Chapter 1

Introduction: Themes in the Study of Life

Overview: Inquiring About the World of Life

Biology - scientific study of life Evolution - process of change that has transformed life on Earth Biologists ask questions such as:
How a single cell develops into an organism? How the human mind works? How living things interact in communities?

Some properties of life

Order

Response to the environment Evolutionary adaptation

Regulation Energy processing Reproduction Growth and development

Fig. 1-3

Concept 1.1: Themes connect the concepts of biology

Biology consists of more than memorizing factual details

Themes help to organize biological information

Theme 1. Evolution, the Overarching Theme of Biology

Evolution makes sense of everything we know about living organisms

Organisms living on Earth are modified descendents of common ancestors

Theme 2: New properties emerge at each level in the biological hierarchy

The study of life can be divided into different levels of biological organization:
from molecules to the entire living planet

12 Levels of biological organization

(from biosphere to atom)
1. The biosphere 9. Cells 6. Organ systems 7. Organs 2. Ecosystems 10. Organelles 3. Communities
1 m 10 m

12. Atoms

8. Tissues 4. Populations 5. Organisms

50 m

11. Molecules

Fig. 1-4

Emergent Properties Emergent properties:

result from the arrangement and interaction of parts in a system characterize nonbiological entities as well

Example: a functioning bicycle emerges only when all of the necessary parts connect properly

The Power and Limitations of Reductionism

Reductionism: reduction of complex systems to simpler components that are more manageable to study
For example, the molecular structure of DNA

Balance of reductionism with the study of emergent properties

For example, new understanding comes from studying the interactions of DNA with other molecules

Systems Biology
System - combination of components that function together Systems biology constructs models for the dynamic behavior of whole biological systems The systems approach poses questions such as:
How does a drug for blood pressure affect other organs? How does increasing CO2 alter the biosphere?

Theme 3: Organisms interact with their environments, exchanging matter and energy
Every organism interacts with its environment, including nonliving factors and other organisms Both organisms and their environments are affected by the interactions between them
Example, a tree takes up water and minerals from the soil and carbon dioxide from the air; the tree releases oxygen to the air and roots help form soil

Ecosystem Dynamics

The dynamics of an ecosystem include two major processes:

1. Cycling of nutrients:
materials acquired by plants eventually return to the soil

2. Flow of energy:
from sunlight to producers to consumers

Energy Conversion
Work requires a source of energy Energy can be stored in different forms:
light, chemical, kinetic, or thermal

The energy exchange between an organism and its environment often involves energy transformations Energy flows through an ecosystem, usually entering as light and exiting as heat

Theme 4: Structure and function are correlated at all levels of biological organization
Structure and function of living organisms are closely related Example 1: a leaf is thin and flat, maximizing the capture of light by chloroplasts

Example 2

Theme 5: Cells are an organisms basic units of structure and function

Cell is the lowest level of organization that can perform all activities required for life All cells:
Are enclosed by a membrane Use DNA as their genetic information

The ability of cells to divide is the basis of all reproduction, growth, and repair of multicellular organisms

Eukaryotic cell vs prokaryotic cell

Eukaryotic cell:
has membrane-enclosed organelles; the largest organelle is usually the nucleus plants, animals, fungi, protists

Prokaryotic cell:
simpler and usually smaller; NO nucleus; NO other membraneenclosed organelles Bacteria and Archaea

Theme 6: The continuity of life is based on heritable information in the form of DNA
Chromosomes contain most of a cells genetic material in the form of DNA (deoxyribonucleic acid) DNA is the substance of genes Genes are the units of inheritance that transmit information from parents to offspring

DNA Structure and Function

Each chromosome has one long DNA molecule with hundreds or thousands of genes DNA is inherited by offspring from their parents DNA controls the development and maintenance of organisms

DNA:
Each DNA molecule is made up of two long chains arranged in a double helix

Each link of a chain is one of four kinds of chemical building blocks called nucleotides

Genes and genomes Genes control protein production indirectly DNA is transcribed into RNA then translated into a protein An organisms genome is its entire set of genetic instructions

Systems Biology at the Levels of Cells and Molecules

The human genome and those of many other organisms have been sequenced using DNA-sequencing machines Knowledge of a cells genes and proteins can be integrated using a systems approach

Fig. 1-11

 Advances in systems biology at the cellular and molecular level depend on:
1. High-throughput technology, which yields enormous amounts of data 2. Bioinformatics, which is the use of computational tools to process a large volume of data 3. Interdisciplinary research teams

Theme 7: Feedback mechanisms regulate biological systems

Feedback mechanisms allow biological processes to self-regulate: Negative feedback:
as more of a product accumulates, the process creating it slows and less of the product is produced;

Positive feedback:
as more of a product accumulates, the process creating it speeds up and more of the product is produced

Concept 1.2: The Core Theme: Evolution accounts for the unity and diversity of life

Nothing in biology makes sense except in the light of evolutionTheodosius Dobzhansky Evolution unifies biology at different scales of size throughout the history of life on Earth

Organizing the Diversity of Life

Approximately 1.8 million species have been identified and named to date Thousands more are identified each year Estimates of the total number of species that actually exist range from 10 million to over 100 million

Grouping Species: The Basic Idea

Taxonomy - branch of biology that names and classifies species into groups of increasing breadth Domains, followed by kingdoms, are the broadest units of classification

The Three Domains of Life

Three-domain system:
currently used replaces the old fivekingdom system

Domain Bacteria and domain Archaea comprise the prokaryotes Domain Eukarya includes all eukaryotic organisms

The domain Eukarya includes three multicellular kingdoms:

1. Plantae 2. Fungi 3. Animalia

Other eukaryotic organisms were formerly grouped into a kingdom called Protista, These are now often grouped into many separate kingdoms

Unity in the Diversity of Life

A striking unity underlies the diversity of life:
DNA is the universal genetic language common to all organisms; Unity is evident in many features of cell structure

Charles Darwin and the Theory of Natural Selection

Charles Darwin:
in 1859 published On the Origin of Species by Means of Natural Selection made two main points: Species showed evidence of descent with modification from common ancestors; Natural selection is the mechanism behind descent with modification

Darwin as a young man

Darwins theory explained the duality of unity and diversity

Fig. 1-18

 Darwin observed:
Individuals in a population have traits that vary; Many of these traits are heritable (passed from parents to offspring); More offspring are produced than survive; Competition is inevitable; Species generally suit their environment

 Darwin inferred:
Individuals that are best suited to their environment are more likely to survive and reproduce; Over time, more individuals in a population will have the advantageous traits;

In other words, the natural environment selects for beneficial traits

Natural selection is evident:

in adaptations of organisms:
their way of life

Bat wings are an example of adaptation

The Tree of Life Unity in diversity arises from descent with modification
Example: the forelimb of the bat, horse and whale flipper all share a common skeletal architecture

Fossils provide additional evidence of anatomical unity from descent with modification

Darwin:
Natural selection could cause an ancestral species to give rise to two or more descendent species: Example: finch species of the Galpagos Islands Evolutionary relationships are often illustrated with tree-like diagrams that show ancestors and their descendents

Concept 1.3: Scientists use two main forms of inquiry in their study of nature The word Science is derived from Latin and means to know; Inquiry:
the search for information and explanation;

2 main types of scientific inquiry:

1) discovery science 2) hypothesis-based science

1. Discovery Science
Discovery science: describes natural structures and processes; is based on:
1) observation 2) analysis of data

Types of Data

Data:
recorded observations or items of information; fall into two categories:
Qualitative:
descriptions rather than measurements;

Quantitative:
recorded measurements, sometimes organized into tables and graphs

Induction in Discovery Science Inductive reasoning: draws conclusions through the logical process of induction:
repeated specific observations can lead to important generalizations; Examples:
The sun always rises in the east. All organisms are made of cells.

2. Hypothesis-Based Science

Observations can lead us:

to ask more questions; propose hypothetical explanations called hypotheses

The Role of Hypotheses in Inquiry Hypothesis:

a tentative answer to a well-framed question; leads to predictions that can be tested by observation or experimentation; Example:
Observation: Your flashlight doesnt work Question: Why doesnt your flashlight work? Hypothesis 1: The batteries are dead Hypothesis 2: The bulb is burnt out; Both of these hypotheses are testable

Deduction: The IfThen Logic of Hypothesis Based Science Deductive reasoning:

uses general premises to make specific predictions; Example: if organisms are made of cells (premise 1), and if humans are organisms (premise 2),
then humans are composed of cells (deductive prediction)

A Closer Look at Hypotheses in Scientific Inquiry

A hypothesis must be testable and falsifiable; Hypothesis-based science often uses two or more alternative hypotheses; Failure to falsify a hypothesis does not prove that hypothesis:
Example:
you replace your flashlight bulb, and it now works; this supports the hypothesis that your bulb was burnt out, BUT does not prove it (perhaps the first bulb was inserted incorrectly)

The Myth of the Scientific Method Scientific method:

an idealized process of inquiry;

Hypothesis-based science:
is based on the textbook scientific method; but rarely follows all the ordered steps;

Discovery science:
has made important contributions with very little dependence on the so-called scientific method

Designing Controlled Experiments Controlled experiment:

compares an experimental group with a control group; only the variable of interest differs between the control and experimental groups (ideally); means that control groups are used to cancel the effects of unwanted variables; does not mean that all unwanted variables are kept constant

Limitations of Science

Science:
observations and experimental results must be repeatable; cannot support or falsify supernatural explanations:
they are outside the bounds of science

Theories in Science

In the context of science, a theory is:

broader in scope than a hypothesis; general, and can lead to new testable hypotheses; supported by a large body of evidence in comparison to a hypothesis

Model Building in Science

Models:
representations of natural phenomena; can take the form of:
diagrams, 3-dimensional objects, computer programs, mathematical equations