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Exam 1 Study Guide/List of Topics (Chapters 1-7)
AAAS Article and Chapter 1:
People (those people not in boldface type will not
be on the exam). Know their century, Historical
period, nation of origin, and important
contributions/writings!
Anaximander
(610 – 547
BCE)
Greek

Heraclitus
(5th century
BCE)
(490-430
BCE)
Greek

Greek

(384-322
BCE)
Greek

Empedocles
Aristotle





Imagined the transition from fish to
reptiles to mammals and birds (first
thoughts of evolution)
thought change=fundamental principal of
the universe
Spontaneous generation from “body
part soup” Only certain combinations
survived.
His writings cover many subjects,
including physics, metaphysics,
poetry, theater, music, logic, rhetoric,
linguistics, politics, government,
ethics, biology, and zoology.
He was a great mind of the time, but
his legacy as an unquestioned
authority held back scientific progress
for centuries.
He made collections of creatures, did
dissections of animals, recognized
different kinds of organisms.
He noted the sequence of organ
development by observing chicken
eggs.
The world can be understood with
observation and reason
a slow rate for geological change,
undetectable in the lifetime of a
human being

Claudius Ptolemy
(90-168 AD)
Ibn al-Haytham
“Alhacen”
St. Thomas Aquinas
(965-1040)
Greceoegyptian
Arabic
(1225-1274)
Italian

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Christopher
Columbus
(1451-1506)
Italian

Nicolaus Copernicus
(1473-1543)
Polish

Ferdinand Magellan
(1480-1521)
Portugese

Gaspard Bauhin
(1560-1624)
Swiss

Sir Francis Bacon
(1561-1626)
English



proclaimed that there was a
hierarchical order of species from
most imperfect to most perfect, a
concept refined over the centuries as
the "Great Chain of Being." Scala
Naturae (Scale of Nature) which
ranked things from the inorganic to
humans to Gods.
believed species were immutable
Geocentric (earth centered) universe
(WRONG)
Father figure of Islamic science
Italian Dominican priest of the
Catholic Church, and an influential
philosopher and theologian in the
tradition of scholasticism.
You can have religious beliefs, but still
be rational.
Foremost classical proponent of
natural theology
Italian explorer, colonizer, and whose
voyages across the Atlantic Ocean led to
general European awareness of the
American continents in the Western
Hemisphere.
He proposed a heliocentric (sun
centered) universe
Explorer who was the first to sail from
the Atlantic Ocean into the Pacific Ocean
and the first to cross the Pacific; his ship
was the first to circumnavigate the globe.
Botanist who first used binomial
nomenclature used in 1623, in his Pinax
Theatri Botanici.
English philosopher, statesman,
scientist, lawyer, jurist, author and
father of the scientific method.
He outlined a new system of logic
(inductive reasoning) to improve on
the old philosophical process of
syllogism [deductive reasoning]
Inductive reasoning - a philosopher
should proceed through inductive

James
Usher/Ussher
Rene Descartes
(1581-1656)
Irish


(1596-1650)
French

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Carl von Linné
(Carolus Linnaeus)
(1707-1778)
Swedish
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Georges Louis
Leclerc, Comte de
Buffon
(1707-1788)
French
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
Albrecht von Haller
(1708-1777)
Swiss

reasoning from fact to axiom to
physical law.
Contributed to the modern scientific
method
wrote Novum Organum (1620)
Bishop, Argued the earth was born
Sunday the 23rd of October 4004 BCE.
A natural philosopher, rationalist and
mathematician
Rational thinking; “Cogito ergo sum” I
think therefore I am.
Vivisection- live dissection; believed
animals felt no pain
Discourse on Method (1637) –
framework for scientific methods
guiding principle
Popularized the binomial
nomenclature
The idea originated with Swiss
Botanist Gaspard Bauhin in 1623 in
his Pinax Theatri Botanici
Attempted to classify the material
world as evidence of the power of the
Christian God with Systema Naturae
(1753)
Naturalist, mathematician,
cosmologist, and encyclopedic author.
Buffon published thirty-six quarto
volumes of his Histoire naturelle; this
included everything known about the
natural world up to that time.
Concluded that species must have
improved and degenerated (change
through time)
Noted that similar environments have
distinct flora and fauna (Buffon’s Law
or the first principle of Biogeography).
Centers of creation/origin
Climate change must have facilitated
worldwide spread of species from
their centers of origin
Botanist, physiologist, lawyer, and poet
who helped solidify evolution with his
theory of encapsulation. Used the term
Charles Bonnet
(1720-1793)
Swiss
James Hutton
(1726-1797)
Scotland
Captain James Cook
(1728-1779)
British
William Paley
(1743-1805)
English
Jean-Baptiste de
Lamarck
(1744-1829)
French
evolution to describe the development of
the individual in the egg.
 Lawyer who believed that all future
generations are preformed within the
egg, his theory of encapsulation.
 Geologist, physician, naturalist,
chemist and experimental farmer.
 Considered the father of modern
geology.
 His theories of geology and geologic
time, also called deep time, came to be
included in theories which were called
Plutonism and later
Uniformitarianism.
 Explorer, navigator and cartographer.
 Cook made detailed maps of
Newfoundland prior to making three
voyages to the Pacific Ocean during
which he achieved the first European
contact with the eastern coastline of
Australia and the Hawaiian Islands as
well as the first recorded
circumnavigation of New Zealand.
 Wrote Natural Theology; or, Evidences
of the Existence and Attributes of the
Deity in 1802.
 The book was a major influence on
Charles Darwin.
 worked most of his life at the Muséum
d’Histoire Naturelle in Paris.
 Vitalism (wrong): Organisms have an
inner disposition, a “purposive force,”
to adapt their characteristics in
response to changes in the
environment (an aspect of vitalism for
Lamarck but similar to the modern
term developmental adaptation)
 hypothesized the Chain of Being or
Scala Naturae as a moving “escalator”
which he called Nature’s Parade = La
Marche de la Nature (1597) (wrong)
 First organisms arose by abiogenesis
(correct)
 Inheritance of acquired traits via use and
disuse. (wrong)

Baron Georges
Cuvier
(1769-1832)
French
Robert Edmond
Grant
(1793-1874)
English
Charles Lyell
(1797-1875)
British
Friedrich Wöhler
(1800-1882)
German
Charles Darwin
(1809-1882)
English
Proposed the continuity of species by
gradual modification through time
without leaving any gaps, a materialistic
explanation for evolution. (correct)
 Coined the term “invertebrates”.
 proposed a Theory of Catastrophism
to explain extinct organisms
 Accepted some fossils as evidence of
extinctions, but did not accept the
concept of life evolving, in opposition
to Buffon
 Recognized evidence of stratification
of rock layers, examples of
sedimentation, uplift and subsidence
 Recognized a Principle of Faunal
Succession used to assign times to
geologic strata
 The Animal Kingdom, Distributed
According to Its Organization (1817)
 The first Professor of Comparative
Anatomy at University College London.
 Described evolution of invertebrate
groups in 1826; one of the first published
uses of “evolution” for the transformation
of organism
 lawyer and the foremost geologist of
his day.
 Best known as the author of Principles
of Geology, which popularized James
Hutton's concepts of
uniformitarianism – the idea that the
earth was shaped by slow-moving
forces still in operation today.
 Lyell was a close and influential friend
of Charles Darwin.
 Synthesizes urea (discrediting vitalism)
(1828)
 Naturalist who established that all
species of life have descended over
time from common ancestry, and
proposed the scientific theory that this
branching pattern of evolution
resulted from a process that he called
natural selection.

Gregor Mendel
(1822-1884)
Austrian
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Wilhelm Weinberg
(1863-1937)
German
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Geoffrey Hardy
(1877-1947)
English
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Ronald A. Fisher
(1890-1962)
English

Stephen J. Gould
(1941-2002)
American

Richard Dawkins
(1941present day)
English
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
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Jeffery Barrick
(1980 present day)
American

The author of the ground breaking
book Origin of Species.
Augustinian monk who provided the
essential basis for understanding the
material basis of biological
inheritance in his genetic experiments
using pea plants.
Although Mendel's work was
published soon after The Origin of
Species, a mechanism of inheritance
was not widely known until the
beginning of the 20th century.
He established several Laws of
Inheritance.
Independently derived a formula for
calculating gene frequencies in
populations under natural selection;
Hardy-Weinberg Principle.
Independently derived a formula for
calculating gene frequencies in
populations under natural selection;
Hardy-Weinberg Principle.
Mathematician who combined
Mendelian inheritance with
population genetics.
An evolutionary biologist and
invertebrate paleontologist who
promoted Punctuated Equilibria as an
explanation for the sudden
appearance/disappearance of species
in the fossil record as communities
replace each other in locations over
geologic time.
Biologist who wrote The Blind
Watchmaker (1986)
Advocated for the gene is an important
unit of selection in The Selfish Gene
(1975)
Contemporary opponent of Intelligent
Design
Demonstrated evolution experimentally
using Escherichia coli bacteria in the
laboratory (2009) and recording the
mutations over 40,000 generations.
AAAS "The Nature of Science" Article and Chapter 1 concepts:
 The Scientific Method
o Observations/Data ➔ Hypotheses ➔ Hypothesis Testing ➔
Models ➔ Laws ➔ Theories
Renaissance - the period of European/Western history during which the cultural
rebirth occurred from roughly the fourteenth through the middle of the seventeenth
centuries, based on the rediscovery of the literature of Greece and Rome. It gave
birth to a new way of scientific thinking and rationalism that eventually led to the
scientific method. It was also the time of the Great Voyages of Exploration which
brought back many kinds of information and specimens that provided the data to
expand scientific thinking.
Age of Reason or Age of Enlightenment - the period of European/Western history
(~1685 - ~1815) during which politics, philosophy, science and communications
were radically reoriented as part of a movement referred to by its participants as
the Age of Reason which produced numerous books, essays, inventions, scientific
discoveries, laws, wars and revolutions. Enlightenment thinkers throughout Europe
questioned traditional authority and embraced the notion that humanity could be
improved through rational change.
The Scientific Method: Produce a Hypothesis based on observations/data; Design
and Perform Experiments, controlled if possible, making detailed observations;
Analyze the data in an objective way against the background of existing knowledge;
and, Draw a conclusion that supports or refutes the hypothesis.
The Experimental Method - the use of controlled observations and measurements
to test hypotheses is the method of choice for having the greatest confidence in
drawing conclusions from hypothesis testing but this method is not available to
answer some kinds of questions posed by scientists. It involves the deliberate
manipulation of one variable, while trying to keep all other variables constant

Scientific World View:
o The Universe Is Understandable.
o The Universe Is a Vast Single System In Which the Basic Rules Are
Everywhere the Same.
o Scientific Ideas Are Subject To Change.
o Scientific Knowledge Is Durable.
o Science Cannot Provide Complete Answers to All Questions.

o
o
o
DIFFERENT SCIENTIFIC DISCIPLINES SHARE FUNDAMENTAL PRINCIPLES:
the reliance on observation and the use of evidence
the use of hypothesis testing to formulate laws and theories
the use of logic, mathematics and statistics
hypothesis - a tentative insight into the natural world; a proposal intended to
explain certain facts or observations ; a concept that is not yet verified but that if
true would explain certain facts or phenomena
o Observe and describe a phenomenon or group of phenomena.
o Formulate hypotheses to explain the phenomena; hypotheses often take the
form of a proposed causal mechanism or mathematical relationship.
o Use the hypotheses to predict the existence or actions of other phenomena,
or to predict quantitatively the results of new observations.
o Perform additional data collection or experimental tests of the predictions by
several independent experimenters using properly performed techniques or
experiments.

Theories, Laws, Models and Hypotheses
o Theories, Laws, Models and Hypotheses are supported by data
analysis using the Scientific Method.
 Confidence in the accuracy of Theories, Laws, Models and
Hypotheses is expressed by a level or degree of Probability (P
value) which is established by the application of various kinds
of statistical analysis.
 A P value of 0.05 is the minimal P value required to support a
conclusion
 As a result of our confidence in the Scientific Method, both
scientific laws and broader scientific theories are accepted to
be “true” (accurate) by the scientific community as a whole
o Theory - is an explanation of a set or system of related observations or
events based upon proven hypotheses and verified multiple times by
detached groups of unbiased researchers; should have predictive
power; a theory will have significant predictive power and be
falsifiable.
 Genuine scientific theories must be falsifiable by means of
additional application of the scientific method (data collection
and hypothesis testing including generating predictions of
what data or observations, if found, would falsify the
hypothesis).
 Falsifiability is the ability of a scientific theory to be disproved
by an experiment or observation. The ability to evaluate
scientific theories against observations is essential to the
scientific method, and as such, the falsifiability of scientific
theories is key to this and is the prime test for whether a
proposition or theory can be described as scientific. If a
scientific theory cannot be falsified, there is no point in even
examining the evidence.
o Law - governs a single action or situation, and can often be expressed
as a mathematical relationship; whereas a theory explains an entire
group of related phenomena
o The biggest difference between a law and a theory is that a theory is
much more complex and dynamic.
o Model - A systematic description of an object or phenomenon that
shares important characteristics with the object or phenomenon;
scientific models can be material, visual, mathematical, or
computational and are often used in the construction of scientific
theories.
COMMON MISTAKES IN APPLYING THE SCIENTIFIC METHOD
Failure to collect appropriate data or perform appropriate experiments
Personal, institutional or cultural bias – interpreting or manipulating data to
produce a desired outcome or ignoring or dismissing evidence which
disagrees with a preferred hypothesis
Failure to recognize or account for errors in description, measurement or
analysis
Failure to review relevant prior scientific evidence
Failure to communicate the results of research honestly or completely
Theories should have predictive power, the ability to predict relationships among
phenomena that previously seemed unrelated. The concept of predictive power
differs from explanatory and descriptive power (where phenomena that are already
known are retrospectively explained or described by a given theory) in that it allows
a prospective test of theoretical understanding in application to new situations, data
or evidence.
Science is not authoritarian (authoritarian is the reliance on the statements or
writings of important figures in an unquestioning way)
Science is self correcting and progressive
Scientific Bias describes the tendency or preference, conscious or unconscious, for
a particular result or outcome; it interferes with the ability to be impartial,
unprejudiced, or objective. The scientist attempts to remove all factors that would
introduce bias into his or her experiment. That is part of the scientific method. A
scientist’s nationality, culture, gender, ethnic origin, age, political convictions, etc.,
may be a cause of scientific bias.
Scholasticism - the system of philosophy, theology, and teaching that dominated
medieval western Europe and was based on the writings of the Church Fathers and
Aristotle; Thomas Aquinas was a major proponent.
Natural Theology - a type of theology that provides arguments for the existence of
God based on reason and ordinary experience of nature which distinguishes it from
revealed theology, which is based on scripture and/or religious experiences.
Age of Reason - a period in history, especially the 18th century in France, England,
etc., characterized by a critical approach to religious, social, and philosophical
matters that seeks to repudiate beliefs or systems not based on or justifiable by
reason.
The Enlightenment - a European intellectual movement of the late 17th and 18th
centuries emphasizing reason and individualism rather than tradition. It was
heavily influenced by 17th-century philosophers such as Descartes, Locke, and
Newton, and its prominent exponents include Kant, Goethe, Voltaire, Rousseau, and
Adam Smith.
Cosmogenesis – the origin of the universe in the Big Bang and the forces which
generated the material nature of the universe, its composition and the laws by
which it operates.
Vitalism - a discredited doctrine that the functions of a living organism are due to a
vital principle distinct from physicochemical forces; a discredited doctrine that the
processes of life are not explicable by the laws of physics and chemistry alone and
that life is in some part self-determining.
Orthogenesis/Orthogenetic Evolution - an obsolete biological hypothesis that
organisms have an innate vitalistic tendency to evolve in a definite phenotypic
direction due to some internal mechanism or "driving force".
Biogenesis/Abiogenesis – the origin of life from non-living chemical precursors.
Scala Naturae/Scale of Nature/Great Chain of Being – a discredited ancient
classification of the world (material universe) describing a continuous hierarchy of
all beings arranged in order of “perfection; this system had religious roots and
pictured beings rising in a linear order, starting with inanimate minerals, and rising
through fossils (which were considered something between the mineral and the
living) to plants, animals, humans, celestial beings, and ultimately, God; it was the
accepted majority view in the Western Tradition from the time of the Greek Natural
Philosophers until the time of Darwinism.
Lamarckism - a discredited theory of organic evolution, proposed by Jean Baptiste
Lamarck in the 18th century, asserting that environmental changes cause structural
changes in animals and plants, through use and disuse of its body parts in response
to the environment, are inherited by its offspring; the mechanism for this mode of
inheritance is termed the inheritance of acquired characteristics.
Intelligent Design - a creationist religious argument for the existence of God, and
that life, or the universe, cannot have arisen by chance and was designed and
created by some intelligent entity, presented by its proponents as "an evidence-
based scientific theory about life's origin” but found to be pseudoscience by the law
and by the scientific method because it cannot be falsified.
Evolution
1.
2.
3.
4.
5.
6.
o Define evolution. Simplest definition: A change in allele frequencies
in one or more genes/loci in a population's gene pool. Also: the
process by which different kinds of living organisms are thought to
have developed and diversified from earlier forms during the history
of the earth
 Be sure to know the different definitions used over time (i.e. in
the 17th century vs. the 18th century, vs. today, etc.)
o What are some of the criticisms of evolution as a science?
o What is some of the evidence that we have to validate evolution
despite these criticisms?
o Evolution that occurred in the past can be observed, documented,
studied and tested. Evidence to test evolutionary hypothesis exists in
the fossil record, and evolution can be tested and demonstrated
experimentally.
o The four levels upon which Evolution operates.
 The Genetic level, through mutations, changes in gene number
and regulation, and changes in gene networks.
 The Organismal level, seen as individual variation and
differential survival through adaption and the evolution of new
structures, functions and/or behaviors.
 The Population level, changes in the populations of organisms,
operating through mechanisms that limit gene flow between
populations.
 The Species level, the subsequent origin, radiation, and
adaption of species.
 -The Twelve (12) Points of Evolution
Organisms exist as Individuals living in populations and communities.
Natural Selection acts on individuals but individuals do not evolve.
Individuals exist in Populations that inhabit discrete ecological Niches.
Populations of sexually reproducing organisms consist of individuals that are
not identical; asexual individuals exist in populations composed of clones,
though asexual individuals may experience genetic recombination due to
HGT = horizontal gene transfer.
Resources are often limited with the consequence that not all individuals
in a population will survive to reproduce as a result of competition for
resources.
Individuals develop and reproduce, Populations may reproduce and
evolve.
7. Heritable Variation is an essential prerequisite for evolution to act.
Variation in an individual arises from 2 factors - the genotype (the alleles an
individual has) and the environment (e.g., poor diet gives poor growth - even
though there may be genes for good growth). The variation due to the
environment is not inherited, e.g., if you double in size due to overeating this
will not be inherited by your offspring. However the genes you possess will
determine the fundamental characteristics of your offspring and this is the
heritable variation.
8. Because resources are limited, natural selection results in survival to the
next generation through reproduction of the individuals (variants) that are
best suited to the conditions of their existence (survival and reproduction).
9. Because the genetic background of individual sexually reproducing
organisms differs, those that are selected on the basis of their fit to the
environment will preferentially pass their genes on to the next generation.
10. Because of differential reproduction the genetic composition/gene pool of a
population can drift (change at random) and spontaneous mutations occur.
11. Populations may subdivide into smaller groups. Differences that emerge in
the subgroups can provide the basis for speciation.
12. Populations or subsets of populations may “crash” or become extinct
because of environmental catastrophes or other problems.
 Evolution that occurred in the past can be observed, documented, studied
and tested. Evidence to test evolutionary hypothesis exists in the fossil
record, and evolution can be tested and demonstrated experimentally.
o The facts of Evolution come from
 Anatomical Similarities and differences.
 Habitats of Organisms
 Metabolic Pathways
 Embryological Stages
 Fossil Forms
 Genetic, Chromosomal, Molecular features
o The four levels upon which Evolution operates.
 The Genetic level, through mutations, changes in gene number
and regulation, and changes in gene networks.
 The Organismal level, seen as individual variation and
differential survival through adaption and the evolution of new
structures, functions and/or behaviors.
 The Population level, changes in the populations of organisms,
operating through mechanisms that limit gene flow between
populations.
The Species level, the subsequent origin, radiation, and
adaption of species.
o -Individuals respond to Natural Selection but Populations Evolve.

Phenotype/Character/Feature - Used interchangeably for any distinguishing
attribute of an organism, whether morphological (blue eyes), behavioral (burrows),
functional/physiological (breaths oxygen), or molecular (has gene for
hemoglobin/has a particular DNA sequence).
Phenotype - the set of observable characteristics of an individual resulting from the
interaction of its genotype with the environment; whereas the "genotype" is the
genetic makeup of an organism, the phenotype is how genetic and environmental
influences come together to create an organism's physical appearance, physiology,
biochemistry and behavior.
Mosaic Evolution (or modular evolution) - the concept that evolutionary change
takes place in some body parts or systems without simultaneous changes in other
parts; the evolution of characters at various rates both within and between species;
different characters in the same population/species evolve at different rates.
Fitness - The adjustment of an organism to its environment leading to relative
reproductive success (including adjustments to other organisms in that
environment) is measured by the biological attribute Fitness/Darwinian fitness.
The Species Problem
o Defining species, why is it a problem?
o What are the definitions of species? (will be covered in future
chapters in more detail)
Evolution:
-First meaning
o Evolution as the development of an Organism ( 17th Century
Definition )
-19th Century Definition
o Transformation of a species or transformation of the features of
organisms.
-from 1859-1900 Evolution was studied as
o The origination and transformation of species
o The transformation of major groups/lineages of organisms and the
search for ancestors.
o The transformation of features (; such as jaws, limbs, kidneys, nervous
systems) within lineages of organisms.
1. Evolution
a. Modern definition: Evolution is now recognized as hierarchical; genes,
structures, populations, species and ecosystems all evolve.
2. Niche/ecological niche
a. All the relationships of a species with its community's other species
and with the physical environment and resources of its habitat
b. Niche is not defined as a place, but by a set of interactions.
c. The unique role and position a species has in its environment; how it
meets its needs for food and shelter, how it survives, and how it
reproduces. A species' niche includes all of its interactions with the
biotic and abiotic factors of its environment. It is advantageous for a
species to occupy a unique niche in an ecosystem because it reduces
the amount of competition for resources that species will encounter.
3. Transformation
a. Change from one variant/form to another
4. Darwin’s phrase
a. Descent with modification
5. Modern evolutionary synthesis/modern synthesis/Neo-Darwinism:
established in the 1930s and continues as the explanation for most
evolutionary change by means of natural, sexual, group/kin, and species
selection or due to random events, especially likely in small populations.
Chapter 2: The Origins of Matter, the Universe
and the Earth
People:
Aristotle
(384-322 BCE)
Greek




His writings cover many
subjects, including physics,
metaphysics, poetry, theater,
music, logic, rhetoric,
linguistics, politics,
government, ethics, biology,
and zoology.
He was a great mind of the
time, but his legacy as an
unquestioned authority held
back scientific progress for
centuries.
He made collections of
creatures, did dissections of
animals, recognized different
kinds of organisms.



Xenophanes of Colophon
(570-480 B.C.E)
Greek

Ibn Sina
(981-1037 AD)
Persian

Shen Kuo
(1031-1095)
Chinese

James Usher/Ussher
(1581-1656)
Irish

Isaac Newton
(1643-1727)
English


Georges Louis Leclerc,
Comte de Buffon
(1707-1788)
French


He noted the sequence of
organ development by
observing chicken eggs.
The world can be understood
with observation and reason
a slow rate for geological
change, undetectable in the
lifetime of a human being
recognized that some fossil
shells were remains of shellfish,
and, therefore, that sea floors
had risen over time
elaborated concepts related to
earthquakes, mountain
building, rock strata formation,
and an understanding of what
we would call the Theories of
Catastrophism and
Uniformitarianism in Geology
Song Dynasty in China used the
evidence of uplifted marine
fossils found in neighboring
mountains to propose gradual
climatic and geological change
Bishop, Argued the earth was
born Sunday the 23rd of
October 4004 BCE.
Physicist and mathematician
who calculated that an Earthsized sphere would require
50,000 years to cool to its
present temperature
As a pious Christian, he felt
obliged to reject his own
calculations
Naturalist, mathematician,
cosmologist, and
encyclopedic author.
Buffon published thirty-six
quarto volumes of his
Histoire naturelle; this
included everything known
about the natural world up to
that time.






James Hutton
(1726-1797)
Scottish





John Playfair
(1748-1819)
Scottish

Abraham Werner
(1749-1817)
German


William Smith
(1769-1839)
English

Concluded that species must
have improved and
degenerated (change through
time)
Noted that similar
environments have distinct
flora and fauna (Buffon’s Law
or the first principle of
Biogeography).
Centers of creation/origin
Climate change must have
facilitated worldwide spread
of species from their centers
of origin
Buffon calculated that the age
of the earth was 75,000 years,
basing his figures on the
cooling rate of iron
Buffon’s law – first principle
of biogeography
Father of modern Geology,
though his “uniformitarian”
proposals were obscured by
his difficult writing style
He recognized both
sedimentation and vulcanism
as sources for rock strata
Plutonism
Responsible for the concept
of deep geological time.
Calculated the earth to be
millions of years old.
restated Hutton’s ideas in
Illustrations of the Huttonian
Theory of the Earth (1802)
18th century Neptunist
advocated that the Noachian
Flood formed all rock strata
Principle of faunal
succession: noted that
different rock strata contain
particular types of fossilized
flora and fauna, and that
these fossil forms and
communities succeed each
Baron Georges Cuvier
(1769-1832)
French






Alexandre Brongniart
(1770 – 1847)
French


19th Century
Catastrophists
William Whewell
(1794-1866)
English

Sir Charles Lyell
(1797-1875)
British



Richard Owen
(1804-1892)
British


other in a specific and
predictable order that can be
identified over wide
distances
proposed a Theory of
Catastrophism to explain
extinct organisms
Accepted some fossils as
evidence of extinctions, in
opposition to Buffon
Recognized evidence of
stratification of rock layers,
examples of sedimentation,
uplift and subsidence
Recognized a Principle of
Faunal Succession used to
assign times to geologic
strata
The Animal Kingdom,
Distributed According to Its
Organization (1817)
improved the Linnaean
system of classification
was an colleague of Cuvier’s
and made important
contributions to geology and
paleontology
accepted the Earth was many
thousands of years old
Coined the terms
Catastrophism and
Uniformitarianism
Uniformitarianism
Mentor to Darwin
Principles of Geology in 3 vols.
(1830-1833)
19th Century Christian
Catastrophist and antiDarwinist comparative
anatomist who never
accepted Darwinism
important comparative
anatomist and paleontologist
who identified homologies to
establish characteristic
Louis Agassiz
(1807-1873)
American

Charles Darwin
(1809-1882)
English



William Thomson, Lord
Kelvin
(1824-1907)
Irish


Platonic "archetypes," "ideal"
body plans / bauplans for
higher taxa, especially
vertebrates
19th Century Christian
Catastrophist and antiDarwinist paleontologist at
Harvard
Father of Evolution - He had
geologic training - focused on
fossils and coral reefs,
(formation by incremental
growth), likened geologic
distribution of organisms to
geology.
Naturalist who established
that all species of life have
descended over time from
common ancestry, and
proposed the scientific
theory that this branching
pattern of evolution resulted
from a process that he called
natural selection.
The author of the ground
breaking book Origin of
Species which relied little on
fossils, accepted
uniformitarianism which
gives time for gradual
changes, documenting the
fact that evolution has
occurred, and mechanisms of
evolution are artificial and
natural selection.
Mathematician and physicist
who estimated the age of the
earth at 15-20 mybp
maximum
Based his calculations of
thermodynamic properties,
comparing the size and
temperature of the sun and
earth, and estimating the rate
of cooling of the earth

Alexander du Toit
(1878-1948)
South
African


Alfred Wegener
(1880 – 1930)
German


Léon Croizat
(1894 – 1982)
Italian



discovery of radioactive
isotope decay in the Earth’s
core as the heat source which
refuted Kelvin’s calculations
Geologist, only major supporter
of Wegener at the time
Wegener first advocated for
continental drift
Our Wandering Continents
(1937)
Meteorologist who proposed
continental drift in 1912
based on fossil and mineral
distributions and continental
coast lines
Proposed the supercontinent
Pangea
Biologist, also proposed
continental drift, more or less
independently, based on
distribution of communities
of living organisms
Croizat developed a new
biogeographic methodology,
which he named
Panbiogeography ― Based on
the metaphor that "life and
earth evolve together" ―
which means that geographic
barriers and biotas co-evolve.
This method was basically to
plot distributions of
organisms on maps and
connect the disjunct
distribution areas or
collection localities together
with lines called tracks
Vicariance
Concepts:
 Cosmogenesis - The origin and evolution of the universe: Big bang 15-12
BYA [approximately 13.73 BYA)  solar system formation 5-4.5 BYA  Sun
formation 4.6 BYA  Planets form 4.5 BYA (BIG WHACK : formation of the
moon when Earth collides with a Mars sized object, “Theia,” soon after the
planets formed.)




Origin of the solar system
1.
Supernova injects matter into space and disturbs nearby interstellar
gases
2.
Gravity causes matter to coalesce into planets, sun, etc.
3.
Requires more than 100 million years
Earth’s Ability to sustain life:
o In the Goldilocks Zone – conditions just right for life/biogenesis
o Size of the Sun
o Orbital distance from the earth to the sun
o Mixture of atomic elements
o Liquid water
o Ozone layer
o Magnetic field
Earth’s early atmosphere
o First Atmosphere:
 Reducing: hydrogen and helium
o Second atmosphere:
 A violent and energy abundant reducing atmosphere produced
by volcanic out gassing
 Gases: H2O, CO2, SO2, CO, S2, Cl2, N2, H2 and NH3 (ammonia) and
CH4 (methane) but with no free O2
 Water vapor condenses from it to form the oceans
 The atmosphere under which life evolves
o Third Atmosphere (current)
 Organic molecules
 H2O, CO2, SO2, CO, S2, Cl2, N2, H2 and NH3, and CH4 from volcanic
out gassing
 Oxygen O2 from cynaobacterial photosynthesis
 Autotrophs consume CO2
 Ozone (O3) layer forms gradually
 Ozone blocks uv radiation which reduces mutation rates
in DNA
 Oxygen most likely arose due to photosynthetic cyanobacteria
some of which form colonies/fossils in shallow marine
environments known as stromatolites
Rock Formation:

o Igneous rocks - molten magma cools
o ~65% of the total crust volume
o
17-20% of the exposed crust
o Sedimentary rocks - small rock particles form from
weathering/erosion and are moved to other locations by wind and
water where they collect and are transformed by heat and pressure
over time
o
~8% of the total crust volume
o
50-55% of the exposed crust
1. Metamorphic rocks - igneous or sedimentary rocks that undergo heat and
pressure after they are buried and transform into new kinds of rocks
o
~25% of the total crust volume
o
25-30% of the exposed crust
 Radiocarbon/Radiometric Dating
o Knowing the rate of decay of radioactive elements and analyzing the
presence of the radioactive isotope and it’s daughter isotopes within a
fossil or rock layer allows for estimates of time frames in which the
layers were formed/ the fossil organisms may have been alive.
o Half Life - the amount of time required for half of the radioactive
element’s atomic nuclei to decay
o Carbon: C12 & C14isotopes: When the organism dies, stable C12
persists, but unstable C14 decays to N14 at a constant rate and is slowly
lost from the fossil To measure the amount of radiocarbon left in a
fossil, scientists burn a small piece to convert it into carbon dioxide
gas, radiation counters are used to detect the radiation given off by
decaying C14 as it turns into nitrogen. More time = less C14 present;
proportion of C12 to C14 = age of fossil.

Principle of faunal succession: noted that different rock strata contain
particular types of fossilized flora and fauna, and that these fossil forms and
communities succeed each other in a specific and predictable order that can
be identified over wide distances
Vocabulary:
1. Neptunism: Noachian Flood or similar global floods formed all rock strata;
developed into Catastrophism
2. Plutonism: volcanic activity formed most rock strata formation with
sedimentation as a secondary process; developed into Uniformitarianism.
The geologic theory that the rocks forming the Earth were formed “in fire” by
3.
4.
5.
6.
7.
8.
volcanic activity, with a continuing gradual process of weathering and
erosion wearing away rocks, which were then deposited on the sea bed, reformed into layers of sedimentary rock by heat and pressure, and raised
again. It proposed that basalt was solidified molten magma. [The theory was
first proposed before 1750, by Abbé Anton Moro who had studied volcanic
islands], and was subsequently developed by James Hutton as part of his
Theory of the Earth published in 1788.
Uniformitarianism: the theory that changes in the earth's crust during
geological history have resulted from the action of continuous and uniform
processes the can be observed by humans around the globe, the action of
weather, erosion, water flows, volcanic and earthquake activities.
Catastrophism: the theory that changes in the earth's crust during
geological history have resulted chiefly from sudden violent and unusual
events.
Continental Drift: the radical early 20th century concept of gradual
movement of the continents across the earth's surface through geological
time advocated for by Alfred Wegener, Leon Crozait, and others; it was finally
accepted in the 1960s by the discovery of the mechanism of plate
techtonics.
Plate Techtonics - a geological theory of global tectonics, which explains
continental drift, in which the lithosphere is divided into a number of crustal
plates, each of which moves slowly on the plastic asthenosphere abnd
underlying molten mantle of the earth more or less independently to collide
with, slide under, or move past adjacent plates.
Vicariance: the geographical separation of a population or community of
taxa, typically by the formation of a physical barrier such as a mountain
range or river, ocean or desert, resulting in a pair of closely related
populations or communities; a concept proposed by Leon Crozait.
Dispersal: the movement of animals over great distances (via flying or
swimming) from one land mass to another across an inhospitable barrier of
some sort.
IMPORTANT PRINCIPLES OF GEOLOGY
Uniformitarianism - central principle; the processes acting on the earth's surface
today are the processes that have always acted and are enough to explain all the
changes on the earth's surface over time, origin of strata, etc.
Stratigraphy – the discipline within geology that deals with the origin, composition,
distribution, arrangement and succession of strata/layers of rock.
Original Horizontality - any tipping or bending of strata layers had to occur later
Superposition - young rocks and fossils are on top of older ones
Intrusive relationships- when volcanic materials penetrate sedimentary strata it is
younger
Inclusions - new strata may surround older material
Cross-Cutting Relationships - strata breaks up and faults form which fill with
rocks which are younger than the rocks of the fractured strata
Fauna Succession - fossils change through time and give relative ages to strata;
fossils deeper into crust are older
Correspondence in age can be from radiometric or geometric dating or index fossils
or other means.
Index Fossil - a widely distributed fossil, of narrow range in time, regarded as
characteristic of a given geological formation and biological community, used
especially in determining the age of related formations.
Geo-magnetism - the earth's magnetic field reverses from time to time and can be
detected in newly formed igneous rock when iron containing crystals orient
according to the magnetic field as they cool and crystalize; a phenomenon that can
be used to date rock strata.
Continental Drift - a theory stating that the Earth's continents have been joined
together and have moved away from each other at different times in the Earth's
history. The theory was first proposed by Alfred Wegener in 1912. While his
general idea of continental movement eventually became widely accepted, his
explanation for the mechanism of the movement has been supplanted by the theory
of plate tectonics.
Plate Tectonics - a theory of geology in which the lithosphere is divided into a number
of crustal plates, each of which moves on the plastic asthenosphere more or less
independently to collide with, slide under, or move past adjacent plates.
Lithosphere - the solid part of a celestial body (such as the earth); specifically, the
outer part of the solid earth composed of rock essentially like that exposed at the
surface, consisting of the crust and outermost layer of the mantle, and usually
considered to be about 60 miles (100 kilometers) in thickness
Pangaea – Mesozoic supercontinent of some 300 to 200 Mya, proposed by
Wegener; composed of northern Laurasia and southern Gondwana
Laurasia – northern supercontinent from the breakup of Pangaea composed of
North America, Greenland, Europe and Asia (except India)
Gondwana – southern supercontinent from the breakup of Pangaea composed of
South America, Africa, India, Australia, and Antarctica
Panbiogeography - originally proposed by the French-Italian scholar Léon Croizat
(1894–1982), is a cartographic (mapping) approach to biogeography that basically
plots distributions of a particular taxon or group of taxa on maps and connects the
disjunct distribution areas or collection localities together with lines called tracks;
Croizat’s data supported the hypothesis of continental drift.
Disjunct Distribution - the geographic distribution of a taxon that has two or more
groups that are related but widely separated from each other geographically; the
causes are varied and might demonstrate either the expansion or contraction of a
species range or the development of a barrier which separated demes.
Vicariance - a biogeographic process, originally proposed by the French-Italian
scholar Léon Croizat, by which the geographical range of an individual taxon, or a
whole biota, is split into discontinuous parts by the formation of a physical or biotic
barrier to gene flow or dispersal.
Vicariant Distribution - the geographic distribution of a taxon, any of several
closely related species, races, etc., each of which exists in a separate geographical
area, their ranges assumed to have originated from a single ancestral population
that became subdivided by barrier formation, at the large scale of geological events,
e.g., plate techtonics, to the small scale of river or stream formation, lakes shrinking
into isolated ponds, forests being fragmented into clumps by drought-induced
grassland formation, etc.
Chapter 3: The Origin of Molecules and the
Nature of Life
People:
John Burdon
(1892-1964)
Sanderson [J.B.S.]
Haldane
British

Harold Urey &
Stanley Miller
(1893-1981) &
(1930-2007)
American


Aleksandr
Ivanovich Oparin
(1894-1981)
Russian



John Desmond
Bernal
(1901-1971)
British

Biologist and mathematician who
independently proposed (1928) a
similar hypothesis that
conditions on the primitive Earth
favored chemical reactions that
synthesized organic compounds
from inorganic precursors:
biopoiesis
“primordial organic soup”
Physical chemists who conducted
experiments beginning in 1953
that simulated hypothetical
conditions present on the early
Earth and supported abiogenesis
by demonstrating that an
"organic soup" could form
spontaneously from the second
reducing atmosphere
Biochemist/botanist who wrote
The Origin of Life (1924/1936)
proposing Abiogenesis
produced some prebiotic
protocell precursors from the
mixture of gelatin and gum arabic
 coacervates
studied biochemistry and
enzymology of plant cells
coined the term Biopoesis:



Sidney Walter
Fox
(1912 - 1998)
American

Carl Woese
(1928-2012)
American




Walter Gilbert
Concepts:



(1932-present)
American

Stage 1: The origin of biological
monomers
Stage 2: The origin of biological
polymers
Stage 3: The evolution from
molecules to cell
found that under certain
conditions proteinoids
assembled into microscopic
spherical balls, which they
referred to as proteinoid
microspheres, experimental
models of hypothetical ancient
abiogenetically produced
protocells
Microbiologist who defined
archae
Wrote The Genetic Code (1967)
an early advocate for the RNA
World
He proposed the three domain
classification of living organisms
1986 – coined the term “RNA
World”
Oparin & Fox experiments
o Demonstrated how the phosopholipid bilayer of cells could
arise through abiogenesis
o Fox and Harada demonstrate the polymerization of
“proteinoids” exposed to high heat; when water was added to
these cross-branched polymers amino acids, proteinoid
microspheres (globular droplets in the water solution which
can coalesce or bud if disturbed) were formed.
Miller-Urey Experiments
o Formed amino acids, sugars, lipids, building blocks for nucleic
acids, etc.
o Supported that biomolecules could form from abiotic factors in
lab
Coacervate - an aggregate of colloidal droplets (lipids and proteins)
held together by electrostatic attractive forces; these structures
exhibit a few characteristics of living cells: outer boundary, osmotic
swelling and shrinking, budding and binary fission, streaming
movement of internal particles




Possible sites for the origin of the fist biomolecules of Earth:
o Hydrothermal vents, volcanoes, marine clays, tidal pools, bare
hot lave splashed with the water of the early ocean's organic
soup.
o carbonaceous meteorites
Bada and Miller's “sub-ice organic gazpacho” theory (ice as a catalyst
for abiosynthesis reactions)
o Amino acids of extraterrestrial (?) origin
Primordial Organic Soup - a term introduced by Soviet biologist
Alexander Oparin and English scientist John Burdon Sanderson
Haldane. In 1924, Oparin proposed a theory of the origin of life on
Earth through the transformation, during the gradual chemical
evolution of particles/molecules that contain carbon, in the
primordial soup. Biochemist Robert Shapiro has summarized the
"primordial soup" theory of Oparin and Haldane in its "mature form"
as follows: [1] Early Earth had a chemically reducing atmosphere. [2]
This atmosphere, exposed to energy in various forms, produced
simple organic compounds ("monomers"). [3] These compounds
accumulated in a "soup", which may have been concentrated at
various locations (shorelines, oceanic vents etc.). [4] By further
transformation, more complex organic polymers – and ultimately life
– developed in the soup.
o Phospholipids (of an appropriate length) can spontaneously
form lipid bilayers, a basic component of the cell membrane.
o The polymerization of nucleotides into random autocatalytic
RNA molecules might have resulted in self-replicating
ribozymes (RNA world hypothesis). autocatalytic RNA
molecules - RNA molecules which can use ribonucleotide
monomers to synthesize additional copies of themselves as
well as, possibly, catalyzing other synthetic reactions to make
other RNAs or proteins; thought to be the main catalysts of the
protocells of the RNA World.
o Natural Selection pressures for catalytic efficiency and
diversity result in ribozymes which catalyze peptidyl transfer
(hence formation of small proteins), since oligopeptides
complex with RNA to form better catalysts. Thus the first
ribosome is born, and protein synthesis becomes more
prevalent.
o Proteins outcompete ribozymes in catalytic ability, and
therefore become the dominant biopolymer. Nucleic acids are
restricted to predominantly genomic use for polypeptide
primary structure blueprints (DNA), regulatory functions (DNA
& RNA) and as participants in protein synthesis (transcription
and translation).
Biopoesis:
o Stage 1: The origin of biological monomers
o Stage 2: The origin of biological polymers
o Stage 3: The evolution from molecules to cells
RNA World Hypothesis - Alexander Rich, Leslie Orgel, Francis Crick, and
Carl Woese proposed the RNA World hypothesis around 1982 stating that
the first chemical world was an RNA World (RNA can catalyze like enzymes
and replicate like DNA)





DNA replication - During S phase of the Cell Cycle, the hereditary
material (DNA) of cells must be copies so that at cell division daughter
cells receive nearly exact copies of the parent cell DNA; the process is
complex, requiring helicases, RNA Primase, DNA replicases, deoxyribo-nucleotide triphosphate monomers and other molecular helpers;
the process is semi-conservative. The RNA primer formed by RNA
Primase must be removed and replaced before DNA synthesis is
completed. These shorts pieces of primer RNA may be considered
vestigial features retained from the ancestral RNA World.
Semiconservative replication – the reactions in which a doublestranded molecule of DNA separates into two single strands each of
which serves as a template for the formation of a complementary
strand that together with the template forms a complete molecule.
Transcription - The synthesis of RNA molecules from DNA
sequences/blueprints using RNA synthetases and other molecular
helpers and ribo-nucleotide triphosphate monomers. In the case of
the production of mRNA which carries the blueprints for polypeptide
chains, the mRNA will be further processed with the addition of a 5'
cap and poly-A tail, and if the mRNA is in a Eukaryote, the processing
will also include excision of introns from a pre-mRNA and the splicing
of exons to form the final mRNA product.
mRNA processing in eukaryotes requires that pre-mRNA undergo
excision of introns, noncoding mRNA base sequences, and splicing of
exons, amino acid coding sequences, in order to generate a functional
mRNA. Excision and splicing is not required for prokaryotic mRNA
because prokaryotic gene sequences contain no introns. All mRNAs
require the addition of a 5’ cap and a poly-A tail.
5' End Capping - Post-transcriptional processing of the 5' end of the
RNA product of DNA transcription comes in the form of a process
called the 5' cap. At the end of transcription, the 5' end of the RNA
transcript contains a free triphosphate group since it was the first
incorporated nucleotide in the chain. The capping process replaces
the triphosphate group with another structure called the "cap". The
cap is added by the enzyme guanyl transferase. This enzyme catalyzes
the reaction between the 5' end of the RNA transcript and a guanine
triphosphate (GTP) molecule. The cap is formed through a 5'-5'





linkage between the two substrates such that the GTP molecule is
oriented in the opposite direction as the other nucleotides in the RNA
transcript chain. Once in place, the cap plays a role in the ribosomal
recognition of messenger RNA during translation into a protein.
Prokaryotes do not have a similar cap because they use other signals
for recognition by the ribosome.
The Poly A Tail - Post-transcriptional RNA processing at the opposite
end of the transcript comes in the form of a string of adenine bases
attached to the end of the synthesized RNA chain. This string of
adenines is called the "poly A tail". The addition of the adenines is
catalyzed by the enzyme poly (A) polymerase, which recognizes the
sequence AAUAAA as a signal for the addition. The reaction proceeds
through mechanism similar to that used for the addition of
nucleotides during transcription. The poly A tail is found on most, but
not all, eukaryotic RNA transcripts. Among other possible functions,
the poly A tail serves to delay the catalysis of the mRNA protein
blueprints by RNA degrading/recycling enzymes
Translation - The synthesis of a polypeptide chain coded for by a
DNA blueprint at a ribosome using tRNAs to carry specific amino acids
into place in the growing chain. For this to happen, a specific tRNA
with a triplet nitrogenous base anticodon must allign with a triplet
base codon on the mRNA. Then the amino acid on the tRNA in the A
site on the ribosome is transferred to the growing polypeptide chain
at the P site until the stop codon is reached and the completed
polypeptide chain is released from the ribosome.
RNA molecules - the several classes of RNA molecules that
participate in protein synthesis: rRNA molecules combine with
ribosomal proteins to form ribosomal subunits which bind to form
functional ribosomes; mRNA molecules which carry the transcribed
DNA blueprint for a polypeptide chain which will be synthesized at
the ribosome; tRNA molecules which carry amino acids to the
ribosome for incorporation into a growing polypeptide chain with the
tRNA's anticodon matching by hydrogen bonds to the mRNA codon to
ensure the correct amino acids are inserted into the growing chain in
the correct sequence; various types of regulatory RNAs which
participate in replication, transcription, or translation to change the
timing, amount, and cell location of protein synthesis.
Codon Dictionary - the listing of 64 codons, nitrogenous base triplets
composed of RNA bases, A, G, C, U, which represent either the Start
Codon, 60 codons which represent twenty amino acids available for
protein synthesis, and three Stop codons. The codons are redundant
but unambiguous and the code is universal except for a few bacterial
variants.
The Genetic Code
o The code is universal because it specifies the same 20 amino
acids in all organisms with only few (bacterial) exceptions
o The code is redundant because there are multiple triplet
codons which code for the same AA
o The code is unambiguous because any one codon codes for
only one amino acid
o The code is a triplet code because 3 bases represent a single
AA in a codon
Lac Operon - Several proteins involved in lactose metabolism in the E. coli cell. They
are:



ß-galactosidase - converts lactose into glucose and galactose
ß-galactoside permease - transports lactose into the cell
ß-galactoside transacetylase - function unknown
Research with this system was greatly added by the availability of constitutive
mutants. A constitutive mutant is one in which the gene product is produced
continually, that is there is no control over its expression. In these mutants, the
above proteins were produced all the time in comparison to the wild type where the
proteins only appeared in the presence of lactose. So in these mutants, the mutation
must be a gene other than those responsible for the structural genes.
All of the genes involved in controlling this pathway are located next to each other
on the E. coli chromosome. Together they form an operon. Another locus, elsewhere
in the genome, is a regulatory gene which codes for the repressor protein.
Without lactose in the cell, the repressor protein binds to the operator site and
prevents the read through of RNA polymerase into the three structural genes. With
lactose in the cell, lactose binds to the repressor. This causes a structural change in
the repressor and it loses its affinity for the operator. Thus RNA polymerase can
then bind to the promoter site and transcribe the structural genes. In this system
lactose acts as an effector molecule.
Without lactose in the cell, the repressor protein binds to the operator and prevents
the read through of RNA polymerase into the three structural genes. With lactose in
the cell, lactose binds to the repressor. This causes a structural change in the
repressor and it loses its affinity for the operator. Thus RNA polymerase can then
bind to the promoter and transcribe the structural genes. In this system lactose acts
as an effector molecule.
The evolutionary significance of the Lac Operon is that it allows the genes for lactose
metabolism to be carried by all E. coli, generation after generation, but to regulate
them on only in the presence of lactose (for the relatively rare E. coli generations
living in the gut of baby mammals nursing on a milk diet) but not to waste energy
and resources synthesizing these proteins when there is no lactose present in the
environment (the majority of E. coli generations living in the gut of weaned
mammals).
Properties of life:
 Organization: Composed of one or more cells, the basic unit of life,
with integrated subunits and biochemical systems inside.
 Metabolism: Transform energy by converting chemicals and energy
into cellular components (anabolism/synthetic reactions) and
decomposing organic matter (catabolism/breakdown reactions) to
generate useful energy. All metabolic reactions liberate some waste
heat.
 Homeostasis: Regulation of the internal environment to maintain a
relatively constant state or dynamic equilibrium (a state of balance
between continuing processes; input of matter and energy to the
system are relatively equal to the output of matter and energy from
the system over time).
 Growth: Maintain a higher rate of anabolism than catabolism to
increase size and complexity and repair damage to the cell or
organism.
 Adaptation: The ability to change over time in response to stimuli
from the environment. Individuals develop and populations evolve.
 Response to stimuli: A change in activity (metabolism, behavior,
etc.) appropriate to the change in the environment which was the
stimulus.
 Reproduction: The ability to produce new individual cells, tissues, or
organisms, either asexually, or sexually.
 Enzymes - Protein (or RNA) catalysts which change reaction rates by
participating in reactions but remain unchanged when the reaction is
over so that they may be reused enormous numbers of times.
The Central Dogma: DNA  RNA  Protein
Vocabulary:
1. Goldilocks zone: There is a relationship between star size and energy
output on the one hand and planetary distance on the other that produces a
zone in which planets will be likely to have water present in all three phases,
vapor, liquid, and solid; the sun and Earth’s orbit is “just right” to sustain life.
2. Biopoiesis: The abiogenetic formation of living systems from inorganic
precursors on the early earth, more than 3.5 billion years ago.
3. Proteinoid microspheres: spherical droplets produced in Sidney Walter
Fox’s lab that represented how cells could have possibly formed via
abiogenesis (protobionts, coavervate droplets); the proteinoids are proteinlike, often cross-linked (branched polymer) molecules formed abiotically
from amino acids in hot acidic environments; when mixed with water these
preteinoids formed microspheres with some properties similar to living cells:
an outer wall, osmotic swelling and shrinking, budding, binary fission
(dividing into two daughter microspheres), and streaming movement of
internal particles; preteinoid microspheres are a model for a likely abiogentic
protocell.
4. Thermophilic: heat loving
5. Zeolites: sponge like clay minerals that can retain and catalyze the formation
of organic compounds and polymers and a possible location for abiogenesis
on the early Earth.
6. Autocatalytic RNA molecules: RNA molecules which can catalyze the
synthesis of other RNA molecules or polypeptide chains. They are thought to
have been important in the early development of life in the "RNA World."
7. Ribozymes: a ribonucleic acid (RNA) enzyme that catalyzes a chemical
reaction. The ribozyme catalyses specific reactions in a similar way to that of
protein enzymes. Also called catalytic RNA, ribozymes are found in the
ribosome where they join amino acids together to form protein chains.
8. Proteins: any of a class of nitrogenous organic compounds that consist of
large molecules composed of one or more long chains of amino acids and are
an essential part of all living organisms, especially as structural components
of body tissues such as muscle, hair, collagen, etc., and as enzymes and
antibodies, etc..
9. Nucleic Acids: any of a group of long, linear macromolecules, either DNA or
various types of RNA, that carry genetic information directing all cellular
functions: composed of linked nucleotides.
10. Phospholipids: Any of various phosphorus-containing lipids, such as
lecithin, that are composed mainly of two nonpolar fatty acids, a polar
phosphate group, and a simple organic molecule such as glycerol.
Phospholipids are the main lipids in cell membranes.
11. Abiogenesis: the theory that the earliest life forms on earth developed from
nonliving matter more than 3.5 billion years ago.
12. Semi-conservative model of DNA replication: The normal process of DNA
synthesis/replication, in which the two original anti-parallel strands of the
molecule separate, and each acts as a template on which a new
complementary strand is laid down by the DNA replication process.
13. Enzyme Active Site - the specific region of an enzyme where a substrate
binds and catalysis takes place or where the chemical reaction occurs.
Chapter 4: From Molecules to Cells and the
Origin of Selection
People:
Sidney Fox
(1912-1998)
American

developed membranebound microspheres
from organic
polymers in the
laboratory
Concepts:






Important Transitions for Living systems:
o Abiotic organic molecules – sheet/droplet membranes
o Concentrating molecules – protocells
o Protocells leading to the first true cells, prokaryotes
First Atmosphere ― a reducing atmosphere
o 4.6 to 4.2 Bya
o Hydrogen and Helium lost to space because Earth's gravity is
not strong enough to hold lighter gases
Second Atmosphere ― a reducing atmosphere
o 4.2 to ~2.3 Bya
o Produced by volcanic out gassing
o Gases produced were probably similar to those created by
modern volcanoes (H2O, CO2, SO2, CO, S2, Cl2, N2, H2) and NH3
(ammonia) and CH4 (methane)
o No free O2 (not found in volcanic gases)
Third Atmosphere – the current oxidizing atmosphere
o Nitrogen, Oxygen predominate
o O2 from cyanobacterial photosynthesis accumulated slowly
o From 3.3 to 1.8 Bya, most of the oxygen combined with metal
ions, especially iron, in rocks and soils
o Free oxygen (O2) only gradually accumulated in the
atmosphere
o Ozone (O3) layer forms gradually from collisions between O2
molecules in the upper atmosphere
o Ozone blocks uv radiation which reduces mutation rates in
DNA
o Photosynthetic Autotrophs consume CO2
o
Earth’s first organisms were most likely prokaryotic methanogens
Oxygen was produced by photosynthetic cyanobacteria around 2.3
BYA
Vocabulary:
Abiogenesis: The study of how life originally arose on the planet, encompasses the
ancient belief in the spontaneous generation of life from non living matter.
Abiotically produced organic molecules: carbon based molecules such as amino
acids, fatty acids, and small peptides
Phospholipid: a lipid (fat) composed of a three-carbon glycerol with a
phosphorous-containing polar group at one carbon and two nonpolar fatty acid
groups at the other two carbons; phospholipid molecules self-assemble with
hydrophilic phosphate heads facing the water solvent and hydrophobic
hydrocarbon tails facing each other to form a monolayer on the surface of water and
are the major structural components of cell membrane lipid bilayers
Cell membrane: phospholipid bilayer with accessory lipids, e.g., glycolipids and
cholesterol, and integral and peripheral proteins; the cell membrane structure is
characterized by the Fluid-Mosaic Model of Membrane Structure
Membranous droplet: important step in the evolution of cells; lipid vesicles that
can grow by adding more fatty acids; grow large enough for concentration gradients
to be established across the membrane which allowed differences to be developed
between the inside and outside of vesicles
Protocells: a membranous droplet; ancient life forms that can maintain their
internal environments in the face of a different external environment but may lack
some of the properties of living systems of the DNA/RNA/Protein World.
Methanogens: early organisms that only survive in absence of oxygen; molecular
fossils provide the evidence of their presence; produced high levels of methane to
atmosphere beginning ~3.8 Bya
Methane: CH4 greenhouse gas; helped warm the Earth by reducing the loss of heat
from Earth's surface
Photosynthesis: synthesis and production of organic compounds from carbon
sources and water using light as the energy source; oxygen is produced when
hydrogen ions are removed from water. The first photosynthetic organisms were
cyanobacteria and related prokaryotes. Later, some eukaryotic lineages acquired
photosynthesis from endosymbiosis.
Cyanobacteria: first organisms preserved as fossils in stromatolite reefs 3.5 Bya;
photosynthetic and single-celled prokaryotic organisms; produced oxygen into
Earth's atmosphere and it began to accumulate 2.3 Bya
Coacervate: spherical aggregation of polymers into colloidal droplets in liquid
suspension formed by mixing hydrophilic and hydrophobic components in the
absence of life; an aggregate of colloidal droplets (lipids and proteins) held together
by electrostatic attractive forces; these structures exhibit a few characteristics of
living cells: outer boundary, osmotic swelling and shrinking, budding and binary
fission, streaming movement of internal particles.
Microspheres: formed by heating then cooling protein polymers in the lab; tiny
and has a double bounding membrane; absorb chemicals selectively from medium.
Molecular selection: competition among catalytic systems for substrates
(resources).
Protocell selection: competition among vesicle populations for substrates
(resources).
Malthusian selection: when energy or raw materials are in limited supply;
Malthus originally predicted that humans would outstrip their ability to provide
themselves with food because human reproduction increase is exponential while
food production is geometric. Geometric growth has a constant rate of change - the
increases per time period are constant. Exponential growth is where the rate of
change is itself increasing.
Living systems: have parts that are heterogeneous and specialized, include a
variety of internal mechanisms, contain diverse organic molecules (including
nucleic acids and proteins), grow and develop, reproduce, repair themselves when
damaged, have a metabolism, exhibit environmental adaptation, construct the
niches that they occupy.
First Living System: protocells that had some sort of catalyzed metabolism with a
functional inheritance system (RNA or DNA) to code for the catalysts, whether RNA
or protein.
Prokaryotes: unicellular, single circular DNA and plasmids for heredity, no
cytoplasmic membrane-bound organelles, prokaryotic cytoskeleton and ribosomes,
most have a rigid external cell wall, asexual reproduction and various forms of gene
recombination, i.e., horizontal gene transfer.
Fermentative Anaerobes: bacteria and archaebacteria that consumed simple
organic nutrient compounds from the "organic soup" of the early oceans; many
lineages of such anaerobes and facultative anaerobes still exist today but few
eukaryotes exhibit this lifestyle.
Heterotroph: An organism that is unable to synthesize its own organic carbonbased compounds from inorganic sources, hence, feeds on organic matter produced
by, or available in, other organisms. Heterotrophs are the consumers in the food
chain, particularly the herbivores, carnivores and omnivores. All animals, some
fungi and most bacteria are heterotrophs. They are not capable of producing their
own food. Therefore, they obtain their energy requirements by feeding on organic
matter or another organism. An organism is heterotroph if it obtains its carbon from
organic compounds. If it obtains nitrogen from organic compounds but not energy,
it is still considered an autotroph (such as carnivorous plants).
Autotroph: an organism capable of synthesizing its own food from inorganic
substances using light or chemical energy. Green plants, algae, and certain bacteria
are autotrophs
Peptidoglycan Cell Wall: a crystal lattice structure in the bacterial cell wall that is
made up of linear chains of alternating amino sugars, namely N-acetylglucosamine
and N-acetylmuramic acid, and short peptide chains of three to five amino acids
(attached to the N-acetylmuramic acid). The peptide chains form cross-links
between them resulting in a 3D mesh-like structure. Peptidoglycan serves a
structural role in the bacterial cell wall, giving structural strength, as well as
counteracting the osmotic pressure of the cytoplasm. Its degradation and synthesis
is involved in binary fission during bacterial cell reproduction.
Glycocalyx/Carbohydrate Capsule: complex carbohydrate/glycoprotein
protective outer coat (“slime layer”) present in many bacteria which serves to resist
phagocytosis by white blood cells in bacterial pathogens, e.g., Streptococcus
pneumoniae.
Selection: the sum of the survival and fertility mechanisms that affect the
reproductive success of genotypes/phenotypes in a population of organisms.
Population: basic ecological and reproductive unit of a species.
Artificial selection: process of variation and selection occurring in the lab or as a
consequence of artificial breeding of animals or plants, or exposure to drugs or
insecticides, i.e., by any form of human intervention into breeding of organisms.
Chromosomes: nuclear structures consisting of DNA and associated proteins that
replicate with each cell division in Eukaryotes.
Binary fission: the process of division in prokaryotes, archaebacteria, some
protists and fungi. After replicating its genetic material, the cell divides into two
nearly equal sized daughter cells.
Mitosis: the nuclear division of cells other than germ cells in (somatic) eukaryotic
cells, typically consisting of four stages, prophase, metaphase, anaphase, and
telophase, and normally resulting in two new nuclei, each of which contains a
complete copy of the parental chromosomes. Also called karyokinesis.
Meiosis: the type of two stage nuclear division found only in eukaryote cell lineages
that produce germ cells (gametes) in which the chromosome number is typically
reduced from the diploid to the haploid state.
Cleavage: type of cell division that characterizes the earliest stages of the
development of animal embryos; during cleavage cell divisions occurs so rapidly
that there is little time for growth and daughter cells are significantly smaller than
their parent cells.
Prions: proteinaceous infectious particles that have alternative three dimensional
configurations, a normal structure and an alternate which can induce disease.
Viruses: acellular entity that can only replicate inside cells of a host organism; DNA
and RNA viruses exist and may infect prokaryotes and eukaryotes.
Robert A. Wilson concluded in 2005 that living systems:
a) have parts that are heterogeneous and specialized
b) include a variety of internal mechanisms
c) contain diverse organic molecules, including nucleic acids and
proteins
d) grow and develop
e) reproduce
f) repair themselves when damaged
g) have a metabolism
h) exhibit environmental adaptation
i) construct the niches that they occupy
It is important to note that the capacity to evolve is another important criterion of
life. Later, Wilson added two criteria to these nine:
1. Belonging to a reproductive lineage
2. Having minimal functional autonomy
Chapter 5: Darwin and the Voyage of the
Beagle
Plato
(428-348 BC)
Greek

Idealism; Organisms are
imperfect representations of a
pure essence, an ideal; Idealism
was the prevailing philosophy in
Aristotle
(384-322 BCE)
Greek
western Europe for almost 2
millennia.
 His writings cover many
subjects, including physics,
metaphysics, poetry, theater,
music, logic, rhetoric,
linguistics, politics,
government, ethics, biology,
and zoology.
 He was a great mind of the
time, but his legacy as an
unquestioned authority held
back scientific progress for
centuries.
 He made collections of
creatures, did dissections of
animals, recognized different
kinds of organisms.
 He noted the sequence of
gradual organ development
by observing chicken eggs and
for him this supported
epigenesis over preformation.
 He rejected pangenesis but
did accept a concept of
inheritance of acquired
characteristics (use and
disuse).
 He believed the world can be
understood with observation
and reason.
 He accepted a slow rate for
geological change,
undetectable in the lifetime of
a human being
 He proclaimed that there was
a hierarchical order of species
from most imperfect to most
perfect, a concept refined
over the centuries as the
"Great Chain of Being." Scala
Naturae (Scale of Nature)
which ranked things from the
inorganic to humans to Gods.
He saw life as progressive and
goal-oriented (vitalist), and
therefore thought there was
no need for adaptation, since
there were no random or
arbitrary influences on the
progression of life
• Favored spontaneous
generation
 believed species were
immutable
naturalist, first Professor of
Chemistry at the University of Oxford,
and the first keeper of the Ashmolean
Museum
believed that most fossils were not
remains of living organisms but
rather crystallizations of mineral
salts with a coincidental zoological
form
mathematician and philosopher
who studied comparative anatomy
and fossils
saw evidence in nature that
suggested the universe and the
living world were progressing
towards a state of perfection
Species may not be fixed
Preformation
Teleology
Unfolding of a preconceived plan in
a Chain of Being; a process
suggesting possibility of change
(evolution)
 Father of modern Geology,
though his “uniformitarian”
proposals were obscured by
his difficult writing style
 He recognized both
sedimentation and vulcanism
as sources for rock strata
 Plutonism
 Responsible for the concept of
deep geological time.
•
Robert Plot
(1640-1696)
English


Gottfried Wilhelm
Leibniz
(1646-1716)
German


Charles Bonnet
(1720-1793)
Swiss
James Hutton
(1726-1797)
Scottish





Erasmus Darwin
1731 - 1802
English



Jean-Baptiste de
Lamarck
(1744-1829)
French








Calculated the earth to be
millions of years old.
Was the grandfather of
Charles Darwin.
One of the first proponents of
evolution.
Incorporated the two Laws of
Nature (principle of use and
disuses, Inheritance of
acquired characters) in
Zoonomia.
Worked most of his life at the
Muséum d’Histoire Naturelle
in Paris.
Vitalism (wrong): Organisms
have an inner disposition to
adapt their characteristics in
response to changes in the
environment (an aspect of
vitalism for Lamarck but
similar to the modern term
developmental adaptation)
hypothesized the Chain of
Being or Scala Naturae as a
moving “escalator” which he
called Nature’s Parade = La
Marche de la Nature (1597)
(wrong)
First organisms arose by
abiogenesis (correct)
Inheritance of acquired traits
via use and disuse. (wrong)
Proposed the continuity of
species by gradual
modification through time
without leaving any gaps, a
materialistic explanation for
evolution. (correct)
Lamarck did not believe in
extinction: for him, species
that disappeared did so
because they evolved into
different species.
Coined the term
“invertebrates”.
Johann Wolfgang
von Goethe
(1748-1832)
German


John Henslow
(1796-1861)
British

Robert McCormick
(1800-1890)
British

Richard Owen
(1804-1892)
British
Robert FitzRoy
(1805-1865)
English




Charles Darwin
(1809-1882)
English



writer was also a serious amateur
student of botany
had ideas on similarities among the
structures of organisms which
could demonstrate relationships, a
more philosophical than biological
approach.
Regius professor of botany at
Cambridge University who
taught Darwin and
recommended Darwin to travel
on the H.M.S. Beagle.
Navy appointed naturalist on
board the Beagle. Was also the
ship's surgeon.
 19th Century Christian
Catastrophist and antiDarwinist comparative
anatomist who never
accepted Darwinism
 important comparative
anatomist and paleontologist
who identified homologies to
establish characteristic
Platonic "archetypes," "ideal"
body plans / bauplans for
higher taxa, especially
vertebrates
Captain of the H.M.S. Beagle.
Devout Christian who believed in
Biblical creation of lfe.
Darwin's primary role on the
voyage was to serve as the dining
companion for FitzRoy.
His work as a naturalist was
incidental to the purpose of the
mapping voyage.
Sailed on the HMS. Beagle (18311836) Galapagos  finches
American Trypanosomiasis,
acquired while he was exploring
in South America: Chagas
Disease via T. infestans bite
In On the Origin of Species
(1859) he coined the terms





Gregor Mendel
(1822-1884)
Austrian


artificial selection, natural
selection, the foundations of the
principles of evolution
Later added a third mechanism
of evolution - sexual selection
Father of Evolution - He had
geologic training - focused on
fossils and coral reefs,
(formation by incremental
growth), likened geologic
distribution of organisms to
geology.
A dispersalist who considered
that long distance dispersal
explained most disjunct
distributions of organisms in
biogeography.
The author of the ground
breaking book Origin of Species
which relied little on fossils,
accepted uniformitarianism
which gives time for gradual
changes, documenting the fact
that evolution has occurred.
Naturalist who established that
all species of life have descended
over time from common
ancestry, and proposed the
scientific theory that this
branching pattern of evolution
resulted from a process that he
called natural selection.
Augustinian monk who provided
the essential basis for
understanding the material
basis of biological inheritance in
his genetic experiments using
pea plants.
Mendel hypothesized that
hereditary information was
represented by physical objects
within the organism which could
be passed to offspring; he called
them “elementen.”


Ernst Haeckel
(1834-1919)
German




Mendel used genetic crosses of
pea plants to establish the
mathematical and statistical
basis of inheritance which were
formalized into his three Laws of
Inheritance.
Although Mendel's work was
published soon after The Origin
of Species, a mechanism of
inheritance was not widely
known until the beginning of the
20th century.
1866 – phylogenetic tree of life
Promoted and popularized
Charles Darwin’s work in
Germany
Developed recapitulation theory
(ontogeny recapitulates
phylogeny)
Coined the term “ecology”
Homology - a state of similarity in structure and anatomical position but not
necessarily in function between different organisms. They may arise from a
common ancestry or evolutionary origin. An example would be the forelimbs of
humans and bats. These structures are described as homologous. These structures
have dissimilar function but have the same fundamental skeletal structure and
developmental origin. Their similarity in this regard could indicate a likely evolution
from a common ancestor.
Chapter 6: Darwin and Wallace’s Evolution by
Natural Selection
People:
Empedocles
(490-430
BCE)
Greek

•
Leonardo Da Vinci
Johann van
Helmont
(1452-1519)
(1577-1644)
Italian
Dutch

Spontaneous generation
from “body part soup” and
only certain combinations
survived.
thought life forms that
adapted to “some purpose”
survived while those that
did not adapt would perish.
Renaissance Human anatomist
 Physician who offered a
classic recipe for the
Francesco Redi
(1626-1697)
Italian

William Harvey
Marcello Malpighi
Anton van
Leeuwenhoek
(1578-1657)
(1628-1694)
(1632-1723)
English
Itallian
Dutch



Edward Tyson
(1650-1708)
British


•
•
Abbé Lazarro
Spallazani
(1729-1799)
Italian

William Charles
Wells
(1757-1817)
Scottish
•
spontaneous generation
of mice from rags and
grain.
Demonstrated that maggots
did not arise spontaneously
from rotting meat,
discrediting spontaneous
generation
Renaissance Anatomist
Renaissance Human anatomist
Asserted that microscopic
“beasties” growing in broth
could be explained as
originating from previously
existing particles
Founder of comparative
anatomy
1680- demonstrates that
porpoises are mammals
1698, he dissected a
chimpanzee and the result was
the book, Orang-Outang, sive
Homo Sylvestris: or, the
Anatomy of a Pygmie Compared
with that of a Monkey, an Ape,
and a Man
He concluded that the
chimpanzee has more in
common with man than with
monkeys, particularly with
respect to the brain
Demonstrated that bacteria
would not spoil broth unless it
was exposed to particles in the
air, discrediting spontaneous
generation
In 1813 wrote a paper about a
white woman with patches of
black skin; in this paper, Wells
reflected on racial differences
among humans and discussed
variation (and local
adaptation) in disease
resistance between different
human races; this led Wells to
•

Thomas Robert
Malthus
(1766-1834)
English





Baron Georges
Cuvier
(1769-1832)
French




postulate a basic mechanism of
natural selection (he did not
use this term) for the
divergence of the human races
Darwin was unaware of this
essay until it was brought to
his attention in 1865
By reflecting on racial
differences among humans,
discussing variation and local
adaptation in disease
resistance among these
varieties, Wells had postulated
the basic mechanism of natural
selection
Political economist and
demographer
An Essay on the Principle of
Population
“Malthusian catastrophe”
"The power of population is
so superior to the power of
the earth to produce
subsistence for man, that
premature death must in
some shape or other visit the
human race.”
Inspired Darwin and Wallace
to see competition for
resources among living
species.
proposed a Theory of
Catastrophism to explain
extinct organisms
Accepted some fossils as
evidence of extinctions, but
did not accept the concept of
life evolving, in opposition to
Buffon
Recognized evidence of
stratification of rock layers,
examples of sedimentation,
uplift and subsidence
Recognized a Principle of
Faunal Succession used to
Patrick Matthew
(1790-1874)
Scottish
Karl Ernst von
Baer
(1792-1876)
German
Heinrich Rathke
(1793-1860)
German
assign times to geologic
strata
 The Animal Kingdom,
Distributed According to Its
Organization (1817)
 He published the principle of
natural selection as a
mechanism of evolution over a
quarter-century earlier than
Charles Darwin and Alfred
Russel Wallace who were
unaware of his writings in
1859 because Matthew failed
to develop or publicize his
ideas
 Founded modern
embryology in the 1820’s
 Extended Pander’s studies of
chick embryo
 Discovered the notochord,
the rod of dorsal most
mesoderm that separates
the embryo into right and
left halves and which
instructs the ectoderm
above it to become the
nervous system
 Discovered the mammalian
egg
 Developed von Baer’s “Laws”
of embryology
 Founded modern
embryology in the 1820’s
 First to describe the
vertebrate
pharyngeal/branchial
pouches/arches, which
become the gill apparatus of
fish but become the
mammalian jaws and ears,
and contribute to the
formation of the vertebrate
skull, and the origin of the
vertebrate reproductive,
Heinz Christian
Pander
(1794-1865)
German
Robert Chambers
(1802-1871)
Scottish
Charles Darwin
(1809-1882)
English






excretory, and respiratory
systems
 Founded modern embryology
in the 1820’s
 Discovered the three germ
layers (endoderm, ectoderm,
mesoderm)
 Also discovered the reciprocal
regulatory tissue interactions
among embryonic cells
(induction)
• Published Vestiges of the
Natural History of Creation
(1844)
• Debate and ridicule of
Vestiges dissuaded Darwin
from publishing his ideas on
speciation for fifteen years
Sailed on the HMS. Beagle
(1831-1836) Galapagos 
finches
American Trypanosomiasis,
acquired while he was
exploring in South America:
Chagas Disease via T. infestans
bite
In On the Origin of Species
(1859) he coined the terms
artificial selection, natural
selection, the foundations of
the principles of evolution
Later added a third mechanism
of evolution - sexual selection
Father of Evolution - He had
geologic training - focused on
fossils and coral reefs,
(formation by incremental
growth), likened geologic
distribution of organisms to
geology.
A dispersalist who considered
that long distance dispersal
explained most disjunct
distributions of organisms in
biogeography.

Asa Gray
(1810-1888)
American
Moritz Wagner
(1813-1887)
German
Joseph Dalton
Hooker
Louis Pasteur
(1817-1911)
English
(1822-1895)
French
Alfred Russel
Wallace
(1823-1913)
British
The author of the ground
breaking book Origin of Species
which relied little on fossils,
accepted uniformitarianism
which gives time for gradual
changes, documenting the fact
that evolution has occurred.
 Naturalist who established
that all species of life have
descended over time from
common ancestry, and
proposed the scientific theory
that this branching pattern of
evolution resulted from a
process that he called natural
selection.
 Botanist and major adviser
and supporter of Darwin
 Naturalist and geographer
 Among the first to emphasize
the benefit of geographical
isolation to species formation;
failed in convincing his
contemporaries that
geographical isolation was
important for speciation
 Botanist and major adviser
and supporter of Darwin
 Microbiologist who in 1859
drove the final nail in the
coffin of spontaneous
generation with his “swan
necked flasks”
demonstrating that bacteria
in the air are necessary for
sterile broth to spoil
• spent 5 years in South
America, 1848-1852; the
ship he was on, Helen,
burned on homeward
voyage along with all of his
work collected over the 5
years
 (1854-1862) explored the
east indies


•




Henry Walter
Bates
(1825-1892)
English
•
•
Thomas Henry
Huxley
(1825-1895)
English



St. George Jackson
Mivart
(1827-1900)
English

contracted malaria in the
indies
dispersalist
Wallace wrote letters to
Darwin outlining his
independent conception of
the theory of Natural
selection (though Wallace
did not use that term)
proposed natural selection
and evolution with Darwin
but took a background role
described natural selection
as favoring the mating
barriers among populations
if hybrid inferiority occur
Father of Biogeography and
proposed six biogeographic
realms for the earth, based
primarily on animal
distributions
The Geographical
Distribution of Animals
(1876) and Island Life
(1880)
Went to Brazil with Alfred
Russell Wallace in 18481852
Characterized Batesian
mimicry systems in South
American butterflies
Comparative anatomist and
major adviser and supporter
of Darwin ("Darwin's
bulldog").
Recognized the importance
of phonotypic variation in
populations.
Evidence as to Man's Place in
Nature (1863).
Biologist who questioned
Darwin’s work in part when he
questioned the adaptive value
of intermediate forms by
John Thomas
Gulick
(1832-1923)
American
Ernst Haeckel
(1834-1919)
German
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Ernst Mayr
(1904-2005)
German/American
Jacques Monod
(1910-1976)
French
asking “What is the use of half
a wing?”
•
Reverend, the first author to
develop a theory of evolution
based on random variation
based on the geographic
distribution of varied snails in
Hawaiian valleys
•
Recognized that each Hawaiian
valley or even region in a
valley had its own snail species
due to the founder effect
 The father of “Geographical
Isolation”
1866 – phylogenetic tree of life
Promoted and popularized
Charles Darwin’s work in
Germany
Developed recapitulation
theory (ontogeny recapitulates
phylogeny) claiming that an
individual organism's
biological development, or
ontogeny, parallels and
summarizes its species' entire
evolutionary development, or
phylogeny
Coined the term “ecology”
 Regarded as the greatest
evolutionary biologist of the
20th century
 Biological species concept in
1942
• His last version, from 2001
states: "Species are groups
of interbreeding natural
populations that are
reproductively isolated from
other such groups."
 Nobel prize winner
associated with the Lac
Operon, and the genetic
control of enzyme and virus
synthesis
•
Willi Hennig
(1913-1976)
German
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Edward O. Wilson
(1929present)
American
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stated that mutation
provides the random noise
from which selection draws
out the nonrandom music
Advocated for cladistics from
1950
argued that taxa/species
should be classified not by
overall similarities among
organisms, by all
"homologies," or similarities
among specific structures,
but rather by only those
homologies that are also
synapomorphies, shared
derived characters only
found in the members of a
clade and its most recent
common ancestor
Harvard evolutionary
biologist who studied ants
Authored Sociobiology
(1975), The Diversity of Life
(1992) and many other
books
Charles Darwin (1809-1882) emphasized the following aspects of nature in his
arguments in support of evolution and the mechanism of evolution by natural
selection with the following elements:
• Darwin extrapolated from artificial selection in agriculture and domestic and
pet animal breeding
• Darwin made the analogy from Malthus's concern for human populations
outstripping their food resources to the competition for resources of
organisms competing for resources in nature
• Darwin accepted Lamarck’s theory of use and disuse
• Darwin assumed differential survival and disproportionate numbers of
offspring for organisms better suited to environment
• Darwin deduced an evolutionary mechanism — natural selection — but was
not the first person to think about transmutation of species
• viewed evolution as descent with modification
• when developing his theory, Darwin gave examples of artificial and natural
selection to explain the mechanism of evolution; included considerable
evidence from comparative anatomy and comparative embryology, and
relied very little on the meager fossil record of the time
•
Did not emphasize discontinuous variations in his initial understanding or
outlining of natural selection
Vocabulary:
Spontaneous Generation - The once popular but now discredited notion that living
organisms arise or develop from nonliving matter; that complex, living organisms
may be produced from nonliving matter in the present world, e.g., it was a popular
belief that mice occur spontaneously from stored grain, or maggots spontaneously
appear in meat.
Preformation - a theory (popular from the time of the Greek natural philosopher
until the 18th century and now discredited) that an individual animal or human
develops by simple enlargement of a tiny fully formed organism (a homunculus)
that exists in the germ cell; some believed the homunculus resided in the sperm cell,
others that it resided in the egg or ovum.
Epigenesis - In biology, epigenesis is the process by which plants, animals and fungi
develop from a seed, spore or egg through a sequence of steps in which cells
differentiate and organs form. The originator of theory of epigenesis was Aristotle
in his book On the Generation of Animals. Prior to the 18th century, most scientists
preferred the theory of Preformation, but with the advent of modern embryology,
Epigenesis, in its modern interpretation, was accepted.
Karl von Baer “Laws”
 General characteristics of the group/taxon to which an embryo belongs
develop before the special characteristics of members of the group
 General structural relations are formed before the more specific structural
relations appear and the most specialized features appear
 The form of any given embryo does not converge upon other definite
embryonic forms but, on the contrary, separates itself from them last / The
embryo of a given species, instead of passing through the adult stages of
ancestral animals, departs more and more from them
 Fundamentally, the embryo of a higher animal form never resembles the
adult of another ancestral animal form, but only resembles its ancestral
embryo
The 3 Primitive Embryonic Germ Layers - the ectoderm, the mesoderm, and the
endoderm are in place at the end of gastrulation.
Ectoderm gives rise to the central nervous system (the brain and spinal cord); the
peripheral nervous system; the sensory epithelia of the eye, ear, and nose; the epidermis
and its appendages (the nails and hair); the mammary glands; the hypophysis; the
subcutaneous glands; and the enamel of the teeth [Ectodermal development is called
neurulation in regard to nervous tissue]
Mesoderm gives rise to connective tissue, cartilage, and bone; striated and smooth
muscles; the heart walls, blood and lymph vessels and cells; the kidneys; the gonads
(ovaries and testes) and genital ducts; the serous membranes lining the body cavities; the
spleen; and the suprarenal (adrenal) cortices
Endoderm gives rise to the epithelial lining of the gastrointestinal and respiratory tracts;
the parenchyma of the tonsils, the liver, the thymus, the thyroid, the parathyroids, and the
pancreas; the epithelial lining of the urinary bladder and urethra; and the epithelial lining
of the tympanic cavity, tympanic antrum, and auditory tube
Embryonic Induction: the embryonic process, the reciprocal regulatory tissue
interactions among embryonic cells, in which one group of cells, the inducing tissue,
directs the development of another group of cells, the responding tissue. Induction
directs the development of various tissues and organs in most animal embryos; for
example, the eye lens and the heart.
The Theory of Recapitulation: also called the biogenetic law or embryological
parallelism—often expressed using Ernst Haeckel's phrase "ontogeny recapitulates
phylogeny"—is a largely discredited biological hypothesis that the development of
the embryo of an animal, from fertilization to gestation or hatching (ontogeny),
goes through stages resembling or representing successive stages in the evolution of
the animal's remote ancestors (phylogeny).
Ontogeny Recapitulates Phylogeny: According to this theory, fetal development
resembles ancestral forms and goes from one form to the next in chronological
order. The youngest fetus resembles the oldest ancestor, and so on. However, this is
not the case. While the fetuses of air-breathing animals retain gills until a certain
stage, the gill stage does not necessarily resemble the adult form of any evolutionary
ancestor. Instead, fetal development often resembles the developmental forms of its
ancestors; the embryos of both chickens and humans resemble the embryos of fish
and lizards.
Natural Selection: Darwin and Wallace's primary mechanism for evolutionary
change in which differential reproduction or survival of well adapted individuals
living in populations of organisms which are competing for resources among
themselves and with other taxa; those aspects of the successful phenotypes which
are under hereditary control will be transmitted to offspring such that future
generations will contain more individuals with those well adapted phenotypic traits;
natural selection was characterized as analogous to similar changes in domesticated
animals and plants "artificially selected" by their human breeders.
Artificial Selection: The process of selection of organisms to be parents in a
domestic animal or plant breeding program by humans to change one or more
phenotypic characters toward some perceived goal, e.g., faster horses or more
nutrient rich grains.
Preadaptation: A phenotypic character that was adaptive under a prior set of
environmental conditions and later provides the initial stage for the evolution of a
new adaptation under a different set of conditions and from which natural selection
over generations can improve the form and function of the phenotype. The
ancestral fish's swim bladder was the preadaptation for the tetrapod lung; the
spore-bearing leaf of an ancestral non-seed plant was the preadaptation for
reproductive cone in gymnosperms; that reproductive cone was then the
preadaptation for the ovary of the angiosperms.
Principle of Divergence: Hypothesis developed by Charles Darwin that
competition between sub-populations/demes in different locations that favors
specialization and separation of the populations to the point of distinction, i.e., that
over time, populations adapting to different environments will become different
enough to be recognized as different taxa, first as distinct species, and if the process
continues, to become different enough to be assigned to different taxa at higher
levels in the classification system. This principle drew a contrast between the
classification of distinct taxa defined by Linnaeus and others who saw each group
originating from separate special creations and the Darwinian view of classification
representing a hierarchy of descent from ever more distant into the past common
ancestors.
Microevolution - the change in allele frequencies that occurs over time within a
species’s population and its demes that leads to phenotypically different varieties
adapted to specific environments within the range of the species. This change is due
to four different processes: mutation, selection (natural, sexual, artificial, etc.), gene
flow (migration), and random genetic drift. This change happens over a relatively
short (in evolutionary terms) amount of time compared to the changes termed
macroevolution which is where greater differences in the population occur.
Macroevolution - Evolution happening on a large scale, above the level of a species,
over geologic time resulting in the divergence of taxonomic groups.
Microevolutionary processes over time may lead to speciation or adaptive radiation,
which is macroevolution. Macro and microevolution describe fundamentally
identical processes on different scales.
Biogeography is the study of the distribution of species and ecosystems in
geographic space and through (geological) time. Organisms and biological
communities often vary in a regular fashion along geographic gradients of latitude,
elevation, isolation and habitat area. Alfred Russel Wallace is considered the father
of modern Biogeography. Zoogeography: The science/study of the distribution of
animals in a particular region and the ecological and evolutionary explanations for
such distributions. Phytogeography is the comparable science for plant
distributions.
Phylogeny: The evolutionary development, ancestor to descendants, and history of
a species or trait of a species or of a higher taxonomic grouping of organisms; often
represented as a "family tree" or cladogram.
Classification: The grouping of organisms into a hierarchy of categories commonly
ranging from species through genera, families, orders, classes, phyla and kingdom,
each category reflecting one or more significant characters expressed in common.
Different methods of classification emphasize different phenotypic characters as the
most important for decision making.
•
•
Taxonomy is the classification of organisms in an ordered system that
indicates natural relationships
Systematics is the science, laws, or principles of classification of organisms
in an ordered system that indicates natural relationships
Taxon (taxa): A taxonomic unit at any level of classification
Morphological/Typological (or Essentialist, Phenetic) Species: A population of
individuals that share more anatomical characters with one another than they do
with any other organism; Typology is based on morphology/phenotype. Stems from
the Platonic "forms" (Platonic ideal). This concept is still applied in museum
research (type method) where a single specimen (type specimen and possibly some
paratype specimens) is the basis for defining the species. In paleontology all you
have is morphology: typology is practiced and species are defined as
morphospecies (e.g., snail shells in fossil beds).
Biological Species Concept: Species are groups of interbreeding natural
populations that are reproductively isolated from other such groups. Proposed by
Ernst Mayr and very widely accepted for many decades.
o Good for living and sexually reproducing species but meaningless for extinct
organisms, and organisms that do not reproduce sexually
Genetic Species: A set of organisms exhibiting similarity of DNA.
Agamospecies: A set of organisms which reproduce asexually, typically
representing a collection of clones, but which share common morphological and
physiological characteristics and are considered as equivalent to a species.
o This species concept is usefully paired with the Biological Species for
sexually reproducing organisms.
o Boundaries may be hard to define.
o Ex: Taraxacum: a genus of dandelions, a very successful world-wide
agamic complex.
Ecological Species: Populations that are adapted to certain ecological niches and
because of their adaptations will form discrete morphological clusters
o Acknowledges the role the environment plays in controlling phenotypes
Ring Species: species with a geographic distribution that forms a ring and but does
not overlap at the ends; with the range, most species exhibit small hybrid range
boundaries but the two opposite ends of the ring are populations that will not
hybridize. Ex: Salamanders that span from Canada to Southern California
Chronospecies: A fossil species which changes in morphology, genetics, and
ecology over time on an evolutionary scale so that the originating species and the
species it becomes would not be classified as the same species had they existed at
the same point in time.
o If connection is recognized both forms will be assigned to a single
evolutionary species
o Implies directional selection
Phylogenetic / Cladistic / Evolutionary Species: A species definition in which a
group of organisms that share a common ancestor and maintains its integrity with
respect to other lineages, through time and space; defined by the presence of a
unique set of shared derived characters / synapomorphies.
o When members diverge the two populations are regarded as separate
species
o Most recent species definition
Monophyletic: A taxonomic group united by having arisen from a single ancestral
lineage, a single last common ancestor.
Paraphyletic: A taxonomic grouping which includes some descendants of a single
common ancestor, but not all its descendants derive from that one common
ancestor or a taxon that contains lineages that do not share a common ancestor; an
invalid taxonomic group from the perspective of cladistics, e.g. Class Reptilia.
Polyphyletic: The presumed derivation of a single taxonomic group from two or
more different ancestral lineages or last common ancestors through convergent or
parallel evolution; modern taxonomists/systematists attempt to eliminate
polyphyletic taxa from their phylogenies and clades.
Cladistics: A mode of classification proposed by Willi Hennig in which taxa are
principally grouped on the basis of their shared possession of similar characters,
synapomorphies, that differ from the ancestral condition; this technique does not
consider all phenotypic characters to be equally important in making taxonomic
decisions.
Plesiomorphy: An ancestral or primitive character, the ancestral trait state, usually
in reference to a homologous character which is a derived trait state
(synapomorphy) in some descendants in the lineage. When a species' trait is similar
in form and function to that character in an ancestral species.
Apomorphy: A feature recently derived in evolution in contrast to an ancestral
character.
Synapomorphy: The possession by two or more related lineages of the same
phenotypic character, a shared derived character, from a different (in form or
function) but homologous character in the ancestral lineage; these are the
significant characteristics to use to make taxonomic distinctions using cladistics; the
characteristics that distinguish one clade from another at any given taxonomic level.
Sister Taxon: A group (taxon) that is the closest relative of another group (taxon);
derives from the concept that each significant evolutionary step marks a
dichotomous split that produces two sister taxa equal to each other in rank.
Adaptive Radiation: The diversification of a single species or group of related
species (or higher taxa) into new ecological or geographical zones to produce a
larger number of descendant species that occupy new niches; this is the common
product of macro-evolutionary change. Adaptive radiations produce branched
phylogenies.
Phyletic Evolution: Evolutionary changes producing a single new taxon that
diverged from a single ancestral lineage over the course of time; aka anagenesis; the
phylogeny of phyletic evolution is a single unbranched transition from ancestor to
descendant taxon.
Founder Effect: The effect caused when a few individuals derived from a large
population disperse to begin a new colony. Since these founders carry only a small
fraction of the parental population’s genetic variability (alleles at all loci), different
gene frequencies with reduced allelic variability become established in the new
colony. The founders will also likely be inbred for many generations and such
populations face a higher risk of extinction though they may also be able to evolve
rapidly in a different environment.
Bottleneck Effect: The Bottleneck Effect occurs when there is a disaster of some
sort that reduces a population to a small remnant of individuals, who rarely
represent the actual original genetic diversity of the initial population's gene pool.
This leaves less allelic variation among the surviving individuals. The survivors will
also likely be inbred for many generations and such populations face a higher risk of
extinction.
Vestigial Feature - A body part or organ, or a behavior or physiological pathway
that is small and degenerate or imperfectly developed in comparison to one more
fully developed in an earlier stage of the individual, in a past generation or ancestral
species, or in closely related forms. It is a special kind of homology that can help
clarify ancestor - descendant relationships.
Atavism/Atavistic Feature - The reappearance in an individual of homologous
characteristics of some remote ancestor that have been absent in intervening
generations; a body part or organ, or a behavior or physiological pathway that is
normally absent in the phenotype of a given species, but appears in a few rare
individuals of the species; it may be reduced in size and function or it may have the
normal size and function that it had in an ancestral species. It is a special kind of
homology that can help clarify ancestor - descendant relationships.
Biogeographic Realms - A large spatial region, within which ecosystems share a
broadly similar biota. Eight terrestrial biogeographic realms are typically
recognized, corresponding roughly to continents (Australasian, Afrotropical,
Nearctic, Oceanic, Antarctic, Indo-Malayan, Neotropical, Palearctic).
A Center of Origin is a proposed location, based on fossil or modern distributional
evidence, for the home of the oldest common ancestor of a taxonomic group.
A Center of Diversity is a region where the greatest proportion of members of the
taxonomic group are present.
A center of origin and a center of diversity are often the same location, or not far
from one another.
Biogeographic Corridor – a dispersal route that permits movement of many
related species from one region to another, a route that has similar environment to
the origin and destination habitats, with few or no significant barriers to the
dispersing organism.
Filter Bridge – a dispersal route that selectively impedes the movement of many
related species from one region to another, but permits the movement of a few
hardy species; a route that has different environment to the origin and destination
habitats, with some barriers to the dispersing organism.
Sweepstakes Dispersal – a dispersal route that only permits rare dispersal events
across significant barriers to the dispersing organism so that the dispersal is likely
to be rare in time.
Dispersal Barrier or Ecological Barrier: An area of unfavorable habitat that
separates two areas of favorable habitat; oceans or rivers for terrestrial organisms,
desert or grassland for of woodland organisms, waterfalls for river/stream
organisms, etc.
Key Concepts
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Charles Darwin purposed a theory of evolution by natural selection
Alfred Russel Wallace proposed a very similar theory. The two theories were
communicated to a meeting of the Linnean Society on July 1 1858.
Ideas of artificial selection were in the air centuries before Darwin’s time.
Darwin made enormous use of artificial selection in explaining his theory.
Darwin was among the first to see the significance of small, continuous
variations in Nature.
Darwin grappled with how selection could get started, invoking the concept
of Preadaptation.
The writings of the Rev. Thomas Malthus showed Darwin and Wallace how
limited resources could lead to competition for these resources.
Competition would result in some individuals leaving more offspring than
other individuals and those parents would be the ones best adapted to the
current environment.
Slowly, natural selection would increase the numbers of individuals best
adapted to the resources and to the environment: survival of the fittest.
Darwin saw that such slow change could lead to the origin of new species.
Darwin placed his emphasis on mechanisms including` geographical isolation
behavior and sexual selection as necessary for speciation.
Darwin initially lacked a mechanism by which phenotypic changes could be
inherited and so proposed a form of pangenesis without the support of data.
Publication of the On the Origin of Species in 1859 revolutionized
understanding of the relationships between organisms and how organisms
arise and change through geologic time.
On the Origin of Species initiated widespread public discussion concerning
science and the place and role of science in society.
Darwin elaborated an evolutionary mechanism – natural selection – but was
not the first think about selection in relation to living organisms.
Darwin continuously referred to natural selection and artificial selection
through combinations of:
o The ease of effecting change via artificial selection,
o The vastness of geological time,
o The application of the geological principle of uniformitarianism by
which present day processes could be extrapolated back in time,
o Identification of a natural selector – the pressure of continuously
limited resources – and with brilliant intuition
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Many more individuals of each species are born than can possibly survive.
Consequently, there is a recurring struggle for existence.
Any individual that varies however slightly in any way that is advantageous
will have a better chance of surviving, of being naturally selected, and of
leaving offspring.
1844-1855 Darwin documented variation in nature; during this time Darwin
did not publish a single word on his theory of evolution; the arrival of Alfred
Russel Wallace's letter prompted the presentation and then publication of
Darwin's ideas.
The evolutionary principle can be summarized:
o Excess reproduction + limited resources →competition, which,
because of natural heritable variation and natural selection allows
those individuals best adapted to pass their existing characters to the
next generation.
o Changing environments + hereditary variation + natural selection
results in the modification of existing characters or the origin of new
characters that become established and spread throughout a
population/species.
Phylogeny happened; Classification did not happen but is a way to arrange or
order the results of evolution.
Taxonomists call each unit of classification, whether it be a particular species,
genus, order or whatever a taxon and give it a distinctive name.
Darwin’s approach accounted for the evolution of a particular species in time,
critics argued that it did not easily account for the multiplication of species in
geographical space or geologic time.
Natural selection is the idea that species that develop adaptations that are
favorable for their environment will pass down those adaptations to their
offspring. Eventually, only individuals with those favorable adaptations will
be more likely to survive and leave the most offspring in the next generation
and that is how the species changes over time, or evolves through speciation.
In the 1800s, after Darwin first published his book On the Origin of Species, a
British economist Herbert Spencer used the term "survival of the fittest" in
relation to Darwin's idea of natural selection as he compared Darwin's
theory to an economic principle in one of his own books. This interpretation
of natural selection caught on and Darwin himself even used the phrase in a
later edition of On the Origin of Species. Clearly, Darwin used the term
correctly as it was meant when discussing natural selection. However,
nowadays this term is often misunderstood when used in place of natural
selection.
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A majority of the general public may be able to describe natural selection as
"survival of the fittest".
When pressed for a further explanation of that term, however, the majority
will answer incorrectly. To a person not familiar with what natural selection
really is, "fittest" means the best physical specimen of the species and only
those in the best shape and best health will survive in nature; they miss the
necessity of increased reproductive success.
This is not always the case. The individuals that survive are not always the
strongest, fastest, or smartest. Therefore, "survival of the fittest" may not be
the best way to describe what natural selection really is as it applies to
evolution. Darwin did not mean it in these terms when he used it in his book
after Herbert first published the phrase. Darwin meant "fittest" to mean the
one best suited for the immediate environment and therefore able to leave
proportionally more offspring in the next generation than those less well
suited for the immediate environment. This is the basis of the idea of natural
selection.
The individual of the population only needs to have the most favorable traits to
survive in the environment. It should follow that individuals who have the favorable
adaptations will live long enough to pass down those genes to their offspring.
Individuals lacking the favorable traits, in other words, the "unfit," will most likely
not live long enough to pass down the unfavorable traits and eventually those traits
will be bred out of the population. The unfavorable traits may take many
generations to decline in numbers and even longer to disappear completely from
the gene pool. This is evident in humans with the genes of fatal diseases that are
still in the gene pool even though they are unfavorable for the survival of the
species.
Darwin’s Theory in Brief:
1. Individuals within species are variable. Not all members of the same species
are alike in structure and function. Some of these variations are passed on to
offspring.
2. In every generation, more offspring are produced than can survive.
Reproductive rates are geometric. The capacity of all organisms to
reproduce is infinitely greater than the capacity of the world to sustain them.
3. The limited resources of the world and the infinite power of reproduction
lead to a competition for resources or a “struggle for existence” between
individuals within species.
4. The survival and reproduction of individuals are not random: the individuals
who survive and go on to reproduce, or who reproduce the most, are those
with the most favorable variations. Those which die have less favorable
variations. The survivors are naturally selected; a process of natural
selection, analogous to the artificial selection practices of animal and plant
breeders, in which the environment determines who lives and who dies. This
results in a survival of the fittest.
5. Those creatures that are most fit and survive will live to produce young that
resemble themselves, so that a particular successful variety is preserved.
The evolution of the eye. An example of historical science and evolutionary
biology that refutes that anti-scientific argument of irreducible complexity. Any
photoreceptor of any degree of complexity would be of benefit to the organism that
has it. Each stage in the evolution of the photoreceptor/eye would serve as a
preadaptation with features that could be acted upon by natural selection to further
improve the structure.
Chapter 7: Darwin, Mendel, and Theories of
Inheritance
People:
Hippocrates
(460-370 BC)
Greek
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Physician, Father of Medicine,
who proposed the concept of
Pangenesis which Darwin
Gregor Mendel
(1822-1884)
Moravian /
Austrian
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Francis Galton
(1822-1911)
English
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August Weismann
(1834-1914)
German
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Walther Flemming
(1843-1905)
German
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Edouard-JosephLouis-Marie van
Beneden
(1846-1910)
Belgian
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Hugo de Vries
(1848-1935)
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Dutch
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reworked as a mechanism of
inheritance
founder of modern genetics
Monk/Friar who developed
three fundamental principles
of heredity from his pea plant
studies
Darwin’s cousin
Disproved pangenesis by
transfusing blood between
rabbit strains and
demonstrating that the
offspring did not acquire
phenotypic traits from the
strains that donated the blood.
coined the term “eugenics” in
1883
Ernst Mayr considered him the
most respected evolutionary
biologist of his generation after
Darwin.
His series of experiments
cutting off the tails of mice
disproved the inheritance of
acquired characteristics
His Germ Plasm Theory stated
that (in a multicellular
organism) inheritance only
takes place by means of the
germ cells—the gametes.
Biologist who discovered
chromosomes and mitosis in
1880
Founder of cytogenetics
discovered that each species has
a fixed number of chromosomes
he also discovered the formation
of haploid cells during cell
division of sperm and ova
(meiosis) in 1887
Botanist who continued
Darwin’s idea of pangenes as
the particulate units of
inheritance which de Vries
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Wilhelm Johannsen
(1857-1927)
Danish
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William Bateson
(1861-1926)
British
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Theodor Boveri
(1862-1915)
German
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Wilhelm Weinberg
(1862-1937)
German
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described in his Intracellular
Pangenesis (1889)
Mutation Theory of Evolution
 Saltationism
Worked with the primrose
Oneothera lamarckiana
Independently rediscovered
Mendel’s work in 1900
Botanist and geneticist who
coined the terms gene (to
replace pangene), genotype,
and phenotype
He demonstrated that not all
phenotypic variation is
controlled by genes, that some
variation is not heritable
Geneticist and Evolutionary
Biologist who coined the terms
genetics and allelomorph (later
shortened to allele)
Emphasized the distinctions
between continuous and
discontinuous variation in
phenotypes and studied other
aspects of phenotypic variation
He was an early Saltationist
Biologist who discovered the
chromatin, the centrosome,
and independent discovery
which led to the Boveri-Sutton
Chromosome Theory of
Inheritance.
He proposed carcinogenesis
was the result of aberrant
mitoses and uncontrolled
growth caused by radiation,
physical or chemical insults or
by microscopic pathogens.
Physician who was one of the
founders of mathematical
genetics
Hardy-Weinberg Equilibrium –
1908
Weinberg pioneered in studies
of twins
Carl Correns
(1864-1933)
German


Thomas Hunt
Morgan
(1866-1945)
American




William E. Castle
(1867-1962)
American


Erich von
Tschermak
(1871-1962)
Austrian



Reginald Punnett
(1875-1967)
British



Walter Sutton
(1877-1916)
American


Botanist and geneticist who
independently rediscovered
Mendel’s work in 1900
He also discovered cytoplasmic
inheritance
Geneticist, embryologist and
evolutionary biologist who
worked with Drosophila
melanogaster  first to
associate a specific gene with a
specific chromosome
He established techniques for
mapping genes on
chromosomes and observed
the importance of
recombination in heredity
(linkage and crossing over)
He was an early Saltationist
and rejected Darwinian sexual
selection
He opposed the Eugenics
movement
Zoologist, one of the founders
of mathematical genetics
The first to use Drosophila
melanogaster in genetics
experiments
He trained Sewall Wright
Botanist who independently
rediscovered Mendel’s work in
1900
He was a major influence in
agriculture and plant breeding
in Austria
One of the founders of
mathematical genetics
He invented the Punnett
Square for calculating monoand di-hybrid crosses
He argued for rapid, not
gradual, evolution of mimicry
patterns in butterflies
Geneticist and physician
His theory that the Mendelian
laws of inheritance could be
Oswald Avery
(1877-1955)
CanadianAmerican


Godfrey H. Hardy
(1877-1947)
British


Richard
Goldschmidt
(1878-1958)
German American




Paul Kammerer
(1880-1926)
Austrian



Colin MacLeod
(1909-1972)
CanadianAmerican

applied to chromosomes at the
cellular level of living
organisms led to the BoveriSutton Chromosome Theory of
Inheritance
Physician who used enzymes to
eliminate the various classes of
biological polymers, one at a time
He, McLeod and McCarty (1944)
demonstrated that DNA was the
“transforming factor” first
identified by Griffith
Mathematician, one of the
founders of mathematical
genetics
Hardy-Weinberg Equilibrium, a
basic principle of population
genetics, he developed
independently from Wilhelm
Weinberg in 1908
Geneticist who was the first to
integrate genetics,
development, and evolution
He advocated a non-Darwinian
origin of species and higher
taxa
The Material Basis of Evolution
(1940)
Goldschmidt advanced a model
of macroevolution through
macromutations known as the
"Hopeful monsters" hypothesis
He was a Saltationist
Biologist who advocated for a
modern form of inheritance of
acquired characteristics and may
represent an early identification
of what today would be called the
effect of epigenetics on heredity
His life is depicted in The Case of
the Midwife Toad, by Arthur
Koestler (1971)
Medical researcher who used
enzymes to eliminate the various

Maclyn McCarty
(1911-2005)
American



Francis Crick
(1916-2004)
British


Arthur Kornberg
(1918-2007)
American




Rosalind Franklin
(1920-1958)
English


James Watson
(1928present)
American

classes of biological polymers,
one at a time
He, Avery, and McCarty (1944)
demonstrated that DNA was the
“transforming factor” first
identified by Griffith
Physician and geneticist who
used enzymes to eliminate the
various classes of biological
polymers, one at a time
He, Avery, and MacLeod (1944)
demonstrated that DNA was the
“transforming factor” first
identified by Griffith
Later he became an expert on
Streptococcal diseases
Molecular biologist and
neuroscientist who was codiscoverer of the DNA double
helix structure with James
Watson
Contributed to the deciphering
of the genetic code
Biochemist who isolated the first
DNA polymerizing enzyme, now
known as DNA polymerase I
(1956)
Won Nobel prize in 1959
first in vitro synthesis of E. coli
DNA in 1968
Made many other contributions
to enzymology and DNA
replication studies
Chemist and X-ray
crystallographer whose data
provided key information for
Watson and Crick in
discovering the DNA double
helix structure
She was also a pioneer in
studying viral structure
Molecular biologist, geneticisy
and zoologist who was codiscoverer of the DNA double


Carl Woese
(1928-2012)
American




J. Craig Venter
(1946present)
American



helix structure with Francis
Crick
He also contributed to cancer
research
First head of the Human
Genome Project
Microbiologist who defined
archae
Wrote The Genetic Code (1967)
an early advocate for the RNA
World
He proposed the three domain
classification of living organisms
Biotechnologist who
sequenced the first genome of
Haemophilus influenza in 1995
Complete sequence of human
genome independent of The
Human Genome Project – 2006
His company created he first
cell with a synthetic genome –
2010
Vocabulary:
Both Darwin and Lamarck believed in evolution and both offered mechanisms to
explain evolutionary change. To explain why some features disappeared, Lamarck
invoked use and disuse and the inheritance of acquired characters as opposed
to Darwin who proposed artificial selection, natural selection, and later, sexual
selection as mechanisms.
The old concept of blending inheritance (the expression in offspring of phenotypic
characters (as pink flower color from red and white parents) intermediate between
those of the parents) sets variation and inheritance in opposition. Blending
inheritance in a now discarded theory in which the genetic material of offspring was
held to be a uniform blend of that of the parents which produces offspring with
intermediate phenotypes to the parents.
Organismal evolution relies on two fundamental aspects of genetics or biological
inheritance: constancy and variation. Constancy resides in the observation that
like produces like. Constancy has the evolutionary significance that all life processes
depend on the transmission of hereditary information from previous generations.
In contrast, variation resides in the observation that like can produce unlike. The
source of hereditary variation was not well understood until the 20th century.
Phenotypic Variation, the small differences in phenotype that exist between
individuals, can be described as being either discontinuous or continuous.
Discontinuous variation - This is where individuals fall into a number of distinct
Phenotypic classes or categories, and is based on features that cannot be measured
across a complete range. Individuals either have the characteristic or they don't.
Blood groups are a good example: you are either one blood group or another - you
can't be in between. Such data is called discrete (or categorical) data. The number
of peas in a pod or the number of kernels on an ear of corn or the number of scales
on the belly of a snake are also examples. Discontinuous variation is controlled by
multiple alleles of a single gene/locus or a small number of genes. The environment
may have little effect on this type of variation. Mendel chose this sort of variation to
study in his experiments.
Continuous variation - In continuous variation there is a complete range of
measurements from one extreme to the other, and so individuals do not separate
into discrete phenotypic classes. Height is an example of continuous variation individuals can have a complete range of heights, for example, 1.6, 1.61, 1.62, 1.625
etc., meters high. Other examples of continuous variation include: weight; hand
span; tooth size; milk yield in cows. Continuous variation is the combined effect of
many genes (known as polygenic inheritance) and is often significantly
affected by environmental influences. Milk yield in cows, for example, is
determined not only by their genetic make-up but is also significantly affected by
environmental factors such as pasture quality and diet, weather, and the comfort of
their surroundings. When plotted as a histogram, these data show a typical bellshaped normal distribution curve, with the mean (= average), mode (= biggest
value) and median (= central value) all being the same.
Mendelian factors and the distribution of chromosomes during meiosis formed
the foundation for the new science of genetics.
Lamarckian inheritance - The discredited concept that somatic phenotypic
changes which develop in an individual's lifetime from some sort of use / disuse
action in a particular environment can be passed to offspring so that offspring will
be likely to demonstrate the phenotype to a greater degree without having to
experience the same lifetime of use or disuse. This inheritance of acquired
characteristics was the main driver of evolutionary change according to JeanBaptiste Lamarck and accepted by Darwin and many of his contemporaries.
Lamarck incorporated two ideas into his theory of evolution, in his day (Age of
Enlightenment) considered to be generally true: (1) Use and Disuse, (2)
Inheritance of acquired traits
Use and disuse – Individuals lose or have diminished phenotypic characteristics
they do not require (or use) during their own lifespan and enhance phenotypic
characteristics that are useful during their own lifespan.
Inheritance of acquired traits – Individuals inherit the modified phenotypic traits
of their parents which have been modified by use or disuse during the parent's
lifetime.
Blending inheritance - The discredited theory that inheritance of traits from two
parents produces offspring with characteristics that are intermediate between those
of the parents.
Isolation - the complete separation of some local populations or demes from others
of the same species; the separation may be due to a variety of circumstances:
geography, season, behavior, etc. It is more likely that an adaptive character trait
could be maintained if those individuals expressing it were isolated from other
members of the species. Most Darwinian taxonomists emphasize the importance of
isolation in increasing the speed of evolutionary changes. Reproductive isolation is
the key feature of Ernst Mayr's Biological Species Concept.
Intraspecific variation - the range of change or difference in condition, amount or
level of some aspect or aspects of the phenotypic characters of the individuals in the
populations that comprise a particular species.
Mendel’s exceptional contribution to science was to demonstrate that organisms
have a distinct hereditary system (now known as the genotype), which transmits
biological characteristics through discrete units ("elementen," now known as genes
and alleles) that remain undiluted in the presence of other genes and alleles.
Mendel developed two fundamental principles of heredity: the principle of
segregation, and the principle of independent assortment
gene - the hereditary controller of a phenotypic trait; the DNA sequence that codes
for a particular polypeptide chain or protein.
genotype - the alleles present at one or more loci in an individual. If the two alleles
are identical, then the genotype is homozygous; if the two alleles are different, then
the genotype is heterozygous.
locus - the physical location of a gene along the length of a DNA molecule.
allele - the different forms of a gene at a give locus, these different forms control
some of the variation seen in the phenotype under the control of the gene (some of
the variation in phenotype may also be controlled by environmental factors).
Dominant trait / allele - a form of a gene and the phenotype that it controls which
will be expressed if the diploid individual receives either one (heterozygous) or two
copies of the allele (homozygous) from its parents.
Recessive trait / allele - a form of a gene and the phenotype that it controls which
will be expressed only if the diploid individual receives two copies of the allele
(homozygous) from its parents.
Incomplete dominance - A kind of gene expression occurring in heterozygotes in
which the the relationship among alleles is neither dominant or recessive; it can be
thought of as a dosage effect, fully expressed when the allele is in the homozygous
state, but only partially expressed in the heterozygous state and usually resulting in
an offspring with an intermediate phenotype.
A typical example of incomplete dominance is the color of the flower in which R
symbolizes an allele for red pigment production and r is the alternative allele for no
pigment production (an allele for a defective enzyme which cannot transform a
colorless precursor into red pigment). In incomplete dominance, the heterozygous
plant carrying both alleles, Rr, will not be able to produce enough red pigment and
therefore will appear pink. (Synonym: partial dominance)
Codominance - A condition in which the alleles of a gene pair in a heterozygote are
fully expressed thereby resulting in offspring with a phenotype that is neither
dominant nor recessive. A typical example showing codominance is the ABO blood
group system. For instance, a person having A allele and B allele will have a blood
type AB because both the A and B alleles are codominant with each other and both
are expressed independently in the phenotype.
Principle of segregation - alleles of a single gene at a locus are discrete entities
that segregate from each other into gametes; they do not blend even when found in
heterozygous individuals.
Principle of independent assortment - allele pairs belonging to two or more
genes at different loci separate independently during the formation of gametes. This
means that traits are transmitted to offspring independently of one another. This
principle of independent assortment of genes always applies when the loci are on
different chromosomes and may also apply if the loci are far enough apart (>50map
units) on the same chromosome.
In practice, the manifestation of Mendel's laws is seen by characteristic ratios of
phenotypic classes, such as 3:1 in monohybrid crosses of heterozygous parents and
9:3:3:1 in dihybrid crosses of heterozygous parents. Further, the Mendelian
principles just stated include the simple assumption that one allele is dominant to
the other allele.
In the time since Mendel's original experiments, we have come to learn that there
are extensions to Mendelian principles, including the fact that some alleles are
incompletely dominant or co-dominant, that some genes have multiple allele
systems (more than two different alleles at a single locus within the gene pool), that
some genes are sex-linked, and that some pairs of genes do not assort independently
because they are physically linked on a chromosome.
Gene Penetrance - the proportion of individuals of a specified genotype that show
the expected phenotype under a defined set of environmental conditions.
Saltations – jumps; large discontinuous phenotypic changes in organisms or parts
of organisms which are caused by macromutations (alleles that individually cause
large dramatic changes in phenotype). During the Mutationist/Saltationist period
of biology (1900 - ~1930), saltations/macromutations were thought to be the main
driver of macroevolutionary change.
Pangenesis – Aristotle had proposed the theory of Pangenesis, which was adopted
with variations by later biologists, including Darwin, which held that particles
(called pangenes or gemmules) produced by all tissues of the body of a parent
migrate from somatic tissues to reproductive tissues and are incorporated into its
eggs or sperm. Darwin’s “provisional hypothesis of pangenesis:” “The chief
assumption is that all the units of the body, besides having the universally admitted
power of growing by self-division, throw off minute gemmules which are dispersed
through the system . . . “But we have further to assume that the gemmules grow,
multiply, and aggregate themselves into buds and the sexual elements; their
development depending on their union with other nascent cells or units. They are
also believed to be capable of transmission in a dormant state, like seeds in the
ground, to successive generations.”
Gemmules – Darwin’s idea of control particles for phenotypic traits shed by the
cells of tissues and organs of the body and carried (in the bloodstream or by some
other means) to the reproductive organs where they accumulate into germ cells or
gametes; this is an aspect of the pangenesis hypothesis. Another names for the
gemmules was pangenes.
Germ plasm theory – only the reproductive tissues transmit the heredity factors of
the entire organism; changes (mutations) that occur in nonreproductive (somatic)
tissues are not transmitted to gametes and therefore not to offspring.
Chromosome Theory of Inheritance - The unifying theory that chromosomes are
linear sequences of genes and that inheritance patterns may be generally explained
by assuming that genes are located in specific sites/loci on chromosomes.
Extranuclear inheritance – traits that do not follow a nuclear pattern of
inheritance but rather transmit through the cytoplasm of the egg; the best known
examples are the transmission of organelle genes, those of the mitochondria and
chloroplasts.
Sex-linked genes – genes that are localized to the X chromosome of the XY (sex
chromosome) system or to Z of the ZW (sex chromosome)system. Sex-linked genes
are more easily expressed in the heterogametic sex (XY males or ZW females)
because they only receive one allele per gene at all their loci on their sex
chromosome.
Gene linkage is the tendency of alleles that are located close together on a DNA
molecule (plasmid, chromosome, etc.) to be inherited together during cell divisions.
In the division I meiosis phase of sexual reproduction, synapsis causes homologous
chromosomes to form tetrads. If chromosome breaks occur within the tetrad and
are followed by improper DNA repair, some alleles may be swapped from one
parent DNA molecule to another (from maternal to paternal DNA or vice versa).
This is termed crossing-over and it is a major source of recombination of genes
(alleles at particular loci) during gamete formation (at Meiosis I Prophase and
Metaphase). This is of evolutionary significance because some changes in
phenotype can occur from the same genotype if phenotypic expression depends on
particular alleles being on the same DNA molecule (cis configuration) versus being
on two different homologous DNA molecules (trans configuration).
Eugenics - the science of improving a human population by controlled breeding to
increase the occurrence of desirable heritable characteristics; developed largely by
Francis Galton as a method of improving the human race, it fell into disfavor only
after the perversion of its doctrines by the Nazis.
Positive Eugenics - the study of or belief in the possibility of improving the qualities of
the human species or a human population, especially by encouraging reproduction by
persons presumed to have inheritable desirable traits.
Negative Eugenics - the study of or belief in the possibility of improving the qualities of
the human species or a human population, especially by discouraging reproduction by
persons having genetic defects or presumed to have inheritable undesirable traits.
Gene recombination - The process of forming new allelic combination in offspring
by exchanges between genetic materials (as exchange of DNA sequences between
DNA molecules from different individuals, even from different species). This
process is a natural process, sometimes also called gene transfer. Different
mechanisms are used by asexual or sexual species. In sexually reproducing
organisms, it is usually the result of crossing over between homologous
chromosomes during meiosis and since the changes are passed from parent to
offspring, it is termed vertical gene transfer. In asexually reproducing organisms,
it is usually the result of transformation (acquisition of naked DNA from the
environment), conjugation (the one-way transfer of of DNA sequences, part or all of
a bacterial genome, usually part of the main circular DNA, but sometimes plasmids,
through a conjugation tube (“sex pilus”) from a donor strain to a recipient strain of
bacteria) or transduction (transfer of a DNA sequence from one cell to another by a
virus vector) and since these alleles are passed from one cell or organism to another
mature cell or organism in the environment,, it is termed horizontal gene transfer.
For many organisms, especially mammals, sex determination is associated with
chromosomal differences between the two sexes. In the XY sex determination
system common in many plants and animals, one typically observes XX females and
XY males, with the Y chromosome often smaller and mostly inactive, except for male
determining and male-fertility genes. In the ZW sex determination common in
some leopidopterans and birds, one typically observes ZW females and ZZ males.
Other species may use the ratio of sex chromosomes to autosome sets or the
presence of particular sex determination genes distributed among the autosomes to
determine sex.
Sex-Linked Genes - A gene located on a sex chromosome, the X-chromosome in XY
systems and the W-chromosome in XW systems. The single allele on the sex
chromosome in the heterogametic sex (XY males or ZW females) will be expressed
in the phenotype of the heterogametic individuals.
Haplo-Diploidy Sex Determination – the unusual genetic method of sex
determination Hymenoptera, the Order of insects that includes the bees, ants and
wasps. Males are haploid while females are diploid. Female Hymenoptera come
about in the usual way, with a sperm from a male fertilizing a female's egg. One set
of chromosomes comes from the father, the other from the mother, yielding a
diploid daughter. Males, on the other hand, have a mother but no father.
Environmental sex determination occurs when the sex of one or both of the male
and female individuals is developed because of sensitivity to agents such as
temperature or hormones or social group organization or body mass, or age, etc.
Temperature Dependent Sex Determination - a type of environmental sex
determination in which the temperatures experienced during embryonic/larvae
development determine the sex of the offspring; seen in all crocodilians, most
turtles, a few lizards and rare birds.
Protandry – A form of environmental sex determination in which animals, e.g.
many reef fish species, develop into males first in their life cycle, and then later, if
the right environmental stimulus in presented, transform into females later in their
life. One advantage to protandry could be reaching a large size before becoming an
egg laying female and needing to have large energy reserves to produce yoik rich
eggs.
Protogyny – A form of environmental sex determination in which animals, e.g.
many reef fish species, develop into females first in their life cycle, and then later, if
the right environmental stimulus in presented, transform into males later in their
life. One advantage to protandry could be reaching a large size before becoming a
male and having to compete with other males for access to females.
Parthenogenesis is a form of asexual reproduction in animals in which females
produce eggs that develop without fertilization.
DNA replication is the process by which DNA makes a copy of itself during cell
division.
1. The first step in DNA replication is to ‘unzip’ the double helix structure of the
DNA molecule.
2. This is carried out by an enzyme called helicase which breaks the hydrogen
bonds holding the complementary bases of DNA together (A with T, C with G).
3. The separation of the two single strands of DNA creates a ‘Y’ shape called a
replication ‘fork’. The two separated strands will act as templates for making the
new strands of DNA.
4. One of the strands is oriented in the 3’ to 5’ direction (towards the replication
fork), this is the leading strand. The other strand is oriented in the 5’ to 3’ direction
(away from the replication fork), this is the lagging strand. As a result of their
different orientations, the two strands are replicated differently:
Leading Strand:
5. A short piece of RNA called a primer
(produced by an enzyme called
primase) comes along and binds to the
end of the leading strand. The primer
acts as the starting point for DNA
synthesis.
6. DNA polymerase binds to the
leading strand and then ‘walks’ along it,
adding new complementary nucleotide
bases (A, C, G and T) to the strand of
DNA in the 5’ to 3’ direction.
7. This sort of replication is called
continuous.
Lagging strand:
5. Numerous RNA primers are made by
the primase enzyme and bind at various
points along the lagging strand.
6. Chunks of DNA, called Okazaki
fragments, are then added to the
lagging strand also in the 5’ to 3’
direction.
7. This type of replication is called
discontinuous as the Okazaki
fragments will need to be joined up
later.
8. Once all of the bases are matched up (A with T, C with G), an enzyme called
exonuclease strips away the primer(s). The gaps where the primer(s) were are
then filled by yet more complementary nucleotides.
9. The new strand is proofread to make sure there are no mistakes in the new DNA
sequence.
10. Finally, an enzyme called DNA ligase seals up the sequence of DNA into two
continuous double strands.
11. The result of DNA replication is two DNA molecules consisting of one new and
one old chain of nucleotides. This is why DNA replication is described as semiconservative, half of the chain is part of the original DNA molecule, half is brand
new.
12. Following replication the new DNA automatically winds up into a double helix.
Primase is an enzyme that creates a primer on a DNA strand by adding RNA
nucleotides to the strand according to the DNA template sequence. This process
occurs during DNA Replication and may represent a biochemical vestige of the RNA
World.
The Genetic Code is the set of rules by which hereditary information encoded in
genetic material (DNA or RNA sequences) is translated into proteins (amino acid
sequences) by living cells.
Specifically, the code defines a mapping between tri-nucleotide sequences called
(triplet base) codons and amino acids; every triplet of nucleotides in a nucleic acid
sequence specifies a single amino acid. The code is unambiguous because any one
codon always codes for the same amino acid. The code is degenerate because
several codons (codon synonyms) may represent a single amino acid. The codons
are found in mRNA molecules. The DNA sequence is a base compliment to the
mRNA codon and is found on the sense strand of the DNA gene. The code is termed
universal because most organisms have exactly the same set of codon to amino acid
relationships though there are some exceptions to that relationship.
The genome (all the structural and regulatory genes) of an organism is inscribed in
DNA, or in some viruses in RNA. The portion of the genome that codes for a
polypeptide chain or protein or an RNA is referred to as a gene.