Chapter 1: The Study of Life

MAGS 202

Introduction

As of 2015, about 2.3 million described species of living things are known on Earth (Pennisi, 2015 1)

The first life forms (microorganisms) appeared on Earth about 3.5 billion years ago (bya).

Mammals, birds, and flowers originated 130 to 250 million years ago (mya).

The earliest members of our own group Homo appeared about 2.5 mya while organisms we would recognize as
“human” appeared about 300,000 years ago.

1.1 The Science of Biology

Broadly defined, biology is the study of living things and how they interact with each other and their internal and
external environments. Fields in this discipline can range from the sub-microscopic (sub-cellular) to global
(environmental) levels and cover topics as diverse as disease causation and protection, food safety, and
environmental protection.

The Process of Science

Biology is a science. Other sciences include fields such as archeology, astronomy, computer sciences, ecology,
geology, logic, psychology, physics, chemistry, and mathematics.

Science (from the Latin scientia meaning “knowledge”) is defined as knowledge that is acquired and tested using
the scientific method (explained below), the formation of hypotheses, and the execution of repeatable
experimentation.

A hypothesis (plural: hypotheses) is a tentative explanation (that generates predictions that can be tested) for an
observed phenomenon. The testing of hypotheses is core to the study of sciences such as physics and chemistry.
However, the concept is more difficult to apply to sciences such as archeology, psychology or geology.

Hypotheses can become theories. A theory is a broad and repeatedly tested and confirmed explanation for
observations or phenomena.

Natural Sciences

The natural sciences are the sciences concerned with the physical world and its phenomena and processes.
Broadly, these can be further divided into the life sciences (the study of living things) and the physical sciences
(study of the nonliving things). Note that some scientists use slightly different criteria to characterize these
divisions.

The natural sciences are broad and include sub-disciplines such as cytology (study of cells), anatomy (study of the
structure of entire organisms), physiology (study of the internal functioning of organisms), botany (study of plants)
and zoology (study of animals) to name just a few. Some fields of natural science such as biophysics and
biochemistry are interdisciplinary and combine life and physical sciences.
1
First comprehensive tree of life shows how related you are to millions of species.
(http://www.sciencemag.org/news/2015/09/first-comprehensive-tree-life-shows-how-related-you-are-millions-
species)

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Some refer to the natural sciences as “hard sciences” because they rely on the use of quantitative data (recorded
observations that can be quantified; note data are plural, a datum is singular) as opposed to “soft” sciences that
rely more on qualitative assessments (descriptions or other observations based on qualities rather than on
measurements).

Scientific Reasoning

Curiosity (the desire to learn or know something) and inquiry (the act of asking questions) are at the core of all
sciences and the quest to understand the natural world and how it operates. Two methods of logical thinking are
used to accomplish this goal: inductive reasoning and deductive reasoning.

Inductive reasoning uses specific and related observations to reach a general conclusion (or formulate a general
rule) and is most common in descriptive studies. Conclusions are inferred from a large number of observations and
the analysis of the many qualitative or quantitative data these generate. Inferred conclusions may or may not be
correct. For example: If an individual gets stung by a bee, a wasp and an ant -- all of which belong to the insect
order Hymenoptera -- that person might infer that all hymenoptera have stingers. (In reality, that conclusion would
not be correct because stingless hymenoptera are known.)

Conversely, deductive reasoning uses generalities to predict specific results that can be tested. This is the type of
logic used in hypothesis-based science. For example: A scientist who discovers a previously unknown type of wasp
-- and has the general belief that all wasps have stingers as reasoned above – may reach the specific conclusion that
the newly found wasp has a stinger. An experiment would have to be conducted to see if this is indeed true.

Two main pathways exist in the pursuit of science: descriptive science and hypothesis-based science.

Descriptive science (aka discovery science) describes and documents observations. It usually involves the use of
inductive reasoning.

Hypothesis-based science begins with specific questions or problems and formulates potential answers or solutions
to those questions/problems that can be tested. This usually involves deductive reasoning.

The boundary between these two forms of science is often blurred. Most scientific studies combine both
approaches.

The Scientific Method

The Scientific Method is the process that describes how scientists perform investigations to provide a systematic
and rational approach to answer questions about the natural world. The goal is to eliminate bias -- and be as
objective as possible -- in what is studied. It is important to note that this process is also used daily -- by people
who are not scientists -- to solve problems associated with routine activities in all walks of life.

Sir Francis Bacon (1562-1626) -- an English philosopher, scientist, statesman and author -- is credited as the first
person to document the process.

The process typically starts with an observation (often a problem to be solved) that leads to a question. A question
leads to a tentative answer that can be tested. That tentative answer is a hypothesis. Note that several potential
answers could be generated to answer a specific question, but only one can be tested at a time. For example, a
common question might concern the fact that a car will not start when a key is turned in its ignition.

Hypotheses are usually stated in an “if … then ...” format. The hypotheses generated to address the above-
mentioned question might be: “If I replace my battery, then my car might start,” or “if I fill my empty gas tank, then
my car might start.”
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A valid hypothesis must be testable and falsifiable, meaning that experimental results can disprove it. Note that
questions related to the supernatural, or spiritual, are neither testable nor falsifiable.

Note, science does not claim to “prove” anything because scientific understandings are always subject to
modification with further information.

Openness about disproving ideas is what distinguishes science from non-science (aka pseudo-science or “fake”
science).

Hypotheses are tested with one or more experiments designed to eliminate one or more hypotheses.

Each experiment should have one or more variables and one or more controls. A variable is any component of an
experiment that can be measured and changed. A control group is the group in the experiment that is not
manipulated in any way. It serves as the basis for comparison to the experimental group, which can have only one
of its variables manipulated at a time.

Detailed steps of the scientific method are pictured below:

The scientific method appears rigid and structured. In actuality it is and is seldom practiced exactly as it appears in
the figure above. Rather, science often proceeds in much less rigid fashion as eloquently stated by AD Johnson
(2009)2:

“No scientist is talented and intuitive enough to ask a perfect question, choose exactly the right methods,
then get enough data from just one set of experiments to reach an unambiguous, publishable conclusion.

2
Johnson, A.D. 2009. Designing Scientific Experiments. Pp. 93-102 in Inquiry exercises for the college biology lab.
NSTA Press, Arlington, VA.
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 In reality, scientists continuously refine the questions they ask. They try different methods for testing their
hypotheses, and they perform multiple trials to get sufficient data for analysis. Once they obtain their data,
they may find that some results conflict with others and require that experiments be redesigned. At other
times, the data may point in an entirely different direction than the original question that spawned the
study. Technical problems may cause an experiment to fail miserably and produce no useful data at all.
Even if everything goes right, the results of one set of experiments usually raise two questions for every one
they answer. In short, like everything else in life, scientific researchers have their share of false starts,
surprising outcomes, and, occasionally, just plain bad luck. Only at the very end, do the researchers have
sufficient hindsight and understanding to package their data into the tidy summary we see in a scientific
paper.”

Two Types of Science: Basic Science and Applied Science

Scientific studies can be broadly grouped into two categories: basic science and applied science.

Basic science (aka “pure” science) is pursued simply to gain and expand knowledge. The purpose of applied science
(aka “technology”) is to solve real-life problems; the results of this kind of science have practical applications.

The line between these two forms of science is often blurred. For example, science that was once considered
“pure” can have practical application after it has been conducted. Conversely, research that was conducted for
practical purposes can also greatly enhance basic knowledge.

Some scientific discoveries, such as the discovery of penicillin by Alexander Fleming, are made by serendipity
(purely by accident).

Reporting Scientific Work

Regardless of how or why they conduct their research, scientists must share their findings in order for other
researchers to expand and build on their discoveries. This also highlights the importance of collaboration in
scientific pursuits.

Communication with peers and the dissemination of results to the scientific community are important components
of science. This is done at scientific meetings and through the publication of research results in peer-reviewed
scientific journals.

Peer-reviewed manuscripts are papers that have been reviewed by other researchers – qualified experts – in a
researcher’s field of expertise. Peer review ensures that the research in a scientific paper, or the grant applications
requesting funding to conduct research, is original, significant, logical and thorough. Scientific papers provide all
the information necessary for other researchers to replicate the reported study, and be consistent with the findings
of other scientists. Using the work or ideas of others – without proper citations – is plagiarism.

Scientific papers are brief, concise, and accurate. Moreover, the papers that report original research results usually
all contain similar components: an introduction, materials and methods, results and discussion (sometimes
separate, sometimes combined depending on the journal), conclusions, and literature cited. An abstract (concise
summary of all the components of the paper) usually appears at the beginning of a paper.

The introduction provides background material about what is known about the research topic and rationale for
why it is of interest. The materials and methods section summarizes all the materials and equipment used as well
as detailed protocols and analysis methods used in the study. The point is to allow others to replicate the study if
they choose. The results section presents the research data collected (in narrative, graph, chart or tabular form),
but does not interpret them. This is saved for the discussion section. The conclusion section summarizes the
importance of the experimental findings.
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1.2 Themes and Concepts of Biology

Biology is the scientific study of life. However, defining exactly what is meant by “life” can be tricky. For example,
viruses are often studied as part of biological investigations because they affect living things. Viruses, themselves,
are not living things.

Biology as a discipline wrestles with three questions. Specifically, what are the shared properties that define “life?”
How are living things and their components organized in terms of their structure? How do we organize the
incredible diversity of living things (more than 2.3 million described species) to better understand them?

Properties of Life

All living things share several key characteristics or functions: order, sensitivity (response to environmental stimuli),
reproduction, growth and development, regulation, homeostasis, energy processing, the need for water,
adaptation and change, and death.

ORDER: Living things are highly organized coordinated structures composed of one or more cells. Single-celled
organisms are unicellular; Organisms with more than one cell are multi-cellular. Cells are made of atoms that form
molecules. Molecules, in turn, make up organelles or other specialized structures in cells. In multi-cellular
organisms, cells form tissues (groups of cells that carry out specific functions). Tissues form organs (major body
structures with a distinct function) and organs can function together to form organ systems.

RESPONSE TO STIMULI: Organisms respond to a diversity of environmental stimuli (sing. stimulus). For example,
plants can bend toward light or change colors as season change. Animals can run away from predators, or search
for mates when they perceive certain chemical cues. Even bacteria move toward certain chemicals (a positive
response) or away from others (a negative response).

REPRODUCTION: All living things reproduce (produce more of themselves). Single-celled organisms reproduce by
duplicating their genetic material (DNA), doubling their contents, and then dividing in half between two daughter
cells. In contrast, most multi-cellular organisms produce specialized reproductive cells (eggs from females and
sperm from males) that fuse to produce a zygote that develops into a genetically unique individual that displays
combined characteristics representative of its parents.

GROWTH AND DEVELOPMENT: Organisms grow and develop according to individual-specific and species-specific
instructions coded in their genetic material (DNA).

REGULATION: All living things require multiple regulatory systems to coordinate all their functions. Examples
include: waste removal, movement of nutrients and other materials throughout the organism, and
thermoregulation.

HOMEOSTASIS: Most systems in living things function optimally within a narrow set of conditions (e.g.,
temperature, pH, ion and other chemical concentrations) that must constantly be maintained. Temperature
regulation in mammals, through the mechanisms of sweating or shivering, and structures such as blubber and fur
are good examples of this.

ENERGY PROCESSING: All living things need a constant source of energy. Organisms such as plants make their
own food by capturing energy from the sun, which they convert into chemical energy (e.g., sugars). Organisms such
as animals and fungi take in food from external sources.

USE OF WATER: All living things require water. Water makes up between about 65% and 95% of all living things
and most chemical reactions in living things take place in water.

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ADAPTATION AND CHANGE: Once formed, an organism’s genetic make-up stays the same even though its
appearance changes as it grows. However, with time, the genetic make-up of populations can change if
environmental conditions change. This results in the appearance of adaptations. An adaptation is any feature that
allows an organism to thrive and enhances its successful reproduction.

DEATH: All living things eventually die. Consequently, they cease to use energy, grow, respond to stimuli,
reproduce, maintain homeostasis or exhibit any of the other characteristics of living things. After death, the
molecules and atoms that make up living things are recycled in the environment

Levels of Organization of Living Things

Living things are highly organized and structured and can be studied at many levels ranging from atoms (what all
living and non-living things on Earth are made of) to the biosphere (all the areas on Earth that support life).

Such a progression, or ranking, from smallest (e.g., atoms) to largest (e.g., biosphere) is called a hierarchy. Every
level of the biological hierarchy has its own characteristics or properties. Higher levels of the hierarchy are more
complex than lower levels, but include all the properties of the levels below them.

The biological hierarchy consists of atoms, molecules, organelles, cells, tissues, organs, organ systems, organisms,
populations, communities, ecosystems, biomes and finally the biosphere.

Atoms are the smallest and most fundamental units of matter and consist of a nucleus surrounded by electrons.

Molecules consist of at least two atoms joined together by chemical bonds. The most important molecules in living
things are large (and called macromolecules) and usually consist of many small repeating units.

Macromolecules in living things can join together to form organelles, which are the small units – each with a
specific function -- inside cells. Examples are the nucleus, mitochondria, chloroplasts, and ribosomes.

Cells are the fundamental units of living things and the smallest biological entities considered to be alive.
Organisms with only one cell are unicellular. Those with more than one cell are multicellular.

Prokaryotes are single-celled organisms without a nucleus or membrane-bound organelles. Eukaryotes are single-
or multi-celled organisms -- the cells of which have a nucleus and membrane-bound organelles.

In large organisms, cells combine to form tissues – groups of cells that carry out specific functions. Examples are
bone and blood in animals or epidermis (outer covering) in a plant leaf.

Organs (e.g., a stomach in an animal or root in a plant) are collections of tissues that work together to carry out
specific functions.

Organ systems (e.g., digestive system in animals, vascular system in plants) contain groups of organs.

Organisms are individual living things (e.g., tree in a forest, bacterium in a petri dish, fish in a ocean).

Populations are collections of individuals of the same species that exist together in a given area and are close
enough together to interact (e.g., a herd of elephants or a stand of red oak trees).

Communities are all the populations of living things in an area (e.g., all the fish and other marine organisms in a
coral reef or all the plants, animals, fungi and bacteria in a forest).

An ecosystem consists of all the living (biotic) things in an area as well as the non-living (abiotic) components such
as the atmosphere, water, rocks, etc.
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Biomes are large-scale geographically recognizable areas with distinctive climates and animal and plant
communities (e.g., deserts, grasslands, tropical rain forests, arctic tundra).

The biosphere is the area on Earth where life exists. It includes land, water and the atmosphere. It exists about 8
km (5 miles) above and below the land surface.

The Diversity of Life

As already stated, about 2.3 million species have been described on Earth. The source of this diversity is evolution
as a result of natural selection (see more in chapter 18), the process of gradual change during which new species
arise from older species.

A phylogenetic tree summarizes the evolution of various life forms on Earth.

This type of diagram dates to the 1970’s and was pioneered by microbiologist Carl Woese. It shows the
evolutionary relationships among biological species based on similarities and differences in physical, biochemical,
physiological and genetic traits (specifically gene sequence data).

Branching points (nodes) represent ancestors that separated to form two species. The length of each branch is
proportional to the time that has passed since the split. Organisms (species) that have evolved the most recently
are at the tips of the branches.

Woese demonstrated that life on Earth evolved along three lineages now called domains. These are the Bacteria,
Archaea and Eukarya. The Bacteria and Archaea are prokaryotic and microscopic and differ in terms of their
genetics and chemistry of their cell walls. Many Archaea occur in, and are believed to have evolved in, extreme
conditions (e.g., sulfur vents, manure, gastrointestinal tracts, high salt environments, etc.). Such organisms are
called extremophiles.

The Eukarya are all the other living things on Earth. They include familiar groups such as all the animals, plants, and
fungi as well as many lesser known major groupings collectively known as the Protista (chapter 23). All Eukaryotes
have cells with a nucleus and membrane-bound organelles.

How Organisms are Classified (from OpenStax Biology 2e, Chapter 20)

Taxonomy is the science of naming, describing and classifying all living things on Earth. Taxonomists use a
combination of available morphological, genetic, biochemical and behavioral data to identify, describe and place
organisms (living, currently undescribed and extinct) in groupings (taxa; singular taxon) from largest and most
general (domain) to smallest and most specific (species or subspecies) based on shared characteristics.

This taxonomic classification system was developed by eighteenth century Swedish botanist Carl Linnaeus.

The smallest unit of classification is the species – individuals that are most related to each other and can breed to
produce viable offspring.

Closely related species are grouped together to form a genus (plural: genera).

Every species receives a unique, two-word Latin name called its scientific name, which is italicized. The first word
identifies the genus to which an organism belongs. The second defines the species. Consequently, Homo sapiens
(human beings) and Homo neanderthalensis (Neanderthals) are two separate species but both belong to the genus
Homo.

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Each species is then placed in progressively larger and more inclusive rankings beyond genus. Closely related
genera are grouped into a family.

Closely related families are grouped into an order.

Closely related orders are grouped into a class.

Closely related classes are grouped into a phylum (plural: phyla).

Closely related phyla are grouped into a kingdom. Finally, closely related kingdoms are grouped together into a
domain.

Current phylogenetic trees -- and the groupings to which organisms are assigned – do not necessarily align with
historic views of evolutionary relationships based solely on morphology. The evolutionary relationships among
living things can be modified as new information becomes available.

Branches of Biological Study

Biology is a broad field and contains many branches and sub-disciplines. Some biologists are very focused in their
pursuits. Others are truly interdisciplinary and ask research questions – and combine research techniques -- that
span several of the major scientific disciplines (e.g., biophysics or bioacoustics) and even science and non-science
fields (e.g., bioethics).

See “Additional Material” for this chapter for an expanded list of some biological sub-disciplines.

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