The initial impressive feat from Baker’s group was that they designed an enzyme de novo using Rosetta design (this was reported in 2010).  The FoldIt addition was an 18-fold increase in activity, which came from targeted redesign (redesigning a loop to increase contact between the protein and one of the reactants, stabilizing the new loop, and so forth).  The FoldIt players were not not choosing the goals of the redesign (that was done by postdocs in Baker’s group), but they were exploring the protein space in ways that conventional optimization programs do not (such as adding 13 amino acids).

This is not the first success for FoldIt.  They had a Nature paper in 2010, which reported on the success of FoldIt players at predicting protein structure on a target that had eluded automatic methods for a few years.

So far as I know, FoldIt is the only computer game so far to have made any real advances in molecular engineering. (The main other contender, EteRNA, though fun to play, does not capture enough in its scoring function for EteRNA play to do anything very useful.)

Disclaimer: my former PhD student, Firas Khatib, was an author on both the FoldIt papers mentioned here, though he was not part of the original enzyme design team.

Rosie Redfield have openly posted data using better lab procedures that show no arsenic in the DNA. The latest post in the series addresses some incorrect assertions about Dr. Redfield’s protocols that appeared in the Nature News article Study challenges existence of arsenic-based life.

With this new data, the burden is clearly on Dr. Wolfe-Simon to either retract her paper or provide some more convincing evidence for her astonishing claim.  I am doubtful that Science will put any pressure on her to retract, since they have a long history of presenting sensational, but wrong, science papers.

Originally, we were going to an ADXL335 accelerometer (with a breakout board by Adafruit Industries) and an MPXHZ6250A pressure sensor (no magnetometer), for which I designed a small PC board, but once the specs for this year’s mission came out, we saw that they wanted us to determine compass headings for a “sunken ship”, so it seemed a natural thing to add a magnetometer to the hardware.  After looking at what was available, I chose the MAG3110 breakout board from Sparkfun, because it provided a triple-axis magnetometer for only $15.

The MAG3110 is an I²C interface, which means we need only 2 wires to hook it up (and the wires can be shared with other I²C devices).  If we are going to all the trouble of figuring out an I²C interface, I figured we might as well use it for the accelerometer as well, so I got a MMA8452Q breakout board from Sparkfun also.

I decided to do a simple test program for the I²C parts before handing them over to the robotics club, so that they could be sure they had working parts.  It was a good thing I did, because I spent more than an entire day trying to get the parts to work.  I finally gave up on the “Wire” library from the Arduino website, and tried using the i2c.h file from Sparkfun (example code linked to from the accelerometer web page).  I got that working and rewrote the library as a proper .h and .cpp file, so that it could be installed as a normal Arduino library, adding some of the utility calls that had been buried in the MMA8452 demo code.

The MMA8452Q code was working fine, so I tried using the same i2c library for the MAG3110 magnetometer.

I had gotten MAG3110 working with the Wire library, but running at 5v (I’d not noticed that it was a 3.3v part—rather, I thought I’d checked that it was a 5v part, but I was wrong).  I’d left it powered at 5v all night, and I think I burned it out, as it was quite warm in the morning.  Today, I can read and write the registers of the MAG3110, but the xyz values are not coming out reasonable at all—I frequently get the same values (like 0xF9F9)and 0x1DF9), independent of the orientation. If I read all the registers, a lot of them come out as 0xF9 or 0x1D.  Even the WHO_AM_I register (which should be 0xC4) often comes out 0x1D.  I seem to get intermittent correct values for registers, but mostly bogus values.

I’ll feel stupid if I order another part and it turns out to be a software bug, but I’m pretty sure the chip is fried.  But I guess it is time to do another Sparkfun order. (I owe them some business, after calling them for the replacement photointerrupter.)

Incidentally, I tried finding a usable pressure sensor with an I²C interface, but it doesn’t look like anyone is making them except for barometric pressure ranges for dry gases.  I suppose Freescale will eventually come out with a full range of I²C pressure sensors, but my guess is that will be a long time coming, as the automotive and industrial applications have a pretty long product design cycle (unlike consumer electronics, which is driving the barometric pressure sensors).

I think I owe Sparkfun a couple of bucks for that replacement, because I now no longer believe that the part was faulty.

The replacement part arrived yesterday, so this morning I unsoldered the part that I believed was faulty and put in the new one.  Getting the holes clear enough to insert the new part was a bit difficult with just a soldering iron and a solder sucker, but I eventually managed to do it.  Since I already had the good photogate set up for the physics lab, I did not get a chance to test the spare until after lab was over.  It didn’t work either!

Now, I’m willing to believe in one random part failing, but two in a row seemed unlikely.  That lead me to suspect problems with either the soldering or with the breakout board.I had already checked thoroughly for shorts (I always do that before powering up a board), and I knew there were none.

I had noticed when taking pictures of the photogate that the IR LED is clearly visible on the camera’s LCD display (strangely, it comes out looking blue, not red), so I looked at the IR diode through the camera—not lit up!  I double checked with the good part and it lit up very visibly.

I then checked the bad board for open circuits.  I quickly found that the resistor, which should be connected on one side to the ground plane was not connected to the ground pin of the header.  I re-examined all the solder joints, and one of the ones on the resistor looked a little bit less than perfect, so I reflowed the solder joints on the resistor.  Still nothing.

In desperation, I tried reflowing the solder joints on the header, although they all looked good.  Success!  It seems that the solder to the ground pad, though looking like a perfect connection, was not connecting. Now the second photogate is working just as well as the first, and I’m feeling very sheepish about having trusted visual inspection of a solder joint—I should know better than to do that.  I certainly should have done a better job of debugging before complaining to SparkFun, who were very nice about replacing the part, no questions asked.

So what can I do?  I feel I owe Sparkfun for the $1.95 part they sent me, but I’m not sure that the effort to get them the money wouldn’t cost them so much in labor costs for handling something unusual that they would lose money on my attempt to pay them.  About all I can do is encourage others to do business with them, since they seem to have real superb customer service.

If anyone does get Sparkfun’s photogate and breakout board, look at the easy Lego mounting I have in More on pendulums, which was easy to set up and worked very well. And check your solder joints carefully!

Fall

• How to be a grad student.  That’s not its official name, but that’s what its purpose is.  I created this course and have taught it (except for Fall 2011) ever since.  I’ll find out if anything new was added this year, but otherwise this course is pretty straightforward for me to teach.
• Bioinformatics: Models and Algorithms.  I’ve been teaching this forever also.  I definitely plan to talk to the person who taught it this year, as we may be alternating years from here on, and I’d like to incorporate any novel stuff he did.

Winter

no courses, but I’ll have to do some course design and prep work for Spring

Spring

• Introduction to Programming for Biologists and Biochemists. I’ve never taught this course—for that matter I’ve never taught any large introduction-to-programming course, so I’m definitely going to have to do some prep work.  I need to find out what has been taught in this class in the past, what pedagogical tricks are needed to get math-phobic biologists to program, what texts (paper or on-line) are available and suitable, and so forth.  I suspect a big chunk of my winter quarter will be prepping for my first lower-division course in over a decade.
• Senior Thesis Presentation. I assume that this course is an attempt to get the senior thesis students to write their theses and prepare poster and oral presentations.  It strikes me that the last quarter of senior year is far too late for this.  They needed to start writing their senior theses when they started doing the projects updating drafts as they go, but I doubt that even one in ten will come in with an outline, much less a draft. Half of them probably will not be able to reconstruct what they have done from their inadequate notes in their lab notebooks, since their research advisers never made them write anything up in any detail and never looked at their lab notebooks or taught them what to record. (Not all the research advisers are so unhelpful with their undergrads, but enough are to make this course be too little, too late.)
  I’ve done something like this before, but a quarter earlier in the year, when students were still working on their thesis research.  The work load for providing student feedback is incredibly high (practically a full-time job for just this one course), and I expect it to be worse this coming year.

There are no surprises for me in the official CLP—these are the courses that I had agreed to.  It is a higher than usual load, because the budget cuts meant we could not afford to hire instructors for some of the courses we usually use them for, and I volunteered to take on the intro programming course, so that we could continue to hire a lecturer for the popular Human Genome course.  It isn’t quite as high as the load I had last year, so I should survive it, but Spring will be rough.

Here is a table of the measurements (and calculated g) we made for the circular pendulum:

The range of estimates for g is larger than I would like.  I think that the decay of the oscillation of the pendulum makes quite a difference.  The average of all the estimates of g is 967 gm/sec^2, which is rather low.

And for the simple pendulum:

The pendulum ticked reliably for quite a while, and the periods were remarkably consistent.  The estimates of g from the simple pendulum are good to about 0.5%, which is the limitation of accuracy on our pendulum length measurements and close to the limit of the accuracy of the small-angle approximation.  The average of the 5 measurements looks good to about 0.2%, which seems pretty good to me, since we certainly weren’t measuring the lengths that accurately.

I looked up the gravitational field in Santa Cruz on Wolfram Alpha’s gravitational fields widget:

While the lab was running, one of the students wrote a Python script (using numpy for mean and standard deviation) to read the data and compute the numbers in the table.  We could have talked directly to the Arduino, but it was simpler to cut the numbers from the Arduino serial monitor and paste them into a file for the script to read. That allowed us to keep the Arduino running throughout, and just cut and paste the good numbers, discarding the junk from starting or stopping the pendulum.

I’m quite pleased with the photogate setup, which was very simple to build and worked reliably during the experiment. Crudely wrapping tape around the string made a lumpy opaque object, whose rotation probably contributed to the standard deviation of the  period—having a smoother cylinder for the optical blocker would probably make the period measurement much more consistent.  But that would not improve the mean estimates much since errors in adjacent period measurements cancel.  I believe that our mean periods are much more accurate than the standard deviations suggests, with errors less than 1 per thousand.

I had to make one change in the Arduino code during the lab to accommodate all the different pendulum lengths—I had a dead time before recognizing the next pulse, to prevent getting 2 pulses per period as the string passed through the beam twice.  I started with a dead time of 1 second, which as a bit too long for the smallest pendulum.  Reducing the dead time to 500 msec for that pendulum made it count reliably.  Note that for the 2nd and 3rd pendulum, we measured for about 3 minutes without a bad time measurement, and could have gone longer if we had had the patience.

Thanks to John Burk for suggesting that I forget about the motor—that seems to be the best approach, even though I then can’t use the photogate to time the period.  I’m hopeful that we can measure the height and the period accurately enough to get within about 2% of the right value for .

This week in addition to doing the circular pendulum right, I wanted to do simple pendulums.  I’ve assigned problem 4.P.89 in Matter and Interactions, which seems to be the only place in the book that simple pendulums are done.  It is a computational problem, since there isn’t an analytic solution (though the small-angle approximation works pretty well up to about 45°).  I hope the students have done that by tomorrow!

I wanted to measure the period of the pendulum directly (not averaging over many periods), to demonstrate that the amplitude does not matter much.  Unfortunately, I’ve not yet built a sensor that works for this. I tried using the photogate, but I could not hit the 1 cm gap consistently, even with a shorter pendulum.

I also tried using a magnetic sensor (using the circuit I used for the speed-of-sound lab) with a magnet for the pendulum weight, but that triggered at random times as the magnet came close.  Even 20cm away the field was enough to trigger the detector, and I got almost random timings.  A magnetometer was no better than the coil and comparator, as the magnetic field varied chaotically (from movements of the magnet other than the simple pendulum swing, such as twirling on the string).  The magnetometer was usable as a compass, though, which is good, because I originally bought it for the robotics club to use as a compass.  There are some tricky points to using it as a compass, which I’ll talk about in a different post.

I then tried marking the top of the string with a bit of electrical tape and using the photogate there.  That was the most successful so far—if I hold the photogate steady enough, I can get readings repeatable to ±20msec, which is much better than I can do with any other approach I’ve tried.  For one pendulum hanging from the edge of my desk, I either got  two pulses at about 1.11 and 0.45 seconds or one pulse every 1.56 seconds, depending on whether the marker on the string passes all the way through the beam or blocks it continuously at the end of the swing. The random variation I get is probably because of holding the sensor by hand (to align with the string).

If I had a more rigid way to mount the sensor, I should be able get more consistent readings, so my main engineering task was to get a rigid pivot point on the ceiling beam (without making any holes) and mount the photogate in a rigid, but adjustable, way.  Of my two standard mechanical engineering techniques, duct tape and Lego, I chose Lego:

A view of the photogate mounted on the Lego beam next to the pendulum string.

Closeup of the photogate, showing the breakout board and sensor wedged between a plate and a beam, with a 2-plate spacer.

Having come up with a nice way to grip the photogate and still be able to swing a pendulum string into the gap, I connected the beam holding the photogate to the same right-angle platform that we had used last week for the motorized pendulum. This left a little gap that I could rest the Arduino board in, so that there was no tension on the wires to the photogate.

I was a bit worried that I might have to put my laptop on top of a ladder, since the USB cord is not very long, but I have a spare pair of USB-to-Cat5 converters (one set is for the robotics project), so I was able to make an extension cord out of a flexible Cat-5 Ethernet cable, giving me enough length to put my laptop safely on the desk.

The same Lego that holds the photogate can also support the Arduino, so I don't need to hold anything in my hands.

I had two other ideas I haven’t tried: using one of the ultrasonic range finders to track the pendulum motion and using a video camera to time the motion.  These require interpolation of position data to estimate the period, so I’d rather avoid them for now. The top-of-string photogate will work (I think) for the simple pendulum, and the circular pendulum can be timed with a stopwatch averaged over many periods.  (I could even use the photogate timer as a stopwatch, though the resolution of the stop watch on my Casio wristwatch is 0.01 seconds, and human reflexes make anything less than 0.1 second pretty much noise.)

The “virtual tour” is not a tour so far as I can tell, but heavy Street View coverage of the campus.  The coverage of UCSC campus is adequate, including major roads and the bike paths, but not including many of service roads and footpaths that a real tour would cover.  It would be good for Google to hire a student to walk a number of the paths (particularly some of the single-track trails in the woods, which are not properly mapped) with a geotagging street-view camera, to capture the campus more thoroughly.

I think that Mr. Zimmer may have been fooled.  The process described in the article, of yeast cells clumping together is known as flocculation and it a natural property of yeast that evolved (most likely) millions of years ago.  It has been well studied as it is critically important for beer brewers (even Wikipedia has an article  on yeast flocculation). Standard lab strains often have a disabling mutation in one of the flocculation genes (for instance, strain S288C has a mutation in FLO8), since lab strains have been selected for non-flocculation. Some of these mutations are frame shifts and  it is generally very easy to restore flocculation to yeast by having a compensating mutation that restores the correct reading frame to the disabled gene.

Of course, Mr. Zimmer may have left out some crucial information from the paper. The article itself is

William C. Ratcliff, R. Ford Denison, Mark Borrello,  and Michael Travisano
Experimental evolution of multicellularity
PNAS 2012 ; published ahead of print January 17, 2012, doi:10.1073/pnas.1115323109

and is open-access, so anyone can read it.

The authors claim that their “snowflake” phenotype differs from the flocs of flocculent strains of yeast:

During this time each cell was seen to give rise to a new snowflake-type cluster, whereas aggregation was never seen, demonstrating that clusters arise via post-division adhesion and not by aggregation of previously separate cells [as would be the case for flocs].

They also distinguished their phenotype from another way yeast cells are known to cluster:

The snowflake clusters are distinct from S. cerevisiae pseudohyphal phenotypes, which have filamentous elongate cells and arise under conditions of nutrient stress. Clustering in snowflake-phenotype yeast is independent of pseudohyphal growth, as the snowflake phenotype is stable under both high- and low-nutrient conditions. Individual cells within clusters retain the ancestral ability to form pseudohyphae when starved, but remain oval (not elongate) during standard culture conditions

So they do seem to have observed a new phenotype for yeast, but it is it a new evolution (as they claim) or simply a new observation of something that evolved a long time ago? They do “evolution” but do not then look to see what has changed in the genome—probably because they know that they have just turned on a pre-existing gene and don’t want to spoil their fantasy of “evolving multicellularity”.

I’d need a lot more data to show that multicellularity had evolved within 60 days, as they claim.  It is so much more likely that they turned on a pre-existing pathway that is not normally on in the yeast strains people study.  If I had been refereeing this paper, I would have made them tone down their claims for having evolved something new—given that all replications resulted in the same phenotype, it was almost certainly a pre-existing possibility in the genome.  (I fault PNAS, which has such a crummy refereeing process that I refuse to referee for them.)

Disclaimer: I’m not a yeast biologist.  If the “snowflake” phenotype really is a new evolution, I’d like to hear about it from someone who is an expert on yeast, and what the evidence is that it is really newly evolved.

If students can do a complex task, that really only means that they can do that one problem, no matter how much understanding is applied. If they can’t, it’s very difficult to find the gap or problem in understanding. It reminds me of unit testing versus system testing in programing. Testing doesn’t start at the “authentic” system level. You might define tests that work, but you will never properly exercise the code.

For any complex system, you have to validate the parts before you put them together to test and validate the whole. For education, you have to validate that students have mastered basic skills before letting them loose on complex “authentic” or real world problems.

This analogy seemed pretty reasonable at first, so I thought about how in interacts with my own assessment methods.  I’m usually dealing with students at a fairly advanced level, and there is no way that I could assess them on all the basic skills they are supposed to have acquired over the preceding 16 years of their education.  The new skills I want them to develop are layered on top of the writing, math, biology, and programming skills and knowledge they are supposed to already have.  I can test some of the new skills incrementally (and I do to some extent, having usually 6 programs of gradually increasing difficulty, plus a couple of papers), but most of the problems I uncover tend to be underlying problems in their previous training.

I disagree with him that evaluating a complex task results in only one bit of information (they can or can’t do it).  The complex task produces a complex output that can be debugged—though not always easily. So my teaching and assessment is often more like debugging someone else’s poorly tested and undocumented library.  I can’t write unit tests for everything in the library—I can’t even figure out what is in the library, but I can look for errors in the output and try to trace them back to their sources. That is why it takes me forever to grade programs or papers—I’m not doing a pass/no-pass assessment, but attempting to debug the underlying thought processes of the person. Like all debugging tasks, it is difficult and the first guess at the problem is usually wrong.

I would love it if the students I taught had all been excellently educated and I knew precisely what their skills were (like tested and documented libraries).  But that is a fantasy world.  Every one of my students comes in with a different skill set, often with great strengths in some areas and unexpected holes in others. Part of my job is to try to identify some of those holes and point them out to the students, so that they can patch them up. Another part is to help them build new capabilities on top of what they already have.

One commenter, Derek Bruff, summarized the pro-flipped-classroom position well:

As Eric Mazur often points out, in the traditional model, the “transfer” of information happens during class and the “assimilation” of that information—the much harder step—happens after class when students are on their own. Why not move the harder step to class time, during which the instructor and other students are around to help?

In the inverted classroom, it’s still important that students spend time outside of class doing work (and that can be problematic for the reasons you point out in your blog post), but the hardest work happens during class when the teacher is around to help.

[Derek is responding to a comment by Ira Socol which pointed to several blog posts. I think the one he means is Changing Gears 2012: rejecting the "flip" .]

I’ve been thinking about that pedagogical assumption: that assimilation of information works best if it happens during class when the teacher is around to help.  I can’t decide if I really believe it.

Certainly my deepest understanding of material has come when I’ve worked with it extensively on my own—writing programs, doing mathematical derivations, writing papers, … .  Having other people around when I’m doing this just makes it harder to focus, and does not aid in the assimilation.

But initial entry into the material is aided by having a guide who can quickly point me to productive lines of thought, so that I don’t flail around on trivia.  Some forms of learning are definitely helped by having interaction with the teacher as the practice is done (physical training like martial arts, dance, and sports seem to particularly benefit from supervised practice).

My son is taking an online calculus class that meets in a chat room once a week.  That time is spent doing a lecture with students asking questions for clarification, and he often refers back to the lecture transcript (an advantage of the chat-room format is that you get a full transcript, which is much easier to search than a video) rather than to the book for clarification of methods. Even my son, who is a diligent, top student, rarely reads the calculus book before class (or afterwards for that matter—he seems to get most of his information from the chat-room lecture, though I think that the book they are using is one of the best I’ve seen for top students).

But most of the learning takes place when he does the problem sets, not in the class.  There is an opportunity for the students to interact on the homework: there is a forum where the students can publish their solutions, ask one another for help, or read other students’ solutions (there is a social convention of hiding the solutions so that it requires an extra click to get them, so that no one looking at the forum is forced to see solutions before they want to).  My son posts solutions to all the problems, and I believe that there is some social status associated with doing so, though no explicit recognition from the instructors.  Still, the learning is not happening on the forum—it is happening when the problems are solved, with the forums providing an incentive for doing the individual work. The forums do also provide for communication with the instructor—particularly for clarification of confusing points in the homework problems or lectures.

Just this last week, we experimented with another approach: he and I each took a small (2′ × 3′) whiteboard and simultaneously worked independently on the same problem.  I sometimes had to ask him about what they had covered in class, as I’ve not done integration for 30 years  and have forgotten some of the techniques. I admit that I struggled a bit with , though I eventually came up with a simpler solution than my son did, by “cheating” and using .  Integration by parts was always the least fun part of calculus for me. When we both finished a problem, we compared solutions, and then each looked for algebra errors if we got different results.  This provided more social interaction than working alone on a problem and the slightly competitive nature of trying to finish quicker with a more accurate answer resulted in the homework problems being done faster.

I think that this sort of synchronized but mostly independent work can be a good way to combine the individual effort needed for learning with some social incentives for doing it, as long as the problems are small enough ones and the people working on them are working at about the same pace.  (I’m rusty enough on my calculus that I’m at about the same pace as my son who is just learning it.)  I can’t see it working in a classroom, where students are likely to have a 5-fold different range of the pace at which they work—the faster students will be bored to tears and the slower students will be left behind.  I also don’t see it working in classes involving bigger problems (like programming projects that take >10 hours to do).

My son has developed a very different way of working on his science-fair project, which involves talking with me or his postdoc mentor at the university about the problem he is working on, then going and spending hours coding and testing.  He learns little bits from books, from Wikipedia, and from conversations (like what a decision tree is, or feature selection, or how to calculate entropy), but it is the hours of coding and testing by himself that really makes the ideas his.  He needs the contact with others to talk through points where he gets stuck, though often all he needs is a sympathetic ear and not guidance by an instructor.  The need for interaction is hard to schedule, though, as it does not come a fixed intervals—sometimes he needs to be left alone for days to write his programs, other times he wants to check on ideas every half hour.  This is one advantage of home schooling or (for the fantastically rich) a live-in tutor: learning on demand, without the tyranny of a class schedule.

I’ve often wondered whether the desirability of the flipped classroom is in extravert/introvert thing: as an introvert, I find working in a group that is trying to interact as they work extremely draining.  So much effort for so little accomplished! The traditional lecture classroom is much more suited for introverts, as there are only occasional social interactions required, and they are more like performances than like ordinary social interactions, and so are less stressful. (I know, extraverts can’t imagine performance being less stressful than ordinary social interaction, but introverted actors and professors may understand.) I think I might not have made it through college and grad school if my classes had all been “flipped classrooms” that relied on having “instructors and students around to help”.

I thought about using some of my sabbatical to record mini-lectures on various topics to experiment with a “flipped classroom” next year, but I doubt now that I’ll do it.  My lectures are extemporaneous performances that would be very hard to do without the interaction with a live audience, and I’m not convinced that flipping would really help learning any—the students are still going to have to spend many hours outside class struggling with their programs, and having to watch videos as well just reduces the time they have for the programming.

A much more eloquent article on the subject by Susan Cain was just published in the NY Times: The Rise of the New Groupthink.

There are nice sound bites like

But decades of research show that individuals almost always perform better than groups in both quality and quantity, and group performance gets worse as group size increases.

She does suggest that on-line brainstorming may work better than in-person brainstorming, quoting Proust’s description of reading as a “miracle of communication in the midst of solitude”.  Her prescription for effective teamwork seems reasonable to me:

To harness the energy that fuels both these drives, we need to move beyond the New Groupthink and embrace a more nuanced approach to creativity and learning. Our offices should encourage casual, cafe-style interactions, but allow people to disappear into personalized, private spaces when they want to be alone. Our schools should teach children to work with others, but also to work on their own for sustained periods of time. And we must recognize that introverts like Steve Wozniak need extra quiet and privacy to do their best work.

I certainly have found that my best collaborative work has come out of fairly incidental contacts (meeting someone from another department in a hallway, chatting after a research seminar, talking with a student in someone else’s research group), followed by days or weeks of intensive work on the problem.

My sabbatical this year has been going through fertile and dead periods.  The dead periods have been times when I was not getting any contact with students and colleagues, and was not getting anything done.  The fertile periods were intense bursts of activity by myself after a chance contact with someone sparked an interest in a particular problem.

Most recently, I’ve been working on putting together a bioinformatics protocol that will let us reconstruct the cagY genes from hundreds of strains of Helicobacter pylori using PacBio sequencing.  Most of the sequencing technologies are not suitable for this gene, as it has long blocks of many repeats that vary from strain to strain.  Because the tandem replication is very recent (divergence between the strains may be only a few generations earlier) and there is selective pressure to maintain the open reading frame, the different repeats are often identical for long stretches, making short-read data nearly impossible to assemble. Even Sanger sequencing to confirm the gene assembly is difficult, as it is hard to find unique primer locations.

I started this project as a result of a short discussion with a couple of H. pylori researchers, but I spent weeks writing programs and Makefiles, testing them, twiddling parameters to see if they were robust, and so on.  I could not have done the work without the collaboration (I needed someone who had a difficult, interesting problem and the data to work on), but I could not have done the work if someone had kept interrupting me or making suggestions either.  The project would probably have died halfway through if I had had to do it with my usual teaching load, as I was spending 12–16 hours a day on it for weeks.

I need to alternate between working alone and contact with others. Sometimes talking through a problem with someone who understands and can ask good questions helps me clarify my thinking, after which I need hours or days to work out the details, after which I want to share again.

At some of the Bay Area’s most competitive public and private high schools, teachers and counselors have started pushing for a cap on the number of Advanced Placement courses a student can take.

The problem she outlined is clear: many students are taking so many AP classes that they have no time for anything else.

Why? A lot of colleges (including University of California) give a bonus point on grades for honors and AP courses, and with grade inflation causing most grades now to be As, there is no way to distinguish good students from mediocre ones except by how challenging their courses are.  She mentions that last year the average GPA of accepted freshmen at UCLA was 4.34, but the official UCLA freshman profile for 2011 says 4.11 (UCB is higher at 4.14, and no UC is close to 4.34).

For a student to get a 4.14 GPA with a typical high-school load of 24–28 classes, they must get straight As and take at least 4 honors courses (or get an occasional lower grade but take even more honors classes to compensate).

AP classes are intended to be college-equivalent classes taken in high school. When the program was started it was used for small numbers of students who needed more challenge than the high schools normally provided (about 40 students in my high school class of around 600 were taking AP-level courses, and that was an unusually academic school).  Now, with everyone who wants to get into a name-brand college taking AP courses, they have gotten watered down to the point where they are roughly the equivalent of the standard “college track” courses of 40 years ago, and more and more colleges are refusing to give credit for passing the AP exam.

The workload in the courses is often large, because teachers remember how many hours of homework they had in college and think that they should assign the same amount in high school, forgetting that college students have fewer classes at once and spend many fewer hours in class.  So the workload (class+homework) of AP classes is often much larger than for the corresponding college classes, but the quality is highly variable (some are much better than corresponding college classes, some are much worse).

What is a student or parent to do?  Taking no AP or honors courses generally makes the student look like they are not interested in academics, so even those colleges that don’t give bonus points for AP courses are likely to downgrade the student somewhat.  Taking huge numbers of AP courses gives no room for students to pursue their passions, and often indicates an education heavy on memorization and cramming for tests, rather than deep understanding.

Probably the most reasonable course is for students to take AP courses (and exams!) in those subjects that most interest them and pursue interests outside the AP classroom.  Community college courses that go beyond the AP courses are also a cost-effective choice, if you can get in.

For students interested in STEM majors, I recommend taking AP calculus (at least AB, and BC if it is offered), AP Physics B (or C, though that is rare for high schools to offer), AP statistics, and AP chemistry.  Those interested in bio or health careers could take AP Bio, but at the moment it is too much work for too little reward—a non-AP bio course may cover less material but get students to end up understanding more.  (That may get fixed in the next couple of years as teacher adapt to the new AP Bio curriculum and reduce the “memorize a million factoids” approach.)  In addition to the core AP courses, only one or two others should be taken, based on student strengths (a foreign language, English, art, or history, for example).  More important for a STEM student is to do research projects and enter them in county (and state and international, if possible) science fairs, or to join robotics clubs and do engineering projects.

I don’t know what advice to give humanities students—I guess the corresponding advice would be to enter essay contests, write for local literary magazines, do book reviews for the student paper, send history articles to Concord Review, and so forth.  Intensive immersion programs in foreign languages might also look good.

Showing independent interest in a subject by doing it outside of courses is more impressive than getting an extra point for the GPA by taking an AP class.

Schools, however, should not ration the AP courses, as they have not shown great ability in the past in being able to determine who can and who can’t benefit from the courses.  It is far better to let students and parents choose, as long as students meet the prerequisites for the courses (so the courses don’t get further watered down).  The schools should not be pushing everyone into AP courses (as some schools seem to be doing), but neither should they be holding back kids who want to take them.

I’d be a lot faster if I did not make so many mistakes and have to keep back-spacing. I actually had a typing class in high-school, back in the days when you had to hit the keys pretty hard and slipping off a key could mean getting your finger caught between the keys. My first typewriter was an extremely heavy manual “portable” with an 11″ carriage (so you could put paper in sideways). Its keys were so stiff that I could not operate them with my little fingers, so I quickly lost the typing technique taught in class and created my own style which used only three fingers on each hand, plus the right thumb for spaces. I was trying to observe what I do now, and it seems that I use all the fingers of the left hand, and only two on the right, plus the right thumb. Of course when I’m trying to be aware of my fingers, the usage of them changes, but I think I use the little finger of the left hand only for shifting.

The motor for the circular pendulum mounted on a ceiling beam, with a short string attached.

In Chapter 5 of Matter and Interactions, the authors describe an experiment that Newton did to measure , the gravitational field at the surface of the Earth.  The idea is a simple one: have a pendulum moving in a circle.  The size of the circle is a function of the length of the pendulum, the speed of rotation, and . So I thought it would be fun to do an experiment along those lines in physics lab today.

The first step was to make a circular pendulum that could be driven to move at a constant speed.  My idea here was to build something out of Lego, so that we could adjust the speed as needed with pulleys and belts. My son and I built such a device early in the week and put it up on one of the ceiling beams in the room where we do our physics labs.  I put it up that high so that we could have a long string for the pendulum that would be easy to measure.  I had not done any calculations, just guessed that the bead on the string would fly out as we spun the shaft.

We had quite a surprise when we tried it out with a fast-spinning motor (about  9Hz or 540rpm) and a 2m long string.  The bead hung straight below the motor, but the string bowed out in several places, forming a nice pattern of nodes and antinodes. Changing the speed of the motor changed the number of nodes and antinodes. That is where I stopped the pre-lab preparation—the rest of the lab was done with the students.

The first thing we did was rederive the formulas the motion of the mass at the end of the pendulum, using the new whiteboards I had made for the class.  The whiteboards cost under $8 each for 2 2′×3′ boards—the lumberyard sells dry-erase hardboard for $1 a square foot (less if you buy a full sheet, but that was too hard to get home on my bike), plus $1 for the cutting.  The rest was the cost of the duct tape for the edge and taxes.

The cone formed by the string can be described as having height , base radius , and hypotenuse , the length of the string.  The idea was to measure , , and the period of the pendulum , and from these try to calculate .

One of the new whiteboards.

We neglected air resistance (probably not a good idea) and so had just two forces acting on the mass: the gravitational attraction to the Earth and the diagonal pull from the string with magnitude . We can get the horizontal and vertical components of the force exerted by the string: . The vertical component must match the force due to the Earth as the mass is not moving vertically, so , or . The magnitude of horizontal component is .

The horizontal component is what is accelerating the mass around the circle.  We rederived the formula for that by describing the position of the mass in the complex plane and taking the derivative twice: .  One of the students was very comfortable with this, the other (who had ostensibly had more calculus), had never seen .  I gave a very brief mention of doing it with sines and cosines, but did not take the time to do the derivation in those terms.  Note that the magnitude of the force is and it is directed towards the center of the circle, as we would expect.  The angular frequency is just the speed in radians per second, so .

Combining the two formulas for the horizontal force, we get .  We can simplify this to .  If we don’t want to measure ,we can use Pythagoras’s Theorem to get . After demonstrating the unexpected behavior of the long string, I challenged the students to compute from the known value of .

To do the calculation we needed the period . In preparation for this, I had bought a “photo interrupter” from Sparkfun and a breakout board to mount it. (Actually, I ordered 2, which was a good thing, since one of them did not work—Sparkfun is sending me a replacement).

Photo interrupter with a 1cm gap between the infrared LED and the detector.

I hooked up the photo interrupter to my Arduino microprocessor, which I programmed to measure the time between falling edges of pulses (with a 20msec minimum pulse width). By letting the Lego beam on the motor pass through the gap, I could get pretty consistent measurements of the period. Because the beam is not quite centered, I believe I was getting just one end to pass through the gap. I could have made the measurement easier by having a piece of opaque tape sticking out the end of the beam to pass through the gap. I believe that the period as the motor was initially set up was 119 msec. The students computed that this should result in lifting the mass by 3.5 mm, which is a bit small to measure at the end of a 2m string!

Photo interrupter hooked up to an Arduino microprocessor, connected in turn to a laptop.

Pendulum on desk with short string.

The next step was to have the students compute a period that would involve a decent value for , say 20 cm. They computed it to be about 0.9 seconds, which was easily arranged by changing the pulleys on the motor and shaft. We then shortened the string to about 30 cm, and put the motor on the desk. I forget exactly what the period turned out to be: something close to 910 msec, I believe. We did not take careful notes, because we were still playing around with the setup when it was time to end the class (one student’s mother came to fetch him, another had to go off to improv class, and I had a meeting with 4 grad students and an AP bio teacher about a bioinformatics lesson the students are going to do for his classes in 2 weeks).

Why were we still fussing around? Well, when we turned on the motor the pendulum mass did indeed move out into a big circle, but it didn’t stay there! Instead the circle slowly shrank until the bead was hanging almost straight down, then grew again to a big circle, then shrank again, and so on. This was the second, even less anticipated result from the lab. I still don’t have a good explanation for it. Am I getting some sort of beating between the natural period of the pendulum and the forced rotation? I think I’ll have to play around with the setup this weekend to see the effect of different variations. Some things I plan to play with include

• using a heavy weight for the mass, instead of a tiny one.  Originally, I had thought the I would need to allow the mass to pass through the gap in the photo interrupter, and I didn’t want to risk damaging it. But now I see that I can measure the period using the beam, so the mass can be larger.
• adjusting the length of the string, to change the natural period of the pendulum.
• adjusting the speed of rotation.  It would be nice to have a real slow rotation, so that I could do a decent measurement with a long string.

Question for the physics people who read my blog: have any of you done the circular pendulum experiment in class?  Are there some things I should have known about to make this work better? Do you have an explanation for why I got such a varying amplitude in the size of the circle with the short pendulum? Will the long string with a fairly fast motor always produce nice nodes and antinodes, or did I get lucky on the two speeds I tried?

The idea is simple: students acquire enormous debt in the hopes of getting a better life, but they are required to labor for many years to repay that debt.  The main differences from indentured servitude are that the debt-holder doesn’t guarantee the existence of a job that will repay the debt, the student loan period lasts much longer than indentured servitude did, and indentured servitude is now illegal.

I wonder how many people will sign up for Code Year, and how many will make it through the year.

I’m curious about the pedagogy of the Codecademy lessons, but not curious enough to sit through the slow pace of interactive lessons on stuff I either already know or am not interested in learning.  I’d be interested to hear reactions from anyone who is in the intended audience (that is, complete novices at programming who want to learn JavaScript).

Intellectual Merit has always been clear to grant writers and grant reviewers (though they often disagree about the merits of any particular proposal).  “Broader Impacts” has always been rather murky with different grant writers and grant reviewers interpreting it in incompatible ways.  It has also been very difficult to evaluate whether “Broader Impacts” have been achieved by a funded project.

To try to clarify things, NSF just approved a report titled National Science Foundation’s Merit Review Criteria: Review and Revisions December 14, 2011, subject to final edits.  Unfortunately, they have not put the report on their own web site yet, so I had to get a copy from scienceinsider.  After reading the report (the body, not the hundreds of pages of appendices), I’m at least as confused as I was before about what the h*** NSF expects for Broader Impacts.

It seems that the guidance they offer is pretty much limited to one page:

Merit Review Criteria

When evaluating NSF proposals, reviewers should consider what the proposers want to do, why they want to do it, how they plan to do it, how they will know if they succeed, and what benefits would accrue if the project is successful. These issues apply both to the technical aspects of the proposal and the way in which the project may make broader contributions. To that end, reviewers are asked to evaluate all proposals against two criteria:

Intellectual Merit: The intellectual Merit criterion encompasses the potential to advance knowledge; and
Broader Impacts: The Broader Impacts criterion encompasses the potential to benefit society and contribute to the achievement of specific, desired societal outcomes.

The following elements should be considered in the review for both criteria:

1. What is the potential for the proposed activity to
   a. advance knowledge and understanding within its own field or across different fields (Intellectual Merit); and
   b. benefit society or advance desired societal outcomes (Broader Impacts)?
2. To what extent do the proposed activities suggest and explore creative, original, or potentially transformative concepts?
3. Is the plan for carrying out the proposed activities well-reasoned, well-organized, and based on a sound rationale? Does the plan incorporate a mechanism to assess success?
4. How well qualified is the individual, team, or institution to conduct the proposed activities?
5. Are there adequate resources available to the PI (either at the home institution or through collaborations) to carry out the proposed activities?

They deliberately avoided further clarity:

Because of the great breadth and diversity of research and education activities that are supported by NSF, the Board has decided not to recommend a specific set of activities related to Broader Impacts, just as it would not recommend particular types of research–those decisions are best left to the PIs to describe and to the NSF to evaluate, for relevance to programmatic priorities and alignment with NSF’s core strategies for achieving its mission, as described in the NSF Strategic Plan for FY 2011- 2016 “Empowering the Nation Through Discovery and Innovation:”

• Be a leader in envisioning the future of science and engineering.
• Integrate research and education and build capacity.
• Broaden participation in the science and engineering research and education enterprises.
• Learn through assessment and evaluation of NSF programs, processes, and outcomes.

So grant writers and reviewers are left with nothing more specific than “benefit society or advance desired societal outcomes”. Different people will have very different ideas about what societal outcomes are “desired”, and Broader Impacts will continue to be used as a blunt instrument to reject intellectually worthy proposals based on the whims of reviewers.  If there were a list of “desired societal outcomes” then it might be possible to compare proposals, but without such a list, politics, religion, and random taste prevail.

More likely, there is a secret list of what NSF really wants for broader impacts, which is supposed to be “understood” without ever being stated.  So far as I can tell, NSF has just said “read our minds, we’re going to judge whether you address our goals without ever telling you what those goals are”. When this is combined with NSF’s new policy of funding bunches of stuff without external review, it becomes absolutely critical that there be clarity on what the goals are.

I hate guessing games like this.

Related articles

• NSF Tweaks Its Merit Review Rules (news.sciencemag.org)
• NSF takes broad look at broader impacts (blogs.nature.com)
• NSF Broader Impacts Broadened (writedit.wordpress.com)
• New NSF program without peer review (gasstationwithoutpumps.wordpress.com)
• New NSF Program Sidesteps External Peer Review (news.sciencemag.org)

The International Society for Computational Biology has sent e-mail to all its members:

As many of you may be aware, the U.S. House of Representatives has recently been presented with a bill called the Research Works Act (HR 3699) that threatens the current U.S. requirements of public access to federally funded research results. ISCB strongly opposes this bill. Burkhard Rost, ISCB President, and Richard Lathrop, ISCB Public Affairs & Policies Committee Chair, are drafting a letter to the bill’s authors that expresses our opposition and emphasizes the importance of the ISCB Public Policy Statement on Open Access to Scientific and Technical Research Literature that was released in 2010. If you are a member of ISCB and have not yet signed on to our statement, you are invited to do so at your earliest opportunity via the link to current signatories from the above URL.

I’m glad to see that the ISCB is taking action.  It would be valuable for people to write letters to their congressional representatives.  Those who are members of professional societies should write letters to the president or board of the society asking them to take action.

Of course, some professional societies behave more like publishing houses than like member-serving societies, and may be perfectly happy getting back the right to keep all taxpayer-paid research behind a paywall.  Has anyone gotten ACM or IEEE to recognize the importance of open access to scientific literature?

Note: the NIH rule does not prevent publishers from making money selling articles, as the articles don’t become open access until a year after publication, and the user interface for getting access to the publications is rather awkward.  Several journals had already adopted an “open after a year” policy before the NIH ruling took effect.

The article offers 13 alternative assignments for the usual “book report” or “literary analysis” assignment (which I have ranted about before in posts like Death to high school English and Reluctant Writers).  I don’t know that we will use any of them exactly, but they did help spur some thinking about some of the assignments my son has done for his “Alternative Realities” English class so far this year:

• description of the caste system in Brave New World
• sociolinguistic analysis of NewSpeak in 1984
• extra chapter for Alice in Wonderland, describing her adventures in a land that looks a lot like Minecraft
• map of Gethen, the world (or part of the world) in Left Hand of Darkness
• travel guide for Arde, the world in Planiverse

He has not been having the huge problems with writer’s block that he had last year.  I think that being able to craft his own style of response to each book (in consultation with his mother, who is choosing the books, discussing them with him, and giving him feedback on his drafts) has helped a lot in allowing him to keep moving on the assignments.  His consultant teacher has indicated that he needs to do six assignments each semester to get full credit for an English class, and he seems to be on track for that.  We’re thinking of a dramatic reading (with sound effects) for the 6th project.

He’s been doing writing in his other classes also.  His time-line for history class requires a lot of one-paragraph summaries, he’s done one lab report for physics (I should require a couple more), and he has been doing fairly detailed write-ups for his calculus homework sets (the Art of Problem Solving faculty provide feedback on the writing, so his math writing has improved enormously since he started precalculus with them last year). His science fair and robotics projects have not generated much writing yet, but he’s been keeping notes in his science-fair lab notebook and has a draft of the general introduction to his science fair project, so I’m hopeful that he’ll produce a decent report this year without too much prodding.  (His previous science fair reports are good, but took a lot prodding to get him to complete.)

Overall, I think that the writing he has done this year has been good for him and has not been much different in quantity than if he had been in school.  He’s felt less pressured about it, because each writing project has been one he has chosen, or at least agreed is a necessary component of something he has chosen.  We’ll see whether he can do the writing needed for the Shakespeare class he is taking this spring (in preparation for a trip to Ashland), or whether the prompts there turn out to be too inflexible for him.

Joss Ives, on The Science Learnification blog had a nice post on this today, Learning Before Class Strategies – Quick Update, which included pointers to  other blog posts and articles by various people about pre-reading.

Unfortunately, the data from Joss’s own class do not show any correlation between completing “pre-lecture and checkpoint assignments” and the final exam scores.  It is not clear whether this means that the pre-reading was not effective, or whether the scoring on the pre-class assignments was measuring the wrong thing.  It was an effort measure, but it may well be that the students were just going through the motions of doing the pre-reading, and not actually engaging with the material.

Or maybe students were only reading the material once, in which case it may not matter much whether it is before or after the class in which the material is “covered”.

My own experience trying to learn physics this fall with my son is that I learn very little from reading the book—I have to work several exercises to get the ideas firmly into my head.  The book (Matter and Interactions) has several places where the reader is supposed to stop and think about an example, but I rarely find myself doing so.  Only when I’m working a problem “for real” do I actually think in much detail about the models and formulas.  Sometimes the formulas stick in my head without much effort, but other times not (I particularly have problems with arbitrary constants like ).

So perhaps the secret is not pre-reading, but discussing homework problems after students have struggled with them a bit.  That is the approach our home-schooling class is taking, where we spend our 2 hours a week either comparing solutions to homework problems (and clarifying any confusion brought up by the problems) or doing a lab.  I find the lab classes more fun, though they take more prep time, as I have to design and build or buy whatever equipment we need.  I just got a pair of “photo interrupters” from Sparkfun, together with breakout boards that I hope we’ll use next week for timing the period of a circular pendulum to do Newton’s measurement of .

Comparing solutions has turned out to be useful, even when we have all made the same mistake, because we talk through the method and compare intermediate results as well as the final result. On one mass and spring exercise in Chapter 4, I noticed that we had all left out the force due to gravity, which happened to matter for that exercise.  We re-worked the exercise in class, and got a slightly different solution.

TaxpayerAccess has started a letter-writing campaign opposing this bill, and scientists who value the NIH open-access policy may want to add a letter of their own to this.

There is a good explanation of the advantages in scientific education to having open-access literature, especially for community colleges, on the Discovering Biology in a Digital World blog: Raising the barriers: restricting access to scientific literature will hurt STEM education.

The International Society for Computational Biology has an official policy supporting such open-access policies for funding (see my post ISCB open access policies and the official policy statement).  Perhaps the President of the ISCB needs to write a letter in opposition to HR 3699.

I want to start discussing Chapter 5 tomorrow (2012 Jan 6) and have homework due next week 2012 Jan 13.  I’d also like to do a lab next week: perhaps estimating g from measurements of circular pendulum.  We should be able to set up a circular pendulum with a lego motor on one of the ceiling beams and have a nice long pendulum so that we can measure length of the string, radius of the circle, and period of the circle.  My son and I will work on building the Lego contraption so that we can get different speeds.  He also suggested that we use two weights (on equal length strings) so that we can keep the motor balanced. With any luck, the optical gate I ordered from Sparkfun should have arrived by then so that we can do very precise timing of the period.

Homework due Friday 2012 Jan 13:

5P14, 5P16, 5P19, 5P46, 5P52(this is the lab we’ll do together), 5P54, 5P56, 5P59, 5P65, 5P67.

Here’s an excerpt:

The concert hall at the Sydney Opera House holds 2,700 people. This blog was viewed about 58,000 times in 2011. If it were a concert at Sydney Opera House, it would take about 21 sold-out performances for that many people to see it.

Click here to see the complete report.

I offered to help her choose a new system and looked at several, including Follett, Koha, Greenstone, and a few others.  Initially, I was drawn to the open-source solutions (Koha and Greenstone), but her school does not have any IT staff, and installing and maintaining a big package would be too much effort for too little reward.  It would also be difficult to provide on-line access from her library through the school firewall. We decided that a cloud-based solution, with someone else doing all the software maintenance, would be the best solution, if we could find a cheap enough one.

Although there are several companies providing cloud-based service using the open-source packages, they are generally marketing to much larger libraries (colleges, universities, and public libraries), and their fees were too high for a tiny library.

LibraryWorld, the cloud-based solution we chose for a small school library.

We finally settled on a cloud-based system using proprietary software: LibraryWorld.  They offer a flat fee of $395/year (less that the annual license fee for the antique version of the Follett software), and appear to provide all the features she needs, including providing on-line (even phone) access to the catalog for students and parents, e-mail of overdue notices, and adequate cataloging capabilities (though it would be good to have more databases to search for matching records, as the Library of Congress rarely catalogs book club editions, which the school library gets a lot of, and LC is very slow during the day).

One nice feature is that LibraryWorld gives a 30-day free trial, so we could try uploading the MARC records and patron records from her current system and see whether everything works as claimed.  There does not seem to be any way to transfer current circulation records, which would make LibraryWorld almost impossible for a large library to transfer to, but there are usually not more than a few dozen books checked out from this tiny library, so reentering the circulation information from a report would only take a few minutes. LibraryWorld also does not seem to support RFID tags in books, only bar codes, but her library couldn’t afford the $1/book cost of RFID tags anyway.

We did a trial transfer into a temporary account, and there don’t seem to be any problems with either the catalog data or the patron information.  Although the MARC record format is an ancient one, it is very well standardized, and so library catalog records are very easy to port from one system to another.  The OPAC (Online Patron Access Catalog) seems fairly well designed for school use, with different levels of sophistication for the youngest students, the middle schoolers, and the teachers.   We don’t have a cellphone, so have not been able to investigate the mobile access to the catalog.

I think that early next week we’ll probably transfer the library over to LibraryWorld for real.  Once that happens, one of the first things my wife will do is get rid of the antique Windows98 computer and replace it with something smaller, faster, and easier to use—probably a Mac mini.  Then she’ll get more shelving for the library, so she can start cataloging the books she has stored under our dining-room table (she has no storage at the library, and all her shelves there are full).  Those purchases and the LibraryWorld annual fee will probably eat up most of what she made from the book fair this year, but the library will be much better as a result.

Coil (about 0.5H) with refrigerator magnet on top. Magnet is stuck to the core of the coil just by its own magnetism.

I used a setup inspired by the one in the Chapter 4 Lecture 3 video at http://courses.ncsu.edu/py581/common/podcasts/.  That is, a long metal bar tapped with a metal striker at one end.  A clock is started when the tap is made (a simple electrical connection), and stopped when the wave is detected at the other end.  As mentioned in my earlier post More on the slinky and the speed of sound, I used an electromagnet and a small refrigerator magnet to detect the sound wave.  The coil has a  68.3 Ω resistance and a laminated iron or steel core, and I estimated the inductance at about 0.5 Henry (the estimate  may easily be off by a factor of 2—I should measure it better some day when it matters). When I rested a piece of aluminum bar stock on the magnet and tapped the other end, I got a signal of about 0.3 v, which I could see clearly on my oscilloscope.  (Note: the analog view of the signal was not done in the lab with the students, because we were pressed for time and moving the analog oscilloscope out to the room worked in and setting it up would have taken too long.)

The signal is not large enough to be measured by a digital input on the Arduino that we used for timing, and the Arduino analog-to-digital converter (accessed with analogRead()) is a very slow one, that would limit our time resolution to about 100 µsec, rather than 4 µsec as we can get with the “micros()” function call. I happened to have an LM311 comparator chip from about 30 years ago, so I made a comparator circuit to convert the analog signal to a clean digital signal.

Comparator circuit used to convert the small electrical signal induced in the coil to digital levels for input to the Arduino. The pair of 15kΩ resistors serve as a voltage divider to set the bias voltage for the inputs to about 2.5 volts, in the middle of the range. The output pull-up resistor provides a load for the comparator. The two capacitors filter out high frequency signals picked up by the coil—they were not part of the circuit provided in the LM311 datasheet, but turned out to be essential.

I did have to modify the circuit a little from the one for a magnetic pickup given in the data sheet, as the output remained high with that circuit.  Adding small capacitors to the input and output seemed to fix things.  I arbitrarily used 47000pF capacitors, because I happened to have several of them, but I also experimented with some other sizes (560 000 pF and 1000pF) which did not work.  One effect of the capacitor on the input is to make a resonant circuit that rings with a period of about 800 µsec (eyeballed from the oscilloscope trace), which would make the inductance of the coil about 0.34H.  This ringing has a couple of consequences: 1) if the magnet is the wrong way around, the polarity of the impulse is reversed and the comparator will detect the impulse half a cycle later, adding about 400 µsec to the reading, and 2) the signal ramps up slowly in response to an impulse, and the delay in the comparator circuit is dependent on the magnitude of the input signal.  This will add noise to the timing measurements.

Because the magnet we used had residues of paper and glue on one side, it was easy to check that it was oriented correctly.  For one set of measurements, the coil and magnet had to be moved, and the magnet may have been upside down for that set of measurements, resulting in a different offset for those measurements.

To keep the noise from differences in amplitude to a minimum, we took several measurements (generally 10 or 20) of each time, discarding obviously bogus numbers (like 8 µsec when the comparator had already detected something before the strike, or > 10 msec, when an impulse had been missed).

On the Arduino, the following program was used measure times.  Pin 2 of the Arduino was connected with a long wire to a metal striker, with the object being struck connected to Arduino’s GND with another wire.  Contact between the two metal objects pulled pin 2 down (overpowering the 20kΩ pull-up in the Arduino), recording the time in start_1. As soon as the comparator detects the sound, pin 3 is pulled down, and the time is recorded on stop_1.  The resolution of the timer is about 4 µsec, but the repeatability of the times varied more, depending in part on how consistently the strikes were made (one of us appeared to have much more consistent technique than the others, and the times from his strikes had lower spread—we did not record who did the strikes on our data log, and so we can’t quantify this observation).

void setup()
{
  //  put a 20k pullup resistor on pin 3 (sound detector)
  pinMode(3,INPUT);
  digitalWrite(3, HIGH);
  //  put a 20k pullup resistor on pin 2 (striker)
  pinMode(2,INPUT);
  digitalWrite(2, HIGH);

  Serial.begin(115200);
}

void loop()
{
  Serial.println("Ready");

  // wait for pin 2 to go low (contact with striker)
  while (digitalRead(2)>0) {}
  long start_1=micros();

  // wait for pin 3 to go low (sound detected)
  while (digitalRead(3)>0){}
  long stop_1=micros();
  long diff = stop_1-start_1;
  if (diff > 10000)
  {   Serial.print(F("rejecting large delay: "));
  }
  Serial.print(diff);
  Serial.println(F(" microseconds"));
  delay(200);  // wait 200 msec

  // wait some more if the striker still in contact
  while (digitalRead(2)==0) {}

}

The vertical rod is the one being measured. The sensor is on the floor and the rod is struck at the top end. The breadboard has the comparator circuit connected to the Arduino, which in turn is connected to a laptop (not in the photo).

The setup for most measurements was simple: the coil was put on the floor with the magnet resting on top. A rod was held vertically on top of the magnet and struck at the far end with another rod. Initially, we used a small screwdriver as the striker, but this turned out to be hard to hold, and so we switched to using a foot-long piece of ¼” steel rod, which was also used for some of the timing tests.

Because the delay in the comparator is unknown, but likely to be substantial compared to the time of flight, we tried to measure the same material at different lengths, and do a straight-line fit of the data to estimate the offset. By doing many measurements at each length, we could average out a lot of the noise. We could also see how well the data fitted a model that assumed that the time delay for the sound arriving would be proportional to length—that is, does the speed-of-sound model make sense for this data?

The simplest set of data was for 3 rods ¼” in diameter, made of hot-rolled weldable steel (that’s all the information about the material that the hardware store had on the tag). I’ve put the data in a page on the blog: Steel rod speed of sound lab data.

We also measured one aluminum bar (Aluminum bar speed of sound lab data), one long copper tube (Copper tube speed of sound lab data), and two wood dowels (Wood speed of sound lab data).  Because wood is not conductive, we added a washer on the striking end of the dowel, to provide a conductive contact. The copper tube was about 3m (10′) long and very soft, so we laid it on the floor and duct-taped the sensor to one end.

Perhaps the most interesting data set comes from an aluminum ladder (Aluminum ladder speed of sound lab data).  We removed one foot from the ladder and duct-taped and bungey-corded the sensor to the bottom of the ladder.  We then struck the ladder inside the hollow rungs, providing a nicely spaced series of different ten different lengths.  Because of the difficulty in getting the duct tape to stick to the ladder, the magnet fell off and was replaced a few times in setting up the sensor.  The final orientation was not checked, but I believe that it was backwards, so that the delays of the sensor were substantially larger for the ladder than for the other measurements.  Luckily, there are enough different lengths that we can get a very good linear fit even with a large offset.

I did a fit for the steel-rod data using the following gnuplot script:

unset key

set title "Time of flight for compression wave in 1/4\" hot-rolled steel rod"
set xlabel "length (meters)"
set ylabel "time (seconds)"

set xrange [0:*]
set yrange [0:*]

fit a*x+c 'steel-rod.txt' using (0.01*$1):(1e-6*$2) via a,c

print "velocity=", 1/a, "m/s"

plot a*x+c, 'steel-rod.txt' using (0.01*($1+2*rand(0))):(1e-6*$2)

which produced an estimate of 5292 m/s for the speed of sound in the steel rod. I was noticing on the web that the speed of sound in thin rods may be a bit different from the speed of a planar wave in bulk steel, so I’m not sure what the “right” value is for this measurement, but it sure seems reasonably close to reported values around 5000–6000 m/s.  I also get from the same fit an estimate of the delay in the sensor and comparator of 33.7 µsec, which I can use for the aluminum bar and copper tube data. How does the fit look?  See for yourself:

The linear model seems like a pretty good fit for the data on the steel rod, but the scatter on the data is a little high. Note: small random jitter was added to the x values, in order to spread the points out.

If I remove outliers (the two largest and two smallest measurements from each length), I get a tighter fit (naturally), but one with is also likely to be more accurate, as outliers have a large influence in linear regression:

After eliminating the outliers, the estimated speed of sound is 5267 m/s and the sensor delay is 31 µsec.

Using a similar script, but with a fixed 31 µsec offset, for the aluminum bar data and the copper tube data (again eliminating the two largest and two smallest measurements), we get 4412 m/sec for the aluminum bar and 3857 m/s for the copper tube. (Of course, we don’t have anywhere near 4 significant figures, so I should probably round these to 4400 m/s for aluminum and 3900 m/s for copper.)

The ladder data used essentially the same script as the steel-rod, but even after censoring the data had a pretty wide spread:

The ladder data, after removing the two largest and two smallest times at each data point, got an estimated speed of sound in aluminum of 3955 m/s. The offset was 256.6 µsec, confirming that the magnet had been reversed. (It also implies that one period of the ringing is about 450 µsec, which is shorter than the period I thought I saw on the oscilloscope.)

If I fit the data from the wood dowel using the 31 µsec offset, the line does not fit the data at all well. If I fit with a 2-parameter model, I get an offset of 162.6 µsec (between the ones for the steel rod data and the ladder data), and a velocity of 6150 m/s, which is unusually high for wood. It is a very light wood, so perhaps the number is reasonable, but I’d be more comfortable if we had had more different lengths to test. The difference in the delay introduced by the sensor suggests to me that I should have used multiple lengths for each of the materials, despite the inconvenience (I only had one piece of aluminum bar and did not want to cut it—similarly, I did not want to cut the copper tube.)

Comparing our speeds with typical speeds from engineeringtoolbox.com:

The best match is for the copper, with our aluminum alloys having a much lower speed of sound than typical for pure aluminum (does our alloy have higher mass? lower stiffness?), and our wood dowel having a much higher speed of sound than typical for wood. The steel rod was a little low, but within the range of reported speeds of sound in steel.

This report took me several hours to write, in part because producing the graphics took a while, and in part because I fussed around a lot with seeing if removing outliers from the data helped get better results.  My son produced a substantially similar lab report, with graphs but no pictures or schematic of the comparator, in 2–3 hours.  He did not play with removing outliers.  He also correctly reported the velocities with only 2 significant figures (in cm/µsec).