by Greg Bear
Exon: regions of DNA that code for proteins or RNA.
Gamete: a sex cell, such as egg or sperm, capable of joining with an opposite gamete — egg plus sperm — to make a zygote.
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 a protein. Besides the nucleo-tides 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.
Genotype: the genetic character of an organism or distinctive group of organisms.
HERV or 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 the sum total 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 cell to cell, in lateral or horizontal transmission. Many HERV do produce viruslike particles within the cell, 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 retrovirus, are found in many other organisms, as well.)
Homosome: the complete complement of usable genetic material both inside and outside a cell or organism. Bacteria exchange circular loops of DNA called plasmids and may have some genes carried by lysogenic phages; this total pool of genetic material constitutes the bacterial homosome.
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.
Intron: regions of DNA that do not generally code for proteins. In most eucaryotic cells, genes consist of mingled exons and introns. Introns are clipped out of transcribed messenger RNA (mRNA) before it is processed by ribo-somes; ribosomes use the code contained in lengths of mRNA to assemble specific proteins out of amino acids. Bacteria lack introns.
Lysogenic phage: phage that attaches to a bacterial capsule and inserts genetic material into the bacterial host, where it then forms a circular loop, integrates with the host DNA, and lies dormant for a time. During this stage, the host bacterium reproduces the prophage or integrated phage genome with its own. Damage or “stress” to a host bacterium may result in the transcription of the phage genes, which then replicate new phages, releasing them by lysing or breaking open the host. In this stage, they are called lytic phage. Lysogenic/lytic phages may also transcribe and carry host genes, along with their own, from one bacterium to another. Many bacteria that cause severe disease in humans, such as cholera, can have their toxicity triggered by the transfer of genetic material by lysogenic phages. Such phages, understandably, are dangerous in their natural form and useless in controlling bacterial pathogens.
Marker: distinctive or unique arrangement of bases or a distinctive or unique gene within a chromosome.
Modern human: Homo sapiens sapiens. Genus Homo, species sapiens, subspecies sapiens.
Movable element (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 poly-merase. Retrotransposons contain their own reverse tran-scriptase, which gives them some autonomy within the genome. Movable 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. Others believe that movable elements in the DNA contribute to novelty in all genomes, and perhaps even help regulate 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 geneticists 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, pro-lists (formerly known as protozoa), and metazoans such as nematodes.
Phage: virus that uses bacteria as hosts. Many kinds of phages kill their hosts almost immediately and can be used as antibacterial agents. Many 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. (See Lysogenic phage.)
Phenotype: the physical structure of an organism or distinctive group of organisms. Genotype expressed and developed within an environment determines phenotype.
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.
Provirus: the genetic code of a virus while it is contained within the DNA of a host.
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 complementary copy of DNA; messenger RNA or mRNA is used by ribosomes as templates to construct proteins.
SHEVA (HERV-DL3, SHERVA-DL3): fictitious human endogenous retrovirus that can form an infectious virus particle, or virion; an infectious HERV No such HERV is yet known.
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. In a few years, we will understand the sequence of the entire human genome.
Sex chromosomes: in humans, the X and Y chromosomes. Two X chromosomes result in a female; X and Y result in a male. Other species have different types of sex chromosomes.
Transposon: see movable elements.
Trisomy, trisomal: having an extra copy of a chromosome in a diploid cell. In humans, having three copies of chromosome 21 leads to Down syndrome.
Vaccine: a substance that produces an immune response to a disease-causing organism.
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 virus. 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.
Zygote: the combination of two gametes; a fertilized ovum.
ACKNOWLEDGMENTS
Special thanks to Mark E. Minie, Ph.D., for introducing me to the Puget Sound Biotech Society and many of its members. One of my first contacts was Dr. Elizabeth Kutter of the fac
ulty of the Biology Department of Evergreen State College in Olympia, Washington. She helped me with details about her specialty, bacteriophages, as well as with many facts about one of her favorite places on Earth, the Republic of Georgia. Her assistants, Mark Alan Mueller and Elizabeth Thomas, were constructively critical and encouraging. Our discussions have been both formative and informative!
Mark E. Minie also introduced me to Dr. Dennis Schwartz, whose work on the early chemistry of life may prove revolutionary.
Many other scientists and friends have read and critiqued this book, and a few have given me tours of their facilities. Dr. Dominic Esposito of the National Institutes of Health shepherded me around the NIH campus and made copious notes on an early draft. His friends, Dr. Melanie Simpson and Martin Kevorkian, also provided substantial help.
Benoit Leblanc, Ph.D., working with Dr. David Clark at NIH, in the Laboratory of Cellular and Developmental Biology, did an excellent critical reading, and straightened out many errors in the text.
Brian W. J. Mahy, Ph.D., Sc.D., Director of the Division of Viral and Rickettsial Diseases at the Centers for Disease Control and Prevention, was kind enough to meet with me and share some of his insights into viruses and their possible contributions to evolution. He also critiqued a later draft of the book. Barbara Reynolds of the Public Information Office of the CDC helped arrange a tour of the facilities at 1600 Clifton Road.
Dr. Joe Miller, of Texas Tech University Health Sciences Center, read the book in its earliest draft and provided details about the chemistry of human hormones and vomeronasal receptors.
Julian Davies, Professor Emeritus of the University of British Columbia, kindly agreed to look over the final draft.
Katie and Charlie Potter provided sage advice on mountain climbing, its history and terms.
Even with the help of all these excellent readers, errors certainly remain. They belong to me, not them. Also, at every step of the way, these scientists have expressed both support and doubts about my theories, sometimes severe doubts. Their aid in no way implies that they agree with any or all of the theories in Darwin s Radio.
Greg Bear is the author of twenty-four books, which have been translated into a dozen languages. He has been awarded two Hugos and four Nebulas for his fiction. He was called the “best working writer of hard science fiction” by The Ultimate Encyclopedia of Science Fiction. He is married to Astrid Anderson Bear. They are the parents of two children, Erik and Alexandra.
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