Prodigal machine

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

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.

Ruts

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?

Harper, 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.

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."

"Photoshop."

"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.

And they call economics the dismal science...

MILLER, 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.

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."

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

The 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.

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.

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.)

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.

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

A 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.

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.

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.

Popcorn personalities

There 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?