Genes encode the programs that build organisms out of molecules. Genes have two major functions: they provide a description of how proteins are built, and they regulate other genes to determine how much of any given protein will be synthesized at any one time. Genes are contained mostly within chromosomes (some also are found within mitochondria), and are encoded mostly by deoxyribonucleic acid (DNA).
During reproduction, the genes from the parent organism are passed down to the descendent; if the reproduction is sexual, the descendent receives one copy of every gene from each parent. Elements within the cell continually repair the genome, so that it remains stable. As a result, the descendent organism closely resembles the parent organisms. However, a small fraction of genes are copied with errors, and these allow diversity to develop within a population of organisms.
Gene theory was first developed by Gregor Mendel based on his experiments breeding plants. Mendel found that when he bred two plants, the descendent was not a blend of the two parents, but appeared to inherit distinct, discrete features from each parent, with fixed probabilities. To explain this, Mendel proposed that the descendent receive one copy of a gene for any feature from each parent. Some of the genes were dominant, that is, they would be expressed whenever at least one copy of the gene was present. Others were recessive, and would only be expressed if two copies of the gene were present. Mendel published his work in 18XX, but it was not noticed for several years.
Gene theory was re-discovered (and Mendel's work finally appreciated) in 1900, by several scientists who were thinking about the mechanisms by which evolution might work. Genes were needed to explain two aspects of evolution. On the one hand, evolution appeared to be a slow process, so some mechanism was needed by which information was passed down faithfully from parents to children, without major changes. On the other hand, mutations needed a way to remain within the population for a species to evolve into another species. At the time, most biologists assumed that the child was a mixture of the parents. However, if traits were mixed, new traits would become diluted, and one would not end up with variation within a population. The persistence of mutations was best explained by Mendel's gene theory, because changes in genes would be kept in the genome as discrete units, even if they were not expressed. Therefore, mutations could accumulate over time, eventually generating a new species.
While trying to understand how genes might operate to develop and sustain an organism, scientists made an enormous number of discoveries about how cells operate at a molecular level.
For instance, the discovery of DNA was a result of predictions based on gene theory and the theory of evolution. In order for genes to exist, there had to be some element within cells that could pass down information from parent to child. This element would have to remain stable and be copied faithfully, although some errors would have to be introduced in order for evolution to occur. In 192X, it was hypothesized that chromosomes carried the genes within cells that contained nuclei; by 1943 is was suggested that DNA might be involved in genes. Finally, in 1953, Franklin, Watson, and Crick identified the double-helix structure of DNA, and the latter two scientists showed that it encoded information by the positions of base-pairs that formed ladder-rungs that connected the two helixes.
Once DNA was discovered, molecular biologists were able to determine how it operated to produce proteins, the building blocks of cells. It was realized that genes were needed that not only produced proteins, but also that regulated whether other genes were to produce proteins. Both sets of genes were found in portions of the DNA.
The idea that genes dictate the production and expression of chemicals in organisms had led to several technologies that are in varying stages of development. First, it has allowed scientists to develop organisms that develop chemicals that they never had in nature, such as genetically-modified crops that produce natural pesticides, bacteria that produce medically-useful chemicals, and animals that glow in the dark or that can contract human diseases.
Gene theory has also led to the realization that errors in genes are responsible for many diseases. The specific genes responsible for Tay Sachs, Huntington's disease, cystic fibrosis, thalassemia, and phenylketonuria, for instance, have been identified. Diagnostic tests have been produced to identify these diseases, and the hope is that treatments will be developed to repair or counteract the errors responsible for these diseases.
Gene theory is intertwined with evolutionary theory as the basis of modern biology. Genes provides the mechanism by which information is passed from parent to child, and are the elements that are modified to produce new species.
The idea of genes has also been adapted to the philosophical study of how ideas propagate through society as "memes."
For all of gene theory's successes, an enormous amount remains uncertain about how genes remain stable, how they are encoded, how they interact with other elements to produce proteins, and how they operate to build organisms.
Scientists have been surprised to find that the mechanisms that copy sequences of DNA are fraught with more errors than would be expected, given that organisms reproduce themselves in their offspring fairly faithfully. It turns out that there are a number of additional mechanisms to repair errors within the cell, and that their activity depends on environmental cues. It appears that their are at least two modes of repair: one that is careful, and one that fills in large gaps when the damage is catastrophic. It is thought that some of the modes might encourage mutations that lead a species to evolve, although how this works is not well understood.
Scientists have also been surprised to discover that some genes that encode for the production of proteins can be spread over disjoint portions of DNA. It also appears that some sequences of DNA can be transcribed in multiple ways to produce different proteins. It is not clear what mechanisms control the rearrangement of DNA to yield a specific function. However, it is now clear that a gene is not merely a contiguous bit of DNA, but involves the interactions of multiple pieces of DNA, and possibly other elements within a cell.
Given the above uncertainties, it should not be surprising that scientists are uncertain of the process that turns a set of genetic instructions into a complex living organism, with multiple functions within a cell, and many different types of cells making up a body. Important chemical markers have been identified that instruct cells to grow to fit specific functions, but we are nowhere near identifying where in the DNA (or elsewhere in the cell), all these instructions are encoded.
The Century of the Gene, Evelyn Fox Keller, 2000, Harvard University Press
Like science itself, these pages are under construction. OK, so they are in a lot worse shape than science. I welcome your comments.