Tuesday, July 22, 2008

So here we go again...

Here we go again in Kansas, haggling about evolution. In the mean time evolution keeps on happening and in unexpected ways. For example, you may be familiar with the infectious cancer that is threatening the Tasmanian Devil (AKA Taz) with extinction. This cancer is spread when the Devils bite each other's faces during mating leading to spread of cancer cells from animal to animal.

The infectious cancer cells are genetically identical and their spread is believed to be made possible because inbreeding has led to a loss of genetic diversity so that the animal's immune systems are not able to recognize the foreign cancer cells.

See this link for background.

In an interesting twist, natural selection seems to be operating, at least in the short run, to favor precocious sexual activity and breeding. According to the research published in the Proceedings of the National Academy of Sciences, this is the first time where an infectious disease has been shown to bring about these sorts of life history changes in mammals.

Often times natural selection favors the spread of genes conferring increased resistance to a disease so the scientist's findings are some what surprising.

The other interesting thing is that even though genetic diversity in the Tasmanian Devil has apparently been reduced by genetic drift there is still enough genetic diversity for natural selection to lead to a rapid shift in the timing of reproduction.

Presumably the scientists will now follow up with research looking at the sorts of genes that are involved and try to related the life history changes they see to genetics. Might there also be long term responses in other aspects of the animal's behavior and physiology driven by natural selection?

Aside from it's implication for the survival of the Tasmanian Devil as a species, this research may provide insight into the ability of endangered species to evolutionarily adapt to rapid environmental changes be they due to disease or to human activity.

Meanwhile back in Kansas...sigh.

Cross posted with Dangerous Ideas.

Nota Bene:

Here is a very balanced discussion of the PNAS paper over at Not Rocket Science. Note in particular this comment:

"Jones clarifies that so far, all she has found is a physical response. Rather than reflecting genetic evolution, the changes in the devil's life cycle over such a short time span is almost certainly due to "phenotypic plasticity" - the ability of an organism to change its body and its behaviour to match its environment, without changing its genes."

So while there is clearly selective pressure for early reproduction, the immediate response of the population may be a physiological adaptation rather than a longer term evolutionary adaptation.

Sunday, July 20, 2008

A matter of survival

There is an in depth article about Larry King, the "gay" Junior High student who was killed by a classmate last year. The article raises a number of issues about gender and sexual identity. One thing the article notes is that the age at which young people come out is decreasing and is now 13 years with the parents finding out a year later.

I am not surprised at this given the more liberal and tolerant attitudes our society is supposed to have. The problem is that this tolerance is not uniform; lots of kids are very insecure about their sexuality and gender identity and as the article notes schools are not well equipped to handle these sorts of issues even when teachers and administrators have the best of intentions.

The article notes:

"What you might call "the shrinking closet" is arguably a major factor in Larry's death. Even as homosexuality has become more accepted, the prospect of being openly gay in middle school raises a troubling set of issues. Kids may want to express who they are, but they are playing grown-up without fully knowing what that means."

I am not going to try to second guess the school and parents on this one, but one thing GLBT kids need to learn at a young age is how to survive and that means being discrete. In my own experience, kids figure out who's different very early on anyway and in my day that meant a fair amount of bullying. So you learn to hide or "cover", to find a safe niche and bide your time. For me that meant a lot of time alone, being one of the smart kids knowing that some day I will be able to go to college, be an adult and then be able to do what I want. Of course that was a naive hope, but it at least kept me alive, though not entirely free of bullying. Kids after all, do know who is different.

I knew I was different and I knew who else was as well. For Larry, and for Brandon the kid who killed him, the system failed all the way around and it shouldn't have failed. Larry has become the poster boy for the need for tolerance; yeah tolerance is a great ideal and its great that queer kids have a vocabulary to express how they feel about themselves, vocabulary and concepts we didn't have in the 50's and 60's. In my day, the bullies had chains and knives, today they and confused kids of all sorts have guns. In my day kids had good old face to face gossip, today kids have "social networks" which can destroy a kid's standing with his or her peers instantly and deliver threats.

So I think it is a bit unfair of the article to blame the "shrinking closet" for Larry's death. On all levels kids are pushed into adult roles with out the skills to handle adult considerations. It's easy-blame the gay vice principle-blame the "shrinking closet" that empowers queer kids today when the problem really is much broader. Kids are not taught how to cope with bullies be they armed with guns, computers or use sexuality as a weapon.

Parents don't seem to be any more understanding of their kids today than in my generation. If the article is any indication, things are worse today. Survive, just get through, because if you do, things will get better.

"Larry's life was hard from the beginning. His biological mother was a drug user; his father wasn't in the picture. When Greg and Dawn King took him in at age 2, the family was told he wasn't being fed regularly."

"Like Larry, Brandon had his share of troubles. His parents, Kendra and Bill McInerney, had a difficult, tempestuous relationship. In 1993, Kendra alleged that Bill pointed a .45 handgun at her during a drunken evening and shot her in the arm, according to court records. She and Bill split in 2000, when Brandon was 6. One September morning, a fight broke out after Kendra accused her husband of stealing the ADHD medication prescribed to one of her older sons from her first marriage."

Larry had a hard road to travel. The article pegs him as gay but who knows if he was gay, or perhaps transgendered. Who really knows what path he would have chosen. Knowing you are different doesn't easily translate into understanding how you are different or what to do about it.

So don't use Larry as a poster person for a cause unless the cause is fixing a system that fails to help kids cope. Anti bullying efforts help. Straight-Gay alliances, yup go for it; greater tolerance of sexual and gender related issues, sure, go for it. What about Brandon? He needed help too. The tolerance message had not gotten to him, nor had any one taught him how to cope with Larry's behavior toward him.

The sad thing is this whole mess is going to to get litigated in the courts and used by all sorts of people with political agendas and there will be a whole bunch of people projecting their issues onto this case. I admit it is real tempting to do, projecting my desire for tolerance and acceptance of queer youth. But it was hard enough for someone such as myself to cope and I had psychic resources and support that Larry and Brandon did not have. What about them?

Maybe the best immediate message, the message I got which was survive, just get through it, and things will get better. Not politically correct advice for queer youth or any youth. After all, part of us wants kids to make the sorts of brave decisions we didn't always make when we were young. Come out, take a stand. We do want to help kids explore their identity. But I also want kids to able to survive and cope; maybe "just get through it things will get better" ought to be a part of what we do. Meantime we can clean up our own adult world so that things really will be better.

Other Links:



Here's a sad story of how attempts to deal with bullying can get derailed politically. Tip of the antennae to Pam's House Blend for this one.

Wednesday, July 16, 2008

Election time again!

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Sunday, July 13, 2008

A Script Generator for Second Life

Anyone who scripts in Second Life knows that the scripting language has a pretty steep learning curve, especially if you are not used to event driven programming. So it would be nice to have a code generator-maybe something a novice could use. Well today a post on SLED, the Second Life Educator's list, had a brief mention of a system called Scratch for Second Life (S4SL).

S4SL can be down loaded for Macs and Windows machine. I tested the Windows version on my home Vista machine and hope to test the Mac version on my iMac at work later this week.

S4SL is developed by Eric Rosenbaum at MIT, using Scratch . Scratch allows you to program graphically by snapping together little "modules." It sounds like a lot of fun in itself! But getting back to S4SL, the program has 8 classes of modules including one called pen which apparently requires an extra set of tools. Here is the opening window loaded along side the Second Life client. The left hand part of the window shows the eight modules, and the shapes associated with motion commands.

opening screen

Click on the image to go to my Flickr stream to see a large version of this screen. The basic idea is to snap together modules in S4SL. Then you press the copy code button. This copies the generated SL script into your clip board. So all you need to do is to rez an object SL, and paste the code in place of a new script.

S4SL is loads of fun and I spent a delightful evening making little Second Life "pets" that follow my Avatar around. The next image shows a Scratch program for a pet that exhibits random motion, but then attempts to find my avatar if it gets too far away.


The "modules" are color coded based on function and notice how the "modules" can be snapped together. This sort of approach ought to be appealing for novice programmers including biology types who are of course used to thinking of shape as related to function.

There are some limitations to S4SL. First, since it is in development, only some of the capabilities of SL's language are implemented. The code is fat, meaning there is a lot of non functional material in the code depending what sorts of features are enabled or disabled. Also the resulting code, because not everything is implemented may not work the way the user expects.

Originally I pasted the script into a cube prim for testing but it so happened I had a flexi prim representation of a phospholipid hanging around and I thought it would make a cool bacterium complete with flagella. So here is a brief movie (A still is here) of the resulting "bacterial cell:"

I think S4SL has a lot of potential as a learning tool. For instance someone interested in behavior could use the system, as my example suggests, let students design bots which mimic different sorts of orientation behavior. Students without any programming experience can give their simple prims behaviors and there are good pre-made S4SL projects that come with the down load to show how this can be done.

S4SL, a neat learning tool and lots of fun and it doesn't require any scratch for the fun.

Friday, July 04, 2008

Dappled Water Lilies

dappled water lilies
Originally uploaded by pdecell
As a friend commented...you can't go wrong shooting pictures of water lilies but I really like the dappled light on these flowers. So enjoy. By the way these this year's blooms from the plant pictured back in 2006 here.

Dragon Fly Eyes

dragon fly eyes
Originally uploaded by pdecell
I try to see something new every day. Look at this dragon fly's eyes closely. The eye is divided into at least two regions. The upper region seems to have slightly larger sections(ommatidia), perhaps for detecting movement. The lower region's ommatidia are smaller, perhaps for seeing detail.

Click on the image to see larger versions on my flickr photostream.