Bateria

Archaea

Archaea or Archaebacteria, common name for a group of one-celled organisms, many of

which do not require oxygen or sunlight to live. Before the discovery of archaebacteria,
scientists divided all living organisms into prokaryotes (organisms without a cellular
nucleus), which consisted primarily of bacteria, and eukaryotes (organisms with a cellular
nucleus), which consisted of fungi, plants, and animals. Archaebacteria were initially
grouped with bacteria because like bacteria, they lack a well-defined nucleus. Recent
evidence, however, has demonstrated that archaebacteria have a genetic makeup that
more closely resembles the eukaryotes, organisms that have a well-defined nucleus. This
unique structure means that archaebacteria cannot be accurately grouped with either the
prokaryotes or the eukaryotes. Instead, scientists have proposed that these
microorganisms be classified in a new branch of life, or domain, called archaea.
Archaebacteria often live in extreme conditions that were once considered inhospitable to
life. Some archaebacteria live in deep-sea hydrothermal vents in the Pacific Ocean.
Located at depths of 3 km (2 mi), the hot vents provide a dark environment with
extremely high temperature and pressure where few creatures can survive. Instead of
deriving energy from the sun, these microorganisms obtain energy by oxidizing inorganic
chemicals that spew from the hot vents. In a process known as chemosynthesis,
archaebacteria harvest energy from chemical reactions involving hydrogen sulfide and
other inorganic compounds. These deep-sea archaebacteria make up the bottom of the
food chain for clams, tube worms, mussels, and other animals that live near the vents (see
Marine Life).
Scientists initially found archaebacteria only in harsh environments, but recently these
microorganisms have been found in the guts of animals, compost piles, saturated
marshes, and other common places. Knowledge gleaned from studying a third branch of
life could provide insight on the common ancestry of all living organisms.
Scientific classification: Archaebacteria are members of the domain archaea. The
archaebacterium found near deep-sea hydrothermal vents is classified as Methanococcus
jannaschii.

Bacteria
I. INTRODUCTION
Bacteria, one-celled organisms visible only through a microscope. Bacteria live all
around us and within us. The air is filled with bacteria, and they have even entered outer
space in spacecraft. Bacteria live in the deepest parts of the ocean and deep within Earth.
They are in the soil, in our food, and on plants and animals. Even our bodies are home to
many different kinds of bacteria. Our lives are closely intertwined with theirs, and the
health of our planet depends very much on their activities.
Bacterial cells are so small that scientists measure them in units called micrometers (µm).
One micrometer equals a millionth of a meter (0.0000001 m or about 0.000039 in), and
an average bacterium is about one micrometer long. Hundreds of thousands of bacteria
would fit on a rounded dot made by a pencil.
Bacteria lack a true nucleus, a feature that distinguishes them from plant and animal cells.
In plants and animals the saclike nucleus carries genetic material in the form of
deoxyribonucleic acid (DNA). Bacteria also have DNA but it floats within the cell,
usually in a loop or coil. A tough but resilient protective shell surrounds the bacterial cell.
Biologists classify all life forms as either prokaryotes or eukaryotes. Prokaryotes are
simple, single-celled organisms like bacteria. They lack a defined nucleus of the sort
found in plant and animal cells. More complex organisms, including all plants and
animals, whose cells have a nucleus, belong to the group called eukaryotes. The word
prokaryote comes from Greek words meaning “before nucleus”; eukaryote comes from
Greek words for “true nucleus.”
Bacteria inhabited Earth long before human beings or other living things appeared. The
earliest bacteria that scientists have discovered, in fossil remains in rocks, probably lived
about 3.5 billion years ago. These early bacteria inhabited a harsh world: It was
extremely hot, with high levels of ultraviolet radiation from the sun and with no oxygen
to breathe.
Descendents of the bacteria that inhabited a primitive Earth are still with us today. Most
have changed and would no longer be able to survive the harshness of Earth’s early
environment. Yet others have not changed so much. Some bacteria today are able to grow
at temperatures higher than the boiling point of water, 100oC (212oF). These bacteria
live deep in the ocean or within Earth. Other bacteria cannot stand contact with oxygen
gas and can live only in oxygen-free environments—in our intestines, for example, or in
the ooze at the bottom of swamps, bogs, or other wetlands. Still others are resistant to
radiation. Bacteria are truly remarkable in terms of their adaptations to extreme
environments and their abilities to survive and thrive in parts of Earth that are
inhospitable to other forms of life. Anywhere there is life, it includes bacterial life.

II. THE IMPORTANCE OF BACTERIA

Much of our experience with bacteria involves disease. Although some bacteria do cause
disease, many kinds of bacteria live on or in the human body and prevent disease.
Bacteria associated with the human body outnumber body cells by ten to one. In addition,
bacteria play important roles in the environment and in industry.

A. Bacteria and Human Health

We have all had bacterial diseases. Bacteria cause many cases of gastroenteritis,
sometimes called stomach flu. Perhaps the most common bacterial disease is tooth decay.
Dental plaque, the sticky film on our teeth, consists primarily of masses of bacteria.
These bacteria ferment (break down) the sugar we eat to produce acids, which over time
can dissolve the enamel of the teeth and create cavities (holes) in the teeth.

Tooth decay provides a good example of how multiple factors contribute to bacterial
disease. The human body hosts the bacteria, the diet supplies the sugars, and the bacteria
produce the acid that damages the teeth.

A1. Bacteria That Inhabit the Body

Communities of bacteria form what are called biofilms on many body surfaces. Dental
plaque is a biofilm covering the teeth. Biofilms also cover the soft tissues of our mouths
and the inner surfaces of our nose, sinuses, throat, stomach, and intestines. Even the skin
has bacterial communities that extend into hair follicles. Bacterial communities differ in
each region of the body, reflecting the environmental conditions in their specific region.
Bacteria that inhabit the surface of the stomach, for example, must deal with extremely
strong acid in the digestive juices.
Some regions in the interior of the body are sterile—that is, devoid of living organisms
other than the cells of the body. Sterile regions include the muscles, the blood, and the
nervous system. However, even these regions face constant invasion by bacteria. The
body’s immune system is designed to rid the body of these invaders.
A healthy, balanced community of bacteria is extremely important for our health. Some
of these organisms protect us from disease-causing organisms that would otherwise infect
us. Animals raised in a completely germ-free environment, without any contact with
bacteria, are highly susceptible to infectious diseases if they are exposed to the outside
world. Bacteria in our bodies also provide us with needed nutrients, such as vitamin K,
which the body itself cannot make. The communities of bacteria and other organisms that
inhabit the body are sometimes called the normal microflora or microbiota.

A2. Disease-Causing Bacteria

In most cases the bacteria that cause disease are not part of the bacteria that normally
inhabit the body. They are picked up instead from sick people, sick animals,
contaminated food or water, or other external sources. Bacterial disease also can occur
after surgery, an accident, or some other event that weakens the immune system.

A2a. Opportunistic Infections

When the immune system is not functioning properly, bacteria that usually are harmless
can overwhelm the body and cause disease. These organisms are called opportunistic
because they cause disease only when an opportunity is presented. For example, cuts or
injuries to the skin and protective layers of the body enable normally friendly bacteria to
enter the bloodstream or other sterile parts of the body and cause infection. Surgery may
enable bacteria from one part of the body to reach another, where they cause infection. A
weakened immune system may be unable to prevent the rapid multiplication of bacteria
and other microorganisms.
Opportunistic infections became more important in the late 20th century because of
diseases such as acquired immunodeficiency syndrome (AIDS), a viral disease that
ravages the immune system. Also contributing to an increase in opportunistic infections
is the wider use of cancer-fighting drugs and other drugs that damage the immune
system.

A2b. Bacterial Killers

Some dramatic infectious diseases result from exposure to bacteria that are not part of our
normal bacterial community. Cholera, one of the world’s deadliest diseases today, is
caused by the bacterium Vibrio cholerae. Cholera is spread in water and food
contaminated with the bacteria, and by people who have the disease. After entering the
body, the cholera bacteria grow in the intestines, often along the surface of the intestinal
wall, where they secrete a toxin (poison). This toxin causes massive loss of fluid from the
gut, and an infected person can die of dehydration (fluid loss) unless the lost fluids, and
the salts they contain, are replaced. Cholera is common in developing regions of the
world that lack adequate medical care.
Another major bacterial killer is Mycobacterium tuberculosis, which causes tuberculosis
(TB), a disease of the lungs. Tuberculosis is responsible for more than 2 million deaths
per year worldwide. Although antibiotics such as penicillin fight many bacterial diseases,
the TB bacterium is highly resistant to most antibiotics. In addition, the TB-causing
bacteria readily spread from person to person.

A2c. New Bacterial Diseases

While tuberculosis and cholera have been with us for centuries, in recent decades new
bacterial diseases have emerged. Legionnaires’ disease, a severe form of pneumonia, was
first recognized at an American Legion convention in Philadelphia, Pennsylvania, in
1976. It is caused by a previously unknown bacterium, Legionella pneumophila, which is
most often transmitted through infected water.
Lyme disease, a form of arthritis caused by the bacterium Borrelia burgdorferi, was first
recognized in Lyme, Connecticut, in 1975. A bite from a deer tick that carries the bacteria
transmits the disease to human beings.
A food-borne disease currently causing major concern in the United States, Canada, and
Western Europe is caused by a particular variant of the common intestinal bacterium
Escherichia coli, or E. coli for short. Although E. coli is normally present in the human
intestines, the variant E. coli O157:H7 produces toxins that cause bloody diarrhea and, in
some cases, far more severe problems, including kidney failure and death. A person can
become infected by eating contaminated meat. Thorough cooking kills the bacteria.

A3. How the Body Fights Bacterial Disease

Our immune system is designed to protect us against harmful bacteria. It works to keep
our normal microflora in check and also to eliminate invaders from outside the body.
Some immune-system defenses are built in: The skin acts as a barrier to bacterial
invaders, and antimicrobial substances in body secretions such as saliva and mucus can
kill or stop the growth of some disease-causing bacteria. We acquire another immune-
system defense through exposure to disease-causing bacteria.
After recovering from many bacterial infections, people have the ability to resist a second
attack by the same bacteria. They can do so because their immune system forms disease-
fighting proteins called antibodies designed to recognize specific bacteria. When next
exposed to those bacteria, the antibodies bind to the surface of the bacteria and either kill
them, prevent them from multiplying, or neutralize their toxin. Vaccines also can
stimulate the immune system to form disease-fighting antibodies. Some vaccines contain
strains of the bacterium that lack the ability to cause infection; others contain only parts
of bacterial cells.

A4. Treatment and Prevention of Bacterial Disease

A4a. Antibiotics
In many cases the immune system can wipe out a bacterial infection on its own. But
sometimes people become so sick from a bacterial disease that they require medical
treatment. Antibiotics and other antibacterial drugs are the major weapons against
disease-causing bacteria. Antibiotics act in a number of ways to kill bacteria or suppress
their activity. Over time, however, bacteria can become resistant to antibiotics. As a
result bacterial diseases have become more and more difficult to cure.
In an effort to control antibiotic resistance, physicians have tried to limit the use of
antibiotics. In addition, they have advocated more vigorous efforts to improve the
antibiotics we now have and to find new agents active against bacteria.

A4b. Vaccines
Immunization through vaccines is important in the prevention of infectious diseases
caused by bacteria. Vaccines expose a human being or other animal to a disease-causing
bacterium or its toxins without causing the disease. As a result of this exposure, the body
forms antibodies to the specific bacterium. These antibodies remain ready to attack if
they meet the bacteria in the future. Some immunizations last a lifetime, whereas others
must be renewed with a booster shot.
Tetanus provides a good example of a successful vaccine. The bacterium Clostridium
tetani, found in soil and ordinary dirt, produces one of the most lethal toxins known. The
toxin affects nerves, resulting in muscle rigidity and death. Tetanus infection has become
very rare in developed countries such as the United States where nearly everyone is
immunized against the toxin. The vaccine immunizes the body by means of toxins that
have been chemically treated so they are no longer toxic. Health officials recommend
getting a tetanus shot every ten years. In less developed countries where vaccination is
not so common, tetanus is a major cause of death, especially of babies.

A4c. Public Health Measures

Public health measures provide major controls against infectious disease. Especially
important are those measures leading to ready availability of clean water, safe food, and
up-to-date medical care. Waterborne diseases, such as cholera and typhoid fever, kill an
estimated 5 million to 10 million people worldwide each year, according to the United
Nations. Sufficient sources of clean drinking water in developing countries could help
prevent these deaths. Food-safety guidelines can help prevent the spread of disease
through contaminated food. Proper medical care can prevent transmission of infectious
diseases to others. Tuberculosis, for example, kills more people worldwide every year
than any other single disease. But if identified early, cases of tuberculosis can be treated
effectively with antibiotics and other means, thereby stopping transmission to others.
Maintaining a clean environment for medical care is also important in preventing the
spread of infectious diseases. For example, medical instruments, such as needles and
syringes, must be sterile and proper infection-control procedures must be followed in
hospitals, medical and dental offices, and industries that use bacteria. However, it is
never possible, or even desirable, to have an environment entirely free of bacteria.
B. Bacteria and the Environment
Bacteria play a major role in recycling many chemical elements and chemical compounds
in nature. Without such bacterial activities as the recycling of carbon dioxide (CO2) life
on Earth would be impossible. Plants use CO2 to grow and in the process they produce
the oxygen humans and other animals breathe. Moreover, we would drown in garbage
and wastes if bacteria did not speed the decomposition of dead plant and animal matter.

B1. Nitrogen Fixation

Bacteria play a key role in making soil fertile. They convert nitrogen in Earth’s
atmosphere into the nitrogen compound ammonia, which plants need to grow. Bacteria
are the only organisms able to carry out this biochemical process known as nitrogen
fixation. The bacteria able to fix atmospheric nitrogen usually live in association with
plants, often integrated into the plant tissue. Bacteria in the genus Rhizobium, for
example, form nodules (knobs) on the roots of beans and other plants in the legume
family.

B2. The Carbon Cycle

Bacteria and fungi (yeasts and molds) are vital to another process that makes life on Earth
possible: the carbon cycle. They help produce the gas carbon dioxide (CO2), which
plants take from the atmosphere. During a part of the carbon cycle called photosynthesis,
plants turn sunlight and CO2 into food and energy, releasing oxygen into the atmosphere.
The carbon cycle continues after plants and animals die, when bacteria help convert the
material of which those organisms are made back into CO2. Bacteria and fungi secrete
enzymes that partially break down dead matter. Final digestion of this matter takes place
within bacterial and fungal cells by the processes of fermentation and respiration. The
CO2 released by this action escapes back into the atmosphere to renew the cycle.

B3. Chemosynthesis
Bacteria are major players in cycles of other elements in the environment.
Chemosynthetic bacteria use chemical energy, instead of the light energy used by plants,
to change CO2 into something that other organisms can eat. Chemosynthesis occurs in
vents at the bottom of the ocean, where light is unavailable for photosynthesis but
hydrogen sulfide gas, H2S, bubbles up from below Earth’s crust. Life can develop around
these vents because bacteria use the H2S in changing CO2 into organic nutrients. The
H2S coming up from Earth’s mantle is extremely hot, but bacteria in these vent
communities are adapted to the high temperatures. Bacteria’s ability to react chemically
with sulfur compounds is useful in certain industrial processes as well.

B4. Bioremediation
Bioremediation refers to the use of microorganisms, especially bacteria, to return the
elements in toxic chemicals to their natural cycles in nature. It may provide an
inexpensive and effective method of environmental cleanup, which is one of the major
challenges facing human society today.
Bioremediation has helped in cleaning up oil spills, pesticides, and other toxic materials.
For example, accidents involving huge oil tankers regularly result in large spills that
pollute coastlines and harm wildlife. Bacteria and other microorganisms can convert the
toxic materials in crude oil to harmless products such as CO2. Adding fertilizers that
contain nitrogen, phosphorus, and oxygen to the polluted areas promotes the
multiplication of bacteria already present in the environment and speeds the cleanup
process.

C. Bacteria in Agriculture and Industry

Many of bacteria’s beneficial roles in agriculture have been described in the previous
section on Bacteria and the Environment. By recycling certain chemical elements and
compounds, bacteria make plant and animal life possible. Bacteria’s chemical
interactions have also found uses in industry. In recent decades, scientists have
engineered bacterial genes to produce sought-after substances, such as human insulin, to
use in the treatment of disease.

C1. Bacteria in Agriculture

Through the process of nitrogen fixation, bacteria turn nitrogen in the air into nutrients
that crops and other plants need to grow. Some of the nitrogen-fixing bacteria attach to
the roots of plants. Through the carbon cycle, bacteria produce the carbon dioxide that
plants require for photosynthesis. Bacteria that live in the stomachs of cud-chewing
animals, such as cows and sheep, help the animals digest grasses.
Bacteria also can be harmful in agriculture because of the major diseases of farm animals
they cause. Many of the bacteria that cause infectious diseases in farm animals resemble
those that cause similar human diseases. For example, a variant of the bacterium that
causes human tuberculosis causes tuberculosis in cattle, and it can infect humans through
cow’s milk. To prevent transmission of the disease, milk for human consumption should
be pasteurized (heated at a temperature between 60° and 70°C (140° and 158°F) for a
short time. Pasteurization kills most bacteria in milk.
Other disease-causing bacteria primarily affect animals other than humans. For example,
the bacterium Brachyspira hyodysenteria causes a type of diarrhea in pigs that can be
disastrous for pig farmers. Many infectious diseases of farm animals also affect wild
animals, such as deer. Wild animals, in turn, can infect domestic animals, including cats
and dogs.

C2. Bacteria in the Food Industry

Bacteria are of major importance in the food industry. On the one hand, they cause food
spoilage and foodborne diseases, and so must be controlled. On the other hand, they
improve food flavor and nutrition.
The dairy industry provides prime examples of bacteria’s harmful and helpful roles.
Before the introduction of pasteurization in the late 1800s, dairy products were major
carriers for bacteria that caused such illnesses as tuberculosis and rheumatic heart
disease. Since that time regulation of the dairy industry has greatly reduced the risks of
infection from dairy products.
On the helpful side, bacteria contribute to the fermentation (chemical breakdown) of
many dairy products people eat every day. Yogurt, considered a healthful food, is
produced by bacterial fermentation of milk. The bacteria produce lactic acid, which turns
the milk sour, hampers the growth of disease-causing bacteria, and gives a desirable
flavor to the resulting yogurt. Cheese also is produced by fermentation. First, bacteria
ferment milk sugar to lactic acid. Then, cheese makers can introduce various
microorganisms to produce the flavors they desire. The process is complicated and may
take months or even years to complete, but it gives cheeses their characteristic flavors.
The variety of fermented foods we eat ranges from pickles, olives, and sauerkraut to
sausages and other cured meats and fish, chocolate, soy sauce, and other products. In
most of these fermentations, bacteria that produce lactic acid play major roles. Alcohol-
producing yeasts are the primary fermentors in the manufacture of beer and wine, but
lactic-acid bacteria also are involved, especially in making wine or cider. Bacteria that
produce acetic acid can convert wine, cider, or other alcoholic beverages to vinegar.

C3. Bacteria in Waste Treatment

Bacteria are very important in sewage treatment. Standard sewage treatment involves
multiple processes. It usually starts with settling during which large items sink to the
bottom. Next, air is bubbled through the sewage. This so-called aerobic phase encourages
oxygen-using bacteria to break down organic material in the sewage, such as human
wastes, to acids and CO2. Most disease-causing organisms are also killed in this phase.
The sewage sludge left behind is attacked in a subsequent phase by anaerobic bacteria
(bacteria that cannot tolerate oxygen). These bacteria break down the sludge to produce
methane gas, which can then be used as a fuel to power the treatment facility. In
treatment plants today, this anaerobic phase sometimes precedes the aerobic phase.
Bacteria are also effective in cleaning up harmful wastes through bioremediation. In this
process bacteria and other microorganisms convert toxic or otherwise objectionable
wastes, such as pesticides and oil spills, to harmless or even useful products.

C4. Bacteria in Mineral Extraction

An interesting industrial process carried out by bacteria is the recovery of valuable
minerals such as copper from ores. The most important copper ores are copper sulfides,
which may contain only a small percentage of copper. Bacteria of the genera Thiobacillus
and Sulfolobus are able to oxidize sulfides—that is, cause a chemical reaction of sulfides
with oxygen—yielding sulfuric acid. This action produces the acid conditions necessary
to leach (remove) the copper from the ores. The use of bacteria in extracting minerals,
though slow, is environmentally friendly compared with the standard process of smelting.
Smelting requires energy to heat the ore to extremely high temperatures for extracting
minerals, and it also releases gases that pollute the air.
Some chemical reactions in which bacteria participate are harmful rather than helpful to
industry. Bacteria are major agents of metal corrosion (wearing away) through the
formation of rust, especially on metals containing iron. During the early stages of rust
formation, hydrogen is produced, and it acts to slow the rusting process. However, certain
bacteria use the hydrogen as a nutrient with the result that they greatly speed up rust
formation.

C5. Bacteria in Biotechnology

Bacteria have been at the center of recent advances in biotechnology—the creation of
products for human benefit through the manipulation of biological organisms.
Biotechnology itself dates back at least as far as ancient Egyptian civilization. Paintings
on the walls of Egyptian tombs depict the brewing of beer, which uses microorganisms in
the fermentation process. However, the existence of bacteria did not become known until
the development of sufficiently powerful microscopes in the late 1600s. During the
centuries that followed, scientists became aware that living organisms were responsible
for many biotechnological processes.
Biotechnology grew steadily during the 20th century. In the 1970s scientists used
information about replication of viruses and bacteria and about DNA synthesis
(manufacture) to begin the genetic engineering of bacterial cells. When scientists
combined human DNA with the DNA in bacterial cells, recombinant DNA technology
was born. Human DNA is the “recombinant.” DNA contains the instructions for creating
proteins. With their recombinant DNA, bacteria became factories for turning out human
proteins, such as the hormone insulin or antibodies that fight disease. Because they
multiply so rapidly, bacteria produce multiple copies of proteins in a short time. The
process of taking genetic information from one organism and placing it in a different
organism was patented by American biochemists Stanley Cohen and Herbert Boyer in
1980. The genetic revolution was underway.

C6. Other Industrial Roles

Bacteria play a role in the production of other products, including certain plastics and
enzymes used in laundry detergents. They also produce many antibiotics, such as
streptomycin and tetracycline. Since the 1980s, bacteria have gained importance in the
production of many bulk chemicals, including ethanol, a form of alcohol made from
fermented corn. Ethanol is an ingredient of gasohol, a fuel that burns more cleanly than
gasoline and uses less petroleum. Chemical production using bacteria and other
microorganisms results in less pollution to the environment than standard chemical
production. The growth of genetic engineering has opened the way to even greater use of
bacteria in large-scale industrial manufacturing and environmentally friendly processes.

C7. Controlling Bacterial Growth

Sterilization and disinfection—processes for destroying microorganisms—are integral
parts of the food industry. For example, canning involves heating foods to temperatures
of 121oC (250oF) to kill all organisms, including the most heat-resistant bacterial cells.
Failure to kill bacteria and the spores they produce can result in fatal disease such as
botulism. If spores of the bacterium Clostridium botulinum are not destroyed, they can
grow in canned foods and produce a toxin that attacks the nervous system. The botulism
toxin is one of the most deadly toxins known.
Demand for better sterilization and disinfection methods in medicine and other industries
has increased since the 1970s because of fear of spreading infection by the human
immunodeficiency virus (HIV) and other disease-causing microorganisms. Industry has
developed a wide array of products oriented to killing bacteria and other organisms. The
industry has grown to be a huge one with a wide array of products oriented to killing
bacteria and other microorganisms.

III. CHARACTERISTICS OF BACTERIA

Bacteria are so small that they can be seen only under a microscope that magnifies them
at least 500 times their actual size. Some become visible only at magnifications of 1,000
times. They are measured in micrometers (µm) and average about 1 to 2 µm in length.
One micrometer equals one-millionth of a meter (0.0000001 m or about 0.000039 in).
Bacteria not only have many uses, they also occur in diverse shapes and types. As a
group they carry out a broad range of activities and have different nutritional needs. They
thrive in a variety of environments.

A. Types of Bacteria
Scientists use various systems for classifying bacteria into different types. One of the
simplest systems is by shape. Other systems depend on oxygen use, source of carbon, and
response to a particular dye.

A1. Classification by shape

Most bacteria come in one of three shapes: rod, sphere, or spiral. Rod-shaped bacteria are
called bacilli. Spherical bacteria are called cocci, and spiral or corkscrew-shaped bacteria
are called spirilla. Some bacteria come in more complex shapes. A hairlike form of spiral
bacteria is called spirochete (see Spirochetes). Streptococci and staphylococci are well-
known disease-causing bacteria among the cocci.

A2. Aerobic and Anaerobic Bacteria

Scientists also classify bacteria according to whether they need oxygen to survive or not.
Aerobic bacteria require oxygen. Anaerobic bacteria cannot tolerate oxygen. Bacteria that
live in deep ocean vents or within Earth are anaerobic. So are many of the bacteria that
cause food poisoning.

A3. Autotrophic and Heterotrophic Bacteria

All bacteria require carbon for growth and reproduction. Bacteria called autotrophs
(“self-feeders”) get their carbon from CO2. Most bacteria, however, are heterotrophs
(“other feeders”) and derive carbon from organic nutrients such as sugar. Some
heterotrophic bacteria survive as parasites, growing within another living cell and using
the nutrients and cell machinery of their host cells. Some autotrophic bacteria, such as
cyanobacteria, use sunlight to produce sugars from CO2. Others depend instead on
energy from the breakdown of inorganic chemical compounds, such as nitrates and forms
of sulfur.

A4. Gram-Positive and Gram-Negative Bacteria

Another system of classifying bacteria makes use of differences in the composition of
cell walls. The difference becomes clear by means of a technique called Gram’s stain,
which identifies bacteria as either gram-positive or gram-negative. After staining, gram-
positive bacteria hold the dye and appear purple, while gram-negative bacteria release the
dye and appear red. Gram-positive bacteria have thicker cell walls than gram-negative
bacteria. Knowing whether a disease-causing bacterium is gram-positive or gram-
negative helps a physician to prescribe the appropriate antibiotic. The stain is named for
H. C. J. Gram, a Danish physician who invented it in 1884.

A5. The Cell and Its Structure

The cell wall generally determines the shape of the bacterial cell. The wall is a tough but
resilient shell that keeps bacterial cells from drying out and helps them resist
environmental stress. In some cases the cell wall protects the bacterium from attack by
the body’s disease-fighting immune system cells. Some bacteria do not have much of a
cell wall, while others have quite thick structures. Many species of bacteria move about
by means of flagella, hairlike structures that project through the cell wall. The flagellum’s
rotating motion propels the bacterial cell toward nutrients and away from harmful
substances.
Like all cells bacteria contain the genetic material DNA. But bacterial DNA is not
contained within a nucleus, as is DNA in plant and animal cells. Most bacteria have a
single coil of DNA, although some bacteria have multiple pieces. Bacterial cells often
have extra pieces of DNA called plasmids, which the cell may gain or lose without dying.
Surrounding the DNA in a bacterial cell is cytoplasm, a watery fluid that is rich in
proteins and other chemicals. A cell membrane inside the wall holds together the DNA
and the constituents of the cytoplasm. Most activities of the bacterial cell are carried out
within the cytoplasm, including nutrition, reproduction, and the manufacture of proteins.

B. How Bacteria Function

Bacterial cells, like all cells, require nutrients to carry out their work. These nutrients
must be water soluble to enter through pores in the cell wall and pass through the cell
membrane into the cytoplasm. Many bacteria, however, can digest solid food by secreting
chemicals called exoenzymes into the surrounding environment. The exoenzymes help
break down the solid food outside the bacteria into water-soluble pieces that the cell wall
can absorb. Bacterial cells use nutrients for a variety of life-sustaining biochemical
activities known collectively as metabolism.

B1. Anabolism and Catabolism

The metabolic activities that enable the cell to function occur in two ways: anabolism and
catabolism. Simply put, anabolism is the manufacture of complex molecules from simple
ones, and catabolism is the breakdown of complex molecules into simple ones. Cells use
the energy from catabolism for all their other tasks, including growth, repair, and
reproduction.
A single bacterial cell takes up small molecules from the environment by means of
specific transport proteins in the cell membrane. In the case of more complex molecules,
such as proteins or complex carbohydrates, bacteria first secrete digestive enzymes into
the environment to break the nutrients down into smaller molecules, which are
transported across the membrane. Enzymes (proteins that speed chemical reactions)
within the cytoplasm then digest the molecules further. This breakdown, called
catabolism, results in energy transfer through the processes of respiration and
fermentation. During metabolism, some of the small molecules are converted into the
molecules the cell needs to synthesize (manufacture) its own proteins, nucleic acids
(building blocks of DNA), lipids (fatty substances), and polysaccharides (sugars and
starches). The metabolic processes for synthesis of these complex cells are anabolism.

B2. Adaptation to Environmental Stress

All organisms have some capacity to adapt to environmental stress, but the extent of this
adaptive capacity varies widely. Heat, cold, high pressure, and acid or alkaline conditions
can all produce stress. Bacteria easily adapt to environmental stress, usually through
changes in the enzymes and other proteins they produce. These adaptations enable
bacteria to grow in a variety of conditions. Gradual exposure to the stress, for example,
may enable bacteria to synthesize new enzymes that allow them to continue functioning
under the stressing conditions or that enhance their capacity to deal with the stressing
agent. Or they may resist environmental stress in other ways. Some bacteria that live in
extremely acidic conditions can pump out acid from their cell.
Extremophiles are organisms that can grow in conditions considered harsh by humans.
Some kinds of bacteria thrive in hydrothermal vents on the ocean floor or in oil reservoirs
within Earth, at high pressures and temperatures as high as 120oC (250oF). Other kinds
can live at temperatures as low as –12oC (10oF) in Antarctic brine pools. Other bacteria
have adapted to grow in extremely acid conditions, where mines drain or minerals are
leached from ores and sulfuric acid is produced. Others grow at extremely alkaline or
extremely salty conditions. Still others can grow in the total absence of oxygen. Bacteria
able to function in these extreme conditions generally cannot function under conditions
we consider normal.

B3. Reproduction and Survival

Bacteria reproduce very rapidly. Replication in some kinds of bacteria takes only about
15 minutes under optimal conditions. One bacterial cell can become two in 15 minutes,
four in 30 minutes, eight in 45 minutes, and so on. Bacteria would quickly cover the
entire face of the globe if their supply of nutrients was unlimited. Fortunately for us,
competition for nutrients limits their spread. In the absence of sufficient nutrients,
however, many bacteria form dormant spores that survive until nutrients become
available again. Spore formation also enables these bacteria to survive other harsh
conditions.

B3a. Binary Fission

The simplest sort of bacterial reproduction is by binary fission (splitting in two). The
bacterial cell first grows to about twice its initial size. Toward the end of that growth, the
cell membrane forms a new membrane that extends inward toward the center of the cell.
The cell wall follows closely behind, bisecting the cell. The membrane then seals to
divide the enlarged cell into two small cells of equal or nearly equal size, and a new wall
forms between the membranes.
The growth and division of a bacterial cell has two main phases. In one phase, the cell
replicates its DNA and makes all the other molecules needed for the new cell. The second
phase—cell division—occurs when DNA replication stops. In the bacterium E. coli
replication takes about 40 minutes and cell division lasts about 20 minutes. The entire
cycle takes about an hour. Yet the time for one cell to become two cells still takes only
about 20 minutes. How is this possible? The cell does not wait for one cycle of
replication to end before it starts another. Thus, a rapidly growing bacterial cell is
carrying out multiple rounds of replication at the same time.

B3b. Spore Formation

In response to limited nutrients or other harsh conditions, many bacteria survive by
forming spores that resist the environmental stress. Spores preserve the bacterial DNA
and remain alive but inactive. When conditions improve, the spore germinates (starts
growing) and the bacterium becomes active again.
The best-studied spores form within the bodies of Bacillus and Clostridium bacteria, and
are known as endospores. Clostridium botulinum spores cause deadly botulism
poisoning. Endospores have thick coverings and can resist environmental stress,
especially heat. Even boiling in water does not readily kill them. But they can be killed
by heating in a steel vessel filled with steam at high temperature and high pressure.
Endospores can live for centuries in their dormant state.
Some bacteria form other types of spores. These spores are usually dormant but not as
heat resistant or long-lived as endospores. Some aquatic bacteria, for example, attach to
surfaces and produce swarmer cells during division. The swarmer cell swims away to
attach to another surface and give rise to still more swarmer cells. Still other bacteria
survive by forming colonies made up of millions of cells that act in a coordinated way to
keep the organism alive.

B3c. Genetic Exchange

Bacterial cells often can survive by exchanging DNA with other organisms and acquiring
new capacities, such as resistance to an antibiotic intended to kill them. The simplest
method of DNA exchange is genetic transformation, a process by which bacterial cells
take up foreign DNA from the environment and incorporate it into their own DNA. The
DNA in the environment may come from dead cells. The more the DNA resembles the
cell’s own DNA, the more readily it is incorporated.
Another means of genetic exchange is through incorporation of the DNA into a virus.
When the virus infects a bacterial cell, it picks up part of the bacterial DNA. If the virus
infects another cell, it carries with it DNA from the first organism. This method of DNA
exchange is called transduction.
Transformation and transduction generally transfer only small amounts of DNA, although
bacterial geneticists have worked to increase these amounts. Many bacteria are also
capable of transferring large amounts of DNA, even the entire genome (set of genes),
through physical contact. The donor cell generally makes a copy of the DNA during the
transfer process so it is not killed. This method of exchange is called conjugation. DNA
exchange enables bacteria that have developed antibiotic-resistant genes to rapidly spread
their resistance to other bacteria.

IV. CLASSIFICATION AND STUDY OF BACTERIA

Scientists long had difficulty classifying bacteria in relation to each other and in relation
to other living things. Because bacteria are so small, scientists found it nearly impossible
to identify characteristic structures on or in the organisms that would help in
classification. For many years bacteria were considered to be plants and named according
to the botanical system of classification, by genus and species. For example, Escherichia
coli belongs to the genus Escherichia and to the species coli within that genus. The genus
name starts with a capital letter; the species name, with a small letter. Both are written in
italic letters. For convenience, people often use only the letter of the genus name, as in E.
coli, for example.
A. A New Classification System
The development of the field of molecular phylogeny in the 1970s changed our view of
bacteria. Phylogeny relates organisms through their evolutionary origins. In molecular
phylogeny, scientists look for similarities in the molecules of organisms to figure out
relationships. Initially, scientists looked at proteins, which are made up of long strings of
amino acids. They figured that if a particular protein in two organisms contained exactly
the same amino acids in the same order, then the two were very closely related or even
identical. If there were only a few differences, the organisms were closely related. The
more differences there were, the more distant the relationship would be.
Carl Woese, a microbiologist at the University of Illinois, discovered that it was easier to
work with nucleic acids, such as DNA and RNA. He found that the best molecules were
ribonucleic acid molecules from ribosomes (rRNA). Ribosomes are the biochemical
machines inside cells that coordinate the synthesis of proteins. It was relatively easy to
obtain rRNA, to identify its chemical building blocks known as nucleotides, and to
determine the order of the nucleotides in the molecule. Because rRNA shows relatively
little variation from one generation to the next, it proved to be an excellent tool for
determining evolutionary relationships.
Molecular phylogeny indicated that there are three major groups, or kingdoms, of
organisms. One kingdom, called Eukaryotae, consists of all organisms with a true nucleus
and includes all plants and animals. The two other kingdoms, called Archaea and
Eubacteria, consist of prokaryotic bacteria without a true nucleus. Archaea, or
archaeabacteria, were once classified with other bacteria and the two kingdoms share
many characteristics. Many of the archaea are extremophiles and can live in extremely
hot, salty, or acid environments, but so can many eubacteria.
The classification of bacteria into two kingdoms, a system proposed by Woese, is based
almost entirely on the structure of ribosomal RNA. But it appears to agree with other
findings regarding the basic structures of the organisms, their metabolism, and their
evolution.

B. Sequencing Bacterial DNA

Amazing advances in technology have enabled scientists to sequence the entire genome
of many bacteria—that is, identify the nucleotides that make up the DNA and the order in
which the nucleotides are arranged. This knowledge, and the sciences that have
developed around it, will enable scientists to harness the useful capabilities of bacteria in
agriculture, industry, and other fields and to develop new drugs. In one example,
scientists have turned bacteria into factories for producing the hormone insulin by
inserting human insulin-producing genes into bacteria. The insulin produced can be used
to treat human diabetes.
Insulin is a protein, and genes govern the production of proteins by a cell. The study of
protein production will help scientists understand the process of disease at a cellular level
and help them develop new means of combating diseases. As scientists study how
bacteria attach to and enter healthy cells, cause illness, and spread, they are learning
useful details about the molecular structure of cells.

V. EVOLUTION OF BACTERIA
The oldest fossils of bacteria-like organisms date back as many as 3.5 billion years,
making them the oldest-known fossils. These early bacteria could survive in the
inhospitable conditions when Earth was young, extremely hot, and without oxygen. With
the help of molecular phylogeny, scientists have pieced together a view of the evolution
of bacteria. They believe that the kingdoms Archaea and Eubacteria had a common
ancestor but separated very early on, a few billion years ago. Archaea may be the most
common organisms on Earth today. Many of them can live without oxygen and without
sunlight and inhabit such places as deep-sea vents. However, scientists currently know
much more about the kingdom Eubacteria than the kingdom Archaea, because humans
have more contact with disease-causing Eubacteria, such as streptococci and E. coli, and
with Eubacteria such as lactobacilli used in food processing and other industries.
Over time, bacteria evolved to capture energy from the Sun’s light and thereby carry out
the process of photosynthesis, converting sunlight into nutrients. Next they developed the
sort of photosynthesis that plants today carry out by splitting water molecules to produce
oxygen. With oxygen available, organisms that require it, such as animals, could inhabit
Earth.
Recent discoveries suggest that Eukaryotae (plants and animals) probably evolved from
Eubacteria. Many of the organelles (structures within the cytoplasm) of plant and animal
cells are actually bacterial. Among organelles derived from bacteria that invaded plant or
animal cells are mitochondria and chloroplasts. Mitochondria in plants and animals
convert nutrients into energy-storage molecules. Chloroplasts house the photosynthetic
machinery of plant cells. Not only do bacteria live on us and in us, but we ourselves are
in a way partly bacterial.

VI. SCIENTIFIC STUDY OF BACTERIA

Before the development of the microscope, some people speculated that small, invisible
particles caused diseases and fermentations. But not until the late 1600s did anyone
actually see bacteria. In the 1670s Dutch lens maker Antoni van Leeuwenhoek first saw
what he called “wee animalcules” under his single-lens microscopes. Leeuwenhoek
noticed cells of different shapes within a variety of specimens, including scrapings from
his teeth and rainwater from gutters. His findings laid the foundation for the growth of
microbiology.
The microscope was improved over the following centuries, but bacteria still appeared as
tiny objects, even with magnifications of 1,000 times. In the 1930s, the first electron
microscopes were developed. Using beams of electrons instead of light, these
microscopes could magnify objects at least 200 times more than light microscopes could.
With magnifications of 200,000 times actual size, it became possible to see structures
within bacterial cells in detail.
Early studies of bacteria were difficult. In any environment many types of bacteria
compete and cooperate, and all this activity makes it nearly impossible to figure out what
each organism is doing. The first step was to separate different types of bacteria. One
way of isolating bacteria was to grow them on a solid surface. Scientists first used kitchen
foods, such as a potato slice cut with a sterile knife, on which to grow bacteria that attack
plants. This method was not very convenient, however.
The perfect medium (environment) for growing bacteria also came from the kitchen,
although its usefulness was demonstrated in the laboratory of German scientist Robert
Koch. The medium was agar, a gel-forming substance that comes from seaweed. A
coworker of Koch’s noted that his wife’s puddings remained solid in summer heat,
whereas the gelatin on which he grew bacteria dissolved or got eaten by the bacteria. The
firm puddings contained agar.
Agar dissolves in water only at temperatures close to boiling. When it cools, it forms a
stable gel. Most bacteria cannot digest it. Bacteriologists could transfer a bacterial
specimen onto a plate of agar using sterile wires or loops, and obtain a colony of
organisms. If more than one type of bacteria formed a colony, the scientists could repeat
the process, growing each type on a separate agar plate to obtain a pure culture
(laboratory-grown specimen) for study. They could also add nutrients to agar to provide
the bacteria with the food they need for growth. In addition, they could add substances to
suppress the growth of unwanted bacteria but not the growth of those the bacteriologist
wished to isolate. Growing bacteria on agar has become routine in laboratories.
Bacteriologists have become accustomed to studying individual types of bacteria in pure
cultures. In nature, however, bacteria usually live in diverse communities, often with
hundreds of types of organisms. These communities form sticky masses called biofilms
on soil particles, ocean debris, plants and animals, and just about any solid or liquid
surface. In our bodies, biofilms develop on teeth, on the soft tissues of the mouth and
throat, on the membrane lining the nose and sinuses, in the gut, and on all other exposed
body surfaces. In nature, organisms form microbial mats on surfaces between water and
air. In sewage treatment, bacteria clump together in masses. All these communities are
highly diverse, harboring many kinds of organisms. They can be compared to cities in
which the different members have different functions, all important to maintaining the
community.
Bacteriologists are realizing more and more the need to move from studying pure cultures
containing only a single species to the study of communities in biofilms and microbial
mats. The growth of molecular biology and the capacity to study bacteria in molecular
detail have demonstrated that the bacterial world is far more diverse than previously
thought. It seems possible that we currently have discovered only a small fraction of
existing types of bacteria in the world. Perhaps as many as 95 percent of total types
remain unknown.
Scientists have already sequenced the entire genome for many bacteria. Researchers can
cut pieces from bacterial DNA and replicate it in many copies. Through DNA transfer,
the pieces can be inserted in bacterial cells. The cells with the new DNA may then start to
make new proteins they were unable to make previously. Thus, bacteria can be
genetically engineered to make a whole range of products and to develop new functions.
Genetic engineering has opened up a new world of biology and a tremendous opportunity
to explore bacteria and other microorganisms and to benefit humanity from the resulting
knowledge.

Contributed By:
Robert E. Marquis

Cyanobacteria
Cyanobacteria or Blue-Green Algae, members of a group of photosynthetic prokaryotes
single-celled organisms that lack an enclosed nucleus and other specialized cell
structures. Like green plants, cyanobacteria contain chlorophyll but the chlorophyll is not
located in chloroplasts; rather it is found in chromatophores, infoldings of the plasma
membrane where photosynthesis is carried out. In many species, other pigments mask the
chlorophyll and impart a bluish or sometimes reddish color. Some species are free-living,
but most aggregate in colonies or form filaments. Reproduction is by simple cell division
or by fragmentation of the filaments.
Cyanobacteria are found throughout the world in diverse habitats. They are abundant on
tree bark and rocks and in moist soil, where they carry on nitrogen fixation. Some
symbiotically coexist with fungi to form a lichen. In hot weather some species form large
and occasionally toxic blooms on the surfaces of ponds and coastal waters. In shallow
tropical waters, mats of the cyanobacteria grow into humps called stromatolites. Fossil
stromatolites are found in rocks formed more than 3 billion years ago, during
Precambrian time. They suggest that cyanobacteria played a role in changing the ancient
carbon dioxide-rich atmosphere into the oxygenated mixture that exists today.
Scientific classification: Cyanobacteria make up the phylum Cyanophyta, in the kingdom
Prokaryotae.

Microsoft ® Encarta ® 2006. © 1993-2005 Microsoft Corporation. All rights reserved.

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Senin, 30 Juni 2008

About Biology Science

1.1 The Process of Science

The statements made by Jake’s friends and family about what actions will help him
remain healthy (for example, his mother’s advice to wear a hat) are in some part based on
the advice-giver’s understanding of how our bodies resist colds.
Ideas about “how things work” are called hypotheses. Or, more formally, a hypothesis is
a proposed explanation for one or more observations. All of us generate hypotheses about
the causes of some phenomenon based on our understanding of the world (Figure 1.1).
When Jake’s mom tells him to dress warmly in order to avoid colds, she is basing her
advice on her belief in the fol lowing hypothesis: Becoming chilled makes an individual
more susceptible to becoming ill.

The hallmark of science is that hypotheses are subject to

rigorous testing. Therefore, scientific hypotheses must be testable—it must be possible to
evaluate the hypothesis through observations of the measurable universe. Not all
hypotheses are testable. For instance, the statement that “colds are generated by
disturbances in psychic energy” is not a scientific hypothesis, since psychic energy
cannot be seen or measured—it does not have a material nature. In addition, hypotheses
that require the intervention of a supernatural force cannot be tested scientifically. If
something is supernatural, it is not constrained by the laws of nature, and its behavior
cannot be predicted using our current understanding of the natural world.

Scientific hypotheses must also be falsifiable, that is, able

to be proved false. The hypothesis that exposure to cold temperatures increases your
susceptibility to colds is falsifiable, because we can imagine an observation would cause
us to reject this hypothesis (for instance, the observation that people exposed to cold
temperatures do notcatch more colds than people protected fromchills). However,
hypotheses that are judgments, such as “It is wrong to cheat on an exam,” are not
scientific, since different people have different ideas about right and wrong. It is
impossible to falsify these types of statements.

The Logic of Hypothesis Testing Of all the advice Jake

has heard, he is inclined toward that given by his lab partner. She insisted that taking
vitamin C supplements was keeping her healthy. Jake also recalls learning about vitamin
C in his Human Nutrition class last year. In particular, he remembers that:
1. Fruits and vegetables contain lots of vitamin C.
2. People with diets rich in fruits and vegetables are generally healthier than people who
skimp on these food items.
3. Vitamin C is known to be an anti-inflammatory agent, reducing throat and nose
irritation.
Given his lab partner’s experience and what he learned in class, Jake makes the following
hypothesis:
Consuming vitamin C decreases the risk of catching a cold. This hypothesis makes sense.
After all, Jake’s lab partner is healthy and Jake has made a logical case for why vitamin C
is good cold prevention. This certainly seems like enough information on which to base
his decision about how to proceed—he should start taking vitamin C supplements if he
wants to avoid future colds. However, a word of caution: Just because a hypothesis seems
logical does not mean that it is true. Consider the ancient hypothesis that the sun revolves
around Earth, asserted by Aristotle in approximately 350 B.C.This hypothesis was
logical, based on the observation that the sun appeared on the eastern horizon every day
at sunrise and disappeared behind the western horizon at sunset. For two thousand years,
this hypothesis was considered to be “a fact” by nearly all of Western society. To most
people, the hypothesis made perfect sense, especially since the common religious belief
in Western Europe was that Earth had been created and then surrounded by the vault of
heaven. It was not until the early seventeenth century that this hypothesis was falsified as
the result of observations made by Galileo Galilei of the movements of Venus. Galileo’s
work helped to confirm Nicolai Copernicus’ more modern hypothesis that Earth revolves
around the sun. So even though Jake’s hypothesis about vitamin C is perfectly logical, it
needs to be tested. Hypothesis testing is based on a process called deductive reasoningor
deduction. Deduction involves making a specific predictionabout the outcome of an
action or test based on observable facts. The prediction is the result we would expect
from a particular test of the hypothesis.
Deductive reasoning takes the form of “if/then” statements. Aprediction based on the
vitamin C hypothesis could be:
If vitamin C decreases the risk of catching a cold, then people who take vitamin C
supplements with their regular diets will experience fewer colds than people who do not
take supplements.
Deductive reasoning, with its resulting predictions, is a powerful method for testing
hypotheses. However, the structure of such a statement means that hypotheses can be
clearly rejected if untrue, but impossible to prove if they are true (Figure1.2). This
shortcoming is illustrated using the “if/then” statement above. Consider the possible
outcomes of a comparison between people who supplement with vitamin C and those
who do not: People who take vitamin C supplements may suffer through more colds than
people who do not, they may have the same number of colds as people who do not
supplement, or supplementers may in fact experience fewer colds. What do these results
tell Jake about his hypothesis?
If people who take vitamin C have more colds, or the same number of colds as those who
do not supplement, the hypothesis that vitamin C alone provides protection against colds
can be rejected. But what if people who supplement with vitamin C doexperience fewer
colds? If this is the case, should Jake be out proclaiming the news, “Vitamin C—A
Wonder Drug that Prevents the Common Cold”? No, he should not. Jake needs to be
much more cautious than that; he can only say that he has supported and not disproven
the hypothesis.
Why is it impossible to say that the hypothesis that vitamin C prevents colds is true?
Primarily because there could be other factors (that is, there are alternative hypotheses)
that explain why people with different vitamin-taking habits are different in their cold
susceptibility. In other words, demonstrating the truth of the thenportion of a deductive
statement does not guarantee that the if portion is true.
Consider the alternative hypothesis that frequent exercise reduces susceptibility to
catching a cold. Perhaps people who take vitamin C supplements are more likely to
engage in regular exercise than those who do not supplement. What if the alternative
hypothesis were true? If so, the prediction that people who take vitamin C supplements
experience fewer colds than people who do not supplement would be true, but not
because the original hypothesis (vitamin C reduces the risk of cold) is true. Instead,
people who take vitamin C supplements experience fewer colds than people who do not
supplement because they are more likely to exercise, and it is exercise that reduces cold
susceptibility.

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Beranda
Langgan: Entri (Atom)
Biodiversity
First published Wed Jun 11, 2003; substantive revision Tue Dec 4, 2007

“Biodiversity” is often defined as the variety of all forms of life, from genes to species,
through to the broad scale of ecosystems (for a list of variants on this simple definition
see Gaston 1996). "Biodiversity" was coined as a contraction of "biological diversity" in
1985, but the new term arguably has taken on a meaning and import all its own. A
symposium in 1986, and the follow-up book BioDiversity (Wilson 1988), edited by
biologist E. O. Wilson, heralded the popularity of this concept. Ten years later, Takacs
(1996, p.39) described its ascent this way: "in 1988, biodiversity did not appear as a
keyword in Biological Abstracts, and biological diversity appeared once. In 1993,
biodiversity appeared seventy-two times, and biological diversity nineteen times". Fifteen
years further on, it would be hard to count how many times "biodiversity" is used every
day by scientists, policy-makers, and others. The global importance of biodiversity now
is reflected in the widely accepted target to achieve a significant reduction in the rate of
loss of biodiversity by the year 2010 [see 2010 Biodiversity Target].

While the history of this term is relatively short (compare it to other terms covered in this
encyclopedia), it already has raised important, distinctive, philosophical issues. Some of
these are entangled in the very definition of "biodiversity", an issue treated in the first
sections below. A challenge is the reconciliation of process-based and elements-based
perspectives on biodiversity. Overall, the major issue for biodiversity is how its
conservation may be integrated with other needs of society.

• 1. Concepts of Biodiversity
• 2. From Species Values to Biodiversity Values
o 2.1 Species Values and Triage
o 2.2 Species as Equal Units and SMS
• 3. Alternatives to Unit-species
o 3.1 The Shift from Elements to Processes
o 3.2 Option Value and Hierarchy of Variation
• 4. Integrating Process and Elements Perspectives
• 5. Biodiversity and Growth of Knowledge
o 5.1 Phylogenetic Hypotheses
o 5.2 Species Hypotheses
o 5.3 Biodiversity and DNA barcoding
• 6. Conclusions
• Bibliography
• Other Internet Resources
• Related Entries

1. Concepts of Biodiversity
The sequel to that first biodiversity book, naturally titled Biodiversity II (Reaka-Kudla et
al. 1997), documents the rapid rise of the term "biodiversity" in importance and
influence. But it also traces the study of aspects of biodiversity back as far as Aristotle.
To some extent, biodiversity merely offers a new, emotive, term for some older ideas and
programs. In fact, "biodiversity" is now used sometimes to mean "life" or "wilderness" or
other conservation values. "Biodiversity" also has served on occasion as a catch-all for
"conservation" itself.

The scientific literature illustrates how most any conservation activity might use the label
"biodiversity". On the one hand, workers taking advantage of the acknowledged
importance of the term have expanded its meaning to capture concerns at a fine scale,
such as that focussing on a favourite single species. This focus might be referred to more
accurately as one of "biospecifics". At the coarser scale, one important interpretation,
discussed below, advocates a primary linkage of biodiversity to the maintenance of
ecosystem processes — what might be called the "bio-processes" approach.

The nub of the problem of defining biodiversity is that it is hard to exclude anything from
a concept that is taken so easily to mean "everything". Sarkar (2005) has argued that
interpreting biodiversity across all biological levels, from genes to ecosystems, amounts
to considering all biological entities, so that biodiversity absurdly "becomes all of
biology".

Callicott et al. (1999) examined "biodiversity" as one of the current normative concepts
in conservation. They concluded that it remains ill-defined, and that distinctions can be
made between "functional" and "compositional" perspectives in approaching biodiversity.
"Functional" refers to a primarily concern with ecosystem and evolutionary processes,
while "compositional" sees organisms as aggregated into populations, species, higher
taxa, communities, and other categories. Callicott et al. call for a better integration of
these different perspectives, an issue discussed below in the section on Integrating
Process and Elements Perspectives.

Norton (1994) has argued that there will never be a single "objective scientific definition"
of biodiversity, in the sense of a prescription for how to measure it. In fact, Norton claims
that any increase in our understanding of biodiversity will make it less likely that there
will be a single objective measure. This biodiversity pluralism is based on an argument
that inevitably there are many different "theory bound" versions of biodiversity and many
different ways to value it. This perspective is in accord with recognition of functional-
compositional perspectives on biodiversity. For example, Norton (1994; 2001) points to
recent emphasis on structure and process regarding ecological "health" or "integrity" that
is seen as going beyond a conventional elements-oriented perspective for biodiversity.
One cannot aggregate all these different versions of biodiversity. Instead, we are to
"describe in ways appropriate given certain purposes" and the choice among these
different biodiversity "models" will depend on what values are important to the decision-
maker.
This perspective is characterized as "post-positivist" because it recognizes biodiversity as
inevitably value-laden — there is no one, correct, measure of biodiversity to be
discovered but many, each having different values. Roebuck and Phifer (1999) lament
what they perceive as current "positivism" in biodiversity conservation, described by
them as based variously on processes of verificationism and falsificationism in seeking
facts. They argue that biodiversity conservation is rooted primarily in ethics and we must
not continue to back away from values and advocacy.

The idea that the choice of a measure of biodiversity depends on values finds support in
Sarkar (2005). He argues that biodiversity operationally amounts to whatever is the
valued target of conservation priority setting for different localities.

Biodiversity may be a catch-all for various aspects of conservation, but the fresh
perspectives arising from recognition of "biodiversity" suggest possible unifying
concepts. E. O. Wilson (1988) sees "biodiversity" as corresponding to a dramatic
transformation for biologists from a "bits and pieces" approach to a much more holistic
approach. Wilson describes this change in perspective as a realization that biological
diversity is disappearing and, unlike other threatened things, is irreversible. Wrapped up
in the term therefore is the idea of a "biodiversity crisis". Ehrenfeld (1988) similarly
reinforces this idea of the value of diversity in the aggregate. He argues that diversity
previously was never regarded in itself to be in danger, but that biodiversity now is
recognised as endangered in its own right. Wrapped up in the term therefore is the idea of
a "biodiversity crisis". While the case for such a crisis itself raises debates about
measures and definitions (see Sarkar, 2005), the definition of "biodiversity" sometimes
explicitly reflects these links to an extinction crisis. Takacs (1996) reviews cases where
the definition of biodiversity is wrapped up in the idea of strategies needed to preserve
variation. In accord with this perspective is a shift to a focus on valuing ecosystem
processes. This focus arguably will ensure maintenance and ongoing evolution of these
systems, and therefore all of biodiversity.

Holistic perspectives on biodiversity have emerged also through another important focus.
For Wilson (1988), biodiversity captures the idea of a "frontier of the future", presenting
a dazzling prospect of largely unknown variety, with unanticipated uses. Biodiversity is
seen by many as a symbol for our lack of knowledge about the components of life's
variation, and their importance to humankind (see Takacs 1996). These arguments
suggest that core biodiversity values might be based more on what we do not know than
what we do know. Biodiversity can be viewed as primarily capturing the two-fold
challenge of unknown variety, having unknown value.

Anticipated future uses and values of the unknown are captured in the idea of "option
values" (for definitions, see World Conservation Union 1980). A species, or other
element of biodiversity, has option value when its continued existence retains the
possibility of future uses and benefits. Option value corresponds not just to unknown
future values of known species, but also to the unknown values of unknown species (or
other components of variation). This concept is at the core of biodiversity because it links
"variation" and "value". Estimating and quantifying the largely unknown variation that
makes up biodiversity is one and the same as quantifying corresponding option values of
biodiversity. According to this emphasis, a basic definition of biodiversity might be
expanded as: the variety of all forms of life, from the scale of genes through to species
and ecosystems …so forming a "calculus" — a means for measurement and comparison
— of option values.

Focussing on this important aspect of biodiversity does not throw away the other possible
"biodiversity" values that might be listed (process-based "resilience" of ecosystems,
current commodity values of species, etc.), but facilitates integration of biodiversity's
option values with those other values. These possibilities are discussed further in the
section on Integrating Process and Elements Perspectives.

Given that holistic approaches may integrate functional and compositional aspects, the
following sections address these different biodiversity perspectives. The next section
addresses the early attempts to address values of biodiversity as a whole that emerged
from dissatisfaction with the "bits and pieces" focus on individual species. A later
section, Alternatives to Unit-species, presents attempts to address some weaknesses of
this initial approach.

2. From Species Values to Biodiversity Values

2.1 Species Values and Triage

In developing ideas about the overall value of biodiversity it has been natural to draw on
existing arguments about values of individual species (for review, see World
Conservation Union 1980; Norton 1988). Commodity value and other direct use values
have intuitive appeal because they reflect known values. But a key problem is that
species need to be preserved for reasons other than any known value as resources for
human use (Sober 1986). Callicott (1986) discusses philosophical arguments regarding
non-utilitarian value and concludes that there is no easy argument to be made except a
moral one. Species have some "intrinsic value" — reflecting the idea that a species has a
value "in and for itself" (Callicott 1986, p.140) — and there is an ethical obligation to
protect biodiversity.

A philosophical issue is whether such species values depend on a human-centered

perspective. The environmental ethics entry notes that assessments of issues concerned
with biodiversity allow for "commitment either to a purely anthropocentric or purely non-
anthropocentric ethic". Regan (1986) argues that we need "duties that are independent of
out changeable needs and preferences." Callicott (1986) sees the intrinsic value of species
as not independent of human values, because such values can be linked to Hume's theory
of moral values. Norton (1986) sees all species as collectively embraced by an
environmental ethic that is anthropocentric.

Randall (1988, p. 218) has argued that preference is the basis for value and that it is
possible to treat all species values as preferences of humans. Preferences-based
approaches to valuation can provide economic (dollar) estimates of value. This valuation
process may include methods for assessing and quantifying option values. A claimed
advantage of such approaches is that the only good way to protect species is to place an
economic value on them. Randall argues that such quantification is advantageous because
the species preservation option will fare well when the full range of values is included in
conservation priority setting.

The context for many of these arguments has been a consideration of various criteria for
placing priorities among species for conservation efforts. These considerations have led
to debates about the role of "triage" based on species prioritization. Triage recalls the
medical context in which priorities are set for investments in saving patients. Applied to
conservation, individual species are differentially valued and assessed relative to
differential opportunity costs. The best conservation package is to be found through a
process of calculating costs and benefits of protection of individual species.

2.2 Species as Equal Units and SMS

Many biologists have rejected the idea of triage and argue that we must try to save all
species (Takacs 1996). Philosophical issues arise in the debate as to whether biodiversity
should be approached through the process of differentially valuing species, so that
choices could be made in the face of a budget, or regarding species as the fundamental
unit and trying to protect them all. The latter option is arguably more holistic and in
accord with a focus on all of biodiversity (the individual species focus is sometimes
viewed as the first of three phases of growth in biological resources assessment; see the
section on The Shift from Elements to Processes).

If one nominated a "prequel" to Biodiversity (1988) it might be The Preservation of

Species (Norton 1986). The title suggests a species focus, but the book's subtitle refers to
biological diversity. This book documents an attempt to move from values of species to
some overall value of biodiversity, rejecting typical triage arguments based on benefits
versus costs for individual species. Here, Norton criticizes the "benefit — cost"
approaches as piecemeal because every species must exhibit actual or potential use to
justify itself. He argues that every species arguably has utilitarian value and that species
perceived values are hard to estimate. For this reason, trying to place dollar values is
"doomed to failure" (1986, p. 202). Norton concludes that we can't try to sum up values
(in accord with his general advocacy of no aggregation of biodiversity values). It is
argued that we should abandon the "divide and conquer" approach and look at total
diversity, with species as a unit: "each species in an area can be viewed as a unit of total
diversity." Ehrenfeld's (1988) position is even more sharply defined: "value is an intrinsic
part of biodiversity; it does not depend on the properties of the species in question."

This perspective demands some alternative to species-based triage that will still
accommodate the reality of limited resources. The idea of a "safe minimum standard"
(SMS) for biodiversity has been proposed as a suitable alternative to triage. Norton
advocates an SMS based on unit-species, interpreted to mean that all species are saved
unless costs are intolerable; he argues for "preservation of species as a general policy".
Wilson (1992, p. 310) also has advocated an SMS in which all species are to be protected
unless costs are too high. He argues that we "treat each as an irreplaceable resource for
humanity". This is directly in preference to a cost-benefit approach, characterized as
examining single species and their properties and deciding how much to invest.

The SMS leaves the idea of "too high a cost" open to different interpretations. These vary
with philosophical perspectives about the nature of values. For example, "deep ecology",
where biodiversity is independent of human value, responds differently to
"utilitarianism", where biodiversity might be preserved to extent that measurable benefits
to humans exceed costs (see The Preservation of Species). Randall's (1986, p. 103)
utilitarian position considers intrinsic or option value of unit-species in conjunction with
any recognized utilitarian value: all species not already distinguished in having
recognised human-use values "would be treated as having a positive but unknown
expected value; implicitly all would be treated as equally valuable."

Despite difficulties in actual implementation, the ideal of an SMS based on species as

units of biodiversity has remained popular from the 1986 The Preservation of Species
through at least to Takacs' review (1996). In the latter book, objections to attempts to
differentiate and prioritize among species are extended to take into account approaches
developed in the early 90's that quantify taxonomic distinctions among species. These
methods address the idea that a species that is taxonomically (or phylogenetically)
distinctive may deserve a higher priority for biodiversity conservation (see World
Conservation Union 1980). Takacs (1996; p. 61) cites early proposals of this kind for a
"calculus" of biodiversity, and objects to the resulting "intricate" calculations to prioritize
species based on taxonomic distinctiveness. He claims that "we can avoid tedious
mathematical calculations of relative species value by switching to biodiversity". Takacs
joins others in arguing that we do not know enough about species to assign different
values (for further review, see Faith 1994). As an alternative to such a triage approach, an
SMS-style approach again is advocated based on the number of unit-species saved within
a budget.

In conclusion, the SMS is compatible with an all-of-biodiversity perspective that views

species collectively, avoiding the seemingly arbitrary "bits and pieces" approaches to
individual species priorities that arguably are poorly justified given our poor knowledge.
The SMS approach, however, arguably suffers from a double-barrelled arbitrariness of its
own, in the choice of a level of variation (species) and the choice of a threshold on costs.
Alternative approaches are considered in the next section.

3. Alternatives to Unit-species
We can recognize two alternatives to the use of species as equal-weight units for an SMS.
One of these (see the section on The Shift from Elements to Processes) consciously
moves further away from units or items of any kind. Here, the valuation of species is seen
as problematic, with arbitrary solutions. Valuation is to encompass all of biodiversity but
through a functional perspective, shifting the focus to ecosystems processes (Norton
1994, 2001).
The other alternative [see the section on Option Value and Hierarchy of Variation] might
be viewed as going to the other extreme. Units or elements of biodiversity are seen (at
least implicitly) at every level of biological variation, and the quantification of variation
is to provide relative valuations (e.g. of different places) for priority setting.

These two perspectives provide different responses to the issues concerning taxonomic
distinctiveness valuations on species — so providing one benchmark for comparisons. In
the ecosystem processes case, this has provided a prototype example of problems with
attempts to value species-units. In the hierarchical variation case, it has provided a
prototype example of the quantification of unknown variation and option value at one
nominated scale of biodiversity.

3.1 The Shift from Elements to Processes

Norton (2001) summarizes the development of the process perspective on biodiversity by

describing three phases of growth in "biological resources" conservation over the past
years. The first was the focus on individual species. The second phase was a
"problematic" perception of biodiversity as all about protection of "objects" — merely
expanding the list of "items" from the first phase. Here, Norton (2001) objects to an
"atomistic" bias of western culture towards objects. He argues that biodiversity has been
wrongly focussed on "inventory" of species, genes, ecosystems and has neglected
processes that create and maintain natural values. This inventory perspective is described
as "static", not dynamic (see also Frankel and Soule 1981; Takacs 1996).

Norton argues that the inadequacy of this second phase, being "ill-suited" to an emerging
process orientation, has lead to the third phase based on ecosystem processes. Here,
values are not to be attached to objects; instead, we should value (or "abhor") processes.
This approach is characterised as more dynamic in its perspective, as systems oriented,
and therefore more "holistic". The focus is on maintaining functions of healthy
ecosystems, such as provision of clean air and water. This process orientation is
compatible with much recent work internationally on ecosystem services [Takacs 1996;
Millennium Ecosystem Assessment].

The term "biodiversity" is used in this context largely as an assumed foundation for
ecosystem processes. Norton (2001) sees the process focus as replacing, not
complementing, the "increasingly obsolete" inventory/items perspective of biodiversity,
arguing that we "will likely move away from the inventory-of-objects approach
altogether". The processes perspective is to determine how we look at biodiversity: "…
applied to biodiversity policy, we can focus on the processes that have created and
sustained the species and elements that currently exist, rather than on the species and
elements themselves" (2001; p. 90). Further, "it is reasonable to interpret advocates of
biodiversity protection as valuing natural processes for their capacity to maintain support
and repair damage to their parts" (2001; p. 91).

Related arguments are found in the advocacy of "biological integrity" (Karr 1991), in
preference to biodiversity, as a focus for conservation management. Biological integrity
is primarily concerned with the persistence of biogeographic, evolutionary, and
ecosystem processes, such as those relating to energy flows. For Angermeier and Karr
(1994), "integrity is reflected in both the biotic elements and the processes that generate
and maintain those elements, whereas diversity describes only the elements." They
conclude that "resource policy would be most effective if based on the more
comprehensive goal of protecting biological integrity." Biological integrity is discussed
further in the section Integrating Process and Elements Perspectives.

3.2 Option Value and Hierarchy of Variation

The other alternative to the unit-species approach departs from it by increasing not
decreasing our focus on items or elements. The unit-species perspective has been justified
through option values and a response to a lack of knowledge — we do not know enough
to differentially value species. But consideration of option values also has been used to
justify a move away from a species-as-units approach, to embrace a whole hierarchy of
possible units. Suppose, for example, that the units of interest are features of species (a
feature might be some morphological characteristic shared by all members of that
species). These features in general have unknown future values. It follows that total
option value would be increased by having more features protected. If we apply the
rationale that all these features should be treated as units of equal value, then some
species (those that are phylogenetically distinctive; see below) will make larger
contributions to the overall feature diversity represented by a set of species. thus, equal
value at the fine scale among features leads to differential values at the coarse scale
among species. We see that the same argument used to justify species as equal-value
units can be used to justify differential valuation of species (Faith 1994).

Feature diversity can provide a basis for valuation, but it raises measurement challenges.
Not only do we not know, in general, the future value of different features, but also we
cannot even list the features for most species. Phylogenetic pattern provides one way to
estimate and quantify variation at the feature level. A species complements others in
representing additional evolutionary history (Faith 1994), as depicted in the branches of
an estimated phylogeny. The degree of complementarity reflects the relative number of
additional features contributed by that species. For example, given some subset of species
that are well-protected, and two species in that taxonomic group that are endangered, the
priority for conservation investment may depend on the relative gains in feature diversity
(the complementarity values) expected for each species. We do not know in practice what
all the actual features are, but can make a prediction about relative gains and losses. The
predicted total feature diversity of a set of species is referred to as its "phylogenetic
diversity" (PD; Faith 1994).

In practice, PD calculations may be integrated with species' estimated extinction

probabilities ("probabilistic PD"; see Witting and Loescke, 1995). Priorities for
conservation efforts for endangered species then can respond to both threat and the
potential loss of PD. One such conservation program, attracting much attention, is the
EDGE program (“evolutionarily distinct and globally endangered”; for discussion see
Faith (2007)).
A nice illustration of the contrast between biodiversity assessments at the species and
features levels is found in the recent study of Yesson and Culham (2006). They showed
that, while many cyclamen plant species are likely to be impacted by expected climate
change, the expected loss of cyclamen PD nevertheless would be relatively low. The set
of cyclamen species resistant to climate change would retain high PD because they are
dispersed throughout the phylogenetic tree. Such a potential retention of feature diversity,
and corresponding evolutionary potential (for discussion, see Forest et al., 2007),
suggests that future climate change impacts studies may focus on PD as an important
complement to species-level studies. This link from option values to processes is
discussed further below in the section Integrating Process and Elements Perspectives.

This phylogenetic diversity perspective can be reconciled with the rejection (Takacs
1996) of "intricate" calculations of phylogenetically based valuations of species. Some
proposed taxonomic distinctiveness methods indeed simply have been species-based
attempts to assign differential values. But when the focus is on biodiversity units at a
lower level, it is not an attempt to apply differential values to species as fundamental
units of biodiversity, but equal values to those lower-level units. The focus on these units
rather than conventional species is highlighted by the fact that for subsequent priority
setting on places, species sometimes are ignored altogether (Faith 1994). We return to
this issue below, in discussing ways to side-step contentious species designations in DNA
barcoding (see the section on Biodiversity and DNA barcoding).

A conclusion is that a taxonomic/phylogenetic distinction among species is not a fruitless

distraction from "biodiversity" — it is all about biodiversity. Features of species
quantified in this way are just one part of a whole hierarchy of variation. Sarkar and
Margules (2002) emphasize that, when we speak of genes, species, and ecosystems, it is
not that these form the specific entities of interest but instead are benchmarks for the full
hierarchy of variation: "there is heterogeneity at every level" (2002, p. 301).

The value of all of biodiversity is in this full hierarchy of variation — measuring one
measures the other. These values may also encompass intrinsic values of biodiversity.
Callicott (1989) and others have followed Aldo Leopold's (1949) work in arguing that all
levels of biological organization (species, biotic communities, ecosystems) have intrinsic
value. This suggest that any calculus of relative option values (indicating relative value
contributions made by species, places, etc) is also a calculus of relative intrinsic values.

For conservation priority setting, each new place (for example) adds some biodiversity to
the total for a set of places. This open-endedness means we must consider costs; there is
no possible policy position that can ask to "save all the pieces". However, this
comparison among places is arguably made easier also because we only require
complementarity — marginal gains in variation — rather than total amounts. Sarkar and
Margules (2002, p. 302) argue that, if we are considering conservation actions in different
places, then "an absolute concept or measure of biodiversity is not needed," and "the
relative concept of biodiversity built into the definition of complementarity has the level
of precision needed to undertake conservation planning."
This perspective, while useful, may be too narrow. Sarkar and Margules (2002) describe
biodiversity as rooted in place, but this is just one scale of decision making. We can apply
the same complementarity principle to species not places, as in the example of
complementarity values at the underlying feature level estimated from phylogenetic
pattern (a general conceptual model for complementarity at different levels of
biodiversity is found in Faith 1994).

Sarkar and Margules describe the use of a relative concept of biodiversity based on
complementarity as "philosophically uncharted territory." At issue are the empirical and
"conventional" elements involved in estimating complementarity values. These issues are
addressed in the section on Biodiversity and Growth of Knowledge.

An appealing property of unit-species approaches was that quantification of option values

allowed the political process to balance these with other values of society. A full
hierarchical perspective suggests a continuum of variation rather than a countable number
of objects. The relative complementarity value (say, of a place) is not the relative number
of different species but the relative amount of the hierarchy of variation gained in that
place. Thus, quantifying complementarity values provides the ability to balance these
with other kinds of values, through the political process and the use of tools such as
multi-criteria analyses [e.g., see A Biodiversity Conservation Plan for Papua New Guinea
Based on Biodiversity Trade-offs Analysis] that work with values naturally expressed in
different measurement units. This capacity potentially helps integrate option values with
process-based values, as discussed in the next section.

4. Integrating Process and Elements Perspectives

The functional/process (see the section on The shift from Elements to Processes) and
elements/inventory perspectives (see the section on Option Value and Hierarchy of
Variation) each try capture all of biodiversity, but have different emphases. Consideration
of biodiversity option/intrinsic values will not in general capture all important
considerations about processes. Also, taking processes into account will not always
capture option values defined at the level of elements. Here, the danger in ignoring
elements-option values is that priority-setting and management in a given place may be
able to address ecosystem resilience and other process goals, but still also allow loss of
components of biodiversity of global value.

The two alternatives, presented as dichotomous above, may be viewed as partly

overlapping, and not mutually exclusive. An option value approach based on units does
not neglect process. The descriptor, "static", has been used to describe this so-called
"inventory" approach (e.g. Norton 2001), with clear negative connotations relative to the
desirability of "dynamic" approaches. But the biodiversity measures based on phylogeny,
for example, capture evolutionary processes that support future variation. Consideration
of a hierarchy of elements of biodiversity can be expected to include diversity of
processes (following Noss 1990; but see Angermeier and Karr 1994). Further, "static"
entities of biodiversity typically are protected using dynamic approaches to biodiversity
conservation, as in methods that set conservation priorities on different places taking
climate change into account. Such links between what we protect and how we protect it
suggest that concerns about biological integrity (see the section on The Shift from
Elements to Processes) may be reconciled with biodiversity goals. Management focussed
on biological integrity will be critical for the persistence of biodiversity in those places
recognised as having high complementarity values.

While process considerations clearly support biodiversity conservation, the maintenance

of option values based on elements of biodiversity also ensures processes and services.
For example, Turner (1999), using the similar term "insurance value" rather than "option
value", observes that "the number of species … serves as a valuable index of ecosystem
reliability. These results support the hypothetical ‘insurance’ value of biodiversity, that is,
insurance against the failure of ecosystems to provide goods and services." This is one
way in which biodiversity option or insurance values apply at the "local" scale.

The perception of conflict between process and elements perspectives appears sometimes
as a tension between global and local aspects of biodiversity. For example, Vermeulen
and Koziell (2002) see global biodiversity values as ignoring important local values of
biodiversity, relating to ecosystem services. They argue that treating biodiversity as one
composite property corresponding to global values is not helpful, and is a consequence of
the fact that "the global consensus is that of wealthy countries" (2002, p. 89). They
recommend the consideration of biodiversity in terms of services derived from it, and not
as an end in itself. Thus, the claim is that "the most useful biodiversity assessments are
those based locally" (2002, p. 83).

An alternative to a proposed preference for local values of "biodiversity" is to pursue

balanced trade-offs (and synergies) among local and global values. As long as local
values and opportunities, whatever their source, are given weight in these trade-offs,
there is no need to try to define (or re-define) the "important" values of biodiversity as
local not global. Apparent conflict is resolved also by realizing that often the local values
and opportunities have little to do with the biodiversity (biotic variation per se) of the
place (though they typically will link to its "biospecifics").

A trade-offs perspective based on complementarity suggests that there is good capacity

for balancing different values in setting priorities in a given region. Every place has
biodiversity, but its contribution to the global option values of biodiversity is indicated by
its complementarity value, not its total diversity. It is the comparison of the place's
current complementarity value to the other values/opportunities in that place that matters
when considering trade-offs at a regional scale. There may be apparent high conflict in a
region, in that places with high biodiversity have high values for some other land use
opportunity, but in such cases the region may well be able to satisfy both needs. Trade-
offs applications based on complementarity have suggested that other values can be
integrated without much penalty to biodiversity goals [an example is A Biodiversity
Conservation Plan for Papua New Guinea Based on Biodiversity Trade-offs Analysis].
The Millennium Ecosystem Assessment [Millennium Ecosystem Assesment web pages]
emphasized trade-offs of this kind to find a balanced provision of the various ecosystem
services provided by the world's ecosystems. The assessment also called for further work
on developing a calculus of biodiversity, so that these trade-offs approaches could
integrate the biodiversity gains from a wide range of conservation instruments (protected
areas; payments to private land owners; control of invasive species, etc.)

Recent work has suggested that the most effective pathway to achieving the 2010
biodiversity target for a significant reduction in the current rate of biodiversity loss [see
2010 Biodiversity Target] is to find balanced trade-offs and synergies between
biodiversity and other needs of society. (See “Actions for the 2010 biodiversity target in
Europe: How does research contribute to halting biodiversity loss?”) The Global
Biodiversity Information Facility (GBIF) has a major campaign to address the 2010
target, based on mobilising extensive museum species collections data to form the
biodiversity calculus needed for exploring trade-offs and synergies in different regions
[see GBIF 2010 Campaign]

In conclusion, a possible resolution of the conflict between elements-based and

processes-based interpretations of biodiversity may be part operational, part conceptual.
Operationally, trade-offs processes can balance different values, whatever their labels.
Conceptually, biodiversity may retain its original connotation of biotic variation at all
levels. This does not deny that attention to processes is a good way to protect
biodiversity, nor that ecosystem services represent important values of society, including
provision of resources. It is interesting that Takacs (1996) points to Ehrenfeld and others
as making early attempts to move beyond the "resource" school in valuing biodiversity as
a whole. Yet Norton (2001) and others, in linking "biodiversity" to maintenance of
ecosystem processes, move back to the resource perspective — as evidenced in Norton's
reference to three phases of "biological resources", not "biodiversity", protection.

An earlier section (Concepts of Biodiversity) referred to a call for "post-positivism" and

greater focus on advocacy in the context of a biodiversity concept seen as properly value-
laden. Such a perspective has some compatibility with trade-offs; advocacy and society's
values may determine how well biodiversity conservation fares in the course of trade-
offs. But a "new positivism" may be required also, in trying to better estimate and
quantify unknown aspects of biodiversity in order to better inform the inevitable trade-
offs processes. The final section of this SEP entry addresses this problem of growth of
knowledge, which itself has raised philosophical issues.

5. Biodiversity and Growth of Knowledge

The sections above highlighted the role of complementarity — the additional contribution
made by a place (or other entity, such as a species) to the overall representation of the
hierarchy of variation that makes up biodiversity. But the true biodiversity
complementarity of a place inevitably is unknown and must be estimated using some
known, "surrogate", information. We may not know enough in a particular case to
consider surrogates that are to reflect a fine scale of variation. For example, at a whole
country scale, to a first approximation all species may be judged equal in comparing
biodiversity contributions of different places. A whole country study may not focus
directly on variation at the genetic or even species scales, but might use ecosystem types
or similar as the surrogates to assess representativeness of its protected areas system. If
the assessment reveals that a whole ecosystem type is not represented, then this directs
priorities for land acquisition. If all types are already represented, then variation within
these can be the focus, perhaps as indicated by representation of species.

Sarkar and Margules (2002) discuss the role of biodiversity surrogates, arguing that even
the relative concept of complementarity has a "conventional" element built into it because
it relies on "estimator" surrogates (say, a set of butterfly species) for "true" surrogates
(say, the use of species as the basis for assessing complementarity of places). Whereas
estimator surrogates, they argue, are subject to empirical justification, true surrogates are
still dependent on convention. They defend this conventional element: "a philosophical
point, widely appreciated by philosophers of science, but often not explicitly
acknowledged by scientists, deserves to be noted in relation to this: conventional
elements almost always enter into theoretical reasoning in science (Nagel 1961; Sarkar
1998). But ‘conventional’ does not mean ‘arbitrary’: it means that there were choices to
be made, no single option was dictated by the facts at hand, and a choice was justified
instrumentally by its ability to achieve the purpose for which it was intended" (2002, p.
307).

The empirical approaches for determining effective "estimator" surrogates for

biodiversity have raised philosophical issues as well. There are plenty of observations
about the congruence (or not) of surrogates with other components of biodiversity (for
review, see Faith 2003), but what constitutes good evidence for an effective biodiversity
surrogate?

Popperian corroboration provides one pathway to assess evidence for such hypotheses.
Corroboration is attractive because it does not attempt to assign probabilities of truth to
hypotheses (Popper 1982, p. 346), but instead focuses on the evaluation of the particular
evidence at hand. Proposals have focussed on the idea that corroboration assessment asks
whether apparent good evidence for an hypothesis is "improbable" without the hypothesis
— it cannot easily be explained away by other explanations (possible explanations
suggested by our "background knowledge"). Popperian background knowledge is
assigned an important role in this interpretation — the investigator is obligated to try to
discover any background knowledge that would suggest that the evidence is probable
even without the hypothesis (for discussion, see Faith and Trueman 2001; Faith 2006).

The interest in the role of corroboration in biodiversity studies has prompted debates
about its role and meaning. As background to these issues, it is revealing to examine one
of Popper's own examples of falsification/corroboration, as presented in the entry on Karl
Popper. This example, based on the discovery of the planet Neptune, effectively
highlights the limited prospects for actual falsification, but may be under-appreciated as
an example of corroboration. The hypothesis of interest in this example is Newton's
theory, and the evidence is the observation of the new planet, in a position predicted by
this hypothesis. Popper (1982, p. 247) argues that "a moving star, planet, would have
been significant, because unexpected." Popper argues, "the unexpectedness of an event
can be identified with a low probability, in the sense of the calculus of probability, on the
background knowledge" and that the "predictions which lead to the discovery of Neptune,
were such a wonderful corroboration of Newton's theory because of the exceeding
improbability that an as yet unobserved planet would, by sheer accident, be found in that
small region of the sky where their calculations had placed it". Corroboration was
achieved because "the success of the prediction could hardly be due to coincidence or
chance".

This example supports the idea that Popperian corroboration for a biodiversity hypothesis
arises only if the evidence is judged to be improbable — in spite of attempts to identify
background knowledge that suggests that the evidence is probable even without the
hypothesis. For biodiversity surrogates, a common hypothesis is that the pattern of
species "turnover" over different geographic areas for one taxonomic group will indicate
the pattern for all biodiversity. Good evidence for the surrogacy hypothesis is typically
claimed when the pattern for the surrogate taxonomic group is congruent with that of
some target set of taxa. However, on many occasions such evidence can be explained
away as probably arising simply because of a shared bias in the geographic sampling of
the surrogate and target taxonomic groups (for review, see Faith 2003). The evidence
based on congruence can be explained away as a probable result even without the
hypothesis. Based on such evidence, corroboration for the surrogacy hypothesis is low.

The following sections address the potential role of such corroboration assessments in
two other areas of biodiversity assessment: phylogenetic inference and species inference
(discussion of corroboration assessment in the context of biodiversity monitoring can be
found in Downes et al. 2002). The section, Biodiversity and DNA barcoding, then links
all these issues to the controversies surrounding an emerging area of biodiversity
assessment, called “DNA barcoding”.

5.1 Phylogenetic Hypotheses

The problem of inferring phylogenetic patterns within a taxonomic group from character
data has long raised philosophical issues. Popperian falsification has been used to argue
for the justification of one inference method over others (one out of many ways of
measuring goodness-of-fit of characters to phylogenetic trees is claimed as uniquely
capturing the idea of falsification; for review, see Faith and Trueman 2001). An
alternative perspective is that Popperian corroboration embraces all inference methods in
phylogenetics. In this interpretation, the Popperian evidence for a phylogenetic tree
hypothesis is a measure of the goodness-of-fit (as defined by any given inference
method) of observed character data to that hypothesis. Degree of corroboration of a
phylogenetic tree hypothesis is given by improbability of that goodness-of-fit — that is,
the difficulty in explaining fit that good by other factors, including elements of chance,
that make up our "background knowledge". This reflects the obligation to try to explain-
away evidence through identification of some background knowledge that implies that
the evidence was probable anyway (Faith and Trueman, 2001; Faith, 2006). The goal of
the search is a high probability of the evidence given only background knowledge, even
while the desired outcome may be a low probability.
5.2 Species Hypotheses

Testing an hypothesis that a set of populations is a single species is important to

conservation management. Also, sets of recognised species often form the basis for
surrogates for geographic priority setting. Corroboration may play a role in the ongoing
debates about the definition of a species and how species status is to be determined. The
entry on species discusses the issue of species pluralism — the idea that there is not just
one correct species concept. While twenty or more different concepts have been
identified (some based on a designated species discovery process), a possible emerging
consensus (e.g. see Claridge et al. 1997; Mayden 1997) is that all of these may be unified
under an evolutionary lineage concept. This is based on the idea of an evolutionary
species, defined as: "a single lineage of ancestor-descendant populations which maintains
its identity from other such lineages and which has its own evolutionary tendencies and
historical fate." (Wiley 1981, p. 25).

This "primary" concept arguably is compatible with most other proposed species
concepts (for discussion, see Mayden 2002). However, a difficulty is that this seems to
simply produce many so-called "secondary concepts", corresponding to all the previously
proposed ways of detecting and/or defining species. For example, Mayden (1997) refers
to these as "operational concepts" that are "tools" for discovering all the different ways to
realize the primary concept. The unconstrained use of these tools suggests a "grab-bag"
that amounts to reliance as much as ever on expert opinion. An issue therefore is whether
a unified species concept can be matched by some unified operational framework for
identifying species. Mayden (2002) does claim that there is Popperian "testability" and
possible "falsification" for species hypotheses. He argues that the typical process is one in
which we do not reject species status if there is no falsification.

Corroboration assessment may be an important missing element in this framework. In

much the same role it plays for phylogenetic hypotheses, it can allow many different
kinds of evidence (suggested by different secondary concepts), all brought to bear on a
single species concept. Evidence for a species hypothesis will be some fit of observations
to the hypothesis, and corroboration will depend on the improbability of such goodness-
of-fit without the hypothesis (Faith and Trueman 2001; Faith, 2004). This supports a
unified species concept as something more than just a shifting of the pluralism problem
down one level — the inevitable pluralism now properly reflects the various kinds of
evidence that may bear on the same concept. There are no a priori restrictions on the
form of the evidence for species hypotheses, but assessment of improbability of evidence
is important in avoiding an arbitrary, grab-bag, approach. Further, over time, experience
in corroboration assessment in different contexts — for example, for different kinds of
organisms — may have lessons about the context-dependent pitfalls of certain kinds of
evidence. This process will help evaluate new kinds of evidence, such as that from DNA
barcoding, discussed below in the section on Biodiversity and DNA barcoding.

5.3 Biodiversity and DNA barcoding

The philosophical issues concerning biodiversity surrogacy, phylogenetic inference, and
species inference are all relevant to a new, and controversial, source of biodiversity
information — DNA barcoding. A DNA “barcode” refers to a short region of a gene that
changes over evolutionary time at a rate that results in measurable distinctions among
species (analogous to the barcodes on products in stores). The Consortium for the
Barcode of Life [see CBOL] has brought together natural history museums and other
research organizations with the goal of producing DNA barcoding information for all
named species on the planet. Such a large-scale DNA barcoding program potentially
offers a wealth of new information for biodiversity assessment, filling both taxonomic
and geographic knowledge gaps. However, much of the controversy over the past few
years (for review, see Rubinoff et al., 2006) arises from the proposed link from one short
bit of DNA (e.g., approximately 600 base pairs of mitochondrial DNA) to the supposed
identification and discovery of actual species. While some recent reviews (e.g., Vogler
and Monaghan 2007) have pointed to the success of DNA barcodes over many different
taxonomic groups, there remains the concern that the use of one small bit of molecular
data cannot be used to determine species status.

DNA barcoding programs can address two different goals. First, such programs may be
concerned about diagnosis and identificaiton of already-known species (e.g., invasive
species that are difficult to identify by morphological characters). Second, such programs
may be interested in the discovery of new species, including "cryptic" species that may
not be revealed by morphological or other characters. The second goal raises issues about
species concepts and the nature of DNA bracoding based evidence for species status.

The use of limited molecular data for inferences about species identification and
discovery points to some interesting philosophical issues. For example, “hypothesis-
driven science” is seen as abandoned through the adoption of degree-of-difference
thresholds and other simple recipes for DNA-barcoding-based species delimitation
(deSalle et al, 2005). A related concern is that the scientific requirement for “total
evidence” is neglected when DNA barcoding is used on its own for species inference
(Fitzhugh, 2006, citing Carnap 1950). Fitzhugh argues that "for one to rationally believe
a conclusion on the basis of some set of evidence, then all available relevant evidence
must be taken into consideration. Barcodes cannot be used, even initially, to understand
biodiversity because they are incomplete and often incongruent with other sources of
data." Similar arguments are used in calling for an "integrative taxonomy" that includes
DNA barcoding in combination with other lines of evidence (e.g., Dayrat, 2005).

The philosophical arguments for total evidence would seem to place severe limits on the
role of DNA barcoding for biodiversity assessment. An alternative argument is that DNA
barcoding, in providing one form of valid evidence for species hypotheses, clearly can be
charactersied as “hypothesis driven”. The limited evidence from DNA barcoding here is
not taken to be the only possible evidence, but nevertheless is regarded as potentially able
to provide some degree of corroboration for a species hypothesis. This corroboration
assessment process does not strictly require "total evidence", because the focus (as
described in the overview on Popperian corroboration above) is about probing the current
evidence to see if it can be explained away. The different ways that barcode data
potentially can mislead should be integrated into such assessments. Only evidence from
DNA barcoding that is improbable — not easily explained away — provides high
corroboration.

An effective integrative taxonomy will depend on Popperian corroboration assessments

to provide the necesary critical questioning of evidence, from various sources, for species
hypotheses. It is premature to claim (as in Rubinoff et al., 2006) that an integrative
taxonomy based on corroboration is already in place. The required corroboration process
goes well beyond the simplistic view of corroboration as depending on the number of bits
of evidence. Because it is improbability of evidence that matters, a small number of bits
of evidence might provide higher corroboration, compared to that provided by some
alternative large number of bits of evidence.

Missing from emerging DNA barcoding programs is any well-defined process for such
Popperian corroboration assessments of species hypotheses. This limits the capacity to
combine corroborated evidence for species hypotheses from DNA barcoding with
corroboration derived from evidence from other data sources.

While the definition of “the barcode of life” is clearly focused only on the species level
("a short DNA sequence from standardized portions of the genome, used as an aid in
identifying species"; see the Consortium for the Barcode of Life — CBOL), others have
suggested that this wealth of new information need not be tied to species hypotheses in
order for it to be useful for biodiversity assessment. One proposal is that it is possible to
side-step the contentious species designations and make use of corroborated phylogenetic
patterns (e.g., Faith and Baker, 2006). Such an approach then uses PD calculations (see
the section on Option Value and Hierarchy of Variation) to quantify gains and losses in
biodiversity, without counting changes in species numbers. Such an application of PD
makes an assumption that the limited DNA sequence data provides useful information
about phylogenetic pattern.

The vast biodiversity knowledge gap suggests that DNA barcoding applications makes it
tempting to consider barcoding data for any one taxonomic group as valuable information
for making predictions about other taxonomic groups. Application of PD to inferred
phylogenetic patterns may boost surrogacy in reflecting historical processes and
relationships among geographic areas that are shared by many different taxonomic
groups. For example, the phylogeny for one taxonomic group may reflect historical
processes/relationships among geographic areas that are shared by other taxonomic
groups, so that observed differences among areas in PD-complementarity values also
reflect the values that would have been calculated for the other groups. Such a surrogacy
hypothesis remains largely untested, and requires corroboration assessments (see the
section on Biodiversity and Growth of Knowledge).

6. Conclusions
There is a nice parallel to be found in the debates about the definitions/concepts of
species and the broader definitions/concepts of biodiversity. In both cases, an
unnecessary pluralism has developed because operational issues have become intertwined
with definitions (for species — the meaning sometimes is to include information about
the process of species detection; for biodiversity - the meaning sometimes is to include
information about the process of biodiversity protection). In both cases, there is perhaps a
good case for monism regarding the concept, with pluralism welcomed at the operational
level (for species — many kinds of evidence for hypotheses; for biodiversity — many
kinds of protection strategies and many kinds of values of society to be traded-off).

Despite a wide range of usage, biodiversity remains a concept strongly linked to the idea
of biological variation that is largely unknown in its extent, and its future values. Any
"calculus" of biodiversity providing quantitative estimates of this unknown variation
automatically provides at the same time a measure of those values that link to the need to
maintain variety — option values and intrinsic values. Such values broadly reflect values
of elements of biodiversity having unknown present value. These quantified values
typically will not be in conventional units (e.g. dollars), but nevertheless can be balanced
with other values of society. Decision making (for example, deciding whether we should
invest in conservation of area A or area B) may require only estimates of relative gains in
represented variation offered by different places (their "complementarity" values).
Complementarity helps integrate biodiversity option values with other values attributed to
biodiversity, and with values of society more generally. This integrative process, together
with processes for the growth of knowledge about components of biodiversity, provide an
alternative to the "post-positivism" perspective that sees biodiversity conservation as
predominantly value-laden.

The perspective that biodiversity reflects option and intrinsic values, to be balanced with
other values, appears to be compatible with the broader discipline of conservation
biology: "the field is rooted in a philosophy of stewardship rather than one of
utilitarianism or consumption. The latter has been the basis of traditional resource
conservation, that is, conserving resources solely for their economic use and human
consumption" (Meffe 2000).

Bibliography
• Angermeier, P. L. and Karr, J. R., 1994, "Biological integrity vs. biological
diversity as policy directives: Protecting biotic resources", Bioscience, 44: 690-
697.
• Callicott, J. B., 1986, "On the intrinsic value of nonhuman species", in The
preservation of species: the value of biological diversity, B. G Norton (ed),
Princeton, NJ: Princeton University Press.
• Callicott, J. B., 1989, In defense of the land ethic: essays in environmental
philosophy, Albany: State University of New York Press.
• Callicott, J. B., Crowder, L. B. and Mumford, K., 1999, "Current normative
concepts in conservation", Conservation Biology, 13: 22-35.
• Carnap R., 1950, Logical Foundations of Probability, Chicago: University of
Chicago Press.
• Claridge, M.F. Dawah, H.A. and Wilson, M.R., (eds), 1997, Species: the Units of
Biodiversity, London: Chapman Hall Ltd.
• Dayrat B., 2005, "Towards integrative taxonomy", Biol J Linn Soc., 85: 407-415.
• DeSalle, R., Egan, M. G. and Siddall, M., 2005, "The unholy trinity: taxonomy,
species delimitation and DNA barcoding", Phil. Trans. R. Soc. B,
doi:10.1098/rstb.2005.1722.
• Downes, B. J., Barmuta, L. A., Fairweather, P. G., Faith, D. P., Keough, M. J.,
Lake, P. S.. Mapstone, B. D. and Quinn, G. P., 2002, Assessing Ecological
Impacts: Applications in flowing waters, Cambridge: Cambridge University Press.
• Ehrenfeld, D., 1988, "Why put a value on biodiversity?", in E.O. Wilson (ed),
Biodiversity, Washington, DC: National Academy Press.
• Faith, D. P., 1994, "Phylogenetic pattern and the quantification of organismal
biodiversity", Philosophical Transactions of the Royal Society of London, Series
B, 345: 45-58.
• Faith, D. P., 2003, "Environmental diversity (ED) as surrogate information for
species-level biodiversity", Ecography, 26: 374-379.
• Faith D. P., 2004, "From species to supertrees: Popperian corroboration and some
current controversies in systematics", Australian Systematic Botany, 17: 1-16.
• Faith D. P., 2006, "Science and philosophy for molecular systematics: which is
the cart and which is the horse?", Molec. Phylog. Evol., 38: 553-557.
• Faith D. P., Trueman, J. W. H., 2001, "Towards an inclusive philosophy for
phylogenetic inference", Systematic Biology, 50: 331-350.
• Forest, F., Grenyer, R., Rouget, M., Davies, T. J., Cowling,R.M., Faith, D.P.,
Balmford, A., Manning, J.C., Proches, S., van der Bank, M., Reeves, G.,
Hedderson T.A.J. and Savolainen, V., 2007, "Preserving the evolutionary
potential of floras in biodiversity hotspots", Nature, 445: 757-760.
• Frankel, O. H. and Soule, M. E., 1981, Conservation and evolution, Cambridge:
Cambridge University Press.
• Fitzhugh, K., 2006, "DNA Barcoding: An Instance of Technology-driven
Science?", BioScience, 56: 462-463.
• Gaston, K. J. (ed)., 1996, Biodiversity: a biology of numbers and difference,
Oxford: Blackwell.
• Karr, J. R., 1991, "Biological integrity: a long neglected aspect of water resource
management," Ecological Applications, 1: 66-84.
• Leopold, A. A., 1949, A sand county almanac, London: Oxford University Press.
• Mayden, R. L., 1997, "A hierarchy of species concepts: the denouement in the
saga of the species problem", in Species: the Units of Biodiversity, M. F. Claridge,
H. A. Dawah and M. R. Wilson (eds),f London: Chapman & Hall Ltd.
• Mayden, R. L., 2002, "On biological species, species concepts and individuation
in the natural world", Fish and Fisheries, 3: 171-196.
• Meffe, G., 2000, in Nature and Human Society: The Quest for a Sustainable
World, National Research Council (NRC).
• Nagel, E., 1961, The structure of science, New York: Harcourt, Brace and World.
• Norton, B. G. (ed), 1986, The preservation of species: the value of biological
diversity, Princeton N.J.: Princeton University Press.
• Norton, B. G., 1988, "Commodity amenity and morality: the limits of
quantification in valuing biodiversity," in E. O. Wilson (ed), Biodiversity,
Washington, DC: National Academy Press.
• Norton, B. G., 1994, "On what we should save: the role of cultures in determining
conservation targets," in P. Forey, et al. (eds), Systematics and conservation
evaluation.
• Norton, B. G., 2001, "Conservation biology and environmental values: can there
be a universal earth ethic?," in C. Potvin, et al. (eds), Protecting biological
diversity: roles and responsibilities, Montreal: McGill-Queen's University Press.
• Noss, R. F., 1990, "Indicators for monitoring biodiversity: a hierarchical
approach," Conservation Biology, 4: 355-364.
• Popper, K., 1982, Realism and the aim of science: from the ‘Postscript to the
logic of scientific discovery’, W. W. Bartley (ed), London: Routledge, 1992
(reprint).
• Randall, A., 1986, "Human preferences, economics, and the preservation of
species", in B. G Norton (ed), The preservation of species: the value of biological
diversity, Princeton, NJ: Princeton University Press.
• Randall, A., 1988, "What mainstream economists have to say about the value of
biodiversity", E. O. Wilson (ed), Biodiversity, Washington, DC: National
Academy of Sciences/Smithsonian Institution.
• Reaka-Kudla, M. L., Wilson, D. E. and Wilson, E. O. (eds), 1997, Biodiversity II:
Understanding and Protecting Our Biological Resources, Joseph Henry Press.
• Regan, D. H., 1986, "Duties of preservation", in B. G Norton (ed), The
preservation of species: the value of biological diversity, Princeton, NJ: Princeton
University Press, 1986.
• Roebuck, P. and Phifer, P., 1999, "The persistence of positivism in conservation
biology", Conservation Biology, 13: 444-446.
• Rubinoff, D., Cameron, S. and Will, K., 2006, "A Genomic Perspective on the
Shortcomings of Mitochondrial DNA for ‘Barcoding’ Identification", Journal of
Heredity, 97: 581-594.
• Sarkar, S., 1998, Genetics and reductionism, New York: Cambridge University
Press.
• Sarkar, S., 2005, Biodiversity and Environmental Philosophy: An Introduction,
(Cambridge Studies in Philosophy and Biology), New York: Cambridge
University Press.
• Sarkar, S. and Margules, C. R., 2002, "Operationalizing biodiversity for
conservation planning", Journal of Biosciences, 27: 299-308.
• Sober, E., 1986, "Philosophical problems for environmentalism", in B. G Norton
(ed), The preservation of species: the value of biological diversity, Princeton, NJ:
Princeton University Press.
• Takacs, D., 1996, The idea of biodiversity: philosophies of paradise, Baltimore:
The Johns Hopkins University Press.
• Turner, R., 1999, "Environmental and ecological economics perspective", in
J.C.J.M. van den Bergh (ed), Handbook of environmental and resource
economics, Northampton, MA: Edward Elgar, pp. 1001-1036.
 • Vermeulen, S. and Koziell, I., 2002, Integrating global and local values: a review
of biodiversity assessment, London: IIED.
• Vogler, A. P. and Monaghan, M. T., 2007, "Recent advances in DNA taxonomy",
Journal of Zoological Systematics and Evolutionary Research, 45: 1-10.
• Wiley, E. O., 1981, Phylogenetics: The Theory and Practice of Phylogenetic
Systematics, New York: John Wiley and Sons.
• Will, K., Mishler, B.D., Wheeler, Q.D., 2005, "The Perils of DNA Barcoding and
the Need for Integrative Taxonomy", Syst. Biol., 54: 844-851.
• Wilson, E. O. (ed), 1988, Biodiversity, Washington, DC: National Academy of
Sciences/Smithsonian Institution.
• Wilson, E. O., 1992, The diversity of life, Cambridge: Belknap Press.
• Witting, L. and Loescke, V., 1995, "The optimization of biodiversity
conservation", Biological Conservation, 71: 205-207.
• World Conservation Union, 1980, World conservation strategy: living resource
conservation for sustainable development, Gland: IUCN- UNEP-WWF.
• Yesson, C., and Culham, A., 2006, "A phyloclimatic study of Cyclamen", BMC
Evol. Biol., 6: 72.

Other Internet Resources

• The Millennium Ecosystem Assessment
• The Global Biodiversity Information Facility (GBIF)
• The Consortium for the Barcode of Life (CBOL)
• Perspectives on Biodiversity: Valuing Its Role in an Everchanging World,
Committee on Noneconomic and Economic Value of Biodiversity, National
Research Council, 168 pages, 1999.
• Biodiversity II: Understanding and Protecting Our Biological Resources, Marjorie
L. Reaka-Kudla, Don E. Wilson, and Edward O. Wilson, Editors; A Joseph Henry
Press book, 560 pages, 1997.
• Biodiversity, E.O. Wilson, Editor; National Academy of Sciences/Smithsonian
Institution, 538 pages, 1988.

Related Entries
ethics: environmental | Popper, Karl | species