Course Syllabus

Psych 50: Introduction to Cognitive Neuroscience

Course Description: How does our brain give rise to our abilities to perceive, act and think? Survey of the basic facts, empirical evidence, theories and methods of study in cognitive neuroscience exploring how cognition is instantiated in neural activity. Representative topics include perceptual and motor processes, decision making, learning and memory, attention, reward processing, reinforcement learning, sensory inference and cognitive control

NOTE: This class will be taught online in the winter and summer quarters. We are working to adapt this course for online learning and this syllabus is likely to change over the coming weeks. The material covered will be similar to previous years, however, we will use a "flipped classroom" style in which lectures will be pre-recorded and class times will be for online discussion and group activities. To allow for more interaction with the teaching team across zoom we are limiting class enrollment. Also, students will be assigned either the Tuesday or Thursday 2:30 - 3:50pm time period for discussion. That is, you will be required to come to class via zoom on one of those days each week, but not both. If you are in a timezone in which you are unable to attend one of those times or have limited internet connectivity and have a compelling reason that you must take the course this quarter, please contact the instructor for exemption to the requirement to attend during class period. Instead of a midterm and final, we will require weekly graded assignments and a group project. 

Instructor:  Justin Gardner, PhD

Open office hours: Feel free to stop by on zoom here without appointment on Fridays 12:30 - 1:30 pm PST

One-on-one, by appointment, office hours: If you would like to meet one-on-one, for example, to discuss cognitive neuroscience, how you can learn more about the field, or become involved in neuroscience research, please free to schedule a one-on-one appointment with me here.



Meeting time: Winter quarter, TTh 2:30 - 3:50PM

Location: Zoom

Pre-requisite: None

Undergraduate Requirements: Disciplinary Breadth: Natural Sciences, Ways: Scientific Method and Analysis, Ways: Social Inquiry

Teaching Assistants: 

Name Email Office Hours Office Hours Zoom link
Head TA: Akshay Jagadeesh  Sun & Thurs 9:30am Link
Josh Ryu  Wed 2:30pm Link
Mohammed Abdal Monium Osman  Tues 10:30am Link

Learning goals

We are our brains. The overall goal of this class is to introduce you to the scientific study of how our brains work to make us who we are. This class should prepare you to take more specialized upper level classes in specific areas of cognitive neuroscience.

The overall learning goal is to teach you how to think like a cognitive neuroscientist. This is not just about learning basic facts about the workings of the brain, but developing the instinct to question those facts. When presented with new information about the brain, a cognitive neuroscientist will ask themselves, how do we know that "fact" about the brain? What experiment was performed to establish that "fact"? What type of evidence supports that "fact" about the brain? Is that "fact" consistent with other things we know about the brain. 

After taking this course you should be able to...

...demonstrate familiarity with basic anatomy and physiology of the brain. You should gain familiarity with fundamental terminology and basic knowledge about brain systems and functions. You should be able to recognize and understand these terms when you encounter them in reading literature (both popular press and primary) or listening to lectures about cognitive neuroscience. Chapter reading and quizzes will be used to build this knowledge. Examples of basic factual knowledge:

What is an action potential? Why is it important for cognitive function? How do Na+ and K+ currents make it possible?
Where is prefrontal cortex or the hippocampus? What might happen to someone if they had damage to it?
What is dopamine? What it is thought to signal in the brain?

...use Marr's levels to explain how the brain allows us to do everyday behaviors. Cognitive neuroscience aims to provide explanations for how the brain gives rise to behavior. You should be able to take common behaviors and break them down into the goals, the algorithms that could achieve those goals, and ways they may be implemented in the brain. We will practice this through weekly thought questions discussed in section. For example: 

My goal is to swing at a pitch while playing whiffle ball. How would the drift diffusion model explain my reaction time and choice? How might drift diffusion be implemented in the brain?
My goal is to recognize a cat. How would hierarchical computation allow me to achieve this? How might simple and complex cells implement hierarchical computation?
My goal is to learn how to balance on my new RipStik casterboard. How would a reinforcement learning algorithm be used to explain my learning? How might dopamine neurons implement the learning signal?

...reason about how experimental evidence supports or does not support conclusions about how the brain functions. Cognitive neuroscience is a rapidly changing field in which sometimes what we thought we knew one year is overturned by new experimental evidence the next year. It is therefore important not to just accept a set of facts about the brain, but be able to evaluate evidence that supports those facts. For example:

What do we learn from observe, remove or add experiments?
What are ways to operationalize cognitive behavior so that brain mechanisms can be formally tested?
What experimental methods are used to measure neural activity and what can be learned from the use of those techniques?
When confronted with a new experimental technique, what sorts of questions should one ask about that technique to understand what it can tell us about the brain?
What can be learned by probing the brain at different scales such as synapses, neurons, populations or areas?


We will not cover everything there is to know about cognitive neuroscience in one quarter. Cognitive neuroscience is a rich field that draws on many disciplines from biology, chemistry, psychology, computer science, engineering, mathematics, philosophy and beyond. The objective is not to be exhaustive (and exhausting!) in what we cover. Instead the goal is to give you basic background and conceptual knowledge as outlined above by going in to depth in a few areas to illustrate the concepts and knowledge that structure the scientific study of cognitive neuroscience. 

  1. Input Our brains have many sensors and systems that allow us to get information about the outside world. For example, touch, smell, balance, etc. We will use the visual system as a canonical system for understanding how information about the world gets into the brain. This will allow us to understand what is meant by bottom-up processing from sensory transduction to cortical streams of processing supporting high-level categorization and sensory inference. 
  2. Output We will next flip our thinking about the brain from something that passively takes in information and processes it to something that generates movement. 
  3. Feedback If the brain can act to contract muscles and make movements it can also act on itself to change things like sensory processing. We will discuss in depth a canonical system that does just that: attention.
  4. Broadcast We will next turn from cognitive processes like attention that offer very specific control of information processing to ones that can distribute information widely and modulate activity across lots of the brain; neuromodulatory systems. We will discuss in-depth the one we know the most about - the dopamine system and its role in reinforcement learning.
  5. Memory Memory will give us a chance to see many of the above concepts put together to explain a cognitive function. It will also show us how neuroscience can inform our understanding of cognition as we see different systems and process underlie different forms of memory.

Along the way, various topics will come up - emotion, language, decision-making, consciousness, free-will, psychoactive drugs, disease, mental illness, brain metabolism, brain-machine interfaces, mind-control - we will try to fit these into the above frameworks for thinking about the brain. Undoubtedly, there will be a part of cognitive functioning that we do not cover (hey, why haven’t we talked about why I sneeze when I see a bright light? - you are wired funny. Yes, that’s true. It really happens). You will have opportunities in sections to take the framework that are discussed in lectures and apply them to understanding other things that were not covered. So, for example, in section we might talk about the auditory system and how it is the same or different from the visual system. 

Ethics and morality

Some aspects of the material covered in a cognitive neuroscience course may bring up ethical and moral considerations for you that you feel strongly about. For instance, it might challenge your religious beliefs. It might challenge notions of when someone should be culpable for behavior that is abhorrent but for which they might not have control. They may challenge your notions of self, of memory, of personality. All these are extremely important issues since they bear on how we act as a society, how we educate, how we deal with crime and punishment, how we think about who we are and how we act with others. Much foundational work in cognitive neuroscience has been done using animal experiments which raise important questions of how we weigh humane treatment of animals against the quest for knowledge and betterment of human society and health. 

We encourage you all to think about these issues openly and frankly as they should be in an academic environment like Stanford. Having said that, we hope that you will come in with as open a mind as possible and not pre-judge what you are learning about. We will have opportunities to discuss issues related to ethical and moral considerations that come out of the study of cognitive neuroscience. For those particularly interested in these issues, we would recommend the excellent course offering: NBIO 101: Social and Ethical Issues in the Neurosciences.


Chapter readings will be from the following textbook, but will be supplemented by occasional readings posted on Canvas. The textbook is available in the Stanford bookstore and on a 2-hour course reserve at Green Library.

Brain and Behavior: a Cognitive Neuroscience Perspective, 1st Edition (2015) David Eagleman and Jonathan Downar. Oxford University Press.

 All students should retain receipts for books and other course-related expenses, as these may be qualified educational expenses for tax purposes. If you are an undergraduate receiving financial aid, you may be eligible for additional financial aid for required books and course materials if these expenses exceed the aid amount in your award letter. For more information, review your award letter or visit the Student Budget website


The schedule is broken up into one week modules, you can find all the resources for each week organized by clicking on the modules link in the menu on the left of Canvas.

Weekly study guide

We will provide a weekly study guide (links are found under modules). This is a central document that summarizes learning goals each week. In it you will find an overview of the week and a set of learning goals for each of the lectures and sections. There will be a reading guide which will provide you some detail about what we hope you should be taking away from the readings. In particular, lists of key terminology that we expect you to learn. We will also provide some of the key slides from lectures with brief explanations as a reference for some of the main take-aways. Note that full slides and section materials will be posted to Files. 


Readings and recorded lectures: Each week there will be assigned readings and one or two recorded lectures for you to watch. You will be expected to finish the readings and watching of the lectures before coming to your assigned class period (either Tuesday or Thursday).

Quizzes: Education research shows that quizzing is an effective way to improve learning, so we will provide quizzes that are based on the material covered each week. They should be done closed-book at home after you have done the weekly reading, watching of lecture videos and review of the study guide. After taking the quiz once, you may go back and take the quiz a second time, open book. Your grade will be based on the second taking of the quiz. Both quiz attempts are to be completed on Canvas before your assigned class period (either Tuesday or Thursday).

Weekly worksheet: Each week we will provide a worksheet that includes a thought question to aid in the development of conceptual thinking. We will go through the worksheet during your assigned class period (either Tuesday or Thursday). You will be required to complete whatever was not finished during the class period and post your worksheet after your assigned class period on Canvas by 11:59PM (either Tuesday or Thursday). Worksheets are to be done open-book and we encourage you to work with others.

Weekly graded assignment: Each week you will have a graded assignment that will closely follow the format of the weekly worksheet. This graded assignment is to be completed on Canvas by 11:59 PM on Friday for those assigned to the Tuesday class period and 11:59 PM Sunday for those assigned to the Thursday class period. The assignment is open-book, but must be done by yourself as it is representative of the development of your conceptual understanding of course material.

Final group project: You will work in groups of students (ideally, 3 students, but 2-4 is acceptable) on a topic related to cognitive neuroscience of your own interest. The goal is to take your conceptual understanding of cognitive neuroscience developed during the class and explore an area that you are particularly interested in. Your group will make an "explainer" presentation about the area of cognitive neuroscience you have chosen. You will make a recorded video presentation (via zoom) with slides (10-15 minutes per student, e.g. 30-45 minutes for a group of 3) and a 5 minute in-class teaser presentation. There will be a series of assignments related to the group project through-out the quarter and your grade will be based on your individual contribution to the project as assessed through your Canvas submissions related to the project and participation in the video presentation.

Midterm and Final: There will not be a midterm or final this year.

Your final grade will be based on the following:

10% Quizzes (2 lowest grades will be dropped)

15% Weekly worksheet and attendance in class (2 drops allowed)

35% Weekly graded assignment (2 lowest grades will be dropped)

40% Final group project

Policy on missed classes and work

Attendance at all lectures and sections is expected. If you are sick, have a commitment like an athletic tournament or assignment from another class which makes you unable to complete a quiz or thought question, then you may drop at most 2 quizzes and 2 thought questions without affecting your grade, as noted above. You do not need to inform the instructor or your TA. No further accommodations for missed assignments can be provided on an individual basis without an official Accommodation Letter (see below). Late assignments are not graded and count against the 2 allowable drops.

Sections are an important part of the course in which we dive deeper into subjects covered in lecture and reading. We also have numerous demonstrations and labs which we hope will more deeply develop your conceptual understanding of cognitive neuroscience. Whether these sections achieve their learning goals depends in large part on you - being engaged, asking questions, helping each other understand what you find difficult and teaching each other.

However, if for unavoidable reasons such as away games beyond the normal 2 absences you cannot attend a section or exam please have your coach or responsible official email your TA (please cc the Head TA) to confirm that you were absent for an official Stanford event. These excused absences will be graded solely on the written portion of the thought question -- make sure you turn it in on time even if you are not on campus! In your assignment, please leave a comment as a reminder to your TA that you have an official reason to be absent so that your TA will remember to ignore attendance for that week.

Take-home exam deadlines and in-class exams cannot be changed without an OAE accommodation (see below). In the event that you suffer from a major injury or very serious debilitating illness (i.e. not a seasonal cold) that unexpectedly incapacitates you and have done all the rest of the work in the class, you may petition for an incomplete in the class and take the exam at a later date. In this case, we would ask that you document your injury or illness with a written letter from a nurse, doctor, coach or other person in a supervisory role.

Use of laptops and phones in class

We ask that you refrain from using laptops, tablets and phones in class as their use can be very disruptive to others. While note taking on a computer is permitted, we recommend taking notes with pen and paper (you can take pictures of them and digitize later if you wish) because research has shown that the act of writing helps retention of concepts.

Students with Documented Disabilities

Students who may need an academic accommodation based on the impact of a disability must initiate the request with the Office of Accessible Education (OAE).  Professional staff will evaluate the request with required documentation, recommend reasonable accommodations, and prepare an Accommodation Letter for faculty dated in the current quarter in which the request is being made. Students should contact the OAE as soon as possible since timely notice is needed to coordinate accommodations.  The OAE is located at 563 Salvatierra Walk (phone: 723-1066, URL: Please send your letter to your TA (cc the Head TA) at the start of the quarter to give us time to plan accommodations.

Honor code

We will abide by the Stanford University Honor code. Please familiarize yourself with it.

Course Summary:

Date Details Due