If we want to talk about really huge numbers of living organisms, we will have to discuss the bacteria (singular: bacterium). These are the world's simplest living things, and the most numerous. They are multitudinous in the habitats that we are familiar with, but they also survive on the ice fields of Antarctica and in rocky fissures deep within the Earth. Bacterial activity supports strange sightless animals living at fumaroles on the bottom of the sea, and bacteria are an important component of the phytoplankton that captures the energy of sunlight near the ocean surface. Trillions of bacteria, of several hundred kinds, live within our intestinal tract, helping us digest our food, providing us with essential vitamins, and helping us defend ourselves against disease (though the wrong kinds can kill us).
Recently, using newly developed DNA screening, microbiologists have also discovered that there are huge numbers of bacteria in the sea and in the soil. Earlier, we would culture bacteria on petri plates to find and identify them, but many bacteria cannot survive on a dish of agar, remaining undetected and unknown. Using recently developed DNA surveys, we are now able to identify bacteria without having to culture them. One study claims that there may be as many as 1010 (10,000,000,000) bacteria in a gram of dirt.1
In discussing bacteria, we are being quite specific. Bacteria may be microbes, but microbes include a great variety of other minute organisms as well. Protozoa and flagellate amoeba are microbes, but these have larger cells containing nuclei; they are fundamentally different from bacteria. With few exceptions, bacteria are so small that we cannot see them without the aid of a microscope. Before going further with bacteria, however, let's dispense with the even smaller “life form” called viruses.
Viruses do not truly qualify as living beings. To make sense of that statement, let's think about the operations that define life. First of all, living things have to have some way of keeping themselves intact in a changing environment. Bacteria are encased in a tough wall to protect themselves, and many can even transform themselves into tough spore-like devices when the going gets really rough. Just as important is the ability to capture energy in order to carry on life activities. Food, digestive enzymes, and metabolic systems help keep the bacterium supplied with energy. Another key responsibility for all living things is that they must have a way of replicating themselves. This necessitates a genetic program that can be duplicated and transferred from generation to generation. The long double-stranded DNA helix, held together by precise base pairing, is the principle information storage and duplication mechanism for life on Earth. By having the double-stranded DNA helix unwind, each separate strand can then be duplicated to form two new double-stranded helices. These then become the hereditary information for two newly divided “daughter cells” in the process of reproduction.
Viruses do carry short strands of DNA (or RNA) for replication, but they lack two major life criteria. They cannot garner energy for themselves, nor can they reproduce themselves. Then how can they make us so ill? Viruses seem to be a horrible example of “Murphy's Law,” where something that could go wrong did go wrong! Viruses appear to be rogue snippets of DNA or RNA—the basic stuff of genetic information—that got themselves a proper protein coat “and learned how to travel.” What these snippets of DNA or RNA do is to travel around until they encounter a cell they can parasitize, attach to that cell, and insert their short genetic program into the cell. Once within the cell, the viral genes commandeer the gene-replication machinery of the infected cell, which then begins to churn out more viruses. What went wrong here—in the sense of Murphy's Law—was that a small fragment of DNA or RNA got itself a proper encasement, allowing the fragment to travel, to attach, and to infect specific host cells. Viruses are the simplest of parasites; they are “alive” only in their hosts, and each kind of virus is limited to a narrow range of cells it can infect. Among humans, viruses are responsible for influenza, polio, the once-devastating smallpox, and AIDS (caused by the HIV virus). Viruses are so simple that they can even be crystalized and their structure studied by X-ray diffraction. Parasitism, moreover, is a lifestyle that many other living things have also adopted, including bacteria, protozoa, many fungi, a number of animals, and even a few plant species. In many of these, drastic reduction in body size and loss of complexity has occurred, as the parasite depends more and more upon the host. However, and unlike viruses, these larger parasites reproduce—often prodigiously—on their own. But enough of parasites, let's get back to the world's smallest form of independent life: bacteria.
MICROSCOPIC BUT SUCCESSFUL
The most singular aspect of bacteria is their very small size and the lack of organelles within their cells. There are larger bacteria, especially in the lineages that carry on photosynthesis, but most bacterial cells are about one-tenth of the length of an average animal cell. (Bacteria average 1–2 microns thick and 1–4 microns long. A micron is a millionth of a meter, or a thousandth of a millimeter. There are 25.4 millimeters in an inch.) Considering that many bacterial cells are similar in all three dimensions, and that they are about one-tenth the size of animals cells, we can multiply one-tenth (length) by one-tenth (width) by one-tenth (depth), with the result that most bacterial cells have only one-thousandth of the volume of an average animal cell. This is a difference that accounts both for the ubiquity of bacteria and for limitations in what they have been able to accomplish.
Despite their small volume, different lineages of bacteria display a wide array of biochemical activities—more than in all the rest of the living world. Surely this is due to the fact that they have been active here on Earth for a longer period of time than any other lineage—a span of over three billion years! To gain nourishment, most bacteria exude enzymes that digest the food around them. They then absorb their digested dinner. Not a very efficient way to get chow, but it works well in a wide variety of environments. Just as important, each bacterial cell carries a genetic code of DNA, allowing it not only to repair and maintain itself but also to replicate that code for future generations. Efficient energy harvesting and effective reproduction are essential to all forms of life.
Studies of ancient rocks suggest that some kind of bacterial life was in place on planet Earth 3,500 million years ago. These bacteria must have gained energy from a variety of chemical reactions. Breaking down sulfur compounds was an early strategy, and such sulfur-utilizing bacteria are still with us today. But finding just the right energy-rich substrates limited the expansion of early bacterial life. A grand advance took place when one lineage of bacteria developed the biochemical means to capture the energy of sunlight. We call this process photosynthesis: transforming the energy of sunlight into the energy of chemical bonds. The world's earliest photosynthetic bacteria used compounds of hydrogen and sulfur to gain the hydrogen atoms they needed to construct carbohydrates. Transforming the energy of sunlight into chemical energy requires a complex system, including chlorophyll molecules and additional pigments, all within an elaborate molecular framework. By using sunlight to build carbohydrates and other complex molecules, photosynthesizing bacteria became food for others.
Early photosynthesis was a major advance in the history of life, but finding appropriate sulfur molecules limited this process. Then came a world-changing advance: water-splitting photosynthesis! This was accomplished by the Cyanobacteria (called blue-green algae in older literature). Cyanobacteria can be much larger than average bacteria and are often connected in long filaments big enough to produce the dark green glop and yellow-green mats we often see in ponds and streams. At the other end of the size scale sits Prochloroccus, less than a micron in size. So minute, this marine cyanobacterium was not described until 1988! Its photosynthetic ability is essential to life in the ocean, its minute size probably a response to filter-feeding predators.
What the Cyanobacteria accomplished was phenomenal: they were able to rip apart the water molecule in order to get the hydrogen needed to build carbohydrates. This new kind of photosynthesis utilized the hydrogen of water, expelling free oxygen into the air. Oxygenic photosynthesis was probably operational by 2,700 million years ago.2 Coupling the hydrogen of water with carbon dioxide by using the energy of sunshine, Cyanobacteria empowered a vastly larger biosphere and—with time—gave rise to breathable air!
Another biochemical triumph, nitrogen fixation, is also exclusive to the bacteria. This resembles photosynthesis in an important respect. Pulling the water molecule apart in photosynthesis is no ordinary reaction. Hydrogen and oxygen really like each other. When they get together there is a hot time, as the burning of the hydrogen-filled Hindenburg zeppelin displayed. But once together, the two hydrogen atoms are tightly embraced by oxygen, and they want to stay that way. Pulling them apart takes a lot of effort. The biochemical process of nitrogen fixation faces a similar challenge. Our atmosphere is full of nitrogen, to the tune of about 79 percent nitrogen. So what's the problem?
The problem is that the nitrogen in air is made up of molecular nitrogen. Here, two nitrogen atoms hold each other close with three covalent bonds, and they like to stay that way. Because of this strong bonding, molecular nitrogen remains inert to most life activities. And this is why “nitrogen-fixing” bacteria are so important: they can separate the two nitrogen atoms and build them into nitrates or ammonia. Once in this form, other living things can use the “fixed,” or “available,” nitrogen for their life activities. Because nitrogen is a central component of nucleotides (in DNA and RNA), amino acids (in proteins), alkaloids, and more, all living things require accessible nitrogen for growth and reproduction.
HOW DO BACTERIA MAKE MORE BACTERIA?
Bacteria multiply by division. That is, the individual cell divides into two, forming similar daughter cells. Before this important aspect of the life cycle takes place, the bacterium has to have been well-fed and in an agreeable environment. During this time of growth and prosperity, the thin circular chromosome within the bacterium will have made a duplicate copy of itself. (It is the chromosome that carries the long double helix of DNA, the genetic information for keeping them running). The two thin filament-like chromosome loops will then attach themselves at the same point on the inside wall of the bacterium. This single attachment point will split, and here is where the bacterium will pinch in two. Some bacteria carry two chromosomes but divide in much the same way. All told, both daughter cells will come away with a complete chromosome complement, carrying all the genes needed to continue being a busy bacterium. In fact, when conditions are good, many bacteria can grow and divide every twenty to thirty minutes. With plentiful resources, bacteria can multiply exponentially, as rotting food often makes clear.
But did you notice something else? We've been discussing bacterial reproduction and we haven't mentioned sex. That's because there isn't any. There are no male bacteria searching for female counterparts in this story. There is only the simple internal duplication of the chromosome into two, followed by a separation of the two strands to become the chromosomes for each of the two new daughter cells. Simply stated, bacteria do not have sexual reproduction as more complex creatures do. Yet we all know that bacteria are highly adaptive—they mutate frequently, and new strains can make us very ill. How can they be so adaptable without having their genetic material scrambled around in the process higher organisms use?
Turns out, bacteria do have ways of getting together, called conjugation. In this closely positioned state, they can exchange bits of genetic information (DNA) and that's about as close they get to having sex. They can also exchange or acquire packets of genes from other bacteria via plasmids, or by virus-like intermediates. In other words, bacteria do have effective mechanisms for exchanging sections of DNA, thus gaining new hereditary information, new variability, and new possibilities. All this is in addition to naturally occurring mutations as they grow and divide. Though the vast majority of mutations may be deleterious, a very few will give an advantage, helping in the struggle for survival. Clearly, we must monitor bacterial diseases constantly; our foe is ever changing.
Despite extraordinary biochemical diversity, fast life cycles, thousands of different lineages and diverse genetic strains, the bacteria remain sharply constrained. Because they are so small, and because they carry only one or two chromosomes, they are limited in the amount of information they can carry. If they pick up packets of new genes from other bacteria, they cannot just keep making their chromosome longer. They must, in fact, jettison some genetic information when they get too much. They're simply too small to carry around an expanding file cabinet. Remember that these things are really small; the period at the end of this sentence provides enough area for about ten thousand average-sized bacteria to congregate.3 Our skin hosts an estimated three hundred million bacteria, and our large intestine is thought to be teeming with around seventy trillion of them.4
Because they are so small and so versatile, bacteria are impossible to stay clear of. True, some of these bacteria can cause disease or reduce the efficiency of animals, which is why our hog farmers and cattle ranchers add tons of antibiotics to animal feed. But, over the longer run, this may be stupid! Yes, these antibiotics improve the growth of the animals we eat and, in that way, make meat more affordable. But there are two serious reasons that these short-term strategies might backfire. The first is simple: by using large quantities of antibiotics in raising our livestock, we are creating environments saturated with antibacterial compounds. And you get only one guess as to how Mother Nature is going to respond: natural selection! This is a gargantuan program screening for resistance to antibacterial medications, the same agents we use in guarding ourselves from bacterial attack. And then there is a second problem. We are learning that low levels of bacteria may help protect animals from microbial attack! Thanks to intense study of the laboratory fruit fly (Drosophila melanogaster), we have discovered that a persistent low-level bacterial commensal within the fruit fly protects the fly from further serious microbial infection! Since insects have been around for over three hundred million years—subject to bacterial attack over that entire length of time—it makes sense that they have developed a lot of defenses to deal with microbial challenges. Extrapolating from insects to other animals and ourselves, investigators have found that at least some “native microbes are symbionts that shape our immune response and help us stay healthy.”5
We've mentioned how bacteria can transfer DNA between themselves. Interestingly, it turns out that many bacteria can pick up packets of genes from bacteria to which they are not closely related. This is called horizontal gene transfer, a phrasing that reflects the metaphor of an “evolutionary tree.” Such a tree places contemporary living species at the ends of distal twigs, with their earlier ancestors along the branches, and their deep evolutionary origin along the trunk. On such an evolutionary tree, with an ancient trunk and more modern branches, contemporary gene transfer between unrelated species appears to be “horizontal” across distal branches. In contrast, complex animals get their genes from parents, who received their genes from their parents in an “up-from-below” pattern—not horizontally from our contemporaries.
Effective horizontal gene transfer is rare in more complex living things. Rose breeders can only use other roses for their breeding program. Until the advent of genetic engineering, there was no way of getting a petunia gene into a rose. The same was true for animals; animal breeders were stuck with the close relatives of the animals they were breeding. And that's why antelopes all look like antelopes; they are highly restricted in their choice of mates. Because horizontal gene transfer is so rare in higher organisms, we can talk comfortably about thousands of beetle species. Lacking horizontal gene transfer, each beetle keeps looking like all the other members of his or her species.
But in the case of bacterial species, how can we distinguish species among bacteria when they are busy tossing genes back and forth between lineages? With so many bacteria in so many places, with such a long history, and with so many looking so similar, how can we recognize, designate, or even hope to find species in the world of bacteria? This question brings us back to the fundamental unit of biological diversity: the species.
DO THE BACTERIA REALLY HAVE SPECIES?
The biological species concept in higher plants and animals goes something like this: “A species is a population (or series of populations) of interbreeding individuals that cannot exchange genes with other such species.”6 In other words, a species should be genetically isolated from other closely allied plants or animals. Whether the isolation is by long distances, inability to mate, or offspring that are sterile, the result should be the same: no gene exchange with individuals outside the species! In an ideal world, a species is a collection of plants or animals that are advancing through time, down the evolutionary road, all by themselves. Genes from outside sources simply can't get into this species, to mess up its morphology, or obscure its past. Philosophically, the biological species concept is a great idea, and it works well for a large percentage of plants and animals. Unfortunately, the biological species concept seems inappropriate for the world of bacteria. They can and they do exchange genes across different lineages. Our common intestinal bacterium (Escheria coli) is thought to have some 25 percent of its genome acquired from other species.7
The sad truth seems to be that we cannot use the generally accepted concept of species when we are talking about bacteria. If you can pick up genes from far and wide, you have extraordinary potential for doing new and interesting things. But after you have acquired those distant genes, you may suddenly become quite different from even your own ancestors. Bacterial species don't seem to have a tree of close relationships. Rather, they seem to be moving through time as if they were on an interconnected trellis.8 However, bacteria are important; they are a huge component of the living world. If we want to understand them, we must have a means of classifying them. And though the horizontal-gene-transport problem obscures some of their relationships, perhaps we can still find effective ways of arranging the world of bacteria.
When it was discovered that some human diseases were caused by bacteria, the medical community had to find ways of identifying and classifying these critters. In a medical setting, getting a bacterial identification correct could mean the difference between life and death. Some bacteria do differ clearly in form or color, such as the spiral Spirochetes, the small spherical Cocci, or the larger filamentous Cyanobacteria. These were easy to segregate. But the vast majority of bacteria are little rod-shaped things, differing little in appearance. An important test was to see how the bacterium responds to specific staining reagents. Gram-positive bacteria were distinguished from Gram-negative bacteria by how their walls reacted to stains. Also, biochemical and nutritional tests were devised as means of identification. Growing the unknown bacterium on agar with different nutritional qualities was a way to tease out their identity. This may not produce a classification of clear “evolutionary branches,” but it worked well enough to help identify them. Now, with piles of new DNA data, we can seek those genetic traits that are basic to the working of the bacterium and unlikely to be easily exchanged. We may not get clear-cut species out of this activity, but we will develop a better classification.9 More important, these studies revealed a big surprise: the so-called “bacteria” included two very different assemblages!
A major breakthrough in the understanding of bacteria came about after Carl Woese and his colleagues at the University of Illinois found that bacteria really comprised two profoundly different groupings. These groupings were first separated as the Eubacteria and the Archaebacteria. Further studies confirmed this dichotomy, and the two are now called the Bacteria and the Archaea. Certain gene complexes and biochemical traits made clear that Archaea weren't paddling the same boats as were the other bacteria. For one thing, the cell walls of Archaea differ in chemical structure from the walls of other bacteria. In addition, RNA transcription in Archaea differs significantly from transcription within the Bacteria. Even more striking was the fact that many of the Archaea are found living in extreme environments. These ranged from the steaming water of hot springs to the ice fields of Antarctica, and from sulfur-belching fumaroles on the deep ocean floor to water of extremely high salinity. Perhaps it was their ability to live at very high temperatures that made scientists assume these microbes might be ancient survivors of Earth's earliest history, when our oceans were near the boiling point. Nevertheless, and regardless of their origins, the more the Archaea were studied, the more obvious it became that they are distinctive. None of the Archaea are human pathogens and, as we've just noted, many are extremophiles. Today, they are seen as one of the three major living domains or “super kingdoms” of life: Bacteria, Archaea, and the Eukaryota.10
ARE THE ARCHAEA REALLY ARCHAIC?
As more data was gathered regarding the three large domains of life, odd similarities were noted. Clearly, eukaryotic (nucleated) cells had some genetic traits that were closely similar to those of the Bacteria. One of the grand surprises at the end of the late twentieth century was that we could put a human gene into a bacterium and have that bacterium produce a human enzyme! Today, we are busy manufacturing human insulin for diabetics in exactly this way! No one had expected this. After all, our lineage and the bacterial lineage have been separated for at least two billion years. Apparently, Mother Nature has been following the old maxim: “If it works, don't fix it!” Our ability to get bacteria to make human insulin makes clear that some of our basic biochemical-genetic machinery has remained unchanged over billions of years. These biochemical facts are strong evidence for evolutionary continuity since early bacterial times. However, as regards RNA transcription and some other features, the Eukaryotes resemble the Archaea more than they do the Bacteria. It appears that Bacteria and Archaea have both played a role in the later origin of eukaryotic cells.
Let's back up a minute here and review our nomenclature. The cells of Eukaryotes have a nucleus; their name declares “true nucleus.” Prokaryotes have no nuclei, and their name means “before the nucleus.” The prokaryotes include all the Bacteria and the Archaea. In addition to not having a nucleus, prokaryotes do not have organelles within their little cells. The word prokaryote implies that these cells existed before the more complex eukaryotic cells evolved. Indeed, the fossil record supports such an inference (more about this in chapter 8). Not only are bacteria cells generally much smaller than eukaryotic cells, they are not as complex. Though they carry on a huge variety of different biochemical activities in their many different lineages, and are found in every nook and cranny on the planet, the individual bacterium is quite limited in what it can do.
Fossil evidence for the earliest forms of life is meager, and minute eukaryotes are difficult to distinguish from bacterial-grade life. It seems likely that the “eukaryotic cell” may have emerged around 1.5 billion years ago, a full two billion years after bacterial life began. Whatever the actual dates, the greater complexity of eukaryotic cells was a later development in the history of life. But what about the two grand divisions of the prokaryotic world? Those bacteria that survive in the hottest water—close to the boiling point—are nearly all Archaea. While some Bacteria can live in water up to about 180°F (82°C), few can handle the turbulent heat in which some Archaea thrive. Keep in mind that temperature is a measure of molecular motion. The higher the temperature the greater the motion, which is why complex organic molecules begin breaking apart above the boiling point of water and why metals melt in thousand-degree heat. Staying together and carrying on one's life activities at the boiling point of water is no simple task. Nevertheless, some scientists thought that life might have originated under such fierce conditions, and that the Archaea were the living descendants of those earliest forms.
Not so, claimed Thomas Cavalier-Smith of Oxford University. In bold contrast to the received wisdom of earlier work, Cavalier-Smith argues that the Archaea are, in fact, a more modern assemblage of bacteria.11 Because the Archaea have RNA transcription protocols and some other characters found in the later-evolved Eukaryota, it would seem logical that the Archaea are also a more modern development. More telling may be the fact that some Archaea live at temperatures that no other living things can tolerate. Does it seem reasonable that the earliest life forms developed under such severe conditions? Just as polar bears and penguins are recently evolved residents of our most severe polar climates, it would also seem that Archaea were a later development in the history of life. Despite their name, the Archaea may not be especially archaic. Furthermore, Professor Cavalier-Smith addressed an even more fundamental question: Why haven't the Bacteria been more progressive?
Why have bacteria spent more than three billion years being so small? True, they're hugely successful in biochemical diversity, as well as invading every corner of the globe, but why haven't they been able to do anything along the lines of plants and animals, or even protozoa? Bacteria do have an ability, called quorum sensing, that lets them know about others of their kind nearby. And they can form some larger aggregations in this way. Also, Cyanobacteria can form long filaments made up of very large cells. But this is nothing comparable to a simple plant or animal that is, in fact, a functional union of many millions of differing eukaryotic cells. What is it that has kept the bacteria from becoming more than just bacteria?
Professor Cavalier-Smith claims that one of their most important traits has kept bacteria trapped in an evolutionary vise from which they have been unable to escape. That vise, he argues, is the bacterial cell wall itself. This wall must protect the interior of the bacterium from toxic substances or high concentrations of chemicals in the exterior environment. It must prevent the leakage of essential substances from within the bacterium. It must sense the environment and keep the interior of the cell informed of danger. The wall must also allow for the secretion of digestive enzymes and waste products, even as it enables the absorption of nutrients. All this is in addition to being able to pinch itself in two during division, and repairing itself in the face of environmental stress. The bacterial wall allows the bacterium to remain a sensitive and dynamic living being in a huge variety of inhospitable environments. Obviously, when you are enclosed within something as solid and efficacious as the bacterial wall, any change in that protective armor might prove disastrous. This, Cavalier-Smith argues, is why the bacteria have remained so consistent: their protective encasement has not permitted them to expand and enlarge.
The importance of Cavalier-Smith's argument is that it helps us understand why, over more than three billion years, the bacteria were unable to do what the larger, more complex eukaryotic cells have been able to do—become the building blocks for larger and more complex life forms. Unable to change the nature of their walls, a defensive bulwark against an often hostile world, bacteria are doing today most of the same things they've been doing for a very long time.
Bacterial success combined with bacterial stasis reminds us that there are two general ways of increasing biodiversity. The first, as in the bacteria, is to achieve a certain level of complexity and then diversify “laterally,” filling more and more niches with additional variants of your kind. The second, and a major theme in our story, is to increase one's inherent complexity and diversify from this new state. A larger, more complex cell, in fact, proved to be the platform required for building increased biological complexity on planet Earth.
A MAJOR ADVANCE: THE EUKARYOTIC CELL
A revolution in the nature of the cell wall, in fact, ushered in a major new chapter in the history of life. This new kind of cell wall allowed the ancestors of eukaryotes to engulf their prey, just as protozoa do. Swallowing one's dinner is a lot more efficient than exuding enzymes and then absorbing the digested food through the cell wall. A more flexible and more versatile cell wall did more than help early eukaryotes swallow dinner; this was the beginning of entirely new possibilities. Surely the most profound innovation was forming an intimate and permanent relationship with an energy-processing bacterium. By engulfing a new bacterial partner that became the mitochondrion, the eukaryotic cell was empowered to achieve new levels of complexity. Because the mitochondrion is about the size of a bacterium, and has interior membranes that resemble bacterial membranes, early biologists speculated that the mitochondrion had once been an independent bacterium. Lynn Margulis championed this idea in the late 1960s, calling it endosymbiosis. She suggested that a close symbiotic partner—the bacterium—finally became a necessary organelle within the much larger eukaryotic cell itself. The term symbiosis implies that both partners are benefiting from the relationship, though it could be that the bacterium was essentially enslaved by the larger eukaryotic cell.12 Either way, slave or partner, mitochondria became a central feature of the eukaryotic cell. Margulis's endosymbiotic hypothesis found confirmation with the discovery that mitochondria still carry a few of their own genes—evidence that they had once been independent life forms. By providing the eukaryotic cell with a more efficient metabolism, the acquisition of the mitochondrion was an essential early innovation in the advance of complex life forms.13
A new, more flexible wall structure may have been the first fundamental step forward, but getting more efficient energy processing from the mitochondria opened the door to other advances. Think about the small bacterial chromosome. When bacteria acquire new genetic information, they often have to jettison part of the information they're already carrying; they simply can't handle an additional load. But with a larger cell, and more efficient energy delivery, the eukaryotic cell was able to build, maintain, and duplicate much larger file cabinets! This cell could carry not one chromosome but lots of chromosomes. Neatly enclosed within the nucleus of the larger eukaryotic cell, chromosomes and their genetic information were protected from the rough-and-tumble dynamics in the cytoplasm (the aqueous cell contents outside the nucleus). Cellular dynamics include building and destroying proteins as needed, renewing and repairing cell constituents such as enzymes that regulate reactions, digestion of food particles, and preparing for cell division. Unlike bacteria, eukaryotic cells have “motor proteins,” which move materials around within the larger cell. All this takes energy, provided by the oxygen-utilizing mitochondria and information from a larger genome. (The genome is all the genetic information carried by an individual organism, whether simple bacterium or larger animal.)
Nick Lane points out that much of the energy generation in biology involves forcing protons and electrons across membranes. This means more membranes are necessary for increasing energy acquisition. And since the bacterial membrane is closely tied to the bacterial wall, bacterial energetics is limited. Because volume increases faster than surface area as things get bigger, larger bacteria have proportionally less membrane surface for energy production, and they cannot provide sufficient energy to the increased demand of greater cell volume. In contrast, Eukaryotes, armed with lots of mitochondria (each with folded interior membranes), have what's needed to power ever higher levels of complexity. Lane argues that incorporation of mitochondria into the early eukaryotic cell was a truly momentous innovation, without which we simply wouldn't be here.14 Not only are you the reader and the oak tree down the street constructed of eukaryotic cells, but you and the oak tree in fact originated from such a solitary cell—the fertilized egg cell!15
Endosymbiosis, where a bacterial-grade life form became an essential organelle within the larger eukaryotic cell, has occurred several times and in different lineages. Lynn Margulis also believed that the complex eukaryotic cell had acquired significant elements from spirochetes (spiral bacteria that move very rapidly). These bacteria, Margulis claimed, gave the eukaryotic cell the machinery to move chromosomes apart during cell division, and they were the origin of wiggly tails in sperm and other cells. While these ideas remain speculative, there was another grand endosymbiotic event in the history of life, which everyone does agree on.
This second union was the inclusion of a photosynthetic cyanobacterium into a eukaryotic cell, giving rise to the algae. The resultant organelle is called a chloroplast, making plants green and allowing them to photosynthesize. This advance expanded photosynthesis beyond the Cyanobacteria to a host of larger, more complex algae and, eventually, land plants. Capturing more sunlight, this new symbiosis was another major advance in the escalation of biodiversity on planet Earth. In addition, red algae, brown algae, and a few other lineages were the benefactors of yet additional symbiotic unions within their cells.16 However, because of stiff cellulose cell walls, plants have been limited in their ability to form varied morphological forms, unlike animals with their thin flexible cell membranes. But whether plant or animal, the more complex eukaryotic cell has a problem: how to divide and reproduce.
HOW EUKARYOTIC CELLS MULTIPLY
Before moving to the world of eukaryotic creatures, we must examine another fundamental aspect of the eukaryotic cell: replication. We need to understand how the eukaryotic cell divides and multiplies—a process called mitosis. The first sign that a eukaryotic cell is going to divide is the disappearance of the nucleus, as the nuclear membrane is dissolved. At the same time, the chromosomes condense into thick visible structures. During the regular activities of the cell, chromosomes are not visible under a microscope. Even staining does not show them. But as cell division begins, the chromosomes condense, becoming dark little sausages under the microscope. (We observe this process after the cell has been killed and stained.) The chromosomes move toward the center of the cell and align themselves along a central plane within the cell (called the metaphase plate). This is the same plane along which the cell will divide, or pinch itself in two. So now we've got all the chromosomes hanging out along this saucer-like area at the center of the cell. They then begin to align themselves in such a way that each chromosome will separate into two strands, with the two strands ready to move in opposing directions. Lines appear to form within the cell, reaching toward the center of each chromosome. Like stars, these lines radiate inward from two distal poles, and it is along these lines that the sister strands are pulled in opposite directions, and the cell is ready to divide down the same plane on which the chromosomes had aligned themselves. Voila—two new cells, each with the same number of chromosomes as the original cell!
Before cell division could occur, preparations were made in advance. During the period of time when the cell was going about its normal business, it was also doubling its chromosome strands. Each double-helix strand of DNA had to be transformed into two double-helix strands. Thus, when cell division began, the chromosomes were already two-stranded. Let's review this process again: Once mitosis begins, the nucleus disassembles its membrane, freeing the chromosomes to move to the center of the cell and align themselves properly. Set to travel in opposing directions, each of the two sister DNA strands separate and head to one of the two poles of the now-dividing cell. At the same time, mitochondria and other cell organelles are also dividing, to ensure that each daughter cell has what's required to be a successful new cell. In short, mitosis produces two identical cells where there had been only one. And, with over a trillion cells making up a human being, you can understand how critical cell division is to our growth and health. Since many of our cells are being continuously lost, whether on our skin, in our bloodstream, or along the walls of our intestine, cell division maintains our active bodies even as we age. But this is just one aspect of the game of life. Eukaryotic organisms have another game they like to play—we call it sex.
WHAT GOOD IS MEIOSIS AND SEX?
Meiosis is the starting gun of sex. Meiosis is the process of cell division that produces sex cells (gametes) in eukaryotic organisms. Meiosis differs significantly from mitosis, the common form of cell division we've just been talking about. Looking at stained cells, killed during the process of meiosis, one sees much the same activities as in mitosis. However, there are two main differences. The first is that meiosis is a two-stage process, comprising two cell divisions. The second difference is how the chromosomes line up and then divide during their first cell division. In meiosis, before lining up on the metaphase plate, homologous chromosomes form pairs. Most organisms received one set of chromosomes from their female parent and a second set from their male parent; thus their cells contain two sets of chromosomes (the diploid condition). Humans carry forty-six chromosomes in their cells; twenty-three came from Mom, and twenty-three came from Dad. Each of these twenty-three chromosomes is different from the other twenty-two, and each will link up with its own homologue during meiosis. Thus, instead of having forty-six chromosomes crowding the center of the cell, in meiosis we've got twenty-three pairs ready to divide and head in opposite directions. Thus, the first division of meiosis gives rise to two daughter cells with half the normal adult number of chromosomes: twenty-three in the case of humans (the haploid state). The second division of meiosis follows in the manner of mitosis and results in four cells, all with half the regular chromosome number. In animals, meiosis usually produces four sperm cells, but in the female line meiosis often results in one very plump egg cell and three skinny sisters that are cast aside. Unfair but pragmatic: the larger female egg cell will have more nutrition to begin a new life. The smaller male sperm carries only enough nutrition to power its flagella, swim to the egg cell, and donate its haploid genome for the new diploid organism.
Meiosis takes ordinary cells with two chromosome sets—the diploid condition—and reduces them down to sex cells with only one set of chromosomes: the haploid condition. Meiosis yields sex cells that are utterly and completely useless (in most organisms) until they get together with another sex cell to restore the diploid condition. Consequently, most eukaryotic cells in larger organisms are diploid: they have two chromosome sets within the nucleus of each cell. There are exceptions (this is biology): many algae, mosses, and liverworts live most of their lives in the haploid condition. Nevertheless, sperm and unfertilized egg cells represent the haploid part of the life cycle in most eukaryotes. (We'll discuss the chromosome compliment of a plant or animal—ploidy—in the next chapter).
WHY IS SEXUAL REPRODUCTION ADVANTAGEOUS?
Why produce sex cells; cells that are useless until and unless they unite with another haploid sex cell? This has been a central conundrum for biology over several centuries. Why waste time and energy making sex cells when complex organisms could simply divide in two and produce little copies of themselves? Why should a huge Alaska brown bear mother do all the work of bearing young, nursing them, and teaching them, while brown bear males do little more than defend their territories? Like most animals, date palms also come in two sexes. Again, it is the female palm that produces all the sweet dates we are so found of; male date palms produce nothing more than large inflorescences and a lot of pollen. The troublesome question is: Why is sex so widespread in the living world?
Biological systems are complex systems—the products of many processes and many interactions, all with a very long history. Again, this isn't physics. Two fundamental explanations for the existence of sex are found in the process of meiosis itself. Recall that homologous chromosomes must pair together before becoming aligned on the metaphase plate. Precise pairing of strands in meiosis is necessary for the accurate separation into the two diverging daughter cells. Just as significantly, this pairing allows for chromosome repair in a way that ordinary mitosis does not.
The second advantage of precise pairing is called crossing over. This allows sections along the paired chromosomes to be exchanged—a terrific way to get new gene combinations onto the same chromosome. Imagine a chromosome with a bad gene at point q, while its chromosome partner has a bad gene at point t. With crossing over there is the possibility of forming a single chromosome with good genes at both points q and t. Of course, this results in the other chromosome getting stuck with both bad genes. Tough luck! The good news is that we've now got a new combination, with both good traits on the same chromosome. What meiosis does is allow both for repair and recombination. And that's just the beginning.
Sexual union, when sperm and egg unite, brings together two gametes from two separate individuals, who may be quite different themselves. Each of the parent's sex cells (gametes) is a sample of that parent's genetic resources. Think of this in terms of your grandparents. Your parents gave you a sampling of your four grandparent's chromosome sets, via their sperm and egg. Theoretically, your parents could have had two million children, each with a different sampling of their four grandparent's chromosomes. No wonder families can have such markedly different children!
Now let's expand our view to look at sex from the perspective of the entire species. Sex means that the genetic heritage of a species can be reshuffled every generation, rather like a huge deck of playing cards. From the perspective of a large population of individuals, sex constantly produces individuals with both old and new gene combinations. This has several profound advantages. Genetic diversity means that a species can have individuals doing well in both drier and wetter, or warmer and colder, parts of its habitat. Constant genetic reshuffling also means that a species is more likely to adapt when there is a change in climate. And finally, a diverse and constantly variable species may be the only way to withstand incessant attack by parasites and pathogens. It is not “Lions and tigers and bears, oh my!” that are likely to end your days. Rather, it is these smaller, quickly changing enemies, which cause devastating losses among plants, animals, and people. A sexually reproducing host species is more likely to contain individuals who can survive in the face of attack by a new pathogen. Sex, and the constant scrambling of genetic combinations, may be the only way for a species to survive in a hostile world of unpredictable climate perturbation and ever-variable pathogens.
Fundamentally, sex serves the population and species—not the individual! Meiotic division and sexual union are constantly shuffling the cards to produce a grand variety of hereditary outcomes. Those with nonadaptive traits or mutations will be cleared away (sacrificed, you might say) for the good of the species. While many species regularly reproduce without sex, they do undergo sexual reproduction from time to time, taking advantage of genetic recombination. In experiments, sexless strains of the tiny nematode worm Caenorhabditis elegans, coevolving with their parasites, became extinct within twenty generations! Perhaps this is why sex is found in virtually all eukaryotes, from amoebas and redwoods to fish and fowl. Sex appears to be a necessary attribute for survival in a dynamic and unfriendly world.17
There are additional advantages to sex. One huge advantage is being diploid: having two sets of genes! In the diploid condition, you might be carrying a nonfunctional gene on chromosome number thirteen, but if your other chromosome number thirteen has a functional gene at the same position you're home free! Your good gene will be perfectly functional, “covering for” its nonfunctional partner. This has further advantages. Lots of individual genes differ only slightly from each other (called alleles). One allele may be advantageous in today's environment, but another allele may be more effective if the climate gets warmer. In effect, each of us diploid organisms carries two genomes—one from our male parent, the other from our female parent. Returning to the larger population, diploid species carry a large reservoir of diverse genes, all “held in waiting” for new environmental challenges. Sex, despite its costs, is ubiquitous among complex living things because it provides them a larger collection of genetic resources and keeps mixing them up. Though sex can be disastrous for individuals born with bad genes, it has proven essential for species-survival over evolutionary time.
COOPERATION AND BUILDING LARGER LIVING THINGS
Surely the invention of the eukaryotic cell, with all its internal components working together to carry on its life activities, was a major advance in the history of life. But that internal cooperation was followed in a few lineages by something even more extraordinary: the working together of many cells—cooperatively—to form larger multicellular entities. But how might unitary, independent cells, centered on their own reproduction, abandon those drives to form larger multicellular beings? Forming cooperative entities required that individual cells first develop mechanisms for sticking together. Next, they had to acquire communication abilities allowing them to interact with other cells and “do what they were supposed to do” on behalf of the larger organism. Such cooperating cells had to play by new and very restrictive rules.
Fundamentally, the basic purpose of all cells is to divide and make more cells. But that directive must be strongly modified if the cell is to be a functional member of a larger multicellular organism. In this case, the cell must take orders from its close neighbors. The tragedy of cancer begins when a few cells lose these constraints, proliferating at the expense of other tissues around them, and, finally, threatening the health of the entire individual. Cancer reminds us of how important the cooperation of cells is in maintaining the complex individual as a single well-functioning organism.
One of the simplest of animals, a sponge, has recently had its genome analyzed. Sponges are filter-feeders that lack symmetry. While very simple, their genome includes a basic genetic toolkit shared by all multicellular animals. Among these are genes responsible for some human cancers! These must be genes essential to forming the larger multicellular organism, instructing cells how to behave, and when to divide. Because they are multicellular, the lowly sponges require these genes just as we do. Multicellularity was one of the great advances in the elaboration of life on Earth. More remarkable, this advance in living complexity took place independently in animals, plants, and fungi! However, it did not come quickly. Larger multicellular organisms did not make their appearance in the fossil record until around 560 million years ago, a full four thousand million years after our solar system began!
We began this chapter focused on the most numerous and prolific of living things, the bacteria. From these simple cells, endosymbiotic unions allowed more voluminous cells to upgrade their energy processing. Utilizing the atmosphere's free oxygen, mitochondria gave the eukaryotic cell more energy more efficiently. Sequestered within a nucleus, the eukaryotic genome was protected from a metabolically turbulent cytoplasm. Meiosis and sex gave eukaryotic lineages the ability to reshuffle their genes to confront environmental change and to counter ever-diversifying pathogens and parasites. Together, these advances provided a platform from which eukaryotic cells would make new and innovative advances.
Though bacteria may have the highest numbers and greatest variety of impacts on our planet, the larger eukaryotic cell was the advance from which even greater complexity would emerge. Only the Eukaryotes have given rise to multicellular organisms, and they've done this multiple times. A recent mathematical analysis estimated that our planet has about eight million different eukaryotic species, both on land and in the sea.18 I suspect that three to five million is a more reasonable estimate but—either way—these numbers are huge. Why so many? In the next chapter we confront the phenomenon of increasing numbers of species.