by Peter Ward
Viruses are parasites. They are technically termed obligatory intracellular parasites, as they are unable to reproduce without a host cell. In most cases, viruses infiltrate cells of living organisms and hijack the protein-forming organelles and start making more of themselves, turning the invaded cells into virus-producing factories. Viruses have a huge effect on the biology of their hosts.
Our revised version of the tree of life, which includes viruses and now-extinct RNA life. This requires a new taxonomic category, one that is higher than domains (which are above kingdoms). RNA life is currently not definable on the accepted tree of life. (From Peter Ward, Life As We Do Not Know It, 2006)
The greatest argument against including viruses as alive is the fact that they are unable to replicate on their own—and thus seemingly fail this major test of whether or not an object is living. But it must be remembered that viruses are obligate parasites, and parasites tend to undergo substantial morphological and genetic changes in adapting to their hosts.
We can also ask if other parasites are alive. Parasitism, which is essentially a highly evolved form of predation, is generally the result of a long evolutionary history. Parasites are not primitive creatures. But like our viruses, they have stages that do not seem fully alive. Cryptosporidium and Giardia, both parasites on humans and other mammals, have resting stages that are as dead as any virus outside of its host. Without the hosts, these two organisms (and thousands of other species as well) will not live, perhaps cannot be classified as living. Yet when in their hosts, they show all the hallmarks of life as we know it: they metabolize, they reproduce, and they undergo Darwinian selection. But if we accept that viruses are alive, and this is increasingly accepted, we must radically reassess the tree of life as it is currently accepted.
In studying life on Earth, two questions can be posed: What is the simplest assemblage of atoms that is alive? And what is the simplest life form on Earth, and what does it need to stay alive? To answer these questions we must look at what current Earth life needs to attain and maintain the state of life described above. To do this we must briefly digress into chemistry of the materials that all Earth life uses to attain and then maintain life.
THE NONLIVING BUILDING BLOCKS OF EARTH LIFE
Of all the molecules making up Earth life, perhaps none is more important than water, and water in a single phase: it has to be liquid water, and not ice or water vapor (a gas). Earth life is composed of molecules bathed in liquid, and while the number of molecules that can be found in life is staggeringly large, in fact there are only four main kinds of molecules used by Earth life: lipids, carbohydrates, nucleic acids, and proteins. All of these are either bathed in liquid, in this case water with salt in it, or serve as an outer wall to contain the other molecules and water.
Lipids—what we call fat—are key ingredients in the cell membranes of Earth life. They are water resistant due to an abundance of hydrogen atoms, but they contain few oxygen and nitrogen atoms. Lipids are the major components of the cell boundary or wall that separates the outside environment from the fluid-filled interior of what we call life. These membranes, although delicate, provide control of substances in and out of cell.
Carbohydrates are the second major class of structures that Earth life is made of, and they are what we informally call sugars. By linking together a number of them, we can form a polysaccharide, which means “many sugars.” Sugars, be they linked or single, are important building blocks in that they can be combined with themselves or with other organic and inorganic molecules to form larger molecules.
Sugars are also important in forming the next category of building block, nucleic acids. This group contains the stored genetic information of any cell. They are giant molecules that combine sugars to nitrogen-containing compounds called nucleotides, themselves formed from subunits called bases, phosphorus, and more sugars. In this arrangement the bases are crucial, for they become the “letters” in the genetic code.
DNA and RNA are sugars that are among the most important of all molecules of life. DNA, composed of two backbones (the famous double helix described by its discoverers, James Watson and Francis Crick), is the information storage system of life itself. These two spirals are bound together by a series of projections, like steps on ladder, made up of the distinctive DNA bases, or base pairs: adenine, cytosine, guanine, and thymine. The term “base pair” comes from the fact that the bases always join up: cytosine always pairs with guanine, and thymine always joins with adenine. The order of base pairs supplies the language of life: these are the genes that code for all information about a particular life form.
If DNA is the information carrier, a single-stranded variant called RNA is its slave, a molecule that translates information into action—or in life’s case, into the actual production of proteins. RNA molecules are similar to DNA in having a helix and bases. But they differ in usually (but not always) having but a single strand, or helix, rather than the double helix of DNA.
Why the enormous complexity of DNA and RNA? The answer lies in the need for information to first build (blueprints) and then maintain the many tasks that staying alive requires. DNA is the blueprint, instruction manual, repair manual, and directions for building copies of itself and all that it codes for. In computer terms, DNA is the software, in that it carries information but cannot itself act on the information. Proteins can be thought of as the computer’s hardware, needing the DNA software to provide information of when and where specific chemical changes should occur in time and space, and to produce material necessary for life. RNA has the interesting characteristic of being either hardware or software, and in some cases both at the same time.
Proteins, the last building blocks, perform four functions in Earth life: building other large molecules, repairing other molecules, transporting material about, and securing energy supplies. Proteins also modify both large and small molecules for a variety of purposes and are involved in cell signaling. There are a huge number of different proteins, and we are only now learning how these work and what they do. A new insight is that their topology, or folding pattern, is as important to their function as their chemical makeup.
All proteins used in Earth life are formed from the assembly of the same twenty amino acids. A new twenty-first-century area of research is asking an old problem: are these same twenty used because they are the best building blocks out there—or because they were common where life was first forming and then became permanently “coded” into life? In fact it looks like it is the former; they work the best, at least according to research in 2010.11 This group is specific to Earth, and perhaps diagnostic of Earth life.
Proteins are constructed in the cell by stringing together the various amino acids in a long, linear chain that folds into its final shape only when all its amino acids have been joined together. Sometimes they fold as they are still being synthesized. Because the assembly of amino acids into a protein is done one at a time in linear and specific order, that protein is often analogized to a written sentence, each amino acid being a word. Within its cell walls, a living cell is packed with molecules, arranged in rods, balls, and sheets, all floating in a salty gel. There are about a thousand nucleic acids and over three thousand different proteins. All of these are going about some sort of chemistry that combined makes up the process we call life. Many chemical processes can go on simultaneously in this one-room house.
There are about also about ten thousand individual spheres within the cell, known as ribosomes, which are distributed rather evenly throughout. Ribosomes are composed of three distinct types of RNA, and about fifty kinds of proteins. Also present are chromosomes, which are long chains of DNA connected to specific proteins. The DNA in bacteria is usually localized in one part of the cell, but is not separated from the other interior material by a plasma membrane, as is the case in higher forms of life known as eukaryotes, which have an interior nucleus. It can be asked just what in this cell is “alive.”
A bacterium is composed of
inanimate molecules. A DNA molecule is certainly not alive, in any sense that any rational person would accept. The cell itself is composed of myriad chemical workings, each, taken alone, being but an inanimate reaction of chemistry. Perhaps nothing is alive but the whole of the cell itself. If we are to understand how life first arose, we need to find the minimum cell that can accomplish this with the fewest molecules and reactions.
One of the pressing problems in looking at this simple cell is that when examined in detail, it is in no way simple. Freeman Dyson has explicitly looked at this aspect of modern life, asking, “Why is life (at least life today) so complicated?”12 If homeostasis is a necessary attribute of life, and if all known bacteria contain a few thousand molecular species (coded by a few million base pairs in the DNA), it looks as if this might be the minimum-sized genome. Yet all bacteria come to us today at the end of more than 3 (and perhaps more than 4) billion years of evolution. Perhaps the simplest Earth life is among the most complicated of life forms in the cosmos.13
The eventual tree of life as it is now viewed. The shaded areas are those organisms that thrive in high heat. What is missing are the presumably many kinds of organisms and “pre-organisms” that evolved from inorganic chemistry step-by-step to produce the first living cell.
CHAPTER IV
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Forming Life: 4.2(?)–3.5 GA
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On July 28, 1976, a robotic claw extended from a huge one-ton machine that only days before had completed the long, silent flight from the Earth to Mars and then had successfully landed there. The claw scooped Martian soil into the Viking spacecraft. This sample collection was the first time such an engineering achievement had ever been accomplished off the Earth. With this sediment now contained in its complicated interior, NASA’s Viking performed four basic experiments, all designed to look for chemical evidence of life or its processes. That was the entire reason for Viking coming to Mars: to search for life.
The initial experiments1 raised hopes that Mars indeed harbored extant life in its soil, for it was soon found that the soil contained more oxygen than was expected, and furthermore that chemical activity of the soil at least hinted at a microbial presence in the Martian regolith. These first-blush experiments created such a wave of optimism in the Viking scientific team that one of the mission’s chief scientists, Dr. Carl Sagan, was optimistic enough to tell the New York Times that he thought that life on Mars, even large forms of life, was not out of the question. By large life, he meant really large, for in the same interview he went on to posit the existence of Martian polar bears!
But the onboard spectrograph, after carefully analyzing the Martian soil, could find no evidence of organic chemicals in the soil. Mars, as viewed from this first Viking lander, not only seemed dead, but inimical to life, leading to speculation that any life that might be there would soon be killed by the toxic chemicals in the soil. Sagan, ever the optimist, could now only hope that the second Viking lander, on that same day already orbiting Mars, would yield telltale evidence for life.
On September 3, 1976, the second lander safely parachuted onto the Martian surface at a place named Utopia Planitia. Like the first, this huge machine functioned perfectly.2 And also like the first, no evidence of life was found in any of the separate and crucial life-detection experiments. Viking had been conceived as a multi-investigative program. But while its study of the chemistry and geology of the soil and atmosphere was important, its primary mission, and most of the instrumentation crammed into the crowded spacecraft, as noted above, was dedicated to the search for extraterrestrial life.
The Viking results suggested that Mars was sterile,3 and NASA began to lose interest in Mars, because NASA was and is driven by the search for life beyond Earth. NASA’s lack of interest began to benefit another branch of science, one that also was bent on studying alien worlds, and perhaps alien life: the oceanographers.
In the immediate post-Viking years, huge new sums went into the technology necessary for deep-ocean exploration, and soon another kind of spacecraft made its own successful descent onto an alien surface. In this case, however, life was found, but of a kind that was totally unexpected. First in the Atlantic Ocean, and then in rapid succession in the deep sea off the Galápagos Islands followed by dives in the Gulf of California, the small yellow submarine Alvin photographed and sampled a kind of life using a radically different source of energy than sunlight.
This discovery of deep-sea “vent” faunas would radically change our understanding of where and how life on Earth came into being, if in fact it originated on Earth at all, for there is a possibility that life formed elsewhere and then was transported to Earth. If life on Earth formed soon after our Earth coalesced into a large and ultimately habitable planet, it suggests that life is not all that hard to make. But how old really is the oldest Earth life—and where was this first life formed?
Usually when historians try to find the “first” of anything, they look into records of ever-older time units, and so it has been with the Earth historians. Their problem has been the paucity of rocks of sufficient age, and the near impossibility of a bacterium-like early cell to actually fossilize.
For more than two decades it has been axiomatic that the oldest sign of life on Earth came from a frozen corner of Greenland, at a place named Isua.4 No fossils were found. Instead, small minerals called apatite were reported to contain microscopic amounts of two different isotopes of carbon that showed a ratio quite similar to one that is characteristic of life today. The Isua, Greenland, rocks were well dated at about 3.7 billion years in age, and later, new dating suggested that they were even older, about 3.85 billion years, in fact, and this is the date that has long been codified into textbooks.
The date of 3.7 to 3.8 billion years old made a lot of sense to those looking for the oldest life on Earth. As we saw earlier, asteroids bombarded the Earth along with every body in the then-young solar system and other junk left over after planet formation from about 4.2 to 3.8 billion years ago. We mentioned earlier that life, while it may have formed (or have been even older that this), would have been wiped out by the process of “impact frustration.”5 Thus the age of the Isua rocks was perfect; the heavy bombardment would have been just over, and life could start. Unfortunately for this tidy package, new instruments developed in the twenty-first century discovered that the small bits of carbon in the Isua, Greenland, samples were not formed by life at all.6
The next-oldest life was 3.5 billion years in age, and in this case, the claim was based on fossils, not just chemical signals. Filamentous forms in an agate-like rock dated to be around 3.5 billion years in age7 were discovered by American paleontologist William Schopf. The fossils came from a previously obscure and ancient assemblage of rocks located in one of the least habitable places on current Earth, a highly deformed rock assemblage called the Apex Chert in Western Australia. The exact geographic position of these fossils, in the dust-dry enormity of Western Australia, was the “North Pole,” a whimsical name given some years earlier because the locality is, in fact, one of the hottest places anywhere on Earth, and about as removed both geographically and especially climatically from the Arctic as a place could be.
Schopf’s discovery galvanized science, for it showed that life on this planet began very early in Earth history indeed. For almost twenty years these ancient Australian fossils were accepted as the planet’s oldest fossil life. Then these too were cast into doubt by Oxford’s Martin Brasier, who claimed that the so-called oldest fossils on Earth were only tiny crystal traces, not life relicts at all.8
What came next was a scientific donnybrook. Scientists on both sides unleashed attacks and counterattacks, most polite (but some less so). Back and forth it went for some years, with Schopf gradually losing ground, not only from attacks from the Oxford crew about the interpretation of the small traces in the Apex Cherts, but also soon after about the age of Apex Chert itself.
Around 2005, Roger Buick of the University of Washing
ton claimed that even if the tiny objects in the Apex Chert are fossils at all, the rocks themselves are far younger than Bill Schopf has claimed, more than a billion years younger, in fact, which would still make them old (any fossil with billions attached to its birthday qualifies for old-age discounts), but nowhere near the oldest life on Earth. With these one-two punches, the Apex fossils were knocked out of the ring.
So matters rested until the summer of 2012, when the same Martin Brasier coauthored a paper9 demonstrating the presence of life that is at least 3.4 million years old—which, according to the authors, makes it the oldest fossil life ever discovered. What makes the discovery even more important is the identity of the fossils themselves, all microscopic, of the size and shape of a specific kind of bacteria living on Earth today. The oldest life on Earth lived in the sea, appeared to need sulfur to live, and quickly died if exposed to even a small number of oxygen molecules. While this life is still what we might call a carbon-based life form, it brings the element sulfur front and center in our assessment of how life came about.10
The fossils described in the Brasier paper appear to be related to minute bacteria still living on our planet—bacteria that need the element sulfur to live, and that die quickly if exposed to the thinnest whiff of oxygen. If this discovery holds, it will confirm that life on our planet began in a place utterly alien to most of the Earth today, and depended on sulfur, not oxygen.
Earth life is usually associated with the forests, seas, lakes, and skies of our present-day Earth—with the creatures living in clear air, clean blue water, on grass-covered hills. Yet the tiny fossils found by Brasier came from an environment of temperatures far higher than those of today, with air composed of the toxic gases methane, carbon dioxide, ammonia, and not a little of the poisonous gas hydrogen sulfide.11 It lived on a planet certainly without continents, or virtually any land of any consequence at all, beyond strings of ephemeral, volcanic isles. In this setting, life began (or arrived, a major possibility to be explored in the pages to come) and then thrived for billions of years. The majority view is that we are all descendants of this Hades on Earth cradle, bearing the scars and genes of a sulfur-rich origin of life.
