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Faculty of Science School of Biological Sciences

BIOL1001: Concepts in Biology Semester 1 , 2016 | 6 Credit Points | Coordinator: A/Prof Charlotte Taylor ([email protected])

1 Introduction BIOL1001 is a 6 credit point unit of study that introduces the major themes of modern biology. The material we present in the unit emphasizes how biologists investigate important issues, and introduces tools we use in studies of molecules, cells, whole organisms and communities. Topics covered in lectures and practicals include: introductory cell biology, with an emphasis on how cells function and obtain and use energy; introductory molecular biology, including the role of DNA in protein synthesis including the genetics of organisms and current developments in DNA technology; theories of evolution and phylogenetic analysis, and how they are used to interpret the origins of the diversity of modern organisms; introduction to animal and plant biodiversity, with an emphasis on Australian organisms, as well as the biogeographic processes which gave rise to them. 1.1 Assumed Knowledge and Prohibitions It is assumed that students have studied the equivalent of 2 unit HSC biology. Students who have not completed HSC biology (or equivalent) are strongly advised to take the Biology Bridging Course (in February). For more information on the Biology Bridging Course, see http://sydney.edu.au/science/biology/studying_biology/bridging-course.shtml

2 Course Aims, Learning Objectives and Graduate Attributes 2.1 Course Aims

This unit of study introduces the major themes of modern biology. The material we present in the unit emphasizes how biologists investigate important issues, and introduces tools we use in studies of molecules, cells, whole organisms and evolutionary processes. 2.2 Learning Outcomes After successfully completing this unit, you should be able to demonstrate: 1. an understanding of the concepts and language of modern biology; 2. understanding of complex biological issues; 3. the capacity to find and analyse information; 4. enhanced skills in written, oral and interpersonal communication; 5. a team approach both to scientific investigation and the process of learning; 6. basic skills in computing, numeracy and data handling; 7. basic skills for use of technical equipment in laboratories 8. a sense of responsibility and independence as a learner and a future scientist

2.3 Graduate Attributes Graduate Attributes are generic attributes that encompass not only technical knowledge but additional qualities that will equip students to be strong contributing members of professional and social communities in their future careers. The overarching graduate attributes identified by the University relate to a graduate’s attitude or stance towards knowledge, towards the world, and towards themselves. These are understood as a combination of five overlapping skills or abilities, the foundations of which are developed as part of specific disciplinary study. For further details please refer to the Science faculty website at: http://www.itl.usyd.edu.au/graduateAttributes/facultyGA.cfm?faculty=Science Graduate Attributes

Learning Outcomes

A Research and Inquiry A1.

Apply scientific knowledge and critical thinking to identify, define and analyse problems, create solutions, evaluate opinions, innovate and improve current practices.

1, 2, 3, 5, 6, 8

A2.

Gather, evaluate and deploy information relevant to a scientific problem.

1, 2, 3, 6, 8

A3.

Design and conduct investigations, or the equivalent, and analyse and interpret the resulting data.

1, 2, 3, 4, 5, 6, 7, 8

A4.

Critically examine the truth and validity in scientific argument and discourse, and evaluate the relative importance of ideas.

1, 2, 3, 4, 8

A5.

Disseminate new knowledge and engage in debate around scientific issues.

1, 2, 4, 5, 8

A6.

Value the importance of continual growth in knowledge and skills, and recognise the rapid, and sometimes major, changes in scientific knowledge and technology.

2, 3, 5, 8

B Information Literacy B1.

Use a range of searching tools (such as catalogues and databases) effectively and efficiently to find information.

3

B2.

Access a range of information sources in the science disciplines, for example books, reports, research articles, patents and company standards.

3, 6

B3.

Critically evaluate the reliability and relevance of information in a scientific context.

1, 2, 3, 4, 5

B4.

Consider the economic, legal, social, ethical and cultural issues in the gathering and use of information.

2, 3, 8

B5.

Use information technology to gather, process, and disseminate scientific information.

3, 8

C Communication C1.

Explain and present ideas to different groups of people in plain English.

3, 4

C2.

Write and speak effectively in a range of contexts and for a variety of different audiences and purposes.

1, 2, 4

C3.

Use symbolic and non-verbal communication, such as pictures, icons and symbols as well as body language and facial expressions, effectively.

4, 6

C4.

Present and interpret data or other scientific information using graphs, tables, figures and symbols.

1, 3, 6

C5.

Work as a member of a team, and take individual responsibility within the group for developing and achieving group goals.

4, 5

C6.

Take a leadership role in successfully influencing the activities of a group towards a common goal.

5, 8

C7.

Actively seek, identify, and collaborate with others in a professional and social context.

4, 5

D Ethical, Social and Professional Understanding D1.

Demonstrate an understanding of the significance and scope of ethical principles, both as a professional scientist and in the broader social context, and a commitment to apply these principles when making decisions.

2, 8

D2.

Appreciate the importance of sustainability and the impact of science within the broader economic, environmental and socio-cultural context.

1, 2, 8

D3.

Demonstrate empathy with, and sensitivity towards, another's situation, feelings and motivation.

E Personal and Intellectual Autonomy E1.

Evaluate personal performance and development, recognise gaps in knowledge and acquire new knowledge independently.

8

E2.

Demonstrate flexibility in adapting to new situations and dealing with uncertainty.

5, 8

E3.

Reflect on personal experiences, and consider their effect on personal actions and professional practice.

2

E4.

Set achievable and realistic goals and monitor and evaluate progress towards these goals.

E5.

Demonstrate openness and curiosity when applying scientific understanding in a wider context.

2.4 Threshold Learning Outcomes

8

The Threshold Learning Outcomes (LTOs) are the set of knowledge, skills and competencies that a person has acquired and is able to demonstrate after the completion of a bachelor degree program. The TLOs are not equally weighted across the degree program and the numbering does not imply a hierarchical order of importance. Threshold Learning Outcomes

Learning Outcomes

1 Understanding science 1.1

Articulating the methods of science and explaining why current scientific knowledge is both contestable and testable by further inquiry

1, 2, 3, 4, 8

1.2

Explaining the role and relevance of science in society

1, 2

2 Scientific knowledge 2.1

Demonstrating well-developed knowledge in at least one disciplinary area

1, 2, 3

2.2

Demonstrating knowledge in at least one other disciplinary area

1, 2, 3

3 Inquiry and problem solving 3.1

Gathering, synthesising and critically evaluating information from a range of sources

2, 3, 8

3.2

Designing and planning an investigation

1, 2, 3, 5, 8

3.3

Selecting and applying practical and/or theoretical techniques or tools in order to conduct an investigation

2, 5, 6, 7

3.4

Collecting, accurately recording, interpreting and drawing conclusions from scientific data

1, 2, 3, 6

4 Communication 4.1

Communicating scientific results, information or arguments, to a range of audiences, for a range of purposes, and using a variety of modes

2, 4

5 Personal and professional responsibility 5.1

Being independent and self-directed learners

3, 8

5.2

Working effectively, responsibly and safely in an individual or team context

5, 6, 7, 8

5.3

Demonstrating knowledge of the regulatory frameworks relevant to their disciplinary area and personally practising ethical conduct

3, 8

For further details on course learning outcomes related to specific topics see Blackboard.

3 Work, Health and Safety 3.1 University Work, Health and Safety Policy We are governed by the Work Health and Safety Act 2011, Work Health and Safety Regulation 2011 and Codes of Practice. Penalties for non-compliance have increased.

Everyone has a responsibility for health and safety at work. Information about the Uni-versity’s Work Health and Safety policy http://sydney.edu.au/whs/policies/legislation.shtml. explains the responsibilities and expectations of workers and others, and the procedures for managing WHS risks associated with University activities. Your staff, lecturers and supervisors must do what they can to eliminate or minimise risks to health and safety so far as is reasonably practicable. Students and visitors - are required to take reasonable care that their acts or omissions do not adversely affect the health and safety of themselves or others, and to comply with any reasonable instructions given to ensure health and safety. With respect to working in the practical classes, “reasonable care” includes wearing a lab coat and closed in shoes (the top of the foot must be covered), and complying with safety instructions when handling hazardous materials and/or equipment. 3.2 General Laboratory Safety Rules · No eating or drinking is allowed in any laboratory under any circumstances · A laboratory coat is mandatory · Appropriate footwear is mandatory · If you are thirsty, you can leave the laboratory to have a drink · Covered shoes must be worn at all times in laboratories. You will not be allowed in the laboratory in open toed shoes · Follow safety instructions in your manual and posted in laboratories · In case of fire, follow instructions posted outside the laboratory door · First aid kits, eye wash and fire extinguishers are located in or immediately outside each laboratory As a precautionary measure, it is recommended that you have a current tetanus immunisation. This can be obtained from University Health Service (http://www.unihealth.usyd.edu.au/). 3.3 Emergency Evacuation Procedures If you hear the alert signal (interrupted beeping sound), prepare to evacuate: 1. Check for any sign of immediate danger 2. Shut down equipment and processes 3. Collect any nearby personal items If you hear the evacuate alarm (rising repeated tone): 1. Listen to the instructions given over the loudspeaker 2. Follow the instructions to evacuate the building and proceed to the assembly area 3. Escort visitors and those who require assistance 4. Do not use lifts 3.4 Risk Assessment

Risk Assessment aims to identify any foreseeable hazard that may arise in the workplace and to assess the risk of harm arising from the identified hazards. MSDS provide employees, self-employed persons, workers and other health and safety representatives with the necessary information to safely manage the risk from hazardous substance exposure. For each practical class, a risk assessment and relevant MSDS will be available for viewing. It is the responsibility of each student to read the relevant RA before each practical class. Risk assessments are posted on BlackBoard and complete MSDS will be available in a yellow folder in the laboratory as required.

4 Study Commitment The current standard work load for a 6 credit point unit of study is 3-6 hours per week of face-to-face teaching contact hours and an additional 6 hours per week of student independent study. Below is a breakdown of our expectations for this unit. It should be noted that ‘independent study’ is based on what we believe to be the amount of time a typical student should spend to pass an item of assessment. Times are a guide only. In class activities

Hours

Independent Study

Hours

Lectures (25 @ 1 hr each)

25

Preparation for lectures (25 @ 0.5 hr each)

12.5

Practicals (11 @ 3 hrs each)

33

Review and self assessment (12 weeks @ 1 hr each)

12

Preparation for practicals (11 @ 1 hr each)

11

Total

58

Scientific writing

12

Revision for tests/exams

18

Total

65.5

Study Tips

You are now in control of your own study strategy, and as an adult learner it is up to you to devise a study plan that best suits you. Many resources are available to assist your learning, and can be found linked from the Concepts in Biology Blackboard site. The Lizard Lounge (Room 507 Carslaw Building F07) is available during semester from 9:00am 4:45pm Monday to Thursday and 9:00am - 12:00pm on Fridays. It is a place to relax, work with friends on a project, and use computers and microscopes outside of class. We also have resources (e.g. textbooks) available for you to borrow. Student consultations are available by appointment. Please email your lecturer, or Matt Pye ( [email protected])

5 Learning and Teaching Activities Weekly Schedule Lecture times and venues: Lecture 1: Monday 9am Eastern Avenue Auditorium Monday 1pm Footbridge Theatre Lecture 2: Thursday 3pm Eastern Avenue Auditorium Friday 10am Eastern Avenue Auditorium TIMETABLE - 2016 Week, starting

Lectures

Practical

Assessment/ Activity

1. Introduction to Biology Practical 1:Introduction to Labs 1 (CT) and safety induction 29 Feb 2. Organisation of life (DB) 3. Building blocks of cells (TN) 2 Practical 2.Cells, scale, 7 Mar 4. Cellular membranes & substructure and dimensionality communication(DB) 5. Proteins and enzymes Practical 3.Investigating cowpea Laboratory notebook (TN) 3 feedback 14 Mar 6. Searching the literature phosphatase functionality (CT) 7. Respiration (DB) Practical 4.Cellular Respiration in 4 NO LECTURE Yeast 21 Mar (Friday 25th March) Mid-semester break 25 Mar to 4 April Enzyme paper: peer Practical 5.Review of cowpea 8. Photosynthesis (DB) review 5 short paper and design of 9. Cellular Reproduction Extra lecture: Using the 4 Apr photosynthesis experiment (DB) primary literature (CT)

6 11 Apr

7 18 Apr

8 25 Apr

9 2 May

10 9 May

11 16 May 12 23 May 13 30 May

10. Molecular basis of inheritance (BO) 11. Mendelian inheritance (BO) 12. More than one gene, character (BO) 13. Sex and single chromosome (BO) 14. Mapping (BO) (Friday 22nd April) NO LECTURE (ANZAC DAY) 15. Genomes and proteomes (BO) 16. Darwinian selection (MB) 17. Population genetics (BO) 18. Mechanisms of evolution (MB) 19. The evidence for evolution (BO) 20. Species and speciation (NL) 21. Phylogenies and radiations (NL) 22. Biodiversity (MB) 23. Evolution of earth & biogeography (MB) 24. Major transitions & macroevolution (MB) 25. From cells to ecosystems (MB)

Lecturers: Charlotte Taylor (CT) Ben Oldroyd (BO) Madeleine Beekman (MB) Nate Lo (NL) Deborah Barton (DB) Tim Newsome (TN)

NO PRACTICAL CLASS (Preparing Literature review for Photosynthesis paper)

Revision Tutorial Molecules & Cells test

Practical 6. Photosynthetic responses to light regimes

Practical 7.Draft Photosynthesis paper review and Sordaria setup

Practical 8.Viral DNA forensics

Revision Tutorial

Practical 9.The chromosomal basis of inheritance.

Final photosynthesis paper Genetics test

Practical 10. Population genetics

Practical 11. Selection in Slaters: Slater vs Predator

Revision Tutorial.

Practical 12. Measuring Biodiversity

Laboratory notebooks Evolution test

6 Teaching Staff and Contact Details Unit Coordinator

Email

A/Prof Charlotte Taylor

[email protected]

 Teaching Staff

Charlotte Taylor

Matthew Pye

Ben Oldroyd

Madeleine Beekman

Nathan Lo

Debbie Barton

Tim Newsome

Email

Room

Phone

Note

[email protected]

Room 201 Botany Annexe Building A13

+61 2 9351 5788

Unit Coordinator

[email protected]

Room 506 Carslaw Building F07

+61 2 9114 0797

Deputy Unit Coordinator

[email protected]

Room 247 Macleay Building A12

+61 2 9351 7501

Lecturer

[email protected]

Room 249 Macleay Building A12

+61 2 9351 8779

Lecturer

[email protected]

Room 306 Edgeworth David Building A11

+61 2 9036 7649

Lecturer

deborah.barton @sydney.edu.au

Room 239 Macleay building A12

+61 2 9351 2384

Lecturer

[email protected]

Biochemistry and Microbiology Building G08

+61 2 9351 2907

Lecturer

7 Learning Resources NECESSARY LEARNING RESOURCES All the necessary learning resources will be available from the course website, delivered via the University's Blackboard learning management system. PRESCRIBED TEXTBOOK Ladiges, P., Evans, B., Saint, R., & Knox, B. (2010) Biology: An Australian Focus 4th Edition. McGraw-Hill Australia Pty Ltd, Sydney. Textbooks can be purchased at the Co-op Bookshop or borrowed from SciTech Library. A limited number of textbooks can also be borrowed from the First Year Biology Student Enquiries Office, Room 519, Level 5, Carslaw for use only in the Lizard Lounge. You must leave your student card with staff to borrow the textbook. Additional readings may be suggested from supplementary textbooks and scientific literature. The readings will be available in Special Reserve in Badham Library. Brief Description

Learning Outcomes

Percentage Mark

Due Date

Pre-work quiz

5

Weekly (weeks: 2, 3, 4, 5, 7, 8, 9, 10, 11, 12 and 13)

1, 3, 6, 7, 8

Enzymes short communication and peer review

2

Week 5 (week starting Sunday, 03 April 2016)

1, 2, 3, 4, 6, 8

...