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.