31 January 2008

Prodigal machine

My office computer came back into my office after six weeks of repairs. Hooray.

30 January 2008

Texas Higher Education and Creation Research, Part 17

I was listening to the Scientific American podcast on my way into uni this morning. Host Steve Mirsky has a regular feature called "Totally Bogus!", in which the reader is challenged to find the one fake science story amoid three real ones.

This morning, one story was about whether it was true that Texas was considering an application for graduate degrees in creation science. Well, readers of this blog know that one is true!

I mention this because in describing the story, Mirsky noted that the Institute for Creation Research's websites includes tenants including that humans were created in their current form, the first humans were Adam and Eve, and that the earth was created in six days.

He then asks, "So since everything's already known, what would the theses be about?"

While it's a good quip, it misses a bit about the story. Mirsky seems to be under the impression that the ICR is asking for permission to do Master's degrees in staight science...which they are not. They are asking for permission to do science education degrees.

Graduate degrees in education typically do not involve original scientific research. They may involve research into teaching practices, if they are Master's degrees with a thesis. Many programs have non-thesis Master's, even in strict science degrees. So it's not appropriate to mock a program for what scientific questions students might ask, because science education are not typically asked to do those sorts of questions.

I appreciate Mirsky bringing the story up as one that could be -- and one wishes was -- totally bogus, it creates the wrong impression about what the institute is asking for. I think the ICR knows there's no way they would have a prayer of getting a degree in a science.

Could it truly be...?

Could my office computer truly be on its way back to my office, six weeks after it went away for repair?

Fingers crossed. Because heaven knows I like my PocketPC, but it's not in the same league as my desktop. And it's been awful running back and forth to my lab to use my lab computer.

Of course, I know I'm going to have to undo all the "improvements" that the Helpdesk will have made while fixing it.

But it will be a happy day if and when the machine rolls back into my office.

29 January 2008


This morning, I selected all the music on my iPod and hit "Delete." Sometimes, it's good to rebuild differently.

If only all ruts were so easily solved.

Was Columbus to blame?

ResearchBlogging.orgHarper, K., Ocampo, P., Steiner, B., George, R., Silverman, M., Bolotin, S., Pillay, A., Saunders, N., & Armelagos, G. (2008). On the Origin of the Treponematoses: A Phylogenetic Approach PLoS Neglected Tropical Diseases, 2 (1) DOI: 10.1371/journal.pntd.0000148

I remember way back in junior high science class hearing that Columbus was to blame for introducing syphilis to Europe. At the time, I didn't appreciate whether that was well-supported or not, and just remembered it as one of those little factoids. So I was a little surprised that this has actually been very contentious, and that there was a new paper about that subject.

This new paper by Harper and colleagues on the origin of syphilis is more interesting to read about than it is to read itself. The paper is very focused on molecular biology paper, with lots of As, Ts, Cs, and Gs. It's not very approachable. I had the good fortune to listen to some interviews with one of the co-authors, Dr. Mike Silverman, and those are far more interesting and accessible.

The new paper takes a lot of DNA sequence data from bacteria in the genus Treponema. These cause several diseases other than syphilis, most notably a condition I had never heard of before called yaws. Yaws hadn't been reported in the Americas for a long time, but when it was recently rediscovered in Guyana, Silverman and his team initially thought they might be looking at syphilis. Except that the disease wasn't showing up on the genitals, like syphilis, but rather on knees, arms, and so on.

Silverman got a call while he was waiting for his plane just before he was to go to Guyana to ask if he could collect DNA samples of yaws. He did, but found only two cases, and because the request came so late, they couldn't preserve the tissue very well. That is undoubtedly the biggest strength and weakness of the paper. The American yaws samples are absolutely crucial to the story, but the quality of the samples are poor. Still, 50% of something is better than 100% of nothing.

Once they had those DNA samples, the authors use some evolutionary theory. The more recently diverged species are, the more alike their genes should be. With the aid of a computer, you can group the samples into clusters based on their similarity. This is usually shown in a tree-like diagram.

The Guyana samples aren't included in that tree, presumably because they were quite degraded compared to the others, and they couldn't quite get enough DNA sequence information to analyze.

The bottom line is that although the bacteria are very similar, yaws is more diverse than syphilis, and appears to be older. Syphilis is extremely similar worldwide, suggesting it is very recent. And the most genetically similar is the American yaws.

This pretty strongly supports an hypothesis that indeed, syphilis was yaws that was passed on by sex between natives and Columbus's crew.

The next step in this research would be to get better preserved samples of American yaws. But because of medical missions, it's quite possible that the disease has been eradicated in the Americas. Great for health, but a shame for research.

27 January 2008

Texas Higher Education and Creation Research, Part 16

I missed this editorial in the Austin American-Statesman last week. I feel a little weird picking on a couple of points in an editorial that I agree with so much:
The other is the recent request by the Institute for Creation Research, a proponent of "intelligent design" to the Texas Higher Education Coordinating Board, for certification to grant graduate degrees in science education in Texas.
If there is one thing I respect about the Institute for Creation Research, they don't advocate intelligent design. Intelligent design does not specify who or what hypothetical "designer" might be -- only that a designer is somehow involved in the living systems we see.

ICR, to its credit, does not play this game. ICR is not coy about what they are: they are fundamentalist Christians who believe the Bible is literally true. They advocate creationism, not intelligent design. They don't pussyfoot around that there might be a "designer," they say flat out, "Life is creation of God."

Back to the editorial:
"Intelligent design" is a belief and is not subject to testing or validation; thus, it has no place in our educational system.
I have to disagree here again. I think intelligent design could be totally valid to talk about intelligent design in a class on religion or perhaps politics or in several other areas. (That said, I don't know if K-12 public schools can teach classes on religion.) Little statements like this can really make it seem like like scientific organizations really are trying to keep all religious ideas out of all arenas.

There's also a more recent piece in the Houston Chronicle that talks about prospects for a "meeting of minds" on evolution.
With clergy members and scientists banding together to proclaim that their fields have much to teach us about the world, with both demonstrating they can work collaboratively, there's now hope we can put the divisiveness that's been the hallmark of this struggle behind us.
I cannot be optimistic here.

Conflict is the essence of drama. So there is always a good story about those who disagree with majority views. This is partly how small minorities can very easily get a disproportionate amount of attention: they make for good copy.

Intelligent design is an excellent example. It was promoted incredibly successfully by a few individuals. (Pure creationism, as I noted above, is a different beast, not the least of which is that it is undoubtedly supported by a much bigger group of people.) I've seen a lot of "God versus Darwin" headlines, and with good reason. Conflict is interesting.

Destructive denials

Imagine you introduced yourself as John Smith. And someone overhears you and says, "No you're not."

"But here's my friend who can vouch for me."

"He only knows who you say you are."

"Here's my driver's license."


"Here's my mother who gave birth to me!"

"Babies have been switched in hospitals."

How long would you go on trying to convince this person that you are who you say you are?

Fast successions of quick denials are a surprisingly effective way of attacking a proposition. This is particularly true if the proposition is even slightly complex.

26 January 2008

And they call economics the dismal science...

ResearchBlogging.orgMILLER, G., TYBUR, J., & JORDAN, B. (2007). Ovulatory cycle effects on tip earnings by lap dancers: economic evidence for human estrus?☆☆ Evolution and Human Behavior, 28 (6), 375-381 DOI: 10.1016/j.evolhumbehav.2007.06.002

Sometimes, science reporters find a really interesting paper that you wouldn't have known about and you think, "Okay, I have to read that." This was one. The issue of human estrus is interesting to start with, and when you throw lap dancers into the title, well, that's paper that warrants a trip to the library. I took a risk and suggested it for our journal club.

So did the paper get attention for the obvious prurient reasons, or is it good science? Some of the other participants in journal club were very down on it, and didn't think there was much to be concluded from it.

Humans are definitely unusual in that it is not obvious when females are ovulating, In many mammals, including many primates, it's blazingly obvious when a female is fertile, and this is the only time females are receptive to mating. I've heard sort of "science legends" that humans and dolphins are about the only mammals that don't have obvious estrus cycles. To my surprise, it seems to be true that dolphins don't show pronounced behavioural changes with fertility. I don't know whether there are other mammals that show very reduced estrus or not.

Since the whole idea of estrus is to indicate readiness for mating, it follows that if human females show some subtle signs of when they are fertile, males should consider fertile female more attractive. Problem is, it's really hard to get people to talk about what turns them on to a complete stranger -- like a researcher.

The idea here is simple: people vote with their dollars.

The authors of this paper contacted exotic dancers indirectly and set up a website where the study participants could enter in their data. And here's one of the worries about this paper: they had a small sample size, with only 18 participants.

The subjects were asked basic demographic information, but the key pieces of information were how much money did they make dancing each night, where were they in their menstrual cycle, and were they on the pill?

And here's the second worry. The subjects didn't log in as often as they were asked to (i.e., daily). Over 70% of the data were missing. That's a lot of missing data.

Nevertheless, the researchers found big swings in earnings over the course of the month, but not for dancers who were on the pill (which suppresses ovulation). Dancers who were not on the pill earned over 80% more during their estimated fertile period.

The effect is large, so I'm inclined to believe that the effect is real. In fact, it's almost puzzling that the dancers hadn't learned that they can make more money being off the pill (say).

The interpretation of what's causing that effect is more more difficult, however. In particular, is there any cue above and beyond some behavioural differences? Some manner of pheremone? Can those behavioural differences be identified? (I can just imagine being the ethics reviewer on that proposal...)

The third worry is that self-report data is always tricky, particularly when the key question is, "When were subjects ovulating?" This is not easy for anyone to determine, as the low success rate of using the rhythm method of contraception testifies. Testing this rigourously would require regular blood samples to test for hormone levels.

Assuming the effect is real, one way to test whether is is specifically related to estrus would be to look at tipping in a non-sexual context. For example, waitress's tips. In some ways, probably easier in that you'd probably be more likely to be able to find more waitresses who were willing to participate. In some ways, it might be harder, because the tips would probably be lower and it would be harder to see any effect. But if waitress's tips varied over the course of the month, it would suggest that whatever is going on may be more related to general feelings well-being than estrus as such.

Regardless of its limitations, this paper should be a leading candidate for an Ig Nobel prize for Economics this year.

25 January 2008

Texas science standards, Part 3

Several papers are reporting today about the recommendation of university "readiness standards" for K-12 students, including the Austin American-Statesman, which focuses on how few students can actually do some of the requested tasks, the Houston Chronicle, and the Dallas Morning News. The Morning News article actually links to the actual standards, which is helpful.

What's it say about evolution? Here's a quick sample: "Know multiple categories of evidence for evolutionary change and how this evidence is used to infer evolutionary relationships among organisms." No waffling language, no "strengths and weaknesses."

24 January 2008

Texas Higher Education and Creation Research, Part 15

The Dallas News reports that the Texas Higher Education Coordinating Board has been getting an earful about the ICR's proposal to grant Master's in science education.
The coordinating board provided 286 pages of e-mails in response to an open-records request from The Dallas Morning News. Many of the notes are from Texas. But others come from all corners of the U.S. and the world – from Florida to the Philippines, Nevada to Nigeria. ...

Just as many people, if not more, wrote to defend the institute's proposal.
Support at this level is not too surprising. Fundamentalist Christians are often very good at mobilizing their fellows.

I'll comment on one question from an email:
Robert Bashaw, a doctor who sits on the Stephenville school board, wrote: "I think that presenting all sides to theories of origin and other matters is healthy. What better way to encourage critical thinking and evidence-based evaluation of controversial topics?"
This would undoubtedly work if you have an honest broker who is willing to evaluate evidence in a way that is fair and free of bias. The ICR has made it abundantly clear that they will not accept anything that contradicts the literal truth of the Bible.

Incidentally, you won't find me in those emails, several samples of which are online.

I wrote a letter.

Additional: The Austin American-Statesman has a similar story.

Texas Education Agency and Chris Comer, Part 28

Washington Independent logoThe Washington Independent has an article that focuses on Arkansas and its former governor and current American presidential candidate Mike Huckabee. It refers a bit to Chris Comer's situation in Texas:
Chris Comer, who held the same position in the Texas schools, was not so lucky. The Texas Department of Education forced out Comer in November after she forwarded an email to colleagues about an upcoming speech by a pro-evolution philosopher. Her boss, Lizette Reynolds, whom George W. Bush had hired while governor of Texas, called her on the carpet and removed her. “I’ll never get hired in Texas education again,” she said. ...

The removal of Comer was deeply preoccupying to Fulton and other biology teachers, both because was a manifestly unjust, stupid act (Emphasis added. -ZF), and because Texas science textbooks are used by Arkansas and other states. “All Chris did was forward an email, which is exactly what my boss wouldn’t have wanted me to do and exactly what I would have done,” Fulton said. “It could have been me.”
The most disturbing part of the article for me was that it claims fully 10% of teachers teach pure creationism. Now, the article doesn't say whether those are public school teachers, because that would be illegal. I suppose it's possible those 10% belong to private schools.

23 January 2008

Proud of evolution

In an earlier post, I talked about other people's responses to a question about "Why are you passionate about teaching evolution?"

I went up to the guy who asked the question a little later, and thanked him for a great question. I talked to him a bit and I told him part of my answer.

I'm passionate about evolution because I have professional pride.

I'm proud of the few tiny little dents I've made in ignorance.

Evolution informs my research. It informs the questions I ask, how I ask them, and how to interpret them. And it's been a pretty successful guide to me to find interesting questions to asked.

So yeah, when I see evolution getting dismissed out of hand, flippantly, with claims that have been known to be wrong for decades, of course I feel injured pride. It's not even so much that evolution is being attacked -- it's the dismissive attitude that makes me crazy. Because you can't have a thoughtful conversation if all the amassed evidence is dismissed in one sentence that takes a long time to explain why it's wrong.

22 January 2008

Repairs and lack thereof

I'd like to point out that my office computer, which went down about 40 days ago, still isn't repaired. It's the second week of classes. Maybe it should just be given up as dead...

Passion for evolution

Near the end of a teaching evolution roundtable discussion at the recent SICB San Antonio meeting, someone asked the gathered speakers, "Why are you passionate about this?"

The response was immediate and united. But I think Randy (A Flock of Dodos) Olson was the first to respond, "Truth."

But Barbara (Creationism's Trojan Horse) Forrest wasn't far behind. She said that the first principle of philosophy was the ability to distinguish between true and false statements.

After that, because there were a slew of academics in the room, the conversation broke down a bit into the difference between well supported by evidence (scientific truth) versus eternal verities that always have been and always will be (what most people think of when they think about truth).

Which sort of supports Randy Olson's point that scientists don't do a great job of making simple points. They are highly trained to make qualified statements and deal in subtleties and nuance.

But maybe sometimes we should just say, "It's the truth."

(I'll give my own answer to the question in a later post.)

21 January 2008

Texas Higher Education and Creation Research, Part 14

The Beaumont Enterprise has an article looking at the Institute for Creation Research application to grant Master's in science education. Henry Morris III is quoted:
"We are forensically interpreting the data based on our presupposition," Morris said. "The evolutionists do the same thing. They have a presupposition that there is no supernatural intervention of any kind. We have a presupposition that there is supernatural intervention in the past, not in the present."
Arguable. It's probably more accurate to say that science does not deny supernatural events could occur, but that they are not within the realm of science. Regardless of how one breaks down the philosophy of methodological naturalism, the bottom line is:

Miracles are not allowed in science. The instant you invoke miracles, you're not doing science, whether you're doing biology, chemistry, physics, or anything else.

The article gives some details about the way the degree is structured:
Students in the current master's degree program must complete 33 semester hours of work, according to the Institute's Web site. This coursework is a combination of 15 credit hours of education and research courses, three hours of advanced creationism studies, and 16 credit hours of sciences.
I hadn't noticed this before, because surfing the Institute's web site is a very depressing experience: it's never fun to experience open hostility.

In any case, 33 credit hours is about standard for a non-thesis degree; our non-thesis Master's is a 36 credit hour program. Although it sounds like the creation studies aspect is very small, one also has to be concerned about the accuracy of the 16 credit hours in science making up almost half the degree.

Finally, the article notes:
If approved by the coordinating board, this would be the first online master's degree in science education offered in Texas.
This little factor would be another reason to look at this program carefully.

20 January 2008

Texas Education Agency and Chris Comer, Part 27 and Texas science standards, Part 2

Chris ComerA lengthy post at The Atheist Experience blog describes a meeting in Austin concerning science standards, especially evolution.

I particularly wanted to note that Chris Comer spoke at this event. She provided an interesting -- okay, distressing -- inside view:
Comer did tell us that the "forces at play here are huge" and that the whole situation concerning science education in Texas is "far worse than I ever, ever dreamed it would be." As an indicator of just how thin the ice is on which we're all skating: there is an end-of-course biology test, currently optional, that will be required of all Texas students as of 2012. Last month there was an attempt to remove all references to evolution from this test, and it almost worked.
The whole post is worth looking at, although as an atheist blog, it contains some opinions that are not charitable to the religious, fundamentalist or not. But the information seems credible.

19 January 2008

Texas science standards, Part 1

The old saying goes, "Never assume malice when stupidity will suffice." I fall back on that a lot, because it prevents me from spiraling into the world of conspiracy theories and paranoia. But sometimes the degree of ignorance is depressing.

Today's Fort Worth Star-Telegram has an article about the upcoming review of the Texas K-12 science standards. I've been looking at this a lot, because of all the blogging I've been doing about Chris Comer's forced resignation.
Board member Gail Lowe of Lampasas said she doesn't believe in interjecting religion into a science class. However, she agrees that there are weaknesses to evolution that should be pointed out in the textbooks.

"They present evolution in the same terms as gravity," she said. "We can be honest that there are some weaknesses and that Darwinian evolution is still controversial in the science community." (Emphasis added.)
Reading something like that makes me want to scream. It is so profoundly wrong. It is so untrue. But I wish I could see malice, because the level of not understanding is so deep.

Within the science community, there isn't controversy about evolution by natural selection. And it frankly angers me that such people make statements like that, but never, ever back them up with examples.

In some ways, from a scientific standpoint, gravity is arguably more controversial than evolution, because gravity doesn't work well with quantum physics. So physicists imagine a hypothetical partical called a graviton that nobody has any evidence for whatsoever, except that if true, it would explain certain other kinds of data. But it's by no means the only possible explanation.

So gravity gets a free pass as non-controversial (even when there are genuine questions about the science of the thing) because we deal with gravity on a regular basis in real time. Evolution -- which is scientifically just as well-founded as gravity -- gets attacked because it occurs over long time scales that are difficult for humans to get an intuitive sense of.

17 January 2008

The point of doubt

Back in this post, I wrote:
While McLeroy wants to been seen as a friend to critical thinking, I think what he's really trying to sell is doubt.
Something about how I phrased that bugged me, and I thought it warranted more explanation.

Doubt is absolutely necessary to critical thinking. My comment wasn't an attempt to undermine its importance. You can't accept everything unreservedly. You have to look at evidence carefully, and you need to be willing to doubt conclusions, interpretations, how data were collected, and do on.

But the point of doubt, and of critical thinking generally, is not to live in a continual state of doubt: it's to arrive at a conclusion.

A lot of people who toss around the idea of "critical thinking" are purely in the business of getting people to hold off on making conclusions. Just keep pushing doubt, awaiting more evidence, and the status quo can continue even when strong evidence suggests change is warranted.

Texas Education Agency and Chris Comer, Part 26

I'm not sure if this should be a new thread, as it only tangentially concerns Chris Comer, but it does follow directly from concerns about the Texas Board of Education, led by Don McLeroy. The Dallas News reports that the Board rejected a school math textbook:
Conservative individuals and groups that say they favor traditional math instruction have voiced several concerns about Everyday Mathematics.

In general, they say it relies too much on calculators and peer activities rather than focusing on more traditional approaches such as having students memorize multiplication tables for automatic recall.
Interestingly, there is some data about the book's performance:
In Dallas, officials rolled out Everyday Mathematics books in kindergarten through sixth grade at 19 schools with low math scores during the 2000-01 school year. By the end of the year, only two of those schools still had low scores; a year later, none of them did, said Camille Malone, DISD's director of mathematics.
If there's this sort of quarrel over math, which is about as cut and dry as it gets, imagine what's going to be happening over science textbooks.

16 January 2008

Popcorn personalities

PickerThere are two kinds of people in this world:

Shovelers and pickers.

Shovelers grab popcorn by the handful. No delicacy, no pretense. Use all five fingers and the palm.

Pickers take a small number of popped kernels in their fingertips at a time. No contact of the popcorn to the palm of the hand.

Similar patterns of behaviour can also be observed with certain candies. I wonder what personality traits correlate with each behaviour?

Are you a shoveler or a picker?

Texas Higher Education and Creation Research, Part 13

And just when I was worried about what I would blog about today...

The Austin American-Statesman, Dallas News, and Inside Higher Ed. are all reporting that the decision on whether to allow the Institute for Creation Research to grant Master's degrees in science education has been pushed back, and won't be this month. April appears more likely.

The Inside Higher Ed article has the most substance of the three. It quotes Raymund Paredes, with bureaucratic understatement, as saying of ICR:
“Their curriculum doesn’t line up very well with the curriculum available in conventional master of science programs here in Texas,” he said. “I wanted them to either revise the curriculum or explain why it departed from the norm.”
Also pleased to note that Paredes is asking not just about faculty degrees, but the research they claim to do:
Paredes said that the institute “claims that their faculty do actual research,” so he asked for “material that documented the research activities under way” and that show the research to be “based on solid scientific research.”
It seems Raymund Paredes may be trying to move the application towards creation studies rather than science education. In any case, I am pleased to see that the Coordinating Board seems to be taking concerns about this application seriously.

15 January 2008

The Zen of Presentations, Part 16: Tell a story

Everybody loves a good story. In a very real sense, it's how we make sense of our lives.

Presentations are little one act plays. Anyone giving a presentation should think about who to make it a better story. And that may be easier than you think.

I think there are three story elements can be meaningfully incorporated into almost any presentation.

Character. Who is this presentation about? In a lot of cases, it's about you, so you should try to give the audience a sense of who you are. Your foibles, motivations, background, and so on. A long while back, I read Joe (Babylon 5) Straczynski creator describing a story:
As someone (E.M. Forster - ZF) noted, "The king died, and the queen died" is not a plot or a story; "The king died, and the queen died of grief" IS a story, IS a plot; there is connective tissue.
We recognize "The queen died of grief" is a more effective story, because we get a sense of relationship and therefore character.

Conflict. It's the essence of drama. Chris Carter (The X-Files) was once as saying that all you need for drama are two people, in a room, with different opinions. Any time there are differing opinions, you have the start of a story.

Mystery. We love mysteries, as one of the marks of the best stories is to be asking, "What's going to happen next?" Create puzzles for your audience, and bring them along for the solution. This is where scientific talks can really excel, because the whole scientific process is aimed at uncovering a mystery. Unfortunately, scientific presentations rarely do excel at this, because people are often so poor at laying out why we should care. Here's where understanding character (who the puzzle matters to) and conflict (do people have different ideas about the puzzle solution?) can help bring forth a greater level of intrigue and desire for people to know what will happen next.

In that vein, below is a presentation from J.J. Abrams (creator of the TV series Alias, Lost, and producer of the upcoming film Cloverfield, which I am eagerly anticipating) talking about storytelling and mysteries. I give him minus ten points for veering around a bit from topic to topic, but plus several hundred for energy, humour, enthusiasm, passion, and insight.

14 January 2008

First days of semster are always like this

Three new classes, a bunch of graduate students who can't register who should be able to, and a grant proposal submission due. The proposal got in on time (just), the grad students I'm trying to help, and I'm just about ready to relocate myself home...

Why teaching luddites win

Today is the first day of class for the spring semester. These classes use a lot of different technologies to assess students other than paper and pencils. Every time I've told fellow university instructors about various kinds of technology I've introduced into my class, I get the same objection.

Students will cheat.

Online learning? "Students can look up the answers, or have someone else do their tests. Clickers? "Their friends can bring in the clickers and push buttons for them."

Fear always tries to quash innovation.

Of course, it doesn't help when our IT Department promises to upgrade teaching software on class computers before classes start on Monday morning and don't. Leaving it for me to do myself. Splud. I'm not surprised. Just disappointed.

12 January 2008

Peoples of the Earth, please attend carefully

What Doctor Who villain are you?
created with QuizFarm.com
You scored as The Master.

Sly, lonely, powerful, cunning, horrid.

The Master










The Editor


Black Guardian


Henry van Statten


Davros's 2nd Dalek






Lady Cassandra




I will add that I actually do, in fact, own a laser screwdriver.

11 January 2008

Texas Education Agency and Chris Comer, Part 25

From NCSE's Eugenie Scott:
Dear Friends,

You all know about Chris Comer, the director of science curriculum at the Texas Education Agency who was forced to resign after forwarding an announcement of a talk by “intelligent design” critic Barbara Forrest. The grounds for forcing her out were insubordination, because she “took a position on” the subject of evolution. Apparently, her superiors believe that the person responsible for science education in the state should somehow be “neutral” on the organizing principle of biology.

Chris is undergoing what we hope will be a temporary cash flow problem until she can find a new job. If you feel that you can help — even $5, $10, $20, or $50 would help— you can make a donation directly to Chris. You would not only be helping a good person who stood up for the integrity of science education, you would also be showing appreciation for her many years of working at the TEA to improve science education in Texas.

If you wish to contribute, you can send a donation of whatever amount to Chris’s PayPal account. Go to PayPal.com, click on the “send money” button, and put Chris’s e-mail address in the “To” box. Chris’s e-mail address is chris.comer@live.com. For those of you who would prefer to send a check, make it payable to Chris Comer and send it to Chris Comer, c/o NCSE, 420 40th Street, Suite 2, Oakland CA 94609, and we will forward it to her.

Thanks so much for reading this.


Ow. Ow. Ow. Ow.

I go away to San Antonio, have a good time at SICB, come back, and the building bit me. First thing Monday morning.


I didn't take my finger out of the door frame of my lab fast enough. And my lab door is surprisingly heavy.

Going to be a few months before that's gone.

The Zen of Presentations, Part 15: The Gore Method

I finally managed to watch An Inconvenient Truth a few weeks back, because I has heard so much about how effective a presentation it was, and I wanted to try to figure out what made it so effective.

The number one lesson and reason for its success, in my mind, is this:

Make what you're talking about concrete. Make it real and tangible.

Climate change has got to be one of the most abstract subjects imaginable. It covers thousands of years of data, highly complex computer simulations, and so on.

But Gore find something concrete to make the point: a devastating series of pictures showing snow and ice retreating in mountain range after mountain range. Suddenly, you're sitting thinking, "This is not something to worry about in the next two hundred years, it's been happening in front of my eyes."

And he shows the pictures right next to each other, not right after the other, so the images are within "eyespan," as Edward Tufte puts it, and can be immediately compared.

Whenever possible, show real physical objects, not just graphs. Our brains seem highly responsive to these. Just think of how many of our common expressions make abstract things understandable by referring to physical objects. To attempt to lead is to "step up to the plate." To set high ambitions is to "raise the bar." And so on.

Gore had lots of other advantages, too. Superb rehearsal, which showed in the perfect synchrony of his speech as years are ticking by in a timeline behind him. The biggest screens I've ever seen, allowing him to pull off the great visual point to get up on a cherry picker to indicate the predicted top of a exponential trend. And just excellent, low key, simple graphics. I think some those graphs could have been improved somewhat, but that is quibbling over details. An Inconvenient Truth is a fantastic presentation.

10 January 2008

Texas Higher Education and Creation Research, Part 12

Austin American-Statesman logoI've been gaining a lot of respect for the Austin American-Statesman for its continued and very good coverage of Texas education, starting with its uncovering of the Chris Comer story. Today, it has a new article on the Institute for Creation Research's application to grant Master's degrees in higher education, and an interesting postscript.

I can't help but snicker at this somewhat reserved statement:
Paredes has asked an informal panel of scientists and science educators to comment on the institute's curriculum, which is flavored with a Christian worldview.
Saying the institute is "flavored" with a Christian worldview is a little like biting into a mouthful of habanero peppers and saying it's "a little spicy."

But I'm also reminded of something Kevin Padian said at the SICB meeting in San Antonio. He really objects when students say they don't accept evolution "because I'm a Christian." He points out that many Christians have no problem with evolution, so if you're going to let religion be a sticking point, be honest enough to admit that you're rejecting evolution because you're a fundamentalist. Similarly, I think ICR should be tagged as a fundamentalist Christian institution, because the qualifier really is important in distinguishing their particular point of view. Their views are not supported by all -- probably not even most -- branches of Christianity.

For instance:
(T)he institute's bylaws, tenets and other records show that students and faculty members are required to believe that humans did not evolve from animals but were created in fully human form from the start, that God created all physical and living things in the universe in six days, and that anyone who rejects Jesus Christ will be consigned to "everlasting fire prepared for the devil and his angels."
Not exactly an institution that's big on the idea of academic freedom, really. I'm sure they allow people lots of freedom within that framework, but it's a very narrow framework indeed.

The associated postscript notes that Paredes is being extraordinarily careful over this situation, as ICR has shown a tendency to sue when things don't go their way.

09 January 2008

Great balls of fire!

What Doctor Who character are you?
created with QuizFarm.com
You scored as The Third Doctor.

A man of science, a gadget king, you can put up a good fight. You are just what the doctor ordered.

3rd Doctor


9th Doctor


4th Doctor


10th Doctor


8th Doctor


7th Doctor


1st Doctor


A Dalek


6th Doctor


2nd Doctor




5th Doctor


07 January 2008

The Zen of Presentations, Part 15: Take a bow

Soprano Melina Pyron, tenor Scott Ramsay, and conductor Karen Lynne DealIt’s kind of fun to search blogs for comments on things that you yourself went to. Since I’ve been writing about the SICB meeting, I looked for that and found this post, which had good presentation advice. So I thought I would elaborate on it.

I was reading a book on magic once, and the author said it was important when you finished an illusion to bow. Now, he immediately elaborated that he didn't literally mean “bend at the waist.” He meant that you should do something to indicate clearly that the trick was done. It was also important not to immediately start the next one, but to create a space for the audience to show their appreciation – to applaud.

Because people’s attention may drift, it’s also helpful to cue them that the talk is coming to a close. Say something like, “In conclusion...” or “To sum up...” or “The take home message is...”.

Several bad ways to end a presentation include:

  • Just not talking. Definitely the worst way to go, as people are really unsure of whether they should listen or clap.
  • Ending with a perfunctory, “That’s it,“ or “That’s all.” This is usually thrown in as a desperate sign to the audience after the above method (just not talking) fails.
  • Anything mentioning questions (as in the linked blog post), as people don’t know if they should stick up their hands or clap.

My typical way to end is to put up an acknowledgments slide, which I do not read, but leave it up during questions. Then, I say, “I thank these people for help with my science, and I thank you for your attention.”

By thanking the audience, you create a chance for them to say, “You”re welcome,” with their applause.

Workin' at SICB

SICB poster
Got a lot of comments about the T-shirt. Geek to the end!

Turning up the heat

Randy Olson and friendsAt the SICB meeting I had a chance to see Flock of Dodos and sit in on some discussions with filmmaker and former scientist Randy Olson. He revealed that he has another movie coming out, a comedic documentary about global warming called Sizzle.

The film isn't listed on IMDB's database yet, so just consider this your insider entertainment scoop for the day.

In it, Olson describes how he tried to subvert the normal science documentary process, which is to take cameras to campuses and film a bunch of scientists talking. Interviews start out that way, but then a "skeptical" cameraman starts throwing in questions about climate change. Olson said it was really interesting to watch the dynamic change at that point...

Olson also said that he thought that people who saw both films would find the similarities. The data and the issues are different, but the kinds of people who argue against the scientific consensus and the kinds of arguments they use are almost identical. Olson mentioned that the skeptics / deniers in both the intelligent design issue and the climate change issue are very fond of conspiracy theories, for instance.

I'm really looking forward to it.

Texas Education Agency and Chris Comer, Part 24

Lauri LeboLauri Lebo (pictured at left), the local reporter who covered the Kitzmiller v. Dover trial and author of the upcoming book Devil in Dover, has an article in the Washington Spectator that discusses Chris Comer's situation in some detail and has a few new comments from some of the people involved, such as Don McLeroy.
Leaving the constitutional legal matter of such a maneuver aside, what aspects of evolution does McLeroy consider controversial? He cites the principle of common descent, in particular the idea that humans and apes evolved from a common ancestor, as one debatable issue. Yet in the science community, there is no controversy over the idea that all living organisms are descended from a shared ancestor. The mapping of the genetic code in recent years has only confirmed anew scientific support for life's universal connection.

Still, McLeroy says he isn't interested in pushing creationism. "I resent the notion that I'm speaking in code," he said. But in Texas, just as in Dover and in other earlier battles in Kansas and Ohio, the scientific arguments of evolution's critics are intertwined with their religious views.
And the article ends with a description of what Comer has been facing since her forced resignation. I've added the emphasis, because I do think it needs to be emphasized that Chris Comer has been harmed.
As both sides wait to see how this will play out, Christine Comer is adjusting to caring for her disabled father and paying her bills on a pension that provides less than the salary she lost. "But I feel like this is my contribution," she said. "This is my time to draw my line in the sand for science."

She had watched what took place in Dover and remembers being outraged at the time. "But I guess I wasn't outraged enough," she said. Because she never did anything about it.

Now, teachers she knows in small towns across Texas have come to her to say they've been forced to teach creationism in science class for years. She asked them why they didn't do anything about it. "Come on," they told her. "What can I do? It's Texas."
I had the good fortune to talk to Eugenie Scott at the SICB meeting about the Comer and ICR stories, which I've been blogging so much about. I asked her why the ICR story has been so much quieter than the Comer story, and she said it was partly the writer's strike, and partly because Comer was a martyr, so to speak. I certainly have been avoiding that term, because it is emotional and easy to overuse. But during her presentation, Dr. Scott mentioned that Chris Comer is struggling financially right now. She indicated that anyone who was interested in finding out what they could do to help support Ms. Comer could email Eugenie Scott at the NCSE.

06 January 2008

SICB, Day 5

And for the final talks today: pot luck! I went to talks with no rhyme or reason. During each talk, I looked through the list to see which was the one coming up that looked the most interesting.

An easy and uneventful drive home. Now is the time to set wheels in motion for some of the plans hatched during the conference...

05 January 2008

SICB, Day 4

Today was definitely crustacean day for me. I pretty much saw decapod crustacean talks all day. It was kind of nice, because I don't get to interact with that crowd very much and met a lot of people whose names I had previously only known from reading their papers.

Then my Master's student Sandra and I both gave our posters. I generally had only one person at a time, but there was pretty much always someone in front of my poster talking to me, asking the right questions and agreeing with what I thought the data were showing me. Sandra was also busy at her poster.

Then -- socials! Crustacean social, then neurobiology social, then the general student appreciation social (Hi Candace! Hi Mike! Hi Turkesha!). The poor hotel staff was spending a long time trying to get the clueless scientists out of the social room. Turn lights up -- turn lights down. Turn them up -- turn them down.

One half of one day to go!

04 January 2008

SICB, day 3

Argh! Why does wi-fi work on Thursday but not Friday?

Lots of stuff going on today. Today was tough for me personally, because there were talks on evolution and neurobiology and crustaceans -- which is kind of my trifecta. I gave up on neurobiology, and just flitted back and forth between the other two.

Barbara Forest gave one of my favourite talks today -- wonderfully energetic, forceful, direct, concise. She dedicated her talk to Chris Comer, about which I have written much recently, as it was an announcement of Forest's talk that precipitated Comer's forced resignation. The dedication received some applause throughout the audience. Not a huge number, as I think not everyone was aware of the story. But more know now. Forest's talk was, "Still creationism after all these years," showing that intelligent design is creationism, end of story. A lot of other fine talks on teaching evolution, too, talking about the inadequacies of lecturing, and how creationist ideas can be talked about in a class in an effective way.

Another highlight was seeing an IMAX film called "Volcanoes of the Deep." I love movies, I like the IMAX format a lot, and this one has some brilliant undersea footage from deep sea hydrothermal vents. Carrying on with a theme, this film was not allowed to play in some cities because some people objected to some of the evolutionary content. And it had lots of crustaceans in it, which I also liked.

I was also pleased to talk to several people about Marmorkrebs, which generated uniformly high interest. That I also liked, and does help convince me I might have something useful for people. (That website again: http://marmorkrebs.org!)

Tomorrow: two posters to give!

SICB, day 2

High light of the day has been seeing a screening of Flock of Dodos, a film about intelligent design. I really enjoyed it and found it much funnier than most of the rest of the audience, judging by the amount of laughter. My laughter, that is.

The screening was followed by a discussion and Q&A with filmmaker / former biologist Randy Olson. He's given a lot of thought to how scientists communicate. His assessment: he'd rather play poker with the intelligent design crowd.

Sheila Patek's talk was a close second. Search the blog; I've linked to a TED talk of hers you should be able to find. I think this was the first time I'd seen film taken at 100,000 frames per second. Wow.

A thought experiment

Imagine you had a friend who was smart, funny, and charming. There was just one thing.

Every time you asked that friend where he was, he invariably said, "I am in my home in Moscow, Russia."

This friend has never been to Russia. No matter where he goes, the answer is always the same. He could be in the middle of the Arizona desert and insist he was at home in Moscow. When asked where his house was, he might say, "I have a really big backyard."

On every other matter under the sun, you would have a perfectly reasonable conversation. Just as long as you didn't ask him where he was. It's just on this one quirky issue that this person has an unshakable -- but obviously false -- belief.

(There are cases of people with particular brain damage who do, in fact, have these sorts of convictions. So this is not purely a hypothetical case.)

What would you say if that person ran for Mayor of your town? Would you recommend him?

03 January 2008

SICB, Day 2

Hooray to SICB for providing free wi-fi at their meeting!

Already have seen four cool talks- 2 on crayfish fighting, dinosaur singing, bird bill shape...

Fun stuff!

SICB Day 1

Will this day never end?!

This day has had a series of gaffes and mistakes and confusions. Student running behind, the big one- me forgetting my own posters!- and a veritable comedy of errors trying to get the rooms for the REU students straightened away.

Some days can only be improved by how fast you can hit unconsciousness.

02 January 2008

Rethinking granting, part 2

Research grants in the U.S. (and many other countries) are so competitive that many, many good ideas go unfunded. When funding success is at 10%, many researchers think applying for a grant is just rolling the dice. Obviously, there are certain things that can improve the likelihood of getting a grant, but there seems to be a large component of luck in the process now.

Why not just admit it and award some grants through a lottery system?

They do it for green cards in the United States.

Obviously, there would have to be some criteria to insure that grants do not go to poorly written proposals. Make them small -- micro grants, even. Make them just as accountable as large grants.

It could help ensure greater diversity of ideas (just like the green card lottery helps promote diversity). It would provide insurance that “old boys networks” and coalitions of researchers don't have complete control over the review process.

Texas Higher Education and Creation Research, Part 11

Texas Citizens for Science is reporting this morning that Raymund Paredes (pictured) has asked for a second site visit and report on the Institute for Creation Research. This would be consistent with several earlier hints of Paredes not being satisfied with the first report, which recommended approval to give Master's degrees in science ed.

01 January 2008

Who owns ideas?

I'm working at the lab today, mostly to write a grant proposal. Now, many people would think I could do that easily from the comfort of home. It's a holiday, there is nobody but nobody else in the building (as far as I can tell), so why not just work at home?

Turns out it's very difficult to do any serious scientific writing (a grant proposal or manuscript) at home, because I constantly need to look up references. When I write something serious, I'm always being forced to track down papers I haven't read before. Or I have to find papers where I've read the abstract, but not the main text.

And I can't get to most of those papers from home.

I can from my lab, because it's a university. And the university has paid various publishers for the right to have electronic access to many of the journals I need to refer to when I do serious scientific writing.

That's a direct consequence of copyright and intellectual property issues, and the business models of scientific publishers, most of which are run by for-profit companies.

This week's Science Show has a really wonderful, thought-provoking set of talks about intellectual property issues. Highly recommended.

Indeed, to harken back to the last post, one of the things I think I've changed my mind about is about intellectual property. I used to be much more supportive of copyright protection overall. Now, I see more and more benefits of a more relaxed attitude towards accessing information, thanks to programs like the one above, Creative Commons (particular Lawrence Lessig's advocacy), the push towards Open Access, and more.

(And in addition to all the stuff about copyright, there's a bonus revelation about just how much power internet computing is using up. I never considered how much juice Google HQ must suck back.)

Changing your mind

Given that much of what I've been writing about recently concerns people who have consistently failed to revise their hypotheses in light of contrary evidence (much of what I've been writing about ICR, for instance; a lot of posts on skepticism), I absolutely love this page:

What have you changed your mind about?

And, paradoxically, one of the first ones I come across is one that I like a lot, but I don't think is easily digestible to non-scientists, and indeed, runs counter to much of what I've been writing. Irene Pepperberg talks about the the importance of doing more than hypothesis testing.

As to her first point, my favourite version of that is from Niko Tinbergen, who, in one of his most famous papers, wrote:
Contempt for simple observation is a lethal trait in any science(.)
As for Pepperberg's third point: strong inference, baby.

I'm going to be reading this page a lot, methinks. Fantastic.

Texas Higher Education and Creation Research, Part 10

You're not fooling anyoneHenry Morris III, the ICR director, has a letter in the Dallas News this morning objecting to their recent editorial. Time for a fisking.
It came as a surprise to both faculty and administration when the editorial stated that the Institute for Creation Research "rejects so many fundamental principles of science."
That shouldn't be a surprise, since people have been pointing out that creationism isn't science for years now. There have been court cases about it. McLean v. Arkansas Board of Education in 1982 (summarized here -- # 3) was a prominent one. And ICR, then under Henry Morris's grandfather, Henry Morris, Sr., featured rather prominently in that case (search the linked text for ICR).

Odd that Henry Morris III wouldn't know about that court case.

Funny that it would come as a surprise to Mr. Morris that people don't think his institute is doing science.
ICR would like to know which "principles of science" are supposedly rejected by our school.
Methodological naturalism and willingness to revise hypotheses in light of contrary evidence.
Surely not Newton's gravitational theory.
Not a principle of science. That's a particular body of information generated by the principles of science, but it is not the principle itself.
Nor Mendel's laws of heredity.
Not a principle of science.
Nor do we deny natural selection, suggested by Edward Blyth 24 years before Charles Darwin's writings.
Yes, natural selection was recognized before Charles Darwin. Nevertheless, Darwin's contribution was huge. Darwin was the first to recognize natural selection as a creative force with the ability to create new forms of life. Stephen Jay Gould writes about this quite a bit in The Structure of Evolutionary Theory.
All were creationists.
Irrelevant. They probably all had two legs, too. Nobody disputes that many scientists have been and are Christians. This is about evidence, not authority.

Also, it's a total shell game to say, "Newton and Mendel were creationists" because there really were any strong competing theories at the time! If you were able to go back, bring Newton or Mendel or any of those people to the present day, show them the evidence that we have now... would they still hold to the doctrine that the earth is a few thousand years old and that species were specially created? There's no way to say. Mendel, for example, was an Augustinian monk -- a Roman Catholic. And the Catholic Church has no problem with evolution. Indeed, one of my colleagues learned evolution from a nun.

If Mendel were alive today, he would probably not be a creationist.
What ICR scientists openly question is Darwin's "descent with modification" or macroevolution. Even renowned evolutionary biologist L. Harrison Matthews wrote that "evolution is the backbone of biology, and biology is thus in the peculiar position of being a science founded on an unproved theory."
Oooh, a quote mine! No context, no date, no source. Let's see if I can find this in Talk Origins... and yes, here it is. It's from 1971 or 1972. And we've learned a few things since then.
Despite what The News implies, ICR is a science-oriented institution, employing experts since 1970 whose credentials meet or exceed the qualifications of numerous secular universities and who conduct research across various disciplines. Many researchers bring extensive experience from such recognized facilities as Los Alamos, Sandia Labs, Cornell, UCLA and Texas A&M.
Do they make predictions, conduct experiments, analyze data, and publish results in peer-reviewed journals? They probably have in the past, but what's their output recently?
The graduate programs of ICR, while similar in factual content to those of other graduate colleges, are distinctive in one major respect: ICR bases its educational philosophy on the foundational truth of a personal Creator-God, as opposed to the naturalistic, atheistic presuppositions of evolution.
And here comes the wedge: A real Christian can't support evolution. Only atheists support evolution. Choose!

What a tremendous disservice -- actually, an insult -- to the many, many Christians and other believers who see no incompatibility between their faith and scientific evidence.

And it also shows the the ICR does not abide by one of the working assumptions of scientific inquiry: no miracles allowed.
Perhaps before suggesting that men and women of faith have no place in teaching science, The News should verify the credentials and scientific contributions of those it impugns who are both committed Christians and recognized, productive scientists.
Interesting how the letter ends without mentioning how many peer-reviewed papers come out of the ICR. How many externally funded grants ICR personnel currently hold. I'm willing to guess that the number is low.

Not surprising to see familiar and not very substantive arguments here.