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Biology 162--Freshman Biology for Science Majors, 2nd semester

The first half of the semester, Dr. Lago will cover structure and function of the major organ systems of animals, with an emphasis on human organ systems.  
The second half of the semester, Dr. McCook will focus on the amazing diversity of living things out there and the study of ecology.  I hope you will come to recognize that humans are dependent upon that diversity for the air we breathe, the food we eat, much of our building materials and fibers, our fuel.....even the clean water that we drink.  But for many professional biologists, including myself, it is a fascination with other forms of life that led us to our careers (and to really cool hobbies).

Links to information from Ecology section:

World food crisis a "Silent Tsunami":  http://www.nicholas.duke.edu/institute/water/eeewaterreport.pdf

Calculate your carbon footprint:  http://www.carbonbalanced.org/index.asp

Take a break from studying and send some rice to hungry people!:     http://www.freerice.com/

CHAPTERS & LEARNING OBJECTIVES FOR 2nd half of semester

Chapter 21: Origin & Evolutionary History of Life.      Read pages 447-454.  Learning Objectives 1-5.
Chapter 23: Biodiversity.                                            Read pages 482-493.  Learning Objectives 1-3, 8.
Chapter 24: Viruses & Prokaryotes                            Read entire chapter.  Learning Objectives 1-3, 6-11
Chapter 25: Kingdom Protista                                    Read entire chapter.  Learning Objectives 1-7, 9-10 (only groups covered in lecture)  
Chapter 26: Kingdom Fungi                                       Read entire chapter.  Learning Objectives 1-4, 6 (zygos & basidios only), 7-9
Chapter 27: Kingdom Plantae                                    Read pages 581-584. Learning Objective 1 and Alternation of Generations life cycle.
EXAM 3

Chapter 27: Kingdom Plantae                                    Read pages 584-587.  Learning Objectives 3, 5, 6, 8 & 9
Chapter 28: Kingdom Plantae                                    Read pages 600-602, 607-612.  Learning Objectives 1, 5 & 6.
Chapter 36: Reproduction in Flowering Plants            Read pages 767-770, 774-776.  Learning Objectives 1, 2, 5-7.
Chapter 29: Kingdom Animalia                                  Read pages 619-622, 630-636.   Learning Objectives 1 & 2, 4, 6 & 7.
Chapter 30: Kingdom Animalia                                  Read pages 640-641 & pages on taxa covered.   
                                                                                            Learning Objectives 1,  3-6, 9 (only groups covered in lecture).
Chapter 31: Kingdom Animalia                                 Read pages 667-668.  Learing Objectives 2,3 & 6 (only groups covered in lecture).
Chapter 52: Population Ecology                                Read pages 1126, 1129-1131, 1139-1143.  Learning Objectives 2, 3, 9-11.
Chapter 54: Ecosystems & the Biosphere                  Read pages 1166-1178.  Learning Objectives 1-2, 4. (only those covered in class)
Chapter 56: Global Environmental Issues             Read entire chapter and expect 3-4 questions on your exam from this important information.   
                                                                                       Focus on headings and highlighted terms---not tiny details.

Why aren't these infectious particles included in our formal classification of life?  We currently define "life" on the basis of cells and what those cells can do, such as reproduce, metabolize, gather energy, etc.  Viruses, viroids and prions are not cells, but particles of organic molecules that take over cells and use the host cell to reproduce the particles.  We are clearly interesed in them because they often cause disease, but they are everywhere and may have played a huge roll in the evolution of organisms.  In the future, will we change our definition of life to include these "life-like particles"?  Stick around and find out.

As discussed in class, most scientists now recognize THREE DOMAINS in SIX KINGDOMS based on recent molecular data.  Here is an outline of the domains and kingdoms we will study this semester.  Use this outline as you study to keep your thoughts in order and organize your notes.  Remember, there are more Phyla, Classes, Orders, Families, Genera and Species out there in nature.  We are just covering those that you are most likely to encounter or that are of particular importance to us or to the study of biology.
To see scientific data on the relationships among organisms, click on this site:
           http://phylogeny.arizona.edu/tree/phylogeny.html

            Also, consult APPENDIX C in your text for a complete classification--

Prokaryotes  are the most diverse organisms on Earth in terms of the range of metabolic processes included within the two major domains, Eubacteria and Archaea.  Here is a list of terms that we have already learned and that can now be applied to prokaryotes, as well as other taxa.  A discussion of each is included on pages shown.

DOMAIN BACTERIA
I. Kingdom Bacteria: Single-celled prokaryotes.  
    Two groups of Eubacteria covered in lecture are:
      1. Gram positives (including Lactic acid bacteria, Actinomycetes, staphylocci & streptococci)
       NEW RESEARCH!!  Using a phage to kill strep bacteria!!
       Info on anthrax from the CDC!!  http://www.bt.cdc.gov/agent/anthrax/
     
    2. Gram negatives (including E.coli, nitrogen-fixers, & Cyanobacteria)
          What are cyanobacteria? http://www.ucmp.berkeley.edu/bacteria/cyanointro.html
      
Learn more about Antibiotic Resistant Bacteria!!!

Learn more about Quorum Sensing:  http://www.nottingham.ac.uk/quorum/index.htm

DOMAIN ARCHAEA
II. Kingdom Archaea: Single-celled prokaryotes that are genetically and ecologically distinct from the Bacteria.
Many occur in harsh environments, and so they have been called "extremophiles". 
Click here for 2 great sites on Archaea      http://www.ucmp.berkeley.edu/archaea/archaea.html
                                                                 http://library.thinkquest.org/CR0212089/home.htm
3 groups of Archaea covered in lecture are:
    1. Methanogens.  See a student-posted page on these creatures:  http://microbewiki.kenyon.edu/index.php/Methanogens
     
    2. Extreme Thermophiles
       explore deep sea hydrothermal vents where thermophiles live!!        
                http://seawifs.gsfc.nasa.gov/OCEAN_PLANET/HTML/oceanography_recently_revealed1.html
                 http://www.ocean.washington.edu/people/grads/scottv/exploraquarium/vent/intro.htm

     3. Extreme Halophiles   http://library.thinkquest.org/CR0212089/halo.htm    

DOMAIN EUKARYA
        Includes all eukaryotic organisms, classified in 4 Kingdoms:
        Protista           Fungi                Plantae            Animalia

III. Kingdom Protista: Single-celled and multicellular eukaryotes of many kinds.   Chapter 24
This Kingdom is NOT a monophyletic group.  We simply do not know enough about them and so they are lumped into this giant taxon. Scientists will soon break this taxon into small units, but for now.....
We will cover 7 groups of Eukaryotes that include protists: see Table 25-1 in text!! 

IV. Kingdom Fungi     Chapter 26
Monophyletic group of multicellular (and some single-celled) eukaryotes.  All heterotrophic.
You can't have bread or alcohol without these guys (not to mention Athlete's Foot, or mushrooms on your pizza).  
  Fungi Photos!!!

We are covering 2 phyla in depth: 
        Phylum Zygomycota--bread molds
        Phylum Basidiomycota--mushrooms, shelf fungi & puffballs

V. Kingdom Plantae     Chapters 27 & 28
Multicellular eukaryotes.  All autotrophic. Four groups covered in lecture.
If you don't breath or eat, or wear jeans or take medicine, you really don't need to know anything about plants.
Link to plant photos:     http://images.botany.org/      
    Careers in Botany!!    http://www.botany.org/bsa/careers/

END MATERIAL FOR EXAM 1
Remember to bring your Scantron Form F-289 and your Student ID

Seedless Nonvascular Plants with a dominant Gametophyte Generation----The Bryophytes     Chapter 27
    1. Phylum Bryophyta--mosses            
                              http://scitec.uwichill.edu.bb/bcs/bl14apl/bryo1.htm

Seedless Vascular Plants with a dominant Sporophyte Generation---The Ferns and Fern Allies     Chapter 27
    2. Phylum Pterophyta--Ferns      
     A great website on ferns posted at Univ. Cal. at Berkely:
        http://www.ucmp.berkeley.edu/plants/pterophyta/pteridopsida.html

 Vascular Plants with Naked Seeds---The Gymnosperms      (heterosporous) Chapter 28
    3. Phylum Coniferophya---conifers, such as pine, cypress, fir, sequoia & redwood
        Can't afford to visit Sequoia National Park?  Visit this site and learn about the Giant Sequoias:   http://www.fs.fed.us/r5/sequoia/

Vascular Plants with Flowers, Fruits and Seeds---The Angiosperms   (heterosporous) Chapter 28 &  36 (but only what we covered)
    4. Phylum Anthophyta--the flowering plants

Check out this site, called eNature.com: http://www.enature.com/
It offers online searchable information from 35 field guides to over 4,800 plant and animal species.

VI. Kingdom Animalia We will study 8 phyla in Chapters 29-31.
Multicellular eukaryotes.  All heterotrophic.      
Animals R Us.  Plus, cockroaches, worms, sharks, owls, dinosaurs, crawfish, sponges,etc.
**Be able to use the terms describing symmetry highlighted on page 623 of text!!**
Check out the Animal Diversity Web!!http://animaldiversity.ummz.umich.edu/index.html
Or, visit this AMAZING site on animals:    http://www.pbs.org/kcet/shapeoflife/index.html       

PARAZOA---Asymmetrical animals with no true tissue development
    1. Phylum Porifera--sponges--see link below
           http://www.pbs.org/kcet/shapeoflife/animals/porifera.html
RADIATA---Radially symmetrical animals with tissue development from 2 embryonic germ layers
    2. Phlyum Cnidaria--cnidarians (corals & sea anemones, jellyfish & hydrozoans)
        Class Hydrozoa--Hydra---a hydrozoan
                      http://www.pbs.org/kcet/shapeoflife/animals/cnidaria.html

Go here for photos and info on sponges (Phylum Porifera) & corals (Phylum Cnidaria):
http://www.enature.com/guides/show_species_thumb.asp?curGroup=Seashore_Creatures&shape=1065

Bilaterally symmetrical animals with tissue development from 3 embryonic germ layers

PROTOSTOMIA
    Acoelomate animals
      3. Phylum Platyhelminthes--flatworms  http://www.pbs.org/kcet/shapeoflife/animals/platyhelminthes.html
                  To learn more about tapeworms on dogs and cats: http://www.marvistavet.com/html/body_tapeworm.html 
              Planarians- a Class of free-living flatworms.
              Don't miss the penis-fencing worms ( I am not kidding!) http://www.pbs.org/kcet/shapeoflife/episodes/hunt_explo2.html 
   
   Coelomate animals

        4. Phylum Mollusca--mollusks      http://www.pbs.org/kcet/shapeoflife/animals/molluscs.html
           a. Class Gastropoda--snails and slugs
                Do you love snails (with garlic)?  This site is for you: http://escargot.free.fr/eng/cooking.htm
           b. Class Bivalvia--clams, oysters, etc.
           c. Class Cephalopoda--octopods and squid:  http://is.dal.ca/~ceph/TCP/index.html
                  Action photos of a new species of deep sea squid     http://www.sciencemag.org/cgi/content/full/294/5551/2505/DC1
      5. Phylum Annelida--the annelids, or segmented worms
                      http://www.pbs.org/kcet/shapeoflife/animals/annelids.html
              Class Oligochaeta--earthworms    Learn about earthworms with kids--    http://www.urbanext.uiuc.edu/worms/                           
    
      6. Phylum Arthropoda--arthropods--includes spiders, crustaceans and insects
                                  http://www.pbs.org/kcet/shapeoflife/animals/arthropods.html
              Class Malacostraca:  Crustaceans
              Class Arachnida: Spiders
              Class Insecta: Insects.

                            
   DEUTEROSTOMIA---Deuterostome Coelomates
      7. Phylum Echinodermata--echinoderms, including sea urchins, sea stars, & sand dollars
                  http://www.pbs.org/kcet/shapeoflife/animals/echinoderms.html
               Class Asteroidea--sea stars   http://www.perspective.com/nature/animalia/starfish.html  

      8. Phylum Chordata--the chordates
                        http://www.pbs.org/kcet/shapeoflife/animals/chordates.html
           A. Subphylum Cephalochordata--Invertebrate chordates---lancelets
           B. Subphylum Vertebrata--Living classes of Vertebrate chordates include Mammals, Birds, Reptiles, Amphibians, and many groups of Fish.

Remember to bring your scantron, #2 pencil and Student ID to #FINAL EXAM.

You will not be allowed to take the final without your student ID.  No exceptions!!!
No electronic devices of any kind allowed in test.

 
ANALYZE YOUR TESTS!!
No matter what class you are in, you should always sit down and analyze a test after it is returned to you.  If you want to improve your grade, you must first determine the types of questions you are missing and then you can alter your study habits to reflect those needs.  Look for patterns in the kinds of questions that you missed and those that were correct.
Going over your test, ask yourself the following about the questions that you missed:

1. Was the material in my notes?
 If not, work on note-taking skills.   Go over notes in a study group.
 Beware!!!!  Other peoples' notes can be lousy or incorrect!!!  If you are skipping class and depending on others for notes, you could be hurting yourself immeasurably.
If the answers are in your notes but you still missed the question, you need to examine your study methods.

2. Did I miss questions covering particular topics?
As an example, did you miss most of the questions covering atomic stucture?  Then, you need to go back and work on that topic.  Knowledge of atomic structure is important for an understanding of how bonds form and molecules work, and is fundamental to an understanding of biology.  Also, it will be on the comprehensive final.

3. Did I miss questions covering straightforward details?
 Or, did I miss questions where I needed to have a broader understanding of a topic?
You need to understand both the details (the "little picture") as well as the "big picture".
When studying details, always stop and ask yourself:
 --Where is this happening?
 --What is its importance?
 --What other topics can I link directly to this?
 The summary at the end of each chapter in the book can be very helpful here.

Think hierarchically!!
 ---atoms, molecules, membranes, cells, tissues, etc.
 Organizing your notes may be very helpful here.

4. Can you find the correct answers using your notes or the book?
 Doing this will ensure that you come to an understanding of what you missed and why you missed it. And, you will be preparing for the comprehensive final!
 NEVER BE SATISFIED with "the answer is C" because you will not have learned anything.

5. Did you tend to miss the questions that offer multiple answer options (a & b are correct), or those questions that are phrased as a negative (which one is NOT correct?)?
These questions involve logic and reasoning.  You can improve your ability to perform these questions, and you must learn to be especially careful when answering these.

6. Are you "second-guessing" and changing answers on the test?
 If you have studied, have confidence in your knowledge.  Go with the knowledge you have, use your knowledge to work out questions that you are not certain of, and use that knowledge to think through difficult questions.  Only change an answer when you are certain----not when you are "second-guessing".
Remember---your ability to think during an exam is based on your knowledge and on your state of mind.  GET SOME SLEEP BEFORE EXAMS!!

Scholarships:

All pre-med. students, Air Force & Army Cadets, and Navy Midshipmen, are invited to attend a presentation given by COL. Charles Serio, Ph.D, Uniform Services University of the Health Sciences (USUHS), on Monday January 29th, at 2 P.M. at Old Chemistry Auditorium (Room 107)
If you are considering attending Medical School at USUHS and/or serving our country as a Doctor in uniform, you are encouraged to attend this presentation.
Questions? Coordination: Call LTC Bill Hollowell 915-7085, Army ROTC.

Here is a list of TERRIFIC web sites that offer opportunities for students interested in Biology.
My advice to you: invest an hour browsing these pages.    If you come up with some other sites of value, let me know and I will post them here.   Have fun......Dr. McCook

Join SCA as we celebrate our 50th year!
	SAVE THE DATE! The Student Conservation Association will be visiting the University of Mississippi on February 28 and 29! My name is Kat Deely and I am the Southeastern Recruitment Representative for SCA.  SCA is the leading provider of conservation internships in the nation and offers opportunities in such areas as Anthropology, History, Public Relations and Outreach, Biology, Natural Resources, and Project and Land Management to name a few. SCA interns complete over 1 million hours of service annually, receive outstanding career training, work on our nation’s land, and are even eligible to receive an AmeriCorps Educational Award. Please contact me if you or your students would be interested in learning more about the SCA experience. I would be happy to meet with you, give a class presentation, hold an information session, or speak with student groups. Thank you for you time, and we look forward to placing some of your students in an SCA internship this year. To learn more about SCA, visit us at www.thesca.org.

Cedar Creek Ecosystem Reserve, formerly Cedar Creek Natural History Area, 
offer several internships every summer for undergraduate and newly 
graduated students.  marot019@umn.edu. 

Great site for summer internships in all fields of biology--from natural history to medicine and engineering             http://www.yale.edu/necuse/

MOUNTAIN LAKE BIOLOGICAL STATION  www.virginia.edu/~mtlake
2008 Summer Courses and Undergraduate Research Opportunities 
     Our field station is located on a mountaintop in southwestern Virginia and is home to a lively research, teaching and social community.  For details on these programs, full course descriptions, application material, and a list of research areas see our web page: www.virginia.edu/~mtlake
    The Mountain Lake Biological Station (University of Virginia) announces credit courses in field biology, and paid research opportunities for undergraduates.  We offer students hands-on experience and training in a wide variety of biological field studies.  Join us for an exciting and unforgettable summer in a first-class field biology teaching and research environment. To see this seasons Courses:  http://www.virginia.edu/~mtlake/courses.html
MLBS home page - http://mlbs.org/
You can also contact us by email, mail, fax or phone:
  Mountain Lake Biological Station
  238 Gilmer Hall, PO Box 400327
  University of Virginia
  Charlottesville VA 22904-4327
  E-mail:  mtlake@virginia.edu
  voice:   (434) 982-5486
  fax:     (434) 982-5626

The Dauphin Island Marine Lab..Students interested in marine sciences must check this out!!!
http://www.disl.org

National Interniships--you must pay a fee to get their listings of regional interships, but they also give you lots of info about what to expect and how to apply.
http://www.internships.com

REAL JOBS in Biology & Related Areas

Biology careers--a listing of real jobs out there.  This is a terrific site to see the range of employment opportunites that biology majors have, and to see the experience employers are looking for!!
http://www.furman.edu/~snyder/careers/careers.html

A huge listing of real jobs out there in all areas of science all over the world!!    http://recruit.sciencemag.org/

Environmental Opportunities and Career Planning --- both summer internships and real jobs in environmental work, from research, to management, to computer & database analysis
http://www.ejobs.org

Pharmacological and Biotech Jobs in Human and Agricultural Sciences --mostly with private companies
http://www.symbiosinc.com

Careers in Botany!!  http://www.botany.org/bsa/careers/index.html