Friday, January 16, 2015

Teaching Computers to Predict (1/11/2015)

Last Sunday we presented the first of the current series of four Born To Do Science programs a the Stillwater Public Library. My guest was Allan Axelrod, who studies machine learning. 

Allan has developed an algorithm (or set of computer instructions) he calls EIEIO, which helps computers get clever about how they collect and analyze data in situations where numbers are collected continuously, but the entire set cannot be seen at once.

The situation that brought about the need for this algorithm is this: How do we monitor carbon sequestration sites for potentially dangerous leaks of CO2 back into the atmosphere?

We began with a song inspired by Allan's whimsical EIEIO acronym.

Introducing the topic with a song.

We had some discussion about whether carbon sequestration (storing waste carbon dioxide under ground) is a good idea in the first place. I know it's a controversial topic! But we needed to put a pin in that, in order to get to Allan's algorithm. Given that CO2 is already being sequestered under ground, it's good that people like Allan are coming up with ways to monitor it!

We set up a game to mimic the situation Allan has to deal with. There are monitoring stations on the ground spread over a large and hard-to-get-to area of land. Each one takes CO2 measurements every hour. The computer can use this information to model the system and attempts to predict leaks before they occur.

The problem is that all the current CO2 data is not available instantly. Drones are used to fly by each station and pick up the data. The question is - should the drones visit every station once, then every station again, etc.? Or is there a more useful way of gathering the data?

One of our sampling stations "collecting" data.

For the game, we set up seven sampling stations around the room. Two volunteers became drones, and two others were the computer. The computer sent drones from station to station collecting data. The computer then tried to make good decisions about where to send them next based on the numbers collected.

(If you're wondering - I created a set of measurements for each station ahead of time. The station-masters flipped through a stack of cards slowly, one every ten seconds. Each card they put down represented taking a measurement. At each station, the drones collected all the measurements taken since the last visit.)

The object of the game was to find a leak (if the numbers went high enough, they turned red on the page representing a leak) as quickly as possible.

A "drone" picks up data from a sampling station.

The "computer" analyzes data, trying to decide where to send the drones next.


The kids tried a couple of basic strategies. One was to send drones randomly to different stations and hope to find the leak. Another was to notice if the numbers were going up from a given station and send drones back there, or to a nearby station. It was challenging to process all those numbers during the game. But sending drones to a station where the numbers were rising is very similar to Allan's actual strategy!

If I'd had the chance to test the game out first, I would have changed a few things about how we did it to make it easier and clearer for the kids to think about strategy. But we did successfully get a handle on the basics of how the station, drones, and computers work together in real life.

Allan answers questions.

Allan's strategy with the EIEIO algorithm is to compare data collected from each station to the numbers the computer would have predicted. A "metric" - a measure of how close the numbers are to the predicted value - is calculated for each station. The stations that are the farthest off get the next drone visits.

This way the computer can collect the numbers it most needs next at any given time.

Allan has tried several versions of his algorithm on several sample data sets and compared the results of his EIEIO strategy to the strategy of sending drones methodically or randomly to all the stations every time. His EIEIO results are much better!

Taking info on Allan's computer class at the library.
Allan teaches a computer class on designing videos and video games at the Stillwater Public Library.

Looks like I forgot something but I can't remember what.
Can I get witness for science!
Sunday January 25 - Particle physics with Dr. Flera Rizatdinova! We've found the Higgs Boson, so what's next for the ATLAS detector at CERN?

Friday, March 28, 2014

Loser Lizards and Motherly Winners (March 23, 2014)

Our most recent program was on the Sunday after Spring Break. In hindsight, not the best date for a program! We had two kids show up, and their parents. So, a small group, but we had a great time anyway, and asked lots of good questions.

In preparation for this program I visited my guest, Jess Magaña, at the OSU Zoology Department where she does her research. I took some pretty good photos of lizards in their cages...

Brown anole lizards in their cages at the OSU Zoology Department

Jess holding one of her subjects.

This is just one section of one wall of the lizard room!

I kicked the program off with a new song, "My Lizard Brain," which is basically about how mysterious it is the way we humans make decisions, and maybe that it has a lot to do with the way other animals make decisions, since we've retained a lot of ancient circuitry in our brains through the process of evolution. I expressed all that in the form of a love song, which my wife, Lisa, finds intriguing - it's the second lizard love song I've written. I don't know if that's a coincidence or a "thing." Maybe a lizard love CD is in the works.
I kicked us off with a brand new song.
Jess's research was inspired by thinking about how lizards make decisions about allocating their energy. In particular, how does a female lizard decide (and we use the word "decide" loosely here, since it probably isn't a conscious decision being made) how much energy to put into making eggs and babies? I asked everyone to think like a lizard and allocate some energy to various lizard activities such as finding food, defending territory, and reproduction.

Giving some thought to how much energy a lizard should allocate to various lizard activities such as finding food, defending territory, and reproduction.

Collecting data from our imaginary lizards.
Just like in real life, we got lots of different answers for our imaginary lizards. We talked about different kinds of things that might effect a lizard's choices. The thing that Jess was most interested in is what's called "the experience effect." Lots of animals' behaviors are known to be effected by things they've experienced in the past. Jess wanted to know whether a female lizard would put more or less energy into her eggs and offspring according to whether she has won or lost fights for territory in the past.

Answering questions.
To find out, she paired female lizards in conflict situations by putting one lizard into another's territory. After ten minutes she removed the interloping lizard, effectively making it the loser. Then she followed the winners and losers over time to see how they did with their eggs and offspring.

During our program tried putting two males together in a cage, so we could observe some of the aggressive behaviors. We saw the lizards move toward one another and bob their heads. We didn't see them display their dewlaps, though, as they often will.

Lizard fight! We introduced the light brown lizard on the right into the cage to see if the darker lizard on the left would defend his territory.

The lighter lizard made aggressive moves up the stick.

The darker lizard finally turned to face the interloper. They never got too energetic about the confrontation, though. Maybe they felt too cold or too "on display" for an energetic fight.

Jess found in her study that the lizards who lost territorial fights put less energy into their offspring and more energy into their own upkeep. Those who had won the fights gained less weight and hatched heavier babies. Moreover, the effect was increased with the number of fights. The heaviest babies came from the lizards who had won two or three fights instead of just one.

One of our attendees suggested that the lizards who win fights can get the best territory with the most food, and therefore it makes sense that they would spawn larger offspring. That's probably true of lizards in the wild.

However, Jess went to a lot of trouble to make sure the lizards in her study got the same amount of food, and lived in very similar "territories." The only difference between the winning group and the losing group was that the winning group won their fight and the losing group lost theirs. I think it's really interesting that just losing a fight or two triggers the lizard to put less energy into her eggs.

Next time we'll be delving into the teeny tiny world of proteins and trying to figure out how those micro-machines that run our bodies do what they do! 

April 13, 2:00 at the library. I hope to see you then!!

Saturday, March 22, 2014

Imperiled Bats of Tar Creek (March 9, 2014)

Whew, it's been a while, but we did it - another Born to Do Science program for the books!

My guests were Dr. Karen McBee and her student, Rachel Eguren, whose study we talked about.

Rachel, who did the bat study, Karen, her advisor, Monty (me) the host, Elizabeth the children's librarian

I performed a brand new song based on Rachel's research. She wanted to find out whether the bats at the Tar Creek superfund site are affected by toxins in the area. She had to come up with a really clever way to answer that question, since you can't just ask a bat how it's feeling. The song, "Figure It Out" takes the form of a few journal entries where the researcher is trying to feel her way through the process. Scientists don't get to follow directions in a lab book - they're figuring out how to do things as they go!

Me singing a brand new song, "Figure It Out," inspired by Rachel's research project. 

What Rachel ended up doing is flying bats through an obstacle course made of strings that would drop when hit by a bat's wing. She charted the time each bat spent in the air against the number of strings dropped. As you would expect, for the control group (bats from a healthy habitat), the longer the bats flew the more strings they knocked down. However the Tar Creek bats showed almost no such correlation!

To get us in the question asking mood, we ran the kids through their own obstacle course, made from sections of carpet tubes. In hindsight, we should have placed the tubes closer together, or maybe had the kids stick their elbows out like bat wings, because even when we spun them with their eyes closed to simulate bats whose brains are addled with lead, hardly a tube got knocked over. Rachel had more time than we did to design her obstacle course. She made sure the strings were placed so that the bats could get through without knocking strings, but it was a challenging for them.


We timed each kid's run through the obstacle course, just like Rachel did with the bats.

After our activity we discussed lots of details about Rachel's study, including how she video taped the bats using a night-vision (infra-red) camera. She needed a marker in the bat cage to show depth so she could tell on the video whether the bats were flying through the obstacles. The marker had to be warm, to show up on camera, it had to stay warm for a long time, it couldn't require an electric outlet since she did her trials outdoors where the bats live, and it had to be relatively inexpensive. See the photo caption to find out what she used...

Karen passing around a "hot hands" - this is what Rachel used as a marker in her night vision (infra-red) video.

Rachel is still compiling results from the lab so she can correlate each bat's performance in the obstacle course with the levels of toxins found in their body tissues. But judging from the bats' performance in the obstacle course, the is definitely something different going on with the Tar Creek bats. The heavy metals in the area, including lead, may be affecting the bats' brain function, which could interfere with their ability to maneuver. This would make it more difficult for them to hunt at night.

The heavy metals in the soil and water around Tar Creek were left there by mining operations started over 100 years ago. In 2009 the town of Pitcher was completely evacuated due to the toxins. Dr. McBee and her students are studying many different aspects of how wildlife in the Tar Creek area has been affected.

Bats from the OSU Zoology Department collection.

Looking through the night vision camera!

Bat skeleton.

Thanks to Rachel, Karen, and the Stillwater Public Library for making this program possible, and for support from the National Science Foundation.

See you next time for "Loser Lizards and Motherly Winners!"

Thursday, February 20, 2014

Lizards Protons, Bats, and Ions, Oh My!!

New Programs are On the Calendar!

March 9, 2014
Imperiled Bats of Tar Creek
With Dr. Karen McBee and Rachel Eguren, OSU Zoology Department
Are toxins knocking these critters off course?
The Tar Creek superfund site in Northeast Oklahoma is one of the most toxic areas in the United States. How is the wildlife coping? Dr. McBee and her students shoot night vision video of bats flying obstacle courses to help find out!

March 23, 2014
Loser Lizards and Motherly Winners
With Jess Magaña, OSU Zoology Department
Can losing a fight make you less of a mother?
Mother reptiles have only so much energy. How do their bodies decide how much to invest in their offspring? Can winning or losing a fight make a difference for future babies? Jess Magaña finds out by pitting female against female!

April 13, 2014
Probing Proteins’ Secret Tricks
With Drs. Wouter Hoff and Aihua Xie, OSU Microbiology & Physics Departments

Infrared spectroscopy gives us the clues!
Proteins that can move protons from here to there enable our sight and power our cells, but how do they do it? Nobody knows! Drs. Hoff and Xie use infrared spectroscopy to peek at the inner workings of these mysterious biological nano-machines!

April 27, 2014
Battling Bacterial Biofilms
With Dr. Marianna Patrauchan, OSU Microbiology Department
Decoding chemical conversations could save lives!
Pseudomonas aeruginosa is a common bacterium, usually harmless to humans. But in the lungs of people with Cystic Fibrosis, it forms a deadly biofilm. Why? How? Dr. Patrauchan uses a variety of approaches to help figure it out!

Can you help spread the word by printing this flyer and sharing with friends? Thanks!

More details are here: click the schedule tab.

Friday, September 13, 2013

Digesting Sunshine - How Mother Nature Turns Light Into Chemical Energy

Howdy, Science Fans!

I've been on hiatus from BTDS, but I'm back, and gearing up for some new programs soon. More about that later. First order of business - the last few programs in 2012 never got write-ups, so I'm posting them now!


In February 2012 our speaker was Dr. Rob Burnap from the Department of Microbiology at OSU. Dr. Burnap is trying to work out a very important and very difficult puzzle - how exactly do plants accomplish photosynthesis?

Photosynthesis is that trick we all know plants like to do. They turn carbon dioxide, water and sunshine into oxygen (good for us!) and chemical energy that they use to grow.

This is an important trick to understand. Part of the process involves splitting water molecules into hydrogen and oxygen. If we knew how to do that as efficiently as plants, we'd have have our energy problems solved! That's because the reverse process, putting oxygen and hydrogen together to form water, releases a lot of energy quickly.

We CAN split water using a process called electrolysis. Dr. Burnap brought a special electrolysis set-up that allowed us to see (using a ph indicator that changed colors) how it works. We connected electrodes to a battery, put them in the water, and watched the bubbles of hydrogen forming on one end and oxygen on the other.

We used a nine volt battery to supply the power needed to pull those water molecules apart, and the bubbles came out pretty slowly. A plant could do the same thing with just one volt's worth of sunshine! We tried using a one volt battery, but nothing happened.

Electrolysis in action!
Unfortunately electrolysis uses up way more energy than you can ever get back by burning the hydrogen it releases. But if we knew exactly how plants use sunlight to split water, maybe we could do it that way. Then it wouldn't cost much at all to produce lots of hydrogen (or possibly hydrocarbons, similar to gasoline).

At this point in the program, I shared the song I wrote, inspired by Dr. Burnap's research. It's called "Photosynthesis Machine."

You've probably heard of chloroplasts and chlorophyll. Chloroplasts are the structures inside plant cells where photosynthesis happens, and chlorophyll is the chemical in the chloroplasts that makes plants look green and allows photosynthesis to happen.

Dr. Burnap uses green algae in the lab as a stand-in for plants. Its photosynthesis machine is pretty much the same, but the algae is easier to work with.

But if you're like me you probably never realized that chlorophyll doesn't do the job alone. Dr. Burnap studies the protein structure that contains the chlorophyll. It's called the "reaction center," and it's a molecular machine that brings all the ingredients for photosynthesis together, recombines them, and moves the resulting products apart.

It's a photosynthesis machine!

That blobby shape on the screen behind Dr. Burnap is a computer model of part of the reaction site.

How exactly does the photosynthesis machine work? We know a lot about it already, but there are still many details to figure out. The challenge is: how do you study a machine so small you can't even see it with a microscope?

One way Dr. Burnap studies the molecular machine is by measuring how fast it works, then messing with it to see if he can slow it down. He uses a strobe light and an oxygen detector as a speedometer. The light flashes; the plant makes oxygen; the detector measures how much and how fast. We're talking super-fast speeds here. The video below shows how quickly the strobe light flashes on and off.

Some questions Dr. Burnap was working on were: Why don't the hydrogen and oxygen just bond back together right after the photosynthesis machine pulls them apart? How exactly does the photosynthesis machine move hydrogen away from the reaction site so that doesn't happen?

To slow down the machine, Dr. Burnap gave his algae heavy water instead of regular water. Heavy water is made with deuterium instead of hydrogen. Deuterium is a hydrogen isotope, containing one proton AND one neutron, so it weighs about twice as much as regular hydrogen. Heavier things are harder to move, so...

Would the machine have a harder time moving these heavy hydrogens out of the way? If so, would that also slow down the rate the oxygen gets released? It turns out: yes, and yes!

We made a human photosynthesis machine, using balloons to represent hydrogens and oxygens.

Dr. Burnap suspects that certain parts of the photosynthesis machine act like a bucket brigade. A series of proteins pass each hydrogen atom down the line in order to move it out of the way once it's been freed. One way to test this hypothesis is to change the machine and see what happens. Dr. Burnap was able to grow a special algae by "knocking out" one of the proteins in the bucket brigade. With this protein missing, would the hydrogen pile up? Would that slow down or stop the photosynthesis process?

Next we put our bucket brigade behind the screen, since Dr. Burnap can't see directly what's happening in real life either, and we took one of the proteins (people) out. Did the hydrogens (black balloons) still make it across to the other side? Surprise surprise - they did! How did they do that?

Using the strobe light and oxygen detector speedometer, Dr. Burnap discovered that even with one of the proteins missing, the machine worked just fine! This suggested to him that the proteins are not arranged in a straight line, but are interconnected so that the hydrogen has more than one path out.

We had a blast during the program re-creating Dr. Burnap's bucket-brigade experiment with people standing in for proteins and balloons representing hydrogen and oxygen molecules!

It's pretty amazing what we can figure out about how a machine is put together, even if it's too small to observe directly! If we keep piecing together details, one day maybe we'll be able to build our own photosynthesis machines to convert sunlight into chemical energy that we can use!

Playing with the electrolysis after the program.

Me on the left, Dr. Burnap on the right.

Friday, May 18, 2012

Fungus Among Us! Saturday May 19!

Yes, our last scheduled Born to Do Science is tomorrow!!

May 19, 2012
The Fungus Among Us!
When Fungi Attack, Science Fights Back

Stephen M. Marek PhD from the Department of Entomology and Plant Pathology at Oklahoma State University will speak about his use of molecular tools to investigate "who done it" and how to stop it when important crops suffer damage from pathogenic fungi.

We will have microscopes on hand with lots of fungi to observe!

10:00 AM at the Stillwater Public Library. I hope to see you there!

Friday, April 20, 2012

Predators and Prey this Saturday!

Yes, we are having a Born to Do Science tomorrow!!

April 21, 2012
Predators, Prey, and the Games They Play!
Computer Models Reflect Real-World Animal Behavior
Dr. Barney Luttbeg from the Oklahoma State University Department of Zoology will speak about his research using tadpoles, dragonfly larvae, and computer simulations to understand the complex interactions between predators and their prey.  

If you can, please bring a chess board, chess pieces (or any game pieces you like), checkers (or any flat tokens with two colors), and a coin to flip or dice to role.

We will also have live tadpoles and dragonfly nymphs to observe!

Sunday, April 1, 2012

New Music Video - Science Frontier!

I'll get caught up soon with photos from the last to BTDS events. In the meantime, please enjoy this brand new video for my song "Science Frontier!" Many thanks to Brian Collins, who wrote, produced, and directed it!!

Thursday, March 8, 2012

This Saturday - My One and Only Vole!

Don't forget we're meeting a week early this month! Saturday March 10. I hope to see you there! We're working on setting up a live vole-cam in the lab! Here's what the program is about:


Vole pups! I borrowed this photo from a Mother Nature
Network article, 11 Animals that Mate For Life.
Zoology student Tomica Blocker will share the science of "voles in love" in a program for children Saturday at the Stillwater Public Library.

Blocker, a master's student in zoology at Oklahoma State University, will present "My One and Only Vole" at Monty Harper's "Born to Do Science." "Born to Do Science" is a monthly program that gives students a chance to meet scientists and learn about their research. The series is hosted by Monty Harper, a local children's musician who composes a song for each program inspired by his guest scientist's work.

Three brother voles moved nesting material
one mouthful at a time from one end of
their tub to the other while I interviewed
Tomica about her research.
"Prairie voles are a fascinating species to study," said Harper. "It's a rare mammal that sticks with a single mate for life. It's even rarer to find a mammal species where mothers and fathers both care for their young. That's why certain types of prairie voles are useful model species for investigating human behavior and physiology; they are rodents with family values. We can learn a lot about ourselves by studying these cute little monogamous mammals."

The presentation will include hands-on activities for the participants. "This one will be a lot of fun," said Harper. "We'll have kids up acting out vole social recognition using olfactory cues, analyzing vole behaviors in videos from the lab, and even designing their own vole research!"

One of the voles gets a sunflower seed treat.
"Born to Do Science" is free and open to students in at least third grade. Parents are encouraged to attend, participate, and learn along with their children. It will begin at 10:00 a.m. in Room 119 of the library. Registration is requested at (405) 377-3633 or

For more information about "Born to Do Science" or to listen to podcast interviews with past guest scientists, visit Stillwater Public Library is at 1107 S. Duck St.