Lecture 0: General Information- 1/12/22
● Monday- in person lecture and a quiz due at 10pm
● Wednesday- recorded lecture and quiz due at 10pm
● Midterms: Feb 9, Mar 2, Apr 6, May 2
● Final: May 12
Lecture 1: Diversity of Life- 1/12/22
Organismal Diversity
● Zoo/Aquarium/Botanical garden diversity: The view most have of organismal diversity is
based on variation among large animals and plants.
● These differences are in fact fairly trivial compared to the spectrum of biological diversity.
● Not only are life forms diverse, they are much more diverse than most people can
imagine.
Bacteria
● While animal and plant diversity is impressive, it is largely morphological
● Bacteria have modest morphological variation, but enormous biochemical variation
● They are found in every possible environment, including deadly hostile ones
● Bacteria growing in the middle of these salt crystals
● The study of life in such extreme environments has provided significant new insights on
two of the most important questions in biology: How did life start? Is there life beyond
earth? If so, what features (if any) does it share with life as we know it?
How can we account for
● The apparent adaptability of these life forms to their environments?
● The diversity of life forms?
● "Nothing in biology makes sense except in the light of evolution" Th. Dobzhansky (1973)
What is life?
● Life is historically defined as the ability to – Self-replicate – Evolve (change over time) –
Take in raw materials from the environment and modify them
● Single human cells are “alive”, but not really an organism • Viruses: are these alive? –
Inject RNA or DNA instructions into a host to make copies of themselves
● Prions: only protein. Are these alive? – Really are acting like a virus • Bottom line: The
distinction between living and nonliving is a blur, not a sharp line
Basic questions about life
● What’s out there?
● How is it built?
● How does it work?
● How did it get that way (i.e.How has it evolved?)
● The effect of past history on the story of life separates it from the other sciences (e.g.,
chemistry, physics), where the past history leading to an event often has little bearing on
the outcome of some process
Biology is also the study of interactions
● The diversity of individual life forms is dwarfed by the diversity in how these individuals
forms interact with the environment and each other
● Ecology is the study of these interactions
Basic questions about ecosystems
, ● What’s out there? – How do we define, and delineate, ecosystems
● How is it built? – What “parts” (species/interactions) are involved
● How does it work? – How do interactions structure an ecosystem?
● How did it get that way (i.e., how has it evolved? – How do parts coevolve?
● Of course, some life forms are unexplainable
○ One working theory = Basic genetics: crosses
Lecture 2: Evidence for Evolution- 1/19/22
Overview
● Early views of evolution
● What is Evolution? –often misunderstood
● Science and religion
○ Scientific “facts” vs. “theories”
● What is the evidence for evolution?
How can we account for
● The apparent adaptability of these life forms to their environments?
● The diversity of life forms?
● “Nothing in biology makes sense except in the light of evolution” Th. Dobzhansky (1973)
The Early seeds of Evolutionary thinking
● The classical view (greeks)
● Buffon 1770
● Erasmus Darwin 1770
● Lamarck 1810
● Charles Darwin
The classical view of the Greeks
● Living organisms are constant and unchanging (short period of time -life time)
● The roots of this notion traces back to the Greeks, but even the great naturalist Aristotle
pondered over bizarre life forms that he could not easily classify, e.g. Sponges, which
look like plants but feed like animals (continuum not boxes to put things in)
This view gets shaken up:
● Global explorations starting in the 1500s turned up extraordinary diversities of life forms,
some of which appeared related to European forms, others with no resemblance
● Humans rarely traveled before the global exploration period
The world distribution of organisms puzzling:
● Interesting observations of distribution of animals and plants:
○ Biogeography: distribution of plants and animals across the world
● Marsupials mammals generally very rare, but all Australian mammals were marsupials
● Cactus plants common in North and South American deserts, absent in Austrials and
Asian deserts
● If all species were created at the same time in the same place, how could so many be
restricted to particular parts of the world?
Buffon (1770s)
, ● Noted that if there had been only a single center of creation, species spreading out from
this center would have eventually been stopped by the mountains or seas. He suggested
that the creation of species is spread out in space.
● Buffon also noted that species might not have been created in a perfect state (e.g., pigs
have lateral toes that are too high to reach the ground). He suggested that perhaps
species become modified over time
Erasmus Darwin (1770s)
● Was impressed by the diversity of domesticated animals generated by selective
breeding. Suggested that all organisms had a common ancestor
● Grandson Charles Darwin later used these ideas
Jean Baptiste de Lamarck (1809)
● Suggested that life had been created long ago in a simple state, and had been gradually
improving. He proposed a specific mechanism for how this change occurs: the
inheritance of acquired characteristics
● Misbelieved that acquired characteristics are passed onto to offspring
● Lamarck thus suggested that species change over time and that the environment was a
factor in this change
What is evolution?
● Charles Darwin defined it as descent with modification
● Darwin was not the first to suggest that evolution occurs, but he was the first to suggest
a plausible mechanism as well as present an overwhelming case that evolution occurs.
● What do we mean by descent with modification?
Descent with modification
● Phylogenetic tree: read it as E is the common ancestor across all shown species (each
point is called a node) A, B, C descend from E and D
● All organisms can be traced back through a series of common ancestry (here, D and E).
If tur, should find evidence of this
● Descent with modification allows for tests of Evolution
● House example: if a house has been renovated one or more times, if we look hard
enough, we can find vestiges of the original house. For example, a wall with a
plasterer-over door frame
Scientific theories and scientific facts
● Gravity as a scientific fact
● Dropping a pencil does not “prove” gravity. What about other times?
● What about gravity and other planets or stars?
● Key: all experiments designed to test for gravity has shown it occurs
Science vs. Religion
, ● Not incompatible, as are designed for different tasks
● Religion is a system of beliefs generating set of values and culture
● Science is a specific tool for asking questions and rigorously testing them
● Scientists of different faiths still use the same approaches for asking and testing
questions
● Many scientists are religious and many people of strong faith have a deep interest in
science
Science is about testing
● The key feature of science is making predictions and testing them
● Testable predictions
○ Hypothesis: there is a cold beer in the fridge
○ Science: Open fridge and see if there is a beer (test your hypothesis!)
● A strong scientific idea is one that brings order to a set of apparently disparate set of
facts
● In science, the burden of faith is on the believer —you have to make a case, based n
repeatable tests that supports your assertions
● Hence, you have to pout your most fundamental ideas on trial and constantly try to prove
them wrong!
Evolution as a Scientific fact
● If evolution has occurred, there are a variety of signs we should be able to detect
● Key: signatures of shared ancestry -descent with modification
● Why a “fact” – each time we “test” for evolution, we see evidence of it. It’s the
undefeated champs for over 150 years of aggressive testing!
● For example, each new genome sequence is a test of evolution
Evidence for descent with modification
● Biogeography
● Functional morphology
● Paleontology
● Comparative embryology
● Animal and plant breeding
● Molecular evidence
The voyage of the HMS Beagle 1831-36
● Darwin was hired as a naturalist for a 5 year mission
Armadillos and fossil Glyptodonts
● Both found in the same location on South America
● If these had been created separately, why would both living and extinct forms be
restricted to the same area?
● Darwin thought it made more sense to assume the armadillo evolved from the glyptodon
or a close relative
Variation between species on the Galapagos Islands
● Darwin observed that each island has a slightly different species of finch, all of which
appear close to a single species found on the South American mainland
● Island radiation: rapid propagation of a certain species because of isolation
● Monday- in person lecture and a quiz due at 10pm
● Wednesday- recorded lecture and quiz due at 10pm
● Midterms: Feb 9, Mar 2, Apr 6, May 2
● Final: May 12
Lecture 1: Diversity of Life- 1/12/22
Organismal Diversity
● Zoo/Aquarium/Botanical garden diversity: The view most have of organismal diversity is
based on variation among large animals and plants.
● These differences are in fact fairly trivial compared to the spectrum of biological diversity.
● Not only are life forms diverse, they are much more diverse than most people can
imagine.
Bacteria
● While animal and plant diversity is impressive, it is largely morphological
● Bacteria have modest morphological variation, but enormous biochemical variation
● They are found in every possible environment, including deadly hostile ones
● Bacteria growing in the middle of these salt crystals
● The study of life in such extreme environments has provided significant new insights on
two of the most important questions in biology: How did life start? Is there life beyond
earth? If so, what features (if any) does it share with life as we know it?
How can we account for
● The apparent adaptability of these life forms to their environments?
● The diversity of life forms?
● "Nothing in biology makes sense except in the light of evolution" Th. Dobzhansky (1973)
What is life?
● Life is historically defined as the ability to – Self-replicate – Evolve (change over time) –
Take in raw materials from the environment and modify them
● Single human cells are “alive”, but not really an organism • Viruses: are these alive? –
Inject RNA or DNA instructions into a host to make copies of themselves
● Prions: only protein. Are these alive? – Really are acting like a virus • Bottom line: The
distinction between living and nonliving is a blur, not a sharp line
Basic questions about life
● What’s out there?
● How is it built?
● How does it work?
● How did it get that way (i.e.How has it evolved?)
● The effect of past history on the story of life separates it from the other sciences (e.g.,
chemistry, physics), where the past history leading to an event often has little bearing on
the outcome of some process
Biology is also the study of interactions
● The diversity of individual life forms is dwarfed by the diversity in how these individuals
forms interact with the environment and each other
● Ecology is the study of these interactions
Basic questions about ecosystems
, ● What’s out there? – How do we define, and delineate, ecosystems
● How is it built? – What “parts” (species/interactions) are involved
● How does it work? – How do interactions structure an ecosystem?
● How did it get that way (i.e., how has it evolved? – How do parts coevolve?
● Of course, some life forms are unexplainable
○ One working theory = Basic genetics: crosses
Lecture 2: Evidence for Evolution- 1/19/22
Overview
● Early views of evolution
● What is Evolution? –often misunderstood
● Science and religion
○ Scientific “facts” vs. “theories”
● What is the evidence for evolution?
How can we account for
● The apparent adaptability of these life forms to their environments?
● The diversity of life forms?
● “Nothing in biology makes sense except in the light of evolution” Th. Dobzhansky (1973)
The Early seeds of Evolutionary thinking
● The classical view (greeks)
● Buffon 1770
● Erasmus Darwin 1770
● Lamarck 1810
● Charles Darwin
The classical view of the Greeks
● Living organisms are constant and unchanging (short period of time -life time)
● The roots of this notion traces back to the Greeks, but even the great naturalist Aristotle
pondered over bizarre life forms that he could not easily classify, e.g. Sponges, which
look like plants but feed like animals (continuum not boxes to put things in)
This view gets shaken up:
● Global explorations starting in the 1500s turned up extraordinary diversities of life forms,
some of which appeared related to European forms, others with no resemblance
● Humans rarely traveled before the global exploration period
The world distribution of organisms puzzling:
● Interesting observations of distribution of animals and plants:
○ Biogeography: distribution of plants and animals across the world
● Marsupials mammals generally very rare, but all Australian mammals were marsupials
● Cactus plants common in North and South American deserts, absent in Austrials and
Asian deserts
● If all species were created at the same time in the same place, how could so many be
restricted to particular parts of the world?
Buffon (1770s)
, ● Noted that if there had been only a single center of creation, species spreading out from
this center would have eventually been stopped by the mountains or seas. He suggested
that the creation of species is spread out in space.
● Buffon also noted that species might not have been created in a perfect state (e.g., pigs
have lateral toes that are too high to reach the ground). He suggested that perhaps
species become modified over time
Erasmus Darwin (1770s)
● Was impressed by the diversity of domesticated animals generated by selective
breeding. Suggested that all organisms had a common ancestor
● Grandson Charles Darwin later used these ideas
Jean Baptiste de Lamarck (1809)
● Suggested that life had been created long ago in a simple state, and had been gradually
improving. He proposed a specific mechanism for how this change occurs: the
inheritance of acquired characteristics
● Misbelieved that acquired characteristics are passed onto to offspring
● Lamarck thus suggested that species change over time and that the environment was a
factor in this change
What is evolution?
● Charles Darwin defined it as descent with modification
● Darwin was not the first to suggest that evolution occurs, but he was the first to suggest
a plausible mechanism as well as present an overwhelming case that evolution occurs.
● What do we mean by descent with modification?
Descent with modification
● Phylogenetic tree: read it as E is the common ancestor across all shown species (each
point is called a node) A, B, C descend from E and D
● All organisms can be traced back through a series of common ancestry (here, D and E).
If tur, should find evidence of this
● Descent with modification allows for tests of Evolution
● House example: if a house has been renovated one or more times, if we look hard
enough, we can find vestiges of the original house. For example, a wall with a
plasterer-over door frame
Scientific theories and scientific facts
● Gravity as a scientific fact
● Dropping a pencil does not “prove” gravity. What about other times?
● What about gravity and other planets or stars?
● Key: all experiments designed to test for gravity has shown it occurs
Science vs. Religion
, ● Not incompatible, as are designed for different tasks
● Religion is a system of beliefs generating set of values and culture
● Science is a specific tool for asking questions and rigorously testing them
● Scientists of different faiths still use the same approaches for asking and testing
questions
● Many scientists are religious and many people of strong faith have a deep interest in
science
Science is about testing
● The key feature of science is making predictions and testing them
● Testable predictions
○ Hypothesis: there is a cold beer in the fridge
○ Science: Open fridge and see if there is a beer (test your hypothesis!)
● A strong scientific idea is one that brings order to a set of apparently disparate set of
facts
● In science, the burden of faith is on the believer —you have to make a case, based n
repeatable tests that supports your assertions
● Hence, you have to pout your most fundamental ideas on trial and constantly try to prove
them wrong!
Evolution as a Scientific fact
● If evolution has occurred, there are a variety of signs we should be able to detect
● Key: signatures of shared ancestry -descent with modification
● Why a “fact” – each time we “test” for evolution, we see evidence of it. It’s the
undefeated champs for over 150 years of aggressive testing!
● For example, each new genome sequence is a test of evolution
Evidence for descent with modification
● Biogeography
● Functional morphology
● Paleontology
● Comparative embryology
● Animal and plant breeding
● Molecular evidence
The voyage of the HMS Beagle 1831-36
● Darwin was hired as a naturalist for a 5 year mission
Armadillos and fossil Glyptodonts
● Both found in the same location on South America
● If these had been created separately, why would both living and extinct forms be
restricted to the same area?
● Darwin thought it made more sense to assume the armadillo evolved from the glyptodon
or a close relative
Variation between species on the Galapagos Islands
● Darwin observed that each island has a slightly different species of finch, all of which
appear close to a single species found on the South American mainland
● Island radiation: rapid propagation of a certain species because of isolation
