Course Syllabus

Biology 10B

Diversity of Life on Earth:  Structure Function and Ecology

 

Prerequisite: Chem 001A and Biol 010A. 

Explores the diversity of living organisms, the structure and function governing their form and function, and the ecological principles that guide their interactions. Second in a 3-course series for Biology majors (Biol 010ABC). Total of 54 hours lecture and 108 hours laboratory. 
Transfer Credit: CSU; UC

   Student Learning Outcomes (SLOs)

When a student successfully completes this course they will be able to;

1. Identify and characterize the diversity of life at the phylum level and critically evaluate the hypotheses regarding the overarching phylogenetic patterns. 

2. Explain the major patterns in the form and function of organisms across the diversity of life uniting cell structure and anatomy with the physiology of their function.
3. Critically evaluate current theories governing our understanding of population, community, and global ecology and their relationships to evolution of life on earth.

 

Materials

Books

1. Textbook:  Campbell Biology, Reece, Urry, Cain, Wasserman, Minorsky, Jackson,

10^th Edition, Pearson ISBN 10:0-321-77565-1

2. Notebook - wait until first day of class for options

 

Instructor Information

Russell DiFiori   redifiori@pasadena.edu

Office: 

Office Hours:

Monday 1-3PM (every other will be live online through Canvas)

T R  11AM-1PM & 6-6:30PM

W  8-8:45AM & 3:30 -4:30PM at Field Site 

What I’m Teaching Fall 2016:

Biology 14: Field Biology  (4 units)

 73855 8:45AM – 11:55 PM  &  70159 12:15-3:25 PM  W

Biology 10B Diversity of Life on Earth: Structure Function and Ecology (5 units)

72633  T R    1 - 2:25 & 2:30 - 5:40PM  SV 32

 Physical Sciences II, Scientific Method as Critical Thinking

74355   Online

 

Structure: Full online or Web enhanced and Project Based

All of my classes are web enhanced and the online portion of the class is delivered through CANVAS (https://canvas.pasadena.edu/).

Note: If you do not have access to a computer off campus, there are many computer labs on campus you can use to participate in the course. Most public libraries also have computers with internet access that you can use for free.

 Requirements

 You will need:

1. Internet access for the CANVAS (https://canvas.pasadena.edu/) site and you should check the browser and system requirementson the PCC Distance Education website. 
2. Transportation to field sites, entrance & parking fees.
3. Willingness to work in teams on projects and communicate regularly with team members
4. The text book

 

Communication

Etiquette: It is expected that everyone in the class will demonstrate professionalism in all communications and interactions both in person and online.  

Turn-around/response:  I will normally respond to any email or message within 24 hours typically I review all messages first thing in the morning and respond at that time unless I need to do some research or look something up first.  Grading and comments on work will normally be within one week of your submitting or posting your work.

 Announcements:  I may post an Announcement  just to keep everyone up on what’s going on in the class and I may use additional announcements for special occasional like a change in our meeting locations.  I will try to avoid any same day changes but may post something the night before or meeting in an emergency.  Be sure to check all Announcements for this class.

Email: Message me anytime through Canvas and I will respond within 24 hours.  The message system through Canvas is linked to an email address so you can also use that function for any questions you may during the class. Always put a clear topic in the subject heading of your email and be sure your name is somewhere in the email.                      

Policies 

Drop :  If you want to drop the class you must do it yourself before the drop deadlines to be sure of your status.  That being said, if you do not participate for 2 weeks you may be dropped by the instructor.   If you attend but do not submit work at a passing level you may be dropped at any time.

Student Conduct :  It is expected that you will meet the standards of the Pasadena City College policy of Student conduct.   Cheating or plagiarism of any kind can result in an F in the class.  Your behavior at field sites reflects upon our whole class and can influence how future classes are treated when we visit locations around Los Angeles and I take this very seriously; we will always leave a site better and cleaner than we found it and treat people with a courteous manner where ever we go.

Participation

 It is expected that you will do the weekly assignments in during their open periods and participate in a meaningful way in the discussions and comments.  Superficial and uninformed participation will be result in a lower grade.  It is also expected that you will attend all meetings and be prepared and on time every time.   

Grading

Grade or Symbol Meaning interpreted from the PCC general catalog:

A Excellent ............... 4 HONOR GRADE indicating EXCELLENCE earned as a result of:

1. consistently superior examination scores;

An A grade on at least 1 practical exam (passing on the other) and A's on 2 of the 4 written exams (passing on the others)

2. consistently accurate and prompt completion of assignments;

Passing grades on 90% of all coursework turned in on time and

3. ability to deal resourcefully with abstract ideas;

A grades on at least 2 written exams, overall A grades on the ePortfolio and Notebook 

4. superior mastery of pertinent skills;

A grade on one of the practical exams (passing on the other)

A grades on at least 3 major projects (poster – papers- debates), and passing grades on all other major assignments in the ePortfolio

5. promise of success in a field relating to the subject.

Demonstrated by the achievement in 1-4 above and satisfactory completion metacognitive assignments 

To earn an A grade in the class in addition to the necessary A grades mentioned above, the grades that are not A's must be at least a C.  Thus you must still pass all assignments even after you have secured an A in the class.

 

 

B Good ........................... 3 HONOR GRADE indicating COMPETENCE earned as a result of high examination scores; accurate and prompt completion of assignments; ability to deal well with abstract ideas; commendable mastery of pertinent skills; promise of continued success in sequential courses.

Specifically you can replace the A grades in the description above with at least a B grade and you will have the definition for an overall B grade.

 

C Satisfactory ...................... 2 STANDARD COLLEGE GRADE indicating SUCCESSFUL PERFORMANCE earned as a result of satisfactory examination scores; generally accurate and prompt completion of assignments; ability to deal with abstract ideas; fair mastery of pertinent skills; sufficient evidence of ability to warrant entering sequential courses. A “C” is the minimum course grade necessary to meet a prerequisite.

Specifically you can replace the B grades in the description above with at least a C grade and you will have the definition for an overall C grade.

 

D Less Than Satisfactory ............... 1 SUBSTANDARD GRADE indicating the MEETING OF MINIMUM REQUIREMENTS ONLY earned as a result of low examination scores; generally inaccurate, incomplete or late assignments; inadequate grasp of abstract ideas; barely acceptable mastery of pertinent skills; insufficient evidence of ability to make advisable the enrollment in sequential courses. A grade of “D” would indicate the student is not likely to be successful in a higher level course and would not meet prerequisite requirements.

 

 

Special Needs

Please let me know if you have adaptive software and hardware to assist you with taking this course or if you have any specific needs I should be aware of. The PCC Disabled Students Programs and Services Department (RM D209) is available to assist you during this course. You can also email dsps@pasadena.edu or call (626)585-7127 for assistance. 

 

Additional Resources

Distance Education Website:  online.pasadena.edu

Tech Support : If you need technical assistance at any time during the orientation or to report a problem you can contact PCC’s 24/7 Technical Support Center at http://online.pasadena.edu/canvas-support.

You can get in-person help on-campus at the D Building Learning Assistance Center. Tutors at the center are trained to help students with CANVAS and its tools.

There are many services on campus to help you achieve success in your courses. Check out this Student Services link for information on 24/7 library services, online tutoring computer lab hours and research help.

 

 

Biology 10B Itinerary / Schedule

Week 1

Day 1   Aug 29

1) Role, admission and Introduction to the class with a review of the Syllabus.

Notebook styles and choice

2) Maximum Diversity (Max D): View 2 Unknown samples under the microscope – asking questions about observations

Diversity defined & which sample is more diverse and how do you know? How do you measure diversity?

Workshop – what factors influence diversity? Experimental design to answer this question and what do you need to know?

3) Animal Phylogeny debate Introduction

Article Presentation Team formation time for team planning & How to read a scientific paper

 

Before the next class

Read you article for the debate team so you can contribute to an outline of the major points.

 

Day 2    Sept. 1

1) Paper presentation planning – putting together the presentation (for a 15 minute max presentation).

2) Max D project: Designing an experiment to test diversity hypotheses. Identifying Protists and other micro-organisms to phylum and Cataloging the samples by phylum to make yourself a field guide and a dichotomous key.

 

Notebook assignments:

1) Catalog of samples of all organisms in the cultures to phylum and a field guide and dichotomous key that will help you to identify them in the future. (Oh, and in case you were wondering, that future includes a practical exam)

2) Preliminary experimental design for the Max D project

3) A summary of the paper you are now an expert in – what were the conclusions and what was the evidence. What is your opinion of the paper?

 

 

 

Week 2

Day 3      Sept. 6

1) Present Animal Phylogeny papers (15 minute max presentation), Jigsaw into new teams for the Animal Phylogeny debate, meet new teammates decide upon your hypotheses for now and do some planning for the coming weeks: who is going to do what?

2) Meet with your Max D Team and prepare for the wet set up on Thursday.

3) Workshop: How will we measure diversity?  Write an SOP and Lets try it out – how can we get reproducibility?

 

Day 4      Sept 8

1) Set up the Max D experiment and get baseline diversity data & sample one other teams culture to verify diversity numbers.

2) How to: Blasting your animal genes to get phylogenies: Try some Blasting and verify the results of at least 2 different gene searches

 

Notebook assignments week 2 :

Animal Phylogeny Debate team: what are the roles of each member and what are your hypotheses so far. Lab like report of Blast results for the Animal Phylogeny debate, basic phylogenies for each and your conclusions based upon those results.

Max D project – Diagram you experimental design list the parts of the experiment for your set up like the control, how did you replicate, what is your independent variable? Put in your data table and preliminary results. How did the replication go with sampling another groups culture?

ePortfolio Assignment:

SOP (Standard Operating Procedure, aka, Methods) for sampling diversity for the Max D project - What is an SOP?

 

Week 3

Day 5     Sept 13

1)Neuropharmicoevolutionary lab: Introduction and the Planaria protocol - Developing hypotheses for the evolution of the autonomic nervous system and who cares?   Brainstorming: How to make modifications of the Planaria protocol for other phyla?   Do Part 1 (First) of the System diagrams assignments – diagramming nervous systems across phyla and making a phylogeny.

2) Sample your Max D experiment and one other teams

3) Work on the Animal Phylogeny debate

 

Day 6     Sept 15

1) Part 2 (Second) for the Systems diagrams, neurophylogenomics, and Brain-builder Blasting, and finishing this exercise.

2) Sample your Max D experiment

 

Notebook Assignments week 3

Max D data table and graphs so far

Sketches of the nervous systems of animal phyla, a neurophylogeny, blast results for neurodevelopmental genes, diagram of the membrane physiology for the sympathetic nervous response including pharmacokinetics of caffeine an the drug you’ll be testing, and the Blast results and phylogenies for the molecules involved. Lastly, your conclusions from this exercise.

 

Week 4

Day 7   Sept 20

1) Animal Phylogeny Debate; each team presents (20 minute max) and then a question round, and general discussion of how to draw conclusions from multiple perspectives.

2) Introduction to the Megafauna Project

3) Sample your Max D project

Before the museum read Chapter 40 in Campbell

 

Day 8     Sept. 22

Los Angeles Natural History museum activity

Homework- Megafauna thought exercise (see notebook assignments)

 

Week 4: Notebook Assignments

1) Los Angeles Natural History Assignment

2) Megafauna Project: Some thinking ahead: Read Chapter 40 in Campbell and answer the following questions:

1. What are the energetic constraints on the size of animals that eat meat or for those that eat plants?  
2. Do you think this has limited the size of animals in past or is there something else that ultimately limits their size?  You should provide an argument here with evidence.
3. What are some of the homeostatic challenges to overcome as animals get very big?  Consider which physiological systems would face more severe challenges as you scale up size.
4. Explain the thermoregulatory challenges if really big animals are endotherms or ectotherms; consider the largest dinosaurs. 
5. What is the largest animal possible and what constrains it's size.  This is not asking for an animal that ever existed - what is the largest possible, use your imagination but stay within the constraints as we know them. 

 

Week 5

Day 9     Sept. 27

Neuropharmico SOPs: Modify the Planaria protocol to fit the behavior of the other phyla we will test. Write the SOPs.

Max D- final samples, verification of diversity numbers for all teams (every team samples all other teams)

Workshop – Max D: How could this be improved?

Redesign the Max D, plan to reboot.

 

Day 10     Sept 29

1) CORE 1 (Cognitive Open Resource Exam)

2) Megafauna project refined; What is an insightful question? How do I think up 10 of them and then how do I answer them?

3) Dissecting the mini-megafauna (A frog, a rat, and a pigeon walk into a lab…)

4) Max D: Back from the Dead! Set up the new and improved version.

 

Week 5 Notebook:

1. Neuropharmicoevolutionary SOPs
2. Maximum diversity Round 2: The new experimental design and Preliminary data and graph for the reboot.
3. Mini-megafauna dissections sketches fully labeled.
4. Megafauna Project:   Read Chapter 41 in Campbell and answer these questions:
5. How long would the intestine of a Argentinosaurus huinculensis,and how would you know?
6. Did T-Rex need a gall bladder, and how would you know if they had one?
7. What would the other organs of the dinosaur digesitive system look like, how big would they be in tons? Make a list for the Argentinosaurus huinculensis.
8. What are the size constraints on a digestive system?

 

Week 5 ePortfolio

This week you will add a reflective article to your eportfolio focused on the reproducibility of our diversity data.  You should analyze the data getting the mean and standard deviation for the measurements we did for each sample.  What should the data look like if we are, in fact, able to reproduce our experiments?  What would improve the process?

How does this experience reflect on the larger controversy over reproducibility in science?

Check out this Nature news article and use that as a baseline for the crisis.

 

Week 6

Day 11     Oct 4

1) Planaria protocol experiment day; troubleshooting the protocol and getting preliminary data.

2) Max D 2.0 sampling

3) Replication crisis discussion

4) Introduction to the Menstrual debate. Setting parameters for the menstrual debate and choosing teams.

5) Workshop: CORE exam results and discussion on how to excel at this type of assessment.

 

Day 12     Oct. 6

FLEX Day: No school for you

 

Week 6 Notebook

1) Planaria experiment data table, graphs, conclusions and trouble shooting notes for the scale up to the multiple phyla - did you learn any important things about the procedure and how will you modify your protocols to adapt.

2)  Max D 2.0 data and comments so far.

3) Megafauna project:   Read Chapter 42 in Campbell and answer the following questions:

1. How big was the heart of a Argentinosaurus huinculensis?
2. What are some of the challenges of circulation in animals with really long necks?
3. What are some of the constraints to size with regards to maintaining circulation?
4. What are the challenges in respiration for giant animals?
5. Did dinosaurs have diaphragms? How did they breath?
6. Since you have read to reproduction chapter - how did dinosaurs have sex?

Week 6 ePortfolio

Reflect on your CORE results and make a plan to improve that includes how you will assess your next performance.

 

Week 7

Day 13     Oct 11

• Neuropharmicoevolutionary experiment: We should have all the representatives of the various phyla and we’ll need to carefully extract the data from our living partners. You should bring all the things you need for this experiment especially the chemicals you intend to test.
• Workshop: If you could visit the museum again what would you observe to answer your questions?
• Max D 2.0 sampling

 

Day 14     Oct 13

1) Neuropharmicoevolutionary experiment completion

2) Prepare for the Menstrual debate

3) Max D 2.0 sampling

 

Week 7 Notebook

Neuropharmicoevolutionary experiment : Preliminary data and graphs for all phyla and preliminary conclusion and comments for the experiment.

Megafauna project: Read Chapter 44 and answer these questions

1. How big was the kidney of Argentinosaurus huinculensisand how do you know? How much urine would it produce in a day?
2. What is the challenge to going from terrestrial to living in the sea like mammals did in the evolution of cetaceans and then what might have prevented dinosaurs from doing this?
3. What are the biggest constraints to being giant and osmoregulation.

 

Week 7 ePortfolio

Max Diversity short Paper posts

 

Week 8

Day 15     Oct 18

1) Menstrual Debate: Present your argument – prepare and then a round of questions followed by a workshop to come to the best conclusions.

2) Max D 2.0 sampling

 

Day 16     Oct 20

Los Angeles Natural History Museum and the observations to answer your questions! This should complete the observations you need to build your website.

 

Week 8 Notebook Assignment

Final List of 10 questions for your website and a reflection on how this second trip to the museum was different than the first trip.

 

ePortfolio week 8

Post your Neuropharmicoevolutionary mini paper

 

Week 9

Day 17     Oct 25

1) CORE II

2) Plant Diversity and Histology

3) Megafauna website post

4) Max D 2.0 sampling

 

Day 18     Oct 27

1) Plant Morphology and Adaptation

2) Workshop: Measuring adaptive characters & making predictions for next week experiments

3) Max D 2.0 sampling

 

Week 9 Notebook:

1.  Plant descriptions, gross anatomy of leaf and stem and cross sections of the leaf and stem for 7 phyla or plants, and monocots and dicots for the angiosperms.  
2. Conclusions regarding the comparison of the phyla and the usefulness of the descriptions in Campbell with suggestion to improve. 
3. All anatomy and histology sketches labelled for different morphological adaptations.  these include gross anatomy, xs of leaf and xs of stem for each.
4. A list of traits that vary among the adaptation samples that you will be measuring, how you will measure each, a data table and graph of the measurements and a prediction of how each will effect the transpiration rate. 
5. Design for the potometer that you will use next week and the SOP for its use. 
6. Hypotheses for the Transpiration lab for next week

 

Week 10

Day 19     Nov 1

Transpiration experiments

Finish sampling Max D 2.0, verify all teams diversity numbers

Workshop: CORE II – How did your plan work – what can you do to improve next?

 

Day 20     Nov 3

Transpiration experiments

Clean up Max D 2.0, verify all teams diversity numbers (if they were not finished yesterday)

Workshop: How did the Max D reboot work out? What did you learn from the process?

 

Week 10 Notebook:

1. Experimental design and critique of your potometer
2. Data from the experiment graphed and a first rough conclusion. This involves graphing the transpiration rates against the traits you quantified from the week before. 

Max D2

1. Graph of new and old data and rough conclusions
2. Draft of reflection on the process of redoing and experiment and your insights in the controversy of replication in science. 

 

 

ePortfolio week 10

1) Add to your week 6 post reflecting on your plans to improve, evaluate your assessment, and update you plan for the next round.

2) Write a reflection on the value of repeating the Max D experiment what was learned and how does this reflect upon replication and the entire process of science in general.

 

Week 11

Day 21     Nov 8

Practical preparation – review materials in lab

Plant adaption lab finishing if anything needs resampling or redoing.

 

Day 22     Nov. 10

Practical exam starts around 2:30PM finishes at 4PM, we’ll clean it up and then discuss the next major project and our field work at Chantry Flats next week.

 

Week 12

Day 23       Nov. 15

Introduction to the field site, hiking along the Upper Winter Creek Trail, choosing the 3 sites for your study.

 

Day 24     Nov. 17

Sampling individual ecology for the plasticity of the forest at your 3 sites

Field practical scavenger hunt

Notebook week 12

Map with your field sites labeled, photos of each site and graph of plasticity among the 3 sites for the 3 factors you measured.

ePortfolio

Max D 2.0 mini paper

 

Week 13

Day 25     Nov. 22

Sampling the demography and dispersion at your 3 sites

Field practical scavenger hunt

 

Day 26     Nov. 24  

Thanksgiving Holiday!

 

Week 14

Day 27     Nov 29

Sampling the species diversity at your 3 sites

Field practical scavenger hunt

 

Day 28       Dec 1

Finish all fieldwork at Chantry

Field practical scavenger hunt – collect microscopic samples

Week 14 Notebook

Demography, dispersion, and diversity data and graphs for all 3 sites and some conclusions as to how they are all related and concept map and written description will do here.

 

Week 15

Day 29     Dec 6

1) CORE III

2) Examine your microscopic samples

3) Work on posters, making concept map towards an ecological model

 

Day 30     Dec 8

1) Poster Presentation

2) Turn in the scavenger hunt

3) review CORE 3 and plan for the final

 

Week 15 ePortfolio

1) Upload your poster and a reflection on the project

2) Update your CORE reflection and plans

 

Week 16

Day 31     Dec15

Final CORE