Biology 104: Summer 2014JOHN JAY COLLEGE OF CRIMINAL JUSTICE

THE CITY UNIVERSITY OF NEW YORK

Professor Lissette Delgado-Cru;zata, Ph.D., M.P.H. (Lecture and Recitation Instructor)Email: Idelgado-cruzata@jjay.cuny.edu Phone: 212.621.3743 Room: NB 05.66.17Office Hours: By appointment

Course description: Biology 104 is the second half of the modern biology sequence. It continues the in-depthexploration of the basic properties of living systems on the cellular, and organismallevels. In addition, evolutionis introduced. Representative organisms from the plant and animal kingdoms are studied in detail. Thelaboratory portion of the course emphasizes phylogeny and teaches basic microscopy and dissection skills.

Learning Goals of Bio104:

1. Knowledge: Students will understand the basic concepts in the field of modern biology:• Tissue structure and function• Anatomy and physiology of the digestive, circulatory, respiratory, excretory, reproductive, and nervous

systems• Evolution• Plant anatomy and physiology

2. Reasoning: Students will use knowledge of evolution to solve problems regarding phylogeny andorganismal development

3. Practical Skills: Students will learn laboratory skills and experimental techniques:

• dissection techniques• phylogenetic classification

4. Communication: Students will apply communication and analytical skills by orally presenting researcharticles related to the content of the course. Students will also engage in scientific writing by preparing areview of a scientific article.

Text and Laboratory Manuals

Available in the Bookstore:• Campbell, N. & Reece, J. (2008). Biology (8th ed.) New York: Pearson- Benjamin Cummings, ISBN-10:

0321560493. Volume 2: John Jay College Custom Edition

Online Resources:www.masteringbiology.com. course id: MBDELGADOCRUZA TA13468

Access codes are provided with the custom textbook, if bought in the John Jay Bookstore. Students that havepurchased the text separately must purchase an access code through the Mastering Biology website. Thiswebsite will have the homework assignments, these are required and wiff be graded.

Available on Blackboard:• Laboratory Manual for Biology 104 at John Jay College.• Recitation articles and instructions for presentation and writing the paper• Lecture assignments, lecture readings and study guides

Students are responsible for accessing Blackboard frequently to complete assignments and findreading material

Blackboard: Important course announcements, lecture notes, homework assignments, review questions, adiscussion forum for Q and A, and other resources will be posted to the course on Blackboard. Please checkregularly. Furthermore, students are responsible for checking their John Jay e-mail account regularly forimportant announcements. Contact blackboardstudent@jjay.cuny.edu or DolT (212.237.8200), not your Bioinstructor, for help with e-maif or Blackboard.

You must check Blackboard and your John Jay E-mail account regularly.You are responsible for any and all course information, assignments, announcements,

and communication that occurs through blackboard and/or your email account.

Grade Distribution and Class Policies 93.0 and above A90.0 - 92.9 A-87.0 - 89.9 B+83.0 - 86.9 B80.0 - 82.9 B-77.0 - 79.9 c+73.0 - 76.9 C70.0 - 72.9 c-67.0 - 69.9 0+63.0 - 66.9 060.0 - 62.9 0-below 60.0 F

Grading Scale:Lecture (50%):Exams 35%Assignments 10%Homewo~ 5%

Recitation (20%)Laboratory (30%)

The grading scale here (7) isthe official grading scale for this course. There will be no exceptions to this scaleand grades will not be rounded up, except as explained here. Following allcomputations, the grade will be rounded to the nearest tenth of a point in MicrosoftExcel (one decimal place, e.g., 97.2%). This is the final grade and no furthermanipulations will be made. The scale here (7) will then be strictly used. Thismeans that a 72.949% is a "C-" and a 72.950% is a "C." These calculations aredone by the computer so there are no judgment calls or "leniency."

Lecture Attendance: You are required to attend the lectures. An attendance sheet will be circulated duringclass. It is your responsibility to sign the sheet during class. You will be allowed three absences with norequired documentation. However, beginning with the fourth undocumented absence, your final course gradewill be penalized by two pOints (2%) for each undocumented absence. Arrivals later than five minutes after thestart of class will count as a one-half absence. Attendance is also required for recitation and lab.

Lecture Exams: There are five in-class lecture exams. All exams are of equal weight, including the final.There is NO AUTOMA TIC DROP TEST in this class.

If you miss an exam (or foresee that you will miss an exam) for any reason, you MUST contact the instructoras soon as humanly possible. You may be allowed to take the exam late (or early). However, you areONLY eligible for this one-time consideration if you contact the instructor immediately and you arrange to takethe exam BEFORE the corrected exams are handed back to the class. In all other cases, the missed examWILL count as a ZERO. (Exception: a documented medical or family crisis may result in being excused froman exam, but this will only be allowed ONCE. Further missed exams will count as a zero, regardless ofreason.)

Class Protocol: All electronic devices, except for laptop computers, must be turned off in class. Recording isnot permitted except with the specific permission of the DSS office.

CUNY John Jay College expects students to maintain standards of personal integrity that are in harmony withthe educational goals of the institution; to observe national, state, and local laws and University regulations;and to respect the rights, privileges, and property of other people. ANYONE disrupting the class will beremoved.

Disruptive behavior will result in 5 points being taken from your final grade.

Accommodations for Students with Disabilities: Qualified students with disabilities will be providedreasonable academic accommodations if determined eligible by the Office of Accessibility Services (OAS).Prior to granting disability accommodations in this course, the instructor must receive written verificatio.n of astudent's eligibility from the OAS which is located at L66 in the new building (212-237-8031). It is the student'sresponsibility to initiate contact with the office and to follow the established procedures for having theaccommodation notice sent to the instructor.

Statement of the College Policy on Plagiarism: Plagiarism is the presentation of someone else's ideas,words, or artistic, scientific, or technical work as one's own creation. Using the ideas or work of another ispermissible only when the original author is identified. Paraphrasing and summarizing, as well as directquotations require citations to the original source. Plagiarism may be intentional or unintentional. Lack ofdishonest intent does not necessarily absolve a student of responsibility for plagiarism. It is the student'sresponsibility to recognize the difference between statements that are common knowledge (which do notrequire documentation) and restatements of the ideas of others. Paraphrase, summary, and direct quotationare acceptable forms of restatement, as long as the source is cited. Students who are unsure how and when toprovide documentation are advised to consult with their instructors. The Library has free guides designed tohelp students with problems of documentation. (JJC Undergraduate Bulletin, see Chapter IV AcademicStandards). In this course, we will use www.turnitin.com for all the submitted written work.

Lecture Schedule

Date DAY LECTUREMay 28 Wed CHAPTER 22: Descent with Modification

CHAPTER 23: Evolution of Population

Jun 02 Mon CHAPTER 24: The Origin of SpeciesCHAPTER 25: History of Life on Earth

Jun 04 Wed CHAPTERS 27: Bacteria and Archaea

Jun09 Mon EXAM #1: Chapters 22-25

Jun 09 Mon CHAPTERS 28: Protists

Jun 11 Wed Cont. Protists ChapterCHAPTER 31: Fungi

Jun 16 Mon CHAPTER 29: Plant Diversity ICHAPTER 30: Plant Diversity II

Jun 18 Wed CHAPTER 35: Plant Form and FunctionCHAPTER 40:Animal Form and Function

Jun 23 Mon EXAM #2: Chapters 27-31

Jun 23 Mon CHAPTER 41 :Animal Nutrition and Digestion

Jun 25 Wed CHAPTER 42: Circulation and Gas Exchange

Jun 30 Mon CHAPTER 44: Osmoregulation and Excretion

Jul02 Wed CHAPTER 45: Hormones & Endocrine SystemCHAPTER 49: Nervous Systems

Jul07 Mon EXAM #3: Chapters 35,40,41,42,44

Jul07 Mon CHAPTER 46:Animal Reproduction

Jul09 Wed CHAPTER 52: Introduction to EcologyCHAPTER 53: Population Ecology

PAGES452-467468-485

487-506507-533

556-574

576-599

636-653

600-617618-636

738-754852-874

875-897

898-929

954-975

976-9971064-1086

998-1020

1148-11731174-1197

Jul 14

TBD

Mon CHAPTER 54: Community Ecology

EXAM #4: Chapters 45, 46, 49, 52, 53, 54

1198-1221

Bio104 Recitation

Group work: Students will work with classmates in groups of up to four students. Groups will be created in thefirst Recitation class. If a student is absent, he or she should approach the instructor as soon as possible to beassigned to a group. The group assignments include: in-class presentations, discussions and a paper. Theassignments will be graded as a group and all members of the group will receive the same grade. Students willoutline the rules for the functioning of their own group, will typed them and hand them in to the professor at thebeginning of the second recitation class. Find below some aspects to consider in creating the rules for yourgroup; however, add others that you find appropriate:

• Best method to communicate• Designate a point person• Group deadline for assignments (for instance, if an assignment is due on Tue in class, the group

deadline could be Fri for editing and reviewing)

Recitation Attendance and Participation is mandatory. Following one "freebie," for every missed recitationclass, a deduction of five (5) percentage points will be taken off of the final recitation grade. Absences may beexcused only with valid written documentation. Because class will NEVER let out early, students are expectedto come to recitation sections with questions about the selected topic or lecture material. Following onewarning, any student that does not actively participate in the in-class activities will be charged an absence.

Recitation Grades: The recitation section comprises 20% of the BI0104 course grade and is based on in-class assignments, attendance and participation, and a final group paper.

AttendanceFinal paperPresentationQuestion/in-class discussion

10%25%50%15%

Assignments: Every week, students will be assigned readings through Blackboard. Students are responsiblefor reading posted articles and each week one or two groups will be assigned to prepare a short Power Pointpresentation based on the readings. The presentation will be of one article, it is expected to be 20-30 min longand will be assigned at least one week in advance. Everyone in the class is expected to prepare at least onequestion for the discussion and ask the question to the presenters. Instructions for all assignments will beposted on Blackboard. it is the student's responsibilitv to follow the rubric for presentation and paperassignments.

At the end of the semester, each student will hand in a short paper. Instructions for the paper will be providedin a separate hand-out by the fourth week of class.

Recitation Schedule

Date TOPICMay 28 Wed Description of class assignments and policies

Reading and presenting scientific literature

Jun 02 Mon Evolution Group #1

Jun 04 Wed Microbiology Group #2

Jun 09 Mon NO PRESENTATION/IN-CLASS GROUP WORK

Jun 11 Wed Fungi Group #3

Jun 16 Mon Plants I Group #4

Jun 18 Wed Plants" Group #5

Jun 23 Mon NO PRESENTATION! IN-CLASS GROUP WORK

Jun 25 Wed Animal Nutrition and Digestion Group # 3

Jun 30 Mon Gas Exchange Group #4

Jul02 Wed Osmoregulation and Excretion! Endocrine System Group #5

Jul07 Mon NO PRESENTATION! IN-CLASS GROUP WORK

Jul09 Wed Human population growth and health Group #1

Jul 14 Mon Ecology Group #2

Jul 16 Wed REVIEW

BIOI04 Laboratory Policies

Dr. Brian Raffertyrafferty.bj@gmail.com

Office NB 03.62Hours: Beforel After lab or by appointment

Laboratory Manual and Course Materials

Laboratory manual: The manual is posted on Blackboard (Lab manual tab) and students are responsiblefor printing each lab in advance and bring it with them. Reading the material in advance is mandatory andwill be tested in a short quiz at the beginning of each lab.

Lab notebook:a. Need to obtain a Marble composition notebook (preferably 100 page)b. To complete the pre-lab portion of your notebook, you need to access the lab manual for

that week on Blackboardc. Pre-lab portion (Sample posted on Blackboard)

i. Pre-Lab HW: Need to complete the pre-lab HW questions embedded in the labmanual (Labeled HQ-l, HQ-2, etc.)

ll. Procedure/Protocol: Need to write out the procedure, which you can fmd in thelab manual. You can summarize and put in your own words, but you needenough info to complete the experiments with only your notebook in front ofyou.

lll. This will be checked before you enter the lab each week and will be graded (10points per lab) and go towards your overall notebook grade

d. In-lab portioni. In-class lecture/discussion notes: Unlike Bio 102/103 lab, taking notes about

each weekly topic and discussion in lab will be key to complete comprehensionof the lab material.

ii. Experimental results and observations: Neat and organized in charts and/orgraphs when possible. Some labs maybe have a chart setup while others requireyou to make your own.Any microscopic observations which you are required to document must bedrawn to take up at least 1/3 of the page and must include size of the field ofVIew.

lll. Interpretations and conclusions of what your results mean and whatconclusions can be drawn from them. Some labs will ask for you to drawspecific conclusions and in the case they do not, either Iwill ask for whatconclusions to draw or have you come up with them on your own

The notebook will be checked weekly for progress and must be handed in for a grade on the day of themidterm and final exams.

Lab safety:You must bring protective eyewear to each lab, and it is available for purchase at thebookstore.You should wear a lab coat or sensible clothing relevant for lab work.No food and drinks are permitted in the lab.The use of cell phones, iPods, mp3 players may not be allowed at any time.

Lab Participation and Attendance

Attendance and Lateness: You are required to attend the laboratory - it is considered a necessary hands-on learning experience. More than three (3) unexcused absences are considered excessive and you willreceive a zero for the lab part of the course.

Lateness (missing first roll call or a class quiz administered at the start of a lab) is considered one-half(112) an absence. Missing second roll call is considered a full absence. Any quiz missed due to unexcusedabsence or lateness cannot be made up and will count as a zero. You are responsible for providingacceptable written documentation for each excused absence or lateness or it will not be excused.

Participation: Many lab activities are hands-on and you are expected to actively participate even whenpart of a group - otherwise, you will not get full credit for attendance.

Grade distribution

Lab quizzes and exams: A quiz will be administered at the start of ALL labs. You are responsible forbeing prepared by doing the assigned pre-lab reading. Quizzes will be based on this prelab reading as wellas material from the previous lab class.

There will be a mid-term and fmal exam. Both exams will have practical and written sections.

Lab homework: Homework problems will be assigned at the end of most labs, which will help youprepare for both next week's lab quiz and the midterm and final exams. These will be collected andgraded on a weekly basis. Any uncollected HW assignments will be graded at the midterm and finalnotebook checks.

Laboratory Grades: The laboratory section will comprise 30% of the course grade for BI0104. In-classquizzes will cover material from the assigned reading. Thus, the assigned reading MUST be done beforethe laboratory. Lab Grades will be based on the following required components:

20% In-class quizzes20% Lab Notebook **30% Midterm lab exam30% Final lab exam

** (Notebookfor Lab#1-6 due at the midterm exam, Lab#7, #12 and dissection notes due atfinal exam)

Laboratory Schedule

Date Lab#: Topic Covered

Wed 5/28 Lab#1 Course Description, policies and grading.Introduction to Cladistics

Mon 6/2 Lab#3 Molecular Phylogenetics

Wed 6/4 Lab#4 Introduction to the microscopeMicrobiology: Eubacteria and Protista

Mon 6/9 Lab#5 Cont. Protist (Algae, Volvocine Series) and Fungi

Wed 6/11 Lab#6 Plants

Mon 6/16 Lab#2 Field Trip to the American Museum of Natural History

Wed 6/18 LAB MIDTERM EXAM (Labs #1-6)

Mon 6/23 Lab#7 Animal Diversity I

Wed 6/25 Lab#8 Animal Diversity II

Mon 6/30 Lab#9 Animal Diversity III

Wed 712 Lab#10 Dissection of the Pig

Mon 7/7 Lab#11 Dissection ofthe Pig

Wed 7/9 Lab#12 Dissection of the Pig

Mon 7/14 LAB FINAL EXAM (Labs #7-14)