Thursday, August 11, 2011

Does it quack like a duck?

A recent analysis of the classic intermediate fossil Archeopteryx in light of new fossils has reclassified it from a basal bird to a group of dinosaurs that are close cousins to the basal birds. It is a minor move that we see all the time in paleontology. It is unlikely any of our intermediate fossils are direct ancestors of modern species because the fossil record is so incomplete. That doesn't mean they are not intermediate. The features are intermediate, and the species is a close cousin of the actual intermediate. All that has happened with Archeopteryx is that it has been moved from a first cousin to a second cousin. It still has intermediate features. This is a new analysis and it might change, but for this post, I will assume it is correct.

Any change in the status of such an iconic specimen will produce the inevitable crowing from creationists, and plenty of others have analyzed the basic misunderstanding of the creationists (which I summarized very briefly above). But I have not seen anyone else comment on one other irony of the creationists reaction to this, so I thought I would point it out. For decades, creationists have insisted Archeopteryx is not an intermediate fossil. The most common way to do this is to say this it is obviously a bird. It had feathers and could fly. Creationists like to force intermediate fossils into one category or another, rather than being intermediate between the two categories. Historically, they have almost always forced Archeopteryx into the bird category. I have never once read a creationists say that it is a dinosaur.

So how does this new analysis affect their interpretation? The new analysis says that Archeopteryx was a dinosaur, more closely related to Deinonychus than to birds. It shows that every creationist was wrong--if it must be forced into one category or another, it is into dinosaurs, not birds. But the creationists are crowing thatevolutionists were wrong, and say not a word that they have all been wrong as well. The change for evolution is minor--a change from first to second cousins, but still intermediate. But it seems to me the mistake for the creationists is great. If you insist all species clearly fit into one category or another and there can be nothing in between, then it is hard to explain how a creature that is now clearly a dinosaur could once have been universally considered clearly a bird. It is a minor change for evolution, it is a complete blow to creationists.

It is funny that they do not see this inconsistency in their own view, but not surprising. Their mode of argument is entirely negative. Any percieved mistake by evolution is considered evidence for creation, even if the mistake is even more harmful for creation. Thus they nitpick over whether peppered moths evolved, even though powerful microevolution is an absolutely essential part of the creationists model. And they declare victory in the fluidity of taxonomic classification, even though a rigid classification is essential to the creationists model.

Thursday, June 9, 2011

Recently the Intelligent Design community has become more obsessed with so-called junk DNA. Jonathan Wells has just published a book on it (The Myth of Junk DNA), and it comes up more and more in their discussions. Plenty of others have and will dissect all of the ways in which they misrepresent the science. Larry Moran does a good job at Sandwalk (search for Junk DNA). I am interested in how this emphasis is a surprising change from the usual creationists tactic. At first it seems like they are actually trying to be a science.

First I should say a little bit about the misrepresentations going on. "Junk DNA" never really was a recognized term. It includes a wide variety of DNA. Creationists try to make it refer to everything except protein coding DNA. There has never been a time that biologists thought all non-coding DNA is junk. We have always known about regulatory DNA and rRNA and tRNA, for example. Much of our DNA is selfish DNA, such as the various transposable elements. Some might consider this junk, some might not.

The most important thing to understand is that evolution does not predict the existence of junk DNA. It can explain it, but it does not require it. In fact, the existence of so much junk was a surprise at first, because many biologists had a strong adaptationist bias and assumed most structures (including DNA) have an adaptive function. One of the usual meanings of junk DNA is functionless DNA. Evolution can account for non-adaptive features and the existence of such DNA feeds into the question of how important selection is compared to other processes, such as genetic drift (selection will produce functional features, drift can produce functionless).

So the existence of junk DNA is not really an argument for evolution, since evolution neither predicts it nor denies it. It can explain it, which is necessary for any theory. Junk DNA may be an argument against design, as we will see below, but it is not a positive argument for evolution. The great strength of the junk DNA for evolution is not so much its existence, but the patterns that it forms. The presence of the exact same pseudogene inactivated with the same mutations in the same position is several organisms is strong evidence for common ancestry.

So now we get to the surprising part: the embrace of junk DNA denial by the ID movement. It appears that they have genuinely embraced a prediction. They are saying that ID predicts there will be no junk DNA. They admit its existence is a genuine problem for ID. If that is the case, then they are admitting the existence of junk DNA is a way to falsify ID.

Why would ID predict there would be no junk DNA? If you assume a logical, optimal designer, like a human engineer, who would not make wasteful or useless features, then junk DNA is a problem. Junk DNA is clearly not good engineering. So if ID predicts no junk DNA, it based on a particular version of the designer. This is a breakthrough. ID is very careful not to say anything specific about the designer, but they now seem to have done so. I wonder if they will stick with it.

Junk DNA is just one version of a common argument against creationism. There are various arguments that show evidence of poor design in nature. For example, the vertebrate eye is poorly designed in many ways--light has to pass through nerves and blood vessels to get to the photoreceptors and it has a blind spot. It is not good engineering. The panda's thumb is another classic example of an oddly designed object. Vestigial organs are similar, and analogous to junk DNA (some of it is "vestigial DNA").

How have ID proponents responded to these arguments? Sometimes they argue that the features are well-designed, but they eventually almost always fall back on the mysterious designer argument. Who are we to tell the designer how to design? God may have had some mysterious purpose. He may even have been whimsical. We cannot expect the designer to be like a human designer or engineer. If God wanted to give the panda a thumb made out of a wrist bone he could have, and just because it seems odd to us means nothing. We can't dictate how the designer designs.

When they make that argument, they move out of science and into the land of the unflasifiable. Although well designed things are evidence for a designer, poorly designed things are not evidence against the designer. The designer can make whatever he wants. The designer can be an optimizer or engineer, or he can be whimsical and mysterious. Therefore, no observation is inconsistent with design. ID actually can be a theory that makes predictions, but only if they dare to pin the designer down, and clearly say what kinds of things a designer would and would not do.

Generally, ID has not been willing to do that. All of the many examples of poor design mean nothing. For some reason, they don't do that with junk DNA. They seem to actually be saying that the designer would not make junk DNA. The designer is an optimizer, an engineer. They have pinned him down and made a prediction. If we take them at their word, ID is now testable. If much of our DNA has no function, then we have disproven ID.

It would be great if they stuck to this. The history of the movement isn't too promising. I suspect one of two possible outcomes. Either they will forever deny the evidence for junk DNA, as Wells is doing now, or they will eventually go back to the mysterious designer argument. They are good at denying clear evidence. They have denied the clear evidence of the fossil record for decades. The first tactic should work for quite awhile, but eventually they may switch to the second choice and invoke the mysterious purposes of the designer. I guess there is a third choice--treat it as a genuine prediction and reject ID when the prediction fails. I'm not holding my breath.

It seems to me that accepting the threat of junk DNA also opens ID up to the classic argument from bad design. They have nailed down their designer. He is an optimizer. Now the structure of the eye, the panda's thumb, or the recurrent laryngeal nerve are all arguments against ID. If God wouldn't make junk DNA, he wouldn't make any of them either. If an ID proponent makes an argument about junk DNA, the first thing you should do is to confirm that they are admitting the designer would not make such non-adaptive, non-optimal features.

Wednesday, June 8, 2011

A Bite of Chalk

Since I've mentioned urban legends at least in passing in the last two posts, I thought I would write one more about my personal experience with apparently creating a mild urban legend. Perhaps urban legend isn't the proper term, since it is only a story amongst a handful of students, but I still find it interesting how my own actions became distorted to make a better story.

I occasionally eat chalk in the classroom. OK, I don't actually eat chalk. But I palm a candy lick-it-stick that looks like chalk. I write on the chalk board with chalk, and then secretly switch the chalk and the candy. I pause, look at the "chalk", take a bite, and then go back to writing on the chalkboard with the chalk that I switch back into my hand. There is no reason to do this other than entertainment. I do it early in the semester to try to introduce some humor into the class and lighten the load. I also enjoy the response of the students. Many aren't sure what they saw. They rarely say anything, rather they just look somewhat dumbfounded. I eventually reveal the trick and there is much relieved laughter.

I've been doing this for around ten years now. Recently some students were talking about it, and they mentioned that they heard one time I messed up and actually ate the real chalk instead of the candy. Apparently this story is circulating. It makes for a good story--the professor's trick backfiring on himself. The picture of the professor spitting out chalk when he was trying to be clever is quite funny. It is also entirely false. I have never made that mistake. But apparently it is now part of the lore about the chalk-eating stunt.

I wonder how such distortions arise. Does someone knowingly make up a lie? Or does someone say "what if one time..." and then later the "what if" gets lost? Does it somehow become a bigger story by the small incremental embellishments that we all make when telling a story? Once the change is made and believed to be true, I can readily see why it would spread--it is a good story. However it arose, it is a good example of how easily a story changes. We need to remember that the next time you hear about a UFO or a ghost or a dramatic coincidence or any of the many other extraordinary stories we hear. If there are two versions of a story, one true and commonplace and one false and entertaining, the entertaining one is the one that will be repeated.

Monday, June 6, 2011

Random Collisions with Knowledge

In my previous post, I told the story of picking up a book on urban legends and quickly devouring it. That made me reflect on how frequently I have picked up an odd book lying around and how that habit has given me a breadth of knowledge. I doubt it would happen today.

One constant resource for me as a kid was the World Book Encyclopedia. We had a set on our shelves, and I was constantly running to it to look up some information. But the important thing is that I never went straight to the article I was interested in. If I was interested in something beginning with S, I would pull out the S volume and open it to a random page. I would then need to move forward or backward in the book depending on where my word was alphabetically. But first, I would look at the page and usually find something interesting and read up on it. I would then move closer to my article, but stop again, and read something again. It would typically take me at least 30 minutes before I actually got to the topic I was originally looking for, and on the way I would learn about a dozen unrelated topics. I think paging through those volumes was more critical for my education than anything I ever got in school. I learned lots of useless trivia that I still know to this day, but I also got a background in almost every field of knowledge, so that I could make sense of any more information that came my way. If I have one major intellectual strength, it is breadth of knowledge. I may not be an expert on much, but I know something about almost everything.

I was at the younger end of a large family of readers. That means there were always books lying around, from casual reading to college textbooks. I don't know how many times I would find some book, pick it up, and start reading. For almost all of the books I can remember, I have no idea whose they were. They were just sitting around and I read them. Chariots of the Gods by Van Danniken was one such book. I was fascinated and started to believe we were visited by ancient astronauts and became fascinated with the Mayans. There were other books on ESP and other kinds of pseudoscience, which I generally read uncritically. I don't know exactly when I started to become critical of these, but I eventually did. I remember looking for things on Mayans at a later age and finding none of it seemed as cool or mysterious as I remembered. Of course, that is because I was finding facts, not fantasies.

I also picked up higher quality material. One that I remember best was a college textbook that dealt with logical fallacies. I devoured that and was fascinated with it. I would start to look for logical fallacies in my life. By the time I was in high school, I already had a decent understanding of how our logic can go wrong. I was disappointed when I went to college and logical fallacies were not covered in any class I had. I assume there is some philosophy class that I could have taken that would have covered it. A day spent reading that section of a book was one of the most important readings I had in my life. I still think logical fallacies should be part of the general education requirements of every student.

One day I saw The Stranger, by Albert Camus lying around, and I picked it up and read it in one sitting. I had no idea who Camus was and was only vaguely familiar with existentialism. I appreciated the book and had that background when I was exposed to some of these ideas later.

I could go on with many examples of random books in a other areas--history, literature, psychology (actually very little natural science--I got that at the library). That was my education. Formal education only became helpful when I reached college. I learned little of use before that. I guess I learned a lot about the constitution while in high school, but that is because I actually read the constitution in the appendix of the history book when I was supposed to be doing something else. We never actually covered or read the constitution in class. It was fascinating, I don't know why it isn't read by everyone.

That doesn't happen as much now. Of course, I no longer have random books from other people lying around. The books are my books now. I get books I like and enjoy, but they are books I chose, not random collisions with knowledge. When I look things up now, I go directly to what I want. I do love the internet. There is more information at your fingertips than ever before, and I like that if I want to know what other movies I saw that actor in, I can find out in 30 seconds. But in the past, it might have taken me 30 minutes and I would find out 20 other interesting things on the way. There is something lost there. It is reflected in how the internet allows us to only find what we already agree with or already know and associate with people who think like us. It has its advantages, but it also cuts into that breadth and wider associations. I am glad I read both Van Danniken and Camus.

A fascination with errors

It is standard practice for skeptics to emphasize that they are not debunkers or naysayers, and I generally agree. The point isn't to show someone is wrong, but to determine the truth, which is a positive thing. We focus on the many ways in which truth is lost or science is misused. However, I wonder if many of us in fact do have an inner fascination with things being wrong, regardless of our protests. My recent pile of summer reading books make me think that about myself.

Every summer I go through my reading list and order a stack of books to dig into for the summer. I usually try to get a variety of topics, and this time I avoided biology. I got books on psychology and law and politics instead, but most of them are still of a skeptical nature. The two books I started reading first are the two that made me reflect on whether I just like to find mistakes. They are But They Didn't Read Me My Rights!: Myths, Oddities, and Lies About Our Legal System by Michael Cicchini and , and 50 Great Myths of Popular Psychology: Shattering Widespread Misconceptions about Human Behavior by Scott O. Lilienfeld....

As I've studied why people believe wrong things, one thing that often comes up is that most people hold on to cherished beliefs. They do not like to be told that they are wrong. They are slow to change their minds or reject previously held beliefs. Debunking a myth is as likely to reinforce belief in it as to correct it. I seem to be the opposite, and I wonder if a lot of other skeptics are too. I love to find out I was wrong. I get a thrill when I find out something I always thought was true is in fact false. The two books above both deal with correcting widely held myths.

I can't really argue that this is just my interest in science. One of the books has nothing at all to do with science. It deals with myths about the law. But it does the same thing I often do with science--exposed widely held beliefs that are wrong. Why am I attracted to this book? Is my skepticism not just a love of science, but a fascination with errors?

Many years ago, long before I was familiar with the skeptical movement or called myself a skeptic (although I definitely had a scientific and critical mind at the time) I happened to find a book on urban legends, by Harold van Brunvand. It was just lying around at the library, I picked it up, and was fascinated. I finished the book and soon read all of the other books on the topic by Brunvand. Again, these books did not deal with science. It simply dealt with stories that many people believe are true but are not. Yet again I was fascinated with the discovery of widely held beliefs that are wrong. I loved the debunking of these stories.

I very rarely find myself resisting these corrections. I change my mind readily, almost eagerly, and I remember the corrections. I guess there are a few examples I have used in my lectures that I later find out are wrong, and I do resist those for awhile. The viceroy butterfly mimicking the monarch butterfly is such a great example of Batesian mimickery, and I have used it in my teaching. When I discovered it may actually be Mullerian mimickery, I resisted and wasn't so happy to accept the correction, but usually that is not the case.

I don't know why I like finding errors. Maybe it is still just a love of the truth. Maybe I secretly feel superior by having privileged knowledge. Maybe I am fascinated by what leads to falsehood in all areas, not just science. But if I am honest, I have to admit I rather do like debunking. I like finding the truth but especially like it when the truth is contrary to popular belief. I wonder if this is common in skeptics.

I don't think that a fascination with common misconceptions makes me, or any skeptic, a negative naysayer. I do not dismiss things out of hand, and do not denigrate people who believe in errors nor do I constantly point out mistakes. I require evidence before I accept something is wrong. I very happily reject my previous beliefs if the evidence suggests I should. I am simply fascinated with errors.

While many people err by holding on to beliefs that are wrong, I wonder if I err by too readily accepting something is wrong. Have I rejected a common belief too quickly when in fact it is true? I cannot quickly think of any such examples, but I should reflect more on that. We all need to monitor ourselves for our biases.