In Defense of Expelled: No Intelligence Allowed and Intelligent Design


"I cannot believe this shit. Ben Stein makes some movie that nobody ever even hears about. Then a year later it gets posted here. Then we see that in that year, over 100,000 articles centered around the National Academy of Sciences spend all of their time bashing the movie... Yeah I definitely see what is going on here."
~ Sane/Dig, Prison Planet forum moderator

"If you want to debunk dishonesty and sleaze in documentaries, the BBC is far more worthy of your attentions." ~ William Dembski

"Science provides evidence for the unobservable via inference" ~ TalkOrigins

"People write to me that evolution is only a theory. Well, it is not a theory. Evolution is as solid a historical fact as you could conceive. Evidence from every quarter. What is a theory is whether natural selection is the mechanism and the only mechanism. That is a theory. But the historical reality that dinosaurs led to birds and mammals produced whales, that's not theory." ~ Sir David Attenborough

"The first point one has to get straight in discussions like this is that ID is not the opposite of evolution. Rather, it is the opposite of Darwinism." ~ Michael Behe

"There is a difference between observations of evolution, and the cause of the changes that have been observed. We're not talking about gaps, we're talking about the creative power of the mutation/selection mechanism." ~ Stephen C. Meyer

"The supposed creative powers of the Darwinian mechanism of random errors filtered by natural selection will go down in history as one of the most stupid ideas ever proposed in the name of science. Future generations of legitimate scientists will shake their heads in disbelief that that this idea was taken seriously in the information age of the late 20th century." ~ Gil Dodgen

"We think of natural selection as tuning the piano, not as composing the melodies." ~ Jerry Fodor and Massimo Piattelli-Palmarini, What Darwin Got Wrong (2010)

"Like Behe's irreducible complexity, the concept of specified complexity can also be tested." ~ Ker Than, anti-ID science writer

"I suppose it's possible that you might find evidence for that if you look at the details of biochemistry, molecular biology you might find a signature of some sort of designer." ~ Richard Dawkins

"To find out what's true has a value all of its own. If it has additional good consequences, so be it." ~ Paul Nelson

"Smart people believe weird things because they are skilled at defending beliefs they arrived at for non-smart reasons." ~ Michael Shermer

"It was hard to be an atheist before The Origin of Species." ~ Richard Dawkins

"There are many hypotheses in science which are wrong. That's perfectly alright. It's the aperture to finding out what's right. Science is a self-correcting process. To be accepted, new ideas must survive the most rigorous standards of evidence and scrutiny ... The suppression of uncomfortable ideas may be common in religion, or in politics, but it is not the path to knowledge, and there's no place for it in the endeavor of science." ~ Carl Sagan

"In questions of science the authority of a thousand is not worth the humble reasoning of a single individual." ~ Galileo Galilei

"A fair result can be obtained only by fully stating and balancing the facts and arguments on both sides of each question." ~ Charles Darwin

A couple of years ago, I was listening to Jason Bermas' Infowarrior show and he was discussing his views on intelligent design and evolution. He mentioned the movie Expelled: No Intelligence Allowed and how it "debunks" evolution and also discusses eugenics. Back then I didn't really care much about the creation/evolution controversy, but I was interested in eugenics so I decided to watch it. For those of you who haven't seen it, the entire movie is embedded below. I recommend you watch it before reading this article.

I've seen a lot of mind-blowing, eye-opening, life-changing documentary films over the last few years - documentaries like Starsuckers, Loose Change, Wake Up Call, EndGame, Truth Rising, Selective Hearing and What In The World Are They Spraying? - but out of all of them, the one that has changed the way I look at the world the most is Expelled. Not just the film itself but also the reaction to it on the internet. It definitely touched a lot of nerves!

Most of the movie was nothing new to me. I already knew about eugenics and from my research into the global warming debate I was already aware of how the scientific establishment suppresses dissent. I just had no idea the same thing was going on in evolutionary science. I was also well aware of the so-called 'skeptics' - people like Michael Shermer - and how, when it comes to things like 9/11 truth, they're an insult to the word! But I always assumed they had it right on Darwinian evolution. Expelled made me question those assumptions.

The claim that the only people who doubt Darwin are fundamentalist conservative Christian creationists stands refuted by me! I'm not a conservative (although I do agree with many of their criticisms of the left), I'm not even remotely religious and in fact find religion pretty ridiculous (just ask my sister what I was like at my Dad's church wedding!) and I have no real objection to the idea of descent with modification from a universal common ancestor (so I'm not 'anti-evolution'). I do believe in mind-brain dualism and some form of afterlife, but that's about the extent of my religious and philosophical views. And if when I die it turns out I'm wrong about that, what do I care? I'll be dead! On my Facebook profile I've put my religious views as "Agnostic Darwin Heretic".

A month after first watching Expelled, I mentioned it during an argument on Facebook with a "left-wing intellectual elitist" (his words) friend of mine who I went to school with, his response was:
Did... Did you just try to use Expelled as a source of viable information? Expelled was a bunch of retarded IDers whinging because they didn't actually understand the scientific process.

Evolution is a fact. As time goes on, mutations in reproduction occur. These mutations can be either beneficial, negative, or do f**k all. Beneficial will lead to a higher chance of survival, Negative less so, and f**k all effect will have f**k all effect.

The organisms that have a higher chance of survival have a higher chance of reproducing, and as such, the mutated genes have a higher chance of progressing.

There is a vast (and I mean VAST) supply of literature on the subject of evolution, and it is about as close as a fact as is humanly possible to discover.

Just because the fossil record doesn't preserve every possible developmental attribute, does not mean that those stages weren't there. We just have no way of seeing them.
What was immediately interesting to me was that it seemed like he hadn't actually watched the movie! The ID proponents in the movie all accept "evolution" to some degree - and certainly understand and accept the fundamental premise of adaptation via mutation and natural selection - and at no point in the film did anyone say anything about a lack of transitional fossils. He seemed to be attributing creationist talking points to the movie that it doesn't actually make.

But since I knew he was a lot more informed than I was about evolution, I thought maybe I had been misled by the movie and so I decided to do more research. I started off by reading articles critical of Expelled. I read the Wikipedia article and all the Scientific American articles about it, numerous ScienceBlogs blogs and every page of the website Expelled Exposed. And again, I was surprised because it was as if the authors of these articles hadn't actually watched the movie. The movie exposes the very tactics that they were employing in these debunking pieces!

The movie is essentially a response to common criticisms of ID, and the counter arguments in the film seem perfectly valid to me. The critics of Expelled, rather than addressing these counter arguments, simply reassert the same weak arguments that the movie was countering!

In this article I will counter the main talking points of the Expelled debunkers. Over the last 18 months I've done a lot of research into the intelligent design controversy, and have written a number of ID posts on this blog. I decided to write this post after sorting through my old emails and stumbling upon the email from Facebook notifying me of the above comment from my friend.

Please don't take this post as an endorsement of the Discovery Institute. I know all about the Wedge Strategy and am fully aware of the Discovery Institute's political agenda - and I'm not saying I agree with that agenda. But as far as I'm concerned, whatever agenda they may have doesn't discredit their scientific arguments any more than Richard Dawkins' secular/atheist/humanist/whatever they're calling it now agenda discredits his. This post is simply about debunking the Darwinist misrepresentations of ID and the movie Expelled. I have no agenda, I simply don't like misinformation; especially when it's spouted by people who claim to pride themselves on reason and critical thinking.

"The producers misled pro-Darwin participants about the title of the movie"

Scientific American writes:
As Richard Dawkins, PZ Myers, Eugenie Scott, Michael Shermer and other proponents of evolution appearing in Expelled have publicly remarked, the producers first arranged to interview them for a film that was to be called Crossroads, which was allegedly a documentary on "the intersection of science and religion." They were subsequently surprised to learn that they were appearing in Expelled, which "exposes the widespread persecution of scientists and educators who are pursuing legitimate, opposing scientific views to the reigning orthodoxy," to quote from the film's press kit.

When exactly did Crossroads become Expelled? The producers have said that the shift in the film's title and message occurred after the interviews with the scientists, as the accumulating evidence gradually persuaded them that ID believers were oppressed. Yet as blogger Wesley Elsberry discovered when he searched domain registrations, the producers registered the URL "" on March 1, 2007—more than a month (and in some cases, several months) before the scientists were interviewed. The producers never registered the URL "". Those facts raise doubt that Crossroads was still the working title for the movie when the scientists were interviewed.
Not only is this complaint a load of fuss over nothing, but it's also totally hypocritical. So the producers lied about the title of the movie? ... Who cares?! It's not uncommon for otherwise honest journalists and filmmakers to use somewhat sneaky tactics to expose hidden truths - covertly recording people, using false personas, not fully disclosing intentions etc. - it's called going undercover! If the Expelled producers had told people like Dawkins that the movie was going to be about persecution of ID proponents, I doubt they would have taken part in it. It had to be done.

Besides, it's not as if the other side is any better. In 2006, the BBC made an anti-ID documentary entitled A War on Science. Do you honestly think the ID proponents featured in that program were told it was gonna be called a "A War on Science"?! As William Dembski comments:
I find it remarkable that the Darwinists are belly-aching about the treatment they received from EXPELLED producers. Our side experiences far worse. When the BBC interviewed me for their documentary on ID, they didn’t tell me it would be titled A WAR ON SCIENCE and that my colleagues and I would be portrayed as those trying to destroy science. Whereas the Darwinists were filmed in their offices and made to look professorial, they had me walking down a railroad track, Behe suspended in mid-air on a carnival ride looking ridiculous, etc. Finally, they spliced in commentary by Ken Miller ostensibly critiquing my work on probabilities, which he then was forced to repudiate since the criticisms were so patently off target with respect to my work — he attributed the fault to bad editing on the part of the BBC.

So, if you want to debunk dishonesty and sleaze in documentaries, the BBC is far more worthy of your attentions. The worst that can be said about the producers of EXPELLED is that they didn’t tip their hands early. In consequence, we find Darwinists with their pants down and looking unimpressive. I’m sure that hurts. Take the pain.
At 38:45 in this radio podcast, the producer, Mark Mathis, defends himself:
The most incredible part is - and this is why I sleep very well at night - when you hear these scientists speak in this film, they are being entirely consistent with what all of them do in articles, films, books and on the internet. We are not taking anything out of context. Nothing is being twisted. They are saying exactly what they can be heard saying in many other places in the media. And so we don't understand what their problem is.

They wanna have it both ways. They want everything to be done in such a way that it is demeaning to Intelligent Design, it mocks Intelligent Design and it reinforces their atheistic Darwinian view. I mean, how is it that Richard Dawkins can complain about this film, when he made his own film called The Root of all Evil - which is about religion - when he has spoken disparagingly in so many cases, written a book, The God Delusion. He's been interviewed for a film, A War on Science - that if you disagree with atheistic Darwinian view, you're not just wrong, you're part of a war on science itself. It's preposterous!
"There is no conspiracy to 'expel' ID proponents"

Well first of all, no one has ever really said there is a 'conspiracy'. 'Conspiracy' isn't really the right word. The terms I would use are 'groupthink', 'confirmation bias', 'peer-pressure' and 'pseudo-intellectual circle-jerking'. It's nothing sinister, just basic group psychology.

When it comes to the central thesis of Expelled, that ID is being suppressed in academia, the responses from the film's debunkers are very interesting. Sites like the NCSE's Expelled Exposed website on the one hand try to deny that intelligent design advocates are being persecuted, and on the other hand attempt to justify the persecution of intelligent design advocates!

Their denials can be easily refuted. With Richard Sternberg, for example, they claim that the treatment he received had nothing to do with ID, but was due to the fact that the paper by Stephen Meyer that he accepted had not been properly peer-reviewed. Emails obtained by a congressional subcommittee, however, tell a different story. In one email, the President of the Biological Society of Washington, Roy McDiarmid, wrote:
I have seen the review file and comments from 3 reviewers on the Meyer paper. All three with some differences among the comments recommended or suggested publication. I was surprised but concluded that there was not inappropriate behavior vis a vis the review process.
It's clear from the chronology of the emails that the outrage that the paper had been published came before skepticism of its peer-review. Obviously the paper's conclusion was what motivated the attacks. The peer-review stuff was just them looking for an excuse. A similar thing happened in 2009, when the California Science Center cancelled a screening of the documentary Darwin's Dilemma. The official reason was violation of contract, but internal emails again reveal how CSC staff wanted to cancel the screening because the film was pro-ID, and that the alleged pretext was a fabrication.

On September 7, 2004, the Council of the Biological Society of Washington released the following statement:
The paper by Stephen C. Meyer, "The origin of biological information and the higher taxonomic categories," in vol. 117, no. 2, pp. 213-239 of the Proceedings of the Biological Society of Washington, was published at the discretion of the former editor, Richard v. Sternberg. Contrary to typical editorial practices, the paper was published without review by any associate editor; Sternberg handled the entire review process.

The Council endorses a resolution on ID published by the American Association for the Advancement of Science (, which observes that there is no credible scientific evidence supporting ID as a testable hypothesis to explain the origin of organic diversity.
It's interesting that they would cite the 2002 AAAS resolution, since the main argument of the AAAS was that ID is not science because no case for it has been made in the peer-reviewed literature. Before the Meyer paper was published, people would say that intelligent design isn't science because there are no pro-ID papers. Then when Meyer's pro-ID paper was published, the response was that it shouldn't have been published, because it isn't science! So then they retract the paper, and then use the fact that it was retracted to strengthen their case that ID isn't science! The circular logic being employed here is akin to that of a schoolyard bully.

The emails also reveal how Eugenie Scott sent Smithsonian staff a rebuttal to Meyer's paper - a blog post on the anti-ID blog Panda's Thumb. The AAAS also linked to this "scientific critique" when discussing the controversy.

This is something that really annoys me about not just Darwinists, but 'skeptics' and defenders of consensus science in general. They always like to make themselves appear intellectually superior to their opponents by claiming that their views are supported by peer-reviewed science, while their opponents don't publish peer-reviewed science and make their claims only on blogs. They often demonize blogs and frame the debates as a bunch of idiots on the internet going up against a vast amount of authoritative, peer-reviewed literature. Yet when their opponents do publish peer-reviewed papers, and they attempt to debunk them - as Panda's Thumb did with Meyer's paper - suddenly the roles reverse. The 'skeptics' are now the random bloggers on the internet going up against peer-reviewed science. But apparently it's okay when they do it! It seems critiquing peer-reviewed science on blogs is okay, as long as you side with them. If you don't, you're an idiotic, anti-science denialist! The hypocrisy is astounding.

In a Washington Post article, Eugenie Scott admitted - while attempting to justify it - that the treatment Sternberg received was due to his views on evolution:
If this was a corporation, and an employee did something that really embarrassed the administration, really blew it, how long do you think that person would be employed?

They don't care if you are religious, but they do care a lot if you are a creationist. Sternberg denies it, but if it walks like a duck and quacks like a duck, it argues for zealotry.
So in other words, because Scott and others consider Sternberg to be a "creationist", what happened to him was - according to them - totally justified. Here we see them attempting to justify the very thing they are denying occurred!

The movie itself refutes claims that two of the other cases - Guillermo Gonzalez's loss of tenure and Robert Marks' website being shut down - had nothing to do with ID. In the case of Robert Marks, after Dean Kelley attempts to deny that what happened to him had anything to do with ID, Kelley's original email to Marks is shown on screen:
I have received several concerned messages this week about an interview and web site dealing with evolutionary computing associated ID. Please disconnect this web site immediately and Cheryl will arrange a time for us to meet immediately upon my return.
And in the case of Gonzalez, the producers interviewed Hector Avalos from Iowa State University who admitted that "what we wanted to stop is the use of the name of ISU to validate intelligent design ... and we did succeed".

It's true he wasn't explicitly referring to the tenure denial, but it is clear from Gonzalez's tenure file that intelligent design was an issue. Gonzalez's department head wrote in a private Chair's Statement that "The problem here is that Intelligent Design is not a scientific theory ... The fact that Dr. Gonzalez does not understand what constitutes both science and a scientific theory disqualifies him from serving as a science educator."

In a Talk Reason article, Dr Avalos dismisses the evidence of viewpoint discrimination by arguing that all it proves is that "-- drum roll, please—scientists do not like other scientists portraying non-science as science". Again, he is justifying the very thing the Expelled debunkers are denying occurred.

During a recent lecture in Glasgow, Eugenie Scott mentioned Expelled and once again attempted to rationalize intolerance towards ID:
Expelled ... accuses the scientific establishment of conspiring to keep the intelligent design scientists from holding jobs and sharing their groundbreaking ideas. Quite possibly the reason why intelligent design has not been accepted in the scientific community is because it's just really bad science, but that's not the position that's being taken in the Expelled movie.
In perhaps the most blatant condonation of intolerance towards ID, Expelled Exposed states:
What they seek, of course, is for intelligent design to be accepted as a valid scientific alternative to evolution. They have failed to make a convincing case for it, yet they seem to believe that they have an entitlement to a place in academia.
In other words, because the NCSE feels that ID has "failed to make a convincing case", they say ID proponents have no "entitlement to a place in academia".

To on the one hand deny that ID advocates are being persecuted, while on the other hand justifying persecution of ID is Orwellian doublethink at its most blatant. Again, it's a similar mentality to that of a schoolyard bully. Ironically, by denying that intelligent design has a right to a place in academia, the critics of Expelled have justified the central thesis of the documentary!

"ID argues that life is too complex, it must have been designed"

This straw man characterization of the design argument is mentioned in the movie. During the section on media bias, Bruce Chapman says:
We constantly deal with reporters who refuse even to report the correct definition of intelligent design. They over and over again talk about 'life is so complex god must have done it' ... It's a wanton distortion of our position.
And journalist Larry Witham says:
You can look at Associated Press stories, and the same sentence will appear in those stories for ten years: "Intelligent design says that life is too complex ... " - it's called a boilerplate. And the reporter never reports any more or gets any new ways to say it, so the public understanding never advances.
There are two things wrong with this characterization of the design argument. First of all, the claim that ID argues that life is "too complex" is incorrect. This is a common straw man that even leading ID critics like Ken Miller and PZ Myers have employed (see here). I completely agree what they are saying - that you don't need to invoke a creative intelligence to explain an 'improbable' sequence of shuffled cards or a 'complex' pile of driftwood - but ID advocates have never claimed otherwise.

What if you saw a driftwood formation that looked like this though?

Image Credit:

With intelligent design, it's not about 'complexity' or 'improbability', but specified or functional complexity. A letter of the alphabet or a single binary digit is specified but not complex, a randomly generated sequence of characters or bits is complex but not specified, and a meaningful sentence or functional piece of computer code is complex and specified. It is specified complexity that we recognize as being the product of intelligence. The examples cited by Miller and Myers are perfect examples of things which are complex but not functional or specified, so obviously you don't need to invoke a creative intelligence to explain them.

This fundamental distinction between mere 'complexity' or 'improbability' and 'specified complexity' is clearly made in the first two paragraphs of the preface to William Dembski's first foundational work, The Design Inference (1997)!

ID theorists don't simply point to the 'complexity' of life. They point out that life at every level is a specific and functional arrangement of parts. DNA is a specific and functional arrangement of nucleotide bases. A protein is a specific and functional arrangement of amino acids. A molecular machine inside the cell is a specific and functional arrangement of proteins. Etc. etc. It is this functional complexity which they say is best explained by intelligent design.

Either people like Ken Miller and PZ Myers don't actually understand the fundamental design argument or they deliberately misrepresent it. Or, most likely, it's simply their out-of-whack egos driving them to perform impressive feats of mental gymnastics - like Cartman in that Fishsticks episode of South Park.

Secondly, the overall structure of the argument is not as they characterize it. ID critics like to characterize the design argument as an argument from ignorance or incredulity (a 'god of the gaps' argument). Stephen Meyer counters this distortion in his book Signature in the Cell (2009):
As one of my frequent debating partners, Michael Shermer, likes to argue, “Intelligent design…argues that life is too specifically complex (complex structures like DNA)…to have evolved by natural forces. Therefore, life must have been created by…an intelligent designer.” In short, critics claim that ID proponents argue as follows:
Premise One: Material causes cannot produce or explain specified information.
Conclusion: Therefore, an intelligent cause produced specified biological information.
If proponents of intelligent design were arguing in the preceding manner, they would be guilty of arguing from ignorance. But the argument made in this book does not assume this form. Instead, it takes the following form:
Premise One: Despite a thorough search, no material causes have been discovered that demonstrate the power to produce large amounts of specified information.
Premise Two: Intelligent causes have demonstrated the power to produce large amounts of specified information.
Conclusion: Intelligent design constitutes the best, most causally adequate, explanation for the information in the cell.
Or to put it more formally, the case for intelligent design made here has the form:
Premise One: Causes A through X do not produce evidence E.
Premise Two: Cause Y can and does produce E.
Conclusion: Y explains E better than A through X.
In addition to a premise about how material causes lack demonstrated causal adequacy, the argument for intelligent design as the best explanation also affirms the demonstrated causal adequacy of an alternative cause, namely, intelligence. This argument does not omit a premise providing positive evidence or reasons for preferring an alternative cause or proposition. Instead, it specifically includes such a premise. Therefore, it does not commit the informal fallacy of arguing from ignorance. It’s really as simple as that.
Bottom line, the claim that "intelligent design says life is too complex, god must have done it" is a straw man. The movie notes this, yet Darwinists continue to misrepresent ID in this way.

"ID is anti-evolution"

Again, it's as though the people making this claim haven't actually watched the movie. Three times in the movie the ID position on evolution is clarified. When Ben Stein is talking to Paul Nelson, he asks Nelson if there really is a debate among scientists about whether or not evolution occurred, and Nelson's response is:
Well evolution is a kind of funny word. It depends on how one defines it. If it means simply change over time, even the most rock-ribbed fundamentalist knows that the history of the Earth has changed - that there's been change over time. If you define evolution precisely though to mean "the common descent of all life on Earth from a single ancestor via undirected mutation and natural selection", that's textbook definition of neo-Darwinism, biologists of the first rank have real questions.
When we are introduced to William Dembski, Dembski's first words in the film are:
Evolution, from an intelligent design perspective, is perfectly acceptable if the sense is that, how did the design get implemented? The issue is, is there real design there and are these material mechanisms, like natural selection, adequate to account for everything we see in biology? And our argument is, no it's not.
Later, Ben Stein asks Jonathan Wells if he thinks the whole theory is wrong or just certain parts of it, and Wells' response is:
Well again, evolution is a slippery word. I would say, minor changes within species happen. But Darwin didn't write a book called "How existing species change over time". He wrote a book called "The Origin of Species". He purported to show how this same process leads to new species - in fact, every species. And the evidence for that grand claim is in my opinion almost totally lacking.
In the film, people like Richard Dawkins repeatedly state that "evolution is a fact" and that the evidence for "evolution" is overwhelming - as if "evolution" is just one single idea. But it's not one single idea. The word "evolution" has several meanings. The three key meanings are:
  1. Adaptation via natural selection
  2. Descent with modification from a universal common ancestor
  3. The 'Blind Watchmaker' thesis
Even the most hardcore fundamentalist young-earth creationists acknowledge that natural selection is a real process that adequately explains minor adaptations. Everyone agrees, for example, that the dozen or so varieties of Galapagos finches all most likely share a common ancestor, and that the subsequent variation and diversification was due to random variation and natural selection. So no one is denying "evolution" in that sense of the word.

One argument that's frequently made is that rejecting Darwinism would negate 150 years worth of medical progress because "evolution" helps us understand how bacteria and viruses mutate and adapt etc. But which meaning of "evolution" are we talking about here? We're talking about the first meaning - minor adaptations due to variation and selection. Neither ID nor even creationism is opposed to this idea.

As for the second meaning - the idea that all life on Earth is related in a tree of life via descent with modification from a universal common ancestor - creationism in all its forms is typically opposed to this idea. Intelligent design, however, is not. While many ID proponents are also skeptical of common descent - citing things like the Cambrian explosion as evidence against universal common descent - with ID that's not the main issue. In fact there are many ID proponents who accept common descent, Michael Behe for example. In response to Eugenie Scott calling him a creationist, Behe wrote in 2000:
Scott refers to me as an intelligent design "creationist," even though I clearly write in my book "Darwin's Black Box" (which Scott cites) that I am not a creationist and have no reason to doubt common descent. In fact, my own views fit quite comfortably with the 40% of scientists that Scott acknowledges think "evolution occurred, but was guided by God."
William Dembski has also repeatedly stated that he has no stake in the debate either way:
"I'm open to common ancestry ... I don't think I would go as far as Eugenie. I think there is still some question about that but I know there are some very strong lines of evidence for common ancestry ... So I'm open to that. That's not a problem for me if that's how it turns out." ~ William Dembski, December 7, 2001

"I have no dog in this fight. If common descent were true and well supported scientifically, I could make my peace with it. My beef, and that of the ID community, is with non-teleological mechanisms like natural selection being invoked by Darwinists as designer substitutes." ~ William Dembski, March 15, 2011
One day last year, I was able to find, in only a couple of hours of research, numerous quotes by ID proponents and sympathizers clarifying the ID position on common descent. Despite the fact that ID proponents have stated many times that ID is perfectly compatible with common descent, there is a constant effort by the Darwinists to equate ID with denial of common descent. One example of this can be found in the 2007 Nova documentary, Judgment Day: Intelligent Design on Trial:
NICK MATZKE: What's really being advocated is the idea that organisms poofed into existence through the miraculous act of an intelligent designer, i.e., God. That's the view that intelligent design promotes.


NARRATOR: As it turned out, the latest in a large body of evidence to refute intelligent design and support evolution was coming to light just as this case was unfolding.


Darwin believed that evidence for his idea of common ancestry would be unearthed in the form of transitional fossils. For example, if, over millions of years, fish gave rise to land animals, as evolutionary theory predicts, we should find fossils of extinct creatures that are part fish and part land animal.
The program then goes on to discuss the discovery of Tiktaalik, a transitional form between fish and tetrapods. According to PBS, such transitional fossils "refute intelligent design", but that is false. Transitional fossils are, at best, proof of descent with modification - an idea which is perfectly compatible with intelligent design.

The main idea that intelligent design challenges is the whole 'blind watchmaker'/'climbing mount improbable' stuff; and proof of common descent is not by itself proof that natural selection can scale 'mount improbable' and act as a 'blind watchmaker'. As Casey Luskin & Paul Logan Gage write in Intelligent Design 101:
Many assume that if common ancestry is true, then the only viable scientific position is Darwinian evolution—in which all organisms are descended from a common ancestor via random mutations and blind selection. Such an assumption is incorrect: Intelligent design is not necessarily incompatible with common ancestry. Even if all organisms on earth share a common ancestor, it does not follow that the primary mechanisms causing the differences between the species must be blind, unguided processes such as natural selection.
Bottom line, probably the biggest misconception about the "intelligent design vs evolution" debate is the belief that it's between intelligent design and evolution! As William Dembski writes:
According to evolutionist Francisco Ayala, Darwin’s greatest achievement was to show that the organized complexity of living things could be brought about without recourse to a designing intelligence. Given this view of Darwin’s achievement, what evolutionary biology has come to mean by “evolution” is an unintelligent or blind form of it. This was brought home to me two years ago at a debate in which I participated. I was invited, along with my colleague and friend Michael Behe, to debate Darwinists Kenneth Miller and Robert Pennock at the American Museum of Natural History in Manhattan. The debate was initially titled “Blind Evolution or Intelligent Design?” Yet, when the debate actually took place on April 23, 2002, the program bulletin distributed at the event quietly dropped the word “blind” and titled the debate simply “Evolution or Intelligent Design?” The original title was more accurate. Intelligent design, the view for which Behe and I were arguing, is opposed to blind evolution, not to evolution simpliciter.
In the same way man-made global warming activists exploit the ambiguity of the term 'climate change' and accuse the skeptics of being 'climate change deniers', Darwinists employ the exact same semantic sleight-of-hand to discredit their opponents. Reading the writings of both groups is often like watching a three-card Monte or shell game con! The technical name for this fallacy is equivocation.

"Abiogenesis is not evolution"

The movie never claims otherwise. In fact, Jonathan Wells acknowledges that Darwinism strictly defined starts after the first life. But again, intelligent design isn't really challenging "evolution" per se. Whether you consider abiogenesis to be part of Darwin's theory or not, it is a key event in the materialist creation story, which is what ID is challenging.

"ID is untestable/unfalsifiable"

The gold standard for what constitutes a scientific explanation is testability (or falsifiability). In its 2008 booklet, Science, Evolution, and Creationism, the National Academy of Sciences states:
In science, explanations must be based on naturally occurring phenomena. Natural causes are, in principle, reproducible and therefore can be checked independently by others. If explanations are based on purported forces that are outside of nature, scientists have no way of either confirming or disproving those explanations. Any scientific explanation has to be testable — there must be possible observational consequences that could support the idea but also ones that could refute it. Unless a proposed explanation is framed in a way that some observational evidence could potentially count against it, that explanation cannot be subjected to scientific testing.
A frequent charge made against intelligent design is that it is untestable, and therefore unscientific. For example, the NAS argues later in the aforementioned booklet that "Intelligent design is not a scientific concept because it cannot be empirically tested".

However, this claim appears to be at odds with the fact that all the critics of intelligent design do is attempt to falsify it! In an impressive display of Orwellian doublethink, critics of intelligent design in one breath claim that intelligent design is untestable, and in another breath cite experimental results which they believe refute intelligent design. Ken Miller, for example, cites things like nylonase or Barry Hall's E. Coli lactase experiment as observations which undermine the case for design.

Now, whether or not these observations really do undermine the case for design is a matter of debate, but let's assume for the sake of argument that these results are as significant as Ken Miller claims. In that case, intelligent design would indeed be falsified, which is precisely why Ken Miller cites such results!

One cannot have it both ways. The fact that people put forward scientific arguments against intelligent design suggests that it can indeed be falsified. In fact, it can be falsified by simple laboratory tests like those commonly cited by critics.

Let's say for example you grew some bacteria in a laboratory for 100,000 generations or so and in that time we observed the step-by-step Darwinian evolution of an entirely new functional system in one of the populations. That would prove that it isn't necessary to invoke intelligence to explain such intricate complexity and intelligent design would therefore be as good as falsified.

Now let's turn it around. Let's say you grew bacteria in a lab for over a million generations and in that time nothing interesting happened, would that falsify Darwinian evolution? Not at all. Defenders of Darwinian evolution would simply say things like "maybe the environmental conditions weren't right", or "maybe we didn't introduce the right selective pressures" or "maybe we just didn't wait long enough" etc. Darwinists can always make excuses for why nothing happened, there is no result that would absolutely falsify Darwinian evolution.

Now again, when we say "Darwinian evolution", we're not talking about the tree of life. The tree of life is falsifiable. It could be falsified simply by finding a fossil in the wrong strata (a Precambrian rabbit, for example). What we're talking about here is the 'blind watchmaker' idea that the mechanism of random mutation and natural selection can function as a designer substitute. That assertion, it seems, cannot be falsified. So under the National Academy of Sciences' own demarcation criteria, intelligent design is actually the more scientific of the two ideas, not Darwinian evolution.

"ID violates the principle of methodological naturalism"

Intelligent design invokes the supernatural, so the Darwinists say, and science cannot invoke the supernatural. This is the ultimate "your argument is invalid"-type argument employed by Darwinists. When all else fails, they play this trump card.

The problem is, the line between the 'natural' and the 'supernatural' is not clearly defined. What we label as 'supernatural' is often determined by our current understanding of the world. There was a time when the idea of gravity was considered to be an appeal to the supernatural. Today, things like psychic phenomena are often labeled as 'magic' or 'supernatural', but what if we were to ever be visited by advanced aliens who could communicate psychically, would we still think of such a phenomenon as being 'supernatural'?

When ID critics use the term 'naturalism', what they really mean is 'materialism'; because when they say 'nature', they mean the material world. A non-materialist philosopher though would argue that 'nature' is not simply limited to the material world; that there is more to 'nature' than just the material world. A better, more clearly defined dichotomy therefore would be material versus transcendent. At best, intelligent design is an inference to something that transcends the material world, but just because it transcends the material world doesn't necessarily mean it isn't 'natural'. To assume otherwise is to assume the very thing at issue.

If 'methodological materialism' is the rule, then ID does indeed break it. But of course it does. The whole point of ID is that it is contesting the rule of 'methodological materialism'! As William Dembski explains in his rebuttal to Dover expert witness Barbara Forrest:
The point to appreciate here is that Forrest and her fellow expert witnesses, in assuming methodological materialism, have assumed precisely the point at issue. Specifically, to say, as Forrest does, that science is the search for natural explanations of natural phenomena is to presuppose that such explanations exist for all natural phenomena. But how is this claim to be justified? Rather than justify it, Forrest begs the question. To see that Forrest has indeed made a question-begging assumption here, consider the following analogy drawn from the game of chess. In chess, there are initially thirty-two pieces arranged on an eight-by-eight chessboard as follows:

Moreover, chess operates by certain fixed rules. For instance, bishops move diagonally, pawns only move forward and only take one square diagonally, etc. In this analogy, the chess pieces in their initial configuration correspond to the material entities that for Forrest constitute nature and the rules of chess correspond to the laws of interaction that for Forrest govern nature. Given the initial position of chess pieces and the rules of the game, we can ask whether the following position is possible:

It turns out that it is not. There is no way to get from the first position to the second by the rules of chess.

So too, intelligent design purports to show that there exist configurations of material entities (e.g., bacterial flagella, protein synthesis mechanisms, and complex organ systems) that cannot be adequately explained in terms of antecedent material conditions together with processes characterized by fixed laws that act on them. Granted, chess constitutes a toy example whereas the biological examples ID theorists investigate are far more complicated. Moreover, whereas chess operates according to precise mathematical rules, the laws of interaction associated with material entities are probabilistic, so the obstacles to producing complex biological configurations of material entities are not logical impossibilities but empirical improbabilities. But the point of the analogy still holds. Whenever you have a theory about process — how one state is supposed to progress into another — it is perfectly legitimate to ask whether the process in question is capable of accounting for the final state in terms of the initial state.
As I've already pointed out, the logical inference to intelligent design is testable, and that's what science is about: logical inferences that are testable using the scientific method. The objection seems to be that while the inference to design is testable, the 'designer' isn't - and the 'methodological naturalism/materialism' argument is just another way of saying that. The problem is, if logical inferences are unscientific if the thing that is being inferred to is unobservable/untestable, then lots of things that are accepted by mainstream science would also be unscientific. Consider, for example, dark energy. We can't observe or detect dark energy directly. Instead, we infer its existence based on what can observe. We observe galaxies accelerating away from one other and we logically infer that there must be some invisible, undetectable form of energy driving these galaxies apart. The reasoning behind intelligent design is basically the same: we observe functional complexity in nature and we logically infer the existence of some unobservable intelligent entity as an explanation for that. If that's unscientific then so is dark energy. So are lots of things, in fact - even Darwinism!

A TalkOrigins article defending 'macroevolution' makes this exact point:
Science Provides Evidence for the Unobservable via Inference

The primary function of science is to demonstrate the existence of phenomena that cannot be observed directly. Science is not needed to show us things we can see with our own eyes. Direct observation is not only unnecessary in science; direct observation is in fact usually impossible for the things that really matter. In fact, the most important discoveries of science have only be inferred via indirect observation. Familiar examples of unobservable scientific discoveries are atoms, electrons, viruses, bacteria, germs, radio-waves, X-rays, ultraviolet light, energy, entropy, enthalpy, solar fusion, genes, protein enzymes, and the DNA double-helix. The round earth was not observed directly by humans until 1961, yet this counterintuitive concept had been considered a scientific fact for over 2000 years. The Copernican hypothesis that the earth orbits the sun has been acknowledged virtually ever since the time of Galileo, even though no one has ever observed the process to this day. All of these "invisible" phenomena were elucidated using the scientific method of inference.
I completely agree with what TalkOrigins is saying here, but I would argue that you could use the exact same argument in defense of intelligent design!

My personal position on the demarcation issue is either ID is science, or Darwinism isn't. I don't care which one you go with. Whether you allow ID into science or demote the 'blind watchmaker' thesis to 'non-science', I don't care. The only inexcusable position as far as I'm concerned is the one advocated by the anti-ID Darwin lobby: that Darwinian evolution is science, but ID isn't. Because it seems to me that any criteria for what constitutes 'science' that you want to invoke to exclude ID, if enforced consistently, will cut just as much the other way against Darwinism. Both infer to an entity or process that's apparently unobservable, both require a certain amount of faith and both are unfalsifiable if you dismiss the arguments of the other side. So the way I see it, either they're both science, or neither is. Unless the criteria is materialism, but that's begging the question.

"ID is rebranded creationism"

The 'proof' that ID is rebranded creationism is presented in the following NCSE video:

I'll admit, I got a good laugh out of the "cdesign proponentsists" thing, but as 'evidence' I found it pretty unconvincing. As far as conspiracy theories go, and I know conspiracy theories, this is probably the weakest I've ever heard. I know if I were to ever base an anti-establishment conspiracy theory solely on a few old, mined quotations and a typo, the 'skeptics' would laugh in my face - and rightfully so - but apparently when they do it, it's okay.

Terms like 'Creationism' and 'Intelligent Design' are just labels. It is the ideas themselves that are important, not what you call them. In these early drafts of Of Pandas and People that used the word creationism instead of intelligent design, the basic content was the same as the final version. It's not as if in these early drafts they were arguing that the Earth is young or discussing evidence for a global flood, or anything like that, and then took out all that stuff after teaching creationism was ruled unconstitutional. If that was the case then yes, this would be pretty good evidence that ID = Creationism. But that wasn't the case. The fact is, the 'product' was the same in these early drafts, the only difference being that it was labeled 'Creationism' instead of 'Intelligent Design'. The critics have it backwards. This isn't proof that ID is re-labeled creationism. All this proves is that what we now call 'Intelligent Design' was once called 'Creationism'. That doesn't change the fact that what we now call 'Intelligent Design' is distinctly different from what the word 'Creationism' most commonly refers to.

It's pretty shocking to see such flawed logic from people who claim to be champions of reason and critical thinking. Most of these prominent ID critics, like Michael Shermer for example, are the very same 'skeptics' who think all 'conspiracy theories', such as those surrounding the JFK assassination and 9/11, are ridiculous. Two and a half years ago, a peer-reviewed paper was published documenting "active, unreacted thermitic material, incorporating nanotechnology" in samples of World Trade Center dust - a finding which strongly supports the alternative 9/11 theory that the twin towers were destroyed by controlled demolition. But for the skeptics, this is isn't good enough. So it seems in their minds, actual forensic proof of explosives at the World Trade Center site isn't good enough evidence for the 9/11 conspiracy theory, but a few old, mined quotations and a typo is all the proof you need for the ID = Creationism conspiracy theory! It's totally backwards!

One thing the anti-ID crowd doesn't want you to know about the Dover trial is that Judge John Jones' ruling on intelligent design was basically copied verbatim from the plaintiff's proposed "Findings of Fact and Conclusions of Law". Michael Behe highlights some of the word-for-word similarities between the two documents in the video below.

Judge Jones even copied several obviously false claims from the plaintiffs' proposed "Findings of Fact". One example of this is their interpretation of a famous moment in the trial dealing with the evolution of the immune system. As dramatized by PBS here, when Behe was questioned on this topic, the plaintiffs presented him with a stack of papers and books which they claimed refuted his assertion that the scientific literature has no answers for how the vertebrate immune system evolved.

In his 2008 book Only a Theory (2008) (pg. 74), Ken Miller characterizes Behe's response as follows:
Even when presented with every opportunity to make their case, the defenders of design retorted to little more than saying "It's not good enough for me" in the face of overwhelming evidence for evolution.
Miller's statement was in reference to the following quote from Judge Jones' ruling:
He [Behe] was presented with fifty eight peer-reviewed publications, nine books, and several immunology textbook chapters about the evolution of the immune system; however, he simply insisted that this was still not sufficient evidence of evolution, and that it was not “good enough.”
Judge Jones' characterization of the exchange was taken basically word-for-word from the plaintiffs' proposed "Findings of Fact and Conclusions of Law":
He [Behe] was confronted with the fifty-eight peer-reviewed publications, nine books and several immunology text-book chapters about the evolution of the immune system, P256, 280, 281, 283, 747, 748, 755 and 743, and he insisted that this was still not sufficient evidence of evolution – it was “not good enough.”
But let's look at Behe's exact words from the Day 12 PM transcript:
Behe: My answer, or my argument is that the literature has no detailed rigorous explanations for how complex biochemical systems could arise by a random mutation and natural selection and these articles do not address that.

Rothschild: So these are not good enough?

Behe: They're wonderful articles. They're very interesting. They simply just don't address the question that I pose.
The "not good enough" quote was not Behe's words, but Rothschild's. Later, the relentless Rothschild posed the same question again:
Rothschild: Is that your position today that these articles aren't good enough, you need to see a step-by-step description?

Behe: These articles are excellent articles I assume. However, they do not address the question that I am posing. So it's not that they aren't good enough. It's simply that they are addressed to a different subject.
As you can see, Behe did not say "it's not good enough". In fact, he said the exact opposite.

So the plaintiff attorneys distorted the facts, Judge Jones copied their distortions word-for-word without checking the facts and Ken Miller parroted Judge Jones in his book. The Darwinists believe they've found a transitional fossil in the form of "cdesign proponentsists", but we can go one better. Here we have a clear, documented, irrefutable example of descent with modification!

"Darwinism is compatible with theism"

Intelligent design advocates use the word Darwinism (or Neo-Darwinism) not as an ad-hominem, but to distinguish belief in common descent from the belief that all life is the result of purely unguided, unintelligent, material processes like random mutation and natural selection, which is what intelligent design is primarily challenging.

People such as those at the NCSE assert that Darwin's theory of evolution is perfectly compatible with a belief in god. If by "evolution" one simply means common descent, then I agree. It is not logically contradictory to believe that all life on Earth evolved from a common ancestor and that god intelligently guided that evolution in some way. But such a belief would fall under the category of intelligent design. Since the NCSE is so critical of intelligent design, it is obvious that when they say "evolution", they mean Darwinism.

As Stephen Meyer briefly explains in the above video clip, it is logically contradictory to believe in Darwinism and in god, because Darwinism asserts that the appearance of design in life was produced solely via unguided, unintelligent, material processes such as random mutation and natural selection. How can god, an intelligent, transcendent entity, guide an unguided, unintelligent, purely material process?! That's so much a theological problem as it is just a basic logical problem!

In the movie Expelled, both Richard Dawkins and PZ Myers admit that it was their acceptance of Darwinian evolution that turned them atheist. Ask any of their followers and they will likely tell you the same thing. Atheists turn atheist because they can see no logical way to reconcile Darwinian evolution with belief in god. And this is one point that intelligent design proponents agree with them on. Darwinian evolution is a 'blind watchmaker'. The whole point of it is that it takes away the need for an actual 'watchmaker'. The only way god could play any role in evolution is if there was more at work than just the 'blind watchmaker'. But then that wouldn't be purely Darwinian evolution, it would be intelligently directed evolution, i.e. intelligent design!

So it seems theistic evolutionism in general is fine, but theistic Darwinism is an oxymoron.

"Expelled blames Darwin for the holocaust"

While there isn't conclusive evidence that Darwin himself advocated eugenics, the connection between Darwin's ideas and the eugenics movements of the early twentieth century are well documented. But no one is "blaming" Darwin or his theory for the holocaust, we are simply pointing out that connection. And certainly no one is saying that all evolutionists are Nazis. In fact, both Ben Stein and David Berlinski are careful to emphasize this in the movie. It's not that belief in Darwinism automatically makes you a eugenicist or a Nazi, it's that people who are eugenicists/Nazis are attracted to Darwinism. In their minds, Darwin's theory is a scientific rationalization for their ideology.

All of the great twentieth century tyrannical regimes were rationalized 'scientifically'. Except it wasn't actually science though, but politicized dogma heavily propagandized by the state. Consider, for example, the 'race science' that led to the Holocaust. While we know in retrospect that the whole thing was a bunch of pseudo-scientific nonsense, it was widely accepted by the establishment in Germany at the time. You had professors of 'racial science', you had top research institutions endorsing it. If you were alive then, you would likely have been told that it was a "well-established scientific consensus", or something to that effect. And of course, any scientist who publicly challenged it was discredited or worse, so few people did so out of fear.

Hitler didn't round up and exterminate millions of Jews by himself; he had an army to do it for him. Most of those who did the deed were arguably not technically malevolent, they were simply victims of propaganda who genuinely believed they were doing the right thing and were too weak minded to question their orders. That's how tyranny works. Without 'race science', there would have been no justification for the Nazis racial policies, and the end result most likely would not have been possible.

The lesson here is that the scientific establishment tends to go along with the state, regardless of the empirical merit of the state's claims, so we need to be vigilant whenever a politically or ideologically sensitive idea such as climate change or evolution is dogmatically promoted by the establishment, and the intellectual freedom to challenge these ideas is vitally important. That was the central message of the movie Expelled. It's not really warning us about Darwinism per se, but about scientific elitism in general.

Contrary to mainstream history, eugenics did not die with the Nazis. Many leading names in science today are eugenicists. The most infamous is John P. Holdren. He is President Obama's current science advisor and is a former president of the American Association for the Advancement of Science. In 1977, he wrote a book called Ecoscience which called for all kinds of eugenical policies including compulsory sterilization and abortion. Whatever your view on abortion - pro-life or pro-choice - the idea of compulsory abortion should sicken you. In China, mothers who violate the nation's one child policy can have their babies forcefully aborted, even if they are in their ninth month of gestation, and people like Holdren want this sort of thing worldwide. With people like him essentially running science, is it any wonder alternatives to Darwinian materialism aren't allowed?! Again, it's not that belief in Darwinism automatically turns you into a person like Holdren, but certainly Darwinism is attractive to people like him.

One final point on the Darwin-Hitler connection, it's interesting how the critics say THE MOVIE links Darwin to the holocaust. "The movie" is basically a collection of interviews. "The movie" doesn't claim anything. It is the people in the movie that are making the claims. Interestingly, the person in the film who makes the most forceful connection is Uta George, the curator of the Hadamar holocaust museum. When Ben Stein asks her if this was "a Darwinian concept", she says yes. Stein then asks her if it was also Malthusian and she says "yes but the Nazis, they relied on Darwin". Here we have a third-party expert witness who has no stake in the debate over Darwinian evolution. If you have a problem with the movie's claims, take it up with her!

"Ben Stein twisted Richard Dawkins' comment about alien designers"

According to some critics, Ben Stein twisted Dawkins' words to claim he believes life on Earth was intelligently designed by aliens. As Dawkins himself writes:
Stein said something like this. "What? Richard Dawkins BELIEVES IN INTELLIGENT DESIGN." "Richard Dawkins BELIEVES IN ALIENS FROM OUTER SPACE."
Here is a clip of the scene in question:

I'd like to know what movie Dawkins was watching, coz I didn't hear a "ZOMG! Dawkins believes we were intelligently designed by aliens" in there! That may be how some creationists spun it, but that's not how Ben Stein interpreted it.

The damning thing about Dawkins' statement - and this is I think what Ben Stein meant - it's not that he seems to be open to the idea that we were intelligently designed by aliens, it's that he admitted that design is a scientifically testable idea. He said it's possible that we may find evidence for this "intriguing possibility" in biochemistry and molecular biology, in the form of a "signature". This is why Stein said, "Wait a second, Richard Dawkins thought intelligent design might be a legitimate pursuit". He didn't say Dawkins thinks intelligent design is true, he simply commented on how he seems to be advocating scientific inquiry into a design hypothesis.


I think what's going on here is that the Darwinists, atheists, anti-ID people etc. are watching Expelled with the preconceived belief that it is dishonest creationist propaganda. And so rather than simply listening to the raw arguments in the movie, they're twisting everything they hear so it fits that preconceived view. They're convinced there is an agenda, so they are interpreting everything they hear based on the assumption that there is an agenda and so they get very defensive and attribute claims to the movie that it doesn't actually make.

If one watches the movie with no emotional investments one way or another, and actually listens to what's being said instead of getting all defensive and immediately consulting your own internal "how to debate a young-earth creationist" debating manual, like I did, and a friend of mine did (who by the way is an atheist), one comes away with a completely different opinion of the movie. When I read the writings of the film's debunkers, I honestly get the sense that they watched a completely different movie to the one I saw. They're not debunking the movie, they're debunking their own distorted interpretation of the movie. It really illustrates the power of ideological commitment, which was one of the film's points...
John Lennox: What is being presented to the public is, first comes the science and then comes the world view. I would want to argue that that may not be the case, that it may actually be the other way around; that the world view comes first and is influencing the interpretation of science.

Alister McGrath: My deep regret is that some people are so deeply entrenched in their own world views that they will simply not countenance alternatives

The Great Debate: Blind Watchmaker or Intelligent Design?

One thing I've noticed from reading, listening to and participating in numerous debates on the internet is that they tend to go round in circles.

Essentially the entire atheist/Darwinist view is based on a denial of design (1). As Richard Dawkins wrote in River out of Eden (1995):
The universe we observe has precisely the properties we should expect if there is, at bottom, no design, no purpose, no evil and no good, nothing but blind pitiless indifference.
But wait, there are people out there who say there is a case to be made for design (2)! Intelligent design advocates point to the functional complexity of life, making comparisons to human technology and information, to argue that life is most likely the product of intelligence.

Darwinists respond by pointing out that human technology is not made of self-replicating DNA, and therefore the comparison is invalid (3). The problem with this argument is it assumes the very thing at issue. Why do they believe it to be different for things made of self-replicating DNA? Well, because they believe there exists this designer substitute mechanism of random mutation and natural selection that can explain the appearance of design in living things and remove the need for real design. But can random mutation and natural selection function as a designer substitute? That's the question!

Intelligent design advocates note logical problems with the 'blind watchmaker' thesis, pointing to irreducible complexity as an apparent obstacle for the gradual Darwinian mechanism. They also point out that it has never been empirically demonstrated in a lab (4) that the mechanism can produce entirely new functional systems.

The typical Darwinist response at this point is to state that the reason it hasn't ever been observed in a lab is because it can't be, since the process takes millions of years (5). The problem is, this doesn't do them any favours, because they are essentially admitting that the 'blind watchmaker' thesis is untestable (6).

The Darwinist's then distort this valid criticism of Darwinian evolution into an argument from ignorance/incredulity, or what they call a 'god of gaps' (7) argument. They claim the case for design is based solely on not being able to imagine how it could happen via Darwinian means. ID advocates respond by asserting that it's not just a 'god of the gaps', it's an inference to the best explanation. It is not just a negative argument against Darwinism, because there is also a positive case to be made for design (2)! From this point on, the debates just go round in circles.

Debating in this manner isn't going to get us anywhere. I know it's difficult in this age of trolling, but we have to get past this kind of reactionary debate mentality. The simplest, fairest and most rational way to approach this debate is to look at the basic pros and cons of the two hypotheses.

Occam's Razor dictates that when we have multiple competing hypotheses of equal explanatory power, we should tend towards the simplest one. So if Darwinian evolution has the explanatory power to account for everything in biology, then that is the hypothesis we should go with. On the other hand, if it doesn't have the explanatory power, then we should go with the hypothesis that does have the explanatory power: intelligent design.

So it all comes down to one fundamental question: Does Darwinian evolution have the explanatory power? Can it function as a 'blind watchmaker'? To the people who say it can, the burden of proof is on you! I will now take a look at the positive case, or lack thereof, for this grand Darwinist claim.

Probably the most embarrassingly bad efforts to prove that natural selection can function as a designer substitute are the ones which involve computer algorithms. In Richard Dawkins' book The Blind Watchmaker, he attempts to show how a Darwinian process can generate a line of Shakespeare using a computer program he made. In the clip below, he gives a demonstration this "weasel" program.

Now there's nothing wrong with Dawkins' program, the problem is, it isn't Darwinian. Dawkins himself admits that it's "a bit of a cheat", because it looks into the future and homes in on a distant target. However, he also asserts that it's still a "fairly good model" for Darwinian evolution. I agree that it's a cheat, but I disagree that it's a fairly good model for Darwinism. You're giving foresight to a process that by its very definition has no foresight!

As a computer programmer myself, I see how ridiculous Dawkins' logic here is. When the programmer or user of a program specifies a line of text to be printed on screen, it doesn't matter how it does it; whether it fetches the string directly from the memory and prints it, or repeatedly manipulates a randomly generated string until it matches the specified string and then prints that. At the end of the day, the reason that line of text is on the screen is because it was specified intelligently by the programmer or user.

What Dawkins' program is modelling is more of a teleological process. It demonstrates that evolution is possible if information is in some way hard-coded into the universe, but that was never in doubt. The question is, where does the information come from? Rather than refuting the design argument, Dawkins' has proven their point, because the information was specified intelligently by him.

But Dawkins' weasel program is simple. Over the years, evolutionary algorithms have become more sophisticated. Nonetheless, they all suffer from the same basic flaw. Consider, for example, the Avida simulation.

In 2003, a paper by Lenski et al. was published in Nature entitled The evolutionary origin of complex features. The paper was clearly a response to the claims of intelligent design advocates. The abstract of the paper begins with "A long-standing challenge to evolutionary theory has been whether it can explain the origin of complex organismal features" and ends with "These findings show how complex functions can originate by random mutation and natural selection". One of the authors of the paper, Robert Pennock, is a prominent critic of intelligent design. The findings were hailed in scientific magazines as a mortal blow to creationism and ID. And the paper was even used as evidence in the Dover trial. Yet the authors avoided referencing the work of ID proponents. Perhaps because if they did they would be acknowledging that ID is a scientifically testable idea, which of course contradicts their constant assertions to the contrary. By not referencing any pro-ID work, they were able to challenge intelligent design in a leading journal while avoiding legitimising it. The conspiracy theorist in me suspects that was intentional!

And before you say "What pro-ID work?!", they could have cited a pro-ID book. Books are often cited as references in peer-reviewed scientific papers. Take, for example, Charles Darwin's On the Origin of Species!

The Lenski paper reported on research using the Avida artificial life software. Avida is a virtual Petri dish in which digital "organisms" self-replicate, mutate, compete and evolve. When an organism is "born" with a mutation that allows it to perform a logic function, it is rewarded with increased "fitness". The more complex the logical operation, the more fitness the organism is rewarded with.

Sounds good, right? The problem is, the relative fitness of an organism is determined by static, absolute fitness multipliers. As Robert Deyes writes:
Equally striking were the computational merits that were awarded to digital organisms whenever they performed particular logic functions. NOT and AND functions for example were given a computational merit of 2 while 'EQUALS' was given a merit of 32. It seems that even evolutionary biologists would have a problem here since their claim is that in real life, what constitutes evolutionary fitness is never pre-specified. No single trait gives an organism an absolute merit value for every type of situation it encounters. So rather than demonstrating Darwinian natural selection, AVIDA appeared to show what happens in a teleological world where goals and purpose are front-loaded into the fabric of life ... If anything what we see here is an example of goal directed evolution- precisely what Darwinian evolution purports not to be.
Since "fitness" is an absolute numerical value that is increased the closer you get to the target function, it is unsurprising that the target function evolved. It is the exact same flaw that Dawkins' weasel program has.

By rewarding the simpler functions, the simulation pre-supposes a gradual pathway to the target function. The Lenski paper discusses what happened when the simulation was set up so the simpler functions yielded no reward:
50 populations evolved in an environment where only EQU was rewarded, and no simpler function yielded energy. We expected that EQU would evolve much less often because selection would not preserve the simpler functions that provide foundations to build more complex features. Indeed, none of these populations evolved EQU, a highly significant difference from the fraction that did so in the reward-all environment.
In other words, when they modelled a situation where there was no selective advantage until you have the final function - i.e. when they truly modelled irreducible complexity - the final function did not evolve. Avida's success, therefore, depends on there being a gradual pathway to complex functions. As Casey Luskin puts it, Avida "does not test Darwin's theory--it assumes it".

The Lenski paper was hyped as a refutation to irreducible complexity. The truth is, the authors began with the assumption that there is a gradual pathway to the complex function and then ran the simulation and documented how it followed that gradual pathway. If it were a true test of irreducible complexity, the task would be to find a gradual pathway, not follow a pre-specified one.

Casey Luskin also notes how the process of "mutation" in the Avida world is nothing like the process of mutation in biology:
Another way the study granted too much selective advantage was that every mutation inserted a line of code which had pre-set meaning and functionality in the computer-environment. The biological analogy might be inserting a fully functional protein via the duplication of a gene. Such gene-duplication events do occur in biology, but biochemical evolution at the gene-level must also via point mutations (or insertions or deletions of segments of DNA within a gene). Point mutations, insertions, or deletions need not add such discrete and meaningful functionality, however every mutation in the Lenski paper which added code represented the addition a of a complete and discrete function. The paper thus granted the addition of too much functionality for each "mutation" and did not accurately model biology in this respect. Were it to accurately model biology, the study might have randomly substituted, inserted, or deleted code at the lower level of words or even letters into the code of the digital organism. While this might have had the effect of creating many syntax errors in the code of the digital organism, it might have been closer to what really happens in biology when a gene experiences substitutions, insertions, or deletions of nucleotides.
Put simply, the instructions themselves aren't altered, what is altered are the attributes that determine whether or not an organism can execute a certain instruction.

To understand why "digital world" evolutionary simulations miss the point, consider the analogy of video game "unlockables". Lots of video games reward their players when they reach certain milestones in the game by making new weapons, vehicles, areas etc. available to them. When an unlockable is made available to you, the information coding for that unlockable doesn't just spontaneously come into existence, does it? Nor was it created by you playing the game. No, the information was already there, it just wasn't being used before. When you reach the defined milestone in the game, and the unlockable is made available, all the game does is start using the information that was already there in the game's code and data files. And that code, ultimately, was intelligently written by a programmer.

With "digital world" simulations, it's essentially the same principle. When the digital organisms "evolve" certain functions, the information coding for those functions was already there, hard-coded into the digital world by the programmer (or into the physical computer itself if the instructions are machine level). All that's happening is, when a digital organism gets lucky and is born with a certain virtual genome (which was basically homed in on), it can now use that pre-programmed information. So all these simulations really are, essentially, are video games playing themselves!

In summary, Avida shows that evolution will work if:
  • Natural selection works by numbers.
  • An end goal is pre-defined and an organism's "fitness" depends on how close it is to that end goal.
  • It is assumed that there is a gradual pathway to all complex functions.
  • The process of mutation is simply the reordering of lines of pre-programmed, functional code that's stored outside the organism's genome and is immune to alteration.
The problem is, this isn't how Darwinian evolution works in reality!

The central question is, how did the information in biology arise? By an undirected, unintelligent process, or by intelligent design? The only thing evolutionary algorithms demonstrate - whether they're a simple program like Dawkins' weasel program or a digital world - is that evolution will work if there is pre-specified information in some form. They do not demonstrate that an undirected, unintelligent process can create information.

Bottom line, the idea that you can use intelligently designed computer algorithms running on intelligently designed computers to show that intelligent design isn't necessary to explain life is simply ludicrous! The purely Darwinian version of evolution has no pre-programmed goals and no pre-specified functions, and it is not possible to create a simulation of evolution without either. All the Darwinists have proven with their simulations is that computers will do what you tell them to! Shocker! If this is all one has to do to get inducted into the Royal Society, I think I might have a go myself!

More technical dissections of evolutionary algorithms can be found at The Evolutionary Informatics Lab.

Historically, the human eye has been cited by many as a something so intricate that it could only have been designed, but in recent years we have often been told that evolutionary theory has explained how the eye evolved by Darwinian means. In the above clip from an episode of the BBC's Bang Goes The Theory series, Richard Dawkins outlines the leading evolutionary explanation, describing how the "camera" eye is believed to have evolved from a light-sensitive spot, via the intermediary stages of a "cup" eye and a "pinhole" eye.

Mystery solved, right? Well, not according to some. A number of Darwin heretics have criticised this explanation, calling it oversimplified and purely speculative. The fact that these simpler eyes exist in nature is proof of evolution in a sense. It is proof that eyes have increased in complexity. But that isn't proof that the undirected process of random variation and natural selection is what created the camera eye. Michael Behe, David Berlinski, Casey Luskin, Jonathan MacLatchie and Sean Pitman have each written detailed critiques of various aspects of this eye evolution story. See my blog post entitled The Oversimplified Eye Evolution Fairytale for a compilation of key extracts from these critiques.

To summarize, the account starts off with a fully functional eyespot of light-sensitive pigments already present. So in other words, our story begins at the second chapter! We are taking vision as a given with no discussion as to how you go from no vision to vision via a gradual Darwinian process. Even the simplest form of vision is, biochemically, extremely complicated.

And at the other end, when the lens is introduced, there is no mention of how this occurs in embryological development. The development of the lens is a remarkably complex cascade involving numerous chemical triggers. First, the embryo's outer surface thickens and bulges. The bulge then separates into a free-floating element called a lens vesicle as the eye is developing around it. The vesicle cells then differentiate and become transparent lens fibers. Remarkably, subsequent development of the eye depends in large part on chemicals secreted by the developing lens! The process of lens development illustrates that it's a lot more than just "hardened jelly", as the BBC presenter characterized it, and the mutual dependency between the developing eye and developing lens seems inconsistent with the premise that the lens was a relatively late add-on.

The theory also only makes sense if you invoke the abrupt appearance of additional components such as the cornea, the iris, muscles to move the eye and focus the lens and mechanisms for colour vision etc. Each of these things would certainly give an organism a selective advantage over organisms that don't have these things, but where do these things come from in the first place? It's not as if they can each arise fully formed in a single mutation! Like the eye itself, these parts have to come about via a gradual ascent up 'mount improbable'. But again, there's no apparent functional advantage until those parts are fully formed, so they can't arise via that kind of process! It seems natural selection is good at explaining the survival of the fittest, but not the arrival of the fittest!

Furthermore, each stage in the evolution of the eye has to be accompanied by changes to the optic nerve - to transmit the additional information - and neurological changes in the brain - to process the additional information - otherwise there will be no improvement in vision. So each stage in eye evolution is not just one modification, but three modifications. If these three modifications arose simultaneously, then we are no longer talking about a gradual ascent up 'mount improbable'. If they did not arise simultaneously, then there is no logical reason for them to come about at all because there's no reason for natural selection to preserve just one or two of the modifications.

At best this account provides a step-by-step explanation of "numerous gradations" for only one feature of the eye: its concavity. But even that would be giving it too much credit, since no experiments have ever been done to test this theory. It wouldn't be too difficult to test. All you would have to do is take a creature with a flat eyespot, have it produce offspring and artificially select for those with slightly more dimpled eyespots. Repeat this for several generations and see if you can get close to a "cup" eye. If it works, then you can test the new eyes against the old to see if there really is an improvement in vision. If there is, then part of the theory at least would be experimentally confirmed. It could at least be considered science then. At present, it's nothing more than a just so story.

Recently featured on the front page of the parody wiki Uncyclopedia was an article taking the piss out of irreducible complexity. In the article, the writers attempt to ridicule the logic by using the example of an arch. An arch is irreducibly complex in a sense, since the removal of one of the stones will result in the entire structure collapsing. Yet arches are built gradually with the aid of scaffolding.

So if an arch can be constructed gradually with the aid of scaffolding, it has been suggested that irreducibly complex systems in nature could also be constructed gradually with the aid of some form of biochemical "scaffolding". The premise is similar to geneticist Hermann Muller's idea for how "interlocking" complexity could arise by gradual means due to systems changing in such a way that they become dependent on parts that were originally merely an asset.

As Boudry et al. write in an article entitled Irreducible Incoherence and Intelligent Design – a look into the conceptual toolbox of a pseudoscience:
As early as the beginning of the 20th century, geneticist Hermann Muller explained how biological systems that depend on the complex “interlocking” actions of many different components could come about by evolutionary processes: “Many of the characters and factors which, when new, were originally merely an asset finally became necessary because other necessary characters and factors had subsequently become changed so as to be dependent on the former” (Muller 1918, pp. 463-464). Thus, redundant complexity can eventually generate IC (under the weak interpretation). More recently, biochemist and molecular biologist A. G. Cairns-Smith proposed the analogy of “scaffolding” in the construction of an arch to explain the evolution of systems that are IC according to Behe (Cairns-Smith 1986; see also Orr 1997; Pennock 2000). A classical stone arch is IC in the weak sense, because the structure will collapse as soon as one removes either the keystone or one of the other stones. The support of scaffolding is necessary in building a stone arch, but once the arch is completed, the scaffolding can be safely removed. In a similar vein, a biochemical structure may have functioned as a scaffold in the evolution of an IC system before becoming dispensable and disappearing. That is, “Before the multitudinous components of present biochemistry could come to lean together they had to lean on something else” (Cairns-Smith 1986, p. 61).
The scaffolding analogy is a nice idea, but no one has ever suggested a way in which it could apply to biochemical machines and processes. The function of an arch is to stay up, and a partially constructed arch can stay up with the help of scaffolding, but how do you "scaffold" a partially constructed motor so that it can function as a motor? When talking about mechanisms, the scaffolding analogy makes no sense!

The most commonly parroted counter argument to irreducible complexity is Ken Miller's idea of "co-option". Ken Miller agrees that if you remove just one of the bacterial flagellum's 40 parts, it can no longer function as a flagellum. However, he argues, that doesn't necessarily mean it's entirely non-functional. He cites the example of the type-III secretion system, a needle-like structure found in pathogenic bacteria which is built from 10 of the bacterial flagellum's 40 parts. Miller reasons that the bacterial flagellum likely evolved from something like the type-III secretion system, a simpler molecular machine with a different function.

It is unlikely that the flagellum evolved from the type-III secretion system itself. If anything, it was probably the other way around. If you think about it, bacteria have been swimming around in the water a lot longer than they've been acting as pathogens for eukaryotic organisms. As a 2008 New Scientist article reported:
One fact in favour of the flagellum-first view is that bacteria would have needed propulsion before they needed T3SSs, which are used to attack cells that evolved later than bacteria. Also, flagella are found in a more diverse range of bacterial species than T3SSs. "The most parsimonious explanation is that the T3SS arose later," says biochemist Howard Ochman at the University of Arizona in Tucson.
But even if you ignore that, the existence of the type-III secretion system still doesn't explain the evolution of the bacterial flagellum. To understand why irreducible complexity is such a problem for Darwinism, consider Dawkins' analogy of climbing Mount Improbable...

On one side of the mountain we have an unscalable cliff face, which represents the probability of something like the eye arising by chance alone. On the other side, however, Dawkins envisions a more gradual route. This gradual route represents the gradual Darwinian process of random genetic change and natural selection. It is claimed that through incremental tinkering, with each step providing some type of functional advantage, complex structures can arise over several generations.

The problem is, for irreducibly complex systems, there doesn't appear to be a gradual route! The idea of a gradual route depends on there being a series of functional intermediate stages. But for irreducibly complex systems, there is no function until you have the complete system. If there's no gradual route, there's no way it can evolve incrementally via random mutation and natural selection. In order to refute the argument from irreducible complexity, you have to prove that there is, in fact, a gradual route to such a system.

But Ken Miller has not done that. All he has done is suggest one possible step along the route. To say this refutes irreducible complexity is like saying you could travel by foot from Southampton to New York because we know there's an iceberg somewhere in between! Darwinists need to do better than that.

Miller's idea of co-option has been expanded upon by Nicholas Matzke, a former NCSE staff member and contributor to the Panda's Thumb blog, who was the guy who blatantly misrepresented ID in the quote from the PBS documentary I cited earlier. In 2003, he wrote a lengthy article proposing a Darwinian explanation for the bacterial flagellum. His theory is animated in this YouTube video by cdk007 and in 2006 he challenged the design argument in a paper in Nature.

Sean Pitman has written a technical critique of Matzke's 2003 article. In summary, he writes:
Given the TTSS system as a starting point, regardless of the tenuousness of that hypothesis, the next steps in the evolution of the flagellum should be easy - right? With just a few residue changes here and there, the pathway of improved beneficial function should be made up of neat, closely spaced, steppingstones. Consider that Matzke's proposed scenario is one of the most detailed descriptions that I have come across - as superficial as it is. Necessary parts just pop into existence and easily attach to each other in just the right way. No detailed discussion concerning the significant modifications that would be required for such specific attachments to be realized to a beneficial degree is provided. Matzke's discussion is a gross underestimate of the complexity involved in going from one beneficial state to the next along his proposed evolutionary pathway.

In fact, not a single evolutionary step proposed by Matzke or anyone else has ever been demonstrated to be "crossable" in any laboratory experiment - - not one. Without the ability to test such stories in the laboratory, they are simply not falsifiable and therefore are, by definition, not supported by scientific method. It may seem strange for many to even consider this, but such statements concerning the evolution of complex functions, on the order of flagellar system complexity, are not scientific at all - they aren't even theory. At the very best they are untested and perhaps untestable propositions. Simply put, these "stories" about flagellar evolution are just that - - fairytale stories. And, when examined in closer detail, they don't even look good on paper.
I have to commend Matzke for his efforts. As William Dembski said, "he has told the best Darwinian story to date concerning the evolutionary origin of the bacterial flagellum". But that's all it is - a story! Much like the eye evolution story, it's oversimplified, it invokes the abrupt appearance of key parts and most importantly from a scientific standpoint, it isn't testable. It's just another Darwinian fairytale masquerading as science.

Computer algorithms and just so stories do not a science make. For the 'blind watchmaker' to be considered scientific, you need more than that. You need to actually empirically test it in a lab.

But of course there are some interesting experimental results which are cited by Darwinists as examples of the 'blind watchmaker' in action. In Chapter 5 of The Greatest Show On Earth (2009), Dawkins discusses Richard Lenski's long-term E. Coli evolution experiment; specifically, the results of a 2008 PNAS paper reporting on the evolution of citrate metabolism in one of the populations. Dawkins' interpretation of this find is that it "undermines [the] central dogma of ‘irreducible complexity’".

What Dawkins neglected to mention though is that two days after the paper was first published online, Michael Behe - the man who coined the term 'irreducible complexity' - wrote about the paper and argued that it supported his thesis in his 2007 book, The Edge of Evolution.

Not only is Behe's article not mentioned in Dawkins' book, but Behe's name doesn't appear in the book at all. There's a few mentions of 'irreducible complexity', but no mention of the man who came up with the concept, or of any leading ID proponent for that matter. Instead, while discussing Lenski's research, Dawkins sets up a straw man by telling a boring anecdote about some silly dispute with a Conservapedia editor:
Andrew Schlafly, creationist editor of ‘Conservapedia’, the notoriously misleading imitation of Wikipedia, wrote to Dr Lenski demanding access to his original data, presumably implying that there was some doubt as to their veracity. Lenski had absolutely no obligation even to reply to this impertinent suggestion but, in a very gentlemanly way, he did so, mildly suggesting that Schlafly might make the effort to read his paper before criticizing it. Lenski went on to make the telling point that his best data are stored in the form of frozen bacterial cultures, which anybody could, in principle, examine to verify his conclusions. He would be happy to send samples to any bacteriologist qualified to handle them, pointing out that in unqualified hands they might be quite dangerous. Lenski listed these qualifications in merciless detail, and one can almost hear the relish with which he did so, knowing full well that Schlafly – a lawyer, if you please, not a scientist at all – would hardly be able to spell his way through the words, let alone qualify as a bacteriologist competent to carry out advanced and safe laboratory procedures, followed by statistical analysis of the results. The whole matter was trenchantly summed up by the celebrated scientific blogwit PZ Myers, in a passage beginning, ‘Once again, Richard Lenski has replied to the goons and fools at Conservapedia, and boy, does he ever outclass them.’

(Richard Dawkins, The Greatest Show on Earth (2009), pg. 131)
This is a perfect example of how people like Dawkins and Myers approach this issue - it's all straw man! As David Klinghoffer notes:
If you follow the top Darwin blogs you'll notice how eagerly and often they go in for mocking extremely marginal and daffy creationists. PZ Myers specializes in this. So too, in his books, does Richard Dawkins. How about answering the arguments of a real scientist who advocates intelligent design on scientific rather than Bible-thumping grounds -- a Douglas Axe or Ann Gauger, for example? How about a thoughtful critique of The Myth of Junk DNA or Signature in the Cell? A response to serious science bloggers like ENV's Casey Luskin or Jonathan M.?

Uh, no, thank you!

It's quite a contrast with intelligent-design advocates who, like them or not, wrestle with the top scientists and thinkers on the other side, while ignoring the small timers.
In 2009, while both Dawkins and Stephen Meyer were on book tours, Meyer noticed that their tours crossed paths and challenged Dawkins to a debate; Dawkins declined. A few days later, during an appearance on The Michael Medved Show, Dawkins was asked by Discovery Institute President Bruce Chapman about his refusal to debate ID proponents. Dawkins' response was:
I will have a discussion with somebody who has a genuinely different scientific point of view. I have never come across any form of creationism, whether you call it intelligent design or not, which has a serious scientific case to put.

The objection to having debates with people like that is that it gives them a kind of respectability. If a real scientist goes onto a debating platform with a creationist, it gives a kind of respectability which I do not think that your people have earned.
Interestingly, that's the exact same BS excuse Al Gore gives for why he refuses to debate man-made global warming skeptics, and the same reason NIST gives for why they won't debate Architects and Engineers for 9/11 Truth. But the thing is, Dawkins actually DOES debate his opponents, but only his more fringe opponents. A few years ago, he presented a series on Channel 4 called The Genius of Charles Darwin, and devoted an entire episode to debating creationists. And the creationists featured in the program were far less deserving of attention than the ID scientists. Essentially, Dawkins avoids debates by arrogantly appealing to his own authority, but he isn't even consistent about it. I think the real reason he refused to debate Stephen Meyer is pretty clear: he isn't confident he can best him.

I've read The Greatest Show on Earth and actually agree with most of it. Since I have no issue with the age of the Earth or common descent, the only scientific chapter I really have issue with is Chapter 5. It's not so much what's in the book that's the problem, it's what's not in the book! On the back cover of the book there is a quote from The Times praising it as "a beautifully crafted and intelligible rebuttal of creationism and intelligent design", but the truth is, it hardly addresses intelligent design claims at all! Essentially, the book is one big 480-page straw man attack.

Unlike Dawkins, I'm not going to attack my opponents straw man by focusing on the weaker claims and ignoring the better evidence. In fact, I'm now going to address what is cited by many as one of the strongest pieces of evidence that new information and novel functionality can arise by Darwinian means.

In a 2005 MSNBC/LiveScience article, writer Ker Than cites an intriguing scientific discovery as evidence against intelligent design:
In 1975, Japanese scientists reported the discovery of bacteria that could break down nylon, the material used to make pantyhose and parachutes. Bacteria are known to ingest all sorts of things, everything from crude oil to sulfur, so the discovery of one that could eat nylon would not have been very remarkable if not for one small detail: nylon is synthetic; it didn't exist anywhere in nature until 1935, when it was invented by an organic chemist at the chemical company Dupont.

The discovery of nylon-eating bacteria poses a problem for ID proponents. Where did the [Complex Specified Information] for nylonase—the actual protein that the bacteria use to break down the nylon—come from?
'Nylonase' seems to be the Darwinist's strongest scientific argument against ID - the observed rapid evolution of entirely new proteins - and that's why it fascinated me.

The name 'nylonase' is a little misleading, since it's not nylon that the enzyme degrades, but a by-product of nylon-6 production. The enzyme's actual name is 6-aminohexanoate-dimer hydrolase. While the by-product also isn't found in nature, the bonds that hold it together (amide bonds) are nothing unusual, so it's not as impressive as "nylon-eating bacteria" makes it seem. However, it is still an interesting observation.

Ker Than's interpretation of this find is the same as that of an article archived on the NCSE's website entitled New Proteins Without God's Help. This article was written in 1985, so it's more than a quarter of a century old! Since then, more research has been done which challenges the anti-ID crowd's interpretation. Recent studies by scientists at the University of Hyogo in Japan have found that 'nylonase' is simply a slightly modified carboxylesterase enzyme. The carboxlesterase enzyme already had a slight amount of activity towards the nylon oligomer, and a couple of mutations in the catalytic site greatly increased its 'nylonase' activity without significantly affecting its original esterase function.

While this certainly is "evolution" in one sense of the word, and it is a testament to the versatility of bacterial adaptation, it is not new complex specified information, nor is it arguably even a new function. And, as Ker Than noted, "the nylonase enzyme is less efficient than the precursor protein it's believed to have developed from". As an example of the 'blind watchmaker' in action, it's no more impressive than antibiotic resistance.

Last year, during a debate between Michael Behe and Keith Fox on a UK Christian radio show, Fox cited the nylon-degrading enzyme as evidence which refutes Behe:
Fox: One example that is cited of a new function evolving reasonably recently is the production of an enzyme that degrades nylon -- a man made fibre; where organisms who were exposed to, actually the effluent from a nylon factory, evolved the ability to degrade that. It's something that's not out there in nature, it's a new function.

Behe: Well no that's -- yeah it's been reported as that but that's not quite correct. It doesn't degrade nylon, it degrades a precursor, a small organic chemical that's used in the synthesis of nylon.

Fox: That's correct but it's still something that isn't out there in nature and it is a new function.

Behe: Well that may be true but the question is, how hard is it to do that? And I suspect it's not so hard. Hydrolysing some amide bond, or an ester or something like that, is not quite the same thing as, you know, being an outboard motor.
Some might say Behe is moving the goalposts here, but he isn't. Behe's goalposts have always been where he's setting them now. The Darwinist's simply aren't scoring!

So, we return to that fundamental question: Does Darwinian evolution have the explanatory power? Can natural selection function as a 'blind watchmaker'? Well, the computer simulations tell us absolutely nothing and the empirical basis is surprisingly underwhelming, but Darwinist storytellers like Richard Dawkins, Ken Miller and Nick Matzke can always think of ways in which it COULD work. But such exercises in storytelling are more faith-based than science-based.

And this brings me to my main point, and the reason I wrote this blog. The main point I want to argue is that Darwinism, materialism and atheism are world views which are just as much faith-based as their theistic and spiritual alternatives. Atheists of the Dawkinsian variety like to sit on their high horses and look down on all the religious people with an arrogant delusion of intellectual superiority because their world view is based on "science", while those silly theists base their world view on faith. And the reason I like the ID arguments so much is because, regardless of which is actually true - Darwinian materialism or intelligent design - they expose how belief in the blind watchmaker (and by extension, Darwinism, materialism and atheism) actually takes quite a lot of faith. And that's an uncomfortable reality check for those who claim to be rational free-thinkers. Perhaps that's why they hate ID so much!

"The first effect of not believing in god is to believe in anything." ~ Émile Cammaerts

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