Tuesday, November 29, 2005

Come on folks! Buy those Darwin fish!

I can't resist this headline from the Lawrence Journal World about the marketing of the evolution controversy. Hmmmm I wonder how much money Phillip Johnson or Michael Behe make through peddling their pseudoscience. So as Allen Ginsberg might have said: put your unintelligently designed shoulder to the wheel and buy those Darwin Fish!

Monday, November 28, 2005

Is ID even a pseudoscience?

A fellow Lawrencian Ron Pine sent me an article he wrote for CSICOP in which he argues that Intelligent Design does not even qualify as pseudoscience because it is void of any content. I am not sure about this. I am not sure what content astrology for instance has or crop circle science either, but I do see ID as a fraud and a scam...mmm maybe that is a bit redundant. Let's just say fraud or scam. Check his article out for yourself at http://www.csicop.org/intelligentdesignwatch/pine.html.

Oh check out CSICOP,

Committee for the Scientific Investigation of Claims of the Paranormal

Probably the religious right feels the same way about CSICOP as they feel about the ACLU. :-)

Another CSICOP ID critique is, Very Like a Machine by Robert Camp.

Thursday, November 24, 2005

Thinking about thinking....

In a recent post on Pharyngula PZ Meyers attempts to divide people up into Naturals vs unnaturals.

Naturals are "...those people who consider material evidence paramount and regard the real world as a mostly sufficient container of phenomena that define our existence..."


"those who think inspiration and intuition and all the internal imagery of their minds define their external reality; that what they wish to be so will be so if only they can articulate it and select and distort evidence for the purposes of persuasion."

I don't think that he is quite right in how he does this, after for a poet inspiration and internal imagery are all important, but I think he is on to something if we make a slightly more elaborate scheme. I don't think the terms are novel with me but I envision a 2 x 2 matrix distinguishing between the mode of thinking and relationship between the universe. First of all with respect to mode of thinking: the distinction between linear or analytical thinking and analogical thinking. Analytical thinking is sequential and based on explicit rules that can be formalized. Analogical thinking is implicit not based on formal rules..at least not verbalized rules and is not linear. In analogical thinking inspiration and intuition are important. These define the columns of my little matrix.

As for the rows, my distinction is between empirical and magical. Empirical thinking views the operation of the universe as explainable by natural and objectively testable mechanisms. Magical thinking operates outside of and is not consistent with empirical and testable explanations.

So what are representative tasks that fall into these four groups...Recognizing that no one is purely in any one group but rather these are extremes on along two possibly oblique axes:

Analytical empirical: Most engineers and scientists doing every day science. Me analyzing a linkage problem.

Analytical magical: Phillip Johnson, Michael Behe and other ID proponents and vitalists; perhaps religious scholars trying to reason about God or develop rationalizations for their beliefs.

Analogic empirical: Scientists and mathematicians working on a new problem and really struggling. Many modern poets-think Objective poetry. Some religious people, Dr. Coyne, or myself when thinking about the relationship between God and the universe.

Analogic magical: Pat Robertson, New Agers. Believers in Wicca and witchcraft casting a spell. Perhaps Catholics including myself when we are receiving communion. A little kid not stepping on cracks in sidewalks. Poets and writers in their metaphorical internal worlds. Gamers in Second Life and other multiplayer universes.

Notice that I define mental tasks and my classification is mental task oriented rather than person oriented.

Late developments in Kansas...

Eventually I will get back to what I really want to do here...and not seem like just another liberal Kansas blog but since I am an evolutionist as well as a religious person what's happening can't go without more notice. First KU, through Provost David Shulenburger responded to the uproar about the KU religion course that has all the ID and creationists upset. In his response he notes that calling ID a myth is not an affront...

"A myth refers to the common use of stories or rituals to symbolize in a meaningful manner the core beliefs of a religion; it does not refer to any religion as a whole."

He is right but I think he is falling into the fundamentalist trap of equating a narrow set of conservative beliefs with Christianity which is exactly what people do all the time. If you want evidence of this simply look at this most recent flap around an e-mail message (apparently made on a yahoo group by Paul Mirecki) belittling intelligent design proponents. Now the conservatives are really out for blood!

I sympathize with Dr. Mirecki but I do have to wonder about someone so naive as to think e-mail is somehow private.

In today's journal world you will also find my minor contribution to the frey in terms of a letter to the editor. Of course this letter immediately attracted the attention of one of those anti intellectuals who frequent newspaper response boards who called me a:

"Behold the Noodly Appendage of the Great Flying Spagetti Monster!"

Of course feeling great because I had attracted the attention of one of Lawrence's finest illluminaries Ragingbear, I was promptly deflated when search his response history found that he calls any opponent of ID the same thing. Obviously he is unaware of the common public admission on the part of ID advocates that the designer's nature is outside the scope of science and could just be a space alien.

I hope Mr. Bear takes my response in good humor.

Tuesday, November 22, 2005

The Shoe's on the Other Foot...the teaching of ID

A new flap about intelligent design in Kansas: according to the Lawrence Journal World, University of Kansas Professor Paul Mirecki is planning to teach a course that treats intelligent design as a creation myth:


Of course this has angered Intelligent Design Advocates such as John Calvert. Calvert whines:

"To equate intelligent design to mythology is really an absurdity, and it's just another example of labeling anybody who proposes (intelligent design) to be simply a religious nut,Calvert said. "“That'’s the reason for this little charade."”

and then goes on to complain according to the reporter that "the teaching of intelligent design requires an extensive understanding of evolution and science."

Now the shoe is on the other foot. After all Steve Abrams and the gang of six on the board of education have no scientific let alone evolution expertise and none of the ID advocates the Board used as experts has any significant experience in evolutionary biology either, and this includes Michael Behe, in spite of his credentials as a DNA biochemist.

So John Calvert, if the Board of Education can listen to witnesses who are ill trained in evolutionary biology instead of real scientists, then fair is fair and a religious studies professor can teach about ID. At least he is teaching it in a more proper framework as mythology.

Of course, perhaps one ought to make a distinction between mythology and pseudoscience. A legitimate argumentt can be made that ID is not even mythology but just pseudoscience advanced to justify a particular political agenda.

Sunday, November 20, 2005

The Tyranny of the Dichotomous Mind

in his book, The Ancestor's
Tale, bemoans what he calls the Tyranny of the Dichotomous Mind. What he means is that when we look at the world around us, we tend to want to classify everything
into discrete groups. That makes some sort of sense after all, from
our perspective, the world is made out of discrete objects that it is
adaptive in an evolutionary sense for us to recognise. Being able to
distinguish a lion from a gazelle is certainly adaptive. This ability
to classify into distinct groups is not limited to humans. For instance
in a recent study by Chris Templeton (see http://acp.eugraph.com/news/news05/templeton.html
) suggest that at least some birds recognise different predators and
cnvey this information in their warning calls. Many organisms are able
to distinguish individuals that belong to their group from those that
do not. When you think about it this sort of dichotomous behavior in
very basic. Indeed, one of the things the immune system has to do
is discriminate between cells that belong in the body from those that
do not.

So given the obvious adaptive advantage to doing this sort of
classification, why does Dawkins speak of the Tyranny of the
dichotomous mind? First of all not all phenomena have sharp boundaries
as suggested by a dichotomy. Consider color. Most humans can look at an
individual monochromatic color swatch and classify it as to perceived
spectral color(Red, Orange, Yellow, Green, Blue, Violet). But when one
looks at the visible spectrum as a whole this gets more difficult since
it is clear that the colors blend in a continuous or if you will,
analog manner. Second of all, we confuse classification with the
thing itself. For instance Dawkins discusses some of the problems
inherent in trying to distinguish one biological species from another.
The boundaries are not at all clear in many cases. Indeed, I like to
tell my students that even were there no transitional fossils (and there
plently inspite of Creationist claims to the contrary), we have plenty
of evidence that the different kinds of organisms we see arise
from preexisting kinds. The evidence is in the messy boundaries we see
when we try to impose dichotomy on the species around us.

The tyranny of the dichotomous mind is related to another tyranny, I
call the "Tyranny of the Type" or Typological Tyranny. People who are
prone to this tyranny assume that objects have some sort of intrinsic
nature which defines a class of objects uniquely. Clearly this is
many times true, or else classification schemes would not be
feasable. Hunter gatherering tribes, with no formal training in
taxonomy recogise the same sorts of species of birds that a trained
taxomist might recognize at least most of the time. But this sort of
discreteness and non arbitraryness in many classification schemes is
often burdened with extra meaning which makes it difficult to deal with
some fundamental issues our society such as when does human life begin
or end, our identity in terms of gender or race and even our identity
as a species.

For instance Senator Brownback of Kansas proposed a bill
(S. 659—The
Human Chimera Prohibition Act of 2005
), which
bans the use of so called human chimeras. See http://www.asbmb.org/ASBMB/site.nsf/0/AF98278139BC60FB85256FE1006784A6?OpenDocument.
A chimera is defined in biology as an organism composed of cells from
unrelated organisms, two or more species. Chimeras are routinely used
today in plant biology and have become increasingly important in animal
biology to gain an understanding of animal development, including human
development. A good lay person's review of some of the ethical issues
raised by animal chimeras, especially chimeras involving human cells is
an article by Maryann
in National Geographic, which is very
heavily cited today. The ethical issues surrounding chimeras involving
human cells mixed with animal cells revolve around two basic concerns.
First is the concern about blurring the lines between humans and
animals: Brownback in a a recent Lawrence Journal World article ( http://www2.ljworld.com/news/2005/jul/05/brownback_works_ban_humanhybrid_research/
) notes:

“From the moral perspective, to create a human that is less than fully human or to create an animal that possesses particularly unique human aspects should be a serious concern for all of humankind”

and the text of his Senate Bill contains this narrative:

"Congress finds that-- advances in research and technology have made possible the creation of chimeras, which are beings with diverse human and non-human tissue; serious ethical objections are raised to some types of chimeras because they blur the lines between human and animal, male and female, parent and child, and one individual and another individual; respect for human dignity and the integrity of the human species may be threatened by chimeras; the uniqueness of individual human beings is manifested in a particular way through their brain and their reproductive organs/cells";


"...with an increase in emerging zoonotic infection threatening the public health,
both domestically and abroad, chimeras present a particularly optimal means of genetic transfers that
could increase the efficiency or virulence of diseases threatening both
humans and animals."

This narrative points out the second concern, namely that the jump of
viruses and other infectious agents to humans from other animals could
be facilitated by animal human chimeras since the cells are obviously
in contact. Personally I think that Brownback is right to be concerned
about the ethics of chimeras and some sort of ethical guidelines, and
restrictions are needed. Indeed the National Academy of Science has
released a set of proposed ethical guidelines covering stem cell and
and chimera research: http://www.nap.edu/books/0309096537/html/.

I suspect these guidelines will be controversial and it is going to
take sometime to reach a reasonable consensus. What I call your
attention to is Senator Brownback's comment about the integrety of the
human species and about blurring the lines between human and animal,
male and female...one individual and another. These are nice
sounding phrases, and as indivuals we don't like threats to our own
identity. As an aside I fund in amusing that we often want to tell
people what their identity ought to be in addition to be concerned
about our own identity. But banning human chimera research will
not prevent blurring of the lines between human and animal, male and
female parent and child, one individual and another because in biology
these lines are already blurred.

Not only are we perfectly good
animals, but it turns out we are also chimeras or at least have our
origin as a chimeric sort of relationship. First in our gut, we have a
large numbers of bacteria that live in a symbiotic relationship.
Even our cells are chimeral in nature. Consider that the mitochondria
in our cells apearantly arose from free living aerobic bacterial that
became associated with the ancestors of eukaryotic cells. Further there
is appearently lateral gene transfer between the mitochondrial genome
and the genome in the cell nucleus.

Above the cellular level, consider gender. The
concept of male and female useless for many groups of organisms. For instabce,
What's male and female in yeasts or in certain protists which have a
number of mating strains but the 'gametes' are the same size? What's
male and female in flowering plants that often have 'male' and 'female'
flower parts on the same plant and often in the same flower? In
non human animals- certain fish, such as clown fish, change from
male to female situationally. Even in humans- sex and gender lines are
blurred a lot more often the typical person might think. See Lynn
Conway http://ai.eecs.umich.edu/people/conway/TS/TSprevalence.html
for some interesting and eye opening estimates on the frequency of
transsexuality. Some of her numbers are inflated I suspect but the
point is even in humans some of our fundamental boundaries say between
male and female are blurred.

How about the distinction between humans and other animals? I am
astounded that my students seem blind to the fact that we humans
are perfectly good animals. As a species we may well have adaptations
that are unique to us, but as Dawkins notes, genetically the gap
between us and the rest of the apes is quite small. In fact we are so
close that even though chimpanzees are apparently our closest
relatives, some of us actually have certain genes (more precisely
alleles) found in Gorillas but not in Chimpanzees. What makes us human may be the
result of subtle changes in the timing and regulation of
developmental events related to the nervous system. Some scientists
have implied a few key events among them a mutation related to jaw size
and muscle attachment as being critical in human evolution. What
these key events are is not clear, but it seems to me that these events
are probably quite prosaic such that were we to go back in space and
time we would not be able to say "ah this ape is really human and this
one is not." It much the same as in our own lives where little events
may go unnoticed as being critical in shaping us exept with the benefit
of hindsight.

Darwin recognized that we really are not distinct from the rest of the
animals. This evolutionary kinship is reflected in our laws and
ethical stance toward other animals. Not anything goes: we have laws
against animal cruelty; animal experimentation today involves oversight
by animal care committies. Indeed there has been an ethical progression
toward increased concern and oversight about the treatment of animals.
When I was an undergraduate I was repeatedly warned to not be
anthropomorphic about othe animals because they don't have the same
sorts of cognitive abilities and awareness that we have. That is
true to some degree, but carried to an extreme, this
anti-anthropomorphic stance was used to justify cruel experimentation.
I am not an antivivisectionist but the recognition that we are not
separate from animals in a scientific sense clearly affects our ethical
stance toward non human animals and how we treat them as experimental

I don't think it is any accident that the rise of animal
welfare organizations such as the SPCA stems from the time of
Darwin. Darwin was actually sometimes excessively
anthropomorphic, even giving earthworms greater credit for cognitive
abilities they do not really possess.

The tyranny of the type is still wide spread in medicine and
psychiatry, mercifully less so. But the idea is that there is a normal
physiological state for the human organism or perhaps some optimum
mental state and deviations from that are illness. So people
suffer from minor depression or mood swings and they take medication. A
child with ADHD is given Ritalin, a person whose body mass index is
above or below a certain level is considered obese or perhaps the
reverse. a person with a fever might take aspirin or some other
antipyretic to reduce the fever.

Now I am not arguing against use of medications; for me certain types of medications have literally been a life saver but sometimes the symptom may actually be an adaptive response. For instance, today we understand that fever is an adaptive
response to infection rather than an accidental symptom. The immune
system tends to work better at higher temperatures and higher
temperatures aslo seem to inhibit viral replication.

The tyranny of the dichotomous mind, the type: it divides us from
Nature; it divides us from each other and it divides us from ourselves
and from our own identies. It all springs from a logical fallacy that
since recognizing objects is an useful idea, it is therefore an over
arching idea that ought to apply to all spheres of our lives and yet it
clearly does not. The best analogy to the fallacy is from physics in
which we find Newtonian mechanics useful in our every day experience.
And yet, when we get down to very small scales we find that physics
becomes decidedly non Newtonian and particles become wavelike and we
struggle to hold two ideas at the same time and a multiplicity of
possibilities. It is not comfortable and we like comfort and cling to
the notion or either or, that we are human not animal, man or not
woman, normal or not normal and we find ourselves in a dysphoria of
comfort and wonder what is wrong.

Thursday, November 10, 2005

Viruses and Intelligent Design

The last few weeks I have been fighting an on again off again battle with a cold and today I am at hope trying to lick this thing after a sleepless night. It is humbling that a complex organism such as we are can be brought down by a small stretch of genetic material, not even a cell, namely a virus. Actually I feel like maybe several viruses have ganged up on me but that is another matter. I do wonder what viruses are for? After all if life came about through the agency of intelligent design, what about viruses? Viruses, we know evolve, and that point has been made enumerable times, for example about the bird flu in the Daily Kos at http://www.dailykos.com/story/2005/10/11/14551/149 their discussion of ID. But ID proponents don't dispute evolution in the sense of "microevolution" and that viruses are capable of this sort of evolution. But there is a deeper problem for intelligent design proponents, and that is what did the intelligent designer make viruses for?

I know, the ID people claim that all that is sufficient is to show evidence of some aspect of the universe that is inexplicable to have arisen by chance and that the intelligent designer's nature cannot be discussed. See for example this discussion in slate: http://www.slate.com/id/2128238/?nav=navoa

Of course as pointed out in this article Behe and the other leading ID proponents are all party to the Wedge document from the Discovery Institute, and its pretty clear that most ID proponents equate the designer with the Christian God. See for instance this commentary by Phillip Johnson. Viruses and organisms that cause human diseases lead to a question of the intent of the intelligent designer? Is the intent that the universe be for people? And intent is the issue here:

Johnson notes in a Leadership University essay:

"Religion, like science, starts with assumptions or conclusions about reality. If we were created by God for a purpose, that is one starting point. If we are the accidental product of blind natural forces, that is a very different starting point. In the former case we try to learn the will of our creator, and in the latter case we discard that "intervening spirit" as an illusion and proceed to chart our own course."

So what is the will of the creator with respect to viruses and humans? Viruses even though they are not cells show very complex adaptations for penetrating the host cell and also for spreading from one host to the other. If viruses arose independently from cells then either this contradicts the ID premise that one cannot generate new genetic information or if viruses are as currently favored http://en.wikipedia.org/wiki/Virus#Origins.3D.3D_.3D.3DAnd_Beginings, transposons and other bits of host genetic material that have escaped from host cells, what kind of designer would design a genetic system with so many problems? If the designer is intelligent then its intelligence is inexplicable in a very major way from human intelligence and is not designing the universe with us in mind in any way we can see. The ID people cannot wiggle out of this one by claiming the all one has to do is point to design not explainable (allegedly) by evolutionary theory because Johnson has opened the door to just such speculation since if we are created by God then science ought to be able to infer something about the will of the creator not just that the creator exists!

Perhaps Mr. Johnson ought to remember that the path to our modern understanding of evolution began with a natural philosophy with a very similar starting point, namely that by studying the universe we can learn something about the mind of God. See for example this article,http://www.ucmp.berkeley.edu/history/owen.html about Richard Owen, a contemporary of Darwin and who developed the concept of homology. So if Johnson is right once we detect alleged design, the intent of the designer is a legitimate scientific and philosophical concern and you cannot hide behind saying that God(oops) the designer is mysterious and beyond human comprehension. If viruses are designed then here is more evidence that the designer is not designing with us in mind. If viruses are not designed then the designer really messed up when designing genetic systems of organisms that allow bits of genetic material to escape. So the designer is really limited or not designing with us in mind.

Of course if the designer is truly mysterious and beyond human comprehension then this contradicts jouncing assertion that we can try to learn the will of the Creator through science and that Intelligent Design has anything to do with science at all. In fact I don't think Intelligent Design has much to do about anything except as a vehicle to further a religious and political agenda as expressed in the Wedge Strategy document. See http://www.antievolution.org/features/wedge.html for a link to the Wedge document.

As this document says:

"We are building on this momentum, broadening the wedge with a positive scientific alternative to materialistic scientific theories, which has come to be called the theory of intelligent design (ID). Design theory promises to reverse the stifling dominance of the materialist worldview, and to replace it with a science consonant with Christian and theistic convictions."

So much for the argument that ID has nothing to do with religion!

Sunday, November 06, 2005

Small exciting things...

Been putting my gardens to bed for the fall and yesterday found a small skipper that seemed at bit out of place; very pale and so I took a picture. Hard of me to do since I don't have a fancy camera. Today looking at more closely it seems very different from the skippers I am used to, but I am hardly a butterfly expert.

So even though it is dangerous to try to identify insects from pictures, today I went to the USGS Northern Prairie research site,http://www.npwrc.usgs.gov browsed the skipper pictures. The closest species I come up with is the Desert Checkered Skipper, Pyrgus philetas. If so the butterfly is way out of range. I am pretty confident of the genus but good skipper pictures are hard to come by. But compare my picture above with the one from the site and see what you think. The original image is at:


and you should go there to view it. I try to be respectful of copyrights and don't have Dr. Cary's permission to use the image. If you scroll down to the end of the page for this species you will see that it is reported from Southern Texas/Northern Mexico.

There are other Pyrgus species that range into Kansas, so it's possible I have one of those instead...but who knows.

Today I found the butterfly again but not having an insect net, was not able to catch it. But did find a nice female praying mantis. So here she is. Mantids do have some ability to change color and she has a quite appropriate color for this time of year.

Saturday, November 05, 2005

Otters and the Weasel Sex Trade

The other weekend my wife and I went to Big Cedar Resort near Branson. You know that Expedia commercial in which a father is booking a hotel for his kids where he envisions them going to a hunting lodge? If not, in the commercial the father imagines that his children are frightened by all the "stuffed" animals-bears, wolves etc. Well, that commercial could have been filmed at Big Cedar. Associated with the resort is a private nature and fishing park called Dogwood Canyon Park which has a very nice tram ride and lots of wildlife.

The guide, shown in the picture, was showing us this stream loaded with huge German and rainbow trout- the park earns lots of its money from daily fishing tours when he mentioned that they had a mysterious predator that had been eating their trout, and he told how he had tracked it down, killed it and now it was mounted and on display in the park store. The predator turned out to be a male river otter, weighing about 30 pounds. Now the guide said that they had to kill it since it needed to eat 15% of its weight in fish per day. Seems reasonable since otters are active.

Now while I sympathize with the Park's plight I just couldn't help be a tad upset. After all, otters are not that common; I have never seen one in the wild and I happen to have a soft spot for otters ever since when I was young read about a family who kept one as a pet. My wife- evil person that she is- had no sympathy with my arguments that the park might be able to draw more visitors with frolicking otters than through fly fishing. She didn't buy my argument that a little predation might improve the stock of fish, make them more challenging to catch because assuredly the otter would kill only the weak and slow trout.

I couldn't even get her sympathy when I described how the otter was merely scouting out sites for his family and now there was this widow otter and her pups alone in the world and how the mother would have to sell her kids to the weasel sex trade to earn money to buy trout at the supermarket. Sigh...It's all about the all mighty buck...a term the guide claimed was derived from the use of buck skins as currency worth well, about a buck.

Dogwood Canyon is free to enter but the tram and most of the other activities do cost money. But if you are in that neck of the woods and want to see elk and bison up close along with the fattest most tame trout you will ever see, Dogwood Canyon might be worth a a visit unless of course you are an otter.

Friday, November 04, 2005

The force that through

Starting out. The title comes from a poem by Dylan Thomas. If you are not familiar with him, you might check out the Dylan Thomas Home Page at http://www.dylanthomas.com/. My blog is an outgrowth of a running commentary called greenfuse on my academic website, The Entangled Bank at staff.jccc.edu/pdecell. But doing everything in html got to be cumbersome and of course does not allow for the sort of participatory evolution that I wanted.

Woops do I dare use the E word? I have been actively involved in the evolution flap in Kansas: I will not say controversy because that evolution happens is not controversial; we know that evolution happens. So if your faith perspective requires you to treat your sacred text as a science book get over it because that simply is not what science is about and it is not the way the world seems to work.

Several good evolution blogs are Pharyngula at http://pharyngula.org/ . A more complete listing of evolution blogs is at http://www.evowiki.org/wiki.phtml?title=Good_evolutionist_blogs.

Links to evolution and its misguided critics are at http://www.talkorigins.org/origins/other-links.html.

Indeed the whole talk origins site is a wonderful resource.