Transcript ppt1

Outline of Lectures 1 and 2:
I.
II.
III.
IV.
What is Biology?
What is Science?
Context: Ways of Knowing
What Distinguishes Living Systems?
I. What is Biology?
I. What is Biology?
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?
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?
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?
B. Limitations:
- What is studied: the physical world /universe
A medieval, Ptolemeic
view of the universe
II. What is Science?
B. Limitations:
- What is studied: the physical world /universe
- How it is studied (Method): empiricism
“of the senses”, but not “common sense”…
-Methodological Approaches:
1. REDUCTIONISM
Gaining an understanding of a system by
describing its subsystems (components)
-Methodological Approaches:
1. REDUCTIONISM
Gaining an understanding of a system by
describing its subsystems (components)
≠
“emergent properties”
Powerful Approach: living systems are very complex, so
describing the STRUCTURE can give insights into FUNCTION.
-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?
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:
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.
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!?
-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: is this relationship causal?
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)
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
You have just used Inductive logic , using specific
observations to formulate a general principle
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…)
Conduct an experiment in which data supporting either
hypothesis is possible.
To do this, you use deductive logic (general to specific case).
IF my general principle (hypothesis) is true, THEN I can predict
a specific outcome in my particular experiment.
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.
II. What is Science?
A. Definitions
B. Limitations
C. Theories
- tested, explanatory models of how the
physical universe works
II. What is Science?
A. Definitions
B. Limitations
C. Theories
- tested, explanatory models of how the
physical universe works
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.”
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
Is abortion right?
How old is the Earth?
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. Ordered Organization – highly complex and nonrandom 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. Ordered Organization – highly complex and nonrandom 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.
- highly organized at different spatial and temporal
scales
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)
11. Nucleus:
2 x 10-15 m. 5 orders of magnitude smaller than the width of the atom!!!
1.
2.
3.
4.
5.
So, the nucleus is only 1/50,000th the width of the atom.
Atoms are mostly space… matter is 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. Age of Earth: 4.5 x 109 yrs (4.5 billion)
2. History of Life on Earth: 3.5 x 109 years
3. Oldest Eukaryotic Cells: 1.8 x 109 years
4. Oldest Multicellular Animals: 6.1 x 108 years
5. Oldest Vertebrates: 5.0 x 108 (500 million)
6. Oldest Land Vertebrates: 3.6 x 108
7. Age of Dinosaurs - Mesozoic: 240-65 million
8. Oldest Primates: 2.5 x 107 (25 million)
9. Oldest Hominids: 4.0 x 106 (4 million – 1/1000th of earth history)
10. Oldest Homo sapiens: 2.0 x 105 (200,000)
11. Oldest Art: 3.0 x 104 (30,000; 1/100,000th of Life's History)
12. Oldest Agriculture: 1.0 x 104 (10,000)
13. Oldest Organism: Bristlecone pines: 5 x 103
14. Human cell:
brain/muscle 70 yrs
Red Blood Cell - weeks
Skin cell – days
15. Supply of ATP in cell - 2 seconds
16. Rates of chemical reactions - milliseconds (3.1 x 10-10 ms/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.
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
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.