sequencing revealed some 95%-98% similarity. Why are we so different then? Because DNA is not just a molecule containing gene after gene. Like a circuit board, it is a network, where some pieces of DNA function as switches that turn other genes on and off. This is the field of evolutionary development or evo-devo and offers another way for small changes to have big effects. (On a side-note, it would offer a possible mechanism for Noam Chomsky’s proposed single mutation that led to human language, see my review of Why Chimpanzees Can’t Learn Language and Only Humans Can.)
Hox genes control the development of whole body segments and can be repurposed to make other structures, such as limbs. Most DNA does not even code for anything and Susumu Ohno surmised it results from copying processes gone wild, whether gene, chromosome or whole-DNA duplication (biologists call this last one polyploidy, it is common in plants). And then there is Barbara McClintock’s discovery of jumping genes: selfish genetic elements that multiply and willy-nilly insert themselves all over a DNA molecule. If rogue replication sounds an awful lot like cancer, well, that is because it is – evolution and cancer are closely linked. And how about this? If such a jumping gene mutates and becomes a genetic switch, they can insert switches all over a genome. Dramatic new traits that at first sight would require an unlikely number of separate mutations suddenly become a whole lot more plausible. One example Shubin provides is the evolution of pregnancy.
Even viruses are not exempt. You might remember that a virus commandeers a host’s biochemical machinery for its own reproduction. Some viral genes can end up in the host’s DNA by accident or, in the case of retroviruses, by design. This viral DNA can be neutered and repurposed, offering another option for rapid evolution. We even have turned this into a powerful biotechnological tool, CRISPR, that allows fine-scale gene editing, rather than the previous blunt tools of genetic modification.
“DNA is not just a molecule containing gene after gene. Like a circuit board, it is a network, where some pieces of DNA function as switches that turn other genes on and off. This […] offers another way for small changes to have big effects.”
Shubin reveals there is a plethora of pathways to rapid evolution and sudden transformations. Some Assembly Required is a very pleasant mix of the latest science, the historical roots of ideas, and the people behind them. Not infrequently, these stories of discovery show multiple people converging on the same idea at the same time (as was the case for Darwin and Wallace). Or show people being far ahead of their time, resulting in them being ignored or even ostracized for heretical views. The latter, sadly, involves a fair share of brilliant women whose ideas were initially not taken seriously.
Like a spider in a web, this book sits in the centre of a large number of topics I have been reading about, lighting up paths of intellectual enquiry branching off in different directions. For a moment, while reading this book, I was a young student again, attending lectures, and getting acquainted with mind-blowing ideas. Frequently funny and always eloquent, Shubin’s power as a science communicator is to make you fall in love with evolutionary biology all over again.
* It took more than three years after this review, while reading another book, before it occurred to me to ask: wait a minute, is this not the same process that Stephen Jay Gould and Elisabeth S. Vrba termed exaptation in their 1982 paper? Indeed, their definition, “features that now enhance fitness but were not built by natural selection for their current role“, and their inclusion of feathered dinosaurs as an example for me confirm that Shubin is talking about the same process in this book. Though the book is no less brilliant for it, and he mentions Gould in another context, it is odd that he does not mention exaptation here.
Disclosure: The publisher provided a review copy of this book. The opinion expressed here is my own, however.
Other recommended books mentioned in this review:
or 
or 
__________________________________________________________________
or 
or 
, __________________________________________________________________
, __________________________________________________________________
, 
or 
, __________________________________________________________________
, 
, __________________________________________________________________
or 
or __________________________________________________________________
]]>
,