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HUMANS in NATURE

Biol 102
SPRING 2012
SECTIONS: .... 010, 011, 012, 013

11-Jan-2012 - 27-Apr-2012
Tues & Thurs, 12:40-1:55
Walters Life Sciences Bldg room M-311
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Instructor, Neil Greenberg
office / hours

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BlackBoard|My UTK

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"Humans in Nature" is not about nurturing 21st century biologists ... it is about seeing the large picture as well as key details about ourselves as organisms in a world of organisms. I hope we can appreciate the beauty and wonder of nature as well as thinking critically about the causes and consequences of specific phenomena in nature. The approach I will undertake will hopefully put biology as a discipline in the service of whatever you choose to emphasize as a life or career path.


CALENDAR | GRADING | LABORATORY


TEXTBOOK: Campbell Essential Biology with Physiology (3rd edition) (CEBwP3 or CEBwP3)

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SYLLABUS ALWAYS UNDER CONSTRUCTION
topics entered as they emerge from projected topics and as modified by emerging discussion and news; prospective future topics identified near approximate dates

weeks 1 & 2, introduction to the "heart" and "mind" of biology: biophilia and bioeconomics; optimality; levels of organization; disintegration and renewal

weeks 3 & 4, life and determinism: - "nature and nurture" - DEEP biology; the cascade of "Biological Needs" (adaptation, fitness)

WEEK 1 (Jan 12, 17, 19, 2011) "FRAMING THE PROBLEMS"
    (LAB: FIRST MEETING is week of JAN 17)
    (Arcane Word-of-the-Week: ARCANE WORD of the WEEK - Jan 17 2012.ppt
      TOPICS to be DISCUSSED:
      • FRAMING The intellectual context in which information is received influences how it is understood and used. Sometimes models and diagrams are more effective than narrative text
      • HUMANS in NATURE HOW we relate to NATURE: BIOPHILIA and BIOECONOMICS

      READ: (From TEXT (CEBwP3):
      • CHAPTER 1: in particular: "Properties of Life, Life at its Many Levels, Life in its Diverse Forms; Evolution; The Processes of Science; The Culture of Science; Science, Technology, Society; Evolution in our Every Day Lives."
      • Chapter 20: page on "Biophilia and an environmental Ethic" (pp 448-449)
      CONNECT ideas from text to ideas emerging in lectures: in particular: "Internal and external VALIDITY;" hierarchies and emergence, systems biology; biophilia (including Aristotelian "forms" of "philia"), emotions, pleasure; bioeconomics, proximate and ultimate costs and benefits; optimality principles; determinism; nature; nurture; epigenesis; Needs that living organisms must meet"

      QUIZ: available AFTER Jan 19 via Bb DUE by Monday, Jan 23 NOON: based on (1) LAB CONTENT about Galápagos relative to "levels or organization" &/or (2) "macro/micro trade-offs" from Powerpoint in "Framing" notes &/or (3) "VALIDITY" POSTPONED due to Bb issues.
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      TOPICS to be DISCUSSED:
      • "validity," "framing," hierarchies and emergence, systems biology
      • biophilia, emotions, pleasure
      • bioeconomics, proximate and ultimate costs and benefits; optimality principles
      • determinism; nature; nurture; epigenesis
      • Needs that we must meet

    WEEK 2 (Jan 24, 26) "DEEP BIOLOGY; CAUSES and CONSEQUENCES"
      (LAB: FORAGING ... relate to "optimality" in lecture)
      ARCANE WORD of the WEEK - Jan 25 2012.ppt
      "DEEP biology" is a nickname for an integrative perspective on biological phenomena. It contends that biological phenomena cannot be well understood from one perspective alone -- understanding and insight require a perspective that integrates the several different ways that biologists look at things. DEEP BIOLOGY for HUMANS in NATURE
      • (DEEP is an acronym for the four biological points of view that we will explore with a view to putting them in the service of providing an integrated understanding of biological phenomena and human affairs: It stands for DEVELOPMENT, EVOLUTION, ECOLOGY, AND PHYSIOLOGY)
      • brief summary:
        • Traits are adaptive if they serve fitness
        • DEVELOPMENT has FIXED and FLEXIBLE dimensions that are deployed as individual animals change as a result of programmed growth and coping with environmental experiences
        • ECOLOGY describes the context of life and the biotic and abiotic SELECTION PRESSURES that organisms must cope with
        • EVOLUTION reflects naturally selected changes in organisms that serve fitness and are transmitted BETWEEN GENERATIONS
        • PHYSIOLOGY describes the internal mechanisms that organisms use to maintain stability in the face of change

      • DEEP BIOLOGY - emphasis on ECOLOGY
          READ:
            • Essential Biology with Physiology: Chap 18 pp 372-379.
          TOPICS to be DISCUSSED:
          • Optimality
          • biotic and abiotic aspects of environment
          • adaptation


          OPTIMALITY is related to DETERMINISM: key points in Powerpoint attached below:
          NEW on Jan 31, 2012:
          OPTIMALITY and LIFE 2012.ppt


      • POWERPOINT OVERVIEW of CHAP 1 connected to some ideas from class:
      BIOL 102 - 2012 weeks 1-2.ppt
      • DEEP BIOLOGY - emphasis on DEVELOPMENT - including historical and cultural dimensions

          READ:
          • Essential Biology with Physiology:
            • Chap 14, pp 278-279 (development & evolution);
            • Chap 26 pp 562-564 (embryonic development);
            • Chap 11 pp 198-206 (gene regulation & communications between cells - cell signaling)

          TOPICS to be REVIEWED / DISCUSSED:
          • Biological "novelty;" "bricolage" epigenetic aspects of development
          • "determinism" and "nature/nurture" continuum
          • adaptation

          DEVELOPMENT and DETERMINISM, adaptation, genes, memes, fitness, and altruism
          • development relative to disease, to specific traits ... to "human nature" ...
          • determinism relative to national policy
              • Stalin's Russia: Lysenko's environmental determinism cost over 30 million lives in Russia and China;
              • Hitler Nazism and genetic determinism: WW-II cost over 70 million lives)

      QUIZ: At Last! available on Friday, Jan 27 via Bb DUE by Monday, Jan 30, NOON MIDNIGHT: including (but not limited to) (1) readings identified in BIOPHILIA and BIOECONOMICS link (2) "macro/micro trade-offs" from Powerpoint in "Framing;" (3) "VALIDITY" (4) "OPTIMALITY;" (5) "DETERMINISM;" (6) "BRICOLAGE"
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      WEEK 3 (Jan 31, Feb 2):
        (LAB: INTRODUCED SPECIES & BIOLOGICAL CONTROLS ... relate to "ecological homeostasis" in lecture)
        • DYNAMIC BALANCE; interactions: SYSTEMS
        • LIFE (what IS life??) ...Life as understood by research scientists is often profoundly INTERDISCIPLINARY in accord with the view that REAL LIFE is a profoundly interdisciplinary enterprise -- the divisions that scientists often create for convenience often become somewhat rigid and do not always take account of complementary views. At its most inclusive and rich, the study of humans in the environment take us from the epigenetic interactions of an individual's genome with its immediate environment through the highest ambitions of our species for self-actualization as manifest in its art and culture.
        • DETERMINISM: the essence of DETERMINISM


        OPTIMALITY is related to DETERMINISM: key points in Powerpoint attached below:

        WEEKS 3 &4: TOPICS to be DISCUSSED:
        DEVELOPMENT and DETERMINISM, adaptation, genes, memes, fitness, and altruism
            • development relative to disease, to specific traits ... to "human nature" ...
            • determinism relative to national policy
              • Stalin's Russia: Lysenko's environmental determinism cost over 30 million lives in Russia and China;
              • Hitler Nazism and genetic determinism: WW-II cost over 70 million lives)

              REVIEW PPT (also above) that comments on DETERMINISM and HOW we can identify "LIFE"
              OPTIMALITY and LIFE 2012 (3).ppt

          COMMUNICATIONS BETWEEN & WITHIN LEVELS OF ORGANIZATION: BEGIN WITH GENES!
          BIOL 102 - 2012 weeks 3-4 --2-2-2012.ppt

        • begin thinking about team presentations. 3-5 individuals will collaborate, propose a topic from the list provided. The outcome of a team project is a 10-12 minute Powerpoint presentation about the biology underlying a significant issue or concern. You can start with the EXAMPLES of POSSIBLE TOPICS for STUDENT PAPERS or PRESENTATION

      FOR EXAM 1, be very comfortable with use of the terms in black type ... the other terms will be explored in weeks to come. Adaptation, open/closed genetic programs, assimilate/accommodate, ontogeny, experience, epigenesis, costs and benefits of traits (morphological, physiological, behavioral) tabula rasa, biological constraints (on learning) preparedness, instinct, automatization, affect, rationality, non-conscious cognition, cognitive dissonance, pleiotropic, polygenic, teaching, learning (=behavioral plasticity & includes imitation, associative, & non-associative ...) social referencing. What are mirror neurons?




      WEEK 4 (Feb 7, 9): -- the essence of ECOLOGY
        (LAB: VARIATION & CLASSIFICATION / MOLLUSKS ... relate to "categories" and "bias" in lecture)

      TOPICS to be DISCUSSED: WHAT ARE the BIOLOGICAL NEEDS that Humans must meet?.
        • for example, play is a DEVELOPMENTAL phenomenon, what is its ECOLOGY?
        • MORE ABOUT team presentations. 3-5 individuals will collaborate, propose a topic from the list provided. The outcome of a team project is a 10-12 minute Powerpoint presentation about the biology underlying a significant issue or concern. The team may be asked to present this in one of the later class sessions.



      EXAM 1: Tuesday, February 7 ON-LINE (no class meeting on this day) open-book/notes; only 150 minutes; can be taken only ONCE and once you begin you must finish. Available on line through Thursday, Feb 9, 9AM


      Q 10 & POP-UP.ppt
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      WEEK 5 (Feb 14; 16) (LAB: exercise on PROTISTS) DEVELOPMENT continued, emphasizing its connections to ECOLOGY and need for COMMUNICATION
      READ:
      • TOPICS to be DISCUSSED: How communications serves the BIOTIC aspect of ECOLOGY: communicating with predators, prey, and each other.
      • communication
      • Competition and cooperation
      • Assigned: keep results in your own notes:
            • (1) what is the "channel" by which the reproductive process of slime mold is communicated?
            • (2) (connect to DEVELOPMENT): how do adjacent cells in a developing embryo communicate and
            • (3) Can cells "de-differentiate" ?? (connect to "STEM CELLS")
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      WEEK 6 (Feb 21, 23): ECOLOGY: attributes of the ecosystem and how humans in nature relate to them.

      biol 102 - 2012 - ECOLOGY PART 1 (2).ppt Feb 21, through "r & K selection"

      OPTIONAL: excellent paper or presentation themes: SPECIFIC ENVIRONMENTAL VARIABLES and their connections in BIOLOGY and CULTURE:
          INTERDISCIPLINARY APPROACH to INSIGHT about ECOLOGICAL VARIABLES --attributes of the niche-- and specific biological functions.


      Review modules in text that cover (chapter:section numbers are from old text; new text CEBwP3 must be searched):
      • 1.6 ("Evolution explains ...")
      • 1.10 ("Evolution is connected...")
      • 13.7 ("Units of Evolution"),
      • 13.8 (sources of genetic variation),
      • 13.9 (Hardy-Weinberg),
      • 13.11 (changes in gene frequencies in a population);
      • 13.12 (Natural selection);
      • 13.14 (sexual selection); and
      • 13.15 (example of evolution affecting public health)
      • 13.17 (imperfection)


      BIOLOGICAL TIMELINE PROJECT
      Science a few generations ago (1).ppt
      The Powerpoint above makes points about how hard it is to predict significant advances in science and associated changes in culture or life-style. It draws mainly on PHYSICS, but you are going to draw mainly on BIOLOGY


      INFORMATION to put in your NOTES inspired by
      discussion surrounding Dictyostelium:

      keep results in your own notes: (1) what is the "channel" by which the reproductive process of slime mold is communicated? (2) how do adjacent cells in a developing embryo communicate and (3) how is "differentiation" manifest?


      WEEK 7-8 (Feb 28, March 1, 6, 8): CONTINUE with ECOLOGY and ENVIRONMENTAL VARIABLES

      TRIALS of LIFE video: "Living Together" (in class Feb 28)

      (review biotic relationships in ecology)

      (review COMMUNICATIONS: BIOL 102. communication review.ppt)

      TRIALS of LIFE video: "Talking to Strangers" (in class March 1)



      MARCH 6-8-13 -- (LABS: Mar 1-4: FLATWORMS & PARASITES; Mar 8-11: HOMINID EVOLUTION)

      TOPICS to be DISCUSSED in CLASS: PBS / NOVA video on "Becoming Human, Part 3"
      • watch video AND complement video information with CEBwP3 text: Ch 17 on "Human Ancestry" pp361-368
      • Connect to specific previous "overarching" or "integrative" ideas:
          • REVIEW ideas about ECOLOGY ... for example check the link for ideas about "niche" & abort "r- & K- selection"
          • what were the constraints on r when comparing one evolutionary lineage to another, were there hits of "r-selection?"
          • Did human populations ever exceed K -- were there hits of "K-selection?" What were the fundamental and realized niches of competing lineages
          • any evidence for paedomorphosis or neoteny? (Ch14, section on developmental and evolutionary novelty; assigned to read on Jan 26)
          • How can we know about "cognitive" evolution - "consciousness" - evidence of imaginative forethought? ... what's the evidence?
          • LINK NOVA comments on SAPIENS-NEANDERTHAL genetic connections to recent articles on Neanderthal genes

      Lecture on what's so special about humans? by Bob Sapolsky (in class)

      COMPLEMENT with

      REVIEW from TEXTBOOK:
      ("Structural adaptations ...");
      ("Animals regulate...");
      ("homeostasis...")

      CREATIVE THINKING: our DEEP FUTURE and the FUTURE of NATURE in particular [words of the week: HOLOCENE and ANTHROPOCENE ]



      EXAM 2:
      After Class, Tuesday March 13 : ON-LINE (no class meeting on March 15)
      You must work alone but may use your book/notes; can be taken only ONCE and once you begin you must finish within 90 minutes. Available on line through Tuesday March 27, 9AM

      MARCH 19-23 is 2012 SPRING BREAK (no class on Mar 20, 22)

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      (Mar 27,29) MORE on "being human" WHO are you? WHO do you THINK you are? WHERE is your "SELF?" ... HUMAN DIVERSITY and BIODIVERSITY
      1. HUMAN "BEING" -- ON BEING HUMAN: genetic differences between humans and chimps are slight - so why are we so different:? Read Lee Dugatkin's recent blog entry
      2. BIODIVERSITY and STRESS - SELECTION PRESSURES present CHALLENGES to individuals, populations, and even communities: INTEGRATIVE (DEEP) BIOLOGY can consider these in terms of BIOLOGICAL NEEDS ... which are connected to MOTIVATIONAL SYSTEMS ,,, which are connected to STRESS RESPONSES.
      3. A new organizing theme : physiological phenomena that integrate development, ecology, and evolution: Complete your mastery of STRESS from the PHYSIOLOGICAL perspective and consider its influence of the processes seen in DEVELOPMENT, EVOLUTION, and ECOLOGY (see Powerpoint embedded in PHYSIOLOGY link). For example, be confident in your understanding of how it is CONNECTED to AUTONOMIC NERVOUS SYSTEM reflexes that are (a) essential for maintaining HOMEOSTASIS as well as (b) contributing to important COMMUNICATIVE SIGNALS. How does stress affect SEX (see Feb 16, 2012)
      4. Homeostasis involves multiple physiological systems that respond to each other and interact to enable us organisms to cope with change -- that shouldn't be news to you this week ... but apply the principle to the BRAIN and its multiple specialized modules. -- brain representation and coordination of the organism's functions are reasonably easy to understand, but are we our MINDS? What is meant by the idea of a "cerebral symphony" ... and the "juggling act" that involves every biological need we have!

      TARGET READINGS/VIDEOS:
      1. "Our Brain are Getting Smaller..." (connect to "domestication," intelligence, conspecific sociality, autism)
      2. "My Stroke of Insight" (connect to "balance of areas neural activation")

      THURSDAY, March 29 -- no class: take quiz (on-line)
      (April 3, 5)

      BIODIVERSITY
          • what does the snail darter represent?
          • what does the "canary in the cage" represent
          • HOW does one measure the "health" of an ecosystem?
          • what are the most likely causes of the several "great extinctions?"
          • how does the adult version of "intolerance of delaed gratification" bear on concerns about a healthy ecosystem?
      • REMEMBER to consider levels of organization when thinking about ecosystems: for many people, an unexpected "level of ecosystem thinking" involves the fact that WE (human beings) are also ecosystems with countless organisms within us -and we need each other) (exercise: consider the HUMAN BEING as an ECOSYSTEM)

      ALSO read:
      (Fri April 6 is SPRING RECESS)
      (April; 10, 12):
      • ALIEN SPECIES INVADING our ECOSYSTEM? Read Pimentel et al. 2005 -- what is the annual value of introduced species? the cost? what about human diseases, diseases of domesticated animals or plants?
          • "alien species in the United States cause major environmental damages and losses adding up to almost $120 billion per year.
          • There are approximately 50,000 foreign species and the number is increasing.
          • About 42% of the species on the Threatened or Endangered species lists are at risk primarily because of alien-invasive species."
          • "Most plant and vertebrate animal introductions have been intentional, whereas most invertebrate animal and microbe introductions have been accidental."
          • "About 20 species of mammals have been introduced into the United States; these include dogs, cats, horses, burros, cattle, sheep, pigs, goats, and deer (Layne, 1997)." How serious are introduced pests in the Smoky Mountains?
      • EFFECTS of DISEASE on an imuunologically inexperienced population: Read "Population history of indigenous peoples of the Americas" --

      CONTINUE WITH BIODIVERSITY (review: BIODIVERSITY AND MORE ABOUT WHY WE SHOULD CARE about BIODIVERSITY - what needs are being met)
      April 12: in class "class participation" QUIZ: be prepared to comment in class on this recent article about conservation initiative in Mexico from the NY Times: (ARCHIVE VERSION); Comments should involve connections between article and previous assigned web readings (indigenous peoples, alien species -Pimentel et al) on the reasons for preserving biodiversity and the HUMAN NEEDS met (see Feb 7 on "BIOLOGICAL NEEDS that Humans must meet" revised Powerpoint presentation at DEEP site) in-class questions: (a) alien species in Europe originating in the Americas (b) Tennessee had its first brush wit "Africanized" bees ... how are bees "Africanized"? (c) Pimentel article monetized the effect of alien species at about $120 billion in their 2004 article ... what is a good RECENT estimate?
      Buddy Quiz Rules.pptx

      (April 17, 19):
      CONSERVATION
      • APRIL 19: PRESENTATION in preparation for your visit to Knoxville Zoo; Samantha Ogle-led presentation on teaching biology in primary school
      • FOR YOUR ZOO VISIT: schedule of activities and "KEEPER CHATS." Your ASSIGNMENT is to apply your experience and explicit information you learn at the Knoxville Zoo to questions that emerge from reading the more general assigned "RESOURCES for the role of zoos in conservation" (above as America Zoos Info and http://unitedforconservation.org/ ) A major source of explicit information will be one or more of keeper chats in the attached flyer:
            • H&N 102 Spr 2012 chat schedule for UT.pdf ... 2012 Sheela Hira in-class KZG PRERSENTATION.ppt

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      (April 24, 26):
      SPECIAL TOPICS & PRESENTATIONS
          SPECIAL PRESENTATIONS Classmates and conclusion
      OVERVIEW of OPTIMALITY and FREEDOM for H&N 2012.ppt

      APRIL 26: TARGET DATE FOR FINISHED PAPERS; (LAST class meeting)

      APRIL 27: last day of all classes

      MAY 7: EXAM deadline for completion: 2:30 PM


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      scheduled time for BIOL 102 FINAL EXAM: MONDAY MAY 7: 12:30

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      RECOMMENDED RESOURCE: ... B:C&C -- BIOLOGY: CONCEPTS & CONNECTIONS (6th edition) by Neil Campbell et al. (2006) is a valuable resource ... its modular organization will let us pick and choose specific sections that will provide important information. These key sections will be identified in the syllabus and available at the library

      VIEWING: selected episodes of video series ...

      OTHER READING: essays, research reports and book sections identified during the semester, often linked to the website
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      GRADING
      there will be over 800 point opportunities represented in EXAMS, QUIZZES, class attendance and participation.
      cumulatively, this will be 80% of the final grade
      LAB = 20%
      MORE about BIOL 102 GRADING

      UT official grading policy for +/- grades

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      Students who have a disability that require accommodation(s) should make an appointment with the Office of Disability Services (974-6087)
      to discuss their specific needs as well as schedule an appointment with me during my office hours.

      .CAUTION: some subjects are known to hurt your brain, if this happens, click on the nearest butterfly


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      APPENDICES

      2012 SPRING COURSES
      TYPE
      TIME
      PLACE
      Lecture
      12:40PM- 01:55PM
      Walter Life Sciences Building-M311
      Lab Sec 10 (24575)
      03:35PM- 05:30PM
      Neyland Drive Biology Annex-119
      Lab Sec 11 (24577)
      05:45PM- 07:35PM
      Neyland Drive Biology Annex-119
      Lab sec 12 (24578)
      03:35PM- 05:30PM
      Neyland Drive Biology Annex-118
      Lab Sec 13 (24579)
      03:35PM- 05:30PM
      Neyland Drive Biology Annex-118



      Spring 2012 Semester
      Classes Begin . . . . . . . . . . . . . . . . . . . . . .Wednesday . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Jan. 11
      MLK Holiday . . . . . . . . . . . . . . . . . . . . . . .Monday . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Jan. 16
      1st Session Ends . . . . . . . . . . . . . . . . . . . .Wednesday . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Feb. 29
      2nd Session Begins . . . . . . . . . . . . . . . . . .Thursday . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .March 1
      Spring Break . . . . . . . . . . . . . . . . . . . . . . .Mon-Friday . . . . . . . . . . . . . . . . . . . . . . . . . . .March 19-23
      Spring Recess . . . . . . . . . . . . . . . . . . . . . .Friday . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .April 6
      Classes End . . . . . . . . . . . . . . . . . . . . . . . .Friday . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .April 27
      Study Day . . . . . . . . . . . . . . . . . . . . . . . . .Monday . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .April 30
      Exams . . . . . . . . . . . . . . . . . . . . . . . . . . . .Tues – Tues . . . . . . . . . . . . . . . . . . . . .May 1, 2, 3, 4, 7, 8

      may 24, 2012