Understanding Life: Tap Into An Ancient Cellular Survival Program to Optimize Health and Longevity

Introduction

This book is an almost ridiculously ambitious undertaking. It attempts to span an enormous conceptual range, from the development of cellular life on our planet to health, aging, and disease. It covers topics ranging from biochemistry to human physiology and moves from the theoretical to the practical. At the outset, when I described my plans, many people openly scoffed at the notion that a casual reader with little or no scientific background could understand such things—or even want to. However, as much as anything, this book reflects my faith in the average person. I don’t believe you need a doctorate to grasp the principles underlying biology. Further, I think that all of us have a deep fascination with how living things work and what it means for our own health and well-being. I’ve done my best to simplify the more complex topics and to avoid scientific jargon as much as possible.

I’m afraid that there’s no way to explain the development of life without invoking the potentially controversial e-word—evolution. Let me take a few moments to try to convince you that it’s OK for even the most ardent creationist to believe in evolution, or at least the evolutionary process as we observe it today, and recognize its predictive value.

Have you ever fired a shotgun? The shells that are loaded into such weapons are filled with hundreds of tiny metal balls, appropriately called shot. If you fire a shotgun at a target across a field, you’ll find it peppered with little holes that reflect how fast each piece of shot was going and its exact trajectory when it hit the target. The farther you are from the target when you shoot, the more spread out the shot will be, reflecting the dispersion that occurs over time, as demonstrated in figure 1.

If someone gave you a target they had fired at, can you see how it would be possible to work backward and figure out where they were standing when they fired the gun? Such analysis would involve fairly simple physics using math that Isaac Newton developed more than three centuries ago. You could probably do a fairly good job just by eyeballing the target and the amount of dispersion without using any math at all.

However, if you didn’t see the person fire the gun, could you ever be sure where they were standing? What if someone developed a machine that precisely mimicked the position, angle, and speed of every single piece of shot halfway between the hypothetical shooter and the target, as shown in figure 2?

When it leaves the machine, the shot will have the exact overall state (position and velocity) as if it had been fired by a person holding a shotgun at the calculated spot. Newton’s calculations would be accurate in either case, but the point of origin would be different.

The situation with evolution and creation is similar. Evolution is analogous to Newtonian mechanics in the shotgun example above, as something that can be measured and verified. In the same way, we see evolution at work when bacteria become resistant to antibiotics. Even cancer is an example of evolution in action. So even though we talk about evolution as a theory, it is extremely well established. We also have a theory for electromagnetism that similarly works so well that it has led to smartphones and other sophisticated devices. You don’t have to accept the theory to use your iPhone to call your mother.

The controversy begins when we run the theory of evolution in reverse and use it to explain the origin of life. Just as with the shotgun example, we can never know for sure. After all, no one was around when the earth was formed or when life began. In the same way that, given a target, we can estimate where the shooter was but can’t rule out the possibility that the shot pattern was generated elsewhere that could replicate the same state as a shooter, we can’t disprove that the earth and its life arose from some miraculous event just a few thousand years ago. Either way, the theory of evolution is just as valuable. In fact, if there’s anything divine and perfect about life, it’s the process of evolution. If you look closely at living things, it’s clear that they are not the perfectly designed products of some super intelligence, but marvelous Rube Goldberg contraptions that work for a short period of time and then fall to pieces.

So bottom line—it’s OK for even the staunchest creationist to believe in the process of evolution and to recognize its predictive value. Scientists may choose to run the models backward and talk in terms of how things appear to have begun, and religious people may prefer to believe that the world was created by a divine being much more recently. However, both can apply evolution practically to help understand how life, bacteria, cells, and organisms operate. A quote from Theodosius Dobzhansky sums the situation up nicely: Nothing in biology makes sense except in the light of evolution. It really is something we can all agree on despite our different faith backgrounds. In this book, we’ll go ahead and run the models of evolution backward. This will help us understand the apparent development of life because it will allow us to appreciate how our bodies operate.

This book is organized into three multi-chapter sections. The first examines the molecular basis of life and how it might have emerged on the early earth. The second explores aging and death in complex organisms—like us. The third section looks at some of the ancient programs that our cells inherited from their primitive ancestors and how we can leverage these programs to live longer and healthier lives.

There’s no denying that some of the material here may be challenging for people who didn’t study chemistry and biology in college. For that reason, I have partnered with LifeOmic to create easy-to-consume mobile courses that distill the essence of each chapter into short comic books that can be accessed using the Lifeology platform. Lifeology has been used to create dozens of illustrated courses focusing on various aspects of science and medicine. If you really want to understand the information presented in this book, we recommend that you take the following approach:

Go through the Lifeology course(s) for a chapter.

Read the chapter in the book.

Go back through the Lifeology course(s) for the chapter.

The Lifeology courses feature beautiful explanatory drawings by professional artists. These illustrated courses are intended to make learning both easy and fun. You can find the courses for this book online at lifeology.io/understanding-life.

1

The Grand Timeline of Life

Tune your television to any channel it doesn’t receive and about 1 percent of the dancing static you see is accounted for by this ancient remnant of the Big Bang. The next time you complain that there is nothing on, remember that you can always watch the birth of the universe.

Bill Bryson

If we run the various models of physics and chemistry in reverse, all lines converge at a strange event that occurred 13.8 billion years ago, starting with the big bang. At that instant, the entire universe—all of matter and space itself—was compressed into a volume smaller than the head of a pin. At this pressure and temperature, there were no atoms or molecules, let alone stars or planets. All that existed was energy and fleeting subatomic particles. Space itself began to expand. As it cooled, the contents of the universe began to settle into tiny particles such as quarks and leptons. These soon gave rise to protons and electrons, which in turn began to form atoms—initially hydrogen and helium. We’ll go quickly through a crash course in chemistry in the next chapter, but now let’s try to get the whole big picture straight in our minds.

As the cloud of hydrogen, helium, energy, and particles spread, these substances began to appear throughout the expanding universe. They became unevenly distributed, and some aggregated into giant clouds of gas and dust that we call nebulae. In many places, these gas clouds began to spin and over the course of several million years started to aggregate into balls. In our neck of the woods, in the Milky Way galaxy, a solar system formed about 4.6 billion years ago with a central star (our sun) and eight planets.

Around 99.9 percent of the mass became concentrated in the area of the sun, leading to tremendous temperatures and pressures. These quickly built up to the point that hydrogen atoms began to fuse together. Some of the mass was converted into energy, leading to the chain reaction we call nuclear fusion. And so the sun began to shine. Even after all these billions of years, hydrogen atoms are still fusing and generating the tremendous energy emitted by our local star.

The small quantity of matter not sucked into the sun settled into the eight planets that began to orbit the new star at various distances. Violent solar winds blew the light hydrogen and helium atoms away from the inner planets, leaving them mostly rocky with thin atmospheres. The four outer planets became the gas giants we know as Jupiter, Saturn, Uranus, and Neptune. The third planet happened to form in an ideal location about ninety-three million miles (150 million kilometers) from the sun. This Goldilocks distance was neither too hot nor too cold. The newly formed planet was able to hold on to an atmosphere of mostly nitrogen and carbon dioxide, and to develop and retain an ocean of water.

The First Life Forms: Bacteria and Archaea

We’ll talk later about how life might have originated, but there is overwhelming evidence that this occurred about four billion years ago, roughly a half-billion years after the planet cooled. The first forms of life we know of were the single-celled organisms we call bacteria. These creatures were relatively simple and still are today. We can most succinctly describe them as little protein factories surrounded by a fatty (lipid) membrane. The proteins they make are themselves tiny machines that can perform an amazing variety of wonderful tricks. Some proteins facilitate chemical reactions and are known as enzymes. Others help the bacteria move around, while still others act as harbors, transporting material in and out of the cell through the enclosing membrane.

How do the bacterial cells know what proteins to make and how to make them? That’s the job of their DNA. You can think of DNA as a recipe book for proteins. There’s one recipe for a protein that can pump sodium out of the cell and another for a protein that can help repair the DNA if it gets damaged. Early protocells probably started out with only a handful of proteins. The first true bacterial cells had roughly five hundred or so such recipes, producing proteins capable of handling a range of different jobs. Even after four billion years of evolution, modern bacteria are quite similar to these early ones, now making as many as several thousand different proteins.

Bacteria have been spectacularly successful, spreading out all over the earth. They came into being at a time when there was very little free oxygen (O2) in the air or dissolved in the water. In fact, oxygen was a poison to these new creatures. For millions of years, bacteria continued to evolve, mainly to explore different ways of harvesting energy to survive and multiply. After about a half-billion years of existence, a new, tougher kind of single-celled creature came onto the scene as it evolved from bacteria. If bacteria were Honda Civics, these new creatures were armored tanks. They were able to live in places that bacteria couldn’t even visit—hot springs with temperatures above boiling; polar regions that stayed frozen year-round; lakes so salty that you could float without effort; even water so acidic it would melt your boots. These new, badass bacteria were discovered only in the last fifty years and were given the name archaea (singular archaeon), which derives from the Greek word for ancient. Interestingly, scientists have never found an archaeon that makes humans sick, unlike their bacterial relatives.

Under the microscope, bacteria and archaea look pretty much the same—just a tiny rod or sphere about one micron (millionth of a meter) across. Archaea can be slightly larger, but not enough to worry about; you’d have to put ten to twenty thousand of them end to end to make an inch. Bacteria and archaea are both prokaryotes. That is, they lack a nucleus. Their DNA floats in the interior of the cell, the cytoplasm, along with everything else.

These two types of primitive organisms differ in less apparent ways. For one thing, there are important differences in the ways they copy their DNA when they get ready to divide—archaea use copying machinery much like that of more modern organisms such as plants and animals. The other big difference is in their cell membranes. Bacteria use a bilayer membrane structured like a sandwich. Each layer consists of fatty acids with their charged (polar) heads all grouped together. The long tails of the fatty acids hate water (hydrophobic) and stick together in the middle of the membrane—the inside of the sandwich. The polar heads love water (hydrophilic), so they form the top layer of the sandwich, polar heads sticking out to face the outside world, and the bottom layer of the sandwich, polar heads pointing down to face the watery inside of the cell (cytoplasm).

This structure allows bacterial membranes to be soft and to change shape easily. On the other hand, archaeal membranes can sometimes use lipids that run the full width of the membrane. It’s as if the two pieces of bread in the sandwich were held together with toothpicks. It’s easy to see how this helps archaea handle more extreme conditions. Instead of being surrounded by a delicate soap bubble like bacteria, archaea are encased in something akin to clear plastic—much tougher and more durable.

So bacteria arose about four billion years ago, and archaea appeared roughly a half-billion years later. For the next billion years, the picture of life on earth was relatively static. Bacteria spread around the planet into all but the most inhospitable areas. The archaea occupied the places that bacteria feared to tread. Together, they dominated the planet and still do today.

An Amazing New Trick

Around 2.5 billion years ago, one type of bacteria learned how to harness sunlight. Actually, this discovery might be even older, but evidence abounds that at least 2.5 billion years ago some bacteria figured out how to use sunlight to crack hydrogen atoms and their electrons out of water and use them to generate energy. Now, stealing hydrogen atoms and electrons from water is no mean feat because it puts you in conflict with a chemical bully—oxygen. We’ll talk about this a lot more in the next chapter, but know for now that oxygen simply loves electrons. Once it gets them, it hates to give them up. So it took a long time—a billion years in fact—for some bacteria to stumble onto a way to reliably accomplish this theft. This ability to use two plentiful resources—sunlight and water—to produce energy was a game-changing innovation. Suddenly, these photosynthetic bacteria began to proliferate, especially in the top layers of the ocean, where sunlight was plentiful. One fascinating wrinkle to this development was the fact that molecular oxygen (O2) began to accumulate first in the ocean and later in the atmosphere.

Of course, we humans tend to think of oxygen as the elixir of life. After all, all the animals we’re familiar with rely on oxygen to live. However, when photosynthetic bacteria burst onto the scene roughly 2.5 billion years ago, the oxygen they spewed out was like the most toxic environmental spill ever recorded. Although later life learned how to actually use oxygen to produce energy and grow, the bacteria and archaea present 2.5 billion years ago had no idea how to deal with the stuff. For them, oxygen was a lethal poison that interfered with some of their most critical chemical reactions. They and their ancestors had spent hundreds of millions of years in an environment with almost no free oxygen. As the photosynthetic bacteria started to proliferate, countless other bacteria and archaea began to die off—or retreat to the deeper ocean, still devoid of the deadly poison.

At first, the oxygen the photosynthetic bacteria produced was soaked up by other molecules dissolved in seawater, especially iron. Iron acts like a sponge for oxygen. Without oxygen, iron can float free in seawater. However, oxygen combines with free iron to form the ferric oxide (rust) that we all know too well. As we can now see in the geological record, iron and oxygen settled out into huge bands of reddish sediment, and the levels of dissolved iron in the ocean plummeted. Once all the dissolved iron was used up, the amount of free oxygen in the ocean began to rise. When the ocean could no longer hold all the oxygen produced by the photosynthetic newcomers, it began to spill out into the atmosphere.

Today, earth’s atmosphere is around 21 percent oxygen with almost all the rest being nitrogen. Before the advent of the photosynthetic bacteria, atmospheric oxygen levels were close to zero; by about 2.4 billion years ago, they were rising rapidly to levels unseen since the birth of the planet, though barely reaching 1 percent of what we measure in the air today. This is referred to as the Great Oxidation Event, and it led to major changes in the environment. For one, as oxygen accumulated in the atmosphere, it eventually began to form ozone (O3) at higher levels. This ozone layer served as a shield to reduce the penetration of DNA-damaging ultraviolet (UV) radiation from the sun, and eventually made it possible for organisms to live on land.

To this point in earth’s history, we’ve seen four major developments: the first appearance of cellular life in the form of bacteria; the generation of a bigger and badder kind of bacteria called archaea; the evolution of photosynthetic bacteria; and the initial sign of atmospheric oxygen. But what is perhaps the most important innovation in the history of life was still around the corner.

Enter the Eukaryotes

Somewhere around two billion years ago, shortly after the Great Oxidation Event, a new form of life appeared on our planet, and it was unlike anything the earth had ever seen before. It was a type of cell so different that it was given the name eukaryote, which means true nucleus. These new cells were thousands of times bigger than bacteria and archaea. Bacteria and archaea were relatively peaceful species. We can think of them as vegans—consuming only small natural molecules like sugars or even making their own using simpler building blocks such as carbon dioxide and hydrogen gas. In contrast, eukaryotes were hunters. They developed the ability to eat (phagocytize) other cells such as bacteria and archaea. More than anything, they were able to thrive in the new oxygen-rich environment. Within a few million years, they had spread all over the planet.

So how did this incredible new life form come about? This topic was hotly debated for many years. We can think of prokaryotes (bacteria and archaea) as primitive cells. They have no nuclear membrane surrounding their DNA, so their genetic material floats free within their cytoplasm—the liquid interior of the cell. What has become clear over the last few years is that eukaryotes arose from a one-in-a-million union between an archaeon and a bacterium. We don’t know how, and we don’t know why, but a little over two billion years ago, a bacterium invaded an archaeon and they decided to make it a permanent arrangement. The result was the first eukaryote.

Now, this never should have happened. As we’ll learn later, both archaea and bacteria produce energy by means of protein machines embedded in their membranes. Because of their small size and the way their membranes are studded with thousands of these little protein energy generators, there’s really no way for them to swallow an organism of similar size. Perhaps the relationship started as a close-buddy system rather than a symbiosis. After all, the new photosynthetic bacteria had learned to deal with the toxic effects of oxygen—they had figured out how to get close to the fire without getting burned. As oxygen levels began to rise in the oceans, archaea that otherwise would have been poisoned by this corrosive gas might have begun to cozy up to the new types of bacteria that had learned how to