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“Nothing in biology makes sense, except in the light of evolution”. Theodosius Dobzhansky.
All living organisms are the products of the selective pressures that shaped the form and function of their ancestors. Evolutionary biology traces the changes that have occurred to give rise to the diversity of modern organisms. Developmental biology provides information about how tissues, organs and ultimately organisms arise from the single, fertilised egg. We can now understand how changes at the genetic level can lead to changes in cell fate and morphogenesis that allow existing structures to change and adopt new configurations. This course will show how combining the two approaches of evolutionary and developmental biology allows an understanding of the mechanisms by which organisms evolve, which cannot be achieved by either discipline alone.
Course Coordinator: Dr Jonathan Pettitt (ext. 7516) Email: j.pettitt@abdn.ac.uk
1.Know the major groups of animals and their interrelaionships.
2.Understand how the interrelationships between extant animal phyla are determined.
3.Know the major developmental events associated with the evolution of different body plans.
4.Have an appreciation of the likely mechanisms by which specific organs and structures have evolved.
1.The concept of homology and the hierarchy of biological systems (JP)
How do we know when biological systems in different organisms share a common ancestor? And why should we care? This lecture will introduce and revisit important concepts involved in evolutionary biology as it relates to developmental processes. The lecture will also cover the implications of gene, cell, tissue and organ-level views of biological systems, and the problems that can arise when they are inappropriately used.
2.How We Know What We Think We Know About Animal Evolution (JP)
The relationship between humans and each member of the animal kingdom has been the subject of intense research since Darwin and his contemporaries formulated the concept that all life arises from a series of common ancestors. The lecture will discuss our current understanding of the evolutionary relationship between different animal groups (phyla) and why this is important for our understanding of human biology.
3.Geoffroy’s Lobster, Urbilateria and the evolution of bilaterality (SH)
The recent molecular insight into the mechanisms of embryonic development has revealed the originally proposed body plans for different groups of animals in Zoology lectures reflected in reality in the conserved phylotypic stage; but this molecular insight has quite unexpectedly also revealed a much deeper and remarkable conservation which we share with all animals in fundamental organisation, which is called the zootype. This lecture will explore the molecular hallmarks of the zootype, from the Hox cluster and possibly related clusters (which patterns the anteroposterior axis in different germ layers) to the conservation of dorso-ventral patterning (but with a twist as originally proposed in Geoffroy’s Lobster). We will go in search for our Urbilaterian ancestor and discover that the fundamental molecular zootype organisation is conserved even in animals in which asymmetry is not morphologically evident.
4.Chordates and the evolution of vertebrates (SH)
A number of developmental model systems are used because of their position at the base of the vertebrate evolutionary tree. These have been used to shed light on the developmental innovations critical to vertebrate development, such as the notochord, and the formation of somites.
5.The evolution of multicellularity (JP)
The lecture will consider current evidence and hypotheses as to how the first animals evolved. Using recent evidence from a variety of genome projects it will illustrate how the diverse range of animal developmental strategies is based upon a common molecular toolkit that likely predated the evolution of the first animals.
6.Genomic dark matter and its role in shaping the embryo (AMK)
In addition to the requirement for normally functioning proteins it is critical that these proteins be expressed at the right times in the right places and at the correct amounts. Understanding the systems that ensure normal gene expression lags many years behind our understanding of protein function. However, thanks to the sequencing of multiple vertebrate genomes and the new science of "Comparitive Genomics" the regulatory sequences that control gene expression during development are now being identified. This lecture will describe that instead of consisting of "Junk" DNA the non-coding vertebrate genome, often described as "genomic dark matter", contains a wealth of regulatory information that is required to shape the embryo and possibly provide the plasticity required to drive evolution.
7.The evolution of eyes 1(JMC)
Ernst Mayr in 1961 stated that ‘It requires little persuasion to be convinced that the lens eye of a vertebrate and the compound eye of an insect are independent evolutionary events.’ But both invertebrates and vertebrates use rhodopsin as a primary photosensory pigment, and in the last 15 years it has become apparent that at the genetic and cell biology level that there are many similarities between the development of eyes across diverse animal taxa. This lecture will explore the concept of deep homology as it applies to genes involved in eye development, and assess the evidence that the eyes of invertebrates and vertebrates are in fact homologous structures derived from a common ancestor that had an eye.
8.The evolution of eyes 2 (JMC)
Among vertebrates there is an extraordinary range of extant eye morphologies, demonstrating eye developmental pathways are under strong evolutionary selection. This lecture will track some of the developmental specialisations that have been shown to underlie vertebrate eye evolution. The genetics of eye development and degeneration in Mexican cavefish will be used as an example of an animal that has traded in its eyes in exchange for better taste and smell. We will look at the specialisations of eyes in mammals that live underground – mole-rats and true moles – examine the genetic mutations that underlie their eye phenotypes and ask whether they are just ‘mammalian cavefish’.
9.The Evolution of Limb development (NV)
Limbs are complicated appendages; yet show an incredible range of diversity between species in the Animal Kingdom. This lecture will describe how the human limb has evolved into the structures we know and love, using examples from the animal kingdom and in an historical context.
10.If You Want to Get Ahead, Get a Head: the evolution of the vertebrate head (SH)
Vertebrate evolution is characterised by formation of ever more sophisticated heads, to develop ever more sophisticated sense organs and jaws to find, catch and process our food. The prime example in evolution of modifying existing structures for new functions is the evolution from cranial neural crest-derived support structures for gill arches in jawless vertebrates first into integral components of jaws and then further into bones in the mammalian middle ear, which allow us to sense sound waves in the air in our terrestrial habitat.
11.The Human Evolution and Development (JMC)
There are a number of features that distinguish us from our closest-living relatives, the great apes. Recent work has shown that it is possible to identify genes that may have been responsible for the increases in brain size and language acquisition.
Essay and Presentation
You will be required to research and write about a specific piece of research in the area of evolution and development. This will form the basis of an essay and a 10-minute presentation. Guidance about the selection of appropriate papers will be given, and be available throughout the course.
Developmental Biology students are required to attend research seminars in Cell and Developmental Biology (usually Friday afternoons at 4pm in the IMS Level 7 Conference Room), to reinforce and complement the material covered in lectures and practical laboratory work.
General Reading List
Essential Developmental Biology by JMW Slack (Blackwells, 2nd Edition, 2006) will be the main textbook used for the course. Additionally, Principles of Development by Lewis Wolpert et al. (Oxford University Press, 3rd Edition, 2007) and Developmental Biology by Scott F. Gilbert (Sinaur Associates Inc. 8th Edition, 2006) will be useful textbooks’ for some aspects of the course.
The University has strict regulations on plagiarism. If you are unsure about what constitutes plagiarism read the University guide on plagiarism at http://www.abdn.ac.uk/writing
Copying or plagiarising another persons work, either from other students or published material in books or papers and submitted as your own for assessment is considered a form of cheating. This is considered by the University to be a serious offence and will be penalised according to the extent involved and whether it is decided there was an attempt at deliberate deception, or whether bad practice was involved. If you do use information or ideas obtained from textbooks or other published material you must give a precise reference to the source both at the appropriate point in your narrative and in a list of references at the end of your work. Direct quotations from published material should be indicated by quotation marks and referenced in the text as above.
Students are expected to attend all lectures, laboratory classes, and tutorials, and to complete all class exercises by stated deadlines. The minimum performance acceptable is attendance at 75% of the lectures, seminars, practical classes, and presentation of all set course work, written and oral.
Assessment is derived from course work (30%) and a written examination (70%). The continuous assessment (CA) component is a problem-based assignment.
Written Examination: 70% of the total assessment is based on one 1.5 hour written paper. The student has to answer two questions of equal weighting selected from a list of four.
Common assessment scale (CAS) grade: The overall performance of the student is expressed as a grade awarded on the common spine marking scale.
The degree examination is held in January, with the re-sit examination in August.
Dr Martin Collinson
Prof Stefan Hoppler
Dr Alasdair MacKenzie
Dr Jonathan Pettitt
Dr Neil Vargesson
If students have difficulties with any part of the course that they cannot cope with alone they should notify someone immediately. If the problem relates to the subject matter you may be best advised to contact the member of staff who is teaching that part of the course. Students with registered disabilities should contact either the IMS based School Office (Miss Lyndsay McEwan l.mcewan@abdn.ac.uk) or the Old Aberdeen office associated with the teaching laboratories (Mrs S.Jones s.jones@abdn.ac.uk ) to ensure that the appropriate facilities have been made available. Otherwise, you are strongly encouraged to contact any of the following as you see appropriate:
Course student representatives.
Course co-ordinator (NV)
Convenor of the Biomedical Sciences Staff/Student Liaison Committee (Dr Gordon McEwan).
Adviser of studies.
Disabilities Co-ordinator (Dr Derryck Shewan).
Staff are based at Foresterhill (IMS Building) and we strongly encourage the use of email or telephone the SMS office. You may be wasting your time to travel to Foresterhill only to find staff unavailable.
Support Available to Students
The University is keen to help you successfully complete your studies. If at any time you feel you need assistance, there is a range of support services available to help you. These include support to assist with unexpected and/or exceptional financial difficulty, support for disabled students and academic learning support through the Student Learning Service. Further details about all these services area available at http://www.abdn.ac.uk/studenthelpguide/.
We value students’ opinions in regard to enhancing the quality of teaching and its delivery; therefore in conjunction with the Students’ Association we support the operation of a Class Representative system.
The students within each course, year, or programme elect representatives by the end of the fourth week of teaching within each half-session. In this school we operate a system of course representatives. Any student registered within a course that wishes to represent a given group of students can stand for election as a class representative. You will be informed when the elections for class representative will take place.
What will it involve?
It will involve speaking to your fellow students about the course you represent. This can include any comments that they may have. You will attend a Staff-Student Liaison Committee and you should represent the views and concerns of the students within this meeting. As a representative you will also be able to contribute to the agenda. You will then feedback to the students after this meeting with any actions that are being taken.
Training
Training for class representatives will be run by the Students Association. Training will take place in the fourth or fifth week of teaching each half-session. For more information about the Class representative system visit www.ausa.org.uk or email the VP Education & Employability vped@abdn.ac.uk. Class representatives are also eligible to undertake the STAR (Students Taking Active Roles) Award, further information about the co-curricular award is available at: www.abdn.ac.uk/careers.
The University operates a system for monitoring students' progress to identify students who may be experiencing difficulties in a particular course. If the Course Co-ordinator has concerns about your attendance and/or performance, the Registry will be informed. The Registry will then write to you (by e-mail in term-time) to ask you to contact the Senate Office in the first instance. Depending on your reason for absence the Senate Office will either deal directly with your case or will refer you to your Adviser of Studies or a relevant support service. This system is operated to provide support for students who may be experiencing difficulties with their studies. Students are required to attend such meetings with their Adviser of Studies in accordance with General Regulation 8.
Set criteria are used to determine when a student should be reported in the monitoring system. You will be asked to meet your Adviser if any of the following criteria apply for this course:-
either (i) if you are absent for a continuous period of two weeks or 25% of the course (whichever is less) without good cause being reported;
or (ii) if you are absent from two small group teaching sessions e.g. (laboratory/tutorial classes) without good cause;
or (iii) if you fail to submit a piece of summative or a substantial piece of formative in-course assessment by the stated deadline
If you fail to respond within the prescribed timescale (as set out in the e-mail or letter) you will be deemed to have withdrawn from the course concerned and will accordingly be ineligible to take the end of course assessment or to enter for the resit. The Registry will write to you (by e-mail in term-time) to inform you of this decision. If you wish consideration to be given to reinstating you in the course you will be required to meet the Convener of the Students' Progress Committee.
Students who attend and complete the work required for a course are considered to have been awarded a ‘Class Certificate’. Being in possession of a valid Class Certificate for a course entitles a student to sit degree examinations for that course. From 2010/11 class certificates will be valid for two years and permit a total of three attempts at the required assessment within that two year period i.e. the first attempt plus up to two resits.
You will receive a University e-mail account when you register with the University Computing Centre. The University will normally use e-mail to communicate with you during term-time. These e-mails will be sent to your University e-mail account, which you can access using Eudora or SquirrelMail.
It is your responsibility to check your e-mail on a regular (at least weekly) basis and to tidy the contents of your e-mail inbox to ensure that it does not go over quota (see http://www.abdn.ac.uk/diss/email/mailquota.hti for guidance on managing your e-mail quota). It is recommended that you use your University e-mail account to read and respond to University communications. If you already have a non-University e-mail account that you use for personal correspondence, it is possible to set up automatic forwarding of messages from your University e-mail account to your personal e-mail address (see http://www.abdn.ac.uk/local/mail.forward/) but, should you do so, it is your responsibility to ensure that this is done correctly. The University takes no responsibility for delivery of e-mails to non-University accounts.
You should note that failure to check your e-mail or failure to receive e-mail due to being over quota or due to non-delivery of an e-mail forwarded to a non-University e-mail account would not be accepted as a ground for appeal (for further information on appeals procedures, please refer to http://www.abdn.ac.uk/registry/quality/appendix5x17.hti).
Phylogeny Tutorial, Report and Presentation
As part of the course you will be given the chance to build a phylogenetic tree using a variety of Web-based programs. This will give you an appreciation of how phylogenetic information is obtained and interpreted. The results of this exercise will form the basis of a 10 minute presentation to the class and the teaching staff and will be assessed in the form of a short report summarising your findings. Guidance on this exercise will be provided online and during the tutorial session.
TurnitinUK
TurnitinUK is an online service which compares student assignments with online sources including web pages, databases of reference material, and content previously submitted by other users across the UK. The software makes no decision as to whether plagiarism has occurred; it is simply a tool which highlights sections of text that have been found in other sources thereby helping academic staff decide whether plagiarism has occurred.
As of Academic Year 2011/12, TurnitinUK will be accessed directly through MyAberdeen. Advice about avoiding plagiarism, the University’s Definition of Plagiarism, a Checklist for Students, Referencing and Citing guidance, and instructions for TurnitinUK, can be found in the following area of the Student Learning Service website www.abdn.ac.uk/sls/plagiarism/.
Transition into level 4 and beyond
As students progress through their degree programme, they will notice a change in the style and approach of teaching and the expectations upon them as learners. Expectations again change as students progress into Honours year, where they are expected to become more independent and self-directed in their learning. To help with this transition, a variety of activities will be planned to address any new challenges faced by students at level 4. The level 4 retention co-ordinator - Dr Steve Tucker (s.j.tucker@abdn.ac.uk; 01224 437491) will organise such events and is a point of contact for any level 4 SMS students facing any kind of difficulty. Regular activities and workshops will be designed around key issues faced by Honours students much in the same way as it was at level 3. In addition, Dr Tucker will hold regular, advertised drop-in surgeries for students to raise any issues face to face and all level 4 SMS students will have access to a MyAberdeen site that will offer information, feedback, guidance and discussion forums designed to ease students through to the completion of their degree.
Absence from Classes on Medical Grounds
Candidates who wish to establish that their academic performance has been adversely affected by their health are required to secure medical certificates relating to the relevant periods of ill health (see General Regulation 17.3).
The University’s policy on requiring certification for absence on medical grounds or other good cause can be accessed at:
www.abdn.ac.uk/registry/quality/appendix7x5.pdf
You are strongly advised to make yourself fully aware of your responsibilities if you are absent due to illness or other good cause. In particular, you are asked to note that self-certification of absence for periods of absence up to and including eleven weekdays is permissible. However, where absence has prevented attendance at an examination or where it may have affected your performance in an element of assessment or where you have been unable to attend a specified teaching session, you are strongly advised to provide medical certification (see section 3 of the Policy on Certification of Absence for Medical Reasons or Other Good Cause).
Feedback Framework
Feedback on assessment:
The University recognises that the provision of timely and appropriate feedback on assessment plays a key part in students learning and teaching. The guiding principles for the provision of feedback within the University are detailed in the Institutional Framework for the Provision of Feedback on Assessment available at:
www.abdn.ac.uk/registry/quality/appendix7x8.pdf
Enhancing Feedback:
The University recognises both the importance of providing timely and appropriate feedback on assessments to students, and of enabling students to voice views on their learning experience through channels such as Student Course Evaluation Forms and Class Representatives. FAQs, guidance and resources about feedback can be found on the University’s ‘Enhancing Feedback’ website at: www.abdn.ac.uk/clt/feedback
Appeals and Complaints
The University’s appeals and complaints procedures provide students with a framework through which to formalise their concerns about aspects of their academic experience or to complain when they feel that standards of non-academic service have fallen short of that which they expected.
The process has been designed to make the appeals and complaints process as accessible and simple as possible and to provide a robust, fair mechanism through which to ensure that all appeals and complaints are considered in the appropriate way at the appropriate level.
A major feature of the process is the emphasis it places on early or informal resolution. All students should note that there is an expectation that they will take responsibility for seeking resolution of their academic or non-academic concerns by raising and discussing them at the earliest possible stage with the relevant individuals in an academic School or administrative Service.
Further details of the processes for making an appeal or complaint, including where to find further help and support in the process, is given at:
www.abdn.ac.uk/registry/appeals
Transcripts at Graduation
It is anticipated that students who commenced their studies in, or after, 2009/10, will receive a more detailed transcript of their studies on graduation. The increased details will include a record of all examination results attained. For students graduating in 2012/13 transcripts will show details of all CAS marks awarded, including marks which are fails. Where a resit has been required as a result of medical circumstances or other good cause (MC/GC) this will not be shown, but all other circumstances (i.e. No Paper ‘NP’) will be included.
MyAberdeen (the University of Aberdeen’s Virtual Learning Environment)
MyAberdeen replaces WebCT as students’ virtual learning environment. This is where you will find learning materials and resources associated with the courses you are studying.
MyAberdeen also provides direct access to TurnitinUK, the online originality checking service, through which you may be asked to submit completed assignments.
You can log in to MyAberdeen by going to www.abdn.ac.uk/myaberdeen and entering your University username and password (which you use to access the University network).
Further information on MyAberdeen including Quick Guides and video tutorials, along with information about TurnitinUK, can be found at: www.abdn.ac.uk/students/myaberdeen.php.
Information about academic writing and how to avoid plagiarism can be found at www.abdn.ac.uk/sls/plagiarism.
Aberdeen Graduate Attributes
Graduate Attributes are a wide-ranging set of qualities which students will develop during their time at Aberdeen in preparation for employment, further study and citizenship.
There are four main areas of the Graduate Attributes:
• Academic excellence
• Critical thinking and communication
• Learning and personal development
• Active citizenship
Students have many opportunities to develop and achieve these attributes. These include learning experiences on credit-bearing courses and co-curricular activities such as work placements, study abroad and volunteering. In accordance with the University’s commitment to Equality and Diversity, students can request support with any aspect of the Graduate Attributes framework.
The ACHIEVE website offers resources that enable students to assess and reflect upon their present skills and development needs. The website also contains resources to help students to improve their skills and links to a range of university services such as the Careers Service and the Student Learning Service. Students can access ACHIEVE from their MyAberdeen site in the ‘My Organisations’ section. More information about Aberdeen Graduate Attributes and ACHIEVE can be found at www.abdn.ac.uk/graduateattributes.
The Co-curriculum
The co-curriculum enhances a student’s employability and provides opportunities to develop and achieve Aberdeen Graduate Attributes. Co-curricular activities complement a student’s degree programme and include: work placements, study abroad, enterprise and entrepreneurship activities, the BP Student Tutoring Scheme, career mentoring and the STAR (Students Taking Active Roles) Award initiative. Below are examples of credit-bearing co-curricular activities. It is anticipated that these types of activity will be included on an enhanced transcript for students graduating in, or after, 2012/13
ERASMUS is an exchange programme funded by the European Commission which enables students to study or work in another European country as part of their degree programme. Eligible students will receive a grant to help with extra costs while abroad and a number of our partner institutions teach through English. For more information, visit www.abdn.ac.uk/erasmus/. The University also has opportunities for students to study in a non-European country as part of their degree through the International Exchange Programme. International partners include universities and colleges in North America, Hong Kong and Japan (www.abdn.ac.uk/undergraduate/international-exchange.php). The University aims to ensure full academic recognition for study periods abroad, therefore the credits gained from study abroad will count towards the Aberdeen degree programme for students participating in both ERASMUS and the International Exchange Programme.
Work placements can also form an integral part of a degree programme and attract academic credit. Placements are available locally, nationally and internationally, lasting from a few weeks to a full year and are generally paid. Visit the Careers Service website for further placement information and to find available work placements.
Further information about the co-curriculum is available at: www.abdn.ac.uk/careers
School of Medical Sciences - Guide to Citing and Referencing
This guide should be used to assist you when completing any work for disciplines in the School of Medical Sciences. All work should include citations at appropriate places in the text, with a complete reference list at the end of the assignment. If diagrams/ graphs/ tables are copied or adapted from other publications/ websites, the sources must also be cited in the legend for that item, and included in your reference list.
Good citing and referencing not only improves the quality of your work, but it gives credit to the authors of original work, and makes it less likely that you can be accused of plagiarism. Further guidance on writing and plagiarism may be found at http://www.abdn.ac.uk/writing/ . When you submit work for marking, you are declaring that YOU are the author, that you have not copied it or plagiarised any material from other sources, AND that all sources of information have been acknowledged in your text. Students may be penalised by the University if found guilty of plagiarism.
Students are warned to be careful if using websites as sources of information. These may be inaccurate and are often not peer-reviewed. You are strongly encouraged to use advanced textbooks, peer-reviewed papers or reviews as the sources of your information in your work. Students are also advised to avoid quoting chunks of text in their work. Just because you put quotation marks around some text does not mean that you have not plagiarised it. Try and explain ideas and concepts in your own words.
The referencing style used here is Harvard, similar to that recommended by the University Library (see their factsheet for further information on referencing). Students must use this style of citing and referencing for all work. Other styles are not acceptable. Marks may be deducted if students do not cite or reference properly (see specific marking schemes for details).
Citing references within the text
You must provide citations in the text at the appropriate places by putting the author’s surname and year of publication in round brackets immediately after the relevant text (author, date method).
Author, date method
Jones et al. (1999) has argued that….
Studies have produced conflicting results…..(Bloggs, 2000; MacDuff et al., 1993)
Smith stated (1990)…..and then later work confirmed this (2003)…..
Bloggs (2001) investigated…..
One author (Bloggs, 2000)
Two authors (Smith & Jones, 1982)
Three or more authors (Chesterfield et al., 1995)
If the same author(s) wrote two or more papers in the same year Thwaites et al. stated (1990a)…..and then provided further evidence (1990b)…..
N.B. “et al.” should be in italics, as should all other Latin words/phrases in your text (e.g. in vitro). There is also a full stop after “et al.”, since it is an abbreviation of “et alia” (“and others”).
Listing your references at the end of your work
Your list of references must place the surnames of the first authors in alphabetical order. List all authors of a piece of work unless there are a large number.
Format of references at the end of your work
Book - whole Rang, H.P., Dale, M.M., Ritter, J.M. & Flower, R.J. (2007) Pharmacology. 6th Ed. Edinburgh: Churchill Livingstone.
Book – article or chapter within Johnson, D. & Smart, J.S. (1983) Advanced techniques in measuring athletic performance. In: S. Roberts, ed., Sports Science in the Laboratory. London: Macmillan, pp. 3-28.
Journal – article within Furchgott, R.F., Zawadzki, J.V. (1980) The obligatory role of endothelial cells in the relaxation of arterial smooth muscle by acetylcholine. Nature. 288(5789), 373-6.
Website Department for Education and Employment (2000). Student loans: guidance on terms and conditions from April 2000. [online]. Available from: http://www.dfee.gov.uk/loan2000/index.html [Accessed 23rd March 2006]
