Course Syllabus: Bio 301D, Fall 2013

This syllabus describes the scheduling of and procedural details for Bio 301D. This information is subject to change, as described below.  The website for the class, which displays this syllabus, the book, homework assignments, and old exams is

Lecture locations and times

PAI 3.02 MWF 10-11 (#48760)

PAI 3.02 MWF 11-12 (#48765)

Fall 2013 calendar (important dates only; class meets every MWF)



August 28 (Wednesday)

First Lecture (first day of class)

September 2 (Monday)

Labor Day (no class)

September 6 (Friday night)

Rosh Hashanah starts

September 23 (Monday)

First Homework Due

September 25 (Wednesday)

First Exam (during class)

October 12 (Saturday)

Texas OU Weekend

October 16 (Wednesday)

Second Exam (during class)

October 18 (Friday)

Second Homework Due

October 23 (Wednesday)

Last day to change CR/NCR status

October 30 (Wednesday)

Homework ‘test’ in class (counts as one homework)

November 5 (Tuesday)

Last day to drop or change CR/NCR status

November 11 (Monday)

Third Homework Due

November 13 (Wednesday)

Third Exam (during class)

November 28-December 1

Thanksgiving Break

December 4 (Wednesday)

Fourth Exam (during class)

December 6 (Friday)

Last class day, last Bio301D day; Fourth Homework due

No final exam


Course Materials

1)  Class website (for book, syllabus, homework templates, old exams)    

2) Class email          

3) Quest:    $25 (charged after day 12; for questions).

4)  Polleverywhere:  register free as a participant at .  Enter either your name or EID so I can tell who you are.  Use of Polleverywhere does not affect your grade.

5) Videos of lecture:

6) Blackboard:


For personal matters and emergency issues, you may email Jim Bull at (don’t use this email for questions about class material and other routine matters); always use “301” in the subject line


Calendar of lectures

The lectures follow the on-line book (Scientific decision-making).  However, the dates of specific lecture topics are subject to change based on current events, class progress, and guest lectures.  Furthermore, lectures are interactive and involve student input and feedback (with ‘clickers’ provided free, in class).  The pace of most lectures depends on how well the ideas are being understood, so a rigid schedule of topics for each day of the semester is not given here because it does not fit the type of comprehension-based progress used in the class.  More or less, the four exams will cover the chapters listed below (a more specific coverage will be given shortly before each exam).  Furthermore, the lectures tend to go in order of chapter number, but exceptions are sometimes made.  The book is not a complete substitute for lecture, however, as lectures contain examples and demonstrations not included in the book. 

Exam number

Chapters (approximate)


Dates (all Wed)



Scientific Method and Models

25 September




16 October



Interpretation and Conclusions

15 November



Impediments and Conflict

4 December


Weekly topics (see the book for more exact contents):

Week spanning

Topics covered

28-30 August

Introduction to 301D, Scientific Method

4-6 September

Scientific Method, Intro to Models

9-13 September

Models (general and specific topics)

16-20 September

Models (specific topics)

23-27 September

review, Homework 1 due, Exam 1, start Data & Evidence

30 Sept – 4 Oct

Data and Ideal Data (general)

7-11 October

Data (forensics)

14-18 October

finish Data, Homework 2 due, Exam 2, begin Evaluation

21-25 October

Correlation vs. Causation

28 Oct – 1 Nov

Controls, Experiments; an in-class Homework will be undertaken for credit

4-8 November

Experiments, start Impediments

11-15 November

Homework 3 due, Exam 3, Impediments

18-22 November

Conflict & bias

25-29 November

Conflict & bias

2-6 December

Conflict, Homework 4 due, Exam 4



Optional Help Sections: times and locations (not in catalog; you do not register for these and there is no University credit associated with these)

Times will be scheduled during the first week of class; they will meet only for weeks announced.










office hours*

email **





Jim Bull

PAT 131

W 1:00-4:00 (or by appt)





Patricia Salerno

PAT 122

M 3:00-5:00





Mariana Vasconcellos

PAT 121B

T 16:00-18:00





Matt Paff

PAT 130

M 13:00-15:00


*- if office hours overlap with Help Session times, then for those weeks when Help Sessions meet, it will usually be the case that the person’s office hours will be held during the Help Session in the Help Session room.  Also, if you are unable to make scheduled office hour times or Help Session times, you should make arrangements to meet with us at a time of your convenience.



** in case of emergencies, but not for routine class questions, you may contact


Course content

This class teaches an evidence-based method of making decisions: how to evaluate evidence, what alternatives to consider, and what to trust. The main ideas are taken from the scientific method, but the emphasis is on applying that style of decision-making to all sorts of normal problems in daily life. You should learn how to evaluate a newspaper article about some new claim or discovery, what kinds of limitations underlie any study (and thus how to look for weaknesses), and how to improve almost any goal-oriented procedure. The course content consists of lectures and demonstrations (plus a few short videos) in class.  Your course grade is determined by your performance on the exams, written homework assignments, a few on-line quizzes and an on-line survey. 

As noted above, lectures mostly follow the order and content in the class book (Scientific Decision-Making) written by Pease and Bull (modified by Chis Warnock and Konrad Prus in 2012), although lectures also augment the material in the book.  In addition, a few lectures may not be in the book, and lectures will often describe and discuss current events that are not in this book.  So whether you come to lecture or not, you should know what was covered in class for the exams.


Syllabus (this document)

The syllabus describes the procedures, materials and events/schedules for Bio301D.  It is not only useful at the beginning of the semester, but it is also relevant throughout the course, as it tells you how to challenge exam questions, whether late homework is accepted, and many other things.

Updates.  If it is necessary to make changes during the semester in exam dates, homework due dates or other aspects of the course syllabus and conduct, we will announce these changes in lecture and post a new syllabus and post a notice on the class web site. You are responsible for all announced changes, whether or not you attend lecture.

Course book

We do not use a standard text for this course. We lecture from our own material and from various publications in the scientific literature, news, and other sources. We have written a book (Scientific Decision-Making) that contains most of the class material. It is available for free on the class web site .  In the past, a hard copy has been available by request for around $20 at Paradigm Notes, near 24th & Speedway.  Students enrolled in Bio301D may make a personal photocopy or electronic copy of the book for use in this course for free. One way or another, you are likely to want access to it, but don’t feel that you need to spend any money to get it. Furthermore, although the book contains most of the material for this class, the lectures include current events and a few new topics each semester that are not in the book.


Downloading the book, sample problems, and homework

The class website ( has the on-line class material and allows you to download the book.   Note that you may access everything without going through Blackboard and that no password is required (homework assignments do need to be uploaded to Blackboard).  You may choose to purchase hard copy of the book at Paradigm, but you at least have the option of free downloads. 

The syllabus, book and homework assignments may be modified during the semester.  You will be notified of any changes, but you should be aware that any downloads of material done at the beginning of the semester (and the Paradigm hard copy) will not have those updates.

Help sessions (times and rooms given above):

Help Sessions are offered with this course. They are optional, in that your attendance at them does not affect your grade, and they were not part of your registration. They will not meet every week – they meet only during the times announced in class. They are intended as help and practice sessions. They will be used (i) for help with homework, and (ii) to go over practice exams. Students are not assigned to particular sessions; instead, you go to any one you want (or can). If you cannot make at least one time (and in a class of 400, there will be several such cases), you can make other arrangements with the TAs or Bull.

Practice exams. In the 1-2 weeks preceding a scheduled exam, the corresponding exams from the previous 3-4 years will be posted on the class website.  You will be able to "take" the exams and then go over the answers in Help Sessions. Keys will also be posted so that you are not forced to attend a Help Session to obtain the answers.



You will be given timely access to your exam scores and homework scores throughout the semester.  There is a standard 1-week period after you are given access to scores in which you may report mistakes so that we may correct them. This 1-week window applies to any opportunities for points that you are provided in class – exams, homework, surveys or other means of awarding points.  If you have an extended absence, then you should document your excuse within a week of returning to class.  The goal here is to get these matters addressed during the semester rather than at the end.

There are 4 exams and 5 homework assignments, due on the dates given in the calendar above.

There will be at least 11 on-line quizzes/surveys, dates to be determined (all but one administered through CNS QUEST).



Four homework assignments are described on the class web site and in the book, and will also be discussed in lecture; the 5th will be of a different type as described in class.  The QUEST quizzes will be announced during the semester as they become relevant and due. 

Only your 3 highest exam scores will count towards your final grade (If you take all four exams, your lowest exam will be dropped. Or you may choose to not take one exam). Similarly, only your 4 highest homework scores will count towards your final grade.  And you can get credit for at most 8 QUEST quizzes.  Each exam will be worth 100 points, each homework will be worth 40 points, and each QUEST quiz will be worth 12 points.  Your final grade will be determined from the sum of your

+3 highest exam scores (100 each)

+4 highest homework scores (40 each)

+8 highest QUEST quizzes (12 each)


compared to a threshold. There are minimally 3*(100)+4*(40) +8*(12) = 556 points possible in the semester. We will use the following grade thresholds.  Note that a ‘+’ will be assigned grades in the top 25% of the intervals (except for A).


A         (500 and above)            (90% or more of 556 points)


B+, B        (499-445)                      (80%)


C+, C      (444-389)                      (70%)


D+, D        (388-334)                    (60%)


F                         333 and below



We may change these thresholds to make them more lenient -- that is, to benefit you; we will not make them more stringent.  Furthermore, any opportunities for additional points will merely be added to your total and thus make it easier to get a higher grade – we will not rescale your points if there is an opportunity to make more than 556 total points.

We advise against using the "best 3 of 4" policy as an excuse to miss any of the first three exams. The first exam is typically the easiest, and you may later regret not taking it. Likewise, if you miss one of the first three exams for an unexcused reason and then miss another with a valid reason, you will get a zero for one of your three top scores.  Importantly, you are not allowed to make up an exam unless you present documented, timely excuses for missing two exams (see the details below for what constitutes "timely"). So missing one exam without a legitimate excuse means that you will get a zero as one of your top 3 exams if you miss a second exam, regardless of whether you have a legitimate excuse for the second missed exam. 


There are two lecture sections, one at 10:00 and another at 11:00; they are in the same room, and the material for each is the same.  Subject to seating limitations, you may attend either lecture.  But you must attend the exam at the time for which you are registered (subject to a possible penalty unless you have prior permission). If you are registered for the 10:00 class, you must take the 10:00 exam, and if you are registered for the 11:00 class, you must take the 11:00 exam.  This restriction also applies to the day we will do an in-class homework assignment.

Bring a photo I.D. to all exams. You should also bring a #2 pencil and eraser for exams.

Exams use scantron forms.  Exams and keys from previous years will be made available on the web in advance of each exam so that you may familiarize yourself with the types of questions likely to be asked. 


Correcting and challenging exam grading:  a 1-week window

Copies of the exams and keys are posted within hours of the exam so that you can see how the exam was graded.  The complicated nature of many questions leads some students to ask about or even object to the way that questions were graded.  You may ask how questions were graded in person or over email, but there is also a formal procedure for challenging the grading of answers; if successful, these challenges could result in a more favorable grading of your answer.  These formal challenges to the grading of exams must be presented by email or in writing to Jim Bull within 1 week of the date the exam results are posted. Challenges relating to the amount of partial credit given for incorrect answers are never successful - don't bother explaining that you think you should get some credit for getting two of 10 grouped questions correct.  Likewise, you may not challenge an exam on the grounds that you were misled by one of us when you asked a question during the exam; if a question was genuinely misleading, then that should be the basis of the challenge, not the fact that we did not tell you the answer. Some grouped questions don't give any partial credit. The assignment of points and partial credit depends on many factors, such as how difficult the question is, whether you had access to that question in the sample problems, and how serious a misunderstanding is implied by a wrong answer.

Challenges may cost you points.  If your challenge to a question indicates that you do not understand the issues, you can lose 1 point on that question.  This penalty may never be used and is not intended to dissuade you from challenging a question.  Rather, it is intended to ensure that you understand the question and answers before offering a challenge.  You will not lose points by indicating that you interpreted the question differently than it was intended, but you could lose points if your challenge indicates that, after getting your exam back, you still don’t understand the issues needed to answer it. 

You may challenge a maximum of two questions per exam.  If you think that more than two questions had problems, use the best two cases for your challenges and get someone else to challenge the others.  If a question has fundamental problems, then it will be regraded for the entire class, so you can benefit by someone else’s challenge.  Probably at least half the challenges that are accepted lead to regrading of the entire class (done in such a way that no one’s score goes down).

The format for challenges to the key, whether on paper or email must include the following information:

1) Your exam keycode and the number of the exam in the semester (first, second, etc.)


2) The problem number challenged with a brief description of what the problem was about.


3) The letters of the answers required by the key


4) The letters of the answers you put down


5) A (partial) wording of the options that differ between the key answers and your answers. For example, if the key required (A) (B), but you only put (A), you should indicate enough of what option (B) said, so that your challenge can be evaluated without going back to the exam (e.g., "option (B) was violation of protocol.") This information will enable a rapid processing of your challenge.


6) A statement of why you think your answer should be credited (this is the important part).


If your challenge deviates from this format so much that we cannot understand it or cannot evaluate it without going back to your version of the exam or your answer sheet, there is a good chance that your challenge will be dismissed regardless of its content. Class size is large and we need your cooperation in expediting challenges.  Furthermore, we do not engage in a dialogue about challenges or send email responses back.  We will evaluate those that are submitted and regrade where appropriate, but you will not be notified of the outcome except via changes to your exam score.

The fourth and last exam is scheduled for the last week of class in the lecture hall. University rules dictate that we obtain permission from the Chair to be exempted from giving a final exam, and if we obtain that permission (you will be notified during the semester either way), that fourth exam will merely cover the material since the third exam. If we cannot get permission to give the fourth exam on this date, the fourth exam will instead be given at the time and place scheduled for the final, and it will then cover material from the entire semester.  If you wish to submit a written challenge to our grading of the fourth exam, this must also be done within 1 week of when we post scores.

Make-up exam policy – no make-ups for those who miss just one exam.

We do not give make-up exams to students who miss only one of the four scheduled exams. If you miss two or more exams, we will give you a makeup exam only if you present us with a documented, compelling excuse for all exams you missed. Furthermore, when you miss an exam for a documented, compelling reason, you must give us your documentation within one week of the exam date (or your return-to-school date, if your documented excuse indicates that you were unable to attend classes for some time after the exam). For example, we would not give a make-up exam to a student who missed the first and second exams, but who did not provide us with the documentation for missing the first exam until after the second exam. We would give this student a make-up for the second exam only if they gave us a documented excuse for missing the first exam within one week of the first exam, and a documented excuse for missing the second exam within one week of the second exam.  So if you miss an exam (unless it is the last) let Bull know why pronto, so that you don’t get a bad grade by missing a second exam.  If you oversleep but can still get to the exam during the exam period, do so to see if we can accommodate you.

Homework assignments and late homework policy

Homework assignments require you to find an article (newspaper, magazine, web, or other) and fill out a template that relates the information in the article to material presented in class. The 301 home page provides a link to the details about these assignments. 

Turning in Homework.  This year (for the first time ever) your homework should be uploaded to our class in your BlackBoard account.  Each homework assignment has a writeable pdf file with fields that need to be filled in.  You need to upload the filled pdf and the article.  If you have the hard copy of an article, you may need to scan it and upload the scan. 

Homework grading may be challenged, just as exam grading may be challenged. The deadline for a homework challenge is one week from the time its grading is first poste. Like exam challenges, a homework challenge must be presented in the form of an explanation for which part of the grading you are challenging and why you think an error has been made. In addition, homework challenges may entail a blind regrading of the entire assignment, and your score could go down. So be confident that your challenge has merit before turning it back to us (you can ask about it before you challenge). Also, we will do any regrading as blindly as possible. So please don't indicate that you need "x more points" to get an A at the end of the semester.

No End-of-Semester Special Options

Students slightly below a grade threshold often look for ways to get the few extra points at the end of the semester. The options at the end of semester are the same as they are during the semester:

i)                   fix scantron errors on the fourth exam (the deadlines for other exams have passed)

ii)                 challenge the exam 4 key

iii)                challenge HW4 grading (your score could go down)

There is simply no other work that is allowed to get such points – no reports, no redoing homeworks or retaking exams.  The only way to get points for the class is with the four exams and four homeworks, regardless of the grade a student receives, whether passing or failing.

Professor accountability for errors in electronic files and Student responsibility for keeping hard copies and reporting recording errors in a timely fashion.

Keep your returned exam and homework material until the end of the semester.

In handling electronic files for large classes, it is easy for the staff to make mistakes -- both big and little ones. For example, a student may forget to fill in a pad number on an exam, and the instructor may accidentally insert the number of another student in attempting to fix the problem. Or, the professor's manipulation of the class Excel file may inadvertently shuffle some columns but not others so that the posted scores do not correspond to the actual recorded scores for any of the students. Mistakes such as these and others will be corrected whenever detected, and the instructors are under no obligation to honor such errors whenever the student has, in due time, access to information that would reveal the error. Hard copies of all assignments (there may be none this year) and scantrons (Xerox copies) are returned in class, and exam keys are posted, so that any incorrect grading may be identified by the student, and any erroneous recording may likewise be recognized. If we post an incorrect score and then discover our error, don’t expect that the previous score should apply if access to the hard copy records would have revealed the error. Additionally, any challenges to class records must be supported with any originals that were returned in class or files you uploaded (do not delete them until the final grades have been posted).


Attendance is not directly a factor in calculation of your grade. Nonetheless, you are responsible for material presented in class, regardless of whether you attend. And you must attend to take the exams and must complete on-line quizzes and assignments on time (which does not require attendance).  In the past, one student suggested that we should grade their exam more leniently because they missed lecture because of a dentist appointment. That request was denied -- it is your responsibility for making up the missed material, regardless of how legitimate your excuse for missing class. In the event you have missed class, you may wish to consult someone who did attend to determine what was covered.

Other Matters

         Bio301d and the UT core curriculum

Bio301D will count toward the Science & Technology, Part I core curriculum if paired with another appropriate biology class.  The core requirements for this part of the core read as follows (Texas core code 030):

Six hours in a single field of study. The following courses may be counted:

                                             Biology 301D, 301L, 301M, 311C, 311D, 315H, 325H, 326M, 446L, 365S
It is recommended that students complete two courses chosen from Biology 301D, 301L, and 301M; or one of the following pairs of courses: Biology 311C and 311D, Biology 311C and 326M, Biology 311C and 446L, Biology 311C and 365S, Biology 315H and 325H.


Students with disabilities

Any student with a documented disability (physical or cognitive) who requires academic accommodations should contact the Services for Students with Disabilities area of the Office of the Dean of Students at 471-6259 as soon as possible to request an official letter outlining authorized accommodations.

Student grievances, complaints, dishonesty, and other matters

If you have a problem with the conduct of the course (e.g., you take issue with teaching methods, feel that the classroom environment is not conducive to proper education, or another matter), please first discuss the matter with Jim Bull or one of the TAs. If you are not satisfied, you may take the matter higher up. The next step would be to request an audience with the appropriate official of Biology, and an even further step is to speak with the Dean's office (either the Dean of Students or the Dean of the College of Natural Sciences). There are various sources of information about how to proceed with complaints and who can help you, listed below:

Students with disabilities may request appropriate academic accommodations from the Division of Diversity and Community Engagement, Services for Students with Disabilities, 512-471-6259,

Grievances: contact the Ombudsman at 471-3825

Penalties for (and definition of) academic dishonesty:

Prohibition of sexual harassment:

Religious Holidays.  By UT Austin policy, you must notify me of your pending absence at least fourteen days prior to the date of observance of a religious holy day.  If you must miss a class, an examination, a work assignment, or a project in order to observe a religious holy day, you will be given an opportunity to complete the missed work within a reasonable time after the absence.

The following recommendations regarding emergency evacuation from the Office of Campus Safety and Security, 512-471-5767, :

-        Occupants of buildings on The University of Texas at Austin campus are required to evacuate buildings when a fire alarm is activated. Alarm activation or announcement requires exiting and assembling outside.

-        Familiarize yourself with all exit doors of each classroom and building you may occupy.  Remember that the nearest exit door may not be the one you used when entering the building.

-        Students requiring assistance in evacuation shall inform their instructor in writing during the first week of class.

-        In the event of an evacuation, follow the instruction of faculty or class instructors.

-        Do not re-enter a building unless given instructions by the following: Austin Fire Department, The University of Texas at Austin Police Department, or Fire Prevention Services office.

-        Behavior Concerns Advice Line (BCAL):  512-232-5050

-        Link to information regarding emergency evacuation routes and emergency procedures can be found at:


A request from us to you

The coordination of a large class with considerable electronic software faces various logistical problems. In the past, we have had such difficulties as rooms accidentally scheduled for two classes at the same time, classrooms reassigned after they had been published in the Course Catalogue, and a bomb threat for the building in which we were lecturing (which we avoided interpreting as a reflection of student attitudes toward our course). It is difficult for us to anticipate and apprehend all that might go wrong with the administration of peripheral aspects of a large class such as this one, and we solicit your help in identifying problems when they arise. If something is wrong with the class, please contact Jim Bull (471-8266, or 471-5661), or one of the TAs pronto. If they are not available, please leave a message with the Biology office (471-4882) and explain the problem to the staff there.