Chapter I

Biology unifies much of natural science

- A point of convergence for the information and tools from all of the natural sciences.
- Biological systems are the most complex chemical systems
- Constrained by chemistry and physics
- Illustrate the workings of natural laws
- Complexity of living systems is made possible by a constant source of energy-sun
- Science is interdisciplinary
- Biology is the heart of this multidisciplinary approach
- Biological problems require different approaches
Life defies simple definition (7)
- Cellular organization : cells carry out basic activities of living; bounded by membrane
- Ordered Complexity: complex and highly ordered; nonliving things do not exhibit ordered
complexity
- Sensitivity: responds to stimuli
- Growth, development and reproduction: growing; reproducing, possess hereditary molecules.
- Energy Utilization: take in energy and use it to perform many kinds of work.
- Homeostasis: relatively constant internal conditions which is different from the environment.
- Evolutionary Adaptation: interaction which influence survival; evolve adaptations to their
environment.
Hierarchical Organization
- Cellular Level: atoms(fundamental elements of matter) >>>
molecules>>>organelles>>>cells(membrane- bounded units; basic unit of life)
- Organismal Level: tissues (group of similar cells that act as a functional unit)>>>
organs>>>organ system
- Populational Level: population (group of organisms of the same species living in the same
place)>>> species (similar in appearance and able to interbreed) >>> biological community(all of
the populations of different species living together in one place
- Ecosystem: a biological community and the physical habitat within which it lives together.
- Biosphere: planet
Emergent Properties: result from the way in which components interact.
Nature of Science
- There is no one scientific method
- Scientists also attempt to be as objective as possible
- One person’s results are verified by others and if the results cannot be repeated, they are
rejected.
Much of science is descriptive
- In order to understand anything, the first step is to describe completely
- Concerned with increasingly accurate description of nature
- Efforts are currently underway to classify all life on earth
- 21st century: completion of the sequence of the human genome
Deductive Reasoning
- Applies general principles to predict specific results
- Eratosthenes >> Euclidean Geometry >> circumference of the earth
- Reasoning of mathematics and philosophy
- If all mammals have hair and you find an animal that does not have hair, then that animal is not
a mammal.
-
Inductive Reasoning
- From specific to general
- Particular experiments to infer general principles.
Hypothesis driven science
- Science establish which general principles are true through the process of systematically testing
alternative proposals
- How science is done: observations>>>hypothesis(potential explanation) >>> experiments >>>
predictions >>> further experiments (iterative)
- Hypothesis: a suggested explanation that accounts for observations; a proposition that might be
true.
Testing a hypothesis
- Experiment
- A successful experiment is one in which one or more of the alternative hypothesis is
demonstrated as inconsistent
Establishing Controls
- Processes are influenced by many factors called variables.
- test experiment: one variable is altered in a known way to test a particular hypothesis
- Control experimnt: one variable is left unaltered
Using predictions
- A hypothesis is most useful when it makes predictions because predictions provide a way to test
the validity of a hypothesis.
- * Spontaneous generation: there was an inherent property in organic molecules that could lead
to the spontaneous generation of life.
- * Germ Hypothesis: pre-existing organisms in the air could contaminate the nutrient broth
- *Louis Pasteur: constructed flasks with curved necks that would trap any contaminating germs
- * disproved the hypothesis of spontaneous generation.
Reductionism
- Breaks larger systems in their component parts
- A philosophical approach used by scientists to understand a complex system by reducing it to its
working parts.
- General approach of biochemistry
- *enzymes do not always behave exactly the same in isolation as they do in their normal cellular
context.
- *emergent properties cannot be predicted based on the workings of the parts.
Models
- Explain living systems
- Provide a way to organize how we think about a problem
- Gets us closer to the larger picture and away from the extreme reductionist approach
The nature of scientific theories
- Theory is a proposed explanation for some natural phenomenon often based on some general
principle.
- *Newton: Theory of Gravity
- Theory is the body of interconnected concepts supported by scientific reasoning and
experimental evidence.
- Theory brings together concepts that were previously thought to be unrelated.
- *Quantum Theory: physics brings together a set of ideas about the nature of the universe.
- Theories are the solid ground of science, expressing ideas of which we are most certain.
- General public: theory is a lack of knowledge or a guess
 - The key is how well a hypothesis fits the observations.
Research can be basic or applied
- Scientific method: consisting of an orderly sequence of logical, “either-or” steps.
- As if trial and error testing would lead one to the ultimate scientific answer, but science is not
done this way.
- *Karl Popper: scientists design their experiments with a pretty fair idea of how the results are
going to come out >>> “Imaginative Preconception”
- Basic Research: intended to extend the boundaries of what we know; provides scientific
foundation for applied research
- Applied Research: associated with industries: manufacture of food additives, creation of new
drugs, testing of environment quality.
- Peer review: experiments and conclusions are reviewed by other scientists; helps to ensure that
faculty of research or false claims are not given the authority of scientific fact. Provides other
scientists with a starting point for testing the reproducibility of experimental results.
Darwin and Evolution
- Theory of Evolution: explains and describes how organisms on earth have changed over time
and acquired a diversity of new forms.
- Charles Robert Darwin: English naturalist, 30 years of study, wrote “On the Origin of Species by
means of Natural Selection”
The idea of evolution existed prior to Darwin
- Belief that different kinds of organisms and their individual structures resulted from the actions
of a Creator. Species were thought to be unchangeable over the course of time.
- Earlier naturalists and philosophes: living things must have changed during the history of life on
earth.
- Charles Darwin: natural selection
Darwin observed differences in related organisms
- 1831 (22 years old): was part of the 5 year Mapping Expedition around the coasts of South
America. Aboard H.M.S. Beagle
- Darwin studied a wide variety of plants and animals.
- Observed that characteristics of similar species varied somewhat from place to place
- Geographical patterns: suggested that lineages change gradually as species migrate
- At Galapagos Island: encountered a variety of finches which differed slightly in appearance –
“beaks”
- He assumed that the birds had descended from a common ancestor
- Found plants and animals on the relatively young volcanic islands which resemble those on the
nearby coast of South America
- Darwin proposed natural selection as a mechanism for evolution
Darwin and Malthus
- Thomas Malthus: An Essay on the Principle of Population
- Populations tend to increase geometrically while humans are able to increase their food supply
arithmetically
- Populations of species remain fairly constant year after year because of DEATH
- Darwin: Although every organism has the potential to produce more offspring than can survive,
only a limited number actually do survive and produce further offspring.
- Individuals possessing physical, behavioural, or other attributes that give them an advantage
in their environment are more likely to survive and reproduce to pass on their “favourable
characteristics” The nature of the population as a whole will gradually change: selection
Natural Selection
- pigeon breeding- breeders- “artificial selection”
- Natural selection- nature fosters variation
Darwin drafts his argument
- 1842: preliminary manuscript >>> Darwin put it in the drawer for 16 years
- Stimulus: An essay about the hypothesis of evolution by means of natural selection by Alfred
Russel Wallace in 1858
- Expanded the manuscript and submitted it for publication
The predictions of natural selection have been tested
- The fossil record: darwin predicted that the fossil record would yield intermediate links between
the great groups of organisms; palaeontologists found what appear to be transitional forms and
found them at the predicted positions in time.
- The age of the earth: Darwin predicted that the world must be very old; proven by radioactive
decay
- The mechanism of heredity: Gregor Mendel – pea plants
- Comparative Anatomy: comparative studies of animals have provided strong evidence for
Darwin’s theory
Homologous- same evolutionary origin, different structure and function
Analogous- similar function, different evolutionary origin
- Molecular evidence: comparing the genomes: specify the degree of relationship among groups.
A series of evolutionary changes over time should involve a continual accumulation of genetic
changes. Can clearly be seen in the protein hemoglobin.
Phylogenetic tree- obtained pattern of descent “family tee” (agreed well with fossil records)
Unifying themes in Biology
- Cell theory describes the organization of living things:
 Cells were first discovered by Robert Hooke in 1665 with 30x microscope
 Anton van Leeuwenhoek used a 300x microscope; discovered single celled life in
pond water
 Matthias Schleiden and Theodor Schwann – concluded that all living organisms are
composed of cells. “CELL THEORY”
- The molecular basis of inheritance explains the continuity of life
 Deoxyribonucleic Acid – where the information that specifies what a cell is like is
encoded. Formed from two long chains of building blocks called nucleotides
 Four different nucleotides are found in dna
 Gene- specific sequences of nucleotides
 Genome- entire set of DNA instructions that specifies a cell
 Human genome- 3 billion nucleotides long
- The relationship between structure and function underlies living systems
 We study the structure of molecules and macromolecular complexes to learn about
their function.
 Similar structures are used to infer possible similar functions
 Functions give clues to what kind of structures are involved in a process
- The diversity of life arises by evolutionary change
 All life has evolved from the same origin event. The diversity of life arises by
evolutionary change leading to the present biodiversity we see.
 Domains: Bacteria, Archaea (prokaryotes) and Eukarya (eukaryotes)
- Evolutionary conservation explains the unity of living things
 all organisms alive today have descended from some simple cellular creature that
arose 3.5 BYA
 storage of hereditary information in DNA is common to all living things
 retention of conserved characteristics reflect that they have a fundamental role in
the biology of that organism
 Homeodomain proteins- powerful developmental tools that evolved early and for
which no better alternative has risen.
- Cells are information processing systems
 Are highly complex nanomachines that process information
 Information stored in DNA is used to direct the synthesis of cellular components
 Control of gene expression allows differentiation of cell types
 Cells process information that they receive about the environment
 Homeostasis is possible because of elaborate signaling networks that coordinate the
activities of different cells in different tissues.
- Living systems exist in a non equilibrium state
 They are open systems that function far from thermodynamic equilibrium
 Energy is necessary to maintain a stable nonequilibrium state
 Non equilibrium systems exhibit self-organizing properties
 Emergent properties- properties of collection of molecules, cells, individuals that
are distinct from categorical properties described by nonlinear dynamics.