Second Life Biology

Second Life Shadows

2011-07-28T21:05:00.000-07:00

If your graphics card is up for it Second Life Shadows are pretty cool. But be forwarned...even my 1GB 8800 Nvidea card has to be tweaked a bit and performance is really degraded. Of course this computer "only" has 2GB of RAM.

What's cool is that the shadow to the right of me is cast by a prim that has a texture that has transparent regions and that is reasonably well echoed in the shadow! How's that done?

More on Avination

2011-07-26T19:58:00.000-07:00

My initial enthusiam for the $40 price for a sim is a bit tempered by a couple of limitations in Avination. The first is minor-namely it doesn't seem to support SL's media on a prim idea. In SL I am used to being able to have my blogs and my Flickr site open on prims so that I can at least see what's going on. The second is a bit more surprising given the OpenSim background of the owner, namely that Avination does not support OpenSim specific functions some of which are really cool especially the texturing functions.

On the plus side my inquiry about OS functions was quickly answered by their support staff. I also like that you can import prims that you own from SL using the Avination viewer, including scupted prims as my picture shows. Just be aware that it doesn't seem possible to import the scripts in the object- you have to do that separately or use Stored Inventory as explained here.

https://www.avination.com/support/faq/creation-inventory.html

Of course Second Life is not sitting still what with pending rolling out of mesh and if you haven't noticed realistic shadow rendering like that in Blue Mars. Since Avination is billing itself as content creator friendly, I wonder how the introduction of mesh in SL will affect Avination.

Who knows, I may ultimately find it cheaper to set up my own Open Sim server, and link it to OSGrid. Not that I have ever done anything like that mind you. Hmm as cheap as computers are today...might be worth it to take that plunge.

An Alternative to Second Life?

2011-07-23T15:13:00.000-07:00

Somehow I keep getting side tracked. Today I stumbled upon a new virtual world grid based on open sim called Avination and of course checking this out took precedence over cleaning and reorganizing my study.

Avination according to its website was started by an OpenSim developer, Melanie Thielker who has created her own "spin" on Open Sim. See https://www.avination.com/inside-avination/management-team.html for more information about Avination's Staff.

Now I have invested lots of time and energy in Second Life, including on my college's land. Unfortunately Second Life has doubled educational fees for a ful sim to around $4,000 which has my IT people really nervous. Avination right now is advertising full sims with 15,000 prims at the special price of $60.00 a month. Hmm in SL I am at the $40.00 tier level which means I am paying about 6 times what I could be paying in Avination.

Well even a virtual lady can't resist a bargain so I went on over. Joining is easy and similar to Second Life in that you choose your own first name and then select a second name from a predefined list and select your basic avatar form. One slick thing is that Avination has terminals in Second Life. (Wonder if Linden Lab knows about this.) You can go there and use the terminal to assign your Second Life AV name. Which I did right away. You don't get to share your inventories or your appearance but when you log back in to Avination your SL profile name shows in place of your Avination AV name. The system is like SL's new double naming system so my Avination name still shows on my profile if you click on the Avatar.

You can use SL viewers for Avination but I choose to use the Avination viewer. This viewer is clearly based on the SL viewers but is a lot more like the older 1.2 series of SL viewers wth some things out of SL 2.X viewers. Just about everything should be familiar to veteran SL users. I have not had a chance to try any scripting but Open Sim's version of LSL typically has some things on it that are not found in SL's language so I would be suprised if all my scripts will always work.

Buying land. Unlike SL it looks like the best thing to do is buy a whole sim. In fact the map is set up as a huge grid and you pick your sim and which one of a limited number of configurations you want and buy the sim using one of several methods including Paypal.

The advertisements have a promotional code so you might watch out for that. A sim is $40.00 a month for the first three months and then goes up to $60/month. Mmmm sounds to good to be true even at $60 a month but the lure of the bargain was too strong so I am giving it a whirl. I am sure there are some limitations in terms of flexibility and service...we shall see. Supposedly I can port my SL objects to Avination-assuming I have permissions on the objects so we shall see. Probably can't port my nice Kimono collection though.

I had my sim within 5 minutes of the transaction. Seeing all that sunny empty land is a bit intimidation as I have always lived in the mainland in SL. By the way there is apparently no sort of division between PG, Mature and the "Dark side" but you can control access to your sim just as in SL. So I figure at $40 bucks a month for three months this is worth a try.

One risk is that this is a small company-when I was on there were about 850 users online (SL might have 60K users online at the same time) so that perhaps adds a bit of premium to SL. Avination has it's own currency(C$) I haven't compared it closely, but it looks to be valued roughly the same as the Linden. I bought 2,000 C$ for $8.00 so I can upload textures and files. Uploading costs are 10C$ per upload.

I am not ready to give up my SL account so you still find me in Carmine at http://maps.secondlife.com/secondlife/Carmine/137/181/144

More to come.

Today all started when...

2011-07-22T20:04:00.000-07:00

My meat avatar decided to get a web cam to use with his desktop. Well the USB cable was too short so he decided to rearrange the office and computer. That meant a lot of cleaning and throwing away of stuff. Then testing the computer and the new monitor arrangement and the web cam. And then booting up SL and spending a delightful afternoon listening to jazz and doing some simple building. I had forgotten how therapeutic building in SL can be. So here is the first pass at the Tree of Life...

Pretty rough but lots of fun...more to come at http://maps.secondlife.com/secondlife/Carmine/133/181/144

Identity in Second Life

2011-05-06T19:14:00.000-07:00

One of my first life interests is gender identity, so I periodically search the SL forums for gender related posts. Today I ran across a wonderful thread called the Unqueering of Second Life, started by resident Scylla Rhiadra. Scylla argues that one of the things that SL does well is queering our perceptions. Here Scylla isn't quite talking about queer in the sense that the word is being reclaimed by GLBT people but a process related to that notion that forces us to reexamine our assumptions about people and identity. Scylla writes:

" “Queering” in this sense is really a process of “making strange,” a kind of shifting or even distortion of perspective that forces us to perceive anew, and in different ways, objects, ideas, and socially-constructed conceptions that we otherwise take for granted. "

Scylla then argues that this queering process is under threat by social networking such as facebook where one's "real life" identity becomes paramount as well as by groups requiring gender verification via SL voice.

The threats posed by social networking and beyond that, the threats posed by facial recognition software and other technologies is something that I have been thinking about. To me the threat of such systems is that they threaten to take away any sense of sanctuary that one might want online to explore by trying on other identities. Now I don't believe for a second that I have expectation of absolute privacy online but there should be room for relatively safe spaces where a person has some control over what information from these identities they wish to link to their real life information.

For transgender people, this can present a problem because there is the desire and for some the need to keep their transgender issues private, and at the same time be able to talk and share with other people including those outside the transgender community. In my case I am a professor and generally keep my transgender identity separate from my work life. But as a professor I am told "to be authentic" by academic theoreticians and to me being authentic means presenting myself as an integrated whole.

Of course in real life, we take on specific roles but to me the quest for integration implies that I don't keep my gender dysphoria suppressed-been there most of my life and that path is inherently destructive. Besides as professor-I can and do maintain a male persona at work-but unless in my private time I am going to relegate my gender expression to the shadows some bleed through is inevitable. Students do from time to time see me outside of class as a female. So my strategy is not to keep my other self hidden but keep my presentation separate enough so as not to upset the gender binary natives and yet reveal this aspect of my psyche in a sort of matter of fact way. I am for instance co-advisor of my school's GLBT student group and also am a Safe Space trainer for my campus and I can't exactly be hidden there. The whole idea is to open up some psychological space for myself.

Certainly students can find out about me. Now returning to SL, if you check out my profile you will a picture of me in SL but also there is a real life picture of me as I look in RL. When I teach, work, or shop in SL, Simone is my expression-sort of an extended phenotype. She is the face my biology students see when we go into SL. I did create a male AV which I use only rarely. Why should I bring the dysphoria I feel in first life into Second Life? To me that makes no sense. My experiences in SL as Simone have generally been good. I guess most people who might other feel threatened by my alternate identities appreciate the transparency or they don't find a short Japanese -Creole female AV in a Kimono to be threatening or desirable as a SL pick up.

One of my best experiences happened the other Spring when I was on sabbatical and working in SL. One day a strange male IM'd me in SL, and as I normally do, refused the IM since he did not state what he wanted. Well he persisted and on his third attempt said "Paul it's XXXXXX". Now it turns out that XXXXXX was an old friend from South America whom I had lost track of for about 15 years. At any rate he had googled my first life male name, found this blog and made the connection.

He asked me if I was gay since I have a female AV so I took the time to explain the issues I have and even show him a picture of myself "en femme" in real life. For the record, dear reader, "Paula" is pretty conservative in dress-not pick up material at all. But this fellow knows me in first life and my colleagues and friends have pretty much stuck with me. So my friends allow me an oasis where I can be more myself. That gets me through the week sometimes.

Yet even me being relatively transparent feels threatened by social network technology. First all of the sudden my RL "official" identity becomes key-I was dragged kicking and screaming into Facebook by my son who insisted that this how he and his friends communicate. Plus enough of my colleagues are on FB that my morning coffee ritual is to look at FB first rather than opening my campus E-mail. But I was a bit disturbed when FB kept insisting that I had to give my sex as male or female else how could people find me? Ya right. Fortunately FB stopped that nonsense. Maybe they imputed it from my RL name or from the funky stuffed caterpillar that currently graces my FB profile.

Now I really don't mind FB or SL having my legal ID information but why should this be the primary thing for a profile. Why can't FB allow me to establish a profile at variance with my legal identity if by doing so I am giving a more authentic face to myself? Fortunately in the circles I run in-even SL work related circles have not insisted in any sort of voice or verification of gender which would in my case be a verification of assigned gender based on the fact that my gonads produce microgametes with tails (i.e. sperm). SL provides still an oasis for me to the degree that my assigned gender or even my male name is not an issue.

Voice verification, linking SL to other social networks etc threaten the informational oasis because all of the sudden it become too easy for "queering" information to leak out to people who don't know me and may not be so willing to set aside their biases about people who are transgender. Rather than being like a large city where anonymity serves as a buffer against judgmental busy bodies, making first life assigned gender markers etc makes the net even more a city of judgmental busy bodies where the gender binary is enforced and those of us who don't fit are relegated to the shadows of the closet.

Scylla has a lot more to say in the SL forum thread and if you are interested in identity issues in Second Life it's worth a read.

Wiki on SL hardware requirments...

2010-08-28T19:13:00.000-07:00

Torley Linden has just started a Wiki covering hardware requirements for Second Life. He provides generic advice for selecting computers running the major OS's and graphics cards. Definitely worth a look if you are getting a new computer.

http://wiki.secondlife.com/wiki/Choosing_a_computer

Student activity at University of New Orleans

2010-07-20T13:28:00.001-07:00

Today I visited the University of New Orleans in Second Life, where Stephen Gasior (SL Stephen Xootfly) showed off his student's work in Second Life. The assignment was to select an animal and in the space of a three panel display present information about the animal's natural history, classification and phylogeny and distribution. These students are in a non majors class and did a fine job with their assignment. So you might go on over to the University of New Orleans region and have a look. You can start your tour and get a map here:

http://maps.secondlife.com/secondlife/Louisiana%20Regents/53/60/25

But it's just as much fun to wonder around. Here are a few representative displays:

I really liked how he kept the assignment simple and focused-no building was required of the students but they did have to design their own layouts. Steve brought in judges-yours truly was supposed to be one but of course misread the starting time.

Great job students!

An SL Biology Event-call for volunteers

2010-07-02T19:22:00.000-07:00

I just received a note from a Biology professor who is asking for volunteers to help access from student projects in Second Life.

Stephen Gasior(SL=Stephen Xootfly) writes:

Dear Biologists-

Hi. I am teaching a nonscience majors biology class in Second Life this summer. I am having my students make a presentation board about an animal. Basically 3 static textures. I am going to grade the content, but I would like to have biology faculty come talk to them about it. You can also note that they seem to know what they are talking about and confirm that they did the work. In other words, if you can tell me whether they should pass/fail the assignment.

Preferably, I would like to have other university or college faculty with a background in biology. If you would like to volunteer, please send me a link to your faculty profile page.

The event will take place in SL on Tuesday July 20th from 12:40 to 1:40 CST (10:40 to 11:40 SLT). If you are interested in helping me out, please let me know. By July 15th. Location will be on the Louisiana Board of Regents Island (look in my profile).

Thank you.

Stephen Gasior
sgasior@uno.edu

Stephen Xootfly in SL

Sounds like fun and its on a Tuesday when I am not teaching.

Been Kind of Busy with First Life

2010-05-20T11:30:00.000-07:00

Well some first life projects took over for about a month...but finally the semester is just about over. Yesterday I, or rather my meat avatar, met with the our IT people about refreshing our colleges's island to accommodate projects and make the island easier to use (yea!).

So to ease back into SL, I decided to revamp my JCCC office to make it cleaner in appearance, cut down on prim use turn it into more of a floating residence. This is because we are going to flatten the topography and I want my ground space free for my evolution critters.

Speaking of which now I can get back to that project. Yea!

Evolution Simulation IV: Mutating critters at last!

2010-03-23T21:38:00.000-07:00

As noted in my last post I was finding all sorts of problems with my region. Turns out that these were due to two things. First to control my critters I was killing them off bu broadcasting a commmand that triggers the llDie() function. But too many prims dying at once was messing up the asset server.

Also I was duplicating the critters en mass and that I led the server to treat my critters as the dreaded grey goo. Grey goo is a term for excessive rapid self replicating prims. See this discussion of the origin of the term from nanotechnology. When Second Life, and apparently OpenSim as well, detects too rapid prim replication this is treated as grey goo and a defense against this called the grey goo fence is activated.

Open Sim apparently doesn't warn you about this and I only discovered the problem when experimenting with my critters in Second Life. Second Life does warn you about grey goo and I got the warning rezzing even a small number of critters at once. Apparently the limit is about 240 rezzings in 6 seconds. Beyond that the ability to rez those prims is restricted. My inadvertant experiments suggest that in SL the limit may be more stringent than 240 rezzings in 6 seconds.

See http://lslwiki.net/lslwiki/wakka.php?wakka=GreyGooFence for a discussion of Grey Goo and the Grey Goo Fence.

This last week I worked out how to input and represent the critters genetics and the mutation routines. In my earlier systems I had the critters read their initial genetics from a note card. Instead I use the object description field to enter and store the genetics as a string of integers.

Right now the description field has 4 digits

position 1 = "1" or "2" "1" = haploid "2" = diploid. Right now the critters are strictly haploid so this position is ignored for now.

Position 2, 3, 4 are three loci each with 9 possible alleles represented by single character "0" through "9". For the haploid critters, this means there are 1,000 possible genotypes.

Since I mean my evolution simulation to be visual the genotypes in the three loci are used to make a vector that can be used with the llSetColor function.

So in the object description field the legitimate genetic description would be
"1045" . When a new critter is rezzed, the description can be passed to the offspring through the parameter in the llRezObject function.

I also wrote a mutation function:

string mutation(string start, float mforward, float mback)

Where the string is the genetic description, mforward and mback are forward and back mutation rates going forward to the next allele and mback the back mutation rate to the previous allele. So I assume if the allele is "7" then forward mutation would lead to a change to "8", and back would change from "7" to "6".

In addition another function setcolor(string thedata) takes the genetic string, isolated the loci and uses them to set the color of the critter and display the genetic description as using llSetText. I did this because just as in real populations most of the genetic variation leads to subtle variation in the population phenotypes over the short run.

The image shows the results. The critters started out with the color <.9, 0 .9> which sort of a light bluish green. After 4 generations of mutations if you look at the image you can see subtle differences resulting from successive mutations.

The critters still don't really interact with each other and wander around randomly, but not leaving my region. I did some work streamlining this routine so it was much more efficient.

Next up....adding simple natural selection to the mix.

Evolution Simulation III Devastation in Science Sim!

2010-03-08T21:14:00.000-08:00

Well not quite. But I was testing my critters to see how big a population my parcel in Science Sim could hold. Everything was fine until I went to delete them using a listen event with llDie triggered by a chatted command. Guess what, 600 prims dying all at once causes the asset server to have a fit: a bit disconcerting but Mic Bowman got things fixed....

And immediately after Mic's fix:

Thigs were still loading at this point. What Mic recommended is that I use a random number to determine when a particular critter is going to die so that when I issue the command to die the critters don't all die at once.

In SL this bit of code gives a quite realistic movement for my critters:

vector newpos = newcoodinates(llGetPos() ,3.0);

llSetRot(llEuler2Rot(<0,0,-pi/2>)*llGetRot());

llLookAt(newpos,1,0);

llSetPos(newpos);

But in OpenSim the critters don't seem to turn toward the target in response to llLookAt as they do in SL.

SLPro Conference Day 3 Invasion!

2010-02-25T09:39:00.000-08:00

Just down the road from my project is this collection of marvelous insects made with scupted prims...and they are flyable according to the menu options. But I guess you have to be the owner to fly them.

The Dragonfly is spectacular!

The builder by the way is Strat Inshan.

SLPro Conference Day 2

2010-02-24T23:37:00.000-08:00

My humble entry into the Shared Media competition.

Don't expect to win the $L 10,000 but I had fun putting together a little chi square demo showing how Google's Spreadsheet can be used on a prim. The hard part was working around the limitations of Google's Spreadsheet.

Sorry Google, you may be taking over the world but you ought to spend some time improving your spread sheet especially protections. I can't believe your programmers couldn't figure out how to protect just part of a spreadsheet!

I finally figured out that I can protect my original spreadsheet and have people access it and copy it and just work with the copy.

Grrrrrr......

SLPro Conference Day 1: A Rocky Start but...

2010-02-23T09:31:00.000-08:00

The key note got off to a rocky start with most participants not able to get audio and video for much of the time. But the big announcment is SL's Viewer 2 which we get to preview! Looks like a cleaner interface and my impression is that Viewer 2 renders graphics more rapidly than the current viewer.

But what is really cool is the viewer's shared media feature. One thing that I and other "content devlopers" in Second Life have groused about is the inability to display interactive sorts of media such as, well web pages. With the current Second Life viewer the user can display a web page by replacing using the llLoadUrl function but you can't interact with it. But now you can.

After the keynote we got to play for example with a drawing program and we could all interact with it in real time even though it was displayed as a texture on a prim. If you use a web page as a texture you can not only see the web page but you can scroll through the web page and even open new links just as with a standard browser!

Ahhh but there is more. Currently when you display a web page it uses you're parcel media feature which means only one medium per parcel. So if you are a teacher and want to display say multiple web pages you can't have them all display at the same time unless you subdivide your parcel into smaller parcels. Now you can!

This is a big deal for SL content providers and really integrates SL with the web. I just had to try it and works as advertised. So this image shows two of my blogs on separate prim's and these are all on the same parcel. You can do the same thing with media such as Flash sites opening up a new potential for gaming in SL.

I have just started working with this feature so don't have more to say about it...but it looks like web on a prim is here finally. and I think it is really going to improve the immersive experience in Second Life. I can almost forgive the keynote glitches for this.

NMC SL Pro Conference...

2010-02-22T20:15:00.000-08:00

The NMC SL Pro conference begins tomorrow and I will be there in amongst my first life teaching and meetings so I think my laptop will be my special friend through Thursday. The focus is on scripting...so hope to get some good tips. The schedule is here:

http://www.nmc.org/2010-slpro/program

The Selfish Herd: OpenSim Evolution Simulation II

2010-02-20T18:49:00.000-08:00

Been a bit distracted by academics but this week worked a bit on my evolution simulation. First I put limits on my critters so that if they escape my parcel they die. Next I set up a controller that uses or at least attempts to use llGetParcelPrimCount in a timer event to count my organisms and kill them all if the population grows beyond a certain size.

The script is straightforward:

But the script does seem to update the prim count properly in OpenSim unless I touch the prim with the script. What's weird is that I have used a very similar script in SL and it updates fine.

The other thing I have been working on is the duplication script itself. I am using the basic script givenn in the LSL Wiki at this link.

http://lslwiki.net/lslwiki/wakka.php?wakka=ExampleSelfReplication

This gives a pretty complete list of precautions if you want to make self replicating critters. So should you decide that you need some sort of self replicating critters pay real close attention lest you get the grey goo.

Right now I have the basic replication scheme worked into my code but right now the critters replicate only on a command from me...so they are on a pretty tight leash. The picture accompanying this post is after 8 doublings from a single critter. My critter sensing prim did not pick up that there were more than 128 critters so it is good thing I am not letting these things replicate on their own! The critters remind me of a herd hence the Selfish Herd after W. D. Hamilton's famous paper: Geometry for the selfish herd. J. theor. Biol. 31:295-311.

OpenSim Evolution Simulation I

2010-02-04T09:01:00.000-08:00

This is the first progress report on what's going on with my OpenSim Artificial Life/Evolution simulation introduced in this post.

Since I am interested in social behavior I think a good place to start is simulating a population where prisoner's dilemma is operating. The term "game" here used in the game theoretic sense, gets its name from the following scenario:

Two suspects are arrested by the police. The police lack enough evidence for a conviction. The prisoners are kept separate and the prosecutor visits each of them with the same deal. If one testifies (defects from the other) against the other, and the other remains silent (cooperates with the other prisoner), the betrayer goes free and the silent accomplice receives the full 10-year sentence. If both remain silent (they cooperate with each other), each gets only six months in jail for a minor charge. If each betrays the other, each receives a five-year sentence. Each prisoner must choose to betray the other or to remain silent. Each one is assured that the other would not know about the betrayal before the end of the investigation.

(modified from http://en.wikipedia.org/wiki/Prisoner%27s_dilemma)

Now this scenario may not seem related to evolution but it turns out that this is exactly the sort of thing that happens when two animals related or not might have choices to cooperate or not with other animals either of the same species or sometimes other species.

A couple of design issues revolve around topics like how to link the organisms' behavor to genetics, represent the genetics of the interacting organisms and how to pass that genetics to offspring. To get a feel for the general strategy I have used in the past, go to this post.

One new technical issue is that unlike my genetics activities and my discrete generation evolution simulation, the organisms I am using here have to be able to replicate themselves independently of some command from me. Now that a scary thought since I don't want to over run a sim with thousands of little evolving critters.

Fortunately the LSL Wiki gives a good rundown on how to make non invasive self replicating critters. For instance have them be killed if they get out of your parcel. Right now my critters are able to detect the parcel boundary and turn away from the boundary....but I will add the kill feature as an additional safety.

One of LSL's safety features isn't going to work in my case. LSL recommends using a counter that is decremented by 1 each time an offspring is replicated from the parent. The value of the counter is passed as the integer parameter in the llRezObject function and when the counter reaches zero say after 10 generations the critter dies rather than replicating. The problem is that I use this parameter to pass the genetics from parent to offspring.

So I need to figure out how to prevent non invasive critters from over running my parcel. My first impulse was to have each critter sense the number of critters in the parcel and stop them from replicating when the parcel count gets to a certain point-kind of a parcel carrying capacity. And that might be a good idea but the simplest way to do it might be to have one object track the number of critters in in the parcel and periodically send that to all the critters using llRegionSay on a private channel and have the critters individually adjust their replication as required.

A more interesting option might be to use a sensor event to get the number of critters in a set radius around the sensing critter and use that to adjust the rate of reproduction, perhaps make it negative. So critters in a region with few others would be able to multiply more rapidly than those at higher densities. I already use a sensor event to let the critters detect each other so I could modify that to do this as well. This would actually be quite realistic since organism's reproductive rates are often affected by density dependent factors.

So here is what I am thinking on the replication issue:

1. Implement a die if beyond land owned by me along with my current boundary detection routine.
2. Implement a central controller that determines how many critters are in my region and either kills them all or stops them from reproducing further if they get too numerous beyond some large population size say 4,000.
3. Implement the sensor option to determine the density of critters and adjust the rate of local reproduction. Should be possible to tweek this so the population's maximum would tend to run at a lower limit than 4,000, say 2,000.

Maybe I am being paranoid but who knows what sort of chaotic things can happen with 2,000 artificial life forms run around a sim unchecked. It would be the equivalent of pythons in the Everglades and probably really annoy my neighbors.

This may be interesting in its own right as a simple population growth model even with out the complication of prisoner's dilemma! If you want to join the fun and see what's going on, IM me as Paul Decelles in ScienceSim or as Simone Gateaux in SL . Remember, you need to configure your client for OpenSim and set up a user account. Also Avatars do not port between SL and Opensim.

The ScienceSim site will get you started.: http://www.sciencesim.com/ Make sure you read and follow the directions and rules carefully.

PS: SLurls don't work in OpenSim as far as I can tell but if you are in OpenSim I am in
Oregon North 47, 184, 23 in the ScienceSim grid.

I know I have been quiet...

2010-01-30T14:41:00.000-08:00

But there is a lot going on. First of all I am busy moving and tweaking some of my projects from Spring and its always interesting to revisit scripts with a bit more maturity and say to one's self. "Gee that's sloppy" or "hmm why didn't I do it this way".

At any rate some of my online students will be able to work on my college's island and use some of my materials for their course work and I will be using some of the simulations in lecture as well.

Also, as if that isn't enough, I have a six month land grant for a larger scale project at INTEL's Science Sim using OpenSim and am starting an artificial life type simulation to visualize some of the interesting effects spatial distribution and simple behaviors can have on group properties and evolution. This is inspired both by my Second Life sabattical project on evolution but also by my interest in social insects where complex group behavior arises from simple individual behaviors. And it is inspired by Aaron Duffy's work on fern genetics at Science Sim.

The difference between my project and Aaron's is that his is a special purpose project focused on fern genetics while I am working on visualization of more general sorts of models that visitors can work with and watch evolve over time. My project is more like some of the Artificial Life described here:

http://en.wikipedia.org/wiki/Artificial_lif e

So this is quite different than my earlier simulation which uses population wide parameters such as fitness to determine what mix of critters to have as you go from one generation to the next. It is also a bit like the now defunct (unfortunately) ecosystem project in Second Life. One big difference is that I am going to use LSL and Opensim functions to change the characteristics of the critters (within certain limits so as not to blow stuff up and crash servers) in response of changes in an underlying "genetic" system. So organisms of different sizes, shapes and with different rates of movement and types of behavior would be allowed to mutate and evolve.

I will be reporting on this throughout the Spring. The attractiveness of OpenSim is that depending on your server many of the limits of Second Life such as the small number of prims available to the user in a parcel. For instance I have use of an OpenSim region that supports 6,000 plus prims. This is all part of INTEL's land grant program. If you are interested you can learn more at http://www.sciencesim.com/wiki/doku.php or at:
http://shenlei.com/2010/01/03/sneak-preview-of-settlement-land-in-sciencesim/

If want to see what can be done at ScienceSim in terms of large scale simulations check out these pictures of the ScienceSim model of Yellowstone Park: Yellowstone without the bears. The picture in this post show me, actually my ScienceSim Avatar, and some of the critters I am working on. These guys look to me a lot like Paramecia but one visitor thinks they are more like banana slugs. Right now they don't do much but wander randomly around the parcel and when they encounter each other they stop for a bit and alternately blink red and white. I will not tell you what my wife thinks they are doing ...that may be a bit TMI.

For those interested here is a bit more about using geological data with OpenSim at ScienceSim.

As always, you can contact me in SL as Simone Gateaux or now in ScienceSim as Paul Decelles.

Welcome JCCC Autism spectrum conference!

2009-10-15T07:20:00.000-07:00

Virtual World Resources related to Autism

This is a selected list for the JCCC workshop on Second Life and Autism being presented by Marziah Masala and me October 16. You can get an SL notecard with these links and relevant SL land marks by visiting my JCCC home at
http://slurl.com/secondlife/JohnsonCountyCommCollege/36/92/65
You need to have Second Life installed.

Once there touch the rotating box with the brightly colored autism ribbon.

Virtual World Resources including virtual world resources for young children

Second Life
http://www.secondlife.com

Virtual world with over 90% user-created content. Must be 18 to create an account. Basic accounts are free, but "Linden dollars" can optionally be spent and earned in-world. Some users have created in-world businesses that earn enough to support them in "first life," but most view their in-world business as a hobby.

Suggested places to visit: Virtual Ability Island, Autism Society of America, Autism Liberation Front

Second Life Teen Grid
http://teen.secondlife.com

Teens 13-17. This is exactly like Second Life's main grid, except that membership is restricted to teenagers and educators who pass background checks. Teens also have restrictions on how many Lindens they can purchase per month and stricter rules on conduct. Basic accounts are free, but paid accounts are required for land ownership. Parents can also request an activity summary for teens. Teens can "graduate" their avatar and possessions to the main grid when they turn 18.

Alice
http://alice.org
free download

Alice is a programming language designed for kids to make programs that can be uploaded to the Web and shared with others. The 3D virtual world programming environment was designed by Carnegie Mellon and teaches object oriented programming principles that apply to more advanced programming languages like C++ or C#. There are also lesson plans available for teachers.

Although it's designed for kids, they should have strong reading and computer skills.

Project Wonderland
Free
http://wonderland.commonneed.com:8080/Wonderland/

Sun Micrososystems Java environment for virtual worlds. Mainly aimed at higher ed/corporate environments but
see http://isocial.rnet.missouri.edu/ for video about iSocial at the University of Missouri. iSocial is designed to help autism spectrum youth develop social competencies and uses Sun's Wonderland software.

Open Sim
http://opensimulator.org/wiki/Main_Page

Open Sim is an environment similar to Second Life, but open source. It can be run on a single server instead of connected to a large grid. Building content in Open Sim is nearly identical to doing it in Second Life.

Young Children:

Secret Builders
http://secretbuilders.com/
Free
Secret Builders is a virtual world for 5-14 year olds emphasizing education and creativity. Children interact with virtual versions of famous historical figures and characters and can create and publish their own writing, art, and videos.

Club Penguin
http://www.clubpenguin.com/
Free membership, but some activities require a paid membership

Virtual world for kids from Disney where each avatar is a penguin. Attempts to offer personally identifying information like addresses/phone numbers are filtered out by the system. Parents can choose between allowing free dialog or allowing only limited, scripted communication.

Along the same lines, Disney offers:
Pixie Hollow
http://pixiehollow.go.com/
Pirates of the Caribbean (10+ for simulated violence and drinking)
http://piratesonline.go.com
Toon Town
http://play.toontown.com/

And Mattel offers Barbie Girls http:barbiegirls.com/

Webkinz
www.webkinz.com

Membership requires a purchase of a plush Webkinz doll per pet per year ~ $10-15

This is a virtual world where members care for pets that resemble their stuffed toy. They can earn points by playing games and then spend those points on items relating to their pets, such as food, clothing, furniture, etc. The pets have monitors corresponding to their health and wellbeing of the virtual pet.

Articles and videos related to Autism activities in Virtual Worlds.

Naughty Auties from cnn
http://www.cnn.com/2008/HEALTH/conditions/03/28/sl.autism.irpt/index.html

Link to video and article about Amanda Baggs.
http://www.miltonbroome.com/2009/05/autism-awareness-in-virtual-world.html

Autism community forges virtual haven
http://www.guardian.co.uk/society/2006/mar/08/guardiansocietysupplement1

Virtual Worlds Turn Therapeutic for Autistic Disorders
http://chronicle.com/article/Virtual-Worlds-Turn/11607/

Milton Broome Autism and Aspergers in Second Life
http://www.slideshare.net/Milton.Broome/autism-and-aspergers-in-second-life

Internet resources for special neds educators
http://www.emergingedtech.com/2009/07/internet-resources-for-special-needs-educators-this-week-autism-pdd/

Seond Life virtual world: A heaven for autistic people? http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WN2-4TDBMGK-2&_user=4558894&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000063405&_version=1&_urlVersion=0&_userid=4558894&md5=8962aef203a348469c83462b49d9a641

Autistic Acceptance, The College Campus and Technology:Growth of Neurodiversity in Society and Academia
http://www.dsq-sds.org/article/view/146/146

Monitor on Pyschology, Can Second Life Therapy help with Autism?
http://www.apa.org/monitor/2009/09/second-life.html

A Second LIfe for E-Health Prospects for Use of 3-D WOrlds in Clinical Pyschology
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2553247/

A Virtual Environment for Teaching Social Skills
http://www2.computer.org/portal/web/csdl/doi/10.1109/MCG.2009.57

iSocial 3D Virtual Learning: Helping youth with Autism Spectrum Disorders develop social competence
http://isocial.rnet.missouri.edu

iSocial Video
http://vimeo.com/2064686

Welcome SidLit!

2009-07-30T17:18:00.000-07:00

Science Simulations for students in Second Life at SidLit July 31, 2009.

Welcome from Simone Gateaux and her carbon based side kick Paul Decelles!

Install the Second Life viewer first and create your avatar.

SLURL to Sidlit Notecard with landmarks:
http://slurl.com/secondlife/Carmine/87/145/135

When you arrive, touch on the box which will offer you a note card with landmarks to the sites discussed in my presentation. Accept the note card into your inventory.

Other links-not SLURLS:

Some scripting resources:

Scratch for Second Life:
http://web.mit.edu/~eric_r/Public/S4SL/

Autoscript: A web based script generator:
http://www.3greeneggs.com/autoscript/

Other virtual World Systems:

Virtual Worlds: Best Practices in Education 2009:
http://www.vwbpe.org/

Wonderland
Blog Entry about Wonderland:
http://slbiology.blogspot.com/2009/03/wonderland.html

Sun's Wonderland Site:
https://lg3d-wonderland.dev.java.net/index.html

Video about iSocial at U of Missouri in Columbia MO:

OpenSim Links:
Blog entry about OpenSim and Intel's Science Island:
http://slbiology.blogspot.com/2009/03/opensim.html
OpenSim main site:
http://opensimulator.org/wiki/Main_Page

Exit Reality
Blog Entry about Exit Reality:
http://slbiology.blogspot.com/2009/02/another-virtual-reality-system.html

Exit Reality Site:
http://3d.exitreality.com/

Mitosis I Wigglies

2009-07-21T21:01:00.000-07:00

Animated and wiggly duplicated chromosomes (Reddish wormie things*) scripted to separate and behave as they do during anaphase. The green structures are the paired centrioles, the pink box when touched tells the sister chromatids...those are the wigglies... to separate into unduplicated chromosomes.

*notice the precise biological terminology in this post.

Lots of stuff: Part 1

2009-07-21T09:09:00.000-07:00

Been busy teaching in first life this summer but also with Second Life as well. In about 2 weeks I in my first life presence as Paul Decelles will be giving a presentation on doing simulations in Second Life to the SIDLIT conference in Kansas City. My topic is Scientific Simulations in Virtual Worlds and I will cover some of the stuff I did on my sabbatical, lots of which is on this blog, and also discuss alternative virtual world systems for doing simulations.

Also, I am part of a group of Second Lifers working over at Nature Magazine's Second Life site at Elucian Omega associated with their Second Nature site. The idea is to have people share lab space to work on their own projects and by sharing space and working in close proximity hopefully the collaboration engendered will lead to greater productivity.

The group includes a bunch of really talented people including Max Chatnoir, whose Genome Island Site I have visited numerous times. Another really talented person doing some exciting work on visualizing proteins is Hiro Sheridan who does lots of really cook stuff on visualizing protein structure. We each have our own project areas, my project is to build a mitosis and meiosis simulation, something I have wanted to do, but it is a bit more complex than the other things I have done and so its only now do I have the background in scripting to attempt this.

Since we have people at different levels of Second Life experience, we are having some basic workshops to get us started. For instance the first week was basic building, given by Hiro. I don't know about the other participants, but I thought it is really valuable to see how another person explains Second Life.

In Second Life there are often several ways to ummm build a cat. So it is easy to get stuck in one way of doing things. For instance, when I duplicate an object I always do it from the pie menu and had forgotten about the little shift and drag trick, which is actually a lot easier. Another example: our first homework assignment is to build a chair and while I have done some building had not built my on chairs-just quickly slapping things together not not being too concerned with the llSitTarget function.

So this morning, I spent some time building a chair and using llSitTarget...and of course it needed a table, and a nice rug. The result is shown here. Now I can replace those lumpy cushions in my lab space!

Particle fun

2009-06-04T20:31:00.000-07:00

In building my protein synthesis model, I really don't want to use more prims than needed. At the same time I want to display the results in a more interesting way than than as a string. So I have been playing with a particle system.

Here's the result. The script is modified from a snippit of script that generates a particle banner by Debbie Trilling, part of her Random AV profile script.

I tweaked those settings to give two functions that collectively take a text string and converts it into a string of particles. One could use this to display text messages, but here I am using it to display the one letter amino codes of a proteins primary structure. The colors represent the type of amino acid (non polar, acidic, polar non ionizing etc). Of course you have to put a texture for each symbol.

The two functions I developed to represent the protein's primary structure as a string of particles

particleletter(string texture, float distance, float size)

particlemessage(string message, float distance, float size, float speed)

This system unfortunately does not work reliably in that the individual particles are not always produced so the display will have gaps in it. This is a big problem with long polypeptides such as this one here which is the primary structure of an opsin protein.

Another limitation is that the particles only last for a minute or so.

For the student version I will use a small polypeptide with 10-12 residues, that way the DNA template and RNA will require only 30 or so DNA bases. That is a lot more practical.

What's going on at the lab?

2009-05-29T08:33:00.000-07:00

My protein synthesis functions, got me thinking about developing an animated model of protein synthesis that actually does transcription and translation and so I have been trying to figure out a good way to do this. The figure shows a animated prototype for an operon that I have been working on. The model loosely mimics the behavior of the repressor protein and inducer of the lac operon as well as the RNA polymerase.

In the picture the repressor protein (red) is sitting on the operator and the RNA polymerase(purple) cannot attach to the promoter to begin transcription of the operon's coding region (teal). The inducer is the green ball. The can see how the system behaves by touching say the inducer which will then bind to the repressor protein, preventing it from blocking the RNA polymerase.

This view shows the repressor protein not on the operator allowing the RNA polymerase to begin transcription. As the polymerase moves down the coding region the transcript (yellow) grows.

When the RNA polymerase reaches the terminator part of the operon the polymerase detaches, the RNA detaches and the small ribosomal subunit (brown) attaches to the start of the start of the transcript.

Obviously there are some simplifications here. For instance in prokaryotes translation can begin while transcription is still on going and I don't bother with the details of how RNA polymerase works.

The goal is to let the students input a short DNA sequence, animate transcription and show the mRNA in local chat (or perhaps as hovering text above the mRNA) and optionally send it as an e-mail. Then as translation proceeds actually have the tRNA's bring in the amino acids and make a short polypeptide. In this scheme the mRNA is a single prim but carries the codons as data inside. But the development of the polypeptide via translation is explicitly animated in terms of what happens at the ribosome, each amino acid shown as a separate object.

In the foreground are some crude tRNA's (orange rectangles) some of which have amino acids represented by balls attached to them. This is going to be a fairly elaborate scripting effort with some neat tricks involved so stay tuned...

My sabbatical is officially over and have already given my sabbatical report. I will be teaching summer school-just two intro biology lecture sections. Also at the end of July I will be speaking on Science simulations in Second Life at SidLit and giving also giving several local talks about Second Life in general.

Protein synthesis functions

2009-05-14T09:24:00.001-07:00

The chromosome module mentioned previously is part of my JCCC evolution build on the agents of evolution. Mutations are any sort of heritable change in the DNA, that is changes in the DNA passed on to future generations of cells. Chromosomal mutations are large scale rearrangements, involving many nucleotide bases. But a discussion of mutations has to include point mutations-changes on the level of a single nucleotide base.

Discussing these means dealing with protein synthesis first. So the last couple of days I have been scripting core functions to do the basic steps in protein synthesis , namely transcription and translation. Max Chatnoir over at Genome Island has a nice little collaborative game related to protein synthesis, (http://slurl.com/secondlife/Genome/119/144/54) but since my focus is on evolution at JCCC, I've decided to build my module around a series of functions that start with a strand of DNA, transcribe that DNA to get a messenger RNA and then translate that DNA.

Doing this involves a series of string manipulations and here are some functions I've written specifically to manipulate DNA and RNA represented as a sequence of letters:

string stringclean(string toclean, string allowed);

This function takes a string toclean and strips out blanks and any characters that are not allowed after converting upper case letters to lower case. Permissible characters are in the string allowed. For instance DNA nucleotide bases are represented as a,t,g or c so the the string allowed is "atgc". Were the string toclean representing RNA then allowed would be "augc". Just to be safe the function trims any leading and trailing spaces. The reason for this function is to try to catch elementary mistakes and strip out extra characters from genetic information copied and pasted from GenBank or FASTA formatted data.

string compdna(string dna);

This function takes a DNA strand and outputs the complementary strand. This is useful because data bases often give a so called sense strand which is like the RNA only with "t" shown instead of "u". For illustrating transcription you need to start with the complement of the the sense strand as happens in the cell. Hence the need for a function to generate the correct DNA strand.

string transcription(string dna);

This function takes what ever DNA strand is given it and mechanically does transcription. It doesn't recognize any sort of promoter region such as a -35 or Pribnow box. If you don't know what those are..well don't worry.

string transcodon(string codon);

Takes an mRNA codon and uses the standard genetic code table to translate the codon into the corresponding amino acid using the standard genetic code, used by most eukaryotes. This function is needed for the translation function:

string translation(string mrna);

This function takes the mRNA string and using the function transcodon, translates the mRNA into the polypeptide that would be produced in the cell at the ribosome. The function does not recognize the Shine-Dalgarno sequence and mRNA's start for simplicity with the start codon, 'aug'. The function terminates the polypeptide when it recognizes a stop codon. Polypeptides are represented by the now standard one letter abbreviations commonly used in protein data bases. Thus it will allow the student to compare the effects of frame shift mutations caused by insertions or deletions to substitutions on the resulting polypeptide.

These functions work for small genes with on the order of 250 nucleotide bases. One frustrating thing is the limited ability of SL to write data to files and for now the easiest way fo the user to save the output, is to e-mail it to themselves.That will be built into the module as an option. Otherwise users would have to cut and paste from the chat window.

Users will have the option of using data they obtain from another source by configuring a note card with the raw data copied from say NCBI, or using a small gene data set preloaded onto a note card.

Three other core functions are being developed:

string makesubstitution(string dna) makes a random base substitution in an original DNA strand.

string makeinsertion(string dna) makes a random insertion while
string makedeletion(string dna) makes a random deletion.

But these will be easy to make. The activities are being designed around a pencil and paper exercise I use in my classes currently, only now the students will be able to use more realistic data and quickly investigate at a number of different mutations.

Sabbatical Presentation

2009-05-11T11:15:00.000-07:00

Last Thursday I gave my Sabbatical report on my Second Life activities this semester. It is only about 20 minutes long so it is really difficult to say and show everything one might want to show. The video was just posted today so if you want to see my take on what to say about Second Life in less than 20 minutes have a look at:

http://video.jccc.edu/publicvid/innovations/PaulDecelles.asx

JCCC Chromosome module

2009-05-06T21:02:00.000-07:00

Chromosome Build at JCCC site. This is part of the evolution unit being installed at the JCCC site. It currently includes the human chimp ideograms courtesy of ENSI. You can see two of my real simple viewers, the one on the left with some narrative and the one on the right with the human chimp chromosome ideograms.

On the side directly behind me are some red and blue chromosome, that illustrate reciprical and non reciprical translocations. The four cylinders with the colored horizontal stripes illustrate basic chromosomal rearrangements. Because of their importance, I want to have a separate activity for duplications and the evolution of gene families if I can keep it simple.

On the right hand side of the picture a some of my human chromosomes that link into the Ensemble web site.

The chromosome build is at http://slurl.com/secondlife/JohnsonCountyCommCollege/38/94/65

This is open access but the rest of the JCCC sim is currently not.

Mitosis in the Morning...

2009-05-02T22:11:00.000-07:00

As part of my evolution build I wanted to have an activity related to chromosomal rearrangements. We know these are important in evolution, some of the clearest examples are in our own evolutionary history. So I developed a series of human chromosomes similar to those over at Genome Island.

These consist of representations of human chromosomes, textured with the standard banding patterns (ideograms) that geneticists use. When the user clicks on the chromosome, menu dialogue allows the user to look at the similarities between the human chromosome and the chromosomes of selected mammals: mouse, chimp, and the macaque. This is done using a data base portal called Ensembl. This displays regions of synteny, which in the bioinformatics context refers to regions of chromosome that have the same arrangement of genes in both species. Here is a quick example for human chromosome 1 showing the regions of synteny in chimp chromosomes to human chromosome 1.

It's probably hard to see what's going on here. But the big white structure in the center represents huna chromsome 1, and the chimp chromsomes with regions of synteny for human chromosome 1 are shown to the left and right. Human chromosome one has synteny with most of chimp chromosome 1 with just a little region of synteny with chimp chromosome 2A and chimp chromosome 10.

Speaking of chromosomes, Max Chatnoir was wishing for a build related to mitosis and meiosis so to help me think about this, I spent the last couple of days building mitosis at my carmine site. None of this is scripted and it still isn't clear what the best strategy for this is.

Here is a quick look at my mitosis builds. These are quite large and I will probably scale them down a bit. They are relatively simple but do take up a fair amount of real estate-not prims but literally really real estate.

This shows prophase, prometaphase, metaphase, anaphase and telophase. You can see me in the bottom of the picture. Each of the "cells" is 10m in diameter.

I don't normally build this big, but it seemed easier to do this big. The mitosis build is currently at:
http://slurl.com/secondlife/Carmine/120/190/138

Here is a close up of metaphase when the chromosomes (shown in red and blue) are lined up in the middle of the cell.

My thinking is rather than animate mitosis, having this build (maybe on a smaller scale) and then an activity center where students can play with chromsome models like they do in lab. I think it is possible to script the chromosomes to sense a proper arrangement. That would provide a nice collaborative activity.

Speaking of collaborative activities, I also tweaked my predator natural selection module and installed it on my college land site. The module is packaged appropriately with a velociraptor texture so hopefully student predators will get in to the spirit of things.

Here's the module installed at http://slurl.com/secondlife/JohnsonCountyCommCollege/41/95/64. I am also building an activity center just above Predator which students will do first to study natural selection under less challenging conditions.

A Little Break

2009-04-27T21:59:00.000-07:00

Last week we went to Big Cedar in the Ozarks for a little break. No computer work at all. OK I did sneak a quick look at e-mail but that is it. I did take lots of pictures and will get them posted on my flickr stream this week. Since I just had my macro lens took lots of flower pictures. Here are a few shots:

This is a male carpenter bee, Xylocopa virginica. This is a macro uncropped so you can see maybe just how close he was to my lens!

We timed this vacation to coincide with the Dogwood bloom. Maybe we were a week late for the best viewing but the trees were still quite nice!

Most people might think I took this shot for the bee. Actually, no. I had never seen ornamental cabbage when it bolts, or at least had never paid attention to it. But the yellow blossoms against the purple stems are quite striking making me reassess my dislike of ornamental cabbage.

Today I had meetings at school and spent sometime designing a chromosome activity. More on that later this week.

Evolution IV

2009-04-21T12:25:00.000-07:00

Now that I have my drift and selection modules in hand, the next goal is to working on activities that can be fit around them. I know this is a bit backwards on the surface, but what I want to focus on in my evolution module is mainly the agents of evolution. These are basically:

Mutation
Genetic Drift
Non random mating (of which there are several types!)
Migration
Selection

To house the activities related to these agents, I have deviated from my photosynthesis and genetics design and come up with a series of open activity arenas. Each one will have a sensor driven script for tracking visitors, an simple activity rezzer of my own design, built into one of the corner posts. Rather than use my Carmine land, I am building the agents of evolution site at my College's island. The design challenge is to work with in a 281 prim limit.

The natural selection and drift modules use temporary prims so only the rezzers for these count. My 5 activity arenas and office take up a grand total of 67 prims so that leaves me a budget of 220 prims. Now I can stretch that, since activities will not be rezzed all at the same time since each arena but each activity has a "budget" of 40 prims. Ah but each activity arena can hold multiple activities in waiting so the "budget" isn't so draconian after all. 220/5 activity arenas.

Oh and my goal is to have this done by May 7th. At least now I can focus on design more rather than the arcanity of the LSL's llfrand function and other such issues. Plus I will have two radically different design approaches to compare, the module in a box approach of my photosynthesis and gentics builds versus my more open arena centered approach.

Evolution lends itself to the more open approach, and this summer I will install photosynthesis and the Cami genetics modules in Carmine using the arena centered approach. That way I can have the same material side by side with different design features to begin to assess what works best with students.

Evolution III: the Predator version...

2009-04-18T19:03:00.000-07:00

My natural selection module works pretty well but one concern was how to make it a bit more interesting. One obviously way to do that would be to make Cami's that move so that they are harder to spot and catch.

So since I really don't know a whole lot about making things move in Second Life, the first thing I did was develop a cami that will roam around randomly but stay in my land.

The strategy I developed builds on a function I had previously scripted for random movement of a prim:
//--------------------------------
vector newcoodinates(vector pos ,float pathlength, integer start)
{

integer icount;
float deltax;
float deltay;
vector temp;
float ground;
temp = llGetPos();
if (start = TRUE)
{
deltax = llFrand(pathlength)-pathlength/2;
deltay = llFrand(pathlength)-pathlength/2;
temp.x = temp.x + deltax;
temp.y = temp.y + deltay;
ground = llGround(<0.0,0.0,0.1>);

temp.z = ground;
if (llGetLandOwnerAt(temp) == llGetOwnerKey(llGetKey()))
{

return temp;
}
else {

return pos;
}
}

return temp;
}
//---------------------------------------------------

The idea is to take the prim's current position and update it with a "random" number between zero and some maximum path length. That's what this statement does in the one dimension:

deltax = llFrand(pathlength)-pathlength/2;

Since I want the cami's to hug the ground for the vertical dimension I use LSL's llGround function:

ground = llGround(<0.0,0.0,0.1>); the result is the vertical dimension.

One thing that flummoxed me for awhile was how to keep the cami in bounds. My original idea was to have the cami detect when it was on someone else's land and have it turn around and leave. But that turned out to be more difficult to script in a totally fool proof manner to this trigonometrically challenged scriptor. Besides, it seemed much better and nicer, to stop the cami from even entering someone's land in the first place:

So that's what this piece of code does:

if (llGetLandOwnerAt(temp) == llGetOwnerKey(llGetKey()))
{

return temp;
}
else {

return pos;
}

The rest of the basic movement script is deceptively simple:

default
{

state_entry()
{

do {

newpos = newcoodinates(llGetPos() ,2,start);
llSetRot(llEuler2Rot(<0,0,-pi/2>)*llGetRot());
llLookAt(newpos,1,0);
llSetPos(newpos);

llStopLookAt();

}
while (start==TRUE);

}
}

The rotation functions are sort of trial and error on my part but the cami's end up with an interesting waddling motion, so I am pleased with that even if it wasn't quite what I wanted at first.

Deceptively simple because I also needed toggle that stops the cami's so I can catch them and for determining the cami genotypes and phenotypes. Fortunately my previous cami scripts are easily modified to to work with my cami movement script.

The result is Natural Selection the Predator version right now at:

http://slurl.com/secondlife/Carmine/123/151/135

Just touch the light blue prim and 50 maddingly difficult to catch cami's will start swarming around:

The idea is to put yourself in the role of a predator selecting against one of the phenotypes. The phenotypes use my cami genetics scripts and it is possible to select against one of the phenotypes and eliminate the genes for that phenotype, but its harder than it looks.

This version will allow you to keep selecting until the the cami's derez at which point you must touch the blue prim again to rez the next generation of cami's using the ones you didn't get as the parent population. I may change this feature.

The main script in the cube again handles all the book keeping and generates a report tracking the allele frquencies when you touch it to rez the next generation.

By the way, when you touch one of the camis in your role as predators they explode red blood thanks to a little particle script...next will be sound effects.

So even if you don't know squat about population genetics or evolution, at least you get to blow up stuff. I guess there is a bit of adolescent even in the most prim and proper of us.

Oh if you visit, watch out for cami sharks.

This week I will be designing some suggested activities related to evolution using my cami system and also taking a few days for a trip to the Ozarks for springtime dogwood viewing, I hope.

Evolution II 101 Dalmations?

2009-04-14T15:33:00.000-07:00

Well no, how about 30 Caminalcules after selection favoring a recessive allele for 8 generations. The natural selection module beta is finished and works very well. The basic strategy is to have the user or users act as visual predators removing camis from the population. The module might for instance be on a certain background where some cami phenotypes are real obvious while others are not.

The "predators" remove cami's by touching them, and the population is up dated. After a set period of time say 1 minute the remaining cami's are used to make a new population, which the module generates when it is touched and the cycle is repeated until only one genotype remains or until the users give up.

At the start of each generation the module generates a report in chat on the screen showing the allele frequencies for both of the cami loci.

If Cami's are never "eaten" the result is genetic drift. So this module really combines genetic drift and natural selection. It does not use or even compute selection coefficients, but one could add that to a report.

A Scripting Interlude

2009-04-13T11:30:00.000-07:00

While revisiting my genetic drift module and starting my natural selection module, I decided to fix a potentially annoying problem. Since Caminalcules rez as physical objects sometimes they behave really flaky and end up in other regions. Right now they are set to die on their own after a set time but that would be a scant comfort to another land owner who has one of these things appear on her land.

With the help of the good folks in the College of Scripting Music Science group here's the basic strategy...

default {
state_entry()
{
llSetTimerEvent(1.0);
}
timer()
{
// check if the touching person is over the script owner's land

if (llOverMyLand(llGetKey())) {
llSay(0, "the prim is on my land.");
} else {
llSay(0, "the prim is NOT on my land.");
llDie();
}
}
}

Not real hard and experienced scripters probably know about llOverMyLand, but it solves one of life's little mysteries. I can of course shorten this to a single if statement if I just want the critter to die, but I might want different sorts of behavior depending where the critter is, hmmmmm.

By the way, since I have several parcels, I was interested to find that llOverMyLand doesn't care what parcel the object is in just whether or not you own the parcel.

Soror Nishi's at it again...

2009-04-11T23:22:00.000-07:00

I am a big fan of Soror Nishi's phantasmagorical plants and was thrilled to see that she has lots of new stuff on her site. Some of her things are pretty prim intensive and much of my stuff is the same way. So prims are precious. But I do believe in supporting artists I like to the degree that I can so did find a couple things that were low prim.

Here is one of my two buys sited in my land.

Camilab is in the background.

You can visit Soror at http://slurl.com/secondlife/Lifstaen/10/50/228

Definitely worth it.

Also today, actually yesterday now I spent some time in the Costa Rica sims poking around. These are definitely worth a visit as they are very detailed.

Here is a view from the Palo Verde sim:

By the way the Costa Rica builds are so nice that for the first time I have been tempted to buy into a private region...but its quite a bit more expensive than my mainland region.

I recommend Cocos Island which you can visit here:
http://slurl.com/secondlife/Cocos%20Island/128/218/1002

Here are a couple of pictures:

This bridge is quite famous in RL.

An example of the wonderful plant texturing on Cocos Island.

A certain cell membrane...

2009-04-11T13:43:00.000-07:00

My biology viewers might recognise what this SL model is supposed to be.

This is a preliminary prototype for a neuron membrane showing stylised transport proteins (purple). The round guys with the lids are gated sodium proteins the lidless tubes are gated potassium channel proteins. The "lids" on the sodium gates will be scripted to pop open to let Na+ ions through while the bottoms of the K+ channels will flip open and closed.

The oval shaped guy on the right is part of a Na+/K+ pump.

All these proteins are embedded in a stylised plasma membrane (red fatty acid residues connected to white polar heads with phosphorus for the phospholipids).

This project is actually part of a planned metabolism build which uses the neuron to illustrate how cells use active and passive transport for complex processes. So it's not meant as a full action potential simulation though my scripting strategy will take that possibility into account.

Fret no more!

2009-04-05T15:08:00.000-07:00

When at the Best Practices conference several presenters beefed about having to face the slide viewers in use to advance their slides.

Well, heated discussions of the merits of slide presentations in SL aside, I modified my simple viewer discussed in my last post to take care of this problem. So fret no more SL conference presenters because now there is Simone's absurdly simple minimalist podium slide viewer/podium! (AKA Silly viewer)

It consists of a big viewer for the audience and a small viewer that the present er can use to control the slides while facing the audience! All you do is transfer your slide textures from you inventory to the inventory of both the big and small viwers and you are good to go.

I haven't tested it on big sets of slides so I don't know how Erich Bremer'sbuffering system will work with big sets. But it took about 5 minutes last night to whip this together (with a last minute change tonight). By the way I did not start out to make this viewer but it was a proof of concept to myself of another project, namely to update my clunky image map type viewer used in my photosynthesis build. More later.

The picture shows my male AV, Simeon Gateaux who has his own land next to mine and he tests permissions etc.

So if you think my silly little viewer might be of use to you (you can resize and move both prims), you can IM me, Simone Gateaux, in SL or stop by my garden spot (SLurl) in Carmine and grab a copy to try and a note card. It's free but both feedback and donations toward my private tier are accepted.

All you have to do (and this is changed from my desription in SLED BTW, is rez the viewer and insert your slides in the right order (careful here SL will put them in alpha order) into the "podium", resize the main viewer, position the podium and you are ready. Do not mess with the blacked out parts of the prims. They hide the buffered textures.

The Cami Lab is up!

2009-04-03T13:39:00.001-07:00

The Caminalcules (camis for short) have been safely installed in a Mendelian Genetics lab module called the Cami Lab. I use my note card configurable camis to illustrate dominance relations, monohybrid crosses, and dihybrid crosses. The evolution module will be directly underneath.

I have had to readjust my land and merge several parcels to give me some prim breathing room. Feel free to come and visit Cami Lab currently at:

http://slurl.com/secondlife/Carmine/128/144/136

As part of this, I rescripted my simple viewer to use Erich Bremer's double buffering script which makes loading much faster. My essentially new viewer uses LSL's way cool llDetectedTouchST function. This function detects where on a prim's surface you are touching and returns that as the x and y terms of a vector.

You can then access, these to do things like change a slide or teleport. What is really cool is that the coordinates are normalized to the size of the prim so they are presented as a float between 0.0 and 1.0, so if you stretch, say a viewer, the detected function still works properly.

Evolution I: Simulating genetic drift with Caminalcules

2009-04-01T09:29:00.000-07:00

So far I been working with my caminalcules in terms of genetics. But of course-and maybe someone ought to tell creationists about this-evolution and genetics are logically connected and evolution follows from genetics. So naturally I want to use my system to simulate the basic mechanisms of evolution.

Yesterday and today I programed a prototype Evolver (pink square) that simulates genetic drift. Genetic drift is an agent of evolution where a population's genetic make up changes due to sampling error. Drift is particularly important for small populations, such as caminalcule populations which given the prim limits in SL can never be very big.

Genetic drift is actually easier to simulate than natural selection, so it makes a good starting point for scripting and probably also for students to play with.

To look at populations of caminalcules I treat the population as a list containing the genotypes of all the individuals in the population. I use the same phenotype routines developed for genetics crosses and simply can access the approriate caminalcule through the list index.

Next I had to write a series of population functions:

string randommating(list the_pop) chooses two individuals from the population at random to mate and produces one offspring.

initialise(integer popsize) produces an initial random population and stores it in a list called start_pop_list and returns that list after rezzing an offspring:

Here's a snippet form this function:

start_pop_list = start_pop_list + genotype;
pass2offspring = (integer)genotype;
llRezObject("bigpup",llGetPos()+<2.0-llfrand(4),2.0-llfrand(4),0>,<0,0,0>,<0,pi/4,0,0>, pass2offspring);
}
while (++icount
return start_pop_list;

Most of the other routines are functions made before for the Caminalcule genetics module. So there is nothing new here. The simulation is direct in that I do not calculate allele frequencies and sample from that.

Doing random mating is pretty easy and here is the new function that handles that:

string randommating(list the_pop)
{
integer index;
string organism1;
string organism2;
string thezygote;
string gamete1;
string gamete2;
integer pop_size = llGetListLength(the_pop);
index = irandom(0, pop_size-1);
organism1 = llList2String(the_pop,index);
gamete1 = make_a_gamete(organism1);
index = irandom(0, pop_size-1);
organism2 = llList2String(the_pop,index);
gamete2 = make_a_gamete(organism2);

//----pick 2 organisms at random to mate from the_pop, self mating allowed----
//list the_pop must have been checked!

return make_zygote_string("4",gamete1, gamete2);
//4 because we assume independence here
}

Well so what happens with genetic drift? I want to write routines to quantitatively track what happens, but for many situations running the drift script for for a number of trials ought to get the idea across so here are some pictures from two sets of runs.

My first run started with a population that looked like this:

Four generations later...

Notice the pink and green phenotypes are becoming more common. The the genes related to the white caminalcules have apparently been eliminated. Since the genes related to the white photype are recessive the student might think (as did some geneticicts in the early 20th century) that the recessive allele ought to dissappear over time any way.

By the 11th generation all you have are these caminalcules:

Actually the picture shows the population after 14 generations since I wanted to make sure the other types were eliminated. This nicely shows that the effect of genetic drift is to reduce genetic variation in a population.

Now consider a trial starting with this population:

Not very different than the starting population from the previous run. But look what happens now! This is at generation 10. Note the large number of white caminalcules. Remember white is recessive.

And by generation 15:

Only the white caminacules are left and it looks like only one type of spotting! This illustrates two points. First of all as I noted earler, recessive alleles are not eliminated just because they are recessive, but evolution is strongly contingent. Just because you get one result one time, the chance elements in evolution such as genetic drift may cause completely different out comes the following time. This can lead students and teachers into all sorts of interesting avenues of thinking about how evolution works!

If you want to see how this works, look for me in world.

Hopefully later this week I will have worked through natural selection.

Virtual World Best Practices Conference

2009-03-30T15:23:00.000-07:00

Wow its over and I am still mentally going through everything that I saw at this conference. But needless to say seeing all the wonderful things being done in Second Life and other Virtual World systems is exciting. There was just no way to be everywhere at once and the best I can do here is present a few comments and pictures. The presenters are putting up outlines of their talks and slides at the best practices Wiki here.

Rather than try to recap everything, a few general impressions. First the conference was extremely well run with surprisingly few crashes, considering the number of avatars present at any given time.

While the conference was mainly held and dealt with Second Life, one track did look at other virtual world systems. For example here is Nicole Yankelovich presenting on Sun Microsystems wonderland project, which I have blogged about earlier.

In the same vein there were virtual tours of Beyond Space and Time's Forbidden City, a tour I went on. It is visually stunning and photo realistic and I high recommend it as a great resource for anyone interested in Chinese culture.

It's not to use the latest 3D world buzz word interoperable with Second life and from my perspective it is not a virtual word in the same sense as Second Life. Everything is controlled and you can't build and somehow to me that lack of spontaneity makes the experience less immersive than Second Life; there is no sense of being embedded in a larger world.

I did not get to see this, but people interested in accessibility issues ought to check out Max the guide dog designed to help persons with limited vision cope with Second Life which after all is highly visible. Along the same vein, Nichole Yankelovitch mentioned what looks like an interesting Autism site located physically not too far from me at at University of Missouri. This particular project is called iSocia l. This system uses Wonderland so it is not accessible through Second Life.

The talks I was at involved the main presenter using voice rather than chat with background text banter among the avatar's in the audience, and I found myself listening to the presentation, taking pictures and dealing with several chats at the same time. Now that may seem rude but remember several things in SL, the avatar can do all these things while looking perfectly still to the speaker. Secondly the chat generally became entrained to the speaker's topic.

In some cases the presenter was clearly comfortable with this, in other cases the moderator would monitor the chat and relay questions to the presenter. The one thing that did mar a few presentations was sound quality. One otherwise good presentation was very difficult to listen to because the sound was too distorted and I think presenters using voice need to pay close attention to the quality of their equipment and how they use it.

Here is maybe an extreme case of my screen while at a presentation. Those who have seen my computer screens in RL or for that matter my cluttered RL office desk will probably chuckle at this.

Most of the talks were formatted pretty much as standard Avatar sitting and listening to the main presenter while watching power point type slides. I think this was a good strategy since there were lots of new Second Life participants and getting the hang of SL camera controls can take a little time. The most interesting alternative was a walk about presentation by Dona Cady (RL) and Don Margulis (RL) where the slides were on separate panels and the avatars had to teleport to the presentation site high up in the sky. Since the slides were on large panels there was no fussing with camera or slide viewer controls. So again sometimes simple things work best.

This presentation also did a nice job relating virtual worlds to the sorts of paradigms common in oriental cultures. The slides by the way are wonderful and I hope the presenters get them up on the conference Wiki for others to see.

The talks tended to be theoretical or taxonomic in nature rather than quantitative but they all raised lots of neat questions. For example Shailey Minocha and colleagues from Open University gave a fascinating talk on realism versus fantasy in Second Life and how that might relate to the design of learning spaces.

What they found suggests that spaces for social interaction tend to be filled with familiar stuff couches and tables, "vending machines" etc, while less realistic and more metaphorical spaces can be effective for discussions. For example a discussion about test tube babies had a series of test tubes for the avatars to sit in during the discussion.

Other talks dealt with applying pedagogical models to virtual worlds or dealt with the importance play as part of the learning experience. I particularly enjoyed Max Chatnoir's talk where she emphasized this in terms of science in Second Life.

The themes of her talk were some what echoed in a really interesting study by on the effectiveness of collaboration by Jason Breland and colleagues in the use of virtual world systems by architecture students.

Also these two talks were among the most quantitative; Max had some wonderful data on visitors to Genome Island and what they do, much of it very fine grained as she builds sensors into many of her objects. So she can infer for instance, what tasks she has assigned her students are the most challenging in terms of the amount of time they spend on the task or with the object.

Breland's study was almost an analysis of variance type study that attempted to control for experience in determining the effectiveness of collaboration. I think an expert on ANOVA could help Breland and company with their design but they have an interesting approach to getting at some good answers to important questions.

The conference was really intense and even when I got away, for instance to go back to my SL lab to do some scripting, I found myself talking to conferees. And I drank copious quantities of coffee. So to the left is my mug.

But there was plenty of play as well...that's part of learning right? There were lots of fun avatars among the participants and presenters.

Pathfinder Linden from Linden Labs was a constant presence.

Here I am in a Kimono, I either wore this or a two piece pants suit.

Lori Vonn Luster

Here is one of the presenters, Jonathon Richter, during his talk. Those Salamander people really are dedicated. Imagine the effort keeping that skin moist!

Continuing the herpetological theme, this dragon kept asking for cookies.

Of course as any good conference there was a big party at the end. So to close things out we all went to a club for dancing. Now this was pretty new experience for me since I am not a particularly social critter in real life but it turned out to be lots of fun in spite of a fair amount of lag due to lots of avatars in a small space. Plus I had to dig a bit to find an outfit that was a bit more suited for the event. Fortunately I had just the thing.

Here is a general party shot. As people danced there was lots of local chat and it was more fun than I thought it would be. What was interesting is the parallel with real life in that more women danced than men. In real life I am very self conscious about my dancing...but not here and I didn't even work up a sweat.

Of course a party called for switching out the coffee for a glass of...

OK just one.

Configurable Caminalcules!

2009-03-28T12:06:00.000-07:00

One thing I wanted for my Caminalcules to is allow for the instructor to configure different genetic systems via a note card rather than a menu system. Turned out to be pretty easy and so in amongst Best Practices Workshops, I've been squeezing out time for this.

So here is an example of a pair of Caminalcules who have indulged in a little bit of dihybrid Mendelian interaction. I'm making little activity pens or corrals (as Max Chatnoir suggests) for them partly to keep them in but because when the pups are "born" sometimes they don't end up right side up. Visitors can move them around with fear that they are going to escape!

I need to give them some sort of movement but that will need to wait and I will probably introduce that option in a couple weeks when I script my Caminalcule evolution activity.

Caminalcules Spotted at Genome Island!

2009-03-27T05:40:00.000-07:00

No need to panic. I sent Max Chatnoir a pair of them for her to break as a beta tester, which she very nicely did in about 1 minute. So made some changes based on her feedback. The Caminalcules can now do various modes of inheritance and can either mate with each other of self fertilize as any proper organism for genetic studies ought to be able to do. Did I mention they also do linked genes? The picture show Max with her first brood. There had been a problem with permissions which caused a bit of grief until I tracked the problem down.

This coming week will see lots of frantic designing and building for the Caminalcule project including plans for a build on Genome Island once the prototype build is finished at Carmine. But a good part of today and Saturday I will be at the Virtual World best Practices Conference. Oops! Starting in about 10 minutes.

OpenSim and INTEL's ScienceSim

2009-03-21T16:12:00.000-07:00

A group from INTEL has been busy setting up a virtual world called ScienceSim using OpenSim and so over the last few days I took a little look. First about OpenSim: OpenSim can use a scripting language based on lsl and indeed you can use the standard SL viewer for OpenSim sites. However OpenSim is not centralized as is most of SL but is run on servers owned by different people and groups.

According to the OpenSim wiki, OpenSim:

Supports creating multiple 'worlds' in a single application instance.
Supports multiple clients and protocols - access the same world at the same time via multiple protocols.
Extensive ability to customize your avatar, both with custom clothing, skins, and attached objects.
Realtime Physics Simulation, with multiple engine options including ODE, PhysX, Bullet and more.
The ability to create content real time in the environment using in world building tools. What you see is what you get.
In world application development using a number of different languages, including LSL/OSSL, C#, JScript and VB.NET

You can have your own virtual world offline on your own computer or link a server so that people from the outside can visit. Plus its free and you don't have to pay $L to anyone. So let's see, I am at the $40/month tier so that means I pay $480 + $88 or $568/year so maybe it would pay to use my tier money and get my own server and load OpenSim. Also OpenSim has some really cool extensions to LSL. Check these out.

Of course the flip side is I have never run my own server and OpenSim is buggy at least when using the current SL client so it would be very difficult to bring freshmen or sophomore students into an OpenSim region. For example I had great difficulty teleporting and my avatar sometimes would not be easily controllable. How much of that is due to problems with the software vs the servers and connections is not clear to me. As an alternative to the SL viewer you can use a viewer called Hippo.

First getting there- You need to set up an account via the ScienceSim adminstration page. But read these instructions and follow them carefully. You will need to make another copy of your Second Life shortcut, rename it and change the target. Remember that OpenSim is not Second Life so that you need to register a new avatar. ScienceSim prefers that you use your real life name for your avatar; I chose to register Simone again since I am not working in ScienceSim's grid but did register with my carbon based world name.

When you open the log in page, the left hand side has a list of regions run on private servers linked to the ScienceSim grid but I recommend just logging in. It may look at first like you are going to Second Life but you are not!

When you first launch your viewer to enter ScienceSim, you get a default female avatar which you can customize just as in Second Life. But while visiting ScienceSim decided to keep things simple. So here I am rezzing at ScienceSim's orientation site which serves as your default home.

There are four regions in the main ScienceSim grid Galileo, Kepler, Newton and Einstein, the world map is shows just those four regions. However there are currently 46 regions in total as shown here, which is a bit confusing. But it makes sense when you consider that these other regions are not really set up for the most part for public display but used for visualizing scientific data.

Here are some various screen shots I took on my first visit:

Einstein Region

Kepler Region

Newton Region. This shows part of the amphitheater. There also an observatory build in ScienceSim from where you can teleport to some of the other regions connected to the grid.

There is kind of a fun marble launcher and several other goodies like that in the main grid but right now there is not a whole lot to see.

Since I am a biologist I was particularly hot to see some of the biology being done there and sent an inquiry to the site master and got a nice response inviting me to the user's meeting on Friday. Unfortunately people got really confused as to what time the meeting was so it really didn't happen as scheduled.

However I did find a friendly group of users and they invited me to join their discussion and then later on met some other users at the amphitheater. They use Skype for much of their conferencing so I had to download and set up skype on my machine but that was pretty painless and the sound quality was excellent, much better than SL's voice.

One of the people I met is Aaron Duffy who a grad student using OpenSim to simulate the population genetics of ferns and since some of my training is in population genetics, was interested to see that. So today I went back and he graciously gave me a tour and demo of his work which is just starting. His project superficially resembles the ecosystem working group effort in Second Life, in fact Aaron got onto his project from exposure to that group.

This is Aaron and in the back ground are shown the 3 basic stages of the fern life cycle. The tall structure that is not entirely in the frame represents a sporophyte. The upside down "hat" to the left of sporophyte stem is a gametophyte and the brown ball partially hidden by Aaron is the spore which of course is produced by the sporophyte. Guess what gametophytes produce. Hmmm.

His simulation tracks the details of the genetics of the population as the population evolves over time. So for me this was really neat to see. Right now he is working on interpretative slides to make his project more understandable to non population genetics geeks.

Wonderland

2009-03-18T10:07:00.000-07:00

Today Kira Cafe hosted a presentation by Nicole Yankelovich from Sun Microsystems about Wonderland, an environment for creating virtual worlds. Wonderland is quite different than Second Life in a number of respects. So I will briefly summarize my in world notes.

The handsome nautilus to the left is Joshua Linden by the way.

Wonderland is free and developers can make either open source or proprietary applications. One can create data driven worlds or programmatic worlds. Also it has modules that allow you to create just bits of functionality e.g. an audio recorder or a microphone. In fact a big push for her group in Sun is in audio for virtual conferencing. For example, one can dial up or down bandwidth from telephone quality to CD quality for internal meetings. Thus one can get a really immersive experience

Suns' vision is different than Second Life since rather than one big world, Wonderland is decentralized and the idea is to have the possibility of a federation of worlds.
As for how big a world can wonderland make, version 0.4 could only support 20 users and scalability is an issue. Her group is aiming for worlds with several hundred avatars.

Right now they are in the middle of doing their fourth developer release 0.5 version. This involves a complete rebuild with better avatars and graphics.

Sun is very much interested in the education market, and its use for data visualization and teaching. There is also a wireless sensor platform (this is way cool) for bringing real world data into a Wonderland World for processing or visualization. Sounds like Wonderland has a lot of potential given that it is JAVA based and open source. Perhaps learning system providers such as Blackboard and Angel Learning Systems should check this out.

The Wonderland group is not directly involved in interoperability issues between virtual worlds but perhaps one of their community will pick this up.

Makes me wish I knew JAVA!

By the way Friday, Simone will be at Intel's Science Sim for a visit and blogging session.

Related Links:

https://lg3d-wonderland.dev.java.net/index.html

http://www.sunspotworld.com/

The Voyage of the Beagle in Second Life

2009-03-16T15:59:00.000-07:00

So much science in Second Life and so little time. But today I took a little side trip following Darwin's Voyage of the Beagle. This is a wonderful build and very appropriate for the 200th anniversary of Darwin's birth and the 150th anniversary of the publication of Origin of Species.

The basic idea is to put the clues together to release Darwin's Muse, a Galapagos mocking bird, Mimus trifasciatus . I hesitate reporting too much so as to not spoil the fun. I did the voyage by myself but this is an ideal resource for collaborative learning. There is, for instance, a fun puzzle which took me wayy to long to solve. Don't feel handicapped by not knowing much about the real voyage of the Beagle. You still have to find the clues even if you are like a biology geek like me who read the Voyage in grade school.

If you go, dress appropriately, my normal dress in SL is much too fancy and just to be safe I removed my Geisha hair attachment and skin and donned my Science Friday shirt.

There is lots of wildlife some of which are clues for the game and plenty of poisonous snakes which of course I think are cool. Here is a cobra. I don't recall Darwin mentioning cobras in Voyage, but I ought to check that. Needless to say good thing the SL health option was not on, else I would have died several times over from snake bites.

Of course there are the Galapagos tortoises, pretty much in scale. Here's one with Opuntia cactuses. The focus of the build goes beyond evolution and natural selection to include Darwin's hypotheses about coral reef formation and if you want you can even go diving.

You also get some nice details about the wildlife Darwin encountered and a bit about how Darwin was influenced by the then new geology of Charles Lyell.

Here is what every well dressed avatar needs in her wardrobe:

By the way the interface includes a supply pack that provides you with a compass and journal. Both are lots of fun.

And if you get four keys and release Darwin's muse, you get the Darwin Prize which includes several goodies such as the Beagle in a bottle which now takes a place of pride in my lab, Second Life lab that is.

I suppose, now the creationists will follow suite and probably put up a Second Life Creation Museum. I wonder how they will show the intelligent designer. Oh I forget, you're not allowed to infer anything about the nature of said designer.

If you have A Second Life viewer installed you can visit The Voyage of the Beagle sim at:

http://slurl.com/secondlife/Elucian%20Omega/113/79/22

First Life Bursts In...

2009-03-14T13:26:00.000-07:00

Second Life from my perspective is meant to enrich the rest of our lives and in that spirit some people watch for the first robin but I watch for the first...

Virtual Worlds-Best Practices in Education

2009-03-13T12:52:00.000-07:00

I will be attending, but not presenting at this conference in late March(27th -29th)...look for Simone. Not sure where in SL it will be held. They do have a rack on simulation and gaming so I plan to be learning (I hope) and blogging.

Go to

http://www.vwbpe.org/

for registration and schedule information.

A Visit to Kira Cafe

2009-03-10T14:55:00.000-07:00

I really do need to blog more about some of the places and workshops I visit. One of my new places to visit is Kira Cafe sponsored by the Kira Institute. Kira Cafe is for discussion of science and more. As the institute's mission statement notes:

The Kira Institute's mission is to investigate distinct views of reality, taking off from one central question: “Starting with science, what else is true?”

The Institute holds lots of workshops/discussions related to this theme. Some of them are ongoing. For example the other week I attended a really interesting one about the role of virtual environments in scientific visualization as part of an ongoing workshop called Relocatable Laboratories in the Metaverse (ReLaM). This workshop dealt with Open Sim and the Science Sim by Intel.

Today was a weekly science discussion called Nymf's Science Circle which was hosted by Darkeagle Darkstone (left), in real life a computer science instructor in a Californian community college. The discussion revolved around the theme of how virtual reality environments such as SL can help persons with disabilities. Quoting from the note card:

" There are people here, who in real life are strapped into wheelchairs. Here can the walk away from the isolation and prejudice the face in their day to day lives. Here they dance, fly, and mingle. Their bodies here are not ravaged and mangled by disease or genetics in the Virtual worlds. Their speech is not slurred or laborious; we accept them here like everyone else. We discover that they are valuable and treasured friends. "

I was particularly interested in discussion related to use of SL by persons with autism (called in the discussion autists)

Kira has a packed schedule of events and you can view them her e. You can visit the Kira campus in Second Life at http://slurl.com/secondlife/BaikUn/234/95/251.

A Building Frenzy...

2009-03-09T09:06:00.000-07:00

Well not really. But one real nice thing about doing Second Life projects is that there are so many different things to do. So, if you OD on scripting there is always something to build. I like doing both and I decided that maybe when I dream about scripting that it is time to do something else. So last night I played a bit more with Blender and sculpted a pair of very simple guard cells for my photosynthesis project.

This picture shows the result. Probably the sort of thing a master builder would snort at but they are pretty dramatic. Guard cells have a much more complex form than what I show here so for advanced students I might want to show that. Right now these are phantom and the visitor has to walk through them to enter the photosynthesis module. And since Mat Chatnoir has already asked about this...yes eventually they will be scripted to open and close: eventually ;-).

I have also redone the sky box* that my photosynthesis module is in. Originally it was built like the lab where I do my scripting and prototyping as a 20m x 20m x 10m box made from 10 x 10 x .1M prims, plus extra prims for window framing and entrances. My lab module bare bones has 16 prims. But since I currently do my work on my own private region on the mainland I need to watch prim count. You can visit the photosynthesis module in world at http://slurl.com/secondlife/Carmine/118/142/296

In my inventory I have the infamous mega prim package from Alberto Linden, so decided to play with them. Generally I avoid mega prims because the big ones are really intrusive. In fact one of my neighbors has rezzed a big one for some weird reason and it goes right up to my property line...but that is another issue. My neighbor seems to only speak Japanese and while I typically wear a Kimono, I do not. Fortunately my neighbor did blend it so it is textured the same as the region's ground. A few eucalyptus trees and that mega prim is hidden.

At any rate I put together a barebones box, the same size as my SL lab/office but uses only 4 prims rather than 16. Astute biologists will recognise that it is textured with a scanning electron micrograph of the upper epidermis for a leaf. In fact both the inside and the outside were originally textured the same way which is really cool and immersive but maybe over kill. So I retextured the inside with the same sorts of window textures I use in my lab/office and the result is basically what you see in the first picture showing the guard cells at the entrance to the photosynthesis module.

Also this weekend, worked a bit more on the Caminalcule menuing system so that it is a bit more sensible; I was making things way to complex to follow and so I am having to reorganize the scripting a bit.

You're also welcome to stop by my lab/office at http://slurl.com/secondlife/Carmine/174/217/137 You can also TP there from the photosynthesis landing spot.

* Generally I loathe skyboxes..but creatively textured they do have their uses.

A handy little string function...

2009-03-06T12:21:00.000-08:00

For the Caminalcule project I'm finding it easier to represent a genotype as a string because I can easily manipulate strings. But LSL is not real whippy on the string manipulation front.One function I needed was one that would substitute a sub-string starting at a certain position in an original string without making any other changes in the original string.

There are functions that do similar things but they rely on having a recognizable set of characters in the original string as in standard find and replace. But what I wanted was a function that goes to a particular position in the original string where I (or a script) specify where the position starts.

This is important for me because the way I represent genotypes there are some things that change a lot, but somethings may not change very often and yet I want to keep those things together with the more variable stuff-kind of like what happens in a chromosome.

So if I have two sentences:

"The sly big fox is learning scripting." and

"The big sly cat is learning scripting" ,

I might want to change what ever starts at letter 9 with the substring "red". Hence my little function:

replace_string(string original,string sub_string,integer pos).

Try copying the following code and inserting it in to a prim and let me know what you think. Given Blogger's tendency to mess up LSL code, you might have to change a few things by hand. Or IM me (Simone Gateaux) in world and I will send the script to you.

//begin code here
string replace_string(string original,string sub_string,integer pos)
//replaces part of string starting at pos with substring; does not change the original string length
//real handy for me
{

integer orig_length;
integer length;
string new_string;
length = llStringLength(sub_string);
orig_length = llStringLength(original);
if ((orig_length-1) > pos &&( pos >= 0))
{

new_string = llInsertString(original,pos,sub_string);
new_string = llDeleteSubString(new_string,pos+length, pos+length -1+length);

}
else new_string = original;
return new_string;

} //end function

default
{

touch_start(integer num_detected)
{
string newstring;
string oldstring = "The sly big fox is learning how to script.";
string replacement = "red";
integer position = 8; //position start at 0 index so here 8 is the start of "big"
newstring = replace_string(oldstring,replacement,position);
llWhisper(DEBUG_CHANNEL,oldstring);
llWhisper(DEBUG_CHANNEL,newstring);
}
}
//end code

Caminalcules III Colorful pups...

2009-03-05T20:13:00.000-08:00

This week I implemented a version of Eloise Pasteure's suggestion to get genetic data into the Caminalcule's offspring, representing the genetic data as a 7 digit integer. This integer has two positions for each locus or allele pair, a dominance term which is 1 position for each locus and an extra flag telling the program whether to process one or both loci when making the phenotype of the offspring. It's a little less compact than what Eloise suggested but easier for me to keep track of.

This version of the Caminalcule will illustrate Mendel's two laws and does not do linkage...yet. The second locus, by the way, has to do with the type and number of black spots on the critter and I just got that implemented today.

Yet to do are some fixes to the menu system- I've had to think carefully how the lldialog function works-and think out the mechanics of Caminalcule mating. How will they communicate and behave? Right now they can detect each other with sensors but I haven't given them an sort of movement. What happens if two encounter each other and they are genetically incompatible? What sort of reproductive system? We already know that some of them are hermaphroditic. Is there also a non hermaphroditic gender? Hmmmm. Stranger things than this happen in nature. You might look up the life cycle of Caenorhabditis elegans, one of the major organisms in modern genetics.

Lots of potential here for getting students thinking about life cycles and gender that go beyond genetics and collaborating with each other. I've also been to several interesting workshops related to Second Life and I will post more on those later.

Caminalcules II: Mother and her pups

2009-02-26T10:05:00.000-08:00

Continuing along with my Caminalcule genetics activity...

Here is a heterozygous Caminalcule mother with 10 of her pups produced by selfing under incomplete dominance. The maternal script produces two gametes at random, the "pup" is rezzed and the genotype along with the degree of dominance communicated to the pup and the pup then changes phenotype.

This is of course not the way it works in the real world; the pups should be rezzed with the genotype in place but there doesn't seem to be an easy way to do that save maybe with some really clever use of llSetPrimativeParams. But my approach seems more flexible.

Here notice that roughly half the "pups" have the heterozygote's phenotype (grey) and roughly half are one of the two phenotypes (black or white) of the homozygotes.

Right now I represent a gene's locus with an SL vector type. The third position is not currently used but it could be used to store some other type of float type information related to the gene say something about its linkage position along a chromosome.

Coming up soon...Caminalcules make nookie.

Caminalcules I

2009-02-25T21:41:00.000-08:00

I could work on photosynthesis forever, but must move on to get another project started. One thing I have wanted is a creature that might serve as the basis for several different modules. So I whipped together these cute (OK I think they are cute) sculpties. What I had in mind was something like Joe Camin's famous Caminalcules, fanciful, but useful as a teaching tool.

If you are not familiar with Caminalcules here is a pretty good discussion of these little critters. My guys look more like ground beetles than the original Caminalcule but I think they will do for now. I wanted to keep them fairly small and yet large enough to see and manipulate. The blue rod in the picture is an SL meter, so these are pretty small. Any smaller and the scultpie's little legs don't show well. Besides this is a good size for students to manipulate in Second Life.

My first project with these guys is going to be real simple: Mendelian monohybrid and dihybrid crosses followed by linkage. But these guys could easily be used for natural selection or ecology and I have put together a little interface for selecting the sorts of crosses you might want to do, concentrating on monohybrid crosses. Students will be able to self them(they have the potential of being hermaphroditic) or cross them with another one.

Right now there are four color forms: white, grey and black controlled at a single locus with incomplete dominance, though I can adjust the level of dominance. The 4th color form is bright red and that is displayed when one senses a compatible mate. I knew there was a use for sensor functions somewhere!

They will have litters of up to 10 pups at a time. Not to worry- the pups will be genetically modified to be sterile so they won't overrun a region!

Now to write the genetics states and functions I need. Once this is done then I will add more colors and textures controlled by different loci and allow for mutation so there will be plenty of variation for natural selection. I may introduce some genetically based behaviors as well.

Another Virtual Reality System

2009-02-24T08:37:00.000-08:00

Bruce Sommerville, a member of SLED had been exploring a very different Virtual Reality system (really a plugin for your browser) called ExitReality. This system is quite different than Second Life as it is based on VRML (virtual reality modelling language), or rather its descendant X3D. As the name suggests this is meant to be a 3D extension to HTML in the web. VRML has apparently been around for awhile but has not become popular. Maybe though it is worth a look.

Bruce gives a pretty good rundown on ExitReality and he has graciously given me permission to quote from his SLED report. I will intersperse pictures from his site amongst his commentary and follow that with a few additional comments and pictures.

Bruce writes:

"Over the last few months, I have been experimenting with the new
ExitReality browser plug-in, which allows any web page to be viewed in 3D,
and used as an immersive and communicative space.

Although I have not used it in teaching yet, I have constructed a series
of activities, constituting a lesson, which utilises 3D animated models, a
variety of different audio-visual media, and lesson materials in the form of
texts (Word docs), in order to explore the affordances of ExitReality in
education. Since most of my students are international Science and
Engineering students studying in Australia, the lesson materials have a
certain ESL/Literacy flavour. The site may be viewed here:

http://www.users.bigpond.net.au/academic/X3D/EngineeringRoom/index.htm

*Please note that I did not build the bicycle, welding robot, or crane that
are used in the site, but have linked to the two latter at their original
sites on the net, and have given acknowledgements. The bicycle was freebie
from Google Warehouse. The lesson materials (obtained by clicking on the
large books) were written by me. The lesson is based on an RL lesson I have
used with my Foundation Studies students on 'Describing the Functioning of a
Machine'.

- Portal Crane is based on the work done by Mr. Martin Foltin and Mr. Samuel
Bartos, Department of Automatic Control Systems, Slovak Technical
University, Bratislava, Slovak Republic, Source: "Gallery", *Orbisnap*,
http://www.orbisnap.com/gallery.html

- Welding Robot created by University of Michigan Virtual Reality Laboratory
at the College of Engineering, http://www-vrl.engin.umich.edu/projects.html

Thanks Bruce for allowing me to post your comments.

While I was using the ExitReality plugin I decided to explore a bit. I found the interface a bit awkward to use. Avatar customization is extremely limited (Simone was not happy with that!) and there doesn't seem to be any way to fly or use camera features to zoom in close to something far away.

But I really was impressed with some of the places I visited and the ability to view just about any sort of web content in the plug in, something that is lacking in Second Life. You can store sites and inventory items and there is chat including voice. So here are some representative screen captures.

I recommend ExitReality plaza as a first stop to get your bearings. It's analogous to Second Life orientation and has VRML links to various goodies and companies with sites designed for VRML.

A forest site viewed with ExitReality showing some of the texturing potential.

Here some entrepreneurs are using x3d and
the plugin to sell "islands" for 3D conferencing and collaboration. These islands are again only analogous to Second Life Islands.

Simone needs to stop and get a quick drink. Non alcoholic, of course, on work time.

Finally, a quick visit to my college's web site (www.jccc.edu). This shows very nicely what the plug in does with a site NOT designed for X3D. The results are really quite interesting!

By the way the picture in front of me scrolls much as it does on the 2D website and all the links work, though it takes you out of the plugin's viewer in to the regular mundane 2D web.

I don't know how building in X3D compares with building in Second Life but I think that if integration with the web is critical than this sort of system merits a look. You are also necessarily dependent on a 3rd party server.

You can build animations that the user can interact with, there is chat and voice and you can stream other media apparently limited only by what the web supports. It also looks like you can do some limited 3D web editing with the ExitReality but I didn't explore that.

ExitReality doesn't have the same sort of immersive feel to me that SL has and the plugin seemed pretty buggy. But it is still in Beta, so I expect improvements. I'd be interested in what other people's experience with this sort of approach to virtual reality have been and any experences in using X3D in teaching.

Building the Photosynthesis Engine VI :Calvin cycle

2009-02-24T06:42:00.000-08:00

Last night I finished the basic Calvin cycle model. The Calvin cycle is the part of photosynthesis where carbon dioxide is brought into the metabolism of the plant (or other photosynthetic organism).

Next the ATP and NADPH from the light reactions are used to donate energy and hydrogens to the carbon atoms from the carbon dioxide.

The resulting molecule, a three carbon sugar, called G3P then can be used to make glucose or other organic compounds. Making this G3P is the point of photosynthesis!

The model rezzes the molecules involved in the Calvin cycle and it is a real three ring circus to watch. Come visit the model along with the light reactions in Carmine at: http://slurl.com/secondlife/Carmine/116/148/296

There is still more to do in terms of design issues and presentation and particle usage...but as with the Light Reactions, my immediate concern has been with the scripting.

The model can only be toggled on or off but unlike the light reaction model, the molecules move from spot to spot at a more sedate pace.

I want to thank SL educators Azwaldo Villota and Eloise Pasteur for their feedback on this project as well as other visitors who have dropped by from time to time.

Photosynthesis Engine V....more nitty gritty...

2009-02-17T14:11:00.000-08:00

Well the sensor approach outlined last time had some problems. The entire light reaction model has 18 prims. Sensors are limited to the 16 prims closest to the sensor. When the model was running, some of the parts were not conststantly sensing where they needed to go.

So this meant a rework using linked prims and learning about how to get linked prims to communicate.

The big issue was my protons which are rezzed at various times. The problem is that when they are rezzed, they are unlinked prims and so can't communicate with the rest of the model using the link communication functions.

The strategy that worked was to first rezz a proton, then have the linked prim that rezzed the proton get the keys for the required places the protons need to go to and sending that information to the newly rezzed prim using llWhisper functions and listen events in the proton. I was concerned that the proton's listen events might not pick up all the Whispers, but that doesn't seem to be an issue.

The model runs much more smoothly as well!

So come on over and visit at:
http://slurl.com/secondlife/Carmine/118/143/296

Still trying to decide the best way to present the Calvin cycle....and working on some other other goodies. I will also be commenting on the Stepping into Science workshop I attended In World last Friday.

Building the Photosynthesis Engine IV: Nitty Gritty TIme in the Lab

2009-02-09T12:15:00.001-08:00

Finally got a beta version of my light reaction light model to work properly. There were of course some programming issues. Since the model has moving parts, the parts had to be able to tell where they are in relation to other parts, get and send messages to other parts and that takes no small amount of coordination.

Not only that, when I moved the model to another spot, that created a problem since I tried an end run around some issues by using object keys. Well as I was afraid, keys are useless once the model is rezzed , since Second Life generates a new key every time an object as rezzed.

So here is what I did. I set up those parts that need to know where other things are to detect those parts using a sensor event as partly shown here:

The llSensor statement tells the object (in this case a proton) to scan a 10 meter radius for what ever objects are around and then the if statements within the sensor event enable the proton to "tell" Of course real protons move randomly but in Second Life having lots of randomly moving protons presents some problems...so this is a compromise.

Also I could have done the protons as particles, but you can't control where particles go and since they are generated client side, can't interact with the model.

There are always design compromises in modeling and that is true in Second Life as well as in other modeling systems and the modeler has to pick the right compromises for the level of modeling being used for the audience.

The Calvin cycle will be much easier...far fewer moving parts and coordination problems especially since I have dealt with some of the issues involved in the Calvin cycle in Photosynthesis Engine I and II.

If you have Second Life installed you can visit the light reaction model in its temporary home at:
http://slurl.com/secondlife/Carmine/117/140/296

On tap this week:

Calvin cycle.
Look at Max Chatnoir's pedigree program. Max has graciously sent me a copy to study.
Faculty meeting - in person no less...that's so 20th century.
Also in the middle of Angel training.
Friday I am going to be at the Stepping to Science workshop. I was supposed to go to the first iteration of the workshop but my registration got messed up.
Oh yes one more thing: change the cats' litter boxes. Now that really is so 20th century.

Building the Photosynthesis Engine III:Light Reactions

2009-01-23T22:40:00.000-08:00

The light reactions in photosynthesis are where light is absorbed and converted to a flow of electrons. The electrons are used to make energy rich compounds for the rest of photosynthesis. It is also the step where oxygen is produced.

This week I have worked out a way to simulate the light reactions in which all the parts of the model are embedded in a lipid bilayer as in nature (more or less). The model is more detailed model than my more general simulation of the whole photosynthesis process in that the parts are meant to sense each other and communicate with each other. Here both photosystems are glowing purple because they both have absorbed photons. The structures in red or purple are parts of the electron transport systems, the red indicating the passage of electrons.

The user will eventually be able to treat this simulation as a work bench adding or removing parts and putting them in the right order to get their own working model of the light reactions. The parts interact via a series of sensor and listen events. This seems to be an easier approach to implement than the one used in my more general simulation where all the parts are linked into one large object. Again the idea is not to mimic every single detail of the light reactions but allow the user to explore the steps in the light reaction.

Playing with Light

2009-01-20T21:13:00.000-08:00

Visiting Soror inspired me to get back to Blender which I had struggled with last summer and found it very difficult. Part of the problem is that the tutorials are often times confusing especially when it comes to exporting sculptie textures. Fortunately there is new stuff out there. Now there is a site called Second Life Artis t which gives a really clear explanation of how to export sculpted prim textures to Second Life using a set of Python scripts developed by Dominodesigns.

It works great! No more editing meshes by hand and voodoo baking. Soror suggested a good place to start with Blender is with a sphere and use the Sculpting tool.

So here are a few things I did today after the inauguration.

This is a shot showing some of my sculpties. The star was made with Blender, the other glowing sculpties where made earlier as part of an installation for a video.

I thought cactuses would be easy...but I can't get fine enough detail to do spines, but I think these are cute.

Experimental Flora

2009-01-18T21:14:00.000-08:00

When I was in grade school I got into trouble when we had to do one of those infamous class murals. What could possibly have gotten me in trouble? Well my job was paint tree trunks and I painted them as I saw them, not brown but various other shades and encrusted with lichens like this.

Now I wonder what my class mates and teacher would have done if I painted trees looking like this gem?

This bit of experimental flora was created by Soror Nishi who does some of the most inspired objects I have seen in Second Life. Soror has a really keen eye and a wonderful organic sense-organic in the meaning related to life.

All around, one sees cellular shapes, tissues, flowers and seeds that pay homage to evolutionary exuberance. I must confess I spent way too much time last night going from one plant to another, and snapping pictures. So here is a sampling from my Flickr Stream.

This one echoes either a palm or maybe an extreme split leaved philodendron with aerial roots.

Soror titles this one "Bog Lily" but it is really more like a Calla lily complete with spathe.

Everything is fantastic maybe the biologist equivalent of magical realism such as these jeweled mushrooms. In some universes they probably would be down right illegal.

These lily pads are clearly inspired by the real thing.

There is attention to botanical detail everywhere. Consider these wonderful hanging legume pods:

Soror has a clear grasp of the importance of small things too, that the average visitor to a tropical rain forest might miss such as these wonderful beach flowers instantly recognisable to me as a morning glory echoing some I have seen in Florida.

So if you want to visit a great site to see just what you can do with SL...maybe wow first time visitors, check out Soror at http://slurl.com/secondlife/Lifstaen/20/52/228

Soror is currently having a show at LALALALA Gallery at http://slurl.com/secondlife/Avendale/51/76/22

If you send up teleporting to the Avendale town square, let everything rez and click on the Gallery's sign on the sign post for a teleport.

In the artist information notecard Soror says:

"The extensive attempts some make to populate this new world with "realistic" copies of the Old World show a colonial tendency to ignore the native culture and superimpose a pre-formed visual style on this new medium. This medium (SL) has more in common with stained glass than with photography, and failure to recognise this results in poor copies of boring everyday objects, architecture, flora and fauna."

And I think this is an interesting point for someone such as myself who tends to import photos for textures.

I see Soror works with Blender...wonder what tips she has for a novice?

Soror's blog is at http://sorornishi.blogspot.com/.

Molecular Mayhem in Second Life

2009-01-16T06:10:00.001-08:00

Yesterday I visited with Erich Bremer from Stony Brook for a quick tour of Monolith, his Molecular rezzer, discussed in my previous post. He asked me to select a protein from the Protein Data Base(RCSB) so he could test it on his new beta version of Monolith. So many proteins! So I picked three favorites, a cytochrome C (pdb 3CP5), a dicer (2FFL) and a Rubisco (1RXO). The dicer and Rubisco would have required too many prims for the sim-I should have known that- but we had lots of fun rezzing and playing with cytochrome C.

Two big things. First Monolith is fast. It takes roughly one minute to rez a protein. Since a protein such as cytochrome C easily has 5,000 plus atoms, each of which is rezzed as a prim.

Second Monolith provides a fair amount of flexibility to color different regions of the molecule. For instance, cytochrome C has a heme group-this is a set of four carbon rings with an iron atom in the middle, just as in hemoglobin. Erich was able to immediately find the heme group in the pdb format file and color it, just as one might do with a traditional molecular rendering tool such as Cn3D.

Right now Monolith only does space filling models but Erich has plans for ball and stick models, and some ideas for clever use of particles. Monolith is not nearly as powerful as s Cn3D in terms of the types of displays you can use and right now you can't rotate the molecule right now and scaling might be nice, but then these traditional viewers don't let you easily fly through the molecule.

Not quite the holy grail of molecular rendering which for me would be a Cn3D type rendering system in world. But given that Monolith is still in beta, it's pretty impressive given the current constraints of Second Life's environment the Erich has to work around.

Monolith is at http://slurl.com/secondlife/SBU%20Medical%20Center/58/26/28.

A visit to the monolith...

2009-01-14T06:18:00.000-08:00

Imagine being able to fly through a molecule. Well now you can at the Stony Brook School of Medicine SL site where Erich Bremer has put together Monolith. Monolith creates huge complex molecules using a complex Second Life script that is actually able to import data from some of the standard molecular data base files and use that data to create 3D molecules. Way cool!

Here is monolith itself. Straight out of 2001 at the Stony Brook site.

Some molecular views. I made these a little bit dramatic and I bet some of the more artistic SL residents will want to visit.

This is a transfer RNA.

And to show you the scale these models are done at, in this view I am barely visible on the left hand side of the image:

One more view. The metallic looking molecule in the foreground is DNA.

This is a really neat system. I haven't had a chance to play with monolith and the program is still under development.

One weakness of course is that each atom is a single prim. So that tRNA might gobble up 400 prims...so if you don't own an island monolith probably won't work. It might be possible to save on prims if monolith can be pre programmed with certain stock sculpted prims for certain common structures, but suspect it is not practical.

Certainly monolith would not work on my land in Carmine...let's see (teleporting home for a sec), one of my parcels is 1024 m squared and it supports 234 prims. Even the Stony Brook land (teleporting back...) supports roughly 15,000 prims...so Monolith could quickly eat into that. So Linden lab...if you want SL to be able to host these intensive sort of educational environments, we need more prims!

If you have SL installed on your machine visit Monolith at

http://slurl.com/secondlife/SBU%20Medical%20Center/58/26/27

Building the Photosynthesis Engine II

2009-01-13T14:14:00.000-08:00

Here is a working prototype of the Photosynthesis Engine. The Engine consists of eight linked prims, scripted to qualitatively model photosynthesis. This model presented a number of challenges.

First is developing a representation of of photosynthesis that captures qualitative aspects of the process without getting bogged down in heavy model building. I chose to avoid dynamic modeling and and use very general functions to illustrate what is happening in photosynthesis.

The scripting challenge involved getting the parts of the model to talk to each other since the physical model consists of linked prims which pass data to each other. The trick was to develop a system that allows the prims to pass data using SL's llMessageLinked function to send data and the Link_message event to receive data. If you compare this version of the engine, you'll notice it has far fewer parts-important since SL does have limits on how many prims you can have. I also could simply the scripting since each prim has fewer other prims to keep track of.

The next challenge is making the way users interact with the Engine as smooth as possible and this is still being played with along with adjusting the script parameters to give more realistic output.

It is hard to see in this image but the blue horizontal object with the left and right arrows is a tunable lamp. The user can select a particular wavelength of light and "shine" it on the chloroplast to examine the relationship between light wavelength and the rate of photosynthesis. The trick here is to develop a way to represent the spectral color of a wavelength of light in SL's r,g,b color scheme The yellow and light grey boxes show the sugar and oxygen produced by the chloroplast.

The user can also change the level of carbon dioxide and water independently. Note that the user has to manually change the factor she wants to investigate..the engine is not completely automatic.

The model has a thylakoid that receives a wavelength of light from the lamp and uses its own absorption spectrum (input as a notecard) to interact with the wavelength received from the lamp. So the can gets to generate a real action spectrum. I might point out that the thylakoid's color is generated internally with a function based on the its own spectrum. So there is a fair amount of flexible scripting embedded in this innocent looking model!

More details later...

Building the Photosynthesis Engine I

2009-01-02T08:33:00.000-08:00

One of my projects is an interactive photosynthesis module that the students can experiment on. I am just starting to work on an object I call the Photosynthesis Engine. The idea is to roughly...(very roughly I might add) model photosynthesis in a way that students can adjust the inputs: light, carbon dioxide and water and observe how the outputs of photosynthesis behave.

My initial version of the Engine is a set of 14 linked objects representing the steps and reactants and products of the light reactions and the Calvin cycle, avoiding most of the details of what happens in each cycle. The immediate challenge is figuring out what are reasonable parameters to get sensible qualitative behaviors out of the model and getting all the linked parts of the model to communicate properly.

The picture shows a preliminary set up for the Engine, including a nifty(OK that dates me) light source that displays the spectral colors of the wavelength, allowing the students to display the wavelength. Also the light reaction prim's color uses a function that takes a transmission spectrum and converts it to R,G,B values and displays that on the prim. Students will be able to send the light's wavelength to the light reaction as input and generate an action spectrum.

More later...

A Walk in the Garden

2008-12-19T19:57:00.000-08:00

Of course I have a Second Life garden just as I have a first life garden. Most of the plants were bought in Second Life...in the very back is a wall textured with a cool little Ficus-at least I think that is what it is- taken from a photo I shot in Florida over break. And my goal for the garden is to make it completely interactive as an introduction to plants.

Visit my SL garden at:

http://slurl.com/secondlife/Carmine/99/141/135

You can also visit my First Life garden via this Flickr stream set.

Simone's Simple Scripts #2 Image maps in SL?

2008-12-18T15:33:00.000-08:00

One neat feature of the web is the ability to create image maps. We take for granted that you can often interact with images and get different responses depending on where you click. But until very recently this has not been possible in Second Life.

However now it is, thanks to a new function called llDetectedTouchST. This function allows you to return coordinates you have touched on the face of a prim. If you have a rectangular face the upper left corner is 0,0 and the lower right corner is 1,1.

I have found that with successive calls to this function, you can design rectangular hot spots for a texture. The texture can be anything from an image of a leaf, to menu items or a city map that you want a visitor to interact with. For learning purposes, I decided to set up an interactive leaf using this function. The object tells the visitor what the part is and displays a short text explanation as a texture of an object rezzed when the visitor touches on the appropriate spot on the leaf. I thought about displaying the textures as particles but decided that rezzing objects would give me greater flexibility.

I built in an interesting feature and this came about because I haven't quite mastered how SL handles coordinates. When I rotated the leaf prim, the objects with the explanations often ended up behind or on the wrong side of the leaf. Rather than mess with figuring out the right set of coordinate functions. I decided on a different strategy. I made an invisible prim called "positioner" linked to the leaf object and let it determine where the explanations are rezzed.

This is cool because it allows me to customize where the explanations rezz without with any sort of code. I just move the positioner prim to the right position. To make this little feature I linked the leaf prim to the positioner prim and then used the following set of statements in the Leaf's code to rezz the objects:

puthere = llGetObjectDetails(llGetLinkKey(2),[OBJECT_POS]);
llRezObject(part_name, llList2Vector(puthere,0), <0,0,0>, llGetRot(), 0);

The variable "puthere" is a list and the position of puthere has to be extracted from the list by llList2Vector.

The image shows the invisible prim highlighted (translucent red cube) in the middle of the object for Phloem.

Right now the hot spots and object names for rezzing are written into the code, but it should be easy to have all this be somewhat more automated were I to make this tool generally available. Unfortunately you need to find the prim coordinates for the hot spots by hand via repeated calls to llDetectedTouchST.

If you want to play with the leaf, and assuming SL is installed on your machine, just teleport to my home in Carmine at:
http://slurl.com/secondlife/Carmine/102/143/135

Simone's Simple Scripts #1

2008-12-09T15:25:00.000-08:00

One of my pre-sabbatical tasks is to learn the scripting lanquage. So I am starting a new occasional feature Simone's Simple Scripts to share some scripts and amuse more advanced scripters with my fumbling around.

A useful tool in Second Life is a viewer that visitors to flip through textures or text-the holy grail of course is true web on a prim where users could essentially use a prim as a web browser, thus bringing the web into Second Life. Failing that, a standard thing to do is display information as textures and flip through that and there are of course lots of such viewers out there.

Prowling around the SL scripting portal I found a really cool and new function, llDetectedTouchFace(i). This function detects what face of a prim you are touching. Now this has possibilities. So I decided to make a simple viewer that uses only one prim and real simple controls. I like simple.

So I tool a box prim, flattened it out so that the central face is a display and the left and right faces are for flipping through images-which could be text captured as a texture of course.

The accompanying picture shows the result:

The script is pretty simple.

Unfortunately Blogger seems to mangle SL script. So if you want a copy of my one prim viewer that you can copy and modify contact me in world (Simone Gateaux) or e-mail me. sgateaux at gmail dot com and I will send you the script or if you want, in world give you a copy of the one prim viewer.

Of course feedback and suggestions are always welcome.

P.S. If any one has an idea how to stop Blogger from mangling SL code...let me know.

Griefed

2008-09-11T14:01:00.000-07:00

One of the perils of Second Life is getting griefed which can take a number of forms. Last weekend I went hiking in the Ozarks-lots of pictures but no Second Life. When I returned to SL, I had a message from the owner of the sim adjacent to mine that someone had griefed my land and would I please change my options so strangers can't build on my land.

I am usually really careful about building permissions but had just bought two 512m squared parcels to add to my public land holding and had forgotten to set the land permissions. So my poor neighbors were confronted with this wonderful mess.

I guess griefers attract each other and apparently things were actually much worse and a bit explicit. Fortunately my neighbor was able to file an abuse report with Linden Lab against the griefers, and apparently the griefers were immediately banned. I get the impression that use of their particular ISP address was also banned. Not too serious a hassle for them but maybe enough so that they will think a bit before griefing.

All I had to do then is set my access permissions, which I immediately did. Just in case someone hasn't done this here is what to do. Click on your land to access the about land dialogue. Open the options page and unclick the anyone can build option-unless of course you are running a sand box or like to be griefed.

A visit to Dinosaur Park

2008-08-26T09:59:00.000-07:00

What makes Second Life so neat is that you can really play and immerse yourself in a world if only to explore. So yesterday I took a trip, actually several trips to Dinosaur Park (http://slurl.com/secondlife/Dinosaurs%20Park/229/234/22), This a real ambitious sim owned by a group called the Dinosaur's council, started by Nargus Asturias (Nargus Lab website). Nargus runs Nargus Lab whose motto is "The Past is Our Future. The web site has photos and a little history of the park.

The park is a lot like Jurassic Park right down to the labs and electric fences but it is not a slavish imitation of Jurassic park. Here's a view just outside one of the building entrances. This gives a pretty good feel for the build present in the sim:

Right now there are not too many dinosaurs wandering around but the shops and laboratory facilities are fun to visit. You might even find several Park employees hanging around such as these two dinos:

One nice feature in the visitors center is an information Kiosk that gives information on different dinosaurs and rezzes a dinosaur that you can walk around and view from different angles. This is really slick!

Here's a little raptor rezzed with this system. Unfortunately the textures were not quite fully loaded when I snapped this shot:

Another shot of a park Employee talking with me.

Well lest you get jealous as I was of the cool dino AV, never fear you can buy dino AV's at the park. Normally I try to maintain a consistent appearance as Simone but decided to have some fun and buy an avatar, an official Nargus Lab raptor. The are a bit pricey, the one I settled on was around 1500$L, but I am a big believer in supporting good Second Life designers. Besides you get what's you pay for.

So here I am, Simone as velociraptor:

As you can see, the AV is feathered very nicely reflecting current thinking about how dinosaurs. This AV comes with a HUD (Heads up display) that you can use to modify the texture, and coloring of your AV. I did not get the full mod version since I am not really experienced with modifying AV parts.

The next shot shows me wandering around the park's lab and restaurant with another visitor. Here AV is from another designer and is not nearly was well articulated as my Nargus AV.

You buy scripts and other add ons for your AV, and what I really like is you get a little card that you can take to an upgrade station to get the latest version of the AV if one is available which there was for mine. Very painless and free.

Well back at my lab:

You can see the HUD in the left hand corner of the image.

I was getting hungry so decided to go to Torley Lindon's sim Here which had these adorable bunnies and I thought it might be fun to get a shot with the bunnies before I ate them:

Unfortunately the bunnies were either hiding or gone so here I am looking very forlorn going "where the bunnies I'm hungry!"

Warning! If you gt one of these AV's, make sure you properly save your current AV. When I switched back to my usual appearance, I had a little bit of trouble putting myself back together again. For instance the AV's script gives me a male shape-really ugly and so I had to find my female shape again. But the whole experience was lots of fun and my difficulty was probably more related to my lack of experience in radical AV transformations than to the dinosaur AV.

Dinosaur park is really engaging, the scripts operate very smoothly and the AV's are lots of fun and well thought out. There need to be more dinosaurs, yummy dino food in the restaurant and right now the labs are pretty empty. Looks like that will change. I know I will keep going back and even if you are not a dinosaur person, there are lots of neat little ideas that could be incorporated into educational builds.

More about this Blog.

2008-08-22T19:41:00.000-07:00

As noted in the header, this blog is narrowly focused on using Second Life to teach biology. So I probably ought to explain my thinking. One of the problems in teaching biology is getting the students to under stand how the big processes in biology work, such as cellular respiration, photosynthesis, protein synthesis and for that matter evolution.

What attracted me to Second Life was not only the ability to build and texture objects and place them in an immersive environment but also the ability to link objects together and script them and so was born my sabbatical project to develop some simulations tools in Second Life that students could then experiment with.

For example in photosynthesis how about if students could uncover the relationship between light absorption and oxygen production for themselves, much like they would do in a laboratory setting. Or how about if they use working mock ups of lab equipment before doing the real thing.

There are other biology places in Second Life, for instance Max Chatnoir's Genome Island (http://slurl.com/secondlife/Genome/145/84/30). Max has done some really nice genetics work in Second Life and I have even taken my students there and Max has graciously served as our host. See the post about this on my general blog, The Force That Through.

As an aside, you will notice that some links are slurls, literally second life urls. These will take you to the Second Life map and if Second Life is installed on your computer you can teleport you avatar to the place in Second Life I am discussion. I will always show the whole slurl so you don't get surprised by one if you don't have Second Life installed.

So what sorts of things will I cover here? Obviously other biology sites and efforts similar to mine. Also as I fumble through scripting and try to build cool things and explore various aspects of SL's scripting language. So this is my place to get geeky. I am a photographer-OK I take lots of pictures-in real life and really love that I can use these as the basis for realistic textures so you will some of my texturing efforts.

I will cover Second Life Science events and hopefully throw in some interviews with more seasoned users of Second Life for education, of and maybe students(now there is a thought, ya think?). I will continue to blog about SL on my general blog, The force that through and on occasion on my Science Blog, Dangerous Ideas...but geek attack moments and scripting stumblings (all to common!) will be here now.

As absorbing as Second Life is to me and as much as I think it is a useful tool, it does have limitations. These become quite clear to anyone who has tried to visit a large online event in Second Life. I am really interested in what makes a good Second Life experience for Students and how do we figure this out?

Sometimes I wonder if Second Life is still waiting for a "killer app" or some technological breakthrough that will really get people excited. I get excited by the creative possibilities in design and scripting, but students want something that they can use quickly, they want structure and something where they can learn without lots of technical issues getting in the way. I think these needs can be met in Second Life but it is going to take really careful design borrowing from game design. It's a bit like the early days of the web when we didn't know a whole lot about web page design and now we are trying to work in three dimensions? Gaack!

By the way you can always look for me and visit my office in Second Life. The SLurl is http://slurl.com/secondlife/Carmine/171/224/137.