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2016 March 30

Class topic not what was planned

Filed under: Circuits course — gasstationwithoutpumps @ 21:27
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In my Applied Electronics for Bioengineers course, I had planned to spend the lecture time today talking about sampling and aliasing, but that is not what ended up happening.

I am making it a point to answer student questions (unless they are irrelevant) first, before doing whatever I prepared. The point of the lectures is to help students understand the reading and do the design work for the labs, and anything I have prepared is just a best guess at what the students need. Their questions address more directly what they perceive as their need.  Most of the prepared lecture material is in the book (I wrote the book based on what I have covered in lectures), so answering questions from students who have read the book and are still confused is going to be better than my repeating what is in the book.

Today students had some logistic questions about what to write up for Lab 1 (not much, it was just soldering headers onto the Teensy boards and setting up PteroDAQ—I just asked for a description of what they did, whether anything went wrong, and what they did to fix the problem) and about prelab homework for Lab 2 (do it, but don’t turn it in, it is just setting up gnuplot so that they can use it for the lab).  Those only took a couple of minutes.

The big question that diverted the entire flow of the lecture was a request for an explanation of the high-pass filter in Lab 2 that is used for recentering the function generator output at 1.65V. This lead to several things:

  • Description of block diagrams as functional blocks connected by interfaces, and why this was an important concept in engineering. Frequency and voltage information was put on the block diagram  connections.
  • Capacitor symbol and DC-blocking property of capacitors.
  • Resistor to Vref and why that would cause the output to become Vref, if there was no current through the output.
  • Back to the block diagram to add the constraint that the analog-to-digital converter on the Teensy board couldn’t take any current from its input.
  • Definition of “gain” as \frac{dV_{out}}{dV_{in}}.
  • Showing the high-pass filter Bode plot as two lines meeting at the corner frequency, and giving the corner frequency as \frac{1}{2\pi R C}, without derivation.  I promised the students that we would derive that result in a few weeks, once we’ve had complex impedance.
  • Replacing the resistor to Vref with a pair of resistors to 3.3V and Gnd.
  • Introduction of the triangular ground symbol, and rejection of the chassis ground and earth ground symbols as not relevant for the class.
  • Derivation of the voltage-divider formula from Ohm’s Law, using the important constraint that no current is taken from the output node of the voltage divider, so that the two resistors have identical currents. I had the students help with this, in order to elicit the most common mistake
  • Assertion, without derivation or explanation, that the RC time constant for the high-pass filter should treat the two resistors as being “2R” rather than “R”.

For the last couple of minutes of class, I finally got to do the demo with the homemade stroboscope and pendulum of aliasing, but it was not very effective. Even with the lights off in the classroom, there was enough light through the windows to wash out the strobe. I could not easily keep the pendulum swinging with one hand and adjust the strobe with the other.  If I do this again next year, I should make a panel with about 20 of the LED boards, for around 2.35A during the flash.  At 1.64ms for the longest flash, that’s 3.85mC, which would drain 8.2V from the 470µF capacitor, if the power supply weren’t capable of delivering that much current (but I have a 6A 9V supply, so there should be no problem delivering full power).  Hmm, maybe I should make up that panel for the Mini Maker Faire, instead of the wimpy 4-LED strobe I now have.

I’m actually pleased that I didn’t give the lecture I had planned—my book, which was based on my lectures, already covers the material adequately, and I’d much rather spend precious class time explaining the things that aren’t clear in the book.  The only way I can know what the students need to hear is for them to ask for clarification where they are confused.

2015 October 2

What is probability?

Filed under: Uncategorized — gasstationwithoutpumps @ 17:43
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Today’s class in Bioinformatics: Models and Algorithms went fairly well.

I started by collecting the first assignment and asking if there were any questions, about anything in the class.  I used a bit longer wait time than I usually use for that prompt, and was rewarded by having a reasonable question asked by someone who had clearly been hesitant to ask.  I’ve been finding that “Wait Time” is one of the most powerful techniques in Teach Like a Champion.

The first part of class was just a quick summary of DNA sequencing techniques, with an emphasis on the effect the different technologies had on the sequence data collected (read lengths, number of reads, error models).  Many of the students had already had much more extensive coverage of DNA sequencing elsewhere (there is an undergraduate course about half of which is sequencing technology), and several students were able to volunteer more up-to-date information about library preparation than I have (since they worked directly with the stuff in wet labs).

I reserved the last 15 minutes of the class for a simple question that I asked the students “What is probability?”

I managed to elicit many concepts related to probability, which I affirmed and talked about briefly, even though they weren’t directly part of the definition of probability.  This included things like “frequency”, “observable data”, and “randomness”. One volunteered concept that I put off for later was “conditional probability”—we need to get a definition of probability before we can deal with conditional probability.

Somewhat surprising this year, as that the first concept that was volunteered was that we needed an “event space”.  That is usually the hardest concept to lead students to, so I was surprised that it came up first.  It took a while to get someone to bring up the concept of “number”—that probabilities are numeric.  Someone also came up with the idea “the event space equals 1”, which I pressed them to make more precise and rigorous, which quickly became that the sum of probabilities of of events is 1.  I snuck in that probabilities of events meant a function (I usually press the students to come up with the word “function”, but we were running low on time), and got them to give me the range of the function.

Someone in the class volunteered that summation only worked for discrete event spaces and that integration was needed for continuous ones (the same person who had brought up event spaces initially—clearly someone who had paid attention in a probability class—possibly as a math major, since people who just regard probability as a tool to apply rarely remember or think about the definitions).

So by the end of the class we had a definition of probability that is good enough for this course:

  • A function from an event space to [0,1]
  • that sums (or integrates) to 1.

I did not have time to point out that this definition does not inherently have any notion of frequency, observable data, or randomness.  Those all come up in applications of probability, not in the underlying mathematical definition.  One of my main purposes in asking a simple definitional question (material that should have been coming from prerequisite courses) was to get broad student participation, setting the expectation that everyone contributes.  I think I got about 50% of the students saying something in class today, and I’ll try to get the ones who didn’t speak to say something on Monday.  Unfortunately, I only know about 2 names out of the 19 students, and it takes me forever to learn names, so I may have to resort to random cold calling from the class list.

In retrospect, I wish I had spent 5–10 minutes less time on DNA sequencing, so that there was a bit more time to go into probability, but it won’t hurt to review the definition of probability on Monday.

2014 June 4

Random topics in class today

Filed under: Circuits course — gasstationwithoutpumps @ 19:20
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Since students have started on their last lab, there is no more material that I have to cover, so I threw today’s lecture open for questions.  I had prepared some material on Wien-bridge oscillators, in case no one had any questions, but we filled the time with stuff they were confused about from earlier in the quarter.  In roughly the order I covered them, we talked about

  • FETs. I showed the cross-sections of nFETs and pFETs, explained the “back gate” or substrate connection and why it was tied to the source on the power FETs. I also talked about the flyback diodes and why they are needed when driving inductive loads.  This also gave me an opportunity to talk about how ignition coils on cars work.
  • PWM. I redid a lecture that had not gone over well the first time, talking about how the rectangular voltage pulses turn into up and down ramps for current in an inductive load, and how duty cycle gets converted to current level.  I still think I could do a better job of the PWM talk, but the students were feeling better about understanding how their class-D amplifiers worked.
  • I also introduced H-bridges for DC motor speed control, and showed how PWM could control the motor to turn forward or backward at different average current levels.
  • A student asked about how the gain in theirpreamp affected thefinal output loudness, so I redrew a part of the comparator function from their lab handout:
    Example of comparator output comparing a slow signal from a preamp and a fast triangle wave to get a pulse-width modulated wave.

    Example of comparator output comparing a slow signal from a preamp and a fast triangle wave to get a pulse-width modulated wave.

    I then showed how a small signal centered at the same voltage as the triangle wave would produce a 50% duty cycle, with only small fluctuations from 50% as the signal went up or down.

  • Finally, I reviewed sampling and aliasing, explaining where the beat patterns they saw in their lab came from.  I think I need to provide more on that earlier in the quarter, as they did not seem to get as much from the sampling and aliasing lab as I had hoped.

Tomorrow is the last lab (unless students request extra time in the lab to redo something next week), and I expect all the students to finish their EKG soldering.  I did remember to suggest that everyone solder a board, so that they could have one to demo to people, but we’ll see how many takers there are tomorrow.

On Friday, I’ll once again take questions, but I’ll still have the Wien-bridge oscillator to present if they don’t have anything to ask.


2013 April 14

Showing is better than telling, but not by much

Filed under: Circuits course — gasstationwithoutpumps @ 10:34
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Robert Talbert, in Examples and the light bulb – Casting Out Nines – The Chronicle of Higher Education, wrote

I have a confession to make: At this point in the semester (week 11), there’s a question I get that nearly drives me to despair. That question is:

Can we see more examples in class?

Why does this question bug me so much? It’s not because examples are bad. On the contrary, the research shows (and this is surely backed up by experience) that studying worked examples can be a highly effective strategy for learning a concept. So I ought to be happy to hear it, right?

The difficulty, of course, is that the students are asking to see examples, rather than working on the examples themselves—they are asking to be spoonfed mush rather than chewing for themselves.

I have found in my own learning that I can get a certain amount by reading, but that really understanding material requires me to work out problems for myself.  Sometimes this just means doing exercises from the textbook (a boring task which I have trouble forcing myself to do without the structure of a course), and sometimes it means struggling with making something work to solve a real problem. Real problems are both motivating and frustrating—just doing carefully drafted exercises that are designed to work out easily doesn’t always help much in applying ideas to the real world.

Talbert gets the point across well:

Of course at the beginning of a semester, students aren’t experts, and showing them examples is important. But what I also have to do is (1) teach students how to study examples and (2) set and adhere to an exit strategy for giving examples. My job is not to give more and more examples. Instead it’s to say: Rather than give you more examples, let me instead give you the tools to create and verify your own examples.  And then, at some point in the semester, formally withdraw from the role of chief example-giver and turn that responsibility over to the students.

This is the same idea as in my post Descaffolding, which was prompted by a post by Grant Wiggins, Autonomy and the need to back off by design as teachers.  It also fits in with Dan Meyer’s theme to “be less helpful”.

Given how frequently teachers and teacher leaders discuss it, I think that over-scaffolding is a common problem for many teachers.  We all want to help the struggling student succeed, but too often we make them incapable of succeeding without us.  If they always outsource their thinking, they’ll never develop their own skills.

To use analogies from other fields: overscaffolding is like showing the students only great literature and telling them about writing process, but never having them struggle through 5 to 10 drafts of a piece of writing, or teaching art by showing only cast bronzes and mosaics, but never having them do a sketch or sculpt in clay.  Showing or telling students how to do something is often necessary (students can’t be expected to guess non-obvious methods), but it needs to be followed by students doing things for themselves.

A lot of us put a lot of time into polishing our presentations so that the students see the cleanest, most elegant way of doing a proof or solving a problem, but never see the debugging and refinement process that creates such elegant results.  I’ve never been guilty of the over-polished lecture: I give my lectures as extemporaneous performances that are never the same twice.  For one course, I did not even prepare any lectures, but had the students give me problems from the homework that they wanted to see how to do, a process I called live-action math.  That approach required a thorough understanding of the material and a confidence that I could do any of the problems in front of an audience without prior prep.

Not all my classes are so extreme, but when I give examples I always try to make them examples of problem solving (as opposed to examples of solved problems).  In the circuits course last quarter I probably did about the right number of examples in class and got the students involved in solving them, but I did not give the students enough simple problems to practice on.  I was withdrawing the supports too quickly and trying to have them jump from the material in the reading (which they weren’t doing) directly to design problems. Next year I’ll assign some more routine exercises (though I’ve always hated the drill work) to help them build their skills.

So too many examples is not a big problem in my teaching style. The bigger teaching difficulty I have is in not doing debugging for the students.  In labs and programming courses I can find student problems much more quickly than they can, and I have to restrain myself from just pointing out the (to me) obvious problem. I can think of several times in the circuits lab last quarter when I glanced at a breadboard that students had asked for help with and just asked them “where’s the connection to ground for this component?” or “why are all these nodes shorted together?”  That was not quite the right approach—it got them unstuck and left them some of the debugging still to do (that is, it was better than just moving the wires around for them), but did not help them develop the skills needed to see the problem at a glance themselves.

Some other approaches, like “Show me your schematic—I can’t debug without a clear schematic of what you are trying to build,” were probably more effective—there were a couple of students who kept trying to build without a clear schematic and being unable to debug the resulting mess.  I probably walked away from them 3 or 4 times during the quarter, telling them I’d help once they had proper schematics to debug from.

It might be better for me to go through a checklist with the students—for example, having them check that each component has the right number of connections and check the breadboard against the schematic to see if the wiring is the same.  Occasionally I’d still have to step in to correct a misunderstanding (particularly at the beginning when some students don’t understand how the holes of the breadboard are connected together underneath and put components in sideways), but by stepping them through a process I think I could eventually get more of them debugging on their own.

After all, the point of the programming assignments and labs to teach students how to debug, not just to get them to produce working programs or circuits.  It is much harder to teach a student how to debug than to demonstrate debugging—I’m still working on better ways to do that.  I think that what I did in the circuits course worked for some students (they were debugging pretty independently by the end of the quarter), but others were still relying too much on help even at the end of the quarter.

A big chunk of learning how to teach is figuring out how to withdraw the initial support without students failing.  Suddenly yanking it out from under them will make many collapse, but being too slow to remove support will leave them still leaning on the crutch when they should be running on their own.

2010 October 14

Good questions

Filed under: Uncategorized — gasstationwithoutpumps @ 06:09
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I am on a lot of e-mail mailing lists (mainly for teachers, bioinformaticians, and protein researchers), and I like answering questions on the mailing lists, particularly where I have some expertise. But I also often do a fair amount of on-web research to find good answers.  A good question involves some preconditions:

  • The question is formulated as a specific, narrowly focused question, not a broad “tell me everything about proteins” request.
  • The question is appropriate for the forum where it is presented.  Off-topic questions are irritating.
  • The person asking has done some preliminary searching and tells us what was already found.

Questions of the form “A says X and B says Y—how can these approaches be reconciled?” are good, if both A and B are reasonable sources.  Questions of the form “A says X, but I thought Y—who’s right?” can be good also, if Y is at all a reasonable misunderstanding (or X is possibly wrong).  An example of a good question lately: on a mailing list for AP bio teachers (I’m not one, but I had a professional need to communicate with them, see Bioinformatics in high school biology), someone asked

We watched “Inner Life of the Cell” a few times during class last week.  I was pleased when a student asked “How do they know that’s how kinesin works?”

So, perhaps one of you knows how researchers model the function of motor proteins like kinesin?  Any other techniques that guide scientists to understanding these sub-cellular events?

This question is good because it is not trivially answered.  “How do they know” questions are often hard to answer, because most of the sites one can find only talk about the results of scientific work, and not the hard work of getting there.  I don’t know precisely how kinesin model was made, but I knew that dynamic models of  motor proteins are often created from snapshots of frozen states of the protein (usually using X-ray crystallography). I could point to Hongyun Wang’s work with F1 and Fo ATPase (including some nice videos).  I read the Wikipedia article on kinesin, which seems pretty good and has citations to real literature on the protein.

I also pointed the teacher to the Molecule of the Month article on kinesin, which has some explanations of how the structures in PDB were used to figure out how kinesin works.  The Molecule of the Month articles are a great resource and easy to find if you know to look for them (though, as usual, I was better off using Google than trying to fight the navigation system that RCSB provided for the PDB site).   [Actually, they have a decent navigation system as well as the broken one. I highly recommend the sort-by-category view of the Molecule of the Month site.]

Another person on the AP bio list, who had worked as a molecular biologist, described how GFP fusion was used to provide marked proteins that could be tracked by microscope to view motion within cells.  I think that both of us were pleased to share bits of our knowledge, though neither of us was an expert on kinesin.  This is the sort of question I like to answer: one where I can use some of my knowledge to find material or briefly explain something non-trivial, but where I learn a bit in the process of answering the question.

Questions of the form “Where can I find X?” are only good if X is particularly tricky to find.  (“Where can I find Inner Life of a Cell?” would not be a good question, as a trivial Google search finds the site at Harvard that has several good biology animations. Even if you don’t know the title, looking for “animation of a cell” finds a nice article about the creation of the video at, with links to the video.)  A lot of times, such questions are just someone too lazy (or stupid) to do their own searches.  For them, I’ve found a good site: Let me Google that for you (  I type in the obvious search, check that Google does indeed get the desired result in the first few hits, and reply with the short URL that does the search for them.  This answers their question (good even for lazy people), but makes it clear that they should have done it themselves and not wasted the time of hundreds of readers of the e-mail list.

The lmgtfy site would have been more useful to me a few years back, when lots of people thought it was easier to ask a hundred people on a mailing list rather than spend 30 seconds doing their own search.  I had to type up the searches and results (and be mildly sarcastic) manually many times.  Now that someone has automated the process for me, I find I don’t need it nearly as often. For most of the lists I’m on, people know how to do a trivial search and try it before making fools of themselves in public.  This means that “where is it?” questions tend to be more difficult,  requiring expert knowledge, access to subscription databases, or much better than average search skills.  Such questions are much more fun to answer, and asking for help from a large group of people makes sense.

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