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:
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“Discovering Retroviruses: Beacons in the Biosphere“, written by Anna Marie Skalka, published by Harvard University Press in October 2018 (hardback, 177 pages)
I was really looking forward to this book and have mentioned it a number of times in previous reviews as several authors have highlighted that retroviruses are something quite special (see e.g. Viruses: Agents of Evolutionary Invention and Virusphere: From Common Colds to Ebola Epidemics: Why We Need the Viruses that Plague Us). Where normal viruses commandeer the host’s biomolecular machinery for their reproduction, retroviruses are even more intimately entwined with their hosts, transferring their genetic information to them.
Skalka first sets the stage with a short history of genetics, from Mendel to Crick and onwards to the “central dogma” (see my review of Unravelling the Double Helix: The Lost Heroes of DNA for more). That dogma refers to the finding that DNA is copied into single-stranded RNA which is then translated, three letters at a time, into amino acids that, when strung together, make up the workhorses of the cell: proteins. It has become a cornerstone of genetics. And exactly because of this, many scientists were not ready to accept the first suggestions in 1964 that retroviruses do it backwards, turning their little RNA genome into a string of DNA that becomes part of the host genome. Rather than a textbook approach that lays out the facts, Skalka chooses to tell the story chronologically, following the timeline of discoveries and introducing all the key players.
“In answer to the question: “what makes us mammal?” […] ultimately, as Skalka shows here, retroviruses did”
As also mentioned in Human Errors: A Panorama of Our Glitches, from Pointless Bones to Broken Genes, modern sequencing technology has revealed that our DNA is littered with remnants of retroviruses, many of which have become inactive and have suffered random mutations. The numbers are quite staggering: whereas ~1% of the human genome codes for all the proteins that make us tick, another 8% is of retroviral origin and larger fractions still consist of other jumping elements and so-called retrotransposons. Slowly but surely, what was initially deemed junk actually has a function (see also Junk DNA: A Journey Through the Dark Matter of the Genome and The Deeper Genome: Why There is More to the Human Genome Than Meets the Eye).
For one, this extra DNA offers hotspots of so-called recombination (i.e. the re-arranging of parts of an organism’s genetic material), which is one way to generate the genetic variation on which evolution can act. In the process, things sometimes break and diseases are caused. But it is not all bad news. Skalka details how this extra genetic material has been co-opted by our immune system; has added the digestive enzyme amylase, found in the pancreas, to our salivary glands allowing us to digest starch better; and has also been involved in the evolution of the placenta. Liam Drew asked the question: “what makes us mammal?” (see my previous review of I, Mammal: The Story of What Makes Us Mammals). One of his answers was: “the placenta did”. But ultimately, as Skalka shows here, retroviruses did. Without them, the placenta would not have happened. And, amazingly, mammals evolved them on five independent occasions!
There are other fascinating revelations about evolution throughout the book. Retroviruses may have very well been a necessary link in the transition from an RNA world (which is how many scientists believe life started, see Life from an RNA World: The Ancestor within) to a DNA world. I was similarly fascinated to read more about the use of retroviruses as an independent line of evidence when drawing up phylogenetic trees (i.e. family trees based on molecules such as DNA). As stretches of retroviral DNA are initially inserted in identical pairs, one way to mine them for information is by comparing mutation rates. This can reveal a timeline of when certain infections occurred and whether this happened before of after two species evolved to become separate. (My explanation leaves out some subtleties, Skalka goes into far more detail)
“retroviruses [can be used] as an independent line of evidence when drawing up phylogenetic trees”
Two further chapters give detailed accounts of how retroviruses have been implicated in causing both certain cancers and AIDS. Especially the chapter on AIDS and HIV goes into great detail on the biochemical and genetic basis of the disease, the development of drugs, the scary denialism propagated by a small minority (see also Pseudoscience: The Conspiracy Against Science), and the research that traced the origin to a virus that jumped from primates to humans in the 1900s (see also Virus Hunt: The Search for the Origin of HIV/Aids). And, as opposed to Viruses and Virusphere, Skalka does describe the recent discovery and developments around CRISPR, which consists of viral DNA stored in the host as a kind molecular vaccination card (see also A Crack in Creation: The New Power to Control Evolution).
Discovering Retroviruses is a short book, but it is dense and quite technical. I found I had to give it my full attention, sometimes going over certain passages twice to make sure I understood them. The readability is slightly hampered by the many abbreviations and gene and protein names that come with this field (a glossary would have been welcome in that regard), but that is made up for by a large number of clear colour illustrations that are very helpful in schematically showing how certain mechanisms work. The chronological format also means that you have to tease some of the details out of the narrative, although Skalka does an excellent job summarising things at the end of each chapter, and in her epilogue. As far as I know, Skalka’s is the first book on this topic aimed at a wider readership. If you have a serious interest in viruses, and retroviruses in particular, this well-researched and scholarly book is a must-read.
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:
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