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Unit outline_

BIOL1997: From Molecules to Ecosystems (SSP)

Semester 2, 2020 [Normal day] - Camperdown/Darlington, Sydney

Paradigm shifts in biology have changed the emphasis from single biomolecule studies to complex systems of biomolecules, cells and their interrelationships in ecosystems of life. Such an integrated understanding of cells, biomolecules and ecosystems is key to innovations in biology. Life relies on organisation, communication, responsiveness and regulation at every level. Understanding biological mechanisms, improving human health and addressing the impact of human activity are the great challenges of the 21st century. This unit will investigate life at levels ranging from cells, and biomolecule ecosystems, through to complex natural and human ecosystems. You will explore the importance of homeostasis in health and the triggers that lead to disease and death. You will learn the methods of cellular, biomolecular, microbial and ecological investigation that allow us to understand life and intervene in ecosystems to improve health. The same theory will be covered as in the advanced stream but in this Special Studies Unit, the practical component is a research project. The research will be a synthetic biology project investigating genetically engineered organisms. Students will have the opportunity to develop higher level generic skills in computing, communication, critical analysis, problem solving, data analysis and experimental design.

Unit details and rules

Academic unit Life and Environmental Sciences Academic Operations
Credit points 6
Prerequisites
? 
None
Corequisites
? 
None
Prohibitions
? 
BIOL1007 or BIOL1907
Assumed knowledge
? 

90 or above in HSC Biology or equivalent

Available to study abroad and exchange students

No

Teaching staff

Coordinator Samantha Hockey, samantha.hockey@sydney.edu.au
Lecturer(s) Claudia Keitel, claudia.keitel@sydney.edu.au
Samantha Hockey, samantha.hockey@sydney.edu.au
Ann Kwan, ann.kwan@sydney.edu.au
Osu Lilje, osu.lilje@sydney.edu.au
Type Description Weight Due Length
Final exam (Open book) Type C final exam Final Exam
Online open book without invigilation
35% Formal exam period 2 hours
Outcomes assessed: LO1 LO2 LO3 LO4 LO5
Tutorial quiz Post-module quizzes
Only 3 out of 4 quizzes will count.
6% Multiple weeks Details on CANVAS
Outcomes assessed: LO2
Skills-based evaluation Lab skills
Calculations & data interpretation (10%); Skills (7%) Details on CANVAS
17% Multiple weeks During online lab
Outcomes assessed: LO1 LO5 LO4 LO3 LO2
Assignment Electronic notebook (ELN)
recording experimental data and interpretation
7% Ongoing 7 lab write-ups
Outcomes assessed: LO3
Assignment CellPaint (draft)
Draft molecular scene
0% Week 03 Details on CANVAS
Outcomes assessed: LO4
Assignment CellPaint (final)
Final molecular scene
10% Week 04 Details on CANVAS
Outcomes assessed: LO2 LO3 LO4
Assignment group assignment Synthetic biology project - background
Formative
0% Week 05 Details on CANVAS
Outcomes assessed: LO1 LO2 LO3 LO4
Assignment group assignment Synthetic biology report - poster
Poster
5% Week 08 Details on CANVAS
Outcomes assessed: LO4
Assignment group assignment Synthetic biology project - Grant application
Synthetic biology grant application
20% Week 12 Details on CANVAS
Outcomes assessed: LO1 LO2 LO3 LO4
group assignment = group assignment ?
Type C final exam = Type C final exam ?

Assessment summary

  • Synthetic biology project: This is a 12 week project where students will have the chance to explore and contribute to current cutting-edge research on SARS-CoV2, while learning fundamentals of biology, biochemistry and biotechnology. Results will be presented in a poster and a grant proposal.
  • CellPAINT modelling: You will create a realistic scene to show how the SARS-CoV2 virus causes havoc to human cells based on the latest scientific knowledge. You will choose a process that you are most interested in to build your scenario, e.g. attachmnet of the virus to a human cell/protein, virus entry, assembly of new viral particles, the virus budding process etc. 
  • Laborartory skills assessment: This assessment has three parts: basic laboratory calculations, data interpretation and lab techniques.
  • Electronic Lab Notebook (ELN): You will write up each lab session in your ELN, including all experimental data, your analysis and conclusions.
  • Post-module quizzes: This is an open book quiz.  Each quiz has 10 questions in total which you need to complete in 12 minutes. You can attempt the quiz twice. The highest mark will be recorded on Canvas. Only 3 of the 4 quizzes will count towards the final assessment mark (i.e. your top three marks will be used).
  • Final exam: The exam will cover all material in the unit from both lectures and practical classes. The exam will have a mixture of multiple choice questions and short answer questions.

Detailed information for each assessment can be found on Canvas.

Assessment criteria

The University awards common result grades, set out in the Coursework Policy 2014 (Schedule 1).

As a general guide, a High distinction indicates work of an exceptional standard, a Distinction a very high standard, a credit a good standard, and a pass an acceptable standard.

Result name

Mark range

Description

High distinction

85 - 100

  • factual information of an outstanding standard with a sophisticated grasp of the principles and interpretation
  • clear evidence of critical analysis, understanding of experimental design and statistical analysis, integration of knowledge and application to the experimental situation; evidence of originality of thought

Distinction

75 - 84

  • factual information is of a superior standard, with excellent grasp of the principles and interpretation
  • good evidence of critical analysis understanding of experimental design and statistical analysis, and integration of knowledge; good understanding of the application of knowledge; some evidence of application to the experimental situation

Credit

65 - 74

  • factual information is of a high standard, but some information may be incorrect or missing, with sound grasp of the principles and interpretation
  • critical analysis is mainly superficial and relevance of knowledge not always clear, understanding of experimental design and statistical analysis is sufficient and applied to the experimental situation

Pass

50 - 64

  • factual information is of an acceptable standard but basic and contains gaps, errors or inconsistencies/contradictions
  • critical analysis is relatively poor, material may be correct but not entirely relevant; surface understanding of experimental design and statistical analysis with limited application to the experimental situation and limited interpretation.

Fail

0 - 49

  • a significant amount of factual information is incorrect
  • misses the point, fundamental misunderstandings evident
  • evidence of plagiarism

sydney.edu.au/students/guide-to-grade

For more information see guide to grades.

Late submission

In accordance with University policy, these penalties apply when written work is submitted after 11:59pm on the due date:

  • Deduction of 5% of the maximum mark for each calendar day after the due date.
  • After ten calendar days late, a mark of zero will be awarded.

Academic integrity

The Current Student website provides information on academic integrity and the resources available to all students. The University expects students and staff to act ethically and honestly and will treat all allegations of academic integrity breaches seriously.

We use similarity detection software to detect potential instances of plagiarism or other forms of academic integrity breach. If such matches indicate evidence of plagiarism or other forms of academic integrity breaches, your teacher is required to report your work for further investigation.

Use of generative artificial intelligence (AI) and automated writing tools

You may only use generative AI and automated writing tools in assessment tasks if you are permitted to by your unit coordinator. If you do use these tools, you must acknowledge this in your work, either in a footnote or an acknowledgement section. The assessment instructions or unit outline will give guidance of the types of tools that are permitted and how the tools should be used.

Your final submitted work must be your own, original work. You must acknowledge any use of generative AI tools that have been used in the assessment, and any material that forms part of your submission must be appropriately referenced. For guidance on how to acknowledge the use of AI, please refer to the AI in Education Canvas site.

The unapproved use of these tools or unacknowledged use will be considered a breach of the Academic Integrity Policy and penalties may apply.

Studiosity is permitted unless otherwise indicated by the unit coordinator. The use of this service must be acknowledged in your submission as detailed on the Learning Hub’s Canvas page.

Outside assessment tasks, generative AI tools may be used to support your learning. The AI in Education Canvas site contains a number of productive ways that students are using AI to improve their learning.

Simple extensions

If you encounter a problem submitting your work on time, you may be able to apply for an extension of five calendar days through a simple extension.  The application process will be different depending on the type of assessment and extensions cannot be granted for some assessment types like exams.

Special consideration

If exceptional circumstances mean you can’t complete an assessment, you need consideration for a longer period of time, or if you have essential commitments which impact your performance in an assessment, you may be eligible for special consideration or special arrangements.

Special consideration applications will not be affected by a simple extension application.

Using AI responsibly

Co-created with students, AI in Education includes lots of helpful examples of how students use generative AI tools to support their learning. It explains how generative AI works, the different tools available and how to use them responsibly and productively.

WK Topic Learning activity Learning outcomes
Week 01 1. Intro, expectations and overview; 2. Chemistry of Life; 3. Biopolymers Lecture (3 hr)  
SARS-CoV-2 project introduction Practical (3 hr)  
Week 02 4.Central dogma of molecular biology 5. Copying DNA and RNA; 6. Making Proteins Lecture (3 hr)  
Gene hunting Practical (3 hr)  
Week 03 7. Enzymes and thermodynamics; 8. Q&A with lecturer; 9. Photosynthesis I Lecture (3 hr)  
CellPAINT modelling Practical (3 hr)  
Week 04 10. Photosynthesis II; 11. Respiration in plants Lecture (2 hr)  
Designing a protein expression system Practical (3 hr)  
Week 05 12. Q&A with lecturer; 13. Metabolism; 14. Cell diversity Lecture (3 hr)  
Transforming bacteria Practical (3 hr)  
Week 06 15. Compartmentalisation of cells; 16. Cells tissues and communication; 17.Q&A with lecturer Lecture (3 hr)  
DNA extraction and digestion Practical (3 hr)  
Week 07 18. Microbiology and the One Health concept; 19. Microbes, food and nutrition Lecture (2 hr)  
Protein overexpression Practical (3 hr)  
Week 08 20. Planetary health: microbes and ecosystems; 21. Cell factories and biotechnology Lecture (2 hr)  
Protein purification Practical (3 hr)  
Week 09 22. Q&A with lecturer; 23. Individuals, behaviour and groups Lecture (2 hr)  
Group A: Intensive skills session 1 Group B: Introduction to enzyme kinetics Practical (3 hr)  
Week 10 24. Groups and populations; 25. Do species matter? Lecture (2 hr)  
Group A: Introduction to enzyme kinetics Group B: Intensive skills session 1 Practical (3 hr)  
Week 11 26. Trophic ecology; 27. Assemblages and ecosystems; 28. The human footprint Lecture (3 hr)  
Group A: Intensive skills session 2 Group B: Ecology of SARS Practical (3 hr)  
Week 12 29. Conservation; 30. Q&A with lecturer Lecture (2 hr)  
Group A: Ecology of SARS Group B: Intensive skills session 2 Practical (3 hr)  

Attendance and class requirements

  • Study load: You are expected to dedicate at least 5 hours per week face to face on campus for 12 weeks of this unit and at least another 5-6 hours off campus.
  • Attendance: Unless otherwise indicated, students are expected to attend a minimum of 80% of timetabled practicals for a unit of study, unless granted exemption by the Associate Dean.

Study commitment

Typically, there is a minimum expectation of 1.5-2 hours of student effort per week per credit point for units of study offered over a full semester. For a 6 credit point unit, this equates to roughly 120-150 hours of student effort in total.

Learning outcomes are what students know, understand and are able to do on completion of a unit of study. They are aligned with the University's graduate qualities and are assessed as part of the curriculum.

At the completion of this unit, you should be able to:

  • LO1. demonstrate an understanding of biology: (i) value the diverse range of biological sub-disciplines and the complexity, variability and unpredictability of living systems (ii) appreciate the importance of sustainability and the impact of biology within the broader economic, social and environmental context
  • LO2. demonstrate depth and breadth of biological knowledge: (i) describe and explain broad biological concepts with relevant examples (ii) explain the biological organisation from molecules to cells and to ecosystems which integrate to form a dynamic network (iii) describe how structure and function are interrelated from the level of molecules to organisms
  • LO3. demonstrate inquiry and problem-solving abilities: (i) propose and test hypotheses to explain biological phenomena (ii) identify and use appropriate technical and analytical skills to collect data (iii) analyse quantitative data to critically evaluate evidence for biological explanations
  • LO4. demonstrate appropriate and effective communication: (i) produce written, visual, and oral explanations to communicate to a scientific audience and to the general public (ii) contribute to both independent and group tasks
  • LO5. demonstrate development in personal and professional responsibility: (i) evaluate and debate arguments on biological phenomena in a respectful and ethical manner (ii) reflect on your development as a student and the responsibility you have to find and apply information and work ethically, responsibly and safely

Graduate qualities

The graduate qualities are the qualities and skills that all University of Sydney graduates must demonstrate on successful completion of an award course. As a future Sydney graduate, the set of qualities have been designed to equip you for the contemporary world.

GQ1 Depth of disciplinary expertise

Deep disciplinary expertise is the ability to integrate and rigorously apply knowledge, understanding and skills of a recognised discipline defined by scholarly activity, as well as familiarity with evolving practice of the discipline.

GQ2 Critical thinking and problem solving

Critical thinking and problem solving are the questioning of ideas, evidence and assumptions in order to propose and evaluate hypotheses or alternative arguments before formulating a conclusion or a solution to an identified problem.

GQ3 Oral and written communication

Effective communication, in both oral and written form, is the clear exchange of meaning in a manner that is appropriate to audience and context.

GQ4 Information and digital literacy

Information and digital literacy is the ability to locate, interpret, evaluate, manage, adapt, integrate, create and convey information using appropriate resources, tools and strategies.

GQ5 Inventiveness

Generating novel ideas and solutions.

GQ6 Cultural competence

Cultural Competence is the ability to actively, ethically, respectfully, and successfully engage across and between cultures. In the Australian context, this includes and celebrates Aboriginal and Torres Strait Islander cultures, knowledge systems, and a mature understanding of contemporary issues.

GQ7 Interdisciplinary effectiveness

Interdisciplinary effectiveness is the integration and synthesis of multiple viewpoints and practices, working effectively across disciplinary boundaries.

GQ8 Integrated professional, ethical, and personal identity

An integrated professional, ethical and personal identity is understanding the interaction between one’s personal and professional selves in an ethical context.

GQ9 Influence

Engaging others in a process, idea or vision.

Outcome map

Learning outcomes Graduate qualities
GQ1 GQ2 GQ3 GQ4 GQ5 GQ6 GQ7 GQ8 GQ9

This section outlines changes made to this unit following staff and student reviews.

We have created a separate CANVAS site this year following USS requests for one.

Disclaimer

The University reserves the right to amend units of study or no longer offer certain units, including where there are low enrolment numbers.

To help you understand common terms that we use at the University, we offer an online glossary.