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 PART 1 FROM CELLS TO ORGANISMS

“Nothing in biology makes sense except in the light of

evolution.” —THEODOSIUS DOBZHANSKY 189

CHAPTER 1 Life Chemical, Cellular, and Evolutionary

Foundations CORE CONCEPTS 1.1 SCIENTIFIC
INQUIRY: Scientific inquiry is a deliberate way of 190
asking and answering questions about the natural
world. 1.2 CHEMICAL AND PHYSICAL PROPERTIES:
Life works according to fundamental principles of
chemistry and physics. 1.3 THE CELL: The
fundamental unit of life is the cell. 1.4 EVOLUTION:
Evolution explains the features that organisms share
and those that set them apart. 1.5 ECOLOGICAL
SYSTEMS: Organisms interact with one another and
with their physical environment, shaping ecological
systems that sustain life. 1.6 THE HUMAN
FOOTPRINT: In the twenty-first century, humans have
become major agents in ecology and evolution. Every
day, remarkable things happen within and around you.
Strolling through a local market, you come across a
bin full of crisp apples, pick one up, and take a bite.
Underlying this unremarkable occurrence is an
extraordinary series of events. Your eyes sense the
apple from a distance, and nerves carry that
information to your brain, permitting identification.
Biologists call this cognition, an area of biological
study. Stimulated by the apple and recognizing it as
ripe and tasty, your brain transmits impulses through
nerves to your muscles. How we respond to external
cues motivates behavior, another biological
discipline. Grabbing the apple requires the
coordinated activities of dozens of muscles that move
your arm and hand to a precise spot. These
movements are described by biomechanics, yet
another area of biological research. And, as you bite
down on the apple, glands in your mouth secrete
saliva, starting to convert energy stored in the apple as
191 sugar into energy that you will use to fuel your own
activities. Physiology, like biomechanics, lies at the
heart of biological function. Studies of cognition,
behavior, biomechanics, and physiology are all ways
of approaching biology , the science of how life works.
Biologists , scientists who study life, have come to
understand a great deal about these and other
processes at levels that run the gamut from molecular
mechanisms within the cell, through the integrated
actions of many cells within an organ or body, to the
interactions among different organisms in nature. We
don’t know everything about how life works —in fact, it
seems as if every discovery raises new questions. But
biology provides us with an organized way of
understanding ourselves and the world around us.
Why study biology? The example of eating an apple
was deliberately chosen because it is an everyday
occurrence that we ordinarily wouldn’t think about
twice. The scope of modern biology, however, is vast,
raising questions that can fire our imaginations, affect
our health, and influence our future. How, for
example, will our understanding of the human genome
change the way that we fight cancer? How do bacteria
in our digestive system help determine health and
well-being? Will expected changes in the temperature
and pH of seawater doom coral reefs? Is there, or has
there ever been, life on Mars? And, to echo the great
storyteller Rudyard Kipling, why do leopards have
spots, and tigers stripes? We can describe six grand
themes that connect and unite the many dimensions
of life science, from molecules to the biosphere.
These six 192 themes are stated as Core Concepts for
this chapter and are introduced in the following
sections. Throughout the book, these themes will be
visited again and again. We view them as the keys to
understanding the many details in subsequent
chapters and relating them to one another. Our hope
is that by the time you finish this book, you will have an
understanding of how life works, from the molecular
machines inside cells and the metabolic pathways
that cycle carbon through the biosphere to the
process of evolution, which has shaped the living
world that surrounds (and includes) us. You will, we
hope, see the connections among these different
ways of understanding life, and come away with a
greater understanding of how scientists think about
and ask questions about the natural world. How, in
fact, do we know what we think we know about life?
We also hope you will develop a basis for making
informed decisions about your life, career, and the
actions you take as a citizen. 193 1.1 SCIENTIFIC
INQUIRY How do we go about trying to understand the
vastness and complexity of nature? For most
scientists, studies of the natural world involve the
complementary processes of observation and
experimentation. Observation is the act of viewing the
world around us. Experimentation is a disciplined and
controlled way of asking and answering questions
about the world in an unbiased manner. Observation
allows us to draw tentative explanations called
hypotheses. Observations allow us to ask focused
questions about nature. Let’s say you observe a
hummingbird like the one pictured in Fig. 1.1 hovering
near a red flower, occasionally dipping its long beak
into the bloom. What motivates this behavior? Is the
bird feeding on some substance within the flower? Is it
drawn to the flower by its vivid color? What benefit, if
any, does the flower derive from this busy bird? 194
FIG. 1.1 A hummingbird visiting a flower. This simple
observation leads to questions: why do hummingbirds
pay so much attention to some flowers? Why do they
hover near red flowers? Observations such as these,
and the questions they raise, allow us to propose
tentative explanations, or hypotheses. We might, for
example, hypothesize that the hummingbird is
carrying pollen from one flower to the next, facilitating
reproduction in the plant. Or we might hypothesize
that nectar produced deep within the flower provides
nutrition for the hummingbird—that the
hummingbird’s actions reflect its need to take in food.
Both hypotheses provide a reasonable explanation of
the behavior we observed, but they may or may not be
correct. To find out, we have to test them. Charles
Darwin’s classic book, On the Origin of Species,
published in 1859, beautifully illustrates how we can
piece together individual 195 observations to
construct a working hypothesis. In this book, Darwin
discussed a wide range of observations, from pigeon
breeding to fossils and from embryology to the
unusual animals and plants found on islands. Darwin
noted the success of animal breeders in selecting
specific individuals for reproduction, thereby
generating new breeds for agriculture or show. He
appreciated that selective breeding is successful only
if specific features of the animals can be passed from
one generation to the next by inheritance. Reading
economic treatises by the English clergyman Thomas
Malthus, he understood that limiting environmental
resources could select among the different individuals
in populations in much the way that breeders select
among cows or pigeons. Gathering together all these
seemingly disparate pieces of information, Darwin
argued that life has evolved over time by means of
natural selection. Since its formulation, Darwin’s
initial hypothesis has been tested by experiments,
many thousands of them. Our knowledge of many
biological phenomena, ranging from biodiversity to the
way the human brain is wired, depends on direct
observation followed by careful inferences that lead to
models of how things work. A hypothesis makes
predictions that can be tested by observation and
experiments. Not just any idea qualifies as a
hypothesis. Two features set hypotheses apart from
other ways of attacking problems. First, a good
hypothesis makes predictions about observations not
yet made or experiments not 196 yet run. Second,
because hypotheses make predictions, we can test
them. That is, we can devise an experiment to see
whether the predictions made by the hypothesis
actually occur, or we can go into the field to try to
make further observations predicted by the
hypothesis. A hypothesis, then, is a statement about
nature that can be tested by experiments or by new
observations. Hypotheses are testable because, even
as they suggest an explanation for observations made
previously, they make predictions about observations
yet to be made. Once we have a hypothesis, we can
test it to see if its predictions are accurate (Fig. 1.2 ).
Returning to the hummingbird and flower, we can test
the hypothesis that the bird is transporting pollen from
one flower to the next, enabling the plant to
reproduce. Observation provides one type of test: if
we catch and examine the bird just after it visits a
flower, do we find pollen stuck to its beak or feathers?
If so, our hypothesis survives the test.

Note, however, that we haven’t proved the case.

Pollen might be stuck on the bird for a different
reason—perhaps it provides food for the
hummingbird. However, if the birds didn’t carry pollen
from flower to flower, we would reject the hypothesis
that they facilitate pollination. In other words, a single
observation or experiment can lead us to reject a
hypothesis, or it can support the hypothesis, but it
cannot prove that a hypothesis is correct. To move
forward, then, we might make a second set of
observations. Does pollen that adheres to the
hummingbird rub off when the bird visits a second
flower of the same species? If so, we have stronger
support for our hypothesis. We might also use
observations to test a more general hypothesis about
birds and flowers. Does red color generally attract
birds and so facilitate pollination in a wide range of
flowers? To answer this question, we might catalog
the pollination of many red flowers and ask whether
they are pollinated mainly by birds. Or we might go the
opposite direction and catalog the flowers visited by
many different birds—are they more likely to be red
than chance alone might predict? Finally, we can test
the hypothesis that the birds visit the flowers primarily
to obtain food, spreading pollen as a side effect of
their feeding behavior. We can measure the amount of
nectar in the flower before and after the bird visits and
calculate how much energy has been consumed by
the bird during its visit. Continued observations over
the course of the day will tell us whether the birds gain
the nutrition they need by drinking nectar, and
whether the birds have other sources of food. 198 In
addition to observations, in many cases we can design
experiments to test hypotheses (Fig. 1.2 ). One of the
most powerful types of experiment is called a
controlled experiment. In a controlled experiment, the
researcher sets up several groups to be tested,
keeping the conditions and setup as similar as
possible from one group to the next. Then, the
researcher deliberately introduces something
different, known as a variable , into one group that he
or she hypothesizes might have some sort of an effect.
This is called the test group . In another group, the
researcher does not introduce this variable. This is a
control group , and the expectation is that no effect
will occur in this group. Controlled experiments are
extremely powerful. By changing just one variable at a
time, the researcher is able to determine whether that
variable is important. If many variables were changed
at once, it would be difficult, if not impossible, to draw
conclusions from the experiment because the
researcher would not be able to figure out which
variable caused the outcome. The control group plays
a key role as well. Having a group in which no change
is expected ensures that the experiment works as it is
supposed to and provides a baseline against which to
compare the results of the test groups. For example,
we might test the hypothesis that hummingbirds
facilitate pollination by doing a controlled experiment.
In this case, we could set up groups of red flowers that
are all similar to one another. For one group, we could
surround the flowers with a fine mesh that allows
small insects access to the plant but keeps
hummingbirds away. For another group, we would not
use a mesh. The variable, then, is the presence of a
mesh; the test group is the flowers with the mesh; and
the 199 control group is the flowers without the mesh
since the variable was not introduced in this group.
Will the flowers be pollinated? If only the group
without the mesh is pollinated, this result lends
support to our initial hypothesis. In this case, the
hypothesis becomes less tentative and more certain.
If both groups are pollinated, our hypothesis is not
supported, in which case we may discard it for
another explanation or change it to account for the
new information. Using observations to generate a
hypothesis and then making predictions based on that
hypothesis are two steps in what is sometimes called
the scientific method. In reality, however, there is no
single pathway to new knowledge about the world. To
convey the full range of activities by which science
works, we instead use the term scientific inquiry to
describe the process outlined in Fig. 1.2 . Scientific
inquiry encompasses several careful and deliberate
ways of asking and answering questions about the
unknown. We ask questions, make observations,
collect field or laboratory samples, and design and
carry out experiments or analyses to make sense of
things we initially do not understand. We then
communicate what we find with other scientists and
the public. Discussing and sharing ideas and results
often lead to new questions, which in turn can be
tested by observations and experiments. Scientific
inquiry has been spectacularly successful in helping
us to understand the world around us. We explore
several aspects of scientific inquiry, including skills
that scientists use to ask and answer questions, in
your online courseware. 200 To emphasize the power
of scientific inquiry, we turn to a famous riddle drawn
from the fossil record (Fig. 1.3). Since the nineteenth
century, paleontologists have known that before
mammals expanded to their current ecological
importance, other large animals dominated Earth.
Dinosaurs evolved about 240 million years ago and
disappeared abruptly 66 million years ago, along with
many other species of plants, animals, and
microscopic organisms. Because in many cases the
skeletons and shells of these creatures were buried in
sediment and became fossilized, we can read a
record of their evolutionary history from layers of
sedimentary rock deposited one atop another. HOW
DO WE KNOW? FIG. 1.3 What caused the extinction of
the dinosaurs? BACKGROUND Dinosaurs dominated
the Earth for nearly 150 million years but became
extinct about 66 million years ago. OBSERVATION
HYPOTHESIS Geologist Walter Alvarez and his
colleagues hypothesized that a large meteorite struck
the Earth, disrupting communities on land and in the
sea 201 and causing the extinction of the dinosaurs
and many other species. PREDICTIONS A hypothesis
makes predictions that can be tested by observation
and experiments. To support the hypothesis,
independent evidence of a meteor impact should be
found in rock layers corresponding to the time of the
extinction and be rare or absent in older and younger
layers. FURTHER OBSERVATIONS CONCLUSION A
giant meteor struck the Earth 66 million years ago,
causing the extinction of many species, including the
dinosaurs. FOLLOW-UP WORK Researchers have
documented other mass extinctions, but the event
that eliminated the dinosaurs appears to be the only
one associated with a meteorite impact. SOURCE
Alvarez, W. 1998. T. rex and the Crater of Doom. New
York: Vintage Press. Working in Italy, the American
geologist Walter Alvarez collected 202 samples from
the precise point in the rock layers that corresponds
to the time of the extinction. Careful chemical
analysis showed that rocks at this level are unusually
enriched in the element iridium. Iridium is rare in most
rocks on continents and the seafloor, but is relatively
common in rocks that fall from space—that is, in
meteorites. From these observations, Alvarez and his
colleagues developed a remarkable hypothesis: 66
million years ago, a large meteor slammed into Earth,
and in the resulting environmental havoc, dinosaurs
and many other species became extinct. This
hypothesis makes specific predictions, described in
Fig. 1.3 , which turn out to be supported by further
observations. A theory is a general explanation of
natural phenomena supported by many experiments
and observations. As already noted, a hypothesis may
initially be tentative. Indeed, it often provides only one
of several possible ways of explaining existing data.
With repeated observation and experimentation,
however, a good hypothesis gathers strength, and we
have more and more confidence in it. When a number
of related hypotheses survive repeated testing and
come to be accepted as good bases for explaining
what we see in nature, scientists articulate a broader
explanation that accounts for all the hypotheses and
the results of their tests. We call this statement a
theory , a general explanation of the world supported
by a large body of experiments and observations (see
Fig. 1.2 ). Note that scientists use the word “theory” in
a very particular way. 203 In general conversation,
“theory” is often synonymous with “hypothesis,”
“idea,” or “hunch”—“I’ve got a theory about that.” But
in a scientific context, the word “theory” has a specific
meaning. Scientists speak in terms of theories only if
hypotheses have withstood testing to the point where
they provide a general explanation for many
observations and experimental results. Just as a good
hypothesis makes testable predictions, a good theory
both generates good hypotheses and predicts their
outcomes. Thus, scientists talk about the theory of
gravity —a set of hypotheses you test every day by
walking down the street or dropping a fork. Similarly,
the theory of evolution is not one explanation among
many for the unity and diversity of life. Instead, it is a
set of hypotheses that has been tested for more than a
century and shown to provide an extraordinarily
powerful explanation of biological observations that
range from the amino acid sequences of proteins to
the diversity of ants in a rain forest. In fact, as we
discuss throughout this book, evolution is the single
most important theory in all of biology. It provides the
most general and powerful explanation of how life
works. Self-Assessment Questions 1. How does a
scientist turn an observation into a hypothesis and
investigate that hypothesis? 2. What are the
differences among a guess, hypothesis, and theory? 3.
Mice that live in sand dunes commonly have light tan
fur. Develop a hypothesis to explain this coloration. 4.
What are the differences between a test group and a
control 204 group, and why is it important for an
experiment to have both types of groups? 5. Design a
controlled experiment to test the hypothesis that
cigarette smoke causes lung cancer. 205 1.2
CHEMICAL AND PHYSICAL PRINCIPLES We stated
earlier that biology is the study of life. But what exactly
is life? As simple as this question seems, it is
frustratingly difficult to answer. We all recognize life
when we see it, but coming up with a definition is
harder than it first appears. Living organisms are
clearly different from nonliving things. But just how
different is an organism from the rock shown in Fig.
1.4 ? On one level, the comparison is easy: the rock is
much simpler than any living organism we can think
of. It has far fewer components, and it is largely static,
with no apparent response to environmental change
on timescales that are readily tracked. 206 207 FIG.
1.4 A climber scaling a rock. Living organisms like this
climber contain chemicals that are found in rocks, but
only living organisms reproduce in a manner that
allows for evolution over time. In contrast, even an
organism as relatively simple as a bacterium contains
many hundreds of different chemical compounds
organized in a complex manner. The bacterium is also
dynamic in that it changes continuously, especially in
response to the environment. Unlike rocks and
minerals, organisms metabolize—that is, they take in
energy and materials from their environment and use
those resources to grow and do work. Organisms
reproduce, but minerals do not. And organisms do
something else that rocks and minerals don’t: they
evolve. Indeed, the molecular biologist Gerald Joyce
has defined life as a chemical system capable of
undergoing Darwinian evolution. From these simple
comparisons, we can highlight key characteristics of
living organisms: complexity, with precise spatial
organization on several scales; the ability to change in
response to the environment; the abilities to
metabolize and to reproduce; and the capacity to
evolve. Nevertheless, the living and nonliving worlds
share an important attribute: both are subject to the
laws of chemistry and physics. The living and nonliving
worlds follow the same chemical rules and obey the
same physical laws. The chemical elements found in
rocks and other nonliving things are 208 no different
from those found in living organisms. In other words,
all the elements that make up living things can be
found in the nonliving environment—there is nothing
special about our chemical components when taken
individually. That said, the relative abundances of
elements in organisms differ greatly from those in the
nonliving world. In the universe as a whole, hydrogen
and helium make up more than 99% of known matter,
while Earth’s crust contains mostly oxygen and
silicon, with significant amounts of aluminum, iron,
and calcium (Fig. 1.5a ). In organisms, by contrast,
oxygen, carbon, and hydrogen are by far the most
abundant elements (Fig. 1.5b ). As discussed more
fully in Chapter 2 , carbon provides the chemical
backbone of life. The particular properties of carbon
make possible a wide diversity of molecules that, in
turn, support a wide range of functions within cells.
209 FIG. 1.5 Composition by mass of (a) Earth’s crust
and (b) cells in the human body. The Earth beneath our
feet is made up of the same elements found in our
feet, but in strikingly different proportions. 210 All
living organisms are subject to the physical laws of the
universe. Physics helps us to understand how animals
move and why trees don’t fall over; it explains how
redwoods conduct water upward through their trunks
and how oxygen gets into the cells that line your lungs.
Indeed, two laws of thermodynamics, both of which
describe how energy is transformed in any system,
determine how living organisms are able to do work
and maintain their spatial organization. The first law of
thermodynamics states that energy can neither be
created nor destroyed; it can only be transformed
from one form into another. In other words, the total
energy in the universe is constant, but the form that
energy takes can change. Living organisms are energy
transformers. They acquire energy from the
environment and transform it into a chemical form
that cells can use. All organisms obtain energy from
the sun or from chemical compounds. Some of this
energy is used to do work—such as moving,
reproducing, and building cellular components—and
the rest is dissipated as heat. The energy that is used
to do work plus the heat that is generated is the total
amount of energy, which is the same as the input
energy (Fig. 1.6 ). In other words, the total amount of
energy remains constant before and after energy
transformation.
The second law of thermodynamics states that the
degree of disorder (or the number of possible
positions and motions of molecules) in the universe
tends to increase. Think about a box full of marbles
distributed more or less randomly; if you want to line
up all the red ones or blue ones in a row, you have to
do work—that is, you have to add energy. In this case,
the addition of energy increases the order of the
system, or, put another way, decreases its disorder.
Physicists quantify the amount of disorder (or the
number of possible positions and motions of
molecules) in a system as the entropy of the system.
Living organisms are highly organized. As with lining up
marbles in 212 a row, energy is needed to maintain
this organization. Given the tendency toward greater
disorder, the high level of organization of even a single
cell would appear to violate the second law. But it
does not. The key is that a cell is not an isolated
system and therefore cannot be considered on its
own; it exists in an environment. So we need to take
into account the whole system, the cell plus the
environment that surrounds it. Only some of the
energy harnessed by cells is used to do work; the rest
is dissipated as heat (Fig. 1.6 ). That is, conversion of
energy from one form to another is never 100%
efficient. Heat is a form of energy, so the total amount
of energy is conserved, as dictated by the first law. In
addition, heat corresponds to the motion of small
molecules—the greater the heat, the greater the
motion, and the greater the motion, the greater the
degree of disorder. Therefore, the release of heat as
organisms harness energy means that the total
entropy for the combination of the cell and its
surroundings increases, in keeping with the second
law (Fig. 1.7 ). 213 FIG. 1.7 Energy transformation and
the second law of thermodynamics. The second law
states that disorder in any system tends to increase.
Entropy can decrease locally (inside a cell, for
example) because the heat released increases
disorder in the environment. Scientific inquiry shows
that living organisms come from other living
organisms. Life is made up of chemical components
that also occur in the nonliving environment and obey
the same laws of chemistry and 214 physics. Can life
spontaneously arise from these nonliving materials?
We all know that living organisms come from other
living organisms, but it is worth asking how we know
this. Direct observation can be misleading here. For
example, raw meat, if left out on a plate, will rot and
become infested with maggots (fly larvae). It might
seem as though the maggots appear spontaneously.
In fact, the question of where maggots come from was
a matter of vigorous debate for centuries. In the
1600s, the Italian physician and naturalist Francesco
Redi conducted an experiment to test the hypothesis
that maggots (and hence flies) in rotting meat come
from other flies that laid their eggs in the meat. He
found that living organisms come from other
organisms and do not appear spontaneously (Fig. 1.8).
HOW DO WE KNOW? FIG. 1.8 Can living organisms
arise from nonliving matter? BACKGROUND Until the
1600s, many people believed that rotting meat
spontaneously generates maggots (fly larvae).
HYPOTHESIS Francesco Redi hypothesized that
maggots come from flies and are not spontaneously
generated. EXPERIMENT Redi placed meat in three
jars. He left one jar open; he covered one with gauze;
and he sealed one with a cap. The three jars were
subject to the same conditions—the only variable was
the opening. The open jar allowed for the passage of
flies and air; the jar with the gauze allowed for the 215
passage of air but not flies; and the sealed jar did not
allow the passage of air or flies. RESULTS Redi
observed that maggots appeared only on the meat in
the open jar. No maggots appeared in the other two
jars, which did not allow access to the meat by flies.
CONCLUSION The presence of maggots in the open
jar and the absence of maggots in the gauze-covered
and sealed jars supported the hypothesis that
maggots come from flies. FOLLOW-UP WORK Redi’s
experiment argued against the idea of spontaneous
generation for insects. However, it was unclear
whether his results could be extended to microbes.
Applying the scientific process, Louis Pasteur used a
similar approach about 200 years later to investigate
this question (Fig. 1.9). Some argued, however, that
Redi’s results might only apply to larger organisms;
microscopic life might be another matter entirely. In
216 the nineteenth century, the French chemist and
biologist Louis Pasteur conducted another set of
experiments using bacteria and came to the same
conclusion as Redi, further supporting the hypothesis
that life does not arise spontaneously (Fig. 1.9). HOW
DO WE KNOW? FIG. 1.9 Can microscopic life arise
from nonliving matter? BACKGROUND Educated
people in the mid-nineteenth century knew that
microbes (microorganisms like bacteria) grow well in
nutrient-rich liquids such as broth. It was also known
that boiling sterilizes broth, killing the microbes.
HYPOTHESIS Chemist and biologist Louis Pasteur
hypothesized that microbes come from microbes and
are not spontaneously generated. He argued that if
microbes were generated spontaneously from
nonliving matter, they would reappear in sterilized
broth without the addition of microbes. EXPERIMENT
Pasteur filled two flasks with broth and boiled the
broth to sterilize it and kill all the microbes. One flask
had a straight neck and one had a swan neck. The
straight-neck flask allowed dust particles with
microbes to enter. The swan-neck flask did not. As in
Redi’s experiments (Fig 1.8), there was only one
variable—in this case, the shape of the neck of the
flask. RESULTS Microbes grew in the broth inside the
straight-neck flask but not in the swan-neck flask.

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