Science in Trinity

Junior Fresh - TR060

Biological and
Biomedical Sciences
2024–2025
Contents
TR060: BIOLOGICAL AND BIOMEDICAL SCIENCES INTRODUCTION ................................................................... 1
TR060 BIOLOGICAL AND BIOMEDICAL SCIENCES OVERVIEW AND MODULE SELECTION ................................... 2
MODULE SELECTION ........................................................................................................................................... 3
MODERATORSHIPS .................................................................................................................................................. 3
CHANGE OF OPEN MODULES..................................................................................................................................... 3
SEMESTER STRUCTURE ....................................................................................................................................... 4
TR060 BIOLOGICAL AND BIOMEDICAL SCIENCES – CORE MODULES ................................................................. 5
BYU11101: FROM MOLECULES TO CELLS I ................................................................................................................. 5
BYU11102: ORGANISMS TO ECOSYSTEMS I ................................................................................................................ 9
CHU11B01: CHEMISTRY FOR BIOLOGISTS................................................................................................................. 14
MAU11002: MATHEMATICS, STATISTICS AND COMPUTATION 2 .................................................................................. 16
TR060 BIOLOGICAL AND BIOMEDICAL SCIENCES – OPEN MODULES .............................................................. 18
GSU11001: SPACESHIP EARTH: AN INTRODUCTION TO EARTH SYSTEM SCIENCE .............................................................. 18
GSU11005: INTRODUCTION TO GEOLOGY: A BEGINNERS GUIDE TO PLANET EARTH.......................................................... 20
PYU11F10/PYU11F20: FOUNDATION PHYSICS FOR LIFE AND EARTH SCIENCES.............................................................. 21
EDU11001/EDU11002: SCIENCE COMMUNICATION ................................................................................................ 25
IMPORTANT INFORMATION .......................................................................................................................... 28
COLLEGE REGISTRATION .......................................................................................................................................... 28
CLOSING DATES FOR COURSE TRANSFER .................................................................................................................... 28
PROGRESSION AND AWARDS ................................................................................................................................... 28
ATTENDANCE/NON-ATTENDANCE REGULATIONS FOR JUNIOR AND SENIOR FRESH STUDENTS ............................................... 28
NON-SATISFACTORY ATTENDANCE IN SCIENCE............................................................................................................. 30
ACADEMIC INTEGRITY............................................................................................................................................. 30
TRINITY TUTORIAL SERVICE ..................................................................................................................................... 31
DISABILITY SERVICES .............................................................................................................................................. 31
STUDENT COUNSELLING.......................................................................................................................................... 32
HELPFUL COLLEGE WEBSITES:.................................................................................................................................. 32
GRADUATE ATTRIBUTES ................................................................................................................................ 33
DATES TO NOTE: ............................................................................................................................................ 34
TEACHING TERM DATES 2024-2025 ................................................................................................................. 34
CONTACTS DETAILS: ....................................................................................................................................... 35
APPENDIX 1: GENERAL INFORMATION .......................................................................................................... 36

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Welcome to Science at Trinity

TR060: Biological and Biomedical Sciences introduction

Welcome to the Biological and Biomedical Sciences Stream at Trinity College Dublin.

In the Biological and Biomedical Stream students will study the core concepts that are fundamental
to all biological systems. These will be presented in core modules during the first two years and will
include: cell structure and composition, genetics, heredity and biological information, evolution,
molecular biology, metabolism, anatomy and physiology of bacteria, fungi, plants and animals,
ecosystems, and environmental biology. Students will also study core concepts in chemistry with a
focus on aspects that are essential for an understanding of how biological systems function and
those that underpin biomedical science. Students will also acquire mathematical, statistical, and
computational skills that are relevant for the analysis of biological systems.

In addition, students have the opportunity both to expand their scientific knowledge and to pursue
their individual interests by choosing from a cohort of open modules on topics such as physics,
geoscience, history, philosophy and ethics of science, science education and communication,
agriculture and biotechnology, infection and immunity, and behavior.

In the third year, students specialize in one of the 11 moderatorships offered in this stream:
Biochemistry; Botany; Environmental Science; Genetics; Human Genetics; Immunology;
Microbiology; Molecular Medicine; Neuroscience; Physiology; Zoology. The fundamental concepts of
that discipline will be presented in core modules while students will also select from a cohort of
open modules from allied disciplines that enhance understanding of their chosen discipline and
encourage interdisciplinary thinking and research. Students can also experience the wide range of
knowledge and investigation available throughout the university by choosing an elective module
from a cohort that highlights major research themes from across all faculties.

In the fourth year, students choose from a selection of modules on advanced topics within their
discipline. They will also undertake a Capstone project in Trinity College or in a research laboratory in
another university, research institute or hospital. Throughout, students will acquire skills in problem
solving and data handling and in oral and written communication.

This programme of science education is designed to foster and develop a student’s capability for
independent thought and effective communication, an ability to continue their education
independently and to act in a responsible manner. These attributes are a preparation for a career in
science and medicine (e.g., in research, biotechnology, pharmaceutical industry, further medical
training); for a career in related areas where a scientific education is beneficial (e.g., patent law,
forensic science, journalism) and for careers in areas such as education, management, business,
finance, consultancy, industry, communication and policy making.

Professor Andrew Jackson

Director, TR060 Biological and Biomedical Sciences Course

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TR060 Biological and Biomedical Sciences overview and module
selection

The TR060 Biological and Biomedical Sciences Introductory Session will take place on Tuesday 17th
September 2024 with a lecture in MacNeill Lecture Theatre followed by an open module
information session, in the Biology Laboratories, downstairs from the MacNeil. Here you will have
an opportunity to meet with Academic members of staff to discuss your open module choices.

The schedule of events for the 17th of September is outlined below:

• Introductory Lecture: Tuesday 17th September 2024 at 10.00 to 10.30 am in the MacNeil
Lecture Theatre and a second session will be at 13.30 to 14.00 in the MacNeil Lecture Theatre.
• Open module choice session with an academic member of staff as follows in the Biology
Laboratory, downstairs from the MacNeil.
o Surnames A-H 11.00 to 12.30
o Surnames I-R 14.00 to 15.30
o Surnames S-Z: 16.00 to 17.00

Note:
• The choices you make in Junior Fresh year may influence your choices in the second semester of
Junior Fresh year and Senior Fresh year.
• Open module choice forms will not open until 17.00 hrs on the 17th September after all students
have attended the Introductory session in the MacNeill Lecture theatre and the relevant open
module choice session. The module choice form must be completed by 17.00 hrs on the 18th
September.

Please read the following information on pages 2,3, and 4 and then go to:
https://forms.office.com/e/fN3ARpC8mZto select your modules. If you feel that you need assistance
with your choices, please contact us at [email protected] and we will be happy to help.

Students considering a career in teaching at second level (Junior and Senior Certificate) are
reminded of the need to fulfil the requirements of the Teaching Council for each subject they intend
to teach. The requirements for each subject are listed at:
https://www.teachingcouncil.ie/en/Publications/Registration/Documents/Curricular-Subject-
Requirments-after-January-2017.pdf

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MODULE SELECTION
Students must take 40 core credit modules (20 per semester) as follows:

Module
Module title Semester Credits
code
BYU11101 From Molecules to Cells Semester 1 10
BYU11102 Organisms to Ecosystems Semester 2 10
CHU11B01 Chemistry for Life Sciences Semester 1 10
MAU11002 Mathematics, Statistics, and Computation 2 Semester 2 10

Students will choose approved modules to the value of 20 credits (10 per semester) from the
Module code Module title Semester Credits
Spaceship Earth: An Introduction to Earth Systems
GSU11001 Semester 1 10
Science
Introduction to Geology: A Beginners Guide to Planet
GSU11005 Semester 2 10
Earth
* PYU11F10 Foundation Physics for Life and Earth Sciences 1 Semester 1 10
* PYU11F20 Foundation Physics for Life and Earth Sciences 2 Semester 2 10
* EDU11001 Science Communication 1 Semester 1 10
* EDU10002 Science Communication 2 Semester 2 10
following:

* Foundation Physics and Science Education modules may be taken in either semester one or
semester two but cannot be taken in both.

Moderatorships
On successful completion of Senior Fresh, students compete for places in any one of the eleven
moderatorship available at sophister level. Open module choices no not affect moderatorship
eligibility or allocation, you are free to choose as you wish. Please see Allocation of Places
regulations for further details: : https://www.tcd.ie/media/tcd/science/pdfs/science-allocation-of-
places-regulations-tspmc2023.pdf

Change of Open Modules

If you feel that you have perhaps made the wrong choice of open module, please seek advice
immediately from your Tutor, Course Director, or the Science Course Office. It may be possible for
you to change from one module to another within Science. If you do decide to change modules, then
do so quickly – it can be difficult to try to catch up with work in a new module if you have missed
more than two or three weeks of lectures. You should call into the Science Course Office if you wish
to change modules, you can also send an email to [email protected]

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SEMESTER STRUCTURE

TR060: BIOLOGICAL AND BIOMEDICAL SCIENCES

CORE MODULES (mandatory) – 20 credits per semester.

SEMESTER 1 – Michaelmas term SEMESTER 2 – Hilary Term

(23rd September to 25th November 2024) (20th January to 07th April 2025)

BYU11101: From Molecules to Cells

BYU11102: Organisms to Ecosystems (10 credits)
(10 credits)

CHU11B01: Chemistry for Biologists MAU11002: Mathematics, Statistics and

(10 credits) Computation 2 (10 credits)

OPEN MODULES (optional): Students choose 10 credits from each semester

GSU11001: Spaceship Earth: An introduction to GSU11005: Introduction to Intro to Geology: A

Earth System Science (10 credits) beginner’s guide to Planet Earth (10 credits)

PYU11F10: Foundation Physics for Life and Earth PYU11F20: Foundation Physics for Life and Earth
Scientists 1 (10 credits) Scientists 2 (10 credits)

EDU11001: Science Education (10 credits) EDU11002: Science Education (10 credits)

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TR060 Biological and Biomedical Sciences – Core Modules
BYU11101: From Molecules to Cells I
Semester 1, 10 credits
Module Coordinator: Kevin Mitchell Email: [email protected]

Module Learning Aims

This module aims to introduce students to molecular and cellular biology, including key topics in Cell
Biology, Biochemistry, Genetics, and Microbiology. A description of the possible origin of life, from
the abiotic world to single-celled and multicellular organisms is given, and the ultrastructure of the
prokaryotic and eukaryotic cells is covered in detail. The properties and functions of the major
classes of biochemicals found in living systems (carbohydrates, lipids, proteins, and nucleic acids) are
described, the structure and function of membranes and organelles, and the chemical basis of
metabolism and energy transfer in the cell. Students are introduced to basic concepts in Genetics,
how the information contained in DNA (genes) is expressed, replicated, and inherited. Finally, the
sheer diversity of life forms, from viruses to prokaryotic and eukaryotic microorganisms, to more
complex plant and animal life forms is described. Students also study cell and virus structure, cell
growth and viral replication, agents of infectious diseases, and host immunity.

Learning Outcomes
• On successful completion of the module, students will be able to:
• Provide an account of the cellular basis of life: from its origins in the abiotic world, to the
evolution of unicellular and multicellular organisms.
• Describe the diversity of life forms: including viruses, prokaryotes (bacteria), archaea, and
eukaryotes (unicellular organisms, animals and plants).
• Provide an account of the chemical basis of life and the biochemistry on which living systems
depend: the properties and functions of the major classes of biomolecules, the structure and
function of membranes and organelles, and the chemical basis of metabolism and energy
transfer.
• Describe how the information contained in DNA (genes) directs the construction and growth of
an organism, and how this information is replicated and transmitted from one generation to the
next (inheritance; genetics).
• Employ a range of laboratory techniques, demonstrating the development of practical scientific
skills, knowledge of experimental design and the interpretation of results.
• Apply the scientific method as a fundamental approach to experiment-based investigations,
critical analysis of data, and problem solving.

Contact Hours/Methods of Teaching and Learning

Lectures and practicals will be supplemented with information sessions, tutorials and activities that
provide guidance in the use of library resources, laboratory health and safety, writing techniques,
help with avoiding plagiarism and examination techniques. Online learning resources, assignments,
submission instructions and information concerning the day-to-day running of the module will be
published in Blackboard. Sixty-five hours contact time.

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Module Content

Lecture Topic Lecturer Practicals

Introduction and overview Kevin Mitchell
Section 1 Origin of Life – Cellular basis of life – Diversity of Life Forms
1. Origins of Life Luke O’Neill The Diversity of Life Forms
2. Origins of Life Luke O’Neill
3. Cellular Basis of Life Fred Sheedy Liquid Handling
4. Cellular Basis of Life Fred Sheedy
5. Cellular Basis of Life Fred Sheedy Bacterial Growth & Survival
6. The Tree of Life Alastair Fleming
7. Bacteria Alastair Fleming
8. The Archaea Alastair Fleming
9. Fungi & Protists Alastair Fleming
10. Viruses Alastair Fleming
11. Relationship Between Life Forms Alastair Fleming
Section 2 The Chemistry of Life
12. Introduction to Biochemistry Luke O’Neill
13. Nucelotides, Amino Acids & Peptides Luke O’Neill Enzyme Purification
(Chromatography)
14. Protein Structure Ken Mok
15. Protein Function Ken Mok
16. Enzymes Vincent Kelly
17. Enzymes Vincent Kelly Enzyme Characterisation
(Kinetics)
18. Lipids & Membranes Vincent Kelly
19. Metabolism Vincent Kelly
20. Metabolism Vincent Kelly
21. Mitochondria & Respiration Vincent Kelly
22. Chloroplasts & Photosynthesis Vincent Kelly
Section 3 Biological Information – Genetics, Heredity & DNA
23. Introduction to Genetics Matt Campbell Mendelian Genetics
24. Mendelian Genetics Matt Campbell
25. Linkage & recombination 1 Matt Campbell
26. Linkage & Recombination 2 Matt Campbell
27. Identification of DNA as Hereditary Matt Campbell
Material
28. Quantitative Genetics Matt Campbell
29. DNA – Structure & Function Kevin Mitchell
30. Information Flow – The Central Dogma Kevin Mitchell
31. Information Flow – The Central Dogma Kevin Mitchell
32. Information Flow – The Central Dogma Kevin Mitchell
33. Mutation & the Consequences Kevin Mitchell

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Lecture Content:
• Origin of Life: What is Life? How did it arise? The Origin of Life from a chemical and cellular
perspective; the abiotic world; the prebiotic world; Miller-Urey experiment; the first cell;
photosynthesis and oxygen – mass extinction; origin of first eukaryotic cell; multicellular life;
cell specialization.
• Cellular basis of life: Cell structure – prokaryotes, archaea, eukaryotes – animal and plant
• organelles & their prokaryotic origin – mitochondria, chloroplasts, mitosis and meiosis – cell
division – regulation of cell division.
• Diversity of Microbial Life: the tree of life; bacteria, archaea, fungi & protists, cell structure,
morphology, function and habitat; extremophiles; viruses
• Relationship between life forms: the good, the bad and the ugly; concepts of symbiosis and
parasites; plant and animal diseases.
• Structural principles for small molecules: elements and chemical groups in life, bonds, bond
energies, bond lengths; forces between biological molecules and chemical groups;
asymmetry; four classes of biomolecules: amino acids, nucleotides, carbohydrates & lipids
• Nucleotides, Amino acids and peptides: DNA, RNA, chromatin and chromosome structure,
properties of amino acids, chemical features, and physical properties of the R-groups; the
peptide unit and peptide bond
• Proteins and protein structure: the concept that shape dictates function; hierarchical
organization of protein structure; concept of primary, secondary, tertiary and quaternary
structure; introduction to forces that stabilize protein structure.
• Protein function: functional classes of protein; introduction to bioinformatics; proteins and
evolution; relationships between proteins; similarity and identity.
• Enzymes: structure & function; reaction mechanisms; co-factors and vitamins; kinetics;
regulation of enzyme activity
• Lipids and membranes: lipid structures, fatty acids, phospholipids; membranes, chemical
and physical properties, membrane proteins; transport across membranes; concept of
compartmentation and membrane traffic.
• Metabolism & major metabolic pathways: the starting point: introduction to carbohydrates
and fatty acids; organization, energetic principles, key steps, and links between the main
metabolic pathways; glycolysis, TCA cycle, beta oxidation; outline of the reversing catabolic
pathways, gluconeogenesis, and fatty acids synthesis.
• Mitochondria & Respiration: mitochondria, redox reactions, and energy transduction;
electron transport and the electron transport chain; oxidative phosphorylation; coupling of
oxidations to phosphorylation; chemiosmotic view of energy transduction (in brief).
• Chloroplasts and Photosynthesis: chloroplast, architecture and function, overview of the
light and dark reactions of photosynthesis.
• Introduction to Genetics: an outline of some core concepts from classical genetics to the
present; a whistle stops tour of key discoveries in the history of genetics.
• Mendelian Genetics: Mendel’s laws, the 1st law of segregation and the 2nd law of
independent assortment using monohybrid and dihybrid crosses; concepts relating to
genetic analysis and the use of model systems; inheritance patterns for single gene disorders
– pedigree analysis.
• Linkage and recombination: Meiosis and the role of ‘crossing over’ in gene mapping; a brief
recap regarding Mendelian genetics – for example, highlighting that genetic linkage breaks
Mendel’s 2nd law of independent assortment; outline of key concepts underlying the
generation of genetic maps; classical work by Sturtevant / Morgan.

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 • Identification of DNA as hereditary material; key experiments establishing DNA as the
genetic material; bacterial transformation and its significance (Griffith / Avery, McLeod &
McCarthy / Hershey-Chase); the concept of horizontal gene transfer (mechanisms
transformation, conjugation, transduction); differences in vertical and horizontal gene
transfer.
• Quantitative Genetics: an overview of concepts relating to discrete variation versus
continuous variation; experiments demonstrating that quantitative traits are inherited,
examples of quantitative traits in humans; concepts regarding the use of GWAS to elucidate
the genetics architecture of complex traits using an example of one or more disorders.
• DNA, Structure and Function: the double helix – discovery of the structure of DNA – DNA
composition – DNA replication – semi-conservative replication, replication forks, leading and
lagging strand synthesis, DNA polymerases; DNA replication in prokaryotes and eukaryotes.
• Information flow in the cell – The Central Dogma: transcription, RNA polymerases in
prokaryotes and eukaryotes; promoters, repressors, terminators – the lac operon;
transcription factors, enhancers; decoding the information in mRNA, translation; ribosomes
in prokaryotes and eukaryotes, tRNAs and aminoacyl tRNA synthetases, the genetic code;
introduction to the regulation of gene expression – positive and negative regulation.
• DNA –Mutation and its consequences: mechanisms by which mutations are generated –
including errors in DNA replication; the action of chemical and physical mutagens; errors in
chromosome construction and distribution; an outline of the different types of mutation
(missense, nonsense, frameshift mutations) and their molecular consequences in relation to
gene expression and protein function; mutations causing inherited diseases and cancer; DNA
repair – mechanisms of DNA repair, repair deficiency and disease.

Recommended Textbook

Campbell Biology, 12th Edition by Lisa A. Urry, Michael L. Cain, Steven A. Wasserman, Peter V.
Minorsky, Jane B. Reece (Published by Pearson (2021)
Assessment Details:
1. End of semester examination: 50% of module mark. The exam format will be closed book, in-
person, fifty multiple choice questions drawn from across the lecture course.
2. Coursework: 50% of module mark. Coursework includes compulsory attendance at laboratory
sessions, assignments associated with practical’s, in-course essay and MCQ tests of lecture
material. Marks breakdown across the various components will be published in Blackboard.

Students must obtain an overall module mark of 40% to pass the module.

Contacts details:

Module Coordinator: Kevin Mitchell [email protected]

Biology Course Coordinator: Mirela Dardac [email protected]
Phone: 01 8962895
Laboratory Manager: Audrey Carroll [email protected]
Phone: 01 8961049

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 Executive Officer: Daniel McCormick [email protected]
Phone: 01 8961117

BYU11102: Organisms to Ecosystems I

Semester 2, 10 credits

Module Coordinator: Trevor Hodkinson [email protected]

Module learning aims.

Organisms to Ecosystems I aims to introduce students to the biology of individuals, species,

populations, and ecosystems, and explore how humans interact with other living organisms. It
covers the developmental biology of organisms, their physiology, brain function and the
evolutionary and ecological responses of organisms to their environment. Topics incorporate the
diversity of life and its biological development, interactions between organisms and their
environment, the biological context of climate change, human impacts on the environment, future
food sustainability, urban ecology, ecosystem services and the value and conservation of
biodiversity.

Topics are arranged in three sections: 1) Multicellularity and Development, Physiology, Behaviour
and Neuroscience, 2) Evolution: Adaptation, Populations and Biodiversity, and 3) Ecology and
Environment.

A mixture of lectures, self-directed field work and hands-on laboratory practicals are used in the
delivery of this module.

Learning outcomes

1. On successful completion of this module, the student will be able to:

2. Outline the major steps involved in how complex animal and plants are formed and be able to
relate the morphological changes that occur to the molecular and cellular changes that underlie
and drive embryo and organ development.
3. Describe the concept of homeostasis at the cell, organ, and organism level; give examples of the
functional interrelationships that exist between cells, organs and systems; provide an account of
how organisms can sense change in the environment.
4. Describe the basic principles by which the brain functions and outline key experimental steps
and informative clinical cases that have elucidated our current understanding of brain function.
5. Recognize the diversity of life on earth and describe how it evolved over geological time scales.
6. Describe the ecological relationships between individuals, populations, communities, and
ecosystems, and between organisms and their environment.
7. Recognize how humans can positively and negatively influence other living organisms and their
environment and understand the value of other living organisms for humans.
8. Demonstrate practical, numerical, and analytical skills.
9. Collate, synthesize, and present information in written reports.

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Contact Hours/Methods of Teaching and Learning

Lectures and practical’s will be supported by online learning resources.

Essay writing skills will be developed. Online learning resources, assignments, submission
instructions and information concerning the day-today running of the module will be published in
Blackboard. 65 hours contact time.

Module Content

Lecture Topic Lecturer Practicals

Introduction and overview Trevor Hodkinson
Section 1 Multicellularity and Development, Physiology, Behaviour and Neuroscience
1. Multicellularity and Development Paula Murphy
2. Introduction to Development Paula Murphy Development and Floral
Morphology
3. Embryogenesis and Morphogenesis Paula Murphy
4. Intercellular Communication, Paula Murphy
5. Pattern Formation Paula Murphy Physiology
6. Differential Gene Expression Paula Murphy
7. Form and Function Áine Kelly
8. Homeostasis Áine Kelly
9. Physiological Regulation Áine Kelly
10. Pre-neuroscience History of Ideas of Mind & Tomas Ryan
Brain
11. Fundamentals of Nervous System Structure Tomas Ryan
and Function

12. Introduction to the Biology of Memory Tomas Ryan

Storage
Section 2 Evolution: Adaptation, Populations and Biodiversity
13. History of life Trevor Hodkinson First Life
14. Selection/modern synthesis Trevor Hodkinson
15. Species Trevor Hodkinson Diversity of Life
16. Speciation Trevor Hodkinson
17. Extinction Trevor Hodkinson Evolution
18. Phylogeny Trevor Hodkinson
19. Genetic Basis of Selection Aoife McLysaght Species Diversity Evolution &
20. Genetic Basis of Evolution 1 Aoife McLysaght Modularity
21. Genetic basis of Evolution 2 Aoife McLysaght
22. Human Evolution Aoife McLysaght
Section 3 Ecology and Environment
23. Species James Barnett
24. Species – Conservation James Barnett

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25. Trophic Cascades and Rewilding James Barnett Biodiversity & Ecosystems
Services
26. Constructing Ecosystems and Conservation James Barnett
27. Urban ecology James Barnett
28. Ecosystem Services and Natural Capital James Barnett Biological Environmental
29. Global Ecology and Climate Change Richard Nair Systems
30. Biomes, Niches Richard Nair
31. Biomes and Global Productivity Richard Nair
32. Biomes and Biogeochemical Cycles Richard Nair
33. Desiccation Resistance and Space Travel Richard Nair

Lecture Content:

• Introduction to development: core concepts, model organisms, analysis of development;

morphology, genetic, biochemical.
• Embryogenesis and morphogenesis: germ layers
• Intercellular communication: determination, potency, axis formation – anterior-posterior, dorsal-
ventral.
• Pattern formation: morphogens, gradients, and thresholds.
• Differential gene expression: temporal and spatial, master regulators.
• Form and Function: functional characteristics of living things; specialisation of cells/tissues/organs to
fulfil specific functions.
• Homeostasis: the concept of the internal environment; composition, temperature, pH etc. of body
fluids; maintenance of homeostasis by cooperation of different physiological systems; feedback and
feed-forward.
• Physiological Regulation of Function: fundamentals of nervous and endocrine control of function
and comparison of speed and modes of action: how an individual organism senses and responds to
changes in the external and internal environments.
• Pre-neuroscience history of mind/brain ideas: cartesian dualism and materialist and non-materialist
explanations of mind; the brain as the substrate of mind; the effects of head trauma on behaviour
and memory, anatomy of the human/mammalian brain, functions in behaviour and in homeostasis,
overview of human brain regions and attribution of various regions to broad functions (evidence
from lesions, imaging).
• Fundamentals of nervous system structure and function: reticular vs. neuron theory, nervous
system as electrically active, Helmholtz and excitable neurons, action potentials & synaptic
transmission.
• Introduction to the biology of memory storage: challenges of integrating neurobiology and brain
function at multiple levels; reductionism and correlation vs. causation; the biology of memory
storage.
• Short history of life: timeline, major groups, diversity.
• Selection/modern synthesis: adaptation
• Species: definitions, taxonomy, diversity, species rich groups.
• Speciation: allopatric, sympatric, adaptation, radiations, key innovations.
• Extinction: fossils, global change (climate, atmosphere, tectonic).
• Phylogeny: homology, convergence, reversals, methods.

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• Genetic basis of selection
• Genetic basis of evolution: molecular variation, neutral theory, drift; molecular evolution of
population genetic variation.
• Human evolution
• Global ecology and climate change: future climate change – global challenges – projections; pest
diseases, human physiology, how to predict; need to understand fundamentals of ecology to address
these global challenges.
• Biomes, niches: introduction to biomes, what shapes biome distribution? Climate change, climate
niches / fundamental versus realized niche; challenge of predicting future ecological responses to
climate change.
• Commonness, rarity, and population processes: extinction or persistence are processes that
operate at the population level; introduction to concepts of abundance and rarity, competition,
dispersal, demography and its application to conservation (endemism and invasions).
• Conservation: applications of population biology at the species level, including prioritizing species
for conservation management, assessing threat and red listing.
• Trophic cascades and rewilding: what is a community, energy flow, applications of community
ecology to conservation and rewilding challenges; consumption, facilitation & predation.
• Constructing ecosystems and conservation: in the Anthropocene humans have constructed new
ecosystems, what are they, where do we find them and what are their values? Contrast with
“natural” ecosystems.
• Urban ecology: how have organisms adapted to living in urban environments? How can we better
design our cities and buildings to gain more value from nature and support biodiversity?
• Ecosystem services and natural capital: nature provides many valuable ecosystem services
supported by natural capital; introduction to the concepts and controversies surrounding the
ecosystem services and natural capital concepts.
• Food: environmental impacts and ecological process: food security- ecological concepts-
productivity- energy flows through ecological systems/basic concepts of biogeochemical
cycles.
• Future food and a changing planet: food security; ecological concepts, human population increase,
projections for future productivity.
• Biosphere feedbacks on climate system: introduction to biological feedbacks on the climate system;
carbon sequestration/ transpiration/ water budget, within biomes; fire feedbacks/rain seeding;
nature-based solutions to climate mitigation and adaptation; green and blue solutions – cities etc.,
‘The Martian’ closed system.

Recommended Textbook: Campbell Biology, 12th Edition by Lisa A. Urry, Michael L. Cain, Steven A.
Wasserman, Peter V. Minorsky, Jane B. Reece (Published by Pearson (2021)
Assessment Details: Assessment Details:

(A) End of semester examination: 50% of module mark. The exam format will be closed book, in-
person, fifty multiple choice questions drawn from across the lecture course.
(B) Coursework: 50% of module mark. Coursework includes compulsory attendance at laboratory
sessions, assignments associated with practical’s, in-course essay and MCQ tests of lecture
material. Marks breakdown across the various components will be published in Blackboard.

Students must obtain an overall module mark of 40% to pass the module.

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Contacts details:

Module Coordinator: Trevor Hodkinson [email protected]

Biology Course Coordinator: Mirela Dardac [email protected]
Phone: 01 8962895
Laboratory Manager: Audrey Carroll [email protected]
Phone: 01 8961049
Executive Officer: Daniel McCormick [email protected]
Phone: 01 8961117

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CHU11B01: Chemistry for Biologists
Semester 1, 10 credits

Module learning aim:

To provide an introduction to aspects of chemistry which are essential to an understanding of the
operation of living systems and the chemical technology of medicine.

Learning Outcomes:
On successful completion of the module, students will be able to:
1. Explain, using appropriate terminology and physical units, basic concepts in chemistry,
including precipitation and redox reactions.
2. Analyse bonding and molecular structure, hybridisation, and mechanisms.
3. Explain the concepts of entropy and free energy and the control of chemical and
biochemical reactions by free energy changes.
4. Explain the concept of equilibrium and factors affecting the position of equilibrium.
5. Demonstrate an understanding of acid-base, buffers, and electrochemistry.
6. Explain the factors that influence the rate of a reaction and the concepts of order of
reaction.
7. Describe and explain the chemistry of oxygen based functional groups.
8. Recall the structure and properties of the major types of biological organic molecules, and
be able to describe the relationships between structure, properties, and functions.
9. Describe organic reaction mechanisms that impact on biochemical processes.

Module content:

Week Topic and description

1-3 Introduction to chemistry: The atom, chemical bonding, and chemical reactions
9 Lectures Structure and building principles of atoms; element symbols; masses and the
mole; introduction to the periodic table; brief introduction to the structure of the
electron shell.
Atoms, Molecules, and Ions.
Isotopes and radionuclides in medicinal chemistry.
Bonding in chemical substances – lengths, angles, and rotation
Ionic bonding; covalent bonding; weak bonding; molecules and solid-state
structures; electronegativity; the periodic table.
Hybridization
Chemical reactions; symbolizing reactions; balancing equations.
Solutions, concentrations, and dilutions
Limiting reagents and yields; role of water in chemical reactions; important
classes of chemical reactions
Oxidation and reduction reactions, electron transfer; oxidizing and reducing
agents; half-equations.

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 4-9 Chemical energetics, thermodynamics, and chemical equilibria (8L)
(14 Lectures) Ionic equilibria (1L)
Acids, bases, and buffers (2L)
Kinetics (1L) and 1st order rate law
Electrochemistry (2L)

10-12 Nomenclature of carbon chains, simple hydrocarbons, and aromatics.

(10 Lectures) Oxygen-based functional groups; hydroxyls, aldehydes, ketones, carboxylic acids,
esters
Sugars, aminoacids and peptides.
Lipids and nucleic acids
Introduction to substitution, addition, elimination, condensation, and hydrolysis
reactions.

Reading list/ Indicative Resources

• Organic Chemistry, by Jonathan Clayden and Nick Greeves; Publisher: OUP Oxford; 2 ed.
• Chemistry & Chemical Reactivity Hardcover by Paul Treichel, John Kotz, John Townsend, David
Treichel; Publisher: Brooks Cole; 9 ed.
• Atkins, P.W. & de Paula, J. (2011) Physical Chemistry for the Life Sciences, 2nd Edition, W H
Freeman & Co

Methods of Teaching and Student Learning

A mixture of lectures, tutorials and hands-on laboratory practicals are used in the delivery of this
module. The practical sessions are formatted in order to further clarify concepts thus reinforcing
learning.

Methods of Assessment CHU11B01

• Laboratory and in course assessment: 30% of Final Grade
• Examination: 70% of Final Grade

Contact details:

Module Coordinator: Dr Eoin Scanlan E-mail: [email protected]

Phone: 01 896 2514
Fresh Coordinator: Dr Noelle Scully E-mail: [email protected]
Phone: 01 896 1972
Senior Executive Officer: Ms AnneMarie
E-mail: [email protected]
Farrell
Phone: 01 896 1726

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MAU11002: Mathematics, Statistics and Computation 2
Semester 2, 10 credits

Module learning outcomes:

On successful completion of this module, students will be able to
• Use graphs of functions in the context of derivatives and integrals.
• Compute derivatives and equations of tangent lines for graphs of standard functions including
rational, trigonometric, exponential, and logarithmic functions.
• Compute definite and indefinite integrals using substitution and integration by parts.
• Solve maximisation/minimisation problems using the first derivative test and other applied
problems based on population dynamics and radioactive decay.
• Algebraically manipulate matrices by addition and multiplication and use Leslie matrices to
determine population growth.
• Solve systems of linear equations using Gauss-Jordan elimination.
• Calculate the determinant of a square matrix and use Gauss-Jordan elimination to determine a
matrix inverse.
• Find the eigenvalues and the eigenvectors of a given square matrix.
• Learn the basic ideas of descriptive statistics, types of variables and measures of central
tendency and spread.
• Recognise common discrete and continuous distributions and how these naturally arise in life
science examples.
• Extract information from a data set and make inference about a population using ideas of
sampling distributions, confidence intervals and hypothesis testing.
• Carry out basic tasks using the statistical software R such as importing, exporting, and
manipulating data, analysing and graphing data, loading and installing package extensions, as
well as using help files and online resources to either solve error queries or achieve more niche
capabilities.

Module content
• Calculus part: functions and graphs, limits, continuity, definition of derivative, rules of
differentiation, graphical interpretation of derivatives, optimization problems, growth, and
decay applications, semilog and log-log plots, techniques of integration, differential equations
and initial value problems.
• Discrete part: limits of sequences, difference equations, discrete time models, vectors and
matrices, inverse matrices, determinants, systems of difference equations, systems of linear
equations, eigenvalues and eigenvectors, Leslie matrices, matrix models.
• Statistics part: numerical and graphical descriptions of data, relationships and linear regression,
samples and inference, conditional probability and Bayes’ rule, discrete and continuous random
variables, sampling distribution, confidence intervals, hypothesis testing.

Recommended reading lists

• Biocalculus: Calculus, probability, and statistics for the life sciences by Stewart and Day.
• Getting started with R: An introduction for biologists by Beckerman, Childs and Petchey.

Methods of Teaching and Student Learning

11 weeks of teaching with 5 lectures, 2 tutorials and 1 computer practical per week

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Assessment Details.
• This module is examined in a 2-hour examination at the end of Semester 1.
• The mathematics part of the module contributes 70% towards the overall mark (with 50% based
on the exam and 20% based on the tutorials).
• The statistics part of the module contributes 30% towards the overall mark (based on a group
assignment during the last weeks of the semester with groups of 1-3 students working together
on a data analysis project).
• Re-assessment, if needed, consists of 100% exam.

Contact Details

Module Coordinators:
Prof Anthony Brown, (Calculus) E-mail: [email protected]
Prof John McDonagh (Statistics)
E-mail: [email protected]

Prof Marvin Anas Hahn, (Discrete) E-mail: [email protected]

E-mail: [email protected]
General enquiries:
Phone: 01 896 1949

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TR060 Biological and Biomedical Sciences – Open Modules

GSU11001: Spaceship Earth: An introduction to Earth System Science

Semester 1, 10 credits

More than 7 billion people now inhabit the Earth and no corner of the planet is unaffected by human
activity. The rise of our species has been fuelled by our ability to access planetary storehouses of
energy and employ this to manipulate the environments around us. The global-scale of human
impacts has led some to suggest we are entering a new era of Earth history – the Anthropocene.
Dealing with the effects of environmental and climate change is one of the most significant
challenge that our species faces in the 21st century.

This module provides a foundation for understanding global environmental issues by considering the
Earth as an interconnected system in which matter and energy are exchanged between the
Geosphere, Biosphere, Atmosphere, Hydrosphere and the Anthroposphere. It considers the life-
support systems of ‘spaceship Earth’ and aims to provide a theoretical basis for evaluating the role
of humans as agents of climate and environmental change.

Module learning aims

To provide foundation-level knowledge of:
• Fundamental concepts of Earth systems science and the theoretical basis of the ‘systems
approach’ in Geography and Geoscience
• Character and scope of Earth’s principal sub-systems: Geosphere, Hydrosphere, Atmosphere,
Biosphere and Anthroposphere
• Composition / structure of the solid Earth (Geosphere) and the principal processes / drivers
responsible for its formation and evolution
• Composition / structure of atmosphere and ocean, the physical processes / drivers of their
circulation, and the nature of coupling between them
• Weather and climate at a global scale including climate change past, present and future
• Biogeochemical cycling and the role of interconnected biotic and abiotic systems in the
maintenance of life on Earth
• Ecological and historical biogeography including fundamentals of ecology, evolution and
extinction.
• Nature and scope of human impacts on the Earth system including the ‘Anthropocene’ concept.

To develop the following skills & graduate attributes

• Digital skills to manipulate and analyse geographical data, including use of Google Earth and
Excel
• Self-motivated and reflective approach to independent learning, including completion of
assigned reading, activities and formative assessment.
• Make connections between a student’s core subject areas and the field of geography &
geoscience.

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Recommended Reading List:
Holden, J. (2019) An Introduction to Physical Geography and the Environment. 4th Edition. Pearson:
Harlow, UK. 876 pages. Skinner, B.J., Murck, B. (2011) The Blue Planet: An Introduction to Earth
System Science. 3rd Edition. J. Wiley & Sons: Hoboken, USA. 656 pages.

Assessment Details: 100% continuous assessment via in-course tests and assignments.

Module Website: Blackboard

Contact Details:
Course Director TR062 Geography and Geosciences
Dr. Sean Mc Clenaghan [email protected]
Phone: 01 896 1585
Geography Department
Executive Officer: [email protected]
Ms Helen O’Halloran Ph: 01 0896 1576
Geology Department
Executive Officer:
[email protected]
Ms Debora Dias Ph: 01 896 1074

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GSU11005: Introduction to Geology: A beginners Guide to Planet Earth
Semester 2, 10 credits

From the vastness of space to the microscopic crystal structure of minerals; from events which take
billions of years, like galaxy formation, to volcanic eruptions which may last only minutes or seconds.
Geology, or Earth Science, is the all-encompassing study of Planet Earth. Geology sets out to
investigate the origin and development of the planet, the natural principles that govern it, the
processes that act in it, on it, and around it, and finally the life that has evolved with it. Many
sciences are conducted in the laboratory, but to a geologist, the Earth itself is the laboratory.

The module is organised into two main themes. Firstly, we will look at ‘Earth in Space’. We live on a
dynamic and ever-changing planet, where the surface is constantly being destroyed and renewed.
This theme looks at the origin of the Earth, what it’s made of and the processes at work, inside and
out, which drive this change. The second theme, ‘Earth in Time’, then focuses on the evolution of
the planet over time, and the life that has evolved with it. Earth has been around for just over 4,500
000 000 years, and remarkably, we have evidence that life has existed for at least 3,800 000 000 of
those years. There are times in Earth’s history when geological events have changed the course of
biological evolution. And, perhaps more intriguingly, there are times when life has changed the way
the planet operates. So, this theme of Earth and Life evolving together through geological time is
illustrated by looking at eight key episodes in Earth’s history, without which, we simply wouldn’t be
here.

Module learning aims

To provide foundation-level knowledge of:
• Fundamental concepts and principal methods employed in the science of geology.
• Planetary origins and evolution of planet Earth
• Rock types, composition, classification and transformation
• Structure of planet Earth and plate tectonic theory
• The distribution and causes of geohazards (volcanoes, earthquakes, tsunamis)
• Fossil evidence of the origins and evolution of life on Earth
• Geological evidence of past environments and climatic conditions
• Economic geology and the nature of geological resources

To develop the following skills & graduate attributes

• Written and digital / analytical skills

• Critical thinking
• Make connections between a student’s core subject areas and the science of Geology

Module learning outcomes

On successful completion of this module students will be able to:
• Outline the origin and evolution of planet Earth
• Describe and illustrate the dynamic nature of planet Earth with reference to specific geological
processes
• Describe the origins of life on Earth and list the major evolutionary episodes evident in the fossil
record
• Explain the links between the evolution of life and environmental conditions on planet Earth
• Outline the geological history of the island of Ireland
• Make basic geological observations, measurements and interpretations in the field and
laboratory

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Recommended Reading List:
Nicholas, C. J., 2019. A Beginner’s Guide to Planet Earth: Introductory Lectures in Geology. C.J.
Nicholas (ISBN 978-1-911180-33-3)

Assessment Details: 50% examination; 50% continuous assessment via in-course tests and
assignments.

Module Website: https://www.tcd.ie/Geology/undergraduate/modules/year1/

Contact Details
Course Director TR062 Geography and Geosciences
Dr. Sean Mc Clenaghan [email protected]
Phone: 01 896 1585
Geography Department
Executive Officer: [email protected]
Ms Helen O’Halloran Ph: 01 0896 1576
Geology Department
Executive Officer [email protected]
Ms Debora Dias Ph: 01 896 1074

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PYU11F10/PYU11F20: Foundation Physics for Life and Earth Sciences
Semester 1 or Semester 2, 10 credits

Foundation Physics for the Life and Earth Sciences is a foundation module (10 credits) in physics.
It is available as an approved 10 credit module for TR060 and TR062 students, all of whom are taking
Maths, Stats, & Computation (10 credits); as well as for TR061 students (if not taking Physics 1 or
Physics 2) who take both Mathematics 1 (10 credits) and Mathematics 2 (10 credits). It is available in
both semesters for TR060 (but cannot be taken twice); it is only available in semester 2 for TR061 or
TR062 students.

Module Content:

This foundation module comprises lectures, practical work and tutorials, providing an introduction
to: physics of motion, biomechanics, physics of hearing and seeing, electricity, magnetism and
bioelectricity, radioactivity, nuclear physics and related medical applications, heat, pressure, as well
as fluids and their biological, geological and medical applications.

Module Learning Outcomes:

On successful completion of this module, students should be able to:
• Demonstrate the application of Classical Physics within the biomedical and earth sciences.
• Connect the study of wave phenomena and electromagnetism with ultrasound diagnostics and
vision.
• Relate basic knowledge of atomic and nuclear physics to radiation diagnostics and therapy, and
to geological applications.
• Prepare a brief report, including error analysis, on a simple physical experiment.
• Through homework: (i) identify the appropriate concepts, principles, and relations that apply to
the problem; (ii) provide a reasonable and appropriate explanation of why they apply; and (iii)
solve physics problems at a foundation level.

Module Structure
Contact Hours: 42 lectures/tutorials, three-hour practical laboratories, online homework.

Module Personnel: Lecturers: Prof. Lewys Jones; Prof. Martin Hegner; Prof. Matthias Möbius

Summary of Practicals:

In the Foundation Physics for Earth and Life Sciences students complete a minimum of three
practical experiments, including from those experiments available at the bench in the laboratory
during the semester. The emphasis in these practicals whether at home or in the laboratory is on
learning to make physical measurements, record keeping in scientific laboratory notebooks,
estimating uncertainties in measurements, while using these estimates in analysing data in order to
make a quantitative measurement of a physical property. Differing students will attempt a differing
set of experiments selected from those available. There may also be a differing availability of
laboratory experiments on the bench in both semesters. Students are required to record all data and
information related to their experiments in a hardback practical laboratory notebook which is
assessed. At-home physics practical experiments may be assigned and evaluated together with the
laboratory-based practicals.

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Laboratory Practicals:

Experiments are selected from among but are not limited to: Pendulum, Thin Lenses, Density and
the Principle of Archimedes, Surface Tension, Electrical Resistance, Collisions and Momentum
Transfer, Resonance Tube, Leslie’s Cube, Geiger Counter, and Photoelectric Effect among others.

Assessment of practical experiments:

All student’s physics experiments are assessed through both online and submission of written
experimental reports and through an at-the-bench laboratory notebook assessment. These reports
and notebooks must include and require a documented complete data analysis, description, and
concise report of the outcomes of the experiment, and any inferences or conclusions that can be
drawn from the outcome.
Reading List: There is required reading and textbook for this course is an online e-Book, “Physics:
Principles with Applications” by Giancoli from Pearson publishers. The e-Book includes access to the
online homework platform used for assessment, and purchasing this bundle is a requirement for
enrolling on this course. The School of Physics has negotiated a group-discount for this book and
details of how to obtain this discount will be shared with students after enrolment.

Online Assignments: Online assignments are submitted through the online homework platform
associated with the “Physics: Principles with Applications” by Giancoli. The electronic access is
associated with the required textbook and details of how to register once you have purchased the e-
Book will be shared after enrolment.

Methods of Teaching and Student Learning:

A mixture of lectures, hands-on laboratory practicals, lecture demonstrations and weekly on-line
assignments based on both numerical and conceptual questions from the textbook are used in the
delivery of this module. The lecture course follows the material in the textbook very closely with
reading assignments clearly indicated to students as the lecture course progresses. The practical
sessions are structured to provide a firm introduction to the process of physical measurements, as
well as an introduction to estimations of uncertainty (error) and propagation of errors as applied to
physics experiments. Each experiment has its own specific learning outcomes and is structured to
further clarify concepts met in the textbook and lectures to reinforce learning. Weekly homework
assignments, typically alternating between topics, are submitted by students through an online
system and corrected, with some limited feedback to the student available through the online
system post deadline. The lecturer has oversight of the scores and responses to each assignment
and can address these in subsequent lectures and tutorials. Finally, a number of lecturers use class-
based polling of student responses to questions using the available “clicker” technologies.

Methods of Assessment:
Assessment is by a combination of examination and continuous assessment and will include multiple
choice tests (MCQs) examination paper; laboratory and at-home assessed practical work; and online
tutorial homework assignments.

Module website: See links at: http://www.tcd.ie/Physics/study/current/undergraduate/

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Contact details:
Foundation Physics Course
Coordinator: Prof. Plamen E-mail: [email protected]
Stamenov
Phone: 01 896 4350
Junior Fresh Physics Coordinator:
E-mail: [email protected]
Prof. Matthias Möbius
General Enquiries: E-mail: [email protected]
Phone: 01 896 1675
Administrative Officer: Ms Una
E-mail: [email protected]
Dowling

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EDU11001/EDU11002: Science Communication
Semester 1 OR semester 2, 10 credits

Introduction
This module explores science communication as a field of research and practice and how it affects
the relationship between science and society. Communication and collaboration are essential skills
for researchers and on successful completion of this module students should be able to:

● Interpret the key concepts of theory and practice in the field of science communication.
● Assess science communication in terms of science learning, public engagement, citizen science
and the evolving relationship between science and society.
● Critically appraise their own communication skills, in particular: writing, debating, and
presenting

This module will provide practical and theoretical foundations that will enable students to develop
their own communication and presentation skills as well as critical thinking skills. Students will gain
an understanding of how science is taught and communicated, an awareness of how research policy
and public perception is crafted, and a familiarity with interdisciplinary opportunities and challenges
arising at the interface of science and society.

The course will equip students with key communication skills as well as a knowledge of science
education (both formal and informal), policymaking, funding, and ethics that will serve as a platform
to examine the historical impact that science has had on society. It will enable students to identify
responsible research and to propose models of science communication and science learning that
promote cultures of sustainability and participation. Students will be equipped to communicate their
own work and critically reflect on the social context of their field of study.

Module learning aims:

The module aims to support the development of a range of graduate attributes, including:

1. To think independently
• The module will give students a deeper understanding of science communication, science
education, and an appreciation of research beyond their chosen fields.
• Independent research will be encouraged as well as the analysis and synthesis of evidence.
• Self-assessment and peer-assessment aspects of the module will nurture students’ capacity
for critical thinking.
2. To act responsibly
• The module will offer global perspectives on societal challenges by focusing on the United
Nations’ Sustainable Development Goals (SDGs)
• The module will give students a familiarity with contemporary ethical issues arising at the
interface of science and society.
• Responsible, inclusive, and sustainable open research will be explored.
3. To develop continuously
• The module will foster self-motivated learning and the enhancement of academic skills.
• Students will be supported in developing their capacity for critical reflective practice.
• Professional development and career pathways will be highlighted throughout the course
content.

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4. To communicate effectively
• The module will task students with presenting work individually and in groups across a range
of media.
• Students will appraise how science is communicated in public, academic, and political
environments.
• Opportunities will be created for students to improve their abilities to write and speak about
science.

Module content
1. Global Science Communication
2. History of Science and the Scientific Method
3. Paradigms of Science in Society
4. Science Education, Governance, and Policymaking
5. Equality, Ethics, and Moral Dilemmas
6. Citizen Science, Public Engagement, and Societal Challenges
7. Mass Media and social media
8. Writing and Publishing
9. Presentations, Discussions, and Debates
10. Career Progression and Professional Development
11. Reflective Practice, Module Review, and Assignment Support

Recommended reading list

● Broks, P., Gascoigne, T., Leach, J., Lewenstein, B. V., Massarani, L., Riedlinger, M., & Schiele, B.
(2020). Communicating Science: A Global Perspective. ANU Press.
● Sagan, C., & Druyan, A. (1996). The demon-haunted world: Science as a candle in the dark. New
York: Random House
● Trench, B. et al. (2016). Little Country, Big Talk: Science Communication in Ireland. Dublin: The
Pantaneto Press.
● Roche, J. (2022). Essential Skills for Early Career Researchers. London, UK: SAGE Publishing.

Assessment details
The teaching strategy combines a blend of lectures and tutorials. The lectures will utilise interactive
methods to incorporate whole class input, while discussion groups in the tutorials will be led by the
teaching assistants and will facilitate teamwork and problem-based, cooperative/collaborative
learning. This will offer students a flexible approach to learning with a special emphasis on peer-
assessment and self-assessment. College guidelines on universal accessibility will be followed.

The module will be assessed entirely through continuous assessment (using the Blackboard suite of
tools), with both summative and formative assessment components including:
● Online engagement before, during, and after lectures and tutorials
● Reflective journaling
● Group presentations.
● Peer-assessment and self-assessment
● End of semester essay

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Formative assessment will take place regularly during the course, predominantly in the tutorials.
Tutorials will be led by PhD and Postdoctoral researchers, with the guidance of the course lecturers,
and will provide a more informal working space for students to engage in the course content.
Students will be invited to share ideas and will be taught how to critically review each other’s work.
This focus on self-assessment and peer-assessment will build confidence and critical skills.
It will provide students with information based on their performance and monitor their learning to
aid instruction and their comprehension of teaching at regular intervals. Detailed feedback will also
be provided by the teaching team on non-graded student work, which will assist students in
preparing their summative assessment. Formative assessment will aid students and teaching staff to
identify strengths, weaknesses, and challenges. Student feedback will be collected at the end of the
module to help assess the effectiveness of the teaching strategies.

Contact hours
2 hours lectures and 1 hour tutorial = 3 hours per week
X 11 weeks = 33 hours per term

Module Coordinator:
Dr. Joseph Roche ● E-mail: [email protected]
School of Education Phone: 01 896 4851

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Important information

College registration
You will complete College registration online via the website my.tcd.ie. Registration will open on a
course-by-course basis. A communication will be sent to the e-mail address you supplied during the
application process inviting you to log in to the Academic Registry website to register. When you
receive your TCD email address, check it regularly Please check your TCD email address regularly as
that will then be the address to which all Trinity communications will be sent.

All information regarding College registration is available at the following link:

http://www.tcd.ie/academicregistry/registration/

Please Note: Students who have already accessed the my.tcd.ie website should continue to access it
using your current username and password as this will not change. For those who have not
previously logged on, a username and password has been created to give you immediate access.

Closing Dates for Course Transfer

If you decide to transfer out of your course altogether, you must submit an application for transfer
of course to the Academic Registry, following discussion with your tutor. Decisions are based on a)
the availability of places, and b) the entry qualifications of the transfer applicant. It may not be
possible to permit transfers to subjects which already have a full complement of students. Further
details are available on the following link:
http://www.tcd.ie/study/apply/making-an-application/undergraduate/index.php

Students may not register or attend a course until their application to transfer has been formally
approved by the Senior Lecturer

Progression and Awards

Information on progression and awards can be found via the following webpage:
https://www.tcd.ie/teaching-learning/academic-affairs/ug-prog-award-regs/index.php

Information in relation to all undergraduate Regulations can be found via the following:
https://www.tcd.ie/teaching-learning/academic-affairs/ug-regulations/

Attendance/Non-attendance Regulations for Junior and Senior Fresh Students

The following regulations will apply to Junior and Senior Fresh student in the following Science
Courses:
TR060: Biological and Biomedical Science
TR061: Chemical Sciences
TR062: Geography and Geoscience
TR063: Physical Sciences

All students must begin attendance for their course no later than the first day of teaching term and
must fully take part in the academic work of their course. Attendance at Lectures, Labs, Field trips
and tutorials is compulsory in both core and open modules. Timetables are published through the
my.tcd.ie portal and the onus lies with the student to inform themselves of dates, times and venues
by consulting the timetable regularly.

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It is extremely important that students meet all the requirements of their course and that they
submit all continuous assessments, Laboratory practical/Field course reports and assignments by the
required deadlines. Students should ensure that they make themselves aware of the module
weightings which are outlined in the relevant booklets available from the Science Course Office
website: https://www.tcd.ie/science/undergraduate/

Laboratory Practicals, Field courses and Tutorials

The primary function of laboratory practicals, compulsory field courses and tutorials is to equip
students with the skills and knowledge necessary to be successful at sophister level in their chosen
moderatorship. Therefore, they are an extremely important part of the student educational
experience in Science. The learning outcomes for these components are intrinsically linked with the
physical actions of being present. Students who do not attend at least 2/3 of the compulsory
sessions in a module will be returned as “non-satisfactory attendance and may be excluded from
taking their exams: see section below.

Coursework/assignments
Students must complete and submit all coursework, laboratory write ups, field course notes in full by
the published submission date. Deductions for late submission will be applied as follows:
Biology – 10% reduction from final grade per week
Chemistry – 10% for the first 24 hours and 5% ever day after that
Geoscience – 10% reduction from final grade per week

Module handbooks will detail penalties for late submission of individual pieces of continuous
assessment.

It is therefore essential, that students who think they will not be in a position to meet a certain
deadline, contact the module Coordinator or Course Director before the due date. We recognise
that there are times when students will struggle with deadlines, and problems identified at the time
are more easily dealt with than retrospectively when assignments start piling up.

Module coordinators/Course Director details can be found in the Blackboard modules or in the
relevant handbooks available for download from the Science
webpage: https://www.tcd.ie/science/undergraduate/

Absence through illness:

Where a student misses an assigned laboratory/field course/compulsory tutorial class through
illness, they must (a) submit an absence report and upload a med cert via the Science Absence form:
https://forms.office.com/Pages/ResponsePage.aspx?id=jb6V1Qaz9EWAZJ5bgvvlK2pn-
Bcn6aBJpJezeqwuYapUMkpaU1E5SDY5TDZaTUhYU01PMlhBV0kxSyQlQCN0PWcu on the day of
their return to College and (b) inform the laboratory practical supervisor of their absence at the
earliest opportunity and certainly at the next session.

Note: submission of a medical certificate does not automatically initiate excusal from an activity.
The student must obtain excusal from the module coordinator or Course Director after they have
submitted a medical cert.

Other absences:
Students who have sports commitments to the College should supply confirmation from the
appropriate committee to the Module Coordinator/Course Director well in advance of any event.

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Students who anticipate that their sporting commitments may necessitate more than an occasional
absence from College (e.g., Sports Scholars etc.) should discuss their situation with their tutor and
the Associate Dean of Undergraduate Science Education (ADUSE).

Students who have unexpected family commitments should request excusal from the Module
Coordinator/Course Director. Excuses for absence presented after the event, will not be accepted.

Vacations/Holidays/Weddings during teaching term

Students who are absent from College during teaching term for planned
vacations/holidays/weddings etc. must ask the Senior Lecturer, through their tutor, for permission
to be absent from college. No special accommodations will be made for such students. No
replacement tutorials, laboratory/field courses will be scheduled, and no lecture material will be
recorded. The onus in such cases lies with the student to catch up on the worked missed.

The general regulations outlined above will apply however, individual cases will be reviewed on their
own merits.

Non-Satisfactory attendance in Science

All Junior and Senior Fresh students must fulfil the course and module requirements as set out
above with regard to attendance. At the end of teaching term students who have not satisfied these
regulations may be reported as non-satisfactory for that term. Students whose attendance is
reported as non-satisfactory may be refused permission to take their semester one or semester two
examinations and may be required to repeat the year.

Science students will be considered non-satisfactory in a module if:

They fail to attend at least 2/3 of the laboratory practicals/field trips in a module.
OR
They fail to submit at least 2/3 of the required coursework/assignments in a module.

Academic Integrity
Plagiarism is using someone else's ideas, charts, concepts, or words in your assignments and using
them as if they were your own, and without giving credit to the actual author. Plagiarism is
considered a serious offence in Trinity and carries penalties depending on the severity of the
plagiarism.

To ensure that you have a clear understanding of what plagiarism is, how Trinity deals with cases of
plagiarism, and how to avoid it, you will find a repository of information
at https://libguides.tcd.ie/academic-integrity

• Academic Integrity homepage (formerly Avoiding Plagiarism): https://libguides.tcd.ie/academic-

integrity
• Ready Steady Write tutorial: https://libguides.tcd.ie/academic-integrity/ready-steady-write
• Coversheet declaration: https://libguides.tcd.ie/academic-integrity/declaration
• Levels and consequences: https://libguides.tcd.ie/academic-integrity/levels-and-consequences

Correct referencing is essential when crediting your sources and avoiding plagiarism. Your course
handbook will tell you what style of referencing you should use in your assignments so be sure to

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check that out before you start any assignments. You will waste a lot of time if you have to redo your
references.

Resources

Referencite, University of Auckland, New Zealand has some good interactive resources to help you
understand plagiarism and how to avoid it: https://www.auckland.ac.nz/en/law/current-
students/llb-information/academic-information/cheating-plagiarism-turnitin.html

Trinity Tutorial Service

The Tutorial Service is unique, confidential and available to all undergraduate students offering
student support in all aspects of College life. The Tutorial Service is supported and co-ordinated by
the Senior Tutor’s Office which is located on the ground floor in House 27.
Opening Hours
The Senior Tutors Office is open Monday – Friday from 9am – 5.30pm. Closed for lunch from 1-2pm.

Appointments
If you require specific advice or would like a confidential meeting with the Senior Tutor, you can
make an appointment by telephoning +353 1 896 2551 or by emailing [email protected]

What is a Tutor?
A Tutor is a member of the academic staff who is appointed to look after the general welfare and
development of the students in his/her care. Whilst the Tutor may be one of your lecturers, this is
not always the case as the role of the College Tutor is quite separate from the teaching role.

When should I go to see my Tutor?

Whenever you are worried or concerned about any aspect of College life or your personal life, in
particular if it is affecting your academic work. Everything you say to your Tutor is in strict
confidence. Unless you give him/her permission to do so, s/he will not give any information to
anybody else, whether inside College or outside (to your parents/family for example). Your Tutor can
only help you if s/he knows you are facing difficulties, so if you are worried about anything go and
see your Tutor before things get out of hand.

Further information on the Senior Tutors Office and College Tutors may be found via the following
webpage: Senior Tutor’s Office – https://www.tcd.ie/seniortutor/students/undergraduate/

Disability Services
The Disability Service aims to provide appropriate advice, support, and information to help students
and staff with disabilities. The Disability Service has in place a range of supports to ensure that
students with disabilities have full access to the same facilities for study and recreation as their
peers. Most students registering with the Disability Service request access to a range of supports
that help the student reach their full potential while studying. Most students’ needs are
accommodated through these supports. The student decides what level of support they require.

For contact information or to make an appointment, please contact the Disability Service – contact
details are available via their webpage: https://www.tcd.ie/disability/contact/

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Student Counselling
The Student Counselling Service is here to help you to manage any difficulties you are
experiencing so you can enjoy and fully participate in your time here at College.

If you wish to make an appointment with the Student Counselling Service, please consider one of the
options below. If you have any other queries you can call into reception on the 3rd floor of 7-9 South
Leinster Street or contact us on:
Phone: (01) 8961407
Email: [email protected]

For further information visit the following webpage:

https://www.tcd.ie/Student_Counselling/

Helpful College Websites:

In the first few weeks at College, you will hear an array of abbreviations, titles, and place names. So,
visit the jargon buster page: https://www.tcd.ie/students/jargon-buster/

Student life offers information on Supports and Services, Clubs and Societies, Student Unions etc.,
https://www.tcd.ie/students/

For information on Registration, Fees, Grants, ID Cards etc. visit the Academic Registry (AR) in the
Watts Building or the visit the AR website: https://www.tcd.ie/academicregistry/

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Graduate Attributes
The Trinity Graduate Attributes represent the qualities, skills and behaviours that you will have the
opportunity to develop as a Trinity student over your entire university experience, in other words,
not only in the classroom, but also through engagement in co- and extra-curricular activities (such as
summer work placements, internships, or volunteering).

The four Trinity Graduate Attributes are:

• To Think Independently

• To Act Responsibly

• To Develop Continuously

• To Communicate Effectively

Why are the Graduate Attributes important?

The Trinity Graduate Attributes will enhance your personal, professional and intellectual
development. They will also help to prepare you for lifelong learning and for the challenges of living
and working in an increasingly complex and changing world.

The Graduate Attributes will enhance your employability. Whilst your degree remains fundamental,
also being able to demonstrate these Graduate Attributes will help you to differentiate yourself as
they encapsulate the kinds of transversal skills and abilities, which employers are looking for.

How will I develop these Graduate Attributes?

Many of the Graduate Attributes are ‘slow learned’, in other words, you will develop them over the
four or five years of your of study.

They are embedded in the curriculum and in assessments, for example, through undertaking
independent research for your final year project, giving presentations and engaging in group work.

You will also develop them through the co-curricular and extra-curricular activities. If you help to run
a club or society you will be improving your leadership skills, or if you play a sport you are building
your communication and team-work skills.

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 Dates to Note:
Fresh Orientation: 16th September to 20th September 2024

Semester one term dates: 09th September to 29th November 2024

Study Week Semester 1: 21st to 25th October 2024

Semester one examinations: 09th December to 13th December 2024

Semester two term dates: 20th January 2024 to 11th April 2025

Study week semester 2: 03rd to 07th March 2025

Semester two examinations: 22nd April to 25th April 2025

TEACHING TERM DATES 2024-2025

Michaelmas Term Hilary Term
Monday 9 September - Friday 29 Nov 2024 Monday 20 January 2025 - Friday 11 April 2025
Teaching wk. 1 Week 03 09 Sept – 13 Sept Teaching wk. 1 Week 22 20 Jan - 24 Jan
Teaching wk. 2 Week 04 *16 Sept - 20 Sept Teaching wk. 2 Week 23 27 Jan – 31 Jan
Teaching wk. 3 Week 05 **23 Sept - 27 Sept Teaching wk. 3 Week 24 *03 Feb - 07 Feb
Teaching wk. 4 Week 06 30 Sept – 04 Oct Teaching wk. 4 Week 25 10 Feb - 14 Feb
Teaching wk. 5 Week 07 07 Oct - 11 Oct Teaching wk. 5 Week 26 17 Feb - 21 Feb
Teaching wk. 6 Week 08 14 Oct – 18 Oct Teaching wk. 6 Week 27 24 Feb – 28 Feb
Study week Week 09 21 Oct - 25 Oct Study week Week 28 03 Mar - 07 Mar
Teaching wk. 8 Week 10 *28 Oct - 01 Nov Teaching wk. 8 Week 29 10 Mar - 14 Mar
Teaching wk. 9 Week 11 04 Nov - 08 Nov Teaching wk. 9 Week 30 *17 Mar - 21 Mar
Teaching wk. 10 Week 12 11 Nov - 15 Nov Teaching wk. 10 Week 31 24 Mar - 28 Mar
Teaching wk. 11 Week 13 18 Nov - 22 Nov Teaching wk. 11 Week 32 *31 Mar - 04 Apr
Teaching wk. 12 Week 14 25 Nov – 29 Nov Teaching wk. 12 Week 33 07 Apr - 11 Apr

* Orientation week for new entrants

** Teaching begins for all Junior Fresh Students
October bank holiday – Monday 28th October 2024
February bank holiday – Monday 3rd February 2025
St Patrick’s Day - Monday 17th March 2025

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Contacts Details:

Course Director TR060: Biological and Biomedical Sciences

Professor Andrew Jackson E-mail: [email protected]

Biology Fresh Teaching Manager

Ms Mirela Dardac E-mail: [email protected]
Phone: 01 896 2895

Chief Technical Officer

Ms. Audrey Carroll E-mail: [email protected]
Ph: 01 896 1049

Executive Officer:
E-mail: [email protected]
Mr Daniel McCormick
[email protected]
Ph: 01 896 1117

Science Course Office

Associate Dean of Undergraduate Science
Education
Professor Fraser Mitchell E-mail: [email protected]
Ph: 01 896 2025

Science Course Office Manager E-mail: [email protected]

Ms. Ann Marie Brady Ph: 01 896 2829

Administrative Officer E-mail: [email protected]

Ms. Helen Sherwin Murray Ph: 01 896 2799

Executive Officer E-mail: [email protected]

Ms. Andressa dos Santos Melo Ph: 01 896 1970

Executive Officer E-Mail: [email protected]

Ms. Romarey Segura Ph: 01 896 2022

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Appendix 1: General Information
ITEM REFERENCE/Source
Calendar, Part II - General Regulations and Information, Section II, Item 12:
https://www.tcd.ie/calendar/undergraduate-studies/general-regulations-and-
information.pdf

Calendar, Part III, General Regulations, Section 1.20

https://www.tcd.ie/calendar/graduate-studies-higher-degrees/

Attendance Requirements:
Calendar, Part II, General Regulations and Information, Section II, Items 17-23
Calendar, Part III, General Regulations and Information, Sections 1.23; 2.11;
and 3.2
General Regulations
Absence from Examinations
Calendar, Part II, General Regulations and Information, Section II, Item 35
Calendar, Part III, Section 3.5
https://www.tcd.ie/teaching-learning/academic-policies/assets/assess-
nonsub-absence-sep2020.pdf

Plagiarism Policy and information:

https://www.tcd.ie/teaching-learning/UG_regulations/Plagiarism.php
https://libguides.tcd.ie/friendly.php?s=plagiarism

Timetables are available via my.tcd.ie portal:

https://my.tcd.ie/urd/sits.urd/run/siw_lgn

Blackboard:
https://tcd.blackboard.com/webapps/login/

Academic Registry:
General Information https://www.tcd.ie/academicregistry/

Data Protection:
https://www.tcd.ie/info_compliance/data-protection/student-data/

Dignity & Respect Policy

https://www.tcd.ie/equality/policy/dignity-and-respect-policy/

Foundation and Non-Foundation Scholarship: Calendar, Part II

Foundation Science Foundation Scholarship information sheet:
Scholarship https://www.tcd.ie/academicregistry/exams/scholarship/

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Appendix 1: General Information
TR060: Biological and Biomedical Sciences Foundation Scholarship Examination
2024-25 – Information for Scholarship Candidates:

Link? Emailed Helen

Academic Policies:
https://www.tcd.ie/teaching-learning/academic-policies/

Student Learning and Development:

https://www.tcd.ie/Student_Counselling/student-learning/

Student Complaints Procedure:

https://www.tcd.ie/about/policies/160722_Student%20Complaints%20Proce
dure_PUB.pdf

Dignity & Respect Policy

Teaching and Learning https://www.tcd.ie/equality/policy/dignity-and-respect-policy/

Student Evaluation and Feedback:

https://www.tcd.ie/teaching-learning/quality/quality-
assurance/evaluation.php

Academic Integrity:
https://libguides.tcd.ie/academic-integrity

National Framework for Qualifications:

National Framework of Qualifications | Quality and Qualifications Ireland (qqi.ie)

Student Support Services:

https://www.tcd.ie/students/supports-services/

Student Services Booklet:

www.tcd.ie/students/assets/pdf/Student%20Services%20Booklet%20(web%2
0version).pdf

Senior Tutor & Tutorial Service

Student support www.tcd.ie/students/assets/pdf/Student%20Services%20Booklet%20(web%2
0version).pdf

Graduate Studies
https://www.tcd.ie/graduatestudies/

Mature Student Office

https://www.tcd.ie/maturestudents/

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Appendix 1: General Information
Central Societies Committee:
Find new link, awaiting 2024-25
Co-curricular activities DUCAC:
Dublin University Central Athletic Club - Trinity Sport - Trinity College Dublin (tcd.ie)
Student Sport - Trinity Sport - Trinity College Dublin (tcd.ie)

Information on
TCDSU, Including TCDSU
student https://www.tcdsu.org/
representative
structures
In the event of an emergency, dial Security Services on extension 1999
Security Services provide a 24-hour service to the college community, 365 days a
year. They are the liaison to the Fire, Garda and Ambulance services and all staff
and students are advised to always telephone extension 1999.
(+353 1 896 1999) in case of an emergency.
Emergency Procedure
Should you require any emergency or rescue services on campus, you must contact
Security Services. This includes chemical spills, personal injury or first aid assistance.

It is recommended that all students save at least one emergency contact in their
phone under ICE (In Case of Emergency).

NOTE: All of the information contained in this booklet is accurate at time of publication. However,
the Science Course Office reserves the right to modify information, dates and times as necessary.
Students will be notified of any changes via e-mail and the Science webpage

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