Welcome to General Zoology
CSM Biol 210, Bucher

A course in animal biology for science majors.

The students most likely to succeed will be those who have met the prerequisite of MATH 120 or 123 or the equivalent and completed a college-level biology course with lab and a college-level chemistry course with lab. In this class we begin by considering what an animal is, has, and does. We will look at:

Student Learning Outcomes

By the end of this course students will be able to:

Course Description from CSM Catalog:

Introduction to principles of animal biology. Includes the molecular basis of life, structure, function and behavior. One or more field trips may be required. Extra supplies may be required. Plus one hour by arrangement per week. Prerequisite: MATH 120 or 123 or the equivalent. Recommended Preparation: eligibility for ENGL 800; successful completion of a college course in biology with laband a college course in chemistry with lab. (5 units) (CSU/UC) (CAN BIOL 4)

Required tools and materials:

Textbook (see current Syllabus and Calendar for details), a bound laboratory notebook (see Lab Notebook link below for description), and after the 6th week gloves and perhaps dissecting tools (scissors, scalpel, mall probe, forceps).

Downloads

Initial Downloads The ones you'll need to start the semester are the Syllabus, Calendar and information on Lab Notebook format and content.

Lab Exercises (Preview only. Some of these are undergoing revision. As long as this statement persists here these should not be considered final versions.)

Field Trip Downloads One or more of these may be required, optional, with or without extra credit. Ask.

Study Guides (Some of these may be out-dated; replacement in progress.)

Initial downloads for this course for Spring 2010!

210 Lecture & Lab Schedule Calendar of assignments, to pics, exams, key dates, etc.

210 Syllabus Course expectations, contact info, texts, key dates, etc.

Lab Notebooks Some words about your own "Q" Document, the bound volume that contains your original observations; sketches; thoughts; measurements; hypotheses; predictions; experimental designs, protocols, results and tentative conclusions.

Notebook Minimal Content Outline of what-to-include in lab notebook entries.

Basic Logistical Files

How to Create a Great Poster The title says it all.

How to Take Perfect Notes Reformatted from an entry at WikiHow to print on a single page.

Concept Map Introduction to Concept Mapping, a very useful tool for organizing information, note-taking, pre-writing.

evolutionmap.pdf organizes some of the basic ideas related to organic evolution into a Concept map. The map was created using a computer application called Inspiration. You may print out the map, then expand it or simply add your own handwritten notes as a crib sheet. OR you can download a trial copy of Inspiration from www.inspiration.com and install it (versions for Mac and Winblows are available) and make your own.

If you don't have a copy of the Acrobat Reader, it is free.

Your first assignment:

Send me an e-mail message (to link to e-mail address) that includes the 3-digit course number (210) and your real name in the Subject line and tell me what you intend to accomplish this semester and what you see as the barriers, if any, to reaching your goals.

Don't have an e-mail account?

Excuse me, but you have at least one. It was issued to you when you enrolled in this or a previous course offered in the San Mateo County Community College District. Please use it as it will be the one to which your instructors and the college will send important information. If you wish, you can have mail addressed to your yourname@my.smccd.edu account forwarded to another account of your choosing.

There are several good reasons for having one of these accounts:
 

1.

they are not dependent on your being at your own computer, so you could pick up your mail anywhere you could get on-line;

2.

they aren't dependent on your keeping the same job or Internet Service Provider;

3.

they are easily abandoned if you happen to get on a "spam" list and start receiving a lot of unwanted e-mail at that address.

Some possibilities, assuming you already have Internet access:

gmail.com Like your @my.smccd.edu account a regular Google's Gmail provides lots of storage area and access to online applications for wordprocessing, spreadsheets and presentations. It also provides space and tools for creating web pages, a function not supported by the @my.smccd account.

Yahoo Mail Yahoo has also expanded its storage capacity

Laboratory, Field Trip and Extra-Credit Files for 2010

Week Topic Required files Other files & links Details

1

Industrial Melanism 1-page deconstruction of a classic experiment and evidence for natural selection in accounts of Pepper Moths.

"On Being the Right Size" The classic essay by J.B.S. Haldane on issues of size and scaling.

The case of IM

Submit your response to the last question in the IM case by e-mail.

Comment on the risk of taking on Godzilla.

2

sample graph

Spreadsheet Tutorial is a review of electronic spreadsheets as a tool for taming numerical data.

An almost identical Google spreadsheet of this tutorial is available for those who choose not to use Excel.

Submit a copy of your Desert Iguana graphs.

2

nematode mouth

Mitosis & Worms

http://www.wormclassroom.org/ge/cellDivision.html

 

2/3

image of fruit fly
Virtual
Genetics Lab

Intro to VGL
VGL Report

Virtual Genetics Lab is loaded on lab laptops already. For practice at home download your own copy of VGL. VGL 1.4.2 Here are the CSM VGL practice problem

 

4

Punnett square modified for Hardy-Weinberg calculations

Evolve "To Change Gene Frequencies is to Evolve" introduces population genetics and the simulation software called Evolve which will be demonstrated by the intructor. Newly ported to Mac OS X is Evolve3.0.7.6, software to simulate and manipulate the parameters of Hardy-Weinberg Genetics and doing "what if" experiments in evolving populations. Instructions will be given in lab, but amanual developed for version 2 might be helpful too.

 

 

5

small family tree

hemoglobin molecule

Globin1 Use a BioSkills Tool Kit on family trees, phylogeny, DNA databases (in Globin2), cladistics and so much more.

ESTEEM module: EvolSeq. Here is a set of "Distance Matrices" from which to construct "family trees. Try some of the simpler ones (3 to 6 differences) before showing the upper triangle matrix of one with 9 sequences together with its tree.

Log into a supercomputer to access DNA sequence data to get like regions of a few species' genomes; align them and analyze similarities and differences for a new look at who's related to whom.

Is "Intelligent Design" just creationism masquerading as science? Watch the Nova episode on-line http://www.pbs.org/wgbh/nova/id/program.html and decide for yourself.

6

small cladogram

"Taxonomy and Cladistics" This is a link to a site developed by the publisher of the Lab Manual. It provides interactive exercises as well as tutorial review material to support your understanding of issues in animal classification.

   

6

       

7

       

8

 

 

 

 

9

Cnidaria:
chitons, snails & slugs, clams & oysters & mussels, octopi & squid & cuttlefish, and tusk shells

Classically zoology labs have included surveying and learning to recognize representative members of each taxon studied—usually as preserved specimens—and reinforcing that learning with sketches of them. I have long discontinued the practice, but notice that the ability of students to identify and assign animals correctly to their respective phyla, classes or orders has suffered. This semester a new assignment will be associated with specific taxa. It will have several parts to be worked in pairs or singly:
1] Use the software application Inspiration® to produce a cladogram of the specified members of the group under study;
2] Use Safari or Firefox to search of the Internet for a clear image of the assigned animal (begin with the MIller/Harley Zoology website, select a chapter and follow “Relate Web Links” under More Resources);
3] Use the Tools command in Preview: Adjust Size… of the image to a height of 72 pixels and Edit > Copy the image;
4] Select the name of the animal or group in the cladogram and Paste the image.
5] Make any needed adjustments to the arrangement of your cladogram; add a title and your names.
6] Print… the cladogram as a PDF and e-mail it as an attachment to yourself and to me. Save the cladogram as an Inspiration 7 or 8 document and e-mail it to me. Print the PDF file at home and trim it for inclusion in your lab notebook.
To assist you there are two files to download as models. an Inspiration 7 file and a PDF. You can open the first file with the Inspiration application loaded on the Biology Lab iBooks. You might Save as… “test” or similar, play around with its elements to better understand the program. For your first cladogram assignment you could modify the Cnidaria cladogram, replacing its genera with the assigned clades (and images of same) and changing the synapomorphies with ones more appropriate to the Mollusca. You may also start from scratch with a new Inspiration document.

The instructions above and the two versions of the Cnidaria cladogram are in a zipped folder for Cnidaria.

Cladograms as Concept Maps consists of the directions at left and the Cnidaria cladogram. It is also in the zipped folder for Cnidaria with the other two files.

 

10

       

11

       

12

       

13

       

 

What's "Intelligent Design?" Is it just creationism masquerading as science? Watch the Nova episode on-line http://www.pbs.org/wgbh/nova/id/program.html and decide for yourself.


Introducing VGL
constitutes an orientation, guide and strategic hints for using the Virtual Genetic Lab (VGL 1.4.2) to simulate the breeding of fruit flies and to test hypotheses about how specific traits are inherited. You can download VGL 1.4.2 for Windows or Mac and a form to record results of selected problems in VGL Report. Here are the CSM VGL practice problems: (This is a compressed Zip file of a folder containing: 01autoCodom.prb; 01autoSimple.prb; 01XYcodom.prb; 01XYsimple.prb; 01ZWcodom.prb; 01ZWsimple.prb; 03autosomal.prb; 02SexLinkCodom.prb; 02SexLinkSimple.prb; 03Codom.prb; 03sexLinked.prb; 03simpleDom.prb; 04ChallengeSet.prb. That folder (once decompressed) is named "Problems" and should replace the one downloaded with VGL 1.4.2; alternatively the files named above could be added to those with names like "level01" in the Problems folder that came with VGL.

tiny image of mammal supertreeMammal Supertree. A recently developed "family tree" of all the mammals based on analysis of published DNA differences. Download and then zoom in the radiating colored lines in the outer ring. Each line is actually the Latin name of a species of mammal. If you don't recognize these scientific names, go to http://www.alltheweb.com, enter the Latin name in the search field and click on the word "Pictures" to see what it looks like.

VertCompAnat is a set of indications to follow in the examination of vertebrate skeletal specimens arrayed in the lab.

Littoral Meaning Field trip directions and map to Princeton Harbor and tidepool area.

Tidepool Field Trip Field trip directions and map to Bean Hollow State Beach and its tidepool area.

thumbnail image of the scavenger hunt document
Intertidal Scavenger Hunt: find animals that bring these features to the intertidal zone.

map of Bali and Lombok and strait between them
Island Biogeography introduces a problem case: several dipterists want to enlarge their collection of exotic flies and are considering a number of different island destinations. Make a supportable, reasoned recommendation regarding the best insular hunting ground for their purpose. Derive suitable hypotheses by examining several data sets from other islands contained within the Excel file Island Biogeography.xls. Additional help might be found in David Quammen's Song of the Dodo: Island Biogeography in an Age of Extinction, Scribner. ISBN 0-684-82712-3 or in Alfred Russell Wallace's The Malay Archipelago, the land of the orang-utan and the bird of paradise; a narrative of travel with studies of man and nature a founding work on the topic available to download free from gutenberg.org.

Academy of Science (the California Academy of Sciences has been reopened in its original location for a year and half now. Regard the following file(s) as relevant to the new location.

These are appropriate for Spring 2010 and may retain some relevance as perennial exams undergo evolution and continuous improvement.

Genetic Concepts Conceptual terms and vocabulary necessary for first exam.

Darwinian Concepts (Revised 18 Feb 2010) Conceptual terms, short answer question previews and vocabulary necessary for second exam covering evolutionary topics.

Ascon to Ascaris Conceptual terms, short answer question previews and vocabulary necessary for third exam covering Porifera, Platyhelminthes, Rotifera and Nematoda.

Coelomate Invertebrates Taxonomic and conceptual terms for your active vocabulary and S.A. question previews

Vertebrates Taxonomic and conceptual terms for your active vocabulary and S.A. question previews.

Frog Parts.pdf Anatomical features of the frog (Rana) that every young zoologist should know.

Pig Parts.pdf Anatomical features of the fetal pig that every young zoologist should know.

Final210S.G. Anatomical and conceptual terms for your active vocabulary and S.A. question previews.

Name the taxon Here is a pictorial review of the majority of the phyla, subphyla, classes, and orders most likely to appear on the Animal Identification part of the final. If you have Powerpoint, download taxa.ppt which is 13.3 MB in size; otherwise download taxa.pdf which is much larger 37.8 MB. Consider downloading taxa.ppt and then uploading it to your my.smccd.edu account for viewing with GoogleDoc's online presentation software.

 

Some are concepts maps, some are presentations developed using Apple Inc.'s Keynote software and exported as PDF files.

Concept Mapping: how and why you might make notes or pre-write in visually holistic fashion. Software available at www.Inspiration.com can facilitate the process of organizing information.

Cellular Issues for Animals: a concept map reviewing key elements of animals organization at the cellular level.

Eukaryotic Nuclear Division a concept map summarizing elements of mitosis and meiosis.

Gene Stuff a concept map reviewing connections among chromosomes, DNA and Mendelian genetics.

Industrial Melanism: a concept map relating to the "case study" of the same name. The map also includes T.H. Huxley's outline of natural selection. From the "Case of Industrial Melanism" page one can download a single page summary of that case to compare to the concept map.

Photoperiodicity: a concept map relating to the impact of changing daylength on the lives of animals.

Cnidaria An overview of mostly marine diploblasts with unique weapons (cnida), comprising a cladogram within a concept map.


Pseudocoelomates An overview of Rotifers and Nematodes.

Mollusca An overview of "softies."

Annelida An overview of segmented round worms.

Arthropoda Map A concept map of the most diverse phylum. You may be asked to construct such maps yourself.

Hexapoda An overview of insects and their near relatives. A key to selected insects as an editable Inspiration document and as a PDF.

Bees An overview of a social insect.

Echinodermata An overview of the pentaramous deuterostomes, comprising a concept map with cladogram.

Chordata An overview of affinities among the Urochordates, Cephalochordates and Vertebrates.

Pisces An overview of the largest group of vertebrates, comprising a concept map about fish with cladogram. [Missing. Awaiting a volunteer to create it.]

Amphibia An overview of the first terrestrial deuterostomes, comprising a concept map with cladogram.

Reptilia An overview of the first real conquerers of dry land, comprising a concept map about "creapers" with cladogram.

Aves An overview of those "highly glorified, endothermic, flying reptiles," comprising a concept map about birds.

Mammalia: An overview of the warmest, the furriest, the cuddliest and smelliest animals of all, comprising a concept map about mammals with cladogram.

thumbnail image of a sarcomere
Muscle Physiology, an assemblage of textbook and Internet images with minimal commentary on the organization and functioning within the "sliding filament model" of muscle contraction.

Neurophysiology introduction looks at neuron structure and function, including resting potentials, conduction and transmission of action potentials. This leads to consideration of simple innate circuits to mediate response to specific stimuli: Reflexes. More involved are reflexes with inhibitory components, which leads to sensory use of Inhibition to make perceptions better resolved.


Endocrine
Introduction to mammalian endocrine concepts. Endocrine Map connects the concepts.

Circulation gets the goods and wastes delivered when simple diffusion just isn't good enough

Respiration is required by all animals, respiratory systems by the larger ones.


Desert Denizens
Two distinct strategies tied to body size for coping with the combined challenges of keeping hydrated and maybe even cool in an arid place.

Reproduction in mammals has shifted in efficiency and subtlety and produced some startling results in anatomy as well as behavior.