Darwin's Children (54 page)

CAVEATS

M
uch of the science in this novel is still controversial. Science usually begins with speculation, but must in time be confirmed by research, empirical evidence, and scientific consensus. However, all of the speculations found here are supported, to one degree or another, by research published in texts and in respected scientific journals. I have gone to great pains to solicit scientific criticism and make corrections where experts feel I have strayed over the line.

No doubt errors remain, but they are my responsibility, not the responsibility of the scientists or other helpful readers listed in the acknowledgments.

The theological speculations presented here are also based on empirical evidence, personal and culled from a number of key books. But that evidence is remarkably and uniquely difficult to present scientifically, since it is necessarily anecdotal. That does not make its truth any less apparent to the witnesses; it simply puts this type of life experience in the same category as other human events, such as love, abstract and creative thought, and artistic inspiration.

All of these experiences are personal and anecdotal, yet almost universal; none are easily quantified or understood by current science.

In answer to the obvious questions about evolution, do I support neo-Darwinian randomness or theistic external design? The answer must be neither. Do I support fundamentalist or Creationist views of our origins? I do not.

My view is that life on Earth is constituted of many layers of neural networks, all interacting to solve problems in order to get access to resources and continue to exist. All living things solve problems posed by their environments, and all are adapted to attempt, with reasonable success, to solve such problems. The human mind is just one variety of this natural process, and not necessarily the most subtle or sophisticated. See my novel,
Vitals
.

I also make a distinction between self-aware personality and mind. Human self-awareness is a psycho-social phenomenon resulting from feedback in modeling the behavior of one’s neighbors, and, almost coincidentally, modeling one’s own behavior to make sure we’ll fit into social activities. One offshoot of this ability is the writing of novels.

Self is not an illusion; it’s real. But it’s not unitary, it’s not primary, and it’s not always in charge.

It seems apparent that God does not micromanage either human history or nature. Evolutionary freedom is just as important as individual human freedom. Does God interfere at all? Other than my affirming, along with many others, that the presence of something we could call God is made known—a kind of interference, undoubtedly—I do not know.

As Kaye experiences her epiphany, she is made aware that her “caller” is not talking just to her, but to other minds within and around her. Epiphany is not limited to our conscious selves, or even to human beings.

Imagine epiphany that touches our subconscious, our other internal minds—the immune system—or that reaches beyond us to touch a forest, or an ocean . . . or the vast and distributed “minds” of any ecological system.

If the only honest approach to understanding both nature and God is humility, then surely this should help by making us feel humble.

A SHORT BIOLOGICAL PRIMER

H
umans are metazoans, that is, we are made up of many cells. In most of our cells there is a
nucleus
that contains the “blueprint” for the entire individual. This blueprint is stored in
DNA,
deoxyribonucleic acid; DNA and its complement of helper proteins and organelles make up the molecular computer that contains the instructions necessary to construct an individual organism.

Proteins
are molecular machines that can perform incredibly complicated functions. They are the engines of life; DNA is the template that guides the manufacture of those engines.

DNA in eukaryotic cells is arranged in two interwoven strands—the “double helix”—and packed tightly into a complex structure called chromatin, which is arranged into
chromosomes
in each cell nucleus. With a few exceptions, such as red blood cells and specialized immune cells, the DNA in each cell of the human body is complete and identical. Researchers currently estimate that the human
genome
—the complete collection of genetic instructions—consists of approximately thirty thousand
genes
. Genes are heritable traits; a gene has often been defined as a segment of DNA that contains the code for a protein or proteins. This code can be transcribed to make a strand of RNA, ribonucleic acid; ribosomes then use the RNA to translate the original DNA instructions and synthesize proteins. Some genes perform other functions, such as making the RNA constituents of ribosomes.

Many scientists believe that RNA was the original coding molecule of life, and that DNA is a later elaboration.

While most cells in the body of an individual carry identical DNA, as the person grows and develops, that DNA is expressed in different ways within each cell. This is how identical embryonic cells become different tissues.

When DNA is transcribed to RNA, many lengths of nucleotides that do not code for proteins, called
introns,
are snipped out of the RNA segments. The segments that remain are spliced together; they code for proteins and are called
exons.
On a length of freshly transcribed RNA, these exons can be spliced together in different ways to make different proteins. Thus, a single gene can produce a number of products at different times.

Bacteria
are tiny single-celled organisms. Their DNA is not stored in a nucleus but is spread around within the cell. Their genome contains no
introns,
only
exons,
making them very sleek and compact little critters. Bacteria can behave like social organisms; different varieties both cooperate and compete with each other to find and use resources in their environment. In the wild, bacteria frequently come together to create biofilms; you may be familiar with these bacterial “cities” from the slime on spoiled vegetables in your refrigerator. Biofilms can also exist in your intestines, your urinary tract, and on your teeth, where they sometimes cause problems, and specialized ecologies of bacteria protect your skin, your mouth, and other areas of your body. Bacteria are extremely important and though some cause disease, many others are necessary to our existence. Some biologists believe that bacteria lie at the root of all life forms, and that eukaryotic cells—our own cells, for example—derive from ancient colonies of bacteria. In this sense, we may simply be spaceships for bacteria.

Bacteria swap small circular loops of DNA called
plasmids.
Plasmids supplement the bacterial genome and allow them to respond quickly to threats such as antibiotics. Plasmids make up a universal library that bacteria of many different types can use to live more efficiently.

Bacteria and nearly all other organisms can be attacked by
viruses
. Viruses are very small, generally encapsulated bits of DNA or RNA that cannot reproduce by themselves, Instead, they hijack a cell’s reproductive machinery to make new viruses. In bacteria, the viruses are called
bacteriophages,
(“eaters of bacteria”) or just
phages
. Many phages carry genetic material between bacterial hosts, as do some viruses in animals and plants.

It is possible that viruses originally came from segments of DNA within cells that can move around, both inside and between chromosomes. Viruses are essentially roving segments of genetic material that have learned how to “put on space suits” and leave the cell.

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 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, 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.