Is Intelligent Design a Scientific Theory? I Think Not

It is important to separate the issues in this debate.
What the Debate Is and Isn’t About
The debate is over whether Intelligent Design (ID), as articulated, is a scientific theory. The debate is not over whether there is an intelligent designer or whether that intelligent designer is God. It really is not whether the theory of evolution is a scientific theory or, if so, the degree to which it is or isn’t supported by data. In my faith perspective, I happen to believe that creation is due to an intelligent designer, and happen to I believe that Creator is the Christian God (with parts of the Trinity playing a part in creation). However, that is, I believe irrelevant to whether I believe that ID is a scientific theory.

What Do I Believe a Scientific Theory to Be?

I believe that a scientific theory is a grand narrative that unifies models, which in turn unify data (and even define what “data� are) through the interrelating connections of what scientists call “latent variables.� A latent variable cannot be seen. It is a construct. However, indicators can be measured that are related in systematic ways to the latent variable. For example, the latent variable of self-esteem is not capable of being measured. But we can measure correlates, causes, and effects that imply that the latent variable exists.

The grand narrative “theory� is an exalted status in science. Most of what lay people, and even many scientists call “theories� are in fact more limited narratives about the relationships of variables, called “models.� In psychology, for example, cognitive theory might incorporate a variety of models about how mental activities, processes, and structures interrelate with each other. Models relate latent and observed variables, but on a much more limited scale than do theories. Theories usually combine quite a few models.

The Debate Is Not about What a Good Scientific Theory Is

Of course, as Professor Ellis points out, scientific theories might be good ones (explaining a lot, leading to specific research agenda that involve testable hypotheses, interrelating many variables, and explaining mechanisms by which events occur and variables interrelate with each other). But this debate is not about whether ID is a “good� theory. It is about whether it meets the criteria for a scientific theory.
Explanation of My Understanding of ID
ID clearly uses observation and measurement. It also relies heavily on statistical inference—one of the hallmarks of scientific theory. Certainly, it posits a central latent variable (the intelligent designer), which can’t be itself measured, but which it might be claimed has evidence pointing to it. (We will examine that claim in a moment.) However, I believe ID falls down on several other criteria that disqualify it, as it is currently articulated, as a valid scientific theory. First, it is not much of a grand narrative. The way ID is articulated, it is more like an anti-theory than an actual theory. It takes an observed aspect of life, tries to explain as much as possible using science as it now exists, and it finally observes that much is unexplained. Rigorous statistical inferences are employed to quantify the amount of unexplained variance. Usually, a conclusion is drawn that a substantial amount of variance is not explainable. The phenomenon is said to be “irreducibly complex.� This method is repeated with many phenomena.
Critique of This Understanding against My Understanding of What Makes up a Scientific Theory
There is no grand narrative. Let’s suppose that thousands of phenomena could be eventually rigorously shown to be “irreducibly complex.� Does that make a theory? Not really. It does not seem that ID is even a model. That is a whole step away from being a scientific theory. Models of actual behavior are not interrelated by the grand narrative. There is no scientific program. Furthermore, there is no scientific program available—other than keep applying the same method to various phenomena. If the method were shown to be valid, what would I tell my graduate students to do on the basis of the theory? There is no program that is suggested by ID—other than apply the method to a new phenomenon.

Thus, ID seems more of a scientific method to me than a scientific theory. In terms of philosopher of science and historian of science, Thomas Kuhn, this seems like a “shared exemplar�—a recommended procedure for uncovering data. As an analogy, let’s take the model of learning, operant conditioning, developed by psychologist B. F. Skinner. Operant conditioning, used an operant chamber—a “Skinner box�—to train rats, pigeons, or even humans to act in specified ways in order to receive a “reinforcement� (roughly what we would call a reward). ID seems more like the method of using a Skinner box than the set of principles that relate latent variables (i.e., learning)—such as what reinforcement does to create and maintain learning, what punishment does, how generalization occurs, how discrimination occurs, etc. Furthermore, ID, as it is articulated at present, does not explain the relationships among variables even as well as does operant conditioning. And in Psychology, operant conditioning is not even considered a “theory.� It is only a model of learning.

If this is a theory, then “scientific theories� have to be redefined. Let’s examine the “latent variable.� In ID, the latent variable is the presence of an intelligent designer. By accumulating instances of irreducible complexity, the ID-practitioner provides indicators that point repeatedly to a fundamentally unobservable latent variable—the intelligent designer. Does that make ID a science? I again do not think so. First, the latent construct of irreducible complexity is related to to the latent variable of the intelligent designer. That is what science indeed does—relates huge sets of interrelated connections of latent variables. But ID does not related huge sets of connections of two (or usually more than two) latent variables. It merely relates the two again and again with different indicators for demonstrating irreducible complexity. I believe, therefore, that—as a scientific theory goes—ID is irreducibly simple. With its two latent variables, ID is simpler than almost every scientific model. To call it a “theory� one must be willing to admit that there are millions of such “theories.� Taking that position, I believe, defines the term “scientific theory� out of all practical existence.

Conclusion

I am unwilling to exclude the enterprise of ID from the realm of science. It partially meets some criteria for being scientific. However, I believe that ID is clearly not a scientific theory. It is too early to label it as such. Way too early.
Everett L. Worthington, Professor of Psychology

Intelligent Design is not scientific based on the fact that it is not falsifiable through empirical analysis; it is not testable. The foundation, the premise of Intelligent Design is scientifically flawed by "design". Basically, the ID people have reached a conclusion, and are working to find evidence towards that conclusion. That, in it's own essence, is not scientific.

This is why you do not see ID research published in peer reviewed scientific journals.

However, the ID people spend millions of dollars on propaganda PR campaigns, with movies/articles/etc. They do very little scientific work, but claim to be scientific. To allow discussion and planting these seeds of doubt, will undoubtedly bring the downfall to scientific inquiry and thought.

Why bother searching for the truth if the truth is established as a designer? This "theory" perhaps is one that may be thought in a philosophy class, but just like we do not teach math in english class, we cannot teach ID in science class.

First, I'd like to say I was pretty disappointed. This first debate completely ignored the question(s) its title and the summaries in the flyers posed. It was yet another "Evolution (and ID) for Dummies" lecture -- useful, but I wouldn't have gone had I known it would be that. No discussion about what constitutes science or a scientific theory. Anyway, moving on...

Dr. Worthington, it is refreshing to see that, in spite of your personal beliefs, you still stick to the facts and analyze the situation in a balanced way. That's intellectual honesty at its best indeed, and I wish all the debaters would always have it. But then maybe there would be no debate on this issue...

Now, although I do agree with most things you wrote and our conclusion, there are a few aspects I have to question. Specially that ID does meet any criterion at all for being scientific. Here goes my view of it.

Although the "grand narrative" is a valid way of describing a scientific theory, I think you missed and important point: the scientific method, which is how we arrive at such narratives. It seemed from your post that you didn't tackle that.

As you probably know, when we're reading a scientific paper, at least in the biological and physical sciences, we (even unconsciously) look for a few hallmarks to tell if it is scientific or not (regardless of the fact that the editors of the journal have already made that judgement). What was the previous knowledge and question? What was the hypothesis? What are the predictions of such hypothesis? Did the authors test such possible outcomes to a satisfactory degree? It is probably the same in Psychology, I suspect. Some of the terms I used, and how I see them:

Question: something that our previous knowledge hasn't yet (partially or totally) explained. E.g. why do organisms have sexual reproduction when it's clearly disadvantageous and slower (you need males, who don't actively produce offspring).

Hypothesis: statement based on previous observations and knowledge. E.g. sex shuffles genes and creates new combinations, therefore increasing variability in the population -- this is good for making populations more resistant to parasites or sudden changes in the environment, for example.

Predictions: consequences of the hypothesis; have to be testable by experiment and/or observation. E.g. if we find two very similar populations or species which only differ in the fact that one reproduces sexually and the other don't (this does exist), we could bring them in the lab and check their robustness to attack over time.

Tests: experiments or observations that try to isolate some aspect of the hypothesis (a variable) as much as possible when checking the validity of the predictions. In my example so far, we would do even better by creating a mutant that does not recombine or does not reproduce sexually (something like that has been done recently).

Theory: a very well corroborated hypothesis (or set of them). E.g. if both species display similar population growth when under attack, then sex is not affecting the outcome. If on the other hand the assexual population starts to have a disadvantage and leave less progeny, then probably sex is helping the other population (since sex was their only difference). The hypothesis passed a test. Passing many more, from different angles and approaches, will make this a theory, a "grand narrative" as you called it.

Kind of inductive, I know, but please don't tell the philosophers, many of them have a problem with induction. But sorry, that's the way science is done in the real world.

Now why doesn't ID, in my oppinion have anything to do with a science? To me, ID might at the most be called a hypothesis, as I think you would agree (or a method, as you put it): given our inability to explain the complexities in the biological world, there must be a designer to make all we see possible -- because nobody denies it exists and is complex.

So the problem with this hypothesis is that it is not productive -- it simply says its opponent(s) can't do something, but provides no way to test any alternative. Actually, I doesn't provide an alternative at all! As you said, an "anti-theory" -- and in many levels, I would add.

The problem with a negative idea like this, is that it suffers from a logical fallacy called argument from ignorance (or lack of imagination): we don't (yet) know or can't imagine how X would happen by means Y, therefore it is impossible for X to happen by mean Y -- as a bonus, my preferred alternative is by default true. Sometimes this is also called argument from incredulity, specially when people don't know the subject they're talking about: "I can't believe this is possible, therefore it is not".

See how this completely invalidates ID, at least as all IDers now "practice" it? They can't see how evolutionary biology could explain the complex structures of the living world, therefore they must have been intelligently designed. It's not a productive statement, just a negative about another idea.

Do you (or anybody) see a way in which ID would be free from this problem which prevludes ID from ever being scientific? I don't, but it might just be MY lack of imagination this time. ;-)

J. Alves, Postdoctoral fellow (Microbiology & Immunology)

I have to disagree with a few points, Everett. You define a theory as: "a grand narrative that unifies models." Okay, there are many different definitions of the phrase "scientific theory" (about which we could ramble for hours). Call it a model if you like--I don't think anyone cares. The central question regarding ID, however, has simply been "Is it scientific?"

The question we all care about (particularly Larry) is "Is this science, or is it supernatural blather?" I think we all agree that science is intrinsically limited to observing natural phenomena. Theories and models, if they're good, rest on strong empirical data which they explain consistently (or at least better than contemporary theories).

So it seems that the key criteria an idea/explanation/method must meet to be "scientific" is simply the empirical element--testability. That said, ID asks an empirical question and attempts to answer it in empirical ways. "Can design be detected empirically?" "Are there elements in design that we can mathematically define and then screen for that set of elements in certain phenomena?"

What's unempirical about these ideas? What's unempirical about seeking to design an empirical test for design?!

Larry, your statements seemed to describe exactly what ID is not! I did find this idea interesting, though: "Basically, the ID people have reached a conclusion, and are working to find evidence towards that conclusion."

What are Darwinists doing if not this? In fact, what do scientists do on a daily basis if not this?! Nobody blindly searches for raw data. All investigations are carried out under the guidance of some sort of prior hypothesis.

I have to disagree with a few points, Everett. You define a theory as: "a grand narrative that unifies models." Okay, there are many different definitions of the phrase "scientific theory" (about which we could ramble for hours). Call it a model if you like--I don't think anyone cares. The central question regarding ID, however, has simply been "Is it scientific?"

The question we all care about (particularly Larry) is "Is this science, or is it supernatural blather?" I think we all agree that science is intrinsically limited to observing natural phenomena. Theories and models, if they're good, rest on strong empirical data which they explain consistently (or at least better than contemporary theories).

So it seems that the key criteria an idea/explanation/method must meet to be "scientific" is simply the empirical element--testability. That said, ID asks an empirical question and attempts to answer it in empirical ways. "Can design be detected empirically?" "Are there elements in design that we can mathematically define and then screen for that set of elements in certain phenomena?"

What's unempirical about these ideas? What's unempirical about seeking to design an empirical test for design?!

Larry, your statements seemed to describe exactly what ID is not! I did find this idea interesting, though: "Basically, the ID people have reached a conclusion, and are working to find evidence towards that conclusion."

What are Darwinists doing if not this? In fact, what do scientists do on a daily basis if not this?! Nobody blindly searches for raw data. All investigations are carried out under the guidance of some sort of prior hypothesis.

"Can design be detected empirically?" "Are there elements in design that we can mathematically define and then screen for that set of elements in certain phenomena?"

Chloe,

It sounds more philosophical than empirical/ scientific to me, specially in the state ID is now (that's basically what Ratzsch concluded, if I remember well). And you're leaving out the most important thing in a scientific theory: what does it predict, how much does it explain. If it predicts nothing and explains nothing, it's as good as nothing, really.

Anyway, your tackle seems to me like a much better approach to the problem -- but ID as it is now does NOT do this, therefore ID is not scientific (yet?). At least judging by what the main figures in the ID movement (e.g. Behe, Dembski) are talking about. They are doing what I said in my previous post: falling for the argument from ignorance when they say "we don't know how it can be done (or it looks too improbable), so it must be designed".

I think Larry did not say what ID is, in his post. But he described pretty accurately how the movement works and how the ID proponents behave. Just have to watch them in action.

You're right, "Darwinists" are not in blind searches for raw data: they are based on *extremely solid science*, accumulated after >150 years of work on inumerous fields -- they are not acting based on arguments from ignorance/ lack of imagination like ID as currently "practiced". I mean, if you drop a rock, do you have no idea how fast it will accelerate and in which direction? How about the "design thing"?

J

Alves : It sounds more philosophical than empirical/ scientific to me...

It seems you completely dodged my question. Again, what is unempirical about designing an empirical test for elements of design?? This is EXACTLY what Dembski's work is about.

Have you read "The Design Inference" or any of his other books on the topic (not sure how many he has written). If not, you need to. It was hard for me to read due to its heavy probabilistic/mathematical content, but it did help me to understand what he is attempting to construct and what factors would need to be considered in designing such a test for elements of design.

As for predictions and explanations, Steve Meyer does a pretty good job of detailing a few of these specifically in a recent debate. (http://www.arn.org/blogs/index.
php/3/2006/05/22/watch_
stephen_meyer_v_peter_ward_debate_)
Granted, Ward was a pathetic opponent, so don't watch looking for entertainment--just consider Meyer's arguments.

Alves: They are...falling for the argument from ignorance when they say "we don't know how it can be done (or it looks too improbable), so it must be designed".

True, but that's not the argument. The argument is "Look at all these design elements detected in this ATP synthesizing proton pump! In addition, based on every empirical observation man has ever made, complex machines and circuitry containing these design elements have never been observed to arise by unintelligent natural forces."

Alves: ...they [Darwinists?] are based on *extremely solid science*, accumulated after >150 years of work on inumerous fields

Does that "extremely solid science" offer us any insight into a plausible evolutionary pathway for the gradual constuction of ATP synthase (or ANY of the myriad of highly complex molecular wizardry found inside cells...)? It seems that Darwinism explains very little here (and we both agree that explanatory power is a key criteria for a theory to be "scientific"). I think Darwinism is currently impotent in the world of molecular biology. Its multiplicity of adherents owes less to its scientific rigor than to their philosophical committments.

I am a PhD student in the Microbiology/Immunology department here at VCU. I unfortunately missed the debate, however, I have followed this debate for several years and have read much of the "ID literature" which amounts to popular books misrepresenting Darwinian theory, making statements of personal incredulity such as "I can't think of how this pathway came about gradually so I am justified in concluding it was designed." ID proponents base their argument for design on a false dichotomy in which gaps in scientific explanations are filled with design. Michael Behe coined the term "irreducibly complex" and defines it as a biochemical structure or pathway in which removal of one part renders the structure non-functional. He claims that the system could not have formed through gradual addition of parts because he defines such precursors non-functional by definition. This is of course a logical fallicy without empirical data. This is of course in spite of the fact that we know genes duplicate and most proteins have homologues that appear co-opted for various functions.

In fact, their architype example is the bacterial flagellum which they call "irredicibly complex". They claim that the bacterial flagellum is composed of over 40 protein parts, each of which is crucial to its function. They conclude, after knocking a few genes out and complementing mutants that this system is in fact irreducibly complex-and by implication-unable to form by natural processes. I will refer you to a rebutal of these claims published in Nature Reviews Microbiology (Pallen MJ, Matzke NJ. From the origin of species to the origin of bacterial flagella. Nat Rev Microbiol. 2006. 4(10):784-790.) They actually do some research into this that was neglected by Mike Behe and Scott Minnich (who testified at the Dover trial as a flagellum expert).

What this paper points out, and what microbiologists know is that saying "the bacterial flagellum" suggests there is only one. However, as the research points out that within these 40 protein parts, only half appear crucial in each bacterium, and that each protein is homologous to other systems used in secretion or cell-cell attachment. Not to mention that archaebacteria have analogous structures with different protein parts. They conclude that co-option of parts is clearly represented by the data. The design argument suggests the designer created many hundreds or thousands of flagella-not a very parsimonious answer. Occam's razor seems to do away with this nicely.

The problem with intelligent design is that it makes no predictions other than organisms will have structures that require their parts to function-and that this, coupled with their complexity necessitates design. Isn't this stating the obvious? It's like asking if a unicycle will work if you remove the tire. Interestingly, the Templeton foundation asked the Discovery Institute (ID home) to submit grant applications for funding. Nothing was submitted. I had email correspondence with Michael Behe to try and find out where he was in terms of research after the 10 year anniversary of his book "Darwin's Black Box: the biochemical challenge to evolution". He told me that the design inference could not be tested experimentally. I agreed. In fact, he has admitted this on several radio programs but insists that this inference is the best explanation.

The hypothesis is that an intelligent designer created life. Because of the obstacle they claim 'irreducible complexity' is for a natural exlanation the designer has to be supernatural by definition. They claim to have a theory that will overthrow Darwinian evolution; however to do so they must provide a theory with greater explanatory power. They claim the Darwinian mechanism is insufficient; yet they propose only the unobservable act of a supernatural designer as their mechanism. You cannot falsify this claim since it is by definition outside our rhelm of observation. How does this explain the fossil record? Antibiotic resitance? Male nipples? The Panda's thumb? Cave dwelling organisms with vestigial eyes? Why would a designer make non-functional or jury-rigged structures? And if small change is possible, as in the case of antibiotic resitance; why are we to believe that large scale change is not possible over millions of years?

The design argument started with William Paley book Natural theology in which he said something along the lines of 'if you came upon a watch you would know immediately that the watch had an intelligent origin.' This is the same argument used to explain life by the ID crowd. I would say, no we know the watch had an intelligent designer because it says Casio on it. Is the flagellum trademarked?

To all those thinking that ID is a genuine scientific enterprise, you should first read their manifesto that leaked out in 1999, called the "Wedge Document".

It starts as follows:

"CENTER FOR THE RENEWAL OF SCIENCE & CULTURE

INTRODUCTION

The proposition that human beings are created in the image of God is one of the bedrock principles on which Western civilization was built. Its influence can be detected in most, if not all, of the West's greatest achievements, including representative democracy, human rights, free enterprise, and progress in the arts and sciences.

Yet a little over a century ago, this cardinal idea came under wholesale attack by intellectuals drawing on the discoveries of modern science. Debunking the traditional conceptions of both God and man, thinkers such as Charles Darwin, Karl Marx, and Sigmund Freud portrayed humans not as moral and spiritual beings, but as animals or machines who inhabited a universe ruled by purely impersonal forces and whose behavior and very thoughts were dictated by the unbending forces of biology, chemistry, and environment. This materialistic conception of reality eventually infected virtually every area of our culture, from politics and economics to literature and art

The cultural consequences of this triumph of materialism were devastating. Materialists denied the existence of objective moral standards, claiming that environment dictates our behavior and beliefs. Such moral relativism was uncritically adopted by much of the social sciences, and it still undergirds much of modern economics, political science, psychology and sociology.

Materialists also undermined personal responsibility by asserting that human thoughts and behaviors are dictated by our biology and environment. The results can be seen in modern approaches to criminal justice, product liability, and welfare. In the materialist scheme of things, everyone is a victim and no one can be held accountable for his or her actions.

Finally, materialism spawned a virulent strain of utopianism. Thinking they could engineer the perfect society through the application of scientific knowledge, materialist reformers advocated coercive government programs that falsely promised to create heaven on earth.

Discovery Institute's Center for the Renewal of Science and Culture seeks nothing less than the overthrow of materialism and its cultural legacies."

As you can see they are committed to the overthrow of methodological naturalism which forms the basis of the scientific method. They must do this to make their hypothesis scientific-that is to say, they must redefine science to make their views accepted.

If you do some basic searches on some of the more notable ID advocates, you will find interesting conflicts of interest with their supposed objectivity.

For instance, Jonathan Wells, who wrote "Icons of Evolution". He has a website "The Words of the Wells Family" in which he wrote an article called "Why I went for my second PhD" which describes:

"At the end of the Washington Monument rally in September, 1976, I was admitted to the second entering class at Unification Theological Seminary. During the next two years, I took a long prayer walk every evening. I asked God what He wanted me to do with my life, and the answer came not only through my prayers, but also through Father's many talks to us, and through my studies. Father encouraged us to set our sights high and accomplish great things.

He also spoke out against the evils in the world; among them, he frequently criticized Darwin's theory that living things originated without God's purposeful, creative activity. My studies included modern theologians who took Darwinism for granted and thus saw no room for God's involvement in nature or history; in the process, they re- interpreted the fall, the incarnation, and even God as products of human imagination.

Father's words, my studies, and my prayers convinced me that I should devote my life to destroying Darwinism, just as many of my fellow Unificationists had already devoted their lives to destroying Marxism. When Father chose me (along with about a dozen other seminary graduates) to enter a Ph.D. program in 1978, I welcomed the opportunity to prepare myself for battle."

To be fair, Dawkins has said that Darwinian evolution makes it possible to be an intellectually fullfilled atheist. However, in both accounts, this is not the science talking, but rather philosophy.

Chloe,

"Again, what is unempirical about designing an empirical test for elements of design??"

What about the "designing" part? It is not empirical until is used, by definition? And there is no such test for probing nature (as opposed to looking at car crashes, crimes and such) so far, is there? So how can it be used? That's what I meant when I said ID is no more than phylosophy at the best so far -- and I think it will always be so.

No, I have not read Dembski's books directly, but only online lectures and slide shows of his.

His main fault is that he uses the strawman fallacy -- he says evolution "is random" and proceeds from there -- among other things. He just says "this can't be" but never shows proof.

Little mathematical tricks with coin tosses do not amount to much. He comes up with a magical information threshold number, sounds pretty impressive until you actually think about it: does he ever determine how to calculate the probability of an eye? Of an ATPase? Of a bacterium?

He even starts the old, ridiculous talk about closed systems and all that. Life ain't a closed system, period.

And finally, but significantly, it's kind of hard to take seriously someone who shows slides with things like:

"The conceptual soundness of a scientific theory cannot be maintained apart from Christ."

or

"Christ is never an addendum to scientific theories but the completion."

Really. May not detract from his arguments (other things take care of that), but it does not bide well, does it?

"Does that "extremely solid science" offer us any insight into a plausible evolutionary pathway for the gradual constuction of ATP synthase (or ANY of the myriad of highly complex molecular wizardry found inside cells...)?"

I don't know for the ATP synthase specifically, but there are molecular examples where we do have plausible scenarios, yes. Many actually, and not only molecular. For one example look online for "The evolution of vertebrate blood clotting", a part of a book by Kenneth Miller.

Anyway, there you go appealing to the argument from incredulity/ ignorance again, so I don't think any evidence will matter, because there will always be some part still to explain, etc. ad infinitum.

"I think Darwinism is currently impotent in the world of molecular biology."

Interesting. I assume then that you're very knowledgeable in both molecular biology and evolutionary biology to make such a claim. I mean, I've been in both areas for some 10+ years... You should publish your ideas then, please.

J

JA: "What about the "designing" part? It is not empirical until is used, by definition? And there is no such test for probing nature..."

First, since when is this the definition of "empirical"? "Empirical" simply means that it is subject to testing. (I hate to appear nit-picky, but discussion is useless unless we agree to play fair with word definitions.) This is certainly the case with detecting design (evidenced by the fact that we ALREADY ARE in the business of detecting design)! You know the SETI example--why pretend it doesn't exist? You know archeologists screen their findings (probably informally, but they are nonetheless distinguishing design from non-design). That means that certain branches of science ALREADY have systems in place for detecting design.

Can we not at least acknowledge this irrefutable fact?

Second, considering you have not read his work, I'm not sure how accurate your critique of his ideas could possibly be. I can't imagine how trustworthy my own critique would be given that statistics/probability theorems are not my strong point! However the most basic and compelling notion that I took from the book was simply this:

Designed things display characteristic and definable elements, and these elements can be used to distinguish design from non-design.

Would you not agree with that statement? If not, where exactly is it erroneous?

You went on to question Dembski's motives by referencing his religious beliefs. Ridiculous in light of the fact that many Darwinists are rabid atheists trying to foist their religion on the world. Who cares?!

Deal with the arguments substantively.

Jason,

Wow--you sure can bloviate...! Forgive me if I just pick through and respond to the main points.

JR: "[ID proponents make] statements of personal incredulity such as 'I can't think of how this pathway came about gradually so I am justified in concluding it was designed.'"

You (and the Darwinist herd) need to move past this lame argument with all due respect. The claim of ID has NEVER been...

"BECAUSE we can't think of how it could have happened by mutation/natural selection, it must have been designed"...but rather something like...

"This molecular machine is rank with design elements. Things that are rank with design elements are designed (100% of the time in the history of human observation...). Therefore, this molecular machine is very likely to be designed."

It really is that simple.

JR: "[Behe] claims that the system could not have formed through gradual addition of parts because he defines such precursors non-functional by definition. This is of course a logical fallicy without empirical data."

Well actually the empirical data would be all the mutagenesis tests that resulted in nonfunctional flagella for each of the 40 proteins...

JR: "This is of course in spite of the fact that we know genes duplicate and most proteins have homologues that APPEAR co-opted for various functions."

Your use of the word "appear" (at least you were honest) translates into "guesswork." We don't know that molecular machines can be built by co-option. Why are you claiming that they can (and in fact DID) when there is NO empirical evidence for the ability of this mechanism to actually build a molecular machine?! Isn't that a bit spurious?

"Homology" among proteins and "analogous parts" between different bacterial species does nothing to answer the question, "By what mechanism was the bacterial flagellum built?"

Since Darwinists reject the obvious elements of design here, insisting instead that that explanation CAN'T be proposed...under any circumstances (certainly not for philosophical reasons!), we find ourselves asking another question.

"Can co-option, mutations, gene duplications (I feel like I'm watching the witches from Hocus Pokus toss random ingredients into their brew...), and natural selection produce a (POOF!) bacterial flagellum?"

If you claim it can, the ten million dollar question then becomes HOW EXACTLY?! As any good scientist should know, this claim must be accompanied with rigorous testing of proposed intermediate forms leading up to (by degrees) the final product. Anything short of this is pure hand-waving. Speculation is fine, but it needs to be identified as such.

Bottom line:
We know that designers can produce motors and other such devices rich in design elements. That is a conclusion based on thousands of years of observations, innumerable pieces of empirical data.

We don't know if co-option coupled with the other factors can build a motor. Contrary to the mountain of positive empirical evidence that things rich in design elements are invariably designed, there is NO empirical evidence for the claim that co-option and other unintelligent causes can actually build molecular motors.

ID theory is clearly a religious pursuit. Since when has science used supernatural explanations? Imagine yourself funding a research project to explain the emergence of a new disease, only to be told by the senior scientist that God/a god created it. You would be enraged. I know I would. I'd demand another answer. Heck, my four-year-old son could come up with that explanation with no scientific training. ID theory is a pathetic, struggling attempt to add validity to a personal religious or philosophical belief in the face of contrary evidence. The theory itself is not pathetic, but the attempt to prove it using science as the vehicle is pathetic. Get ID theory out of science and put it somewhere else. I can't believe people are still falling for it.

Chloe,

Thanks for the response. First, arguments from personal incredulity are the basis of all ID arguments. They claim that standard neo-Darwinian explanations have NOT yet explained the origin of a given structure/pathway and THEREFORE, design is suggested to be the only other explanation. Funny, they require a ridiculous amount of proof from biologists, but don’t hold their own institute to these strict requirements. Afterall, they have never produced ANY evidence that the flagellum or anything else was created by a designer. Secondly, like all ID arguments, your arguments are unfortunately entirely from analogy; which is a logical fallacy. “We know that designers produce motors� with the implication that the flagellum is a motor; therefore it must have been designed.

I’m glad you brought up Behe’s “40 protein flagellum�. I will allow Behe and other DI fellows to define their own terms before I address this notion:

Behe, Irreducible Complexity from Darwin’s Black Box:

"A single system which is composed of several interacting parts that contribute to the basic function, and where the removal of any one of the parts causes the system to effectively cease functioning"

Behe, Minnich and Meyers, on the irreducible complexity of the bacterial flagellum:

“Thorough genetic studies have shown that about forty different proteins are required for a functional flagellum, either as parts of the flagellum itself or as parts of the system that builds this machine in the cell.�

M.J. Behe. Evidence for design at the foundation of life. The Proceedings of the Wethersfield Institute: Science and Evidence for Design in the Universe. M.J. Behe, W.A. Dembski, S.C. Meyer ed. 1999. Ignatius Press, San Francisco, pp. 124.

Stephen Meyer says: “This machine [flagellum] is made of 40 protein parts….that looks like something that Mazda produced�. (http://bevets.com/evolutionav.htm). Scott Minnich says in the video ‘Unlocking the Mystery of Life’, “With a bacterial flagellum you are talking about a machine that’s got 40 protein structural parts. Yes, we find 10 of them are involved in another molecular machine but the other 30 are unique, so where are you going to borrow them from?�

Just so we are clear here, Behe and other Discovery Institute fellows claim that ‘the flagellum’ contains 40 parts that are irreducibly complex. This suggests that if a flagellum were to be found that did not contain 40 parts, or it a flagellum was to be found that still functioned if one or more protein parts were removed (gene knockout) the concept of irreducible complexity would be false. Furthermore, Minnich, the DI flagellar “expert� is quoted as saying that 30 of the proteins are unique, that is without homologues in the database.

Now that we understand what exactly we are talking about here, we can take a deeper look at these claims. In fact, Mark Pallen and Nick Matzke did just that. They published a paper in Nature Reviews Microbiology which was available online this past September. The full reference was provided above.

First, to set the record straight, there is no “the flagellum�. Pallen and Matzke elaborate on this in great detail:

“As the great evolutionist Ernst Mayr noted, one of Darwin’s greatest achievements was to abolish typological or essentialist thinking from biology; intead, the emphasis in biology is on variation and individuality(3). Therefore, when discussing flagellar evolution it is important to appreciate that there is no such thing as ‘the’ bacterial flagellum. Instead, there are myriad different bacterial flagella, showing extensive variation in form and function. The most well-studied bacterial flagellar system is that of Salmonella enterica serovar Typhimurium. However, in Gram-postive bacteria, flagella lack P- and L –rings (4), and in spirochaetes the flagellar filaments rotate inside the periplasm (5). Some flagella rotate using proton motive force, others depend on a sodium-ion gradient (6,7). In Sinorhizobium meliloti and Rhodobacter sphaeroides, the flagellum rotates unidirectionally, with a fast, slow or stop mechanism, whereas in S. typhimurium reversals in the direction of flagellar rotation are used to re-orientate the cell (8,9). Flagellar filaments vary in vary in their physical properties: some show right-handed helical packing, others left-handed; some are flexible, others rigid; some are straight, others curly(10); some undergo post-translational modifications such as glycosylation or methylation, others do not (11, 12). In Escherichia coli alone there are over forty antigenically distinct flagellins, with good evidence that variation is driven by diversifying natural selection (13)."

They also note that metagenomics is uncovering novel flagellar genes and what this means for the logic of Behe’s gross overgeneralization and oversimplification of this structure:

“Many new flagellar systems have been discovered through genome sequencing-a trend that is likely to increase with time. For example, over three hundred flagellin sequences were obtained in a single sequencing project that focused on samples from the Sargasso Sea (17). By even the most conservative estimate, there must therefore be thousands of different bacterial flagellar systems, perhaps even millions. Therefore, there is no point discussing the creation or ID of ‘the’ bacterial flagellum. Instead, one is faced with two options: either there were thousands of even millions of individual creation events, which strains Occam’s razor to breaking point, or one has to accept that all the highly diverse contemporary flagellar systems have evolved from a common ancestor.�

Next, Chloe has challenged me gene-duplication/co-option arguments:

“Similarly, six proteins from the rod (FlgB, FlgC, and FlgG), hook (FlgE) and filament (HAP1/FlgK) show sequence similarities indicative of common ancestry (25). Therefore, the flagellar rod-hook-filament complex has clearly evolved by multiple rounds of gene duplication and subsequent diversification, starting from just two proteins (a proto-flagellin and a proto-rod/hook protein) that were capable of polymerization into an axial arrangement. When examining homologies between flagellar and non-flagellar (NF) proteins, it becomes clear that several flagellar subunits share common ancestry with components from other biological systems.�

In the paper they show that the FliI, the ATPase that powers the flagellum shows unequivocal homology to F-type and V-type ATPases. I will not cover all of the evolutionary analysis performed, the paper is available.

The same table presented in the Nature review is also found below, which shows characteristics of flagellar genes, including whether they are found in all bacteria, and homologues: http://www.pandasthumb.org/archives/2006/09/flagellum_evolu.html

After reviewing this table, you will likely be left as I was: wondering how the DI could have missed this. Here are a few possibilities(1) the Discovery Institute did no research on the flagellum (2) they did the research, and recognized that for their purposes (targeting the general public) just using the analogy of ‘the flagellum is like an outboard motor’ would suffice to get their intended effect. (3) only one or two of them actually have biology research experience, so they lack the technical ability address these problems.

I support (3), but believe the main reason is (2) since it is not the purpose of the DI fellows to actually present their arguments to their peers, but instead, with no experimental work decided to write books whose targeted demographic are conservative Christians who in turn want their kids taught creation; enter the laywers and politicians.

In any case, it has been clearly established that there is no “the flagellum�, instead there are thousands that vary in mechanism of action, protein components, genetic regulation, sequence, etc. Next, there are many examples of flagella in nature that do not contain Behe’s required 40 proteins. Some contain ONLY 20 PROTEIN PARTS. This falsifies Behe’s definition. Finally, Minnich claims that 30 of the parts are unique-that is with no known homologues-though table 1 from Pallen and Matzke shows that this is far from true. The DI fellows are poor scholars with religious motivations as I have demonstrated above from their own documents.

Chloe, you were very selective of what you addressed. In your opinion, does the above present a significant problem to Behe’s hypothesis of ‘irreducible complexity’. I mean, it seems pretty reducible to me after a few scientists actually took a look at its parts.

My link to the flagellum table contained a period and won't open. Use this link:

http://www.pandasthumb.org/archives/2006/09/flagellum_evolu.html

I think any field uses super natural things to aid here and then.