I. What is Biology?
I. What is Biology?
A. Definition:
Webster’s New World Dictionary: "the science
that deals with the origin, history, physical
characteristics, life processes, habits, etc. of
plants and animals: it includes botany and
zoology."
I. What is Biology?
A. Definition:
Webster’s New World Dictionary: "the science
that deals with the origin, history, physical
characteristics, life processes, habits, etc. of
plants and animals: it includes botany and
zoology."
The scientific study of living systems.
I. What is Biology?
A. Definition:
Webster’s New World Dictionary: "the science
that deals with the origin, history, physical
characteristics, life processes, habits, etc. of
plants and animals: it includes botany and
zoology."
The scientific study of living systems.
Begs two questions – “what is science?” and
“What distinguishes living systems?”
II. What is Science?
A. Definition:
Webster’s: “systematized knowledge derived
from observation, study, and experimentation
carried on in order to determine the nature or
principles of what is being studied. The
systematized knowledge of nature and the
physical world.”
II. What is Science?
A. Definition:
Webster’s: “systematized knowledge derived
from observation, study, and experimentation
carried on in order to determine the nature or
principles of what is being studied. The
systematized knowledge of nature and the
physical world.”
II. What is Science?
A. Definition:
Webster’s: “systematized knowledge derived
from observation, study, and experimentation
carried on in order to determine the nature or
principles of what is being studied. The
systematized knowledge of nature and the
physical world.”
B. Limitations:
II. What is Science?
A. Definition:
Webster’s: “systematized knowledge derived
from observation, study, and experimentation
carried on in order to determine the nature or
principles of what is being studied. The
systematized knowledge of nature and the
physical world.”
B. Limitations:
- What is studied: the physical world /universe
II. What is Science?
A. Definition:
Webster’s: “systematized knowledge derived
from observation, study, and experimentation
carried on in order to determine the nature or
principles of what is being studied. The
systematized knowledge of nature and the
physical world.”
B. Limitations:
- What is studied: the physical world /universe
- How it is studied (Method): empiricism
II. What is Science?
A. Definition:
Webster’s: “systematized knowledge derived
from observation, study, and experimentation
carried on in order to determine the nature or
principles of what is being studied. The
systematized knowledge of nature and the
physical world.”
B. Limitations:
- What is studied: the physical world /universe
- How it is studied (Method): empiricism
- Methodological Approaches:
-Methodological Approaches:
1. REDUCTIONISM
Gaining an understanding of a system by
describing its subsystems (components)
Powerful Approach: living systems are very complex, so
describing the STRUCTURE can give insights into FUNCTION.
-Methodological Approaches:
1. REDUCTIONISM
Gaining an understanding of a system by
describing its subsystems (components)
But the functioning of a complex system is not
entirely described by the ADDITIVE EFFECTS
of their components…
The system functions as a consequence of
how these subsystems INTERACT… these
aspects are called EMERGENT PROPERTIES
-Methodological Approaches:
1. REDUCTIONISM
Medicine: Anatomy (reduction) and Physiology
(systems approach)
Natural History: Taxonomy (reduction) and Ecology
(systems approach)
Genetics: sequencing (reduction) and Functional
Genomics (system approach)
-Methodological Approaches:
1. REDUCTIONISM
2. COMPARATIVE METHOD
-Methodological Approaches:
1. REDUCTIONISM
2. COMPARATIVE METHOD
The function of complex systems may be understood by
comparing them with simpler systems (with fewer
subsystems).
-Methodological Approaches:
1. REDUCTIONISM
2. COMPARATIVE METHOD
The function of complex systems may be understood by
comparing them with simpler systems (with fewer
subsystems).
How could a complex system like a
camera eye, composed of mutually
dependent parts, have evolved
through a stepwise sequence?
(This is Paley’s (1802) ‘argument of
design’, currently repackaged with
molecular and cellular examples by
the ‘Intelligent Design’ movement.)
Half an eye (lens) can’t work…
2. COMPARATIVE METHOD
The function of complex systems may be understood by
comparing them with simpler systems (with fewer
subsystems). Visual systems in molluscs:
2. COMPARATIVE METHOD
The function of complex systems may be understood by
comparing them with simpler systems (with fewer
subsystems). Visual systems in molluscs:
Half an eye
(retina) CAN
work…
2. COMPARATIVE METHOD
Why is this method so powerful in biology? Is there a
REASON why different organisms might have similar
structures and functions?
2. COMPARATIVE METHOD
Why is this method so powerful in biology? Is there a
REASON why different organisms might have similar
structures and functions? Yes… common ancestry.
This is why the use of model organisms (E. coli, fruit fly,
house mouse) illuminates the field of medicine
And the most
dramatic examples of
homology are in the
hox genes, as well.
And the most dramatic
examples of homology
are in the hox genes, as
well.
In fact, the homology is
so good that lineages of
eyeless flies lacking that
hox gene can have the
ability to grow eyes
restored by adding the
homologous gene from a
mouse…and flies
develop compound eyes
with the mouse hox gene
for eye development,
even though mice
have camera eyes…
HOW COOL IS
THAT!?
And the most dramatic
examples of homology
are in the hox genes, as
well.
And, human diseases
have been identified as
hox mutants by
identifying homology with
fruit fly hox genes, and
they have been found in
the genome with ss-DNA
(probe) from the fly
homeobox region of that
gene.
And the most dramatic
examples of homology
are in the hox genes, as
well.
And, human diseases
have been identified as
hox mutants by
identifying homology with
fruit fly hox genes, and
they have been found in
the genome with ss-DNA
(probe) from the fly
homeobox region of that
gene.
And, because of evolution
and common ancestry, we
can use model organisms
like flies to learn about how
heredity and development
work in all animals …
including humans.
-Methodological Approaches:
1. REDUCTIONISM
2. COMPARATIVE METHOD
3. EXPERIMENTATION (EMPIRICISM)
-Methodological Approaches:
1. REDUCTIONISM
2. COMPARATIVE METHOD
3. EXPERIMENTATION (EMPIRICISM)
Observe repeated, correlated physical phenomena/patterns
“On Caribbean Islands with lizards, there are no spiders”
Observe repeated, correlated physical phenomena/patterns
“On Caribbean Islands with lizards, spiders are rare”
GOAL: create GOAL:
a falsifiable
is this
(testable)
relationship
causal
causal
hypothesis
?
Observe repeated, correlated physical phenomena/patterns
“On Caribbean Islands with lizards, spiders are rare”
GOAL: create GOAL:
a falsifiable
is this
(testable)
relationship
causal
causal
hypothesis
?
Bring other observed facts to bear
“They use similar habitats” (could live together)
“Lizards eat spiders”
“Lizards and spiders eat other insects”
“They disperse differently” (so they may have gotten to
different islands by chance)
“Hawks eat lizards but not spiders, so maybe it just happens
that hawks and spiders are together”
“Some warblers eat spiders and not lizards, and maybe it just
happens that warblers and lizards are together”
“Lizards run around and may break spider webs and starve
them inadvertently”
Observe repeated, correlated physical phenomena/patterns
“On Caribbean Islands with lizards, spiders are rare”
GOAL: create a falsifiable (testable) causal hypothesis
Bring other observed facts to bear
“They use similar habitats” (could live together)
“Lizards eat spiders”
“Lizards and spiders eat other insects”
“They disperse differently” (so they may have gotten to
different islands by chance)
“Hawks eat lizards but not spiders, so maybe it just happens
that hawks and spiders are together”
“Some warblers eat spiders and not lizards, and maybe it just
happens that warblers and lizards are together”
“Lizards run around and may break spider webs and starve
them inadvertently”
You can envision many alternative causal hypotheses …and there are
nearly a limitless supply…you can’t test them all (so scientific facts aren’t
eternal truths or PROOFS)… test the simplest explanation first = “principle
of parsimony” or “Occam’s razor”
Bring other observed facts to bear
“They use similar habitats” (could live together)
“Lizards eat spiders”
“Lizards and spiders eat other insects”
“They disperse differently” (so they may have gotten to
different islands by chance)
“Hawks eat lizards but not spiders, so maybe it just happens
that hawks and spiders are together”
“Some warblers eat spiders and not lizards, and maybe it just
happens that warblers and lizards are together”
“Lizards run around and may break spider webs and starve
them inadvertently”
Observe repeated, correlated physical phenomena/patterns
“On Caribbean Islands with lizards, spiders are rare”
GOAL: create GOAL:
a falsifiable
is this
(testable)
relationship
causal
causal
hypothesis
?
Other observations
Hypothesis: Lizard predation causes a reduction in spider
abundance on Caribbean Islands
Observe repeated, correlated physical phenomena/patterns
“On Caribbean Islands with lizards, spiders are rare”
GOAL: create GOAL:
a falsifiable
is this
(testable)
relationship
causal
causal
hypothesis
?
Other observations
Hypothesis: Lizard predation causes a reduction in spider
abundance on Caribbean Islands
Alternative Hypothesis: Lizard predation does not cause a
reduction in spider abundance… (maybe competition does
or maybe it is just a correlated effect of something else…)
Observe repeated, correlated physical phenomena/patterns
“On Caribbean Islands with lizards, spiders are rare”
GOAL: create GOAL:
a falsifiable
is this
(testable)
relationship
causal
causal
hypothesis
?
Other observations
Hypothesis: Lizard predation causes a reduction in spider
abundance on Caribbean Islands
Alternative Hypothesis: Lizard predation does not cause a
reduction in spider abundance… (maybe competition does
or maybe it is just a correlated effect of something else…)
Here is a another critical element of a scientific hypothesis – it must be
falsifiable – you must be able to envision data collected from the
physical universe that would prove your hypothesis is wrong.
Hypothesis: Lizard predation causes a reduction in spider
abundance on Caribbean Islands
Alternative Hypothesis: Lizard predation does not cause a
reduction in spider abundance… (maybe competition does
or maybe it is just a correlated effect of something else…)
Here is a another critical element of a scientific hypothesis – it must be
falsifiable – you must be able to envision data collected from the
physical universe that would prove your hypothesis is wrong.
Conduct an experiment in which data supporting either
hypothesis is equally possible. This is a specific case
derived from a general hypothesis … deductive logic.
Conduct an experiment in which data supporting either
hypothesis is equally possible. This is a specific case
derived from a general hypothesis … deductive logic.
IF: - lizard predation is responsible for low spider abundance
And
IF: - I add lizards to specific islands and remove lizards from
others, with appropriate controls for the manipulations,
THEN: - Spider abundance should decline where I add lizards
and increase where I remove lizards, and spiders should be a
major component of lizard diets (gut content analysis).
IF: - lizard predation is responsible for low spider abundance
And
IF: - I add lizards to specific islands and remove lizards from
others, with appropriate controls for the manipulations,
THEN: - Spider abundance should decline where I add lizards
and increase where I remove lizards, and spiders should be a
major component of lizard diets (gut content analysis).
Then you do it and see!!! And you generalize from your
specific experiment to nature (inductive logic). You use logic
and evidence from the physical world to reach a conclusion
about how nature is and how it works.
(Usually by statistical inference…which we will demonstrate
in lab…)
Then you do it and see!!! And you generalize from your
specific experiment to nature (inductive logic). You use logic
and evidence from the physical world to reach a conclusion
about how nature is and how it works.
Many lines of independent evidence…
Then you do it and see!!! And you generalize from your
specific experiment to nature (inductive logic). You use logic
and evidence from the physical world to reach a conclusion
about how nature is and how it works.
Many lines of independent evidence…
can support a single general explanation
Then you do it and see!!! And you generalize from your
specific experiment to nature (inductive logic). You use logic
and evidence from the physical world to reach a conclusion
about how nature is and how it works.
Many lines of independent evidence…
can support a single general explanation…
These Explanations are THEORIES. They are supported by
experimental results and they can be tested by subsequent experiments
-Methodological Approaches:
1. REDUCTIONISM
2. COMPARATIVE METHOD
3. EXPERIMENTATION (EMPIRICISM)
4. METHODOLOGICAL MATERIALISM
-Methodological Approaches:
1. REDUCTIONISM
2. COMPARATIVE METHOD
3. EXPERIMENTATION (EMPIRICISM)
4. METHODOLOGICAL MATERIALISM
Philosophical materialism – the material is all there is.
Methodological materialism – the material is all we can
test.
III. Context: Ways of Knowing
A. Why You Know - Searching for Truth
1. Faith: Webster’s – “unquestioning belief not
requiring proof or evidence”
III. Context: Ways of Knowing
A. Why You Know - Searching for Truth
1. Faith: Webster’s – “unquestioning belief not
requiring proof or evidence”
2. Logic: “the science of correct reasoning;
science which describes relationships among
propositions in terms of implication,
contradiction, contrariety, conversion, etc.”
III. Context: Ways of Knowing
A. Why You Know - Searching for Truth
1. Faith: Webster’s – “unquestioning belief not
requiring proof or evidence”
2. Logic: “the science of correct reasoning;
science which describes relationships among
propositions in terms of implication,
contradiction, contrariety, conversion, etc.”
Evidence is a "clean argument“, but it does not
have to describe a physical reality.
III. Context: Ways of Knowing
A. Why You Know - Searching for Truth
1. Faith: Webster’s – “unquestioning belief not
requiring proof or evidence”
2. Logic: “the science of correct reasoning;
science which describes relationships among
propositions in terms of implication,
contradiction, contrariety, conversion, etc.”
Evidence is a "clean argument“
3. Science: Logical argument and physical
evidence.
III. Context: Ways of Knowing
A. Why You Know - Searching for Truth
B. Different Problems, Different Tools
“If the only tool you have is a hammer, you tend to see
every problem as a nail.” – Abraham Maslow,
American Psychologist
III. Context: Ways of Knowing
A. Why You Know - Searching for Truth
B. Different Problems, Different Tools
“If the only tool you have is a hammer, you tend to see
every problem as a nail.” – Abraham Maslow,
American Psychologist
Science can’t answer questions about
supernatural things (“God exists”) or morality
(“Abortion is right”) – it is a bad tool for those
questions.
But for questions about the physical universe,
science has demonstrated that it is the best
tool. And all technological applications support
that claim.
I. What is Biology?
Begs two questions – “what is science?” and
“What distinguishes living systems?”
II. What is Science?
III. Ways of Knowing
IV. What Distinguishes Living Systems?
IV. What Distinguishes Living Systems?
A. Characteristics
1. O__
2. R__
3. R__
4. G__
5. E__
6. E__
IV. What Distinguishes Living Systems?
A. Characteristics
1. Order – highly complex and non-random systems
requiring energy input for their maintenance. They are
open systems that can achieve greater order by an
input of more energy or greater efficiency.
IV. What Distinguishes Living Systems?
A. Characteristics
1. Order
2. Reproduction:
asexual/clonal/fragmentation
sexual: production of new genome
Inexact reproduction (through mutation
and sex) creates hierarchical patterns of
relatedness among organisms over time:
genealogies and phylogenies
Me
brother
1st cousin
you!
Genealogy of Human Populations
Genealogy of Primates
IV. What Distinguishes Living Systems?
A. Characteristics
1. Order
2. Reproduction
3. Response to the Environment (internal and external):
- physiologically (cells/tissues)
- behaviorally (organisms)
- genetically (populations adapt/evolve)
IV. What Distinguishes Living Systems?
A. Characteristics
1. Order
2. Reproduction
3. Response to the Environment
4. Growth:
- single cells get larger (but less efficient)
- increase size by increasing cell number
IV. What Distinguishes Living Systems?
A. Characteristics
1. Order
2. Reproduction
3. Response to the Environment
4. Growth
5. Energy Transformations – Metabolism:
- take in energy (radiant and/or chemical)
- use some, waste some (can’t violate
second law) to link atoms together into
biomolecules.
5. Energy Transformations - Metabolism
First Law: Energy is neither created nor
destroyed, but can be transformed
Second Law: No energy transformation is
100% efficient; some is lost as ‘entropy’ (often
heat).
Metabolic process are usually coupled
reactions, pairing a constructive (anabolic)
reaction that builds molecules with destructive
(catabolic) reactions that provide the building
blocks and energy.
IV. What Distinguishes Living Systems?
A. Characteristics
1. Order
2. Reproduction
3. Response to the Environment
4. Growth
5. Energy Transformations – Metabolism
6. Evolve:
Populations change over time. One way they
change is to adapt to their environment. Organisms
with useful traits reproduce more successfully than
others (Natural Selection); the frequency of these
traits change over time and populations diverge.
IV. What Distinguishes Living Systems?
A. Characteristics
B. Patterns of Organization
1. Spatial Scales:
Biosphere: Earth is ~4 x 107 m in circumference
Ecosystem: drop of pondwater (1 x 10-3 m) to Amazon Rain Forest (5 x 106 m).
Community: equally variable
Population: equally variable
Individual:
Smallest Mammal - Pygmy Shrew: 2 inches (5 x 10-2 m)
Largest Animal Ever - Blue Whale: 100 feet (3 x 101 m)
Human - 6 ft... 2 x 100 m
Largest Organism: Fungus covering 37 acres (7 x 102 m)
6. Organs: variable
7. Cells:
Liver Cell: 2 x 10-5 m (2/100ths of a mm)
E. coli Bacterium: 2 x 10-6 (1/10th of a liver cell)
Virus: 2.5 x 10-8 (1/100th of a bacterium)
8. Organelles: Ribosome: 1.8 x 10-8 m
Mitochondrion: 2.5 x 10-6 m (about bacteria sized)
9. Molecules:
Hemoglobin (average protein): 6.8 x 10-9 m (1/1000th of a bact.)
Phospholipid: 3.5 x 10-9 m
Amino Acid: 5.0 x 10-10 m
10. Atoms:
Carbon: 1 x 10-10 m (1/10,000,000,000 m - a ten billionth of a meter)
(a ten millionth of a millimeter)
(a ten thousandth the length of a liver cell)
1.
2.
3.
4.
5.
11. Nucleus:
2 x 10-15 m.
So, the nucleus is only 1/50,000th the width of the atom.
Atoms are mostly space.
In fact, a cubic centimeter of nuclear matter (no space) would weigh 230
million tons (Physics by J. Orear, 1979)
Analogy: If a basketball 1 ft. in diameter represents the nucleus of an atom,
the edge of the electron cloud would be about 5 miles away in either
direction; the atom would be 10 miles wide (~ 50,000 ft.)… that’s a lot
of empty space.
Analogy: You and the Earth are separated by 7 orders of linear magnitude. A
millimeter (about the size of a bold-faced period) and a carbon atom are
separated by 7 orders of linear magnitude. So, to a carbon atom, the
period is it's Earth.... mind blowing... Cells make up living systems that
can be 12 orders of magnitude larger (cell to biosphere).
B. Temporal Scales:
1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
11.
12.
13.
14.
Age of Earth: 4.5 x 109 yrs (4.5 billion)
History of Life on Earth: 3.5 x 109 years
Oldest Eukaryotic Cells: 1.8 x 109 years
Oldest Multicellular Animals: 6.1 x 108 years
Oldest Vertebrates: 5.0 x 108 (500 million)
Oldest Land Vertebrates: 3.6 x 108
Age of Dinosaurs - Mesozoic: 240-65 million
Oldest Primates: 2.5 x 107 (25 million)
Oldest Hominids: 4.0 x 106 (4 million – 1/1000th of earth history)
Oldest Homo sapiens: 2.0 x 105 (200,000)
Oldest Art: 3.0 x 104 (30,000; 1/100,000th of Life's History)
Oldest Agriculture: 1.0 x 104 (10,000)
Oldest Organism: Bristlecone pines: 5 x 103
Human cell:
brain/muscle 70 yrs
Red Blood Cell - weeks
Skin cell - days
B. Temporal Scales:
15.
Supply of ATP in cell - 2 seconds
16.
Rates of chemical reactions - milliseconds
(3.1 x 10-10 milliseconds/year).
The history of life, spanning billions of years,
is dependent on reactions that occur at a
temporal scale separated by 19 orders of
temporal magnitude.
Just a diagram to put
things on a scale we
are more familiar
with… you are not
responsible for the
actual physical scales
(in meters or seconds)
of these phenomena…
just their order for
now…