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  down into fragments with only one or two carbon atoms. Perhaps,

  Harold suggested, higher pressure and temperature would reverse this

  trend and induce pyruvate plus carbon dioxide to form oxaloacetate. If

  so—if we could demonstrate that hydrothermal conditions promote

  such a key metabolic reaction—then hydrothermal vents would be-

  4

  GENESIS

  come even more of a focus for the origin of metabolism. Experimen-

  talists dream of such opportunities—a simple experiment with a big

  potential payoff.

  We agreed on a range of temperatures from 150°C to 300°C and

  pressures from 500 to 2,000 atmospheres—conditions relevant to hy-

  drothermal systems at and below Earth’s deep-ocean floor. But achiev-

  ing such conditions is easier said than done.

  It was time to pay Hat Yoder a visit.

  Every scientific career rests on the support of colleagues who act as

  teachers, collaborators, and employers. In my career, Hatten S. Yoder

  Jr. served in all three roles. He is my scientific hero. Burly, handsome,

  with big, powerful hands, Hat built his high-pressure lab at Carnegie’s

  Geophysical Laboratory from scratch, shortly after returning from ac-

  tion with the Pacific Fleet in World War II. For more than half a cen-

  tury, he maintained this premier facility, working tirelessly in his quest

  to understand the origins of rocks. [Plate 1] Even at the age of 75, I

  knew he would jump at the chance to try something new.

  “What P and T?” he asked.

  My response was somewhat sheepish. Hat’s pressure lab was de-

  signed to achieve extreme conditions: pressures of 10,000 atmospheres

  at more than 1,000°C. Running our proposed experiments at a measly

  2,000 atmospheres and 250°C would be like using a blast furnace to

  bake a cake. But an experiment is an experiment, and after only the

  slightest raising of eyebrows and barely audible “hmmph!” Hat was

  ready to go.

  High-pressure experiments are not for the faint of heart. Even at

  pressures of only a few atmospheres, hot gas can cause a nasty explo-

  sion. Your pressure cooker sustains no more than a pressure of 2 atmo-

  spheres, your car’s tires less than 3, and both can blow out violently.

  Hat’s home-built device, aptly called a pressure bomb, worked at thou-

  sands of atmospheres with a volume about the size—and with the same

  explosive power—of a stick of TNT. A catastrophic, explosive failure at

  those pressures could knock out a corner of the lab building. But no

  such worries attached to the pyruvate project.

  Our experimental strategy relied on a classic metal-capsule tech-

  nique for studying chemical reactions at high temperatures and pres-

  PROLOGUE

  5

  sures: Simply seal reactants into tiny cylindrical gold tubes about the

  size of a large grain of rice. The soft, chemically inert gold crushes

  down on the reactants, providing an isolated high-pressure, high-tem-

  perature environment.

  We crafted our capsules from a cylinder of gold a foot long, like a

  precious soda straw. I cut the cylinder into 1-inch lengths and welded

  each piece shut at one end. Water and pyruvate, both liquids, loaded

  easily into the capsules with a syringe—50 milligrams of water and 3

  milligrams of pyruvate, just a droplet. It’s difficult to weld shut a tube

  containing a gas, so we adopted an old experimental trick and used a

  white powdered chemical called oxalic acid dihydrate, which breaks

  down to water plus carbon dioxide above 100°C.

  My first attempts at welding the gold tubes shut were a mess. I

  weighed and loaded the reactants, crimped shut the tube’s open end,

  and placed the gold capsule into a vise, with the crimped end peeking

  out above thin steel jaws. A successful weld requires one smooth flick

  of the wrist with a carbon-arc welder, a graphite rod the size of a pencil

  that carries an intense electrical current. The gold is supposed to melt

  and flow, zipping up the capsule in a fraction of a second. But as my

  welder heated the gold, a portion of the volatile pyruvate boiled away.

  A sudden burp of smelly gas blew an ugly, gaping hole in the weld,

  ruining the carefully weighed ratios of reactants. After a lot of trial and

  error, I learned to weld one capsule end (using a microscope to see

  what I was doing), while the other end was immersed in ultracold liq-

  uid nitrogen, a frigid –196°C bath that froze the volatile reactants. The

  welder would erupt into blue-white flame and the gold would sputter

  and melt, sealing the tube. Eventually my batting average rose above

  0.500.

  Hat inserted three identical gold capsules into a platinum holder in-

  side a foot-long nickel metal cylinder that would serve as an electric

  furnace. Decades of experience streamlined his routine. After the cap-

  sules are inserted, load the cylinder with ceramic filler rod, thermo-

  couple wires, and ceramic end cap, and pack it all with a fine, sandlike

  powder of white aluminum oxide. Attach that sample assembly to the

  “head,” a fat steel plug that holds in pressure while providing insulated

  channels for wires that carry electric current for the heater and tem-

  6

  GENESIS

  perature sensors. Insert the cylinder and head into the massive metal

  bomb. Seal the bomb with a giant 6-inch-long nut with a 6-sided head.

  Tighten the nut with a 3-foot-long 20-pound wrench; use a 3-foot-

  long pipe as an extension for added torque.

  Hat banged away at the unwieldy wrench, making a horrendous

  racket as he tightened the nut just a bit more for safety. “It’s always

  good to make a lot of noise in the lab,” he said. “That way the director

  will know you’re working.”

  We retreated behind a wall of battleship gray, war-salvage naval

  armor as Hat opened and closed a bewildering sequence of valves to

  fill the system with pressurized argon, an inert gas. Ka-chunk, ka-chunk,

  ka-chunk! The argon gas compressor pumped the bomb to 2,000 at-

  mospheres in a matter of minutes. Hat set the computerized furnace

  controls to ramp the temperature up to 250°C, and we were off. Deep

  inside the steel bomb the gold tubes were being crushed and heated to

  conditions similar to those found several miles beneath Earth’s sur-

  face. In such an extreme environment, the pyruvate was sure to do

  something interesting. We went to lunch.

  Two hours later, we were back in the high-pressure lab to quench

  the run. When the current shut off, the temperature dropped rapidly,

  cooling to below 100°C in about a minute or so. Hat released the pres-

  sure with a whoosh, unscrewed the big nut, and pulled out the sample

  assembly. He dumped the cylinder’s contents into a shallow metal tray:

  end cap, thermocouple, filler rod, platinum holder, lots of fine white

  sand, and three fat, shiny gold capsules spilled out. Success! The cap-

  sules had held! We itched to know what was inside. Two capsules went

  into the freezer, while I took the third upstairs for analysis.

  There is nothing sophisticated about opening a gold capsule; you<
br />
  simply snip open one end and pour out the contents. First I washed

  the outside of the capsule in organic solvents to avoid any contamina-

  tion by machine oil or fingerprints. Then I froze it in liquid nitrogen,

  so that the contents would not leak out during the snip. I positioned

  the capsule over a glass vial to catch the gold and its contents. Just a

  little snip . . . usually does the trick. . . . Kapow! The gold weld blasted off into some remote corner of the lab, propelled by the sudden release of what must have been several atmospheres of internal gas pres-

  sure. A bit shaken, I dropped the capsule into the bottom of the vial,

  where it lay dormant for a few seconds. But then it began to hiss and

  foam as a yellow-brown oily substance frothed out, coating the gold

  PROLOGUE

  7

  and the glass. A pungent odor not unlike Jack Daniels permeated

  the lab.

  The pyruvate had clearly reacted, but it did not look anything like

  colorless, odorless oxaloacetate. What had we made?

  Time to consult George Cody [Plate 1], a recent arrival at the lab

  and an organic geochemist trained to analyze messy, oily stuff. George

  is enthusiastic, loquacious, and—luckily for us—he can’t seem to say

  no. He is also an expert in the chemistry of coal; he tends to snow

  visitors to his office with a blizzard of arcane chemical names and reac-

  tions. He thinks out loud and scribbles diagrams of molecules and re-

  actions on any available surface, including the protective windows of

  his lab’s chemical hoods. When I showed him the smelly goo, he knew

  just what to do.

  “GCMS,” he said, “We probably don’t need CI.” I nodded as if I

  understood what he was talking about. “Let’s use BF propanol as the

  3

  derivatizing agent. The Supelco column should work fine.”

  He had proposed that we analyze our suite of products by passing

  them, together with a chemically inert gas, through a long, thin tube

  filled with specially prepared organic molecules. This technique, gas

  chromatography (the “GC” of GCMS), separates different molecules

  according to how fast they move through the column. In general,

  smaller, less reactive molecules move faster than bigger, “sticky” mol-

  ecules. The gas chromatograph sorts a collection of different molecules

  into separate little pulses, typically over a period of 30 or 40 minutes.

  Then comes the mass spectrometer (the “MS” of GCMS), which

  measures the relative masses of molecules and their fragments.

  George’s mass spectrometer blasts molecules into lots of smaller pieces

  of distinctive weights, so each pulse from the GC can be analyzed sepa-

  rately as a suite of characteristic mass fragments, providing a kind of

  fingerprint of the product molecule.

  It took a couple of hours of chemical processing to prepare the

  concentrated liquid sample for analysis. George filled a syringe with

  the pale yellow liquid and injected a tiny drop into the GCMS with a

  practiced, swift motion. We sat back to watch as a spectrum gradually

  appeared on the computer monitor. The first peak showed up at 10.79

  minutes—a small molecule with probably only two or three carbon

  atoms. Then another peak at 11.71 minutes, and another at 11.96.

  Faster and faster peaks appeared, piling in on top of each other, every

  spike representing additional molecular products. By the 20-minute

  8

  GENESIS

  mark, a broad hump decorated with hundreds of sharp spikes was

  emerging.

  “Humpane,” George muttered in disgust. Pyruvate had reacted in

  our capsules, to be sure. But instead of the simple 3 + 1 = 4 reaction

  that Morowitz had proposed, we had produced an explosion of mol-

  ecules—tens of thousands of different kinds of molecules. Not a trace

  of oxaloacetate was to be found, but a bewildering array of other mo-

  lecular species had emerged. It might take a lifetime to decipher the

  contents of just one such molecular suite.

  One conclusion was obvious. Some very dynamic organic reac-

  tions proceed rapidly at hydrothermal conditions. In one sense,

  Morowitz’s hypothesis had failed: Pyruvate doesn’t react with carbon

  dioxide to form oxaloacetate under those conditions. But we had

  caught our first glimpse of a robust, emergent carbon chemistry in a

  hydrothermal environment. This was chemistry worth exploring.

  Where to begin? We were faced with choosing from among thou-

  sands of simple carbon-based molecules over a wide range of pressure,

  temperature, and other experimental variables—work to devour a

  hundred scientific lifetimes.

  What were we getting ourselves into?

  1800

  1600

  1400

  1200

  1000

  800

  600

  Intensity (counts per second)

  400

  200

  13.00 14.00 15.00 16.00 17.00 18.00 19.00 20.00 21.00 22.00 23.00 24.00 25.00 26.00 27.00

  Time (seconds)

  A diverse suite of molecules emerges when pyruvate is subjected to high temperature and pressure. These products appear as numerous sharp peaks superimposed on a

  broad “humpane” feature on a gas chromatogram.

  Part I

  Emergence and the Origin of Life

  All origin-of-life researchers face the baffling question of how the

  biochemical complexity of modern living cells emerged from a

  barren, primordial geochemical world. The only feasible approach is

  to reduce biological complexity to a comprehensible sequence of chem-

  istry experiments that can be tackled in the human dimensions of space

  and time—a lab bench in a few weeks or months. George Cody, Hat

  Yoder, and I were eager to continue our hydrothermal experiments,

  but what should come next? We knew that the simplest living cell is

  intricate beyond imagining, because every cell relies on the interplay

  of millions of molecules engaged in hundreds of interdependent

  chemical reactions. Human brains seem ill suited to grasp such multi-

  dimensional complexity.

  Scientists have devised countless sophisticated chemical protocols,

  and laboratories are overflowing with fancy analytical apparatus.

  Chemists have learned to synthesize an astonishing array of paints,

  glues, cosmetics, drugs, and a host of other useful products. Yet when

  confronted with the question of life’s ancient origin, it’s easy to be-

  come mired in the scientific equivalent of writer’s block. How does

  one begin to tackle the chemical complexity of life?

  One approach to understanding life’s origin lies in reducing the

  living cell to its simpler chemical components, the small carbon-based

  molecules and the structures they form. We can begin by studying rela-

  tively simple systems and then work our way up to systems of greater

  complexity. In such an endeavor, the fascinating new science of emer-

  gence points to a promising research strategy.

  9

  1

  The Missing Law

  It is unlikely that a topic as complicated as emergence will

  submit meekly to a concise definition, and I have no such

 
definition.

  John Holland, Emergence: From Chaos to Order, 1998

  Hot coffee cools. Clean clothes get dirty. Colors fade. People age

  and die. No one can escape the laws of thermodynamics.

  Two great laws, both codified in the nineteenth century by a small

  army of scientists and engineers, describe the behavior of energy. The

  first law of thermodynamics establishes the conservation of energy.

  Energy, which is a measure of a system’s ability to do work, comes in

  many different forms: heat, light, kinetic energy, gravitational poten-

  tial, and so forth. Energy can change from any one form to another

  over and over again, but the total amount of energy does not change.

  That’s the first law’s good news.

  The bad news is that nature places severe limitations on how we

  can use energy. The second law of thermodynamics states that heat

  energy, for example, always flows from warmer to cooler regions, never

  the other way, so the concentrated heat of a campfire or your car’s

  engine gradually radiates away. That dissipated heat energy still exists,

  but you can’t use it to do anything useful. By the same token, all natu-

  ral systems tend spontaneously to become messier—they increase in

  disorder, or “entropy.” So any collection of atoms—be it your shiny

  new shoes or your supple young body—gradually deteriorates. The

  second law of thermodynamics is more than a little depressing.

  But look around you. You’ll find buildings, books, automobiles,

  bees—all of them exquisitely ordered systems. Despite the second law’s

  11

  12

  GENESIS

  dictum that entropy increases, disorder is not the only end point in the

  universe. Observations of such everyday phenomena as sand dunes,

  seashells, and slime mold reveal that the two laws of thermodynamics

  may not tell the entire story. Indeed, some scientists go so far as to

  claim that a fundamental law of nature, the law describing the emer-

  gence of complex ordered systems (including every living cell), is miss-

  ing from our textbooks.

  THE LAWS OF NATURE

  The discovery of a dozen or so natural laws represents the crowning

  scientific achievement of the past four centuries. Newton’s laws of mo-

  tion, the law of gravity, the laws of thermodynamics, and Maxwell’s

  equations for electromagnetism collectively quantify the behavior of