Syllabus & Schedule
COURSE: General Physiology Laboratory (visit our Blackboard site www.scranton.edu/bb for info and documents)
Credit value: 1.5
INSTRUCTORS: Dr. John Conway and Dr. Robert
Waldeck
Course Coordinator: Dr. Robert
Waldeck (waldeckr2@uofs.edu, Loyola Rm
106)
TEXTS: 1) Lecture Text (includes required reading
for laboratory): Human Physiology: From
cells to systems by Lauralee Sherwood (4th Edition);
2) Physiology Laboratory Manual at Bookstore
3) Material on reserve in Weinberg Library
COURSE DESCRIPTION: Physiological processes underlying functioning of the animal organism. Study of irritability, excitation, conduction, contractility, cellular physiology, and functions of mammalian organ systems.
TENTATIVE
LABORATORY AND EXAM SCHEDULE:
Week of: Experiment Sherwood Readings
2/3 Introduction to Laboratory; Laboratory Safety. Brief Introduction
to Data Acquisition using PowerLab
2/10 Renal Physiology 482–525
2/17 Sensory Lab: Reflexes, Cutaneous, Auditory and Visual
Senses 173-212
2/24 EXAM 1 & Lecture for Action Potential Lab see also web site http://human.physiol.arizona.edu/sched/cv/wright/viewIt.html
(used by permission – requires Java; designed for small font
sizes)
3/3 Action
Potential Simulation see also web figure
listed below: http://134.198.26.114/Gen_Physiology_Biol_245/Lectures_in_HTML_Format/AP_Figure.gif 78-98
3/10 Spring Break. No lab
3/17 Introduction to Data Recording
and Skeletal Muscle Data Analysis Demo with Chart
3/24 Skeletal Muscle Contractility 239-261
3/31 EXAM 2 & Intro to Cardiac Muscle Lab 323-331
4/7 Cardiac Function: The Frog Heart 277-279; 284-311
4/14 ONLY
MONDAY & TUESDAY LAB
Electrocardiogram and Physical Fitness 297-301
4/21 ONLY WEDNESDAY, THURSDAY, & FRIDAY LAB MEETS
Electrocardiogram and Physical Fitness 297-301
4/28 Respiratory Function
5/5 NO LAB 433-457; 469-478
Final Week EXAM 3
Downloading Your Data Away from the Physiology
LabRoom
Data from the Chart file can only be used with Chart which can be found on Macs in the computer room (first floor) of Alumni Memorial Hall (AMH). Follow the procedure below:
1. Turn on the Macintosh computer in
AMH
2. Click on folder on Desktop screen for Internet tools and then click on Internet Explorer icon (usually left top hand corner of desktop). This will connect you to the internet.
3. Click on the bookmark which signifies you lab group number. (top of browser)
4. Select “Physiology Lab Data files” folder.
5. Select “Macintosh Data files” folder.
6. Select “day of lab and group number” folder.
7. Select file of interest. After clicking the file will automatically download and be placed into the “Your files” folder on the desktop (usually right top hand corner of desktop).
8. Click on this folder and you will see your data file.
9. Click on data file and it will open. You can then do analysis or work on making figures.
10. The software will prompt you with a window and you need to choose “Analysis”.
Any printing can only be done at a computer at the printing station. So if you make a table or figure, you will have to save it to a floppy disk or a zip disk and take it over to the printing station where you can print it.
The Chart software that allows you to record data is located on all the Macs at AMH so once you have received your data file from the lab computer to AMH computer you can work on the file. Also found on all the desktop folders of the AMH Macs are the following:
Appleworks: used to make figures
Microsoft Office: Word, Excel for text and graphs and tables.
The computer helpdesk people can help you with basic computer problems but if you have a problem or question related to these specific programs listed above, please see/call/email Dr. Waldeck.
You will be accessing much of your laboratory data via the web, with the iMac computers in the lab operating as servers. Here are the addresses for each of the lab computers; listed by Lab Group number:
|
Group 1: http://134.198.26.136 |
Group 2: http://134.198.26.132 |
Group 3: http://134.198.26.133 |
|
Group 4: http://134.198.26.134 |
Group 5: http://134.198.26.135 |
Instrctr’s iMac: http://134.198.26.143 |
LABORATORY SECTION SCHEDULE:
|
Monday Instructor: Dr. Waldeck waldeckr2; 4324 GA: Tracy Bergen bergent2 |
Tuesday Instructor: Dr. Conway conwayj1; 6216 GA: Andrew Hardisky hardiskya2 |
|
Wednesday Instructor: Dr. Waldeck waldeckr2; 4324 GA: Tracy Bergen bergent2 |
Thursday Instructor: Dr. Conway conwayj1; 6216 GA: Andrew Hardisky hardiskya2 |
|
Friday Instructor: Dr. Waldeck waldeckr2; 4324 GA: Tracy Bergen bergent2 |
|
Grading Procedures
Please note that each
faculty member has their own specific instructions for their section of
laboratory and they will go over these in the first week. Generally the
directions listed below ate followed.
Each laboratory experiment that you perform may be considered a small research project. Although the same experiment has been done many times before by other people, your performance of the experiment is unique in that no one has ever used the same living material you will use nor will the physical conditions of the experiment ever be precisely the same despite the attempt to make them so.
Read your lab directions carefully before coming to class and understand the nature of the experiment before proceeding with it. You may be quizzed at the begin of the laboratory to determine your level of preparation. Read pertinent discussions of the material in your text, lecture material and accessory reading matter to help your understanding of the problem. This may require reading material in advance of the assigned reading associated with the lecture material. But it is helpful and necessary for competent interpretation of the experiment.
Work carefully and keep apparatus clean and neat. Since you will be working in groups, be sure each student is familiar with all phases of the experiment. Rotate tasks so that each student gets some practice in all of the manipulations and observations involved. Realize that there are many different laboratory sections. Due to the intensive use of this laboratory it is essential that each participant be responsible for the cleanliness of the working area and the lab in general. It is therefore important to note the following:
a. Do not eat or drink in the lab.
b. Clean working surfaces, instruments and equipment after use. Cleaning supplies are available in the laboratory.
c Return instruments and materials to their designated locations after their use.
d. Close cabinets and drawers and place stools under the work tables.
Throughout the semester, students will be assessed for participation, attendance, and development of technical expertise. Attendance in all laboratory sessions is mandatory. If a student is unable to attend a specific laboratory session, it is the obligation of the student to complete the experiment by attending during that same week another scheduled laboratory section. This course has several sections of laboratory (see above for scheduled laboratory times). One must seek out the instructor of another section and request the permission to attend that instructor’s section. During the lab, each student will be expected to contribute significantly to each experiment. This contribution may include equipment setup, animal preparation (when required), data recording, notebook maintenance, and area cleanup at the end of the experiment.
There will be one LABORATORY NOTEBOOK maintained by each lab group. It will be used to record each laboratory experience: methods and materials used in each experiment; notes pertinent to the experiment (including errors or unexpected occurrences; and the results of each experiment. Laboratory notebooks MUST BE brought to each laboratory session and also be used during data analysis during or after performance of the experiment. These notebooks will be inspected periodically at the discretion of the instructor.
LABORATORY GRADING PROTOCOL
The
laboratory grading protocol is instituted separately by each instructor. Please
check with your instructor to determine if the protocol described below applies
to your laboratory section.
THREE (3) in-depth lab tests will be administered at the times indicated on the syllabus above. Because of the time required for each lab exercise, lab exams may be given outside of scheduled lab times. The material to be studied for each test will be taken from the laboratory lectures, knowledge of the laboratory equipment, results of the laboratory experiments, information from the laboratory manual, and assigned textbook readings. Fifty-five percent of the laboratory grade will be based upon the above three lab tests. Thirty-five percent of your grade will be based on laboratory reports: 20% from the report on which you are the first author and 15% on the reports on which you are the coauthor. The laboratory reports indicate the overall knowledge gained from the experiment. More important, they are a permanent record of what was learned or what may be of future use to the student. The laboratory reports will be based on data collected during the laboratory and recorded in a laboratory notebook. The laboratory reports are formal write-ups of the laboratory experiments using data and notes recorded in the lab notebook. The laboratory report format is discussed later in this handout. The remaining 10 percent of the laboratory grade will be based on class participation and assigned homework exercises. Changes to the grading protocol are at the discretion of the individual instructor.
Laboratory reports will be assigned, at the discretion of the instructor, to individuals during the first laboratory period. Each student will be responsible for acting as the primary author on one laboratory report during the semester. In addition, each student will be a co-author on each of the laboratory reports written by the other members of his/her lab group. Twenty per cent of your laboratory grade will come from the report on which you are the first author; the remaining 15% (for a total of 35% of your final grade) of your laboratory grade will come from those reports on which you are the co-author. Write your laboratory reports as if they were short research papers. A research report is both a work record and a means of communicating your ideas. It also provides you with an academic experience different from that of a library term paper, since a research report is based on one's own data and personal involvement in organized investigation. The first author is responsible for the overall report preparation and will receive the grade; however, every member of the group is expected to significantly participate in the preparation of the report. All group members must hand in a short statement of their contributions.
Laboratory reports must be handed in by your next scheduled lab period (unless otherwise specified by the instructor). The reports must be double-spaced and typewritten. In addition to content, grammar and spelling will be graded. Further details concerning grading criteria will be found on last page of this handout. The following guidelines should be followed in writing your reports:
1. Always write in the third person, past tense.
2. Avoid long involved sentences and overuse of polysyllabic words. Long, run-on sentences often obscure your meaning, and frequent use of cumbersome words reduces the readability.
3. Be positive in your writing. Don't use non-committal statements. For example, "the data could possibly suggest" implies that the data really may show nothing; simply state "the data show." Reminder: the word data is plural.
4. Refrain from drawing unsupported conclusions. On the other hand, don't pad the report with data irrelevant to the purpose or conclusions of the study.
Your
laboratory reports must follow the
format indicated below:
1. TITLE PAGE
The title should be brief but descriptive of the report contents or principal message. The title page should indicate the primary and secondary authors, laboratory section, and instructor.
2. INTRODUCTION (10 points)
The introduction indicates the justification and relevance of your study and, thus, establishes the framework for the remainder of the paper. It is not an exhaustive review of the topic. It must describe (a) the nature of the problem, (b) the objectives of the experiment, and (c) the experimental model that will be used to carry out the experimental objectives. It is often the last part of the report that is written. Any background information or ideas that are taken from another source should be cited appropriately (see below). The Introduction section must not exceed one page in length.
3. MATERIALS AND METHODS(10 points)
Procedures in research reports are usually detailed enough to give a reader an accurate idea of what was done in the study or to be guided to appropriate literature for this information. Often a diagrammatic drawing of the experimental setup is helpful. Keep to a minimum the details of standard and generally known procedures. This section should contain at least (a) a description of the specific equipment used to make measurements (a list of equipment used is not acceptable), (b) a description of any animal preparation, (c) a description of the experimental protocol, and (d) a description of analysis techniques. The Methods section is limited to a maximum of 2 pages.
4. RESULTS (35 points)
This portion of the report presents the data collected in an objective fashion, even if they are contrary to hypothesis or expectation. It should describe in a well organized and coherent manner the content of tables, figures and graphs that facilitate the presentation and analysis of the data. It may be a maximum of 4 pages in length.
Again, in the Results section, data should be reported objectively, with a minimum of personal interpretation (e.g., the reflex reaction times of frogs were half that of humans). Qualitative as well as quantitative statements may be used when stating findings related to the data, as long as these statements are objective. Please note that presentation of subjective conclusions that the experimenter draws from the data, and with which the reader could reasonably disagree (e.g., frogs have fast reflexes because flies are tough to catch) should be left for the Discussion section.
An appropriate example of a statement in a Results section is:
"Figure I shows that as acetylcholine was administered, the rate of contraction of the heart decreased from 40 beats per minute to five beats per minute over a period of ten minutes. Note that the strength of contraction also decreases over the same period."
Figures introduced in the RESULTS section may consist of graphs, diagrams, tables, or limited chart recordings (see Part 7 below) that accurately depict your results. All illustrations must be individually numbered and cited in the text and referred to as a Figure (e.g. multiple motor summation, as shown in Figure 4 ... ). Charts and tables of numbers are labeled as Charts and Tables, not Figures (note capitalization).
All figures should be placed after the REFERENCE section of the report. The illustrations or figures must be numbered in the order cited in the text and must have a title to be placed following the number of the figure, e.g., Figure 5. Relationship Between Muscle Length and Tension. Descriptive legends for each illustration should follow on a separate page. Figure legends should be sufficiently detailed to make the content of the figure clear without having to refer back to the main text.
5. DISCUSSION (35 points)
This is one of the most important sections of your report. The Discussion is a discussion of your data, and so must be focused on your data. It is where interpretation and conclusions based on your results are presented. This section should attempt to answer the following questions:
a. Are your results in accord with expectation?
b. Do they, therefore, support or not support the hypotheses that the experiment sought to test? Why?
The first paragraph of the Discussion should succinctly summarize the major findings of your experiment, and address (support or refute) the central hypothesis that the experiment tested. The rest of the Discussion should expand upon that summary. The following (from R.W. Jeremy et al. 1992. Circ. Res. 70:1180-1190) is an example of a good opening sentence (note that it does not constitute the entire first paragraph):
"The present findings support the hypothesis that glycolysis continues to play an important role during the early reperfusion period in the postischemic myocardium."
In the Discussion section, you should refer to previously known information to corroborate your findings (i.e., especially of those whose work or information you cited in the Introduction). If so, you must make reference to your sources at the end of your report. Do not make generalized statements that are not based on your data, fact, or reason. Remember, you are discussing your results. The Discussion section is limited to a maximum of 4 pages.
6. REFERENCES (at least 4)
Under References (=literature cited) you present the complete citations for all the factual material you refer to in the text of your paper. This presentation enables the interested reader, including perhaps you at a later date, to obtain quickly the sources you have used in preparing your paper. It provides a convenient way for the reader to obtain additional information about a particular topic, and it also provides the reader with a means of verifying what you have written as fact. It occasionally happens that a reference is used incorrectly; your interpretation or recollection of what was said in a textbook, lecture, or journal article may be wrong. By giving the source of your information, the reader can more easily recognize such errors. If the reader is your instructor, this list of references may provide an opportunity for him or her to correct any misconceptions you may have acquired. If you fail to provide the source of your information, your instructor will have more difficulty in determining where you went wrong. Proper referencing is even more crucial for scientific publications. Misstatements of fact are readily propagated in the literature by others; the References section of a paper provides the reader with the ability to verify all factual statements made, and the careful scientist consults the listed references before accepting statements made by other authors.
The following are Guidelines for writing a REFERENCES section of a scientific paper:
1. References are listed in alphabetical order according to the last name of the author of each publication.
2. If you cite several papers written by the same author, cite them chronologically.
3. Each reference should include the names of all authors, the year of publication, and the full title of the paper, article, or book.
4. When referencing books you must report the publisher, the place of publication, and the inclusive page numbers.
5. When referencing format articles, you must include the name of the journal, the volume number of the journal, and the page numbers of the article.
6. Spell out only last names of authors; initials are used for first and middle names.
7. Latin names, including species names, are underlined to indicate italics.
8. Titles of journal articles are NOT enclosed within quotation marks.
Examples follow:
Eckert, R., D. Randall, and G. Augustine.
1988. Animal Physiology Mechanisms and Adaptations, 3rd Ed. W.H. Freeman,
Vergara, J. and K. Asotra. 1987. The chemical transmission mechanism of excitation-contraction coupling in skeletal muscle. News in Physiological Science, 2:182-186.
NOTE: The general format is: Author(s). Date. Title of paper or book. Edition, Publisher, location (for books). Journal title, volume number: pages.
7. FIGURES AND LEGENDS (10 points)
Figures are used to illustrate concepts and data relationships observed during the experiment. There are some traditional ways of doing this but they do not have to be followed slavishly. Be creative! Relationships between data may be illustrated using a wide variety of figure types including bar charts, histograms, and x-y plots. You will find that most biological data collected in this laboratory are mostly easily illustrated using the standard x-y plot or bar graph. If you have an interesting or different way of depicting your data or making your point, feel free to try it. The most important role an illustration plays in a paper is to support the point you are trying to get across to the reader. Direct recordings of your data are used only rarely, for illustrative purposes.
Below are some guidelines to help you when designing your figures:
a. Keep
the figures simple.
Use
colors if it helps the reader differentiate between several lines or bars (bar
graph). However, don't get carried away with your artistry - keep it simple!
b.
Proportion the illustration so that the data are the center of the reader's
focus. Don't draw a large full-page graph and have all the data points crowded into
one comer. Scale the axes to keep the data evenly centered.
c. It sometimes improves clarity if the data points are connected by a line (especially if the x-axis is time). However, be careful that the line only goes from point-to-point and does not extend beyond the last data point. Also, if the line is a regression line be sure to indicate this in the legend.
d. Place the independent variable (usually time, length, concentration, etc.) on the x-axis and the dependent variable on the y-axis. This is not a hard and fast rule, but it is a strong tradition!
8. HOW TO USE CITATIONS
When citing someone else's work or information gathered from another source, do so by giving the last name(s) of the author(s) followed by the date that the work was published.
with one author:
"Jones (1988) found that..."
OR
“…indicates that the application of acetylcholine increased the rate of contraction (Jones, 1988)."
with two authors:
"Vergara and Asotra (1987) suggest..."
OR
"...is associated exclusively with T-tubules (Vergara and Asotra, 1987)."
with three or more authors:
"Zampighi et at. (1975) have shown that..."
You may occasionally have to cite a reference that you have not
actually read. For example, the results reported by Smith (1964) may be cited
in a book written by Jones (1983) and you have read only the work by
Jones. YOUR CITATION MUST THEN READ:
"(Smith, 1964, as cited by Jones, 1983)".
9. SOME COMMON PROBLEMS
a. Use, evaluate, present and interpret YOUR data. Failure to do so is the most common problem students have in report writing. Many will calculate their results and make figures and tables, but then focus the bulk of their report on textbook information rather than on the group data. Please focus your report on your data.
b. Do not ignore results because they differ from textbook generalizations. Your data are not incorrect just because they do not agree with some general principle or a conclusion in another report.
c. Only use reference material pertinent to your data.
d. Be careful about making small differences seem important. Different values are not necessarily significantly different.
e. Do not discard data because of variability and biases. There is some margin of error in nearly all scientific data. If recognized and accounted for in interpretation of results, errors of reasonable size do not necessarily discredit your data.
f. Round off final quantitative results to no more digits than can be reasonably justified. What sense does it make to compare two numbers such as 17.289761 and 19.82946? Do the last several digits have any special meaning? Reporting 17.3 and 19.8 may suffice in your case.
g. Label figures and tables properly and thoroughly and cite them in your text. Too often, figures and tables are inserted in a report without explaining their purpose to the reader.
h. Play around with your data before preparing the final graphs and tables. Get your mind working over the data; attempt to find clear patterns and trends. Try to organize the data in various ways, since different presentations may elucidate different patterns.
i. Do not select or reject data in order to make desired results apparent. ANY "FUDGING" OF DATA IS DISHONEST AND UNACCEPTABLE.
j. Do not perform calculations on data just for the sake of calculating. Have a reason for, and draw conclusions from, the calculations performed. Padding your report with excess though honest numbers serves no useful function. It is not necessary to show simple calculations in the paper.
k. Document ideas, conclusions, and hypotheses with data, facts from the literature, and sound reasoning.
l.
Relate your results and conclusions to accepted
principles and concepts. Explain any discrepancies.
10.
CRITERIA FOR THE GRADING OF LAB REPORTS
The grading of lab reports will be based, in part, upon the following criteria:
1. Concise descriptions
2. Appropriate use of illustrations, charts, and tables
3. Neatness and clarity
4. How well the Discussion is not based on and focused on the data
5. Originality
6. Proper format utilized (i.e., Introduction, Materials and Methods, Results, Discussion)
7. Grammar
8. Proper spelling
9. Appropriate citations of figures in text
10. Appropriate titles and labels of figures
Proper reference citations
