FPH-21806 Unifying concepts for life sciences


Code last year: (FPH-51306)

Course

Credits 6.00

Teaching methodContact hours
Lecture32
Tutorial36
Course coordinator(s)M Habibi
Lecturer(s)M Habibi
prof. dr. J Molenaar
prof. dr. E van der Linden
Examiner(s)M Habibi
prof. dr. J Molenaar
prof. dr. E van der Linden

Language of instruction:

English

Assumed knowledge on:

This is an introductory course to the topic, mostly aimed at BSc students in their second or third year, and MSc-students. Assumed knowledge is MAT-12806 Mathematics M (Mathematics for Social Sciences) or MAT-14903 Mathematics 2.


Contents:

In our daily life, we often can observe and experience phenomena and systems that are complex, such as for example social networks (among humans but also chimpanzees), traffic jams, climate changes, flying flocks of birds, or the pleasure arising while eating good food. Although these phenomena and systems belong to different disciplines and scales, they all share similar features that are essential to understanding their origin and evolution. One common feature is that on a smaller scale one can observe many components with mutual interactions and feedback couplings. Another common feature is that on larger scales one can use one same set of basic concepts (the unifying concepts in the title of this course) for describing structural morphologies of vastly different systems such as coral reefs, broccoli, artery networks in mammals, the structure of an electric circuitry in a city, or the structural arrangement of protein molecules in a dessert. Moreover, one can also use these unifying concepts to describe how properties at different scales are related.

In this course we introduce the above mentioned unifying concepts, such as scales, networks, universality, self-similarity, and self-organization. Besides these concepts, we introduce basic mathematical methods and tools to analyze a complex system in terms of these concepts, e.g. scaling, fractal analysis and data network analysis. This also involves using computer based graphics analysis and computer software modules. One basic reason for commonalities among small as well as large scales will be briefly addressed as well (energy minimisation). The course is a multidisciplinary course with inputs from elementary physics, chemistry, mathematics and computer usage. The course has many examples and many exercises in applications, ranging from social sciences, agri-food sciences, nutrition sciences, environmental sciences, animal sciences, plant sciences and economic sciences.

The course starts with addressing the complexity and underlying simplicity and unity of life, including growth, aging and mortality. It then addresses a science of cities, and discusses the far reaching consequences of the observed underlying principles. Hereto we discuss mobility and the pace of life, social connectivity, diversity, and metabolism and growth on a city scale. After this an analogy will be presented for a science of companies (including company mortality and implications of open ended growth). It will be discussed where the analogy between cities and companies stops and why companies die but cities do not. These topics build up towards the final part of the course in which a perspective on sustainability is presented that is based on the underlying unifying principles treated thus far and how these are and will be governing the current developments in this area. In the end we also briefly address some aspects of Big Data in the perspective of the course.

The course provides an opportunity to learn about unifying concepts and their practical use to help us understand similarities om organisation, structure and dynamics among vastly different complex systems with relevance to the broader area of life sciences (agri-food, social, animal, plant, environmental and economic sciences).


Learning outcomes:

After successful completion of this course students are expected to be able to:

- describe a complex phenomenon and its basic features ( power law, networks, self-similarity, nonlinear interaction, feedback, and adaptation);

- recall the concepts of  complexity, self-similarity, nonlinearity, scales, and identify  these concepts in the area of life sciences;

- use the basic methods (scaling, network analysis, fractal dimension calculation)  to analyse aspects of a complex system relevant to various areas of life sciences;

- apply the unifying concepts and according methodologies to analyse phenomena in different areas of life sciences.

Activities:

The course consists of 32 interactive lectures (slides, movies, and practical demonstrations) of 40 minutes each, and 34 sessions of tutorials (exercises on paper and by using computer) of 40’each.  So, the teaching load will be 3.5 credits of Le and 2.5 credits of T. There will be 1 teacher for 16 students for the tutorials.

In-class activities during lectures consist of looking at demonstrations, video’s and presentation material of the lecturers, making notes, asking questions to the lecturer and thinking about and answering questions from the lecturer that are put to the audience. The latter serves as the initiator of self-critical thinking and stimulation to think further on the subjects of the class.

In-class activities during tutorial consist of making the exercises, listen to the explanations of the exercises that have to be made outside class before the tutorials.

Outside-class activities consists of preparation of lectures by pre-reading the according text book chapters (before the lectures and tutorials). Furthermore it consists of re-reading the according book chapters, memorising the concepts treated in the lectures, re-making the exercises that are treated in the lectures, making exercises for the tutorials to be handed in on forehand, re-making the exercises presented and made during the tutorials. Furthermore it is advised to also make the available test exam.

Examination:

Final grading is based on a written exam (60%) open question and assignments (40%) open question. For written exam a minimum pass mark of 5.5 is required.
Students can buy the text book from online bookstores e.g. Amazon.com and Bol.com

Literature:

Textbook:  “Scales”, by Geoffrey West, Penguin books, 2018.

Students can buy the text book from online bookstores e.g. Amazon.com and Bol.com.

You-tube movies, PowerPoint presentations,  articles (being relevant references within the text book by Geoffrey West), and exercises for tutorials with answers will be made available in Brightspace.

ProgrammePhaseSpecializationPeriod
Restricted Optional for: MFTFood TechnologyMScC: Product Design5AF
MFTFood TechnologyMScH: Sustainable Food Process Engineering5AF
MFTFood TechnologyMScD: Ingredient Functionality5AF