I'm Going to a Lecture on Intelligent Design

 
Denyse O'Leary is teaching a course on Intelligent Design at the University of St. Michael's College, University of Toronto [Denyse O'Leary's University Course on Intelligent Design].

The outline of the course was posted on Post-Darwinist [ COURSE: By Design or by Chance? An introduction to the intelligent design controversy].

Students in the course are allowed to invite a guest for one lecture and one of my friends, who shall remain nameless for now, has urged me to come along. By all accounts the course is going well and Denyse is presenting both sides of the controversy.

Tonight's lecture is ...

Session 5. Intelligent design: What the ID proponents actually say (and don’t say) Tuesday November 20, 2007

Michael Behe, author of Edge of Evolution (2007), sees actual design where, for example, Richard Dawkins, author of The Blind Watchmaker, sees the illusion of design. Who’s right? Are they both wrong?

Guest: Kirk Durston, biophysics PhD candidate at the University of Guelph.

Kirk Durston (right) is the National Director of the New Scholars Society. According to his biography on their website,

KIRK DURSTON, B.Sc (Physics), B.Sc. (Mech. Eng.), M.A. (Philosophy), Ph.D. Candidate (Biophysics) at the University of Guelph.

Kirk Durston is the National Director of the New Scholars Society. He is currently a Ph.D. candidate in Biophysics at the University of Guelph, specializing in the application of information to biopolymers. His other interests include amateur astronomy, wilderness canoeing & camping, and landscape photography & art.

What is it about creationists that they always seem to have multiple redundant degrees? In this case he has two Bachelor's degrees. What's with that?

It's easy to find out what Kirk believes because there's a Statment of Faith on the website.

The sole basis of our beliefs is the Bible, God's infallible written Word, the 66 books of the Old and New Testaments. We believe that it was uniquely, verbally and fully inspired by the Holy Spirit, and that it was written without error (inerrant) in the original manuscripts. It is the supreme and final authority in all matters on which it speaks.We accept those large areas of doctrinal teaching on which, historically, there has been general agreement among all true Christians. Because of the specialized calling of our movement, we desire to allow for freedom of conviction on other doctrinal matters, provided that any interpretation is based upon the Bible alone, and that no such interpretation shall become an issue which hinders the ministry to which God has called us.

Jeffrey Shallit had a few things to say about Kirk Durston on Recursivity [Kirk Durston: Apologist for Genocide]. This is going to be an interesting lecture.

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The two mistakes of Kirk Durston

Kirk Durston think he's discovered a couple of mistakes made by people who debate evolution vs creationism [Microevolution versus Macroevolution: Two Mistakes].

I often observe that in discussions of evolution, both evolution skeptics and those who embrace neo-Darwinian evolution are prone to make one of two significant mistakes. Both stem from a failure to distinguish between microevolution and macroevolution.

Let's see how Durston defines these terms.

How Does an Intelligent Design Creationist Write a Ph.D. Thesis?

 
Some of you will remember Marcus Ross. He is a Young Earth Creationist who obtained a Ph.D. in paleontology from the University of Rhode Island [Lying for Jesus]. Ross now has a faculty position at Liberty University where he teaches courses in religion and science. PZ Myers has posted an update on his career [So what's Marcus Ross up to nowadays?].

How could Ross write an acceptable Ph.D. thesis if he believes that the Earth is less than 10,000 years old? We know the answer to this question. Ross did not discuss his true beliefs in his thesis or during his Ph.D. oral exam. Instead, he wrote a thesis on the fossil record as though he accepted the scientific age of the Earth. In other words, Ross said one thing in public lectures and another in the exam room.

I was reminded of this episode while listening to Kirk Durston last week in Denyse O'Leary's course. Kirk is a Ph.D. candidate in biophysics at the University of Guelph [Kirk Durston's Proof of God]. At some point he will write scientific papers and a thesis and he will be examined on his understanding of science. I wonder what he will do?

In his talk, Kirk tried very hard to give the impression that his scientific findings point to the existence of an intelligent designer. There was a brief mention of the distinction between science and philosophy but it wasn't at all clear whether he was stepping over the line or not. He concludes that God the intelligent designer exists.

One thing was clear, however. Kirk claimed that his work demonstrated the impossibility of evolving protein folds. He presented some calculations showing the total number of mutations that could have occurred since life began (10⁴¹, if I remember correctly). Then he showed that it would take far more than 10⁴¹ mutations to evolve the known protein folds.

In his lecture he clearly states that the results refute "Darwinism." He repeated over and over again that his thesis work was scientific evidence against evolution and in favor of intelligent design creationism.

It seems to me that Kirk Durston has only two choices at this point. Either he's sincere about his "scientific" claims, in which case they go into his thesis, or, alternatively, he's willing to disguise his true "scientific" conclusion by writing a thesis that's more likely to be accepted by the scientists on his committee.

To my way of thinking, scientific integrity should not be compromised in order to get a degree by trickery. But this presents a serious problem for Intelligent Design Creationists. In their public lectures, and in articles for the popular press, they make a big deal about the "scientific" nature of their findings. If that's what they truly believe then they should have no qualms about defending it in a scientific context. In other words, it goes in the thesis and let the chips fall where they may.

But here's the rub. Intelligent Design Creationists know full well that their version of science will not pass scrutiny by other scientists. Kirk Durston will not get his Ph.D. if he's being honest about his belief in his findings. It is simply not true that protein folding is scientific proof of intelligent design and a refutation of evolution.

So, Kirk like other creationists before him, will write the thesis that his committee will pass and not the one that he would be writing if he were honest.

The next hurdle will be the Ph.D. oral exam. Members of his committee know that he has been making very vocal claims about the significance of his Ph.D. research. They know that he has been making claims that the work refutes evolution even if that's not what's in the thesis. Should they question him about the difference between what he says in the thesis and what he says on the lecture circuit? Do they have a right to fail him if they think that what's in his thesis does not reflect his true opinion about the science—and that his true opinion is scientifically invalid?

I think the committee has this right and I think that a Ph.D. candidate should be prepared to defend any "scientific" claims they make outside of the lab.

There will be a few other problems with Kirk's thesis but they are easily fixed. For example, he claimed that ancient bacteria were complex and subsequent evolution has just been degradation of the genome. In the lecture he showed us several references. We now know that he is misinterpreting these scientific papers.

I assume this will go in the thesis because Kirk seemed to be really sincere when he talked about this as scientific fact. Member of his committee will read the thesis, correct his misconceptions, and point him to other scientific papers that reveal the true nature of bacterial evolution. This will give him an opportunity to learn about good science. At the end of the process Kirk will not be making scientifically inaccurate statements in public because he will know better.

There are quite a few examples of these factual errors but I assume they will all be fixed before the oral exam.

The bottom line is can Kirk Durston get a Ph.D.? If so, how should he do it? What do you think?

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[Photo Credit: Theses from Jackson State University]

By Jove, I Think She's Got it!!!

 
Denyse O'Leary muses about the lecture I attended last Tuesday where Kirk Durston presented the case for Intelligent Design Creationism [Kirk Durston's Proof of God].

Here's what she says on her blog Uncommon Descent [We have the hat, but where’s that rabbit? High levels of information in “simple” life forms]. I'll go through it slowly but the bottom line is that Denyse O'Leary is finally beginning to understand mechanistic naturalism and what science is all about. It's only taken her, what ... ten years? Sheesh.

In Tuesday night, a guest speaker spoke to my adult night school class in why there is an intelligent design controversy. He talked about the central problem of evolution: The fact that high levels of information are present in life forms that are supposed to be early and simple.

We've discussed this on other posting. Kirk Durston did, indeed, say that ancient bacteria were complex and modern ones have become more simple. But his most important point was that the existence of protein folds cannot be explained by evolution, therefore they must have been intelligently designed (i.e., God did it).

Some guests attended the talk, and one of them announced that if intelligent design is correct, scientists would not see the need to do any research because Goddunit. Or something like that.

Actually, it wasn't one of the "guests"—it was one of the regular students. It happened to be the one who invited me as a "guest."

The question referred to the fact that "God did it" is a science-stopper. As soon as Kirk Durston concludes that protein folds are designed by God, that's the end of doing science. What else can be done? Does he plan to design experiments to prove that God did it? Does he plan to investigate how God might have done it, or when? Of course not. It's a science-stopper.

The more I thought about what he was saying, the more it puzzled me. Finally, I realized:

For the materialist, the PURPOSE of science is to show that high levels of information can be created without intelligence.

Therefore, in looking for causes of events, the materialist accepts ONLY a solution that shows that high levels of information can come from random assembly (= without intelligence).

I'm delighted to hear that Denyse O'Leary is capable of serious thought. (Who knew?) She's pretty much got it right.

In science you cannot invoke the supernatural. You are committed to finding naturalistic explanations of the natural world. The procedure is called methodological naturalism or methodological materialism [see Theistic Evolution: The Fallacy of the Middle Ground].

The debate over the conflict between science and religion has been going on for hundreds of years. In the past 50 years the debate has focused on the methodology of science and how it must exclude the supernatural if it's supposed to work properly. I'm shocked (not really) that Denyse has never heard of this before. It's one of the main themes in the writings of Phillip Johnson [see Are You as Smart as a Second Year University Student? Q1 and comments].

He has not shown that high levels of information can be created without intelligence. He assumes that his assertion is true and looks for evidence to support it.

Discoveries that disconfirm his initial belief are not treated as evidence.

Keep looking, he says, keep looking … that magic information mill has GOT to be somewhere!

"Disoveries" that claim to disconfirm the assumption of naturalism are tested against reality. If a hypothesis appears to conflict with a naturalistic explanation then it's back to the drawing board. Scientists will re-examine their assumptions to see where they went wrong. They will devise new approaches and do experiments to collect more data. In other words, the apparent conflict stimulates research, it does not shut it down.

Keep looking, keep looking. This is an approach that has been enormously successful in science over the past several thousand years. Without that attitude we would still believe that all of humanity was wiped out in a flood and that the sun went around the Earth.

Contrast this scientific approach with the typical Young Earth Creationist approach to learning. How many of them are looking for evidence of how God made the Universe 6000 years ago? Where did he get all the atoms, for example? Did he make any mistakes? Belief in the Bible is a science-stopper.

Here's another example. Kirk Durston stops doing science once he's decided that God made proteins. There's nothing else he can do. On the other hand, scientists look at his data and try to explain where he went wrong and why there could be naturalistic explanations. In this case, it's not too hard to discover where Kirk made most of his errors. This is what science is all about and this is why Intelligent Design Creationism isn't science. It's a science-stopper.

Look at bacterial flagella. Michael Behe pronounced that flagella were created by God when he published Darwin's Black Box in 1996. How much research into the origin of flagella did this stimulate among Intelligent Design Creationists? None at all. What's the point?

Scientists did not accept the conclusion that God did it. They continued to work on the problem and now we have a pretty good explanation for the origin of bacterial flagella. Pretty soon the creationists will have to abandon this example but it sure won't be because of any scientific work they did. No scientific advances come for assuming that God did it.

What if random assembly is not in fact the answer? Then either

1. No solution is found (because there never was any solution in the direction in which he is looking)

or

2. An inadequate solution is patched together and defended as the best available solution - usually that means that claims for the solution are overstated wildly to the public.

But it is the materialist scientist’s duty to keep looking for the magic mill even if the fact that random assembly did not occur is overwhelmingly obvious.

Actually the two scientific possibilities are:

1. We found a naturalistic explanation for the claims of religion. Historically, this is what happens most of the time and it's why the claims of religion have repeatedly been shown to be false.


2. We don't know the answer but we'll keep working on the problem. This is what's happening with the most recent claims of the creationists. It takes a few years to demonstrate their nonsense and during that time the correct scientific position is that the questions hasn't been decided. (Sometimes we can say we have a tentative solutions that needs refinement.)

So far, in several thousand years of testing creationist claims there isn't a single one that hasn't fallen to the onslaught of rationalism.

And he displays his virtue to his peers by never questioning the system and by showing hostility and contempt for anyone who does question it.

Given his initial convictions, the materialist cannot believe that a non-materialist is actually doing science. He cannot envision any approach to the fact base that does not have as its base an effort to show that the information was created randomly.

There are many religious scientists who do a pretty good job of being scientific most of the time. They know that methodolgical naturalism is a powerful assumption with a proven track record and that resort to the supernatural has never led to further understanding. As I said above, I'm shocked that Denyse is only now coming to the realization that her understanding of science was seriously flawed. Apparently, in spite of the fact that she has written two books, she never understood the scientific method.

As for "hostilty," yes, it's true. Some of us get very frustrated with so-called scientists who don't understand the fundamental concepts of the scientific methd and what it means to be a scientist.

As a matter of fact, the fact base could easily be approached otherwise, and often more fruitfully, too. If we assume that an object in nature is designed, we do not waste time trying to imagine how it could have come about randomly. We study its characteristics and make predictions about its behaviour, function, and so forth.

That's just a bunch of bull manure. Part of the statement is true—creationists stop trying to find an evolutionary explanation as soon as they conclude that God did it. But the second part is completely false. Creationists stop all investigations once they've concluded that supernatural beings are involved. They don't try to figure out how God's mind worked.

I hope Denyse does some reading in order to catch up. She should look at Philip Johnson's proposal for a God-based (non-materialistic) science. It ain't gonna happen. Why in the world would scientists shop using a method that has bee so successful?

The idea that invoking the supernatural could be a more "fruitful" approach to science, as Denyse says above, is outlandish to the point of idiocy. There are no scientific advances that have come from assuming God did it. That's always a science-stopper.

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A Scientific Test for the Intelligent Designer

 
Kirk Durston has been participating in the discussion on the thread Kirk Durston's Proof of God. He's been having a bit of difficulty keeping up with the scientific criticisms of his proposed proof of the existence of God an Intelligent Designer. I can understand the problem. In an online debate everyone is on a level playing field. When a paper is mentioned, we can all check it out before replying.

So, Kirk proposes another way of handling the discussion.

I thank Larry for extending the opportunity to post a method to test for whether ID is highly probable or not (the way I phrased it in my lecture). I've been mulling this over even before Larry posted the invite. I have reservations about doing it in this particular forum, primarily because the numbers that would be involved are too few to justify the time and, secondly, I would prefer a live lecture where the back and forth dialogue would be greatly enhanced. I've thought that, perhaps, this could be done at the U of T over a 2 hour period. Larry could book a room and chair the event. I could present my proposal (as I repeatedly referred to it in my lecture) of a method to test for ID. I would sincerely hope that Larry et al would be able to set aside the usual hostility and personal attacks and, instead, run a collegial, honest event. As I repeatedly stressed in my lecture this past week, I am NOT claiming to have a 'proof' for ID. Rather, I am proposing a scientific method to test for it that is a work in progress. When this could take place is another question. Certainly not this semester. I am currently swamped with getting the next phase of my research up and running, and a couple of papers in progress. I cannot even afford the time o respond to these posts and will likely have to bow out today. My suggestion would be sometime in 2008, preferably after the winter semester, say, late April or May.

I'm happy to oblige and I've booked a room for either Tuesday April 22nd or Tuesday April 28th. I invite Kirk Durston to come and present his evidence that protein folding studies indicate the presence of an intelligent designer.

This will be an informal scientific debate attended by scientists who are familiar with protein folding. We have a lot of them here at the University of Toronto. Here's a list of the active labs working in this area in our Department [Protein Folding]. Here are the labs in the Dept. of Medical Biophysics [Molecular and Structural Biology]. And here are the labs in the Dept. of Molecular Genetics [Structural Biology].

I'm pretty sure we could get 20-30 graduate students, postdocs, and faculty members to come out and hear the protein folding evidence for intelligent design. They are experts in the same field as Kirk and I'm sure they will be able to show him where he's going wrong. It will be good for them to get exposure to the quality of work on protein folding that's being done at the University of Guelph.

I think it's safe to say that most of my colleagues have no idea of the importance of their work in the Intelligent Design Creationism field of scientific research. This is an opportunity for them to learn from Kirk Durston. Hopefully, after listening to Kirk my colleagues will be more open to the idea of intelligent design when it comes to reviewing research grants, scientific papers, or even sitting on Ph.D. oral exams—provided Kirk makes a convincing case.

I admire Kirk for his willingness to subject his scientific evidence for intelligent design to a group of experts on protein folding. It's very courageous of him since he's putting his scientific reputation on the line.

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[Photo Credit: The Figure is from my textbook, Horton et al. (2006) p. 110. It's taken from the work of my departmental colleague Hue Sun Chan, one of the world's leading experts on the theoretical aspects of protein folding.]

Kirk Durston vs PZ Myers

 
PZ Myers has a brief account of his encounter with Kirk Durston in Edmonton (Alberta, Canada) last weekend [An ugly debate in Edmonton].

PZ discovered what many of us already knew about Kirk ...

He's a good debater, because he relies on a powerful tactic: he'll willingly make stuff up and mangle his sources to make his arguments. I'm at a disadvantage because I won't do that.

Exactly. It's hard to debate someone who lies with a straight face, especially if they act like a Christian while doing it.

Here's what I had to say last year about my encounter with Kirk Durston [Kirk Durston's Proof of God].

It was a very frustrating experience. Like most Intelligent Design Creationists, Durston was all over the map in terms of spreading lies and misconceptions about science. This scattergun approach seems to be very successful for them. I assume it's because no one person can address all of the problems with their presentation. Most people will catch one or two flaws but they'll assume that everything else has to be correct.

Sounds like nothing has changed.

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Kirk Durston appears on Evolution News & Views to announce that "Darwinian Theory" has been falsified

Kirk Durston is a Canadian biophysicist with a Ph.D. from the University of Guelph (Guelph, Ontario, Canada). He's been attacking evolution for more than a decade using all the old tricks and sophistry that we've come to expect from creationists.

I thought you might be interested in his latest attempt to discredit evolution. His post is at: An Essential Prediction of Darwinian Theory Is Falsified by Information Degradation.

He begins by claiming that "Darwinian Theory" (what ever that is) makes an essential prediction. It predicts that information must increase over time.

In the neo-Darwinian scenario for the origin and diversity of life, the digital functional information for life would have had to begin at zero, increase over time to eventually encode the first simple life form, and continue to increase via natural processes to encode the digital information for the full diversity of life.

An essential, falsifiable prediction of Darwinian theory, therefore, is that functional information must, on average, increase over time.

The Guelph Creationists

 
The University of Guelph is located in southern Ontario (Canada) about 2 hours west of Toronto. It has recently gotten a lot of attention because of the presence of several Intelligent Design Creationists among its staff and students.

Here are the main players.

David K.Y. Chiu is Professor of Computing and Information Science and Professor of Biophysics Interdepartmental Group. He has a Ph.D. in Systems Design Engineering from the University of Waterloo (Canada).

Professor Chiu is head of the Pattern Learning Research Group. Most of his recent papers have to do with recognizing patterns in bioinformatics data.

Durston, K.K., D.K.Y. Chiu, D.L. Abel and J.T. Trevors (2007) Measuring the functional sequence complexity of proteins", Theoretical Biology and Medical Modelling 4:47. [doi:10.1186/1742-4682-4-47]

Chiu, D.K.Y. and K. Zhang (2007) Biomolecular data analysis: a post-genomic reflection. Biomolecular Engineering, 24:319-320.

Chiu, D.K.Y. and Y. Wang (2006) Multipattern consensus regions in multiple aligned protein sequences and their segmentation. EURASIP Journal on Bioinformatics and Systems Biology, Vol.2006:1-8.

Ma, P.C.H., K.C.C. Chan, X. Yao and Chiu, D.K.Y. (2006) An evolutionary clustering algorithm for gene expression microarray data analysis. IEEE Trans. on Evolutionary Computation 10:296-314.

Hwang, C., Chiu, D.K.Y. and Sohn, I. (2005) Analysis of exon structure using PCA and ICA of short-time Fourier transform. L. Wang, K. Chen, and Y.S. Ong (Eds.): ICNC LNCS 3611, pp.306-315, 2005, Springer-Verlag Berlin Heidelberg 2005.(also Second Intern. Conf. on Fuzzy Systems and Knowledge Discovery, joint ICNC'05-FSKD'05, 27-29 Aug. 2005, Changsha, China.)

Durston, K. and Chiu, D.K.Y. (2005) A functional entropy model for biological sequences. in supplementary volume of the journal, Dynamics of Continuous, Discrete and Impulsive Systems, Series B, 2005 (also Proc. 4th Intern. Conf. on Engineering Applications and Computational Algorithms), pp.722-725.

Professor Chiu is a Fellow of the International Society for Complexity, Information, and Design. Other fellows include Michael Behe, Paul Nelson, Guillermo Gonzalez, William Dembski, Jonathan Wells and Scott Minnich.

Kirk Durston is National Director of the New Scholars Society whose aim is to "be a resource to those faculty and scholars who have an interest in developing the spiritual area of their lives from a Christian perspective." Durston has a B.Sc. in Physics from the University of Manitoba (Canada), a B.Sc. in Mechanical Engineering from the University of Manitoba (Canada) and an M.A. in Philosophy from the University of Manitoba (Canada). He is currently a Ph.D. candidate in the Biophysics Interdepartmental Group at the University of Guelph [Kirk Durston].

Durston's supervisor is David Chiu (see above). This is not a simple case of a graduate student falling under the influence of his supervisor since Durston was a well-known creationist even before he joined Chiu's group. It's just a coincidence that student and supervisor share the same views on religion and evolution since to suggest otherwise would be like accusing Chiu of selecting a student based on his religious views and not on the normal criteria. Intelligent Design Creationists are vehemently opposed to that kind of discrimination.

I'm sure Durston's previous degrees in physics, mechanical engineering, and philosphy made him well qualified to do Ph.D. research on the evolution of proteins in a bioinformatics lab.

Jack Trevors is a Professor in the Dept. of Environmental Biology [Jack Trevors] and he's also a member of the Biophysics Interdepartmental Group [Jack Trevors].

Professor Trevors has a B.Sc. and an M.Sc. from Acadia University (Canada) and a Ph.D. from the University of Waterloo (Canada). Most of his many publications are on various aspects of microbiology diversity and industrial applications but he is also interested in "Bacterial evolution with an emphasis on the origin and of the first bacterial cells and functional genetic instructions."

Trevors is famous in creationist circles for two papers he has published with David Abel, Director of The Gene Emergence Project at The Origin-of-Life Foundation, Inc. in Greenbelt, MD (USA). These papers are widely quoted as evidence that the origin of life cannot be explained by natural processes.

Abel and Trevors have also just published a paper with creationists Durston and Chiu.

Abel, D.L. and J.T. Trevors. (2006) Self-organization vs. self-ordering events in life-origin models. Physics of Life Reviews 3:211-228. [doi:10.1186/1742-4682-2-29]

Trevors, J.T. and Abel, D.L. (2004) Chance and necessity do not explain the origin of life. Cell Biology International 28:729-739. [doi:10.1016/j.cellbi.2004.06.006]

Durston, K.K., D.K.Y. Chiu, D.L. Abel and J.T. Trevors (2007) Measuring the functional sequence complexity of proteins. Theoretical Biology and Medical Modelling 4:47. [doi:10.1186/1742-4682-4-47]

Jack Trevors is not a creationist according to this profile at the University of Guelph. He's a "self-proclaimed atheist."

Take that question about the origins of life. It's hardly a new line of inquiry for Trevors, who was about 10 when he began wondering about the existence of God. He's still wondering. Indeed, it's a question that has consumed a fair amount of his own life recently, albeit now voiced in the language of a professional scientist: Where and how did the genetic code and its instructions arise?

No small question. “The origin of genetic instructions in the DNA is the most pressing question in science,” he says. “Genetic instructions don't write themselves, any more than a software program writes itself.”

He adds that the issue goes far beyond deciphering the recipes for making proteins. Given that our genetic material constitutes the stuff of our own identity, “it's the search for ourselves, our origins,” he says.

Call it looking for God in our DNA — or at least that's how a person of faith might phrase it. Trevors, a self-proclaimed atheist, is more circumspect. “If you're a religious person, you say God. If you're an evolutionist, you say evolution.”

He notes, however, that not even evolution deigns to tell us where or how life itself first came about or how DNA's instructions came to be. Perhaps the birthplace of those instructions — like the very creation of the universe itself — is, in Trevors' words, both “unknowable and ‘undecidable' at this point in time.”

The same profile article describes his association with David Abel ...

It's a million-dollar question, literally. That's the size of the prize in a contest being run by the Origin-of-Life Foundation based near NASA's Goddard Space Flight Centre in Maryland. All the winner needs to do to claim the reward — actually annual instalments of $50,000 for 20 years — is to explain how the initial genetic code arose — or, in the words of the contest rules, provide "a highly plausible mechanism for the spontaneous rise of genetic instructions in nature sufficient to give rise to life."

The Gene Emergence Project is a program of the foundation, a scientific and educational body of about 200 scientists in 40 countries.

"We want the international scientific community to help us prove that genetic instructions don't write themselves," says Trevors, who got involved by contacting David Abel, the project's program director, two years ago.

"Jack relentlessly looks for evolutionary explanations for everything we observe in biology," says Abel, adding that his Guelph colleague helps ensure that "life-origin theory" remains empirically responsible, or answerable to the test of repeated observation. "He likes to include the full gamut of microbiological phenomena to make sure our models are explaining all aspects of genetic control."

Trevors has written on the topic, including a paper last year with Abel called: "Chance and Necessity Do Not Explain the Origin of Life." There and in a more recent piece, they frame the genesis-of-life discussion in terms that might resonate with a computer programmer, including referring to genes as linear strings of digital instructions and describing DNA's four nucleotide building blocks as four-way switches. If genes are merely algorithms, albeit highly sophisticated ones, another obvious question occurs, says Trevors. “Computer programs don't write themselves. Why would scientists or anyone else think genetic programs write themselves? The question has to be asked and examined from a scientific perspective.”

I don't know about the rest of you but I don't often hear atheists say things like that. Maybe he's thinking of aliens who write genetic programs? I also don't know too many atheists who would publish papers with known creationists who use the data to support their religious agenda.

The Origin-of-Life Prize has a complicated set of rules that must be followed in order to claim victory. The organization has posted a list of suggested texts that candidates should be familiar with (see sidebar on their website). That list is very revealing. There are books by well-known scientists like Michael Behe, Hubert P. Yockey, Walter James ReMine, William Dembski, and David Berlinski.

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Kirk Durston's Proof of God

 
I went to the lecture in Denyse O'Leary's course last night [I'm Going to a Lecture on Intelligent Design]. As promised, the guest speaker was Kirk Durston, a graduate student in biophysics at the University of Guelph.

It was a very frustrating experience. Like most Intelligent Design Creationists, Durston was all over the map in terms of spreading lies and misconceptions about science. This scattergun approach seems to be very successful for them. I assume it's because no one person can address all of the problems with their presentation. Most people will catch one or two flaws but they'll assume that everything else has to be correct.

I'll come back to some of these lies in another posting but right now I'd like to explain his main argument.

Kirk Durston has a background in computer science and his project has to do with analyzing the sequences of conserved gene families.

The Intelligent Design Creationist part of his study relies heavily on the work of Douglas Axe (Axe, 2000; Axe, 2004). Axe is head of Biologic Institute a "research" company in Redmond, WA (USA) with ties to the Discovery Institute [We're in Trouble Now].

The papers Axe published in the prestigious Journal of Molecular Biology represent work he did as a post-doc in Cambridge UK. The goal was to show that the probability of a protein adopting a particular three-dimensional fold is very, very low.

Durston is pursuing this line of work and he described it in his talk last night with plenty of equations and diagrams. There were about 15 people in the room and it's almost certain that nobody other than me had any idea what was going on. But it all sounded very sophisticated.

As it turns out, not understanding the science shouldn't have been such a big deal since the form of his argument was obviously silly. At least I thought it was obvious. Here's the way it went ...

1. By making assumptions A, B, C, and D and constructing equations E and F he is able to predict that no protein will have more than X amount of information.


2. By making a few assumptions about protein families it is possible to measure the amount of information in a folded domain by plugging the data into his equations. It turns out that most proteins have more than X information.


3. Therefore God exists (i.e., the protein must have been intelligently designed).

This are (at least) two major flaws in this argument and it doesn't take an expert in computer science or biochemistry to detect them.

First, when you formulate a scientific hypothesis you test it against scientific reality. If the predictions of your hypothesis are not fulfilled then your hypothesis is falsified. At that point it's back to the drawing board. You need to reconsider your assumptions or your equations because they were not successful. That's how science is done but that's not how Intelligent Design Creationism is done.

Second, the sudden appearance of God in the conclusion is illogical. There's no mention of God intelligent design in the premise. It just pops out of the argument without any warning. This is not how logic works and it's certainly not how science works.

I tried to point this out last night but nobody in the audience was paying attention and Durston was in no mood to discuss logic after having spent close to two hours practicing something else.

We have a word to describe people who can't construct a simple logical argument. It seems to have slipped my mind .... what is it ..... oh, yeah, now I remember ... IDiot.

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Axe, D. (2000) Extreme Functional Sensitivity to Conservative Amino Acid Changes on Enzyme Exteriors. J. Mol. Biol. 310:585-595.

axe, D. (2004) Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds. J. Mol. Biol. 341:1295-1315.

Bacterial Genomes and Evolution

 
I recently became aware of the fact that Intelligent Design creationists are promoting a strange idea. They bacteria were very complex when life first formed and their genomes have been degrading over time. Kirk Durston, a graduate student at the university of Guelph, pushed this idea in a course on intelligent design. Durston used a number of scientific references to prove his point. The main one was a paper by Miraa et al (200) from Nancy Moran's lab [Bacteria Genomes Are Degrading].

Ryan Gregory is one of the world's leading experts on genomes and their evolution. He's also a Professor at the University of Guelph. Ryan has published an excellent description of what the Mira et al. (2000) paper shows and what it does not show. You should all read it [Bacterial genomes and evolution].

For Kirk Durston's sake, I hope Ryan Gregory isn't on his Ph.D. oral committee.

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Bacteria Genomes Are Degrading

 
At one point in his talk last night Kirk Durston mentioned the bacterial flagella. He acknowledged that the "Darwinists" have proposed an evolutionary pathway from a Type III secretory structure to flagella.

This pathway is improbable, according to Durston, because flagella are more complicated than secretory pores so flagella have to evolve first.

What? Yes, that's right. Scientists have now shown that the most primitive bacteria were very complex and evolution has been all downhill from then on. Modern bacteria are less complex. Thus the type III secretory apparatus had to evolve from the more complex bacterial flagella. (The actual situation is complicated [Evolution in (Brownian) space: a model for the origin of the bacterial flagellum]. What I'm addressing here is the claim of general loss of information in bacterial evolution.)

I suggested that this was bull not correct and Durston responded with a slide showing the scientific papers that proved it. The most important paper was

Mira, A., Ochman, H. and Moran N.A. (2000) Deletional bias and the evolution of bacterial genomes. Trends Genet. 17:589-96. [PubMed]

I asked Durston what would happen if I called Nancy Moran (no relation, that's her above) and asked her whether she agreed that primitive bacteria were complex and all modern bacterial lineages are losing information. He affirmed that she would and that's what modern evolutionary biologists are saying. There are other papers that say the same thing. He accused me of not being aware of them.

This is the abstract of the Mira et al. (2000) paper.

Although bacteria increase their DNA content through horizontal transfer and gene duplication, their genomes remain small and, in particular, lack nonfunctional sequences. This pattern is most readily explained by a pervasive bias towards higher numbers of deletions than insertions. When selection is not strong enough to maintain them, genes are lost in large deletions or inactivated and subsequently eroded. Gene inactivation and loss are particularly apparent in obligate parasites and symbionts, in which dramatic reductions in genome size can result not from selection to lose DNA, but from decreased selection to maintain gene functionality. Here we discuss the evidence showing that deletional bias is a major force that shapes bacterial genomes.

I think it's pretty obvious from the abstract that they're discussing a particular problem in bacterial evolution; namely selection for small compact genomes. This point is clear in the paper as well.

At no point in the paper do the authors suggest anything close to what Durston says. There's no mention of primitive bacteria having the full complexity of all modern species including the myxobacteria and photosynthetic bacteria etc. Why in the world do the Intelligent Design Creationists have to lie about things like this? (I assume it's a lie because the only other possibility is ignorance and a Ph.D. student in biophysics can't be stupid enough to misunderstand such a key principle of evolution, right?)

Naturally in a forum like this Durston had me at a disadvantage. He was displaying the scientific papers and I had to admit that I had not read them recently enough to comment. The point was not lost on some members of the audience. The atheist scientist was trumped by the religious graduate student who was more aware of the scientific literature.

"Frustrating," doesn't begin to cover it ...

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Michael Egnor Gets It Right

 
Michael Egnor has posted a number of quotations from me about how I would deal with people who don't understand the basic principles of science [Dr. Larry Moran and Censorship of Intelligent Design].

He get it mostly right. If they are undergraduates who don't understand that evolution is a scientific fact, the Earth is 4.5 billion years old, and humans share a common ancestor with chimpanzees, then they flunk the course. If they are graduate students in a science department, then they don't get a Ph.D. If they are untenured faculty members in a science department, then they don't get tenure.

Readers might be amused at Michael Egnor's comments regarding Kirk Durston. It's further proof that IDiots are irony deficient. (Note that Kirk has not accepted my invitation to give a seminar here in the Biochemistry Department. I guess his "courage" has limits.)

Why should Mr. Durston’s willingness to present his scientific evidence for intelligent design to other scientists require courage? Isn't the presentation of evidence a routine part of science? Why should presenting evidence for intelligent design put Mr. Durston’s "scientific reputation on the line"?

Are you listening Kirk? Michael Egnor M.D. wonders why you don't come here and defend your evidence that protein folding demonstrates the existence of God.

I gave you two dates last November: you can give a seminar on Tuesday April 22nd or Tuesday April 29th.

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Kirk Durston Interview

 
Here's an online interview with Kirk Durston on canadianchristianity.com for those who want to know more about his views on Intelligent Design Creationism [Evolution under fire? -- Part 1]. By all accounts Kirk seems to be a Young Earth Creationist in the sense that he prefers the literal interpretation of the Bible until it has been proven wrong.

Here's a part of the interview that seems unblievable.

I have been doing a great deal of work in ID over the past few years -- and have given presentations of my work in universities, both in Canada and the USA, that are well attended by both students and faculty. I have been very surprised by the fact that no significant objections to the evidence I present are being raised in these venues. I never bash Darwinism, I simply show them the positive evidence for ID -- and it goes over very well indeed.

I am currently working on a paper dealing with functional information, under the guidance of a professor in bioinformatics who wants to see my work published. It will be very low-key, mentioning nothing about ID, yet laying the groundwork for some major advances in this field -- if it is, by some miracle, accepted for publication.

I'm surprised that he has never heard any significant objections to the evidence he presents in his talk. I didn't have any trouble recognizing several lies and distortions and I wasn't the only one on Tuesday night.

Maybe he gives a different talk in other venues? In any case, we'll see whether the experts on protein folding hear at the University of Toronto will be as gullible when they hear the "positive evidence for ID" next Spring [A Scientific Test for the Intelligent Designer].

Oh, I almost forgot, in his Tuesday evening presentation he did bash "Darwinism." I guess that's one more difference between what I heard and his normal talks to students and faculty. Either that or .....

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Mathematical Proof of God

 
Here's Kirk Durston explaining how mathematics can show that evolution is impossible and Intelligent Design Creationism is probable. Durston is a graduate student at the University of Guelph (Guelph Ontario, Canada). At some point he will have to describe his ideas to a group of scientists who will determine whether he should get a Ph.D. Good luck Kirk, you will need it. Unless, of course, if the committee is stacked with IDiots people who don't understand biology.

If this explanation forms any part of Durston's thesis then it would be extremely embarrassing if the University of Guelph awards him a Ph.D. But what if all this is left out of the thesis? Is it still fair game for the Ph.D. oral committee?

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IDiots Don't Bash Evolutionary Biologists

 
How many times have you heard that line? The IDiots are fond of saying that they have positive evidence for Intelligent Design Creationism. According to them, it's not about bashing "Darwinists."^*

So how do you explain the Darwin Daze Sock-Hop on the Expelled site? [The Playground for Expelled] This is nothing less than a blatant attempt to mock the leading figures in evolutonary biology and atheism.

It makes me feel good about calling them IDiots.

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^* It will be interesting to see if any Intelligent Design Creationists object in public to that video. Several of them are on record as saying that they don't bash "Darwinists" (e.g., Kirk Durston, "I never bash Darwinists.")

What She Said

 
Monado of Science Notes has pointed out, once again, the major flaw in Intelligent Design Creationism [ The Masked Man speaks]. In spite of all the blustering and rhetoric, Intelligent Design Creationism boils down to just one thing—arguments against evolution. Here's what Monado says ...

I throw in my two cents' worth:

There is indeed a huge, huge logical fallacy at the base of Dembski's argument. It's the assumption that if you pick enough holes in evolution to let the air out, "God did it" is the only remaining conclusion. That's known as a false dichotomy.

In reality, there are a lot more than two choices. If the received explanation of evolution were not true, it would be back to the drawing board for everyone. If it isn't random mutation plus natural selection plus sexual selection plus genetic drift, then perhaps it's inheritance of acquired characteristics plus natural selection plus sexual selection plus genetic drift. There's no reason to jump to the conclusion that unnatural causes are needed.

The result of pushing the false dichotomy is that ID proponents are ready to use every rhetorical trick in the book, misrepresent evolution, continue to quote falsified "facts," and invent mathematical proofs based on strained assumptions that evolution can't occur without angels pushing the molecules. Dembski's arguments have been falsified again and again. Mutation produces new information. Mutation can produce improvements. Mutation can double the genetic material and then modify it (in spite of the "if I copied this paper I haven't doubled my knowledge" rhetoric). Natural selection is neither directed by God nor random at a particular time and place. It is probabilistic, however. When Dembski claims that something is impossible and actual researchers explain step by step how that could happen, his argument is demolished. The fact that our evidence is always "pathetic" and his evidence is non-existent tells you who has the logic on their side and who is blowing smoke.

Many people have said this before but we need to keep hammering away at this point [see Kirk Durston's Proof of God]. There's no logic to Intelligent Design Creationism other than discrediting evolution on the assumption that God is the only other option.

This is why we call them IDiots.

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Theme: Genomes & Junk DNA

Junk in Your Genome

Transposable Elements: (44% junk)

      DNA transposons:
         active (functional): <0.1%
         defective (nonfunctional): 3%
      retrotransposons:
         active (functional): <0.1%
         defective transposons
            (full-length, nonfunctional): 8%
            L1 LINES (fragments, nonfunctional): 16%
            other LINES: 4%
            SINES (small pseudogene fragments): 13%
            co-opted transposons/fragments: <0.1% ^a

^aCo-opted transposons and transposon fragments are those that have secondarily acquired a new function.

Viruses (9% junk)

      DNA viruses
         active (functional): <0.1%
         defective DNA viruses: ~1%
      RNA viruses
         active (functional): <0.1%
         defective (nonfunctional): 8%
         co-opted RNA viruses: <0.1% ^b

^bCo-opted RNA viruses are defective integrated virus genomes that have secondarily acquired a new function.

Pseudogenes (1.2% junk)
      (from protein-encoding genes): 1.2% junk
      co-opted pseudogenes: <0.1% ^c

^cCo-opted pseudogenes are formerly defective pseudogenes those that have secondarily acquired a new function.

Ribosomal RNA genes:
      essential 0.22%
      junk 0.19%

Other RNA encoding genes
      tRNA genes: <0.1% (essential)
      known small RNA genes: <0.1% (essential)
      putative regulatory RNAs: ~2% (essential) Protein-encoding genes: (9.6% junk)
      transcribed region:  
            essential 1.8%  
            intron junk (not included above) 9.6% ^d

^dIntrons sequences account for about 30% of the genome. Most of these sequences qualify as junk but they are littered with defective transposable elements that are already included in the calculation of junk DNA.

Regulatory sequences:
      essential 0.6%

Origins of DNA replication
      <0.1% (essential) Scaffold attachment regions (SARS)
      <0.1% (essential) Highly Repetitive DNA (1% junk)
      α-satellite DNA (centromeres)
            essential 2.0%
            non-essential 1.0%%
      telomeres
            essential (less than 1000 kb, insignificant)

Intergenic DNA (not included above)
      conserved 2% (essential)
      non-conserved 26.3% (unknown but probably junk)

Total Essential/Functional (so far) = 8.7%
Total Junk (so far) = 65%
Unknown (probably mostly junk) = 26.3%

For references and further information click on the "Genomes & Junk DNA" link in the box

LAST UPDATE: May 10, 2011 (fixed totals, and ribosomal RNA calculations)

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November 11, 2006
Sea Urchin Genome Sequenced

The sea urchin genome is 814,000 kb or about 1/4 the size of a typical mammalian genome. Like mammalian genomes, the sea urchin genome contains a lot of junk DNA, especially repetitive DNA. The preliminary count of the number of genes is 23,300. This is about the same number that we have in our genomes. Only about 10,000 of these genes have been annotated by the sea urchin sequencing team.