9.13 | Spring 2019 | Undergraduate

The Human Brain

Assignments

Learning to read papers is an important skill. A few tips:

  1. Skimming does not work; reading just the abstract does not work.
  2. Reading a scientific paper takes a long time (≥ 2 hours, usually more, even for me). If you are frustrated trying to figure out what the experiment was, this is normal, it just takes a long time. Reading a scientific paper is more like solving a puzzle than it is like reading a novel. Until you figure all this out, you have not understood the paper.
  3. A key skill: what can you skip?
  4. Our strategy in this class: You will struggle for hours on your own first, then post your responses, then work with fellow students, then discuss in class.

Reading Response Assignments

Reading Response Assignment 1

Reading Response Assignment 2

Reading Response Assignment 3

Reading Response Assignment 4

Reading Response Assignment 5

Reading Response Assignment 6

Reading Response Assignment 7

Reading Response Assignment 8

Experimental Design Assignment

Experimental Design Project

Note: Lecture 2 should help but hopefully not be required for this assignment.

Article: Tootell, R.B.H., J.B. Reppas, et al. “Visual Motion Aftereffect in Human Cortical Area MT Revealed by Functional Magnetic Resonance Imaging.” Nature 375 (1995): 139–41.  DOI: 10.1038/375139a0

Assignment: Read the assigned article carefully (expect to spend at least one hour on this, possibly more) and think about it, then provide short answers to the questions below.

  1. What is the characteristic functional (response) property of cortical area MT (V5)? Answer in a phrase or sentence.
  2. Which aspect of Figure 2 shows the central new finding of the paper?
  3. Does activity in cortical area MT reflect what the subject is perceiving, or what visual information is arriving on the retina? Answer and explain in at most 3 clear sentences.

Article: Downing, P.E., Y. Jiang, et al. “A Cortical Area Selective for Visual Processing of the Human Body.” Science 293 (2001): 2470–73. DOI: 0.1126/science.1063414

Assignment: Read the assigned article carefully and think about it, then provide short answers to the questions below. Be clear and concise, points will be taken off for unnecessary words.

  1. Give three pieces of evidence that the selectivity for the EBA does not simply reflect the presence of particular low-level visual features.
  2. The authors state that they identified the EBA in each subject with a localizer scan. What is a localizer scan and why is it important?
  3. Do the findings in this paper show that the EBA meets all the criteria for a distinct cortical area? Explain.
  4. What do you want to know next about the EBA and how might you test it with fMRI?

a) State a specific hypothesis that you could test with fMRI (one sentence).

b) What conditions would you need to include to test your hypothesis? Describe each briefly.

c) What, specifically, would you expect to find empirically in your conditions if your hypothesis is true?

Assignment: Design two fMRI experiments to test whether the brain contains regions that are selectively involved in perceiving snakes. In each case, state i) the specific hypothesis you are testing, ii) the experimental conditions you will test (including what study participants will see and do in your experiment), iii) what exactly you will measure, and iv) what your hypothesis predicts you will see. You can describe stimuli with words, sketch them, or find them and paste them in (with appropriate explanations). Next, list the alternative accounts that might remain even if the data from this experiment are consistent with the predictions of your hypothesis. Then, describe a second experiment to test one or more of those alternative hypotheses. Finally, list two important questions about snake-specific regions in the brain that can never be tested with fMRI, and give a different method that could be used to test each.

Article: Bryan, P.B., J.B. Julian, and R.A. Epstein. “Rectilinear Edge Selectivity Is Insufficient to Explain the Category Selectivity of the Parahippocampal Place Area.” Front. Hum. Neurosci. 10, no. 137 (2016): 1–12. DOI: 10.3389/fnhum.2016.00137

Assignment: Read the paper and answer the questions below.

  1. Describe the main conclusion of the paper in one sentence.
  2. Explain the main point of Figure 4 in one sentence.
  3. Describe the stimulus conditions you would need and the key prediction you would make to test the hypothesis that the FFA contains information about the curviness of faces.

Article: Sugita, Y. “Face Perception in Monkeys Reared with No Exposure to Faces.” PNAS 105, no. 1 (2008): 394–98. DOI: 10.1073/pnas.0706079105

Assignment: Read the assigned article carefully and think about it, then provide short answers to the questions below. Be clear and concise—points will be taken off for unnecessary words.

Notes: This is a hard assignment. Two videos that might also be helpful are:

Figs. 3a,b © 2008 National Academy of Sciences. All rights reserved. This content is excluded from our Creative Commons license, see https://ocw.mit.edu/fairuse for details. Source: Sugita. Y. Face perception in monkeys reared with no exposure to faces. PNAS Jan 2008, 105 (1) 394-398; DOI: 10.1073/pnas.0706079105

1. The above results are from a preferential looking task in monkeys. To conduct a preferential looking task, two objects or pictures are placed side by side within the subject’s field of view. The amount of time spent looking at each object/picture is measured for a fixed period. The above plots are the results of the preferential looking test described in Sugita 2008.  Describe the results and attempt to explain their importance.

Figs. 4a,b © 2008 National Academy of Sciences. All rights reserved. This content is excluded from our Creative Commons license, see https://ocw.mit.edu/fairuse for details. Source: Sugita. Y. Face perception in monkeys reared with no exposure to faces. PNAS Jan 2008, 105 (1) 394-398; DOI: 10.1073/pnas.0706079105

2. A visual paired-comparison procedure (VPC) uses habituation to determine if subjects can discriminate between pairs of stimuli in the same class.* The above plots are from Sugita 2008 and depict the results of a VPC test in face-deprived (A) and typically developed (B) monkeys. What are the key results? Explain their implications.

3. Inspired by Sugita, you decide to test whether you can find an FFA in young monkeys using fMRI. To do so, you design two different experiments described below. For each experiment first state your hypothesis based on the Sugita paper, and then your specific predictions for the following specific findings: (i) the response you might expect to see to faces compared to objects in a region of the ventral temporal cortex (approximately where you would find the FFA in adults); and (ii) the rationale behind your predictions. Feel free to use words or make simple plots. Use only what you know from class (especially the snake homework) and the Sugita paper.

a) Experiment 1: A blocked design with black and white images of faces, bodies, objects, and scenes. Each image is presented for 500 ms and each block is 18 seconds long.

b) Experiment 2: Similar to the protocol established by Sugita et al., infant monkeys are face-deprived for 6, 12, and 24 months. Similar to Experiment 1, the paradigm is a blocked design with black and white images of faces, objects, bodies and scenes. Each image is presented for 500 ms, each block is 18 seconds long, and monkeys are passively viewing the stimuli. Monkeys are scanned twice—once at the end of the face deprivation period (t = 0) and once 6 months later (t = 6).

* If this description of VPC is unclear, a more thorough explanation can be found here: Nancy’s Brain Talks: What is the role of experience in the development of face recognition?

Article: Knops, A., B. Thirion, et al. “Recruitment of an Area Involved in Eye Movements During Mental Arithmetic.” Science 324, no. 5934 (2009): 1583–85. DOI: 10.1126/science.1171599

Assignment: Read the assigned article carefully and think about it, then provide short answers to the questions below. You can do this by responding straight on this document or by submitting a separate document with numbered answers. Be clear and concise—points will be taken off for unnecessary words.

  1. What is the central empirical claim of the paper in a single sentence?
  2. Is the data in this paper consistent with the idea that a brain region exists that is specifically engaged in processing number and arithmetic only? Why or why not.
  3. What is the contrast that Knops et al. used to identify the standard brain regions engaged in saccades (eye movements)? Is this contrast a minimal pair? Is that important for this study?
  4. Can you think of a more general version of Knops et al.’s hypothesis, that applies not just to eye movements but to any rightward versus leftward movement? How might you test this hypothesis using motor cortex? What would the key prediciton be?

Article: Tang, C., S. Hamilton, and E.F. Chang. “Intonational Speech Prosody Encoding in the Human Auditory Cortex.” Science 357, no. 6353 (2017): 797–801. DOI: 10.1126/science.aam8577

Assignment: Read the assigned article carefully (expect this to take at least two hours, possibly more) and think about it, then provide short answers to the questions below. You can do this by responding straight on this document or by submitting a separate document with numbered answers. Be clear and concise, points will be taken off for unnecessary words.

A few things that are not well explained in the paper:

  • I didn’t see a definition of H gamma (indicated as the Greek letter which I cannot get my text editor to make) in the figures – this is just “high gamma power”, which is the main measure of neural response used in this paper and in other intracranial recording studies.
  • When the paper refers to “spectral information” (which I highlighted in orange), that just refers to different amounts of power at different frequencies. See the “spectrogram” in Figure 1A, which shows auditory power (darkness) as a function of time (x axis) and auditory frequency (y axis).
  • You can ignore the stuff about the “missing fundamental” (highlighted in orange).

TA tip: when reading, try to focus on the figures and make sure you understand them. Refer back to the text for supporting information when needed.

  1. What method does this paper use?
  2. What is the main (most important) empirical finding in the paper? What figure illustrates this finding?
  3. What is the design of this experiment? That is, what factors were manipulated (list each), and how many different conditions were used?
  4. What does Figure 1E show?
  5. The middle graph in figure 2N shows 147 electrodes that had information about which sentence was spoken. Could you decode from these electrodes whether the speaker saying those sentences was male or female?
  6. Would you expect the electrodes that can discriminate intonation to be able to discriminate musical melodies (in which each note has a different pitch)? If so, how would you characterize the function of those sites?
  7. If the same experiment were repeated using fMRI, what results would you expect?

Article: Fischer, J., J.G. Mikhael, et al. “Functional Neuroanatomy of Intuitive Physical Inference.” PNAS 113, no. 34 (2016): E5072–E5081. DOI: /10.1073/pnas.1610344113

Assignment: Read the assigned article and think big about the problem it addresses. Think of this article as essentially a first baby step in a broader line of work. What questions does this article answer, and what do you want to know next?

For the next assignment you will have a significant written experimental design assignment (15% of your course grade) designing your own experiment (or two) to ask one of the next questions about intuitive physics in the brain, using any of the methods you have learned about in the course.

For now you are asked only to read this article and answer questions about it. But as you read it, start thinking about the broader space of questions this article opens up, and what you might propose for the larger experimental design assignment.

Provide short answers to the questions below. Be clear and concise—points will be taken off for unnecessary words.

  1. What is the main question addressed in this article?
  2. What is the main answer the article provides about that question?
  3. Briefly contrast the logic of Experiment 1 and Experiment 2. In what way are the two designs complementary?
  4. Scrutinize the data shown for regions P3R and P1R in Figure 3B. What do these data suggest to you?
  5. Are the frontal and parietal regions identified in this study highly specialized for intuitive physical reasoning per se?
  6. List three big questions you might want to answer next in this line of work, and for each one list a method that might be able to answer (or start to answer) that question.

Assignment: Design an experiment using any of the methods of human cognitive neuroscience that we have discussed in the class to address the brain basis of intuitive physics. The biggest part of this task is to come up with a good idea for an experiment that asks an important, interesting, and theoretically motivated question about intuitive physical inference in the human brain. Because a single experiment rarely definitively answers a question, you should include two linked experiments, the second one addressing questions left unanswered by the first. Think hard about and provide important details about your task and stimuli. The difference between a beautiful experiment and a “meh” experiment is often in the specifics of the stimuli. (Work to come up with good ones and show examples!) Extra points for creativity, but note that usually the best experiments are simple and elegant. (Crazy-complicated experiments almost never work.)

Beyond coming up with two successive nicely designed experiments that ask important questions, it is also important to write up your ideas clearly. So, edit your prose multiple times to remove extra words and promote clarity. This assignment counts for 15% of your course grade. Expect to spend many hours on it. You may not propose an experiment that has already been published.

You have already read the very relevant Fischer et al. (2016) paper. I recommend you brainstorm for a while on your own, taking notes, and only after that read Ullman et al. (2017) and/or Kubrich et al. (2017), then revisit and perhaps revise your ideas.

Your writeup may be only a few pages (short is good), but must do the following (for each of your two experiments):

  1. Clearly state your hypothesis and motivate on theoretical and empirical grounds why it is important. This should require 1–3 clearly written paragraphs referring to what we already know from common sense / everyday experience and/or prior studies (including citations, with full references at the end).
  2. Describe your experimental design, listing all factors manipulated, all conditions within each factor, and measures collected.
  3. Describe what subjects will actually do (the task) and what happens in each trial including the precise sequence of events and their timing.
  4. How will the data be analyzed? I don’t need the level of detail of a methods section in a published paper, but I do need enough to understand the logic of the experiment (at the level used in lectures in class).
  5. State or draw the precise predictions of your hypothesis and note which (if any) are main effects and which are interactions.
  6. Discuss what you can infer from each of the main possible data outcomes. Consider alternative accounts of each of these possible outcomes. Especially if the prediction of your hypothesis is borne out by the data, what would you still need to worry about, and what other experiments might address those remaining concerns? This is how you will motivate your second experiment, and even after the second experiment you may still be left with alternative accounts and unanswered questions, which you should describe.

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