Monthly Archives: May 2005

Layla and Ritka

OK, sometimes circumstances cooperate with the photographer, when the light, the subjects, and the machinery all somehow come into alignment and the photographer actually engages the shutter release at pretty much the right time. In going through some recent photos I’ve taken, this one is a standout. If anyone has an idea for a caption, let me know.

Coffee mug with picture

Oklahoma, Textbooks, and Ignorance

In an online press release on 2005/05/25, Oklahoma state Senators Mike Mazzei & Clark Jolley announced, “Henry Nominee for Textbook Committee Opposed”.

Interesting… what, in particular, made them think that the nominee in question, Dr. Virginia Ann Dell, should be opposed?

“Despite her impressive academic degrees and her service as a teacher at the Oklahoma School of Science and Math, her errant belief that the teaching of the Intelligent Design Theory blurs the line between the separation of church and state is the first of many problems to arise with her nomination,” stated Sen. Clark Jolley, R-Edmond.

Sen. Mike Mazzei, R-Tulsa, stated, “Nothing exists in state or federal law that prohibits the discussion of creationism or Intelligent Design theory in the classroom. Let’s encourage open and honest discussion of all theories so students can learn to think critically and, with their parents’ guidance, develop their own worldview.”

Dell’s responses to questioning in the Senate Education Committee showed she is unwilling to even allow a mention or discussion of alternative theories on the origins of the universe.

Hmm… what was Dr. Dell’s training in, I wonder?

Virginia Ann Dell, Ph.D.

Dr. Dell earned her degree in 1987 from the University of Oklahoma, Health Science Center in Biochemistry. She is also the Mentorship coordinator for OSSM. This duty entails pairing interested students with a mentor in a particular field of science, encouraging a hands-on experience. Dr. Dell teaches Genetics, Biochemistry, and Molecular and Cell Biology.

(Source: OSSM Biology Department)

So, someone with actual academic training in science, experience as a science teacher, and apparent familiarity with the legal status of antievolution efforts (such as Epperson v. Arkansas, McLean v. Arkansas, and Edwards v. Aguillard, which show Mazzei to be behind the times as far as legal issues go) is definitely someone to keep away from helping make decisions on textbooks in Oklahoma.

And the same goes for anybody else with half a clue on this topic:

“Since this is Gov. Henry’s second appointee to the Textbook Committee to openly hold this viewpoint, I fear he is trying to stack the Textbook Commission with liberals whose goal is to stamp out all discussion of alternatives to the theory of evolution in Oklahoma classrooms,” Jolley said.

No, Mr. Jolley; what you are seeing is the principled non-partisan stance that we should be teaching science in science classrooms and not teaching non-science there. In order to do right in teaching a scientific alternative to the evolutonary biology you must actually have a scientific alternative to evolutionary theory, not just a lot of long-rebutted antievolution arguments coupled with, “therefore, {God | an intelligent designer} did it.” In other words, first do some science, convince the scientific community that there is a point there, then it will be ready to teach in K-12 science classes. This, I know, is a difficult lesson for those pushing theistic antievolution to learn.

I’m working on the content of a five-day seminar to be given in Oklahoma on the topic of “Evolution and creation”. I had been wondering about how to tie current events to Oklahoma. So, thank you, Oklahoma state Senators Mazzei and Jolley. You have provided me with exactly the sort of hook I needed.

To Olley and Rubinstein

Over on the Social Affairs Unit page there is a post by a Dr. Rubinstein that takes evolution to task using a selection of arguments from the antievolutionist ensemble of arguments. There have been a number of, ahem, abrupt disagreements with Rubinstein posted on that blog. A Dr. Olley (who I unfortunately referred to as “Dr. Oller” there) took some exception to the tone of the responses and suggested that the theory of evolution was not “intuitive” and suggested some historical reflection for people. I left aside problems in Olley’s text in my response to him, taking up Rubinstein’s arguments.

Dr. Olley,

It is a certainty that the tone of the discussion could be improved. So, perhaps a review of the evidence concerning Dr. Rubinstein’s claims would be in order. Was Rubinstein right or wrong in what he wrote?

Is common sense a guide to scientific accuracy? I would think not. To point out an example that does not have to do with the current topic, consider quantum mechanics and such counterintuitive items as the two-slit experiment.

Are there a growing number of doubting scientifically trained commentators? Actually, this claim of Rubinstein’s is ill-formed. One could have a point of view whose “market share” in the marketplace of ideas was monotonically decreasing while the absolute numbers of people involved was increasing. The interesting fact about the claim that “more and more” scientists are doubting the theory of evolution is that it predates Darwin’s Origin of Species and comes close to predating Darwin himself. See Glenn Morton’s essay for the details. Surely it is an odd sort of movement which has been continuously growing a century and three-quarters and yet still only incorporates a tiny fraction of the scientific community?

What of the claim that scientists have “failed to challenge” evolution? I direct your attention to Peter Bowler’s “Evolution: The History of an Idea”, in which the author describes a substantial number of theories in evolutionary biology which were proposed, challenged by scientists, and discarded as being at odds with the evidence.

Certainly Niles Eldredge and Stepehen Jay Gould considered punctuated equilibria to be a challenge to the view of “phyletic gradualism”, and I do not recall anyone calling either of them a “creationist”. A witticism comes to mind, but since the topic was a kinder, gentler exchange I will forego using it.

I want to quote Rubinstein here… “Nevertheless, there are so many deep implausibilities in the Theory of Evolution as it is commonly understood that it seems to me, as a non-scientist, that something must surely be radically wrong.” This is something upon which I can wholeheartedly agree with Rubinstein. The common understanding of evolution is, as is demonstrated by Rubinstein’s further text, composed of common misunderstandings of evolution. Certainly a part of what is wrong is the lack of effective education in this regard.

The claim that “evolution is impossible” and that speciation cannot happen is simply at odds with the scientific literature. See also the FAQs on observed speciation, more speciation events, and common descent. Beyond the insistence of evolution-deniers upon videotaped species transitions, there is an absolutely huge chunk of scientific literature on the topics of incipient speciation and analysis of reproductive isolating mechanisms. As for when one figures out that speciation has occurred, there can be difficulties, as in the cryptic speciation of populations of Cordylochernes scorpioides which look alike, but have genetically diverged such that there is postzygotic reproductive isolation. That sort of situation means that the number of speciation events that are observed in the next few years may be a serious underestimate of the true number of speciations that take place. Another point to be taken is that we can hardly be said to have a handle on knowing what species are in existence right now. The knowledge of populations in regions like the Amazon basin is still pretty sketchy, and yet there is immense biodiversity there (or was, given the habitat loss going on there).

When Rubinstein says that no one expects evolution to occur, he apparently means people who are not biologists and who are not looking at populations in nature. For biologists, though, the view is different. From studies of guppies in tropical streams to finches in the Galapagos to peppered moths to anolis lizards on Caribbean islands, researchers are doing work on characterizing the evolution that does, in fact, happen. Medical researchers are keenly aware of the expectation of evolution in HIV virus strains, and even forensic investigators have used that evolution in their casework. Agricultural researchers deal with evolutionary processes, too, in trying to reduce problems with pests and disease in crops and livestock.

Rubinstein then returns to speciation, and claims that no one has seen one species give rise to another in one generation. This would be a saltational change, and is something that Darwin thought did not happen. Biology is such a confounder of neat principles, though, that biologists have been privileged to see or detect saltational speciation. This is a pretty common occurrence in certain plant taxa, such as orchids. Consult the American Orchid Society list of species and note how many of those say “tetraploid”. Each one is an existence proof to throw light on Dr. Rubinstein’s essential ignorance of the topic. My genetics professor of many years back, Dr. Wallbrunn, was particularly interested in those tetraploid orchid species. Tetraploidy is known to have happened within animal species, too. Consider Hyla versicolor, a tetraploid daughter species of Hyla chrysoscelis. There are systems of differing ploidy in lizards to make your head spin. Speciation in mammals via differing karyotypy is something suggested by the evidence in the Suidae. That would likely take two or three generations to accomplish, but still comes pretty close to Rubinstein’s demand for existing saltation to liven up more staid means of achieving speciation.

The claim that most examples of evolution are “highly dubious” doesn’t stand up to scrutiny. Peppered moths were never claimed to have speciated. The point at issue in that research was whether it was a case of natural selection acting on a population. That’s a different issue than speciation. And those researchers who actually work on peppered moths are quite clear that natural selection has been at work there. Please see Alan Gishlick’s essay on the antievolution objections to peppered moth research.

Rubinstein claims that fossil evidence is arguable or “logically fallacious”. While it certainly is the case that one usually cannot tell from a fossil whether it had offspring and produce a pedigree, one doesn’t see antievolutionists taking this objection to its logical reductio ad absurdum conclusion and say that each foram in the white cliffs of Dover was a special creation of God thereby. While Rubinstein dismisses the fossil record for horse evolution, actual paleontologists say differently. Niles Eldredge says that the fossils are all found in the geologic record just as predicted by evolution in the correct temporal order, and says that these fossils are “every creationist’s nightmare” (see his “Triumph of Evolution” around page 130 for the discussion). Bruce McFadden is a paleontolgist who has specialized in fossil horses (and was also one of my professors a long time ago). His take is the same, that the horse fossil record is a brilliant illustration of historical evolution.

When antievolutionists, and Dr. Rubinstein, claim that there are no transitional fossil sequences, I point them to a gradual and sympatric divergence in foraminifera and ask them to give their technical reasons for saying that that doesn’t count as a transitional sequence. Dr. Rubinstein’s objection falls into a category of responses that I call “non-evidentiary response items” or NERI. The neat thing about issuing a NERI is that one is relieved of the burden of actually looking at the evidence and making an effort to understand what one is looking at. The evidence is completely irrelevant to a NERI, which makes it easy to figure out whether someone is deploying one. If different evidence would not change the effectiveness of the argument, it is a NERI. Does it matter exactly what those horse fossils are to Rubinstein’s argument? No, of course not. However, paleontologists have yet to be convinced of the superiority of simply stating a NERI as opposed to actually studying fossils and making inferences from what one finds there. I’m sorry, I seem to have let some rhetorical content slip into this response. As to the number of expected transitions, I made an estimate based on Charles Darwin’s famous passage and came up with a number fully in accord with what we see today. If Dr. Rubinstein would care to turn his assertion into a quantitative form, we could then compare the two. I find it interesting that Rubinstein relies on Corliss as a source for a grand sweeping negative claim. Botany is not my field, so I will check on that.

Rubinstein repeats the old antievolution claim about organs needing to appear all at once and be integrated into systems. Eyes are certainly interesting examples, coming, as it were, in all forms of differing complexity from simple patches of light-senstive material through “cup” eyes to closed camera-style eyes. Even within a morphological form, one can find examples of differing structure, as in the differences between camera eyes in mammals and those in squid. Evolutionary biology does not hold that an organ like the eye has to appear “all at once”. The critique as given by Rubinstein is an indictment of creationism, not evolution. Evolution posits that new organs are derived from existing organs. Rather than the eye, which is generally soft tissue and unlikely to fossilize, consider the mammalian middle ear and its three-bone impedance matching system. If any of those parts is missing, impedance is not matched and in humans that results in about a 30dB reduction in hearing senstivity. But there is a good fossil record of stages in the development of the mammalian middle ear showing that the middle ear did not “poof” into existence somewhere along the way, but rather was the result of a process that took millions of years in incremental steps.

Rubinstein has a certain fascination for the phrase “survival of the fittest”. There is a historical connection to evolutionary biology, to be sure, but no evolutionary biologist nowadays considers it as anything but historical trivia, and certainly not a regulative principle in evolutionary theory. The role of contingency in historical evolution is widely appreciated in evolutionary biology. Others have already commented on the gap between Rubinstein’s description of ecology and what actually obtains.

Rubinstein’s claim that increasing complexity requires a “guiding hand” is noticeable for the complete lack of scientific research cited in its support. The assertion that “saltation” has any part in “punctuated equilibria” would come as a surprise to Gould, Eldredge, or even Ernst Mayr, whose theory of allopatric speciation forms the basis of PE. Allopatric speciation has nothing to do with saltation. The notion that something does or does not accord with the facts, coolly considered, implies that the person making the decision has actually taken the time to look at “the facts”. It is by no means apparent that Dr. Rubinstein has taken the time to acquaint himself with a sufficient sampling of biological facts to make pronouncements within that field.

Save the Filibuster

It doesn’t have the catchiness of “Save the Whales”, but it is still important. Our Senate leadership is looking to change the rules on filibusters of judicial appointments. I’ve signed an online petition aimed at convincing enough senators to oppose the “nuclear option” that we preserve the filibuster as a means of empowering the minority to reject particular judicial appointments.

Here’s what I put in my personal comment there:

Thirty years ago I was sitting in civics class listening to a description of government in our republic. I was told that our government went about its business by applying the will of the majority with respect to the minority, that the minority viewpoint was not unheeded. The checks and balances in our system of government preserved this state of affairs. Ben Franklin, were he keeping tabs, might be surprised at how long we have managed to keep this republic a republic.

That civics class, by the way, was in a Catholic high school. I’m a Protestant. This makes for layered ironies. Certainly, the Catholic community has been sensitive to the exercise of governmental power where it could prefer Protestantism over Catholicism. And in my time in high school, I got to know what it felt like to be in a minority group of some sort. It seems to me that our majority leadership in the Senate has forgotten what being in the minority is like, and why respecting the views of the minority is important in the maintenance of a republic.

We see news reports nearly weekly about new instances of civil unrest with violence somewhere in the world, even excepting known war zones and occupied regions. From the comfort of our padded recliners, we may feel sympathy for those poor people somewhere far away. What we tend not to think about is just how easily this kind of behavior could become the only way that those with unheeded views feel that they can become heard in the USA.

The action proposed by the Senate in eliminating the denial of particular judicial appointments by the minority has the potential to bring that unheeded feeling to more and more Americans. In their haste for a short-term benefit of rapidly placing any and all judicial nominees on benches, the Senate moves our system of government one step closer to the authoritarian models we see in the news all too often. There are plenty of people qualified for those appointments. Surely we can find the ones who identify with the majority without offending the minority. But this cannot happen if we choose to simply not listen to what the minority tries to tell us through our elected representatives.

Our founding fathers put together a system of government whose revolutionary principle was that the power that came from the people passed on in the appointed ways at the specified times. The transfer of the US presidency from George Washington to John Adams looks like trivia to us today, but to the citizens here and observers abroad at the time it must have been a stunning example of a new principle of governance. Washington’s acceptance of the limitations on his personal power gives us a model of correct behavior in our republic. This is a lesson that the Senate leadership needs to pay close attention to, just as I tried hard to learn my lessons in that long ago civics class. It just means a lot more to the USA whether the Senate leadership passes this test.

Things Cooking Along…

As far as my recovery is going, things seem to be going well. I’m trying to remember to take an iron supplement daily to help boost my hemoglobin content in the blood. I’ve been getting in fairly regular walks. I still have stamina issues. That’s going to be something to work on for a long time into the future, apparently.

And Diane is back from her field research, which is a great thing. Six weeks apart is quite enough. There’s a picture taken with Gail’s digital camera of Diane, Gail, and the Ford Expedition vehicle at the loading bay of Storer Hall at UC Davis. I’ll post that when I get a copy.

Work at NCSE is keeping me busy. But in bits of spare time, I am working on some personal projects. On the evolution/creation issue, I’ve written a web application to help exhaustively catalogue antievolution arguments in sources. Mark Isaak has sent me some suggestions for additions to make the project include a little more information to accomplish a task he wants. I’m also working on a larger-scale web site to help establish a public activist community.

There’s a couple of papers in the pipeline, one on bioenergetics of dolphin biosonar, and another concerning a critique of “intelligent design”. There’s plenty more papers to be done. It’s a matter of making time for working on them.

I’m also looking at passive acoustic localization. This is a pretty cool technology that has been applied both for in-air and underwater bioacoustics. With multiple acoustic sensors (microphones or hydrophones), one can obtain estimates of bearing or locations. This is usually accomplished by noting time-of-arrival differences for the same sound at the different sensors (via cross-correlation) and doing some more math to simultaneously solve for a source location. It seems to me that machine learning may be applied to this problem, and I have some ideas for training that I haven’t found in the literature yet.

And, for the literal approach to the subject line, I’m making a salmon entree a weekly feature on the menu here. Essentially, I take about a half-pound of salmon fillet, a potato, a carrot, and a bit of butter, slice the carrots and potato, put everything in an aluminum foil packet, and bake at 425 degrees for 50 minutes. This is a pretty easy to prepare and very tasty dinner. I just add some lemon juice … I walk out to the lemon tree and get another lemon. Thanks to Marguerite and Sam Blackwood for passing on this bit of culinary knowledge.

The Inflationary Universe of Antievolution

See Jeff Shallit’s Anatomy of a Creationist Tall Tale for the full background for this. Most of the material here is taken directly from that page.

The initial event: Jeff Shallit corresponded with the Smithsonian Institution to find out about collections of designed objects of which we don’t know the functions. Kenneth Burke there told him that in…

one showcase of a 1980-1 exhibition at the then National Museum of History and Technology “a number of unindentified articles were displayed[…]”

(Elsberry and Shallit, 2003)

Then Del Ratzsch in 1998 took notice of this:

The Smithsonian Institution has a collection of obviously designed human artifacts, concerning the purposes of which no one has a clue.

William Dembski then reported in a 1998 article:

There is a room at the Smithsonian filled with objects that are obviously designed but whose specific purpose anthropologists do not understand.

And then again Dembski reports this in 2002:

Consider that the Smithsonian Institution devotes a room to obviously designed artifacts for which no one has a clue what those artifacts do.

In the latter case Dembski cited Del Ratzsch as his source.

This was the state of play where Jeff got involved, where part of a showcase of an exhibit almost 20 years previous became “a collection”, then became a room dedicated to storing such artifacts.

Well, Kansas has added its bit to the inflationary universe of antievolution. In his testimony to the Kansas Kangaroo Court, Dr. William Harris brought up this claim. Now, though, the budget must have gone through the roof, for Harris testified that in Washington, DC, there is a museum that devotes an entire wing to such artifacts!

Mark Twain famously opined that “There is something fascinating about science. One gets such wholesale returns of conjecture out of such a trifling investment of fact.” Obviously, pseudoscience is seeking to one-up science in this regard.

Censorship at PT? I Don’t Think So.

Over on Bill Dembski’s weblog, a couple of people banned for bad behavior from the Panda’s Thumb weblog were claiming that they were censored at PT, therefore Dr. Dembski could do anything that he wanted to with comments on his blog. Other than utilizing moral relativism, the two were wrong at another level, as I documented in a comment made to that thread.

Panda’s Thumb Comment Integrity Policy:

“6. Posting under multiple identities or falsely posting as someone else may lead to removal of affected comments and blocking of the IP address from which those comments were posted, at the discretion of the management.

Simply put, don’t make a jerk out of yourself.”

“Evolving Apeman” writes:

“My comments and IP address were censored at Panda’s Thumb without good reason (and without explanation). If the “premier” pro-neo-Darwinism site is unwilling to allow dissenting viewpoints, why should this site either?”

This is incorrect. There are two comments that explain why “Evolving Apeman” was banned. In between posting as “Andrew Rule, MD” and “Evolving Apeman”, “Evolving Apeman” had a go at posting as “Great White Wonder”, which is an alias used by another PT commenter. I can’t speak to the prevalence of deletions of comments, since each contributor at PT manages their own threads, but I can say that “Evolving Apeman” was quite prolific for someone who claims to have been censored, and quite a lot of his material remains online there.

“DaveScot” wrote:

“Trying to escape that treatment I resorted to using randomly selected names. I was then banned for using multiple names.”

This is incorrect. “DaveScot” was not banned for simply using multiple names; he was banned for making threats against PT and also posting under another person’s name. “Scott Page” is not a pseudonym, but rather an actual person who posts at PT from time to time. Was “Scott Page” “randomly selected” as a posting alias? Apply your EF/DI, Bill, and use a local probability bound. Here’s the data showing that “DaveScot” was well aware of the use of the name “Scott Page”: 1, 2, 3, and 4. The “DaveScot” corpus of material posted at PT is available for review.

PT doesn’t ask much of commenters, not even that they agree with us, given some (very) small modicum of decorum. But there are some behaviors that shouldn’t be tolerated anywhere, and both “Evolving Apeman” and “DaveScot” violated a clearly stated rule at PT.

Low on Energy, but Having a Busy Day

Today I was tired, but still managed to accomplish a fair amount.

I’m preparing for a talk and question and answer session to be held Friday at Stanford University. This is a small bit of information dissemination to counter several days of “intelligent design” disinformation being presented at Stanford courtesy of the Veritas Forum. My colleague, Nick Matzke, and I will try to do our bit for the pro-science community. What that meant was that I was dealing with putting together Powerpoint “slides” today. One point I’ll be making is that “intelligent design” claims have been examined on their merits — and found wanting. Why Intelligent Design Fails is a detailed examination of the ID claims that shows why they don’t hold up to scrutiny. It is heading into its third printing at Rutgers University Press, which means that we are reaching people with the message. The event is “Veritas Forum Follow-Up Event: Presentation and Discussion on Intelligent Design”, 4-5:30pm, in building 370 (Science, Technology and Society program), Room 370. The event is sponsored by Rational Thought.

Bill Dembski had a good idea about making media contact information readily available to people, so I started a page for media contacts for the pro-science activists. This includes links to advice on effective writing for letters to the editor and to already existing media contact link pages. There’s nothing wrong with Dembski’s sense of political cunning.

Another item that I’ve worked on this week is the “Tallying the Arguments” project. This is a collaborative effort to exhaustively catalogue the arguments in antievolution sources. I’ve done the basic programming for a data entry front end and set up a discussion thread for coordination of the project.

I also worked on revisions to a paper on measurement of intranarial pressure in bottlenose dolphins to get it through the clearance process at the US Navy Marine Mammal Program. A chunk of that was just fairly tedious formatting changes. But the thing is done, for this round, and headed back to move along to the next step. Next up will be the paper reporting on bioenergetics of intranarial pressure.

The Response to “Ten Questions to Ask Your Biology Teacher”

The media seems to be finding the antievolution movement’s propaganda without difficulty, but has more trouble locating the mainstream science responses.

A particular example occurred with a CBS news item that listed the Discovery Institute’s “Ten Questions to Ask Your Biology Teacher”. There is a perfectly good response to this specific piece of propaganda at the National Center for Science Education website and there is Nick Matzke’s longer analysis of the arguments of Jonathan Wells. P.Z. Myers at Pharyngula has suggested that all pro-science bloggers prominently link to these resources to make it more visible to media representatives, and I agree. Please pass it on.

For those who claim that “teaching the controversy” is a good thing and are fond of quoting Darwin on how to obtain a “fair result”, I’d say that making sure these resources get linked whenever the DI agitprop is linked would go some way to removing the otherwise strong impression of simple hypocrisy in this matter.