evolutionary & comparative anatomy (anat321)pcnjeffery/evo/handbook.pdf · evolutionary &...
TRANSCRIPT
1
Evolutionary & Comparative
Anatomy (ANAT321)
2012/13 Handbook
Contents:
Timetable 2 Lecture notes 3 Practical Rotations 3 Assessment & Feedback 4 Lecture Synopses 6 Recommended Textbooks 7 Appendix 1: Example individual report 8 Appendix 2: Example Group Declaration 10 Marking and Feedback Proformas Appendix 3: Individual reports 11 Appendix 4: Group Poster 12 Appendix 5: Group Presentation 13 Appendix 6: HARC Rules & Regulations Project Groups
14 18
Dr. Nathan Jeffery
Department of Musculoskeletal Biology Institute of Ageing & Chronic Disease
2
2012/13 Timetable:
Date Week 10am - 12noon 1 - 2pm
25th Sept 1 Practical Rotation 1 (group work, individual report)
Past, Present & Future (NJ)
2nd Oct 2 Genetics & Evolution (JG)
9th Oct 3 Submit 1st individual report (10% of final mark) by 2pm
Diversity & Systematics (NJ)
16th Oct 4 Practical Rotation 2 (group work, group poster presentation)
Skull (NJ)
23rd Oct 5 Feedback Clinic (collect & discuss marks for report
Eyes & Inner Ears (NJ)
30th Oct 6 Poster presentations and marking (5% of final mark)
Nervous System (NJ)
6th Nov 7 Practical Rotation 3 (group work, individual report)
Musculoskeletal System (MG)
13th Nov 8 Digestive System (FP)
20th Nov 9 Submit 2nd individual report by 2pm (10% of final mark)
Respiratory & Circulatory Systems (JQ)
27th Nov 10 Practical Rotation 4 (group work, group powerpoint presentation)
Research Highlight: Biomechanics & Computational Simulations (NJ)
4th Dec 11 Feedback Clinic (collect & discuss marks for report)
Research Highlight: Form Analysis (NJ)
11th Dec 12 Powerpoint presentations & marking (5% of final mark)
Research Highlight: Comparative Anatomy of a Model Species (Mus musculus) (NJ)
Practical (HARC practical classroom, Sherrington Bld.)
Self directed learning and preparation time Lecture (Room 512, Cedar House)
Feedback Clinic (5min slots, Dr. Jeffery's office, Sherrington Bld.)
Lecturers - FC, Mrs Fay Culling; JG, Prof. Jim Gallagher; JQ, Dr. John Quayle;
MG, Dr. Michael Gunther; NJ, Dr. Nathan Jeffery.
3
Lecture Notes
Within “Resources/Lecture Notes” on VITAL there should be notes for each
lecture in the series. These are incomplete copies of the lecture slides, typically
posted on-line the day after each lecture. Students are expected to make notes
during each lecture and afterwards with reference to the recommended
textbook and the lecture slides.
VITAL also contains links to several YouTube tutorials on basic anatomy that
you may find useful.
Practical Rotations
Students work in groups and are provided with a brief introduction to the
nature of the specimens in each scenario. The group is then given the freedom
to dictate the scope and learning objectives of each scenario. For instance, one
group may decide to infer the phylogenetic relationships amongst specimens
whilst another may focus on the functional significance of certain
morphological traits. Students will submit a brief rationale and statement of
their chosen objective(s). Groups rotate through all four scenarios over a
period of 12weeks. The form and timing of assessment is the same for all
students and alternates between individual reports and group presentations
(refer to Assessment & Feedback).
Practical sessions are held in the HARC Anatomy Classroom. This is venue is
licensed under the Human Tissues Act. This means we can only work with
models (no real animal material is allowed) and students must abide by the
HARC rules. By entering the HARC you consent to these rules and to automatic
exclusion from HARC, and any loss of marks that may occur as a consequence,
if you break any of the rules. A copy of rules is given in Appendix 6. To
summarise, students must: i) wear a lab coat at all times; ii) not eat or drink in
the classroom; iii) not take phones, cameras or any other prohibited device
into the classroom. Please refer to the full set of rules.
You will need a sketch and/or a lab book to make hand drawings and notes in
during the practical sessions. Do not panic if, like me, your drawings resemble
cubism rather than photorealism. Marks are allocated on the basis of your
4
analytical insights and ability to visually communicate concepts rather than
your artistic prowess.
Assessment & Feedback
The module has two components of assessment, in-course and exam. The in-
course component relates to the practical elements of the module and consists
of two individual reports (10% each) and two group presentations (poster &
powerpoint presentation 5% each). Reports are marked by an academic whilst
the group presentations are marked by an academic and the peer group. The
overall score allocated for the practical rotations contribute 30% towards the
final module mark. There is no pass/fail mark for the practical rotations and no
opportunity to resubmit if you get a low mark.
Individual reports: should be no longer than 2 A4 sides with a minimum font
size of 11 and a typeset that is easy to read (e.g. arial or times roman). The
report must include a title, your name, a statement of objective(s) and a signed
declaration that the work is your own. An example individual report is given in
Appendix 1. Reports must be submitted (hardcopy) to School of Life Sciences
Teaching Support Office (Sherrington Bld) by the dates and times given in the
Timetable (page 2). Penalties for late submission are outlined in the
University's Codes of Practice on Assessment. As a guide, there will be a 5%
penalty per day. The first 5% deduction starts immediately after the
submission deadline and continues for 5 working days. After 5 days the piece
of work is given zero. Please refer to the full code of practice.
Feedback for each individual report is provided on a proforma along with the
mark allocated. Feedback forms and marks are given out during the drop-in
Feedback Clinics (see Timetable). This also gives students the opportunity to
discuss their progress with an academic (5min slots). The mark and feedback
proforma is given in Appendix 3.
Group Poster: this should consist of one A0 side (landscape) with an
appropriate font size and typeset that can be easily read from approximately
~2metres away. The poster must include a title, names of contributors, a
statement of objective(s) and a signed declaration that the work is that of
contributors. The declaration must also outline the contribution made by each
5
group member and be signed by all members as well (see, for example,
Appendix 2)
Marks will be allocated and feedback provided during the presentation session.
Each poster will be projected onto the large screen in turn and the audience
will mark it using the poster marking proforma (Appendix 4). Marks will be
collated and moderated by an academic. Results will be sent out via e-mail.
Group Presentation: each group is given 10 mins to give an oral presentation
of their study using Microsoft PowerPoint. Presentations should include a title
slide giving the names of the contributors, an objectives slide and an
acknowledgements slide that outlines the contribution made by each group
member. The group must also submit a separate written declaration on
contributions and plagiarism that is signed by all group members (similar to
Appendix 2). Other than these requirements, the group is free to decide on the
content, style as well tempo and mode of delivery. For example, the group may
decide to nominate just one speaker or take it in turns to speak.
Marks and Feedback will be given by the peer group and an academic. Five
minutes is allowed for oral feedback and questions from the audience. The
marking proforma is given in Appendix 5. Marks will be collated and
moderated by an academic. Results will be sent out via e-mail.
Written Exam: The remaining 70% is taken as a 2hr long essay style exam
during the New Year exam period. You will have a choice of answering 3 essay
questions from a choice of 5. Questions will typically ask you to reflect on or
discuss themes, concepts and topics that you have encountered during the
lectures and practical rotations. Example questions include:
- compare and contrast evolutionary adaptations in terrestrial versus aquatic
species of vertebrates
- write about the evolution of the vertebrate brain with reference to the
acquisition and loss of functional capabilities
- give a brief history of the field of comparative and evolutionary anatomy and
outline in detail a recent discovery you have heard about (cite your sources)
- describe the evolution of the vertebrate eye
6
Answers are marked by one member of academic staff, second marked by
another and if necessary moderated by a third, independent academic. Final
marks are also reviewed by the external examiner, the Module Review Board
and Board of Examiners. There will be a resit opportunity in the summer for
students who fail the module.
7
Lecture Synopses
Subject to last minute alterations to accommodate latest ideas and discoveries
Lecture 1 Past, Present & Future: history of comparative & evolutionary anatomy from
Linnaeus, Le Curvier, Huxley, & Owen through to current research and the relevance, and
significance, to clinical sciences as well as environmental philosophy, social sciences &
palaeontology.
Lecture 2 Genetics and Evolution: comparative genetics (molecular phylogeny); HOX
genes & body plans; molecular clocks; population genetics and adaptation; somatic versus
germline mutations.
Lecture 3 Diversity and Systematics: basic phylogeny and taxonomy of the extant
vertebrates; major anatomical attributes of the classes; insights into some fossils that
highlight key speciation events.
Lecture 4 The Skull: a look at different types of bone, joints and sutures in the skull and
how these have evolved in vertebrates.
Lecture 5 Inner Ears & Eyes: Morphological adaptations of the vestibular apparatus,
cochlea and eye, reflecting varied functional demands.
Lecture 6 The Nervous System: evolutionary changes in the brain & cranial nerves
Lecture 7 The Musculoskeletal System: comparative anatomy of the musculature and
postcranial skeleton; modifications to this in relation to support and locomotion
Lecture 8 The Digestive System: evolution of feeding mechanisms, the digestive tract
and the influence of feeding behaviour on whole body morphology
Lecture 9 The Respiratory & Circulatory Systems: examine gills, lungs, accessory
respiratory organs and swim bladders; pulmonary, venous and lymphatic systems.
Lecture 10 Current Research - Biomechanics & Computational Simulations: introduction
to computational anatomy, including kinematics, stress analysis, muscle activation
simulations.
Lecture 11 Current Research - Form Analysis: introduction to geometric morphometrics
as a tool for comparing varying forms and shapes.
Lecture 12 Current Research - Comparative Anatomy of a Model Species (Mus
musculus): review anatomy of the mouse, emphasising functional & morphological
similarities and dissimilarities compared with humans.
8
Recommended Texts
Students are strongly encourage to buy or loan from the library a copy of
Kardong's book. Without it, you will struggle in the practical rotations and in
making additional notes before and after lectures. Evidence of additional
background reading is essential to gain the highest grades.
Kardong K. 2011. Sixth Edition, "Vertebrates: Comparative Anatomy,
Function, Evolution." McGraw-Hill Education
Also useful are:
De Luliis G. & Pulera D. 2007. Second Edition, "The Dissection of Vertebrates: A
Laboratory Manual" Academic Press
9
Figure 1. Series of three bones referred to as (A), (B) and (C).
Scale bar ~25mm and major facets are annotated.
0
10
20
30
40
50
60
70
0 10 20 30 40 50 60
Face
t w
idth
(m
m)
Facet length (mm)
Figure 2. Bivariate plot of facet width against length (mm)
Appendix 1: Example Individual Report
Form variations of the Mammalian astragulus
Author: Smith J
Objective(s): Our two main objectives are to i) document differences of size and shape of
the astragulus and ii) infer functional capabilities as well as assign possible phylogenetic
affinities.
The sample consists of three compact looking bones, each covered in two prominent facets
and a series of smaller facets (see Figure 1). Bone A is large and robust looking with a
principal axis of approximately 75mm in length. The larger articular surface (Ai) is saddle like
with ridges that run obliquely relative to the body of the bone. The second facet is smooth
and almost flat, with only a slight bulge (Aii). Bone B is slightly smaller at around 60mm and
when viewed from the side, perpendicular to the long axis, it resembles a fiddle block pulley.
Paired ridges run parallel along both facets (Bi, Bii) and curve around the ends of the bone.
The facets are almost in alignment with each other and with the body of the bone.
Bone C is the smallest at around 50mm in length. There are traces of two ridges on facet
C(i) but otherwise the surface is curved and relatively smooth. The facet appears to be
Decide on your
aims & objectives
and outline them
here in one or two
sentences (N.B. the
scope of your aims
will determine the
depth of detail that
will be expected ).
Illustrate key features or ideas using
figures, graphs and drawings. You
cannot take photographs so make
sketches and notes during the
practical (no marks for artistic
prowess so keep it simple).
Ai
Aii
Bi Ci
Bii Cii
Use a maximum of two A4 page format with 2.54cm margins and a
minimum 11 pnt font that is easy to read (e.g. arial or times roman).
10
rotated slightly in relation to the body of the bone. Facet C(ii) extends on a neck of bone to
form a head and is similar in arrangement to the neck and head of the modern human femur.
The facet is smooth and rounded. Bones B and C have additional, saddle shaped facets (not
shown) and bones A and C possess other irregular and significantly smaller joint surfaces
(not shown). In total it appears that A and C have four facets whereas B has only three.
Reference to Kardong (2012) suggests that these bones are examples of the astragalus
(syn. talus). Further research (Adams, 2012) indicates that these bones probably belong to
an equid (A), bovid (B) and primate (C), possibly human. The arrangement and relative size
of the ridges indicate that all three bones are from the left side. The astragulus acts as the
articulation between the leg and foot and our study suggests that the facets Ai, Bi & Ci
articulate with the tibia and to a lesser extent the fibula (referred to as the talocrural joint)
The joints Aii, Bii & Cii articulate with the tarsal bones (navicular, humans & bovid; central
tarsal bone, horse). The arrangement of the facets is indicative of certain functions. For
instance, the curved and slightly rotated surface of A(i) suggests that the joint allows for
extension, flexion and a certain amount of rotation whereas the flat A(ii) surface implies a
primarily rotator form of movement. The facets of Bone B appear consistent with extension
and flexion but less rotation than seen with respect to Aii. Facets Ci and Cii also appear
primarily designed for extension and flexion as well as possibly abduction and adduction
around Cii. The larger size of A and it facets indicates that it is subject to much greater
forces than either B or C (see Figure 2). This is consistent with the assignment of A to the
equid family which can grow to several hundred kilograms in weight and practice a cursorial
mode of locomotion. Facet Aii would allow for rotations of the food to meet changes of
ground topography at speed. Bone C also possess two distinct facets of which Cii allows for
a range of motion that would be consistent with an aboreal form of habitat that would require
a degree of inversion to grasp branches.
According to O’Keefe et al (2006) the precursors to the astragalus bone, which include the
tibiale and intermedium, are present in amniotes and evolved with the transition from fins to
limbs. However, it is not clear exactly which combination of bones fused to form the
astragalus proper found in reptiles. Historically the bone is said to have formed from just the
tibiale or from a fusion of the tibiale, intermedium and 4th centrale bones. The authors
advance an alternative model on the basis of new fossil evidence and suggest the
involvement of a fourth bone, the 3rd centrale.
References
Adams, B. & Crabtree, P. (2012). Comparative osteology: a laboratory and field guide of
common North American animals. London, Academic Press.
Kardong, KV (2012). Vertebrates: comparative anatomy, funciton & evolution. Singapore,
McGraw-Hill Press.
O’Keefe, FR et al (2006). Evolution and Homology of the Astragalus in Early Amniotes: New
Fossils, New Perspectives. J. Morphology 267:415–425
Declaration: I declare that is my own work, that I have cited all sources and have not
plagiarised.
Signature.................................................. Name Jen Smith
Always cite
your
references,
avoiding
unsubstanti
ated
tertiary
sources (
e.g.
Wikipedia)
Refer to
papers as
well as
textbooks
include a signed
statement that
this is your work
11
Appendix 2: Example Group Declaration
Declaration: All authors contributed to the poster. JS, PW and NB measured the bones and wrote
notes whilst DA made preliminary sketches and observations. PW formatted and annotated the
Figures and JS, NB, as well as DA conducted the additional background research. All authors concur
with this declaration and that the work is their own and not plagiarised.
Signature.................................................. Name Jen Smith
Signature.................................................. Name Daniel Adams
Signature.................................................. Name Nick Berek
Signature.................................................. Name Pippa Williams
12
Appendix 3: Marking & Feedback Proforma, Individual Projects
ANAT321: Evolutionary & Comparative Anatomy
Assessed Individual Report - Marks & Feedback
Student:
Submission date:
CONTENT
Factually accurate Many factual omissions/inaccuracies
Objective(s) appropriate & clearly defined Superficial treatment
Evidence relevant to objective(s) Material has little relevance
Figure(s)/ table(s) appropriate Absent/inappropriate
Descriptions/concepts clear and logically developed Text lacks coherence, confused
Evidence of deductive reasoning No/little reasoning
Independent thought/analysis Unreflecting/ uncritical account
Evidence of wide reading on topic Limited reading on topic
Conclusions/findings are original, insightful Conclusions/findings are pedestrian and/or
& correspond to objective(s) irrelevant to objective(s)
PRESENTATION AND STYLE
Good structure Material lacks clear structure
Correct English (grammar, spelling) Poor grammar and spelling
Language clear Language confused
Concise ‘scientific’ style Colloquial, convoluted style
Good tables & figures with appropriate legends Poorly constructed figures & tables
Conclusions/findings clearly articulated No discernible findings/conclusions
Appropriate sources, referenced correctly Poor sources, incorrect referencing
Signed declaration present and correct Declaration absent or incomplete
PLEASE NOTE - mark awarded is not simply the sum of ticked boxes. There is some
discretion and flexibility in the weightings of each section to recognise reports that exceed
expectations in one or more aspects and allow for
compensation.
Further comments
Mark (100%)
Mark (10%)
13
Appendix 4: Marking & Feedback Proforma, Group Presentation
Group Poster Presentation
Date:................... Group:........................................................................
Title: ........................................................................................................
Name of appraiser:...................................................................................
Please tick the appropriate box:
CONTENT
Factually accurate Many factual omissions/inaccuracies
Objective(s) appropriate & clearly defined Superficial treatment
Evidence relevant to objective(s) Material has little relevance
Figure(s)/ table(s) appropriate Absent/inappropriate
Descriptions/concepts clear and logically developed Text lacks coherence, confused
Evidence of deductive reasoning No/little reasoning
Independent thought/analysis Unreflecting/ uncritical account
Evidence of wide reading on topic Limited reading on topic
Conclusions/findings are original, insightful Conclusions/findings are pedestrian and/or
& correspond to objective(s) irrelevant to objective(s)
PRESENTATION AND STYLE
Good structure Material lacks clear structure
Correct English (grammar, spelling) Poor grammar and spelling
Language clear Language confused
Concise ‘scientific’ style Colloquial, convoluted style
Good tables & figures with appropriate legends Poorly constructed figures & tables
Conclusions/findings clearly articulated No discernible findings/conclusions
Appropriate sources, referenced correctly Poor sources, incorrect referencing
Signed declaration present and correct Declaration absent or incomplete
Additional comments:
Circle Overall Mark:
Poor 1 2 3 4 5 6 7 8 9 10 Outstanding
14
Appendix 5: Marking & Feedback Proforma, Group Presentation
Group PowerPoint Presentation
Date:................... Group:.........................................................................
Title: .........................................................................................................
Name of appraiser:...................................................................................
Please tick the appropriate box:
1. Audibility and pace
difficult to hear clearly audible
too fast or slow good speed, expressive
2. Use of audiovisual aids
poor quality slides very high quality
crowded, uninteresting easy to follow, informative
3. Explaining the background and rationale to the project
poor explanation excellent understanding
of background and explanation of background
4. Presentation of results and conclusion
very confused clear and logical presentation
hard to follow
5. Time keeping (10 minutes allocated)
far too long/short exact time keeping
6. Handling of questions
inappropriate focused, competent answers
unsure
7. Additional comments:
Circle Overall Mark:
Poor 1 2 3 4 5 6 7 8 9 10 Outstanding
15
Appendix 6: HARC Rules & Regulations
HUMAN ANATOMY RESOURCE CENTRE
SAFETY AND RULES OF CONDUCT FOR USERS OF HARC
After reading the information on this sheet please sign and return the slip attached as
acknowledgement that you have read, understood, and agree to comply, with it.
PLEASE KEEP this information: re-read it regularly so that you are confident you would know
what to do in the event of an emergency.
FIRE SAFETY – AND SAFETY IN GENERAL
FIRE
1. The fire alarm in this area of the building is a continuous sounding bell. When it rings
evacuate the building immediately. The fire escapes are the main staircases at each
end of the HARC floor. There is an additional fire escape which you can reach
through the Practical Classroom. On exiting the building assemble outside the Harold
Cohen Library.
2. In the event of a fire, DO NOT:
Use a lift to exit the building
Stop to collect personal possessions
3. If you discover a fire, sound the alarm by breaking the glass of a RED fire alarm box.
These boxes are located in HARC, and in both the foyer areas at each end of the
floor. Once the alarm is activated, leave the building following steps (1) and (2)
above.
4. When the fire alarm bell rings the locks on all HARC doors are automatically
released. The fire alarm is tested twice a week. If the alarm sounds for longer than
ten seconds, evacuate the building following steps (1) and (2) above.
16
GENERAL SAFETY
1. If an emergency arises when you are in HARC (e.g. an accident or a medical
emergency) inform a member of staff. IF YOU CANNOT FIND A STAFF MEMBER
immediately, telephone the University Security Control desk:
DIAL 2222
There is a wall-mounted telephone near the communicating doors in HARC . There
are additional telephones in the foyers at each end of the HARC floor.
Tell the Security Staff where you are (Human Anatomy Resource Centre, Third floor,
Ashton Street Medical School/Sherrington Buildings) and await further instructions.
2. ALL ACCIDENTS, no matter how minor, which occur in HARC must be reported to a
member of staff and an Accident Report Form must be completed.
3. HARC is designated as a laboratory area. No food or drink may be consumed within
HARC; this includes bottled mineral water.
4. Students MUST wear a white coat at all times in HARC; those not complying with this
regulation will be asked to leave the area. Students must also display the identity
badge issued by their home Department on their white coat.
Disposable gloves should be worn when handling prosected material and disposed of
in the bins provided. Please remember to wash your hands after handling
prosections; there are wash hand basins located in HARC.
Safety glasses must be worn by all students actively engaged in dissection
CONDUCT AND DRESS
1. You should behave in a restrained manner while in HARC. We insist that you respect
the dignity and generosity of those who have bequeathed their bodies to us. Loud
noise and other forms of rowdy behaviour are unacceptable.
2. You should dress in a modest and restrained manner while in the presence of our
donors. No head covering is permitted unless worn for religious reasons. You are
not permitted to wear shorts, three-quarter length trousers, or short skirts. You
must wear appropriate footwear in HARC for health and safety reasons. You are not
permitted to wear open-toed sandals or flip-flops.
17
OTHER REGULATIONS
1. Under NO CIRCUMSTANCES may any student bring visitors into HARC, nor divulge to
anyone the access codes for the digital locks.
2. No bags or coats may be brought into HARC; they should be deposited in the lockers
provided. Please do not leave the HARC area with your locker key.
3. The entire third floor, including foyer areas and locker rooms, makes up the area
licensed under the Human Tissue Act.
No electronic equipment may be used within this area. This includes mobile
telephones, dictaphones, pagers and laptop computers. No MP3, CD or minidisc
players are to be used in HARC.
You may not use any equipment capable of making an image while in HARC. This
includes the cameras associated with mobile telephones.
4. Removal of any material from HARC (including text, images etc.) is theft and
appropriate action will be taken against the person or persons concerned.
Students should be aware that all staff working in this area, including demonstrators
and the technical staff, act with the authority of the Director of HARC. They are
empowered to require an individual to leave the area, if in their opinion, s/he is
contravening the regulations laid out above or if their behaviour constitutes a risk to
safety.
If you are asked to leave HARC you must do so promptly and without question.
Before working in HARC again you must make an appointment with the Director in
order to discuss the circumstances which led to your dismissal.
18
Project Groups
Group A: 200652088 Al-Husaini, Fatemah
200490117 Beglinger, Shanthi
200466196 Burns, Robyn 200711967 Itina, Anna
200719677 Palmer, Megan
200540094 Sahraoui, Yasmina
Group B: 200541635 Brady, Jane
200553034 Gani, Bilal
200695720 Hawkley, Mya
200723040 Nugues, Charlotte
200685436 Warrington, Jessica
200719519 Daly, Kelly
Group C: 200715617 Brydon, Michelle
200710047 Dee, Rachel
200720609 Dorman, James
200576066 Pyatt, Katy
200584558 Tan, Meng
200671032 Goulding, Martin
Group D: 200698672 Brown, Sarah
200704582 Hardy, Elizabeth
200746033 Wasala Mudiyanselage, Lakna
200698872 Niker, Amanda
200733522 Phillips, Leah
200513459 Rowan, Keiran