The Return of the Exiled Elements

The last page in a comic book is often a cliffhanger, so you’ll be more inclined to buy the next issue. It happens so regularly that as I read through the comic (yes, I still read a comic or two), I find myself trying to anticipate what kind of twist will be on the last page. The best twists are the ones you could have seen coming, but didn’t. The story in this book also has a chemical twist here, near the end. This twist is innovative, expensive, and predictable from chemistry. For this twist, the periodic table plays spoiler. Before the Cambrian explosion, hidden in the nets of signaling proteins within cells and signaling molecules outside cells, the cells held a secret chemical potential that could send a much faster signal, built from four elements involved in two of the balances set up in Chapter 5. This form of signaling would be incredibly expensive, but also incredibly fast. It would be electric in its nature and in its effects, the basis of both muscles and brains. Like water flowing randomly down a rocky slope, this fast signaling built from fast chemistry spread out in many different ways in life. At certain points, evolution came together and converged, repeatedly finding that a particular shape or signal was the best solution to a particular problem. Because the liquid flow of life was increased, it could diverge and converge more quickly, while predictably fitting into the shape of its landscape and efficiently moving downhill. The fast chemistry that forms the basis of fast muscles and faster neurons developed with the Cambrian explosion, along with oxygen and calcium use. The explosion of life provided predators that ate and prey that was eaten. Oxygen’s energy (resulting from its place on the periodic table) allowed more complex food chains, with more predators and more prey. For example, some calculate that more oxygen in the late Cambrian made more predators evolve. In response to this oxygen, certain species moved onto dry land, where they had more contact with that element.

The Triple-Point Planet

Let’s move to a vantage point a little quieter: the surface of the moon. It is so still that Neil Armstrong’s footprints remain undisturbed. The only reason the US flag there appears to “fly” is that a wire holds it up. The moon and Mercury stayed still as Mars, Venus, and Earth moved on down the road of geological development. The moon is a “steady” environment, a word whose Middle English roots are appropriately tangled with the word for “sterile.” Nothing moves on the moon, but in its sky Mars, Venus, and Earth move in their orbits, just as they moved on in complexity 4 billion years ago. Out of the whole solar system, Mars and Venus are the most like Earth in size, position, and composition. Mars is smaller, but Venus could be Earth’s twin in size. If Earth and Venus were separated at birth, then something happened to obscure the family resemblance: liquid water brought life. To chemists, liquid is the third phase of matter, between solid and gas, and its presence made all the difference. Mars gleams a bright blood red even to the naked eye, while Venus is choked with thick yellow bands of clouds. Mars is cold enough to have carbon dioxide snow, while Venus is hot enough to melt tin and boil water. Earth’s blue oceans and green continents provide a bright, primary contrast. These three siblings have drastically different fortunes. At first, they looked the same, colored with black mafic basalt and glowing red magma. The original planets were all so hot that their atmospheres were driven off into space. The oceans and the air came from within. Steam condensed into oceans on each planet’s cool basalt surface. Oceans changed the planet. Water is a transformative chemical, small yet highly charged, seeping into the smallest cracks, dissolving what it can and carrying those things long distances. Venus, Earth, and Mars do not look like the moon because they have been washed in water. Mars is dry now, but the Curiosity rover left no doubt that the red planet was first blue with water.

Predicting the Chemistry Inside a Cell

The process of scientific discovery is something like a walk near Freswick Castle. I assume you’ve never been there. (Neither have I, but a friend has.) Freswick Castle stands at the end of Scotland’s northeast end, at the mouth of the Burn of Freswick in the district of Caithness. As of this writing, it is unlisted in Google Maps, and I had to manually scan the coast to find it. Outside the castle is a simple, unlabeled structure that doubles as a biochemical parable. The castle itself is narrow and three stories tall, with orange shingles and gray stone, set on an arc of narrow beach between hills to the north and cliffs to the south. The building is approximately the cruciform shape of a shrunken cathedral, with the rightward wing moved to the top of the structure so it resembles a lowercase f. If you wander the grounds near Freswick Castle, you will discover a stone wall in the wind-blown waves of yellow- green grass, worn but still standing firm like Hadrian’s Wall. From above, it is a period preceding the castle’s f. Let’s approach this as a scientist, with measurement. From the castle side, this structure resembles the circular stump of a roofless tower, eight feet tall and twice that wide. The stones are ancient sand, compacted and weathered, stained different shades of red from iron deposited millions of years ago, but the mortar is new. But inspection is not enough—we should go in. Walk around to the other side, and an opening appears, as shown in Figure 2.1. The structure is not a closed circle, but it is a spiral wall open to the sea, and to you. Inside, a small stone bench invites you to sit. A window slit next to the bench is an eye to the outside. Surrounded by a jigsaw of rocks, you can hear the echo of waves all around and watch the blue-gray sky above. If the spiral’s opening is a mouth, then you are Jonah in the whale. You are both inside and outside at once.

One Step Back, Two Steps Forward

In seventh grade, I picked up The Eye of the World, the first in a series of Tolkienesque novels. The author, Robert Jordan, had built a world with several creative innovations, but at heart it was the familiar story of the farm boy who grew up to be king that drew me in. It was clear to all readers that this boy would be the hero of the prophesied Last Battle, but most characters refused to see it. I was frustrated by this by book four and graduated to acceptance by book eight. (Did I mention this was a long series?) It took 14 books and a second author to reach the Last Battle. Even though the direction was clear, the plot was anything but an upward march. The chemical history of the Earth was also anything but an upward march. Once photosynthesis made oxygen and mitochondria used it, a cycle of oxygen- making and oxygen-breaking generated cheap energy for exploring and processing the planet, spreading out energy in sun-driven cycles. The direction of this story was set, toward oxygen and oxidation. But like any long story, the chemical story of Earth’s development took twists and turns, encountering obstacles and opportunities, as the Earth oxidized and grew in complexity. Of these twists, the biggest may be geological rather than biological. In this story, precipitation changed the early Earth. Not “precipitation” meaning rain, but “precipitation” in the chemical sense, as when a solid precipitates inside a test tube. Chemists work and think in the liquid phase, where the “rain” that falls is solid particles, which happen when two atoms discover that they are more stable together as solid than apart as dissolved ions. For chemists, precipitation is usually a disappointment. Some of the most elegant experiments have been ruined by the chemicals “precipitating out” into a soggy mess. In a sense, it was a disappointment when it happened on the early Earth as well, although this disappointment threatened the continued existence of life.

Wheels within Wheels

Something strange and old lurks under the ice in Antarctica, at a place called Blood Falls. It is an echo of the early Earth. Blood Falls is hard to reach and easy to find. Look through the seas of blue ice, white snow, and gray rocks for the bright-red frozen waterfall, spilling out of the ice around it in a gory cascade five stories tall. This is a red flag made from chemistry, telling that even the coldest environment on Earth is not completely dead. Liquid water can be found there, and in the water is life eking out an existence from the water around it and the dirt under it, just like it did a few billion years ago. The “blood” at Blood Falls spills out of life, but it’s not blood. Like blood, this substance is a form of iron bound to oxygen. In your blood, the protein hemoglobin hosts the iron, but Blood Falls is straight-up iron oxide, similar to rust. I saw some of this chemical last August near Mount Rainier. As we hiked up to Goat Lake, the frozen water looked dirty. The pure white ice was dusted with bright-red powder blown around from the iron-rich rocks surrounding it. The land was red as blood. That was geological, but Blood Falls is biological. It shows that life in an extreme environment eats some pretty strange food—like John the Baptist eating locusts and honey in the wilderness—and outputs blood- red iron as waste. A pocket of liquid water hides behind Blood Falls, sealed under the ice so tightly that air cannot penetrate. Even in solitude, away from the sun and oxygen, liquid water supports life. The microbes under the glacier get energy from adding oxygen to carbon to make stable CO2, just like us. The subglacial lake is sealed off from the air, so the oxygen must come from a solid or liquid source. These bacteria eat sulfate, pulling one of the four oxygens off it and producing the three-oxygen chemical sulfite.

Unfolding the Periodic Table

Our starting point is not hidden, nor is it far off. It is not an extreme place like Mono Lake or Freswick Castle, but it is a central concept expressed on a single page. The periodic table is the center of chemistry, and therefore of this book. You can spot it at a distance from its vaguely cathedral-like shape. You can see the chemical symbols that it contains on magnets and T-shirts and restaurant signs. Its regular columns are not quite symmetric, but that is because it has been twisted out of its natural shape by the contingencies of history. Rearrange it just a little and a simple mathematical pattern appears. To see this pattern, imagine that the periodic table is made out of beads on an abacus, arranged in the familiar U shape. Then push all the beads to the left: … Row 1 = H- He Row 2 = Li- Be- B- C- N- O- F- Ne Row 3 = Na- Mg- Al- Si- P- S- Cl- Ar Row 4 = K- Ca- Sc- Ti- V- Cr- Mn- Fe- Co- Ni- Cu- Zn- Ga- Ge- As- Se- Br- Kr Row 5 = Rb- Sr- Y- Zr- Nb- Mo- Tc- Ru- Rh- Pd- Ag- Cd- In- Sn- Sb- Te- I- Xe … By row, there are 2, 8, 8, 18, and 18 elements. The pattern continues in the rows below, but it is obscured by the fact that on most tables 14 elements have been moved out of the sixth and seventh rows. On the table here I have put them where they belong. These rows have 32 elements each. This can be simplified even more. The rows increase, first by 2, then by 6 more (2 + 6 = 8), then by 10 more (2 + 6 + 10 = 18), then by 14 (2 + 6 + 10 + 18 = 32). The series 2, 6, 10, 14 is the doubles of counting up by odd numbers: 1, 3, 5, 7. Put another way, each row is equal to 2n + 1 with n = integers from 0.

Arsenic Life?

In December 2, 2010, at 11:16 a.m., I received the first of three emails from students in my biochemistry class, all asking if I had heard the news. A press conference at 11 a.m. had announced that scientists had discovered a bacterium that uses arsenic instead of phosphorus in its DNA. Soon there was a hashtag for this: #arseniclife. We were excited and a little puzzled. I had just lectured about how phosphorus was uniquely useful to DNA. I shrugged and mumbled something about how textbooks can be rewritten. Today, the dust has settled—and the textbook reads the same as ever. DNA is made of phosphorus, never arsenic. That December press conference was followed by two full years of multiple experiments in labs around the world. It confirmed what the textbook said all along, yet the story was well worth it. The “arsenic life” story was never just about microbiology. It’s about science itself, how we know things, and the nature of natural history. Everyone should know this story. It will temper expectations when the next press-conference-induced hashtag makes its way halfway around the world while science is still lacing up its boots. More than that, it shows something deep about what kind of world we live in, something underreported because it is so intricate and comes from so many different places. There is a hidden order that makes some sense of biology and even sociology, and that hidden order is chemistry. All life, from a lakewater bacterium to the neurons firing in your brain as you read this, is hemmed in. It is free to randomly adapt to its surroundings with nearly infinite creativity, but its overall path is as constrained as if it were walking on the deck of a ship crossing the ocean. The ultimate movement, on the scale of billions of years, is shaped by chemical rules. One of these rules is that phosphorus makes good DNA, while arsenic does not. To reach this conclusion, we have to start where the arsenic life story started.

A Familiar Refrain

When I was a child, I lived near Kennedy Space Center in Florida. To me, science was all about rocket science: big rockets that flew where no one has gone before, powered by fiery oxidative chemistry and guided by precise measurements. I could watch the space shuttle go up, and trust it would come down, connecting Earth’s orbit to the ground at my feet. That we could send hollow metal capsules on such immense journeys was a wonder I never quite got over, not even when two of the shuttles failed to return home. I had a different view of evolution. It seemed messy, haphazard, cruel, and wasteful, nothing like the sleek engineered rockets at the Space Center. Most of all, I think it just seemed boring. Why study the unpredictable? To be sure about something, you need to see it work multiple times, right? I missed the chance to see evolution work multiple times, right in my home county. In the next lagoon over from where I once dredged up sulfurous muck for my science projects, on six small islands, the tape of life was being replayed six separate times. All six times, it gained the same result. Evolution might be messy, haphazard, cruel, and wasteful, but it is also predictable. In 1995, scientists brought Cuban brown anole lizards to six small islands in Mosquito Lagoon, which only had green anole lizards at the time. Each time, scientists watched what happened and compared the results to five nearby islands that remained green-lizard-only zones. After three years of competition, the green lizards changed their behavior and perched twice as high in the trees. In 2010, the scientists returned and examined the lizards’ feet. On the invaded islands, the green lizards had larger toepads with more wrinkly lamellae than on the non-invaded islands. This difference in feet was mirrored by differences in the lizards’ genes. In a 15-year span, the lizards evolved. (During the same time span, my opinion of evolution also evolved, as I learned about a chemical order behind the biological messiness.)

How Chemistry Shaped History

Evolution accomplished its final major innovation 125 million years ago. Not brains—complex brains had already been around for a few hundred million years. Not flight—animals with wings can be found as far back as brains, although the birds that really flew developed during this time. It was something that is so commonplace that it seems more annoying than astounding. Evolution invented the hive. Hives are annoying because of their success. Only 2% of insect species form hives, but all hive-makers weigh as much as the other 98%. The most complex hive-making species exhibit “obligatory eusociality”: their genes encode physically different levels, or “castes,” each with a specialized job, led by a queen that reproduces for the entire hive. The physical hive itself is easy to see, but the true innovation is the network of life protected inside. The hive acts as a skull for the hive mind. Eusociality was a step forward, on par with the inventions of mitochondria and multicellularity. These other two great evolutionary innovations made specialized organelles inside cells and specialized organs inside organisms. Eusociality made specialized roles outside organisms. Eusocial species changed externally in protection, specialization, and communication. A hive protects; the queen specializes in reproducing (like muscles specialize in movement, and the brain specializes in fast sensing); and external chemical signals like pheromones form parallels to internal chemical signals like hormones. The most telling sign of eusociality may seem mundane: organized, communal child care. One extraordinary day, a termite tended a child not its own. Such au pair termites cannot directly pass on genes to the next generation. But loss is gain—the individual took one step back while the species took two steps forward. Ants and termites succeeded by losing the ability to reproduce. This specialization is coordinated through a chemical communication, mediated by small molecules messaging from bee to bee and termite to termite. Queen bees make a carbon-chain “perfume” molecule that suppresses reproduction in the surrounding bees, which communicate back with molecules of their own.

Cracked Open and Knit Together by Oxygen

The happy insight that biology and geology meet through chemistry has been seen throughout this book when life and rocks interact. A chemical called water transformed this planet’s rocks and opened them to give life its elemental building blocks. The energy in the Earth became the energy in simple cells through chemical wheels. Sunlight split the water with the help of dissolved rocks, and the oxygen from that reaction brought yet more elements out of the rocks and into life. That insight addresses a long-standing mystery here. Long ago, the biggest biologi­cal change in the history of the planet created plant and animal life. What caused the seas to teem with weird new life? I think the periodic table connects that biological event to a previous global geological change. If so, then once again, chemical reactions opened up geology to provide new possibilities for biological complexity. Chemistry shaped the flow of geology and biology at once. The evidence for this connection is like something that happened with the ekko sculpture in northwest Scotland from Chapter 2 (Figure 2.1). After the sculpture had been built, an archaeologist dropped by and found incisions in ekko’s rocks. The archaeologist read the shape and depth of the incisions and concluded that the stones were older than everyone thought, and must have been used for a structure now lost. Like in ekko, there are “incisions” on the Earth made by massive geological processes. Geologists have read these and have concluded that a worldwide event altered the planet’s surface. This geological event was also a chemical event. Soon after, a profusion of fossils filled the rocks. This biological event was also a chemical event. The common denominator of chemistry connects the geology to the biology. The geological event provided chemicals that life used in new ways: especially oxygen, phosphorous, and calcium, resulting in new energy, shells, and signals for life. This hypothesis is that chemical availability drove the evolution of life, and that the periodic table shaped the timing of life’s greatest expansion.