Wednesday, March 29, 2006

Pleo: new life form?

While prowling around the web, I found a link to a new robot toy called Pleo. Pleo is a robot produced by a company called Ugobe and is a robot model of a one week old Camarasaurus, a dinosaur from the Jurassic period. The web site claims:

" Pleo is a 'designer species'. He incorporates all the basic traits of autonomous life. He is specifically engineered and enhanced to mimic life and relate to his owner on a personal level. "

and further that:

"Pleo is capable of expression. He can feel joy and sorrow, anger and annoyance. When Pleo is tired, he will become drowsy and go to sleep, even dream. Two or more Pleos will recognize one another. Be careful though. They can transmit colds to each other. Achoo! Pleo even sneezes!"

Now I am not a vitalist, I believe it one day will be possible to create artificial life forms but Pleo is a poor mechanical analog for the sort of nervous system/hormonal controls involved in real emotion. Is Pleo a nice toy? Looks it to me and at less than $200 I bet Ugobe sells a lot of them. To claim that Pleo is aware, and shows emotion is a bit of stretch. Can you spell anthropomorphism?

Pleo does have some impressive capabilities (video) and one could argue some of the characteristics of life. It even seems capable of some limited learning about its surroundings, but it is qualitatively quite a different thing than an organism. Now when it is able to reproduce and maintain itself then I will change my mind.

Other links:


Meet Pleo, descendent of furby

Tuesday, March 28, 2006

What are we?

When we think of ourselves as organisms, we think of ourselves as being unified, for instance as a eukaryotic organism. But an article in Live Science's "Bad Medicine" reminds us that we are quite different than we think we are. In particular, prokaryotic cells, mainly bacteria, in our body, outnumber our 'human' cells about 10:1. Nor are these bacteria just interlopers to be eliminated by antibiotics or scrubbed away by antibacterial soap.

image from NASA:

Our gut is lined with bacteria which are involved in digestion and in the production of key nutrients. Further by having our own friendly bacteria we are protected from pathogenic bacteria that would otherwise find our bodies great pickings. These friendly bacteria are symbiotic with us. They and we evolved together and the result is mutually beneficial to both us and the bacteria.

So in a sense we really are not a single organism but a whole community of organisms that need each other. This notion maybe unsettling to some, but I find it strangely comforting that the interdependence of organisms on the Earth is reflected in the interdependence of the wildly different organisms that comprise the community of our bodies.

Other links:

War on Bacteria is Wrongheaded.

Double Bonus: Bacteria Eat Pollution, Generate Electricity.

How to Live Long and Prosper: Get Dirty?

The Rise of Antibiotic Resistant Infections.

Bacteria-Animal Symbiosis Site.

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Monday, March 27, 2006

What is good for the goose is good for the platypus...

An anonymous poster commented:

"Not defining evolution and then saying "it" is based on facts and physical evidence without stating such doesn't sound very scientific to me."

I am glad anonymous asked, because there seems to be a lot of confusion in the popular mind about what a biologist means when referrring to biological evolution.

Evolution as a word has a number of meanings, some more general than others. The most general meaning of the word is change through time. But when referring to biological evolution perhaps the most common today is that biological evolution(the type creating all the fuss) can be defined simply as a change in the genetic makeup of a population over time.

The National Academy of Science(1998) defines evolution as:

"..change in the hereditary characteristics of groups of organisms over the course of generations. (Darwin referred to this process as "descent with modification.")"

Note the reference to Darwin's geneological definition as descent with modification.

So biological evolution is not really about species but how about the genetic make up of populations and how this changes over time. This definition can be used to model and empircally test hypotheses about HOW evolution operates. It is after a conceptually trivial problem to demonstrate that biological evolution happens, I suggest a trip to the Science library on this point. So the issue for the scientist is explaining how evolution operates in different situations. Again a trip to your friendly neighborhood science library might be useful.

Sometimes people refer to a change in the genetic make up of a population "microevolution" but there does not seem to be any logical distinction between microevolution and evolution in the sense of the development of new kinds of organisms from preexisiting ones.

Incidentally this definition does not refer to the origin of life problem or the "big bang" or any of the other obfuscations creationists try to use when dealing with evolution.

I wonder what the definition of intelligent design is. Can IT be specifies in a way that allows empirical tests as to HOW intelligent design operates? How about creationism: can IT be defined in a way that allows empirical testing of the mechanisms of creationism? We can do that with evolution. Come on...after all what is good for the goose is good for the platypus.

Other links:

Teaching about Evolution and the Nature of Science

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Saturday, March 25, 2006

Another cool biology blog

For a biology blog with some political bite you might want to visit Mike the Mad Biologist.

Delusional Thinking

Today I had a letter published in the Lawrence Journal World about Dave Penny and his billboard. I expect to get attacked this letter in which I say:

"I want to thank Dave Penny and his band of anonymous businessmen for providing me as a biologist with one of those “teachable moments” I so love. He provides just the illustration I needed to illustrate the distinction between rational and delusional thinking and between how scientists develop understanding through careful study of the natural world versus how delusional thinkers use rhetorical tricks, out-and-out lies and slick slogans to manipulate public opinion about scientific ideas."

So, to forstall that, perhaps a couple of comments about delusional thinking are in order. First, delusional thinking is not all bad. After all, it is the delusional thinking of the optimist that the glass is half full that keeps hope alive in the face of overwhelming odds. Delusional thinking and belief is simply a failure to accept overwhelming contradictory empirical evidence. We engage in this sort of thinking when we get up in the morning and smile in the face of empircal science which seems to say that the universe has no purpose and is not particularly friendly to me as an individual and besides I am out of coffee.

But delusional thinking becomes bad when it interfers with our ability to adapt to new situations, or recognise and handle aspects of our environment that are important (e.g. evolution and global warming). When delusional thinking becomes dogma rational discourse ceases and we put ourselves in grave danger. Delusional thinking becomes bad when it leads us to harm other people such as the religious fanatic (insert your favorite sect) who thinks that by killing their enemies, he or she will find grace or some sort of heavenly reward.

Delusional thinking can be a force for good. It enables us to hope for the future and plan. Positive delusional thinking is faith and that is a powerful thing to have. But some sorts of delusional thinking may become popular and dangerous dogma, spreading because of the hooks they put in our psyche, but dangerous for us as individuals and as a civilization.

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Friday, March 24, 2006

Of Mice and Stem Cells

In an illustration of the unexpected twists science can take, German scientists have found that a type of cell called a spermatogonial stem cell from the testis can be coaxed to behave as a generalized or multipotent stem cell at least in mice. In testis, these cells are what in biology are called "germ cells", that is specialized diploid cells capable of undergoing meiosis and development into gametes.

Image: Slide of spermatogenesis in Grasshopper. Note the sperm bundles.

In males these germ cells are called spermatogonia. Of course we don't know if the corresponding cells in humans have the same flexibility. This research is exciting to some people because it seems to get around the ethical issues posed by harvesting embryonic stem cells. We shall see. But right now it looks like a simple scientific discovery might remove one of the big ethical objections to using stem cells.

I wonder if either germ cells or primary oocytes in females can be used in the same way. Of course this might be difficult since the female's germ cells are found in the fetus and female germ cells don't under go the sort of continuous production that male germ cells do.

Other links:

Stem cells found in adult mouse testes.

Testicles may provide a better kind of stem cell.,,13509-2102393,00.html

Mice cells mimic embryonic stem cells.

Comparison of spermatogenesis and oogenesis.

Text Book Selection Time

Now is the time for all good professors to select new text books so we have been inundated by publisher's reps. It got so bad that I posted the following notice on my door today:


The emergency holographic biology program (Decelles Simulator version 1.0) is currently in the office. If you are a biology student, the program is fully equipped to answer your questions. Otherwise, you should wait until Dr. Paul (Organic version 1.0) returns on Monday."

Shades of Star Trek Next Generation.

Thursday, March 23, 2006

More Creationist Puffery.

Lately I have been seeing stickers that say "Evolution is a fairy tale for grown-ups. " My first reaction was puzzlement: is this pro or anti-evolution. After all, I do have a soft spot for a good fairy tale. They require imagination, something I value. But of course the slogan is anti-evolution and foisted on the public by people who have no imagination. Now a shadowy group of business people fronted by a Lawrence local concrete magnate, Dave Penny are erecting billboards with this slogan and a link to a pseudoscientific creationist site

Dave Penny has a degree from MIT. Presumably he learned how to think there and is not a stupid person. That being the case I can only conclude he has some sort of delusion and ought to consider therapy, or he is pushing this creationist stuff to further his well known conservative ideological bent, much as the conservative Kansas Board of Education. Some family values: pushing lies to further a political agenda.

So here is my slogan: Creationism: not even a fairy tale. :-)

Other links:

Ex-official helps erect anti-evolution billboard

Understanding Evolution

Is Intelligent Design Science?...OK my own essay and a bit dated but hey its my blog.

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Thursday, March 16, 2006

A new plant!

My wife made the mistake of asking me to go the plant store to get a plant for a gift. Well that was a mistake. Fortunately I came home with only one plant, aside from the gift. The plant is a so called carnivorous plant, Nephenthes.

Usually nurseries play up the carnivorous aspect and over charge for these plants but this plant was a steal-only $7.00. So inspite of feeling poor, having just paid my bills I plunked down my money.

Doesn't look too interesting until you examine the plant closely and see the the tips of many of the leaves have a pitcher. I had seen pitcher plants in the wild but those are ground dwelling. This guy is an epiphyte as are many orchids and at least in the wild can get pretty good size with 8" pitchers! Shhhh! Don't tell my wife! She already says that my plants attack her.

What's interesting is that these sorts of pitchers or pitfall traps seems to have evolved independently as a specialization to nitrogen poor habitats in a number of different plant families, and thus represents convergent evolution.

Other links:

International Carnivorous Plant Society

Carnivorous Plants at

Carnivorous Plants at Wayne's Word

"New" data relating to the evolution and phylogeny of some carnivorous plant families
from the ICPS site.

Tuesday, March 14, 2006

a fun meme

What's more fun than reflecting on your past beloved pets and plants? This is courtesy of Nelumba's Garden Blog, where she got it from just go to her site.

#1 What's your earliest memory you have of becoming fascinated with living things- gardens, animals, etc ?

We had a double lot and part of it was let grow semi wild and it was always full of butterflies and had lots of milkweed with these wonderful red longhorn beetles. They would make a squeeking noise when picked up. There were also large dragnflies and my mother would warn me not to try to catch them because they would sew my mouth shut. As for gardening we had an elderly neighbor who gardened and both my sister and I would visit him as he worked in his garden and he would give us fresh vegetables. Mr. Crandell was kind of a "free thinker" and I used to sit with him in the evening and we would talk about plants and animals. He was a big influence on me.

#2 What was your first pet? (I'm adding my own question here- what was your first plant pet?)
Of my own? Do paramecia and brine shrimp count? Actually had a wonderful white cat named snowball. Also had an anole and a spotted salamander.

#3What was your favorite pet?

That is hard!

I guess aside from an Akita I owned as a grad student, probably Snowball. Have also had lots of nice cats in my day. Right now have a 16 year old Siamese with chronic kidney failure.

Sunday, March 12, 2006

Kansas weather.

Kansas weather is never boring. This morning around 8:00 I was in the shower when my wife yelled tornado! So grabbed my pants and cell phone as wind came up over the sirens. No damage here but Lawrence was hit pretty hard with what is either a series of microbursts or a tornado. Some pretty good sized trees were knocked down but the damage was very spotty. Right know power is out to much of the city. We are being told to stay home. Good advice since a new set of storms is on the way.

Image/Text/Data from the University of Illinois WW2010 Project. Used with permission.

Other links:

Was it a Tornado?



Thursday, March 09, 2006


I am getting to hate those funny graphical alphanumeric patterns we use to validate posts in blogger and in other contexts. It seems that the patterns get more and more difficult to handle. Consider the one displayed with this post. I had to really think about the second letter from the right or third letter: is the sequence hm or is it really fim?

Now I have a bit more sympathy with my students who sometimes can't interpret my writing.

That said, pondering these graphics got me wondering, what do the visually impaired do on the web? And that got me fondly remembering Lynx. Lynx for those who don't know is a text based web browser and it was the first web browser I used. At that time, I was a visiting professor at Wasburn U in Topeka and all we had were text terminals. Oh, we could go to the library and use Mosaic's graphics browser but it was so buggy it was not worth it.

Lynx is really compact and fast and even when I finally got a machine with a graphical interface, it was fun to boot the Mac version of Lynx on my Quadra 650 just to see what it would do with my site. My site does not work all that well with Lynx but trying it out with Lynx convinced me that maybe all the frames I was using in my frame happy days probably are not such a good idea. In Lynx you can see the original vision of hypertext that gave rise to what we think of as the web today.

I am pleased to see Lynx still around. Hmmmm supposedly it has been ported to PDA's. Maybe I will see if I can get Lynx for mine.

Other Links:

Blynx: the use of Lynx with speech synthesizers.

Pages enhanced for Lynx: Some of these links don't work, but I see that Kermit lives as well! YES!!!


Finally it is really raining here which means that my garden will get water and the salamanders will run. But my yard is not the only place for water. According to NASA the Cassini probe seems to have detected liquid water in a very unlikely place-Saturn's moon Enceladus. The report claims that images from Cassini show plumes of some substance being ejected from moon's surface and the best physical explanation is that the plumes are liquid water from the Enceladus analog of a cold Old Faithful. Quantities of water has been found in other parts of the solar system but to have it so close to the surface, in what is a presumably a very cold part of the solar system, is unusual.

Perhaps Enceladus is a place to look for life, assuming of course the rest of the chemicals for life are present and the heat source is stable.

Here is how scientists think the water might be produced.

I am not going to get too excited about this but each little discovery of this sort makes it more and more plausible to think that there may be life in other places in the Universe.

Other Links:

Cassini home page


SETI Institute (

Monday, March 06, 2006

A pop music digression

If you are wondering science and poetry consider this wonderful post from Sandra Porter's Blog: Discovering Biology in a Digital World. Her post is about how plants somehow detect volatile organic compounds given off by other plants when the latter are attacked by insects. The listening plants get advanced warning and mobilize their defenses. But what I really love is the title of the post:

"I hear the cottonwoods whispering above"

Naturally this got my interest

This the first line of a song Tammy sung by Debbie Reynolds in 1957 in the movie "Tammy and the Bachelor"; the lyrics are here and here.

"I hear the cottonwoods whispering above
Tammy! Tammy! Tammy's in love!

The ole hootie owl hootie-hoo's to the dove
Tammy! Tammy! Tammy's in love!

Does my darling feel
What I feel
When he comes near?
My heart beats so joyfully
You'd think that he could hear!"


The song appears to be widely recorded but I have never heard it.

As an aside the song was composed by Jay Livingston & Ray Evans who wrote many well known standards including:

Mona Lisa and Silver Bells and
Que SerĂ¡, SerĂ¡. Now those I have heard. Unfortunately most people today may be more familiar with one of their least inspiring efforts, the theme song from the 1960's TV series, Mr. Ed.

Other links:

Salamander Travels

Lest you think the Lawrence salamander rescuers are an odd lot, a quick Google search using salamander migrations as search terms reveals the following links and tidbits:

Salamander Crossing( discusses a mass migration of amphibians in Brattleboro Vermont and the activities of salamander rescuers:

"Environmental groups in the region report that a large-scale salamander migration, with creatures numbering in the hundreds, took place during Tuesday evening's rainstorm.

"Some were running right across the road, others were just taking their time," said Betsy Bennett, curator and educator of the Grafton Nature Museum. "We helped some of them across the road when cars came. It was really fun."

As temperatures reached the 50s during the downpour, about 10 local citizens came out to witness the natural spectacle, Bennett said. Museum officials and local residents watched the migration take place at a beaver brook on Townshend Road."

Jug Bay Wetlands Sanctuary near Washington DC ( conducts research documenting migrations of the marbled salamander Ambystoma opacum shown in the accompanying picture from their web site.

Karen Luepke ( provides a nice discussion of migration in the spotted salamander, Ambystoma maculatum, along with helpful links. She note several things about salamander migrations. First the migrations are very predictable from year to year and at least for the spotted may require more than just the right weather. Also the salamanders seem to be very faithful to the pond they were born in and never stray far, only to about 200m from the pond.

The Federal Highway Administration reports ( on the building salamander tunnels in Amherst MA, not too far from where I grew up. See also

As for the homing aspect of migration between the breeding pond and feeding areas, some writers hypothesize a scent component but in newts at least, experimental evidence suggests that magnetic orientation analogous to that used by some birds in migration may be used. See Phillips, JB 1986 Two magnetoreception pathways in a migratory salamander. Science Aug 15;233(4765):765-7 (Abstract). Of course it is quite possible that several different orientation cues are involved.

Saturday, March 04, 2006


Tonight I joined about 12 other people along 31st Street in Lawrence in a 'salamander rescue' to ferry salamanders Ambystoma texanum across the road to and from their breeding grounds.

I know the typical reaction: good grief get a life; and many probably agree with one of the editorial writers from the Journal World ( who noted:

"The silly season is upon us again and this time it is even sillier than usual. There i’s a local coalition actually trying to organize a mass effort to help salamanders cross a section of 31st Street that supposedly keeps them from making their appointed reproductive rounds."

Of course this whole thing is bound up in a local debate concerning a by-pass through the Baker Wetlands:

"Is this for real, for serious, or just another ploy to impose even more barriers to completion of the South Lawrence traffic way? There is a history of foolishness for political purposes reaching back to the infamous and elusive northern crawfish frog, a species that at one time was considered “threatened."

Well you get the drift.

I am astounded that in the 21st century a supposed educated person doesn't understand the importance of biodiversity and the effects of human activity on wildlife habitat. But I guess some people still cling to notion that the planet was made for us to plunder.

At any rate, we did find 41 salamanders as best as I could tally. Of course the one hitch was uncertainty as to what the salamanders wanted to do. My instinct was to hunt them on the north side of the road figuring they would want to head toward the main body of the wetlands on the south side. But people seemed to be finding the salamanders heading north. However, since we did not get a whole lot of rain, the amphibians were clearly not actively crossing the road.

Dr. Joseph Collins of KU says that at the end of January a student saw the salamanders migrating from the north to the south. But my son Norman who knows the Baker wetlands very well, much better than I, says the salamanders are much more abundant on the south side during the summer, consistent with Dr. Collin's understanding. Perhaps when we get some real rain, we will get a clearer idea of what the salamanders want.

For me the rescue brought back memories of high school when Thom Smith of the Berkshire Museum would lead a group of us on mad salamander hunts in spring rains in Massachusetts. There the quarry was often other Ambystoma species such as the spotted salamander.

The Salamander Rescue was organized by Michael Caron shown here.

Mike is hoping that Tuesday will be a big salamander night. Hope they give the searchers a better clue as to which direction they want to go!

Other links:

Salamander pictures from Jeff Parmelee including A. texanum eggs:

Save the Sacred Baker Wetlands( Has good links to photos from the wetlands. I especially enjoy Wally Emerson's photographs, (

Wednesday, March 01, 2006

For Love of Insects

If you want to see a first rate scientific mind in action a good read is Thomas Eisner's For the Love of Insects(2003) from Harvard university Press. Dr. Eisner is a chemical ecologist from Cornell University and I bought the book in part because I had the pleasure of taking one of his classes but also because I am an entomologist by training. This book though is totally unlike any other entomology books because it shows Eisner in action as a scientist, shows the types of connections he makes when he is observing the natural world. Indeed he notes something that my students (or educators) don't seem to believe:

"...There has to be a readiness to make such connections. Every tidbit of new information, no matter how trivial, has the potential of amounting to more than a speck of color. Properly assigned to the pointillist canvas that constitutes your inner view, the new speck adds dimension to the vision."

This is after he as shown us through following little mysteries about the natural world that he investigated in his long 45 year career at Cornell. These little mysteries that so often we fail as instructors to take advantage of in teaching our students, even our majors so that they come out of our classes perhaps technically competent, able to master course objectives but unable to make the sorts of interconnections so important for critical thinking in biology.

Eisner's book will go down as a classic one that you will dip into over and over again.

The image shows a monarch butterfly larva from my butterfly garden in 2005.

Other links:

Chemical Ecology: Archbold Biological Station: Biennial Report 1997-1998

Chemical Flower Deterrents