27 August 2005

More on the California creationist lawsuit

In a post earlier today, I noted that a group of creationists are suing the University of California system in order to force UC to accept several of their classes that are currently not considered adequate. One of the courses in question is biology. As I already pointed out, UC is not discriminating against Christians by refusing to accept the class; it is simply living up to its responsibility to ensure that applicants are adequately prepared for university study. Nevertheless, I was curious as to what about these particular biology classes was so poor as to attract attention.

The LA Times reported that:
According to the lawsuit, UC's board of admissions also advised the school that it would not approve biology and science courses that relied primarily on textbooks published by Bob Jones University Press and A Beka Books, two Christian publishers.
Now, given what I've heard about Bob Jones University, I figured that any biology text that they produce would be unlike any I'd read before. So I trotted on over to the Bob Jones University Press website to see what I could find. Looking over their list of books for "conventional schools", I found a textbook for a 10th grade biology class. The price is a bit high for me, given the quality, so I didn't order it. However, the website has a nice "see the inside of this book" feature that gives access to the frontmatter, preface, introduction, and a sample chapter. After looking at it, I think I understand why UC has problems with it.

From the Introduction:
Biology for Christian Schools is a textbook for Bible-believing high-school students. Those who do not believe that the Bible is the inspired, inerrant Word of God will find many points in this book puzzling. This book was not written for them.
That's funny. There I was thinking that science is a universal concept, open to anyone who is willing to study the natural world. I had no idea that there are things in science that can only be understood if you believe what these folks do.

The people who prepared this book have tried consistently to put the Word of God first and science second...If...at any point God's Word is not put first, the authors apologize.
Let's see. What we have here is a "science" textbook, written by people who have made a conscious effort to put science second. Wow. What possible reason could the University of California have for being concerned about the quality of classes using this book?

The same encyclopedia article may state that the grasshopper evolved 300 million years ago. You may find a description of some insect that the grasshopper supposedly evolved from and a description of the insects that scientists say evolved from the grasshopper. You may even find a "scientific" explanation of the biblical locust (grasshopper) plague in Egypt. These statements are conclusions based on "supposed science." If the conclusions contradict the Word of God, the conclusions are wrong, no matter how many scientific facts may appear to back them.
It's nice to see how willing they are to keep an open mind about things.

Believe it or not, the book actually seems to get worse. The sample chapter provided on the website is Chapter One: The Science of Life and the God of Life. Page nine is a box that is labeled as one of the book's "Facets of Biology". The title of this particular facet is: "How God Communicates with Man". In it, we find:
Was Joseph Smith's [founder of the Mormons -tqa] revalation from God? Based on Scripture, one must say no! The apostle Paul says that if anyone (including Paul himself or even an angel) comes and preaches any other gospel, he is to be accursed (Gal 1:8).

If you want to know what this has to do with science, or why it appears in a science book, you'll have to ask someone else, because I've got no clue. It must be one of those aspects of science that perplexes those who lack the BJU-approved beliefs.

There's another Facet later in the chapter, dealing with spontaneous generation. It spans three pages, and concludes with this creationist gem:
After Pasteur's swan-necked flask experiment and thousands of other experiments supporting biogenesis, do people today still believe in spontaneous generation? Yes. Anyone who believes in evolution believes that spontaneous generation has occurred. ... If they can create life, they think they can support their belief in life's beginning without God.
This chapter of the text also has some material that discusses evolution:
The idea that life comes from similar life is important. God created humans and all of the other kinds of organisms with the ability to reproduce after their own kind (Gen. 1:12, 21, 25, 28); therefore, humans reproduce humans, oak trees reproduce oak trees, and cats reproduce cats. The idea of all life forms descending from a common ancestor cell that originated from non-living chemicals is absurd.

Right. It's completely absurd to believe that humans have descended from chemicals through a long line of ancestors. It's much more reasonable to believe that humans came directly from dirt which is made from...

Looking at just the available samples from this text, I'm not surprised that UC declines to accept courses using it as the primary material as valid. I am surprised that there are apparently some schools that do.

By the way, the examples that I've quoted are by no means a comprehensive listing of everything that's wrong with the material I read. They are simply a few of the more egregious examples illustrating the comprehensively unscientific nature of this book. A thorough examination would have taken far more time than I have, and would simply have depressed me further.

The consequences of creationism

It appears that yet another creationism-related lawsuit is in the works. This time, the venue is in California, and it is the Creationists who are doing the suing. Apparently, the Association of Christian Schools International and Calvary Chapel Christian School of Murietta are no longer satisfied with being able to teach their students creationism instead of real biology. Now, they also want to make sure that their students will not have to suffer the consequences of this decision, and they are suing for that "right".

The University of California System, quite reasonably, requires that the students that they accept have a certain educational background. Several courses, including biology, offered by Calvary Chapel were determined to be insufficient to meet the UC standards. According to the LA Times article cited above, UC directed Calvary Chapel to instead, "submit for UC approval a secular science curriculum with a text and course outline that addresses course content/knowledge generally accepted in the scientific community." Typically, the creationists don't see this as a university excercising it's duty to ensure that its students are properly prepared for admission. Instead, they see it as yet more evidence of the anti-Christian "bias" that they see anytime they do not get things their own way. From the LA Times article:

"It appears that the UC system is attempting to secularize Christian schools and prevent them from teaching from a world Christian view," said Patrick H. Tyler, a lawyer with Advocates for Faith and Freedom, which is assisting the plaintiffs.
Bird said the schools have no objection to teaching evolution alongside creationism but consider the UC regulations a violation of their rights. "And a threat to one religion is a threat to all," he added.
That is an interesting take on the situation, but one that is not reality-based. The UC system is not expressing an opinion on whether or not the creationists should be permitted to mis-educate their children. They are simply declining to consider such courses as having been an acceptable science education. The creationists do not have to expose their children to the evils of evolution if they do not want to. They just have to recognize that this decision has consequences.

26 August 2005

A little light reading for the weekend...

I just wrapped up at work for the day - nothing like getting out at 8pm on a Friday night - and put together the reading material I'll be bringing home and at least theoretically reading this weekend. It's a somewhat eclectic collection:

Thomas, R. H. and J. A. Hunt (1991). "The molecular evolution of the alcohol dehydrogenase locus and the phylogeny of Hawaiian Drosophila." Mol Biol Evol 8(5): 687-702.

Matzkin, L. M. (2004). "Population Genetics and Geographic Variation of Alcohol Dehydrogenase (Adh) Paralogs and Glucose-6-Phosphate Dehydrogenase (G6pd) in Drosophila mojavensis." Mol Biol Evol 21(2): 276-285.
A couple of papers to read as part of the research toward my proposal.

Talbot, S. L. and G. F. Shields (1996). "Phylogeography of Brown Bears (Ursus arctos) of Alaska and Paraphyly Within the Ursidae." Molecular Phylogenetics and Evolution 5(3): 477-494.

Hennig, Willi. ? Phylogenetic Systematics. p97-116 of something or another (photocopied book chapter)
The assigned reading for the Systematics class I'm taking.

Schluter, D. (2000). The Ecology of Adaptive Radiation. Oxford, Oxford University Press.
Need to read chapters 2 and 3 for adaptive radiation concepts class. Not due until next Thursday, may procrastinate.

Lomolino, M. V. and L. R. Heaney (2004). Frontiers in Biogeography: New Directions in the Geography of Nature. Sunderland, Sinauer.
Need to look through part one for seminar on biogeography. Not actually due for a couple of weeks, but looks a lot more interesting than the Schluter.

It's probably good that I finished the new Harry Potter before classes started.


I just made a change to commenting procedures. I've gotten a bit of comment spam over the past couple of days, and I'm tired of having to go through and manually delete them. I've activated Blogspot's "word verification" feature, so in order to comment you will have to do the whole type the goofy looking word in the box thing. I know it's annoying, and I'm sorry, but it beats having to deal with all those "great job, now come see my [insert commercial blog] blog" type posts.

It also occurs to me that I haven't outlined a comment policy yet. Here it is:

I reserve the right to delete any post at any time for any reason. But I only plan to delete those comments which are either entirely off topic, illeagal, or which use language unsuitable for children. My eight year old looks at the blog sometimes, and I'd like to make sure that it stays a site I'd be comfortable having her read.

25 August 2005

Homeopathy and Intelligent Design

Homeopathy is a form of alternative medicine that is taken seriously by some, and mocked by many - especially those in the reality-based community. There is good reason for the mockery. Homeopathy is based on the medieval philosophy of "similia similibus curentur" (like cures like), and relies on "treatments" that involve administering a substance that causes symptoms similar to those of the disease it is intended to "treat". In order to avoid having the treatment cause more harm, the substance is normally diluted to such an enormous extent that it is present at levels that may be literally undetectable. This is believed to work because it is presumed that the process of dilution releases and concentrates the healing essence of the substance while removing the impure physical presence.

In short, then homeopathy is a classic example of a pseudoscientific enterprise lacking any basis in reality whatsoever. Despite this, it is a very popular form of "alternative medicine", and has many practitioners. There have also been serious scientific studies that have examined the effectiveness of various homeopathic remedies. In the latest issue of the medical journal The Lancet, a group of authors have published a detailed statistical comparison between 110 published, placebo-controlled studies of homeopathic remedies and an equal number of studies of conventional drug trials. Their analysis showed that the effects of the homeopathic remedies in the published trials are so slight that they are best explained as placebo effects. This comes as no surprise to the scientific community.

What I find interesting about this is the way that this contrasts with the Intelligent Design movement. In homeopathy, we see a "medical" treatment philosophy that runs counter to everything that we understand about the way that our bodies function. From a scientific perspective, homeopathy is utter garbage. However, it turns out to be testable garbage. Homeopathy makes predictive statements ("if you take this, it will make you better") that can be tested against what really happens. In this instance, they were tested and massively failed.

Intelligent Design lacks even that virtue. Intelligent Design makes no positive predictions of its own, and therefore cannot be directly tested against reality. The closest that ID comes to anything testable is when they claim that some given trait cannot be explained by evolution, but the jump from that to "ID is therefore right" is totally untestable - it would be like a homeopathic practitioner claiming that, "the cure proposed by conventional medicine does not work, therefore my cure must." Put in those terms it is clear that ID's "logic" is nonsensical. Yet for some reason, people seem to find it a perfectly acceptable argument in that context.

Nobody is so blind...

Yesterday, I got my first chance to TA a lab. I've got a nice deal this semester, since I'm assisting a professor instead of running the whole lab section on my own, and because we've only got six students in the lab at the moment. It's not so easy for the students, however. This lab (400-level ecology) is, for most of them, the first time that they are forced to do very much in the way of planning for the experiments. Most of the prior labs that they've taken have been plug-and-chug, follow the cookbook kind of things. Here, they are given a problem, then told to come up with a way to solve it. Yesterday's introduction to the course involved having them measure seed pods from a local invasive (Koa haole), in an attempt to determine which two (of three) bags of seed pods were taken from the same tree. We suggested that sampling would be better than a census approach, and mentioned that two possible parameters to look at might be length of the seed pods and the number of seeds per pod. We also told them to be sure to try to look at everything, as there might be other characters that might work.

Koa haole seed pods tend to hang around the trees for a while, so the bags contained a number of different age classes of seed pod. There were some that were still green, but the bulk were older brown pods. One of the first questions that they came to us with was whether or not the green seed pods were full grown. We looked at them, grinned, and shrugged. They went off muttering to discuss the question among themselves. They were able to quickly reach the conclusion that they didn't know whether or not the green ones were full grown, so they decided to discard them for the purposes of length measurements. They piled up all the green pods from each bag out of the way, then went on to lay out the brown pods to randomly select their samples. The green pods stayed discarded for the rest of the lab, as the students industriously measured lengths and counted seeds.

Since the green pods had been "discarded", the students never looked at them again. Boy, did they miss out. The lab handout didn't mention looking at the ratio of green pods to brown as a possible way to determine which two sets of pods were from the same source, because in past years virtually all of the pods collected were brown. This year, through sheer coincidence, one of the trees that I collected pods from had lots of green ones. The result was that two of the three piles had loads of brown pods and very few green ones. The third had loads of brown pods, along with a whole bunch of green ones. To anyone who wasn't completely locked into a "brown-only" mentality, it was possible to figure out which two piles were similar from the other side of the room. The students, having discarded the green pods, completely missed it. They're going to be spending a lot of time crunching the length and pod number data that they collected, and I have no idea whether or not they are going to find any significant differences.

This is an example of a common phenomenon - so common that it goes by different names. My wife, who is an army flight surgeon, tells me that it the aviators she works with call it "task fixation". I've also seen it referred to as "situational blindness". You wind up focusing so hard on one task that you can completely miss other things that are going on around you. In aviation, this can be life-threatening. In science, it usually isn't that severe, but it still isn't good. It's always important to make sure, when you are counting trees, that you don't miss the forest. Or that you don't miss the guy in the gorilla suit when you are counting basketball passes.

23 August 2005

More on Iraq.

As I have said before, I believe that the United States has a moral responsibility to ensure the reconstruction of Iraq. I think that this means that we need to keep troops there; others, including the gentleman who commented on the earlier post, believe that reconstruction cannot take place until after we withdraw. It is possible that this is correct, but even if it is, I don't think we could withdraw until arrangements have been made for someone else to take our place. I'm not holding my breath waiting for that to happen.

In the meantime, I do firmly believe that we need to keep troops in Iraq. I also believe that we should have more troops in Afghanistan than we do now, and that we should be doing more to help Afghanistan build a functional and secure nation. That being the case, I guess I can be considered to be a "supporter" of the wars in Iraq and Afghanistan. I certainly support the troops - with a number of family members on active duty, that's pretty much a given.

But as far as the recent AP/IPSOs poll is concerned, I am definitely not in the increasingly small group of people who support the way that the president has been handling the war. Even if I accept, for the sake of argument, that he got us into this thing with the best of intentions, the best I can say is that this thing has been one massive chain of mistakes from the start to the present. The painful fact is that although Bush was once a believer in the importance of a good exit strategy to the success of a military operation, the only exit strategy that we had for this thing - "they'll shower us with flowers and candy and then we'll all go home for the victory parades" - fell through pretty fast.

Since the exit strategy fell through, American casualties have mounted. At this point, more than 90% of American deaths have occurred since the president's ill-advised carrier landing. Nearly 90% of American deaths have occurred since the president took the unprecedentedly stupid step of inviting the insurgents to, "bring it on". More than three quarters of the fatalities have taken place since Saddam was captured. About one-half of one percent of the fatalities have occurred since the president's speech about the war on Monday. And there is no end in sight.

Bush has not done anything in this time that gives me any confidence that he really has anything that looks like a strategy for this conflict, and he's done little to show that he comprehends that some of the problems might actually be his responsibility. He's kept Rumsfeld on, and promoted Rice and Wolfowitz. The closest that he's come to articulating an exit strategy lately is the new, "as the Iraqis stand up, we'll stand down," mantra. There's not a whole lot of detail there, and it's kind of hard to figure out what that will mean. As I type this, I'm looking at a group of troops from various services standing at attention waiting for the president to arrive to start a speech. The president is expected to take this opportunity to tell them that their sacrifices are not in vain, before returning to his extended vacation. I certainly hope that the sacrifices are not in vain, but I really don't know what the reason for them is anymore.

Both of the major groups - Bush & the Bushites and the Disorganized Dems - seem to have grasped the fact that the poll numbers indicate that there are lots of people out there who are not real happy about the way things are going in Iraq. Bush has responded, as he almost always does, with a simple, consistent message: "Stay The Course, Stay The Course, Stay the Course". The Democrats, as is too often the case, have not been able to put together a united position on this issue. More and more, however, prominent Democrats are heard discussing the need for a firm timetable, with dates, for American troops to leave Iraq.

Both messages are wrong.

Iraq, at the moment, is a nation with a population that is split into three major groups (Sunni, Shia, and Kurd). There are an enormous number of current and historical differences and disputes between and within these groups, but they are being asked to work together to forge a new nation. Into this situation, we inject the extra tensions caused by the occupation, add a security situation that allows these groups to address their disputes in very direct ways, and top the whole thing off with an assortment of terrorist groups and foreign fighters. This is not a simple situation, and it does not lend itself to the kind of resolution what you can present as a simple message. If you want to get the American people to support the situation, be honest. Admit errors. Explain the problems that exist right now. Outline the ways that you think you can address the problems, and detail the situation that you would like to see before you start to withdraw troops.

On the other side, recognize that this is a complex situation, and a situation that is not in any way, shape, or form stable. Situations that lack stability require flexible plans to solve. Fixed timetables for pullout do not give much flexibility. Here, too, we need to decide on goals and objectives. Dates don't do much more for the situation than tell the people you are fighting how long they need to hold out. A firm timetable with pullout dates may play well with people who know that they really dislike the war, but it sets unrealistic expectations. If you don't like the way that the administration is handling things, say so. If you think that we should remove our troops now, say so, but also explain why you think this is in the interests of both Iraq and the US. But if you think we should start pulling troops out at some point in the future, you need to explain why having a date to remove troops is more reasonable than having criteria that are based on conditions on the ground.

Right now, we are stuck in a situation that is a massive mess. Getting out of this mess at all is going to be very difficult. Getting out of this mess while still managing to retain any respect in the rest of the world seems to be virtually impossible. If we are to pull off either, we need our politicians to react intelligently to the situation in all of its complexity, instead of just exhibiting simplistic Pavlovian responses to the various polls that come out. We need them to acknowledge the complexities rather than playing for the sound bite. I hope that at least some of them, from either party, will rise to the challenge.

But I'm not optimistic.

22 August 2005

Graduate Workload (or, The Whining Begins)

Well, I survived my first day of classes as a grad student. Remember just a few days ago when I was so blissfully happy about "only" taking seven credits? That moment has passed. I've got the sylabi for three of the four courses I'm taking (one "real" class, one current concepts, and two seminars.) One of the seminars is an introduction to the department that all new grads are required to take, but which does not involve much in the way of work. The second seminar is on biogeography, and has an unknown workload. That's not too bad.

Then we get to the other two classes. The current concepts class is on adaptive radiations, and the "real" class is a systematics techniques course. Those are the two that have already taught me a very valuable/painful lesson: there really is a big difference between 400-level classes and 600-700-level classes. In addition to the reading load, both of the instructors have already mentioned that they think that a good term project for their class will have the potential to be published in a journal. So, hey, no pressure.

Between that and the time involved in TAing (my apologies to all my past TAs for thinking that they had an easy job), it's starting to look like a long semester.

But at least now I know why people were laughing at me when I was so happy about the seven-credit load.

But why should we save the Wiliwili?

One of the comments that was inspired by my earlier post on the invasive gall wasps that are threatening some native Hawaiian plants raised a point that is worth responding to in detail, since it comes up fairly often both in arguments with anti-evolutionists and in discussions about the costs and benefits associated with conservation efforts:

"Big Bill" said:
"And further, letting foreign people plants and animals in always increases diversity. Sure, some native peoples, plants, and animals will die out, but it’s not like they have any right to the land. There is no God-given title. If the native peoples, plants and animals cannot compete and survive, that is their fault. It’s Darwin in action."

Bill's statement does capture a basic fact about the biological effects of invasive species: if the invasive species outcompetes the natives, resulting in the extinction of the native species, it is simply a case of natural selection. I cannot argue with that. There are some who might claim that situations involving invasives do not count, because the invasive arrived as the result of human intervention rather than "naturally". I dislike that argument, both because it ignores the fact that the effects would probably have been the same regardless of the mode of arrival and because it implies that humans aren't really part of nature.

In this case, there isn't any direct competition involved - the gall wasps aren't eating the food of some other species of insect. In fact, they aren't even eating the wiliwili trees to death. They are depositing their larvae inside the leaves. This damages the leaves that are used in this way, and the wasps are currently so successful at reproducing that they are damaging trees beyond repair. But no matter - the gall wasps are a new factor in the wiliwili's environment, and the wiliwili do not seem to be adapting quickly enough to adjust to this new environment. The same general pattern of events has probably occurred with different sets of species countless times over the last few billion years, and such events have likely been a contributing factor in the extinction of many, many species. The loss of the wiliwili would hardly be a unique or even uncommon occurance in the history of life. I wouldn't call it "Darwin in action", as the old man isn't known to have moved much since they stuck him under that old church floor, but the loss of the wiliwili would (will, if nothing changes) be the product of the harsh reality of natural selection.

How do I, as a person who accepts the obvious reality of evolution, justify taking action to preserve the wiliwili - or any other species - when it is failing the test of natural selection? For that matter, how does anyone who understands and accepts evolution justify aiding organisms that do not seem to be fit to survive without our help? Why is there such a field as conservation biology, particularly if it is filled with "Darwinist" scientists?

The answer is simple, it is clear, it is obvious to anyone who understands science, and it is apparently incomprehensible to any number of creationists. Science can provide us with information about the world that we can use to inform moral judgements, but it does not provide moral guidance. Scientific knowledge can tell us what the situation was, what it is now, and what it may or may not be in the future. It does not tell us what we should or should not do.
The question of whether or not we should try to preserve species requires us to make a moral judgement. There may be some people who think that a world that is populated by far fewer species than we see today might be a good place to live. I am not one of them, and I don't know anyone who is. Like many other people, when I look at nature I see something that is wonderful, even awesome - and I mean that in a very literal way: nature often evokes awe and wonder. I believe that a world in which entire communities of diverse species have been destroyed would be a far poorer place to live. I believe that we have a duty to pass on to our children a world that is better than the one we inherited, and I believe that doing our best to preserve the diversity of nature is part of doing that.

My understanding of science allows me to understant that the actions of the gall wasps are likely to lead to the extinction of the wiliwili unless something is done. My moral principles tell me that something should be done. My understanding of science does not change my moral principles, and my moral principles do not change my understanding or acceptance of science. And that is as it should be.

21 August 2005

After a couple of days delay...

...I'm back up and posting.

My mother-in-law is visiting from the mainland right now, so between that and trying to get everything together for the start of classes tomorrow, things have been kind of hectic this weekend.

But right now things are calm. Everyone's been sufficiently entertained for the weekend, things have been taken care of around the house, the website for the class that I'm TAing is finished (but not online yet), and I've read the two of the three chapters that my professors were kind enough to assign as homework before the damn semester even started. Now all I have left to do before tomorrow is finish that last chapter of homework, get back to the reading for my proposal, and get together with the prof I'm TAing for to make sure that the website goes up and that we have worked out any last minute details. Since my schedule for the rest of the week is a bit hectic, I probably also should go out and grab the three big bags of Koa Haole seed pods I'll need for the first lab.

Maybe seven credits really is a lot.