Courses

Obligatory Courses first year

Introduction to Marine Sciences

In this course students will gain a multidisciplinary insight into the marine sciences. The aim of the course is to reach a knowledge and integration level required to follow other MSc courses in marine biology, physics, chemistry, and earth sciences. Moreover, basic insights into issues related to law and policy of the sea will be gained.

The various disciplines will be integrated using a project theme case study that will be studied from multiple disciplines and will be presented at the end of the course. In groups of ~4 students that have different backgrounds, this case study will be treated with a specific research question formulated by the students. Results will be reported in written communication and will be presented in an oral presentation at the end of the course. Within this project you will work on your problem-solving skills, and skills regarding leadership, ability to work in a team, to take initiative in organizing progress and flexibility/adaptability.

The first days of the course will encompass a multidisciplinary introduction, and aspects of oceans law and policy. This is followed by two weeks of physics, followed by chemistry, biology, and finally paleoceanography. Individual thematic blocks of two weeks will yield lectures, (computer) practicals offered on Wednesday afternoon and Friday, and an assignment that will be marked.

Typically, every week will have about 10 contact hours, of which 4-5 hours of interactive lectures and 5-6 hours of exercoises. discussions and practicals to work on your reporting and analytical/quantitative skills. Depending on your background, some themes will be harder to follow than others. For the new themes, you will probably need to invest more time and submit a strong work ethic to keep up. Most themes will include a brief report or exercise that will be graded. About 10 hours will be spent on preparations, the case study and feedback/conversations with instructors.

All individual marks must be at least 5.5. Tests that are marked between 4.0 and 5.5 may be retaken once; grades below 4 are typically not accepted. The final result will be the average of the (sub)-weekly assignments (60%) and the marks for the case studies presented at the end of the course (40%).

Absence for up to two days should be indicated to the specific instructor of that day and the coordinator of the course. For longer periods of absence, contact the coordinator. An extra opportunity for tests will be created in case of sickness or personal circumstances.

Marine Sciences Oceans Law and Policy

The oceans are essential for maintaining life on earth, their mineral resources are increasingly important to the world economy and marine fisheries significantly contribute to ensuring food security. 90% of all international trade is seaborne and most data communication is through submarine cables. Pursuing an effective governance regime for the oceans continues to be a challenge for the international community.

The course will first of all provide the students with some basic knowledge about public international law. That knowledge is essential for understanding the law of the sea as a part of public international law and the actors that play a role in the formulation and implementation of this legal framework.

The current regime for the oceans is built on the United Nations Convention on the Law of the Sea of 1982 (UNCLOS). This framework convention divides the oceans in various coastal state maritime zones and international areas. In all these areas the legal regime seeks to maintain a balance between the rights and interests of individual states and the international community. The course sets out the legal regime applicable to the oceans, how oceans policy to create an effective governance system is taking shape and how disputes over ocean resources may be managed. The course will not only look at the UNCLOS but will also identify and discuss the role of other global and regional conventions and organizations in developing the law and designing effective governance policies.

Science has a role to play in the implementation of the UNCLOS and specific management regimes for ocean uses. The course will illustrate this role of science in oceans law and policy and will also provide an overview of the legal regime applicable to the conduct of marine scientific research.

Academic skills:

  • ability to analyze text to determine issues of legal relevance;
  • ability to determine the relevant legal framework for scientific research in the marine environment;
  • ability to formulate views of this relevant legal framework orally and in written form.

Elective Courses first year

Microbes and Biogeochemistry

This course deals with the interactions between the biosphere and geosphere. The focus is on modern environments and the two-way linkage between organisms and their surroundings. We will cover the basic concepts and approaches in biogeochemistry and the organism involved. The distribution, growth and metabolism of selected organism will be related to the major biogeochemical cycles (e.g. C, N, P, S, Fe) and to processes such as redox transformations and mineral dissolution/precipitation. The course also deals with the basis of molecular techniques, use of isotopes in (microbial) ecology and conceptual models for microbial processes and biogeochemical cycles. The course will be useful for those interested in bioremediation, biogeochemical processes in present and past ecosystems, the effect of climate and global change on the functioning of System Earth. Students will present and discuss debated issues at the interface of the biosphere and geosphere.

Development of Transferable Skills

  • Written communication skills: Students are expected to write term papers and a short research proposal.
  • Verbal communication skills: Students will present a lecture for the general audience about a recent topic in Biogeochemistry.
  • Strong work ethic: students are assigned tasks early in the course with fixed deadlines and have to organize themselves in order to deliver on time.
  • Analytical skills: the material offered comprises many aspects and students are supposed to elucidate complex issues crossing disciplinary boundaries.

Paleoceanography and climate variability

(Paleo)ocean circulation during different climatic regimes and related proxy variability will be discussed while sequentially introducing different concepts and aspects. Theory and application of marine proxies will be illustrated by relevant case studies. In particular the Glacial world will be contrasted to the (present-day) Interglacial, and compared to high-frequency (e.g. El-Nino) paleoceanographic and proxies variations. Amongst the aspects to be discussed are: Glacial climate and its forcing; sediment dating techniques; paleoproductvity; pCO2 reconstruction; oxygenation; sea surface temperature; deep water circulation; and proxy preservation. Current important scientific questions will be addressed and different view points discussed. The course teaches students hands on scientific research so that they can ‘hit the ground running’ in climate related projects.

Development of Transferable Skills

  • Ability to work in the team: Presentations, practicals and final research proposal are organized in teams. Students have to distribute tasks, organize the workflow and are responsible for the time planning;
  • Problem solving: students receive data from previous sea-going expeditions and have to use different approaches to unravel past ocean and climate change;
  • Verbal communication skills: 50% of the lectures are based on the so-called flip-class room concept in which the students have to transfer expert knowledge to to their peers. This implies that they alos have to set teaching goals, plan a lecture and present the lecture. Subjects are setup in such a way as to stimulate discussion and participate in the discussion;
  • Analytical / quantitative skills: students have to setup and run simple numerical (inverse) models to to analyse their data. These model runs are subsequently quantitatively compared with real world data;
  • Technical skills: using the computer programmes Excel for handling large data sets and data transformations. By regularly comparing different analytical approaches students get insight in the prossibilities and limitations of the different techniques.

Ocean waves

Topics: Part 1: tidal forces and tidal potential, free long waves (Kelvin/Poincaré), Taylor problem, forced waves: co-oscillation problem. Part 2: free short waves, wave generation by wind, statistical description of waves, wave spectrum, wave prediction models.

Aquatic and Environmental Chemistry

The course deals with processes that control the composition of water in aquifers, soils, lakes, and in the ocean. The focus lies on using equilibrium approaches to describe and quantify these processes.The course is organized around three main themes:

  1. Speciation of dissolved compounds in aqueous solution:
    Acid-base reactions, complexation of metals, redox speciation, introduction into quantitative methods in aquatic chemistry including the tableau method and speciation models.
  2. Partitioning of compounds between different phases:
    Thermodynamics of equilibrium partitioning, gas – water partitioning, solid-water partitioning, liquid – liquid partitioning
  3. Adsorption at the solid-water interfaces:
    adsorption isotherms, surface reactivity of solids, surface complexation, ion exchange

The course includes project-based work. These projects are devoted to processes controlling the composition of waters in surface and subsurface environments or the phase distribution and transformation inorganic compounds in aquatic environments. Computer equilibrium models will be used to solve quantitative problems related to the different projects.

Development of transferable skills

  • Ability to work in a team: The quantitative problems related to various projects in the course are solved in teams, typically couples. Important part of the team work is the critical assessment and discussion of results obtained from the chemical equilibrium models.
  • Written communication skills: students are introduced to the scientific review process. They write a scientific manuscript, review manuscripts from their fellow students and improve their manuscripts based on the comments.
  • Problem-solving skills: In the projects, students have to find a strategy to answer the given research or practical questions.
  • Analytical/quantitative skills: Students have to learn to conceptualize processes affecting the composition of natural waters. Conceptual understanding is a prerequisite to properly define problem sets in chemical equilibrium models.
  • Technical skills: students are introduced to the methodology to solve quantitative problems in the field of aquatic chemistry including chemical equilibrium models.

Introduction to Marine Sciences

In this course students will gain a multidisciplinary insight into the marine sciences. The aim of the course is to reach a knowledge and integration level required to follow other MSc courses in marine biology, physics, chemistry, and earth sciences. Moreover, basic insights into issues related to law and policy of the sea will be gained.

The various disciplines will be integrated using a project theme case study that will be studied from multiple disciplines and will be presented at the end of the course. In groups of ~4 students that have different backgrounds, this case study will be treated with a specific research question formulated by the students. Results will be reported in written communication and will be presented in an oral presentation at the end of the course. Within this project you will work on your problem-solving skills, and skills regarding leadership, ability to work in a team, to take initiative in organizing progress and flexibility/adaptability.

The first days of the course will encompass a multidisciplinary introduction, and aspects of oceans law and policy. This is followed by two weeks of physics, followed by chemistry, biology, and finally paleoceanography. Individual thematic blocks of two weeks will yield lectures, (computer) practicals offered on Wednesday afternoon and Friday, and an assignment that will be marked.

Typically, every week will have about 10 contact hours, of which 4-5 hours of interactive lectures and 5-6 hours of exercoises. discussions and practicals to work on your reporting and analytical/quantitative skills. Depending on your background, some themes will be harder to follow than others. For the new themes, you will probably need to invest more time and submit a strong work ethic to keep up. Most themes will include a brief report or exercise that will be graded. About 10 hours will be spent on preparations, the case study and feedback/conversations with instructors.

All individual marks must be at least 5.5. Tests that are marked between 4.0 and 5.5 may be retaken once; grades below 4 are typically not accepted. The final result will be the average of the (sub)-weekly assignments (60%) and the marks for the case studies presented at the end of the course (40%).

Absence for up to two days should be indicated to the specific instructor of that day and the coordinator of the course. For longer periods of absence, contact the coordinator. An extra opportunity for tests will be created in case of sickness or personal circumstances.

Making, analyzing and interpreting observations

In this course you will gain practical experience with field measurements related to meteorological or oceanographic processes. When possible you will get the opportunity to participate in ongoing experiments.

Simulation of ocean, atmosphere and climate

1. Numerical models of ocean, atmosphere and ice caps and their numerical aspects, specifically, numerical solution methods (accuracy and stability), parametrisations, model-initialisation and model-validation.
2. Basic programming, debugging and testing in Python, or any other appropriate programming language
3. Setting up a numerical model on a climate-related process, or adaptation of an existing model.
4. Design, performance and analysis of numerical simulations to answer a research question.
5. Presentation of the results of a simulation project in an oral presentation and in a written report.

This course will start on september 1st in BBG 079, see Blackboard for further details

Astronomical climate forcing and time scales

Paleoclimatic research dedicated to unravel natural climate variability is becoming increasingly important in view of current global warming. Astronomical forced climate change related to the Earth’s orbital parameters represent a crucial and integral part of the natural behavior of the climate system in the past on millennial to million year time scales. Paleoclimate studies has solved the problem of the Ice Ages and focused on the orbital theory of the Monsoon. In this course we will focus on climate forcing by the Earth’s orbital parameters computed by means of astronomical solutions for the Solar System. In addition, we will focus on the use of (Milankovitch) cycles to construct geological time scales with an unprecedented resolution and accuracy that are necessary for climate studies of the past and on mathematical methods to statistically detect cyclic variability in paleoclimate records. The course is divided in two parts that are intricately linked:

  1. Astronomical time scales and their applications: Introduction and astronomical solutions; Time scale development and spectral analysis; Ar/Ar dating and geodynamic linkages; Cyclostratigraphy and link to sequence stratigraphy.
  2. Astronomical forcing of climate: Astronomical climate forcing and phase relations; Climate modelling of orbital variations; Sub-Milankovitch cyclicity.

During the computer practicals students will operate in teams of 2 and learn how to use statistical methods (spectral, wavelet) to detect astronomical climate forcing in paleoclimatic archives and determine phase relations between cyclic climate changes and insolation forcing. In addition results of climate modeling experiments will be statistically analysed using the same methods.
Students (in teams of 2) will further have to write an essay on a topic related to the contents of the course and based on scientific publications. They will also have to give a powerpoint presentation of 15-20 minutes that will be marked by fellow students as well.Grading
The course has both a mid-term (“tussentoets”) and final examination. The mid-term examination counts for 20% and the final examination for 45% of the final mark. The remaining 35% is equally divided over the essay and oral presentation. Practical reports and paper summaries have to be accepted.
Final course mark: The final course grade will be satisfactory (pass) or unsatisfactory (fail), expresses in numbers, 6 or higher and 5 or lower respectively. The final grade will be rounded off in one digit. A final course grade of 5 will not have any decimal places; an average grade of 4.50-5.49 is unsatisfactory, an average grade of 5.50-5.99 becomes a 6.
If you have fulfilled all course obligations but failed to obtain a final grade 6 or higher, you will get one chance to repair, via a supplementary test (“aanvullende toets”). However, a non-rounded off final grade <4.00 implies a definite fail, i.e., no right on a repair assignment.
Character and content of the supplementary test will be decided upon in due time. If you pass the supplementary test, a final course grade of 6 will be recorded in the student progress administration system.

Morphodynamics of Tidal Systems

This course is the second course in a series of three (period 1: River and Delta systems, period 3: Morphodynamics of wave-dominated coasts) . Other courses in the MSc that focus on delta and coastal systems are Coastal Ecology and Managing Future Deltas.
During this course the dynamics of tidal systems will be studied at all relevant time scales (few hours to millennia) and spatial scales (kilometers to global scale). We will follow the pathway of the tidal wave from its generation in the ocean to the dissipation of tidal energy in the shallowest regions of tidal basins and estuaries. Along its paths, tidal waves induce current that transport sediment and cause morphological change. Main topics of the course are:

  1. Generation of tides by the gravitational interaction of earth, moon and sun. Tidal dynamics of shallow shelf seas.
  2. Hydrodynamics and morphodynamics of shallow tidal basins.
  3. Tides in estuaries: Effect of geometry on tides, river-tide interactions, estuarine dynamics, fine sediment dynamics and morphological change.
  4. Time series analysis of water level and flow velocity data.
  5. Evolution and depositional architecture of tidal systems under sea level rise.

Development of Transferrable Skills

  • Ability to work in a team: During the course the students have to work in couples to do Matlab exercises, write reports and do research.
  • Written communication skills: Students have to deliver four reports and one abstract. You will get feedback on the content.
  • Problem-solving skills: Students have to work on programming exercises (in Matlab) and apply it to analyse data sets or model tidal phenomena.
  • Verbal communication skills: Student have to give an oral presentation on the results of a case study.
  • Analytical/quantitative skills: Students have to analyze data sets, to apply equations to field cases, and to program Matlab code.
  • Technical skills: Students will have to program in Matlab and will learn to use the codes to study tidal phenomena.

Kinetic processes

  1. Rates of geochemical reactions. Rate equations, reaction mechanisms, elementary reactions, order of reactions, steady state, Arrhenius equation, principle of detailed balancing, Michaelis-Menten kinetics, heterogeneous kinetics.
  2. Theory of chemical kinetics: Collision theory, diffusion controlled reactions in solution, transition state theory, non-equilibrium thermodynamics, kinetic processes under non-hydrostatic conditions.
  3. Applications of geochemical kinetics: Mineral dissolution and growth, kinetics of microbially mediated reactions, kinetics of redox reactions, kinetics of reactions in aqueous solution, geochronology, geospeedometry.

Most of the examples discussed in the course are biogeochemical processes in aquatic environments. As part of the course, the students have to study independently chapters from the textbook Geochemical Kinetics by Y. Zhang. Students have to solve problems in the book and their solutions will be graded.

Development of Transferable Skills

  • Ability to work in the team: (Video) lectures are prepared in teams. Students have to distribute tasks, organize the workflow and are responsible for the time planning.
  • Problem solving: students receive data from (virtual) experiments and have to use different approaches to parameterize empirical rate laws.
  • Verbal communication skills: emphasis is put on transferring knowledge to non-expert audience / teaching, including the definition of teaching goals, planning a (video) lecture and preparing/presenting the lecture. Students are familiarized with techniques required to prepare video lectures.
  • Analytical / quantitative skills: analytical and numerical integration of differential equations. Solving quantitative problems related to kinetic processes.
  • Technical skills: using the computer programmes Excel, Matlab and Stella for numerical integration of differential equations.

Estuarine Ecology

Estuaries are among the most biologically productive ecosystems on the planet--critical to the life cycles of fish, other aquatic animals, and the creatures that feed on them. The Estuarine Ecology module covers the physical and chemical aspects of estuaries, the biology and ecology of key organisms, the flow of organic matter through estuaries, and human interactions, such as the environmental impact of fisheries on estuaries and the effects of global climate change on these important ecosystems.

We will discuss state-of-the-art thoughts and findings based on recent peer-reviewed scientific papers from international journals authored by a team of experts from the estuarine science community. These papers focus on temperate coastal systems and cover key processes that structure these systems (a.o. bio-geomorphology, primary productivity and trophic transfer).

The course will start with introductions on the framework of the course, and how to read and present a scientific paper. Hereafter, the organizers of Estuarine Ecology module will introduce each week two specific scientific papers, one general paper on the background of the process studied and one paper comprising new insights on this matter, which will be made available via the Blackboard.

The students are then requested to read the papers thoroughly. The general paper is discussed within the group. For the second paper, students should prepare questions within small groups with regard to the Introduction, Materials & Methods, Results or Discussion sections. After discussing the questions within the full group, the students will interview one of the authors of the second paper. In addition, students (one group per week) will prepare a presentation on the second paper indicated for a broader audience, which is presented as the start of the discussion with the invited author.

Furthermore, students will learn to execute an experiment within the field of estuarine ecology, including the design, performance, data analyses and reporting. Data analyses will be done using R, a programming language and software environment for statistical computing and graphics, which will be shortly introduced during the course. The one-day experiment will be performed at the Royal Netherlands Institute for Sea Research (NIOZ) on Texel (8 December 2017).

Development of Transferable Skills:

  • Ability to work in a team: research papers and a scientific experiment need to be prepared and carried out in teams. Students have to distribute tasks and organize the workflow.
  • Problem solving: students will measure their own data and have to use different statistical approaches to analyse them and make scientifically valid conclusions.
  • Verbal communication skills: emphasis is put on transferring knowledge to a non-scientific audience; talks need to be prepared to make scientific literature and concepts approachable for the general public.
  • Quantitative skills: univariate statistical methods will be applied to analyse experimental results
  • Technical skills: using computer programs as R for statistical analysis

Morphodynamics of Wave-dominated Coasts

Wind-generated waves are the main driving force for the evolution of the nearshore zone (water depths less than 10 m) on time scales of hours (storms) to decades. As waves approach the coast, they transform by altering, among other characteristics, shape, height, length, and orientation. This results in a wide variety of other processes, including alongshore currents and rip currents. Also, it leads to the transport of sand perpendicular to and along the coast. As a consequence, the morphology of the nearshore zone changes continuously as the offshore wave conditions change with time and when mankind intervenes with coastal processes, for example, by artificially placing sand to enhance coastal safety. This makes the nearshore zone one of the most dynamic and complicated regions within the oceanic domain.

Main topics of the course include:

  • cross-shore transformation of wind-generated waves, and the resulting currents;
  • sand transport and morphological evolution;
  • modelling of waves, currents, and sand transport;

at a range of time scales (hours - decades) and in natural and humanly altered wave-dominated coastal settings. The later setting provides the student with insight into issues related to present-day coastal zone management.

The topics will be treated by means of lectures and computer assignments. As part of the course, the student is expected to apply/develop Matlab code to analyse scientific data and to compare these data to model predictions. This will provide the student with insight into present-day capabilities of models used in both scientific and coastal-zone-management settings, and with basic Matlab programming skills.
The course contributes to the following transferable skills:

  • Ability to work in a team: All computer assignments are performed in teams of 2 persons. Although each team is to provide a report, co-operation between teams during the assignments is encouraged.
  • Written communication skills: Results of all computer assignments are presented in reports.
  • Problem-solving skills: The teams have to define a strategy how to implement code to solve allocated scientific questions.
  • Analytical/quantitative skills: The students have to use the developed code, together with knowledge from the lectures, to answer allocated scientific questions.
  • Technical skills: The students will (further) develop their programming skills for data analysis and modelling.

Evolutionary paleobiology and proxies

The course deals with the evolution, biology and ecology of selected marine microorganisms and terrestrial vegetation and their use as fossils for past environmental and climate reconstructions during the Mesozoic and the Cenozoic. The course will focus on organic and calcareous microscopic remains/fossils (foraminifers, dinoflagellates, pollen and spores). Much attention will be given to the importance of linking changes occurred simultaneously in the marine and terrestrial environment. The course also deals with the (biologically-mediated) process of incorporation of chemical elements into foraminifer shells and thus shells’ chemical composition as proxy for reconstructions of past water column properties.

Next to fundamental knowledge on evolution, paleoecology, and palaeoenvironmental reconstructions, the course will train the students’ taxonomical skills. Students will learn to work with complex data, to perform quantitative and statistical analyses, to think critically, and to present their results orally. All these skills are desired and/or required for successful job applications.

Dynamical oceanography

The ocean circulation is driven by wind-forcing and by density differences, the latter arising through gradients in temperature and salinity. After a brief description of the ocean current systems which are presently observed, this course focuses on understanding the physical processes that determine the spatial pattern and amplitude of the currents and their variability. After a recapitulation of basic principles of geophysical fluid dynamics, the theory of the steady homogeneous wind-driven ocean circulation will be presented. It leads to an explanation of the presence of strong western boundary currents in midlatitude ocean basins (i.e., the Gulf Stream in the Atlantic Ocean). Subsequently, the midlatitude theory is extended to include transient phenomena (waves and instabilities) and the effects of stratification. Next, the problem of the existence of the ocean's peculiar vertical density distribution serves as an introduction to the theory of the planetary density driven (or thermohaline) circulation. In a similar way, the problems of the dynamical existence of the equatorial countercurrent and equatorial undercurrent motivates to consider the theory of the equatorial ocean circulation. Finally, a basic view of the processes governing the Antarctic Circumpolar Current is presented.

Marine Sciences Oceans Law and Policy

The oceans are essential for maintaining life on earth, their mineral resources are increasingly important to the world economy and marine fisheries significantly contribute to ensuring food security. 90% of all international trade is seaborne and most data communication is through submarine cables. Pursuing an effective governance regime for the oceans continues to be a challenge for the international community.

The course will first of all provide the students with some basic knowledge about public international law. That knowledge is essential for understanding the law of the sea as a part of public international law and the actors that play a role in the formulation and implementation of this legal framework.

The current regime for the oceans is built on the United Nations Convention on the Law of the Sea of 1982 (UNCLOS). This framework convention divides the oceans in various coastal state maritime zones and international areas. In all these areas the legal regime seeks to maintain a balance between the rights and interests of individual states and the international community. The course sets out the legal regime applicable to the oceans, how oceans policy to create an effective governance system is taking shape and how disputes over ocean resources may be managed. The course will not only look at the UNCLOS but will also identify and discuss the role of other global and regional conventions and organizations in developing the law and designing effective governance policies.

Science has a role to play in the implementation of the UNCLOS and specific management regimes for ocean uses. The course will illustrate this role of science in oceans law and policy and will also provide an overview of the legal regime applicable to the conduct of marine scientific research.

Academic skills:

  • ability to analyze text to determine issues of legal relevance;
  • ability to determine the relevant legal framework for scientific research in the marine environment;
  • ability to formulate views of this relevant legal framework orally and in written form.

Dynamics of sedimentary systems

Early in the course, emphasis is put on the effect the choice of temporal and spatial scales defined by a research question has on our approach to sediment transport dynamics. Following this, the hierarchy and scaling of the architecture of sedimentary successions is investigated. The structure of this architecture will be built on concepts of sequence stratigraphy. Once a clear perspective on the organization of deposits in parasequences, sequences, and shelf-clinoforms has been presented to the student, attention will shift to forcing mechanisms of deposit characteristics within subsets of deposits and depositional environments: Alluvial systems; transgressive systems and highstand deltas; tidal systems; and deep marine depositional systems. The course will conclude by challenging the students to investigate the validity and application of two oft (miss-)used concepts of Earth Sciences: “Walther’s Law”; and “The present is the key to the past”.

Reactive transport in the hydrosphere

  • Basics of model formulation (from conceptual diagrams to differential equations)
  • Introduction to R (focus on deSolve and ReacTran packages)
  • Spatial components and parameterization
  • Model solution (analytical vs. numerical methods)
  • Stability and feedback analysis
  • Regression analysis (fitting of data by a model)
  • Case studies/Applications:
    • River/Lake chemistry
    • Diagenesis in sediments
    • Aquifers
    • Global ocean biogeochemistry

By the end of the course, students will

  • have a general understanding of concepts and methods needed to quantitatively describe (bio)geochemical reactions and transport processes in various compartments of the hydrosphere;
  • be able to formulate models (conceptually and with mathematical equations) to describe transport and reactions in Earth's surface environments;
  • be able to solve simple models analytically and more complex models numerically using appropriate modeling software (R, with relevant packages such as ReacTran, deSolve);
  • be able to fit data with a model, and interpret the results of the models in the relevant context (e.g., geochemical processes in rivers, lakes, aquifers, sediments, oceans);
  • be able to report the results in written and oral form.

The course will also help develop the following transferable skills:

  • Ability to work in a team: Practical exercises and final projects will be done in teams of two students. Students will need to distribute the tasks, organize and execute the workflow, share responsibility for presentation of the results.
  • Written communication skills: Assignments and final projects will be presented as reports. Feedback will be given after each report, allowing students to improve.
  • Verbal communication skills: Results of the final projects will also be presented orally. Students will receive feedback on the quality of their presentations.
  • Analytical/quantitative skills: Throughout the course students will solve quantitative tasks using analytical and numerical methods. They will also interpret their results in the wider context of environmental biogeochemistry.
  • Strong work ethic: students will be required to follow fixed deadlines for delivering assignments and results of their final projects.

Technical skills: students will write their own code to solve models. This will develop their programming skills in the programming language R. Preparation of written reports and oral presentation will help them develop skills in programs used for word processing and slide shows.

Organic geochemistry

  1. Biochemistry, Organic molecules and Sources of organic matter: Chemical evolution of organic molecules, isotopes, Phylogenetic tree of life, Membranes: Lipid biochemistry, different lipids, i.e. fatty acids, alkanes, acyclic isoprenoids, steroids, terpenoids; Macromolecules: sugars, proteins and peptides, DNA and RNA, resins, lignins, biopolyesters, biopolymers.
  2. Preservation and the Quality of organic matter: Chemical stability versus depositional environment, chemical taphonomy; Preservation models: neogenesis, selective preservation, in-situ polymerization; Export productivity, Oxygen exposure time (OET); Marine versus terrigenous sources; Preservation versus production; Sulphur and Oxygen incorporation, Lignin, soil organic; Soil organic matter.
  3. Molecular palaeontology: Biomarkers: molecular markers based on carbon skeleton, position and nature of functional groups and/or stable carbon isotope composition. Biological markers as indicators of evolution of Life on earth. Biomarkers in relation to the phylogenetic tree of life; Age-related biomarkers: Molecular proxies for palaeoenvironmental and palaeoclimate reconstructions: sea surface temperatures, photic zone anoxia, anaerobic methane oxidation, C3/C4 vegetation shifts, atmospheric pCO2 changes.
  4. Diagenesis, catagenesis, fossil fuel formation, petroleum geochemistry: Diagenetic transformation reactions; Chemical transformation reactions during catagenesis; Coalification; Oil and gas formation; biomarkers as indicators for thermal maturity, oil-source rock correlation and biodegradation; oil exploration and oil exploitation.

Field research instruction geochemistry

In this course students learn how to perform a field campaign and biogeochemical experiments in order to answer research questions related to the nutrient dynamics in aquatic environments. This includes: testing and preparing analytical and experimental methods, collecting and analyzing environmental samples, performing experiments, interpretation of analytical and experimental data, and presentation of the results orally and in a written form.The fieldwork consists of three parts: a preparation period in Utrecht, a field campaign, and a period of data interpretation and report writing in Utrecht. During the preparation period, the students give presentations related to the subject and the objectives of the fieldwork. Furthermore, they practice analytical procedures and experimental methods which are required during the fieldwork. During the fieldwork campaign, water samples from rivers, estuaries, and marine locations are collected and analyzed. Additionally, sediment cores will be taken and analyzed. Laboratory experiments are conducted in order to quantify individual processes related to the nutrient fluxes in the investigated environments. The analytical and experimental data are finally integrated in order to characterize the trophic state of the investigated systems, to determine the nutrient fluxes between the different compartments of the systems, and to investigate the interplay between physical and biological processes in controlling the nutrient dynamics. The results of the fieldwork are presented in reports

Development of transferable skills

  • Leadership: Students work in teams; each day someone takes the task of the team leader who takes the responsibility that the team activities are target orientated and who reports about the team activities.
  • Ability to work in a team: All tasks are performed in teams. The teams often operate independently during field campaigns. Important hereby is making decisions about the selection of sampling sites and sampling approaches.
  • Written communication skills: Results of fieldwork are presented in reports. Feedback is given on the reports and students have to revise the reports based on the comments.
  • Verbal communication skills: Students have to give scientific presentations about a subject related to nutrient dynamics in aqueous environments.
  • Problem-solving skills: In the field, teams often have to define a strategy for fulfilling the assigned tasks, including the identification of sampling sites and performing the sampling.
  • Analytical/quantitative skills: students have to integrate the data collected in the field and in the laboratory, in combination with knowledge from scientific literature and model calcultions, in order to answer the allocated research questions.
  • Flexibility/adaptability: Depending on conditions and observations during field campaigns and during laboratory work, the sampling programme or the analytical / experimental approach have to be adjusted.
  • Technical skills: students are introduced to a variety of methods to characterize the chemical and physical properties of water or sediment samples. They are introduced to methods to determine processes and fluxes in situ or in laboratory experiments.

Please note: There is only 15 places available.Please note: Registration for this course only during the first registration period.

Introduction to Physical Oceanography

The course will start with describing ocean properties, such as sea level, temperature, salinity and density. Their physical relevance and practical measurement techniques will also be discussed. Impact of the earth rotation and the associated Coriolis force on the ocean circulation will be used to explain fundamental ocean phenomena such as geostrophic currents, the large-scale wind-driven ocean circulation and western boundary currents (e.g Gulf Stream). Upper ocean processes in the mixed layer and the Ekman transport will be covered and used to explain upwelling and downwelling phenomena (water moving from depth to the surface and vice-versa). Another large scale dominant feature with impact on the vertical movement of the water, called the thermohaline circulation because it is partly driven by salt and temperature differences in different areas of the ocean will be introduced. Processes that drive large-scale climate phenomena such as the monsoon and El Nino-Southern Oscillation (ENSO) will also be presented. Finally, specific phenomena such as tides and gravity waves will also be introduced to explain shelf sea circulation.

The course includes classes and (student) projects, and will run in the first five weeks of period four.

Academic skills: Presentation, working in groups on exercises, programming

Obligatory Courses second year

Graduation Research, MSc Earth Sciences

The MSc thesis is an individual product that is accomplished by a single student under supervision of a staff member. MSc Research projects can be done in collaboration with other students, but only under the condition that each student works on the basis of an individual problem statement and that the individual performance (and individual thesis) of each student can be properly judged by the supervisor. Together with a thesis supervisor, the student selects a suitable topic of interest that fits within, or has strong links with, one of the Earth Sciences programmes. The topic could be theoretical or practical, could include fieldwork and/or lab-work and/or computer-based simulation/modelling.

Please refer to the MSc Thesis Guidline regarding application, performance, and evaluation of the Graduation Research.
See also: http://students.uu.nl/sites/default/files/geo-es-msc-research.pdf

Internship

Internship

The topic could be theoretical or practical, could include fieldwork and/or lab-work and/or computer-based simulation/modelling. The various options include: a work placement in a company or government organisation working in Earth Sciences or participating in university research. In consultation with the proposed supervisors - one internal supervisor (teacher) and one external supervisor (from the organisation offering the training), a traineeship proposal should be formulated. This should also contain details of credits involved (ECTS), time-planning, deliverables (reports/presentations), confidentiality aspects etc. to avoid last-minute surprises on all sides. The traineeship request form and proposal MUST be submitted for PRIOR approval to, first, the internal supervisor, and then the traineeship coordinator of the relevant MSc-ES programme who will pass it on to the board of examiners for final approval. If the traineeship is also to be used for the mandatory graduation research, the traineeship proposal should also be submitted to the coordinator of the relevant MSc-ES programme for PRIOR approval.According to the examination rules and regulations with regards to the MSc programmes Hydrology and Physical Geography, a student should first hand in a first version of his/her MSc graduation thesis before he/she is allowed to start off with a traineeship.More information and required forms are available on website: enter the page for your master programme and look for “internship”.

MSc Individual Programme

Internship

The topic could be theoretical or practical, could include fieldwork and/or lab-work and/or computer-based simulation/modelling. The various options include: a work placement in a company or government organisation working in Earth Sciences or participating in university research. In consultation with the proposed supervisors - one internal supervisor (teacher) and one external supervisor (from the organisation offering the training), a traineeship proposal should be formulated. This should also contain details of credits involved (ECTS), time-planning, deliverables (reports/presentations), confidentiality aspects etc. to avoid last-minute surprises on all sides. The traineeship request form and proposal MUST be submitted for PRIOR approval to, first, the internal supervisor, and then the traineeship coordinator of the relevant MSc-ES programme who will pass it on to the board of examiners for final approval. If the traineeship is also to be used for the mandatory graduation research, the traineeship proposal should also be submitted to the coordinator of the relevant MSc-ES programme for PRIOR approval.According to the examination rules and regulations with regards to the MSc programmes Hydrology and Physical Geography, a student should first hand in a first version of his/her MSc graduation thesis before he/she is allowed to start off with a traineeship.More information and required forms are available on website: enter the page for your master programme and look for “internship”.

MSc guided research

In addition to the Graduation Research, all Earth Sciences MSc students have to perform a second individual project. This second project can be in the form of a Guided Research or a Traineeship (GEO4-1500). Both types of activities have in common that the student prepares an individual report written in English at the end of the Traineeship / Guided Research. The credit load of a Guided Research can vary between 7.5 and 30 ECTS, while, for a traineeship, the number of ECTS’ can be between 15 and 30.

The difference between Traineeship and Guided Research is, that the latter has, similar to the Graduation Research, distinct research objectives while the objectives of a Traineeship might focus on the application of Earth Sciences based expertise to technical, economical or societal questions. Furthermore, a Traineeship is usually performed at an institution or company outside UU, typically from the non-academic sector.

A Guided Research project can also be performed externally at another academic or non-academic institution. A Guided Research is similar to a Graduation Research (MSc project) but, in comparison to the Graduation Research, the expectations regarding the autonomy and independence of the student in a Guided Research project are lower. This applies particularly to developing the research objectives and methodology. Furthermore, an oral presentation of the results is not obligatory and not part of the assessment.

Summerschools, seminars, or other courses are part of the category Advanced Courses and are not conceived as Guided Research.

Before starting a Guided Research project, the planning has to be approved by the Board of Examiners.