Hi. It's Paul Andersen and this video is mostly for other teachers or students that are interested.
This fall I was looking for a viral replication simulation. I found a few things online, but
nothing that really fit my class and what I wanted to do. So I was going for a run one
morning and thought this up. And so I wanted to share it with you, some of the results.
And I hope that you're able to improve on it. Because I think it's kind of a neat simulation.
Basically the three things that I used were number one Moodle, which is our messaging
system. So we use the instant messaging system within Moodle. We also used Google docs. So
the kids were able to enter in the infection that they got into Google docs. We were able
to track the virus as it mutated and changed over time. This is how it sits today. So we
had by the end something like 89 different strains. 267 people were infected. So we use
a Google docs to track the virus. And the last thing we used were these dice. And so
if you're as old as I am you know that these are Dungeons and Dragons dice. I don't play
Dungeons and Dragons. Haven't done so for quite awhile. But basically I was able to
use some of these 20-sided, 8-sided and 4-sided dice to do some of the randomness in the replication
of the viruses. I basically had the dice in the front of the room because I only had one
set. And then kids would come up when they needed to use the dice. So basically they
infection started on day 1 with a message from Babe Hithertwit that was sent to 3 random
students in each of the 3 different classes. So 3 total random students started with just
3 infections. Basically they got this message. It said you are infected. And then it had
the RNA sequence of the virus. And so that was important. So I started with AAA UUU CCC
GGG AAA UUU. That was the first infection. So that's the first strain. Basically once
you got a Moodle message then if you'd already been infected 5 times, do nothing. And I added
this because I didn't want this to run forever. I wanted it to be a finite amount of infections.
The next things I did is I said if you'd already been infected by this virus, do nothing as
well. And so every time they got infected by a virus they'd enter the strain into a
Google docs so they could see what they got, when they got it. And so if they actually
had that infection before, then we thought of it as you have an immunity to that so you're
not going to get it. So don't do anything. But if neither of these apply to you, then
you follow the following directions. And these were all in Moodle. So first thing. You copy
and paste the received, this should say RNA sequence into the following form. So they
click on a form. And it would just basically say what's your name and what sequence of
RNA did you get. And then the next thing they would do is they would roll the 8-sided die.
So they would role the 8-sided die. Basically if you got a 1 through 3 you would copy it
to 1, 2 or 3 close contacts. Now a close contact I defined as somebody who you spend time around
in class or we have iPads in class, so if you share an iPad with them then you're a
close contact. So basically if you got a 1 you sent this RNA on saying, "You're infected."
to 1 other student. And 2 you'd send it to 2. A 3 you'd send it to 3. But you send it
exactly the way that you got it. If you got a 4 or a 5 then you wouldn't do anything.
We said the virus failed to transfer or replicate to another person. And then the next thing
we had, 6, 7 or 8. If you got a 6 then you'd send it to 1 close contact but it would have
1 mutation. A 7, 2 close contacts with 1 mutation. And an 8 you'd send it to 3 close contacts
with a mutation. And so anecdotally girls were more likely to want to roll a 4 or a
5. Because I think they didn't want to infect somebody else. Guys loved rolling an 8 because
they wanted to mutate it and then send it to 3 others. I'm totally stereotyping, but
I did see that in class. Next thing we did is we determined the mutation. So to determine
the mutation you'd roll a 20-sided dice, so that's a die that looks like this. Basically
if you rolled a 19 or a 20 you wouldn't do anything because there are only 18 nucleotides
in the sequence. And then whatever number you got that would determine what nucleotide
had mutated. Then you'd roll the 4 sided dice and that would tell you what it's going to
change to. In other words if you roll a 1 it's going to turn an adenine. So basically
those were the ground rules. I had no idea what was going to happen. I just sent out
these three messages and then it took off. So example. Let's say that I've been infected.
So I get this first strain. First thing I'm going to do roll the 8-sided dice to see what
happens next. And so I got a 5. And so that would mean I don't send it to anybody. If
I roll it again maybe next time I'm infected I get a 3. And that means that I'm going to
send it to 3 of my close contacts. 3 Moodle messages. But I don't mutate it. And let's
say I roll a 6. So let's say I roll a 6. Then I'm going to, you know, put the data in the
form first but then I'm going to mutate it once and I'm going to send it to 1 other close
contact. So let me show you how the mutation works. Basically you'd roll the 20-sided dice.
And so I got a one. So I got a 1 on the 20-sided dice. That means that basically I'm going
to be mutating this first letter from an A. And now I'm going to roll the 4 sided dice
and I get a 3. If you don't know how to read that, so that would be a 3. And so what that
means is this is going to turn from an A to a C. So this is going to turn to a cystine.
So what am I going to pass on? Well I'm going to send the same message but it's going to
have that 1 point mutation. So now I'm going to make that one change. Leave everything
else the same. I'm going to copy and paste this message. And I'm going to send that since
I rolled a 6. I'm just going to send it to one other person. Now if I were to do this
again, I would make mutations much less likely. You could use a different kind of a dice to
do that. I would make it less likely that it could actually spread. I had too many mutations
and too much viral spreading. If I were to do it again I think that would be a little
more realistic. But I think I had too many different strains. But basically let me show
you the results. So after 1.5 hours, and I used a pivot table to show me the different
types of the virus, you can see after 1.5 hours we basically, 90 percent of the infections
at this point were that original strain. And then we had 2 other strains. If I remember
right we had something like 10 total infections. Now 3 hours in, you can see that the number
of strains we have is greater. We have way more infections. And 4.5 hours we have more.
So basically we have 20 different strains at this point. And then after 6 hours we had
something like 40 different strains. So we started to see exponential growth as I look
back at the data. And I also started to see all of these viruses starting to appear. So
that was pretty cool. Because I could have that up on the board in the front of the room
and the kids could kind of watch as the virus changed over the course of just two class
periods is the data I have right here. So that was neat. The kids were able to see how
a virus can spread really quickly. All of a sudden there's one or two people in the
front of the room rolling dice. But pretty soon it ended up being like a line in the
front of the room. I was infected again, infected again. And the kids really had fun sending
it to somebody else and choosing who that was. I got infected like 5 times as well by
boys of course. But basically I grabbed some of the data right here. And this is not all
obviously of the different strains. We had about 89 strains. But I just copied and pasted
some of them. And so why I like this so much is it was fun. It was interactive. You could
see how viruses change. And how organisms may mutate and change over time. But the cool
thing is now I have this data that I could actually use in class. And so when you're
talking about evolution, and you're talking about like phylogeny and how species are related,
this is great data. In other words there were 38 people of 86 people in my classes that
were infected by this strain. So this is that original strain. So the most popular strain
of course is going to be first one that was spread out. Now we also had some other ones.
So this one is pretty popular as well. So this, 10 people were infected by that. If
we look at this one right here, AAA UUU CCC so here's our mutation right here. You can
see that there was a mutation right there. That was spread to 10 people. So this 1 person
you can see rolled probably, if we think about parsimony or the easiest explanation for that
is there is probably one mutation that was passed off. If you look at the one right above
it, that one had this mutation so we could say that maybe these two were related, so
they came off that same branch. But you can see that there was another mutation there
that was popular. Whereas this one only infected one person but it didn't spread from there.
So I could, I'm confident, I could give this data to people maybe to make it reasonable,
make it this chunk. And then say could you construct a phylogenetic tree of that data?
And so they could draw, so this is my original strain, and they could try to construct a
phylogenetic tree showing all of the branching of all of the different types of viruses.
And so I think that's neat. Because that's what life is. Remember life starts with that
first genetic material. It's mutated. It's replicated. The only thing that I don't show
in this simulation is natural selection. So I was asking one of the kids in my class this
question. How could we make this model natural selection? And he's being much smarter than
I am said, "Well, maybe we could make there an advantage to have As for example. If you
have more As then you're more likely to infect." He was thinking maybe it would reach some,
you know, evolutionary stabilized selection where it's good to have a lot of As. But if
you have too many As then humans are going to start to develop immunity. It's cool when
the kids in your class are much smarter than you and they come up with ideas. And so basically
I would love to get ideas from you as well. Or feedback. And thanks for listening.