by Greg Bear
SHORT GLOSSARY OF SCIENTIFIC TERMS
Antibody: molecule that attaches to an antigen, inactivates it, and attracts other defenses to the intruder.
Antibiotics: a large class of substances manufactured by many different kinds of organisms that can kill bacteria. Antibiotics have no effect on viruses.
Antigen: intruding substance or part of an organism that provokes the creation of antibodies as part of an immune response.
Bacteria: prokaryotes, tiny living cells whose genetic material is not enclosed in a nucleus. Bacteria perform important work in nature and are the base of all food chains.
Bacteriophage: see phage.
Chromosome: arrangement of tightly packed and coiled DNA. Diploid cells such as body cells in humans have two sets of twenty-two autosomes as well as two sex chromosomes; haploid cells such as gametes—sperm or ova—have only a single set of chromosomes. The total number of chromosomes varies between apes and humans. Chromosome numbers for so-called ancestral species such as Homo sapiens neandertalensis and Homo erectus are not known; any DNA extracted from even relatively recent (~20,000 years) fossil specimens is generally limited to mitochondrial DNA. Polyploidy—having extra sets of chromosomes—results in infertile offspring or totally precludes reproduction between organisms and can often define a barrier between species. This should prevent successful mating between SHEVA individuals and older variety humans. Apparently, it does not. This puzzles scientists, and further research is in order.
Cro-Magnon: early variety of modern human, Homo sapiens sapiens, from Cro-Magnon in France. Homo is the genus, sapiens the species, sapiens the subspecies.
DNA: Deoxyribonucleic acid, the famous double-helix molecule that codes for the proteins and other elements that help construct the phenotype or body structure of an organism.
ERV or endogenous retrovirus: virus that inserts its genetic material into the DNA of a host. The integrated provirus lies dormant for a time. ERVs may be quite ancient and fragmentary and no longer capable of producing infectious viruses.
Exogenous virus: virus that does not insert its genes into host DNA on a long-term basis. Some viruses, such as MMTV or mouse mammary tumor virus, seem to be able to choose whether to insert or not insert their genetic code into host DNA. See ERV.
Exon: region of DNA that codes for proteins or RNA.
Frithing: also, flehman. Sucking air over the vomeronasal organ to detect pheromones. See vomeronasal organ.
Gene: the definition of a gene is changing. A recent text defines a gene as “a segment of DNA or RNA that performs a specific function.” More particularly, a gene can be thought of as a segment of DNA that codes for some molecular product, very often one or more proteins or parts of proteins. Besides the nucleotides that code for the protein, the gene also consists of segments that determine how much and what kind of protein is expressed, and when. Genes can produce different combinations of proteins under different stimuli. In a very real sense, a gene is a tiny factory and computer within a much larger factory-computer, the genome.
Genome: sum total of genetic material in an individual organism. In humans, the genome appears to consist of approximately thirty thousand genes—half to one-third the number predicted at the time of the publication of Darwin’s Radio.
Genotype: the genetic character of an organism or distinctive group of organisms.
Glycome: the total complement of sugars and related compounds in a cell. Sugars can form links with proteins and lipids to make glycoproteins and glycolipids.
Herpes: HSV-1 or -2. Herpes simplex virus types responsible for cold sores and genital herpes. Though herpes viruses are not retroviruses they can lie dormant in nerve cells for years, and often reactivate in response to stress. Chicken pox and its recurrent form, shingles, or herpes zoster, are also related to herpes.
HERV: human endogenous retrovirus. Within our genetic material are many remnants of past infections by retroviruses. Some researchers estimate that as much as one third of our genetic material may consist of old retroviruses. No instance is yet known of these ancient viral genes producing infectious particles (virions) that can move from host to host, in lateral or horizontal transmission. Many HERV do produce viruslike particles within the cells and body, however, and whether these particles serve a function or cause problems is not yet known. All HERV are part of our genome and are transmitted vertically when we reproduce, from parent to offspring. Infection of gametes by retroviruses is the best explanation so far for the presence of HERV in our genome. ERV, endogenous retroviruses, are found in many other organisms, as well.
Homo erectus: general classification for fossils of the genus Homo dated chronologically and evolutionarily prior to Homo sapiens. Homo erectus was a very successful human species, surviving for at least a million years. Calling any of these fossils “ancestral” is problematic both scientifically and philosophically, but it’s a simple and easily understood description of a complex relationship. There are many interpretations of these relationships in the literature, but growing sophistication in genetics will probably lead to a general shaking out and clarification over the next ten to twenty years.
Immune response (immunity, immunization): the provoking and marshaling of defensive cells within an organism to ward off and destroy pathogens, disease-causing organisms such as viruses or bacteria. Immune response may also identify nonpathogenic cells as foreign, not part of the normal body complement of tissues; transplanted organs cause an immune response and may be rejected. Autoimmune diseases such as multiple sclerosis and various forms of arthritis may occur or reoccur in response to viral activation due to stress. In humans, ERV activation has been suggested as a cause of some autoimmune diseases.
Intron: region of DNA that generally does not code for proteins. In most eukaryotic cells, genes consist of mingled exons and introns. Introns are clipped out of transcribed messenger RNA (mRNA) before it is processed by ribosomes; ribosomes use the code contained in lengths of mRNA to assemble specific proteins out of amino acids. Bacteria lack introns.
Lipids: organic compounds such as fats, oils, waxes, and sterols. Lipids make up many of the structural components of cells, including much of the cell wall or membrane.
Lipome: the total complement of lipids within a cell. Lipids may also form alliances with sugars and proteins (see glycome and proteome).
Mitochondrion, mitochondria: organelles within cells that process sugars to produce the common fuel for cells, adenosine triphosphate, or ATP. Generally regarded as highly adapted descendants of bacteria that entered host cells billions of years ago. Mitochondria have their own loops of DNA constituting a separate genome within every cell. Mitochondrial DNA, being shorter and simpler, is often the target of choice for fossil analysis.
Modern human: Homo sapiens sapiens. Genus Homo, species sapiens, subspecies sapiens. Homo sapiens sapiens could be read as “Man who is wise, who knows.” Also, “Man who is discreet, who savors.”
Mobile element: movable segment of DNA. Transposons can move or have their DNA copied from place to place in a length of DNA using DNA polymerase. Retrotransposons contain their own reverse transcriptase, which gives them some autonomy within the genome. Mobile elements have been shown by Barbara McClintock and others to generate variety in plants; but some believe these are, more often than not, so-called selfish genes which are duplicated without being useful to the organism. More and more, geneticists have found strong evidence that mobile elements contribute to variation in all genomes and help to regulate both embryonic development and evolution.
Mutation: alteration in a gene or segment of DNA. May be accidental and unproductive or even dangerous; may also be useful, leading to the production of a more efficient protein. Mutations may lead to variation in phenotype, or the physical structure of an organism. Random mutations are usually either neutral or bad for the health of the organism.
Neandertal: Homo sapiens Neandertalensis. Possibly ancestral to humans. Modern anthropologists and gen
eticists are currently engaged in a debate about whether Neandertals are our ancestors, based on evidence of mitochondrial DNA extracted from ancient bones. More than likely, the evidence is confusing because we simply do not yet know how species and subspecies separate and develop.
Pathogen: disease-causing organism. There are many different varieties of pathogen: viruses, bacteria, fungi, protists (formerly known as protozoa), and metazoans such as nematodes.
PERV: Porcine endogenous retrovirus. Ancient retroviruses found in the genome of pigs. See ERV.
Phage: a virus that uses bacteria as hosts. Many kinds of phages kill their hosts almost immediately and can be used as antibacterial agents. Most bacteria have at least one and often many phages specific to them. Phages and bacteria are always in a contest to outrun each other, evolutionarily speaking.
Phenotype: the physical structure of an organism or distinctive group of organisms. Genotype expressed and developed within an environment determines phenotype.
Pheromone: a chemical message produced by one member of a species that influences the physiology and the behavior of another member of the same species. Whether or not this chemical message is consciously detected (smelled), pheromones have the same effect. Mammalian pheromones, in the form of “social odors,” that one member of a species is exposed to during interaction with another member of the species, cause changes in hormone levels and in behavior. See vomeropherin.
Polyploidy: see chromosome.
Protein: genes often code for proteins, which help form and regulate all organisms. Proteins are molecular machines made up of chains of twenty different types of amino acids. Proteins can themselves chain or clump together. Collagen, enzymes, many hormones, keratin, and antibodies are just a few of the different types of proteins.
Proteome, Proteomics: the total complement of proteins within a cell or group of cells, or in an individual organism as a whole. Different tissues will produce different proteins from a standardized set of genes; gene activation in different tissues at different times causes variation in a cell’s proteome. Knowing which genes have been activated can be traced through identifying proteins and other gene products. (See glycome and lipidome.)
Provirus: the genetic code of a virus while it is contained within the DNA of a host.
Radiology: imaging of the interior of a body using radiation, such as X-rays, PET scans (positron emission tomography), MRI (Magnetic resonance imaging), CAT scans (Computerized axial tomography), etc.
Recombination: exchange of genes between or within organisms or viruses. Sexual reproduction is one such exchange; bacteria and viruses can recombine genes in many different ways. Recombination can also be done artificially in a laboratory.
Retrotransposon, retroposon, retrogene: see movable elements.
Retrovirus: RNA-based virus that inserts its code into a host’s DNA for later replication. Replication can often be delayed for years. AIDS and other diseases are caused by retroviruses.
RNA: ribonucleic Acid. Intermediate copy of DNA; messenger RNA (mRNA) is used by ribosomes as templates to construct proteins. Many viruses consist of single or doubled strands of RNA, usually transcribed to DNA within the host.
SHEVA: fictional human endogenous retrovirus that can form an infectious virus particle, or virion; an infectious HERV. No such HERV is yet known. In Darwin’s Radio and this novel, SHEVA carries first-order instructions between individuals for a rearrangement of the genome that produces a new variety of human. In effect, SHEVA triggers preexisting genetic “set-asides” that interact in time-proven ways to create a subtly different human phenotype.
Sequencing: determining the sequence of molecules in a polymer such as a protein or nucleic acid; in genetics, discovering the sequence of bases in a gene or a length of DNA or RNA, or in the genome as a whole. Research into the sequence of the entire human genome has made huge strides, but our understanding of the implications of this growing knowledge is in its infancy.
Sex chromosomes: in humans, the X and Y chromosomes. Two X chromosomes results in a female; an X and a Y results in a male. Other species have different types of sex chromosomes.
Shiver: hypothetical activation of dormant endogenous retroviruses in women who have undergone SHEVA pregnancies. Recombination of exogenous and endogenous viral genes may produce new viruses with an unknown pathogenic potential.
Transposon: see mobile elements.
Vaccine: a substance that produces an immune response to a disease-causing organism. See antibody, antigen, immune response.
Virion: infectious virus particle.
Virus: nonliving but organically active particle capable of entering a cell and commandeering the cell’s reproductive capacity to produce more viruses. Viruses consist of DNA or RNA, usually surrounded by a protein coat, or capsid. This capsid may in turn be surrounded by an envelope. There are hundreds of thousands of known viruses, and potentially millions not yet described. See exogenous virus, ERV.
Vomeronasal organ (VNO, also known as Jacobson’s organ): consisting of two pitlike openings in the roof of the mouth or in the nasal septum, this organ, in non-human mammals, provides a pathway that links pheromones to a hormone response and to sex differences in behavior. “Frithing” is a term used to describe sucking in air over the pit-like entrance to this organ, which is in the roof of the mouth in some animals. Cats can sometimes be observed curling their upper lip when smelling something funky; this is also called the flehman response, usually associated with examination of urine, marking scents, etc. Snakes perform similar sampling by drawing in scents from the air on their flicking tongues. Humans have vomeronasal pits, though they are very small and somewhat difficult to find; they may play a role in mate choice and other behaviors. A 1995 journal article warned plastic surgeons to preserve the human vomeronasal organ during reconstructive surgery, lest damage lead to loss of sexual interest and subsequent litigation.
Vomeropherin: a marketing term for a pheromone detected by the human vomeronasal organ (the same as a mammalian pheromone detected by the mammalian VNO).
Xenotransplant: transplant of nonhuman tissues and organs into humans. Xenotransplants in the past have involved baboon and other ape organs. Most xenotransplant research now focuses on pig tissues and organs. Xenotransplants could be risky because of the existence of latent viruses within the donor tissues. (See ERV, herpes, PERV.) The case of Mrs. Carla Rhine described in this novel is unlikely in real life; Mrs. Rhine’s maladies come from the unfortunate combination of a relatively rare evolutionary viral event and transplantation. Nevertheless, the possibilities of viral contamination or viral recombination within human recipients of animal tissues is very real, and demands further research.
ACKNOWLEDGMENTS
Special thanks to Mark Minie, Ph.D., and Rose James, Ph.D.; Deirdre V. Lovecky, Ph.D.; Dr. Joseph Miller; Dominic Esposito of the National Cancer Institute; Dr. Elizabeth Kutter; Cleone Hawkinson; Alison Stenger, Ph.D.; David and Diane Clark; Brian W. J. Mahy, Ph.D., Sc.D., director of the Division of Viral and Rickettsial Diseases at the Center for Disease Control; Karl H. Anders, M.D.; Sylvia Anders, M.D.; Howard Bloom and the International Paleopsychology Project; Cynthia Robbins-Roth, Ph.D., James V. Kohl, Oliver Morton, Karen Anderson, Lynn Caporale, and Roger Brent, Ph.D.
A BRIEF READING LIST
A concise, elegantly written and conservative view of neo-Darwinian evolutionary theory is available in Richard Dawkins’s River out of Eden: A Darwinian View of Life, BasicBooks, 1995. Dawkins is one of our best science writers and an excellent whetstone for anyone wishing to challenge institutionalized views of biology and evolution. It is my belief that he is wrong on many points, but he defines the debate in ways few others can.
Published more recently, and going into more detail, Ernst Mayr’s summing up of a life’s work, What Evolution Is (2002, Perseus Books) makes another clear and unyielding statement of the paradigm of modern Darwinism. There will probably be no finer exponents of the old view of Darwinian e
volution.
The new view is emerging even as we speak.
Stephen Jay Gould is unfortunately no longer with us. I recommend all of his learned and impassioned books and essays, but in particular the flawed, and for that reason no less fascinating and instructive, Wonderful Life (Norton, 1989).
A good bridge to a larger understanding of the turmoil in evolutionary theory is Niles Eldredge’s Reinventing Darwin: The Great Debate at the High Table of Evolutionary Theory, Wiley, 1995. Eldredge and Gould are currently credited with a particular view of evolutionary leaps known as punctuated equilibrium, but the idea can be traced back at least to masters such as Ernst Mayr, and even back to Darwin. Wherever it comes from, punctuated equilibrium was one of the key stimuli to my writing Darwin’s Radio. Gould and Eldredge should not be blamed for my elaborations, however.
Peter J. Bowler’s The Non-Darwinian Revolution: Reinterpreting a Historical Myth (1988, Johns Hopkins) is scholarly and entertaining at once.
A fine introduction to genetics is Dealing with Genes: The Language of Heredity by Paul Berg and Maxine Singer, 1992, University Science Books. Though a decade old, its information is still useful and its attitude is forward-looking. It could prepare the reader for the following books.
Lynn Margulis and Dorion Sagan have published an excellent critique of neo-Darwinianism in Acquiring Genomes: A Theory on the Origins of Species, 2002, BasicBooks. Margulis is a pioneer in thinking about cooperative and symbiotic systems, and she and her son Dorion make up the single most stimulating popular writing team in modern biology.
More radical still, but just as polite and level-headed as Margulis, is Lynn Caporale, whose Darwin in the Genome: Molecular Strategies in Biological Evolution (2003, McGraw-Hill) is a clear and thoughtful examination of how genomics will shape and mutate the debate on evolution.