Unfortunately, for a lot of ID proponents (though certainly not all), what your saying is often left out by the evolution proponents. What I mean is that for a number of ID proponents, he problem isn't that the Theory of Evolution is taught, it's that its taught as the "Law" of Evolution, and specifically that it is exclusionary to ID.

The problem is that with our current knowledge, Evolution and ID are not necessarily mutually contradictory, they can be reconciled; however IMHO a majority of Evolution supporters and a signifigant portion of the ID supporters have a vested interest in making sure that doesn't happen.

StargazerA5

"The problem is that with our current knowledge, Evolution and ID are not necessarily mutually contradictory, they can be reconciled; "

Just as Buddhism and the Copenhagen Interpretation of quantum mechanics can be reconciled. But you wouldnt teach Buddhism in science class anymore than you would teach quantum mechanics as a philosophy.
I am all for teaching ID in philosophy class, i happen to think its a fascinating subject and one I believe in many respects. But its not science.

I think ID advocates are making a huge mistake... for their own cause. Amac is right, science has a long track record of solving todays questions. By tieing themselves to the current crop of mysteries, ID has planted the seeds of their own defeat unnecessarilly. What happens when the supposed 'show-stopper' criticisms of evolution they bring up solved? I think we all have a pretty good idea judging from how they have argued to date... they will attack the science behind work and smear the scientists themselves. Thats bad for science and faith. Potentially real bad.

"The problem is that with our current knowledge, Evolution and ID are not necessarily mutually contradictory, they can be reconciled; "

"Just as Buddhism and the Copenhagen Interpretation of quantum mechanics can be reconciled. But you wouldnt teach Buddhism in science class anymore than you would teach quantum mechanics as a philosophy."

I think both of those are true. However, there is naturally a "philosophy" that comes out of science, which is not acknowledged - that goes "beyond the evidence". As Bohr said about light (is it a wave or a particle?), don't go beyond the evidence of science, to larger conclusions.

So I believe (and AMac will correct me if I am wrong, I'm sure) that science shows:

a. There is a fossil record with a lot of congruency and progression of species and forms.
b. In labs today, can be observed a certain percentage of mutations that naturally occur. These mutations can have effects - such as an organism being more or less resistant to certain diseases - this resistance/lack of resistance is observable and documentable now.

So AMac, Mark - would you add anything else to the "observable" evidence? Or would you agree that the above about covers it?

"Natural selection" is a proposed principle then, on top of the evidence we have for evolution of forms, and mutations that occur in cells observable in the lab.

Is this correct?

As I've said, natural selection really only means "that which survives is that which survives".

Perhaps I misunderstand what is meant by "random" or "blind", but it simply seems to me that "awareness" - the ability to adapt, be sensitive to the environment, and keep going and going - seems to be present in the smallest living things. For purposes of explanation, I'll "anthropomorphize". (And please, this is only a metaphor). We'll call this "Mother Nature".

Mother Nature seems like the Terminator, but FOR life.

The Terminator quote is " It can't be bargained with! It can't be reasoned with! It doesn't feel pity, or remorse, or fear. And it absolutely will not stop, ever, until you are dead!" (change the last part to "until it survives and propagates!)

Whatever you want to call "the life principle", it seems to have the same WILL - except as a WILL TO LIFE. The qualities are: incredible adaptability (from plants that bend to meet the sun, or that bend around objects, etc) to the ability to become resistant (how many times have we attempted to eradicate mosquitoes, and then become "resistant"?), the principle of "life" and those things that are alive, simply FINDS A WAY to go on, in the most dire of circumstances.

My AWE of this driving life principle - this awareness, this purposiveness, responsiveness, and adaptability - simply doesn't get captured by blind "random mutation" and "natural selection".

This intelligence disguised as microbe, plant, and animal. This LIFE.

Teilhard de Chardin said that the driving life principle above was one of the faces of God, masked in nature, constantly evolving.

I don't know if that is true. But I WILL say that the most advanced computers we currently have, do not have the consciousness of the lowly microbe. The DRIVE, the responsiveness, the adaptability, the energy, the awareness.

Perhaps it will one day be proven that the above qualities evolved mechanistically.

But for science to go from the evidence - of evolution of forms, of mutation - and then say that "evolution is blind adaptation to the environment" - well, that's a philosophic statement too, and goes beyond the evidence of science.

Agreed Mark Buehler.

I'm perfectly willing to believe in an I.D. that doesn't impose weak-minded human limits on the design itself. I mean, its preposterous that ID proponents try to counter the obvious "mutation leads to speciation, eventually" central tenent of evolution by saying "prove it", and then pooh-poohing every example as "mere mutation and selection (usually human mediated)".

I've said it before, but being a programmer (the height in 'genetic coding', I might argue), I value most highly programs and algorithms that have been designed NOT to have specific limits, but that can be mutated and re-used for a variety of unforseen purposes. I therefore submit, that if life really was "designed" by an extraordinary civilisation - that it most definitely would include that seed of self-repair, self-mutation and self-selection called "evolution". I mean, who would want one's creation to go catywumppus and kaput every time the designer decided to take an eonic vacation or three?

No, the ID group are simply put New Age crystalarians, under new guise and cover. You know, "woooooo... this shit is all too complicated to conceivably have been happenschance... it therefore must have been created by some great spiritual force that we can't know, but only infer. Pass the patchouli oil, and don't Bogart the spliff friend!!! Want to put an order in for one of my commune's energy pyramids or a bottle of hyper-pure Graetan space water?"

To me, ID is proof positive that the Era of Psychohistory has begun (Asimov, Foundation trilogy). Arthur C. Clark's "Any sufficiently advanced technology is indistinguishable from magic" thesis just about wraps it up: when that which can be known advances to a sufficiently deep level of specificity, detail, non-intuitive rules and systems, humanity becomes divided into those who attempt to understand ("scientists"), and those who attempt to simplify to any point that approaches a holomyth. Crystalarians.

Disturbingly, fundamentalists of Christian origin tend toward The Book explanation in order to simplify their existences, thus rejecting anything produced by science that directly undermines their favored creation myth. The crystalarians are on for the ride, the Great But Somewhat Challenged prez is just mouthing whatever it takes to keep Kansas a Red State, and on it goes. But by the grace of all that's good, at least one's belief in Evolution or any alternate theory doesn't impact society economically one scintilla. Nothing we're doing in science is creating gadgets based on Darwin's or Smiths's, Abraham's or Jehovah's theories of from whence it all began. Except the dino-bone recoverers and fossil mongers.

Well, need to get to work. Is a great discussion - and remember: if it really is ID, then evolution MUST be built into it. [!!!]

GoatGuy

I'm all for culture war, in its proper place, but now we've got two culture wars raging (over ID and Global Warming) in the midst of some sensitive machinery that ought to be allowed to work undisturbed.

Everybody blames everybody else, of course.

Dr. Steinberg, who has been attacked for allowing an ID article to be submitted for peer review, was interviewed on FOX. The claim was made that the National Center for Science Education has taken the position that "no article challenging Darwinian evolution should be submitted for peer review."

I can't find confirmation of that, but it seems clear that the NCSE is doing these objectable things:

1. Claiming that ID is illegimate because proponents do not publish in peer-reviewed journals.

2. At the same time, they do everything they can to block such publication.

3. When it's pointed out that ID proponents are publishing in peer-reviewed journals anyway, in spite of the NSCE's efforts, the NCSE demeans the value of peer review.

Pseudo-scientific heresy is an enemy of science, of course. But so is deaf and blind conservatism. What's wrong with allowing articles to be peer reviewed? Even articles on dead aliens and spontaneous combustion? Isn't peer review supposed to weed out the obvious crap?

Science isn't an abstract body of received wisdom that operates all by itself. It's a human process, inevitably prone to error and politics. But science has a very good record at overcoming error, and in the end either you believe in the system or you don't.

Some critics of ID are accusing some ID proponents of having insufficient faith in God. I think they have a point. But it goes the other way, too - some of the champions of orthodoxy have no faith in science.

Scientists: I highly recommend reading "Origins of Life" by Rana/Ross. Presents scientific hypotheses and evidence. Stunning analysis.

I'm rather certain you'll be surprised.

Glen,

I hate to point out the obvious, but a "peer reviewed paper" is just that: if its pap, then it stands the same chances as a snowball in Hell of being published.

That's the reason why AAAS Science isn't full of every couch-astronomer's theory of the universe, every napkin-bioligist's theory of protein folding, or every weekend physicist's theory of free energy from magnetic fields. Peer review laughs them right out of existence, back into the backwaters of home-made websites, pet-theory harbors, hamster heaven. (Crystalarians)

As soon as some truely scientific enterprise goes into creating a set of hypotheses, theories, and tests for them, with the accepted standards of scientific inquiry being applied, then the journals peer-review boards will likely jump on the opportunity to stir the mud a bit, from the science standpoint. Until that time, as they continue to evoke magic, superior intellect, mysteries of the unknown being proof of their theory's prowess... they ain't gonna be published.

Period.

GoatGuy

GoatGuy: a "peer reviewed paper" is just that: if its pap, then it stands the same chances as a snowball in Hell of being published.

Well, yes. We should hope so. That's my entire point.

Peer review isn't the entire process, but it's an important part of the process. There is no reason for anybody - from either side - to try to block that process from working.

I'm pretty sure I can resolve almost everyone's issues here, but first I have to have one question answered: is science a theology or is theology a science?

fun topic y'all

Glen:
There are alot of fringes of science; in chemistry, biology and physics. Anytime someone says something which does not sit with the current train of thought, there are almost always outright rejected. That's true of anything, not just ID.
Scientists (as non-biased as we try to be) are still people, who have placed alot of time and energy proving a theory, and will actively work against something that disagrees with their work. (there are thousands of examples)
Note: this is not an inherently bad thing. New 'radical' theories pop up from time to time (like darwin), and if the 'science' is written well, it will invite other scientists to try and disprove this radical new theory. In spurring scientists to debunk this theory, they may actually create experiments that unintentionally show this theory is correct.
The key is that the founding science has to be rock solid, and open to new methods of experimentation. Unfortunately, I can't think of a way that you could directly test for ID.

Here are some links on the "ID and peer-review" controversy that Glen Wishard referred to in Comment #5.

Les Lane’s has a website with a link-rich page devoted to the decision by journal editor Richard Sternberg to publish a pro-ID paper by Richard Meyers. The WaPo and NYT both weigh in. Lane’s suggestions on How to get good scientific advice are germane.

Courtesy of the anti-evo Discovery Institute, here is Meyer’s paper, “Intelligent Design: The Origin Of Biological Information And The Higher Taxonomic Categories.”

As Comment #31 of this thread, my two cents on what “peer review” can and can’t reasonably be expected to accomplish.

We believe all problems, ragradless of how conjured, are solvable by us, all questions, regardless of how specious or profound, are answerable by us. It occurs to me that we might be, even in the aggregate, too dumb to know everything. There is no "irreducible complexity". Perhaps there is not even any complexity. Perhaps we are too dumb to get it. Perhaps we are simply too dumb to do anything but demand a solution, an answer, even to questions which have no legitimacy. We are the spoiled child of the universe.

Our retreat from ignorance is to the mystical. Let us all light a candle to the ID'er. Praise he did not make us paisley for, truly, that would certify his being and we could never wear plaid.

AMac -

Thanks for that link. But why should there be any controversy here?

Right or wrong, Meyer's paper has been published. Now its errors can be dissected and exposed. If some think that it wasn't good enough to be published, then the journal that published it will accordingly suffer loss of prestige.

So far all fair and square, and John Stuart Mill would be pleased.

So tell me what purpose is served by digging into Sternberg's background nad questioning his motives? If it turns out that Sternberg is an awful person, does that have any bearing at all on the truth or falsity of Meyer's paper?

Because if that's how scientific truth is determined, we can dispense with the scientists and hire some private investigators. And instead of peer review, we can have polygraph tests.

Glen Wishard #13,

We agree. (Or, we agree!)

Meyer's article is a review, not a piece of original research. He points out problems with the current interpretation of the "Cambrian Explosion" early in multicellular life's history (600 MY bp), does some calculations, makes some statements about plausible mutation rates, and then suggests that Intelligent Design may be the answer to the conundrum.

Now, this isn't close to my specialty. It may be that the objections he raises are specious, on the order of "since 2 plus 2 = 5, evolution can't account for the observed diversity." Lord knows, enough creationism/ID criticism is along those lines. But I didn't see such arguments enunciated by critics of him and Sternberg in the WaPo piece or elsewhere.

Although Meyer's answer (ID) is speculative, even non-scientific, it takes critics to point out potential problems in any system. It may not be perfect that the peer-review system ends up with journals accepting articles that combine genuine definitions of problems with bogus solutions. But this is much better than the alternative of avoiding insightful challenges to current orthodoxy for dogmatic reasons.

One difficulty is that, in practice, most crummy articles aren't decisively rebutted. They are ignored, and left uncited by other authors. The Discovery Institute and others have been credibly accused of playing the game of creating an alternative network of anti-evolution journals that generously cite each others' articles, thus driving up citation scores: Look, ID is indeed real science, check out our articles' standings in Science Citation Index (etc.).

But for the reasons already discussed, I don't see any prospect that a useless theory that doesn't conform to scientific norms will replace a useful, scientific one. If some unforeseen Kantian synthesis leads to the evolution of a hybrid evo/ID scientific hypotheses, then great.

Why do we believe in electrons, but not in fairies?

I enjoy teasing my students with this question. No one has directly observed either electrons or fairies. Both of them are theoretical constructs, useful to explain observations that might be difficult to explain otherwise. The "theory of fairies" can actually explain more things than the "theory of electrons". What's not to like?

Is the issue a political one, where the "electron" fans got the upper hand in the nineteenth century, so by the twentieth century the "fairy" fans were a scorned and persecuted minority? Or, have we proved for sure that fairies don't exist?

No, to both. The real difference is that for electrons, we have accumulated a set of quite narrow and specific rules about how electrons will behave under various circumstances. Those rules let us make very specific predictions about electron behavior, and about the observations that will result. If those predictions don't come true, we know that either we didn't set up the circumstances correctly, or there is something wrong with the rules. But over many decades, we have repeatedly fixed problems with the rules, so we can now make really good predictions about electrons, especially in certain highly contrived circumstances (i.e., circuits).

Fairies are much more free. A fairy does what it decides to do. We haven't been able to find any useful rules for predicting how a fairy will behave under particular circumstances, or even for telling when a fairy has been involved in a particular observation. (At least I don't know of any such rules. I stand ready for correction on this.) Over many, many decades, it has not been possible for people to try out pretty-good sets of fairy-prediction rules, find out where they make mistakes, and replace them with better sets of rules.

It's always possible that there really are fairies. But the theory of electrons has been far more successful because it makes testable predictions. Because it doesn't make testable predictions, the theory of fairies hasn't enjoyed the same process of incremental improvement. So we have lightbulbs and microprocessors and the Internet, all based on electrons, and no fairy processors.

The scientific method is an amazing procedure for incrementally improving certain kinds of theories: those that make testable predictions. A theory that doesn't make testable predictions could still be true, but it doesn't participate in the scientific method. (There are people who believe that the only truths are scientific truths, but this is essentially a religious faith on their part.)

The theory of evolution is a scientific theory, because it implies a large number of specific testable claims. The specific rules leading to testable predictions have been tested, modified, and refined over many decades (roughly as many as the theory of electrons). Simple versions of the rules for evolution have been tested and refuted long ago, and replaced by better, more specific ones, just as they have for electrons. We are about as confident in the theory of evolution as we are in the theory of electrons.

The theory of intelligent design could be true. The biological world is a marvelous place, with truly amazing complexity. The theory of evolution assumes certain random processes for generating mutations. If an Intelligent Designer could influence those random processes, then perhaps both theories could be true simultaneously. But the theory of intelligent design does not make testable predictions, just like the theory of fairies. The Designer does what He does because He decides to, not because He is governed by rules. (See Matthew 4:5-7.)

The scientific method is an enormous intellectual asset to the human race. All citizens should understand what it can and cannot do, and all children should be taught to appreciate and apply it. It is important for them to understand why the theory of electrons is a scientific theory, while the theory of fairies is not. Likewise, of course, for evolution and intelligent design.

In the debate between evolution and intelligent design, I believe that we scientists are missing an important opportunity to educate people about the difference between "truth" and "scientific truth". There is a perfectly reasonable role in society for faith in truths that are not scientifically testable. But we and our children need to understand and respect the difference.

While one driver in this controversy comes from people with a fundamentalist religious agenda, there are scientists on the other side who pursue an essentially religious belief that "There is no Designer." We don't know that. Precisely because the intelligent design hypothesis is not a scientific hypothesis, it cannot be refuted by scientific testing. Occam's Razor is a useful piece of practical advice about preferring simpler theories, but it has no more empirical content than the Apostle's Creed.

Science education is about teaching the scientific method, and about teaching some of the knowledge that the human race has acquired by applying the scientific method. It would be a useful part of a science class to teach the distinction between theories that are scientific because they make testable predictions, and other theories that could be true, but are not scientific because they don't. Comparing fairies with electrons, or comparing evolution with intelligent design, should be an opportunity to teach better science.

Prof. Kuipers (#15):

Thanks--the relative virtues of electrons and fairies highlight a deep difference between neo-Darwinist thought and intelligent design. Your essay prompts two thoughts.

1. Theories of history face extra challenges that theories of current events don't have to meet. There is no framework for understanding the last billion-or-so years of life-on-earth that offers very much in the way of specific predictions. The experiment ran only once, and random processes played a very large role. Neo-Darwinism also makes predictions about the present, and these have proven to be useful and powerful (e.g. comment #45 here). This makes most of us more willing to apply neo-Darwinism to the past, but proponents of creationist theories are correct to point out that evolution hasn't been proven to fully explain the record. As alluded to in the comment I linked, the generally-accepted geologic explanation of sedimentary formations is vulnerable to a theory of Intelligent Rockdesign, on exactly the same grounds.

2. The main difficulty with intelligent design isn't that it offers a plausible alternative explanation of life's history to neo-Darwinism. It is that its proponents insist that it is a legitimate scientific premise, and thus insist that it be taught as science. For all I know, some variant of intelligent design may be true. But I am certain that a theory that invokes the supernatural, has no predictive power, and is non-falsifiable must not be presented to students as science. This applies equally to irreducible complexity and to fairies.

AMac,

I'm glad you enjoyed my little parable. In fact, the point I was trying to get across was exactly what you said in your second point.

As to the first point, there are a number of ways to assess the relative values of different proposed explanations of a singular (non-repeatable) observation, like the history of life on Earth, or the nature of the universe. A particularly fine example of this is a short, delightful book called The First Three Minutes, by physicist Steven Weinberg, where he explains current thinking about the Big Bang and the origin of the Universe (at least as of 1977 when the book was written).

You also need to remember that scientific theories are never "proven". No scientist would claim that one had been. But a theory that has been repeatedly refined and improved through many decades of challenges and testable predictions is one you can be pretty confident in.

Creationists like to exploit the public's use of the word "theory" to mean "uninformed guess", and "not proven" to mean "probably false", where to scientists, they mean something enormously different.

Let me start off by saying I think that scientific ID is very bad theology. That being said, I can't understand how it's not science. To demonstrate, I have a proposed experiment series to test for ID.

Take a complex structure. Let's say the flagellum of a bacteria. Work out the genetic code that codes for that, remove it all. Does a flagellum provide an advantage over not having one? Is the flagellum an evolutionary advantage over its presumed non-flagellum equipped ancestor?
Let's assume the question is answered yes and the flagellum lacking bacteria is still functional, but at a lower level.

Now take every genetic permutation and combination between the two organisms (with flagellum and without). Test them both against the modern bacteria with flagellum and its presumed non-flagellum equipped ancestor (if we happen to know of any actual populations of the non-flagellum equipped ancestor, use the real thing).

If a partial flagellum bacteria is selected against in both competitions, it's reasonable to assume that nature would have selected against the population and that mutation would have died whenever it arose. It's also reasonable to think that there must be some sort of pathway to get from here to there, where discrete mutations stair-step their way up the functional chain or are at least neutral in their effects on the general success of the organism. If there is no pathway, it is reasonable to conclude that you've discovered an actual example of irreducible complexity.

Evolution must be revised to take account of a discrete mutation of the complexity of this irreducibly complex structure or, if the theory can't stretch that far, you've got to recognize that evolution just doesn't work in all cases and something else is going on. There is no current alternative theory beyond ID challenging evolution. ID is adopted as the last theory standing until some other theory arises that can fit the facts as we know them at the time and can account for known irreducible complexity without positing an intelligent designer.

ID is very difficult to test for. If every structure in the flagellum was coded by one gene, you'd be running around 40! tests. The actual number is probably even larger. The number of tests, however, is a finite number. With a sufficient store of grant funding and patience, you can run all those tests. Can any ID opponent tell me why isn't this science and whatever the results are, why shouldn't a peer reviewed journal publish the paper coming out of the experiment series?

Won't work TM, because you can't account for changes in function that way. Your pre-flagellum might not have been any good at propelling a bacterium through the water, but may have been useful for something else. It's been suggested that pre-flagellum structures might have been useful for stirring water, thereby bringing food to a organism. Further, there are a class of structures known as Type III secretory systems that share nearly all of the flagellum's proteins. Useless for movement but nice for spraying a neighboring cell with something nasty, as a prelude to an invasion.

Further, it turns out that some bacteria use a modified type III system to excrete a slime that lets them glide on a surface. In at least some species, there is a suggestion that the motor proteins that flagellum use are involved.

So, removing parts and seeing if a bacterium can still swim isn't likely to tell us anything. The flagellum itself is probably lacking parts that were present in its precursors, so just removing a protein won't tell us anything about the evolution of the flagellum.

And of course, even if you do show that a structure is irreducibly complex, you still haven't shown that it didn't evolve. Gaining a part is one way to evolve, but losing a part is another.

An organism may have a structure A that does jobs 1 and 2, both of which are necessary for its survival. A copying error can duplicate the gene complex that controls A, producing an identical structure B that also does jobs 1 and 2. If structure A then mutates so that it no longer does job 1, the organism can survive because B still does job 1. If B then mutates to stop doing job 2, we have an irreducibly complex structure. The organism needs both to survive, and either alone is useless.

And I should probably point out that there is no theory of Intelligent Design. Or if there is, no one's bothered to mention what it is. ID is an assertion, not a theory.

Amac, the problem is that the backers of ID aren't interested in doing science. In short, the Meyer paper didn't go through peer review. Or if it did, it wasn't reviewed by competent peers. And any evolutionary biologist who comments on this finds that he's being used as evidence of a "controversy" in science about evolution.

Tony: Amac, the problem is that the backers of ID aren't interested in doing science. In short, the Meyer paper didn't go through peer review. Or if it did, it wasn't reviewed by competent peers.

Well, you won't stop bad science (or bad peer review) with bad logic, and this is what you call "presuming the conclusion".

A hundred years ago, prestigious journals in Britain were publishing articles on Spiritualism. The Church of England was mightily protesting this attempt to clutter up already overly-complex Victorian decor with ghosts.

They were not interested in the scientific value of the ghosts, they just wanted the ghosts out of their drawing rooms. And they prevailed. Obviously, pointing out their lack of scientific credentials was not sufficient to stop the assault on Spiritualism.

Stephen Jay Gould often said that Evolutionary Biology's great weakness was the way it dealt with criticism - or rather, didn't deal with it. As such, it has become remote, suspicious, monolithic, hyper-defensive, and even litigious. There is no more of the collegial courtesy that Darwin gave to Lamarck. Too bad.

Interesting OpEd in NYTimes today: Daniel C. Dennett on Intelligent Design.

Ugh...this discussion is riddickulous.
home truths:
1. Attacking a competing theory is not at all the same as proving yours.
2. Stephen Jay Gould is not a scientist. He is a populist.

What if a law were passed to force ID to be taught in schools tomorrow? Who would teach it? What standards would it be taught to?

Let ID make its bones in academe before it gets pushed into high school classrooms. Let the Discovery Institute fund chairs and research assistantships, let there be ID 101 for underclassmen and graduate students and teaching assistants. (As opposed to funding propaganda for school boards) Let there be papers, reviewed or not, let there be a technical Journal of ID.

Then we'll talk.

TM Lutas #18 proposed a series of experiments to see whether bacterial flagella are irreducibly complex.

Tony in WV #19 rebutted, then concluded:

the problem is that the backers of ID aren't interested in doing science.

One step back.

TM Lutas, great idea and great post! You are practicing science, by devising a testable hypothesis. (This is in contrast to much pro-ID flimflammery, as sketched out in the NYT piece linked in comment #21.)

Like many hypotheses, including some of my own (sigh), you might not be testing what you think you're testing. I'll stipulate that the experiments are doable, and that the results would turn out as you suggest. In other words, you'd find that

[all] partial flagellum bacteria [were] selected against in both competitions.

But I don't think it would be exactly correct

to conclude that you've discovered an actual example of irreducible complexity.

The Modern Synthesis doesn't predict that your experiment would give a positive result. That's because the sequences of the flagellum-related genes that are present today in creatures with functional flagella are not identical to the sequences of the ancestral genes of a long-ago-vanished non-flagellar precursor bug. At every level, evolution has taken place. Of the prototype genes, some have been deleted. Other have been duplicated, once or many times, or subject to recombination with unrelated genes. All of the genes, duplicated genes, and pseudogenes have been subjected to the mutational processes that we observe in the laboratory today. In addition to the just-mentioned duplication, deletion, and recombination, there are the errors made by DNA polymerases (point-mutations, frameshifts, triplet repeats), damage from ionizing radiation, chemical (free-radical) damage, single-stranded DNA repair, double-stranded DNA repair, viral integration, transposon insertion and excision... and other things I haven't thought of!

From the non-flagellar starting point X million years ago until today, all of the genes in every generation of bactera have, potentially, been subject to all of these forces.

Let's return to the points on fitness brought up by Tony in WV #19, who knows flagella better than I do. (For an evolutionary biologist's argument, with references, see Brown U. Prof. Ken Miller's website.

• Some pre-flagella might have been useful for tasks not undertaken by modern flagella.
• Some genes of modern flagella share ancestry with some genes of modern Type III secretory systems.
• In addition to performing complex Type III functions, some of these genes allowed bacteria to secrete a slime--a potential survival-enhancing benefit of an intermediate-stage organism.

So, TM Lutas' proposed experiment would only prove that flagella are irreducibly complex, given today's genes and today's gene sequences, and absent the actions of known evolutionary processes over a long stretch of time. This work could still be useful, say in setting realistic goals for exploiting molecular evolution in a business setting, as outlined in comment #45 here.

As alluded to earlier, the challenge of serious discussion about the history of our planet is that it's about the past (d'oh). Life is an experiment that is run just once, with long-gone random events having played large roles in determining specific outcomes. We have peepholes through which to view the past, such as fossils, bugs in amber, PCR'd ancient DNA, changes in isotopic composition of plankton, and, of late, the ability to compare the sequences of the genomes of closely- and distantly- related species.

By today's standards, the theory of evolution as I learned it was simplistic, and in places wrong. By many small steps and a few large leaps, with controversy and acrimony along the way, 1985 best-knowledge became 2005 best-knowledge. Bio-bloggers of 2025 will see the omissions and errors of today's neo-Darwinism in just as stark a light.

This is the way Science is supposed to work. If and when a variant of Intelligent Design can be reformulated as a workable Popperian theory, it will become a welcome addition. Until such time, biologists will scrap among themselves to advance the field. And evolutionists will keep fighting creationists, so that the next generation of students can learn the principals of scientific inquiry in the classroom.

AMac, so, TM employs the scientific method--so what? Why are we wasting time with this silly controversy?
As a pragmatist, i just don't understand why is anyone expending energy over this? Even if ID could be taught in highschools, who would teach it? There are no trained teachers, because there is nothing in academe to support it. Build the academic support network first, if ID is real science.

We need to be doing other things, like string theory, quantum gravity, nanotech, ESCR AND ASCR, genetherapy, quantum biology, and fighting the WoT.
'Kay?

Well, you won't stop bad science (or bad peer review) with bad logic, and this is what you call "presuming the conclusion".

Um, no. It's called being literate in respect to science. There isn't anything new in the Meyer paper, or ID in general. It's 747 in a junkyard combined with misunderstandings about probability with a few mistakes about biology thrown in. Talk Origins has a good overview of just how evolution improves fitness. Section 1.2.3 deals with the statistical arguments Meyer is making. You might notice that article dates from 1999.

Here and here are a few bits on the Cambrian Explosion. These might help explain why the CE is isn't a problem for science.

Obviously, pointing out their lack of scientific credentials was not sufficient to stop the assault on Spiritualism.

Maybe I'm not being clear. I'm not objecting to a lack of credentials per se, I'm objecting to an attempt at passing a paper off as peer reviewed when it contains obvious errors that someone with Biology 101 should notice, let alone evolutionary biologists. Lysyl oxidase, which Meyer says would need to have been developed from scratch because of its role in maintaining large bodies (which didn't exist much before the CE), is found in microbes, like yeast and archaeobacteria. One would think that decent peer review would have caught that.

All of the criticisms of creationism aka ID were answered years or decades ago. Complex Specified Information is just another kind of the old mutations are always harmful saw that creationists have been pushing since the 70's. At what point, Glen, are scientists allowed to say, "We answered that 20 years ago. You go read (cite) while we get back to work" ?

Not having credentials is just fine, if your work stands up. If it doesn't, credentials don't help.

Stephen Jay Gould often said that Evolutionary Biology's great weakness was the way it dealt with criticism - or rather, didn't deal with it. As such, it has become remote, suspicious, monolithic, hyper-defensive, and even litigious.

Too many advocates of science are first and foremost advocates of atheism. With a significant portion, perhaps a majority (don't remember the actual figure) of American scientists identifying themselves as Christian, I'm sure that's not a good thing. Gould was, in my opinion, the best advocate science has had in some time, but it's probably worth noting that he was also the favorite of creationists to quote out of context. I seem to recall it vexing him.

Is science remote? I've never thought so, but perhaps it has. Are scientists suspicious or hyper-defensive? Again, it doesn't seem that way to me, particularly in light of the 70 year Cindy Sheehan camp out that the creationists have maintained. Monolithic? Glen, read the literature. There's plenty of lively disagreement, but the basic question of whether evolution has occurred is pretty well settled, barring some new evidence. Bring on the fishbian and the chimera and we'll reconsider common decent and evolution.

Litigious? I'm not aware of much in the way of litigation originating from supporters of evolution, aside from the occasional suit against a law requiring the teaching of creationism. Can you back that up, please?

Let's return to the points on fitness brought up by Tony in WV #19, who knows flagella better than I do.

Nooo! I'm no expert. It's just that flagella have been whipped to death. (Pun intended) My point was two fold:

One, conversion of function makes such an experiment much more challenging. If the scenario I posted above is correct, then flagella went through stages where they were weapons, gliders, maybe stirrers before becoming outboard motors. Any of those stages could have required parts and associated genes that were lost after the structure changed to a new function. So, removing modern genes might well not produce an analogue of the actual precursor. Evolution works by not just adding new or changing old, but also by removing the old.

Two, even if you prove that the flagellum is irreducibly complex, you haven't shown that it didn't evolve, because IC structures can evolve by shedding parts.

So I think we're in rough agreement. I still stand by my statement that the backers of ID (and I wasn't thinking of TM when I said this) aren't interested in doing science. Behe has talked about flagella for two decades and did no work on actually showing that they were irreducibly complex or if they were, that they couldn't evolve.

I think scientists, and those of us non-scientists who have some understanding of the issues, need to work on some way of communicating that while a lot of the details are still up in the air, evolution in the sense of common decent by natural selection is an established fact.

matoko kusanagi #24 wrote:

so TM employs the scientific method--so what? Why are we wasting time with this silly controversy?

Fair enough. Answer: We (you included...) are discussing things we find interesting.

Answer the second: My Intelligent Rockdesign analogy is, indeed, silly. Nobody believes it, so its advocates aren't maneuvering to cripple secondary-school science education in order to advance its Lysenkoist agenda. Would that this were true with ID.

Third answer: State-of-the-art evolutionary theory of 2005 is, in important respects, incorrect and incomplete. Not because evolution is fatally flawed, but because that is the nature of science at the cutting edge. It is a great thing when skeptics of evolution make good-faith efforts to engage in the scientific method. I'm fine with religious believers of all stripes, including atheists. The convesation gets better as people come to better understandings of the scientific method, and its limits.

Nobody believes it, so its advocates aren't maneuvering to cripple secondary-school science education in order to advance its Lysenkoist agenda. Would that this were true with ID.

ha ha, dropped your mask AMac. ;-)

Good old Trofim must be laffing in his grave.
There is the biggest problem with theory of ID. We are flirting with a state-sponsored pseudo-science that has no academic or scientific bones.

Just part of the Bush admin's war on science.