A New Second Life Client

I am a CSI freak and interested in Second Life as an educational tool. So I eagerly last week's CSI NY which featured a crime involving a Second Life Avatar and promised a CSI Second Life site with crimes to solve and a CSI crime lab. Also involved was the use of a new Second Life client called Onrez from Electric Sheep. I must admit I was skeptical as was James Au over at New World Notes. He was afraid that Onrez would "AOL-ize" the Second Life experience.






But as he, I was impressed. First the interface is a bit more like using web browser in that there is an address window in the menu bar where you can directly type a Second Life address and teleport there. That saves a step in that you don't have to go to the SL world map first. Next, the menu bar includes a search feature for SL. Typing "education" into the search window gives a list of education sites in SL. Back and forward buttons work much like those of a browser but only within Second Life. Thus novice users might find Onrez more intuitively appealing.


There is more! Second Life supports the opening of web pages via its scripting language, but the Second Life client currently opens the web page externally by launching your default web browser. Onrez is much slicker. It has a built in Browser that opens a window within the client. Granted, the web as a texture on a prim would be slicker yet but Onrez's approach nice and clean. As James notes, right now you can't get certain web features such as quick time to work with in Onrez, but that apparently is coming.

The Onrez client does seem to be tweaked for graphics performance. For instance frame per second rates (fps) are better using Onrez (version 1). Earlier today on my land in Carmine, the SL clent gave fps of 12 and Onrez of 50 fps respectively in consecutive trials. That's is a bit extreme but Onrez seems to give around twice the frame rate as Second Life's current client release (1.18(3)5) on my machine (Specs here).

The average user will notice this speed difference and I found an amusing visual difference in the performance of particle scripts. For instance I have a script that produces little dragonflies around a coy pond in my SL house. (Hey haven't you always wanted a coy pond in your house?)




First, is a shot taken of this particle script's performance in SL. You might get a pulse of 10 dragonflies and they move at a pretty sedate clip. Next is a shot taken from the same vantage point using Onrez. Lot's more dragonflies and they move at a pretty good clip. I suspect this improvement is a graphic's issue rather than faster script execution time, but i don't have any good script bench marks such as are used to compare computer performance. I find it interesting that Second Life viewed via the Onrez client seems to use a lot less bandwidth than when viewed via Second Life's client. I don't know if that is real or how it is done.

Oh as for the CSI Second Life site, I quite frankly haven't played with the crimes scenes yet. I did visit the crime scene lab and was disappointed in the lack of functionality. Most of the equipment is not scripted. I think the CSI people missed a great chance to educate visitors about the science behind CSI. Also I found that novice visitors to the site were confused what to do. But at least they were spared to culture shock of Second Life's normal orientation since Onrez takes the user to CSI island by default.





The SL episode of CSI New York is a "two parter"; the second part to be shown in February. So it will be interesting to see how this experiment melding SL with broadcast television works out. Did I like the episode? Yes I did. There were lots of in world shots, and an arena fight involving some pretty nasty monsters to appeal to the novice gaming set. I am not a gamer but I suspect gamers might not have been impressed with the graphics. Maybe I am missed whether this is possible, but I would like to be able to visit the arena and other spots used to stage the CSI Second Life scenes.

What do you call snail racing?

Obviously NASCARGOT! Check it out.

Harajuku Station, Tokyo

more crazy public service ads, Harajuku Station, Tokyo
Originally uploaded by flashlightfish

One of my of my colleagues at JCCC has a wonderful set of photos from Japan in her flickr photostream including pictures of some really crazy advertisements. This one reads like a found poem but I don't think it is meant to be a poem. The English reads:

After the corner was turned
the trash was tossed away.
It was a blind spot
In the city.

Baker Wetlands and Change

Saturday my son and I went hiking in Lawrence's Baker Wetlands. We were discussing the onset of fall and Norman mentioned that the trees looked very much like it was still summer. Leaves were beginning to fall but there is no real color. Fall is creeping up on us but I too have had the impression that the color is not very vibrant this year.






Quite coincidentally, on Sunday I spotted this report from Vermont that claims that the fall colors in New England have not been as bright for a number of years. The frosts come too late to provide the cold required for vibrant colors. Of course, the tourism board does not agree, but after all getting tourists to come and spend money on foliage trips is it's job.




So who is right-I really don't know. And while the fall here in Kansas seems less bright than normal to me, one really can't tell looking at the bright sumac leaves from the wetlands on Saturday, so bright that I showed this picture to my classes just to show something bright this morning to counteract the rainy grey day.






Humans are always aware of change-I remember growing up the winters seemed harsher than now. The talk among birders even in the 1950's was that Southern birds and mammals were moving north...possums in the Berkshires! Poor things would freeze their tails off in the sub zero weather.

Of course today changes are blamed on global warming, sometimes correctly perhaps but sometimes we confound short term changes with longer term changes that we ought to be concerned about. For instance, consider this article from Science Daily which asserts that the oceans are becoming more acid. The significance of this is that as the oceans become more acid then the ability of coral and other organisms to make calcium carbonate declines as does the ability of the oceans to absorb more carbon dioxide.



This is a big issue since the oceans are assumed to be a major carbon dioxide sink, moderating the increase of carbon dioxide in the the atmosphere. And indeed it appears that the natural sinks (e.g. oceans, the forests) that we rely on to moderate global warming are losing their ability to absorb carbon dioxide. Coupled with reports that carbon dioxide concentrations are increasing more rapidly than expected, this suggests that the biological world is going to become very different more rapidly than we thought possible even five years ago.

The irony of course is that we strive to regulate our immediate environments, air conditioning our homes, managing our landscapes, reducing risk and raising life expectancies. But this requires greater inputs of energy and other resources which we must harvest from more and more diffuse sources. This brings conflict. We see this in Kansas where the head of the Kansas Department of Health and Environment has refused to permit two large coal fired plants in South West Kansas over concerns about global warming. OK good idea. But which would the residents of SW Kansas rather have a coal fired plant or wind farms? The coal is often harvested by leveling mountains with seams of coal that were not economical until we depleted the more concentrated high grade coal resources.

Wind farms harvest a relatively diffuse source of energy as well- easier on the carbon budget perhaps but not without aesthetic and other environmental costs. Statewide, Kansans do appear to back wind or natural gas, but the residents in the flint hills at least have opposed large scale wind farms, calling them "industrial sites" that could destroy the tall grass prairie. Hyperbole perhaps, but symptomatic of the sorts of energy conflicts we have as we use more and more diffuse energy sources.

Tidal power or wave power? Again very diffuse sources of energy-easy on greenhouse gases but with uncertain environmental affects. Some of the proposed projects such as the one to build a massive tidal power facility to supply San Fransisco with electricity look promising on the surface, but we need to go in to these sorts of projects realizing that that they may well be unintended consequences to the life of the Bay.




There is probably no technology that can undo the effects of human activity on the planet and some people argue that even sustainable development is not enough. James Lovelock best known as proponent of the Gaia hypothesis says that the best we can do is a sustained retreat to power sources that can bridge the transition from our current energy mix to a fusion power hydrogen economy. He argues for nuclear power (fission) along with a mix of local renewable energy sources as the best option for weathering the coming environmental changes. He may be right but politically we will be slow to accept nuclear power. He says about nuclear power critics:

"Opposition to nuclear energy is based on irrational fear fed by Hollywood-style fiction, the Green lobbies and the media. These fears are unjustified, and nuclear energy from its start in 1952 has proved to be the safest of all energy sources. We must stop fretting over the minute statistical risks of cancer from chemicals or radiation. Nearly one third of us will die of cancer anyway, mainly because we breathe air laden with that all pervasive carcinogen, oxygen. If we fail to concentrate our minds on the real danger, which is global warming, we may die even sooner, as did more than 20,000 unfortunates from overheating in Europe last summer."

He may be a bit over the top about his description of oxygen as a carcinogen, but on the whole his case is persuasive. But in a counter argument George Monbiot argues that we can save more energy from increasing efficiency than what we can gain from use of nuclear power. Of course no energy source is going to be perfect be it nuclear, wind, geothermal, or as envisioned in this proposal, solar power satellites that beam energy from space using lasers or microwaves.

The world is changing and we have become the agents of much of this change We must look at all our energy options and how to best apply them to reduce dependence on fossil fuels. We need to foster a global energy vision that has as its twin goals reducing the drain on what is left of the planet's natural systems and allowing developing countries to raise the standard of living for their peoples. I think we have the technology now or are on the cusp of developing even better technologies. However, I wonder if our global civilization has the will or the rationality to seriously work toward these goals.

Ren Fest!

Sunday we went to the Kansas City Renaissance Festival in Bonner Springs. Sunday so it was packed. This was good for me though since I wanted mainly to take pictures and just wander around. We did take in a few performances and attended the jousting tourney at the end of the day.


The nice thing about taking pictures at the Ren Fest is that people WANT you to take their pictures if you ask politely that is.




If I have an issue with the "Ren Fest" it is that it is a bit too Anglocentric for my taste. So it's best to ignore these historical lapses, put up with the Pirates singing Frank Sinatra songs and enjoys the colorful people...and birds.

Nature and Nurture

I often get asked if homosexuality is a matter of choice or is it due to nature. It's not always clear what the asker means by nature, but usually they have in their minds something akin to how skin color is largely determined by certain combinations of genes. If homosexuality is controlled in the same sort of way then, the reasoning goes, we should not discriminate against people because of their sexual orientation.

Yet this sort of reasoning and the supposed dichotomy between nature and nurture is a case of correct conclusion but the wrong argument: kind of like chiropractic which may have come up with some good treatments for certain joint and bone problems but from a faulty premise about the cause of disease. Recently though researchers have begun to look more closely at the interaction between genetics and environment in determining certain aspects of human behavior, not specifically homosexuality but I think these studies do have something to say about how we view human behavior in general.

Some of this research is discussed in SCIAM Observations in an article "Can nurture save you from your own genes?" by Charles Glatt. Dr. Glatt reviews a study that considers individuals with genetic variants of a series of genes known to be linked to depression, but who have been raised in different environments. In a nut shell, children with certain combinations of these genes were more likely to develop depression than children lacking these gene combinations if the children were raised in an environment where they were abused.

Nurturing environments where children received support could trump the affects of genetics. The point from my end isn't that the same exact thing happens in homosexuality but that genes and environment interact and indeed genes may or may not be involved in a particular individual's case. After all in this study, depression scores were higher for kids in non nurturing environments even if genes conferring susceptibility to depression were absent. So the environment alone was sufficient to cause depression.

Glatt says something interesting at the end of his article namely that these results will "come as a relief to believers in human free will." But free will in the context of behavior can be reduced by environment and nurture as well as by genetics. As E.O. Wilson once said when he was accused of genetic determinism, that if everything is due to environment then hat amounts to environmental determinism. Free will is internal and comes about from how all the influences on our development genes and environment interact with our developing mind which is always calculating and shaping our trajectory through life and that includes various aspects of our identity.

So yes, don't discriminate against someone because of sexual identity or gender identification not because these are innate but because they are expressions of free will, something that ought to be valued in a society based on the concept of inalienable rights. The model for gay rights and transgender rights from my way of thinking is more akin to why we grant religious liberty rather than analogy with race. Free will exists but it is constrained by history be it genetic, developmental or nurture and experience in very subtle ways.

The ENDA controversy

Currently Congress is considering the passage of the Employment Non-Discrimination Act, or ENDA. This legislation would prohibit firing someone because of their sexual orientation, just as you can't fire someone because of their religion or gender and this year ENDA is as close to passage as it has ever gotten in the 30 years since it was first introduced. Unfortunately the bill has become mired in controversy-not just from the religious right which as you might guess opposes any sort of ENDA passage but also controversy among groups that are at least nominally allies.

The problem is that ENDA, as proposed this year includes gender identity and some gay writers are afraid that adding this provision will make ENDA less palatable politically. An article in Salon by John Aravosis sums up the concerns that some gay leaders have. He observes:

"I support transgendered rights. But I'm not naive. If there are still lingering questions in the gay community about gender identity 10 years after our leaders embraced the T -- and there are -- then imagine how conflicted straight members of Congress are when asked to pass a civil rights bill for a woman who used to be a man. We're not talking right and wrong here, we're talking political reality. Our own community is still grappling with this issue. Yet we expect members of Congress, who took 30 years to embrace a gay ENDA, to welcome the T's into the bill in only five months."

I see his point of view, but I think he misses a couple of points. First of all historically transgendered people have been involved in the struggle for gay rights. For instance, transgendered people were involved in the Stonewall riots which many say marked the the start of the modern push for gay rights. Second of all, the inclusive ENDA does more than protect transgendered but any one whose expression of gender doesn't exactly conform to the norms. This could be a man who is somewhat feminine in appearance, but other wise straight and also a butch appearing woman who may or may not be lesbian.

Finally I agree with him, when he says that the gays are still scratching their heads about transgendered people. But does he really think ENDA opponents such as the Concerned Women for America are any less likely to oppose ENDA without gender identity added? Granted CWFA is currently using scare tactics and misinformation about transgendered people to energize their supporters. For instance consider this gem:

"ENDA would force all Americans who prefer to live within the realm of reality to pretend, by force of law, that a man is a woman — that an apple is an orange, simply because that apple thinks it’s an orange (awkward, fruity pun not intended). It’s “The Emperor’s New Clothes” meets George Orwell, and even if you’re the Mary Lou Retton of mental gymnastics, you land flat on your keister on this one.

ENDA is portrayed by proponents as a panacea against workplace discrimination — a mere extension of the 1964 Civil Rights Act. They claim it simply insulates people against employment discrimination based upon “sexual orientation” (i.e., “gay”) or 'gender identity' (i.e., cross-dressers). But instead, the legislation would actually violate the Civil Rights Act by codifying the very thing it purports to prevent — workplace discrimination."

The people at CWFA aren't stupid. They use this language to play to people's ignorance about gender identity just as Rush Limbaugh recently did on a radio show. I won't quote any of this because it just is not appropriate language. Limbaugh and CWFA are not going to be any less adamant about opposing ENDA. They are simply playing on people's fears to split ENDA supporters. It is we ironically who have deluded ourselves into thinking that ENDA is really more likely to pass if without the gender identity provision.

I am pretty pragmatic, if a less inclusive ENDA is really the best we can get...I say take it. Maybe half a loaf is better than none. I hope some sort of ENDA can pass in the next decade and that if we get the half loaf, we come back soon for the rest. The worse thing that can happen is that ENDA supporters be they gay or transgendered or just not able to fit gender stereotypes get polarized from each other. If that happens the CWFA, and Focus on the Family and the Rush Limbaughs of this world will have won an even bigger victory than the defeat of ENDA. What a deal...Bush vetoes ENDA (You really think he won't?). Conservatives get an energizing issue that is now even more potent because the proponents are now fighting among themselves.

Molecular Beauty

My genetics students have a little assignment. I have been slowly introducing them to some of the major bioinformatics tools available through the National Center for Biotechnology Information.

The idea is to get their feet wet so that they can go further on their own and not be too intimidated by reams of forbidding looking database records.

So far they have looked at OMIM and BLAST. This weekend their task is to load NCBI's Cn3D protein and nucleotide molecular viewer. The next step is for them to find certain important molecules related to genetics so we can make a molecular gallery for the class.

The Cn3Dprogram allows researchers to see and manipulate nucleic acid and protein structures in various ways. Since we have just finished the basics of DNA replication, and are getting ready to do protein synthesis and the regulation of gene expression, I hope that looking at some of the major actors in these processes will help the students become more comfortable with these molecules, more so than looking at a flat amino acid or nucleotide sequence.

Beauty is at all levels of organization; the balance of order and spontaneity that I think makes for beauty, is evident even at the molecular level. So I thought show a few examples beyond the iconic DNA double helix.

My first example, shown in the picture above is a protein that serves as a transcription factor. The proteins polypeptide chains appear pale blue. and it is bound to a DNA molecule shown in the dark blue and brown helical strands on the right. The structure is from a paper by Beth A. Chaney, Kimber Clark-Baldwin, Vrushank Dave, Jun Ma, and Mark Rance
Biochemistry, 2005, 44, (20), pp 7497–7511.

If you want to see and manipulate this and other structures I mention, download the Cn3D viewer, follow the instructions and then go to this structure summary link.

This particular transcription factor binds to a small region of DNA called a homeobox. Homeoboxes are important in the patterning of development. The transcription factor called Pituitary homeobox protein is critical for proper development of the anterior portion of the eye. Mutations in the gene coding for the transcription factor often lead to a syndrome called Rieger syndrome (OMIM = 601542).

Here is a different rendering also rotated a bit, showing a space filling model of the homeobox protein bound to the DNA. The DNA double helix is shown in blue and brown, the homeobox protein is in pink.

One of the nice things you can do with the viewer is highlight different parts of the molecule that might be involved in a binding site with your mouse. The part you select is also highlighted in the sequence data window. This is very useful for activities ranging from drug design to studying protein evolution.





So you can see how this works, here is a screen shot showing a particular amino acid in the protein and a guanine to which it binds in the DNA.

But I stray from my main theme, and that is beauty at the molecular level. Maybe a transcription factor has a beauty only a molecular geneticist can love, but what follows are several beautiful molecular structures, rendered using the viewer along with their structure summary links for those who want to examine them in different ways using the viewer.


A Nucleosome.

Nucleosomes are the basic structural unit of chromosomes in eukaryotic cells, such as the cells in your body. Nucleosomes consist of a core of proteins called histones around which wrap a two coils of DNA. Can you pick out the DNA?

Structure summary.










A DNA mimic.

Gyrases are enzymes that manipulate the coiling of DNA during DNA replication. These are the sorts of enzymes one might which to have when trying to detangle fishing lines or kite strings. Unfortunately Gyrases only work on DNA. In searching for gyrases, I found this wonderful protein which turned out not to be a gyrase but rather a protein called a The Pentapeptide Repeat Protein. It is from the bacterium which causes tuberculosis. These sorts of proteins are wide spread in bacteria and their usual function is not known. But in the tuberculosis organism this protein confers resistance to a class of antibiotics called Fluoroquinolones. I also inhibits the activity of gyrases. It can do this because the pentapeptide repeats (brown) mimic the geometry and charge properties of DNA.

I show two angles so you can see better just how neat this molecule is!


























Structure summary.











Sliding clamp protein.

Clamp proteins hold DNA in place, for example during DNA replication and clamp proteins seem to often have really interesting structures as in my example.

































A different rendering of the same clamp shows that each of the rings is made from three polypeptides. So think of the clamp as a machine with six large molecules for parts!



So I hope you can see some of the beauty I see in these structures. Lest anyone try imbuing these structures with metaphysical freight, to me the real beauty is that even within the confines of the cell evolution has produced adaptations at the nano scale every bit as wonderful as the large scale adaptations of organisms to their environments.