Friday, May 16, 2008

LISE08 talk on Second Life in the Chemistry Classroom

LISE08 talk on Second Life in the Chemistry Classroom screencast

Jean-Claude Bradley: OK. So, thanks very much for the invitation. I think this is a fantastic conference. We've seen many different technologies being used for science education and specifically for chemistry. So I'd like to actually show you in detail how it is that I have been using Second Life to teach chemistry.

Now before I do that, I always like to remind the audience that there is a purpose to these things. As we get new technologies, as we evaluate these new technologies, we have to remember that we are still teachers and there are things that we are trying to do with them. Right?

In terms of chemistry, I want to have students who are competent to understand and generate new chemistry. So keep that in mind whenever you look at these different applications.

The story starts actually a little bit before. I'm going to talk about Second Life but I think it's really important to show how it actually evolved to that. A couple of years ago, I started to record my lectures as I am now actually.

This talk will be made available. I do this in the form of a screen cast. So everything that appears on the screen, in addition to my voice gets recorded.

I would give that to my students after the class so they could review material. I could put these on iTunes or I could put them on a server. There are many, many different ways. We've heard about podcasting, so that is one way that you can deliver this content.

You can see from this small image, I use a tablet PC so I can draw molecules. In organic chemistry it is especially important to not just see the final answer, but see how you arrive to that final answer; how you push the arrows and all that.

So what happened is I started to track the attendance in my class as I made these available. You can see here, this yellow line is the attendance from the first day of class until the end.


The same thing in this class. It starts off here and ends up here. So, by the last lecture there are only 10 to 20% of students that are still showing up. Now what is interesting about that is that I look to the performance in both these classes, between those two groups of students and the performance was the same.

So, in other words, if they just watched my lectures and never came to class, they did just as well as the small minority of students who still came.

So, I started to re-think what it means for me to be a teacher. Does it necessarily mean for me to repeat myself term after term with exactly the same material? We have a lot of stuff to go through and if I am going to be lecturing, there is only a certain amount of time I have left to do other things.

So, I started to just actually assign the recorded lectures. I started to do other things with my class time. So for a couple of terms now I've been basically using the class time as workshops.

The kinds of things that we do here is a lot of what we saw here today in terms of games, in terms of Second Life. You have students who are watching the lectures with headphones and then when they come to a problem that they are having difficulty with, they come up and join the group.

It's either one-on-one attention or if there are several students, it may be group work. Whatever it is, I am spending the same amount of time teaching, but I'm doing something completely different. I'm actually being a learning catalyst as opposed to a parakeet. I think it actually is better for the students, I think.

The other thing that is really useful by having these workshops, and don't underestimate this, the technical implementation for these software packages. Don't believe that all the students are already on YouTube, that they know how to use Second Life. In my experience that's not true. It's actually pretty unusual that a student will already have been in Second Life. It requires me to show them how to create an account and how to get on.

There is all kind of issues with that. For example, a lot of student's computers don't have a good enough video card. So their experience is quite poor in Second Life. They think, "Why is everybody going on this thing? It's so lousy." It's just simply they don't know what to expect.

So having the face-to-face workshop is extremely useful for just taking five to ten minutes in helping them create an account.

I'm going to show a couple of different technologies. Last year I talked in much more detail about this. I'm just going to gloss over it. I have used blogging. Were my students to write something about imine formation for example. They would write a blog. They would upload pictures.

Each one of these technologies has its advantages and disadvantages. I'm going to try to point those out as I go through. The advantage of a blog is that it is really easy to create one, especially with Blogger. So it doesn't take that much time for me to set it up.

The disadvantage is when the student corrects their mistakes; there is no track of that. So I can't actually follow how they have actually arrived at the final presentation. So it has some uses. It is very simple.

If I'm going to be doing student assignments and I want to see basically that interchange between me and the student or between the student and other students, I will probably want to use a Wiki. A Wiki, is again, very simple to set up. It's a little bit more complicated for the student to edit, but really not that much more. It has advantages that I could look at the different versions.

Now here is an example of a Wiki project where a student went into my lab notebook. I have an open laboratory notebook. I do anti-malarial research. So we make compounds of the synthetic organic group. She went in and looked at actual and our spectra of an on-going project.

This is an NMR, it is not really that important to go into details. But in the class material, this would have been predicted to be a single peak. But it turns out, when you blow it up, it's actually a triplet. That's something I learned actually, from looking at these things more closely.

This is the kind of thing where the student is learning something. The teacher is learning something. The graduate student is doing the work of learning something. By using a Wiki, everyone can actually watch in real-time.

Some of the other things I've done using tablet PCs. This game here I call Wheel of Wargo. You put a starting material like benzene in this case and put a final product. The students will take turns trying to come up with either a step from a starting material to anything, any reaction that we saw in class. Or try to write a step that goes toward the product.

The idea was to connect one of the trees with the other tree. Students will get a point for having the right reagents for example. A student might get three points for completing the synthesis. I found this to be actually very useful for organic synthesis.

The difficulty with this is that a lot of students are shy. So it is actually a big deal for some students to come up and write on the tablet PC. So all these have pluses and minuses. That would be the minus when it comes to this. But it certainly was very effective for students who didn't have a problem with it.

So now we're going to move towards the world of more classical games. How many of you have heard of "Un-rule Tournaments." It's a first-person shooter, kind of like Halo. There are a lot of these games where you walk around in a virtual world. You can actually get a version that doesn't have any weapons.

There's a commercial version that has it. I used more extensively the version that didn't have any weapons. It was free. It was easy for the students to download it. It would basically consist of these rooms where there would be pictures of some chemical concept.

Here we're looking at a hybridization, plus a Lewis structure. Here we're looking at a chirality with a Fischer projection. There are actually four walls here, and three of the images are incorrect somehow and only one of the images is correct.

What I would have the students do is a race. If you went through a door that was correct, you ended up in the second room, and then as long as you kept picking the right answers, you would keep progressing through the maze. If you got any of them wrong, you had to start over.

So it was a pretty easy way for me to do races, actually a game. I didn't give out any points for this, but I did give out prizes, like a molecular model kit or something like that. So there was definitely motivation for the students to do it. I thought this went pretty well.

Sometimes, we actually did it with the weapons. This was with the commercial game, but it was all the same content. So I could reuse all these images, just put them in a different context. In the weapons version the idea is to survive, right?

So if you get through a correct door, you might get some more ammunition or help or something like that. So it was another way of engaging. Again, pluses and minuses. You may not want to have weapons in your games [audience laughter] but some students do find that more engaging.

Now I would probably still be using "Unreal Term" or some sort of game like that if I hadn't come across Second Life. Second Life has a whole other dimension that hopefully I will give you a taste of today in my talk. It turns out that you can do exactly the same kind of game, but instead of having rooms that you move through, we created these little obelisks.

By the way, this is the shot of Second Life. The avatar here, that's going to be me. So whenever there's a picture and you see the back of the head, that's me moving through the world. When you click on these obelisks, again four images pop up, and three of them are incorrect; one of them is correct.

Instead of going to another room you just get another set of questions. So I do the same thing. I still do races. I still give out prizes like that. I think that it works pretty well.

The advantage is that students can come from around the world at any time and they can actually take the same quizzes and they can interact with my students. So for me, the huge advantage of Second Life is really this ability to network.

I want my students to network with educators, other students. What you find in Second Life is that the content on the islands is what governs the type of person that visits it. So it's like a chat room. Basically, if you're on Nature Island or you're on Drexel Island or any kind of educational island like that, we really haven't had any negative experiences. But if you go out in the real world there's all kinds of things out there and you have to be aware of that.

So that's how I started with Second Life. After awhile I actually met people that I started to collaborate with. Andrew Lang is a very close collaborator and we've done a lot of stuff together. I put his name up on relevant slides here.

That's a perfect example of why as an educator you'd want to use Second Life. It's actually not so much teaching the students; it's just tapping into this huge reservoir of very intelligent people who are very skilled at doing things. Andy is very skilled at writing script or making buildings in Second Life, and he's a mathematician.

So when we come together I have my chemical knowledge, and we couple that to his skill in terms of rendering objects. We can do some things that we can be comfortable that are actually scientifically accurate.

Here's an example of a student project that was done in Second Life. The student is actually trying to show the concept of chirality using camphor because it's a particularly difficult molecule to visualize in 2D. This is the size of the avatar here. You can see that the molecules are actually much bigger than the avatars. So this is a completely different way of interacting with molecules.

Normally, if you make a molecule set, you hold it in your hand or you draw it on a piece of paper. Here you can actually go all around it, you can sit on it, you can do all kinds of things that you can't otherwise do. It's very interesting to see learning chemical concepts this way.

Now the reason this is possible is because with Andy you manage to create rezors that don't require any computing skill whatsoever. In terms of doing things on Second Life, what's becoming exciting now is not so much the stuff you can do as how easy it is to do it. With very minimal training. anyone could actually make these molecules.

I'll show you that in a little bit here. So students can have fun with this. You can actually sit on the molecule and fly around with it. You can try to simulate docking. There are so many things you can do if you let students play with it. We have a Bucky Ball here, which is pretty popular.

In terms of how you actually teach students to do this, I don't want to be sitting there showing them how to code. It's a chemistry class; it should be about organic chemistry. So what we've done, Andy has basically written these scripts that will take as input smiles, inchies or inchiekeys, and will actually hit a bunch of web services, one in Indiana, one in North Carolina, will actually do a minimization so that the molecule has a realistic shape, and then will actually build the molecule in 3D right in front of you.

So as a student, and more importantly as a teacher, I only have to teach students how to find the smiles code. Luckily, there are some great services out there, like ChemSpider. The student simply typed in camphor in the search box, and camphor pops up and here's the smiles.

You copy it, paste it into Second Life, and it just pops up. It becomes quite feasible then to have students doing projects at a pretty high level of sophistication because it doesn't require a lot of my time.

Some other things we've done more recently, is try to correlate molecules with NMR spectra. So again, this molecule here see the acetylphenone, this was created using the same rezor just the student found the smiles code, dumped it in, and it created it. And here's the NMR spectrum.

And then the student explains how each proton corresponds to each peak in the spectrum. Now this particular spectrum is just an image. The student went on the web, took a picture of an NMR and then put it in Second Life. What we've managed to do quite recently, actually, just a few days ago, is actually interact with the spectra.

So this is an NMR spectrum and I can actually talk to it, and I can tell it to zoom between 2.1 and 2.3 ppm, and the spectrum will actually respond and zoom to any region. So again, this is very simple, right? To interact with it, you just have to type in the chat box.

I think this is going to make it very easy to bring a whole bunch of people together: students, teachers, whatever, and be able to discuss pretty sophisticated chemical concepts. If we want to look at an NMR, we can just pull it up and we can just zoom it in and talk about it.

So a few other things that we've been able to do in Second Life. We've been able to demonstrate docking. As I think I mentioned, my lab focuses on making antimalarial compounds. This is one of those compounds that we've made. This here is actually the receptor site of enoyl reductase. It's a malarial enzyme that we've been trying to inhibit.

This is set up in such a way that if you click on the molecule, you will see it drift down and connect into the receptor site. So this is actually, you're there and you're watching this thing in 3D come down. There's actually four hydrogen-bonding points. It turns out that its actually really tricky to see that.

This is a very interesting way to understand what does it mean when you have a drug molecule interacting with an enzyme. Its just another way to do it, it doesn't replace the paper, it doesn't replace all the other software programs, but its one more way of visualizing it.

There's all kinds of things that you can do in terms of the chemistry, you can display the entire enzyme. Peter Miller has done quite a bit work. This is the same enzyme, it's the whole thing instead of just the receptor site.

And again recently with Andy Lang, we can actually go from a file in PDB and actually go to a fully rendered protein, using up only one prim in Second Life. If you're not familiar with Second Life, everything comes down to prims. You only get so many of them per island, so right now Drexel island is about 90 percent saturated so we couldn't actually do a massive project because there's not enough prims.

This here is the 3D structure of the Avidin and it only took one prim to make this. So you can imagine you could have much larger projects than you could with the other way of rendering, so this thing is very detailed and it uses up a lot of prims.

So again, I don't have to know how to code in Second Life, all I have to do is show my students this is where you get PDB files, this is what you use to make this. And then have them go and actually do their projects. Some other things that we've done, we can actually show reactions taking place.

So this is a reaction between an aldehyde and an amine, to make an imine and there are actually three steps, at least with this mechanism. You can see here this is the blue nitrogen and here's the carbonyl.

And you actually talk to these molecules, you say "Next, Next or Back" and it will actually go to the intermediate, now what's special about that is that each intermediate has actually been minimized so that it's realistic. It has a realistic shape, which is something that you don't often get when you look at these reactions on paper. On paper everything is flat.

But actually these intermediates are not flat at all, they're twisted, the hybridization changes, so there's tremendous changes in the angle. That's something that you get a really good feeling for when you're in Second Life doing it.

We're accumulating this information. Right now there's not a search engine that will actually go into objects in Second Life in the way that you might think Google would do it. One of the things I've set up is this Second Life molecules Wiki, where if we do create new molecules, we can just create a new page. Those pages will be indexed by Google. So if someone searching for this particular molecule, they will find this page, and then there will be a link.

They are called "SLURL's" Second Life URLs, where people can click on it and end up at a specific location in Second Life. This is another way, very simple thing to do, but very effective in terms of indexing.

Again, with Andy we've made a 3D periodic table. So, each one of these atoms, if you click on them it will actually show you more information about each element. And this is freely available. It's on American Chemical Society Island, if any one of you want to see that.

We can also have offices. So, this is how I'd like to look in real life, but I can't. So, I have to do that as an avatar. But, here's a picture of myself and this is an area where you can meet student's or, you know if students are visiting and want to find out more about the Drexel Chemistry Department. They can look it up.

I can put information about my lab. So, here are pictures of my student's, pictures of our equipment, chemicals, things like that.

And something that works very well in Second Life are posters. So, there are posters on Natures Island. The Nature publishing group has actually three islands called Second Nature. And there are these areas that have a whole bunch of posters. In this particular area this is an example of someone that I me...I think she's from the Netherlands, and she works on Crohn's disease.

We met at Second Life and I found out she was going to a conference and she was interested in putting her poster here. This is actually a whole PowerPoint presentation. If you click on it, it will walk you through the entire presentation and there is a little bell here that you can click it and it will summon the presenter. So, if she's in Second Life, she'll get an instant message saying, "come on over."

If she's not in Second Life, she'll get an email. Then if it's convenient, she can actually go in. And I've actually met quite a few people that way, from these bells. In fact, the posters are so effective that we've actually run entire conferences using them.

On Second Nature, there's actually a whole area called Sci Foo lives on, which is an extension of the Sci Foo conference that happens every summer over at Google. And, basically, this is an example of what happens at a conference.

We put up posters and the speaker will go up and talk. You can use voice in Second Life or you can chat. The advantage to chatting is that you can get a transcript really easily. So, we generally have used more of the chat than the voice. But people have done either. Then you basically get to meet all these people.

So, these are all people who are interested in whatever topic that you happen to be talking about. And in this particular case, this is about open science. It's about new ways of doing science. So, those are the people precisely that I want to meet. OK. So again, that networking concept in Second Life.

So, because this is Chemical Heritage Foundation, I'm going to focus more on the chemistry. There's a lot of other stuff in terms of biology, there's Genome islands.

All kinds of things that are wonderful. But in terms of chemistry, I'd just like to point to you this recent project that I was a part of that Kate Seller at American Chemicals Society spearheaded over there, to get an actual island for A.C.S. Maybe you guys will be next? Right?

This island actually has the shape of the Phoenix icon. So, this stuff here in green is land and the blue here is water. I'll just give you a few screen shots. If you're interested, you can contact me and I can show you how to get to all these.

There is actually a headquarters building where you can download some free stuff. You can get this rezor that will let you make molecules that I have my student's use. You can actually get a copy of it right here in the A.C.S. headquarters. Very convenient.

There's a section...I don't know if you guys are familiar with this A.C.S. Landmarks Program, American Chemical Society. I get one or two per year. Pick parts of chemistry that particularly important like purification of aluminum or chemical abstracts. There's this little museum area where those landmarks are located. If you click on these obelisks it will go to the web and give you more information about these. So that's another part.

For the first time, I helped them out with this with actually having a poster area for the Sci-mix session. If you have ever been to an American Chemical Society meeting, there is a Sci-mix where it's a varied group of people. They give posters.

Twenty people out of that group agree to put their poster on Second Life. So there is this whole area where all these posters are still there and still will be there for several months to come.

Some of them have on-line indicators, so you can see if the presenter is on-line. Again, it's that whole fostering, that networking. What we tried to do for this is if there was some molecule that was particularly interesting, we would put it next to the poster. So it is not just a question of replicating what you can do in real life, but to do things that are quite specific to this new technology.

Some fun things, too. It is kind of nice to be able to see a nano-tube in 3-D. You can go in the middle of it. You can see what it actually looks like. Then there are some interesting things like this molecule here is called Felasene. It actually looks like a cat.

It was part of this talk from ACS that basically, they were picking interesting molecules or interesting findings from their database. I thought this was a perfect molecule to represent this collection of molecules. You can not only put the molecule but you can add eyes. There are all kinds of things you can do.

The ACS also has a resident chemist program. What that means is that there are areas that are dedicated. If you have a chemistry lab and would like to share what you are doing, you can go on this platform and you can put different things on it.

The Anastrozol Lab, for example, has posters that they've given at various talks. Gus Rosania has a pretty interesting area. He actually does a lot of fluorescence microscopy. He has lots and lots of these little images in a cube.

So you're in the middle of this cube and you can actually try to see patterns in the data. For him, it's a way to visualize his lab information in a way that he simply can't do in real life.

If any of you are interested, there will be a little party going on at 1:30, May 6th at the Geodesic Dome at the American Chemical Society. It's always nice to pick a time and place to meet people, because often times you're interested in the island and you go there.

Maybe there is one person there or there is nobody there and you don't get to interact.

Sometimes if we can set a specific time and if anyone is interested in that, let me know. I'll make sure that you're set up and you can explore it.

Really, that pretty much covers what I wanted to say. In terms of what technology to use, I get these emails from my friends. Sometimes you get these articles that say, "Your learning doesn't work." Like a big conclusion. Or Second Life can't be used for education and it's pretty annoying because it can not be boiled down to that. It all depends on the details of how you use it.

So if you are using Second Life and you want to record hour-long lectures and you want to display them, it's not going to work well. But, if you wanted to have a poster or if you want to have students make 3-D molecules, well, now we can do that. We couldn't do that easily a year ago but now we can do that really easily.

So, it all depends on what you're trying to do. I would recommend, the easiest way to do it, is find someone who is already doing something close to what you are interested in and have them bring you into the world. Have them show you how to do it simply.

A big mistake people want to learn about Second Life, they just dive in. You end up on this place called Orientation Island, which is kind of like a purgatory.


You can't leave. They sort of rig it so that you have to go through certain tasks. I understand the concept, but the reality is most people just get really annoyed. It takes them two hours to finish it. You don't really need that. For our purposes, I want students to be able to fly around, to walk, to teleport and to chat.

That takes two minutes to show someone how to do that. Yeah, you can learn how to write code and all these kinds of things, but it's really not necessary for the kind of applications that we are doing.

Again, if you are interested in this, talk to somebody who is already doing it. You can use things like Wikis and blogs to interact with students. Second Life, yes, there are some specific chemical things that I showed, but I can't overemphasize this, the major benefit of Second Life is the networking.

If I have a student that does a project on Second Life, fine. They'll learn how a molecule looks in 3-D. That's great. But if they get to meet someone for their next co-op or if they get to meet someone that is going to hire them someday or they get to make a friend that is also a chemist; that actually is the greatest reward.

That is something that you will not find on sites that are closed in. There are other sites that have a virtual world but there is not a lot of interaction.

Second Life on average has 50, 000 people on it at any given point in time. So the odds are you are going to find someone pretty quickly that is like-minded, that you guys have the same objectives.

The other thing that I have done here to ensure my success is I have not made this mandatory. That is another big difference. This is not for everyone. Some students definitely get it and enjoy it. But typically, I only have about 10% of students that do the races for example.

I use multiple channels. I'm a big believer in this. So I care if you've learned the material. I use quizzes. I use tests, objective tests to make sure that students know stuff but I don't really care if you use the screen casts or if you meet me at the workshop or if you are in Second Life or if you are in Second Life next to me or if you are in Second Life in the dorm.

I'm not concerned with that. Do what makes sense for you. If you do that, you should do OK in my class. If you don't, you probably won't, but it's not mandatory. I don't think it is applicable to all students. If you do these things on a voluntary basis, I think you'll find the experience to be pleasant. It's not going to be a big stress.

The worse thing that will happen, if it's not for points, it it's not for grades, it just may not work, but it's not going to have very many consequences. So I would just suggest starting slowly.

Yes, everything I've talked about here is essentially free. In Second Life we bought an island. Drexel has bought an entire island. The American Chemical Society has an entire island. But if you just want to play around, there are plenty of places that will let you, give you a little area for educators and will let you experiment.

That's how I started. I started on Nature Island. They invited scientists to participate. I thought, "Why not?" I tested it out one term with my students and I started to use these quiz objects and it worked out. We eventually got an island. But to get started you don't need an entire island. You can actually just start with some friends. Then have them put up some stuff that you'd like to see.

And I guess that's it.


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