01 October 2005

Some musings on science and intelligent design

I wasn't really planning to be blogging right now. In fact, I was planning on being asleep right now. I put in a nice, relaxing, 13-hour day in the lab today, so I was feeling a bit tired by the time I was ready to go home. Unfortunately, the caffine is still with me, and I was too wired (and too tired) to get to sleep right away, so I decided to take a few minutes to catch up on some of the things that I'd missed during the last couple of days of the Dover trial. Boy, was that a stupid idea. Now, I'm too wired to get to sleep, too tired to get to sleep, and way, way too pissed off to get to sleep.

Strangely, though, it took me a while to figure out exactly why. The quotes from creationists that popped up in the articles weren't really anything that I hadn't seen hundreds of times before. Some complete schmuck of a lawyer asserts that evolution requires atheism:
Creationism requires a student to first affirm the creed that God created the heavens and the earth, and the theory of evolution requires that a student affirm the creed that there is no God. Both are exclusive claims, neither is scientific, neither can be empirically verified.

An utter jackass of a columnist tries to simultaneously argue that Intelligent Design isn't a scientific theory, and that it is science:
In truth, intelligent design isn't a scientific theory but a restatement of a timeless argument: that the regularity and laws of the natural world imply a higher intelligence -- God, most people would say -- responsible for its design. Intelligent design doesn't argue that evidence of design ends all questions or disproves Darwin. It doesn't make a religious claim. It does say that when such evidence appears, researchers should take it into account, and that the weaknesses in Darwinian theory should be acknowledged as forthrightly as the strengths. That isn't primitivism or Bible-thumping or flying spaghetti. It's science.

A second idiot with a law degree tries to paint the ID proponents as being on the side of America, mom, and apple pie:
As the courtroom drama unfolds in Harrisburg, consider the words of one parent — a mother of five — who lives in the school district.

Sheree Hied told a reporter: “I think we as Americans, regardless of our beliefs, should be able to freely access information — because people fought and died for our freedoms.” That’s what America represents — the freedom to explore all sides of an issue.


For some reason, I don't even find it as funny as usual that, despite all the assertions that Intelligent Design isn't religion, pretty much everyone pushing it is a proud member of the Christian right.

None of this is news to me. I'm used to seeing people who call themselves Christians pissing in the well of truth in a frantic effort to discredit evolution. I'm used to seeing assertions that evolution is a weak theory, packed with gaps. I'm used to reading the argument that when it comes to learning about evolution, students shouldn't be taught what the right answer is, they should get to pick whatever answer they believe is best.

So why, tonight, am I so totally pissed off?

It's probably got something to do with reading that bullshit after putting in a very long day, on a weekend, doing original research in evolutionary biology. It might have something to do with seeing a pair of lawyers and a columnist confidently, despite their own lack of scientific credentials, expressing the opinion that the work I do is nonsense. It might just be that I've finally reached the end of my patience. Or all of the above. Or all of the above, coupled with the revelation that a Dover High School janitor was apparently allowed to get away with burning a mural depicting human evolution.

Actually, after reading that last article again, I'm starting to feel my anger fade away a bit. More than anything else, it clarifies the issues for me, and reminds me that this really isn't about science. This is a conflict between worldviews, pure and simple. On one side, we have empirical fact. On the other, we have a group of people who find themselves, sadly, feeling threatened by what they believe empirical fact is telling them. I could almost feel sorry for them, if it wasn't for the way that they keep demanding that my children be exposed to the version of "reality" that they've cooked up to save their own religious perspective.

I see the future...

...and it's going to be light on updates for the next couple of days.

I've got my first real grant proposal due on 15 October, and my advisor wants to see a full draft by Tuesday. That's a bit painful, since I've barely started. But this is an in-house grant, and if he doesn't sign off as recommending funding, I don't get funded. So I'll be finishing a draft by Tuesday. There's even a chance that I can finish this without having my brain liquify and dribble out my ears. But I'm not optimistic.

30 September 2005

Circus of the Spineless

The first edition of Circus of the Spineless is now available at Milkriverblog. Take a look. There's an enormous about of diversity within the inverts, and you'll find posts discussing strange worms, giant squid, flies, bugs, and a host of other invertebrates.

29 September 2005

Some more on relevant expertise

It really never ceases to amaze me. Perfectly rational people, most of whom would never consider having their barber do their heart surgery (or their surgeon do their hair, for that matter), have no problem rendering judgement on the validity of complex scientific theories. In an earlier post, I mentioned an example of this happeining with evolution. At the moment, another example of this sort of thing can be found in the comments section of a recent post that mentioned Einstein.

Personally, I'd be the first to say that there are things in relativity that sound silly to me. They sounded silly to a lot of physicists when the theory was first published, too. Yet relativity was accepted fairly quickly by most physicists. It might be that relativity is wrong, and if so, I expect that we'll find that out someday. At the moment, however, a hell of a lot of physicists who understand the math and the experiments that have gone into establishing relativity think that it's a pretty good explanation of the way things work. That's good enough for me.

I still don't understand why this doesn't work for everyone.

28 September 2005

Ahhh. A nice way to start the day.

I turned on the TV this morning, to some nice news. Tom DeLay, who has come to symbolize nasty politics at its worst, has just been indicted.

I'd love to blog more on this now, but it's time to run to school.

27 September 2005

A few anniversary musings.

On 27 September 1905, a paper was published in the journal "Annalen der Physik". The paper, titled, "Ist die Trägheit eines Körpers von seinem Energieinhalt abhängig?" ("Does the Inertia of a Body Depend Upon Its Energy Content?"), was only three pages long. It was the fourth published by the same author that year. None of the four papers was immediately embraced by the scientific community. In fact, most were initially considered to be fairly controversial. At the time, the author of the papers had neither a doctoral degree nor an academic position. He had a few prior papers to his credit, but was essentially an unknown in the field of physics.

Within a relatively short period of time, those four papers would be recognized as having revolutionized the field of physics. The author, who was a relatively obscure Swiss patent clerk in 1905, would become one of the icons of our time.

One of the interesting things about these papers is that all of them were theoretical. Not one presented experimental data. What they did do, however, was make predictions that could be experimentally tested. As the various hypotheses proposed in those papers past test after test, they became more and more accepted within the scientific community. One of the equations - the one published in the 27 September 1905 paper - is probably the best known equation in physics: E=mc2.

It is one hundred years to the day from the publication of that paper. At this time, science is faced with a group of people who claim that they have a brand new theory that explains how life started on the planet, and how individual species may have originated. Their theory has, thus far, not had much of an impact on the way that scientists actually conduct science. The proponents claim that their new hypothesis has sparked a controversy within science. The vast majority of the scientific community, including every major scientific organization in the United States, disagrees, saying that the "hypothesis" in question is too atrocious to make it even that far.

What separates them from Einstein? The proponents of the atrocious hypothesis would probably say that there isn't much that separates them from Einstein. More rational people disagree. Einstein worked within the established proceedures of the scientific community. They do not. Einstein's work made testable conditions. Theirs does not. Einstein's hypotheses were tested a number of times before becoming accepted. Theirs cannot be tested.

The biggest difference is this: Einstein did not appeal to the public and to school boards to have his work taught to public schoolchildren. Some of his work is taught to schoolchildren, but that came naturally, as his work gained respect and acceptance within the scientific community and made its way into textbooks.

Our modern Intelligent Design proponents have no hope of their work taking that course, and they know it. Their hypotheses make no testable positive predictions. This does not bother them much, however, because they do not appear to be investing much in the way of resources toward doing actual scientific research.

As a result, 100 years after Einstein's paper on mass-energy equivalence was published, there is a trial in Pennsylvania. The ID folks bypassed the normal scientific process, and forced their religiously-motivated fake science into a school, in flagrant disregard of the rights of those who do not want their children to be exposed to religious lies disguised as science.

Happy anniversary, Albert.

More amusement, courtesy of the Discovery Institute.

From an article in the York Daily Record:

Luskin said Miller inaccurately characterized intelligent design as a concept that focuses on what evolution doesn'’t explain. Luskin said intelligent design stands on its own as an explanation of life and the origins of species.

It is untrue that intelligent design requires a supernatural being. Intelligent design doesn’t suggest who a designer is, Luskin said.

Contrary to Miller'’s comments, Luskin said, intelligent design is a testable theory.

Michael Behe, a professor of biological sciences at Lehigh University, has written about how protein and protein interactions could not evolve. His article was printed in 2004 in Protein Science, a publication of the Protein Society, Luskin said.


So let's see if I've got this right:
It is wrong to suggest that Intelligent design merely focuses on what evolution doesn't explain. ID stands on it's own, and makes testable predictions. This can be clearly seen if you look at Behe's paper, which argued that evolution can't explain the evolution of protein interactions.

Wow. I guess even a hint of anything that remotely begins to faintly resemble something that might once have been briefly exposed to intellectual honesty is just too much to ask from these guys.

26 September 2005

More on Dover

I don't have as much time to blog tonight as I'd like. Instead, I'm working on a couple of things that aren't on my top ten favorite things list - designing PCR primers and grading lab papers. I did steal a few minutes here and there to look at some of the news stories relating to the Dover lawsuit, which opened today.

Some good articles:
There are three articles that are especially worth a look:
There's a truly outstanding article in the Washington Post, that provides a nice, simple explanation of evolution. There's a couple of places where I think that they might have simplified a bit too much, but as a whole this article is the best treatment of the issue that I have seen in the media in years. (hat tip: Pharyngula)
The New York Times also has some decent coverage, http://www.guardian.co.uk/religion/Story/0,2763,1579199,00.html.

The WaPo piece, in addition to the good coverage on evolution, has an amusing little quote from the Discovery Institute's John West:
Asked to provide examples of non-obvious, testable predictions made by the theory of Intelligent Design, John West, an associate director of the Discovery Institute, a Seattle-based ID think tank, offered one: In 1998, he said, an ID theorist, reckoning that an intelligent designer would not fill animals' genomes with DNA that had no use, predicted that much of the "junk" DNA in animals' genomes -- long seen as the detritus of evolutionary processes -- will someday be found to have a function.

(In fact, some "junk" DNA has indeed been found to be functional in recent years, though more than 90 percent of human DNA still appears to be the flotsam of biological history.) In any case, West said, it is up to Darwinists to prove ID wrong.


A few things worth noting here:

The Intelligent Design "prediction" is interesting for a couple of reasons. To begin with, one must wonder as to exactly how they develop their expectations for this designer. They expect the designer to be intelligent enough not to leave lots of junk in the genome. Yet they are entirely unconcerned by any number of features in humans alone that smack of incompetent engineering. Why, for example, do our eyes have blind spots? Who put together the specs for my lower back? Flatfeet don't seem too intelligent to me, either. Of course, all of that pales next to the decision that was made to, as the old engineering joke puts it, run the sewer piping right through the middle of a recreational area. It's funny. Anything intelligent about the way that organisms are put together is, they feel, good evidence for an Intelligent Designer. Anything unintelligent about the way that organisms are put together, on the other hand, is just proof that we can't know the Ineffable Plan of the Designer. Who isn't necessarily God. Really.

Another interesting thing that I noted is that, somehow or another, the Discovery Institute doesn't seem to have focused anything in the way of research funding or energy into trying to find the purpose for the junk DNA. One really must wonder why. They are the main source of ID funding, and they think that they have a testable hypothesis out there. So why were they lobbying school boards instead of testing that hypothesis?

Finally, it is not up to us to prove them wrong. That's not how it works. If you think that you have come up with a good hypothesis, you need to go out and test it. You don't get to say, "This is how things are, and I'm right about that unless you prove me wrong." That sort of thing might work on a kindergarten playground. It doesn't work in science.

25 September 2005

Dover News carnival.

This morning, I took a few minutes to look at a number of the various news articles about the upcoming Dover Intelligent Design lawsuit. The articles that I looked at seem to present a wide range of views, and a few of them were actually quite good. Initially, I was just planning on commenting on one or two. After reading a few, I thought it might be a little more fun to present a bunch of them blog-carnival style.

So, without further ado, here they are: the good, the bad, and the ugly.

The good:

One of the best things about Google's News Search is that it allows you to read articles that you would not ordinarily have access to. In particular, it gives you access to local columnists at small newspapers. The quality of these columnists varies widely - almost as widely as the quality of blogs. However, there is at least one thing that can be said for the local columns: they give you a chance to see a take on a story that isn't the same as that in the endlessly duplicated wire-service stories.

The Dover coverage in the Sunday papers included a couple of pretty good articles from local guest columnists. In the South Carolina newspaper The State, there is an article by Furman University professor Wade Worthen. Worthen tackles, head on, the major reason that the debate over Intelligent Design has taken place in the public arena: "There is no debate within the scientific community; that's why intelligent design proponents seek to legislate their truth in the political arena."

A former high school science teacher wrote a good op-ed piece for the Springfield News-Leader. Mr. Cunningham, pulling no punches, begins his article by presenting his opinion of how Intelligent Design should be taught: "Since intelligent design has no scientific substance, there is no controversy with evolution to teach to a science student. What should be taught about intelligent design, if anything, is that it is a hoax." The wording may not be the most diplomatic I've seen, but I really can't argue with that assessment. He also makes a good point about the scientific status of Intelligent Design: "If intelligent design had any substance, young biologists worldwide would be straining to win laurels by disproving current evolutionary theory in favor of intelligent design." Truer words haven't been spoken. There's nothing like being right at the center of a big, massive, ugly, blood-on-the-floors scientific debate when it comes to making a name for your self.

Brad Kurtzburg, writing for Elites TV, put together a nice little piece that tells the story as-is, without searching for "balance". I particularly liked the way he juxtaposed two short paragraphs:
The Dover school board claims it just wants students to be aware of the existence of intelligent design as an 'alternative to evolution.' It also denies that intelligent design in 'religion in disguise.'

The school board is being supported by The Thomas More Law Center which uses litigation to promote what it calls 'the religious freedom of Christians and time-honored family values.'


Bill Toland of the Pittsburg Post-Dispatch has two articles, both good, on the upcoming trial. The first article starts out on a light note:
If "intelligent design" supporters weren't so quick to rebuke those who connect their mission to the Bible, it would be tempting to borrow from the Old Testament and describe the upcoming federal trial over the issue as a legal version of David vs. Goliath.

Instead, we'll let the defendants in this case, which pits Dover Area School District against parent plaintiffs, to describe the trial in their own words.

"It's almost David vs. Goliath," says Richard Thompson, of Michigan's Thomas More Law Center, which is defending the York County, Pa., district.
The rest of the article is a touch more serious, and raises some excellent points that have been overlooked in too much of the press coverage:
"It's an attempt by the ACLU and Americans United for the Separation of Church and State to intimidate this tiny school district in Pennsylvania," he said. "They want to make an example of this small school district."

The parents, their attorneys and most scientists and educators see it the other way around.

Intelligent design is pseudo-science, they say, but a well-orchestrated one, funded by Christian literalists who oppose the theory of evolution and promoted slickly during the past 10 years by religious groups. They say intelligent design supporters are disingenuous when they claim their argument has no religious implications, because intelligent design's top advocates have already let the cat out of the bag. Intelligent design opponents point to the words of Phillip Johnson, devout Presbyterian and father of the theory:

"Our strategy has been to change the subject a bit so that we can get the issue of intelligent design, which really means the reality of God, before the academic world and into the schools."
Toland's second article is largely based on an interview with Ken Miller, and discusses the scientific failings of Intelligent Design in some depth.Perspectivess from other scientists are featured in a couple of more articles - one good example is from a North Carolina TV station.

Mary Warner, writing for the Newhouse News Service, has an a excellent article in the Cleveland Plain-Dealer. She gives a nice description of the scientific standing of evolution:
Evolution - the theory that all life descended from common ancestors over eons through natural selection - is a mainstay of modern science.

"There are probably more scientists who believe Elvis is alive" than scientists who reject evolution, says Ed Larson, a Pulitzer Prize-winning author on America's battles over evolution.
She then goes on, later in the article, to give a slightly different perspective on the matter, from one of the lawyers for the defense:
Attorney Richard Thompson, arguing now for the board, says its purpose was "valid and clearly secular" - to inform students of "the existing scientific controversy" about evolution.
That's a vitally important point that all too frequently is missed when reporters try to be balanced: this is not a controversy of two evenly matched sides, or even one where a significant minority is struggling against the majority. This is a "controversy" where an extremely tiny minority (the Discovery Institute claims 400; there are hundreds of thousands of scientists in the US alone) is waging a political battle against the vast majority of scientists. This point is also made in a column available on the News 24 website.

The York Daily Record continues it's extraordinarily good coverage of the Dover Biology policy with a few more noteworthy articles. One of these examines what is at stake in this trial. The other http://ydr.com/story/doverbiology/86717/ discuss the issues surrounding the testimony being demanded from reporters for two local papers.

Last in this category, but by far not least, there is an interesting column written by a Presbyterian pastor from Virginia. I'm not sure that I agree with everything that he's written in the article, but the overall perspective is definitely thought-provoking.

The Bad: (or at least not too good)


Two of the major wire services, AP and Reuters, have written articles that are, for the most part, factually accurate, but which make far too much of an effort to "balance" their coverage by presenting statements from both sides. As a result, both articles let some real whoppers from ID proponents slip by unchallenged.

The AP article has this doozy, from the head of the law firm representing the defense:
"All the Dover school board did was allow students to get a glimpse of a controversy that is really boiling over in the scientific community," Thompson said.
It might have been reasonable to note at this point that virtually every major scientific organization in the country has issued some sort of statement saying that Intelligent Design is unscientific, or that the body of peer-reviewed Intelligent Design research is small enough that even an incompetent carpenter could count it with ease.

In the Reuters article, the Discovery Institute's Director is given a pass on this bit of hyperbole:
"It's a disturbing prospect that the outcome of this lawsuit could be that the court will try to tell scientists what is legitimate scientific inquiry and what is not," West said. "That is a flagrant assault on free speech."
It really would have been reasonable for the reporter to note that the lawsuit does not seek to limit scientific research in any way. It simply wishes to limit material taught in public school science classrooms to actual scientific material, rather than badly-disguised religion.

A community columnist for the La Crosse Tribune seeks balance, as well:
There is one more rule to this debate. Students must listen to each other and be respectful of other ways of looking at the issue. Evolutionists need to give up their attitude of intellectual superiority. Intelligent design or creation advocates need to give up their attitude of moral superiority.

Debating evolution and exposing its flaws might inspire some young student to find the answers for those flaws. Then again, maybe some other theory is correct. Maybe this kind of critical discussion will show us that alternative answer.
Would that it were that simple. I'd personally love to see students taught about the controversies within evolutionary biology. Unfortunately, there are two problems with this approach. The first is that doing so would require students to learn far more biology than they have been. This isn't necessarily a bad thing, but it may not be realistic given time and resource constraints. The second problem is even simpler: none of the things that the Discovery Institute people claim are "flaws" in evolutionary theory actually are. Adding them to the curriculum would reduce the quality of scientific education, not improve it.

The Christian Post doesn't seem to be any more of a fan of balanced coverage than I am. Unfortunately, their lack of balance leans far to the other side - they include a lengthy section on Behe, but don't mention any of the scientific opposition to his claims.

The Ugly:
In addition to letting you see columns from places you never would have otherwise looked, Google News also lets you see letters to the editor that you never would have seen. I'm convinced that seeing the columns is a good thing. I wonder a bit about the letters.

A letter to the Danville Advocate-Messenger raises a number of old creationist talking points, then concludes with this gem:
Yet it [evolution] continues to be promoted as fact. Why? Because evolution is nothing more than the denial of the existence of a Creator.

The greatest asset evolutionists have is the reluctance of ordinary people to explore and learn the true scientific evidence - and therefore the deception continues to be perpetrated. You don't have to be a scientist or engineer to understand the facts. Many competent scientists have written a great deal about these truths in plain, everyday English.

My study of scientific research proves that "we are fearfully and wonderfully made," or in other words, we have been awesomely, intelligently designed by an infinite, benevolent God. The question is: Are we really looking?
His study of scientific research.... It's funny. I didn't find this sort of thing to be quite so irritating a couple of years ago. Of course, I've invested at least a couple of thousand hours in studying evolutionary biology over the past couple of years.
OK. It is true that you don't need to be a scientist or an engineer to understand the facts. But it helps. (Actually, I'm not sure why someone would expect an engineer to understand evolutionary biology. I don't necessarily expect them to not understand it, but it's not exactly something that they are trained in.)
The problem here is that the creationists are good at putting their message into simple and easily understood prose. Scientists are not as good at this. The fact that the entire message of creationism is simplistic plays a large part in this, as does the fact that science is vastly complex.

The final letter to the editor, and final entry in this post, comes from someone who has a very valuable message to share. Youwon'tt find it in the text of the message - it's just in the subtext. The message is this: there really are places for kooks outside of the internet.

That wraps it up for this brief and biased digest of the Sunday paper coverage of the Dover Battle. I hope you've enjoyed it.