WFSC 616 ­ PHYSIOLOGICAL ECOLOGY OF THE VERTEBRATES (3-3 4)

Fall 2008

INSTRUCTOR:  W.H. Neill (212B Nagle Hall; w-neill@tamu.edu; 979-845­-5759)

OBJECTIVE:

To guide graduate students in organized study of vertebrates' autecological responses to environment, and in synthesis of information about those responses in the form of mechanistic, quantitative models.

FORMAT:

 

WFSC 616 is offered as a course fully accessible to students both on campus in College Station ("local" students) and to those located elsewhere ("distant" students).  All class transactions--lectures, discussions, demonstrations, and workshops--will pass through a computer whose monitor display is projected "live" for the local audience and whose audio input and monitor display are captured via Camtasia and saved as an .avi file, uploaded to the WFSC "disted" server  (http://wfscdisted.tamu.edu/courses/), and made available for dump-downloading (as opposed to streaming) to all students, whether distant or local.  Camtasia .avi files are efficient: With the recording parameters I use, an hour-long presentation requires only 12-15 Mbytes of memory.  So, a download takes only a "reasonable" amount of time, even with a 56 K modem; still, a fast connection, via cable or DSL, is much to be preferred.  For easy-to-play sample downloads (Camtasia .avi files converted to ShockWaveFlash files), follow the links at the bottom of this page.

The Camtasia Player and required codec (TSSC Codec) are available as free downloads, from http://www.camtasia.com/download.asp.  Camtasia .avi files also will play on Widows Media Player, Real Player, IrfanView and several other platforms.  But, you will need the TSSC Codec before any of these will work. And, most folks think the Camtasia Player and IrfanView give best overall quality.   IrfanView (freeware available from http://www.irfanview.com) offers the additional advantage of faster-than-normal-speed playback with good image/audio synchronization.

As the course begins, please download only the TSSC Codec and perhaps Camtasia Player.  Once we are well started, I will give each participant in the course a license for the full Camtasia Studio package.  Toward the end of the course, you will use the Camtasia Recorder (and maybe the Producer, too) to generate a presentation of your project for distribution and playback to the class (see "Research Project/Paper," below).  This arrangement will be essential for distant students and instructive for all:  I want every registrant to find out what it's like, being one's own actor, director, and producer--the proverbial "one-man band."   The Camtasia Studio license is un-expiring, and the software will be yours to keep and use after the course is over. 

The primary tool for functional representation and study of ecophysiological processes will be the symbolic systems simulation software STELLA.  See "LAB" and "Research Project/Paper," below, for more on that.

TEXT (optional):        Animal Physiology: Adaptation and Environment, 5th edition (1997), by K. Schmidt-Nielsen

LECTURE:                 Local:  TTh 12:45 - 2:00 p.m.; 110 Nagle
                                    Distant:  Archival Camtasia record posted to WFSC's "disted" server, normally within 2 h after end of live session.

LAB:                           Local:  Th 2:20 - 5:45 p.m.; 110 Nagle
                                    Distant:  Archival Camtasia record posted to WFSC's "disted" server, normally within 2 h after end of live session.

Lab will consist of several modeling-workshop and model-demonstration sessions during the first weeks of the semester; then a series of informal sessions for work on individual research projects; then, a final marathon session, on the last class day, devoted to presentation and discussion of project reports.

I will work one-on-one with local students, in person, at the reserved lab time and at other times by arrangement.  I will work one-on-one with distant students via telephone and/or Internet conferencing, using Centra.  And, of course, I will be pleased to meet and work with distant students in person, whenever and wherever we can get together.

EXAMS & GRADING:
 

Midterm Exam: “take home”—due in by

 14 October, 5 p.m. CST

  300 points

Final Exam: “take home”—due in by

 Scheduled Final Exam Time, TBA

  400 points

Research Project/Paper

 4 December, 5 p.m. CST

  300 points

Total for course:

 

1000 points


 

Total Points Scored

Course Grade

900­-1000

A

800­-899 

B

700-­799 

C

600­-699

D

0-599

F

 

 

 
 
 
 





 
 
 
 
IMPORTANT NOTE:  Handouts used in this course are copyrighted.  "Handouts"
means all materials generated by the instructor(s) for this class, including
but not limited to, syllabi, exams, lab exercises, simulation models, computer 
files, data sets, notes, and drawings.  Because these materials are copyrighted, 
you do not have the right to copy or distribute them, unless the instructor(s)
expressly grant permission.
 
     As commonly defined, plagiarism consists of passing off as one's own the
ideas, words, writings, etc., which belong to another.  In accordance with
this definition, you are committing plagiarism if you copy the work of another
person and turn it in as your own, even if you should have the permission of
that person.  Plagiarism is one of the worst academic sins, for the plagiarist
destroys the trust among colleagues without which research cannot be safely
communicated.  If you have any questions regarding plagiarism, please consult
the latest issue of the Texas A&M University Student Rules, under the section
"Scholastic Dishonesty."

                                                            Aggie Honor Code
                            “An Aggie does not lie, cheat, or steal or tolerate those who do.”

Upon accepting admission to Texas A&M University, a student immediately assumes a commitment to uphold
the Honor Code, to accept responsibility for learning and to follow the philosophy and rules of the Honor System.
Students will be required to state their commitment on examinations, research papers, and other academic work.
Ignorance of the rules does not exclude any member of the Texas A&M University community from the requirements
or the processes of the Honor System. For additional information please visit:  www.tamu.edu/aggiehonor/.

On all course work, assignments, and examinations at Texas A&M University, the following Honor Pledge shall be
preprinted and signed by the student:
         “On my honor, as an Aggie, I have neither given nor received unauthorized aid on this academic work.”

                            Americans with Disabilities Act (ADA) Policy Statement

The Americans with Disabilities Act (ADA) is a federal antidiscrimination statute that provides comprehensive
civil rights protection for persons with disabilities. Among other things, this legislation requires that all students with
disabilities be guaranteed a learning environment that provides for reasonable accommodation of their disabilities.
If you believe you have a disability requiring an accommodation, please contact the Department of Student Life,
Services for Students with Disabilities in Room 126 of the Koldus Building or call 979-845-1637.

 


WFSC 616 - Physiological Ecology of the Vertebrates: Lecture
Fall 2008

Topical Outline

1. Some Guiding Principles of Autecology (Overview)

     F.E.J. Fry said it all (or much of it) in 1947:

    • The organism is "fundamentally an organized section of the environment."
    • The complex of environment can be resolved into its physiological effects: controlling, lethal, limiting, masking, and directive.
    • Environment acts on activity through metabolism.
    • Activity regulates environment.

2.  Metabolism and Metabolic Scope

 

               2.1  Definitions, units of measure, and experimental approaches

                              2.11   Aerobic vs. anaerobic; volume vs. mass; oxycaloric equivalent; RQ; keeping track of units

                               2.12   Direct calorimetry

                               2.13   Indirect calorimetry

                                              2.131   Respirometry

                                              2.132   Materials/energy loss upon starvation

               2.2  Standard and basal metabolism

                              2.21   Effect of body size; the "surface law"--and more recent power plays

                               2.22   Climatic, seasonal, and diel correlates

               2.3  Locomotory metabolism, active metabolism, and maximum sustained speeds

                              2.31   Swimming vs. running vs. flying

                              2.32   Metabolic scope for locomotion

               2.4  Hypermetabolism, and burst swimming, sprinting

               2.5  Routine metabolism and optimum speeds

               2.6  Metabolic scope for (holistic) activity: grand integrator of  physiological ecology

3.  Controlling Factors

               3.1  Distinguishing features: Influence metabolism by influencing rates of diffusion and molecular activity; operate at cellular and subcellular levels

               3.2  Temperature

                              3.21    Heat transfer

                              3.22    Ahrennius effect on standard metabolism; Q10

                              3.23    Effect on active metabolism

                              3.24    Maximum metabolic scope and thermal optima

                               3.25    Capacity acclimation to temperature; Precht's types of  compensation

               3.3  Other controlling factors: pressure, hardness ions, pH, ?

4.  Lethal Factors

               4.1  Distinguishing feature: Kill by complete interdiction of metabolism

               4.2  Temperature

                              4.21    Incipient lethal levels

                              4.22    Resistance acclimation and ultimate lethal levels

                              4.23    Thermal tolerance polygons

                              4.24    When is temperature a "pure" lethal factor?

               4.3  Other lethal factors: toxic materials, supersaturated gases, pathogens, predators

5.  Limiting Factors

               5.1  Distinguishing features: Restrict active metabolism, thereby reducing metabolic scope; operate at systemic level

               5.2  Oxygen

               5.3  Energy substrates (food, tissue stores)

                              5.31    Bioenergetics and energy budgets

                              5.32    Growth models

   5.4  Other limiting factors:  micronutrients, certain metabolites (incl. CO2) and pollutants (e.g., silt and pulp fines) that interfere with oxygen                               transport

6.  Masking (Loading) Factors

 

               6.1  Distinguishing feature: Load metabolism, increasing metabolism at a given level of locomotory activity; increase metabolic work  for physiological             regulation

 

               6.2  Ionic concentration and composition of medium: ion-osmoregulation

               6.3  Temperature: warm bodiedness and physiological thermoregulation

               6.4  Pressure/depth: regulation of swimbladder volume and buoyancy

               6.5  Food: processing costs, including SDA (?)

7.  Directive (Unloading) Factors

               7.1  Distinguishing feature: Stimulate "transducive" responses of two types, 1) distributional movements and 2) anticipatory adjustments.  Serve to "unload"           metabolism.

               7.2  Distributional movements = orientative responses = spatial maneuvers: accomplish or facilitate behavioral enviroregulation

                              7.21    Predictive movements = transferred adjustment; e.g., surfacing of fish when O2 is low

                              7.22    Reactive movements

                                              7.221   Taxes = orientation to source of stimulus in "transparent" environment

                                             7.222   Kineses = distributional responses brought about by dependency of locomotory rate on intensity of  factor in "opaque"                                                        environment; might permit aggregation at preferred levels of temperature and some dissolved substances, but efficacy in un-bounded                                               gradients debatable

                                             7.223   Klinokinetic avoidance = distributional effects brought about by increase in turning under worsening conditions; modeling                                                  studies suggest this is sufficient mechanism for behavioral thermoregulation

                              7.23    Both predictive and reactive mechanisms reflect a physiological goal or set-point--the [joint] preferendum

                                             7.231   Preferendum seems to correspond with optimum; in case of temperature, preferendum is the temperature for maximum                                                           metabolic scope

                                             7.232   Temperature preferendum vs. acclimation relationship varies among species (re Zahn's scheme), perhaps in accord with type                                   of capacity acclimation

               7.3  Anticipatory adjustments: prepare animal for seasonal, diel change

                              7.31    Photoperiod is chief factor; other possibilities are diet and salinity

                               7.32    Hormonally mediated

8.  Conclusion

               8.1  Interrelations of Fry's factors: a conceptual model

               8.2  A plea for mechanistic synthesis:  Toward an "integrated field theory" for ecology


WFSC 616 - Physiological Ecology of the Vertebrates:  Laboratory
Fall 2008

Research Project/Paper

The move to make the course more "distance friendly" (and to free it from ethical and regulatory concerns about animal use) has obligated changes in format and logistics, relative to those prior to Spring 2003.  One of those changes has been to abandon "hands-on" research projects with live vertebrates, in favor of projects that involve analysis and/or modeling of animals' ecophysiological processes, based on extant data.   I will assist each registrant in analyzing relevant data and/or building and evaluating an appropriate simulation model, using as the basis information from the literature and/or the individual's own past research.   The analysis/modeling effort and consequent report will constitute the "lab" part of the course.

For those who would like to try a modeling project, but have no experience in simulation modeling...be not afraid.  In WFSC 616, you will learn not only about vertebrate ecophysiology, but also you will become acquainted with this tremendously powerful tool for better organizing and integrating what you learn (not just in WFSC 616, but throughout your future life).  To find out how modeling studies are put together, have a look at some recent papers in the journal Ecological Modelling.  For the why and how of systems simulation itself, especially as applied to natural-resource issues, see the excellent textbook by our own Dr. Bill Grant (and two of his former students), Ecology & Natural Resource Management:  Systems Analysis and Simulation (Wiley, 1997).  Students who have completed WFSC 604, or similar course in systems modeling and simulation, are especially invited to continue in WFSC 616; not only will you be able to exploit and further develop your own skills, but also you will be able to help the rest of us.

We will build and "run" our models using the symbolic systems-simulation software "STELLA," available from isee systems, at http://www.iseesystems.com/.  As a student registered in this course, you will be provided a personal copy of STELLA 9, at no additional cost to you (i.e., the $129 cost of your “perpetual” license will be paid from course fees—quite a bargain, when you consider that the cost of the regular, non-expiring license to STELLA now ranges from $649 to $1,899, depending on user category—check the isee systems website.)  [STELLA version and prices, current as of 24 June 2008.]

Timetable:

i)    11 September, project proposal―one or two machine­-printed pages indicating your name, project title, description of problem or statement of hypothesis, intended approach (statistical or mathematical analysis, simulation modeling, or a combination).

ii)    2 October, interim progress report, including data and preliminary analysis and/or model. 

 

iii)    20 November, first submission of project report, in manuscript form―­­not to exceed 10 double-­spaced, machine-­printed pages of text (exclusive of figures and tables); follow the manuscript format specified by Ecological Modelling or another appropriate journal of your choosing.

iv)    25 November, 15-­minute presentation of project uploaded to server, for download and presentation to class on 2 December.

v)    4 December, final submission of manuscript, with complete analysis or working simulation model, for grading.

 


To access sample lecture and lab presentations, click on the links below.  The Flash files called by these .html leaders should download and play automatically inside Internet Explorer or other browser.  The " Lecture Sample:…" presentation plays about 41 min; the "Lab Sample:..." presentation plays about 16 min.  By right-clicking at any point during playback and then checking "Full Screen," you can access Camtasia's controls for navigating within the file.

       Lecture Sample:  Poikilotherm and homiotherm metabolism vs. temperature

       Lab Sample :  Modeling metabolism of swimming fish
 
  


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