Causation in in Biology.

There is an interesting post over at Alex Palazzo's blog, The Daily Transcript, on the distinction between proximal and ultimate causes in biology. As he notes proximal causes and (proximal explanations) deal with how things work where as ultimate explanations are evolutionary explanations: why was a certain structure or behavior selected for-what causes certain genes to spread as opposed to others in a population.

This distinction sometimes creates as Alex notes a divide among scientists in terms of their view points. For example when I was a graduate student there was a lot of interest in "r" vs "K" selection. Populations that are r selected invest heavily in reproduction and reproductive structures whereas K selected species or populations invest in structures that give them a competitive advantage. I went to a dissertation defense of a graduate student working on r and K selection in populations of a certain plant and the evidence seemed to support the student's hypothesis that in unstable environments with fewer competitors the plant should show attributes of an r selected species and in stable environments with more competitors the plant should show attributes of a K selected species.

To make a long story short, the poor graduate student was savaged by a plant physiologist in the audience who argued that the results were just due to physiological responses of the plant and had nothing to do with evolutionary explanations at all. There were weaknesses in the study and the student should have anticipated this sort of criticism. But the physiologist did not pick up on these weaknesses in terms of what the student needed to do to really test the hypothesis, instead ultimate causation was not even on his radar screen.

I have always been bothered by the use of the terms proximate vs ultimate causation explanations in biology and wrote a response to Alex's post. Basically my concern is with the use of ultimate. To me, ultimate implies teleology. Teleology implies directedness toward some sort of final goal, usually some sort of cosmological goal, or metaphysical goal, as opposed to intentional behavior on the part of an individual organism. To illustrate: my goal in writing this article is intentional but not teleological in the sense the word is usually used. I suppose were some one to say "water tends to seek it's own level" ,as students often do by the way, that is a sort of teleological statement, again seeming to imply intent.

So here is the scheme I proposed in my comments to Alex (cribbing heavily from my response on his blog, and correcting typos).

Teleological causality and explanations involve progression toward a final goal (teleos). This is metaphysics and outside the scope of science...at least science has found no empirical evidence that the universe's unfolding involves this sort of intentional movement toward a final goal.

Scientific causality and explanations are about the universe in terms of natural causation. These are "how questions" and it doesn't matter whether you are talking about cells or evolution. It their core all scientific explanations are explanations about mechanism-they are" how explanations."

Scientific causality and explanations in biology (I will ignore physics here) would include:

1. Proximal explanations-explanations about the immediate operation of organisms.

2. Evolutionary explanations-historical explanations about how the structure and adaptations of organisms and groups of organisms came to be in terms of modification with descent and the mechanisms by which modification with descent operates.

So in my scheme, ultimate is relegated to the sort of explanation that is outside the realm of empirical science because how do you know what the final goal is. What I am proposing is related to the problem of design since design implies intent. Evolutionists, myself included, often talk about the adaptations that organisms show as giving the illusion of design. After all, evolution is not intentional. It is not as Darwin realized, directed toward some sort of final goal. Evolution is not teleological, even though it has given rise to creatures that show intent and directedness toward immediate goals-teleonomy.

Whether or not teleology exists, or is an illusion is really what the intelligent design advocates are asking. The problem is that teleological explanations have not proven useful in terms of understanding the universe. Since they have never proven useful -water seeking it's own level is after a pretty useless explanation of fluid dynamics, the intelligent design advocates have a very difficult task ahead of them if they believe that teleological causality and explanations are needed to understanding the universe. If they have not been shown useful in biology whether we are talking cells or evolution, why should teleology even be on our radar screen as scientists?


Other links:

Setsuya Fujita (2001) Evolution of the Brain and the System of Value - Origin of Morality in
Bioethics and the Impact of Human Genome Research in the 21st Century pp 161-169
http://www.eubios.info/BHGP/BHGP161.htm

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Monkey Girl at JCCC

Last night at JCCC we had the privilege of hearing Ed Humes discuss his latest book, Monkey Girl, subtitled evolution, education and the battle for America's soul. Humes' book is at one level about the famous Dover Pennsylvania court case Kitzmiller et al v Dover Area School District (archived here)in which the Federal Judge struck down the Dover School Board's attempt to inject "intelligent design" into the science curriculum.

Humes noted as have many others, that there is a disconnect between what scientists believe about evolution and what the public believes. As most people know, and as Humes documents, more than half of Americans are skeptical of evolution-almost two thirds wanting some form of creationism taught along side evolution in science class. Humes attributes this disconnect to the existence of two separate "theories of evolution.

The first "theory" he called the "talk radio theory" or the "goo to you theory". This theory claims that:

• Evolutionists (called "Darwinists" in talk radio theory)believe that the origin of life is through random processes;
• Scientists are engaged in some sort of conspiracy to suppress or censor the truth;
• Evolution is in its last legs as a theory because of new scientific challenges;
• Evolution leads to Atheism and is connected to Hitler.

Humes notes that Americans are quite right to reject these ideas. The problem of course is that these ideas are either wrong or a distortion of what modern evolutionists believe about what evolution means and how it operates.

What scientists believe is the second theory-the REAL theory of evolution.

• Evolution is not about the origin of life but instead focuses on events once life has arisen. There is however an active research program looking at abiogenesis-the development of life from non living materials on the primordial Earth.
• Evolution is not strictly random since natural selection is not random. As an aside, it is true that we don't have any reason to postulate that natural selection is anything but unguided, but that is a different issue. After the talk I had a somewhat intense (but friendly) discussion with a fellow who failed to grasp the distinction between random and unguided.
• Evolution is not about denying God but is about common ancestry.
• As for Hitler, Hitler seems to have been influenced by a document called "Jews and their Lies" written in 1542 by Martin Luther.

Humes gave a good summary of the Dover case and notes that the ruling has not eased the culture wars-indeed the Judge in the case, a conservative Republican appointee, received death threats. Further Humes argues, and I see lots of hints of this at my school, that the battle ground is broadening to one about Church and State separation. He cited the example of a teacher who was teaching creationism in a science class. A student recorded this and when he complained, the STUDENT was vilified and the TEACHER argued that it was HIS religious freedom that was at risk. So the teaching of evolution becomes a violation of religious freedom! The school board's solution-ban taping in class.

Humes is very concerned about, what he views, a growing mistrust of science and he connects this mistrust to the decreasing number of American students going into science, resulting in a loss of America's competitive edge in various areas of science. Humes may be oversimplifying the causes of this loss, but this is something I really worry about because most of the scientists and science teachers, including myself, are products of the last great push for science education that took place in the 1960's in response to Sputnik.

He briefly touched on the Kansas Board of Education hearings where the scientists chose NOT to participate, and yet Kansas in sense provided a prelude to Dover according to Humes. In particular he discusses how Michael Behe got "skewered" by the Dover Lawyers in way that was not possible in Kansas.

Humes made a big push for increased support for science education at all levels including a commitment on the part of administrators to support their science staff in the the proper teaching of science including evolution.

Oh on another note...almost forgot. Just before the Humes presentation, Jack Krebs was presented with the National Center for Science Education's Friend of Darwin award, something that is well deserved. Jack has been tireless in his advocacy of science, including but not limited to evolution. His work is a major reason for the recent political victory of moderates over the conservatives in the last Kansas Board of Eduction election. Congratulations Jack!


My shots of the presentation did not come out so see Red State Rabble's coverage. This shot is a candid shot of Jack with Liz Craig and the last shot is Jack with Ed Humes.



Thanks to Kansas Citizens for Science for arranging the Humes lectures at KU and at JCCC.

Other Links:

Pat Hayes over at Red State Rabble has related coverage here ,here and here.

Quite a different reaction to Humes' talk at KU on Wednesday is from the Creationist blogger "For the kids" over at Reasonable Kansans

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Vernal Pond

Sometimes I see something that begs to be painted, such as this small feeder stream. I paint on occasion with acrylics and this had so many possibilities. I particularly love the flow of the reflected branches. I am also a sucker for the sort of very restrained color pallets this image would require. Also, I have not done a scene with lots of reflection so thought this would be fun.






I normally paint on masonite but had this old canvas from a failed experiment so decided to try again. I have a small project in mind that masonite would be better suited.









Initial rough in with mars black. In retrospect, I might have been well off to do the sky reflection with a pale yellow wash.










Adding some details of the stones and leaves underneath the reflections of the branches. Didn't want too much detail but to give the impression of things going on under the surface. At this point I started thinking of Three Worlds by M.C. Escher and what else I should put in the water.






Escher's carp wouldn't work but instead I began to think of the image as of a spring pond rather than a stream so put something I miss from spring ponds back in Massachusetts, namely spotted salamanders (Ambystoma maculatum). So how many to put? I decided on just two, though quite frankly thought about a real mating scene.

The salamander outlines are shown to the left...

















Spotted salamanders have nice yellow spots and I wanted to feature them and brighten up the painting a bit without getting garish. You may notice I tend to work the whole painting with a particular set of colors as in the greys and blacks. The salamanders were done in ivory back and shades of grey made from ivory black. The yellow and lighter shades of yellow were made with cadmium yellow and titanium white. Note the yellow used in the reflections. This was cadmium yellow and titanium white diluted with gloss medium.

The final painting after initialing is shown below:


Click on the image for a larger view from my flickr photo stream.

It also may not be obvious from the image, but the white areas are just the underlying gesso. This is a larger painting than I normally attempt - 24" x 36". I will probably frame it either in a silver metal flat put together frame or use redwood moulding...cedar might be nice as well. Have miter box will travel!

Enjoy!

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Update! Transgendered City Manager Fired...

Steve Stanton, the Largo Florida city manager who was fired after it came out that he was planning to transition to a woman lost his appeal. In spite of the presence of hundreds of supporters, the City Commission voted 5-2 to terminate Stanton according to the St. Petersburg Times today.

One of the commissioners, Andy Guyette, according to another article was upset that Stanton allegedly went to some seminars at the National League of Cities as Susan. Guyette says he doesn't care that Stanton wants to be come a woman but that he "misrepresented himself on the City's dime" and has been "living a lie".

Guyette does have a point here, given the stereotypes many people have about transgendered individuals. But transgendered people who desire to transition, typically have to go through (or at least should go through) a standard protocol called the Harry Benjamin Standards of Care, which includes real life experience living as the desired gender, so in some sense what Stanton was doing made sense.

Another Headline in the St. Petersburg Times summed up the facts for many transgender people who decide to transition: "Change Sex? Lose Job."

Stanton may not have handled his situation in the best way, but my gut reaction to the charge that Stanton "was living a lie" is to ask could Stanton really have done things in a way to save his job? Somehow I think not. Not in Largo, and unfortunately not in many other places either, not yet.

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Conscience and Love Reign Supreme...

Christians often get characterized as being "homophobic" but I think that at least some Christians are really trying to grapple with homosexuality, even those whose theology points them in a direction some of us might not like.

Two good examples stand out from this week. First of all is this dialogue on NPR between Nathaniel Frank, senior researcher at the Michael D. Palm Center at University of California, and Richard Mouw, president of Fuller Theological Seminary in Pasadena, Calif. My son and I listened to this dialogue about homosexuality and we came away with the feeling that both men were trying hard to understand the other's position and view point. There was no accusations of homophobia, no scare tactics but good honest dialogue.

I am sure Richard Mouw would not agree with my next example, namely the recent pronouncement of the American Episcopal Church concerning the Dar es Salaam Communiqué of February 19, 2007 which attempts to provide "pastoral guidance to the American Church from the Anglican Community. I cannot do any better than to quote a key paragraph from the Episcopal Church pronouncement (My apologies for the length):

"It is incumbent upon us as disciples to do our best to follow Jesus in the
increasing experience of the leading of the Holy Spirit. We fully understand
that others in the Communion believe the same, but we do not believe that Jesus
leads us to break our relationships. We proclaim the Gospel of what God has done
and is doing in Christ, of the dignity of every human being, and of justice,
compassion, and peace. We proclaim the Gospel that in Christ there is no Jew or
Greek, no male or female, no slave or free. We proclaim the Gospel that in
Christ all God's children, including women, are full and equal participants in
the life of Christ's Church. We proclaim the Gospel that in Christ all God's
children, including gay and lesbian persons, are full and equal participants in
the life of Christ's Church. We proclaim the Gospel that stands against any
violence, including violence done to women and children as well as those who are
persecuted because of their differences, often in the name of God. The Dar es
Salaam Communiqué is distressingly silent on this subject. And, contrary to the
way the Anglican Communion Network and the American Anglican Council have
represented us, we proclaim a Gospel that welcomes diversity of thought and
encourages free and open theological debate as a way of seeking God's truth. If
that means that others reject us and communion with us, as some have already
done, we must with great regret and sorrow accept their decision.It is incumbent
upon us as disciples to do our best to follow Jesus in the increasing experience
of the leading of the Holy Spirit. We fully understand that others in the
Communion believe the same, but we do not believe that Jesus leads us to break
our relationships. We proclaim the Gospel of what God has done and is doing in
Christ, of the dignity of every human being, and of justice, compassion, and
peace. We proclaim the Gospel that in Christ there is no Jew or Greek, no male
or female, no slave or free. We proclaim the Gospel that in Christ all God's
children, including women, are full and equal participants in the life of
Christ's Church. We proclaim the Gospel that in Christ all God's children,
including gay and lesbian persons, are full and equal participants in the life
of Christ's Church. We proclaim the Gospel that stands against any violence,
including violence done to women and children as well as those who are
persecuted because of their differences, often in the name of God. The Dar es
Salaam Communiqué is distressingly silent on this subject. And, contrary to the
way the Anglican Communion Network and the American Anglican Council have
represented us, we proclaim a Gospel that welcomes diversity of thought and
encourages free and open theological debate as a way of seeking God's truth. If
that means that others reject us and communion with us, as some have already
done, we must with great regret and sorrow accept their decision."

It is hard to predict history, but we may have in the Episcopal document something that 30 years from now will be recognized as a key document in the evolution of Christianity, even as the debate we are having as a civilization about diversity will seem hopelessly quaint.

Other Links:

Episcopal Bishop's Statement

NPR Talk of the NAtion Interview with Mouw and Frank (audio-no transcript)

Richard Mouw's Blog

Nathaniel Frank article in LA Times

Nathaniel Frank on Don't ask Don't tell

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Late night DNA fun in Second Life

Simone's shown here with an attempt to make a single prim DNA strand through careful use of transparent textures. I think the concept works and I know what you are thinking...so this is what biologists do when it's too wet to go outside?

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The Obligatory Spring Goose

Because every blog needs one...


Actually this ties in to my posts about endemic invasive species since Canadian Geese are sometimes thought to a nuisance, especially around golf courses because they eat the grass and leave green droppings behind especially in Overland Park where I took this picture today. Let's see now..geese or golf courses, not much of a choice-give me the geese. They are the biggest bird the average person is likely to encounter. My only worry is that the geese might get an overdose of herbicides.

Geese are certainly opportunistic and have taken well to urban and suburban haunts. A similar urban bird phenomenon has been noted with crows, another traditionally rural species that has adapted to urban life, sometimes making pests of themselves. It's not clear if these shifts from rural to urban life are due to natural selection (Can you say evolution?) or due to learned behavior.

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A Deer Skull and Other Finds.

My son and I went on a hike yesterday at the Clinton Wildlife Area, along the Wakarusa and we found this intact deer skull. I was tempted to take it, but decided to leave it for the woods.



Along with this old foundation:



Here is cloesup showing faint chisel marks:



We were suprised by this herd of bison, or perhaps "beef-falo"



The Wakarusa:


There was lots of odd junk along the shore...

For instance

A lost idea:


and

a Kansas Puffball: