Sunday, December 30, 2007

Sedum and ice

Originally uploaded by pdecell
Hope you enjoy this macro of Sedum peeking through the snow.

Saturday, December 29, 2007

The Abominable Snowman in Lawrence!

Inspired by true events...

Thursday morning I received a call from my wife asking me if I had seen the footprints in the yard. She had noticed them when she was leaving for her job in Topeka.

"Definitely human footprints only the person was barefoot and my boss said that there could be a homeless person living in the woods."

"Kay, that sounds really unlikely to me but this is Lawrence, and we've had other strange things happen such as the escaped cows in our I will go look."

So out I went and I did find some prints, but they were not very deep...

"Hey Kay nope not human, I think rabbit"

"But they look like bare feet you can see the toes and everything."

"Nope rabbit"

"Well how do you know? Were you there? After all you can't test anything that happened in the past"

"Kay, I have seen rabbit footprints before and these are rabbit."

"Just because you are trained as a biologist doesn't mean I am are just plain dogmatic. They looked human to me. You are being dogmatic."

"This is just based on experience...Kay look at this picture. I wasn't about to freeze my toes off here but notice how much deeper my shoe print is than the the ones like you found."

"I still think they are human. Why do you always have to explain everything away as something ordinary? Just a rabbit...huh maybe they are that hobbit man or a gnome. A baby Sasquatch. There all kinds of strange sightings even in Kansas."

"Kay I am a scientist and we look for the simplest explanations first."

"That is silly, all you scientists think alike. It is some sort of liberal group think. You need to think outside the box. Maybe you should go work for the government."

"What does that have to do with anything?"

"Well everyone knows those government scientists fake data..if you are told to think rabbit then you're going to think rabbit."

"Besides that rabbit idea is just a theory and scientists deal with empirical facts-not interpretations."

Sigh...fortunately at that point my cell phone died.

**any relationship to current public discussions about science is purely coincidental.

Friday, December 28, 2007

Body Identity Disorder

While traveling to Disney World the other week, I picked up a copy of Scientific American Mind to keep myself from being too bored on the flight. One by Sabine Miller called "Amputee Envy" concerns what she terms "Body Identity Disorder" (BID). People with this extremely rare disorder desire to have one or more of their appendages removed, and some actually have such discomfort that they request that the appendage be removed. A summary of the article is here.

A clarification: "Body Identity Disorder" is a term proposed by Dr. Michael First. See this link:

I had heard about this sort of thing and chalked it up to being a sexual fetish. The reality appears to be much more complex. Some appear to be seeking attention rather than any sort of sexual gratification. But most interesting to me is that at about two thirds of the disorder report that amputation will enable them to express their "true" identity. Thus, there may be a parallel between this disorder and Gender Identity Disorder (GID), which is of personal interest to me. Indeed there are some interesting parallels-both disorders arise early in life, and sometimes the discomfort (which can be extreme) is only resolved through surgery.

One might think that these sorts of identity statements are merely part of our modern cultures preoccupation with identity or authenticity, but some cases of BID appear to arise from irregularities in how the body is mapped out in the cerebral cortex. Indeed, sometimes temporary cases of body image problems result from brain tumor, injury or disease. When the disease or injury is fixed, the body image problem goes away.

The article also address the issue of surgery for BID cases. Some ethicists argue that, as in the case of certain types of GID, if the person is fully informed of the risks and is not psychotic then surgery ethical. Other ethicists consider this wrong headed and that the Doctor must protect the patient from his or her "irrational desires."

Again this sort of debate parallels that about Gender Identity Disorder. Since Gender Identity Disorder is much more common, there is actually standard of care called the Benjamin Standard of Care to provide a way to select those most likely to benefit from sexual reassignment surgery. So lots of interesting things in this article to chew on. What makes our identity? Is it merely socially constructed as some would have us believe? How much is changeable about our identity? What are the boundaries of ethically acceptable medical intervention?

There are lots of other interesting articles in this you might look for it at your newsstand or for purchase online at

Citation: Sabine Miller(Dec 2007/Jan 2008) Amputee Envy Scientific American Mind 18(6) pp 60-65

Other links:

World Professional Association for Transgender Health

Wednesday, December 26, 2007

Poor Ann Coulter!

She's lost her place as a wacko to Mike Huckabee and SHE DOESN"T LIKE THAT! Check out her latest hissy fit: "There is a Huckabee born every minute". Here is one little gem in reference to Huckabee's beliefs about evolution:

"I went on a massive book tour for "Godless" just last year, including a boffo opening interview with Matt Lauer on NBC's "Today," a one-on-one, full-hour interview with Chris Matthews on "Hardball," and various other hostile interviews from the organs of establishmentarian opinion.

But I didn't get a single question from them on the topic of one-third of my book.

If the mainstream media are burning with curiosity about what critics of Darwinism have to say, how about asking me?"

Well gee Ann, You're not running for President, Huckabee is.

Climate change sites...

My wife and I returned from Florida last Friday just in time for last week's snow. And as I write, it is snowing again. But the discussion section in the Lawrence Journal World is hot today because of a column by Cal Thomas in which he accuses Al Gore and other believers in global warming as being fundamentalists. He cites a global warming skeptic "Paleoclimate scientist" Bob Carter as writing:

“In one of the more expensive ironies of history, the expenditure of more than $50 billion (U.S.) on research into global warming since 1990 has failed to demonstrate any human-caused climate trend, let alone a dangerous one...”

This is an interesting comment which flies in the face of the general scientific consensus. So who is the average person to believe? This is important because if Gore and the vast bulk of climate scientists are right then we have an environmental problem that can't wait another 50 years to fix. We are going to have to make both personal and policy decisions either directly or indirectly about this issue.

The first thing we need to do is cut partisanship out of the loop. Second of all we need to look at the information that is out there and try to evaluate it as best we can. Fortunately there are several good sources of information. The U.S. government's EPA site ( is much improved in terms of its coverage and I strongly exploring its links. Another site is the National Oceanic and Atmospheric Administration's Global Warming FAQ which gives a quick synopsis the current consensus on global warming. There is plenty of room to discuss what sorts of solutions - free market, government incentives and mandates, individual action.

As for non governmental sources, Science Daily keeps tabs on climate change at and this is perhaps the site for the latest developments in our understanding of climate change.

If you are a regular blog reader, a good unbiased site is Real Climate ( This blog's contributors are climate scientists-not geologists and not ideologues. Of course look at some of the advocacy sites on the left and the right-what ever your ideological fancy, but do yourself and civilization a favor and check the claims that are made on those sites against each other and come to an honest judgment for yourself about where the truth most likely is. Don't just believe some numskull on the left or the right because you agree with their ideology, unless the numskull happens to be me of course.

In the interest of full disclosure I am pretty much in agreement with the scientific consensus but some of my conclusions about where we stand probably go beyond the scientific consensus:

1. Global warming is real and not just an artifact of changes in data collection.
2. Much, but probably not all, of recent global warming is due to human activity including burning of fossil fuels but also deforestation and increased agricultural production.
3. Global warming may be to the point that we can do little to affect it quickly.
4. Climate change happening more rapidly than we thought possible even five years ago and may be happening more rapidly than many populations can adapt to.
5. There is no magic bullet to solving global warming and we probably will need to make some uncomfortable choices concerning energy sources and (dare I say it?) some sacrifice of living standards.
6. Poorer countries will be more severely affected than developed countries.
7. We have exceeded the ability of the planet to sustain our current population are global warming is interacting with other human disturbances to bring about an irreversible biodiversity crisis.
8. There is still hope for our species but our environment is going to become biologically impoverished in ways we might not like.

Of course all comments are welcome; just play nicely.

At Disney World...Part II: the pictures.

I've posted pictures from our trip on my flickr photostream. I estimate I took 3GB of photos and I have edited them down to the best and have grouped them as follows:

Epcot-General pictures.

Didn't spend as much time roaming around Epcot is we have in the past. But we did spend more time at the aquarium and most of those fishy pictures are grouped by themselves.

Epcot- Aquarium pictures


Most of the fish pictures were shot in the Coral Reef Restaurant. We were seated right by the aquarium which made for great shooting to my wife's dismay. She claims I only spoke 10 words to her since I was so intent on trying to get good pictures. She exaggerates-it was more like 20 words.

MGM Studios

<span class=

We spent part of an afternoon exploring MGM and this set includes some action shots from an Indiana Jones show.

Magic Kingdom which includes some great fireworks pictures.

<span class=

At least I like them since I was just experimenting with taking pictures under low light conditions. Also have some nice parade shots. Disney does wonderfully choreographed parades.

Disney Flowers and Plantings.

<span class=
December probably isn't the best time to see flowers at Disney, but what can I say except "Florida: where the houseplants are outside"... and a lot bigger than mine. There were lots of nice plants out if you looked carefully beyond the mass plantings. Disney uses lots of ferns and cycads which I definitely appreciate.

Saturday, December 22, 2007

At Disney World...part I

<span class=

Last week Mme. D and I went to Disney World in Orlando. This is our 3rd trip together and my first since I began blogging. We left last Sunday the 16th and got back early on Friday morning just in time to encounter the snow that hit today.

I have always had a sort of love/hate relationship to Disney.
On the love side-as is the case with many of my generation, I grew up with Disney characters and movies. Watching the Walt Disney show on Sunday night was something I looked forward to. I fondly remember movies such as Flubber, and Swiss family Robinson.

My favorite movie when I was 10 or so was 101 Dalmations-not the recent remake but the original cartoon. I am not sure what I liked about this movie but was thinking about this just last night and I believe it had to do with the dogs communicating the plight of the kidnapped Dalmatians. I knew even at that age that animal communication is generally not so detailed but I remember thinking that there must be a whole secret world of communication we humans are not aware of. Of course this insight proved to be correct if the particulars were wrong.

At any rate, the movie was serialized in the comics and I loved the movie so much that I actually collected all the strips, taped them together in sequence and made a viewer out of a cardboard box and some pieces of wood so that I could run the strip backwards and forwards and pretend it was a TV-today we might say a VCR or DVD. What's odd is that 101 Dalmations also sensitized me to the flip side of Disney. Cruella Deville is totally dastardly and I can remember thinking that she has a French name. At that time I had become sensitized to a sort of mild ethnic dislike between the Irish and the French communities in my home town and wondered if Deville wasn't some sort of anti French swipe.

<span class=
The characters are very one dimensional
-that is part of the appeal for children and I don't think adults are immune from that appeal either. Disney today is a lot more than the cartoon characters-not only is it a media empire in all sorts of ways but the theme parks have expanded to vast merchandising and real estate empires. For instance we own a time share so we are able to stay in a Disney World resort, get transport to the parks do everything at the parks. For us it is a great vacation since my wife can no longer walk very far. Disney does take good care that its resorts and parks are friendly to persons with mobility related disabilities.

<span class=

But Disney today is I think in disconnect both from its roots and also from the natural world and very carefully manages the information the visitor receives about the the resort. Now some of this is because Disney is all about fantasy and part of what makes fantasy work is control of information. But several things strike me as odd about Disney World in Orlando. First of all while you can get maps of the individual parks that is Magic Kingdom, Epcot, Animal Kingdom etc, there does not seem to be a readily available map showing the whole complex and how the different parks are connected. Second. When we first arrived the Disney Tour driver pointed out that Disney World in Orlando is the largest single site employer in the United States with 60, 000 employees-read cast members and also that by agreement with the State one half of the Disney property must be left natural. Yet I have not been able to find anything out about the natural side of Disney World and it does not seem accessible to visitors except as glimpsed while on the monorail system. What happens to the waste produced by the millions of visitors? How is Disney caring for the natural parts of its land, or is it?

<span class=

Another curious thing is the lack of insect life. Orlando ought to be swarming with insects and yet I saw very few insects on site-a couple of ants, a katydid and one zebra Long wing butterfly. Now you might go so what? Probably most people are like my wife and think I take pictures of strange things. As she said...most people go to Disney for the characters but you shoot pictures of plants. But consider this-last May there was a butterfly garden in Epcot; my wife had taken her Mom down last May and saw it. But the the whole thing was just temporary. The larvae are reared indoors and trucked outside and allowed apparently to emerge in a screened in area. Not quite what I had pictured for a butterfly garden.

<span class=

The whole Disney approach is technological, Julian Simon run amok. Now don't get me wrong I am not a luddite and I have always approved of the sort of forward vision that Disney has. But there is something curiously 20th century, curiously quaint and not in a nice way-about the disconnect between the corporate technology can solve everything and we really don't need nature and the the messiness of the real world. As I remind my students the real world is not Disney World.

This is the year of million dreams at Disney so I entertained myself and my wife... by dreaming of an alternative to Disney World called Paul's World. This would attractions such as:

  • The natural selection walk. Leave your I-pods at home and match wits with the natural world including big cats and not so friendly snakes.
  • The invasive species walk. Avoid the stinging fire ants, cut your way through Kudzu and help defend bluebirds from starlings.
  • Germ pavilion. Test your immune system against 20 great old time pathogens including Mycobacterium tuberculosis, Plasmodium vivax and Yersinia pestis!
  • Global warming water park. Experience the Florida of the the next century full of wonderful tropical parasites and snakes to challenge even the most seasoned survivalist.
  • Creationist wonder park. Thanks to the wonders of synthetic biology combined with genetic archeology, come to the Jurassic and see just how well Adam and Eve would fare if they lived with dinosaurs. By the way, you play Adam or Eve.

Somehow my wife doesn't think these would be popular attractions. Perhaps not. But if I can dream more realistically then I dream that Disney will find a way to get out of the whole Spaceship Earth 20th century technology can do everything rut and turn its considerable resources to bringing about better understanding of the natural world-lessen that disconnect we have as a civilization towards nature at precisely the time when understanding the connection between humans and the rest of the natural world is so critical.

Yes I know, Disney is about fantasy but fantasy can be consciousness raising and it doesn't have to be heavy handed about it either. Maybe all it takes is a real butterfly garden with native butterflies and native vegetation. Maybe all it takes is a bit more transparency and a bit more show casing of the natural side of Disney and just a bit less merchandising of prepackaged dreams.

<span class=

Tuesday, December 11, 2007

My Daemon?

Yesterday, my wife and I took advantage of school being canceled, in spite of relative benign weather in Lawrence, to go see the Golden Compass. We like this sort of fantasy and our interest was piqued because of the Catholic League's claim that the film is anti Catholic. The League claims that Catholics and other Christians should avoid the film because it it "bait" which might cause unsuspecting parents to buy the books by Phillip Pullman upon which the movie is based.

The League accuses Pullman of being a militant atheist with the goal or denigrating Christianity, especially Catholicism and the League claims that the film sanitizes much of the anti Catholic rhetoric in the book. Further, the League dismisses the claims Pullman and others associated with the film that the film is benign. You can download the League's report here.

I have not read the books, so can't comment on that particular controversy except to say that I have never been impressed with arguments that one should avoid such and such work simply because the author's theology, or lack of it, is a problem. Arguments, be they couched in fiction or not, have to stand on their own merits.

Harm to kids? I think not. Perhaps the League's leaders did not go through any sort of questioning of their faith as a teenager...but from what I remember and experienced with my kids-questioning of all sorts is part of being a teen.

Now to the movie. The movie was lots of fun. Mrs Coulter (Nichole Kidman) was the ultimate female villain; the Magisterium appropriately sinister, the good guys appropriately good. So yes, the Golden Compass's characters are very one dimensional from an adult perspective. However, what kid or adult can possibly resist having their "soul" taking the form of an animal daemon? What kid or adult can resist a film that promotes free thinking? OK... don't answer that.

Given the 'controversy' about the film, my antennae were all a quiver for anti Christian references. But aside from the the Magisterium the only swipe at Christianity was a comment Nichole Kidman makes to the young heroine, Lyra to the effect that many of our problems stem from a couple of our ancestors who did not obey authority. This could be a reference to the Fall. But that doesn't disturb me since I have strong Pelagian sympathies, as you might suspect.

The movie's pacing was a bit frenetic and choppy giving the impression that a lot was cut out..which it probably was. But I don't think the director and screen writers did as good a job as other attempts to condense large fantasy books to a movie; certainly the editing is not up to the quality of the Harry Potter films. The special effects are generally good and not too obtrusive. I really liked the daemons which by the way ranged from a snow leopard to a praying mantis to a ferret.

Oh, I suspect now we will buy the books if only to see what the League's fuss is all about. Given the overtly Christian themes of some other fantasy writing-C.S. Lewis comes to mind here-fantasy from an overtly atheist perspective might be refreshing.

The movie has an official web site of course ,and just out of curiosity I visited it and had fun with the choose your daemon game which asks you some basic personality questions and purports to match you with your daemon. Mine is below. Not sure I agree with the choice but it is appropriate for an evolutionist don't you think? At least I didn't get the praying mantis.

Monday, December 10, 2007

Tonight in Kansas

As everyone knows the Southern plains have been hammered with freezing rain and sleet. Well it looks like it is our turn in Northeast Kansas.

When I was young I used to hear about Kansas Blizzards and thought that would be really cool to be in. Snow? Bring it on! I love storms but some sorts of stormy weather I can do without. Tornadoes. Or ice storms.

Check out the radar from tonight. Be safe folks. And if you go out tonight or tomorrow, remember there be ice under those wheels. You might want to review these instructions for driving on snow and ice.

Mendel's Garden #21 is now up!

Check out the best in genetics blogging at Inoculated Mind. Hard to believe this is the 21st edition of Mendel's Garden.

A Big Day in Boston!

If you are a Boston single, as of today you have a new option to find a mate. A company called has a new wrinkle in the match making game-matchmaking based on DNA analysis. The idea is to find a mate based on the compatibility of the genes related to characteristics of the immune system. The company's website claims:

"When you share chemistry with someone:

  • 1. You love their natural body odor. They smell “sexier” than other people.
  • 2. You have a more satisfying sex life.
  • 3. If you’re a woman, you have more orgasms.
  • 4. There’s significantly less cheating in your relationships than if your DNA isn’t matched properly.
  • 5. As a couple, you're more fertile.
  • 6. Your children have a better chance of being healthy."
And there is peer reviewed science to back up at least some of these claims individually, much of which is cited on the company web site. In fact, I talk about some of this literature in my classes. But it is quite a leap from the basic scientific literature to the claim that DNA analysis can make for better matchmaking. Testing that hypothesis would seem would seem to require a whole other layer of analysis which doesn't appear to have been done. Also the site is a bit vague about how the genetic testing is done and what genes are examined.

I must remain very skeptical for now. By the way, a one year membership costs $1,995.95. So if this system is an improvement over the old fashioned way of finding a mate-is that improvement great enough to make the cost worth it? This is especially true since the company makes the case that odor is an important part of compatibility. Maybe the company's owner ought to consider making little scratch and sniff tabs with arm pit odor that clients can give to each other. But perhaps that is not as sexy as DNA analysis.

The web site suggests that the company is planning on expanding to other cities, so have a look and let me know what you think.

Saturday, December 08, 2007

Some personal news and a new blog.

The Force celebrated it's 2nd birthday last month. My first blog post is here if you want to see how this started and I have been thinking of what else to do blog wise that might be a bit more focused. Last Spring I was in the Lawrence Journal World's Citizen Journalism Academy and the LJW has been expanding community blogging activities. So as part of that effort I have set up a new blog on their site called Dangerous Ideas. This is meant to be a strictly science blog, focusing more on local science than this blog does.

The idea is best explained by the opening post to Dangerous Ideas where I say in part:

"I use dangerous here in a positive sense. For me science is a liberating force. It doesn't do away with a sense of wonder, a sense of poetry or wonder. But science does not worship mystery but replaces it with a sense of awe at the quirky creativeness of the universe. This blog will focus on science. I will try to stay away from politics and religion...there are plenty of other blogs that do that including my companion blog at The Force that Through".

My aim there is to try to present science with a minimum of jargon, keep the really geeky and philosophical stuff here and let the local readership in Lawrence doing their own reacting. But here will continue to luxuriate in geekiness and poetry and the other stuff. Of course visitors here are welcome to hop on over there and vice versa.

Unlike here, comments do not have to be approved by me which will probably make the occasional trolls that accuse me of censorship happy. There will be some cross posting between the blogs, just as I occasionally build blog entries here from comments I make else where. My last post here is a good example as it is built from a comment I made on the LJW site.

There is yet more bloggy experimentation to come, so stay tuned.

Synthetic Biology

One of the hottest areas of biology today is synthetic biology. Synthetic biologists are not content to take a gene from one species and insert it into the genetic material of another species.

Instead, synthetic biologists are attempting to build a set of standard building blocks often by synthesizing DNA from scratch. The idea is to have a set of modules that can be plugged together to make the biological equivalent of electrical devices.

So just as an electrical engineer designs new circuits by plugging together standard parts on a breadboard, the synthetic biologist attempts to create custom organisms by inserting these biological circuits into cells.

The field has progressed to the point where there is an annual student competition at MIT dedicated to designing custom devices called iGEM which stands for International
Genetically Engineered Machine Competition. The winners of the 2007 competition have just been announced and they include teams that developed applications of synthetic biology to medicine, environmental sensing, energy and information processing.

For example a team from Alberta Canada developed a synthetic set of genes involved in the production of butanol, an organic compound that could serve as a fuel alternative to ethanol.A team from University of Missouri at Rolla, the Missouri Miners developed a biological breathalyser and a biological timer.

Synthetic biology is in its infancy and the power of this technology is rapidly increasing, much like the power of computers, so that soon synthetic biologists may be able to construct synthetic organisms entirely from scratch!


Synthetic Life, Scientific American 2004


Missouri Miners

Cross posted to Dangerous Ideas

Teddy Bears and Symbolism

All right, I have resisted discussing the Teddy Bear controversy. After all the whole thing strikes me as a silly distraction from more pressing issues, but I found Leonard Pitts' comments: to be a shallow analysis of the Teddy Bear incident.

Pitts writes:

"And then there is Darfur, the western region where four years of government-backed genocide has left an estimated 200,000 people dead. Some might say they are the lucky ones. Luckier than the man whose eyes were gouged out with a bayonet. Luckier than the people burned alive inside their huts. Luckier than the women raped so brutally they can no longer walk, so brutally that urine trickles constantly down their legs.

What a pious, holy nation. Their God is offended by a teddy bear.

If anything, God is offended by them."

I agree with the sentiments but what Pitts is discounting is the power of symbols to take hold of peoples emotions. Maybe he ought to take a closer look at the equally silly things that we get incensed about in our culture. For instance, try burning an American flag and see the way many of us react. In the history of Christianity there have been huge fights over symbolism including how God is to be represented. The English word Iconoclast comes out of just such a fight. FYI I think these sorts of fights are odd too. But I am not immune to reacting to symbolism either. Books for me are highly symbolic and book burning or banning is way up there on the list of symbolic offenses one can make.

The point being that in our culture we generally chalk these sorts of offenses as the price we pay for the right to free expression and some one has to get really extreme before we consider banning them. I don't like fundamentalism any more than Pitts does, but what's going on in Sudan gets at a much deeper aspect of symbols namely their power to hook onto our emotions and I don't think those of us who are not fundamentalists are immune to the power of symbols.

What symbols and related cultural faux pas press other people's buttons?

Friday, December 07, 2007

Power outage


The lights stuttered and then back on
And I thought nothing of it
Until driving east
In the owl eye night.

Thursday, December 06, 2007

What are they afraid of?

Here is a disturbing article from the Telegraph out of England. It seems a group of Dutch creationists are distributing copies of Sir David Attenborough's natural history documentaries that they have doctored to omit or minimize basic facts of science with which they don't agree.

Sir Attenborough comments that:

"Instead of saying "70 million years ago, something happens," they say "a very long time ago something happens". They also omit paragraphs such as: "This is inherited from my warm-blooded ancestors,"" Sir David told the Telegraph. "I would much rather they kept to the letter, as far as that is possible, of what I said."

But of course they won't, because the creationists want to indoctrinate their own kids with their scientific misunderstandings. To me not teaching kids about what science believes about how the world operates is a form of child abuse needs to recognized for what it is. If it was just their own children that were being so abused that would be bad enough but as the article notes:

"BBC documentaries have been made compatible with creationist views by replacing spoken English text by an adapted spoken Dutch text, or by cutting whole scenes."

This editing seems to be much like the sort of authoritarian massaging and muzzling of science that the Bush administration engages in routinely to gain political advantage. What are these creationists afraid of? Don't they think their faith can stand up to science?


Creationists rewrite natural history

Tip of the antennae to a poster from Skepticality for pointing this article out.

Monday, November 19, 2007

The Woods by the College:sustainability and synchronicity

Sustainability and Synchronicity? Now this seems as an odd combination of concepts, so let me explain. The whole thing started a couple of weeks ago when and another faculty member and I were discussing our College's push to promote sustainability across the JCCC campus. Several faculty members and one of our vice presidents had gone to a League of Innovation conference about sustainability and came back all fired up. This of course from my way of thinking is quite laudable and has led to lots of discussion about sustainability on campus.

But I wondered aloud to my colleague if people really understood the sort of sacrifices that true sustainability might entail. For example there are studies which have looked at our civilization's use of planetary resources and the damage we have done to the ability of our planet's systems to sustain our population. Several studies claim that we have effectively overshot the planet's capacity to sustain our population and that we would need to have the resources, biological and otherwise of several Earths to have a sustainable planetary population with the standard of living equal to that enjoyed by people of this country. See for example

Since we only have one Earth we have a little problem of insuring that everyone has a decent standard of living. Now one might argue that technology might help us here, but our track record on mobilizing new technologies has not been particularly good, unless you count the development of hybrid SUV's mobilizing technology in a sustainable way. We can hope for a transforming technology to save us. Scientific and technological development is notorious hard to predict, but the trend in resource use, destruction of habitat seem pretty clear and hard to avoid in the short run even we to develop a set of new sustainable technologies. Sustainability is important but I wondered to my colleague if it isn't in danger of becoming a feel good buzz organic or ecology.

At any the woods. At JCCC we have a wonderful campus wonderful resources for teaching, great staff and an energetic new President. Last week I was riding to work on the bus and was noting the contrast between the college's brick work architecture and well groomed appearance and the scruffy looking patch of woods next to the college's entrance. What a contrast-we are thinking of sustainability in terms of the engineering and management systems we use and how we can tweak them to reduce waste-kind of the Spaceship Earth paradigm. And yet natural systems as epitomized by this patch of woods manage to sustain themselves quite nicely even though the self regulatory nature of biological communities is really an illusion compared to the designed regulation of our technological systems. So from here came this poem that attempts to capture in a few lines some of these ideas:

So to the poem:

The Woods by the College

Not all that long ago this whole space
Was prairie of tall and mid grasses
Swaying across the decades following
The shifting rains east then west,
Except here where a spring feeds
The roots of mock orange and locust
And hack berry and brambles.

Somehow this lot survived by a whim
The building of the campus.
But no one visits here unless
We take our students to see
The stream cut in the grey clay,
Let them pick among the briers,
Trees muffling traffic and shouts
From the tennis courts.
We let then scrape samples
From the wood's trickling womb
And a cardinal scolds us over the water sounds
As we leave for the geometry of brick,
Leave behind the illusion of design
That sustains itself in the real world,
One Earth deep as we say we want
Though our design is many Earth's deep
Beneath the illusions we create.

Now to the synchronicity. That night my wife and I decided to get Chinese food and my "fortune" which by the way I pasted into my poetry journal reads:

"The one that recognizes the illusion,
does not act as if it real."

Wednesday, November 07, 2007

What's in bloom now...

This wonderful fly pollinated plant (Huernia plowseii) is in the milkweed family (Asclepiadaceae) and these plants are sometimes called carrion flowers because some species smell like-well-carrion. Makes sense since these guys are fly pollinated. This species doesn't have much of an odor and is a wonderful easy to grow and propagate succulent.


For more pictures of succulent Asclepiads check out this site:

Sunday, November 04, 2007

Sexism and Creationists...what a combo

I like to tell my Biology and Genetics students that we are for the most part out of the sexist bad old days when women were thought to be incapable of doing science...but Michael Behe-he of the irreducible bacterial flagellum has demonstrated that sexism is alive and well. Seems he is playing the gender card in the case of grad student virologist, SA Smith when she had the gall to correct the Dr. Behe about the evolution of the HIV virus.

Well I had to check what Behe said for myself, because I had met Behe and watched his testimony at the Kansas Creation Science hearings and he seemed like a nice sort of guy though majorly confused about what his own paper on the evolution of proteins was really saying.

Behe says of SA Smith:

"Although she calls herself a “pre-grad student,” the tone of the post is decidedly junior high, the tone of someone who is trying hard to compete with all the other Mean Girls on that unpleasant website. I’ll pass over all that and try to stick to the substance."

Hmmmm I had to look up Mean Girls and I assume Behe is really referring to this site connected to the movie, Mean Girls. Sounds to me as if Behe has taken to imitating a real life Mean Girl Ann Coulter. I guess Behe is a bit grumpy given the failure of his irreducible complexity ideas to explain anything about biology. Or maybe its simply that 19th century scientific beliefs go hand in hand with misogyny.

To be fair to Dr. Behe, maybe he is really meaning to play the "I'm the professor she's the grad student" card. As if THAT is going to win any friends and influence people. Also to be fair misogyny along with racism is found in other scientists including some who are decidedly NOT creationist, James Watson being a recent and ancient case in point.

Ann Coulter image from

Saturday, October 27, 2007

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.

Thursday, October 25, 2007

What do you call snail racing?

Obviously NASCARGOT! Check it out.

Tuesday, October 23, 2007

Harajuku Station, Tokyo

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.

Sunday, October 21, 2007

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.

Tuesday, October 16, 2007

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.


Tuesday, October 09, 2007

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.

Sunday, October 07, 2007

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.

Sunday, September 30, 2007

Operating systems

Here is a snapshot from Sitemeter of visitors to The force that through... in terms of operating systems used. Two things standout. First MacOS is running about 7%, as is Vista. Windows XP is still the most popular system, most Windows users choosing not to upgrade on their current machines. That is quite understandable as older machines can't handle Vista's graphics requirements.

For the record, I run Mac OS at work, Vista Home premium on my home desktop and XP on my laptap. The laptop most certainly would choke on Vista. Since most of my visitors come via Google-roughly 75%, looking for answers to such questions as "Why are plants green?" or "What is weasel sex?" or.. How do I do problem 5 on my evil genetics test?", these may represent a pretty good cross section of users.