Arrival of the Fittest: Solving Evolution's Greatest Puzzle (6 page)

Until a few years ago this principle was not merely unknown but beyond reach, and this book could not have been written. Because life is built of molecules, we need to understand molecules to understand innovation: not only the genotype embodied in DNA, but how this genotype helps build a phenotype. And a phenotype like that of a human body is not just a string of DNA. It is a hierarchy of being that descends from the visible organism, its tissues and cells, to the molecular webs formed by metabolic molecules, signaling molecules, and many others, extending down to the level of individual proteins. New phenotypes can originate at each level. A mere thirty years ago, we knew little of this staggering complexity.

And if
we
knew little, just imagine how much less Darwin knew. The list of things that he didn’t know is practically an encyclopedia of modern biology. He wasn’t just ignorant of how phenotypes were inherited. He also had no knowledge, in those pre-Mendelian days, of genes, to say nothing of DNA and the genetic code. He also knew nothing of population genetics and little of developmental biology—he was oblivious to how molecules build bodies. He had no inkling of life’s true complexity (and many after him thought they could safely neglect it). But to crack the secret of innovation, we need to embrace it.

The time-honored way to study life’s complexity is to focus on one or a few genotypes and their phenotype. This is how early geneticists found many genes in the first place—by tracking a phenotypic change back to its origin in a mutated gene. Later in the genome era, the same idea worked well to find out what a stretch of DNA does: Mutate it and see what happens to the phenotype. These strategies led to striking discoveries, mutations in genes that create flies with two pairs of wings instead of one, plants with transformed leaves, microbes able to survive on new foods. They created many examples of mutant genotypes and strangely altered phenotypes.

The problem is that examples are not enough. Explorers cannot chart a newly discovered continent by making a single landfall and taking a walk on the beach. They need to circumnavigate it to draw its contours. They have to sail into its interior from its river deltas. And they need to traverse its mountain ranges, deserts, and jungles. We need to do just that to draw the elusive maps of life’s creativity—the genotype-phenotype maps that chart each change in a genotype and how it affects the phenotype. We need genotype-phenotype maps to complete Darwin’s job.
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Even with the best technologies, these maps are not easy to draw. For a high-resolution map, we would need to understand the intricately folded phenotypes of more than 10
¹³⁰
different amino acid strings, and that’s before adding any of the higher layers of a phenotype, brought forth by thousands of genes and proteins. In other words, drawing a high-resolution map is not just hard but impossible. Luckily, though, we do not have to map every grain of sand in this new continent. If we care just about its topographical features, we can get away with studying fewer genotypes. But we still need to examine thousands to millions of them. And therefore we need to choose carefully which of the myriad aspects of phenotype we study. We need to choose those that are important for innovation in life’s history, and where existing information or predictive technology is sufficient to draw the map.

In these maps, Platonic essentialism is making a comeback, after decades in which it served as the antihero of evolutionism.
⁵⁶
The essentialism of the twenty-first century, though, is much richer than Plato’s world of simple geometric shapes. It reveals a world full of meaning, compatible with Darwinism but going far beyond it, that is key to understanding how nature creates. This world is inaccessible to our naked eyes, just like the question of whether all four legs of a galloping Sallie Gardner leave the ground, but we can explore it with the best technologies currently available.

These technologies have helped us reveal a Platonic world of crystalline splendor, the foundation of life’s innovability, which began with life’s very origin some four billion years ago.

H
ere is an amazing experiment you can try at home. Put wheat in a container and seal the opening with dirty underwear. Wait twenty-one days, and mice will emerge. Not just newborn mice, but grown adult mice. At least that’s what the seventeenth-century physician and chemist Jan Baptista van Helmont reported.
¹
(He also revealed that scorpions would emerge from basil placed between two bricks and warmed by sunlight.)

Van Helmont wasn’t the first to postulate the doctrine of spontaneous generation, which dates back at least to Aristotle, though he was among the last. Today, any scientist reporting that wheat and underwear conspire to create new life would be forever branded as a crackpot, but Van Helmont’s sloppy experiment did not cause much of a stir, and he died a respected man in 1644. Spontaneous generation was so widely accepted in his time that his experiments just proved the obvious.

A few decades after Van Helmont’s death, the Italian physician Francesco Redi showed us how experiments like this should be done.
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Dump meat in a jar and in good time it will be crawling with maggots. But not spontaneously created ones: When Redi covered the jar with muslin, no maggots emerged, because flies could no longer deposit their eggs in the meat.

Redi helped speed the decline of spontaneous creation. So did the seventeenth-century Dutch fabric merchant and lens grinder Antonie van Leeuwenhoek, whose microscopes opened the door to the world of microbes. For a time, microbes, being so much smaller than visible life, offered refuge to the remaining advocates of spontaneous generation. These were people like the Scottish priest John Needham, who argued in the mid-eighteenth century that decaying organic matter created microbes.
³
Another century later Louis Pasteur would show that Needham had it backward: Microbes cause the decay of organic matter, not the other way around. Pasteur hammered the last nail into the coffin of spontaneous creation when he sterilized a nutrient broth and the air around it and showed that it remained lifeless.
⁴

Pasteur could show that spontaneous generation didn’t exist, but he and his contemporaries could not have known why: The origin of life is a problem for chemists, not biologists. And chemists in the nineteenth century suffered from the same disease as the Mendelists who tried to understand new variation in the early twentieth century: They were born too early. Dmitri Mendeleev had barely worked out the periodic table of the elements, and the chemistry of life was a big blank spot. Chemistry in general took a long time to become a respectable science in its own right, perhaps because of its deep roots in alchemy. Well into the twentieth century, after his first wife had run off with a chemist, the Nobel Prize–winning quantum physicist Wolfgang Pauli would remark to a friend that “had she taken a bullfighter I would have understood, but an ordinary chemist . . .”
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A century later we know that the overwhelming obstacle facing spontaneous generation is probability, or rather improbability, resulting from life’s enormously complex phenotypes. If even a single protein, a single specific sequence of amino acids, could not have emerged spontaneously, how much less so could a bacterium like
E. coli
with millions of proteins and other complex molecules? Modern biochemistry allows us to estimate the odds, and they demolish the spontaneous creation of complex organisms.

This does not mean that spontaneous creation did not occur in life’s early history. A natural origin of life even requires it, but in a much humbler form than a modern cell or even a modern protein. Earth’s first life form was far more like an oxcart than a Ferrari. In fact, it was a lot more like a wheel than an oxcart. And even this wheel was not created in one giant leap, but in many modest steps. Although the muck of deep time has eroded their footprints, chemists have reconstituted some of these steps, which are the subject of this chapter. They not only illustrate how it could have happened but prove an even more important point: Even before life itself arose, nature’s creativity used the same principles it uses today. Then and now, the new and improved arrives through new chemical reactions and molecules.

The Hadean Eon, which marks the beginning of earth’s geological history more than four billion years ago, is aptly named after the Greek underworld, because the early earth was a hellish place. It began with a surface of liquid magma surrounded by an atmosphere of vaporized rock.
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And even after the surface had congealed into a solid crust, Mother Earth was not an inviting place. Had you visited the Hadean earth from outer space, you would have seen a tortured skin pockmarked with countless volcanoes, steamed by scalding rains that poured into the primordial oceans. Only the enormous pressure of the atmosphere—much denser than today—prevented these oceans from boiling away. Needless to say, breathing this atmosphere would have felled you instantaneously, noxious as it was from deadly amounts of carbon dioxide and hydrogen.
⁷
Ducking for cover might also have been smart, for multiple giant asteroids tore into early earth during a period called the Late Heavy Bombardment. You can still shudder at their scars, giant craters visible nightly on the moon, even though the churning continents here on earth have erased most visible traces of these ancient cataclysms. We know their age—and that of earth itself—from ancient rocks that contain slowly ticking chemical clocks, materials like uranium, whose radioactive decay marks the passing eons.

Most remarkable about this period is the speed with which life got going once the worst was over, just about 3.8 billion years ago. A mere few hundred million years later—less than 10 percent of earth’s age today—the first fossilized microbes appear.
⁸
Even closer to the magic boundary of 3.8 billion years ago, telltale traces of an ancient metabolism in the form of light isotopes of carbon appear in rocks from West Greenland.
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Life wasted no time, and appeared almost as soon as it
could
appear. This tells us that life’s origin and the innovations behind it might not be that hard to come by. And that innovability is as old as life itself.

Life’s early appearance on earth demands a theory of its chemical origin. Among the earliest ones is the “primordial soup” theory, usually credited to Alexander Oparin and J. B. S. Haldane, the Haldane of modern synthesis fame, who wrote about it in the 1920s.
¹⁰
Remarkably, however, the ever-prescient Charles Darwin had this idea half a century before them. In an 1871 letter to his friend Joseph Dalton Hooker, he speculates, “If (and oh what a big if) we could conceive in some warm little pond with all sorts of ammonia phosphoric salts, light, heat, electricity etc present, that a protein compound was chemically formed, ready to undergo still more complex changes.” And in the same breath Darwin gives us a good reason why we might look in vain for such a warm little pond today: Its content would be instantly “absorbed or devoured” by today’s organisms.
¹¹

The primordial soup remained speculation for decades, until 1952, when it received a huge boost from Stanley Miller, a graduate student in the laboratory of Nobel laureate Harold Urey at the University of Chicago. Based on an informed guess at the composition of the gases that were present in the early atmosphere, Miller sealed these gases in a container, showered them with electric sparks to simulate primordial lightning, and washed the mixture in a rainfall of condensing water. After mere days, many organic molecules—those normally created by living organisms—had appeared in Miller’s miniature world. This was a monumental discovery, for it showed how organic molecules could have emerged from inorganic matter during the turbulent youth of our planet.
¹²
And Miller’s primordial ocean produced not just any organic molecules. It created amino acids such as glycine and alanine, basic building blocks of modern proteins.
¹³
Later experiments produced many other of life’s construction materials, including sugars and parts of DNA.
¹⁴
But even more important was that Miller’s experiments moved life’s origin from philosophical speculation to the realm of hard, experimental science.

In September 1969, the world learned something that Miller had not known in 1952: Life’s molecules can emerge in environments even more hostile than that of the early earth. That September an exploding fireball briefly created a second sun in the sky over Murchison, an Australian town of a few hundred souls some one hundred miles north of Melbourne. After fracturing, the meteorite left a trail of smoke and smaller fragments, the largest of which fell harmlessly into a barn. This cosmic accident happened two months after man had first walked on the moon, at a time when scientists were itching to study extraterrestrial rocks.

As they scratched this itch, they found that the Murchison meteorite ferried a most unusual cargo. As old as the earth itself, it had wandered through outer space for eons, yet it contained several of the amino acid building blocks of proteins, as well as purines and pyrimidines, which are important DNA building blocks. Later work used twenty-first-century spectroscopy to show that it harbored more than ten thousand different kinds of organic molecules, although many of them in exceedingly small quantities.
¹⁵

The Murchison meteorite, it is important to know, is not a freak of nature. Similar meteorites have landed on earth, and countless other rocks ferry organic cargoes through the heavens.
¹⁶
Fortunately, we no longer need to wait until another one of them drops. Because molecules in the universe absorb or emit radiation that reveals their structure, the hypersensitive ears of radio telescopes can distinguish hundreds of different organic molecules whose voices whisper to us in multitudes from clouds of interstellar gas. Actually, they shout, since three-quarters of the molecules in these interstellar clouds are organic, and include key constituents of life, such as the amino acid glycine.
¹⁷
Incidentally, the single most abundant three-atom molecule in interstellar clouds is water, another blow to the notion that we and our planet are oh so very special.

Life’s simpler building blocks are so prevalent in the universe that molecules from space may have seeded life on earth itself. Meteorites and comets, especially those that bombarded the early earth, discharged ten times more water than currently fills all of the earth’s oceans, and a thousand times more gases than its present-day atmosphere.
¹⁸
What is more, they also delivered the rich buffet of organic molecules we find in interstellar space, and in a staggering number of servings. At least ten trillion tons of organic carbon, and perhaps a hundred times as much, have entered our atmosphere from outer space.
¹⁹
That is at least ten times more than all the carbon that circulates in living cells today. Especially important is the dust trailing behind comets that pass our orbit. Unlike large meteorites whose white-hot temperatures destroy some of their organic cargo during their explosive landing, cometary dust merely blankets the earth in an invisible but unceasing rain of life’s seeds.
²⁰
Perhaps we really are made of stardust.

We may never know whether most of life’s molecules were created in outer space or on earth. But regardless, these observations contain some simple and important lessons. The first is that life’s molecules emerge spontaneously in the right environment. The second is that this environment need not be, like Darwin’s warm pond, a nearby and very special place in the universe. It could be light-years away or as ubiquitous as interstellar gas.

The third is a lesson about innovation—I already mentioned it—that is still valid today: Innovation revolves around new molecules and the reactions that create them. To understand innovability, we need to understand the origins of these molecules.