lizzie3622biol121ch1 Elizabeth A. Morrison
  Biol121
 
I.Biology, the science of life. What is life?
  A.All life:
    1.Order, complexity. Living things are non-random, particular, and the number of functions are huge.
    2.Sensitivity. Responds to Stimuli. All life respond with environment, they are proactive.
    3.Growth, development, and reproduction.
      a.Growth: increase in mass
      b.Development: unicellular or multicellular. Cells are not always the same, they change/evolve over time (baby to adult). This is less important for single-celled organisms (bacterium). Multicellular organisms have not only more than one cell, but also more than one type of cells.
      c.Reproduction: production of identical or similar offspring. Only some cells reproduce themselves. Trivial in classification.
      d.Under control of special hereditary molecules, molecular specialization (self explanatory), evolution, and adaptation. DNA, same cell with same information. Evolution is a change in something. Adaptation is if the change/evolution allows organism to survive.
    4.Regulation of functions of organisms. Goes back to sensitivity -- everything is in control.
    5.Homeostasis internal conditions maintained. Homeo = stays same; Stasis = internal conditions.
  B.Known life on earth
    1.Made up of cells. Components: membrane, nucleus or region containing DNA. There is always at least one membrane. We all use the same DNA code.
    2.Consistent information flow: the central dogma:  DNA makes DNA, copies instructions. DNA is protected and never broken. DNA is copied to make RNA. RNA makes only protein using it's information. Like a research book (DNA), copied (RNA) to make a paper (protein).
    3.Requirements for life: raw materials, energy, information. Energy is constantly needed for maintaining systems, like circulation.
All living things found are related to each other through common ancestors.
  C.Levels of biological organization
    1.Higher levels are more complex and are characterized by emergent characteristics: traits that are more than the sum of the parts.
    2.Within cells
      a.Atoms - elements - chemistry
      b.Molecules and macromolecules: simple biological functions are their emergent characteristic
      c.Organelles and cytoplasm complex biological functions (emergent characteristic). Organelles are small organs of the cell, much like our bodies' organs.
      d.Cells: life. May be whole organism. Cells are the smallest life form; each lives individually. If they are a single cell, they are an organism.
    3.Within multicellular organisms. Additional levels between cells and organisms:
      a.Tissue: Cells together
      b.Organs: tissues together
      c.Organ systems: organs together
      d.Multicellular organism: organ systems together
    4.Among organisms (single or multicellular)
      a.Population: group of same species. Emergent characteristic: social order and evolution. Individuals do not evolve, they can't pass on acquired traits. Potentially, every member could interbred, and genes would be intermixed
      b.Species: whole potentially interbreeding group, largest evolving group.
      c.Community: all living organisms in environment: species interactions. Every species in an area.
      d.Ecosystem: organisms plus inanimate environment. Typically in small areas with distinct species.
      e.Biome: a group of related ecosystems. Includes a lot of variability.
      f.Biosphere: all ecosystems: entire earth, everything.
II.Science is a rational process that seeks to explain the nature of the universe. Prior causes. It rests on established facts: information that can be unambiguously proven. Facts tend to be fairly minor. Objective or subjective.
  A.Two types of reasoning
    1.Deductive: understanding specific instances by applying general principles. Eratothenes and the Earth's diameter. Much scientific measurement. Eratothenes was a Greek in Egypt, and used geometry and the sun's rays to figure the sphere, because the rays hit parallel there. General principle = Geometry.
    2.Inductive: formulating general principles by examining specific instances. How science is expanded. Theories based on facts.
  B.The scientific method. A general principle starts as a hypothesis (educated guess), and many become a theory (widely accepted principle). Some steps/issues:
    1.Identify a problem and examine the relevant facts that are already known.
    2.Develop a hypothesis(es), or educated guess to explain the facts. Often there will be several competing hypotheses. A working idea, a starting point.
    3.Test hypothesis by collecting further facts.
      a.Observations of nature as it is. No change, just observe. Ecologists.
      b.Models, mathematical simulations of nature, often done on computers. Useful for diseases and Astronomers.
      c.Experiments: natural phenomena are observed under artificial conditions. The conditions are carefully controlled so that only a desired factor (variable) varies between treatments. (Treatment 1 receives poison, Treatment 2 does not.). Poison = variable; T2 mice = control. Controls are negative (no response or positive (with response). T2= negative.
      d.Need for control experiments, especially the negative control.
    4.Compare new facts to predictions (of things not obvious outside of hypothesis.
    5.Report results to scientific community. May take many reports
    6.Theory: a hypothesis, or group of related hypotheses, that have been widely accepted. "Stood the test of time." A grown-up hypothesis. Some factors that lead to the acceptance of theories:
      a.Ability to explain known facts.
      b.Gathering of new facts in support of theory. Most important.
      More observations and repeated observations are best.
      Statistics: very important, but they don't always prove.
      c.Lack of facts that oppose theory. Experiments are often designed to look for such facts.
      d.Elimination of alternate theories. Opposite -- used to disprove a hypothesis in order to prove another.
      e.Usefulness of theory in relation to other ideas. Evolution, for example is useful.
      f.Length of time theory holds up.
      g.Simplicity or elegance of theory. Ockham's razor (Occum). Simplicity is accepted more because complexity looks like an excuse. Razor = cut away the unnecessary.
    7.No theory or hypothesis is ever absolutely certain. New facts may always lead to change. "Relative certainty"
    8.Beware of logical fallacies:
      a.Anecdotal evidence is backed only by a list of stories. False significance means the results work, but don't really prove anything, like using one mouse. Statistics can have false significance.
      b.Causality (something being caused) vs. Coincidence. Just because two things happened doesn't mean one caused the other.
      c.Bias: double blind procedures, that is when neither the patient nor the doctor evaluating them in a test know who does or does not have the drug -- both are blinded.
  C.Limits of science. Science is objective only, it cannot answer subjective questions about the meanings of events or moral/ethical/philosophical/religious questions. The strength of science, this, also defines the limits of it.
III.Case Study: Theory of Evolution by Natural Selection
  A.Background. Scientists felt living things were created without change at that time.
    1.Creationism: all living organisms created at  once and did not change: no prior cause. Everything that was made was unchangeable and perfect.
    2.Jean-Baptiste Lamark. In 1809, he was the first to seriously propose full-blown evolution of one species into another. Unfortunately, his details were all wrong, and his ideas were rejected: the inheritance of acquired characteristics. He coined "Biology." His proposed mechanism was the inheritance of acquired traits, which turned out wrong.
  B.The first successful attempt at explanation by Charles Darwin
    1.Born 1809, studied medicine but didn't like it, and the clergy but again found it not to be his area of interest.
    2.Influences
      a.Grandfather, Erasmus Darwin, a doctor, believed that all species were related by descent.
      b.Charles Lyell: geologist. Theory that the landforms of earth have arisen gradually over millions of years. Uniformitarianism is the theory that processes acting on the Earth today is the same as those that always were. Deep time is the theory that the earth is actually very old.
    3.In 1831-1836, Darwin sailed on the Beagle, and observed the natural world. The mission was to survay the coastline of South America, and Darwin was asked on as compainionship to the captain.
    Armadillo: was it descended from a similar animal now only found as a fossil?
    Finches on the Galapagos islands are far more diverse than elsewhere. Did they all arise by the modification of a species similar to those on the mainland?
    4.After Darwin returned home he paid his dues and made his name.
      a.He read Thomas Malthus: believed that many individuals were doomed to starve because population growth can always exceed the food supply. Competition. This is the key to natural selection
      b.Became a respected naturalist, but kept his developed ideas about evolution private. In 1858 Alfred Wallace was about to publish the same ideas, and Darwin had to join him in finally putting out papers, later book "Origin of Species" based on theory of natural selection.
  C.Theory of natural selection
    1.1st part: competition within the species
      a.Observation: all populations can and will outgrow resources.
      b.Observation: populations do not outgrow without limit.
      c.Observation: limits are imposed by resources.
      d.Conclusion (hypothesis): when population exceeds resources, competition results:
      e.Conclusion: some individuals fail to reproduce
    2.2nd part: variability in the face of competition yields natural selection
      a.Observation: members of population are variable for many traits, some of which are heritable (passed on to future generations genetically).
      b.Conclusion: some heritable traits are adaptive: they give the organism an advantage.
      c.Conclusion: natural selection is the result of the reprove advantage of organisms with adaptive traits/
    3.Change in traits (and genetics) of population: evolution, not into new species, but still changed.
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