Prokaryotes Eukaryotes Yeasts People

Non-biologists often fail to appreciate the tremendous number of different kinds of organisms in the world. Although no one really knows, estimates of the number of currently extant species range from 5 million to 50 million (May, 1988).^ There are at least 300,000 different kinds of beetles alone, and probably 50,000 species of tropical trees. Familiar kinds of plants and animals make up a relatively small proportion of the kinds of living things, perhaps only 20%. Vertebrates (animals with backbones: fish, reptiles, amphibians, birds, mammals) make up only about 3% of the species in the world.

Since Aristotle, scholars have tried to group these myriad species into meaningful classes. This pursuit remains active, and the classifications are, to some degree, still controversial. Traditionally, these classifications have been based on the morphology of organisms. Literally, morphology means shape, but it is generally taken to include internal structure as well. Morhpology is only part of phenotype, however; other parts include physiology, or the functioning of living structures, and development. Structure, development and function all influence each other, so the dividing lines are not entirely clear.

In recent years, these traditional taxonomies have been shaken by information gained from analyzing genes directly, as well as by the discovery of an entirely new class of organisms that live in hot, sulphurous environments in the deep sea.

*A virus is arguably alive, and is not a cell, but it depends on infecting a cell in order to reproduce.

tMay also notes that it is possible that half the extant species on the planet may become extinct in the next 50 to 100 years.

All Life

All Life

Fungi

Green Plants

(yeast, planaria) (Mushrooms, Athlete's foot) (trees, flowers, grasses)

Protists

Fungi

Green Plants

(yeast, planaria) (Mushrooms, Athlete's foot) (trees, flowers, grasses)

Animals

Vertebrates

Invertebrates (insects, worms, shellfish, snails)

Vertebrates

Invertebrates (insects, worms, shellfish, snails)

Fish Reptiles Amphibians Birds

(sharks, trout) (snakes, lizards) (frogs, newts) (eagles, finches) Mammals

Fish Reptiles Amphibians Birds

(sharks, trout) (snakes, lizards) (frogs, newts) (eagles, finches) Mammals

Monotremata Marsupials Leptictida Rodents Carnivores Pinnipedia Pteropidae Primates (platypi) (kangaroos) (rabbits) (mice) (wolves) (seals) (bats) (people)

Figure 1. A very incomplete and informal taxonomic tree. Items in italics are common names of representative organisms or classes. Most of the elided taxa are Bacteria; Vertebrates make up only about 3% of known species.

Here I will follow Woese, Kandler & Wheelis (1990), although some aspects of their taxonomy are controversial. They developed their classification of organisms by using distances based on sequence divergence in a ubiquitous piece of genetic sequence As shown in Figure 1, there are three most basic divisions: the Archaea, the Bacteria and the Eucarya. Eucarya (also called eucaryotes) are the creatures we are most familiar with. They have cells that contain nuclei, a specialized area in the cell that holds the genetic material. Eucaryotic cells also have other specialized cellular areas, called organelles. An example of organelles are mitochondria and chloroplasts. Mitochondria are where respiration takes place, the process by which cells use oxygen to improve their efficiency at turning food into useful energy. Chloroplasts are organelles found in plants that capture energy from sunlight. All multicellular organisms, (e.g. people, mosquitos and maple trees) are Eu-carya, as are many single celled organisms, such as yeasts and paramecia.

Even within Eucarya, there are more kinds of creatures than many non-biologists expect. Within the domain of the eucaryotes, there are generally held to be at least four kingdoms: animals, green plants, fungi and protists. From a genetic viewpoint, the protists, usually defined as single celled organisms other than fungi, appear to be a series of kingdoms, including at least the cili-

ates (cells with many external hairs, or cillia), the flagellates (cells with a single, long external fiber) and the microsporidia. The taxonomic tree continues down about a dozen levels, ending with particular species at the leaves. All of these many eucaryotic life forms have a great deal in common with human beings, which is the reason we can learn so much about ourselves by studying them.

Bacteria (sometimes also called eubacteria, or prokaryotes) are ubiquitous single-celled organisms. And ubiquitous is the word; there are millions of them everywhere — on this page, in the air you are breathing, and in your gut, for example. The membranes that enclose these cells are typically made of a different kind of material than the ones that surround eucarya, and they have no nuclei or other organelles (they do have ribosomes, which are sometimes considered organelles; see below). Almost all bacteria do is to make more bacteria; it appears that when food is abundant, the survival of the fittest in bacteria means the survival of those that can divide the fastest (Alberts, et al., 1989). Bacteria include not only the disease causing "germs," but many kinds of algae, and a wide variety of symbiotic organisms, including soil bacteria that fix nitrogen for plants and Escherichia coli, a bacterium that lives in human intestines and is required for normal digestion. E. coli is ubiquitous in laboratories because it is easy to grow and very well studied.

Archaea are a recently discovered class of organism so completely unlike both bacteria and eucarya, both genetically and morphologically, that they have upset a decades old dichotomy. Archaea live in superheated sulphur vents in the deep sea, or in hot acid springs, briney bogs and other seemingly inhospitable places. They are sometimes called archebacteria even though they bear little resemblence to bacteria. Their cell membranes are unlike either Bacteria or Eucarya. Although they have no nuclei or organelles, at a genetic level, they are a bit more like Eucarya than like Bacteria. These organisms are a relatively recent discovery, and any biological theories have yet to include Archaea, or consider them simply another kind of procaryote. Ar-chaea will probably have a significant effect on theories about the early history of life, and their unusual biochemistry has already turned out to be scientifically and commercially important (e.g. see the discussion of PCR in the last section of this chapter).

Viruses form another important category of living forms. They are obligatory parasites meaning that they rely on the biochemical machinery of their host cell to survive and reproduce. Viruses consist of just a small amount of genetic material surrounded by a protein coat. A small virus, such as fX, which infects bacteria, can have as few as 5000 elements in its genetic material. (Viruses that infect bactieria are called bacteriophages, or just phages) Their simplicity and their role in human disease make viruses an active area of study. They also play a crucial role in the technology of molecular biology, as is described in the last section in this chapter.

8 Artificial Intelligence & Molecular Biology 1.3 Evolutionary Time and Relatedness

There are so many different kinds of life, and they live in so many different ways. it is amazing that their underlying functioning is so similar. The reason that there is unity within all of that diversity is that all organisms appear to have evolved from a common ancestor. This fundamental claim underpins nearly all biological theorizing, and there is substantial evidence for it.

All evolutionary theories hold that the diversity of life arose by inherited variation through an unbroken line of descent. This common tree of descent is the basis for the taxonomy described above, and pervades the character of all biological explanation. There is a great deal of argument over the detailed functioning of evolution (e.g. whether it happens continuously or in bursts), but practically every biologist agrees with that basic idea.

There are a variety of ways to estimate how long ago two organisms diverged; that is, the last time they had a common ancestor. The more related two species are, the more recently they diverged. To the degree that pheno-typic similarity indicates genotypic similarity, organisms can be classified on the basis of their structure, which is the traditional method. Growing knowledge of the DNA sequences of many genes in many organisms makes possible estimates of the time of genetic divergence directly, by comparing their genetic sequences. if the rate of change can be quantified, and standards set, these differences can be translated into a "molecular clock;" Li & Graur, (1991) is a good introduction to this method. The underlying and somewhat controversial assumption is that in some parts of the genome, the rate of mutation is fairly constant. There are various methods for trying to find these areas, estimate the rate of change, and hence calibrate the clock. The technique has mostly confirmed estimates made with other methods, and is widely considered to be potentially reliable, if not quite yet so. Most of the dates i will use below were derived from traditional (archaeological) dating.

in order to get a rough idea of the degrees of relatedness among creatures, it is helpful to know the basic timeline of life on Earth. The oldest known fossils, stromalites found in Australia, indicate that life began at least 3.8 billion years ago. Geological evidence indicates that a major meteor impact about 4 billion years ago vaporized all of the oceans, effectively destroying any life that may have existed before that. in effect, life on earth began almost as soon as it could have. Early life forms probably resembled modern bacteria in some important ways. They were simple, single celled organisms, without nuclei or other organelles. Life remained like that for nearly 2 billion years. Then, about halfway through the history of life, a radical change occurred: Eucarya came into being. There is evidence that eucarya began as symbiotic collections of simpler cells which were eventually assimilated and became organelles (see, e.g. Margolis (1981)). The advantages of these specialized cellular organelles made early eucarya very successful. Single-celled

Eucarya become very complex, for example, developing mechanisms for moving around, detecting prey, paralyzing it and engulfing it.

The next major change in the history of life was the invention of sex. Evolution, as you recall, is a mechanism based on the inheritance of variation. Where do these variations come from? Before the advent of sex, variations arose solely through individual, random changes in genetic material. A mutation might arise, changing one element in the genome, or a longer piece of a genome might be duplicated or moved. If the changed organism had an advantage, the change would propagate itself through the population. Most mutations are neutral or deleterious, and evolutionary change by mutation is a very slow, random search of a vast space. The ability of two successful organisms to combine bits of their genomes into an offspring produced variants with a much higher probability of success. Those moves in the search space are more likely to produce an advantageous variation than random ones. Although you wouldn't necessarily recognize it as sex when looking under a microscope, even some Bacteria exchange genetic material. How and when sexual recombination first evolved is not clear, but it is quite ancient. Some have argued that sexual reproduction was a necessary precursor to the development of multicellular organisms with specialized cells (Buss, 1987). The advent of sex dramatically changed the course of evolution. The new mechanism for the generation of variation focused nature's search through the space of possible genomes, leading to an increase in the proportion of advantageous variations, and an increase in the rate of evolutionary change.

This is probably a good place to correct a common misperception, namely that some organisms are more "primitive" than others. Every existing organism has, tautologically, made it into the modern era. Simple modern organisms are not primitive. The environment of the modern world is completely unlike that of earth when life began, and even the simplest existing creatures have evolved to survive in the present. It is possible to use groups of very distantly related creatures (e.g. people and bacteria) to make inferences about ancient organisms; whatever people and bacteria have in common are characteristics that were most likely shared by their last common ancestor, many eons ago. Aspects of bacteria which are not shared with people may have evolved as recently as any human characteristic not shared with bacteria. This applies to the relation between people and apes, too: apes are not any more like ancestral primates than we are. It is what we have in common with other organisms that tells us what our ancestors were like; the differences between us and other organisms are much less informative.

Whether or not it occurred as a result of the advent of sexual recombination, the origin of multicellular organisms led to a tremendous explosion in the kinds of organisms and in their complexity. This event occurred only about a billion years ago, about three quarters of the way through the history of life.

Of course, nearly all of the organisms people can see are multicellular (although the blue-green algae in ponds and swimming pools are a kind of bacteria). Multicellular organisms gain their main evolutionary advantage through cellular specialization. creatures with specialized cells have the ability to occupy environmental niches that single-celled organisms cannot take advantage of. In multicellular organisms, cells quite distant from each other can exchange matter, energy or information for their mutual benefit. For example, cells in the roots of a higher plant exist in a quite different environment than the cells in the leaves, and each supplies the other with matter or energy not available in the local environment.

An important difference between multicellular organisms and a colony of unicellular organisms (e.g. coral) is that multicellular organisms have separated germ line (reproductive) cells from somatic (all the other) cells. Sperm and eggs are germ cells; all the other kinds of cells in the body are somatic. Both kinds of cells divide and make new cells, but only germ cells make new organisms. Somatic cells are usually specialized for a particular task; they are skin cells, or nerve cells, or blood cells. Although these cells divide, when they divide, they create more of the same kind of cell. The division of somatic cells and single celled organisms is a four stage process that ends with mitosis, resulting in the production of two identical daughter cells. The process as a whole is referred to as the cell cycle.

Only changes in germ cells are inherited from an organism to its offspring. A variation that arises in a somatic cell will affect all of the cell's de-scendents, but it will not affect any of the organism's descendents. Germ cells divide in a process called meiosis; part of this process is the production of sperm and egg cells, each of which have only half the usual genetic material. The advent of this distinction involved a complex and intricate balance between somatic cells becoming an evolutionary deadends and the improved competitive ability of a symbiotic collection of closely related cells.

Multicellular organisms all begin their lives from a single cell, a fertilized egg. From that single cell, all of the specialized cells arise through a process called cellular differentiation. The process of development from fertilized egg to full adult is extremely complex. It involves not only cellular differentiation, but the migration and arrangement of cells with respect to each other, orchestrated changes in which genes are used and which are not at any given moment, and even the programmed death of certain groups of cells that act as a kind of scaffolding during development. The transition from single-celled organism to multicellular creature required many dramatic innovations. It was a fundamental shift of the level of selection: away from the individual cell and to a collection of cells as a whole. The reproductive success of a single cell line within a multicellular individual may not correlate with the success of the individual. Embryology and development are complex and important topics, but are touched on only briefly in this chapter.

Most of the discussion so far has focused on organisms that seem very simple and only distantly related to people. On a biochemical level, however, people are much like other eucaryotes, especially multicellular ones. Genetic and biochemical distance doesn't always correlate very well with morphological differences. For example, two rather similar looking species of frogs may be much more genetically distant from each other than are, say, people and cows (Cherty, Case & Wilson, 1978). A great deal of human biochemistry was already set by the time multicellular organisms appeared on the Earth. We can learn a lot about human biology by understanding how yeasts work.

We've now covered, very briefly, the diversity of living things, and some of the key events in the evolution of life up to the origin of multicellular organisms. In the next section, we'll take a closer look at how these complex organisms work, and cover the parts of eucaryotic cells in a bit more detail.

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