July 30, 2020

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Decoding Four Billion Years
of Life, from Ancient Fossils to DNA.

by Neil Shubin.
Pantheon Books, 2020 (i-xii, 267 pages)

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PROLOGUE (ix-xii)

1) FIVE WORDS (3-27)




5) COPYCATS (124-145)


7) LOADED DICE (168-192)


EPILOGUE (215-218)




INDEX (257-267)

Selected Topics Highlighted:
    Contingency and chance
    Darwin, Charles
    Developmental abnormalities
    Developmental biology
    Fruit flies
    Genetic duplication
    Genome sequencing
    Gould, Stephen Jay
    Hox genes
    Huxley, Thomaas Henry
    Jumping genes
    Mayr, Ernst (evolution book)
    Molecular Clock Hypothesis
    "On the Origin of Species" (Darwin's book)
    Pauling, Linus
    Sacral vertebrae
    Single-celled creatures
    Sonic hedghog gene
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AUTHOR NOTES = Neil Shubin is the Robert R. Bensley Professor of Organismal Biology and Anatomy at the University of Chicago and is Associate Dean of Biological Sciences. He was elected to the National Academy of Sciences in 2011. He lives in Chicago.

SUMMARY = The author of the best-selling book, Your Inner Fish, gives us a lively and accessible account of the great transformations in the history of life on Earth — a new view of the evolution of human and animal life that explains how the incredible diversity of life on our planet came to be. Shubin takes readers on a journey of discovery spanning centuries, as explorers and scientists sought to understand the origins of life's immense diversity.

BOOK DESCRIPTION = Over billions of years, the great transformations in the history of life brought about whole scale shifts in how animals live and how their bodies are organized: the beginnings of bodies in single-celled creatures, ancient fish evolved to walk on land, reptiles transformed into birds that fly, and apelike primates evolved into humans that walk on two legs, talk, and write. Paleontology has been transformed over the last 50 years by tools and techniques of molecular biology — and it is that revolution in our understanding of the evolution of life that Shubin traces here.

For more than a century, paleontologists have traveled the globe to find fossils that show how such changes have happened. In addition, Shubin describes how over the last half-century, scientists have been able to explore how genetic recipes build bodies during embryological development — how these inventions and adaptations occur in a nonprogressive manner in different contexts, at different speeds.

We have now arrived at a remarkable moment — prehistoric fossils coupled with new DNA technology have given us the tools to answer some of the basic questions of our existence: How do big changes in evolution happen? Is our presence on Earth the product of mere chance? This new science reveals a multibillion-year evolutionary history filled with twists and turns, trial and error, accident and invention.

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LIBRARY JOURNAL REVIEW = Expanding on his previous two best sellers (Your Inner Fish; The Universe Within), Shubin (organismal biology & anatomy, Univ. of Chicago) shows how evidence from fossils combines with discoveries from DNA to promote new understandings of evolution. Taking a tour of the ideas of scientists over centuries, Shubin explains how creatures often did not develop new organs over time, as science once asserted, but rather repurposed existing organs to serve new functions. The author notes that changes in the timing of embryonic development, controlled by DNA, lead to differences in bodies. These changes, he says, act as recipes for bodies, encoded in DNA, passed along generations. Minor alterations in the code can have outsized ramifications, sometimes resulting in genetic defects or disease. Remnants of the molecules formed from these recipes can be traced through the ages, as clear a history as that found in fossils. Shubin explores deviations in genetic code, copycat codes, invasions of viruses and bacteria (co-opted for our use) into human DNA, and current experiments in genome editing. VERDICT In the end, the genetic constructions of all creatures are variations on a theme; we are all related. An engaging, must-read for anyone with an interest in evolution.-- Karen Nichter, University of Tennessee at Martin

PUBLISHERS WEEKLY REVIEW = Making complex scientific ideas both accessible to and enjoyable for the general public is a rare skill, but one that Shubin (Your Inner Fish), a University of Chicago biology professor, has mastered in his eloquent survey. He explores two complex and related evolutionary questions: how organisms bearing no immediately perceptible resemblance to each other — such as dinosaurs and birds — can be closely related; and how new traits — such as feathers or lungs — can appear. Writing for a lay audience, Shubin takes a historical perspective and describes the gradual accumulation of scientific knowledge. He explains that Darwin, without possessing the data available today, grasped that body parts evolve through "a change in function." In recent years, genetic testing on fish with lunglike organs has revealed that "lungs are not some invention that abruptly came about as creatures evolved to walk." Instead, lungs already existed in certain species of fish, but changed function when their descendants became land-dwellers. Shubin also covers discoveries about the genetic mechanisms behind such changes, such as studies pinpointing the specific areas in DNA that turn genes on and off during fetal development. This superb primer brings the intellectual excitement of the scientific endeavor to life in a way that both educates and entertains.

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[1] "An engaging, must-read for anyone with an interest in evolution."—Library Journal (starred review)

[2] "A rollicking ride . . . It's light of touch, anecdote-rich and funny . . . satisfyingly informative . . . Fossils, DNA, scientists with a penchant for suits of armour—what's not to love?" -- BBC Wildlife Magazine

[1] "Another winner from Dr. Shubin, who skillfully and thoughtfully steers us through the incredibly fascinating world of DNA and fossils. Dr. Shubin's clear and engaging writing rewards us with a deeper understanding of how all life on our planet is interconnected. Steeped in the paradigm of evolutionary theory, he inspires us to think more deeply about our connectedness with the natural world. Charles Darwin would applaud Dr. Shubin's clear explanations and insightful rendering of the incontrovertible evidence for the evolution of all life on planet Earth."-- Donald Johanson, director, Institute of Human Origins; discoverer of "Lucy"

[3] "Neil Shubin shows himself to be a natural storyteller and a gifted scientific communicator."—Wall Street Journal

[4] "Intimate and thoughtful . . . Exciting . . . [A] sweeping evolutionary history . . . One of the book's best features is a 30-page notes section at the end, in which each note could be fodder for an entire volume. These notes are separated by chapter, and many tell a short, engaging story, often accompanied by annotated suggestions for further reading. Readers will want to peruse this section and follow up on some of those readings." -- Science

[5] "Neil Shubin has been one of my favorite science communicators ever since I took his undergraduate anatomy course. In this ambitious and readable book, Shubin blends his own research, epic tales from the history of science, and the latest discoveries in paleontology and genetics to tackle some of the biggest mysteries of evolution. This is an engrossing account from a scientific storyteller at the height of his talents." -- Steve Brusatte, University of Edinburgh paleontologist and author of The Rise and Fall of the Dinosaurs

[6] "Shubin is a brilliant scientist storyteller—an eloquent narrator, who draws you into his rich, evolving world of walking fish and mutant flies, prehistoric birds and precocious biologists. Part adventure, part mystery, with twists and turns you couldn't make up if you tried, Some Assembly Required is an irresistible read!" -- Robert M. Hazen, Carnegie Institution for Science, and author of Symphony in C

[7] "Through tales of remarkable creatures, and some even more remarkable people who study them, Neil Shubin unravels the mystery at the heart of evolution—how nature invents. From bacteria to brains, fish lungs to ballistic salamander tongues, Shubin decodes the surprising origins of the marvelous gadgets that have driven the riot of life's diversity." -- Sean B. Carroll, author of The Serengeti Rules and Brave Genius

[8] "[Shubin's] four-billion-year history from ancient fossils to DNA presents the true picture to the general reader, with engaging portraits of contributing scientists past and current." -- Nature

[9] "He has done it again. Shubin gives us an insightful, fun, and authoritative look at the big story of life and its major transformations. In Some Assembly Required, one encounters curious scientists, surprising histories and a clear sense of the ways in which a diversity of scientific perspectives provides a richer view of life than could any one perspective on its own. This terrific book is new and exciting enough to engage a biology professor (Rob) and clear and engaging enough to fascinate a high school student (Olivia). We couldn't put it down (or rather, one of us would put it down for a minute only to have the other pick it up)." -- Prof. Rob Dunn, author of Never Home Alone and Olivia Sanchez Dunn, high school student

[10] "Enjoyable . . . Eloquent . . . This superb primer brings the intellectual excitement of the scientific endeavor to life in a way that both educates and entertains." -- Publishers Weekly (starred)

[11] "A welcome new exploration of the evolution of human and animal life on Earth . . . Shubin explores it with his characteristic enthusiasm and clarity . . . A fascinating wild ride." -- Kirkus Reviews (starred)

[12] "Exhilarating . . . [Shubin] is one of the best." -- Booklist (starred)

[13] "A pleasure to read . . . The exposition is clear enough to be followed by readers without background scientific training, but the range of topics discussed, the choice of illustrative details, and the historical and biographical background are such that I would expect even experts to find much in this book to inform and delight. The endnotes, as well as providing leading references and background material of interest to those who wish to dig deeper, add numerous interesting details worthy of the attention of any reader." -- 3 Quarks Daily

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When Napoleon Bonaparte invaded Egypt in 1798, he brought more than ships, soldiers, and weapons with his army. Seeing himself as a scientist, he wanted to transform Egypt by helping it control the Nile, improve its standard of living, and understand its cultural and natural history. His team included some of France's leading engineers and scientists. Among them was Étienne Geoffroy Saint-Hilaire (1772-1844).

Saint-Hilaire, at twenty-six, was a scientific prodigy. Already chair of zoology at the Museum of Natural History in Paris, he was destined to become one of the greatest anatomists of all time. Even in his twenties, he distinguished himself with his anatomical descriptions of mammals and fish. In Napoleon's retinue he had the exhilarating task of dissecting, analyzing, and naming many of the species Napoleon's teams were finding in the wadis, oases, and rivers of Egypt. One of them was a fish that the head of the Paris museum later said justified Napoleon's entire Egyptian excursion. Of course, Jean-François Champollion, who deciphered Egyptian hieroglyphics using the Rosetta Stone, likely took exception to that description.

With its scales, fins, and tail, the creature looked like a standard fish on the outside. Anatomical descriptions in Saint-Hilaire's day entailed intricate dissections, frequently with a team of artists on hand to capture every important detail in beautiful, often colored lithographs. The top of the skull had two holes in the rear, close to the shoulder. That was strange enough, but the real surprise was in the esophagus. Normally, tracing the esophagus in a fish dissection is a pretty unremarkable affair, as it is a simple tube that leads from the mouth to the stomach. But this one was different. It had an air sac on either side.

This kind of sac was known to science at the time. Swim bladders had been described in a number of different fish; even Goethe, the German poet and philosopher, once remarked on them. Present in both oceanic and freshwater species, these sacs fill with air and then deflate, offering neutral buoyancy as a fish navigates different depths of water. Like a submarine that expels air following the call to "dive, dive, dive," the swim bladder's air concentration changes, helping the animal move about at varying depths and water pressures.

More dissection revealed the real surprise: these air sacs were connected to the esophagus via a small duct. That little duct, a tiny connection from the air sac to the esophagus, had a large impact on Saint-Hilaire's thinking.

Watching these fish in the wild only confirmed what Saint-Hilaire inferred from their anatomy. They gulped air, pulling it in through the holes in the back of their heads. They even exhibited a form of synchronized air sucking, with large cohorts of them snorting in unison. Groups of these snuffling fish, known as bichirs, would often make other sounds, such as thumps or moans, with the swallowed air, presumably to find mates.

The fish did something else unexpected. They breathed air. The sacs were filled with blood vessels, showing that the fish were using this system to get oxygen into their bloodstreams. And, more important, they breathed through the holes at the top of their heads, filling the sacs with air while their bodies remained in the water.

Here was a fish that had both gills and an organ that allowed it to breathe air. Needless to say, this fish became a cause célèbre.

A few decades after the Egyptian discovery, an Austrian team was sent on an expedition to explore the Amazon in celebration of the marriage of an Austrian princess. The team collected insects, frogs, and plants: new species to name in honor of the royal family. Among the discoveries was a new fish that, like any fish, had both gills and fins. But inside it also had unmistakable vascular plumbing: not a simple air sac, but an organ loaded with the lobes, blood supply, and tissues characteristic of true human-like lungs. Here was a creature that bridged two great forms of life: fish and amphibians. To capture the confusion, the explorers gave it the name Lepidosiren paradoxa--Latin for "paradoxically scaled salamander."

Call them what you will — fish, amphibian, or something in between — these creatures had fins and gills to live in water but also lungs to breathe air. And they were not just one-offs. In 1860 still another fish with lungs was discovered in Queensland, Australia. This fish also had a very distinctive set of teeth. Shaped like a flat cookie cutter, such teeth were known from the fossil record from a species that was long extinct — an animal named Ceratodus found in rocks over 200 million years old. The implication was clear: lunged, air-breathing fish were global and had been living on Planet Earth for hundreds of millions of years.

An aberrant observation can be a game changer for how we see the world. Fish lungs and swim bladders spawned a generation of scientists interested in exploring the history of life by looking both at fossils and at living creatures. Fossils show what life looked like in the distant past, and living creatures reveal how anatomical structures work, as well as how organs develop from egg to adult. As we'll see, this is a powerful approach.

Linking studies of fossils and embryos was a fruitful area of inquiry for the natural scientists who followed Darwin. Bashford Dean (1867-1928) had an unusual distinction in academic circles — he is the only person ever to hold a curatorship at both the Metropolitan Museum of Art and, directly across Central Park, the American Museum of Natural History. He had two passions in life, fossil fish and battle armor. He founded the armor collection and displays at the Met, and he did the same for the fish collection at the Museum of Natural History. Befitting a person with such interests, he was a quirky individual. He designed his own armor and even took to wearing it on the streets of Manhattan.

When he was not donning medieval faulds, Bashford Dean was studying ancient fish. Somewhere locked inside the embryo's transformation from egg to adult, he believed, were answers to the mysteries of history and the mechanism of current fish's descent from ancestral species. Comparing fish embryos with fossils and reviewing the work in anatomy labs at the time, Dean saw that lungs and swim bladders look essentially the same during development. Both organs bud from the gut tube and both form air sacs. The major difference is that swim bladders develop on the top of the tube, near the spine, while lungs bud from the bottom, or belly side. Using these insights, Dean argued that swim bladders and lungs were different versions of the same organ, formed by the same developmental process. Indeed, some kind of air sac is present in virtually all fish but sharks. Like many ideas in science, Dean's comparison has a long history. Its antecedents can be seen in the work of nineteenth-century German anatomists.

But what do air sacs say about Mivart's critique and Darwin's response?

A surprising number of fish can breathe air for extended periods of time. The six-inch-long mudskipper can walk and live on the mud for over twenty-four hours. The aptly named climbing perch can wiggle from pond to pond as needed, sometimes even climbing branches and stepping over twigs in the process. But that perch is only a single species. Hundreds of species can gulp air when the concentration of oxygen in the water they inhabit declines. How do these fish do it?

Some, like the mudskipper, absorb oxygen through their skin. Others have a special gas-exchange organ above their gills. Some catfish and other species absorb oxygen through their guts, gulping air like food, only to use it to breathe. And a number of fish have paired lungs that look like our own. Lungfish live in water and breathe with their gills most of the time, but when the oxygen content of their stream is not sufficient to support their metabolism, they will push to the surface and gulp air into their lungs. Air breathing is not some crazy exception in an oddball fish — it is the common state of affairs.

Recently, researchers at Cornell University revisited the comparison of swim bladders to lungs, using new genetic techniques. Their question: What genes help build fish swim bladders during development? In looking at the catalog of genes that are active in fish embryos, they found something that would have pleased both Dean and Darwin. The genes that are used to build swim bladders in fish are the same ones used to make lungs in both fish and people. Having an air sac is common to virtually all fish; some use them as lungs, while others use them as buoyancy devices.

Here is where Darwin's answer to Mivart becomes so prescient. DNA clearly shows that lungfish, Saint-Hilaire's bichirs, and other fish with lungs are the closest living fish relatives to land-living creatures. Lungs aren't some invention that abruptly came about as creatures evolved to walk. Fish were breathing air with lungs well before animals ever stepped onto terra firma.

The invasion of land by descendants of fish did not originate a new organ — it changed the function of an organ that already existed. Moreover, virtually all fish have some kind of air sac, whether lung or swim bladder. Air sacs shifted from being used for a life in water to later enabling creatures to live and breathe on land. The change did not involve the origin of a new organ; instead the transformation was, as Darwin said more generally, "accompanied by a change of function." (page 9-16)

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RECOMMENDATION: You can re-read this summary according to a reinforcement schedule, such as a few hours later and a few days later and then several times in the next week or two. This strategy can help you take advantage of the power of the spaced-repetition method of memorization. Such deep introspection can strengthen your willpower and change your adaptive self-identity to increase your self-esteem.

You are your adaptable memory!

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Neil Shubin


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