Heart Health, Explosive Gas, and Mexican Mollies (2/8/15)

Last Sunday's program with Dr. Jennifer Shaw from the OSU Department of Integrative Biology, was about how we might learn something about our own body chemistry by studying some amazing fish from Mexico.

I kicked us off with a new song called "Team Science." This is a topic I've wanted to work into a song for a while - how scientists always work as part of an enormous team. Since Jennifer made an unexpected connection with another researcher, using Dr. Michi Tobler's fish evolution studies to further her investigation of how we humans regulate hydrogen sulfide, it seemed like a great way to illustrate the point that scientists do not work alone.

Brand new song, "Team Science"

Hydrogen sulfide is an important signaling molecule that helps our bodies know when to grow new blood vessels, among other things. On it's own, it's a poisonous gas, and it stinks. So of course we wanted to smell it!

Jennifer prepares to release some hydrogen sulfide gas.

Adding powder to water to release the gas.

Jennifer wafts the gas gently so I won't get a harmful dose. I take a whiff - whew! Smells like rotten eggs!

Dr. Tobler's fish are nearly identical except that one group evolved the ability to live in hydrogen sulfide springs. Since the two fish are so similar we can assume that any genetic differences probably have something to do with processing hydrogen sulfide. This can help us figure out which genes are most involved, by comparing how genes are expressed between the two types of fish, when they live with and without hydrogen sulfide in their water. 

And guess what, we humans have a lot in common with fish! The same mechanisms are at work in our own bodies.

Amazing Mexican Mollies that live just fine in pools poisoned by hydrogen sulfide.

Nearly identical mollies collected from nearby pools without hydrogen sulfide. These fish can't survive in the sulfide pools.

Jennifer's lab setup - this is how she delivers hydrogen sulfide to the fish in her experiments.

Hydrogen sulfide is something our bodies need, in small amounts. Too much is poison. There are human diseases related to both having too much and having too little hydrogen sulfide available in our bodies. Understanding how these sulfide tolerant fish can manage will help us figure out how to correct the balance when it goes wrong for us! 

Higgs Boson Found! Now What? (1/25/15)

Last Sunday's program was a doozie! My guest was Dr. Flera Rizatdinova from the physics department at OSU. Flera analyzes data from the Large Hadron Collider (LHC).

So we were talking about particle physics and it went long - very long. It's good though, because there were lots of questions. I think particle physics is really fun to think about.

When you hear an explanation in particle physics and it feels like you don't understand it, that's probably because it's very weird how things work on the smallest scales. Fundamental particles don't behave like things we're used to. Particle physicists understand all the mathematical models that describe particle behaviors. Yet even they seem to have trouble describing what's "really" going on.

So with that in mind, I'll take a stab at summarizing the program. We started with a sneak peek at my new song and video "Quarks and Electrons." Then I tried to give a quick summary of the Standard Model of Particle Physics. 

I tried to give a quick overview of the Standard Model of particle physics. There were lots of questions!

Basically Quarks (up and down, held together by gluons) and Electrons are the fundamental particles that make up regular matter - all the stuff you and I can touch or see. The Quarks and Leptons have mass. The Gauge Bosons, including Photons and Gluons, cary forces. The Higgs Boson gives other particles their masses.

Here's a chart. It's something like the periodic table of elements, only everything here is a fundamental particle, which means that as far as we know it can't be broken down into smaller parts:

Standard Model of Particle Physics

And that's it. If the universe is a giant Lego playset, then these are all the types of Lego bricks we know about. 

However, we also know the Standard Model is missing pieces! 

Until recently we didn't have the Higgs Boson on the chart. We thought it might exist but until we gathered good evidence for it from the LHC (Large Hadron Collider) we didn't know for sure. Now we do.

Other particles are probably missing as well, and we're looking for them next. 

For one thing, there's dark matter. We know it exists because we can observe its effects on galaxies. But from its properties we can tell it isn't made out of anything on the list.

Another problem is gravity. The other fundamental forces have their particles - for example electromagnetic force is carried by photons - but gravity is not accounted for.

And we don't understand a whole lot about exactly how the Higgs Boson gives particles their masses. It's possible there are several different kinds of Higgs Bosons yet to be found.

Physicists have guessed at many ways of extending the Standard Model. (One example is "Super Symmetry.") These hypotheses all include the model as we know it, and add additional particles of different sorts. All of the extended models make mathematical sense, but which one is right? Which one represents the way the world actually is? The only way to tell is to run an experiment. That's where the LHC comes in.

We took a break at this point to remind ourselves that fundamental particles are real. We had a cloud chamber set up to detect them. The chamber is filled with evaporated alcohol. Whenever a particle zips through it leaves a trail of droplets that you can see. We could see lines appear that let us know muons were zipping through. Muons are generated by particles from outer space slamming into our atmosphere - we call those "cosmic rays."

Looking for particle trails in the cloud chamber!

Whew - we are about halfway through the program now! We talked about how the LHC (Large Hadron Collider) at CERN works by slamming protons together at very high energies. The protons plus energy create a whole bunch of new particles. These decay, or fall apart into smaller pieces.

The particles we're looking for, the unfamiliar ones, do not exist long enough for the detector to detect them. Instead we detect the pieces they generate. From those pieces, we have to work backwards to see if we have evidence that one of the new particles was there.

I demonstrated my "photon detector" by taking this photo. The ATLAS detector at the LHC works in a similar way, only it records lots of different types of particles in addition to photons.

This is a very hard problem to solve. The ATLAS detector collects information from millions of particles per second. All those signals are mixed up together. It's difficult to tell one particle from another.

Flera uses computer programs to help her sort through the data. She's part of a large team that includes scientists from all over the world. They each tackle a different piece of that hard problem. Together they can decipher the signals from the ATLAS detector to find out if any exotic particles were created in the proton collisions.

Scientists are still working on the data generated last time the LHC was running. Next time they turn it on it will run at a higher energy. This increases the chances that exotic particles will be formed. It's exciting to think that the new data set may add to our fundamental model of the universe!

Coming up next:

February 8, 2015
Heart Health, Explosive Gas, and Mexican Mollies
With Jennifer H. Shaw, Ph.D., Department of Zoology, OSU
Regulation of hydrogen sulfide in our bodies is important to our health, but how do our cells know exactly how much to make? Find out how some special fish from Mexico can help us understand our own body chemistry!

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.

Processing...

Processing...

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?

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!!

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!"

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!

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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.