Arctic bush pilots are a special breed. Years of solo flying endow them with a crusty independence and deep familiarity with the landscape below. After countless hours looking down on terrain, pilots’ eyes can discern patterns hidden from the rest of us. During one flight in 2002, our pilot suddenly pushed the plane into a steep dive and veered into a tight bank, a maneuver that dropped us from 10,000 feet to about 200 over the water in a small fjord. While I was seeing my life flash before my eyes, he saw a school of fish and, being a fisherman in his spare time, wanted to get a closer view. Even if my eyes weren’t closed, there was no way I could have perceived swimming arctic char from such an altitude.

During one chopper run in 1985, a pilot named Paul Tudge was shuttling supplies between distant camps on Canada’s Axel Heiberg Island and Eureka Sound, two of the North’s most spectacular places. When the air is clear and the ground free of snow, the colors and images are so sharp that tiny details can be visible miles in the distance. In this part of the Arctic barren mountain ranges border gentle valleys. The enduring action of ice, wind, and intense cold sculpts the bedrock into a range of obelisks, sheer walls, and potholes that almost seem unnatural. The sensation of otherworldliness is magnified by the lack of large plants: there are no trees, shrubs, or even grass in this area.

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Scanning brown, gray, and red vistas below his chopper, Tudge noticed something odd on the bedrock floor. Wind had winnowed a depression out of which poked objects that looked like trees. Not believing that there are trees in the Arctic, let alone ones that grew out of rock, Tudge set the chopper down. Lying in wait for him were not only tree stumps, but piles of branches, logs, and other tree parts jutting from the ground. He dutifully collected samples and shipped them to one of the Arctic’s leading fossil plant experts, James Basinger of the University of Saskatchewan. Basinger dropped everything and mounted an expedition as soon as money and permits could allow—of course, in the Arctic this process can take a year or more.

Awaiting Bassinger’s spade was an entire buried forest mummified in eroding rock. The cold dry air left fine anatomical details of the leaves and wood intact, including their original cellular structure. The wood of these trees even burns. There is a big difference between these logs and a Duraflame™; the Arctic ones come from a forest over forty five million years old.

The stumps that jut from this frozen landscape expose redwood trees that would have reached heights of one hundred and fifty feet or more. In the past, this place was no barren wasteland—it was alive with plants much like Northern California is today. Of course, nowadays the tallest tree up north is a little willow that rises mere inches off the ground. It is almost as difficult to see these willows from six feet as Tudge’s fossil forest from the air.

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About 20 years before Paul Tudge’s flight, the eminent paleontologist Edwin Colbert received a box in his office at the American Museum in New York City. Addressed from a famed geologist from Ohio State University, it contained a sheet of official letterhead wrapped around an isolated bone the size of a human finger. The colleague had collected this fragment in the field and wanted Colbert’s expert opinion.

From his many years on expedition to the American Southwest, Colbert was able to identify the bone in a split second: it had the distinctive texture and shape of a jaw from an ancient amphibian that lived over 200 million years ago. Looking somewhat like fat crocodiles, these creatures were widespread throughout the globe for a good chunk of geological time. But this ordinary looking fragment was very special—it came from the Transantarctic Mountains, a range two hundred miles from the South Pole.

As a longtime fossil hunter, the sirens in Colbert’s head went off. Opportunity knocked: here was a continent completely unexplored for fossils. Colbert wasted no time assembling a dream team of experts from the U.S. and South Africa, who from years of working on the rocks of this age, had the eyes to find new fossils. If fossil bones were present in Antarctica, this was the team to find them.

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Once their boots hit the Antarctic sandstones, Colbert and his team had a field day picking bones from the sides of barren hills. Fossils were virtually everywhere they looked. One creature had a body shaped like a medium-sized dog, only instead of a jaw like a carnivore it had a large bird-like beak. What stopped Colbert in his tracks was not this creature’s bizarrely chimeric form, but something far more mundane: paleontologists had known of this creature for decades. In the 1930s, South African geologists identified an entire layer that contains thousands of them extending across a wide swath of the Karoo Desert. This so-called “Lystrosaurus Zone” even reaches South America, India, and Australia. Now, with a Lystrosaurus level in Antarctica, Colbert and his colleagues uncovered yet another clue exposing the reality of continental drift. With the match of the rocks, coastlines, and fossils, an utterly new view of Antarctica emerged: the continent in the past sat as a keystone at the center of a vast supercontinent that included Africa, Australia, and India. This clump of continents covered much of the south of the planet.

The pile of fossils that Colbert’s group discovered revealed something else about the continent. Lystrosaurus, like the amphibian that led him there in the first place, was a cold blooded animal that could only live in warm tropical or subtropical climates; think big salamanders or lizards. Ditto the fossil plants. Colbert and his team labored near the center of a vast frozen continent, close to where Scott and his party froze to death nearly sixty years before. But everything inside the rocks pointed to one conclusion—Antarctica was once a warm and wet world teeming with tropical life.

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Expeditions that followed Colbert’s only exposed more of Antarctica’s disconnect between its desolate present and lush past. For much of its history, Antarctica was a natural paradise. The world that Colbert uncovered was followed by another filled with dinosaurs and their kin. In rocks even more recent, 40 million years old, this tropical continent was home to modern rain forests, amphibians, reptiles, birds and a whole menagerie of mammals.

Then, starting over 30 million years ago, the entire continent went into the freezer and with it came one of the most devastating events in the history of living things. Antarctica witnessed the greatest and most complete extinction of any continent in the history of the planet. From a world rich in plants and animals, virtually every landliving creature simply disappeared.

There is symmetry to Tudge’s flight near the North Pole and Colbert’s exploration of the South: one unveiled temperate forests, the other tropical animals in regions that today house frozen deserts. The story of the poles is that of the entire planet. Our present —with its polar ice—is an aberration. For most of history our planet was warm—almost tropical. Palm trees even dotted the landscape of what is today Wyoming. If the rocks of the world are a lens, they are one that reveals that our modern, relatively cold, landscape is not the normal state of affairs for the planet.

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In this great cooling lies one of the major events that shaped our bodies, our world, and our ability to see all.

Taking our Temperature

Carl Sagan once offered a paradox about our planet’s climate. The sun is not a constant beacon of light: it started its stellar life as a relatively dim star about 4.6 billion years ago and has increased in brightness ever since, being about thirty percent brighter and warmer now than when it formed. With such a dramatic increase in heat over the years, the earth should have been a frozen waste in the past, and now be a roiling cauldron of molten crust. Yet all our thermometers paint a different picture. Glaciers exist today during an era when the temperatures should be downright hellish. There are signs of liquid water inside three billion year old rocks—at a time when the earth should have been a ball of ice. Sure, we’ve had our moments of hot and cold, but compared to Venus’ surface temps of 900 degrees Fahrenheit and Mars’ of -81 degrees, the earth has been a stable eden relative to its celestial neighbors. Somewhere on the planet lies a thermostat that buffers it from dramatic extremes in temperature.

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Inroads to the thermostat were discovered by a student who was as persistent as he was headstrong. He started his graduate career by loudly proclaiming to his thesis advisor that he had a brand new theory of electrical conductivity. The response to this arrogant introduction was one word—“goodbye.” Perseverance paid off however and, probably to the relief of his teachers, Svante Arrhenius graduated from the University of Uppsala in 1884—albeit with the lowest possible passing grade. He then went on to think of other scientific problems.

One scientific puzzle was right in front of Arrhenius’ eyes. He saw the factories of the industrial revolution belching coal smoke, in his words, “evaporating our coal mines into the air.” Arrhenius knew from previous work that carbon dioxide, a major constituent of the fumes, could capture heat. He made a few calculations that revealed how increased carbon dioxide in the air would trap heat on the earth and raise global temperatures. This idea was to lay fallow for a number of years during which time Arrhenius won the Nobel Prize for work derived from the seemingly lackluster doctoral thesis that had so annoyed his professors.

The famous greenhouse effect is based on Arrhenius’ work. The more carbon dioxide there is in the atmosphere, the more heat is trapped by the planet, the hotter things get. Of course the reverse is true. But there is a deeper meaning to carbon in the air, one that only emerges when you take the long view, timescales that extend millions of years in the past.

The television character Archie Bunker once famously said of beer, “you don’t own it, you only rent it.” The same holds true for every atom inside us; we are the temporary owners of the materials that compose our bodies. Few of these constituents are more important to the balance of life and climate than carbon. The connection among parts of the earth depends on how carbon moves through air, rock, water, and bodies. To see this we need to consider living things, rocks, and oceans—not as entities in their own right, but only as a carriers of carbon. This perspective in science is utterly humbling: all of us living things are just stopping places for one class of atom as it marches along during our planet’s evolution.

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Viewed in this way, the amount of carbon in the air depends on a delicate balance of conditions. Carbon in the atmosphere mixes with water and pours down to the surface as a slightly acid rain. We see the effects of this in our daily lives; in my university built largely in the late 1800s, few gargoyles still have faces. Acid rain works on exposed rock everywhere—on mountainsides, rubble fields and sea cliffs. Once the acid rain breaks down rocks, the water—now also enriched with carbon that was inside the rocks—eventually winds its way, through streams and rivers into the oceans. At this point the carbon gets incorporated into the bodies and cells of the creatures that swim there: seashells, fish, and plankton. When sea creatures’ remains, loaded with carbon, settle to the bottom of the ocean they ultimately become part of the sea floor. And as we’ve known since Marie Tharp, Bruce Heezen, and Harry Hess, the sea floor moves only to be recycled deep inside the earth.

This chain of events removes carbon from the atmosphere, taking it from the air and moving it to the hot internal crust of the earth. Alone, these steps would suck all the carbon out of the air, not a happy state of affairs. The good news is that there is a recycling mechanism for carbon. Carbon in the interior of the earth gets injected back into the atmosphere by volcanoes that eject gasses. That is the long term source of much of the carbon we breathe: acid rain and the weathering of rocks remove carbon from the air, and volcanoes spewing gasses return it. Volcanoes typically release huge amounts of water vapor, carbon dioxide, and other gasses: by some estimates they spew over 120 million tons of carbon dioxide each year.

Like a chain reaction in which each step makes sense but the endpoints are completely counter intuitive, the conclusion to draw from carbon’s movement is that rock erosion is linked to climate. Lowering the amount of carbon dioxide in the air will move to drop the planet’s temperature. On the other hand, planetary events that increase the amount of carbon in the air—enhancing volcanic activity or slowing removal of carbon from the air—will, of course, serve to raise temperatures. Increasing erosion leads to lower temperatures, decreasing erosion to higher ones. Rock erosion by acid rain is like a giant sponge that pulls carbon dioxide from the atmosphere.

The movement of carbon links rocks to climate and ultimately answers Sagan’s paradox about the sun. The planet’s temperatures are kept within a narrow range by the dance of carbon molecules through air, rain, rock, and volcano. Hot weather leads to more erosion which leads to more carbon being pulled out of the air, which leads to colder weather. Colder weather leads to less erosion, increasing amounts of carbon in the air, and hotter temperatures. Liquid water is only possible on our planet because of the movement of tiny atoms from air to water to rocks—neither we, nor our vistas, would exist except for them. But liquid water is like the miner’s canary. Too much of it, or too little, reveals a shift in workings of the planet, changes that give it fevers and chills.

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What happened when the poles started to freeze about thirty million years ago? The shift from hot to cold occurred at the same time that the levels of carbon in the atmosphere dropped precipitously. But this begs the question: what changed the levels of carbon in the air?

Maureen (Mo) Raymo went to school to study climate and the kinds of geological changes that could impact it. And, like Ahrennius, she produced a thesis that elicited memorable comments from advisors. One went so far as to comment that her Ph.D. dissertation was “a total crock.”

Her path to that fine moment began like any other graduate student’s—she took a string of classes representing the core knowledge of her field. In geology seminars of the 1980s, much of the buzz was about global carbon and the earth’s thermostat. A classic paper, read by every student at the time, was written by Robert Berner and Antony Lasaga of Yale and Robert Garrols of Penn State and described this link chemical detail. The paper became affectionately known as BLaG after the initials in the last names of each author. Everybody read BLaG and everybody was tested on BLaG, despite the fact that virtually everybody, including the BLaG authors themselves, realized key details of their brilliant model had yet to be filled out.

Raymo took the usual class where the details of BLaG were presented. She also took classes on modern rivers, mountain formation, and tectonics. But unlike everybody else who sat through the same curriculum, she connected the dots.

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Everybody knew that the climate cooled drastically 35 million years ago but there was no known geological mechanism that could possibly have done this. What could drop the temperatures? Only a major planetary change could have possibly removed enough carbon to allow the such a major drop in temperature.

Then she looked at a globe and remembered her plate tectonics. The period of drastic cooling commenced at a pivotal time in the history of the planet. This was the time when the continental plate of India, which had been traveling north for hundreds of millions of years, began to slam into Asia. The result of this collision is like sliding two pieces of paper along a tabletop until they scrunch together—they crinkle and rise. A similar kind of mashup of the continents led to the rise of the Tibetan Plateau and the Himalaya mountains.

Raymo’s lead advisor (not the one who called her thesis a crock) was thinking about how a new mountain range would affect global wind currents, or serve to make a shadow that could foster storms. Raymo’s insight came from putting pieces together, namely thinking how a massive mountain range and plateau could effect the earth’s thermostat.

The Tibetan Plateau is a vast barren face of virtually naked rock. It contains over 82 percent of the surface area of the planet over 12,000 feet high. With the rise of such a plateau, came ever growing amounts of erosion of rock on its surface. When we look at the Himalayas, most of us see a dramatic series of mountains, but Raymo saw a giant vacuum sucking carbon dioxide from the atmosphere, with the rivers that drain them flushing the carbon into the sea.

The lightbulb in her head went off: the rise of the Tibetan plateau led to the shift from a warm earth to a cold one. And it did so by pulling carbon from the air.

Raymo’s theory makes sense of an enormous amount of data but gaining support for a theory like this is more like winning a criminal case on circumstantial evidence than it is a mathematical proof: only a heap of independent lines of evidence can nail the case. Raymo has made a very specific prediction—the test lies in using tools that can correlate measurements of the rates of uplift of the plateau, the levels of weathering of rock, to the amount of carbon in the air. There are altimeters in ancient rocks—altitude sensitive plants. The chemistry of rocks and oceans provides clues to the weathering rates and carbon. Carbon in the air dropped at the time of uplift, but we still do not have the precision to tie them to the uplift and weathering in detail. Whether weathering of the plateau alone is sufficient for the climate change we see, or it acted in concert with an as yet unknown, remains to be seen.

Excerpted from "The Universe Within" by Neil Shubin. Copyright © 2013 by Neil Shubin. Excerpted by permission of Pantheon, a division of Random House, Inc. All rights reserved. No part of this excerpt may be reproduced or reprinted without permission in writing from the publisher.