CH1 The Science of Biology

1.1 The Science of Life

a. Amount of available data has exploded in last 25 years
i. Scientists sequencing genomes at increasing pace
ii. finding out how one cell gives rise to a complex organization
1. iology unifies much of !atural Science
a. iology is a point of convergence of natural science
b. iological Systems are most complex of all on earth
c. "unctions of chemical systems are determined and constrained by principles
of chemistry and physics
i. Study of biology doesn#t bring about new laws
d. Energy determines levels of biological organization
i. Study of thermodynamics gives info about transitions of energy
ii. complexity of living systems made possible by the sun
e. Science is becoming interdisciplinary
i. !anotechnology
ii. Several disciplines required to solve one problem
2. $ife defies simple definition
a. iology is the study of living things
i. scientists living w% gorillas for research& fossils& listen to whales
ii. 'if it moves& it#s alive' is not always true
b. (ellular )rganization
i. All organisms have 1 or more cells
ii. (ells carry out basic activities of living
iii. cells are bound by a membrane
c. )rdered complexity
i. all living things are complex and highly ordered
ii. !on living things may be complex but not ordered
d. Sensitivity
i. organisms respond to stimuli
1. pupils dilate in the dar*
e. +rowth& ,evelopment& and reproduction
i. all organisms and molecules can grow and reproduce
ii. -ereditary molecules passed on to offsprings
f. .nergy /tilization
i. organisms ta*e in energy
1. obtained from food
ii. energy spent through wor*
g. -omeostasis
i. 0aintaining constant internal conditions regardless of changing
environment
h. .volutionary adaptation
i. )rganisms interact w% one another
ii. organisms evolve to adapt to the environment
1. $iving systems show hierarchical organization
a. 2he (ellular $evel
i. atoms3 fundamental elements of matter
ii. molecules3 clusters of atoms
iii. )rganelles3 molecules 4oined together
iv. (ells3 organelles bound together by a membrane
b. 2he organism level
i. 2issue3 groups of similar cells
ii. organs3 structures composed of several different tissues that act as a
structural or functional unit
iii. organ systems3 grouping of organs
c. 2he population level
i. population3 organisms of the same species living in the same place
ii. species3 members similar in appearance and capable of interbreeding
iii. biological community3 population of different species living together
in one place
d. .cosystem $evel
i. ecosystem3 biological community and the physical habitat within
which it lives
e. 2he biosphere3 entire planet
f. .mergent properties
i. result from the way in which components interact
ii. cannot be deduced from looming at parts themselves
1. individual cell examination doesn#t provide info about animal
g. ,ifficult to define life because living world exhibits many emergent properties
1.2 The Natre of Science
a. Scientific 0ethod3 false claims as to a single way of doing science
i. confusion amongst common population
b. Science concerned w% developing increasingly accurate understanding of
environment
c. Assumptions that natural forces acting same as they have been long ago
d. Scientists attempt to be ob4ective
e. Science is a collective endeavor
i. self correcting
ii. 5f results not repeated by several scientists then it is re4ected
1. 0uch of Science is descriptive
a. )bservations lead to hypotheses& hypotheses ma*e experimentally testable
predictions
b. 0uch of science is purely descriptive
c. iology is concerned with arriving at an increasingly accurate description
of nature
d. Study of biodiversity is descriptive
i. .fforts to classify all life on earth
e. !ost im"ortant accom"lishment of 21st centry# com"letion of
hman genome
i. descriptive science
2. Science uses both deductive an inductive reasoning
a. ,eductive reasoning3 general principles to predict specific results
i. /se of geometry by .ratosthenes to estimate circumference of
earth
ii. 5f mammals defined to have hair then an animal with no hair is not
a mammal
b. 5nductive 6easoning3 specific observations to construct general scientific
principles
i. 7oodles have hair& terriers have hair3388 All dogs have hair
ii. leads to generalizations that can later be tested
iii. !ewton and acon used info from particular experiments to
determine how the earth wor*s
iv. ,rosophilia melanogaster3 some genes cause dramatic changes in
developmental fate
1. in isolation it was determined that similar genes found in
humans and other mammals
2. generalization that homeobox genes act as switches to
control developmental fate
1. -ypothesis3driven science ma*es and tests predictions
a. if proposals inconsistent with observations then re4ected as untrue
b. Hy"othesis3 proposition that may be true
c. iterative# a hypothesis can be changed and refined with new data
i. +eorge eadle and .dward 2atum studied nature of genetic
information
1. 'one3gene% one3enzyme'
2. refined to 'one3gene% one polypeptide'
1. later specified that one gene can define more than one
polypeptide
d. Testing Hy"otheses
i. e$"eriment# test of a hypothesis
ii. hypotheses
1. no light b%c light burned out& light switch turned off& or
going blind
2. experiments done to eliminate possibilities
e. Establishing Controls
i. variables3 factors that influence processes
ii. to evaluate hypotheses about one variable all others must be
constant
iii. 2 parallel experiments
1. test experiment3 one variable altered
2. control experiment3 all variables *ept constant
iv. (hallenge of experimental science in designing control
experiments to isolate particular variable
f. %sing &redictions
i. scientific hypothesis must be valid and useful
ii. if ma*es a prediction then the hypothesis may be tested
iii. more experimentally supported predictions ma*e hypothesis more
valid
iv. Ntrient Broth
1. exposed to air becomes contaminated
2. -ypotheses9
a. inherent properties in organic molecules could lead
to spontaneous generation of life
b. preexisting microorganisms present in air could
contaminate nutrient broth
i. proved correct by louis pasteur
ii. curved nec* prevented contamination
:. 6eductionism brea*s large systems into their component parts
a. 'edctionism3 understanding a complex system by reducing it to its
wor*ing parts
i. approach of biochemistry
1. unrevealing complexity of cellular metabolism by
concentrating on individual pathways and specific enzymes
ii. has limits
1. enzymes behave differently in isolationism and normal
cellular context
a. some behaviors cant be predicted
iii. examination of 6!A is reductionism
1. doesn#t lead to predictions about nature of protein synthesis
2. (anadian goose and floc* example
5. iologists construct models to explain living systems
a. +enetics construct models of interacting networ*s of proteins that control
gene expression
i. 7opulation biologists construct models of evolutionary change
ii. (ell biologists build models of signal transduction pathways
iii. Structural biologists build models of proteins and macromolecular
complexes
b. provides way to organize thoughts about a problem
c. farther away from extreme reductionism approach
d. more *nowledge leads to sophisticated models
i. modeling of bacteria cell
e. 2he nature of scientific theories
;. 2he nature of scientific theories
a. theory# proposed explanation for some natural phenomenon
i. based on general principle
ii. secondary meaning3 body of interconnected concepts& supported by
scientific reasoning and experimental evidence& that explains facts
in some area of study
iii. e$am"le3 quantum theory brings together set of ideas about nature
of universe
b. theories are solid ground in science
c. general public theory means lac* of *nowledge
d. 0odern evolution theory unifies biology as a science
e. (ey is ho) )ell a hy"othesis fits an observation
<. 6esearch can be basic or applied
a. 5n past science was an orderly sequence of steps
b. basic research3 extends boundaries of what we *now
i. provides scientific foundation used by a""lied science
1. a""lied science done by someone employed in the industry
c. results published in scientific 4ournals
i. undergo "eer revie) *evaluation of results=
1. provides starting point for testing of reproducibility of
experimental results
1.+ ,n E$am"le of Scientific -n.iry/ 0ar)in and Evoltion
a. theory of evolution explains how organisms on earth have change over
time and acquired a diversity of new forms
b. Charles 'obert 0ar)in
i. .nglish naturalist
ii. 1> years of study
iii. 1n the 1rigins of S"ecies by !eans of Natral Selection
1. 2he idea of evolution existed prior to ,arwin
a. 5n ,arwin#s time people believed that organisms and structures resulted
from the (reator
i. unchangeable over time
b. .arlier naturalists believed that change must#ve occurred3 evoltion
c. Natral Selection coherent& logical explanation for process of evolution
i. proposed by ,arwin
2. ,arwin observed differences in related organisms
a. 5 year expedition on -0S eagle around coast of south america
b. srudied plants and animals
c. (haracteristics of similar species varied from place to place
i. 6esulted form migration from one area to another
ii. 1: species of finches on various islands in +alapagos
1. variations in bea*s
a. caused by variations in food
2. assumptions that common ancestor
iii. 0escent )ith modification# evolution
iv. (haracteristics not resembled by areas with similar climates but
by areas ad4acent to islands
1. ,arwin proposes natural selection as mechanism for evolution
a. ,arwin#s achievement3 evolution occurs because of natural selection
b. 0ar)in and !alths
i. An Essay on the Principles of Population
1. malthus suggests population of plants and animals
increases geometrically
2. food supply for humans increases arithmetically
1. if unchec*ed& populations would soon cover entire globe
:. death limits population
a. limited number survives to produce further
offspring
ii. -ndividals "ossessing "hysical2 behavioral2 or other attribtes
that give them an advantage in their environment are more
li3ely to srvive an dre"rodce
c. Natral Selection
i. ,rtificial Selection3 animal breeders select species with
beneficial traits to produce certain characteristics
1. produces great variation of traits than natural selection
ii. Natral Selection is the same as artificial selection except occurs
freely in nature
d. 0ar)in drafts his argment
i. drafted in manuscript in 1?:2 and put away for 1; years
ii. @allace from 5ndonesia develops identical theory
iii. 2wo scientists present their ideas together at seminar in london
:. 7redictions of natural selection have been tested
a. 4ossil 'ecords
i. ,arwin predicts that these would yield intermediate lin* between
great groups of organisms
1. fishes and amphibians
2. reptiles and birds
ii. discoveries of microscopic fossils extend life on earth bact to 1.5
AA
b. ,ge of Earth
i. ,arwin predicted that .arth must be very old
1. evolution requires a long time
ii. Some physicists argued earth is few thousands years old
iii. 'adioactive decay proved the physicists wrong
c. !echanisms of Heredity
i. ,arwin criticized for heredity
1. could not explain himself b%c no one had concepts of genes
and heredity
2. /nderstanding of laws of heredity caused criticism of
,arwin to vanish
ii. +eorge 0endel#s pea experiment at simmilar time
iii. +enetics not established until 2>th century
d. Com"arative anatomy
i. 0any vertebrates have the same bones
1. evidence for darwin#s theory
ii. homologos# same evolutionary origin& different structure and
function
iii. analogos# similar function but different evolutionary origins
1. birds and butterflies
e. !oleclar evidence
i. comparing of genomes
1. sequence of genes
ii. specifies degree of relationship among groups
iii. evolutionary changes involve continuing changes to ,!A
1. 0ost simmilar hemoglobin in 6hesus mon*eys and
humans
2. simmilar 1:;3amino3acid hemoglobin 3chain
iv. "hylogenetic tree# pattern of descent obtained
1. represents evolutionary history of gene
2. ,!A changesB footprints of evolutionary history
1.5 %nifying Themes in Biology
1. (ell theory describes the organization of living systems
a. cells# life#s basic units
i. ,iscovered by 6obert -oo*e
b. Schleiden and Schwann
i. cell theory# all living organisms consists of cells
2. 2he molecular basis of inheritence explains the continuity of life
a. deo$yriboncleic acid *0N,63 information that specifies what a cell is
li*e
b. Ncleotides# building bloc*s of ,!A
i. : are found in ,!A
ii. Specific sequences of !ucleotides ma*e up a gene
c. (ontinuity of life depends on faithful copying of cell#s ,!A
d. 7enome# entire set of ,!A instruction specifying a cell
i. -uman genome sequence has 1 billion nucleotides
1. ,ecoded in rough draft form in 2>>1
1. 2he 6elationship between structure and function underlies living systems
a. function in molecules and macromolecular dependent on structure
b. @hen we *now function of structure we can infer functions of similar
structures
c. surface receptor for insulin used for conclusion of a relationship of upta*e
of glucose in worms and humans
:. 2he ,iversity of life arises by evolutionary change
a. ,iversity classified into 1 categories
i. acteria
ii. Archae
iii. .u*arya
1. 7lantae3 have cell walls of cellulose and utilize
photosynthesis
2. "ungi3 have cell walls of chitinC obtain evergy by secreting
digestive enzymes and absorbing product
1. Animalia3 lac* cell walls& digest other organisms to obtain
energy
:. 7rotista3 unicelular eu*aryotes and algae& except yeast
5. .volutionary conservation explains the unity of living systems
a. All organisms alive have descended from a simple cellular creature
b. storage of info in ,!A common to all living things
;. (ells are information3processing systems
a. ,!A directs synthesis of cellular components& differs from cell to cell
b. (ells sense their environment
i. (ritical to function of tissues and organs in multicultural organisms
ii. 6egulate internal conditions
1. maintain p-& temp& and concentration of vital ions
<. $iving systems exist in a nonequilibrium state
a. (onstant supply of energy necessary to maintain nonequilibium state
i. !ucleic Acids and 7roteins are not polymers at equilibrium and
would by hydrolyzed