Blog has moved!

Hello everyone.  I wanted to announce that the blog is going to be moving! I’ve been hosted here for quite some time, but eventually decided that it was most beneficial to combine the blog with my academic site.  Both things will now live on my homepage (www.johnrleeman.com).  All of the content and comments from this blog have been migrated across to the new wordpress platform.  Please move your RSS feeds and commenting over to the new location! This blog will remain online for awhile to allow links from other pages to be changed, but will no longer be updated.

Communicating Science: The Lost Art of the "Chalk Talk"

During this semester our lab group has been holding a weekly seminar in which everyone gets together to hear about the latest and greatest that other members of the group are doing.  In a group with multiple professors and many students it is easy to lose track of what is happening in the lab on a daily basis!  When organizing the meetings it was suggested that the presenter of each ~40-50 minute talk use only the chalk boards, no slides, no handouts.  While there was much grumbling from the group, I was rather excited at the idea of giving such a "naked" talk, and it turns of so was one of the great physicists: John Wheeler. Wheeler was famous for going into the lecture hall before his talk and covering the chalk-boards with very nice color diagrams, then walking through them.  Here I am going to discuss my attempt and giving a John Wheeler style talk, and why you should as well.

John Wheeler giving one of his famous talks with colorful hand-drawn illustrations.

For my talk, I was going to be discussing electrical phenomena surrounding earthquakes such as radio emissions and earthquake lights.  After some background I wanted to discuss some laboratory experiments I've done and propose a model to explain the data.  A few challenges were immediately apparent:

1) I can't show exact data plots or scatter plots with many hundreds of data-points.

2) Showing photographs isn't an option.

3) There is no room for all the content that would have been in a slide presentation.

Having just attended a workshop by Michael Alley on "The Craft of Scientific Presentation," many of these "challenges" resonated with things that presenters do, but shouldn't.  We often overload our audience with information: many words on a slide, complex plots, and us speaking fast to beat the buzzer.  We also depend on our slides to guide our talk instead of having the "story" and path well developed in our heads and just using the slides as visual aids.  Dr.Alley even mentioned that one of his favorite slides is the plain black slide, because then the focus is on the presenter and their words.  

In preparing the chalk-talk I thought about how to tell my story, wrote that down, then decided what visual aids would be helpful.  I drew a sketch of those aids by the notes I had just made and then began cutting many of them.  The drawings on my paper would have taken the chalkboards in the room times two! I didn't want to erase anything and draw in real-time for two reasons: it wasted time that we could be talking about science and it didn't let me draw intricate diagrams.  In the end I drew the final set of diagrams on a separate piece of paper and only had one word list in the introduction to help make a point about the diversity of natural observations.

The morning of the talk I went to the room about an hour before people would be arriving with two boxes of chalk (one plain white and one of many colors).  I spent the hour drawing the figures, erasing, drawing again, refining, removing, etc.  Drawing some data plots was difficult, but let me get away from the audience worrying about noise and other artifacts.  By being able to emphasize the important points in the data it made the plots less confusing for the audience.

The entire talk.  I walked around the boards and presented for about 50 minutes.

During the talk I just walked down the boards and talked through the points I had outlined without bulleted lists.  Doing so I noticed a few things:

- The audience eye-contact was just incredible.  Instead of looking at my slides and reading words, examining detailed plots, or other distractions there was a lot of focus on the topic matter.

- The style of the presentation was very relaxed and let me steer the talk dynamically.  Unlike slides that fix you into a path from the moment you click "Show Presentation," I could adjust the level on-the-fly as the audience showed interest or got lost.

- Making the diagrams made me notice things in my data when looking for ways to simplify it.

- Preparing for this talk I learned where gaps in my knowledge were because I refused to rely on pulling figures directly from a paper as we often do in making slides.

My attempt at summarizing about 20 minutes of talking points in diagrams alone.

Overall the talk was very well received and I got some great feedback on the research.  The biggest drawback was also one of the advantages: plots.  Though my simplified drawings made understanding easier for the audience, my drawing skills also caused some questions that were on "artifacts" in my art skills, not the data.  When drawing a time series, making sure things were precisely lined up was a bit tricky, but showing a real plot would probably introduce more confusion due to the complication.

Next time you have to give a talk to a small group in a classroom you should try a chalk-talk! They are simple and I think you'll be pleasantly surprised at both your own understanding and the reaction and engagement of the audience.  If you do, let me know how it goes!

Liquid Cooled Laptop Stand

This is going to be a short post that was requested during the LifeHacker "How I Work" feature.  In the post (here) I had mentioned my custom laptop stand that has an automotive transmission cooler and there was some interest in its construction.  Since moving I haven't hooked everything (fluid and such) up, so I did make any thermal profiles of the stand, but maybe at some point I'll attach some thermocouples and so just that.  Regardless, here are a few photos and some construction notes.

First off I should state the purpose and design requirements of the stand.  I wanted a stand to that the laptop monitor would line up nicely with my second monitor and wasn't made of books.  At the time I was running lots of rather intensive thermal models and gridding some large data sets, so that my laptop would be running very hot with the fans full blast for anywhere from 5-20 hours straight.  To keep it running a bit cooler I decided to build the stand of something thermally conductive, Aluminium was a good choice since that's what the laptop case is made of and it looks nice.  It's also not bad at conducting heat!

The stand was designed to hold the laptop screen at the same level as my second monitor and give a nice angle of viewing.

I bought some Al sheet a Lowe's, as well as a small strap of metal, and some "L" shaped material.  The channel makes the supports for the sheet and the runners on the desk.  I left them long incase I decide to mount the fluid tank and pump back there.  So far I haven't found a setup that is quiet and that fits in the space.  I will try again soon, but I've played with pumps and small aquarium tanks in the past.  

Using a sheet metal shear and brake I cut and bent the top plate to hold my laptop.  Be sure that the rubber feet on the bottom of the computer are off the stand, we want metal-metal contact for the best heat transfer!

So there were no screw heads to scratch my laptop, I used adhesive to mount the top plate to the frame.  The frame was assembled with nuts and bolts, then set on plastic feet to prevent scratches to the glass desktop.  

Next I made the stand match the computer a bit better by giving it a brushed Al finish instead of shiny metal.  A wire polishing wheel attached to the drill gave a nice, but time consuming finish to the entire stand.  

To further the cooling I wanted to mount a heat-sink to the bottom of the stand.  It so happened that I found a great solution at the automotive store that would allow for liquid cooling! A small generic automotive transmission cooler add-on kit (about $25 at the time) provides lots of surface area and a nice look.  The cooler is mounted with JB-weld and seems to get nice and warm when I'm working the laptop.  I'll probably inject some thermal grease to increase the coupling even more.

The transmission cooler on the bottom of the stand.

The surface where the computer sits.  

  This was a really fun little afternoon project and its not done yet! Eventually I'll run onto a tank/pump combo that I like and will fit onto the stand.  I'll mount it and use some colored water to give a nice effect when I'm cooling.  The easiest control mechanism is a small temperature sensor that turns the pump on and off as necessary to maintain a set-point.  When that happens, I'll be sure to post and update.  

To William (the commenter that requested some details of my stand): Sorry this took so long! The LifeHacker article went live not long before I took my candidacy exam! 

As always feel free to comment/email questions!

Quick Test of Geophone Response

I just wanted to post a quick article about geophones.  Geophones are essentially instruments that allow us to measure the velocity or acceleration of the ground.  Yes, seismometers do this, but generally when we refer to geophones we are talking about single sensor (almost always vertical sensing) devices used for seismic imaging in oil/gas exploration.  I've talked about seismic surveys before (here for example). The "element", or the actual sensor is pictured below.  These sensors have a magnetic element on a spring inside a coil of wire.  Motion of the magnet (resulting from ground motion) generates a small electrical potential in the coil.  If I can find a cheap element/case on eBay I'll do a teardown of one in the future.  The signal generation happens through a process called "electromagnetic induction", described by Michael Faraday in 1831!  Want to know more about induction? Head over to the wikipedia page or shout out and we can put together a demonstration.

Dr. Ammon, whose office is next door, brought over an old element that he wanted to compare with our seismometers in the basement of the building.  Not knowing the output voltage range well, we hooked it up to a Rigol DS1102E oscilloscope on my desk.  I set the trigger of the oscilloscope (when it started collecting data) to just above ground potential so that any appreciable motion will trigger data recording.  We recorded the voltage output of the sensor about 6800 times per second!

The sensor element from a geophone.  (Image: Ebay)

Below is the waveform collected from hitting my desk with moderate force.  Surprisingly these elements put out +/-4 Volts! When shaking the element to it's limits we were seeing voltages of around +/- 10 Volts.  To me this indicates there are many turns in the coil and a very strong, probably rare earth, magnet inside.  Measurement of the coil resistance or a teardown will tell if this is correct! I've also included the power spectral density for those of you interested.  These figures tell us about the frequency response of the instrument.  Depending on how the spring system is setup, the oscillator is very sensitive to some frequencies and not so sensitive to others.  These diagrams help us characterize this response.  

Collected waveform from hitting my desk.

Power Spectral Density

Power Spectral Density: Zoomed in

Sorry for the short post, but I just wanted to share a quick desktop experiment!

The Infrasound Bucket - Part 1 - Hardware

I'd like to write a short series of posts describing my setup of the infrasound unit I've written about before.  This is the same unit we used to look at traveling acoustic energy from the Russian meteorite and will soon use to examine earthquakes! Placing the unit inside my office or even inside the apartment proved to be very noisy as I saw every time someone opened or closed a door!  The makers (Infiltec) suggested that I put it outside, maybe in a drink cooler to shield it from the weather.  I did exactly that (photos below), but the cooler turned out to not be water proof and had about 2 cm water standing in the bottom when I checked it after a small storm.  The data quality while the instrument was outside was amazing though, with seismic signals coming through very clearly.  It was time to design a new system that would: 1) Be safe to leave outside in the weather, 2) Not have thick data cables running inside to a computer, 3) Would not require an inside computer, and 4) Would automatically post the current data online.


For the first post we're going to talk about the casing setup and mounting of all the vital hardware.  One weekend we decided to go wandering about Home Depot to find a suitable shell for the instrument as well as pickup a few other essential supplies.  Lendi had the flash of inspiration that we should use a 5-gallon plastic bucket... the ones at the Home Depot "Homer's All Purpose Bucket" even have an O-ring seal on the lid.  Perfect.

A built in O-ring seal on the bucket.

Now to figure out how to hold the hardware up off the bottom of the bucket.  In an ideal world this isn't needed, but in reality water may get in and I don't want it covering electronics thrown in the bottom of the bucket.  We used 1/4" plywood cut to a keystone shape that just fits the vertical profile of the bucket.  Adding two "L" brackets from the shelving section meant for ~$15 we had the shell and left over plywood.

Test fitting the plywood into the bucket.  Notice the cooler in the background that formerly housed the instrument.

I bolted the infrasound unit to the wood by using "plumber's tape" or metal strap with holes down its length.  This isn't the most elegant solution, but it meant no drilling the infrasound case which is semi-sealed on its own.  It is also very easy to get the unit out for any maintenance.   My RaspberryPi ended up having problems on the circuit board, so I've bolted a Beagle Bone Black to the board as well.

Front of the mounting board.  Infrasound unit (right), Beagle Bone (left), and power plugs (top left).

Rear of the mounting board with power passthrough.  

With no tall standoffs handy I made use of locking nuts, washers, and other assorted 4-40 hardware.

Two holes were drilled in the side of the bucket: one for the power and one for the air tube to the infrasound instrument.  I passed the power cable through (outdoor zip cord) through as well as clear plastic tubing and sealed it with bathroom silicon sealant.  I'd recommend sealing on the inside and outside of the bucket bulkhead.  Make sure to leave extra cable and tube for drip loops. A drip loop like structure was fashioned on the outside of the bucket to ensure no rain would blow up the tube into the unit.  We taped the tube down and then ran beads of silicon to secure it to the bucket.  After the sealant dried we moved the tape and secured the rest of the tubing.

Power and air tube sealed into the bucket and loops to prevent water flow.

Inside the bucket: notice the power plug.

In later posts we'll talk about how the power is actually provided and such, but the part that pertains to the hardware is the mounting of two binding posts on the plywood at the standard 3/4" spacing.  This allows us to power the board from a banana jack on the bench for testing or operationally in the bucket.  I drilled a passthrough hole to send power from the back of the jacks to the front of the panel.

Initially I built a 5V regulator to power the computer with from an LM7805 linear voltage regulator, but this was indeed a poor choice.  Even with a decent heat sink, the chip still got blistering hot when I was drawing 700mA (of the 1000mA rated power).  Considering this would be outside in the summer heat and the fact that I didn't want the failure point of a mechanical fan I decided to use a buck voltage converter.  Linear regulators dissipate all extra power as heat.  For example: I was feeding 12VDC to the converter with a 700mA load running at 5VDC.  That means that (12V-5V)*0.7 = 4.9 Watts of power was being turned into waste heat! No wonder, remember we think of watts as energy/time (Joules/second actually).  That's a lot of wasted electricity and really just a complication to our design, but it was very clean power.

The old linear regulator.  It's now awaiting a new use in the parts bin.

The buck converter is a switching type regulator.  I don't want to get into how switching regulators work current, but it's an interesting topic and you should have a read on the theory if you like.  I bought a small unit (P/N 1385) from Adafruit that is rated to 3A (though it gets warm there).  The power isn't quite as clean from this switching supply, but it's fine for out use here.  It works great with the Beagle Bone and provides lots of extra power for 5V accessories.  Don't want to order and ship from Adafruit? You can get the exact same thing from a model shop.  They are called "battery eliminator circuits" and allow modelers to plug their airplane, car, etc servo electronics (5VDC operation) into a 12V battery they already have in their kit.  Just clip the 3 pin servo plug off the end and you are ready to go.  Don't forget good soldering practice and to use heatshrink tube! Shorts could spark a fire, which we don't want.

The "battery eliminator circuit" or my 5V buck converter to supply 5VDC to the Beagle Bone.

So there it is! Next time I'm going to talk about setting up the power and network infrastructure.  Maybe even the serial communications! We're going to try to avoid using a serial-USB converter since the Bagle Bone has only one USB port (that I'm using for a WiFi adapter), I don't want to use a hub, and it's a chance to learn about signal level shifting and wire into that temping header on the board.

Everything fit into the bucket nicely and powers up from the bench power supply.

Texas Fertilizer Plant Explosion Shakes the Ground

Another quick post of some interesting data concerning the explosion at the fertilizer plant in Texas.  Yesterday (4/17/13) there was a large explosion at approximately 7:50 pm local time.  As of early this morning reports showed around 179 people hospitalized, 24 in critical condition, and 5-15 fatalities.  Currently 3-5 firefighters and one law enforcement officer are unaccounted for.  Over 60 homes were damaged by the very large blast.

The best video I've seen so far is attached below, the explosion happens around 30 seconds in.  Also below is the initial emergency services traffic.


 



Finally, we can look at data from the Amarillo seismic station (US.AMTX).  I've pulled down the data and filtered it to show all frequencies above 1Hz.  We expect the explosion to produce mostly high frequency signals and attenuate, or lose strength, quickly (why I didn't see the explosion on any other stations such as US.WMOK in Oklahoma).  It looks like there are 6 main pulses of energy (possibly tanks failing?) very quickly and the large explosion in a period of around 10 seconds.







If you want to look at the data yourself I've made the SAC file available here or you can download the data from IRIS and duplicate the filtering with the following OBSPy code:
from obspy.iris import Client from obspy import UTCDateTime client = Client() t = UTCDateTime("2013-04-18T00:52:00.000") st = client.getWaveform("US", "AMTX", "00", "BHZ", t, t + 2 * 60) tr = st[0] tr.filter('highpass',freq=1.) tr.plot()

EDIT: The USGS posted a transportable array station that was closer to the event (seismogram below) that shows both the fast ground waves and the slower air blast.  They classify this as a magnitude 2.1 event on the event page, but it's really a larger explosion than that hints at as magnitude is only based upon ground motion.

April 2013 Oklahoma Earthquakes

This morning Oklahoma experienced another small sequence of earthquakes.  (There was also a large earthquake with an estimated magnitude of 7.8 in Iran over night.)  While I'm preparing for a conference very soon I'm a bit crunched for time, but thought a short post would be in order.  I would like to write a few posts concerning what magnitude is, how we calculate it, and other common questions I get asked at some point in the near future.

Okay, here's the synopsis of the most recent events. Early this morning at 01:56:29.875 CDT a magnitude 4.7 earthquake occurred centered northeast of the Oklahoma City metro area.  There have been a few significant aftershocks at magnitude 3.0, 3.6, and 4.6.  It is notable that there was a higher number of seismic events (though all small) beginning yesterday.  All these numbers are from the Oklahoma Geological Survey, the USGS estimates are lower with the largest events at 4.3, 4.2, and 3.3.  These magnitudes are computed on slightly different scales, but either way the largest earthquake released over 10 times LESS energy than the earthquakes last year.

The USGS did you feel it program has already collected around 1600 responses and the shaking reported matches very well with what was expected, probably due to the DYFI scale being pretty accurately calibrated after the large earthquake sequence last year.  It was striking that the vast majority of the responses came within 90 minutes of the quakes indicating the people actually got up and reported as soon as the event was over.  These responses really help the folks at the national earthquake information center (NEIC) and if you felt the earthquake but didn't go fill one out you should!

The moment tensor solution of the earthquake shows a strike slip solution meaning that the rock moved laterally past each other, not up and down.  This is shown by the "beachball" below with the colored regions indicating areas of compression.  There isn't enough information from one earthquake alone to tell if the fault runs SW to NE or SE to NW, but based upon the distribution of the large aftershocks it would be an okay initial guess that the fault trends to the NW.  Also notice the solution isn't perfectly strike-slip.  There is a small amount of oblique motion with a thrusting sense.  

After inspecting the infrasound instrument I have in my office I didn't see the earthquake, but the ground motion wasn't really detectable on the seismic station in Standing Stone, PA either.  It looks like the infrasound may have recorded the Iran earthquake, but I need to move it to a less noisy location.

Just for fun I've thrown in a seismograph below from a station in the Wichita Mountains in SW Oklahoma.  It would be fun to calculate the different arrivals and plot, but that's more fun for another time! I've made the trimmed .SAC file is available here in case you want to download it and try.