At the end of the road in Little @Cottonwood Canyon, near Salt Lake City, @Utah, lies @Alta, a near-mythic location for skiing enthusiasts. In time, though, it may well achieve a similar status among molecular geneticists. In December 1984, a conference co-sponsored by the U.S. Department of Energy (or @DOE) was held there, a conference that pondered a single question: Does modern @DNA research offer a way of detecting tiny genetic mutations -- and, in particular, of observing any increase in the mutation rate among the survivors of the @Hiroshima and @Nagasaki bombings and their descendants? In short, the answer was, "Not yet;" however, in this atmosphere of intellectual fertility, the seeds were sown for a project that would make such detection possible in the future -- the Human Genome Project.
In the months that followed, much deliberation and debate ensued. But in 1986, the DOE took a bold and unilateral step by announcing its Human Genome Initiative, convinced that its mission would be well served by a comprehensive picture of the human genome. The immediate response was considerable skepticism -- skepticism about the scientific community's technological wherewithal for sequencing the genome at a reasonable cost, and skepticism about the value of the result, even if it could be obtained economically.
Over the years, though, things have changed. Today, a worldwide effort is under way to develop and apply the technologies needed to completely map and sequence the human genome, as well as the genomes of several model organisms. Technological progress has been rapid, and it is now generally agreed that this international project will produce the complete sequence of the human genome by the year 2005, if not before.
And what is more important, the value of the project is becoming evident in a wide range of areas. Genome research is revolutionizing both biology and biotechnology, and it is providing a vital thrust to the increasingly broad scope of the biological sciences. The impact that will be felt in medicine and health care alone, once we identify and understand the function of all human genes, is inestimable. To that end, the project has already stimulated significant financial investment by large corporations and has prompted the creation of new companies hoping to capitalize on the burgeoning market.
But the DOE's early, catalytic decision deserves further comment, as the implications are more widespread -- and more controversial -- than initially believed. The project could deliver, and already has developed into, much more than the promised tool for assessing mutation rates. The information generated would contribute not only to a new understanding of human biology, but also to a host of practical applications in the biotechnology industry and in the arenas of agriculture and environmental protection. A 1987 report by a DOE advisory committee provided some examples. The committee foresaw that the project could ultimately lead to the efficient production of biomass for fuel, to improvements in the resistance of plants to environmental stress, and to the practical use of genetically engineered microbes to neutralize toxic wastes. In addition, the project could have an enormous impact on our ability to assess, individual by individual, the risk posed by environmental exposures to toxic agents. We know that genetic differences make some of us more susceptible, and others more resistant, to such agents. Far more work must be done before we understand the genetic basis of such variability, but this knowledge will directly address the DOE's long-term mission to understand the effects of low-level exposures to radiation and other energy-related agents -- especially the effects of such exposure on cancer risk.
The Human Genome Project has other implications for the DOE as well. In 1994, taking advantage of new capabilities developed by the project, the DOE formulated the Microbial Genome Initiative to sequence the genomes of bacteria of likely interest in the areas of energy production and use, environmental remediation and waste reduction, and industrial processing. As a result of this initiative, we already have complete sequences for two microbes that live under extreme conditions of temperature and pressure. Structural studies are under way to learn what is unique about the proteins of these organisms -- the aim being ultimately to engineer these microbes and their enzymes for such practical purposes as waste control and environmental cleanup. (DOE-funded genetic engineering of a thermostable DNA polymerase has already produced an enzyme that has captured a large share of the several-hundred-million-dollar DNA polymerase market.)
And other little-studied microbes hint at even more intriguing possibilities. For instance, @Deinococcus @radiodurans is a species that prospers even when exposed to huge doses of ionizing radiation. This microbe has an amazing ability to repair radiation-induced damage to its DNA, and a sequence of its genome could lead to understanding and ultimately taking practical advantage of its unusual capabilities. For example, it might be possible to insert foreign DNA into the microbe's cells that allows it to digest toxic organic components found in highly radioactive waste, thus simplifying the task of further cleanup. Another approach might be to introduce metal-binding proteins onto the microbe's surface that would scavenge highly radioactive isotopes out of solution.
Biotechnology, fueled in part by insights reaped from the genome project, will also play a significant role in improving the use of fossil-based resources. Increased energy demands, projected over the next 50 years, require strategies to circumvent the many problems associated with today's dominant energy systems. The technology could help address these needs by upgrading the fuel value of our current energy resources and by providing new means for the bioconversion of raw materials to refined products -- not to mention offering the possibility of entirely new biomass-based energy sources.
We have thus seen only the dawn of what is surely a biological revolution, and its practical and economic applications are unquestionably destined for dramatic growth. Health-related biotechnology is already a multibillion-dollar success story, and it is still far from reaching its potential; other applications are likely to beget similar successes in the coming decades. The insights, the technologies, and the infrastructure that are already emerging from the genome project, together with advances in fields such as computational and structural biology, will become our most important tools in addressing a variety of human problems and needs.
The biosciences research community is now embarked on a program whose boldness, even audacity, has prompted comparisons with such visionary efforts as the @Apollo space program and the @Manhattan Project. That life scientists should conceive such an ambitious project is not remarkable; what is surprising -- at least at first blush -- is that the project should trace its roots to the Department of Energy.
For close to a half-century, the DOE and its governmental predecessors have been charged with pursuing a deeper understanding of the potential health risks posed by energy use and by energy-production technologies -- with special interest focused on the effects of radiation on humans. Indeed, it is fair to say that most of what we know today about radiological health hazards stems from studies supported by these government agencies. Among these investigations are long-standing studies of the survivors of the atomic bombings of Hiroshima and Nagasaki, as well as any number of experimental studies using animals, cells in culture, and nonliving systems. Much has been learned, especially about the consequences of exposure to high doses of radiation. On the other hand, many questions remain unanswered; in particular, we have much to learn about how low doses produce their insidious effects. When present merely in low but significant amounts, toxic agents such as radiation or mutagenic chemicals wreak havoc in the most subtle ways, altering the genetic instructions in our cells only slightly. The consequences can be heritable mutations too slight to produce discernible effects in a generation or two but, in their persistence and irreversibility, deeply troublesome nonetheless.
Until recently, science offered little hope for detecting these tiny changes to the DNA that encodes our genetic program until they were well entrenched in the code. Needed was a tool that could detect a change in one base pair among, perhaps, as many as a hundred million. Then, in 1984, at a meeting convened jointly by the DOE and the International Commission for Protection Against Environmental Mutagens and Carcinogens, the question was first seriously asked: Can we, and should we, sequence the human genome? That is, can we develop the technology to obtain a word-by-word copy of the entire genetic script for an "average" human being, and thus to establish a benchmark for detecting the elusive mutagenic effects of radiation and cancer-causing toxins? Answering such a question was not simple. Workshops were convened in 1985 and 1986; the issue was studied by a DOE advisory group, by the Congressional Office of Technology Assessment, and by the National Academy of Sciences; and the matter was debated publicly and privately among biologists themselves. In the end, however, a consensus emerged that we should make a start.
Adding impetus to the DOE's earliest interest in the human genome was the Department's stewardship of the national laboratories, with their demonstrated ability to conduct large multidisciplinary projects -- just the sort of effort that would be needed to develop and implement the technological knowhow needed for the Human Genome Project. Biological research programs already in place at the national labs benefited from the contributions of engineers, physicists, chemists, computer scientists, and mathematicians, working together in multi-disciplinary teams. Thus, with the infrastructure in place and with a particular interest in the ultimate results, the Department of Energy, in 1986, was the first federal agency to announce and to fund an initiative designed to pursue a detailed understanding of the human genome.
Of course, interest was not restricted to the DOE. Workshops had also been sponsored by the National Institutes of Health, the Cold Spring Harbor Laboratory, and the @Howard @Hughes Medical Institute. In the fall of 1988, the DOE and the NIH signed a memorandum of understanding that laid the foundation for a concerted interagency effort. The basis for this community-wide excitement is not hard to comprehend. The first impulse behind the DOE's commitment was only one of many reasons for coveting a deeper insight into the human genetic script. Defective genes directly account for an estimated 4000 hereditary human diseases -- maladies such as @Huntington disease and cystic fibrosis. In some such cases, a single misplaced letter among three billion can have lethal consequences. One of the most widespread of these afflictions is sickle cell anemia, in which a single base code is altered. For most of us, though, even greater interest focuses on the far more common ailments in which altered genes influence but do not prescribe. Heart disease, many cancers, and some psychiatric disorders, for example, can emerge from complicated interplays of environmental factors and genetic misinformation.
The first steps in the Human Genome Project are to develop the needed technologies, then to "map" and to "sequence" the genome. But in a sense, these well-publicized efforts aim only to provide the raw material for the next, longer strides. The ultimate goal is to exploit those resources for a truly profound molecular-level understanding of how we develop from embryo to adult, what makes us work, and what causes things to go wrong. In the offing is a new era of molecular medicine characterized not by treating symptoms, but rather by looking to the deepest causes of disease. Rapid and more accurate diagnostic tests will make possible earlier treatment for countless maladies. Even more promising, insights into genetic susceptibilities to disease and to environmental insults, coupled with preventive therapies, will thwart some diseases altogether. New, highly targeted pharmaceuticals, not just for heritable diseases, but for communicable ailments, as well, will attack diseases at their molecular foundations. And even gene therapy will become possible, in some cases actually "fixing" genetic errors. All of this in addition to a new intellectual perspective on who we are and where we came from.
But how is it possible, with the incredible diversity of the world's five and a half billion people, to determine an "average" genome that can be considered even reasonably accurate? The answer lies in an understanding that DNA, with its millions of base pairs, is not the workhorse of the human body -- proteins are -- and that the body is built and run with fewer than 100,000 different kinds of protein molecules. For each of these proteins, we can imagine a single corresponding gene composed of many base pairs (though there is sometimes some redundancy), whose job it is to ensure an adequate and timely supply of the structural or regulatory materials. In a very real sense, then, all of the subtlety of our species, all of our art and science, is ultimately accounted for by a surprisingly small set of discrete genetic instructions. More surprising still, the differences between two unrelated individuals, between the man next door and Mozart, for example, may reflect a mere handful of differences in their genomic recipes -- perhaps one altered word in five hundred. We are far more alike than we are different. At the same time, there is room for near-infinite variety.
It is no overstatement to say that to decode our 100,000 genes in some fundamental way would be an epochal step toward unraveling the manifold mysteries of life û but only if we understand what those genes produce and how they regulate that production. It is the difference between seeing a string of letters on a page and recognizing which of those letters actually form words, and which of those words form sentences. Meaningful information only derives from the relationship between the words to form discrete ideas.
The human genome is the full complement of genetic material in a human cell. The genome, in turn, is distributed among 23 sets of chromosomes, which, in each of us, have been replicated and re-replicated since the fusion of sperm and egg that marked our conception. The source of our personal uniqueness, our full genome, is therefore preserved in each of our body's several trillion cells. At a more basic level, the genome is DNA, deoxyribonucleic acid, a natural polymer built up of repeating nucleotides, each consisting of a simple sugar, a phosphate group, and one of four nitrogenous bases. In the chromosomes, two DNA strands are twisted together into an entwined spiral -- the famous double helix -- held together by weak bonds between complementary bases, adenine (A) to thymine (T) and cytosine to guanine (C-G); structurally the molecule resembles a twisted ladder. In the language of molecular genetics, each of these linkages constitutes a base pair. All told, if we count only one of each pair of chromosomes, the human genome comprises about three billion base pairs.
The specificity of these base-pair linkages underlies all that is wonderful about DNA. First, replication becomes straightforward. Unzipping the double helix provides unambiguous templates for the synthesis of daughter molecules: One helix begets two with near-perfect fidelity. Second, by a similar template-based process, a means is also available for producing a DNA-like messenger known as messenger @RNA (or @mRNA). This faithful complement of a particular DNA segment transports its information to the cell's cytoplasm where it directs the synthesis of a particular protein. Many subtleties are entailed in the synthesis of proteins, but in a schematic sense, the process is elegantly simple.
Every protein is made up of one or more polypeptide chains, each a series of (typically) several hundred molecules known as amino acids, linked by so-called peptide bonds. Remarkably, only 20 different kinds of amino acids suffice as the building blocks for all human proteins in nature. The synthesis of a protein chain, then, is simply a matter of specifying a particular sequence of amino acids. Each linear sequence of three bases (both in RNA and in DNA) corresponds uniquely to a single amino acid. The RNA sequence AAU (RNA uses the base uracil instead of thymine) thus dictates that the amino acid asparagine should be added to a polypeptide chain, GCA specifies alanine -- and so on. A segment of the chromosomal DNA that directs the synthesis of a single type of protein constitutes a single gene.
As we have seen before, one of the central goals of the Human Genome Project is to produce a detailed "map" of the human genome. But, just as there are topographic maps and political maps and highway maps of the United States, so there are different kinds of genome maps. One type, a genetic linkage map, is based on careful analysis of human inheritance patterns. It indicates for each chromosome the whereabouts of genes or other "heritable markers," with distances measured in centimorgans, a measure of recombination frequency. During the formation of sperm and egg cells, a process of genetic recombination -- or "crossing over" -- occurs in which pieces of genetic material are swapped between paired chromosomes. This process of chromosomal scrambling accounts for the differences invariably seen even in siblings (apart from identical twins, whose genomes are equivalent). Logically, the closer two genes are to each other on a single chromosome, the less likely they are to get split up during genetic recombination. When they are close enough that the chances of being separated are only one in a hundred, they are said to be separated by a distance of one centimorgan.
The role of human pedigrees now becomes clear. By studying family trees and tracing the inheritance of diseases and physical traits, or even unique segments of DNA identifiable only in the laboratory, geneticists can begin to pin down the relative positions of these genetic markers. By the end of 1994, a comprehensive map was available that included more than 5800 such markers, including genes implicated in cystic fibrosis, myotonic dystrophy, Huntington disease, @Tay-@Sachs disease, several cancers, and many other maladies. The average gap between markers was about 0.7 centimorgan.
Other maps are known as physical maps, so called because the distances between features are measured not in genetic terms, but in "real" physical units, typically, numbers of base pairs. A close analogy can thus be drawn between physical maps and the road maps familiar to us all. Indeed, the analogy can be extended further. Just as small-scale road maps may show only large cities and indicate distances only between major features, so a low-resolution physical map includes only a relative sprinkling of chromosomal landmarks. A well-known low-resolution physical map, for example, is the familiar chromosomal map, showing the distinctive staining patterns that can be seen in the light microscope. Further, by a process known as in situ hybridization, specific segments of DNA can be targeted in intact chromosomes by using complementary strands synthesized in the laboratory. These laboratory-made "probes" carry a fluorescent or radioactive label, which can then be detected and thus pinpointed on a specific region of the chromosome. Fishing for genes shows some results of fluorescence in situ hybridization (FISH). Of particular interest are probes known as @cDNA (for complementary DNA), which are synthesized by using molecules of messenger RNA as templates. These molecules of cDNA thus hybridize to "expressed" chromosomal regions -- regions that directly dictate the synthesis of proteins. However, a physical map that depended only on in situ hybridization would be a fairly coarse one. Fluorescent tags on intact chromosomes cannot be resolved into separate spots unless they are two to five million base pairs apart.
Fortunately, means are also available to produce physical maps of much higher resolution -- analogous to large-scale county maps that show every village and farm road, and indicate distances at a similar level of detail. Just such a detailed physical map is one that emerges from the use of restriction enzymes -- DNA-cleaving enzymes that serve as highly selective cleavers of the genetic material. A typical restriction enzyme known as @EcoRI, for example, recognizes the DNA sequence @GAATTC and selectively cuts the double helix at that site. One use of these handy tools involves cutting up a selected chromosome into small pieces, then cloning and ordering the resulting fragments. The cloning, or copying, process is a product of recombinant DNA technology, in which the natural reproductive machinery of a "host" organism -- a bacterium or a yeast, for example -- replicates a "parasitic" fragment of human DNA, thus producing the multiple copies needed for further study.
By cloning enough such fragments, each overlapping the next and together spanning long segments (or even the entire length) of the chromosome, workers can eventually produce an ordered library of clones. Each contiguous block of ordered clones is known as a contig, and the resulting map is a contig map. If a gene can be localized to a single fragment within a contig map, its physical location is thereby accurately pinned down. Further, these conveniently sized clones become resources for further studies by researchers around the world -- as well as the natural starting points for systematic sequencing efforts.
Once the DNA has been mapped, and all the genes placed within the chromosomal framework, the real work begins û making sense of the information encoded within those genes. Specifically, this involves determining whether the genes code for a particular protein, and if so, which one, or whether they are involved in the regulation of other genes. The task then falls to understanding what the proteins' functions are within the body, so that effective therapies can be developed for instances when they malfunction. While much progress has been made in the mapping of the human genome, it is clear to all involved that there is clearly much work yet to be done to gain a full understanding of the complex functioning of the human genetic material.
