A New History of Life

by Peter Ward

  Roth had discovered that sublethal doses of hydrogen sulfide put mammals into a state that can only be described as suspended animation.1 While there is a great deal of popular-culture baggage attached to this appellation (mainly from the science fiction world), in fact these two words quite nicely describe what took place in these gassed animals. Animation, or movement, stopped not only in the observable aspects of the study animals—they no longer moved, had a greatly slowed down respiration rate and heart rate—but also at even more fundamental levels. Normal tissue and cellular functions were greatly reduced in rate. And then even something more surprising occurred: the mammals lost their ability to thermoregulate. They stopped being endothermic, or warm-blooded, and reverted to the more primitive chordate state: ectothermy, or cold-bloodedness. But they were neither dead nor truly alive, for in one of the most basic of mammalian characteristics, they were as if dead. But that death was temporary. It was suspended for a finite amount of time, for when the application of the gas ceased, all normal functions returned. Beyond the obvious medical applications, this new understanding says much about what life is—and is not.

  Roth’s hunch was simple—that there exists a state between life and death that is both unexplored and of potential medical interest—and it also provided clues to why certain organisms survived mass extinctions. Perhaps death is not so final as generally assumed.2 His hope was to be able to take organisms to this place and then bring them back. In fact there is no English word that accurately captures the essence of this place. Moviemakers call it zombie land or some such, and maybe stiff-necked science will eventually adopt that term. But we doubt it.

  Here was one of his critical experiments. He took flatworms, simple animals, but animals nonetheless. Yet compared to any microbe, no animal can be called simple. He lowered the oxygen content that the flatworms were respiring. Like all animals, flatworms need oxygen, and lots of it. So down went the oxygen content in the closed vessel with the confined worms, and gradually they slowed and then ceased motion. No poking or prodding could get any sort of reaction. But Roth did not conclude the experiment there. In fact, he kept dropping the oxygen content of the worm’s water, and they came back to life.3 The flatworms had entered the state of “dormancy” that is neither alive nor dead. Life and death seem to be far more complicated states than most of us currently believe.

  LIFE AND DEATH IN THE SIMPLEST ORGANISMS

  Mammals are among the most complex of all animals. Even in these experiments, interesting as they are, the test subjects were obviously alive: their hearts still beat, blood continued to flow in veins and arteries, nerves fired, and the ion transport necessary for life continued to function, if at slower rates. But questions remain about the workings of life in much less complicated and smaller organisms, such as bacteria and viruses, especially when they are put into environments without gas, or in very cold environments. These are not theoretical questions, because every day microbes are flung skyward into the highest reaches of the Earth’s atmosphere by violent storms, and find themselves so high that the Earth’s protective ozone layer—our major defense against ultraviolet radiation coming from space—can no longer screen them. This is the second frontier in the study of life and death: the study of the Earth’s highest life.

  After spending days or weeks in the upper atmosphere, these members of the most newly discovered ecosystem on Earth, one not so subtly named “high life” by the scientists who now study this tropospheric biota, come back to Earth.4 But when they are in space, are they alive?

  While it has been known since the dawn of the space age that bacterial and fungal spores could be found at some of the highest altitudes achievable by aircraft, there was very little appreciation of just how many different species can be found in this largest of Earth’s habitats, a volume of space utterly dwarfing the volume of the second-largest habitat, the top to bottom of the oceans. But work begun in 2010 demonstrated that at any given time there might be thousands of species of bacteria, fungi, and untold viral taxa. It was also discovered by a University of Washington team, sniffing air high atop a mountain in the Cascades of Oregon, that Chinese dust storms routinely drop fungi, bacteria, and viruses onto the West Coast of North America.5

  Yet beyond an intrinsic biological interest that microbes can be found so high in the atmosphere (or that the atmosphere could be a transport system sending us intercontinental, weaponized viruses), there is a new fundamental understanding that is part of the story of this book: atmospheric transport of life may be how the first life on Earth dispersed away from its site of origin. Why slowly float in an ocean, captive of capricious waves and current, when one can jump from continent to continent through the air in less than a day. Later we will return to the implications of high life for the history of life on Earth; here the issue is whether they are constantly alive during their atmospheric, intercontinental travel, or if they are in dormancy. Here, at the fundamentally basic kind of life, we are finding that the categories of life and death are rather incomplete, if not disingenuous concepts.

  High life is collected in three ways: from retired U.S. military high-altitude spy planes, from high-altitude balloons, and when great storms lift off Asia and pass over the Pacific Ocean, and sufficiently “dent” the atmosphere so that air “sniffers” on high mountains can catch a whiff of a descended troposphere. In that air is a zoo full of microbial life. When collected from the immense atmospheric altitudes where cells and viruses are now known to commonly occur, the bacteria are dead. But when brought back to Earth and given some time to react to the altitude they presumably evolved at, they come back to life.

  Most of us would agree that for mammals, and perhaps all animals, dead is dead. But in simpler life, such is not the case. It turns out that there is a vast new place to be explored between our traditional understanding of what is alive and what is not. And this newly discovered region has important implications about the first chapter in the history of life on Earth, telling us whether “dead” chemicals, when correctly combined and energized, could become alive. Life, simple life at least, is not always alive. But now science seeks to find out if there is a place in between. It could be that the first life on Earth came from the place we call death, or from someplace closer to being alive.

  DEFINITIONS OF LIFE

  The question “What is life?” is the title of several books, the most famous by the early twentieth-century physicist Erwin Schrödinger.6 This short book was a landmark, not just for what was written, but also because of the scientific discipline of its author. Schrödinger was a physicist, and before and during his life, the study of biology had been scorned by physical scientists as not worthy of study. Schrödinger began to think of organisms as a physicist would, in physical terms: “The arrangement of the atoms in the most vital parts of an organism and the interplay of these arrangements differ in a fundamental way from all those arrangements of atoms which physicists and chemists have hitherto made the object of their experimental and theoretical research.” While much of the book dealt with the nature of heredity and mutation (for this book was written twenty years before the discovery of DNA, when the nature of inheritance was still a perplexing mystery), it is late in the book that Schrödinger considered the physics of “living,” when he wrote: “Living matter evades the decay to equilibrium,” and life “feeds on negative entropy.”

  Life does this through metabolism, overtly by eating, drinking, breathing, or the exchange of material, which forms the root of the word from its original Greek definition. Is this the key to life? Perhaps, to a biologist, at least. But Schrödinger, the physicist, saw something much more profound: “That the exchange of material should be the essential thing is absurd. Any atom of nitrogen, oxygen, sulfur, etc. is as good as any other of its kind; what could be gained in exchanging them?” What then is that precious “something” that we call life, contained in our food, which keeps us from death? To Schrödinger, that is easily answered. “Every process, event, happening
that is going on in nature means an increase of the entropy of the part of the world where it is going on. Thus a living organism continually increases its entropy.” This, then, was his secret of life: life was matter that created an increase in entropy, and in this, a new way of comparing living to nonliving was made.

  To Schrödinger, then, life is maintained by extracting “order” from the environment, something that he called (with the self-avowed awkward expression) “negative entropy.” Life was thus the device by which large numbers of molecules maintain themselves at fairly high levels of order by continually sucking this orderliness from their environment. Schrödinger suggested that organisms not only created order from disorder but order from order.

  Is that all that life is—a machine that changes the nature of disorder and order? From the physics point of view, life could be understood as a series of chemical machines, all packed together and somehow integrated, maintaining order by expending energy to do so. For decades this view was the most influential of all concerning the definition of life. But a half century later, others began to question and amend these views. Some were, like Schrödinger, physicists, such as Paul Davies and Freeman Dyson. But others were trained biologists.

  Paul Davies, in his book The Fifth Miracle,7 approached the question “What is life?” by using a different question: what does life do? It is actions that define life, according to his argument. These main actions are as follows:

  Life metabolizes. All organisms process chemicals, and in so doing bring energy into their bodies. But of what use is this energy? The processing and liberation of energy by an organism are what we call metabolism, and they are the way that life harvests the negative entropy that is necessary to maintain internal order. Another way of thinking about this is in terms of chemical reactions. If the organism moves from this state of performing chemical reactions on their own (not in the body of the organism) to a state where the reactions stop, the organism has ceased to be alive. Not only does life maintain this unnatural state, but it also seeks out environments where the energy necessary to stay in this state can be found and harvested. Some environments on Earth are more amenable to life’s chemistry than others (such as a warm, sunlit ocean surface of a coral reef or a hot spring in Yellowstone National Park), and in such places we find life in abundance.

  Life has complexity and organization. There is no really simple life, composed of but a handful of (or even a few million) atoms. All life is composed of a great number of atoms arranged in intricate ways. It is organization of this complexity that is a hallmark of life. Complexity is not a machine. It is a property.

  Life reproduces. Davies makes the point that life must make a copy not only of itself but of the mechanism that allows further copying; as Davies puts it, life must include a copy of the replication apparatus too.

  Life develops. Once a copy is made, life continues to change; this can be called development. This process is quite un-machinelike. Machines do not grow or change in shape and even in function with that growth.

  Life evolves. This is one of the most fundamental properties of life, and one that is integral to its existence. Davies describes this characteristic as the paradox of permanence and change. Genes must replicate, and if they cannot do so with great regularity, the organism will die. Yet, on the other hand, if the replication is perfect, there will be no variability, no way that evolution through natural selection can take place. Evolution is the key to adaptation, and without adaptation there can be no life.

  Life is autonomous. This one might be the toughest to define, yet is central to being alive. An organism is autonomous, has self-determination; it can live without constant input from other organisms. But how “autonomy” is derived from the many parts and workings of an organism is still a mystery.

  Action and constitution are one and the same thing for the living system. The system consists of the continuous generation (and regeneration: a protein exists for only about two days) of all the processes and components that put it together as an operational unit. In this view, it is the constant reproduction and renewal of the life form that defines life itself.

  This last, the temporary life-span of molecules crucial to living, and thus life, has been underappreciated as a major clue in understanding where life may first have formed. The NASA definition of life is simpler, and is from a definition favored by Carl Sagan: life is a chemical system capable of Darwinian evolution.8 There are three key concepts to this. First, we are dealing with chemicals, and not just energy or even electronic computing systems. Second, not just chemicals, but also chemical systems are involved. Thus, there is an interaction among the chemicals, not just chemicals themselves. Finally, it is the chemical systems that must undergo Darwinian evolution—meaning that if there are more individuals present in the environment than there is energy available, some will die. Those that survive do so because they carry advantageous heritable traits that they pass on to their descendants, thus lending the offspring greater ability to survive. The Sagan-NASA definition has the advantage of not confusing life with being alive.

  What was the “driver” that caused dead chemicals to combine in such a way to be alive? Was the main driver leading to life a system of metabolism, one that only later added the ability to replicate, or the opposite of this? If it’s the first case, primitive metabolic systems—necessarily enclosed in some cell-like space—later gained the ability to replicate and incorporate some sort of information-carrying molecule. In the latter, replication molecules (such as RNA or some variant) gained the ability to use energy systems to aid in their replication, and only later became enclosed in cell. So we see a very stark contrast that this metabolism vs. replication problem poses at the chemical-molecular level: Was it proteins first, or nucleic acids first? Is either alive, and at what point does each pass from chemical reaction to chemical reactions powering life? Yet if the essential characteristic of a living cell is homeostasis—the ability to maintain a steady and more or less constant chemical balance in a changing environment—it follows that metabolism had to come first. Eating before breeding seems to be the accepted view at the present time, but as in so much dealing with the origin of life, disquieting questions remain.

  ENERGY AND THE DEFINITION OF LIFE

  The role of energy in maintaining life can now be added to our definition of life. We have already defined life as metabolizing, replicating, and evolving. But let us not consider life from an energy flow and order-disorder continuum. Just having energy is clearly not sufficient as a basis of life; there must be an interaction with the energy, and that interaction at a very basic level is needed to maintain a state of nonequilibrium order. Without energy, life goes to nonlife, so life must be something whose very definition is coupled with energy acquisition and energy dumping. Life maintains itself by having states that allow it to become progressively more orderly through the input of energy flow. Our kind of life does this by maintaining a relatively small number of combinations of carbon, oxygen, nitrogen, and hydrogen (and some other elements in smaller volumes). Eventually, a degree of complexity and integration is reached, and maintained, that we call life. The inflow of energy must be sufficient to overcome the tendency of the chemistry within the body that we call life to revert back to its equilibrium condition—nonlife.

  One of the universally accepted definitions of life is that it metabolizes. For Earth life, the primary sources of energy are from the heat of the Earth or from the sun, itself the energy arising from the sun’s thermonuclear fusion reactions. By far the most common way that life taps into solar energy is through photosynthesis. In this process, sunlight provides the energy to convert carbon dioxide and water into complex carbon compounds with many chemical bonds that store energy. By breaking these bonds, energy is released.

  Life on Earth uses a variety of biochemical reactions, and they all involve the transfer of electrons. But this system works only if there is what might be called an electrochemical gradient: the steeper the gradient
, the more energy that can be realized. This means that some types of metabolism yield far more energy than others, just as some kinds of environments have more energy to harvest than others. The organic (carbon-containing) compounds containing the greatest amount of stored energy are fats and lipids—long chain carbons that have much energy tied up in their chemical bonds.

  Metabolism is the sum of all the chemical reactions occurring within an organism. A virus is very small; typical viruses are from 50 to 100 nm in diameter, where nm stands for nanometer, or 10-9 meter. They come in two general types: one group is enclosed in a shell of protein, the second by both a protein shell and an additional membrane-like envelope. Within this covering is the most important part of the virus, its genome, made up of a nucleic acid component. In some there is DNA, in others only RNA. The number of genes also varies widely, with some having as few as three genes and others (such as smallpox) having more than 250 individual genes. In fact, there is a huge variety of viruses, and if they were considered alive, they would be classified across a great taxonomic spread. But common wisdom treats them as nonliving. The viruses that contain only RNA show that RNA by itself, in the absence of DNA, is capable of storing information, and serving as a de facto DNA molecule.9 This finding is strong evidence that there may have been an “RNA world”10 before DNA and life as we know it originated. And there is an even more striking implication of the presence of RNA viruses.