BioL 101 - Zoology (Lecture notes for chapter 1)
LEARNING OBJECTIVES Readers will be able to:
1.1 Explain the unifying properties of living systems as outcomes of life’s unique evolutionary history.
1.2 Explain the major features unique to the animal branch of the evolutionary tree of life.
1.3 Explain how science consists in testing, possibly rejecting, and improving our simplest and best explanations using data, not in proving the correctness of a conjecture.
1.4 Explain the five major conjectures of Darwin’s evolutionary theory—perpetual change, common descent, multiplication of species, gradualism, and natural selection—and the roles of Mendelian genetics and the chromosomal theory of inheritance in animal evolution.
All descendants of life’s common ancestor, past and present, lie within our concept of life.
Life’s most fundamental attribute is its reproduction of individuals with heredity and variation. Replication of large molecules store information is unique to life and must trace to life’s origin. These properties establish a temporal continuity of ancestral and descendant populations showing extensive and ongoing change, which we call evolution. Through its evolution, life has generated many spectacular features that have no counterparts in the nonliving world. Novel properties emerge at all levels of life’s hierarchical systems, from molecules and cells to organismal form and behavior.
Life’s most outstanding general features
Living systems demonstrate a unique and complex molecular organization.
Living systems assemble large molecules, called macromolecules, that greatly exceed in complexity the small molecules of nonliving matter. Macromolecules contain the same kinds of atoms and chemical bonds that occur in nonliving matter and obey all fundamental laws of chemistry; it is only the complex organizational structure of these macromolecules that makes them unique to life. We recognize four major categories of biological macromolecules: ==nucleic acids, proteins, carbohydrates, and lipids. ==
Living systems demonstrate a unique and complex hierarchical organization.
The nonliving matter is organized at least into atoms and molecules and often has a higher degree of organization as well. However, atoms and molecules are combined into patterns in the living world that do not exist in nonliving matter. In living systems, we find a hierarchy of levels that includes, in ascending order of complexity, macromolecules, cells, organisms, populations, and species.
The organismal level also has a hierarchical substructure; cells combine to form tissues, which combine to form organs, which likewise combine to form organ systems.
Cells are the smallest units of the biological hierarchy that are semiautonomous in their ability to conduct basic functions, including reproduction. Replication of molecules and subcellular components occurs only within a cellular context, not independently. Therefore, Cells considered the basic units of living systems are therefore considered the basic units of living systems.
An important consequence of this hierarchy is that;
we cannot infer the properties at any given level even from the most complete knowledge of the properties of its component parts.
The appearance of new characteristics at a given level of organization is called emergence, and these characteristics are called emergent properties.
Emergent properties expressed at a particular level of the biological hierarchy are certainly influenced and restricted by properties of the lower-level components.
Living systems can reproduce themselves
Life does not arise spontaneously but comes only from prior life, through reproduction.
At each level of the biological hierarchy, living forms reproduce to generate others like themselves.
Evolutionary divergence of character among separated population lineages can produce a multiplication of species, in a process called speciation.
Heredity is the faithful transmission of traits from parents to offspring, usually (but not necessarily) observed at the organismal level.
Variation is the production of differences among the traits of different individuals.
Interaction of heredity and variation in the reproductive process makes organic evolution possible and inevitable.
If heredity were perfect, living systems would never change.
if variation were uncontrolled by heredity, biological systems would lack the stability that allows them to persist through time.
A genetic program provides fidelity of inheritance.
Nucleic acids encode structures of the protein molecules needed for organismal development and functioning.
DNA (Deoxyribonucleic acid) stores genetic information. DNA is a very long, linear chain of subunits called nucleotides, each of which contains a sugar phosphate (deoxyribose phosphate) and one of four nitrogenous bases (adenine, cytosine, guanine, or thymine, abbreviated A, C, G, and T, respectively).
Genetic code is the correspondence between the sequence of bases in DNA and the sequence of amino acids in a protein.
Living organisms maintain themselves by acquiring nutrients from their environment.
Nutrients supply chemical energy and molecular components for building and maintaining a living system.
Metabolism is an interaction of destructive (catabolic) and constructive (anabolic) reactions.
The study of metabolic functions from the biochemical to the organismal levels is called physiology.
All organisms pass through a characteristic life cycle.
Development describes the characteristic changes that an organism undergoes from its origin (usually the fertilization of an egg by sperm) to its final adult form.
The transformation that occurs from one stage to another is called metamorphosis.
All animals interact with their environments.
The study of organismal interaction with an environment is called ecology. Of special interest are the factors that influence the geographic distribution and abundance of animals. The science of ecology reveals how an organism perceives environmental stimuli and responds in appropriate ways by adjusting its metabolism and physiology
All organisms respond to environmental stimuli, a property called irritability.
Living systems and their parts show precise and controlled movements arising from within the system.
The energy that living systems extract from their environments permits them to initiate controlled movements. Such movements at the cellular level are essential for reproduction, growth, and many responses to stimuli in all living forms and for development in multicellular ones.
The first law of thermodynamics is the law of conservation of energy.
Energy is neither created nor destroyed but can be transformed from one form to another.
The second law of thermodynamics states that physical systems tend to proceed toward a state of greater disorder, or entropy. Energy obtained and stored by plants is subsequently released by various mechanisms and finally dissipated as heat.
Living cells maintain complex molecular organization only as long as energy fuels the organization.
Animals form a distinct branch on the evolutionary tree of life. It is a large and old branch that originated in the Precambrian seas over 600 million years ago.
Animals form part of an even larger limb called eukaryotes, organisms whose cells contain membrane-enclosed nuclei. This larger limb includes plants, fungi, and numerous unicellular forms.
We distinguish animals also by the absence of characteristics that have evolved in other eukaryotes but not in animals.
Some organisms that are neither animals nor plants combine the properties of animals and plants. For example, Euglena is a motile, single-celled organism that resembles plants in being photosynthetic but resembles animals in its ability to eat food particles.
The microbiome is a major characteristic of animal life that is often overlooked: animal bodies typically harbor thousands of species of bacteria and archaea, primarily in the gut. These species typically exist in a harmless symbiosis with their animal hosts, with fewer than 100 species of bacteria being sources of infectious disease.
An animal’s microbiome is not strictly constant in species diversity and is subject to change as microbes are exchanged among animals of the same and different species.
A basic understanding of zoology requires understanding what science is, what it is not, and how we gain knowledge using the scientific method.
We examine the methodology that zoology shares with science as a whole. These procedures for constructing data-based explanations of natural phenomena distinguish sciences from activities that we exclude from the realm of science, such as art and religion.
Judge Overton stated explicitly these essential characteristics of science:
It is guided by natural law.
It has to be explanatory by reference to natural law.
It is testable against the observable world.
Its conclusions are tentative and therefore not necessarily the final word.
It is falsifiable.
Pursuit of scientific knowledge must be guided by the physical and chemical laws that govern the state of existence. Scientific knowledge must explain what is observed by reference to natural law without requiring the intervention of a supernatural being or force.
These essential criteria of science form the hypothetico-deductive method.
This method requires us to generate hypotheses or potential answers to a question being asked. These hypotheses are usually based on prior observations of nature or derived from theories based on such observations. Scientific hypotheses often constitute general statements about nature that may explain a large number of diverse observations.
The best hypotheses are those that make many predictions that, if found erroneous, cause rejection, or falsification, of the hypothesis.
The scientific method is summarized as a series of steps:
Observation
Observations are a critical first step in evaluating the life histories of natural populations.
Question
Hypothesis
To test our hypothesis, we construct a null hypothesis. A null hypothesis is one that permits a statistical test of our data to reject its predictions if the hypothesis is false.
Empirical test
Note that a hypothesis cannot be proved correct using the scientific method. If the available data are compatible with it, the hypothesis serves as a guide for collecting additional data that potentially might reject it. Our most successful hypotheses are the ones that make specific predictions confirmed by large numbers of empirical tests.
Conclusions
Publication
If a hypothesis is very powerful in explaining a wide variety of related phenomena, it attains the status of a theory.
Our example of the use of natural selection.
Natural selection provides a potential explanation for the occurrence of many different traits distributed among virtually all animal species. Each of these instances constitutes a specific hypothesis generated from the theory of natural selection. Note, however, that falsification of a specific hypothesis does not necessarily lead to rejection of the theory as a whole. Natural selection may fail to explain origins of a human behavior.
We emphasize that “theory,” when used by scientists, does not mean “speculation” as it does in ordinary English usage.
Nonetheless, evolution, along with all other theories in science, is not proven in a mathematical sense, but it is testable, tentative, and falsifiable.
Darwin’s theory of evolution is now over 160 years old.
Professor Ernst Mayr of Harvard University argued that Darwinism should be viewed as five major theories.
These five theories have somewhat different origins and different fates and cannot be treated as only a single statement. The theories are:
(1) perpetual change
This is the basic theory of evolution on which the others depend. It states that the living world is neither constant nor perpetually cycling, but is always changing, with continuity between past and present forms of life. The varying forms of organisms undergo measurable changes across generations throughout time.
(2) common descent
states that all forms of life descend from a common ancestor through a branching of lineages.
life’s history has the structure of a branching evolutionary tree, called a phylogeny.
Species that share recent common ancestry have more similar features at all levels than do species whose most recent common ancestors occurred early in the history of life. The resulting phylogeny serves as the basis for our taxonomic classification of animals.
(3) multiplication of species
Darwin’s third theory states that the evolutionary process produces new species by splitting and transforming older ones. Species are now generally viewed as reproductively distinct populations of organisms that usually but not always differ from each other in organismal form.
(4) gradualism
States that the large differences in anatomical traits that characterize disparate species originate through the accumulation of many small incremental changes over very long periods of time. This theory is important because genetic changes that have very large effects on organismal form are usually harmful to an organism.
(5) natural selection
A creative process that generates novel forms from the small individual variations that occur among organisms within a population.
Darwin’s most famous theory, rests on three propositions.
First, there is variation among organisms (within populations) for anatomical, behavioral, and physiological traits.
Second, the variation is at least partly heritable so that offspring tend to resemble their parents.
Third, organisms with different variant forms are expected to leave different numbers of offspring to future generations.
Adaptation is the expected result of a process that accumulates the most favorable variants occurring in a population throughout long periods of evolutionary time. Adaptation was viewed previously as strong evidence against evolution, and Darwin’s theory of natural selection was therefore important for convincing people that a natural process, capable of being studied scientifically, could produce new species.
Darwin was never able to counter this criticism successfully. It did not occur to Darwin that hereditary factors could be discrete and nonblending and that a new genetic variant therefore could persist unaltered from one generation to the next. This principle is called particulate inheritance. It was established after 1900 with the discovery of Gregor Mendel’s genetic experiments, and it was eventually incorporated into what we now call the chromosomal theory of inheritance. We use the term Neo-Darwinism to describe Darwin’s theories as modified by incorporating this theory of inheritance.
This theory comes from the consolidation of research done in the fields of genetics, which was founded by the experimental work of Gregor Mendel (see Figure 1.16), and cell biology.
The genetic approach consists of mating or “crossing” populations of organisms that are true breeding for contrasting traits, and then following hereditary transmission of those traits through subsequent generations.
“True-breeding” means that a population maintains across generations only one of the contrasting traits when propagated in isolation from other populations.
LEARNING OBJECTIVES Readers will be able to:
1.1 Explain the unifying properties of living systems as outcomes of life’s unique evolutionary history.
1.2 Explain the major features unique to the animal branch of the evolutionary tree of life.
1.3 Explain how science consists in testing, possibly rejecting, and improving our simplest and best explanations using data, not in proving the correctness of a conjecture.
1.4 Explain the five major conjectures of Darwin’s evolutionary theory—perpetual change, common descent, multiplication of species, gradualism, and natural selection—and the roles of Mendelian genetics and the chromosomal theory of inheritance in animal evolution.
All descendants of life’s common ancestor, past and present, lie within our concept of life.
Life’s most fundamental attribute is its reproduction of individuals with heredity and variation. Replication of large molecules store information is unique to life and must trace to life’s origin. These properties establish a temporal continuity of ancestral and descendant populations showing extensive and ongoing change, which we call evolution. Through its evolution, life has generated many spectacular features that have no counterparts in the nonliving world. Novel properties emerge at all levels of life’s hierarchical systems, from molecules and cells to organismal form and behavior.
Life’s most outstanding general features
Living systems demonstrate a unique and complex molecular organization.
Living systems assemble large molecules, called macromolecules, that greatly exceed in complexity the small molecules of nonliving matter. Macromolecules contain the same kinds of atoms and chemical bonds that occur in nonliving matter and obey all fundamental laws of chemistry; it is only the complex organizational structure of these macromolecules that makes them unique to life. We recognize four major categories of biological macromolecules: ==nucleic acids, proteins, carbohydrates, and lipids. ==
Living systems demonstrate a unique and complex hierarchical organization.
The nonliving matter is organized at least into atoms and molecules and often has a higher degree of organization as well. However, atoms and molecules are combined into patterns in the living world that do not exist in nonliving matter. In living systems, we find a hierarchy of levels that includes, in ascending order of complexity, macromolecules, cells, organisms, populations, and species.
The organismal level also has a hierarchical substructure; cells combine to form tissues, which combine to form organs, which likewise combine to form organ systems.
Cells are the smallest units of the biological hierarchy that are semiautonomous in their ability to conduct basic functions, including reproduction. Replication of molecules and subcellular components occurs only within a cellular context, not independently. Therefore, Cells considered the basic units of living systems are therefore considered the basic units of living systems.
An important consequence of this hierarchy is that;
we cannot infer the properties at any given level even from the most complete knowledge of the properties of its component parts.
The appearance of new characteristics at a given level of organization is called emergence, and these characteristics are called emergent properties.
Emergent properties expressed at a particular level of the biological hierarchy are certainly influenced and restricted by properties of the lower-level components.
Living systems can reproduce themselves
Life does not arise spontaneously but comes only from prior life, through reproduction.
At each level of the biological hierarchy, living forms reproduce to generate others like themselves.
Evolutionary divergence of character among separated population lineages can produce a multiplication of species, in a process called speciation.
Heredity is the faithful transmission of traits from parents to offspring, usually (but not necessarily) observed at the organismal level.
Variation is the production of differences among the traits of different individuals.
Interaction of heredity and variation in the reproductive process makes organic evolution possible and inevitable.
If heredity were perfect, living systems would never change.
if variation were uncontrolled by heredity, biological systems would lack the stability that allows them to persist through time.
A genetic program provides fidelity of inheritance.
Nucleic acids encode structures of the protein molecules needed for organismal development and functioning.
DNA (Deoxyribonucleic acid) stores genetic information. DNA is a very long, linear chain of subunits called nucleotides, each of which contains a sugar phosphate (deoxyribose phosphate) and one of four nitrogenous bases (adenine, cytosine, guanine, or thymine, abbreviated A, C, G, and T, respectively).
Genetic code is the correspondence between the sequence of bases in DNA and the sequence of amino acids in a protein.
Living organisms maintain themselves by acquiring nutrients from their environment.
Nutrients supply chemical energy and molecular components for building and maintaining a living system.
Metabolism is an interaction of destructive (catabolic) and constructive (anabolic) reactions.
The study of metabolic functions from the biochemical to the organismal levels is called physiology.
All organisms pass through a characteristic life cycle.
Development describes the characteristic changes that an organism undergoes from its origin (usually the fertilization of an egg by sperm) to its final adult form.
The transformation that occurs from one stage to another is called metamorphosis.
All animals interact with their environments.
The study of organismal interaction with an environment is called ecology. Of special interest are the factors that influence the geographic distribution and abundance of animals. The science of ecology reveals how an organism perceives environmental stimuli and responds in appropriate ways by adjusting its metabolism and physiology
All organisms respond to environmental stimuli, a property called irritability.
Living systems and their parts show precise and controlled movements arising from within the system.
The energy that living systems extract from their environments permits them to initiate controlled movements. Such movements at the cellular level are essential for reproduction, growth, and many responses to stimuli in all living forms and for development in multicellular ones.
The first law of thermodynamics is the law of conservation of energy.
Energy is neither created nor destroyed but can be transformed from one form to another.
The second law of thermodynamics states that physical systems tend to proceed toward a state of greater disorder, or entropy. Energy obtained and stored by plants is subsequently released by various mechanisms and finally dissipated as heat.
Living cells maintain complex molecular organization only as long as energy fuels the organization.
Animals form a distinct branch on the evolutionary tree of life. It is a large and old branch that originated in the Precambrian seas over 600 million years ago.
Animals form part of an even larger limb called eukaryotes, organisms whose cells contain membrane-enclosed nuclei. This larger limb includes plants, fungi, and numerous unicellular forms.
We distinguish animals also by the absence of characteristics that have evolved in other eukaryotes but not in animals.
Some organisms that are neither animals nor plants combine the properties of animals and plants. For example, Euglena is a motile, single-celled organism that resembles plants in being photosynthetic but resembles animals in its ability to eat food particles.
The microbiome is a major characteristic of animal life that is often overlooked: animal bodies typically harbor thousands of species of bacteria and archaea, primarily in the gut. These species typically exist in a harmless symbiosis with their animal hosts, with fewer than 100 species of bacteria being sources of infectious disease.
An animal’s microbiome is not strictly constant in species diversity and is subject to change as microbes are exchanged among animals of the same and different species.
A basic understanding of zoology requires understanding what science is, what it is not, and how we gain knowledge using the scientific method.
We examine the methodology that zoology shares with science as a whole. These procedures for constructing data-based explanations of natural phenomena distinguish sciences from activities that we exclude from the realm of science, such as art and religion.
Judge Overton stated explicitly these essential characteristics of science:
It is guided by natural law.
It has to be explanatory by reference to natural law.
It is testable against the observable world.
Its conclusions are tentative and therefore not necessarily the final word.
It is falsifiable.
Pursuit of scientific knowledge must be guided by the physical and chemical laws that govern the state of existence. Scientific knowledge must explain what is observed by reference to natural law without requiring the intervention of a supernatural being or force.
These essential criteria of science form the hypothetico-deductive method.
This method requires us to generate hypotheses or potential answers to a question being asked. These hypotheses are usually based on prior observations of nature or derived from theories based on such observations. Scientific hypotheses often constitute general statements about nature that may explain a large number of diverse observations.
The best hypotheses are those that make many predictions that, if found erroneous, cause rejection, or falsification, of the hypothesis.
The scientific method is summarized as a series of steps:
Observation
Observations are a critical first step in evaluating the life histories of natural populations.
Question
Hypothesis
To test our hypothesis, we construct a null hypothesis. A null hypothesis is one that permits a statistical test of our data to reject its predictions if the hypothesis is false.
Empirical test
Note that a hypothesis cannot be proved correct using the scientific method. If the available data are compatible with it, the hypothesis serves as a guide for collecting additional data that potentially might reject it. Our most successful hypotheses are the ones that make specific predictions confirmed by large numbers of empirical tests.
Conclusions
Publication
If a hypothesis is very powerful in explaining a wide variety of related phenomena, it attains the status of a theory.
Our example of the use of natural selection.
Natural selection provides a potential explanation for the occurrence of many different traits distributed among virtually all animal species. Each of these instances constitutes a specific hypothesis generated from the theory of natural selection. Note, however, that falsification of a specific hypothesis does not necessarily lead to rejection of the theory as a whole. Natural selection may fail to explain origins of a human behavior.
We emphasize that “theory,” when used by scientists, does not mean “speculation” as it does in ordinary English usage.
Nonetheless, evolution, along with all other theories in science, is not proven in a mathematical sense, but it is testable, tentative, and falsifiable.
Darwin’s theory of evolution is now over 160 years old.
Professor Ernst Mayr of Harvard University argued that Darwinism should be viewed as five major theories.
These five theories have somewhat different origins and different fates and cannot be treated as only a single statement. The theories are:
(1) perpetual change
This is the basic theory of evolution on which the others depend. It states that the living world is neither constant nor perpetually cycling, but is always changing, with continuity between past and present forms of life. The varying forms of organisms undergo measurable changes across generations throughout time.
(2) common descent
states that all forms of life descend from a common ancestor through a branching of lineages.
life’s history has the structure of a branching evolutionary tree, called a phylogeny.
Species that share recent common ancestry have more similar features at all levels than do species whose most recent common ancestors occurred early in the history of life. The resulting phylogeny serves as the basis for our taxonomic classification of animals.
(3) multiplication of species
Darwin’s third theory states that the evolutionary process produces new species by splitting and transforming older ones. Species are now generally viewed as reproductively distinct populations of organisms that usually but not always differ from each other in organismal form.
(4) gradualism
States that the large differences in anatomical traits that characterize disparate species originate through the accumulation of many small incremental changes over very long periods of time. This theory is important because genetic changes that have very large effects on organismal form are usually harmful to an organism.
(5) natural selection
A creative process that generates novel forms from the small individual variations that occur among organisms within a population.
Darwin’s most famous theory, rests on three propositions.
First, there is variation among organisms (within populations) for anatomical, behavioral, and physiological traits.
Second, the variation is at least partly heritable so that offspring tend to resemble their parents.
Third, organisms with different variant forms are expected to leave different numbers of offspring to future generations.
Adaptation is the expected result of a process that accumulates the most favorable variants occurring in a population throughout long periods of evolutionary time. Adaptation was viewed previously as strong evidence against evolution, and Darwin’s theory of natural selection was therefore important for convincing people that a natural process, capable of being studied scientifically, could produce new species.
Darwin was never able to counter this criticism successfully. It did not occur to Darwin that hereditary factors could be discrete and nonblending and that a new genetic variant therefore could persist unaltered from one generation to the next. This principle is called particulate inheritance. It was established after 1900 with the discovery of Gregor Mendel’s genetic experiments, and it was eventually incorporated into what we now call the chromosomal theory of inheritance. We use the term Neo-Darwinism to describe Darwin’s theories as modified by incorporating this theory of inheritance.
This theory comes from the consolidation of research done in the fields of genetics, which was founded by the experimental work of Gregor Mendel (see Figure 1.16), and cell biology.
The genetic approach consists of mating or “crossing” populations of organisms that are true breeding for contrasting traits, and then following hereditary transmission of those traits through subsequent generations.
“True-breeding” means that a population maintains across generations only one of the contrasting traits when propagated in isolation from other populations.
