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AK2040 Theory and Methodology of Science with Applications (Computational Science) 7.5 credits

Course memo Autumn 2023-50333

Version 1 – 08/22/2023, 3:51:03 PM

Course offering

Period 1 (Start date 28 Aug 2023, English)

Language Of Instruction


Offered By


Course memo Autumn 2023

Course presentation

The aim of the course is to provide a deeper understanding of the methodological and underlying philosophical issues that arise in science, and inspire to reflection on such issues within the student’s own area of study. After having taken the course the student should have acquired basic knowledge of the foundational issues in the methodology and philosophy of science.

Headings denoted with an asterisk ( * ) is retrieved from the course syllabus version Autumn 2022

Content and learning outcomes

Course contents

The following is an incomplete list of topics covered in the course.

  • Scientific knowledge
  • Definitions
  • Hypothesis testing
  • Observations and measurements
  • Experiments
  • Models
  • Statistical reasoning
  • Causes and explanations
  • Qualitative methods
  • Algorithmic reasoning and its limitations
  • Risk and decisions of risks
  • Research ethics
  • Philosophical theories about mathematical objects’ nature
  • Theorethical representation theorems of measurement
  • Theoretical virtues in mathematical models

Intended learning outcomes

After having completed the course, the student should, with regards to the theory and methodology of science, both orally as well as in writing, be able to:

  • Identify definitions and descriptions of concepts, theories and problem areas, as well as identify the correct application of these concepts and theories.
  • Account for concepts, theories and general problem areas, as well as apply concepts and theories to specific cases.
  • Critically discuss the definitions and applications of concepts and theories as they applies to specific cases of scientific research.

These learning objectives are examined in writing via a digital exam and orally via seminars. 

  • chart the main lines of thought in some different philosophical theories about the nature of mathematical objects and our knowledge of them.
  • describe the content of some representation theorems from the theory of measurement, and discuss the import of these theorems concerning the relationship between mathematical structures and the material world.
  • compare different mathematical models of one and the same phenomenon with regard to theoretical virtues such as simplicity, agreement with observations, etc.

These learning objectives are examined in writing via a project work.

Learning activities

Below follows an outline of the course learning activities. Detailed descriptions of the learning activities are found in later sections in this course memo. 

  • Two lectures on campus: Introduction and Scientific Knowledge and Algorithmic reasoning and its limitations.
  • Nine pre-recorded video lectures. Each video lecture has an associated voluntary lecture quiz and a text transcription. Video lectures are included in the TimeEdit course schedule as a planning recommendation but can be viewed throughout the course. Video lecture quizzes however, have deadlines.
  • Two flipped classroom sessions on campus related to a subset of the video lectures. Before each flipped classroom session, you post a question related to the relevant video lectures on a discussion board and upvote questions posted by other students that you wish to be discussed on the flipped classroom sessions. The lecturer selects among the questions and answers these during the flipped classroom sessions. 
  • Four seminars on campus. Each seminar covers selected course contents from the video lectures and course readings. Before attending each seminar, you complete a mandatory seminar preparation quiz. On the seminar you work on group exercises and discussions. You take one seminar per seminar week.
  • A project work devoted to the philosophy of mathematics. The project includes 4 separate lectures and one final submission. No mandatory attendance is required for the lectures, but some material might be brought up during the lectures which cannot be found in the associated literature.
  • Three exercise sessions on campus. 

Detailed plan


This course includes eleven lectures. Lecture 1 is held on campus and lectures 2-11 are available as videos via Canvas and can be viewed at any time during the course. The placement of video lectures in the TimeEdit course schedule is a planning suggestion for when you might view them.  

Each of the video lectures has an associated lecture quiz with a deadline. If you complete lecture quizzes with passing score upon the deadline, you receive course bonus points for the exam (see section on Schedule and see Canvas for quiz deadlines). For more information on bonus points, see section on Bonus point system below. 

  1. Introduction and scientific knowledge (campus lecture), course week 1
  2. Scientific inferences (59 minutes) (flipped classroom 1), course week 1
  3. Observation and measurement (76 minutes) (flipped cl. 1), course week 2
  4. Experiments (49 minutes) (flipped classroom 2), course week 2
  5. Models (62 minutes) (flipped classroom 2), course week 3
  6. Statistics (62 minutes), course week 3
  7. Explanations and causes (81 minutes), course week 4
  8. Algorithmic reasoning and its limitations (campus lecture), course week 5
  9. Qualitative methods (93 minutes), course week 5
  10. Research ethics (103 minutes), course week 6
  11. Anticipating risk in science and engineering (85 minutes), course week 6 

Flipped classrooms 

Flipped classroom sessions function as an opportunity for receiving clarification from the lecturer on lecture contents. The flipped classroom sessions are intended for addressing questions on course topics that students find unclear, challenging or otherwise interesting.  

There are two flipped classroom sessions on campus, each based on two video lectures. Flipped classroom 1 focuses on the lectures on scientific inferences (lecture 2), and on observation and measurement (lecture 3). Flipped classroom 2 focuses on the lectures on experiments (lecture 4) and on models (lecture 5).  

Each flipped classroom session has an associated discussion board. Before each flipped classroom session, you post a question for the lecturer on the board related to the relevant video lectures, and you upvote questions posted by other students that you would like the lecturer to address during the session. See section on Schedule and see Canvas for further instructions and deadlines. 

The lecturer selects a set of questions from the discussion board and devotes the flipped classroom sessions to answering these questions. During the sessions, you will also be invited to participate on voluntary exercise activities.  

If you complete the flipped classroom activities, you receive course bonus points for the exam. For more information on bonus points, see section on Bonus point system below.  

It is possible to attend flipped classroom sessions without having posted on the discussion board and without participating on exercises in the classroom, but this will yield no bonus points. 

The flipped classroom sessions are taken together with students from other, similar courses. 

Bonus point system 

Completing video lecture quizzes with a passing score, as well as posting on the flipped classroom discussion boards together with participating on the classroom activities, gives course bonus points for the exam. Bonus point activities are voluntary, optional activities intended at incentivising students to engage with the course contents continuously throughout the course. 

Each video lecture has an associated video lecture quiz, comprised of 15 questions. If you complete a quiz with a 14 point score or higher, you get 0.5 course bonus points. All video lecture quizzes have deadlines (See section on Schedule and see Canvas for deadlines). There is no limit on number of attempts up until the quiz deadlines. 

Course bonus points can also be awarded for the two flipped classrooms. Attending the flipped classroom session and carrying out tasks as per instructed by the lecturer results in 0.5 bonus points per each of the two flipped classrooms. 

In order to make the number of bonus points fit the exam format, course bonus points are scaled in the following way before the exam (C = course bonus points, E = exam bonus points): E = C * 5/6, rounded up to the closest .5-value. Example: 4.5 course bonus points will be scaled as 4.5 * 5/6 = 3.75, then rounded up to 4 exam points. You can maximally obtain 5 exam bonus points.  

Exam bonus points are added to part 1 of the exam. For example, if part 1 has a maximum score of 15 points, then 3.5 exam bonus points plus 10 points on part 1 results in a total score of 13.5 points on part 1 of the exam. 4 exam bonus points plus 13 points on part 1 results in a total score of 15 points on part 1 of the exam. 

For more information about the exam, see section on Examination and completion. 

Bonus points collected during one and the same course period are valid for, and only for, the scheduled exam and the corresponding re-exam for that period. 


The course includes a mandatory seminar series comprised of four seminars. Each seminar covers selected course contents from the video lectures and course readings, and following the first seminar, each subsequent seminar connects to the previous seminars. Seminars are intended as a collaborative learning activity where you practice critically discussing course contents and practice applying course contents to cases, with instruction and support from teaching staff. The overall topics covered during the seminar series are as follows: 

  1. Definitions, operationalizations and hypotheses (course week 3)
  2. Designing a scientific study (course week 4)
  3. Interpretation, analysis and evidence (course week 6)
  4. Risk and research ethics (course week 7). 

Since completion of the seminar series yields course credits, the seminars feature mandatory activities: (1) preparing and passing a seminar quiz, and (2) actively participating on the seminar. Missing activities result in seminar incompletion and thus no seminar course credits. 

Before each seminar, you read the assigned readings (reading instructions available on Canvas). Before attending each seminar, you must also pass a mandatory seminar preparation quiz (See section on Schedule and see Canvas for deadlines). There is no limit on number of quiz attempts up until the quiz deadline. You must complete the quiz with a passing score of 14 points before the deadline (indicated in Canvas as “Passed”).  

The preparation quizzes are intended to ensure that all participants come prepared to the seminar for a more rewarding seminar learning experience. If you attend the seminar without completing the preparation quiz beforehand, you will not be marked as attending.  

On the seminar, you will be working together with other students on exercises as per instructed by the teacher. The exercises are formulated in such a way as to promote critical reflection and discussion, as well as to practice application of course concepts to case scenarios.  

You are expected to engage actively with the course contents and work on the exercises during the seminar. Passive attendance on the seminar will be marked as not attending. Active participation on the seminar does not mean that you are expected to demonstrate full proficiency of course contents. Rather, it means that you are expected to have properly engaged with the relevant course material beforehand and made an honest attempt at understanding it. Arisen questions and reflections can be addressed on the seminar. 

For information on what to do if you have not completed a preparation quiz or actively attended on a seminar, see the section on Examination and completion. 

Seminar contents and reading instructions. All the texts can be found on Canvas. 

Seminar 1 – Definitions, operationalizations and hypotheses. 


  • Grüne-Yanoff, Till – Justified Method Choice, chapters 1, 2, 3, 13 
  • Optional reading: Hansson, Sven Ove – Art of Doing Science: sections 2.2-2.8, 3.1-3.2, 5.0-5.1, and 5.8 

Topics relevant for the seminar:   

  • Stipulative and lexical definitions 
  • Narrowness and broadness (as applied to definitions) 
  • Vagueness 
  • Hypotheses (and their quality criteria)
  • Direct, aided and indirect observation
  • Operationalization
  • Accuracy and precision (as qualities of observations and measurements)
  • Measurement error (random and systematic error)
  • Convergent validity and divergent validity 

Seminar 2 – Designing a scientific study. 


  • Grüne-Yanoff, Till – Justified Method Choice, chapters 4, 5. 
  • Optional reading: Hansson, Sven Ove – Art of Doing Science: sections 3.7, 4.2-4, and 5.1-3. 

Topics relevant for the seminar:   

  • Experiment, observational studies and model studies 
  • Mill’s method of difference 
  • Internal validity and external validity 
  • Experimental control 
  • Constancy, elimination and effect separation
  • Randomization
  • Control group and treatment group
  • Observer influence
  • Confirmation bias
  • Blinding
  • Epistemic virtues of models (Parameter precision, Similarity, Robustness, Simplicity, Tractability, Transparency) 
  • Analogies (positive, negative, neutral) 

Seminar 3: Interpretation, analysis and evidence. 


  • Grüne-Yanoff, Till – Justified Method Choice: chapters 2, 6, 7.
  • "Seminar 3 Case", see below.
  • Optional reading: Hansson, Sven Ove – Art of Doing Science: sections 1.6-7, 3.7, 3.9, 5.3-5, 5.7, 7, 8 and the box on p. 24. 

Topics relevant for the seminar:    

  • Repeatability, reproducibility and replicability 
  • Statistical evaluation
  • Statistical significance
  • Correlation and causality
  • Explanatory virtues (Accuracy [of explanations], Non-sensitivity, Precision in the explanans, Precision of the explanandum, Cognitive salience)
  • Duhem-Quine thesis
  • Ad-hoc hypothesis
  • Falsificationism (Popper)
  • Inductive and deductive inferences 

Seminar 4: Risk and research ethics. 


  • Grüne-Yanoff, Till – Justified Method Choice, chapters 8, 9, 11, 12.
  • “On Being a Scientist: Responsible Conduct in Research”, National academy of Sciences.
  • Ahlin, Jesper, “Ethical Thinking”.
  • Optional reading: Hansson, Sven Ove - Art of Doing Science: Section 9. 

Topics relevant for the seminar:   

  • Functions (assigned and ascribed)
  • The design process
  • Qualitative data
  • Controlling observer effects
  • Case study
  • Gift authorship and ghost authorship
  • Scientific misconduct (falsification, fabrication and plagiarism)
  • Informed consent
  • Deontology, consequentialism and virtue ethics
  • Precautionary principle
  • Decision making (under certainty/risk/ignorance/deep uncertainty) 

Project, 3 credits

In this project part, we will discuss issues in the philosophy of mathematics, with an emphasis on the role of mathematics in the study of the natural world. The part will consist of four lectures and one final assignment. Readings for each lecture will be made available on Canvas in advance of the lecture in question. While lecture attendance is optional, there is no guarantee that material covered orally in lectures will be available elsewhere. 

Exercise sessions 

The exercise sessions are extra opportunities to practice on the course content. They are held on campus and shared with other course codes. They are voluntary and have no associated submissions. The format is tested for the first time this semester. More information will follow on Canvas. 

Expected workload 

Expected workload is calculated based on number of course credits per period.  

AK2040 = 7.5 ECTS one period: 20 h /week 


The course schedule is available in TimeEdit via To find your schedule, log in and choose "Course" in the drop-down menu and search for your course code. Note that this schedule does not include submission deadlines, nor seminar group schedule. The TimeEdit course schedule displays all seminar slots. The seminar group schedule with one slot per group will be determined after student group sign-up upon course start. Instructions for sign-up and group schedule will be available on Canvas.  

Your course shares seminars with other courses on theory and methodology of science. If you have scheduling issues, there may be other sessions that you could attend. Contact your course coordinator if you wish to attend another seminar slot. 

Overall information on seminar preparation quiz deadlines, video lecture quiz deadlines, and deadlines for posting questions before flipped classroom sessions can be found in this document. The exact dates and times for submission deadlines are available on Canvas.

Seminar preparation quizzes (mandatory) 

Seminar preparation quizzes open Monday the week before each respective seminar. You must pass the quiz before attending your scheduled seminar. Seminar group schedule is determined after course start and made available on Canvas. See general course schedule in TimeEdit for all seminar slots.  

Video lecture quizzes 

All video lecture quizzes open on the Monday the week before the scheduling of a given lecture and close on the Friday the week after the scheduling of the lecture. 

Flipped classroom question posting 

Deadline for posting and upvoting questions on the discussion boards are: 

Flipped classroom session 1: 2 workday before the scheduled session. 

Flipped classroom session 2: 3 workday before the scheduled session.

Preparations before course start


The main text for the course is: 

  • Justified Method Choice - Scientific Methodology for Scientists and Engineers by Till Grüne-Yanoff. Based on the video lectures. 

In addition, there are three supplemental texts: 

  • Some Issues in the Philosophy of Technology, by Sven Ove Hansson. 
  • On Being a Scientist: Responsible Conduct in Research, which is an excerpt from a text by the National Academy of Sciences.
  • Ethical Thinking by Jesper Ahlin.
  • Algorithmic reasoing and its limitations, by Tor Sandqvist 

Finally, there is one additional optional text, mainly targeting the same topics as the main course text: 

  • The Art of Doing Science by Sven Ove Hansson. 

In addition to above mentioned readings, you may be asked to read short texts in preparation for some seminars. All course readings will be available in pdf file format on Canvas together with associated reading instructions. The readings cannot be bought as physical books, but you are welcome to print them. 

Advice from previous students

In course evaluations for previous periods, students wanted to pass on the following advice. 

  • This course is different from many other courses in an engineering degree, and often requires a slightly different approach.
  • It is a good idea to follow along with the course structure, such as watching lectures when they are scheduled and completing the quizzes.
  • Taking time to prepare for the seminars and actively engaging in the seminars makes it much easier to understand the course concepts and pass the exam.
  • Watch the lectures and do the quizes every week, not necessarily to get the points for the exam (although that's a really nice bonus) but because it really helps you learn. 

Examination and completion

Grading scale

A, B, C, D, E, FX, F


  • PRO1 - Project, 3.0 credits, Grading scale: P, F
  • SEM1 - Seminars, 1.5 credits, Grading scale: P, F
  • TEN1 - Examination, 3.0 credits, Grading scale: A, B, C, D, E, FX, F

Based on recommendation from KTH’s coordinator for disabilities, the examiner will decide how to adapt an examination for students with documented disability.

The examiner may apply another examination format when re-examining individual students.

TEN1 is examined via a digital exam. The examiner decides, based on recomendation from KTH’s coordinator for disabilities, if a custom-made examination for students with documented disabilities is appropriate.

The section below is not retrieved from the course syllabus:

PRO1 - Project, 3.0 credits

Submission of one final project essay. The final version of the essay is graded by a senior teacher. This essay can be passed, failed or you might be asked to revise to reach the criteria for passing. Once your final version is passed, you get the grade P. 

SEM1 - Seminars, 1.5 credits

There are four seminars, all mandatory. To pass a seminar you need to: 

  • read the required material 
  • watch the required videos 
  • pass a seminar quiz 
  • actively participate in the seminar 

The seminar module is graded P/F. If you have passed all seminars, you get the grade P. 

TEN1 - Examination, 3.0 credits

The examination is based on the lectures and the seminars, as well as the course literature. It is given on the date and time indicated in the schedule. It consists of three parts. The first part is a multiple-choice part asking you to identify the definitions and applications of course concepts. The second part is an essay part where you are to submit written answers to two problems. In this part you are asked to account for the course concepts. The third part is an essay part where you choose one out of a list of problems, which require you to account for, apply and discuss course concepts to show skills equivalent to the grade levels B and A. This part is only corrected if the student passes parts 1&2. The exam is open-book, which means that one is allowed to use the course literature when answering the questions. During the course there are quizzes and flipped classroom sessions where students can collect bonus points. The bonus points are scaled to fit the exam format: maximum five points. The points are then added to the part 1 exam score, capped at the maximum for that part. Bonus points are valid for the exam and re-exam belonging to the period and year when they were collected. One may collect points valid for another exam by re-registering for that period and re-taking the quizzes. 

Other requirements for final grade

Fullfilled seminar requirements, project requirements and written exam.

Opportunity to raise an approved grade via renewed examination

Students have to right to take the exam on TEN1 up to five times and thus potentially improve (“plussa”) their grade. After that, the examiner has to formally allow such an attempt at improving (“plussa”) one’s grade. 

Ethical approach

  • All members of a group are responsible for the group's work.
  • In any assessment, every student shall honestly disclose any help received and sources used.
  • In an oral assessment, every student shall be able to present and answer questions about the entire assignment and solution.

Further information

No information inserted

Round Facts

Start date

28 Aug 2023

Course offering

  • Period 1 Autumn 2023-50333

Language Of Instruction


Offered By



Communication during course

Please e-mail the course coordinator with all matters, both administrative and content questions. Contact through e-mail is preferred, please do not use the Canvas messaging system. You may communicate in either Swedish or English. Please state your course code, since the course coordinator handles several courses. 

Course Coordinator