Courses

The Master’s programme in Environmental Biology offers different kinds of Master’s courses in various specialisation tracks. 

ECOLOGY & NATURAL RESOURCE MANAGEMENT

Sustainable Development Goals (compulsory)

Description of content
Being involved in research, MSc students should be aware of the potential role their results could play to build a sustainable future. Moreover, students should be able to constructively discuss and connect with other students of the master's program. As such, this inter-track course will encourage the participants to determine and discuss how their research topic may contribute to solving questions related to sustainability. In particular, participants will put their research in relation with one or more of the 17 Sustainable Development Goals set by the United Nations (https://sustainabledevelopment.un.org/?menu=1300). Groups of ten students belonging to the five different tracks will be composed. Based on the project proposal that the students wrote at the start of their major internship, participants will write in no more than 500 words a report containing a clear description of their potential contribution. Each participant will read the reports of two fellow peers and gives peer review. Based on group meetings and discussion of the reviews, each group will choose one report which will be presented in plenary in no more than two slides at the end of the course.

Literature/study material used:
17 Sustainable Development Goals set by the United Nations (https://sustainabledevelopment.un.org/?menu=1300)
Research proposal of student’s major internship.
Mandatory for students in Master’s programme: NO.
Optional for students in other Master’s programmes GS-LS:

Yes, if space allows.
Maximum number of participants: 64

Management of Natural Resources in Context (compulsory)

The course ‘Management of natural resources in context’ (MAN) is a reflection on and exercise in natural resources management in its societal context. The emphasis is on the application of what you already know, what you are able to do in the field of natural resources management and on learning by doing. The main activity of the course consists of working on two major assignments.Assignment A1. In the first assignment you will evaluate practical cases of community-based natural resource management (CBNRM), a form of managing common-pool resources. Many resources worldwide are common-pool resources, e.g. forests which are not privately owned but accessible and available to groups of local people. In this assignment you will reflect on the role of different stakeholders in relation to specific types of natural resources management, including nature conservation.

Assignment A2. In the second assignment you will develop a design for a sustainable multifunctional bio-energy plantation. Biomass is a natural resource that can be used as a feedstock for energy production. Bioenergy can partly replace the use of fossil fuel resources, thus reducing CO2 emissions and mitigating climate change. The area under bio-energy plantations is rapidly increasing. However, there are serious concerns about negative ecological and social impacts of bio-energy plantations, e.g. loss of biodiversity, decrease of food production and increase of food prices.
In a small project team you will design an innovative plan for sustainable production of bio-energy. For an area in the Netherlands, Tanzania or Indonesia, you will develop a plantation, while considering environmental conditions, suitable plant species, and proper management practices, and by applying a multifunctional approach (protecting or enhancing local biodiversity, protecting water resources, landscape-level planning).

Prerequisite knowledge
We recommend to take this course in the second year of the track E&NRM in Environmental Biology. If you would be interested in attending the course, but you are a first year’s master student, or a participant of another master programme, please contact the course coordinator.

Ecology of Natural Resources (compulsory)

Introduction and course set – up
Climate change, expanding human populations and the increasing search for available land, put the natural resources of our world under high pressure. There is a dire need to develop methods to manage these resources in a sustainable manner. To do so, profound ecological knowledge on how natural resources function and respond to management is required. The aim of this course is to strengthen your expertise in plant-, microbial and landscape ecology and to show how this expertise is of vital importance to natural resource management.

The central theme of the course will be ecosystem services. Ecosystems provide many benefits either directly through material goods (e.g. timber, food or medicinal plants) or indirectly as a result of their basic functioning (e.g. carbon sequestration, nutrient cycling, climate regulation, control of water and quality and crop pollination). The main goals of the course are to develop an understanding that many of our natural resources are biological in nature, to examine the mechanisms involved in the procurement of ecosystem services and to critically appraise the impacts of global change as well as conservation and management strategies on ecosystems and the crucial services they deliver. Special attention is paid to carbon and nutrient cycle dynamics and in the combined impacts of microbes and vegetation in the delivery of vital ecosystem services. Furthermore, the course is designed to develop skills in examining primary and secondary (review) literature, the analysis and interpretation of experimental and field data and various forms of scientific communication.
Week 1
General MSc introduction. Organized by the Graduate School of Life Sciences
Week 2-4
The first part provides and overview of biological ecosystem services and the mechanisms responsible for them. The first introductory lectures examine the global carbon and nutrient (with emphasis on nitrogen) cycles, especially regarding the interplay of microbial processes and vegetation. The following lectures examine the procurement of other biological resources, including water purification, food production, bioremediation and attenuation and resources for natural products. Each of the lectures is accompanied by background literature (2 to 3 articles) distributed via Blackboard. At the same time, the course participants run a laboratory experiment designed to examine the impact of microbial diversity on ecosystem functioning. Each student group (of 3 students) tackles a different part of the group experiment and results are exchanged at the end of the experimental work. Each student group presents their results and summarizes the experiment by writing a short research article (Nature letter format) with emphasis on data interpretation and statistics and appropriate use of literature. After submission of the manuscript, the students get feedback from the instructors as to errors and room for improvement and are then given the opportunity to revise their manuscripts based upon these comments.
Week 5-7
The second part of the course includes a number of expert guest lectures that demonstrate the practical and applied issues related to biological natural resources, and their management and conservation. Included in this series is a one-day workshop given by the hold of the Prince Bernhard Chair in International Nature Conservation (currently Jaboury Gazhoul). In addition, a series of PhD and post-doc presentations (5-6 in total) related to ecosystem services are given. Each presentation includes background literature and background to the topic of research. At the end of this series, students are assigned one of the research presentation topics and instructed to write a brief individual commentary (750 words – according to The ISME Journal guidelines for commentaries). This assignment is designed to go beyond simply summarizing research, with emphasis on forming and defending an opinion. After grading, feedback is available regarding the strong and weak points of the commentaries.
Week 8-10
For the third part of the course, student groups (3 students per group – different groups than during the first part of the course) choose a final research project from a list of topics related to the content of the lectures. It is also possible for students to develop their own topic in discussion with the course organizers. The final assignment is to produce an educational movie for your peers (approx.. 10 min) concerning specific research issues related to the chosen topic, as well as a written summary. Each student group is assigned an advisor/mentor to help guide the development of the film project. Each group meets regularly with the group advisor to discuss the project plan and progress. During the final day of the course, the movies of all the groups are presented to the class. Each movie is first introduced by the student group in question, and the film presentation is followed up by a question and answer session as well as a class evaluation of the strong and weaker points of the film. Project grades are determined by the joint scoring of all of the project mentors.
Examination and gradingThe final grade is made up of three parts as follows:

Microbial diversity experiment (35%)
Individual commentary report (20%)
Research project with movie & summary report (45%)

There is no final examination! Attendance to lectures, workshop and laboratory activities is obliged.

Material
We will provide all necessary material on blackboard.

Period
September - November 2016. This course will be given in time-slot A+D.

Contact information
Prof. George Kowalchuk (coordinator); Padualaan 8, Kruyt-building, room N304; e-mail G.A.Kowalchuk@uu.nl; tel 030-2532837
Alternative contact person Marijke van Kuijk Padualaan 8, Kruyt-building, room N305; e-mail M.vanKuijk@uu.nl tel 030-2536846

Registration
Registration for the course can be done by sending an e-mail to the coordinator Prof. George Kowalchuk (G.A.Kowalchuk@uu.nl) and provide the following information:
1) course name; 2) your name; 3) your student number; 4) the MSc programme in which you participate.

PLANT BIOLOGY (choose 2 out of 3 optional courses)

Sustainable Development Goals (compulsory)

Description of content
Being involved in research, MSc students should be aware of the potential role their results could play to build a sustainable future. Moreover, students should be able to constructively discuss and connect with other students of the master's program. As such, this inter-track course will encourage the participants to determine and discuss how their research topic may contribute to solving questions related to sustainability. In particular, participants will put their research in relation with one or more of the 17 Sustainable Development Goals set by the United Nations (https://sustainabledevelopment.un.org/?menu=1300). Groups of ten students belonging to the five different tracks will be composed. Based on the project proposal that the students wrote at the start of their major internship, participants will write in no more than 500 words a report containing a clear description of their potential contribution. Each participant will read the reports of two fellow peers and gives peer review. Based on group meetings and discussion of the reviews, each group will choose one report which will be presented in plenary in no more than two slides at the end of the course.

Literature/study material used:
17 Sustainable Development Goals set by the United Nations (https://sustainabledevelopment.un.org/?menu=1300)
Research proposal of student’s major internship.
Mandatory for students in Master’s programme: NO.
Optional for students in other Master’s programmes GS-LS:

Yes, if space allows.
Maximum number of participants: 64

Plant-environment Interactions

A general lecture on plant-environment interactions will set the stage for an advanced-level course on how plants adjust to their most important environmental factor: light. Although plants rely fully on light as their energy source, they often struggle with temporal and spatial variations in the abundance of this resource. Both excess and shortage of light can be very harmful to plants. Students will study the latest developments in plant plasticity towards variations into light quality and quantity.

Plant-Microbe Interactions

Plant-microbe interactions will be introduced in a general lecture, highlighting recent developments and the importance of the reviewing process. For a set of recent manuscripts the students will act as reviewers and editors following the format provided by high standard international journals. Editor decisions will be presented and discussed.

Applied Plant Biology

This course consists of 4 modules. Information/insights obtained within previous modules will be implemented in later ones.Module 1: Masterclasses by guest-lecturers from the green sector; academia, industry, finance and (semi)governmental organizations.Teaching/learning format: Lectures + discussion, writing assignment Module 2: Identifying current challenges in applied molecular plant biology.Teaching/learning format: Project presentation + discussion Module 3: Developing a research project and writing a proposal on applied aspects of the subject chosen in module 2.Teaching/learning format: Developing and writing of a project proposal Module 4: Reviewing of research proposals as member of a granting committeeTeaching/learning format: Written review, rebuttal, short presentation + discussion

FUNGAL BIOLOGY

Sustainable Development Goals (compulsory)

Description of content
Being involved in research, MSc students should be aware of the potential role their results could play to build a sustainable future. Moreover, students should be able to constructively discuss and connect with other students of the master's program. As such, this inter-track course will encourage the participants to determine and discuss how their research topic may contribute to solving questions related to sustainability. In particular, participants will put their research in relation with one or more of the 17 Sustainable Development Goals set by the United Nations (https://sustainabledevelopment.un.org/?menu=1300). Groups of ten students belonging to the five different tracks will be composed. Based on the project proposal that the students wrote at the start of their major internship, participants will write in no more than 500 words a report containing a clear description of their potential contribution. Each participant will read the reports of two fellow peers and gives peer review. Based on group meetings and discussion of the reviews, each group will choose one report which will be presented in plenary in no more than two slides at the end of the course.

Literature/study material used:
17 Sustainable Development Goals set by the United Nations (https://sustainabledevelopment.un.org/?menu=1300)
Research proposal of student’s major internship.
Mandatory for students in Master’s programme: NO.
Optional for students in other Master’s programmes GS-LS:

Yes, if space allows.
Maximum number of participants: 64

Fungal Biology (compulsory)

Content
The aim of this course is to discuss and understand principles of the ecology, physiology, molecular biology, developmental biology of fungi and biotechnology with fungi. To this end, students will make assignments, discuss articles, have lectures, participate in the annual meeting of the section Mycology of the Royal Netherlands Society for Microbiology, make summaries of scientific presentations, and interview an expert in the field of fungal biology.

Literature/study material used
Participants will read selected articles and do their own literature search.

Registration
Osiris

Mandatory for students in Master’s programme track Fungal Biology: Yes
Optional for students in other Master’s programmes GS-LS: Yes

Entry requirements
Bachelor in Biology or Biomedical Sciences

Food and Indoor Fungi

There is no content available for this course.

Fungal Biodiversity

This course gives a concise overview of the biodiversity of the Fungal Kingdom. The course focuses on systematics (Oomycetes, Chytridiomycetes, Zygomycetes, Ascomycetes, Basidiomycetes, Deuteromycetes) and general ecology of fungi, as well as related topics such as soil mycology and diagnostics of plant pathogens. Both visual and molecular recognition methods will be discussed and practical hands on experience will be gained in the recognition and isolation of fungi.
There is overlap with the course Food and Airborne Fungi. Therefore, a student can only participate in one of the courses.
Registration:
Send an e-mail to the course coordinator (Prof. dr P.W. Crous, p.crous@cbs.knaw.nl). The mail should contain 1) your name; 2) student number; 3) e-mail address; 4) telephone number; 5) current Master track. Please note: the number of participants is limited to 25. Only the first registrations can be accepted.

Mandatory for students in Master’s programme: NO.
Optional for students in other Master’s programmes GS-LS: Infection and Immunity

Behavioural Ecology

Sustainable Development Goals (compulsory)

Description of content
Being involved in research, MSc students should be aware of the potential role their results could play to build a sustainable future. Moreover, students should be able to constructively discuss and connect with other students of the master's program. As such, this inter-track course will encourage the participants to determine and discuss how their research topic may contribute to solving questions related to sustainability. In particular, participants will put their research in relation with one or more of the 17 Sustainable Development Goals set by the United Nations (https://sustainabledevelopment.un.org/?menu=1300). Groups of ten students belonging to the five different tracks will be composed. Based on the project proposal that the students wrote at the start of their major internship, participants will write in no more than 500 words a report containing a clear description of their potential contribution. Each participant will read the reports of two fellow peers and gives peer review. Based on group meetings and discussion of the reviews, each group will choose one report which will be presented in plenary in no more than two slides at the end of the course.

Literature/study material used:
17 Sustainable Development Goals set by the United Nations (https://sustainabledevelopment.un.org/?menu=1300)
Research proposal of student’s major internship.
Mandatory for students in Master’s programme: NO.
Optional for students in other Master’s programmes GS-LS:

Yes, if space allows.
Maximum number of participants: 64

Measuring Behaviour (compulsory)

Introduction
The purpose of this course (1 week) is to acquire working knowledge of the methods for measuring and analysing animal behaviour.
The course is based on the book "Measuring Behaviour. An introductory guide".

Course set-up and study aims
Day 1: Introduction; practising observational methods; self-study
Day 2: Empirical cycle; research design; self-study
Day 3: Self-study and assignment
Day 4: Practising the statistical analysis of behavioural data; self-study
Day 5: Self-study; written exam (on Monday)
On day 3 students have to answer a set of questions pertaining to methodological issues in one or two papers, preferably related to their Masters study topic.
The course is not a course in statistics. Basic knowledge on statistical tests is presumed. On day 4 the application of some tests frequently used in behavioural biology will be reviewed. The emphasis here is on when to use which test and how to perform the test in SPSS.

Registration:
Send an e-mail to the course coordinator (Dr. J. de Vries, j.devries1@uu.nl). The mail should contain 1) your name; 2) student number; 3) e-mail address; 4) telephone number; 5) current Master track. Please note: the number of participants is limited to 25. Only the first registrations can be accepted.
Mandatory for students in Master’s programme: YES

Optional for students in other Master’s programmes GS-LS: Neuroscience and Cognition, especially the tracks Cognitive Neuroscience and Behavioural Neuroscience; Environmental Biology, especially the specialization programme Behavioural Ecology; and any other master programme with relevant basal courses.

Evolutionary Perspectives on Sexual Behaviour (compulsory)

In this course all aspects of sexual behaviour will be presented on the basis of the book "The Red Queen, Sex &The Evolution of Human Nature" of Matt Ridley, 1993, key papers and recent articles. Although the title of the book suggests differently, the major part of the book deals with animal behaviour. Human behaviour is also treated from a biological point of view.

In the book, the different aspects of animal sexual behaviour are discussed following five main questions. These questions will be discussed amongst students in a book discussion meeting. The questions are:

1. Why sex, while sex is expensive?
2. Why gender?
3. Who chooses whom?
4. Monogamy or polygamy?
5. Sexing the mind?

Within each of these main questions several essay subjects are distinguished, one of which will be handed to you as part of an essay writing exercise. The goal of this exercise is that you learn how to set up, write, and critically evaluate a scientific topic in English. We provide reference to a key paper for each essay subject, and we expect an additional in-depth literature review from you.

After writing your own essay, you will critically assess the essays of two fellow students. This task is designed to make you familiar with different writing styles and approaches in how to write an essay, and to look at written text critically.

Having received the comments of your fellow students, you will then edit your own essay again, by incorporating the comments of your fellow students into your essay. The goal of this exercise is that you will learn how to separate useful from non-useful comments and to re-write your own text to improve it relative to the previous version.

In the final exercise of this course, you will present your essay in English in a 10 minute powerpoint presentation. The goal of this exercise is that you will learn how to extract the essential elements from your written text and to effectively convey its message to a broad audience.

Registration:Send an e-mail to the course coordinator (A.M.Schel@uu.nl). The mail should contain 1) your name; 2) student number; 3) e-mail address; 4) telephone number; 5) current Master track. Please note: the number of participants is limited to 20. Only the first registrations can be accepted.

Mandatory for students in Master’s programme: NO.

Optional for students in other Master’s programmes GS-LS: Neuroscience and Cognition, especially the tracks Cognitive Neuroscience and Behavioural Neuroscience; Environmental Biology, especially the specialization programme Behavioural Ecology; and any other master programme with relevant basal courses.

Zoo Conservation Biology

Conservation Biology is a relatively new multidisciplinary field in biology which focuses on biological principles and their applications for the preservation of species and habitats, biodiversity conservation in general and the maintenance of equilibrium within ecosystems. It represents a fusion of relevant ideas from ecology, population biology, genetics, biogeography, behaviour and a number of applied disciplines such as wildlife management and forestry. Zoo Conservation Biology specifically approaches this broad field of research from a zoo perspective, and this course will mainly focus on areas of interest that are related to small population management in captive settings and in field conservation programs.
This course is part of the Master in Environmental Biology at Utrecht University specialization programme Behavioural Ecology.
Registration:
By web subscription at: http://www.zooantwerpen.be/nl/introduction-zoo-conservation-biology

Primate Social Behaviour

Lecture 1: Morality A Darwinian View of the Moral Emotions in Man and Animals Homo homini lupus – “man is wolf to man” - is an old Roman proverb popularized by Thomas Hobbes. Even though it permeates large parts of law, economics, and political science, the proverb fails to do justice to our species’ thoroughly social nature as well as to canids, which are among the most gregarious and cooperative animals. For the past quarter century, this cynical view has also been promoted by an influential school of biology, followers of Thomas Henry Huxley, which holds that we are born nasty & selfish. Accordingly, it is only with the greatest possible effort that we can hope to become moral beings. Charles Darwin, however, saw things differently: he believed in continuity between animals social instincts and human morality. He wrote an entire book about The Expression of the Emotions in Man and Animals. Modern psychology and neuroscience support Darwin’s view about the moral emotions. Human moral decisions often stem from “gut” reactions, some of which we share with other animals. I will elaborate on the connection between morality and primate behavior. Other primates show signs of empathy (see Lecture 2), reciprocity, and a sense of fairness that promote a mutually satisfactory modus vivendi. I will review evidence for continuity to support the view that the building blocks of morality are older than humanity.

Lecture 2: Empathy On the Possibility of Animal Empathy The possibility that animals have empathy and sympathy has received little systematic attention due to an excessive fear of anthropomorphism and the Behaviorist taboo on animal emotions. Actual animal behavior, however, would lead one to agree with Charles Darwin that "Many animals certainly sympathize with each other's distress or danger." In my own work with monkeys and apes, I have found many cases of one individual coming to another's rescue in a fight, putting an arm around a previous victim of attack, or other emotional responses to the distress of others. In fact, the entire communication system of nonhuman primates seems emotionally mediated. In this presentation I will review expressions of empathy in animals, especially nonhuman primates, and present a "Russian doll" model of how animals perceive others. It ranges from a core mechanism of emotional linkage arising from a direct mapping of another's behavioral state onto the subject's representations. This Perception-Action Model provides the basis for higher levels in which there is an increasing distinction between self and other, so that the other is recognized as the source of felt emotions. This permits responses to be geared specifically to the other's situation, thus increasing the effectiveness of sympathetic support, care, and reassurance, as observed in dolphins, apes, and elephants. The connection between perspective-taking and mirror self-recognition (MSR) will be elaborated upon, including our recent demonstration that Asian elephants recognize themselves in a mirror.

Lecture 3: Culture
A Social, Political & Cultural Brain: What Primates Know About and Learn From Each Other Primates live in complex societies in which they compete, try to become dominant, but also help friends and kin. At Living Links we test the knowledge of monkeys and apes about each other, including the power relations among primates, described first in my book Chimpanzee Politics (1982).

Several recent experiments will be discussed, such as a) the role of policing by high-ranking “peacekeepers” and how their behavior stabilizes society, b) how primates distinguish gender - do they have a gender "construct" in that they find it easier to determine the gender of familiar individuals, c) how do chimpanzees and bonobos complement "regular" primate communication (facial expressions and vocalizations) with hand gestures and does this bear on language evolution, d) what do primates learn from each other - do they have cultural capacities in that they adopt behavior shown by others in their group? It is known from the wild that many animals, especially our closest relatives, show cultural variation. That is, their behavior differs from group to group based on the transmission of knowledge, skills, or habits. We now speak of the up and coming field of "cultural primatology."

Examination Multiple choice exam

Further information masterclass.bio@uu.nl
The master classes are given by Prof. dr. Frans de Waal, university professor of the Utrecht University. The master classes consist of three lectures with subsequent discussion, each with their own topic:
1. Morality, 2. Empathy, and 3. Culture in nonhuman primates.

Students will read primary literature to prepare each classes and its discussion. The classes will be examined with a multiple choice exam. At the end of the course, students should have a profound understanding of: a. Current Insights in the topics concerning primate social behaviour and skills. At the end of the course, students should be able to: a. Compare and integrate primary literature b. Formulate questions and discuss the topics
Since Prof. dr. Frans de Waal is a Distinguished Professor, the master classes will be open for students from all master programs of Utrecht University. The number of students that can participate from a certain master program or a cluster of master programs will be restricted. Students will be admitted in the order of registration. The maximum number of students will depend on the size of the class venue, but may be around 200.

Writing assignment (7.5 EC)

You will write a Master’s thesis to demonstrate your ability to provide a clear overview of recent literature addressing the topic in question. The thesis will contains both a discussion/evaluation of the hypothesis and a personal view. Alternatively, you may write a scientific research proposal in the format of a NWO Top Talent application, or a scientific proposal in the format of a STW/EU application.

Major (51 ECTS) and Minor Research Project (33 ECTS)

Major Research Project

The Major Research Project (9 months) is carried out in one of the participating Environmental Biology research groups and will teach you the practice of scientific research. Under the guidance of a staff member, a post-doctoral fellow, or an advanced PhD student, you will work on a well-defined project of your choice, practising all aspects of research: designing experiments, planning, conducting experiments, collecting and interpreting data, drawing conclusions, and writing a report or an article for a scientific publication. Furthermore, you will take part in work discussions and journal club meetings in order to understand the meaning of the work related to that of the research group and of the scientific community as a whole. The project is completed with a written report and an oral presentation.

We offer a wide array of research projects in which you can contribute to ongoing research. As research within the Environmental Biology groups develops rapidly, please visit their websites or contact the professors directly to learn more about the latest opportunities. 

Minor Research Project

For your Minor Research Project (6 months), you can either join one of the Environmental Biology research groups or complete your research training at another university, research institute, or professional organisation. For the specialisation track in Ecology & Natural Resource Management, it is highly recommended to do an internship in a professional organisation, where you can develop a career as a natural resource manager. The Environmental Biology research groups maintain an extensive international network with top universities, research institutes, and professional organisations, offering you ample opportunities to complete your Minor Research Project or internship abroad.

The Minor Research Project may also be replaced by a specific profile. A profile contains theoretical and practical components in the fields of Management (M‑profile) or Teaching and Communication (C&E-profile). See the Study Guide Life Sciences for more information.