Biology

Nothing in biology makes sense except in the light of evolution. —Theodosius Dobzhansky

Biology is the science of life, specifically, the science of Earth's living systems, in all its times, present, past, and future, and in all its manifestations, from organisms to ecosystems to the biosphere; from artificial life to synthetic life, and to the possibility of extraterrestrial life. Biologists study all aspects of Earth's living systems, including the origin of living systems from energy, abiotic matter, and information; their development and evolution; and, the dynamic processes operating within them, and those operating in interaction with their environment — all the characteristics that enable them to develop, survive, cognize, and reproduce. Those vital processes include: the harnessing, conversion, deployment and storage of energy and matter; self-organization of hierarchical dynamic networks and logic circuits through information processing mediated in part through supramolecular (non-covalent) interactions; the synthesis of the submicroscopic, microscopic and macroscopic structures of the body; homeostasis and homeodynamics; allostasis; hormesis; the self-healing of injuries; and, the reproduction of the organism, among many other activities, described in the article, Life.

The mysteries of living systems have fascinated all peoples throughout history, and curiosity about the physical nature and apparent relatedness of people, animals and plants exists in every known society. Some of that curiosity arises from a desire to control or influence life processes, as in medicine, and to exploit natural resources (e.g., plants and animals for food). Pursuit of the answers to biological questions has led to an understanding of organisms that has steadily improved our standard of living. Other questions come from a desire to understand nature, rather than to control it; and, in answering these, biological investigation has changed our view of the world and our place in it.

This introductory article focuses on biology as a formal science. Biologists formally employ the scientific method and the methods of theoretical biology and systems biology. They incorporate into their work the knowledge and methodologies of multiple disciplines, including mathematics, biophysics, chemistry, evolutionary principles, and many others.

The scope of biology

How did life on earth begin? What physico-chemical characteristics separate something living from something dead or inanimate? What physico-chemical characteristics do all living share? How have living things, ranging from microscopic bacteria to towering trees, changed the earth's oceans, atmosphere and geology over time, and how have those changes in turn changed living things over time?

The scientific theories constructed as answers often conflict with religious doctrines. Some religious leaders have deplored the scientist's naturalistic mechanistic approach, because it removes the requirement for active intervention by a Creator. As biologists, physicians as early as the 5th century BCE, like Hippocrates of Cos, sought to explain human health and disease as having a natural mechanistic basis. Some modern scientists, such as Francis Crick, have welcomed biological explanations as providing a rational basis for the world, free of the need to invoke supernatural powers. The evolutionary biologist Richard Dawkins (2006) sets out the secular humanist case in The God Delusion.

Biology based advances in the health sciences have helped prevent many deadly infectious diseases such as typhoid in developed countries.

Although biology addresses fundamental issues about living things, it also addresses practical questions. The applications of biology have enabled the health sciences to become effective healing arts, and the world's food supply to become ever more plentiful and safe.

The development of biology

This article explores just a few selected themes; 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, investigative methods that rely on empirical evidence, and the availability of technological tools have, together, 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 the science of biology has a continuous thread through the centuries that began with the ancient Greek philosophers, and has generally followed the winding pattern of advancement presented here.

Biology in the ancient world

People rely on plants and animals for sustenance, and Paleolithic cave paintings show that meticulously careful observations of prey have been expressed for at least tens of millennia. Human interest in food was not limited to passive considerations since, rather than eaten as found, it was carried from place to place and processed in various ways. In Neolithic times, probably somewhere in the fertile Nile delta, more 'planned' interactions with certain plants and their seeds led to the establishment of agriculture in many societies. When the intellectual consideration of what plants are was combined with experiments to understand their growth, then botany, the science of plants began. Hippocrates of Cos and his followers, in their naturalistic approach to medicine, studied the effects of plants and plant products as medicinals. The Hippocratic Treatises advise: "Nature is the cure of illness. Leave thy drugs in the chemist’s pot if thou can heal the patient with food." The tradition of Hippocratic medicine influenced the development of chemistry as well as botany. Biological study depends heaven on chemistry.

Anatomy and zoology both date back to at least the 4th century BCE, and the ancient Greek philosopher Aristotle. In the first known book that discusses how life in the womb begins, Aristotle suggested that the mother provides the substance needed to create a new life, but that the father provides this base material with the essence of the child. He thought that the female's actual physical contribution to the baby was her menstrual blood, and that the male's corresponding contribution was his semen. Aristotle used logic and observation to arrive at his theory, which, in the main, was still accepted 2,000 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. A popular idea that grew out of Aristotle's musings was that sperm contained a perfect miniature version of the new baby—a homunculus. Ironically, we know now that in the strict biological realm, the mother supplies the child's first cell, filled with the structural and functional organization of a living cell, the oocyte, whereas the father supplies only a complementary set of chromosomes to those already in the oocyte. Some species of sexually reproducing species the female can produce offspring without the male's chromosomes, a process known as parthenogenesis.

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 dissections and vivisections 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.

The European Renaissance and the 'scientific method'

See also: History of scientific method

During the Renaissance, 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').

By the 17th 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 ritualized 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 traveled between organs, and analyzed their findings in an attempt to find general principles of the organization and function of the body.

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 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 Aristotelian 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 18th and 19th centuries: seeing the links between life forms

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 arrangements of body structure were recognized in many different species. In the 18th 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 every known species has a unique name that biologists all over the world recognize. The name has two parts: genus and species. The language is Latin, which was the common written language of scholars in Europe in Linnaeus' time. Human beings, for example, belong to the species Homo sapiens (Latin for 'wise man') under the family hominidae (the great apes).

At first this system of classification did not include the idea that all living things were related. For more than a hundred years afterward, most highly educated thinkers assumed that complicated life forms (even mice!) could spring to life from a setting of inanimate objects (such as old rags and bread crumbs left in a dark corner). In the 19th century, Louis Pasteur showed that this common notion, spontaneous generation, was a fallacy. His work in bacteriology, along with that of Robert Koch, was important in establishing the germ theory of disease - a key turning point in the battle between man and the infectious diseases that were taking an increasing toll of human life.

A zebra finch.

In England, Charles Darwin showed how the idea of natural selection could explain how very diverse creatures share common underlying 'body patterns'. His observations of the variations of animal life on remote islands made him realize that individual birds, mammals and reptiles thrive, or die, according to how well their characteristics suit their particular habitat - and made him consider the inevitable consequences of that self-evident truth. He realized that individuals also differed in ways that made some more successful than others in producing offspring. 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 to realize that, given enough time, new species might arise - and different new species might arise in different habitats. His theories became the key part of the theory of evolution, that all species now living on earth descended from species living in the past, most of which are now extinct. The existence of common ancestors explained why plants and animals form "groups" that share similar features : the very features that Linnaeus had used to formulate his categories in classification. The idea of evolution itself was not new, but it had been hard to understand how such incredibly diverse life forms could have come about by any natural mechanisms 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 previously suspected, and this made the idea that organisms had evolved by many small,incremental changes over thousands of generations plausible. Evolutionary change from ancient life, by the mechanism of natural selection, came to be universally accepted by biologists as an immensely powerful and elegant theory that explained both the diversity of life, and the existence of patterns of common features.

In the late 19th century, an Austrian monk, Gregor Mendel, analyzed how traits were inherited from generation to generation in garden peas, and he concluded that the male and the female parent contribute equally. 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 particulate '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 each pea then determined what the next generation would be like. Mendel also saw that these alleles might be either 'dominant' or 'recessive'. Together, these ideas allowed Mendel to predict the proportion of offspring that would have each characteristic, and the field of genetics began.

Technological advances in 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. This drawing, by the pioneer of microscopy Nicolaas Hartsoeker, shows what he thought sperm must contain, not what he claimed actually to see.

The advance of biological thinking depended on communication, and on technology. The invention of the printing press facilitated the Enlightenment, and today, electronic communication has accelerated the rate of research. The availability of technical tools for experimentation has often been key to progress.

Magnified human sperm cells, approx. 125x in thumbnail image

The features of plants and animals, for example, have been understood on an entirely different level with technological advances that provided new ways to study them. The microscope, modified by Antonie van Leeuwenhoek in the 17th century, revealed details of structure in the bodies of organisms that had never before been suspected.

One of the new sights that van Leeuwenhoek described was individual ova and spermatozoa - the sperm cells he described as "animalcules", tiny animals in which he claimed to discern muscles and nerves [1]—an example of even a great scientist perceiving his expectations, rather than what was really there. van Leeuwenhoek was a Creationist, who disputed the Aristotelian notion that living things could emerge from inanimate matter. He believed that the mother is an incubator for the "homunculus", inherited from the father, which was contained within the sperm cells (although he did not claim to have seen the homunculus itself under the microscope, as is often erroneously claimed).

Science is always influenced by past ideas. No scientist can consider any hypothesis, or analyze any experimental 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 objective, that mind is 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 microscope led to new ideas about living things. It was realized 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 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 a much higher resolution allowing the visualization of dividing cells, and the chromosomes of the nucleus.

Cell biology begins

Cell biology began around 1900, with the discovery of the chromosomes and the understanding of mitosis and meiosis. Application of Mendel's fundamental laws of heredity to genetic linkage analysis allowed the correlation of specific plant or animal traits to be ordered as gene loci in the first genetic maps. The culmination of this work and evidence from cytogenetics, led to the concept of genes as heritable traits that had a physical structure in the chromosomes; in the words of Thomas Morgan "...there is an ever increasing body of information that points clearly to the chromosomes as the bearers of the Mendelian factors, it would be folly to close one's eyes to so patent a relation."

Towards the mid-20th century, with the development of the electron microscope, ultra-high power examination of cells was possible and the field of cell biology began to unravel the inner structure of cells, discovering discrete organelles that could only be seen well at such high magnification. Closer examination of the structure of the cell was combined with the ability to separate the components of the cells by their density and chemical properties and analyze each fraction using methods from biochemistry and biophysics. Advances in this new field of cell biology confirmed that living things were composed of cell units and extended the understanding of just how cells carried out life processes.

Science differs from religious and political dogmas in at least one major manner: its tenets are not 'sacred', but are always there to be questioned and tested. Thus over time, ideas have changed and many theories have been abandoned or disproved, including the homunculus theory of fetal development. With the resolving power of the electron microscopes, able to image cell structure at a magnification of tens of thousand-fold, that 'little man' inside the sperm cell vanished forever.

Molecular biology, and a revolution in understanding

In the 20th century, the properties and roles of some of the large molecules (macromolecules) found in living things were examined. Proteins have three-dimensional shapes that give them special properties. Some proteins, known as enzymes, have specialized sites able to catalyze the chemical reactions critical for metabolism. Other proteins act as building blocks that make up the filaments that support the cytoplasm of cells, or lend such qualities as waterproofing to skin (keratin) or tensile strength to tendons (collagen). Proteins also provide an elaborately configured signaling network that guides responses to the environment. These sophisticated activities range from the selective transport of ions and food in and out of cells, to the ability of immune cells to recognize and attack foreign germs.

As protein sequences were compared between species, biologists appreciated a new variation on the old theme that research in comparative anatomy had raised three hundred years before. First, recurring anatomical patterns had been recognized, like the arrangement of bones in a bat's wing, a seal's flipper and a man's arm; and later, the molecular structures and shapes of the various families of proteins were recognized to be similar. The amino acid sequences within the protein families even show similarities between kingdoms like bacteria and animals, confirming that all living things are related.

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 painstaking 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 revealed how information might be coded and passed from generation to generation, 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. Work advanced, but successful experiments required labor-intensive manipulations that could take several days in refrigerated 'cold rooms', without substantial delay between steps. Consequently, unraveling 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 procedures (often performed by scientists dressed in parkas!).

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. By the end of the 20th century, the technique of PCR conceived by Kary Mullis allowed experiments on tiny samples of DNA to be done very efficiently, and progress in molecular biology accelerated. 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 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 found in almost all cells, and these are the factories that produce energy for the cell. Mitochondria have their own DNA, but their form is more similar to those of bacteria rather than mammalian cells. These observations led Lynn Margulis to advocate an outlandish hypothesis for the origin of mitochondria being derived from bacteria assimilated into eukaryotic cells. Her endosymbiotic theory was finally published after being "rejected by about fifteen scientific journals", but is widely accepted today. These energy-producing organelles of animal cells are not the only organelles found that derived from a different life form; the chloroplasts of plant cells are another.

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 from which every human develops does not receive equal genetic contributions from mother and father, after all. Each individual human being is made up of cells which obtain mitochondria and their mitochondrial DNA (mtDNA) exclusively from the mother.

Even genes in the nucleus of germ cells (egg and sperm) do not always act identically in the newly fertilized egg. Some genes are marked in the germ cells to be either active or inactive in the new embryo, by the addition of chemical modifiers to the DNA. This imprinting of genes by parental origin is another asymmetry that had been unsuspected. Oddly, this confirmed some of the suspicions of Aristotle after all, but in the 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 whereas the same genes, when inherited through the mother, act differently. The placenta grows from the same fertilized egg that builds the baby, and nourishes the new infant from the mother's womb—but it is the father's genes that are more important for the placental membrane's success in obtaining nutrients. It is as though there is a 'battle' between the father's genes and the mother's genes—as if 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 20th century, progress in molecular biology had given rise to the 'human genome project', an ambitious vision to determine the nucleotide sequence the DNA of every human gene. That vast project drew on the inputs of hundreds of scientists in many different countries, and saw completion ahead of schedule. That unexpected speed was another of technology's boons to biology.

So, in 2006, we can map out how chromosomes have evolved across species, as well as use these genomic resources to trace our own distant ancestry back to the enigmatic traces of a preceding world. Biologists may have once predicted that reaching this level of understanding would open up the answers to some of our deepest questions about life. However, for all the advances that have been made over the centuries, biology has only begun to clarify the living world. The genome projects, far from settling all uncertainties, have raised a whole new set of questions. One of the biggest surprises was the realization of how few genes underpin a human being—just 28,000 or so, not many more than underpin simple animals, and fewer than the number of genes in many plants.

We have learned that simply identifying the sequence of nucleotides in DNA does not suffice to reveal the informational constitution of a human living system. Biologists must go beyond DNA sequences and start the process of understanding all the ways that genes interact at the level of whole plants and animals, and all the ways of 'epigenetic' mechanisms of function and inheritance. Systems biologists, who aim to develop models (or representations) of whole organisms, their organ systems, and the larger categories (e.g., species, ecosystems), in which the individual organism is only a part, are becoming increasingly important. And so we come full circle, again relying on the more traditional fields of biology to probe the secrets that are not apparent from focusing only on molecular information. This circular route may not have solved the riddle of life, but it has advanced our knowledge tremendously rather than returning us to the start.

Biology will need new mathematics to reveal the working of living systems. "Biology will increasingly stimulate the creation of qualitatively new realms of mathematics. Why? In biology, ensemble properties emerge at each level of organization from the interactions of heterogeneous biological units at that level and at lower and higher levels of organization (larger and smaller physical scales, faster and slower temporal scales). New mathematics will be required to cope with these ensemble properties and with the heterogeneity of the biological units that compose ensembles at each level."

Sadly, with science literacy declining in the United States in the late 20th and early 21st centuries, biology literacy has declined in parallel. Andrew Knoll, professor of natural history at Harvard's Earth and Planetary Sciences Department is quoted as saying: "The average adult American today knows less about biology than the average ten-year-old living in the Amazon, or than the average American of two hundred years ago."

The future of biology

As quantitative methods continue to penetrate the workflows of biologists and professionals in neighbouring fields, the character of biology will change. Further changes can be expected from the wider use of web-based science communication, which allows to perform more and more steps of scientific research in the open. This includes participation of the public as well as the sharing of data, of the scientific literature and of background knowledge (as provided by wiki articles like this one), thoughts, ideas and comments on the process in a way that is much more elaborate than what we have seen so far.

The philosophy of biology

The science of biology itself, even with the collaboration of the other natural sciences, cannot provide answers to questions of biological nature that arise in the minds of both the scientific community and the public. Scientific methodologies have no approaches to answer such questions as:

• What does it mean, if anything, to speak of human nature?
• Does life depend only on physicochemical processes, or must we invoke non-physical processes, and if so, of what nature?
• What does it mean, if anything, to speak of the meaning of life?
• What role does biology play in answering questions of interest to social scientists?
• Why cannot the science of biology answer, in principle, all questions that arise out of biology?

Such questions, among many more, biology leaves to philosophers, including philosophers who themselves qualify as biologists or scientists who specialize in other disciplines.

Philosophy antedated science, then incorporated science as natural philosophy. Gradually, scientific disciplines split off from philosophy, leaving questions behind, and inspiring new questions, that remained the purview of philosophy.