Transcript Ch 1

Chapter 01
Lecture Outline
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**Important study hint**
• Review the study hints at the end of the
syllabus.
• Multitasking does NOT work! Eliminate
distractions while studying.
–
–
–
–
–
Don’t watch TV
Don’t text or watch for texts.
Turn off your phone.
Don’t log in to social media.
Don’t email or use social media in class.
http://www.slate.com/articles/health_and_science/science/2013
/05/multitasking_while_studying_divided_attention_and_technol
ogical_gadgets.html
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The Science of Biology
Chapter 1
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The Science of Life
• Biology unifies much of natural science
• Life defies simple definition
– Living systems are the most complex chemical
systems on Earth
– Life is constrained by the properties of chemistry
and physics
• Science is becoming more interdisciplinary
– Combining multiple fields
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The Science of Life
7 characteristics of all living organisms
1.
2.
3.
4.
5.
6.
Cellular organization
Ordered complexity
Sensitivity
Growth, development, and reproduction
Energy utilization
Homeostasis
7. Evolutionary adaptation – at population level
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The Science of Life
• Living systems show hierarchical organization
– Cellular level
– Organismal level
– Populational level
– Ecosystem level
– Biosphere
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http://iws.collin.edu/biopage/faculty/mcculloch/1406/outlines/chapter%201/chap01.html
The Science of Life
• Living systems show
hierarchical organization
– Cellular level
• Atoms, molecules,
organelles, cells
• Cell is the basic unit of life
CELLULAR LEVEL
Atoms
Molecule
Macromolecule
Organelle
Cell
O
C
H
N
O
H
N
C
O
0.2 µm
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Cellular Level
CELLULAR LEVEL
Atoms
Molecule
Macromolecule
Organelle
Cell
O
C
H
N
O
H
N
C
O
0.2 µm
(organelle): © Dr. Donald Fawcett & Porter/Visuals Unlimited; (cell): © Steve Gschmeissner/Getty Images
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The Science of Life
• Living systems show
hierarchical organization
ORGANISMAL LEVEL
Tissue
Organ
Organ system
Organism
– Organismal level
• Tissues, organs, organ
systems
• individual organism
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Organismal Level
ORGANISMAL LEVEL
Organ
Tissue
Organ system
Organism
10
100 µm
(tissue): © Ed Reschke; (organism): © Russell Illig/Getty Images RF
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The Science of Life
• Living systems show
hierarchical organization
– Populational level
• Population (interbreeding)
• Community (all populations
within a habitat)
POPULATIONAL LEVEL
Population
Species Community Ecosystem
Biosphere
– Ecosystem level
– Biosphere
• Earth is an ecosystem
we call the biosphere
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Populational Level
POPULATIONAL LEVEL
Population
Species
Community
Ecosystem
Biosphere
(population): © George Ostertag/agefotostock; (species): © PhotoDisc/Volume 44 RF; (community): © Ryan McGinnis/Alamy;
(ecosystem): © Robert and Jean Pollock; (biosphere): NASA
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The Science of Life
• Each level has emergent properties
– Result from interaction of components
– Cannot be deduced by looking at parts
themselves – “whole is greater than the sum of
the parts”
– “Life” is an emergent property
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The Nature of Science
• Science aims to understand the natural
world through observation and reasoning
• Science begins with observations,
therefore, much of science is purely
descriptive
– Classification of all life on Earth
– Human genome sequencing
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The Nature of Science
• Science uses both deductive
and inductive reasoning…

Deductive reasoning uses
general principles to make specific
predictions
(big idea  specific situation)

Inductive reasoning uses
specific observations to develop
general conclusions
(specific observations  big idea)
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http://toknow-11.wikispaces.com/Inductive+Reasoning
The Nature of Science
• Scientists use a systematic approach to
gain understanding of the natural world =
Scientific Method
– Observation
– Hypothesis formation
– Prediction
– Experimentation
– Conclusion
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http://www.bcps.org/offices/lis/researchcourse/develop_writing_method_quantitative.html
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Observation
Note the use of
alternative hypotheses
Question
Potential
hypotheses
Hypothesis 1
Hypothesis 2
Hypothesis 3
Hypothesis 4
Hypothesis 5
Remaining
possible
hypotheses
Hypothesis 2
Hypothesis 3
Hypothesis 5
Last remaining
possible
hypothesis
Hypothesis 5
Experiment
Reject
hypotheses
1 and 4
Experiment
Reject
hypotheses
2 and 3
Modify hypothesis
Predictions
Experiment 1
Experiment 2
Experiment 3
Predictions
confirmed
Experiment 4
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The Nature of Science
• A hypothesis is a possible explanation for an
observation – NOT just an “educated guess”
• A hypothesis (the “if”)
– Must be able to be tested to determine its validity
– Allows for predictions to be made if hypothesis is
true
– Is often tested in many different ways
• Iterative
– Hypotheses can be changed and refined in light of
new data
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The Nature of Science
• Predictions (the “then”)
– Valid hypotheses must provide
testable predictions
– Predictions provide a way to test
the validity of hypotheses, …
– Hypothesis must be rejected if
the experiment produces results
inconsistent with the predictions
– The more experimentally
supported predictions a
hypothesis makes, the more
valid the hypothesis
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http://www.bcps.org/offices/lis/researchcourse/develop_writing_method_quantitative.html
The Nature of Science
• Experiment
– Tests the hypothesis thru
predictions
– Must be carefully designed to
test only one variable at a time
– Consists of a test treatment(s)
and a control(s)
– Must have replication
– Results must be reproducible
Control (0 mg drug)
1 mg drug
2 mg drug
4 mg drug
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SCIENTIFIC THINKING
Question:
What is the source of contamination that occurs in a flask of nutrient
broth left exposed to the air?
Germ Hypothesis: Preexisting microorganisms present in the air contaminate
nutrient broth.
Prediction: Sterilized broth will remain sterile if microorganisms are prevented
from entering flask.
Spontaneous Generation Hypothesis: Living organisms will spontaneously
generate from nonliving organic molecules in broth.
Prediction: Organisms will spontaneously generate from organic molecules
in broth after sterilization.
Test: Use swan-necked flasks to prevent entry of microorganisms. To
ensure that broth can still support life, break swan-neck after sterilization.
Note that the alternative
hypotheses have different
(mutually exclusive)
predictions
Broken
neck
of flask
Flask is sterilized
by boiling the broth.
Unbroken flask
remains sterile.
Broken flask becomes
contaminated after
exposure to germ-laden air.
Result: No growth occurs in sterile swan-necked flasks. When the neck is
broken off, and the broth is exposed to air, growth occurs.
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Conclusion: Growth in broth is of preexisting microorganisms.
The Nature of Science
• Complimentary philosophical
approaches to science
– Reductionism
• To break a complex process
down to its simpler parts
– Systems biology
• Focus on emergent properties
that can’t be understood by
looking at simpler parts
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http://likethedew.com/2013/03/23/sciences-sacred-cows-reductionism/
http://en.wikipedia.org/wiki/Graphical_model
The Nature of Science
• Models in science
– Way to organize thought
– Parts provided by
reductionist approach
– Model shows how they fit
together
– Suggest experiments to
test the model
– Mathematical, graphical,
computer
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http://www.treehugger.com/clean-technology/xmas-is-early-for-climate-scientists-new-cesm-modeling-software-is-out.html
The Nature of Science
• Scientific theory – more than “just a theory”
– Body of interconnected concepts
– Supported by much experimental evidence
and scientific reasoning
– Expresses ideas of which we are most certain
• Compare to general meaning of theory
– Implies a lack of knowledge or a guess
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Darwin and Evolution
• Example of how a scientist develops
a hypothesis and a theory gains
acceptance
• Charles Darwin served as naturalist
on mapping expedition around
coastal South America
• 30 years of observation and study
before publishing On the Origin of
Species by Means of Natural
Selection
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Voyage of the HMS Beagle
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British Isles
NORTH
PACIFIC
OCEAN
NORTH
AMERICA
Galápagos
Islands
Western
Isles
NORTH
ATLANTIC
OCEAN
Valparaiso
Society
Islands
ASIA
NORTH
PACIFIC
OCEAN
Canary
Islands
Cape Verde
Islands
SOUTH
AMERICA
Bahia
Marquesas
EUROPE
Philippine
Islands
AFRICA
INDIAN
OCEAN
Ascension
Madagascar
St. Helena
Rio de Janeiro
Keeling
Islands
Mauritius
Bourbon Island
Equator
AUSTRALIA
Friendly
Islands
Sydney
Montevideo
Buenos Aires
Port Desire
Straits of Magellan
Falkland
Islands
Cape Horn Tierra del Fuego
Cape of
Good Hope
SOUTH
ATLANTIC
OCEAN
King George’s
Sound
Hobart
New
Zealand
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http://www.theguardian.com/science/blog/2012/jan/04/new-hms-beagle-2013
Darwin and Evolution
• Darwin was not the first to propose
evolution
– It was known that living things
have changed over time
• Darwin’s contribution was a mechanism
for evolution
– Natural selection
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https://en.wikipedia.org/wiki/Human_evolution
Darwin and Evolution
• On the Beagle, Darwin saw that
characteristics of similar species varied
from place to place
• Galápagos Finches
– 14 related species differ only slightly
– “Descent with modification” or evolution
Woodpecker Finch (Cactospiza pallida)
Large Ground Finch (Geospiza magnirostris)
Cactus Finch (Geospiza scandens)
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Darwin and Evolution
• Darwin studied Thomas Malthus’s An
Essay on the Principle of Population
– Populations of plants and animals increase
geometrically (multiplicative, example x3)
– Humans can only increase their food supply
arithmetically (additive, example +2)
– Populations of species remain constant
because death limits population numbers
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Darwin and Evolution
Darwin saw that:
• Every organism
has the potential
to produce more
offspring
• But, only a limited
number survive
and reproduce
themselves
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geometric progression
arithmetic progression
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Human Growth is
Geometric
Human food
production is
Arithmetic
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6
2
6
8
4
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Darwin and Evolution
Darwin made an important association:
• Individuals with attributes that give
them an advantage in their
environment are more likely to
survive and reproduce
• Pass these characteristics on
to their offspring
• The population will gradually
change over time
• Darwin called this selection
http://www.historyrv.com/blog/en/2012/01/broken-natural-selection/
Darwin and Evolution
• Evidence supporting Darwin’s theory has
only grown
– Fossil record
– Earth’s age
– Mechanism for heredity
– Comparative anatomy
– Molecular evidence
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http://itlaligarcia.blogspot.com/2011/02/why-is-fossil-record-hard-to-interpret.html
Darwin and Evolution
• Evidence supporting Darwin’s
theory has only grown
– Fossil record
• Transitional forms have been
found at predicted positions in
time
– Earth’s age
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• Physicists of Darwin’s time
were wrong
• Earth is very old – 4.5 billion
years old
Image by B. Tyler
Darwin and Evolution
• Evidence supporting Darwin’s theory has
only grown
– Mechanism for heredity
• Mendel’s laws of inheritance were unknown to
Darwin
• At time of Darwin there was no concept of
“genes” or how heredity worked
• Darwin could not completely explain how
evolution worked
• Now have detailed understanding of heredity
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Darwin and Evolution
• Evidence supporting Darwin’s theory has only
grown
– Comparative anatomy
• Vertebrate forelimbs all share the same basic array
of bones
• Homologous – same evolutionary origin but now
differ in structure and function (forelimbs of verts)
• Analogous – structures of different origin used for
the same purpose (butterfly and bird wings)
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Human
Cat
Bat
Porpoise
Horse
Darwin and Evolution
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Human
Cat
Bat
Porpoise
Horse
Homologous – same evolutionary origin but
now differ in structure and function
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Darwin and Evolution
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• Evidence supporting
Darwin’s theory has
only grown
– Molecular Evidence
• Compare genomes or
proteins of different
organisms
• Phylogenetic trees –
based on tracing
origin of particular
nucleotide changes to
reconstruct an
evolutionary history
Human
0
Rhesus
10
Dog
20
30
Frog
Bird
40
50
60
70
Number of Amino Acid Differences in a Hemoglobin Polypeptide
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Unifying Themes in Biology
• Cell theory
– All organisms
composed of cells
– Cells are life’s basic
units
– All cells come from
preexisting cells
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a.
b.
60 µm
500 µm
a: © Dennis Kunkel/Phototake; b: © Karl E. Deckart/Phototake
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Unifying Themes in Biology
• Molecular basis of inheritance
– Deoxyribonucleic acid (DNA)
– Sequence of 4 nucleotides encode
cell’s information
– Gene – discrete unit of information
– Genome – entire set of DNA
instructions
– Continuity of life depends on faithful
copying of DNA into daughter cells
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http://employees.csbsju.edu/hjakubowski/classes/ch331/dna/chromosome.gif
Unifying Themes in Biology
• Structure and function
– Study structure to learn function
– Know a function – look for that
structure in other organisms
– Example
• Receptor on human cell for
insulin known
• Find similar molecule in a worm
• Might conclude this molecule
functions the same in the worm
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http://www.nature.com/nrd/journal/v1/n10/images/nrd917-i1.gif
Unifying Themes in Biology
• Diversity of life arises by evolution
– Underlying unity of biochemistry and genetics
argues for life from the same origin event
– Diversity due to evolutionary change over
time
– 3 domains of life
• Bacteria – single-celled prokaryote
• Archaea – single-celled prokaryote
• Eukarya – single-celled or multicellular eukaryote
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http://www.bacterialphylogeny.com/img/archaea/three_domain.jpg
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Domain
Kingdoms
Plantae
Fungi
Eukarya
Animalia
Protista
(plantae middle): © David M. Dennis/Animals Animals; (plantae right): © Corbis/Volume 46 RF; (fungi left): © Royalty Free/Corbis; (fungi middle):
© Mediscan/Corbis; (fungi right): © PhotoDisc BS/Volume 15 RF; (animalia left): © Royalty-Free/Corbis; (animalia middle): © Tom Brakefield/Corbis;
(animalia right): © PhotoDisc/Volume 44 RF; (protista left): © Corbis/Volume 64 RF; (protista middle): © Tom Adams/Visuals Unlimited;
(protista right): © Douglas P. Wilson/Frank Lane Picture Agency/Corbis
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Unifying Themes in Biology
• Evolutionary conservation
– All organisms today descended
from a simple creature 3.5 BYA
– Many characteristics preserved
– Ex: use of DNA
Tree of Life
– Conservation reflects that they
have a fundamental role in life
 Evidence for evolution
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http://learn.genetics.utah.edu/content/variation/tracktraits/
Unifying Themes in Biology
• Cells are information-processing
systems
– Information in DNA used to direct
synthesis of cellular components
• Control of gene expression leads to
different cells/ tissue types
– Cells process environmental information
• Glucose levels, presence of hormones
– Cells in multicellular organisms must
coordinate with each other
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https://upload.wikimedia.org/wikipedia/commons/thumb/7/7f/Tet-ON_inducible_transgene_expression_cells.svg/500px-TetON_inducible_transgene_expression_cells.svg.png
http://www.eoearth.org/files/115001_115100/115006/300px-Ecosystem_matter_energy.gif
Unifying Themes in Biology
• Nonequilibrium state
– Living systems are open
systems
– Constant supply of energy
needed
– Self-organizing properties
at different levels
– Emergent properties from
collections of molecules,
cells, and individuals
Cells to ecosystems
are open
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http://origin-ars.els-cdn.com/content/image/1-s2.0-S0005272899000651-gr1.gif