Magnolia

Here is a pink Magnolia from campus. One thing I didn't realize is that it is possible to isolate DNA from Magnolia fossils going back to the Miocene (17-20 million years ago)  and use it to help understand the phylogeny of these trees.  See Kim et al (2003)  http://www.amjbot.org/content/91/4/615.full doi: 10.3732/ajb.91.4.615 Am. J. Bot. April 2004 vol. 91 no. 4 615-620

Intelligent Design Monkey Business-again.

There is an interesting article in this month's Chronicle of Higher Education about intelligent design. Apparently some of ID's leading luminaries held a conference at Cornell University, my alma mater, and conned convinced Springer, a major science publishing house, to publish the conference papers as a volume called Biological Information, New Perspectives.

Apparently Springer posted a web page advertising this forth coming book on its web site but it was quickly pulled when science bloggers such as Nick Matzke over at Panda's Thumb discovered this page and posted about it here.

Springer immediately pulled the web page advertising the ID volume deciding that maybe it needs more complete peer review. Apparently, even as noted by this sympathetic review of the conference, participants were told to tone down their religious perspectives so that the conference would be more scientific.

In an update on Panda's Thumb more details have surfaced. First the conference was not well attended. There were 27 or so attendees and that apparently included the presenters.  Second the conference really had nothing to do with Cornell officially but was merely held in the auditorium at Cornell's fine hotel school. This auditorium is rented to the public and that is what happened here.  The conference apparently was not publicized and indeed was held in that in between time before summer semester. To be fair to the conference organizers, that time of year is a wonderful year to be in Ithaca as I spent four delightful summers working there as an undergrad.

That said, one wonders if the University is too happy about having its reputation besmirched by implied association with this conference.

http://www.insidehighered.com/news/2012/03/01/book-intelligent-design-proponents-upsets-scientists

http://pandasthumb.org/archives/2012/02/springer-gets-s.html

http://pandasthumb.org/archives/2012/02/update-on-sprin.html

Science From Multiple World Views?

Recently I stumbled upon a small publisher of home school materials called Gravitas Publications. This publisher's main product is called Real Science 4 Kids by Dr. Rebecca Keller. I have no expertise in home school curricula, and from what I have seen some aspects of her approach seem sensible.

What bothers me is her claim that science can be taught from the point of view of multiple world views in a strictly neutral sort of way.

She writes:

"Yes! Real science doesn’t choose sides. So when teaching science, it’s important that the lessons let kids explore all sides. Otherwise, choosing one side can get in the way of understanding the real science. Darwinism, creationism, intelligent design theory, and all the other “isms” are simply paradigms (or “lenses”) through which science is viewed. The “-isms” are philosophies based on perceptions for how science is interpreted. Students need to learn how “-isms” play a role in science."

Ok, science doesn't choose sides in that is ideologically neutral- there is no conservative science, or Christian science, or Buddhist science. There ideally is just science. And she is right- our world view does affect how we interpret science. But is science really neutral in terms of the world view it admits?

Personally I think not. For example I don't see much support in science for the notion that the Universe or the Earth is say 10,000 years old or that the goal of a liquid is to seek its lowest level, or that magic is real. At the very least science since it is empirical forces scientific explanations and tests of scientific ideas to be mechanistic and transparent.

At any rate, check out Dr. Keller's video discussing the issue of multiple world views and see what you think:

Half Full or Half Empty?

There is a new Gallup poll surveying American's belief in evolution. The bad news is that 40% of Americans believe that God created humans in their present form within the last 10,000 years. The good news is that the percentage of people who believe this has fallen to its lowest level since the first such survey in 1982. Also the pace of decline seems more rapid since the year 2000.

Check out the survey at http://www.gallup.com/poll/21814/evolution-creationism-intelligent-design.aspx

Religious Discrimination or Mere Whining?

An astronomer is suing the University of Kentucky alleging that he was refused a position because of his religious beliefs. Martin Gaskell was supposedly the top candidate for a new observatory position but didn't get it. Dr. Gaskell is an evangelical who has written and lectured on science and his faith. Apparently this got people nervous that his religious beliefs might influence his science.

This statement in particular from an essay Dr. Gaskell wrote seems to have caught people's attention:

"The main controversy has been between people at the two extremes (young earth creationists and humanistic evolutionists). “Creationists” attack the science of “evolutionists”. I believe that this sort of attack is very bad both scientifically and theologically. The “scientific” explanations offered by “creationists” are mostly very poor science and I believe this sort of thing actually hinders some (many?) scientists becoming Christians. It is true that there are significant scientific problems in evolutionary theory (a good thing or else many biologists and geologists would be out of a job) and that these problems are bigger than is usually made out in introductory geology/biology courses, but the real problem with humanistic evolution is in the unwarranted atheistic assumptions and extrapolations. It is the latter that “creationists” should really be attacking (many books do, in fact, attack these unwarranted assumptions and extrapolations)."

However on the surface I am not sure his views are that much different from theistic evolutionists such as Ken Miller. But looking more closely I am bothered by his inclusion in a positive light of groups like "Leadership U" which try to push ... "Intelligent Design".

Also as noted here his attorney refers to Gaskell as an "openly Christian man". Seems like a clever appeal for sympathy in spirit of diversity promoting acceptance of GLBT people. If so this strategy is not going to garner much support from me. I have seen attempts to use this strategy by whiny conservatives whose only motivation is to use the rhetoric of diversity to silence discussion of diversity.

Related Links:

http://www.nytimes.com/2010/12/19/us/19kentucky.html

http://www.examiner.com/creationism-in-national/astronomer-alleges-anti-religious-discrimination-by-university

http://www.courier-journal.com/article/20101210/NEWS01/312110011/Job+candidate+sues+UK++claiming+religion+cost+him+the+post

http://blogs.sciencemag.org/sciencecareers/2010/12/should-a-scient.html

Ah for the good old days!

...when convictions were convictions and martyrs were martyrs. Apparently William Dembski, has had to recant some of his moderate views on creation. In his latest book, End Of Christianity, he had the temerity to admit that he believes that scientists ARE right-the Universe really IS around 14 billion years old and that "the Flood" was NOT world wide. I guess that didn't set well with his overlords (I mean bosses) at Southwestern Baptist Theological Seminary. According to Michael Zimmerman writing in the Huffington Post, Dembski was called on the carpet for his writings. Since the inquisition is long gone, presumably his bosses used less drastic means than hot pokers or racks to get him to recant. Maybe they water boarded him- I don't know.

At any rate Dembski has at least partly recanted claiming that his statement about the flood NOT being universal was based on incomplete reflection:

"Before I write on this topic ( the Flood) again, I have much exegetical,
historical, and theological work to do. In any case, not only Genesis 6–9 but also
Jesus in Matthew 24 and Peter in Second Peter seem clearly to teach that the
Flood was universal. As a biblical inerrantist, I believe that what the Bible teaches
is true and bow to the text, including its teaching about the Flood and its
universality."

quoted in:

http://www.baptisttheology.org/documents/AReplytoTomNettlesReviewofDembskisTheEndofChristianity.pdf

Intelligent design advocates have long claimed that their beliefs about intelligent design are NOT Biblically motivated but I wonder how we are to take an advocate of intelligent design placing the Bible above empirical data.

To be fair, Dembski does not entirely recant but argues:

"My book The End of Christianity is a work of speculative theology. It
assumes that the earth and universe are old and, given that assumption, attempts
to answer how the Fall of humanity could be responsible for natural evil, such as
animal suffering. Since, on the assumption of an old earth, animal suffering
precedes the arrival of humans, the challenge is to explain how the effect (natural
evil) can temporally precede the cause (human sin and the Fall). My solution is to
argue that just as the effects of salvation at the Cross of Christ reach both forward
in time (saving contemporary Christians) and backward (saving the Old
Testament saints), so the effects of the Fall reach forward in time as well as
backward. What makes my argument work is the ability of God to arrange events
at one time to anticipate events at a later time."

OK so Dembski argues that the Fall was an actual event whose affects rippled both into the present and also into the past. So I guess all those veggie eating dinosaurs in the Creation Science museum mysteriously got transformed into evil T. rexes.

Speculative theology indeed!

Practical pantheism?

The movie Avatar must really be a great movie because it has struck so many nerves on the left and the right. My favorite (and I use that word advisedly) take is from the loony right by Phil Kline Kansas's former attorney general. I am not going to dissect his whole scree which you can read here:
http://www.freerepublic.com/focus/news/2415427/posts?page=64

Kline predictably thinks it is pro-environmental propaganda, for he writes:

"The natives are one with their native planet, including their mother-god Eywa. Eywa is the planet, and the natives reach oneness by entwining fibers from their bodies with the fibers of the planet. This representative sexual union allows them to hear their departed ancestors and gain rhythm with the planet — a séance orgy so to speak. All life on the planet is one, with one spirit and one energy."

Notice how nicely he works in the evil SEX into his rhetoric.

Later on we get the evil bugaboo of evolution:

"Such a prayer represents atheistic Hollywood's dilemma. The only way to reconcile a godless Darwinistic worldview with a deeply spiritual American culture is to convert environmentalism into religion. For what greater purpose for man than to save mother earth, or Pandora? And thus, our purpose in a purposeless world."

And he says that that culture of the Pandorans is Pantheistic. Well that is true I suppose but if Kline would take off his blinders a bit he would see that it is really a practical pantheism. After all, on Pandora evolution (sorry Phil that is the way the world works) has led to a system where the Pandorans can little plug into each other and indeed that is necessary for their survival. So it's not some really some sort of mystical new age Pantheism, but quite practical.

Now we don't have the same explicit connections to our environment that the Pandorans have but we are interconnected much more and need the rest of the biosphere a lot more than Kline seems to care about. At simplest level we are not even a single organism but a community of roughly 100 trillion human cells and 10 times that many bacterial cells that are symbiotic with us. And I don't think that includes the mitochondria which were believed derived from free living bacteria. And examples of how we are interconnected can be multiplied repeatedly at other levels of biological organization.

So Kline and company may scream but maybe we need a good dose of practical pantheism.

A lesson from my plants

Here are three plants from my collection:

Plant number 1














Plant number 2



















and finally...

Plant number 3















Which are cacti?

A little more information. At least one is a cactus.

The first plant grows in warm semi arid regions in South America. Some members of this group of plants get to be mid sized trees but most are shrubby.

The second plant has reduced leaves that function as thorns and it is found in deserts in the SW United States and Mexico.

The third plant lives in the jungles of Southern Mexico and into Central America.

All three plants have very similar looking and distinctive complex flowers, all organized in the same basic way.

So which are cacti? How do you know?

Oh Good Grief!

Just when I think anti-evolutionists can't get any sillier some politician comes along to demonstrate that I am wrong. Seems that a mayoral candidate in Tulsa feels the zoo doesn't properly honor Christianity and needs an exhibit on the first book of Genesis.

"Today we are announcing that God will be glorified in this city. He shall not be shunned. Upon our election, we hereby commit to honoring Him in all ways that He has been dishonored," said Anna Falling.

OK...check it out for yourself at:
http://www.newson6.com/global/story.asp?s=10888260

Oh Really?

Well it is either Loonie Toons time or time for another school board race in Lawrence Kansas. If you really want quality schools then check out Michael Riley and consider carefully what he says:
"

Those beliefs lead him to maintain that parents should have a primary say in the public school system before the teachers, district, state and federal government.

“I think when I say decentralized, I feel that our primary responsibility is to the parents and then up from there,” Riley said."

Sounds good until you really think about it. After education involves more than just the parents.

And consider this tidbit:

"He says he does know some issues are on the minds of parents and Lawrence residents.

“Sex education and science standards have come up repeatedly,” Riley said. “These are issues that they’re concerned about and they’re concerned to know what school board members feel about these things.” " Oh oh.

Really he must hang out with a different crowd than I do.

He might really be OK, after all his kids did go to public school. But really do you want some of the parents you've met to be the ones that have primary say about running of local schools? Does my stake in the school system stop because my kids are grown and married? Doesn't business have a say here as well?

Come on Mr. Riley. Get real.

Check out the Journal World forums where yours truly has been accused of:

"Pdecell: Way to come out and bluntly tell us that public education is State indoctrination 100%. I'm sure we all want to line up for your brand of brainwashing for each and every one of our children. As a parent, I want you to keep your taxpayer opinions out of my child's easily manipulated mind."

Notice the nice scary rhetorical touches-"state indoctrination", "manipulated mind" oh yes and "brainwashing". Kind of reminds me of an old Rocky and Bullwinkle cartoon.

Happy Birthday Mr. Darwin!

We love birthdays and anniversaries , especially ones that end in zero. This year there are two such numbers related to Charles Darwin-200 years since his birth and 150 years since publication of Origin of Species. Of course there is all sorts of commentary and there should be. After all Darwin's way of looking at the world really did revolutionize biology and society as a whole.

What was it really that Darwin did that was so great? After all he wasn't the first person to speculate that evolution happens, or even to propose how it might happen. Maybe he was just the right person at the right time to be remembered. But I think there is more. Perhaps the best way to answer the question from my perspective is to briefly contrast Charles Darwin with Jean Louis Agassiz. Agassiz was one of the most popular scientists of the 19th century, especially in biology, Harvard Professor, did lots of important work on fossils and glaciation. Yet he never accepted evolution.

I encountered Agassiz in Edward Lurie's biography, Louis Agassiz: A Life in Science. Lurie observed, as I recall, that Agassiz was a proponent of the notion that the geological features of the Earth were molded mainly by a series of catastrophic events and that that the distribution of species could be best explained by a series of creation events. As new data about geology and the distribution of species came out-Agassiz would simply postulate a new catastrophe or a new creation event. So the data are explained.

Darwin was different. Not only did he synthesize masses of data to support his ideas, but he confronted the weaknesses in his ideas head on. After all, Darwin knew that contradictions between observation and theory are not to be feared but provide new opportunities to learn by empirical means what makes the universe work. Agassiz was an accomplished scientist as well and probably understood this idea as well. The difference is that Agassiz did not understand the universality of the principle that contradictions provide new opportunities in all spheres of science, and, I argue, life as well.

So happy birthday Mr. Darwin and here's to biologists today who see contradiction as something not to be feared, or glossed over with rhetorical tricks, but as opportunity for understanding.

This shouldn't come up, but it has.

You would think that today in America a person's sexual orientation wouldn't be an issue in an election any more than whether or not a person is married, single or divorced. But in one Kansas Board of Education race apparently partisans have not gotten the message. Seems that Kathy Martin and her supporters are trying to make an issue of the fact that her opponent, Christopher Renner is openly gay.

According to this article in the Hutchinson News Online, Martin's supporters argue that this is a valid issue, as voters have the right to know everything about a candidate. Carolyn Simms, a Martin supporter says

"...that voters should also be given all the information possible about the candidates they'll be choosing from."

Really, now. Maybe I should hire a private detective to see what juicy non election related things are in Mrs. Martin's background. Of course I really don't have to do that since Mrs. Martin has embarrassed herself enough as one of the gang of six that spent thousands of dollars on sham evolution hearings a couple of years ago and was a supporter of a completely unqualified Board of Education Commissioner who ended up resigning.

So hello Mrs. Martin! This is the 21st century. We don't fight about whether the Earth is only 6,000 years old or so anymore and we don't care about a person's sexual orientation as a job issue. How laughable this would seem except that there are still folks out there who are blissfully unaware that time has moved on. Mrs. Martin you are so 19th century!

A motivational poster of Richard Dawkins

A motivational poster of Richard Dawkins
Originally uploaded by Torley

A Flickr and Second Life contact recently put together this wonderful poster for Richard Dawkins. Me thinks Dawkins would love it!

Sex ed problem to be solved in Kansas!

It's easy according to Alan Detrich who is running for a spot on the State Board of Education:

"When you teach children that they are apes, they will reproduce like apes," he wrote in a questionnaire. "Stop teaching evolution, and the sex ed issue will take care of itself."

Right...

link:

http://cjonline.com/stories/073108/sta_311695380.shtml

Now do I file this under humor?

So here we go again...

Here we go again in Kansas, haggling about evolution. In the mean time evolution keeps on happening and in unexpected ways. For example, you may be familiar with the infectious cancer that is threatening the Tasmanian Devil (AKA Taz) with extinction. This cancer is spread when the Devils bite each other's faces during mating leading to spread of cancer cells from animal to animal.

The infectious cancer cells are genetically identical and their spread is believed to be made possible because inbreeding has led to a loss of genetic diversity so that the animal's immune systems are not able to recognize the foreign cancer cells.

See this link for background.

In an interesting twist, natural selection seems to be operating, at least in the short run, to favor precocious sexual activity and breeding. According to the research published in the Proceedings of the National Academy of Sciences, this is the first time where an infectious disease has been shown to bring about these sorts of life history changes in mammals.

Often times natural selection favors the spread of genes conferring increased resistance to a disease so the scientist's findings are some what surprising.

The other interesting thing is that even though genetic diversity in the Tasmanian Devil has apparently been reduced by genetic drift there is still enough genetic diversity for natural selection to lead to a rapid shift in the timing of reproduction.

Presumably the scientists will now follow up with research looking at the sorts of genes that are involved and try to related the life history changes they see to genetics. Might there also be long term responses in other aspects of the animal's behavior and physiology driven by natural selection?

Aside from it's implication for the survival of the Tasmanian Devil as a species, this research may provide insight into the ability of endangered species to evolutionarily adapt to rapid environmental changes be they due to disease or to human activity.

Meanwhile back in Kansas...sigh.

Cross posted with Dangerous Ideas.

Nota Bene:

Here is a very balanced discussion of the PNAS paper over at Not Rocket Science. Note in particular this comment:

"Jones clarifies that so far, all she has found is a physical response. Rather than reflecting genetic evolution, the changes in the devil's life cycle over such a short time span is almost certainly due to "phenotypic plasticity" - the ability of an organism to change its body and its behaviour to match its environment, without changing its genes."

So while there is clearly selective pressure for early reproduction, the immediate response of the population may be a physiological adaptation rather than a longer term evolutionary adaptation.

Such details

I suppose one could postulate a creator that pays special attention to us. We are made in the creator's image, right? But notice the wonderful detail of this moth:



Check out the poofy front legs.

Here's another view more from the top:



Each organism seems to be sculpted to the same detail that we are. Now who does the creator love more, me or the moth, eh?

Don't creationists ever think about the issues raised by the personal God as pet notion?

Oh the moth is a Noctuid called a Wood Nymph, genus at least is Eudryas-a true wood nymph!
See http://bugguide.net/node/view/110093

The Evolution of Beauty

I am never away from thinking about evolution. Being at Disney last week taking lots of pictures of flowers, got my thinking about evolution and beauty. Take this shot of a flower from Disney:



Actually this structure is called a spathe and it really a group of fused flowers wrapt around by a leaf. Think of Jack in the Pulpit and you have idea.


At first glance, not a traditionally beautiful picture and yet if you really look at it I suspect you will see a certain sensuousness to this image. I am reminded of Georgia O'Keeffe who allegedly said she painted flowers because she couldn't afford models. The traditional explanation for why flowers are beautiful is that that this is a by product of the coevolution between flowers and pollinators. But that really doesn't explain why they are beautiful for us. Part of the answer maybe that flowers also coevolved with us and breeders selected for beauty. But why beauty in the first place?

In terms of sexual beauty and attractiveness, it appears that humans and other animals have innate neurological biases that operate in conjunction with Darwinian sexual selection leading to elaboration of certain characteristics. But why these biases? Why not just respond to the narrow signs required for our reproduction and not feel rewarded emotionally by flowers and other things that we see as beautiful be it a flower, a poem or a butterfly?




Of course, I would want an evolutionary explanation because of my (innate perhaps?) desire for explanation. How do things come about? How do they work? But just because scientists are interested in these sorts of questions no way diminishes the emotional response and appreciation of beauty in all its forms.

Nor does beauty exist in a vacuum. Our innate neurological biases may be enhanced or over ridden by our experience or cultural preconceptions. For instance for me the beauty of the Rhododendron in the picture above is enhanced by the presence of these little bug (actually Katydid) nymphs:



There is a richness of connection that the nymphs add that for me is itself part of beauty and would be missing if I had taken a shot of the flower alone.

Trouble Ahead for Science?

I have been following the controversy about Ben Stein's "documentary" Expelled and no I have not seen it yet. But Ken Miller sums up scientist's fears about the effect of this "documentary" and the intelligent design movement in general.

Miller in an op ed piece in the Boston Globe writes:

"It deceives its audiences, slanders the scientific community, and contributes mightily to a climate of hostility to science itself. Stein is doing nothing less than helping turn a generation of American youth away from science. If we actually come to believe that science leads to murder, then we deserve to lose world leadership in science. In that sense, the word "expelled" may have a different and more tragic connotation for our country than Stein intended."

So why should I even waste money on seeing Expelled? Now I don't want to hearing any intelligent design whining about not having an open mind. I have looked at the trailers and read the reviews and oh by the way spent several excruciating days biting my tongue at the Kansas Board of Education hearings several years back where I heard the best the ID proponents can give and I have waded through much of the ID literature. And you know what? There is nothing there!

Nothing.

Scare tactic alert

The Intelligent Design Community is eagerly awaiting the release of that boffo documentary exposing the academic cabal surrounding Darwinism (gee maybe I should write for the Discovery Institute), "Expelled", starring that well known scientist Ben Stein.

Since I am clearly in a boffo mood today, I call your attention to the latest buzz. According to the New York Times, Michael Moore he of Sicko fame was dis-invited from a screening of Expelled.


Allegedly, according to the film's promoters, the film has some rough edges and not considered ready for "professional scrutiny". Of course it is ready for screening at various mega church groups who have lost any ability to think critically so rough edges won't bother them so long as the film is appropriately anti evolution and paints evolutionary scientists as totally dogmatic and picking on the poor Intelligent Design Advocates.

What I found interesting is that Stein in commenting about the film says:

“there’s just a lot of people who don’t believe that big science and Darwinism should have a stranglehold on academic life, and they have been waiting for a voice.”

Notice how now there are two enemies. One is Darwinism, but the other is "big science." I suppose that is something like big Church (oops). But the term "big science" perhaps harkens to a more innocent time when scientists labored alone in their labs-that's the type of science the Intelligent Design people do except they don't have labs.

Big science....hmmm yes a lot of science is done on a massive scale and there are certainly a number of reasons for that. Some of that has to do with the complexity of the problems that face us today. But big science- and lets throw in big technology to boot- has been around since the 1930's and is not going away. Anyone read about the Manhattan Project?

Big science-sounds scary but Mr. Stein can pine for the good old days but remember that he and others who use this phrase in a disparaging way are simply trying to avoid applying critical thinking to understanding the world around them. They don't want to because critical thinking would show the weakness in the Intelligent Design idea and that would mean no one would go see his film.

A Row about Testing Evolution...

...is ongoing now on my Science blog at the Lawrence Journal World. Most of the discussion has been at a fairly high level considering how such discussions usually go. Take a look here:

http://www2.ljworld.com/weblogs/dangerous-ideas/2008/feb/18/can-evolution-be-tested/