A Seacoast in Bohemia

Catching up the Chromosomes
October 6, 2009, 8:38 pm
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Yesterday, a new build of the human genome was published to the NCBI genome viewer.  I checked it when a student had a question about the number of genes on a particular chromosome, and discovered that the chromosomes in the Gallery of Human Chromosomes on Genome Island needed updating!

Max updates the chromosomes

New genes everywhere!  Even the little Y chromosome has picked up a fair few.  It raises the interesting question of just what a gene is.  The genes with known functions are relatively easy to spot, since there are chunks of sequence that can be compared to the sequences of the same gene somewhere else. 

Nature doesn’t reinvent the wheel any more often than necessary.  Once it arrives at a workable beta globin or a methyl transferase, that gene becomes part of the archive and just turns up everywhere.  I remember how impressed I was when I first learned about the leghemoglobin in plants.  Who knew? 

Genes that don’t have a known relative can sometimes be recognized by their possession of known motifs — a sequence that binds Ca++ or DNA or ATP in some other protein.   If a DNA sequence encodes a bit of a protein that does something, then it’s probably part of a gene, even if you don’t know exactly why it might be binding Ca++.

But what about REALLY unknown genes –genes with no recognizable homologs or motifs, especially in eukaryotes, whose sequences are usually complicated by introns.  What you need is an open reading frame.  A bit of sequence that has a start codon and a reasonable string of amino acid codons following in the same translational frame.  But codons can break across an intron, that is, part of the codon may be in one exon and the rest of it thousands of nucleotides away in the next exon.   Fortunately introns have markers:  they tend to begin with GT and end with AG, which helps to guess where they might be interrupting the coding sequence. 

Nevertheless, none of this gene hunting is as simple as it might sound, and I’m in awe of the annotators who have added the new genes to the NCBI database.  And Max has now added them to the Chromosome Gallery!

Tejano Tech
April 20, 2009, 12:35 am
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For one of the oldies at Second Life, I don’t get around much. 

However, this evening I went to look around a new SciLands Sim, over on the other side of the NOAA islands, from U. T. San Antonio.  The island is called Tejano Tech (http://slurl.com/secondlife/TejanoTech/154/159/21) and will be combining science with history and culture.  Of course, I have a soft spot for other Texas Techies.  So far, I’m the only serious SL user at my own university, so I’m thrilled to find other Second Life Educators only a few hundred miles away! 

ConstructivIST Solo showed me around the island.  Tejano Tech is still in the early stages of development, but already has a number of learning spaces suitable for student groups of different sizes.  From a coastal fishing shack, you can watch the sun rise with a few friends.  There is a small cafe that will accommodate several groups of 5-6 students.  There is a open colosseum that can seat about 85.    A library area effectively combines an open-air structure with cozy seating alcoves.  A stage area with stadium-type seating is set up for powerpoints or other media presentations. 

One of my favorite spots is the Learning Tree, where about 20 students can sit in delicate flower-like cups in UTSA colors around a small demonstration platform.  I like this so much I may have to building something like it on Genome!  There is a lovely underwater art gallery where students can experiment with both 2D and 3D art projects.   A Learning Maze has been designed and built by a Ed. Tech student; in the maze students will turn left or right, depending on their answers to questions posted at various points in the maze.  To get to the center of the maze.  all the answers have be be correct.  This looks like a fun and flexible assessment game. 

The terraforming on the island has been cleverly done to give each structure its own visual space, as in a Japanese garden.  The island is already being used by students in some classes at UTSA, and I’m sure they are enjoying it.  I’m looking forward to watching this SciLands neighbor continue to evolve.  It is off to a super start!

April 15, 2009, 4:25 pm
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About a year and a half ago, I was whining about the isolation of Genome Island.  Genome had a corner connection to Science School, but in SL, corner connections are “invisible” — you can’t see across to the neighboring island, and if you try to fly or walk across, you bounce off the corner.

What a difference a year and a half makes!  SciLands has grown from about 30 islands to over 50 and the Seacoast of Bohemia is now much reduced.  Genome Island is almost entirely landlocked, as is the real Bohemia —  Biome on the West, ToxTown to the North, the impressive multisim NHS complex to the east and Science School to the South.  There is still one open space on the northwest corner, where I hope Cell Island will someday be.  I have kept my coastlines, breaking waves, and seabirds, but Genome has landbridges to Science School and to Biome.   I had set up possible entry points on the North and East sides, but NHS has quite a lovely void sim (this doesn’t mean it’s empty — just low-prim) to my east, and ToxTown has a pier with sailboats on the north, so a land connection would disrupt their design.   However, if you don’t mind a little underwater stroll, you can walk to either destination.  It’s very nice to be connected to the neighbors!

Oddly enough, the intervening year has taught me something about how people move around in Second Life.  Genome gets a fair number of visitors, but almost NOBODY comes in at the entry points.  This makes perfect sense.  I almost never stroll over to Biome or Science School.  I just pick a spot on the map and do an instant teleport.  I checked how people come into Genome recently, using Maya Realities (http://mayarealities.com) visitor monitors, and it looks like this:


Each green dot marks the spot where somebody came into the sim.  As you can see, there are few dots at the land bridges.  Most people teleport directly in.  The concentrations of entrance points correspond to the places on the island where the activities are located, so a lot of these entrances are return visitors who logged out from one of the activity locations.  A lot of people also come in at the Landing Point, which is the teleport location given in the search utility.  Nevertheless, it’s been nice to have a seacoast with a view!

April 15, 2009, 2:30 pm
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I have the deepest respect for anybody who can keep up with a blog.   Two of my biology buddies on SL, Clowey Greenwood and Simone Gateaux, are both champion  bloggers.  See Clowey’s blog on Biome (http://simbioticbiome.wordpress.com/) and Simone’s Blog Second Life Biology (http://slbiology.blogspot.com/) and you’ll be equally awed. 

I AM A SLACKER.  However, in the interest of being a good SciLands (http://scilands.wordpress.com/) citizen, I will try to do better.   I actually had two new posts started at the time that I became an aspirant to slackerhood.  “Started” in this case means that I had a title that was supposed to remind me to come back later and fill in.  One of them was called “Linkage” and the other was called … um, something else.  Actually, I think I remember what Linkage was supposed to be about.  So maybe I’ll reinstate that one in a separate post.

Wish me luck and a sturdy character!

The Empty Horizon
June 8, 2007, 3:03 am
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Genome is an island.   There are neighboring islands close by.  Science School II is on my southeast corner, but I can’t see it from that corner, nor can anybody at Science School II see Genome.  Islands connect only across their north/south or east/west sides.  Corners don’t connect, so if your only neighbors are on corners, you are visually alone in the middle of a boundless sea. 

There is one exception to this peculiarity.  If I transport to any of the adjacent SciLands, for about one minute I can see the landscape and buildings on Genome on their horizon.  Then they disappear, like Brigadoon or the Elflands.  The same thing happens when I teleport back from the scilands.  For a minute I can see the buildings of Science School, and the thrilling panoply of rockets at Spaceport Alpha.  Then, poof! They’re gone!

Eastern Welcome CenterBut neighbors are coming!  The spots to the east of me are to be occupied soon by four new sims.  This raises an interesting problem.  Genome was constructed as an isolated island, and all of the different sections — the Abbey, the Terrace, the Gene Pool, the Tower — are oriented towards the teleport point at the center of the island.   If you approached the island from its eastern border, you would see the waves breaking on the Seacoast of Bohemia, and the back of the Abbey.  It doesn’t look particularly friendly.  In fact it looks, well, insular.  So I’m working to remedy that defect by constructing a welcome area on the slope behind the Abbey.   This will include a small gazebo, a welcome sign with teleport buttons to the major areas of the island, and a long flight of steps leading into the Abbey garden.   Hurry, neighbors!  And welcome to Genome.