CHAPTER
Biology and the Tree of Life
1
Learning Objectives: Students should be able to...
• Describe the five fundamental characteristics of life.
• Describe the three unifying ideas of biology.
• Explain how biologists use predictions of the theory of evolution and genetic sequence
analysis to construct a tree of life.
• Describe key steps in the scientific process.
Lecture Outline
I. What Does It Mean to Say That Something Is Alive?
A. All living organisms share five fundamental traits:
1. Organisms are made up of membrane-bound cells.
2. Organisms can reproduce.
3. Populations of organisms evolve.
4. Organisms have hereditary information encoded in genes.
5. Organisms acquire and use energy.
II. Life Is Cellular
A. Are all organisms made of cells?
1. Cells were first described and identified in cork tissue (Hooke, 1665) and in water and
a variety of living tissues (van Leeuwenhoek). (Fig. 1.1)
2. Scientists have examined thousands of plant and animal samples and have concluded
that all organisms are composed of cells.
3. A cell is an organized compartment bounded by a thin, flexible plasma membrane and
contains concentrated chemicals in an aqueous solution.
4. Most chemical reactions important to life occur inside cells.
5. Cells reproduce via cell division.
B. Where do cells come from?
1. Two components of theories: observable pattern and the mechanism or process that
creates the pattern
2. Spontaneous generation hypothesis (Virchow) versus all-cells-from-cells (Pasteur)
hypothesis
a. Pasteur’s experiment supported the all-cells-from-cells hypothesis. (Fig. 1.2)
Copyright © 2017 Pearson Education, Inc. 1
, 3. All individuals in a population of organisms are related by ancestry.
4. All cells in a multicellular organism are descended from the same ancestral cell.
C. Statement of the cell theory: All organisms are made of cells, and all cells come from
preexisting cells.
1. Theories are explanations for phenomena or observations supported by evidence.
2. Chemical evolution: Biologists have evidence that life arose from non-life early in
life’s history through this process.
D. Life replicates through cell division.
1. New cells arise when preexisting cells split.
2. All species are connected by common ancestry was also a founding idea published in
the same year as all-cells-from-cells hypothesis.
III. Life Evolves
A. What is evolution?
1. Species are related by common ancestry (pattern component).
2. The characteristics of a species can be modified from generation to generation
(process component).
a. Darwin and Wallace (1858) proposed that this happens by natural selection
(descent with modification, Darwin).
3. Evolution is a change in heritable characteristics of a population over time.
4. Population is a group of individuals of the same species living in the same area at the
same time.
B. What is natural selection?
1. Natural selection occurs whenever two conditions are met:
a. Individuals within a population vary in characteristics that are heritable.
b. Certain heritable traits help individuals survive and produce offspring.
2. How do these two conditions lead to evolution?
a. If certain heritable traits help individuals produce more offspring, then those traits
become more common (more frequent) in the population over time.
3. Natural selection acts on individuals, but evolutionary change affects populations as a
whole.
4. Speciation: In recent decades, natural selection has caused populations of one species
to diverge and form new species.
5. Fitness is the ability to produce offspring.
6. Adaptation is a trait that increases an individual’s fitness in a particular environment.
IV. Life Processes Information
A. Chromosome Theory of Inheritance (1902): Inside cells, hereditary or genetic informa-
tion is encoded in genes, the units located on chromosomes.
1. Chromosomes consist of a molecule of deoxyribonucleic acid (DNA).
B. The Central Dogma (DNA RNA Protein) (Fig. 1.5)
1. Watson/Crick double-stranded helix (Fig. 1.4)
2. DNA encodes a message in the sequence of its building blocks: A, T, C, and G.
2 INSTRUCTOR GUIDE FOR BIOLOGICAL SCIENCE, 6e Copyright © 2017 Pearson Education, Inc.
, 3. A pairs with T, C pairs with G.
4. DNA is made into RNA (ribonucleic acid), messenger RNA is read to make a protein.
C. Life requires energy.
1. Two fundamental nutritional needs are required by organisms: ATP (adenosine
triphosphate) and obtaining molecules that can be used as building blocks for the
synthesis of complex functions of the cell.
V. The Tree of Life
A. Evolution leads to speciation, the generation of new species.
1. This implies that all species come from preexisting species and that their ancestry can
be traced back to a single common ancestor.
2. Therefore, we should be able to reconstruct the tree of life—a family tree of all
organisms.
B. How can we use molecules to understand the tree of life?
1. Evolutionary relatedness should be reflected in molecular similarities.
2. Woese and colleagues proposed using RNA to assess the relatedness (phylogeny) of
all living groups of organisms.
C. What does it mean to analyze genetic variation?
1. Looking at genetic variation means looking at the DNA or RNA of that organism
and its close relationship to related species. (Making Models 1.1 and plant/algae
example)
2. The goal in analysis is to then produce a diagram, a phylogenetic tree, that describes
those organisms being compared. (Fig. 1.6)
D. How is the tree of life estimated from genetic data?
1. Construction of a phylogenetic tree is done using computer programs to find the
arrangement of branches that is most consistent with the similarities and differences
observed in the genetic data.
2. The tree of life contains a diverse array of species with a main node that extends to
the last universal common ancestor (LUCA).
a. There are three major lineages in the tree of life: Bacteria, Archaea (barely known
prior to this analysis), and Eukarya. (Fig. 1.7)
b. Fungi are more closely related to animals than to plants.
c. The data did not support older models, such as the five-kingdom model.
E. The tree of life is a work in progress.
a. Students should understand that the lines in the tree of life, specifically the length of
the lines between species, reflect the variation in nucleotide sequences between
species. (BioSkills 13)
F. How should we name branches on the tree of life? (BioSkills 15)
1. The three major lineages of life⎯Bacteria, Archaea, and Eukarya⎯are called
domains.
2. A phylum (plural: phyla) is a major lineage within one of the three domains.
3. Several (or more) distinct phyla per domain are each represented by distinct major
branches on the tree of life.
Copyright © 2017 Pearson Education, Inc. CHAPTER 1 Biology and the Tree of Life 3
, 4. Each species has a unique, formal, two-part (Genus species) scientific name. This
system was developed by Linnaeus (1735) and is still used today.
VI. Doing Biology
A. What is the nature of science?
1. Biologists test the predictions made by alternative hypotheses, either by making
observations or by setting up carefully designed experiments.
2. Biologists explore only those types of questions that can be tested by collecting data
from the observable world.
3. Are science and religion compatible?
a. Science explores the what (patterns) and how (processes) questions of life.
b. Religion explores why we exist and how we should live.
B. Why do giraffes have long necks? An introduction to hypothesis testing
1. State the hypothesis as precisely as possible, and list the predictions that it makes.
(Example: Giraffes have long necks for food competition.)
a. Remember to search for alternative hypotheses, too. (Example: Giraffes have long
necks to compete for mates.)
2. Design an observational or experimental study that can test the predictions. (Where
do giraffes feed? Prediction for food competition would be high in trees.)
3. Interpret the results.
a. If the predictions are accurate, the hypothesis is supported.
b. If the predictions are not accurate, the hypothesis as originally stated is not correct.
(Fig. 1.8a) It may need to be modified or discarded altogether in favor of an
alternative hypothesis.
4. Example: Why do giraffes have long necks?
a. Students should be able to state whether the giraffe study was an observational or
experimental study. Students should also be able to develop hypotheses, generate
ideas for studies, and interpret hypothetical data for similar questions, such as,
“Why do zebras have stripes?”
C. Let’s look at an introduction to experimental design.
1. Experiments allow researchers to test the effect of a single, well-defined factor on a
particular phenomenon.
2. Example: Navigation by Saharan desert ants—How do ants find their way back to
their nest? (Fig. 1.9)
a. Hypothesis: Ants know the distance back based on number of steps taken and stride
length.
b. Variable tested—stride length (stubs, normal, and stilts) (Figs. 1.10, 1.11)
3. Important features of experimental design:
a. It is critical to include control groups to rule out the effect of other factors. (Control
with normal ants to ensure that manipulating ants doesn’t alter ability to attain an
accurate distance.)
b. Control groups and experimental groups are exposed to exactly the same
conditions.
c. Repeating the test is essential; larger sample sizes reduce the effect of “noise” in
the data.
4 INSTRUCTOR GUIDE FOR BIOLOGICAL SCIENCE, 6e Copyright © 2017 Pearson Education, Inc.
Biology and the Tree of Life
1
Learning Objectives: Students should be able to...
• Describe the five fundamental characteristics of life.
• Describe the three unifying ideas of biology.
• Explain how biologists use predictions of the theory of evolution and genetic sequence
analysis to construct a tree of life.
• Describe key steps in the scientific process.
Lecture Outline
I. What Does It Mean to Say That Something Is Alive?
A. All living organisms share five fundamental traits:
1. Organisms are made up of membrane-bound cells.
2. Organisms can reproduce.
3. Populations of organisms evolve.
4. Organisms have hereditary information encoded in genes.
5. Organisms acquire and use energy.
II. Life Is Cellular
A. Are all organisms made of cells?
1. Cells were first described and identified in cork tissue (Hooke, 1665) and in water and
a variety of living tissues (van Leeuwenhoek). (Fig. 1.1)
2. Scientists have examined thousands of plant and animal samples and have concluded
that all organisms are composed of cells.
3. A cell is an organized compartment bounded by a thin, flexible plasma membrane and
contains concentrated chemicals in an aqueous solution.
4. Most chemical reactions important to life occur inside cells.
5. Cells reproduce via cell division.
B. Where do cells come from?
1. Two components of theories: observable pattern and the mechanism or process that
creates the pattern
2. Spontaneous generation hypothesis (Virchow) versus all-cells-from-cells (Pasteur)
hypothesis
a. Pasteur’s experiment supported the all-cells-from-cells hypothesis. (Fig. 1.2)
Copyright © 2017 Pearson Education, Inc. 1
, 3. All individuals in a population of organisms are related by ancestry.
4. All cells in a multicellular organism are descended from the same ancestral cell.
C. Statement of the cell theory: All organisms are made of cells, and all cells come from
preexisting cells.
1. Theories are explanations for phenomena or observations supported by evidence.
2. Chemical evolution: Biologists have evidence that life arose from non-life early in
life’s history through this process.
D. Life replicates through cell division.
1. New cells arise when preexisting cells split.
2. All species are connected by common ancestry was also a founding idea published in
the same year as all-cells-from-cells hypothesis.
III. Life Evolves
A. What is evolution?
1. Species are related by common ancestry (pattern component).
2. The characteristics of a species can be modified from generation to generation
(process component).
a. Darwin and Wallace (1858) proposed that this happens by natural selection
(descent with modification, Darwin).
3. Evolution is a change in heritable characteristics of a population over time.
4. Population is a group of individuals of the same species living in the same area at the
same time.
B. What is natural selection?
1. Natural selection occurs whenever two conditions are met:
a. Individuals within a population vary in characteristics that are heritable.
b. Certain heritable traits help individuals survive and produce offspring.
2. How do these two conditions lead to evolution?
a. If certain heritable traits help individuals produce more offspring, then those traits
become more common (more frequent) in the population over time.
3. Natural selection acts on individuals, but evolutionary change affects populations as a
whole.
4. Speciation: In recent decades, natural selection has caused populations of one species
to diverge and form new species.
5. Fitness is the ability to produce offspring.
6. Adaptation is a trait that increases an individual’s fitness in a particular environment.
IV. Life Processes Information
A. Chromosome Theory of Inheritance (1902): Inside cells, hereditary or genetic informa-
tion is encoded in genes, the units located on chromosomes.
1. Chromosomes consist of a molecule of deoxyribonucleic acid (DNA).
B. The Central Dogma (DNA RNA Protein) (Fig. 1.5)
1. Watson/Crick double-stranded helix (Fig. 1.4)
2. DNA encodes a message in the sequence of its building blocks: A, T, C, and G.
2 INSTRUCTOR GUIDE FOR BIOLOGICAL SCIENCE, 6e Copyright © 2017 Pearson Education, Inc.
, 3. A pairs with T, C pairs with G.
4. DNA is made into RNA (ribonucleic acid), messenger RNA is read to make a protein.
C. Life requires energy.
1. Two fundamental nutritional needs are required by organisms: ATP (adenosine
triphosphate) and obtaining molecules that can be used as building blocks for the
synthesis of complex functions of the cell.
V. The Tree of Life
A. Evolution leads to speciation, the generation of new species.
1. This implies that all species come from preexisting species and that their ancestry can
be traced back to a single common ancestor.
2. Therefore, we should be able to reconstruct the tree of life—a family tree of all
organisms.
B. How can we use molecules to understand the tree of life?
1. Evolutionary relatedness should be reflected in molecular similarities.
2. Woese and colleagues proposed using RNA to assess the relatedness (phylogeny) of
all living groups of organisms.
C. What does it mean to analyze genetic variation?
1. Looking at genetic variation means looking at the DNA or RNA of that organism
and its close relationship to related species. (Making Models 1.1 and plant/algae
example)
2. The goal in analysis is to then produce a diagram, a phylogenetic tree, that describes
those organisms being compared. (Fig. 1.6)
D. How is the tree of life estimated from genetic data?
1. Construction of a phylogenetic tree is done using computer programs to find the
arrangement of branches that is most consistent with the similarities and differences
observed in the genetic data.
2. The tree of life contains a diverse array of species with a main node that extends to
the last universal common ancestor (LUCA).
a. There are three major lineages in the tree of life: Bacteria, Archaea (barely known
prior to this analysis), and Eukarya. (Fig. 1.7)
b. Fungi are more closely related to animals than to plants.
c. The data did not support older models, such as the five-kingdom model.
E. The tree of life is a work in progress.
a. Students should understand that the lines in the tree of life, specifically the length of
the lines between species, reflect the variation in nucleotide sequences between
species. (BioSkills 13)
F. How should we name branches on the tree of life? (BioSkills 15)
1. The three major lineages of life⎯Bacteria, Archaea, and Eukarya⎯are called
domains.
2. A phylum (plural: phyla) is a major lineage within one of the three domains.
3. Several (or more) distinct phyla per domain are each represented by distinct major
branches on the tree of life.
Copyright © 2017 Pearson Education, Inc. CHAPTER 1 Biology and the Tree of Life 3
, 4. Each species has a unique, formal, two-part (Genus species) scientific name. This
system was developed by Linnaeus (1735) and is still used today.
VI. Doing Biology
A. What is the nature of science?
1. Biologists test the predictions made by alternative hypotheses, either by making
observations or by setting up carefully designed experiments.
2. Biologists explore only those types of questions that can be tested by collecting data
from the observable world.
3. Are science and religion compatible?
a. Science explores the what (patterns) and how (processes) questions of life.
b. Religion explores why we exist and how we should live.
B. Why do giraffes have long necks? An introduction to hypothesis testing
1. State the hypothesis as precisely as possible, and list the predictions that it makes.
(Example: Giraffes have long necks for food competition.)
a. Remember to search for alternative hypotheses, too. (Example: Giraffes have long
necks to compete for mates.)
2. Design an observational or experimental study that can test the predictions. (Where
do giraffes feed? Prediction for food competition would be high in trees.)
3. Interpret the results.
a. If the predictions are accurate, the hypothesis is supported.
b. If the predictions are not accurate, the hypothesis as originally stated is not correct.
(Fig. 1.8a) It may need to be modified or discarded altogether in favor of an
alternative hypothesis.
4. Example: Why do giraffes have long necks?
a. Students should be able to state whether the giraffe study was an observational or
experimental study. Students should also be able to develop hypotheses, generate
ideas for studies, and interpret hypothetical data for similar questions, such as,
“Why do zebras have stripes?”
C. Let’s look at an introduction to experimental design.
1. Experiments allow researchers to test the effect of a single, well-defined factor on a
particular phenomenon.
2. Example: Navigation by Saharan desert ants—How do ants find their way back to
their nest? (Fig. 1.9)
a. Hypothesis: Ants know the distance back based on number of steps taken and stride
length.
b. Variable tested—stride length (stubs, normal, and stilts) (Figs. 1.10, 1.11)
3. Important features of experimental design:
a. It is critical to include control groups to rule out the effect of other factors. (Control
with normal ants to ensure that manipulating ants doesn’t alter ability to attain an
accurate distance.)
b. Control groups and experimental groups are exposed to exactly the same
conditions.
c. Repeating the test is essential; larger sample sizes reduce the effect of “noise” in
the data.
4 INSTRUCTOR GUIDE FOR BIOLOGICAL SCIENCE, 6e Copyright © 2017 Pearson Education, Inc.
