Biology/Citable Version

collage image needed: fabulous shot of earth from space, juxtaposed to images of plants, animals, and people

Biology is the science of living things. Biologists study all aspects of Earth's known living things, including the dynamic processes within them that enable them to live and reproduce. Those vital processes include the harnessing of energy and matter, the synthesis of the materials that make up the body, the healing of injuries, and the reproduction of the entire organism, among many other activities.

The mysteries of life have fascinated all peoples throughout history, and, accordingly, the roots of biology go back to earliest mankind. Curiosity about the physical beings of people, plants, and animals still runs deep in every human society. How is it that these living bodies change; develop, grow, and age? What is it that underlies the divide between inanimate objects and living entities? Some of those questions stem from our desire to control life processes and to exploit natural resources. Pursuit of the answers has led to an understanding of organisms that has steadily improved our standard of living through the ages; but questions also come from a desire to understand nature, rather than to control it. The very core of that desire is sparked by a commonly felt need to understand the nature of the world. Biology brings its own answers to these questions and provides a useful way of learning about living things.

Although the word 'biology' is sometimes used conversationally to refer to matters that concern flesh and blood, and living creatures, this introductory article focuses on biology as a formal science. As such, it incorporate an understanding of mathematics, physics, chemistry and other sciences, and it employs the scientific method. Still, all human interaction with nature eventually contributes, whether it generates ideas from evidence in the laboratory or from the studbook of the breeder, from the notebook of the ecologist or the field notes of the hunter.

The Scope of Biology

How does life begin? What features separate something alive from something not? Biologists use science to try and answer such fundamental questions, questions that also concern the philosopher, the rabbi, the iman, or the priest - as well as every person who retains a sense of wonder. Scientific thinking and religious beliefs about such issues often disagree. Some religious leaders have deplored the scientist's mechanistic view of nature, that seems to remove the need for active intervention of a Creator. Some notable scientists, such as Francis Crick, welcomed biological explanations as providing a rational basis for the world, free of the need to invoke mysterious supernatural powers. Some other great thinkers, however, including the physicist Albert Einstein, found no conflict between the varying teachings of science and religion; he considered divinity and the natural universe to be one and the same . In this view, mathematical equations and the language of prophets are simply two different forms of human expression, each attempting to describe a higher dimension than ordinary human experience.

Although science addresses fundamental issues about life, biology is also used to answer practical questions, which are posed to advance medical and dental care, agriculture and animal husbandry. It is through applied biology that the health sciences became such effective healing arts and that the world's food supply has become safer and more plentiful.

Many independent scientific fields make up biology, but all are related. Natural history (the study of individual species like white-tailed deer, sugar maple trees, box jellyfish and timber wolves) was one of the first areas to develop. In natural history, whole organisms are studied in an attempt to make sense of the order of nature. When the natural histories of plants and animals are considered in a context of how each affects the other and their environment, then the biologist's focus is on ecology. Some fields of biology focus on the natural history of living organisms and their interactions within a certain realm of the earth, as in marine biology; others focus on particular aspects of the bodies of living organisms, like their structure (anatomy) or function (physiology). Studies of animals form the field of zoology, whereas the study of plants is called botany. Medicine and the health sciences apply biology to understanding disease and to improving health.

The development of biology

The rest of this article explores selected themes in biology while giving a short overview of the development of the science. Those themes center on the origin of life (both 'life on earth' and the creation of a new infant) and are followed through the centuries from ancient Greece to the present day. It is apparent that a philosophy of critical thinking, the use of investigative methods that rely on empirical evidence, and the availability of technological tools have, in combination, accounted for how these ideas have changed. The development of biology has drawn on many more topics, and a much larger geographical area than referred to here, but, as outlined below, the science of biology has had a continuous thread through the centuries that began with the ancient Greek philosophers, advanced in Europe during the Enlightenment, and matured during the Nineteenth and Twentienth Centuries with widespread investigations performed according to the scientific method.

Biology in the Ancient World

Whether foragers or farmers, hunters or herders, people have always relied on plants and animals for sustenance, and turned their thoughts to food. Paleolithic cave paintings show that careful observations of prey have been expressed for at least tens of millennia. Human interest in food is not limited to passive considerations. Rather than take sustenance simply as found, we generally carry food items from place to place, and process them in various ways. At some point, probably somewhere in the fertile Nile delta, interactions with certain plants, and their seeds, began to be planned, and, in neolithic times, agriculture became established in many societies. When intellectual consideration of what plants are was combined with evidence-based experiments used to understand their growth, then botany, the science of plants, joined agriculture as a human endeavor.

The beginnings of Anatomy and Zoology both date back at least to the Fourth Century BC, and the ancient Greek philosopher Aristotle. In the first known book that discusses how life in the womb begins, Aristotle suggested that the woman provides the substance needed to build a new baby while the man provides the essence that gives this substance its humanity; he thought that menstrual blood and semen were the female and male contributions to a new life. Aristotle used logic and observation to arrive at his theory, which, in the main, was still accepted 2000 years later. His conclusion that the woman's portion was the mere soil for the man's seed, and that the man's donation supplied all the essential humanity, was probably influenced by the assumption, in his society, that women were less highly developed than men. It might also have come from examining the seeds of some trees, where the entire immature plant is contained within the husk, and springs into independent life as a young tree once planted. A popular idea that grew out of Aristotle's musings was that sperm contained a perfect miniature version of the new baby - a homunculus.

The writings of the Greek scholars were preserved and cherished by the Romans, who added literature on the structure and function of animal and human bodies. The most influential of these was Galen, who was one of the most noted physicians in Rome. Galen performed public dissection and vivisection of animals and used his findings to try to explain human illness. His writings survived the fall of Rome, and they formed a basis for the continuing advance of medicine.

Medieval Europe and the Arab World

With the Fall of Rome, many of the great Greek and Roman works were lost in Europe. Only a few survived, and few people could read them - both the literature and the readers often cloistered together in religious orders. The University of Padua was one of the rare places in Europe where organized learning continued, and later, Padua was to become one of the seats of the Enlightenment. Arab writers, in contrast, continued the work that had been established in the Roman empire. Copies of the old manuscripts were made, and new books of empirically derived medical procedures and theory were written. Later, when the Moors invaded Europe, these books became available to scholars there.

Early Modern Biology : The European Renaissance and the 'Scientific Method'

When the authority of the 'classical' authors (such as Aristotle and Galen) and of religious doctrine (such as the teachings of the medieval Catholic Church) on the nature of living things began to be questioned in light of actual observation and experiment, the scientific method became established. In the early 16th century, scholars had returned to reading Galen in the original Greek, and they emphasized his superiority over his later interpreters, stressing his learning and the importance of anatomy in his view of medicine. The Dutch physician Vesalius (1514-1564), although contemptuous of Galen, followed his methods to produce a new anatomy of the human body, De humani corporis fabrica (On the Workings of the Human Body). He is often called the founder of modern human anatomy.

By the Sixteenth and Seventeenth Century, the advantages of firm empirical evidence over the opinions of authorities were seen by such influential writers as Girolamo Fabrici of Italy and Francis Bacon of England (who coined the phrase knowledge is power). Rather than memorize the texts of Galen, or perform ritualised dissections as 'homage' to Galen's findings, the anatomy and physiology of animals began to be carefully explored in completely new directions. The early European biologists mapped the paths taken by the nerves and veins that travelled between organs, and analyzed their findings in an attempt to find general principles of the organization and function of the body. Theories in biology were still very preliminary, but the evidence for ideas that explained an order to living things revolutionized thinking in biology.

The Englishman William Harvey studied how embryos develop by observations of hens' eggs and by dissecting pregnant deer and other mammals. He speculated that development proceeded from one to another of the fetal forms he found, imagining that each of these forms was a stage in a continuous process. Although other of his experiments famously revealed the circulation of the blood, and identified the workings of the heart as a pump, when it came to early development he failed to see any sort of rational explanation. He could not understand how discrete organs in the developing fetus could form out of the amorphous materials in the just pregnant womb or newly fertile egg. He chose a spiritual rather than a mechanistic explanation, postulating that the soul of the new individual was derived from the placement of sperm in the female tract, invoking the gist of the old Aristotlean argument. Still, he modified Aristotle's explanation by insisting that the male and female contributions were equally important. He refuted the notion that the fetus is made up by the specific materials contributed by the male, that grow because of the separate materials contributed by the female. Instead, he argued that "the material out of which the chick is formed in the egg is made at the same time it is formed" and that "out of the same material from which it is made, it is also nourished"

The Eighteenth and Nineteenth Centuries: seeing the links between lifeforms

As detailed examination of plant and animal species became common, and the knowledge was shared among people in many different parts of the world, similar structures were recognized in many different species. In the Eighteenth Century, the Swedish naturalist Carolus Linnaeus proposed a way of systematically classifying all living things. His method gives a unique name to each kind of plant and animal, and organizes them in a way that stresses similarities of physical features - based on their comparative anatomy. This naming system is still used today, and each known species has one unique name that biologists all over the world recognize. The name has two parts: genus and species, the two most refined categories in the classification scheme. The language of these names is Latin, which was the common written language of scholars in Europe in Linnaeus' time.

Although this systematic classification of living things became widely accepted, at first it did not include the idea that all living things were somehow related. For more than a hundred years after, even highly educated thinkers assumed that complicated life forms (even mice!) could spring to life from a setting of inaminate objects (such as old rags and bread crumbs left in a dark corner). In the Nineteenth Century, Louis Pasteur of France showed that this common notion, spontaneous generation, was a fallacy. His life's work in bacteriology, along with the later work of the German physician Robert Koch, was important in establishing the germ theory of disease. That work helped bring the traditional practice of Medicine into the health sciences and establish a scientific basis for the field of public health.

The varying types of island bird's beaks caught Darwin's attention. Was it just co-incidence that the shape so perfectly managed each bird's particular food?

In England, Charles Darwin built on the idea of natural selection as a way to explain how different life forms might have common patterns of form. His observations of the variations of animal life on remote islands made him realise that individual creatures might thrive, or die, according to how well their characteristics 'fitted' their immediate habitat. He realised that individual members of any species were different from each other in ways that made some more successful than others in producing offspring, and that, if these differences were passed on to the offspring, then the features that made some individuals successful would become more common in each generation. From this insight, he made the bold leap in understanding to realise that perhaps, in enough time, entirely new species might arise. His theories became incorporated into the theory of evolution which suggests that all present living things descended from past living things. The existence of common ancestors would account for similar body forms among descendents, and provided a plausible basis for the wide-spread existence of patterns of very similar features among groups of plants and animals: the very patterns that Linnaeus had used to formulate his categories in classification. This idea was not entirely new, but previous proponents had found it hard to understand how such incredibly diverse life forms might come about in the few thousand years that the world was thought to have existed. By Darwin's time, advances in Earth Science had found evidence that the earth was millions of years older than had been previously suspected. Acceptance of this magnitude of time scale made the idea of incremental change over generations a more reasonable possibilty. Evolutionary change from ancient life was accepted by biologists as a theory that explained both the diversity of life forms and the existence of patterns of common features.

In the second half of the Nineteenth Century, an Austrian monk, Gregor Mendel, analysed how traits were inherited from generation to generation, and he concluded that the male and the female parent contribute equally. (This egalatarian view was perhaps helped by the fact that Mendel studied garden peas, not men and women). Instead of a fuzzy 'blending' of the characteristics of parents, Mendel saw that discrete traits of each individual were inherited intact, apparently based on a sort of 'binary system' of alleles that coded for the quality of each of them. A pea might be wrinkled or smooth, for example, and the particular pair of alleles inherited by the young sprout determined what the next generation of peas would be like. Mendelian also saw that these alleles might be either 'dominant' or 'recessive'. Together, these ideas allowed Mendel to predict the number of offspring that would have each characteristic, and the field of genetics began.

Technology advances Biology

First Glimpses of the Microscopic World

When sperm were first seen under the microscope, it was thought that each contained a perfect miniature human being

The advance of biological thinking depended on the communication of these ideas, and also on technology. Even the communication of ideas in science has depended on technology; in a sense, the printing press was an invention that facilitated the Enlightenment, and today, electronic communication has accelerated the rate of research. The availability of technical tools for experimentation has in a large part determined the course of progress.

The features of plants and animals, for example, have been understood on an entirely different levels with technological advances that provided new ways to study them. The microscope, modified by Antoni van Leeuwenhoek in the Seventeenth Century, revealed details of structure in the bodies of organisms that had never before been even suspected. That amorphous material that Harvey could not fathom as the progenitor of organs might have seemed to him to be of a wholly different nature had he the advantage of magnification. One of the new sights that van Leeuwenhoek described were individual ovum and spermatozoa. Being familiar with the theories of Aristotle, and their popular interpretation, he reported that he could actually see homunculi in the heads of the living sperm - an example of even a great scientist perceiving his expectations, rather than what was really there. Science is always influenced by past ideas. No scientist can consider any hypothesis, or analyze any set of experiemental results without using his or her mind, and all the blinkers and biases that come with it - however hard the good scientist tries to shake free and be rational and objective, that mind is both consciously and unconsciously stamped with the culture that produced it.

Not only was the structure of flesh and plants seen in new detail with the microscope, but new types of organisms were also revealed: micro-organisms that could not be detected with the naked eye. And so, like all important technological advances in biology, the microsocope led to new ideas about living things. It was realised that tissues were composed of cells, the field of microbiology was born, and the ground was prepared for the germ theory of disease, an idea that helped bring the traditional practice of western medicine (sometimes called allopathy) into the field of health science and modern medicine.

Further developments led to the modern compound microscope by the end of the 19th century, with much higher resolution. Cytology included studies of dividing cells, and the chromosomes of the nucleus became recognized as containing the genetic material that lay behind Mendel's laws of inheritance of traits.

Eventually, in the 20th century, electron microscopes were built that could reveal the structure of cells at a magnification of tens of thousands of times. Science differs from religious and political doctrine in at least one major manner – tenets are not to be held sacred forever, but are always there to be questioned and tested. This has proved damaging for many of them, including the homunculus theory of fetal development. With improved optics and the new imaging techniques of scanning and transmission electron microscopes, that "little man" inside the sperm cell vanished forever.

magnified human sperm cells

Cell Biology begins

Cell biology began around 1900, with the discovery of the chromosomes and the understanding of mitosis and meiosis. Fifty years later, the field was revolutionized by the development od the electron microscope, with its ultra-high power examination of cells. Another new discipline within biology began to flourish; the field of cell biology began to unravel the inner architecture of cells, discovering discrete organelles that could only be seen well at high magnification. Closer examination of the structure of the cell was combined with the ability to physically separate out the components of the cells in bulk by weight and chemical properties and analyze each fraction using methods from biochemistry and biophysics. The important techniques that allowed this analysis include ultracentrifugation and gel electrophoresis.

Molecular biology, and a revolution in understanding

In the Twentieth Century, the properties and roles of some of the macromolecules found in living things were examined. Proteins were found to have complex three-dimensional structures that were important for making up physical structures, and some, known as enzymes, included specialized sites able to catalyze the chemical reactions critical for metabolism. Over the decades, proteins were found to take on a variety of roles from being building blocks for cells and tissues, to receptors for signaling, critical for transport in and out of cells, and to guide immune cells to recognize and attack foreign germs. Strikingly, it was found that the molecular structures were conserved, even between kingdoms, in the various families of proteins, thus confirming the ideas of previous centuries that had noted the similar patterns between the organ structures of different plants and animals.

The 'double helix' of DNA. Watson and Crick declared “It has not escaped our notice that the specific pairing ... suggests a possible copying mechanism for the genetic material.” DNA animated

By 1953, the meticulous x-ray studies of Rosalind Franklin allowed the imagination of James Watson and Francis Crick to seize upon the structure of DNA. The double helix structure of that molecule, published in 1953, revealed how information might be coded through the generations, by showing how the DNA molecule could act as a 'template' for the synthesis of both itself, and a related molecule, RNA. Crick and others went on to propose that small RNA molecules might serve as adaptors that could be made from such a template, and be used to assemble amino acids to build proteins.

With these advances in organic chemistry, biochemistry and molecular biology, a new view of the origin of life forms on earth emerged. "It is now widely believed that almost four billion years ago, before the first living cells, life consisted of assemblies of self-reproducing macromolecules".

Studying the biochemistry of RNA and proteins involved purifying unstable compounds from sources that also contained enzymes for their breakdown. Unravelling the movement of RNA out of the nucleus to the endoplasmic reticulum and ribosomes, and pinpointing the mechanics of how proteins were assembled in the cell, were heroic enterprises requiring marathon experiments. Work advanced, but, needed labor-intensive manipulations that could take several days in refrigerated 'cold rooms', without substantial delay between steps. DNA is much more stable, and with DNA chemistry, biologists could take off their parkas and come out of the cold rooms. By the last part of the Twentieth Century, the technique of PCR allowed experiments on tiny samples of DNA to be done in many ordinary laboratories, and progress in molecular biology accelerated.

Attention turned to the DNA sequences that coded for proteins, and the genetic traits that Mendel had observed in his peas were found to have physical correlates in the genes that these sequences provided. Superfamilies of genes were found in different organisms that underlay the existence of those families of related proteins that were identified in diverse tissues and diverse species.

Mitochondria are the 'power plants' of cells that convert organic materials into energy. Mitochondria have their own DNA and may be descended from free-living prokaryotes that were closely related to rickettsia bacteria

Understanding the ultrastructure of cells along with the chemical and physical properties of the organelles brought more new ideas to biology. Mitochondria are tiny organelles that are found in almost all cells, and these are the factories that produce energy for the cell; the complicated chemical process that produce high energy compounds from the breakdown of food molecules is called oxidative phosphorylation. These mitochondria, so essential for living cells, were found to have their own DNA - but its form was that of bacteria rather than mammalian cells. The mitochondria in active human cells were not really human at all, at least not in origin. These organelles had been assimilated into eukaryotic cells and divided along with them, keeping pace with all the generations of the cell, but according to their own genetic code, a circular strand of DNA that resembles the genome of bacteria. These energy-producing organelles of animal cells were not the only organelles found that derived from a different life form; the chloroplasts of plant cells are another. The novel concept that at least some organelles might be the descendants of ancestral 'hitch-hikers' was conceived.

Back to the baby

The age-old question of how a new baby came to be born of man and woman took equally unexpected turns. The single cell that every human begins with does not receive identical types of genetic contributions from mother and father, after all. One of the biggest differences between what each parent gives their baby was found to do with what’s in the egg, but not in the sperm, and that would be cell organelles, specifically mitochondria. Each individual human being is made up of cells with mother's mitochondria only, including the mitochondrial DNA.

Imprinting of genes by parental origin is another asymmetry that had been unsuspected. Even the genes in the nucleus of germ cells are not always treated identically in the newly fertilized egg, but can act differently depending on whether they came from the sperm's nucleus or the ovum's before they joined. Some parental genes were found to be marked in the germ cells (egg and sperm) to be either active or inactive in the new embryo, by the addition of chemical modifiers (like methyl groups) to the DNA.

The suspicions of Aristotle turned out to have an oddly co-incident basis in genetics after all, but in the very opposite way to that imagined by the ancients! "Genes expressed from the paternally inherited copy generally increase resource transfer to the child, whereas maternally expressed genes reduce it." In other words, the genetic material provided by the father has a role slanted to provide nourishment to the fetus. The same genes, when inherited through the nucleus of the egg rather than that of the sperm, act differently. The placenta nourishes the new infant from the mother's womb - but it's the father's genes that are more important for its success in obtaining nutrients. It's as though there is a 'battle' between the father's genes and the mother's genes - it seems almost as though the father's genes want the biggest baby possible, while the mother's genes want a small baby to protect the mother.

The continuing story

By the end of the twentieth century, progress in molecular biology had given rise to the Human Genome Project, an ambitious vision to sequence every single human gene. Not only was that vast project, involving hundreds of laboratories in many countries, completed ahead of schedule [2], but we now also have the complete genomes of many other species with which to compare the human genome. We can actually trace how individual genes have evolved across species, and map out our ancestry to the most primitive life forms in detail. However, for all the advances that have been made in the study of living things, biology remains a science that has only begun to provide a basis for understanding life. The human genome project, so far from answering all our questions, instead opened up many new ones. One of the biggest surprises from the project was the realisation of how few genes it takes to make a human being - just 28,000 or so, not many more than is needed to make the very simplest of animals. It seems that to really unravel our genetic code, we must start the difficult process of understanding all the ways that these genes can interact with each other. The 'vital spark' of life might have its origins in molecules, but knowing just what those molecules are has brought us only a step into the light of its fire.

References

Citations

Notes and Links

Main topics and discoveries

Further reading

Timothy Shanahan The Evolution of Darwinism: Selection, Adaptation and Progress in Evolutionary Biology (2004) ISBN 0521834139

Michel Morange A History of Molecular Biology ISBN 0−674−39855−6; see review here

Stephen Jay Gould Full House: The Spread of Excellence From Plato to Darwin (1996), ISBN 0-517-70394-7 (Released outside North America as Life's Grandeur: The Spread of Excellence From Plato to Darwin (1996), ISBN 0-099-89360-6)

Richard Dawkins The Ancestor's Tale (2004) ISBN 0-618-00583-8; Audio (2005) ISBN 0-7528-7321-0

Selected external links

The following links are recommended because, at the time of their inclusion, they provided accurate information and portals to excellent web resources. Many other excellent links have been omitted.

• The American Institute of Biological Sciences (ABIBS) Virtual Library is free to all visitors
• The Bio-Web reviews and gives access to information in Cell and Molecular Biology, includes "news" in plain language
• Cell and Molecular Biology Online is a resource for professionals that includes links and some information for all
• Kimball's Biology Pages are a online elementary college biology textbook, based on the author's 1996 printed edition.