Chapter 2-Basic Chemistry

2.1 Chemical Elements

• matter-anything that takes up space and has mass
• matter can exist as a solid, liquid, or gas
• elements-basic substances that cannot be broken down to substances with different properties (a property is a physical or chemical characteristic, such as density, solubility, melting point, and reactivity)
• only 92 naturally occurring elements
• 6 elements: carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur make up the body weight of most organisms (CHNOPS)
• atoms-tiny particles
• early 1800s, John Dalton proposed elements contain one type of atom individually
• atomic symbol-one or two letters that stand for the element's name (H for hydrogen, Na for natrium/sodium in Latin)
• most stable subatomic particles: proton, neutron, electron
  
• proton-positive subatomic particle, located in the nucleus and having a weight of approximately one atomic mass unit
• neutron-neutral subatomic particle, located in the nucleus and having a weight of approximately one atomic mass unit
• electron-negative subatomic particle, moving about in an energy level around the atom
• most of an atom is empty space
• atomic mass-sum of protons and neutrons
• mass is constant while weight changes according to gravitational force
• atomic number-number of protons
• the atomic number is written as a subscript while the atomic mass is written as a superscript
• isotopes-atoms of the same element that have the same number of protons and differ only in the number of neutrons
• radioactive isotopes-an isotope that emits radiation in the form of radioactive particles or radiant energy when decaying
• radioactive isotopes are used in medicine since they are absorbed by metabolically active tissues and can be tracked (PET, positron emission tomography)
• 1913, Niels Bohr proposed that electrons orbit in concentric energy levels about the nucleus; although electrons have the same mass and charge, they vary in energy content
• electron shells-energy levels
• electrons differ in amount of potential energy, and the shells indicate the relative amounts of stored energy electrons have: electrons with the least amount of potential energy are located in the K shell, closest to the nucleus, then L and M
• it takes energy to keep an electron farther away from the nucleus as opposed to closer to the nucleus
• octet rule-outer shell is most stable when it has eight electrons
• atoms with eight electrons normally do not react and are inert
• orbital-volume of space where a rapidly moving electron is statistically predicted to be found
• electrons occupy an orbital rather than orbit
• an orbital has a characteristic energy state and a characteristic shape
• at the first energy level, at most two electrons are found about the nucleus in a single spherical orbital because the most likely location for each electron is a fixed distance in all directions from the nucleus
• at the second energy level, there are four orbitals and a maximum of eight electrons; one is spherical but the other three are dumbbell shaped, which allows electrons to be the most distant from one another
  
• when bonding occurs, the orbitals of the L shell sometimes hybridize, forming teardrop-shaped orbitals that point to the corners of a triangular pyramid called a tetrahedron
• photosynthesis: 6CO₂ + 6H₂O → C₆H₁₂O₆ + 6O₂
• equation is balanced

2.2 Compounds and Molecules

• molecules can form when two or more atoms of the same element react with one another
• compound-when two or more different elements react or bond together (O₂, H₂O is a compound that contains the elements hydrogen and oxygen)
• molecule-the smallest part of a compound that still has the properties of that compound
• ionic bonds form when electrons are transferred from one atom to another
• electron transfers may cause a charge imbalance in each atom
• ions-charged particles
• ionic bond-attraction between charged ions
• covalent bond-when two atoms share electrons in such a way that each atom has an octet of electrons in the outer shell
• molecules have a three-dimensional shape that determines their biological function
• hormones have shapes that allow them to be recognized by the cells in the body
• one form of diabetes occurs when the receptors of cells fail to recognize the hormone insulin
• AIDs occurs when blood cells have receptors that bind to the HIV virus, allowing it to enter, multiple, and destroy the cell
• nonpolar covalent bond-when the sharing of electrons between two atoms is fairly equal
• polar covalent bond-the unequal sharing of electrons in a covalent bond
• in the case of water, the sharing of electrons between oxygen and each hydrogen is not completely equal; the larger O atom has a greater number of protons and thus dominates the association, as it is more electronegative than the hydrogen atom and can attract the electron pair to a greater extent, assuming a negative charge (δ^-) and caushing the hydrogen atoms to assume a slightly positive charge (δ⁺)
  
• electronegativity-the attraction of an atom for the electrons of a covalent bond
• hydrogen bond-an attractive force creating a weak bond
• in water
• a hydrogen bond is more easily broken than a covalent bond, but many hydrogen bonds together are quite strong and help maintain proper sutrcture and function of cellular molecules

2.3 Chemistry of Water

• the first cells evolved in water, and all living things are 70-90% water
• water is a polar molecule and water molecules are hydrogen bonded together
• taken together, hydrogen molecules cause water molecules to cling together
• because of hydrogen bonding, water boils at 100°C and freezes at 0°C
• the temperature of water rises and falls more slowly than other liquids under the same conditions
• a calorie is the amount of heat energy needed to raise the temperature of one gram of water 1C
• the many hydrogen bonds that link water molecules help water absorb heat without a great change in temperature
• water has a high heat of vaporization and thus a high boiling point
• hydrogen bonds must be broken to change water to steam
• water facilitates chemical reactions bother outside of and within living systems
• water dissolves a lot of things because it is polar
• when a salt, such as NaCl, is put into water the negative ends of the water molecules are attracted to the sodium ions and the positive ends of the water are attracted to the sodium ions, and the positive ends of the water molecules are attracted to the chloride ions, causing the sodium ions and the chloride ions to separate and to dissociate in water
• water is also a solvent for larger molecules that contain ionized atoms or are polar molecules
• when ions and molecules disperse in water, they move about and collide, allowing reactions to occur
• hydrophilic-(molecules) attracting water
• hydrophobic-(nonionized and nonpolar molecules that) cannot attract water
• water molecules are cohesive and adhesive
• water molecules flow freely, but do not separate from each other; they cling to each other because of hydrogen bonding, and because they have poles, they adhere to surfaces and particularly polar surfaces
• water can fill a tubular vessel and still flow, dissolved and suspended molecules are evenly distributed throughout a system
• water is an excellent transport system both outside of and within living organisms
• one-celled organisms rely on external water to transport nutrient and waste molecules
• multicellular organisms often contain internal vessels in which water serves to transport nutrients and wastes
• the liquid portion of our blood is 90% water that contains dissolved and suspended substances
• contributes to the transport of water in plants
• plants have roots anchored in soil where they absorb water, but the leaves are uplifted and exposed to solar energy. A plant contains a sytem of vessels that reaches from the roots to the leaves, so water evaporating from the leaves is immediately replaced with water molecules from the vessels. Because water molecules are cohesive, a tension is created that pulls water up from the roots. Adhesion of water to the walls of the vessels also helps prevent the water column from breaking apart
  
• unlike most substances, frozen water is less dense than liquid water
• as water cools, the molecules come closer together (densest at 4°C)
• at temperatures below 4°C there is only vibrational movement, and hydrogen bonding becomes more rigid but also more open, so water expands as it freezes and is less dense)
• bodies of water freeze from the top, acting as an insulator to protect water underneath and making life possible instead of accumulating at the bottom of lakes and oceans
• hydrogen ions (H⁺)
• hydroxide ions (OH^-)
• H-O-H ↔ H⁺ + OH^-
• only a few water molecules at a time are dissociated, and the actual number of these ions is very small (10^-7 moles/liter)
• acids-molecules that dissociate in water, releasing hydrogen ions (H⁺)/higher concentration
  
• strong acids dissociate almost completely, strong bases dissociate almost completely
• bases-molecules that either take up hydrogen ions (H⁺) or release hydroxide ions (OH^-)/higher concentration
  
• pH scale-indicates acidity and basicity (alkalinity) of a solution
  
• ranges from 0 to 14
• logarithmic as opposed to exponential
• devised to simplify discussion of the hydrogen ion concentration [H⁺] and hyroxide ion concentration [OH^-] by eliminating th use of cumbersome numbers
• each pH has 10 times the amount of hydrogen ions as the next higher unit
• 7 is neutral pH, pure water has an equal number of hydrogen and hydroxide ions
• source: one mole of pure water contains only 10^-7 moles/liter of hydrogen ions
• in living things pH needs to be maintained within a narrow range or there are health consequences
• pH of our blood is always about 7.4, slightly basic
• buffers-most important of mechanisms to prevent pH changes; keep pH within normal limits because they are chemicals or combinations of chemicals that take up excess hydrogen or hydroxide ions
• blood always contains a combination of some carobic acid and some bicarbonate ions, so in case:
  H⁺ + HCO₃^- → H₂CO₃, then
  OH^- + H₂CO₃ → HCO₃^- + H₂O
• these reactions prevent any significant change in blood pH
  

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Lecture Notes 8/31-9/21

• characteristics of life
• life shows organization-cell theory
• life acquires nutrients for survival-photosynthesis/respiration
• life uses energy to maintain organization-homeostasis
• life respons to its environment-adaptation/evolution
• life needs to reproduce to maintain itself through time
• nutrients: water, minerals (Na, K, Ca, Mg, Fe, Cu, Zn, etc.), vitamins, hydrocarbon molecules that are C-, H- based (carbohydrates, proteins, lipids/fats)
• methodology to learn about the natural world
1. identify a problem to study-natural curiousity
2. examine the literature to find out what is already known
3. formulate a hypothesis to test to learn new information
4. design and run an experiment to test the hypothesis
5. collect observations and measurements (data)
6. analyze and interpret your observations and measurements
7. draw a conclusion about the truthfulness of the hypothesis
   
• supernatural-religion, cannot be tested
  
• pure research-no practical applications, just "because it's there"
• applied research-business, commerical exploitation, practical use
• evolution-
• descent with modification through time (paleontology def.)
• change through time such that one species changes into one or more new species
• active form, it's still occurring but extremely slow
  
• descent through many generations
• survival of the fittest (e.g. black pague, smallpox in North Africa, etc.)
• humans have existed for only a short amount of time, as opposed to cockroaches or the bristlecone pine
• Earth is about 4.5 billion years old
• mechanism: Darwin was influenced by Malthus theory on limiting factors
1. natural populations' reproductive capacity exceeds environment's capacity to support offspring
2. environment interacts with overproduction to "select" those best adapted which "survive"
3. those best adapted to environment survive
   
• sexual reproduction provides new combinations of existing genetic material upon which the environment interacts/has survived the environment
• most mutations are harmful
  
• Origin of Species was highly controversial
• continental/genetic drift is the driving force of evolution-a slow, steady movement over millions of years resulting in climatic changes which "selects" the "best adapted"
• times of bounty and scarcity, wintertime is harder so more "selection"
  
• fossils-first/oldest evidence of life, relatively rare as conditions must be perfect
• many fossils in Montana and southwestern America
• from fossils, you can divine their behaviour, what has happened in the geological past, and support evolution
• comparitive anatomy
• homology-same structure, different function (i.e. human arm, bird wing, whale flipper, horse leg)
• scales are the origin of teeth
• new genes are never created, they already exist just as different combinations of genes; there is a tremendous variety of traits
  
• recessive alleles appear only when there are no dominant traits
• start with the phenotype, then infer the genotype (begin with recessive)
• Hardy-Weinberg equilibrium is the mathematical proof of evolution

p² + 2pq + q² = 1
p + q = 1
q² = 16%
q = √.16 = .4
p + .4 = 1
p = .6
.6² + .4(.6) + .4² = 1
.36 + .48 + .16 = 1

Chapter 20-Origin and History of Life

20.1 Origin of Life

• chemical evolution-an increase in the complexity of chemicals
• the solar system probably formed over a 10-billion-year period from aggregates of dust particles and debris, settling around 4.6 billion years ago
• the primitive atmosphere consisted mostly of water vapor (H₂O), nitrogen (N₂), carbon dioxide (CO₂), with a small amount of hydrogen (H₂) and carbon monoxide (CO)
• at first the earth was so hot that the water vapor formed thick, dense clouds that rained heavily, forming the oceans
• or, the oceans were fed by celestial comets that entered Earth's gravitational field; the ice from the icy comets became water vapor that later came down as enough rain to raise the oceans
• other comets may have carried the first organic molecules to Earth
• Aleksandr Oparin suggested that the first organic molecules could have been produced on Earth from primitive atmospheric gases in the presence of strong energy sources (heat from volcanoes and meteroties, radioactivity from isotopes in the earth's crust, powerful electric discharges in lightning, ultraviolet/solar radiation)
• ocean ridges-where molten magma wells up and adds material to the ocean floor
• amino acids polymerize abiotically when exposed to dry heat
• proteinoids-small polypeptides that have some catalytic properties
• microspheres-structures composed only of protein that have many properties of a cell
• protein-first hypothesis-DNA genes came after protein enzymes arose (Sidney Fox)
• clay was the source of energy for polymerization, and both polypeptides and RNA arose at the same time (Graham Cairns-Smith)
• RNA-first hypothesis-only RNA was needed to form cells
• protocell-a structure that has a lipid-protein membrane and carries on energy metabolism
• if lipids are made available to microspheres, they tend to become associated with microspheres producing a lipid-protein membrane
• coavercate droplets-under appropriate conditions of temperature, ionic composition and pH give rise to complex units that have a tendency to absorb and incorporate various substances from the surrounding solution
• liposomes-droplets formed by phospholipid molecules in a liquid environment
• DNA directs protein synthesis, and there is a flow of information from DNA => RNA => protein
• general view of origin of the first cells
1. there was an abiotic synthesis of small organic molecules such as amino acids and nucleotides in either the atmosphere or hydrothermal vents
2. these monomers joined together to form polymers either on land or at the vents; they could have been rna, proteins, or evolved together
3. the aggregation of polymers inside a membrane produced a protocell, which had some enzymatic properties so that it could grow; if it developed in the ocean, it was a heterotroph, and if it developed at hydrothermal vents, it was a chemoautotroph
4. once the protocell contained DNA it became a true cell; the first genes may have been RNA but later DNA became the information storage molecule of heredity

20.2 History of Life

• fossils-remains and traces of past life or any other direct evidence of past life (trails, footprints, burrows, worm casts, or even preserved droppings)
• sedimentation-the process of embedding fossils in sedimentary rock
• stratum-a recognizable layer in the stratigraphic sequence
• paleontology-science of discovering and studying the fossil record and, from it, making decisions about the history of life
• relative dating-stratum of the same age tended to contain the same fossil, so the sequence of fossils helped determine relative strata dates
• absolute dating-radioactive techniques that assign an actual date to a fossil
• geological timescale-the division of the history of the earth into eras, then periods and epochs
• the Precambrian encompasses the first two eras: Archean and Proterozoic
• during the Precambrian, the first cells (probably prokaryotes that do not have a nucleus or any membrane-bounded organelles) came into existence
• today the archea live in hot springs, very salty lakes, and airless swamps
• stromatolites-strange looking boulders that littered beaches and shallow waters whose outer surfaces are live with cyanobacteria
• cyanobactera in ancient stromatolites added oxygen into the atmosphere
• the presence of oxygen caused photosynthetic cyanobactera and aerobic bacteria to proliferate and anaerobic prokaryotes declined
• ozone shield-oxygen in the upper atmosphere that filters out UV rays of the sun
• eukayotic cells are nearly always aerobic and contain nuclei as well as membranous organelles
• endosymbiotic hypothesis-a nucleated cell engulfed certain prokaryotes, which became organelles
• flagella/cilia may have arisen by endosymbiosis
• the first multicellular forms were most likely microscopic, and later fossils of soft-bodied invertebrates were found
• extinction-total disappearance of all memebrs of a species or higher taxonomic group
• the Paleozoic era lasted over 300 million years
• mass extinctions-the disappearance of a large number of species or higher taxonomic group within an interval of just a few million years
• molecular clock-the principle that DNA differences in certain parts of the genome occur at a fixed rate and are not tied to natural selection
• the number of DNA base pairs tells how long two species have been evolving separately
• no fossil evidence occurs until the Cambrian period, as skeletons are capable of surviving forced that are apt to destroy fossils
• skeletons may have evolved during the Cambrian period to protect animals from predators
• during the Paleozoic era, algae began to grow in fresh water and then invade damp land
• mycorrhizae allowed plants to live on bare rocks, absorbing minerals and passing them to the plant, who passes carbohydrates (photosynthesis) back
• in the Silurian period, fossils of vascular plants with tissue for water transport were found
• in the Carboniferous period, club mosses, horsetails, and seed ferns flourished
• various arthropods (spiders, centipedes, mites, millipedes) proceeded insects on land, who entered during the Carboniferous period
• invertebrates have an outer skeleton and jointed appendages
• vertebrates are animals with a vertebral column that began in the early Ordovician period with jawless fishes and then fishes with jaws
• cartilaginous and ray-finned fishes appeared in the Devonian period (Age of Fishes)
• amphibians are thin-skinned vertebrates that are not fully adapted to life on land and developed during the Carboniferous period (Age of the Amphibians)
• at the end of the Carboniferous period, cold and dry weather ended the Age of Amphibians and turned Carboniferous forests into coal/fossil fuel
• plant and animal evolution continued into the Triassic period (first of the Mesozoic era)
• nonflowering seed plants became dominant in the Permian period (conifers, cycads)
• cycads are short and stout with palmlike leaves, and developed during the Jurassic period (Age of the Cycads)
• reptiles can be traced back to the Permian period
• during the Jurassic period, pterosaurs ruled the air, marine reptiles with paddlelike limbs ruled the sea, and dinosaurs ruled the land
• since dinosaurs were ectothermic, they were so large as to maintain a favorable volume-to-surface ratio for retaining heat
• the Cenozoic era consists of the Paleogene period and the Neogene period, our current time
• at the end of the Mesozoic era, other mammals began to adapt to environments vacated by the dinosaurs
• mammals are endothermic, have hair, and use mammary glands to produce milk to feed their young; they were still small at the end of the Paleocene epoch, but began to diversify during the Eocene epoch
• angiosperms (flowering plants) evolved at the end of the Mesozoic and began their adaptive radiation during the Cenozoic era
• primates are mammals that live in angiosperms; apes diversified during the Miocene epoch and gave rise to the first hominids
• the latter two epochs of the Neogene period are known as the Ice Age (humans, giant ground sloths, beavers, wolves, bison, woolly rhinoceroses, mastodons, and ammoths)

20.3 Factors that Influence Evolution

• continental drift-the continents' positions and positions of the oceans change over time (Alfred Wegener)
• the continents used to be part of Pangaea, then Gondwanaland and Laurasia, and then the continents of today
• they are still drifting
• explains why some coastlines are mirror images of each other and unique distribuation patterns of some fossils
• plate tectonics-branch of geology that studies movements of the earth's crust
• ocean ridges-seafloor spreading that occurs as molten mantle rock rises and material is added to the ocean floor
• at subduction zones, the forward edge of a moving plate sinks into the mantle and is destroyed
• two plates meet along a transform boundary where they scrape past each other
• there have been mass extinctions at the end of the Ordovician, Devonian, Permian, Triassic, and Cretaceous periods
• Walter and Luis Alvarez proposed in 1977 that the Cretaceous extinction was due to a bolide (asteroid), as Cretaceous clay contains an abnormally high level of iridium, an element common in asteroids and meteorites
• in 1984, David Raup and John Sepkoski suggested mass extinctions have occurred every 26 million years, since then the solar system will appraoch other members of the Milky Way that could lead to a bollide
• continental drift contributed to the Ordovician extinction
• the Permian extinction could have been caused by excess carbon dioxide, which would have led to global warming and altered the pattern of vegetation
• the Triassic period extinction is attributed to a meteorite collision, as Quebec has a huge crater

Chapter 19-Process of Evolution

19.1 Evolution in a Genetic Context

• population-all the members of a single species occupying a particular area at the same time
• microevolution-evolution that occurs within a population
• gene pool-various alleles at all the gene loci in all individuals
• population genetics-study of gene frequencies and their change within a population
• sexual reproduction alone cannot bring about a change in allele frequencies
• Hardy-Weinburg law-an equilibrium of allele frequencies in a gene pool (p² + 2pq + q²) will remain in effect in each succeeding generation of a sexually reproducing population as long as there are:
1. no mutations: allele changes do not occur, or changes in one direction are balanced by changes in the opposite direction
2. no gene flow: migration of alleles into or out of the population does not occur
3. random mating: individuals pair by chance and not according to their genotypes or phenotypes
4. no genetic drift: the population is very large, and changes in allele frequencies due to change alone are insignificant
5. no selection: no selective agent favors one genotype over another
   
• this usually never happens; therefore evolution has occurred
  
• a change in allele frequencies results in a change in phenotype frequencies
• industrial melanism-increased frequency of darkly pigmented (melanic) forms in a population when soot and pollution make lightly pigmented forms easier for predators to see against a pigmented background
• the conditions that cause a deviation from the Hardy-Weinburg equilibrium are mutation, gene flow, nonrandom mating, genetic drift, and natural slection (only element resulting from adaptations to the environment)
• mutations are the raw material for evolutionary change
• once alleles have mutated, certain combinations of several alleles might be more adaptive than others in a particular environment
• gene flow-gene migration; movement of alleles between populations by migration of breeding individuals
• there can be constant gene flow between adjacent animal populations due to migration
• gene flow can increase variation with a population by introducing new alleles due to natural selection and genetic drift
• gene flow among populations can prevent speciation
• nonrandom mating-breeding/mating between relatives to a greater extent than chance
• inbreeding doesn't change allele frequencies, but it changes the proportion of heterozygotes and increases the proportions of homozygotes at all gene loci
• in human populations, inbreeding increases the frequency of recessive abnormalities in the phenotype
  
• assortative mating-when individuals tend to mate with those that have the same phenotype with respect to some characteristic
• assortative mating causes the population to subdivide into two phenotypic classes, when there is reduced gene exchange, so homozygotes increase and heterozygotes decrease
• sexual selection-when males compete for the right to reproduce and females choose to mate with males that have a particular phenotype (e.g. peacocks)
• genetic drift-changes in allele frequencies of a gene pool due to chance
• larger populations suffer less sampling errors than smaller populations
• when genetic drift leads to a loss of one or more alleles, other alleles over time become fixed in the population
• genetic drift is a random process
• bottleneck effect-if a species is subjected to near extinction because of a natural disaster/overharvesting/habitat loss, so it's as if most of the population has stayed behind and only a few have passed through the neck of a bottle
• founder effect-example of genetic drift in which rare or combinations of alleles occur at a higher frequency in a population isolated from the general population

19.2 Natural Selection

• natural selection-the process that results in adaptation of a population to the biotic and abiotic environments
• the biotic environment includes organisms that seek resources through competition, predation, and parasitism
• the abiotic environment includes weather conditions dependent chiefly upon temperature and precipitation
• relative fitness-the fitness of one phenotype compared to another
• most traits on which natural selection acts are polygenic and controlled by more than one pair of alleles located at different gene loci; the range of phenotypes' frequency distribution resembles a bell-shaped curve
• directional selection-when an extreme phenotype is favored and the distribution curve shifts in that direction; this can occur when a population is adapting to a changing environment
• stabilizing selection-when an intermediate phenotype is favored which can improve adaptation of the population to those aspects of the environment that remain constant; individuals near the average are favored
• disruptive selection-two or more extreme phenotypes are favored over any intermediate phenotype
• a population always shows genotypic variation
• the maintainence of variation is beneficial because populations with limited variation may not be able to adapt to new conditions and thus become extinct
• only alleles that are exposed (phenotypic difference) are subject to natural selection
• in diploid organisms, this makes the heterozygote a potential protector of recessive alleles that otherwise would be weeded out of the gene pool
  
• in a changing environment, the recessive phenotype may then be favored by natural selection
• when the ratio of two or more phenotypes remains the same in each generation, it is called balanced polymorphism

19.3 Speciation

• speciation-the splitting of one species into two or more species or the transformation of one species into a new species over time
• species-group of similarly constructed organisms capable of interbreeding and producing fertile offspring; organisms that share a common gene pool; taxon at the lowest level of classification
• whenever reproductive isolation develops, speciation has occurred
• allopatric speciation-variations due to different mutations, genetic drift, and directional selection build up, causing first postzygotic adn then prezygotic isolation to occur
• sympatric speciation-a population develops into two or more reproductively isolated groups without prior geographic isolation
• adaptive radiation-the rapid development from a single ancestral species of many new species, which have spread out and become adapted to various ways of life

Chapter 18-Darwin and Evolution

18.1 History of the Theory of Evolution

• Charles Darwin sailed on the Beagle when he was 22 in 1831
• pre-Darwinian view
• Earth is young
• each species is specifically created
• adaption is the work of a creator
• observations substantiate the prevailing world view
• post-Darwinian view
• Earth is old
• species are related by descent
• adaptation is the interplay of random variations and environmental conditions
• observation and experimentation test hypotheses, including evolution
• evolution-species change with time
• descent with modification
• Carolus Linnaeus came up with binomial nomenclature, but believed each species was individually created and occupied a specific rung on the ladder of life, with humans at the top
• Georges-Louis Leclerc provided evidence of descent with descent with modification
• Erasmus Darwin suggested the possibility of common descent
• Georges Cuvier founded paleontology
• paleontology-the study of fossils
• catastrophism-Cuvier hypothesized that a series of local catastrophes occurred whenever a new stratum showed a new mix of fossils. After the catastrophe, the region was repopulated by surrounding species, and the result of all these catastrophes was the appearance of change with time. Others suggested that after there were worldwide catastrophes, and after each one, God created a new species.
• Jean-Baptiste de Lamarck was the first to believe evolution occurred, and concluded that more complex organisms descended from less complex organisms, but believed the increasing complexity was a resultant of an inherent desire for perfection in all species
• Lamarck supported inheritance of acquired characteristics-the environment can bring about inherited change (giraffes' necks stretched when they ate, and passed this on)

18.2 Darwin's Theory of Evolution

• James Hutton believed the earth was subject to slow but continuous cycles of erosion and uplift
• Charles Lyell proposed uniformitarianism-slow erosion changes occurred at a uniform rate
• biogeography-the study of geographic distribution of life-forms on Earth
• Darwin noticed how similar species replaced each other
• Darwin wondered if the types of tortoises was correlated with the types of island vegetation
• Darwin speculated if the different types of finches could have descended from a type of mainland finch
• natural selection-mechanism for evolutionary change
1. the members of a population have heritable variations
2. in a population, many more individuals are produced each generation than the environment can support
3. some individuals have adaptive characteristics that enable them to survive and reproduce better than do other individuals
4. an increasing proportion of individuals in succeeding generations have the adaptive characteristics
5. the result of natural selection is a population adapted to its local environment
• Darwin emphasized variations, and suspected they were completely random and essential to the natural selection process
• Thomas Malthus prophesized that death and famien were inevitable because the human population increased too quickly
• each generation has the same reproductive potential as the previous generation, so there is a constant struggle for existence and only certain members will survive and reproduce
• fitness-the reproductive success of an individual relative to the other members of a population
• artificial selection
• adaptation-a trait that helps an organism be more suited to its environment

18.3 Evidence for Evolution

• fossil record-history of life recorded by remains from the past
• fossils are at least 10,000 years old (pieces of bone, impressions of plants pressed into shale, insects trapped in tree resin)
• extinct-died out
• Darwin concluded there were no rabbits in South America because they had no means to get there
• physical factors determine where a population can spread
• homologous structures-structures that are anatomically similar because they are inherited from a common ancestor (e.g. vertebrate forelimbs)
• analogous structures-structures that serve similar functions but are not constructed similarly nor inherited (e.g. wings)
• vestigial structures-anatomical features that are fully developed in one group of organisms but are reduced and may have no function in similar groups (e.g. tailbone)
• vertebrate homology extends to their embryological development
• degree of similarity in DNA base sequences
• evolution is now considered a theory
  

Chapter 1-A View of Life

1.1 How to Define Life

• cells are the basic unit of life
• energy-capacity to do work
• energy is needed to maintain the organization of the cell and the organism
• metabolism-the chemical reactions occurring in a cell
• the sun is the ultimate source of energy for life on earth
• photosynthesis-process that transforms solar energy into chemical energy in the bonds of organic nutrient molecules
• homeostasis-the maintenance of internal conditions within certain boundaries
• homeostasis is needed for metabolic processes to continue
• some organisms depend on behavior to regulate internal environment, while others have control mechanisms
• living things find energy/nutrients by interacting with their surroundings
• the ability to respond results in movement, which ensures survival and allows organisms to carry on daily activities
• behavior-daily activities
• reproduce-make another organism like itself
• genes-specific information for how the organism is to be ordered
• genes are made of long molecules of DNA (deoxyribonucleic acid)
• adaptations-modifications that make organisms suited to their way of life
• organisms become modified over time by natural selection
• natural selection-groups that inherit favorable characteristics increase their and their offspring's chances for survival, so the attributes of the species' members change over time
• living things have similar cell organization, their genes are composed of DNA, and carry out the same metabolic reactions to acquire energy and maintain organization
• evolution-descent with modification

1.2 How the Biosphere is organized

• individual organisms belong to a population, the members of a species belong to a community, communities make up the biosphere-a thin layer of life that encircles the earth
• communities are highly dynamic
• ecologists study the movemtn of energy and nutrients though communities
• ecosystem-populations with a community interacting within themselves and with the physical environment
• food chain
• plants take in inorganic nutrients, plants and animals return carbon dioxide to the atmosphere when they respire, when organisms decay, inorganic nutrients are absorbed by plants again
• plants use solar energy to produce organic nutrients, which is also converted to heat
• ecosystems are either terrestrial or aquatic
• tropical rain forests have the greatest diversity (central and west Africa, South America, Southeast Asia)
  
• most populations live in the canopy and interact
• rain forests act as giant sponges and absorb carbon dioxide, a pollutant
• an increased amount of CO₂ would cause a temperature and acid rain increase
• biodiversity-number and size of populations within a community

1.3 How Living Things are Classified

• taxonomy-the discipline of identifying and classifying organisms according to certain rules
• biologists give living things a binomial, a two-part name
• species, genera, families, orders, class, phyla, kingdoms, domains
• 5 kingdoms (Monera, Protista-unicellular to multicellular organisms and include algae and protozoans, Fungi-molds and mushrooms, Plantae-multicellular photosynthesizers, Animalia-multicellular and ingest food), 3 domains (Bacteria-unicellular prokaryotes, Archea-unicellular prokaryotes, Eukarya)
  

1.4 The Process of Science

• biology-the scientific study of life
• science-only what is observable by the senses or by instruments that extend the ability of the senses as a way to understand the natural world
• observations can be made by any of the 5 senses and help scientists conduct investigations
• phenomenon-observable event
• inductive reasoning-when a person uses isolated facts and creative thinking to come up with a possible explanation
• hypothesis-a possible explanation
• experiments-artificial situations devised to test hypotheses
• deductive reasoning-a general statement that infers a specific conclusion (if, then)
• David P. Barash tested the hypothesis that aggression of the male mountain bluebirds varies during the reproductive cycle
• control group-a group that experiences all the steps but does not contain the experiment variable
• data-results of an experiment
• conclusion-whether the results support or falsify the hypothesis
• falsify-show to be untrue
• variable-a factor that can cause an observable change during the experiment
• experimental variable-the deliberately manipulated step of the experiment; component of the experiment being tested
• dependent variable-the effects of the experiment; results or change that occurs due to the experimental variable
• scientific method-process of science

1. observations
2. previous data
3. formulation of hypothesis
4. observations and/or experimentation
5. new data
6. conclusion
7. theory

• scientific theories-concepts that join together well-supported and related hypotheses
• cell theory-all organisms are composed of cells
• biogenesis theory-life comes only from life
• evolution theory-all living things have a common acnestor and are adapted to a particular way of life
• gene-organisms contain coded information that dictates their form, function, and behavior
• principle/law-theories that are generally accepted by an overwhelming number of scientists

Basic Terminology

1. control group-a group used as a standard of comparison in a control experiment
2. experimental group-a group being studied to evaluate the effect of an event, substance, or technique
3. independent variable-a variable whose value determines the value of other variables; a factor that can be varied or manipulated in an experiment
4. dependent variable-the outcome variable; what you measure in the experiment and what is affected during the experiment
5. controlled variable-quantity or condition which is measured and controlled; independent variable
6. randomization-a method based on chance by which study participants are assigned to a treatment group. Randomization minimizes the differences among groups by equally distributing people with particular characteristics among all the trial arms. The researchers do not know which treatment is better. From what is known at the time, any one of the treatments chosen could be of benefit to the participant.
7. sampling error-the degree to which a sample might differ from the population
8. random error (+/-)-the irreproducibility in making replicate measurements and affects the precision of a result; the scattering of a measured value around a mean or
   average value
9. systematic error-a persistent statistical error having a nonzero mean that cannot be attributed entirely to chance but to inaccuracy inherent in the statistical system
10. experimental investigation
11. observational investigation