Biology L111 Notes for Exam 1

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BIOL-L 111
Michael J Wade

Biology L111: Chapter 1 8/26/2013 6:01:00 AM What is Science?  Latin Scientia= to know  Science: A way of viewing the world that focuses on objective info, and putting that info to work to build an understanding of processes that operate in the natural world to cause patterns  Scientists test hypotheses using observations, manipulations or experiments, or mathematical models. What do scientists do?  All science begins with observations about the natural world; scientists are „pattern detectors.‟  Scientists suggest an hypothesis to explain or to account for the pattern of observations o Hypotheses must be falsifiable(i.e.testable)  Experiments are used to test an hypothesis, and/or to eliminate one or more competing hypotheses o In a controlled experiment, all variables, but one, are kept constant Theory= a set of tested and data supported hypotheses  A theory is o A set of hypotheses with supporting evidence (data) o A body of interconnected concepts, supported by mathematical or logical reasoning and experimental evidence.  This is different from the colloquial use of “theory” o Opinion-based rather than evidence-based o A hunch, a guess, or a belief about cause and effect.  Scientific Theories are constantly compared with new physical discoveries and new experimental results  New theories explain more not less than old theories  What a Scientist Does ( look at the picture in his online notes 8/28: lecture 2 week 1)  Process Of Science = What the community of scientists do Hypothesis 5 becomes part of “Theory”  1. Make observations  2.speculate, ask a ????  3.form a hypothesis to answer the question  4.make a prediction: what else would be true if your hypothesis is correct  and conduct an experiment that uses quantifiable data to test your prediction  use statistical test to evaluate the significance of your results o significant results support hypothesis  ask new questions  Experiment repeated and results verified by other researchers o Results do not support hypothesis  Reexamine the experiment for uncontrolled variables  Revise your hypothesis  Rejected Hypotheses Are NOT part of Theory Biology is the study of life  Greek word bios= life and ology= science or study of  WHAT IS LIFE? o Basic characteristics of life:  Cellular organization:1 or more cells  Use energy: extract energy from environment  Interact with the environment: convert molecules from the environment into bio-molecules  Maintain homeostasis: stable internal state  Grow and development: get larger and change state  Contain Genetic info: DNA and RNA, information molecules  Evolution from one generation to the next to better fit their environment All life shares a common ancestry   Eukaryotes: cells with a nucleus; may have arisen by the fusion of a bacterium with an archean o Protist: single-cell eukaryote  Archaea: single-celled, no nucleus, no organelles, glycol-ether lipid membranes  Bacteria: single-celled, no nucleus, no organelles, glycol-ester lipid membranes  Eukaryota: animals, plants, and fungi A phylogenetic tree of life, showing the relationship between species whos genomes had been sequenced as of 2006. The very center represents the last universal ancestor of all life on earth.  Hierarchical Organization of Life  Cellular level: o Atoms o Molecule o Macromolecule o Organelle o Cell  Organismal Level: o Tissue o Organ o Organ system o Organism  Population level (DARWIN): o Population o Species o Community o Ecosystem Evolution: 23.1+23.2 8/26/2013 6:01:00 AM What do evolutionary biologists do?  1. Identify patterns in the diversity of life, especially puzzling ones, that appear to be problematic for Darwin‘s theory.  2. Hypothesize processes or forces that might be creating those patterns. Provide an explanation for the pattern in terms of one or more of the 5 evolutionary processes  3.Test the adequacy of their hypotheses by experiments and by further study of the history of life using many different disciplines The Term ―evolution‖ appears many times a week in national on-line newspapers --- not just in science In colloquial contexts, ―evolution‖ is a synonym for ―change over time‖  Usually for the better o Evolution is interpreted to mean improvement over time  Evolution is a process of change in a population and it does result in adaptation over time. But, NOT all change is evolution and adaptation is NOT always improvement. o ―Populations evolve; individuals do not.‖ Evolution is the change in kinds of organisms  Can be seen in evolutionary trees Ecology is the change in numbers and distribution of organisms  Can be seen in ecological interactions o Sporormiella is a coprophilus or dung fungus, obligate symbiont of large herbivores. Fossilized spore abundance indicates abundance of its hosts o Clovis Culture is a Paleo indian human culture associated with unique spear points. Remains of extinct megafauna, such as sloths, mammoth, bison, tapirs, lamas, have been found at Clovis sites Darwins Theory of Evolution by Natural Selection is the corner stone of modern biological science.  ―nothing in biology makes sense but in the light of evolution.‖ o Theodosius Dobzansky (1900-1975)  Evolutionary geneticist  Genetic model of speciation Charles Robert Darwin  Born 1809  Voyage of the H.M.S. Beagle o Dec 1831-Oct 1836 o On the Origin of Species (1859) his book Two Fundamental Patterns of Nature  Adaptation: the functional fit of an organism to its Environment  The diversity of organisms: o Why there are so many different species (5 to 50 million living species)? o Fossil record indicates that >99% of species that have ever existed are extinct o 5000,000 beetle species alone Origin of life on earth—3.5-3.9 billion years ago  Since then, 3 billion different kinds of organisms have arisen  The 5-50 million species alive today are only a tiny fraction, 0.25- 2.5%, of all the species that have ever existed. What forces create all the new species to replace the ones going extinct ?  The most striking feature of the biological world is the diversity of morphology(shape and size), physiology, and behavior exhibited by living organisms. How do we classify 5-50 million different species?  Patterns  Fundamental unit of classification in biology is the SPECIES o A species is a group of (potentially)interbreeding organisms that is reproductively isolated from other such groups (not capable of interbreeding with them) IMPORTANT  There are many different sizes within a single species  Ex: honey mushroom, Armillaria ostoyae  A founding spore is smaller than a bacterium. Its 2,400 yr old fruiting body is more than 3.5 miles across! How Evolution Effects your Life 8/26/2013 6:01:00 AM Sample Multiple Choice Question in LEct 1 Week 2 Wed post SLIDE Voyage of the Beagle  Dec 27, 1831 the HMS Beagle sailed from Devonport, England and returned on Oct 2,1836  Purpose o The objective of the expedition was to complete the survey of Patagonia and Tierra del Fuego,… to survey the shores of Chile, Peru, and some islands in the Pacific—and to carry a chain of chronometrical measurements round the world.  Captain: Robert FitzRoy o Wanted a companion and naturalist onboard o Later became Admiral and developed the First weather forcasts, posting telegraphed reports of weather at Lloyd‘s of Londons coffee house Voyages of the Beagle before Darwin  Beagle set sail from Plymouth on May 22,1826 on her first voyage under the command of Captain Pringle Stokes. The mission was a hydrographic survey of Patagonia and Tierra del Fuego.  Faced with more difficult part of the survey in the desolate waters of Tierra del Fuego, Captain fell into a DEEP DEPRESSION. At Port Famine on the Strait go Magellan he locked himself in his cabin for 14 days, then after getting over-excited and talking of preparing for the next cruise, shot himself on August 2,1828  Robert FitzRoy, a meticulous surveyor, was given command of the Beagle. When a group of Fuegians stole a ship‘s boat, FitzRoy took two men, a girl, and a boy from their families hostage. He took them with him to England in Oct 1830 o Had strong relious conviction. Placed natives under care of Rev. William Wilson(a member of the Anglican Church Missionary Society). He taught them English, dressed them according to british custom, and trained them in ―civilized‖ behavior. o In 1833, Fitzroy returned with the Feugians, installing them in a simple hut, with the catechist Richard Matthews. They were supposed to educate the local groups in enlightened ways. But after 10 days: Matthews was severly harassed and had to be withdrawn.  Darwins Voyage o Charles Darwin  1809-1882  Born a Naturalist o Father a physician, mother from the Wedgwood china family  BA from Cambridge 1831 o Studied to become an Anglican pastor o School was a burden hated school  Encouraged to go on voyage by his Professors John Henslow and Rev. Dr. Adam Sedgwick  Left on the Beagle- Age 22 The orthodox view of Nature in Darwin‘s Day  William Paley,1809. Natural Theology: or Evidences of the Existence and Attributes of the Deity, Collected from the Apperances of Nature  Cataloged the remarkable physical and social order of organisms, which was considered evidence for design o Design implies designer  Famous example of a watchmaker  Immutability: Species do not change Darwins Ideas before the Voyage  In order to pass the BA exam , it was necessary to get up Paleys Evidences of Christianity, and his Moral Philosophy. The logic of this book and as I may add of his Natural Theology gave me a much delight as did Euclid. o He did not at that time trouble himself about Paley‘s premises; and taking these on trust he was charmed and convinced of the long line of argumentation  Fixity or Immutability of Species o Each species was a single, unchanging entity, separate from other species and constant in its fundamental, defining characteristics.  Evolution or the transformation of Species o A speculative idea, espoused by some(including his grandfather, Erasmus Darwin) but with little evidence and no mechanisms or processes. Orthodox View was changing in Geology  Charles Lyell 1830-1833. Principles of Geology being an attempt to explain the former changes of the Earths surface by reference to causes now in operation o Prior to ―Principles‖ dominant view was of Catastrophism( ex: The great flood) o Lyell‘s work popularized the ideas of Uniformitarianism and Gradualism o Darwin‘s professors, Sedgwick and Henslow, and most geologists believed the earth was about 6,000,000 yrs old. Key insigts from Lyell for Darwin  Gradualism: weak forces acting over long periods of time could produce geological changes as large as those the catastrophic forces produce in a short period of time.  Uniformitarianism: geologic processes acting today are similar to those occurring throughout Earth‘s geological history. They account for all of Earth‘s geological features: ―the present is the key to the past‖. There were no ‗special past forces‘ no longer acting. o These were both proposed in Geology Darwin and Geological Research on the Beagle  In Chile on Feb 20,1835, Darwin experienced a strong earthquake  Lyell‘s concept of a steady-state Earth whereby the 4 geological forces of uplift, subsidence, erosion, and sedimentation were in balance over time. o First Applied this in Coral Reefs: the interaction of geology and biology for Darwin  Atoll: a coral reef island that surrounds a lagoon(oldest)  sedimentation and erosion  Fringe coral reef: grows close to the shore of an island with only a small shallow or no lagoon behind it (youngest)  Volcanic Origin= Uplift… formation of oceanic island  Barrier coral reef: grows far from shore with deep lagoon behind it  Subsidence= the sinking of the island  Pattern in nature: if arranged in order from Fringe, to Barrier, to Atoll, oceanic islands form a developmental series indicated by the age and depth of the coral reefs surrounding them.  Hypothesis: The pattern of development of oceanic islands is caused by a series of Geological Forces o Origin of Island:Uplift by volcanism o Decline of Island: subsidence, Erosion, Sedimentation young---------------------------------------------------- Old Darwin and Geological Research pubished  3 papers after voyage o Structure and Distribution of Coral Reefs (1842), Volcanic Islands (1844), and South America(1846):  Proposed theories which combined volcanism, subsidence, and erosion. Darwin‘s theory is the accepted theory of coral reef formation today.  He saw infinite superiority of Lyell‘s views Bio-Geologic evidence from voyage  2 kinds of islands o 1. Oceanic Islands  formed by volcanoes  far from mainland  species on each island were a unique group of species o 2. Continental islands  formed by breaking from the mainland  species were a subset of those species on the nearby mainland  near to mainland  Darwin‘s Hypotheses o Oceanic Islands  Species descendants of a colonizing single ancestor species with modification  Mechanism of modification was unknown o Continental Islands  Source of species was same species colonizing from mainland.  Mechanism was Recurrent Migration Galapagos finches differ in beak shape and diet   Darwin believed there was an ancestral seed-eating finch that started the lineage of all the finches  Hawaiian Honeycreepers were like Galapagos Finches descended with modification  Bio-Geographic Evidence from voyage  South American Fossils o Extant species resemble the fossils of S.A. more closely than fossils of Europe from the same strata.  European Fossils o Extant species resembled the fossils of Europe more closely than fossils of S.A. from the same strata.  Darwins Hypothesis o South American Fossils  Extant species descended with modification from ancient fossil species  Unknown mechanism of modification o European Fossils  Extant species resembled the fossils of Europe more closely than fossils of S.A. from the same stata.  Unknown Mechanism of modification The Orgin of Species  Genetics: 50 years after origin of species  DNA and Molecular Genetics: 120 years after origin of species o The only figure in The Origin of Species o The most important figure for you to understand in regard to this class. o o left side:  Present time: Descendants  Living species o Right side:  Extinctions: brtanches that terminate before the present  Past time: ancestors  Speciation: splitting of branches at nodes of tree Darwin‘s Ideas after the Voyage  Fixity or Immutability of species: Unlikely  Evolution or the Transformation of Species: likely o Much bio-geographic evidence o No mechanisms Chapter 16.1 8/26/2013 6:01:00 AM TODAYS NOTES ARE NOT IN THE BOOK!!!!!! Aves(the birds) have almost 10,000 named species  o x axis= year new species discovered o y axis= Ln of the Number of NEW bird Species  Peak period for naming new bird species- 1850 (150 yrs ago)  Fewer than 7-8 new bird species named per year today Why discuss a Failed theory of classification?  To illustrate the new theories better account for more patterns than the older theories they replace. o New theories explain more in terms of a better, more coherent, general process Quinary Theory  The Quinary theory was used in systematics as an organizing principle for biodiversity at the time of Darwin.
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