Essays - Winter 2016

How Chemistry Became Biology

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And how LUCA, Earth’s first living cell, became Lucas, my adorable grandnephew

Photo-illustration by David Herbick

By Priscilla Long

December 7, 2015


 

 

LUCA is the ancestor we’re all descended from: the Last Universal Common Ancestor, the first living cell on Earth. It was nothing much—a single cell. A cell made up of molecules able to exist apart from myriad other molecules. A cell contained by some sort of membrane. An actual cell, one that could metabolize, meaning it could obtain energy from food. One that could replicate itself. One whose copies could form a population that could evolve. A living cell.

And Lucas? He’s my first grandnephew, five years old, energetic and bright. Cute. Adorable, actually. He was born in Ecuador, about four billion years after LUCA became the first living cell. Now he lives in Vermont. Lucas’s full name is Lucas Samay Yunga Korn. Lucas means light. Samay means, in the Kichwa language, vital energy, whether of an inanimate or a living thing. Yunga is Lucas’s father’s surname; Korn, his mother’s. He has a little brother—Asha. Today, Lucas Yunga Korn told his mother that he drew a “perfect frog.” He’s learning to sound out words. He plays with his friends in their snow fort.

How could this amazing child have evolved from one single cell, this LUCA that originated some four billion years ago? How could all the rest of us have come from this one single cell? Because that is what happened. All life on Earth came from one single first living cell. Therefore, all life on Earth is related. We are related to the frogs, the pond scum, the whales, the petunias. How do we know? Scientists do not prove this or that; they gather evidence. A strong bit of evidence that we all descend from the same single cell is the existence of “old genes,” shared by virtually every form of life on Earth. These old genes were, it’s thought, the genes in LUCA, the cell we evolved from.


Before Life

What do we know about Earth before life? Earth formed, along with the rest of our home solar system, about 4.6 billion years ago from coalescing gases and debris whirling about, the result of a supernova, or star explosion. (Contemplate that 4.6 billion years for a moment. That would be 4,600 times one million years. By comparison, our species, Homo sapiens, evolved just 200,000 years ago.)

We call the time that runs from Earth’s formation to about 3.8 billion years ago the Hadean Eon. Hadean, meaning Hades, Hell. It was hot around here. At a certain point the Earth was all magma. During the Hadean Eon of Late Heavy Bombardment, Earth got whacked by comets, planetesimals, planets. One of these hits, the Giant Impact, happened about 105 million years after the beginning. A Mars-sized planet collided with Earth. Earth got bigger, and debris spewed out and began orbiting and eventually coalesced into the moon. At first, the sun was dimmer, the moon closer to Earth. With all this excitement, Earth lost its entire atmosphere (originally hydrogen and helium) at least once. At some point, likely after another big smashup, Earth’s rocks liquefied and iron and nickel sank to the core, leaving a crust composed of lighter, silicon-based rocks like granite and quartz.

Heat rises. Open the oven to check the pie—rising heat blasts your face. Deep within the Earth, semiliquid iron heats up, rises, then cools and sinks. It heats up again, rises again, cools again, sinks again. These convection currents create a magnetic field around Earth that protects all living things from deadly sun flares. Colliding comets donated water vapor. Or maybe it was the large, soaking-wet meteorites known as carbonaceous chondrites—chips and chunks off asteroids orbiting out there halfway to Jupiter. At Earth’s creation time, a lot of space debris was whizzing about. Collisions were common. Earth cooled, and water vapor turned to water. The rains came, and it rained for centuries. The oceans filled. “I luv reyn,” wrote five-year-old Lucas in his journal. Don’t we all.

Picture Earth covered with ocean, but with volcanic islands sticking out of the water. Volcanoes vomited methane, sulfur, hydrogen, carbon dioxide, nitrogen, water vapor, and chlorine, making a new atmosphere. (Free oxygen, the sort we breathe, had no place in that old air.)

That was the Hadean Eon. Toward the end of that eon (or at the beginning of the following Archean Eon), LUCA appeared. Life. Very old rocks hold the evidence.


Life

LUCA had an abiotic genesis. Nonliving molecules became living molecules. Abiologic became biologic. Today, at home, Lucas did his favorite thing. He made a discovery, what he used to call a “discoverment.” It was a mixture of sugar, flour, baking soda, paprika, and lemon. He then applied heat (baked it). The discoverment was delicious!

In 1952, at the University of Chicago, Stanley Miller and Harold Urey, two
ex-children with a chemistry set, made the discoverment of a lifetime. They made a glass tube-and-bulb trap for four gases—water vapor, ammonia, methane, and hydrogen—each prominent in the gaseous giants Jupiter and Saturn, and thought to be the ones that composed Earth’s early atmosphere. Miller and Urey put water into the bottom bulb (representing the original freshwater ocean). They heated the contraption. The water evaporated and rose through the tubes to the top bulb. The top bulb had electrical charges attached to it, simulating lightning, an energy source on early Earth. The atmosphere cooled, condensed, rained into the bottom bulb, heated up again, evaporated again … They let this run for a week. At the end of the week, they discovered black muck—sugars! And amino acids, the components of proteins, those essential engines of all bodily functions. They were the very type of amino acids coded by “old genes,” the genes shared by virtually every form of life on Earth.

Miller and Urey did not make life. And subsequent experiments using the various gases spewed by volcanoes also got sugars and also got amino acids and also did not make life. As it turned out, these organic compounds—molecules containing carbon—were common, not only on Earth but in space. They were common, but they did not commonly occur in the long molecular chains called polymers that life requires.

Life began in a world of violent storms, volcanoes, gigantic tides pulled by the much-closer moon, tsunamis beyond imagination, and comet and meteorite impacts. Or LUCA may have ridden into town on a meteorite from Mars. Evidence of life on Mars was claimed for a meteorite collected in 1984 in the Allan Hills area of Antarctica. NASA scientists studied this rock for years and in 1996 unveiled their conclusion (to headlines worldwide) that it showed evidence of life. Yet other scientists disputed every piece of the alleged evidence for life on this particular rock.

Living microbes can survive in space for eons—this we know. So it’s still possible that we’re all Martians. We also know that Archaea, the most primitive microbes in existence, can survive deep in hot lavas spewing from vents at the mid-oceanic ridges, or in hot springs such as those shooting up in Yellowstone.

LUCA may have arrived on the Mars express or developed as an “extremophile” in the extreme environment of early Earth. Many such Archaea expel methane as a waste gas. Methane is a global-warming gas; a methane-infused atmosphere would solve the paradox that the early, very-much-dimmer sun should have left Earth too cold to support life.


Chemistry

Chemistry may be as dull as an old shoe, but it gave us life. It gave us ourselves. It gave us Lucas, who is being read Charlotte’s Web. Who drew a toucan in his sketchbook and captioned it: “Lucas droo this.”

Life—of the Lucas kind and of every other kind—requires polymers. Life metabolizes: it obtains and uses energy. Life replicates itself, makes copies of itself, but with variation in the copies. If there were no variation in the copies, then the first living entity would have functioned like a Xerox machine, producing duplicate after exact duplicate. Evolution could not have begun. We could never have evolved. Evolution based on natural selection, in which organisms with features most suited to the given environment survive to reproduce, depends on variation. Finally, life requires a membrane, a wall that separates inside from outside. Or so most, but not all, scientists agree.

Here’s a paradox. Every living thing on Earth has two separate chemical systems that interact; one cannot function without the other. These are genes and metabolism. DNA holds the codes (genes) for amino acids that make proteins that set off metabolism. Metabolism is the chemical process by which all living things gather the energy and atoms required for the maintenance of life (including DNA). How could life have begun with only one of these? Yet how could genetics and metabolism have sprung up together? Or did they develop separately and then meet up? And how did polymers form? When researchers stir all the molecules that were present on prebiotic Earth into a soup and just let it sit, or even heat it up, these small molecules do not form longer chains. They just sit there. They do nothing.

Something must have forced these small molecules to polymerize. Quite possibly that something was clay. Clay takes the form of minuscule compartments that carry a slight charge. Over millions of years, random molecules were presumably jammed together with other random molecules within billions of tiny clay compartments. Surely some would have polymerized. It may be that a clay vessel was the alchemical urn in which life began.


Metabolism

Metabolism is the battery that makes life run. And it looks very similar in all forms of life—one more piece of evidence that all life on Earth evolved from LUCA. Metabolism breaks apart some substances to release (provide) energy, and it synthesizes other substances required by living cells. All life today, every cell, is run by ATP—adenosine triphosphate. But ATP’s series of steps to store energy and release it to the cell are far too complex to have sprung into use by first life.

This metabolism requires (we require, in order to live) an inorganic molecule, phosphate. Phosphate is one atom of phosphorus hitched to four atoms of oxygen. Electrons have negative charges and protons have positive charges and these charges want to bond. In triphosphate the oxygen atoms taken together have four extra negative electrons that want want want want to attach to some positive proton. In that urge of unbonded electrons to bond lies the principle of chemical energy. Add water to ATP, and the marriage has been arranged. In our own cells, ATP becomes ADP—adenosine diphosphate, with two instead of three phosphate molecules—plus water, plus energy. Then this ADP is returned to the mitochondria (the cell’s energy shop). Within the mitochondria, a molecule of phosphate is added back to make a new ATP molecule, and the process begins again.

Each step in this many-step process is catalyzed by proteins called enzymes. Life today runs on lots of proteins, including lots of enzymes. For example, one single bacterium cell, an E. coli cell, contains some 4,000 proteins, most of them enzymes.

This is now, but what about then? Then, no protein molecule existed to catalyze anything. But organic molecules such as adenosine did exist. And minerals such as iron and sulfur existed in ocean-bottom hydrothermal vents, and might have donated electrons in a simple metabolic process. Even if it was unbelievably inefficient, who or what would care? There was no competition.

One principle in the search for first life is that whatever is thought to have happened to begin life must be compatible with life as we know it, since all life on Earth evolved from LUCA. And indeed, one of the metabolic steps in the ADP-ATP cycle is quite ancient and does not require oxygen. This step is called glycolysis. A phosphate molecule is added to the sugar glucose, and that breaks the glucose molecule and releases its energy for use by the cell. Glycolysis is ubiquitous in life. And the step immediately following glycolysis, the citric acid cycle or Krebs cycle, is also ancient and also ubiquitous. And—it can replicate itself! As Robert M. Hazen explains it in The Story of Earth:

It starts with acetic acid, which contains only two carbon atoms. Acetic acid reacts with CO2 to form pyruvic acid (with three carbon atoms), which in turn reacts with more CO2 to make the four carbon oxaloacetic acid. Other reactions produce progressively larger molecules, up to citric acid, with its six carbon atoms. The cycle becomes self-replicating when citric acid spontaneously splits into two smaller molecules, acetic acid (two carbon atoms) plus oxaloacetic acid (four carbon atoms), which are also part of the molecular loop. One cycle of molecules thus becomes two, two become four, and so on.

The molecules in these reactions, Hazen elaborates, easily synthesize sugars and at least one amino acid. Is this life? No. But “it does have the potential to replicate the inner circle of molecules at the expense of less fecund chemicals.”

This has led to the “metabolism first” hypothesis for the beginning of life on Earth.


Genetics First: The RNA World

The RNA world hypothesis counters that the first self-replicating molecular entity was some type of RNA. RNA (ribonucleic acid) is similar to DNA (deoxyribonucleic acid but composed of only one strand, in contrast to DNA’s double strand. RNA is made up of linked nucleotides. (A nucleotide is a molecule composed of a base, a sugar, and phosphate.) The RNA world hypothesis imagines an RNA polymer enclosed in some sort of membrane. This RNA would carry genetic code (later taken over by DNA) and would also replicate itself.

As in metabolism, enzymes set off each reaction that enables RNA to copy the code, assemble the correct amino acids, and synthesize a new protein. But first life had no proteins. So how could any of this have gotten started? During the 1980s, Thomas Cech and Sidney Altman made a major breakthrough. They found that a type of RNA could itself catalyze reactions. They called these catalyzing RNA molecules ribozymes. With ribozymes to catalyze simple reactions, proteins were not required. A lucky thing, since proteins did not exist.

Inspired by this discovery, molecular biologist Jack Szostak, in the forefront of the quest to solve the puzzle of how chemistry became biology, has labored to create in his lab a self-replicating, metabolizing cell that can evolve. In other words, life. He has not succeeded yet. But he’s getting closer.

Szostak and his colleagues have gotten short RNA strands (from a lab-supplied template) to polymerize. They have gotten RNA to replicate itself. They have gotten populations of RNA molecules to evolve. They have solved the following problem: on early Earth, charged magnesium ions may have catalyzed RNA molecules into replicating themselves. But magnesium also rips up the fatty acid membrane and destroys growing RNA chains as fast as it catalyzes their duplication. Szostak’s lab associate Katarzyna Adamala enhanced the mix, adding, one at a time, hundreds of compounds to see whether any of them would tame this magnesium ion. No luck. She finally discovered that if she added a citric acid derivative to the mix, it bonded to the magnesium enough to keep it from chewing the proto-cell to bits but not enough to prevent it from catalyzing the RNA. Problem solved.

Progress! But so far, no one has gotten RNA to form all by itself in a proto-cell using only elements available on prebiotic Earth. All the successes have been achieved by using lab-supplied templates. RNA is fragile and breaks easily, and although it’s simpler than DNA, it’s not all that simple. What could the explanation be? Could LUCA have used a molecule simpler than RNA to catalyze and replicate a molecule that evolved into RNA?


The Membrane

Cells today have membranes made of fat molecules called lipids. Lipids repel water. This is good for preventing the surrounding water from dissolving the contents of the cell. The problem is that the insides of a cell are also mostly water. In modern cells, a molecule comprising phosphorus and a lipid makes a phospholipid. The phosphorus part of the molecule adores water, and the lipid part abhors it. Dump these molecules into water and the lipid parts clump together to escape the water. In this way they form a vesicle, a double-layered membrane that has an outer layer that adores water and an inner layer that repels water, letting it through its structures only very selectively.

And yes, vesicles, or something like them, were present in the early solar system. Biochemist David Deamer studied bits of the Murchison meteorite, which fell into Murchison, Australia, at 11 A.M. on September 28, 1969, and which is older than Earth itself. Not only did this rock contain numerous organic molecules, but, as Deamer discovered and reports in his book First Life, it contained lipid-like molecules that assembled themselves “into cell-sized membranous vesicles.”

These were membranous vesicles, but they were not cell membranes. Cell membranes have elaborate protein-controlled pores and pumps to allow for the entrance of food and exit of waste. The first cells, the cells before proteins, could not have had protein-controlled pores and pumps. How could they eat? How could they excrete?

Szostak discovered that fatty-acid molecules could form leaky cell-like structures that could admit nucleotides, the components of RNA. Then the nucleotides would start growing chains that got too big to get back out. Hah!


How Did Life Happen?

How did the long chains of molecules assemble from the many smaller organic molecules floating about? How did metabolism begin? How did replication begin? When did the membrane materialize to contain the molecules that carried out metabolism and replication, and to separate outside from inside? Where did this happen? The short answer is, we don’t know. But we’re getting closer to a plausible scenario. Life may have started in hot hydrothermal vents that open in the floor of the ocean. Iron or sulfur or both could have catalyzed reactions.

Or maybe David Deamer and Bruce Damer are on the right track. They hypothesize that life began in a hot springs environment that alternated between wet and dry. When water is present, trillions of fatty-acid molecules form vesicles, enclosing trillions of random organic molecules. When the rocks dry up, the fatty acids coagulate into layers. These layers trap organic molecules between them, monomers that are thereby forced together, making polymers. Then the water spouts once again, releasing trillions of new fatty-acid vesicles enclosing new random polymers. Trillions of new vesicles surround trillions of random organic molecules each time the hot spring spouts. If, over millions of years, one or more of these enclosed polymers began chemical reactions for splitting and metabolizing, there you would have life—LUCA.

We can never go back. There’s no time machine. But we’re not far from comprehending the ways in which life may likely have developed out of nonliving molecules and energy.


Life After LUCA

However it came about, LUCA was the big bang of life on Earth. And it’s remarkable to think that from LUCA’s entrance, four billion years ago, until 700 million years ago, all life was single-celled life. Whereas Lucas’s body will ultimately have 37.2 trillion cells.

Long after LUCA arrived—2.4 billion to 2.35 billion years ago, according to a new interpretation elaborated by Peter Ward and Joe Kirschvink in their book A New History of Life—a second great event occurred: photosynthesis. Cyanobacteria evolved. These single-celled bacteria began using the energy of the sun, plus water and carbon dioxide, to make glucose—sugars. Their waste gas was oxygen. The ocean began to be oxygenated. The air began to be oxygenated. An isotope of oxygen, O3, began to form an ozone layer at the top of the atmosphere. This was the Great Oxygenation Event.

Cyanobacteria gave oxygen-dependent organisms—such as young Lucas and all the rest of us—air to breathe, food to eat, and an ozone shield that protected Earth from the sun’s killing ultraviolet rays.

Other great events happened on the road from LUCA to Lucas. Plate tectonics shifted land masses around, making and remaking continents. Multicellular life began some 700 million years ago. Land plants evolved from pond scum (green algae). The explosion of multicellular life forms began in the Cambrian period, about 542 million years ago. Several disastrous extinction events changed everything, each time. The most catastrophic was the end-Permian extinction, the mother of all extinctions, which, 251 million years ago, wiped out 90 to 95 percent of life on Earth. (Memo to ourselves: this event was due, in part, to ocean acidification and global warming.) After the end-Permian extinction, dinosaurs evolved. Birds evolved. Small mammals evolved.

Once again, disaster, when the Chicxulub asteroid smacked into Earth 65.5 million years ago. Hundreds of species of dinosaurs were wiped out. Slowly mammals diversified further and took up more niches. Primates, our kind, evolved. One early proto-primate (Purgatorius) made it through the Chicxulub catastrophe. True primates evolved some 55 million years ago. These squirrel-sized mammals had forefeet and hind feet good at grasping things. Then came the monkeys. Then came the great apes. In the 1970s, the bones of our cousin Lucy, a bipedal upright primate with a small brain, were found and dated to about 3.2 million years ago.

Walking releases the hands. Hands are useful. Lucas, coming in from playing in the snow, announced that the snow had given him new superpowers. He could now grow more hands, and one of these hands could turn into a hammer.

Lucas is right. Hands gave us superpowers. Hands could extend their usefulness by using tools. Figuring out tools requires brainpower, and those with more of that survived better to reproduce more. Homo habilis, an early member of our genus, means “handyman.” We evolved from Homo habilis through Homo erectus through a possible Homo heidelbergensis, ending up about 200,000 years ago as ourselves—Homo sapiens.

Then language happened. Here’s Lucas, speaking to his mother:

—Hey, Mommy, what’s Jengdin?
—What?
—Jengdin.
—I don’t know. Where did you hear the word?
—Oh. I just made it up.
—And what does it mean?
—I don’t know.

What does it mean? That is the question. That is our question. Starting with LUCA, we who strive to find meaning evolved. And because we evolved, the amazing Lucas Samay Yunga Korn was born. Lucas, named for light, for vital energy. Lucas who watches Teenage Mutant Ninja Turtles on YouTube. Who plays ninja turtles versus the bad guys with his mommy, using a shoelace for a sword. Who yells “hai-YA!” every time he swings his shoelace.

Lucas is one consequence of the abiotic genesis of life on Earth. There are zillions of others. But right now I can’t think of a better one.


Clarification

A distinction should be made between the first cells and LUCA (Last, or most recent, Universal Common Ancestor). The first cells, when chemistry became biology, were simple systems, protocells, barely alive, and were different each from the other. Most had their components dispersed but, in David Deamer’s words, “at some point, in a way that we don’t yet understand, a few of these happened to find a way to grow by polymerization, and maybe the polymer was something like RNA.” These cells evolved for perhaps a billion years into LUCA, ancestor to all life extant on earth today. LUCA was a microbial but nevertheless advanced organism with proteins, DNA, metabolism and so on. Thanks to Jack Szostak, David Deamer, and Peter Kessler for this clarification.


Priscilla Long is the author of Crossing Over: Poems. Her two new books, both published in 2016, are a collection of essays, Fire and Stone: Where Do We Come From? Who Are We? Where Are We Going? and Minding the Muse: A Handbook for Painters, Composers, Writers, and Other Creators. Her essay “Genome Tome,” which appeared in our Summer 2005 issue, won the National Magazine Award for Feature Writing.


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