Thursday, September 29, 2011

My Annotation of NOVA's 'Judgment Day' Dover Trial Special

While my next post would be my ripping apart the so-called doctoral dissertation of one of my Arch-Rival's young-earth creationist role models (starting here), it's taking such a long time that I thought I'd post something else, which I had previously written, in longhand, just for him.

Back in February, the Arch-Rival brought up the subject of Intelligent Design and claimed that the evil atheists were suppressing its acceptance as real science. Having studied the subject extensively on and off since the late 90's, I of course argued otherwise, but as he was about to leave for work, he recommended that I watch the 'documentary' with Ben Stein called Expelled: No Intelligence Allowed.
` He also asked me how scientists explained how life was supposed to have begun, and that the theory of spontaneous generation had been debunked long ago. I started off by telling him that the theory of abiogenesis (beginning of life) has nothing to do with the theory of evolution (change of life), nor the completely wrong concept of spontaneous generation, and that it's quite a large and complex area of study, which I could tell him more about if he didn't have to leave just then.
` On his way out the door, smirking, he winked and said something like "I think you'll be surprised" or "impressed" or something like that, as though he expected that I would be stunned by what the movie 'reveals'. I immediately went to my computer and found Expelled for Instant Download on Netflix.

I watched it no fewer than three times, becoming less impressed with each viewing, let's just say.

On one level, I became so deeply offended by its childish demonization and Nazification of evolution and the people involved in its study that I actually started to get angry and teary-eyed. On another level, I vowed to clear up this distortion, so I wrote down each of the movie's claims, and, over the next few months, I managed to use the power of facts to debunk every last one of them.
` Within the next few days after viewing, however, I did manage to write up about fifteen pages of criticism and gave it to him to read. To my surprise, he conceded that I had indeed exposed some actual 'yellow journalism', and I'll have to type that up for this blog.
` However, as that would take way too long, and because I already have a massive project going here, I should probably just wait until I post that.

As a teaser, though, just after I wrote those fifteen pages shredding Expelled, I remembered a rather good documentary that my biology teacher (years ago) had assigned for us to watch because she was terrified that some of the students would think that trying to teach them evolution was some attempt to subvert their religious beliefs.
` (And she was terrified -- shaking in fact -- because she's probably had to deal with such people!)

` This documentary was a PBS Nova special called Judgment Day: Intelligent Design On Trial, and I had thought it was such a good choice that I actually began to write up a blog post about what the other students had to say about it. As was common at the time, I didn't publish it, although someday I will dredge it up for all to see.

This documentary, I thought, might at least impress the Arch-Rival in the fact that it contains lengthy commentary from both 'sides', rather than sound bites which are taken out of context to make one 'side' look bad -- as I saw in Expelled. Also, its informativeness and its utter lack of Lord Privy Seals might also give him some idea of its level of quality.
` I told him that if he was interested in seeing a documentary that I would regard as accurate, that he should watch Judgment Day, and he agreed to the next time he went to the library.
` To help him out, I wrote him up five pages of notes of my narration/commentary of what I thought was most important, for his own reference, and his own use in formulating a response.


To my knowledge, he still hasn't watched this documentary, even though I've sent him a link two separate times to the online video, last spring after he had gotten himself a computer!
` If you want to beat him to it, you can watch it at
this link, and there's also another one at the bottom of the post.

I am not sure if he has read the notes I've given him, but as I have them back now, I can transcribe them here for my loyal readers (assuming I have any) so that at least someone can really appreciate this!
` Plus, I've added just a few more bits and pieces for your own enjoyment -- including a video demonstrating the evolution of a bacterial flagellum!



My notes/annotation/augmentation:

One Dover high school student did a very well-done mural of human evolution, which mysteriously disappeared one day. This seems to have to do with the fact that many Doverians were angry that only Darwin's theory was taught in exclusion to anything else, and suggested Intelligent Design as an alternative, which they claim is based in science, not religion.
` They wanted a statement read in class, informing the students of its existence, and that there is a textbook called Of Pandas and People in the library explaining what it is.

I am not suggesting that a court of law should settle scientific matters, because the evidence should -- but that is another issue. The issue here is whether or not "ID" is even based on scientific research, and, failing that, whether or not it is based in scripture.

The Dover residents talk about "creationism" versus evolution. Is ID based on biblical creationism? We go back to earlier court cases of evolution and creationism -- Scopes losing his trial, and evolution removed from textbooks so as to prevent any more trouble from creationists.
` When Sputnik sparked new interest in science, evolution started going back into the textbooks, and creationists spoke out again. Since creationism is bible-based, it violates our Constitution's Establishment Clause if taught as a fact of the world in government-run schools, and was banned in 1987.

Creationist Bill Buckingham was appointed by creationist Adam Bonsell to review Dover's textbooks. Buckingham did not like the 9th-grade biology textbook by Ken Miller and Joe Levine because it was "laced with Darwinism," and said he did not feel comfortable approving it. The book was put on hold.
` Then, we have a very brief overview of the discovery that broke the back of Darwin's proverbial camel: When finding help in classifying Galápagos' various birds, which looked like woodpeckers, mockingbirds, etc., he found that they were all different species of finches.
` Instead of different types of birds having been separately created on different islands, it seemed that the most likely explanation was that they were all made by one species of finch having spread to different habitats and adapting to different niches.
` Whoa, that one finch has a more than 'slightly' larger beak! There were, of course, many more different types of finch beaks than the ones shown. We see a simplistic explanation of natural selection and descent with modification. Nevertheless, all this is based on the observation of countless species and not some religious text.

Some people feel that this idea takes God out of the picture, including Bill Buckingham, who was allegedly the one who had destroyed the evolution mural, and enjoyed watching it burn.
` In looking for a way to mitigate evolution's being taught in school, the Thomas More law firm directed him to websites about Intelligent Design and the Discovery Institute, which was consistent with his creationism views.
` He and Adam Bonsell wanted to add Of Pandas and People to the curriculum, but it didn't happen. A few weeks later, 60 copies of Pandas turned up at the school, with a statement to be read to students about 'problems' with evolution, and pointing to the textbooks.
` Six school board members resigned in protest, and their reason was that it's creationism. In September of 2004, eleven parents filed suit against the school board, saying it was violating their Constitutional Rights -- the government should not endorse/discourage the practice of any religion. They were represented by the ACLU.

[This fact doesn't win any Brownie Points with the Arch-Rival, because according to him, the ACLU is atheistic, evil and communistic, which was especially amusing when I started to do my own investigation into the matter -- but, I digress.]

Teachers refused to read the statement, so it was read for them. As we'll see a tiny hint of, ID is far from being a scientific theory because scientific processes are what decide valid and useful theories, not interference with the school board, just so we're clear on that.
` After all, when was the last time you heard of scientists trying to force unaccepted theories on kids, for any reason? There's a reason for that; bypassing the scientific community doesn't prove a thing -- but evidence does!
` ACLU was to find evidence that ID is a clever way to disguise creationism as science so that creationists could use it to get creationism in a science classroom, skipping the scientific process. Thomas Moore was to show that ID is to "make students aware of another scientific theory" and that "it is not religion."

This was what President G.W. Bush and Senator Santorum had thought too, evidently, so they made sure that the conservative Judge Jones would be presiding over the case. The first thing he would examine was whether or not ID was science. ACLU assembled some science expert witnesses. (Pay attention to the way they word their explanations.)

Tiktaalik, an even more dramatic transitional fish-tetrapod fossil than Acanthostega, Ichthyostega, etc., had been discovered too late to be used in the trial as one of the transitional fossils, a few of which we see in this documentary.
` What is a theory? The ID proponents complain that evolution's not a fact, but in science, the word 'theory' means something much greater than a fact, as is explained.
` Also, the word 'law' means something quite different from a theory -- laws are simple descriptions, like the law of gravity. A theory is a complex explanation, like gravitational theory, which is meant to explain why the law of gravity exists.
` So, to review; law = description of a very simple natural phenomenon; theory = complex explanation for described phenomena. It's like apples and oranges.
` Though evolution through natural selection and other processes has been described, there is no 'law' of evolution because the number of variables (i.e. type of organism, type of niche, environment, what changes could happen, what DNA is available and what mutations occur, etc.) make it impossible to predict with complete accuracy as to what the next 'move' will be.

Genetics was an enormous test to Darwin's theory -- it could have contradicted this explanation, but instead confirmed it. (The "great details" are left out of this documentary, presumably for simplification's and time's sake.)
` A simple example is shown -- why humans have 23 pairs of chromosomes whereas our closest genetic relatives have 24. It turns out that we all have the same chromosomes, except that two of these in chimps correspond to one large human chromosome that has been found to be made up of two chromosomes fused together.

Darwin proposed his theory in 1859, and his basic ideas have been built upon and used for practical purposes (which depend on his theory being true), including medical research and even self-designing technology (through selection), as well as understanding virtually any given detail of the living world.
` What understanding does ID give us? What predictions does it make? What practical purposes does it have?
` Its proponents say that looking at nature as if it were designed is supposed to be a practical value unique to ID, but it is not; looking at the 'machinery' of nature as though it should be put together in a semi-orderly way -- by evolution's somewhat sloppy processes -- has always been helpful in figuring out how it works.

When you think about it, Intelligent Design doesn't have anything new to offer because it is almost entirely based on (unsubstantiated) claims that evolution doesn't make sense, and not on positive arguments for what one should expect in nature.
` So, even if evolutionary theory were overturned, we would then have no theory to explain all of biology, only that "something somehow designed species and it isn't evolution." It doesn't tell us what the designer is, how it designed or when. If you can't even define what it is you're arguing for, then how can you possibly test this idea?

See how that's a negative argument and not an independent concept that explains facts? It's not even a scientific hypothesis because it doesn't actually try to explain anything at all!
` And, because it isn't testable, as any scientist would explain -- even my Oceanography teacher, come to think of it -- it isn't science. How can you determine if something is true or not if you can't even check the idea against the real world?

By now, 8 of 9 seats on the school board were empty, including Buckingham's, and the situation for the people in Dover is getting very hairy -- as in death threat-hairy -- for the people who are trying to keep ID out of schools.
` What do the ID advocates in court have to say? Five of their witnesses dropped out. The remaining ones were asked whether there was a valid reason for teaching ID other than religious purposes.
` So, Michael Behe explains that design is the inference that parts which look designed are actually designed, and the most 'visually striking' example is the bacterial flagellum, which has parts he claims are ordered for a purpose. He asserts that if any of the parts are missing, then it can't function, thus there would be nothing for natural selection to act upon.
` He cites a 1998 paper by Dr. Daniel DeRosier, who studies such flagella, saying that this type of flagellum "resembles a machine designed by a human." So, De Rosier himself is asked and he says that he doesn't think it actually is designed, because it is clearly an evolved system, built up gradually by the messy process of natural selection.

So, does a 'half-formed' flagellum have anything for natural selection to act upon? Yes.

Just one example is the one they showed here, a 'half-formed flagellum', which is actually a 'syringe' that Yersinia pestis uses to inject poison into human calls -- it functions just fine as evidenced by the historical success of the bubonic plague.
` There are also other examples not included in the documentary, including a version that uses even fewer parts. Importantly, the proteins making up the flagellum are used in other structures in the cell, so it isn't as though they would have to appear just for the purpose of making the flagellum, as Behe would have you think.

* In one of my reams of Expelled-analysis, I drew a full-page illustration explaining how the flagellum could have plausibly evolved, and which has been backed up by actual biological experiments.
` Since it's on notebook paper and would have to be shrunk to show on screen, it would look very hazy and undecipherable, so I found a YouTube video that shows a somewhat informative animation of the same thing:



Also, the genetic evolution of each of these proteins is now understood. Cell biologists can see that the gene for one protein has been duplicated, that is, an extra copy was made, and this is seen to occur in nature. Because only one gene is all that is necessary to make a certain protein, one of these genes was now free to mutate without disrupting the production of that protein.
` A beneficial mutation caused one of the genes to make a different protein with a different job. This kind of thing has happened again and again, for each of the proteins, splitting and changing into new versions as different beneficial mutations accumulated in different lineages, creating new and different proteins:
` (Ignore the white dots -- they're supposed to be black but I can't get them to be!)

Original Protein
. ..|.|
. .\ . /. . . . . . . . . (mutation) . . . . . . . . . . .(subsequent mutations)
. . .V. . . . . . . . . . . . . . V. . . . . . . . . . . . . . . . . . .V. . . . . . . . . .V
TAAACGTGA -- TAACCGTGA -- TAACCGTGT -- TAACCGGGT
` \\ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . \\
` . --TACACGTGA -- TACACGTGC . . . . . . .-- TAACCCTGT -- TAACCCTTT
` . . . . . . . . . . . . . . . . . .\\
` . . . . . . . . . . . . . . . . . . . -- GACACGTGC -- GCCACGTGC

...and so on.

[My original illustration was more extensive and didn't use short strings of letters, but I hope you get the idea. As this text-illustration is off the top of my head, it does not represent an actual genetic sequence, but rather represents the basic explanation for the patterns that are seen to occur in actual genomes over longer stretches of DNA.]

This pattern of genetic diversification is also seen in the genes coding for the proteins in our immune system and our blood-clotting factors. Let me emphasize that this is one way that new information arises in our DNA, from which natural selection can work with.
` Another way is when retroviruses insert their genomes into their host's DNA, adding all their genes! When this happens in a germ cell, the retrovirus can be passed on to the offspring, and host cells have even been observed to use retroviral DNA for their own purposes!
` I mention this, of course, because one of the claims of creationists and ID proponents is that no new information can be naturally created. Since it actually does happen, that claim is disproved.

In the court reenactment (from the transcript), we see how Michael Behe testified that we have no sufficient answers for the evolution of the immune system. He says he hasn't ever read the stacks of books and scholarly articles on the subject that the lawyer presents to him, yet confidently (enough) maintains that there are no sufficient answers.
` But... if he hasn't even examined the research, then how can he judge that for himself?

After weeks of 'science class' in the courtroom, ID is not deemed any sort of science -- although, that does not mean it is religion. So, they ask, is it?
` According to a catalog in the bottom of one of the boxes of donated books, Of Pandas and People is listed under 'Creation Science' (i.e. biblical creationism). Since Pandas is the manner in which ID has been presented in the school, the question is: Is Pandas, and by extension Intelligent Design, actually just 'creation science'?

An old newspaper article was found, about a biology book which 'presents both evolution and creation' by Charles Thaxton. This article was published just before the 1987 trial where creationism was banned in schools for violating the constitution.
` Charles Thaxton is also the editor of Pandas. Was this 'creation and evolution' textbook the same as Pandas? An investigation into earlier drafts shows that this is the case. (Also, the documentary doesn't mention that the original title was Creation Biology! Really!)

Looking at two drafts of this book, one just before the 1987 verdict and one just after, they show that the texts are very similar, except that in the former draft, language such as 'God' and 'creation' are used, and in the latter, these words are changed to 'Intelligent agent' and 'design' (and references to the bible are also omitted).
` According to the former draft, 'creation' is defined as 'various forms of life began abruptly through the agency of an intelligent creator, with their distinctive features already intact -- fish with fins and scales, birds with feathers, beaks and wings, etc."
` In the latter draft, the same definition is given for Intelligent Design except that it's through an 'intelligent agency.' In making this transition, one of the editors mistakenly replaced 'creationists' with 'design proponents', resulting in a 'transitional fossil' of sorts -- 'cdesignproponentsists.'

Another good question comes; does ID offer only a critique of evolution, or does it offer something more? ID proponent and leader Paul Nelson, was asked this question, and here was his response:
"Easily, the biggest challenge facing the ID community is to develop a full-fledged theory of biological design. We don't have such a theory right now, and that's a real problem. Without a theory, it's very hard to know where to direct your research focus. Right now, we've got a bag of powerful intuitions, and a handful of notions such as "irreducible complexity" and "specified complexity" -- but as yet, no general theory of biological design."
(BTW, even to this day they haven't reported making progress on this objective.)

In other words, ID is not a scientific theory and Nelson presumably knows this. Or, is it scientific? Michael Behe, whose definition of a scientific theory includes supernatural (i.e. non-testable) phenomena, says that astrology would be considered a scientific theory under his definition.
` Science is known as 'science' because it is based on empirical evidence, which astrology has none of, other than evidence against. Which reminds me, I remember a bill being proposed to re-define what kids are taught that science is, that it doesn't need empirical evidence.
` The point of this bill was to allow ID to be taught in government-run schools. Of course, lying to our kids that about science being something other than science only serves to keep them from understanding how science actually works and how it actually requires evidence.

The Wedge Document, which highlights the ID Movement's strategy, reveals their motives and ideals. It starts out, "The proposition that human beings are created in the image of God is one of the bedrock principles on which Western civilization was built..."
` Wait... what about the Ancient Greeks? Their philosophy, arts, mathematics, architecture, science, etc. were instrumental in the development of Western civilization. What happened when Christianity took over? The Dark Ages -- that is, the decline of civilization and the spread of ignorance!
` And what happened when people started paying more attention to the Greeks' and others' ancient texts, and rediscovered all that literature and critical thinking and science? The Renaissance -- that is, the flourishing of Western culture!
` If it weren't for people who didn't believe that we're created in God's image, Western civilization might still be floundering in superstition and oppression, and wouldn't have modern technology and medicine unless another civilization invented it!

The Wedge Document also argues that the idea that we come from nature causes people to give up objective moral standards -- as though nature could possibly command us to do so!
` I can't think of anything more ludicrous -- the more-or-less objective portion of my morality certainly dictates that mass-murder is wrong, but if I thought a deity which created me wanted me to go on a suicide bombing mission, or a crusade, or kill all the Jews, or go to war in Iraq, and that anything this deity told me to do was right regardless of my compassion and concern for others, then I would have to abandon my objective moral standards in order to do it!
` It is is difficult to get people to do things they generally know not to do -- the aforementioned atrocities, excommunicating family members, genital mutilation, etc. -- unless they believe that it's for the best. This is true of any ideology, of course, not just religions -- however:
` If it's based on a 'crazy ideology' of 'mere humans', there's a small chance they could bring themselves to question it. But; what if they think that an action is being proposed by something that is supposed to be looking out for them, is all-knowing, all-good, and who promises them an eternal reward for believing, obeying, and loving -- and an eternal punishment for not doing so? It would be much more difficult to back out.

Additionally, this idea that we either come from nature or from God is a false dichotomy -- most Christians in the world also accept evolution, and in this country, because there are so many Christians, most Americans who accept evolution are Christians.
` In other words, these people think that God made them through evolution, that both things are true. How would accepting evolution mean that God wasn't responsible? Most people have a way around such black-and-white thinking.

But, back to the point -- is there religious motivation behind ID? The documentary does not mention this, but there is plenty of other documentation, including records from church meetings and public religious forums, which are hard to interpret in any other way.
` An example I can recall from the top of my head was a 1999 article for Church and State magazine entitled Missionary Man, which is about the scarily-fanatical speakers at a Right-Wing Christian conference:

Johnson calls his movement "The Wedge." The objective, he said, is to convince people that Darwinism is inherently atheistic, thus shifting the debate from creationism vs. evolution to the existence of God vs. the non-existence of God. From there people are introduced to "the truth" of the Bible and then "the question of sin" and finally "introduced to Jesus."

"You must unify your own side and divide the other side," Johnson said. He added that he wants to temporarily suspend the debate between young-Earth creationists, who insist that the planet is only 6,000 years old, and old-Earth creationists, who accept that the Earth is ancient. This debate, he said, can be resumed once Darwinism is overthrown. (Johnson, himself an old-Earth creationist, did not explain how the two camps would reconcile this tremendous gap.)

I can't picture this as being quote-mining, due to other, more direct sources I've seen, but if you'd like to challenge me on that, go ahead.
` Also, the second paragraph is important, because a big part of the object of Intelligent Design is to get rid of the details of which creation story one goes by. Did it occur over a long time? Just how much of Genesis do you have to take literally?
` These details are deliberately left out in order to garner maximum support. At the same time, without these details, there can be no hypotheses in order to test how this thing is supposed to have happened -- automatically making it not science!

The other thing is that the goal is to get evolution out of our culture, which one can only do if one has sufficient reason. If the entire object of your operation is to put forth a conclusion and then find supposed evidence to rationalize it, that's the opposite of science!


Continuing on with the documentary, the Wedge strategy's twenty-year goals include "to see intelligent design theory as the dominant perspective in science." and "To see design theory permeate our religious, cultural, moral and political life."
` In order to do that, they would need to do scientific research that supports their claims of ID as valid -- and they haven't! Phillip Johnson explains that the goal is to reverse cultural changes. This is their motivation, but where is their evidence of ID, and of supposed 'cultural changes'?

Now, Judge Jones must find the motivations of the Dover School board members, who proposed the teaching of ID. In the courtroom re-enactment, they show the tape of William Buckingham suggesting that evolution should be balanced with "creationism", but he says the meant to say "intelligent design."
` Also, Buckingham and Bonsell had sworn in their depositions that they did not know who had donated the books to the high school. In the trial, Buckingham admitted that he had given the check he had written for buying these books to Alan Bonsell, and that the 'unknown businessman' who had bought the books was Bonsell's father. Alan Bonsell must have known who this 'unknown businessman' was, yet he claimed that he hadn't! Accused of lying under oath, Bonsell claimed he misspoke.

Dover's local school board election was national news -- all eight elected opposed ID. December 2005, Jones' decision -- ID is not science, and was introduced for religious reasons, and thus is unconstitutional to teach in Dover science classes.
` Jones says, "Both defendants and many of the leading proponents of Intelligent Design make a bedrock assumption which is utterly false. Their presupposition is that evolutionary theory is antithetical to a belief in the existence of a supreme being, and to religion in general. To be sure, Darwin's theory of evolution is imperfect, however, the fact that a scientific theory cannot yet render an explanation on every point should not be used as a pretext to thrust an untestable alternative hypothesis, grounded in religion, into the science classroom, or to misrepresent well-established scientific propositions. The citizens of the Dover area were poorly served by the members of the board who voted for the Intelligent Design policy."
` "The crushing weight of the evidence indicates that the board set out to get creationism into the science classrooms, and intelligent design was simply the vehicle that they utilized to do that."
` "In an era where we're trying to cure cancer, where we're trying to prevent pandemics, where we're trying to keep science and math education on the cutting edge in the United States, to introduce and teach bad science to ninth-grade students makes very little sense to me. You know, garbage in, garbage out, and it doesn't benefit any of us. We benefit daily from scientific discoveries."
` Of course, Buckingham and Bonsell disagree, as did the ID proponents, and were somewhat appalled. Even Jones received death threats, and he and his family needed police protection. Although the trial is over, he's right -- this issue isn't settled!


The End!


Assuming you, my reader, have read all these annotations/additions to
Judgment Day, I hope you have appreciated it! To watch the actual documentary, now with the information I've provided in mind as a background reference, click here.

As for my Arch-Rival, I am not really surprised that he apparently hasn't seen this documentary, despite repeatedly assuring me that he would. I guess that when you think you're right about something, it's not worth taking a good look at your opposition.
` Which reminds me, in order to tie up the abiogenesis conversation we'd had, I later did try to show him a science magazine article about the various different studies that show how life could have arisen, and handed him the magazine, but he literally rolled his eyes and did not even look at the article!

Well, I hope at least someone out there has enjoyed my annotation -- now back to destroying Hovind's dissertation!

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