B.Sc. HONOURS

DISCIPLINE OF BIOCHEMISTRY AND MOLECULAR BIOLOGY
Molecular Sciences Bldg 21, James Cook University,
Townsville, 4811, Queensland, Australia
Telephone: 61-7-4781 6265 Fax:  61-7-4781 6078



HONOURS IN GENETICS, BIOCHEMISTRY AND MOLECULAR BIOLOGY
 
  • The Department of Biochemistry and Molecular Biology incorporates the Comparative Genomics Centre and is one of the most research-active Departments at James Cook University. Both basic fundamental and applied biotechnology research are conducted within the department and its research activities are supported by grants from national and international funding agencies such as the National Health and Medical Research Council, Australian Research Council, the March of Dimes Foundation, Sugar Research and Development Corporation, Welcome Foundation, Clive and Vera Ramaciotti Foundation as well as industry.  These grants permit the Department to engage in research that is at the cutting edge of the field and to provide a vibrant and well-resourced environment for the development of research skills.
     
  • An active seminar program that brings distinguished scientists from Australia and overseas to JCU is another unique feature of the Biochemistry Department, and the honours and graduate students benefit immensely from this activity. 
     
  • The Department has a very strong commitment to research and the students who have completed honours have had no difficulty in finding employment or Ph.D. positions at JCU or other campuses. 

WHAT IS HONOURS?
       The aim of an Honours degree is to develop and assess the ability of a student to undertake independent research. Above all, the Honours degree program provides training in research skills. Attendance at the CGC seminars, laboratory based mentorship, regular meetings with the Honours coordinator, assignments relevant to research goals and professional development, and the advice of academic and research staff, support this training. Honours students are traditionally required to complete a thesis, which functions as an essential test of the candidate’s capacity to be trained as a scholar and a researcher.
        There are many different reasons why students take the Honours year: you may be contemplating an academic career, you may wish to improve your employment prospects, you may wish to complete a particular piece of research, or you may do Honours because it is considered the 'right' thing to do. It is important that you identify your reasons for participating in this most demanding academic program. In terms of a career, an Honours degree is a more prestigious degree than a pass degree and in many cases it qualifies people to start employment on a higher pay scale. A first class Honours degree is a compulsory prerequisite for winning most competitive scholarships to do a higher degree.
        Honours qualifies a person for normal membership of professional bodies such as Australian Society for Medical Research, Australasian Society for Immunology and The Genetics Society of Australia, Australian Society for Biochemistry and Molecular Biology, and The Australian and New Zealand Society of Developmental Biology. Honours is also the principal prerequisite for entry to higher degrees such as the Masters and PhD. It must be stressed that Honours is not simply a precursor to a PhD. It is also an interesting and highly rewarding year of study prized by employers who seek to employ people with a
demonstrated capacity for independent thought and research. It is a qualification that improves one’s earning potential and opportunities for promotion. Therefore, every student should contemplate doing Honours.



To download the Honour in Biochemistry handbook, click here.


PLANNING AN HONOURS PROJECT:
       The Honours year forms a transition period between the didactic style of undergraduate study and the self-motivated,  mentor-guided study of the postgraduate. Honours projects there therefore in part determined by the interests of the individual students and you are requested to speak with potential supervisors regarding potential projects. It is particularly useful for prospective students to talk to as many staff members as possible so that an informed decision can be made regarding the choice of project(s). Please note that positions will be allocated on the basis of merit and discussions that you hold with the prospective supervisor. 

APPLYING FOR AN HONOURS PROJECT:
       Candidature for honours in Biochemistry, Molecular Biology or Genetics requires successful completion of a full major in Biochemistry with grades of at least a credit average. Under exceptional circumstances students not reaching these criteria may be able to negotiate a position. They should confirm the support of a potential supervisor before contacting the Honours Coordinator Dr Bill Leggat.
       After discussions with prospective supervisors, students intending to complete honours in Biochemistry and Molecular Biology should submit a copy of the application form below either by email or in hard copy to
Bill Leggat by the 1st November.

THE ROLE OF THE SUPERVISOR:
        Good supervision is usually essential to a successful Honours degree, although there is no set formula for how this supervision should be done. The variation derives primarily from the nature of the student, his or her willingness to engage in independent research combined with the sense of need to report on progress and/or seek guidance. The structure of supervision follows a general pattern:
•    Initial discussion of potential thesis topics and general advice on the study skills associated with independent research.
•    Determination of the topic and suggestions for reading.
•    Reporting on research done, sources identified and ideas for the thesis.
•    Modification of the thesis topic if necessary.
•    Preparation of thesis plan, structure of chapters and writing schedule.
•    The supervisor attending whenever possible a student’s work-in-progress_ presentations during the year.
•    The supervisor submitting a report on the student's progress to the Discipline Honours coordinator at the end of the first semester of full-time enrolment and first year of part-time enrolment.
•    The student submitting a progress report to the Discipline Honours coordinator at the end of the first semester of full-time enrolment and first year of part-time enrolment identifying any issues that may have arisen concerning supervision.
•    The supervisor reading and commenting on draft thesis chapters and/or whole draft thesis.
•    The supervisor checking final draft for corrections, format, style, etc.
        The requirement in the Discipline of Biochemistry for supervisory contact is one hour per fortnight (or 30 minutes/week) over the whole academic year. This time is best utilised according to the needs of the student as these are worked out in consultation with the supervisor. Some students feel they simply must touch base on a short weekly basis, while others prefer a less frequent supervisory session during the year with more intensive hourly meetings towards the end. Critically, supervisors cannot always be available when students want them to be. The best arrangement is to determine early on a suitable time for both parties and to stick to that time as best as one can, with the flexibility of mutually changing the arrangement if either or both party feels the need.
    If a student misses appointed supervision sessions, it is not up to the supervisor to make up the time. Nor is a supervisor required to chase up a student for absenteeism. The onus is on the student and it is designed in this way to reflect a student’s capacity for independent scholarship. However, if a supervisor unreasonably fails to meet his or her commitment to a student, the student must immediately raise the matter with the Honours coordinator, who may refer the issue to the Head of Discipline or Head of School.
        A staff member who will be away during the year is usually not expected to supervise, especially if they are away in the second half of the year when theses are written and submitted. Honours supervision is part of an academic’s teaching load, which includes undergraduate teaching and postgraduate supervision. As a result of variations in this load, some academics do more Honours supervision than others. One cannot assume, therefore, that one will have the supervisor of choice. Students can contact a lecturer to discuss the possibility of supervision. However, the allocation of supervisors is not done on a “first-come first serve” basis, but must wait until the members of each discipline meet at the beginning of the year to make an equitable allocation of workload.
 

THE ROLE OF THE HONOURS COORDINATOR:
       The coordinator is responsible for the following:
•    Inducting students into Honours and going through the contents of the Honours Handbook
•    Teaching at least one of the Discipline seminars.
•    Overseeing the progress of each student through liaising with the supervisors and collecting the progress reports.
•    Ensuring the appropriate allocation of supervision
•    Dealing with any issues that may arise between supervisor and student
        All student queries of a general nature that cannot be addressed to the supervisor in the first instance should be addressed to the coordinator. In addition, the coordinator is responsible for creating and holding a confidential file on each student that contains the student's contact details, supervisor's name and a print-out of the student's academic record. The transcript includes the notation of the numerical marks the student has achieved in each subject that has counted towards the Discipline Major. This last requirement stems from the fact that a number of Australian universities use these marks to assist in ranking students for scholarship applications. The practice derives from the traditional English Honours system where the Level 3 marks in the discipline one "read" at university are counted as a component of the Honours mark. JCU does not do this and instead requests the Level 3 GPA. However, other universities do make the request and it is much easier if the marks are recorded from School assessment records in advance.


The Honours Coordinator in Biochemistry is Bill Leggat.

To download the Honours in Biochemistry handbook, click here.


HONOURS TIMETABLE:




Beginning January 2009 Beginning July 2009  
Apply to honours coordinator 14.11.09
15.5.09 Apply to honours coordinator
Start 2.2.09 6.07.09 Start
Introductory seminar 19.3.09 20.8.09
Introductory seminar
Literature review due 31.3.09 1.9.09
Literature review due
Mid year seminar 9.7.09 18.2.10
Mid year seminar
Assignment due 11.8.09 2.3.10
Assignment due
Poster due 16.10.09 23.4.10
Poster due
Cessation of lab work 21.10.09 27.4.10 Cessation of lab work
Thesis due 10.11.09 18.5.10
Thesis due
Final seminar 17.11.09 25.5.10
Final seminar
Oral defence 23.11.09 27.5.10
Oral defence
Release of grades 24.11.09 28.5.10
Release of grades


Introductory seminars
        Early in the first semester students will be required to give a 15 minute informal talk about their chosen research project; this talk, which will form no part of the final assessment, should cover the basic aims of the project and the approach to be employed. It is hoped that these talks, and the ensuing discussions, may result in constructive suggestions and new ideas for the further development of the projects.

Attendance at Honours Meetings and Research Seminars
        Attendance at the honours meetings and CGC research seminars is mandatory. The honours meetings are a forum for the cohort of students to present their work to each other as it progresses, to gain experience and confidence in talking about science, and (if necessary) to raise any practical or personal issues. These meetings will be held at least fortnightly, and will take the format of a first general gossip about laboratory matters, a short research presentation by one student, followed by a journal club presentation by another student. For your journal club presentation(s), you should select a recent research article that is both topical and of general interest. You must get the honours coordinator to confirm that the article is suitable for a presentation, and you should circulate copies of the article to the other students at least one week before the talk. All students must read the articles before the meetings, so that anyone can be asked to explain data or figures from the paper.

Health and Safety
All honours students are required to adopt safe working procedures. There will be a full day biosafety course early in the first semester. The full details of this will be provided by the Honours coordinator and all honours students must attend this course. A radiation safety course will be conducted on about the same time and again this is compulsory for all honours students. Information on this will be posted to all students when the arrangements are finalised by the University Radiation Safety Committee.

ASSESSMENT:
        Assessment of honours is based on the following components:
10%  Literature review 
5%  Assignment (2 page Ph.D. funding proposal)
5% Poster
10%
Final seminar
15% Supervisor's mark and lab book assessment
45%  Thesis
10%
Oral defence (viva)

Please note that attendance at the CGC seminar series is compulsory and content presented may be examined.

  Format for literature review:
        The literature review should cover the literature relevant to the research project to be conducted by the student. It should contain references to papers describing original work, not just to reviews, and should include descriptions of some of the theory of the techniques to be used in the research project. Diagrams are likely to assist in the presentation of the material and particular care should be taken to avoid plagiarism. The literature review should resemble the introduction of a thesis and should include the aims of the research project. It should consist of no more than 4,000 words, and include
Background (literature review, hypotheses and aims) and References sections. Due to the breadth of subjects presented, assessment will be made on scientific criteria; an excellent literature review will be one in which:
•    Background provides a literature review of sufficient depth to justify project
•    Appropriate citation of literature
•    Adherence to academic citation format
•    One or more hypotheses or aims is explicitly stated
•    The rationale for the work is provided
•    High standard of general presentation
•    Adequate binding
   
Submit 5 hard copies and one electronic copy to the honours coordinator.

Format for assignment:
        Research scientists must apply for funding from bodies such as the ARC (Australian Research Council) or NH&MRC (National Health & Medical Research Council) as well as other government and non-government bodies.  The process is highly competitive and it is important that you gain an understanding of how this works if you go on to pursue a career in research. Realistic expected outcomes, relevance, profitability, good science and excellent communication will affect the success of grant applications.
        As part of honours you are required to write a research proposal for a three year PhD project ($15 000 /year). It may be an extension of your honours project but it does not have to be. It must be carefully thought out, precise, concise and specific and it will be marked critically, as a real grant application would be.

Format (modified from NH&MRC NOI)
•    Scientific Title - Ensure the title of your project reflects the topic, area and type of research to be undertaken
•    Aims - Describe the aims of your project (maximum of three aims) and include your hypothesis.
•    Background - Describe the background of your proposal taking into consideration the minimum information that is required for the panel to understand your research proposal.
•    Research Plan - A short and concise plan of your research
•    Significance - Should describe clearly the impact of your proposed project.

Marking Criteria
1) Significance
Would the project, if successfully carried out, make an original and important contribution to a scientific discipline in the field of biochemistry, molecular biology, cell biology or genetics?

2) Approach
Is the experimental approach, model system, experimental methods and data analyses proposed well conceived and appropriate to the aims and hypotheses of the project?

3) Feasibility
Could the proposed project be accomplished by a single student within a 3 year timeframe with access to materials and resources costing less than $15,000 per year? Could the project be performed with currently available equipment and infrastructure at James Cook University?

4) Presentation
Is the assignment of two (2) A4 pages or less in length, written in 12 point Times New Roman Font, single-spaced, with margins no less than 2cm? Is the assignment clearly written and presented with a logical flow of information that includes background, hypotheses, aims and a research plan?

Laboratory book assessment:
        Laboratory books are expected to be kept up to date, provide an accurate record of methods, work performed and results, and to conform to the standards required for the work within them to withstand patent defense. Specifically:
•    Entries are to be dated
•    Errors are not to be overwritten, covered over, deleted or removed, but are     to be ruled out, corrected, dated and signed
•    Pages are to be numbered
•    Methods should be in sufficient detail to allow replication by a third party
•    Blank spaces are to be ruled out
Your supervisor will provide a mark based upon your laboratory book but also your conduct and application throughout the year. This mark will reflect how effectively you have functioned in a laboratory environment and be based upon:
•    Your general laboratory skills
•    Your ability to interpret data, design and conduct experiments
•    Your ability to effectively communicate your results to your supervisor and other members of the laboratory where appropriate
•    Your punctuality for meetings and other lab events
•    Your general contribution to the laboratory, for example in lab meetings or lab maintenance
•    Your professional conduct as a scientist, including how you interacted with other members of the lab

Format for final seminar:
        Twenty minute Powerpoint™ presentation and five minutes for questions. Due to the breadth of subjects presented, assessment will be made on scientific criteria; an excellent seminar will be one in which:
•    One or more hypotheses or aims are explicitly stated
•    The rationale for the work is provided
•    Data are clearly presented
•    Logic is sound
•    Conclusions are justified by the data presented
•    Future directions or final conclusion of the study are/is indicated
Format for poster:
       On the day of the viva voce examination, candidates will be required to present a poster on their research findings. The poster will be assessed in the days before the oral defence on:

1.    Content - scientific content, critical assessment of the topic
2.    Presentation - visual clarity and conciseness
3.    Questions - understanding of questions and the ability and skill in response.

Posters should be no larger than 1.0 x 1.5m and clearly presented. They should contain a brief abstract, methods and results and a conclusion. As a general rule, they should not contain more than 750 words of text, but are expected to conform to the standards of the particular subdiscipline in which the student is studying. Students should seek guidance from their supervisors in this regard. It is advisable that you look at those posters that are present around the building and use these as a guide for your poster. Posters should be printed on A0 size paper (or equivalent) and be laminated. The poster will be assessed by a number of academics and examined on clarity of presentation and quality of the research. Remember to make sure that the text and figures are easily read from a distance.


Format for thesis:
        Between 10,000 and 20,000 words, consisting of Background (literature review, hypotheses, aims), Methods, Results, Discussion and Conclusions, References. Due to the breadth of subjects presented, assessment will be made on scientific criteria; an excellent thesis will be one in which:
•    Background provides a literature review of sufficient depth to justify the     project
•    Appropriate citation of literature
•    Adherence to academic citation format
•    One or more hypotheses or aims is explicitly stated
•    The rationale for the work is provided
•    Methods described with sufficient clarity to allow replication
•    Data are clearly presented
•    Logic is sound
•    Conclusions are justified by the data presented
•    Future directions or final conclusion of the study are/is indicated
•    High standard of general presentation.
•    Adequate binding

Assessment Criteria
•    The development of research aims and outcomes
•    Analysis and presentation of results
•    Use of literature in the thesis
•    Originality of the thesis and quality of argument
•    Quality and standard of illustrations, tables and overall production
•    Overall style and accuracy of the thesis
•    Overall understanding of the project and methods used during completion of the project
You must submit 5 bound copies and one electronic copy to the honours co-ordinator.

Oral defence of thesis:
        The poster will be used as a centre point for discussion. Staff will have already read it, but would appreciate a brief reminder of its major points. You will then be asked questions related to your work, but other scientific issues may be raised, such as those that have arisen from work presented in honours meetings and the CGC seminar series.

Guide To grades:
The following is a broad guide to what the thesis grade and overall Honours grade means. The points relate to the thesis quality and the general statement relates to the overall assessment of the student’s potential for further study.

Class 1 (HD, 85-100%)
•    Outstanding command of expression and logical argument
•    Coherent use of research sources and data
•    Critical evaluation of extant literature appropriate to the topic
•    Strong sense of issue in relation to the discipline
•    Command over a particular theoretical approach
•    Originality of project and ideas
•    Excellent overall production including tables, illustrations, etc.

Upper H1s (90-94 & 95-100)
Display excellence in all these areas.

Lower H1s (85-87 & 88-89)
Are still excellent, but less well balanced in overall quality. All Class 1 students are considered to be capable of pursuing a higher research degree.

Class 2A (D, 75-84%)
Class 2A students are considered capable of pursuing a higher degree.
•    Well-written, logically argued and well-structured
•    Good use of sources and data, but a key example is missing
•    Strong sense of the literature and good integration with text
•    Sense of issue and demonstrated knowledge of discipline
•    Attempt to grasp an appropriate theoretical approach
•    Evidence of original thought but could be better integrated
•    Overall good production

Class 2B (C, 65-74%)
Overall, a H2B student is capable of pursuing postgraduate work, but would be encouraged to complete a Masters degree before attempting a PhD.
•    Generally good written expression and organisation of thesis
•    Adequate coverage of extant literature, but noteworthy omissions
•    Intimations of relevance of topic to the discipline
•    Weak understanding of appropriate theory or use of inappropriate theory
•    Little evidence of originality of thought
•    Solid overall production

Class 3 (P, 50-64%)
While a student_s undergraduate degree may show evidence of suitability for Honours, their performance in Honours may raise doubts about their potential for higher degree research. Students awarded an H3 should consider pursuing a coursework Masters if they want to do further study.
•    Not well written with flaws in expression and logic, needs editing
•    Weak coverage of extant literature with glaring omissions
•    Weak understanding of research methods and analysis of data
•    No strong sense of overall issue and relevance to the discipline
•    Lacking in originality and superficial in interpretation
•    Inadequate grasp of theoretical approaches
•    Poor presentation of data

Fail (N, <50%)
•    Poorly and hurriedly written, badly integrated
•    Serious flaws in the coverage of extant literature
•    Misunderstanding of key concepts
•    Misunderstanding of research techniques and data analysis
•    Inability to demonstrate the finding of the research in a clear manner

PENALTIES:
Late submisson
       Escalating penalties will be imposed for submission of an honours thesis or assignments after the date specified in the honours guide.  The formula of the penalty is “Percentage Reduction = 1 x days squared” including part-days, weekends and public holidays. Extensions may be granted for genuine circumstances at the discretion of the honours co-ordinator and head of discipline.

In extenuating circumstance extensions for submission of work MAY be granted, if in the opinion of course co-ordinator and head of discipline the circumstances have significantly affected the students ability to perform their study. If you are contemplating a request for an extension you should consult the honours co-coordinator as soon as possible, requests for extensions must be made at least 2 weeks prior to the due date.

Medical conditions which have affected your work may be used for an extension request however the honours co-ordinator and academics reserve the right to not grant an extension, or grant an extension for only part of the period of illness, if they feel the student was able to undertake some or all of their honours study during their illness. Original medical certificates should be submitted to the honours co-ordinator within 1 week of the date in which you return to study. Medical certificates MUST include as a minimum:
i. The dates of illness
ii. The date you were seen by the doctor (this must be in the period you were ill or within 1 week of the illness)
iii. Within the bounds of patient privacy, clearly indicate which duties that you are able to complete and those which you can not (e.g. The patient was unable to perform laboratory duties due to a broken leg but was able to use a computer). A general statement that you were unable to perform your studies will not be accepted..

Plagiarism
        Plagiarism means "publishing borrowed thoughts as your own" (OED). It has been defined by the university for disciplinary purposes as "Reproduction without acknowledgement of another person's words, works or thoughts (including a fellow student's) from any source... The definition of words, works or thoughts includes such representations as diagrams, drawings, pictures, objects, text artistic works and other such expressions of ideas." Plagiarism is a serious offence and will not be tolerated in any form - in the scientific community, people lose jobs if they are found guilty of plagiarism. When you write your literature review, assignment and thesis (and scientific papers), you are obliged to express all of the material in your own words; read the background material, think about what it means and say what needs to be said in your way. If you use sentences from the background material (or from anywhere else) without acknowledging that the sentence is not yours by putting it in quotation marks (as well as including a citation at the end of the sentence), you are guilty of plagiarism. Note that this kind of device is hardly ever used in scientific writing, so use it sparingly in your own work; in general you will receive better marks if you use your own words on all occasions.
        You may not copy any published (or unpublished) work of others without acknowledging that the sentence is not yours by putting it in quotation marks (as well as including a citation at the end of the sentence). If in any assessable material a student uses a single sentence that is demonstrably not their own, that student will be penalised severely.


To download the Honours in Biochemistry handbook, click here.

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