Wednesday, April 02, 2008

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.


13 comments :

  1. A lot of those books look pretty good (not that I've read any of them, to know -- but there's some respectable names in there). So duds like Behe and Remine(!) stick out like a sore thumb.

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  2. 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.”

    Correct me if I am wrong, but I don't think that nucleotide strands are digital. Analogy from DNA and RNA to computer programs are weak, at best. I suppose they can be compared to templates for proteins; casts for molding proteins.

    The analogy isn't the thing. While a program may need a program, a covalent bond doesn't need an engineer in order to work. An enzyme doesn't need a controller.

    I am kind of sick of programers setting this analogy for DNA and coding. It's where the Salem Hypothesis gets its strength.

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    1. >>>>Correct me if I am wrong, but I don't think that nucleotide strands are digital.


      "Digital" = "discrete" and "distinguishable." Instead of the cellular apparatus distinguishing between just two values — "0" and "1", or "yes" and "no", or "on" and "off", etc. — it distinguishes among four values — "A" or "C" or "G" or "T" — ergo, the system is digital.


      >>>>I suppose they can be compared to templates for proteins; casts for molding proteins.


      A "template" requires an overlay or physical contact — like a reticle, or dough and cookie-cutter. There is no overlay, physical contact, or chemical interaction between nucleotides and amino acids, any more than there is physical contact or chemical interaction between three dots of ink in a straight line like "..." and a curvy line of ink like "S".

      "..." is not a reticle, model, overlay, or template for "S"; it is an arbitrarily chosen symbol that is mapped onto another arbitrarily chosen symbol. The mapping between "..." and "S" is what constitutes the code.

      Similarly, "CAA" and "CAG" are not templates for glutamine; there's no reticle, model, overlay or physical interaction between the nucleotide triplet and the amino acid. It's a mapping.


      >>>> While a program may need a program, a covalent bond doesn't need an engineer in order to work...


      A bit like saying that, while a program may need a programmer, a piston+cylinder don't need an engineer to work. True. Once they appear and have been machined to a precise fit inside an engine, basic deterministic laws of physics do the rest. The question is: are those same laws sufficient to explain the appearance of a piston+cylinder perfectly machined to fit in an engine, when there are so many more imperfect and non-fitting configurations that pieces of metal can assume when left to those same laws?


      >>>>An enzyme doesn't need a controller.


      Like the piston+cylinder analogy above, once the enzyme has appeared, it doesn't require a controller. The question is: are basic deterministic laws of chemistry enough to explain how the enzyme came into existence in the first place, simply because they can explain its function after it has appeared?


      Enzymes are proteins, and as such, are themselves products of genetic coding, i.e., pre-programming.


      It's circular to argue that the product of the genetic pre-programming was responsible for the appearance of the program itself.

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  3. ..in a contest being run by the Origin-of-Life Foundation based near NASA's Goddard Space Flight Centre in Maryland.

    What blatant lying-by-association! If my house happens to be near Rome, should I be assumed to be Catholic? Isn't there some rule out there in delusion-land about "false witness"?

    Also, the title of this post made me very angry, and reading the rest of it didn't lower that emotion any. I'm not angry at Dr. Moran for posting it, I'm angry at MY university for accepting IDiots like Durston into MY graduate program, and for failing to use the opportunity, nay, DUTY, of the PhD Qualifying exam to boot his duplicitous ass out of here. I am a PhD student, Mr. Durston is apparently a PhD candidate, someone who has passed that exam. I have not yet passed that exam. Who was on his examination committee?

    There are people in the department of Environmental Biology, presumably with offices and labs nearby those of Dr. Trevors, who I respect greatly and hope to work with more closely over the course of my time here. I can't help thinking they should be as outraged as I am at this situation.

    This bullshit sullies the name of the University of Guelph, and devalues the degree I hope to get here.

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  4. While I am horrified by this information about my old university, I found another person from the University at the Fellow of the International Society for Complexity, Information, and Design: Bonnie Mallard.

    Obviously these people must be excellent researchers, and one cannot dismiss people because of their faith.
    it is however a little disturbing. It makes me glad I'm not there now.

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  5. I'm not angry at Dr. Moran for posting it, I'm angry at MY university for accepting IDiots like Durston into MY graduate program, and for failing to use the opportunity, nay, DUTY, of the PhD Qualifying exam to boot his duplicitous ass out of here.

    Why did they have a duty to kick Durston out? For a start, he's already published a paper based on his research, which suggests it does have some merit. When he turned up in the comment boxes here last year, it struck me that he was pursuing an interesting line of research.

    I don't know all that much about evolution, but it strikes me that protein evolution is one area that still requires some work. If he is able to contribute to knowledge about the possibilities of protein evolution in sequence space then fine by me. We should welcome such knowledge, in the same way that we should welcome Axe's work on protein evolution that IDists often crow about (probably mistakenly). Of course, as Larry pointed out at the time, leaping from protein evolution is difficult to God did it, doesn't make much sense.

    When Kirk turned up here, particularly in the thread linked to below, I actually thought there was quite an interesting discussion going on. I contributed a little, particularly based on something he had written for church groups and then others chipped in with some back and forth. I'm not an expert, so I wasn't all that qualified to rip his arguments to shreds, though my readings of the literature do suggest possible routes for protein evolution.

    http://sandwalk.blogspot.com/2007/11/bacteria-genomes-are-degrading.html

    Perhaps you could point out what specifically is wrong with his research and why it is so flawed as to prevent him from pursuing a PhD. If it's solely that he draws an ID inference from it, that doesn't seem reasonable to me.

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  6. Trevors does have a whiff of crankdom surrounding him. I'm surprised Larry, that you didn't point out that he has also published his origin of life ideas in the joke (and often creationist) journal Rivista di Biologia:

    Trevors, J.T. (2004) Origin of genetic instructions is presently unknowable and undecidable and requires scientific experimentation that is not readily possible - Viewpoints. Rivista di Biologia, 98, 23-31.

    The chance and necessity paper has been cited a few times (two of which by Abel and Trevors). One of these is the following odd looking paper:

    Sharov, A.A. (2006) Genome increase as a clock for the origin and evolution of life. Biology Direct, 1, 1-17.

    Background: The size of non-redundant functional genome can be an indicator of biological complexity of living organisms. Several positive feedback mechanisms including gene cooperation and duplication with subsequent specialization may result in the exponential growth of biological complexity in macro-evolution.

    Results: I propose a hypothesis that biological complexity increased exponentially during evolution. Regression of the logarithm of functional non-redundant genome size versus time of origin in major groups of organisms showed a 7.8-fold increase per 1 billion years, and hence the increase of complexity can be viewed as a clock of macro-evolution. A strong version of the exponential hypothesis is that the rate of complexity increase in early (pre-prokaryotic) evolution of life was at most the same (or even slower) than observed in the evolution of prokaryotes and eukaryotes.

    Conclusion: The increase of functional non-redundant genome size in macro-evolution was consistent with the exponential hypothesis. If the strong exponential hypothesis is true, then the origin of life should be dated 10 billion years ago. Thus, the possibility of panspermia as a source of life on earth should be discussed on equal basis with alternative hypotheses of de-novo life origin. Panspermia may be proven if bacteria similar to terrestrial ones are found on other planets or satellites in the solar system.


    Hmmmmm. What do you make of this Larry.

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  7. Regression of the logarithm of functional non-redundant genome size versus time of origin in major groups of organisms showed a 7.8-fold increase per 1 billion years, and hence the increase of complexity can be viewed as a clock of macro-evolution.

    This would seem to require a "ladder" view of evolution, that "major groups" stopped increasing their genome size when they cleared another rung (except for those special few who were chosen for the next rung.) This is not the prevailing view in biology, the branching bush view is.

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  8. There would also be the matter of what is meant by "non-redundant genome size." If several similar genes with obvious (to a non-Creationist) homology but separate cellular roles, as e.g. cell-signalling phosphatases and kinases, would they be counted as non-redundant or not?
    Animal genome size database

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  9. Remind me again when the meeting you set up with Kirk Durston is to take place.

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  10. Perhaps you could point out what specifically is wrong with his research and why it is so flawed as to prevent him from pursuing a PhD. If it's solely that he draws an ID inference from it, that doesn't seem reasonable to me.

    A fair challenge. I'll attempt to address it.

    Any research program or research project that ends up at "goddidit" or something similar hiding behind euphemisms is non-scientific, and not appropriate for a science PhD program. Publication is no guarantee of quality; peer-review is imperfect because scientists are human, mistakes happen, and subjective biases and other influences can impact the dissemination of scientific discoveries. Publishing scientific papers is a necessary, but not sufficient, component of a PhD.

    I was concentrating on Mr. Durston's apparent success at his PhD Qualifying exams. I myself am about half-way through this process: I passed the verbal component, but I must re-write the written component to bring it up to the standards expected of my department's PhD program. I am a student in the department of Integrative Biology, not the same department as Mr. Durston, so I expect there are some differences between the departments in the way they administer the qualifying exams. The verbal examination, in which the student answers a wide range of questions posed by an examination committee composed of several professors in the department, is very common at Canadian universities, as far as I have been able to determine.

    One set of questions I was asked during my exam concerned experimental design. Given a particular research question, how would you go about generating and testing hypotheses? And, given you found a particular result from your experiments, how would you interpret it? What conclusions could you draw?

    I think Mr. Durston's honest answer of intelligent design would be just cause to fail that exam. Falling back on the old argument from personal incredulity of "it must be a creative agent of unknown and unknowable powers" is NOT SCIENTIFIC, because that hypothesis is completely untestable.

    It is not sufficient to publish a number of high-quality research papers during the course of one's work to achieve a PhD. One must show the abilities of a critical researcher, and that includes being able to make and defend arguments based on reason and evidence. Resorting to the collection of logical fallacies that constitutes intelligent design creationism (or any other psuedo-scientific ideology) demonstrates a failure to achieve that critical scientific training, and is grounds for denial of a degree such as a PhD.

    In summary, yes, it's solely that he draws an ID inference from his studies. No ID inference I've yet seen qualifies as a scientific inference, and thus all ID inferences I have encountered are invalid in a scientific context.

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  11. Trevors does seem to be assuming his conclusion with statements like, "Functional algorithms can only come from consciousness" or words to that effect.

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