Flagellum evolution in New Scientist

I LOVE to read the article but it's subscription-only!
Why tease us like this?

Why tease us like this?

Rolf Aalberg:

Why tease us like this?

Seconded!

DJ and Rolf,

I don't like to be teased either, but with a little money one can access the article. But in Behe's case, all the money in the world can't seem to get us to the good part - how, where and when that first designed flagellum came to be.

I'm registered! Here is the article in full. It's a long one.

Uncovering the evolution of the bacterial flagellum

16 February 2008
From New Scientist Print Edition. Subscribe and get 4 free issues.
Dan Jones

[snipping]

The relevance to flagellum evolution? Variants of at least seven T3SS proteins are also found in the flagellum, within a subsystem called the protein export system. This sits within the basal body and funnels replacement flagellin subunits to the filament, using a mechanism remarkably similar to the T3SS. In fact, the two systems are so similar that the flagellar protein export system is now considered to be a subclass of the T3SS (Trends in Microbiology, vol 14, p 157).

Such similarities, or "homologies", are strong evidence that the two systems evolved from a common ancestor - analogous to the way that the arrangement of bones in the limbs of horses, bats and whales reveal their common ancestry despite their very different outward appearance and function. Similar homologies can be seen in the DNA sequences of genes, and in the amino acid sequences and 3D structures of proteins - all are clear evidence of shared descent.

The evolutionary events linking flagella and T3SSs are not clear, but the homology between them is a devastating blow to the claim of irreducible complexity. This requires that a partial flagellum should be of no use whatsoever - but clearly it is. "The T3SS is a useful model of how a 'partial flagellum' could function in protein export," says Nicholas Matzke of the University of California, Berkeley, a prominent defender of evolution and author of a number of academic articles on the flagellum. Miller adds: "The notion that these proteins can only be used in flagella simply falls apart." This argument helped swing the outcome of the "ID trial" in Dover, Pennsylvania, in 2005, in which irreducible complexity formed a key plank of the ID movement's failed bid to have ID taught in school science classes.

So how exactly is the flagellum's protein export system related to the T3SS? One possibility is that the T3SS evolved first and was later co-opted as part of the flagellum. A second is that the flagellum evolved first and its protein-export system gave rise to the T3SS. It is also possible that both evolved in parallel from a common ancestor.

[snipping more -- sorry, I don't like copyright either but we don't want to be sued -- thanks for the thought though! Nick]

I wrote the above article, and while I'm not sure how the folks at New Scientist will feel if they see the text being pasted here, I'm glad PT readers have a chance to read the article - although you don't get to see the nice pictures and graphics that the NS art team put together for the piece!

Cheers,

Dan.
http://psom.blogspot.com/

Oooops...

It is a great article and I thought since no one was able to access it then I would do them a favour by reproducing it here. I do hope NS doesn't mind, but no doubt the administrators will pull it if they do.

Hey Maxi, didn't mean to admonish you for putting the peice up - that's someone else's job! ;-) I'm pleased it's 'out there'. And pleased you like it.

Cheers,

D.

Maxi, could you please edit your post. Posting the full article, rather than a short excerpt for scholarly purposes, is violation of copyright.If you could put in an excerpt and your own brief summary of the article that would be fine.

Dan Jones, thanks for writing the NewScientist article, it is a very nice summary of the recent work on flagella. The Panda's crew does not condone copyright violation though.

AHHRGGG, of course Maxi can't edit his/her post. My brain does not work at this hour of the night.

I've summarised some of the relevant points on my blog, at http://psom.blogspot.com/2008/02/evolutions-engine.html.

D.
http://psom.blogspot.com/

Hope the admins pull the full post, even if the author does not object. The copyright is owned by NS and it clearly wants to sell subscriptions. I subscribe to its newsletters even then it would not let me access the full article.

The author's blog http://psom.blogspot.com/ and our old thread on this
http://www.pandasthumb.org/archives/2007/04/flagellum_evolu_1.html
have lots of interesting info without copyright encumbrances.

It is sad to see great news sources like New Scientist and NPR beg for a few dollars and operate on shoe string budgets while peddlers of ignorance seem to be awash in cash. They claim 10% of the income of the
adherents, (even though the actual collection is much less).

Lurkers please subscribe to at least one of National Geographic, Scientific American or New Scientist or some such mag. And my fellow Americans, please pledge some money to your local NPR station. Today is, after all, the last full day of the pledge week.

To be honest, I wasn't sure how NS would feel about a non-profit/educational-type site such as PT using the text, but Ravilyn's advice above seems on the money. A subscription to NS isn't that much (just $89), and you get 50-odd glossy issues a year (and, of course, acces to archived content)! Listen to me, I'm turning into a salesman (as the mantra from David Mamet's superb 'Gelngarry Glenross' goes, "ABC: alwasy be closing, ALWAYS BE CLOSING!").

D.

Hey, I subscribe to the print edition of NS, and I need to register separately to access the web articles. Since I invariably throw away the cover in which the print edition arrives before I remember that I need the code number from it to access the web articles, I've given up trying to access the subscription-only web articles of NS.

Hmm, reading back that looks rather clumsy, but I hope it is not too hard to parse out the intended meaning.

I would like to apologise for my thoughtless copyright infringement. I was trying to be helpful but I see now what damage I have caused.

I would glady erase it myself, but cannot.

I do subscribe to New Scientist, and would recommend it to everyone!

I expect maxi's post to be changed as soon as someone* wakes up.

I subscribe to the print edition of NS, and I need to register separately to access the web articles.

The sentence "The study of complex molecular systems has been given added impetus by the “intelligent design” (ID) movement - the intellectual heirs of Paley." should more correctly end "...the anti-intellectual heirs of Paley."

Richard Simons:

I subscribe to the print edition of NS, and I need to register separately to access the web articles.

That seems odd. Last night I took out a subscription to the print edition (Can$72 plus a few dollars for the mail) and was immediately able to access the article. While browsing I came across a good idea for a ketchup sachet submarine to show my basic science class (taken from a book with the title 'How to fossilize your hamster').

For all the ID proponents

This should save time and energy when reading and digesting the posted article from the New Scientist. All quote mined with 6 words added.

“In an oft-quoted passage from On the Origin of Species, Charles Darwin wrote: “If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down.””

“Biologists have been interested in the bacterial flagellum for decades, not least because it is a prime example of a complex molecular system - an intricate nanomachine beyond the craft of any human engineer.” “With its intricate arrangement of interconnecting parts, the flagellum looks no less designed than a watch, and would surely have had Paley reaching for the existence of its “maker”.” “The bacterial flagellum is one of the most complex and elegant pieces of biological machinery known.” “It is the bacterial world’s outboard motor, rotating at high speeds to propel bacteria through their watery environments.”

““It’s very difficult to work out the evolution of a complex system when you don’t understand how the system works.” “In the absence of this knowledge, biologists all too often fell back on the assertion that “bacterial flagella evolved and that is that”, according to Mark Pallen, a microbiologist at the University of Birmingham in the UK.”

To counteract this “[t]he study of complex molecular systems has been given added impetus by the “intelligent design” (ID) movement - the intellectual heirs of Paley.” In the case of the flagellum, “each of its interacting components is essential for the system to function, and if you remove any one of them the whole thing grinds to a halt.” “[B]ecause of this irreducible complexity, such systems cannot be explained by the stepwise process of natural selection and therefore must be the handiwork of an “intelligent designer”.”

Delta Pi Gamma (Scientia et Fermentum)

I wrote the above article, and while I’m not sure how the folks at New Scientist will feel if they see the text being pasted here, I’m glad PT readers have a chance to read the article - although you don’t get to see the nice pictures and graphics that the NS art team put together for the piece!

It is sad to see great news sources like New Scientist and NPR beg for a few dollars and operate on shoe string budgets while peddlers of ignorance seem to be awash in cash

If they are one of the many scientific publishers that allow it, you can make the article downloadable from your blog and post the link here.

Dan,
Very nice article - thanks. I'd like to ask you a question about it. Behe's flagship claim is of course that the flagellum was intelligently designed. I'd have expected to see a reaction from him about this latest research. Did you in fact approach him for a comment? If so, did he respond at all?

Good article, but sadly, even if creationists/idists read it closely, they will mine a few bits to COUNTER the article's argument.

I'd see this being quote-mined:

"Most researchers think the best options are flagellum-first or parallel evolution. One fact in favour of the flagellum-first view is that bacteria would have needed propulsion before they needed T3SSs, which are used to attack cells that evolved later than bacteria. Also, flagella are found in a more diverse range of bacterial species than T3SSs. “The most parsimonious explanation is that the T3SS arose later,” says biochemist Howard Ochman at the University of Arizona in Tucson."

Right before this paragraph, you're using the example of T3SS as flagellum-proteins being used in non-flagellum ways to show how an example of functioning "partial-flagellum", but this paragraph shows scientists tend to favour the idea (in THIS case) of flagellum coming first. You know the IDiots would jump on it in this way: "scientists say there exists functioning partial-flagellum, but they also say the FULL functioning flagellum had to come first". That's what I'd expect from an IDiot who actually reads the article.

I've removed the comment that had the full article.

Great article Dan, but what I'd really like to see is how the IDists react to it. I love to read their squirming semantics. If anyone has any good links to ID 'refutations' please post!
Here is my prediction - continued research will make it impossible for them to use the flagellum as an argument. A new, more covert, movement will be initiated in which the ID/creationist 'scientists' keep their theological motivation hidden. There will be no 'Wedge' document error next time. Look forward to a more devious and cunning breed disguised as atheists!

Reed A. Cartwright: I've removed the comment that had the full article.

Drats! My library subscribes through some sort of service, but there is a one month delay for electronic access.

Hasn't this whole T3SS thing been answered ages ago by the ID people? See:

http://www.discovery.org/scripts/viewDB/index.php?command=view&id=1364

What would be said to that?

Such similarities...are strong evidence that the two systems evolved from a common ancestor.

Without knowing enough of the details, such assertions seem odd,

William Wallace:

Such similarities...are strong evidence that the two systems evolved from a common ancestor.

I am setting a goal of studying more about how biologists go from noting coincidences to glibly asserting common descent. Without knowing enough of the details, such assertions seem odd, and very much akin to the specious assertion that this program (wave.c) and this program (bubble sort) are obviously descendants of this program (hello world) simply because they all contain the same "extra operator error" in the sequences '/*' and '*/' instead of just a '/' or a '*'.

halo: Hasn't this whole T3SS thing been answered ages ago by the ID people? See: http://www.discovery.org/scripts/viewDB/index.php?command=view&id=1364 What would be said to that?

Kevin B: Curiously, removing the entire /* ... */ sequence does *not* change the meaning. (The framework of this was worked out in the 1960s; however, the problem of how to specify unambigously[sic] exactly what a program *means* continued to perplex computer scientists.)

David B. Benson: Comments are junk tokens? :-)

Actually, what a sequential program *means* is completely worked out.

WW said: I am setting a goal of studying more about how biologists go from noting coincidences to glibly asserting common descent.

Kevin B wrote: A couple of "knock-out" type experiments will show that replacing /* with / or * or / * will change the meaning of the program. Further, you would appear not [to?] have much understanding of how compilers for high-level programming languages are constructed.

William Wallace: But the computer program analogy of DNA only goes so far, in that there is no sentient and sapient author--at least that is the premise of the PT crowd. And from such a premise, all other findings follow.

OOPS!

dpr (Layman in the ELCA, former member of his congregation’s council)

Steven Laskoske:

I agree that Behe's Irreducible Complexity argument was not properly clear to start with, but the ID people have since clarified it, and this clarification is what needs adressing now - irreducible complexity makes a logical point ruling out a direct darwinian pathway (by definition), leaving only indirect pathways (i.e co-option) as a possibility, which the ID people have addressed. If a good counter-argument is to be furnished I think it is only fair to address the current state of debate, which from the ID side is here encapsulated (I hope fairly) using some excerpts from an article by Dembski called 'Irreducible Complexity Revisited':

QUOTE "A direct Darwinian pathway is one in which a system evolves by natural selection incrementally enhancing a given function. As the system evolves, the function does not evolve but stays put... In ruling out direct Darwinian pathways to irreducibly complex systems, the argument from irreducible complexity is saying that irreducibly complex biochemical systems are provably inaccessible to direct Darwinian pathways.

At any rate, critics of the argument from irreducible complexity look to save Darwinism not by enlisting direct Darwinian pathways to bring about irreducibly complex systems but by enlisting indirect Darwinian pathways to bring them about. In indirect Darwinian pathways, a system evolves not by preserving and enhancing an existing function but by
continually transforming its function...

How does the argument from irreducible complexity handle indirect Darwinian pathways? Here the point at issue is no longer logical but empirical. The fact is that for irreducibly complex biochemical systems, no indirect Darwinian pathways are known. At best biologists have been
able to isolate subsystems of such systems that perform other functions. But any reasonably complicated machine always includes subsystems that perform functions distinct from the original machine. So the mere occurrence or identification of subsystems that could perform some function on their own is no evidence for an indirect Darwinian pathway leading to the system. What’s needed is a seamless Darwinian account
that’s both detailed and testable of how subsystems undergoing
coevolution could gradually transform into an irreducibly complex system. No such accounts are available or have so far been forthcoming. Indeed, if such accounts were available, critics of intelligent design would merely need to cite them, and intelligent design would be refuted.

At this point the standard move by critics of intelligent design is to turn the tables and charge that the argument from irreducible complexity is an argument from ignorance. A common way to formulate this criticism is to say, “Absence of evidence is not evidence of absence.” But as with so many overused expressions, this one requires critical scrutiny. Certainly this dictum appropriately characterizes many everyday circumstances. Imagine, for instance, someone feverishly hunting about the house for a missing set of car keys, searching under every object, casing the house, bringing in reinforcements, and then the next morning, when all hope is gone, finding them on top of the car outside. In that case the absence of evidence prior to finding the car keys was not evidence of absence. Yet with the car keys there was independent evidence of their existence in the first place. But what if we weren’t sure that there even were any car keys? The situation in evolutionary biology is even more extreme than that. One might not be sure our hypothetical set of car keys exist, but at least one has the reassurance that car keys exist generally. Indirect Darwinian pathways that account for irreducible complexity are more like the leprechauns supposedly hiding in a child’s room. Precisely because the absence of evidence for the existence of leprechauns is complete, it is unreasonable to cite “Absence of evidence is not evidence of absence” as a reason for taking leprechauns seriously. And yet that, essentially, is what evolutionary theory counsels concerning the utterly fruitless search for credible indirect Darwinian pathways that account for irreducible complexity. If after repeated attempts looking in all the most promising places you don’t find what you expect to find and if you never had any evidence that the thing you were looking for existed in the first place, then you have reason to think that the thing you are looking for doesn’t exist at all.

That’s the argument from irreducible complexity’s point about indirect Darwinian pathways. It’s not just that we don’t know of such a pathway for, say, the bacterial flagellum (the irreducibly complex biochemical machine that has become the mascot of the intelligent design community). It’s that we don’t know of such pathways for any such systems. The absence here is pervasive and systemic. That’s why critics of Darwinism like Franklin Harold and James Shapiro (neither of whom is an intelligent design proponent) argue that positing as-yet undiscovered indirect Darwinian pathways for such systems constitutes “wishful speculations.”" END QUOTE

So do you see the issue? I perhaps think Dembski's challenge of a 'seamless Darwinian account that’s both detailed and testable' is a bit much but I agree that at least a substantial pathway is needed, otherwise Darwinism is both unproved and unfalsifiable at the same time. This only seems fair and reasonable, what do you think?

“At best biologists have been able to isolate subsystems of such systems that perform other functions. But any reasonably complicated machine always includes subsystems that perform functions distinct from the original machine. So the mere occurrence or identification of subsystems that could perform some function on their own is no evidence for an indirect Darwinian pathway leading to the system. What’s needed is a seamless Darwinian account that’s both detailed and testable of how subsystems undergoing coevolution could gradually transform into an irreducibly complex system. No such accounts are available or have so far been forthcoming. Indeed, if such accounts were available, critics of intelligent design would merely need to cite them, and intelligent design would be refuted.”

“It’s not just that we don’t know of such a pathway for, say, the bacterial flagellum (the irreducibly complex biochemical machine that has become the mascot of the intelligent design community). It’s that we don’t know of such pathways for any such systems. The absence here is pervasive and systemic.”

I perhaps think Dembski’s challenge of a ‘seamless Darwinian account that’s both detailed and testable’ is a bit much but I agree that at least a substantial pathway is needed, otherwise Darwinism is both unproved and unfalsifiable at the same time. This only seems fair and reasonable, what do you think?

halo quoting Behe:

"But any reasonably complicated machine always includes subsystems that perform functions distinct from the original machine. So the mere occurrence or identification of subsystems that could perform some function on their own is no evidence for an indirect Darwinian pathway leading to the system."

Halo, I don't see that the ID people have "clarified" irreducible complexity with statements like this. Instead, all I see is that they have "moved the goalposts".

http://www.discovery.org/scripts/viewDB/index.php?… What would be said to that?

Behe’s Irreducible Complexity argument was not properly clear to start with, but the ID people have since clarified it,

critics of the argument from irreducible complexity

the computer program analogy of DNA only goes so far, in that there is no sentient and sapient author–at least that is the premise of the PT crowd.

Kevin B:

David B. Benson: Comments are junk tokens? :-)

Comments are strongly conserved in environments where persons senior to the programmer (eg lecturers, managers) review the program.

Actually, what a sequential program *means* is completely worked out.

I deliberately wrote "continued to perplex", rather than "continues...", so as to point up the state of art in 1970, rather than the current position.

Steven,

Actually Agile programming results in less comments because the code is easier to read.

We (I am a professional as well.) have a long history of comments which are assumed to be some human readable description of value to be of little value because the program had evolved but the comments had not. This is because the evolutionary pressure to change is captured in the code - not the comments. The comments become junk.

Daoud said: Good article, but sadly, even if creationists/idists read it closely, they will mine a few bits to COUNTER the article's argument. I'd see this being quote-mined: "Most researchers think the best options are flagellum-first or parallel evolution. One fact in favour of the flagellum-first view is that bacteria would have needed propulsion before they needed T3SSs, which are used to attack cells that evolved later than bacteria. Also, flagella are found in a more diverse range of bacterial species than T3SSs. "The most parsimonious explanation is that the T3SS arose later," says biochemist Howard Ochman at the University of Arizona in Tucson." Right before this paragraph, you're using the example of T3SS as flagellum-proteins being used in non-flagellum ways to show how an example of functioning "partial-flagellum", but this paragraph shows scientists tend to favour the idea (in THIS case) of flagellum coming first. You know the IDiots would jump on it in this way: "scientists say there exists functioning partial-flagellum, but they also say the FULL functioning flagellum had to come first". That's what I'd expect from an IDiot who actually reads the article.

Peter Ridsdale said: Great article Dan, but what I'd really like to see is how the IDists react to it. I love to read their squirming semantics. If anyone has any good links to ID 'refutations' please post!

Here is my prediction - continued research will make it impossible for them to use the flagellum as an argument.

A new, more covert, movement will be initiated in which the ID/creationist 'scientists' keep their theological motivation hidden.

There will be no 'Wedge' document error next time. Look forward to a more devious and cunning breed disguised as atheists!

halo said: Hasn't this whole T3SS thing been answered ages ago by the ID people? See: http://www.discovery.org/scripts/viewDB/index.php?… What would be said to that?

But in pointing out that a third of the proteins in the flagellum are closely related to components of the TTSS, Miller tacitly admits that two-thirds of the proteins in the flagellum are unique. In fact they are (indeed, if they weren't, Miller would be sure to point us to where the homologues could be found). Applied to those remaining two-third of flagellar proteins, my calculation yields something like 10^(-780), which also falls well below my universal probability bound.

William Wallace said: Such similarities…are strong evidence that the two systems evolved from a common ancestor. I am setting a goal of studying more about how biologists go from noting coincidences to glibly asserting common descent.

Without knowing enough of the details, such assertions seem odd, and very much akin to the specious assertion that this program (wave.c) and this program (bubble sort) are obviously descendants of this program (hello world) simply because they all contain the same "extra operator error" in the sequences '/*' and '*/' instead of just a '/' or a '*'.

You'd need a compiler for this type of experiment, and the reason I constructed this example was because I do have an understanding of compilers, strings, information theory, randomness—and see some possible similarities between computer programs and "genetic instructions" (where my understanding has room for growth). But simply spewing jargon and ascribing meaning while the bobbleheads nod in agreement is no compiler.

So, in the world of analyzing DNA, what makes you think your "complier" is complete, and that it discloses all meaning and function? For example, endogenous retroviruses have been deemed to be genetic crumbs from ancient germs in the human genome. How do you know they are not '/* comments */' or the basis of some other as yet latent function? Coincidence does not establish causation. After all, in C, '/' and '*' are operators, while '/*' and '*/' are delimiters. (And the Monkey looking at a sea of clouds does not mean that all such forms are created naturally.) This would not be obvious to somebody who had never studied programming languages. But the computer program analogy of DNA only goes so far, in that there is no sentient and sapient author–at least that is the premise of the PT crowd. And from such a premise, all other findings follow.

halo said: Steven Laskoske: I agree that Behe's Irreducible Complexity argument was not properly clear to start with, but the ID people have since clarified it, and this clarification is what needs adressing now - irreducible complexity makes a logical point ruling out a direct darwinian pathway (by definition),

leaving only indirect pathways (i.e co-option) as a possibility, which the ID people have addressed. If a good counter-argument is to be furnished I think it is only fair to address the current state of debate, which from the ID side is here encapsulated (I hope fairly) using some excerpts from an article by Dembski called 'Irreducible Complexity Revisited': QUOTE "A direct Darwinian pathway is one in which a system evolves by natural selection incrementally enhancing a given function. As the system evolves, the function does not evolve but stays put… In ruling out direct Darwinian pathways to irreducibly complex systems, the argument from irreducible complexity is saying that irreducibly complex biochemical systems are provably inaccessible to direct Darwinian pathways. At any rate, critics of the argument from irreducible complexity look to save Darwinism not by enlisting direct Darwinian pathways to bring about irreducibly complex systems but by enlisting indirect Darwinian pathways to bring them about. In indirect Darwinian pathways, a system evolves not by preserving and enhancing an existing function but by continually transforming its function… How does the argument from irreducible complexity handle indirect Darwinian pathways? Here the point at issue is no longer logical but empirical.

The fact is that for irreducibly complex biochemical systems, no indirect Darwinian pathways are known.

At best biologists have been able to isolate subsystems of such systems that perform other functions.

But any reasonably complicated machine always includes subsystems that perform functions distinct from the original machine. So the mere occurrence or identification of subsystems that could perform some function on their own is no evidence for an indirect Darwinian pathway leading to the system.

What's needed is a seamless Darwinian account

that's both detailed and testable of how subsystems undergoing coevolution could gradually transform into an irreducibly complex system.

Indeed, if such accounts were available, critics of intelligent design would merely need to cite them, and intelligent design would be refuted.

At this point the standard move by critics of intelligent design is to turn the tables and charge that the argument from irreducible complexity is an argument from ignorance. A common way to formulate this criticism is to say, "Absence of evidence is not evidence of absence." But as with so many overused expressions, this one requires critical scrutiny. Certainly this dictum appropriately characterizes many everyday circumstances. Imagine, for instance, someone feverishly hunting about the house for a missing set of car keys, searching under every object, casing the house, bringing in reinforcements, and then the next morning, when all hope is gone, finding them on top of the car outside. In that case the absence of evidence prior to finding the car keys was not evidence of absence. Yet with the car keys there was independent evidence of their existence in the first place. But what if we weren't sure that there even were any car keys? The situation in evolutionary biology is even more extreme than that. One might not be sure our hypothetical set of car keys exist, but at least one has the reassurance that car keys exist generally. Indirect Darwinian pathways that account for irreducible complexity are more like the leprechauns supposedly hiding in a child's room.

Precisely because the absence of evidence for the existence of leprechauns is complete, it is unreasonable to cite "Absence of evidence is not evidence of absence" as a reason for taking leprechauns seriously. And yet that, essentially, is what evolutionary theory counsels concerning the utterly fruitless search for credible indirect Darwinian pathways that account for irreducible complexity. If after repeated attempts looking in all the most promising places you don't find what you expect to find and if you never had any evidence that the thing you were looking for existed in the first place, then you have reason to think that the thing you are looking for doesn't exist at all.

That's the argument from irreducible complexity's point about indirect Darwinian pathways. It's not just that we don't know of such a pathway for, say, the bacterial flagellum (the irreducibly complex biochemical machine that has become the mascot of the intelligent design community). It's that we don't know of such pathways for any such systems. The absence here is pervasive and systemic. That's why critics of Darwinism like Franklin Harold and James Shapiro (neither of whom is an intelligent design proponent) argue that positing as-yet undiscovered indirect Darwinian pathways for such systems constitutes "wishful speculations."" END QUOTE

So do you see the issue? I perhaps think Dembski's challenge of a 'seamless Darwinian account that's both detailed and testable' is a bit much

but I agree that at least a substantial pathway is needed, otherwise Darwinism is both unproved and unfalsifiable at the same time. This only seems fair and reasonable, what do you think? Comment #143139 on February 15, 2008 7:33 PM | Quote

So, in the world of analyzing DNA, what makes you think your “complier” is complete, and that it discloses all meaning and function?

— William Wallace

For example, endogenous retroviruses have been deemed to be genetic crumbs from ancient germs in the human genome.

How do you know they are not ‘/* comments */’ or the basis of some other as yet latent function?

Coincidence does not establish causation.

After all, in C, ‘/’ and ‘*’ are operators, while ‘/*’ and ‘*/’ are delimiters. (And the Monkey looking at a sea of clouds does not mean that all such forms are created naturally.) This would not be obvious to somebody who had never studied programming languages.

But the computer program analogy of DNA only goes so far,

in that there is no sentient and sapient author–at least that is the premise of the PT crowd.

halo quoting Dembski: A direct Darwinian pathway is one in which a system evolves by natural selection incrementally enhancing a given function. As the system evolves, the function does not evolve but stays put... In ruling out direct Darwinian pathways to irreducibly complex systems, the argument from irreducible complexity is saying that irreducibly complex biochemical systems are provably inaccessible to direct Darwinian pathways.

How does the argument from irreducible complexity handle indirect Darwinian pathways? Here the point at issue is no longer logical but empirical.

The fact is that for irreducibly complex biochemical systems, no indirect Darwinian pathways are known. At best biologists have been able to isolate subsystems of such systems that perform other functions.

So do you see the issue? I perhaps think Dembski's challenge of a 'seamless Darwinian account that’s both detailed and testable' is a bit much but I agree that at least a substantial pathway is needed, otherwise Darwinism is both unproved and unfalsifiable at the same time. This only seems fair and reasonable, what do you think?

Jeff McKenna: This is because the evolutionary pressure to change is captured in the code - not the comments. The comments become junk.

I agree that Behe’s Irreducible Complexity argument was not properly clear to start with,

— halo quoting Dembski

but the ID people have since clarified it, and this clarification is what needs adressing now - irreducible complexity makes a logical point ruling out a direct darwinian pathway (by definition)

, leaving only indirect pathways (i.e co-option) as a possibility, which the ID people have addressed.

If a good counter-argument is to be furnished I think it is only fair to address the current state of debate, which from the ID side is here encapsulated (I hope fairly) using some excerpts from an article by Dembski called ‘Irreducible Complexity Revisited’: QUOTE “A direct Darwinian pathway is one in which a system evolves by natural selection incrementally enhancing a given function.

As the system evolves, the function does not evolve but stays put…

In ruling out direct Darwinian pathways to irreducibly complex systems,

the argument from irreducible complexity is saying that irreducibly complex biochemical systems are provably inaccessible to direct Darwinian pathways.

At any rate, critics of the argument from irreducible complexity look to save Darwinism not by enlisting direct Darwinian pathways to bring about irreducibly complex systems but by enlisting indirect Darwinian pathways to bring them about.

In indirect Darwinian pathways, a system evolves not by preserving and enhancing an existing function but by continually transforming its function…

How does the argument from irreducible complexity handle indirect Darwinian pathways? Here the point at issue is no longer logical but empirical.

The fact is that for irreducibly complex biochemical systems, no indirect Darwinian pathways are known.

At best biologists have been able to isolate subsystems of such systems that perform other functions.

But any reasonably complicated machine always includes subsystems that perform functions distinct from the original machine.

So the mere occurrence or identification of subsystems that could perform some function on their own is no evidence for an indirect Darwinian pathway leading to the system.

What’s needed is a seamless Darwinian account that’s both detailed and testable of how subsystems undergoing coevolution could gradually transform into an irreducibly complex system. No such accounts are available or have so far been forthcoming. Indeed, if such accounts were available, critics of intelligent design would merely need to cite them, and intelligent design would be refuted.

At this point the standard move by critics of intelligent design is to turn the tables and charge that the argument from irreducible complexity is an argument from ignorance.

A common way to formulate this criticism is to say, “Absence of evidence is not evidence of absence.” But as with so many overused expressions, this one requires critical scrutiny. Certainly this dictum appropriately characterizes many everyday circumstances. Imagine, for instance, someone feverishly hunting about the house for a missing set of car keys, searching under every object, casing the house, bringing in reinforcements, and then the next morning, when all hope is gone, finding them on top of the car outside. In that case the absence of evidence prior to finding the car keys was not evidence of absence. Yet with the car keys there was independent evidence of their existence in the first place. But what if we weren’t sure that there even were any car keys?

The situation in evolutionary biology is even more extreme than that. One might not be sure our hypothetical set of car keys exist, but at least one has the reassurance that car keys exist generally. Indirect Darwinian pathways that account for irreducible complexity are more like the leprechauns supposedly hiding in a child’s room.

Precisely because the absence of evidence for the existence of leprechauns is complete, it is unreasonable to cite “Absence of evidence is not evidence of absence” as a reason for taking leprechauns seriously.

And yet that, essentially, is what evolutionary theory counsels concerning the utterly fruitless search for credible indirect Darwinian pathways that account for irreducible complexity.

If after repeated attempts looking in all the most promising places you don’t find what you expect to find and if you never had any evidence that the thing you were looking for existed in the first place, then you have reason to think that the thing you are looking for doesn’t exist at all.

That’s the argument from irreducible complexity’s point about indirect Darwinian pathways. It’s not just that we don’t know of such a pathway for, say, the bacterial flagellum (the irreducibly complex biochemical machine that has become the mascot of the intelligent design community). It’s that we don’t know of such pathways for any such systems.

The absence here is pervasive and systemic. That’s why critics of Darwinism like Franklin Harold and James Shapiro (neither of whom is an intelligent design proponent) argue that positing as-yet undiscovered indirect Darwinian pathways for such systems constitutes “wishful speculations.”” END QUOTE

So do you see the issue? I perhaps think Dembski’s challenge of a ‘seamless Darwinian account that’s both detailed and testable’ is a bit much but I agree that at least a substantial pathway is needed, otherwise Darwinism is both unproved and unfalsifiable at the same time. This only seems fair and reasonable, what do you think?

Well, I guess I should read all of the comments before sticking my oar in.

That was a very comprehensive answer, Nick (Matzke). I guess there is no substitute for knowing the relevant literature.

I am setting a goal of studying more about how biologists go from noting coincidences to glibly asserting common descent.

— William Wallace

Bobby: Dan, find out the NS policy on self-archiving your publications. If they are one of the many scientific publishers that allow it, you can make the article downloadable from your blog and post the link here.

Alan Bird: Dan, Very nice article - thanks. I'd like to ask you a question about it. Behe's flagship claim is of course that the flagellum was intelligently designed. I'd have expected to see a reaction from him about this latest research. Did you in fact approach him for a comment? If so, did he respond at all?

Daoud: Right before this paragraph, you're using the example of T3SS as flagellum-proteins being used in non-flagellum ways to show how an example of functioning "partial-flagellum", but this paragraph shows scientists tend to favour the idea (in THIS case) of flagellum coming first. You know the IDiots would jump on it in this way: "scientists say there exists functioning partial-flagellum, but they also say the FULL functioning flagellum had to come first". That's what I'd expect from an IDiot who actually reads the article.

halo,

Please feel free to tell us whether you agree with Behe that, regardless of mechanism or whether design actuation events occurred:

1. Humans share common ancestors with dogs and dogwoods.

2. Life on Earth has a ~3-4 billion year history.

Note that Dembski agrees with 2, and is keeping us guessing on his best guess on 1. Although a big clue is that he has never challenged Behe on it.

Speaking of "best guess," please state yours, even if you are genuinely unsure.

William Wallace, that goes for you too.

Before anyone chimes in that Dembski denies common descent, all he said is that he doubts that humans and other apes evolved from a common ancestor. He never denied saltation or front loading.

When IDists start to publish testable hypothesis or new empirical results in peer-reviewed scientific journals, then perhaps they might deserve a bit more space in future articles along the lines of mine.

— Dan Jones

Dembski: If after repeated attempts looking in all the most promising places you don’t find what you expect to find and if you never had any evidence that the thing you were looking for existed in the first place, then you have reason to think that the thing you are looking for doesn’t exist at all.

What they rule out by definition is the gradual accumulation of increasing complexity to form a system that is IC.

Wallace's blog, in absolute seriousness, entitles "Ann Coulter, Renowned evolution expert".

Good luck with your questions, FrankJ.

We need a good EE to design better irony meters...

Come on guys, stop complaining about the ID'ists moving the goalposts. Irreducible complexity is not so hard to understand. Even for a housewife like me!

Use the mousetrap example of Mr Behe as your guide...Just because the spring in the mousetrap under your table is also used in the spring file on top of your table, does NOT explain or show how the mousetrap was the ancestor of the spring file.

Simple really.

They have already moved the goalposts to “we won’t be satisfied until you provide us with every single point mutation over billions of years of evolution” plus “oh and you also have to explain the origin of life before you can consider the evolution of the flagellum solved.”

JohnK wrote Wallace’s blog, in absolute seriousness, entitles “Ann Coulter, Renowned evolution expert”.

Pete Dunkelberg:

What they rule out by definition is the gradual accumulation of increasing complexity to form a system that is IC.

No, they don't. You don't prevent something happening by making up definitions. There are lots of remarks similar to what I quoted in the comments here. It is true that IC might arise by simplification, but there is no reason to think that is the usual way. See for instance Ken Miller's The Evolution of Blood Clotting, and some commenters might go back to basics with good old Irreducible Complexity Demystified.

For goodness sakes, are we forgetting that this bacterial flajellythingy is actually an efficient motor, with all the parts and more than a human invented one. Is the emperor wearing clothes?

Dolly Sheriff: Come on guys, stop complaining about the ID'ists moving the goalposts. Irreducible complexity is not so hard to understand. Even for a housewife like me! Use the mousetrap example of Mr Behe as your guide...Just because the spring in the mousetrap under your table is also used in the spring file on top of your table, does NOT explain or show how the mousetrap was the ancestor of the spring file. Simple really.

William Wallace:

JohnK wrote Wallace’s blog, in absolute seriousness, entitles “Ann Coulter, Renowned evolution expert”.

I am still trying to find the citation for this...I am pretty sure it came from a post by PZ Myers or somebody similar. And while I did recognize it as sarcasm, this was only because I know how much the PT crowd loathes Coulter.

Nigel D: It is a relatively trivial task to demolish the mousetrap argument. This has been done elsewhere in detail, but the essence is twofold: (1) it is not irreducibly complex, and (2) it is not analogous to a biological system.

Dolly Sheriff: For goodness sakes, are we forgetting that this bacterial flajellythingy is actually an efficient motor, with all the parts and more than a human invented one. Is the emperor wearing clothes?

Nigel,
Sorry, you just provided a convenient example of a type of statement that occurs too many times in this comment stream.

Irreducible complexity, short version

IC is a misleading name for co-adapted parts, which evolution can't avoid producing. If ever a reason is found why something couldn't have evolved, IC won't be that reason.

Nigel D: Actually, it bears only a superficial resemblance to motors designed by humans (e.g. it contains a rotor and a stator but there the resemblance ends). Proteins are large, often flexible, molecules. They do not behave in a way that mimics anything that is familiar to anyone without the relevant experience in chemistry or biochemistry or cell biology.

Dolly - you're lying about being "just a housewife " Why?
http://darwinstories.blogspot.com/

Stacy, do you not know of any housewives that have a blog? Nick Matzke, has commented on my blog before, as you will see if you take the trouble to read it!

Dolly Sherrif, mechanical mousetraps are not relevant to biological evolution. Saying "Biology is complicated" is not an argument against evolution. Both complexity and co-adapted parts are natural outcomes.

I'm not opposed to evolution, in fact I'm all for it - I just don't buy the explanation on how it works. They sound like stories to me. Randomness and survival of the fittest just don't seem enough to build a functional motor. It's time scientists came up with a better explanation - then maybe ordinary people like us would believe it!

William Wallace:

JohnK wrote Wallace’s blog, in absolute seriousness, entitles “Ann Coulter, Renowned evolution expert”.

I am still trying to find the citation for this...I am pretty sure it came from a post by PZ Myers or somebody similar. And while I did recognize it as sarcasm, this was only because I know how much the PT crowd loathes Coulter.

Dolly Sheriff: Stacy, do you not know of any housewives that have a blog? Nick Matzke, has commented on my blog before, as you will see if you take the trouble to read it!

Stacy S.: No I don't ... I don't know who Nick Matzke is

Dolly, variation plus genetic drift plus natural selection work much better than you seem to think. You can't be taught everything in a blog comment, you have to study how natural processes work. Meanwhile, scientists don't "come up with" things. Research goes on all the time, and more is learned about nature nonstop, but we make no apology for the complexity of nature. If you don't "get" biology, consider the possibility that this does not mean no one does.

They sound like stories to me. Randomness and survival of the fittest just don’t seem enough to build a functional motor. It’s time scientists came up with a better explanation - then maybe ordinary people like us would believe it!

Dolly Sheriff: Come on guys, stop complaining about the ID'ists moving the goalposts. Irreducible complexity is not so hard to understand. Even for a housewife like me!

Sorry Stacy, Nick Mattzke posted this article that you are commenting on. So you see I am not trying to hide my identity as you not very politely pointed out.

Try starting with simpler stories (e.g., how a snowflake came to be).

I'm not 100% convinced that William Wallace (or "Braveheart," as I'm tempted to call him) isn't a parody troll, especially with that name and that Ann Coulter remark quoted just above.

Leaving that aside for the moment... If Wallace thinks that similarities at the cellular level are just coincidences and not evidence of relatedness, can we assume that he's outraged at the many innocent people put in prison (and the many guilty released) on the basis of DNA evidence? After all, just because the DNA left at the crime scene and the DNA of the prisoner show lots of similarities doesn't prove they're from the same person. It could be just coincidence. (Or a mystical designer inserting fake evidence to mess with us.) Ditto for the poor men forced to pay child support on the basis of similar "evidence."

Pete Dunkelberg: Mike Elzinga said (almost)

Try starting with simpler stories (e.g., how a snowflake came to be).

Pete Dunkelberg: Mike Elzinga said (almost)

Try starting with simpler stories (e.g., how a snowflake came to be).

I swear, it's getting to the point where I almost can't distinguish between tongue-in-cheek satire and genuine creationist claptrap. Dolly's site had me scratching my head. I've rarely seen so much writing and design effort and so much superficial cleverness expended to say so little.

The entire argument Dolly Sheriff makes, in her comments here and on her blog, is "Well, that just sounds far-fetched and hard to understand, so it's not true." I once saw a creationist commenter on the Evolution vs. Creation Forum (evcforum.net) say, and I believe this is almost an exact quote: "The truth is always simple and straightforward. Only lies have to be complicated and hard to understand." It's mind-boggling to me that a functioning adult could believe this, but it's the assumption under much creationist thought (not to mention other anti-intellectual beliefs).

Similarly, it's utterly perplexing to me that an articulate and apparently somewhat educated adult (even one who's "just a housewife") could apparently believe that any explanation, to be correct, must be immediately obvious and intuitive to an ordinary layperson who's done no study into the subject. Dolly, would you accept such reasoning when it came to, say, how to build a suspension bridge or how to keep an airplane aloft or how to operate on a damaged human brain?

Dolly Sheriff:

Nigel D: It is a relatively trivial task to demolish the mousetrap argument. This has been done elsewhere in detail, but the essence is twofold: (1) it is not irreducibly complex, and (2) it is not analogous to a biological system.

Nigel, thank you for your thoughtful reply. What I don't understand is, how is the mousetrap not analogous to a biological system?

Pete Dunkelberg: Nigel, Sorry, you just provided a convenient example of a type of statement that occurs too many times in this comment stream.

Dolly Sheriff:

Nigel D: Actually, it bears only a superficial resemblance to motors designed by humans (e.g. it contains a rotor and a stator but there the resemblance ends). Proteins are large, often flexible, molecules. They do not behave in a way that mimics anything that is familiar to anyone without the relevant experience in chemistry or biochemistry or cell biology.

Well, I think it looks very much like a motor and works very much like a motor. I don't have the "relevant experience in chemistry or biochemistry", but I'm not dim either. I saw those special "photos" that those clever eastern scientists took and it looks like a motor to me!

Dolly Sheriff: I'm not opposed to evolution, in fact I'm all for it - I just don't buy the explanation on how it works. They sound like stories to me. Randomness and survival of the fittest just don't seem enough to build a functional motor. It's time scientists came up with a better explanation - then maybe ordinary people like us would believe it!

William Wallace: I am setting a goal of studying more about how biologists go from noting coincidences to glibly asserting common descent.

Dolly Sheriff:

Stacy S.: No I don't ... I don't know who Nick Matzke is

Sorry Stacy, Nick Mattzke posted this article that you are commenting on. So you see I am not trying to hide my identity as you not very politely pointed out

Dolly Sheriff: It's time scientists came up with a better explanation - then maybe ordinary people like us would believe it!

You will find Intelligent Design is not only bad science, it is also bad theology.

— Ravilyn Sanders

Wallace pitching a slow one right over the plate: For example, endogenous retroviruses have been deemed to be genetic crumbs from ancient germs in the human genome. How do you know they are not ‘/* comments */’ or the basis of some other as yet latent function?

Phoenix rising: Scientists resuscitate a 5 million-year-old retrovirus VILLEJUIF, France (Tues., Oct. 31, 2006) -- A team of scientists has reconstructed the DNA sequence of a 5-million-year-old retrovirus and shown that it is able to produce infectious particles. The retrovirus--named Phoenix--is the ancestor of a large family of mobile DNA elements, some of which may play a role in cancer. The study, which is the first to generate an infectious retrovirus from a mobile element in the human genome, is considered a breakthrough for the field of retrovirus research. The findings are reported in Genome Research. "Phoenix became frozen in time after it integrated into the human genome about 5 million years ago," explains Dr. Thierry Heidmann, lead investigator on the project. "In our study, we've recovered this ancestral state and shown that it has the potential for infectivity." continues

I’m not opposed to evolution, in fact I’m all for it - I just don’t buy the explanation on how it works. They sound like stories to me. Randomness and survival of the fittest just don’t seem enough to build a functional motor. It’s time scientists came up with a better explanation - then maybe ordinary people like us would believe it!

I once saw a creationist commenter on the Evolution vs. Creation Forum (evcforum.net) say, and I believe this is almost an exact quote: “The truth is always simple and straightforward. Only lies have to be complicated and hard to understand.” It’s mind-boggling to me that a functioning adult could believe this, but it’s the assumption under much creationist thought (not to mention other anti-intellectual beliefs).

Wallace’s blog, in absolute seriousness, entitles “Ann Coulter, Renowned evolution expert”. Good luck with your questions, FrankJ.

— JohnK

Nick (Matzke)): ...the original IC argument, which was supposed to be a logical trap blocking evolution, has failed.

“Even if a system is irreducibly complex (and thus cannot have been produced directly)... one can not definitively rule out the possibility of an indirect, circuitous route. As the complexity of an interacting system increases, though, the likelihood of such an indirect route drops precipitously...” Micheal Behe, p40 Darwin's Black Box:

ID proponents would just switch the goalposts again by mumbling "not...enough...detail!"

Neither knew anything about immune system evolution or the evolution of IC degradation pathways, so why should anyone listen to them?

Stacy

Sheep Sheriff....I mean Dolly Sheriff is a DI spokesperson who pops up every now and then on PT

JJ: Sheep Sheriff

Halo babbling: The reason we should listen to them is because they are making admissions contrary to their darwinian position and so therefore these are very likely to be honest admissions.

One more question for you, does your Flagellum article propose a fairly detailed, step-by-step possible evolutionary scenario for the flagellum where:

— halo

Have you ever considered that the reason ID proponents ask for more detail is because they feel that you are making claims that go way beyond the evidence you give to back up those claims? Is that really so unreasonable?

Without knowing enough of the details, such assertions seem odd, and very much akin to the specious assertion that this program (wave.c) and this program (bubble sort) are obviously descendants of this program (hello world) simply because they all contain the same “extra operator error” in the sequences ‘/*’ and ‘*/’ instead of just a ‘/’ or a ‘*‘.

And have you ever considered that the reason that ID proponents ask for more detail is because they are so conceptually out of the ballpark that they can’t even begin to comprehend the meaning of the answers they are given?

— Mike Elzinga

As peddlers of pseudoscience, they merely exploit the double standard that most nonscientists have unwittingly adopted. Specifically that mainstream science can never supply enough detail to satisfy them, while the “oppressed underdogs” of alternative science only need to supply a few feel-good sound bites.

Dolly Sheriff: What I don't understand is, how is the mousetrap not analogous to a biological system?

Halo, your first questions are covered in the very basic Irreducible Complexity Demystified. Then you evidently give up on the IC argument, that IC systems are unevolvable in principle (or so improbable that it comes to the same thing) and switch to "not all molecular details of events a billion years ago are known" which everyone agrees to.

So, your point?

Mousetraps don’t have babies.

Mousetraps don't have babies.

the missing letter: t

One more question for you, does your Flagellum article propose a fairly detailed, step-by-step possible evolutionary scenario for the flagellum where: 1) each intermediate confers a functional advantage (or at very least serves some kind of function) 2) the gap between each step can be analyzed probabilistically to gauge if it is reasonably probable or not. If this has been done all credit to you and I’d love to read it. If this has not been done then could you please tell me how it is anything more than an unproved suggestion that is untestable (with regard to probability) and so therefore unfalsifiable?

Frank J wrote Speaking of “best guess,” please state yours, even if you are genuinely unsure. William Wallace, that goes for you too.

MPW wrote If Wallace thinks that similarities at the cellular level are just coincidences and not evidence of relatedness, can we assume that he’s outraged at the many innocent people put in prison (and the many guilty released) on the basis of DNA evidence?

William Wallace wrote: So, in the world of analyzing DNA, what makes you think your “complier” is complete, and that it discloses all meaning and function?... (And the Monkey looking at a sea of clouds does not mean that all such forms are created naturally.)

Shouldn't one use the "Blogging on Peer-Reviewed Research" icon when citing a Super Bowl commercial?

Again, really, I don't know whether you're joking or not. But I guess that, as near as I can tell under the verbiage, you're saying you consider it highly doubtful whether DNA is an indicator of identity or relatedness. Fascinating. Just what do you think DNA does? Do you really think it likely that it has nothing to do with, say, the fact that my dad and I are so similar physically and psychologically?

Just for the sake of completeness, how many other commonplace areas of science are there where you consider the scientists who work on it daily to be just making stuff up, while you know better than them despite having done no research?

Pretty good commercial, though.

Even so, I am unafraid of science. Science should be pursued with an eternal questioning of all premises, and recognition that what we think we know and reality are not necessarily one in the same.

William Wallace: God—whom I avow, and who needs not my acknowledgment, and who many of you blaspheme as imaginary supernatural caulk, exists.

This God is: holy; wise; worthy of worship and awe; beyond description; beyond comprehension; existed before time; will exist after time; and is far more intelligent than human kind—this God, the creator, is infinitely greater than the entire universe he created.

And, as a study of history confirms, and as present and future times will continue to show, human ignorance is a universal constant.

Even so, I am unafraid of science. Science should be pursued with an eternal questioning of all premises, and recognition that what we think we know and reality are not necessarily one in the same.

A scientific theory is not a fact—it is a model. And a model is a representation—never to be confused with the thing it represents.

Wallace evading all questions and changing the subject: God—whom I avow, and who needs not my acknowledgment, and who many of you blaspheme as imaginary supernatural caulk, exists. This God is: holy; wise; worthy of worship and awe; beyond description; beyond comprehension; existed before time; will exist after time; and is far more intelligent than human kind—this God, the creator, is infinitely greater than the entire universe he created. And, as a study of history confirms, and as present and future times will continue to show, human ignorance is a universal constant.

raven: Salvation is by faith, faith or good works, or both depending on which gospel one quote mines. Treating a book written by bronze age sheepherders as a science textbook is not required.

To be fair, I've recently read a book called "Mutants: On the Form, Varieties and Errors of the Human Body" by Armand Marie Leroi, in which he says (if I remember correctly) that sometimes embryos fuse and a baby is born with some body parts that belong, in fact, to his or her absorbed twin (chimerism). And there are cases where a person might have testicles of his non-identical twin, in which case he might, indeed, leave DNA traces of another person when he commits rape. The author was worried that at least some cases of people released because of DNA evidence might be because of this.

Wallace

"God, whom I avow..." etc. This is the equivalent of sticking your fingers in your ears and babbling loudly so that you can't hear what your opponents are saying. Why have you still not answered the simple questions posed by FrankJ earlier in the thread?

Stanton

"your religious handlers.." That hits the nail on the head!

Richard Simons:

Dolly Sheriff: What I don't understand is, how is the mousetrap not analogous to a biological system?

Mousetraps don't have babies.

God—whom I avow, and who needs not my acknowledgment, and who many of you blaspheme as imaginary supernatural caulk, exists. This God is: holy; wise; worthy of worship and awe; beyond description; beyond comprehension; existed before time; will exist after time; and is far more intelligent than human kind—this God, the creator, is infinitely greater than the entire universe he created.

— William Wallace

What makes you think that computer code is in any way analogous to DNA? Since you assert knowledge of information theory, you must see that the parallels are outweighed by the differences.

Nor is it necessary or even advisable to treat the Bible as a science textbook, either.

— Stanton

If this has not been done then could you please tell me how it is anything more than an unproved suggestion that is untestable (with regard to probability) and so therefore unfalsifiable?

"A Minimal Definition of Evolution"

Evolution is a process that results in heritable changes in a population spread over many generations.

A scientific theory is not a fact—it is a model.

I am unafraid of science.

halo: Nick Matzke:

Nick (Matzke)): ...the original IC argument, which was supposed to be a logical trap blocking evolution, has failed.

Would you mind explaining to me why the original IC argument was supposed to logically block all evolutionary scenarios when Behe himself clearly stated:

“Even if a system is irreducibly complex (and thus cannot have been produced directly)... one can not definitively rule out the possibility of an indirect, circuitous route. As the complexity of an interacting system increases, though, the likelihood of such an indirect route drops precipitously...” Micheal Behe, p40 Darwin's Black Box:

In light of this explicit statement do you really feel you are representing him fairly??

Thanks for the link to the immune system article, I'd like to have a read of it when I get a chance. I've always thought that Miller's tactic of just slapping down a pile of books in front of Behe

would have been much better substituted for just reading out the relevant pieces from them that describe the detailed, step-by-step and testable model for the evolution of the immune system

which is so well known amongst evolutionary biologists, and has been for years. I trust I'll find that in your article...

One more question for you, does your Flagellum article propose a fairly detailed, step-by-step possible evolutionary scenario for the flagellum where: 1) each intermediate confers a functional advantage (or at very least serves some kind of function) 2) the gap between each step can be analyzed probabilistically to gauge if it is reasonably probable or not.

If this has been done all credit to you and I'd love to read it. If this has not been done then could you please tell me how it is anything more than an unproved suggestion that is untestable (with regard to probability) and so therefore unfalsifiable? And when you say:

ID proponents would just switch the goalposts again by mumbling "not...enough...detail!"

Have you ever considered that the reason ID proponents ask for more detail is because they feel that you are making claims that go way beyond the evidence you give to back up those claims? Is that really so unreasonable?

Dolly Sheriff said: Well, I think it [the bacterial flagellum] looks very much like a motor and works very much like a motor. ... I saw those special "photos" that those clever eastern scientists took and it looks like a motor to me!

William Wallace
I knew you would not answer me. I am writing this post for the
benefit of lurkers who might be non-programmers to enable them
to counter similar arguments strongly if they come across this at the watercooler or an airport concourse. Sorry fo the long
post.

I proved

in this comment that your example involving sort.c, wave.c and hello_world.c is a classic straw man. Scientists do not take the short snippets of DNA, the equivalent of these tiny programs,
pounce on one error or similarity and say, "yeah, there is
enough evidence for descent."

You have caricatured the real work of scientists, which is more
like looking at all the versions of source code of FireFox,
InternetExplorer, Opera and draw up distance maps. Like
FireFox.1.1 is closer to Firefox 1.2 than Opera.0.9, and on and on for every version. This
distance relationships are built as a tree. Now the theory that
best explains the tree of relationship is descent.

(Aside: You hint that you are programmer, and your much maligned blasphemer Dawkins is not a professional programmer. And he
describes how these distance relationships are inferred using
the typos in the existing hand-written copies of
Beowulf. He takes pains to explain the difference between
rooted and unrooted trees, something I find even software
consultants charging 100$ an hour are unaware of.)

But just because you are burying your head in sand does not
mean the science of statistical analysis and descent inference
will go away. It is applied not just to DNA, not just to
manuscripts of Beowulf, it is very heavily applied to the Holy Bible.
They are coming up with amazing theories like the Gospels of Mark and Luke had a common ancestor, these sections of the OT were written when the tribes were pastoral and these sections were written after they urbanized etc. These studies are not
done by atheists, it is done by religious scholars who devote
their life studying the scriptures. Most people don't know
much about proteins and coding DNA and genotype, phenotype and
alleles. That goes for the religious folks who are hoodwinked
into supporting ID too. But they quote the Bible chapter and
verse. They would immediately "get" the similarity and distance
analysis of various books and versions of the Bible. At that
time they themselves will realize that your example is a
very weak straw man caricature of comparative DNA analysis.

The reason we should listen to them is because they are making admissions contrary to their darwinian position and so therefore these are very likely to be honest admissions.

— Halo

And if to escape this you say that they were just ignorant can you please back that up?

halo, Please feel free to tell us whether you agree with Behe that, regardless of mechanism or whether design actuation events occurred: 1. Humans share common ancestors with dogs and dogwoods. 2. Life on Earth has a ~3-4 billion year history. [snip] Speaking of “best guess,” please state yours, even if you are genuinely unsure. William Wallace, that goes for you too.

— Frank J

God—whom I avow, and who needs not my acknowledgment, and who many of you blaspheme as imaginary supernatural caulk, exists. This God is: holy; wise; worthy of worship and awe; beyond description; beyond comprehension; existed before time; will exist after time; and is far more intelligent than human kind—this God, the creator, is infinitely greater than the entire universe he created. And, as a study of history confirms, and as present and future times will continue to show, human ignorance is a universal constant.

— William Wallace

tell us whether you agree with Behe that, regardless of mechanism or whether design actuation events occurred: 1. Humans share common ancestors with dogs and dogwoods. 2. Life on Earth has a ~3-4 billion year history.

— Frank J

And, as a study of history confirms, and as present and future times will continue to show, human ignorance is a universal constant.

— William Wallace

God—whom I avow, and who needs not my acknowledgment, and who many of you blaspheme as imaginary supernatural caulk, exists. This God is: holy; wise; worthy of worship and awe; beyond description; beyond comprehension; existed before time; will exist after time; and is far more intelligent than human kind—this God, the creator, is infinitely greater than the entire universe he created.

— William Wallace

Peter Ridsdale: Stanton "your religious handlers.." That hits the nail on the head!

Frank J:

Nor is it necessary or even advisable to treat the Bible as a science textbook, either.

— Stanton

Michael Behe himself said that doing so is "silly."

Nigel D: OK, am I the only one to spot the inconsistency here? William, you clearly state that human ignorance is constant, and then you claim knowledge of something for which there is no physical evidence. All I can say is this: how do you know?

Even so, I am unafraid of science. Science should be pursued with an eternal questioning of all premises, and recognition that what we think we know and reality are not necessarily one in the same.

— William Wallace

A scientific theory is not a fact—it is a model. And a model is a representation—never to be confused with the thing it represents.

Dan:

Do you mean you saw pictures like the one presented here? Or perhaps you mean pictures like figure 2 in this article? http://www.aip.org/pt/jan00/berg.htm Read the caption: "Rotationally averaged reconstruction of electron micrographs of purified hook-basal bodies." This is a manipulation of photographs, not a photograph.

Figure 2 looks very much like the structure of a motor to me. I've seen my hubby, Ben dismantle machines in his garage many times before and the structure is uncanningly similar to those. Excuse me for not using the scientific definition. Okay so its an electron micrograph and not a photomicrograph. I don't think this changes my point.

Dan: Do you mean you saw pictures like the one presented here? Or perhaps you mean pictures like figure 2 in this article? http://www.aip.org/pt/jan00/berg.htm Read the caption: "Rotationally averaged reconstruction of electron micrographs of purified hook-basal bodies." This is a manipulation of photographs, not a photograph.

Dear William Wallace

You say that God is far more intelligent than human kind and yet it appears to me that He has created a greatly flawed kind of universe in which the "forces of darkness" seem to have a pretty free rein. As a human being I can easily imagine a universe that was not quite so hostile (black holes, radiation, meteors, seismic activity etc.) and a planet where selfishness and greed were not so well rewarded and where poverty and suffering were not so widespread. If God could have created any kind of universe why did he create one in which he continually needs to tinker - "Damn, there goes another species! I'll have to create something else now! I know, I'll try something invisible to the naked eye that's got a little motor in it - then when my great prophet Michael Behe comes along, he will prove that I exist!"
And if we are created in God's image does that mean that when He moved over the face of the waters He was already equipped with testicles, toe-nails and a vestigial appendix?

I know you will have fun answering this posting as it doesn't have any hard science in it, and your reply will be more or less predictable, so please answer Frank J's questions instead. We are all still waiting.

Yet, the vast majority of Mr Behe’s colleagues, along with all other creationists, give us the opposite impression.

— Stanton

MPW:

Apologies for being a bit behind the curve. Your creationist may have been referring to the following:

"Science is always simple and always profound. It is only the half-truths that are dangerous."

George Bernard Shaw (1856-1950)

A couple of possible rejoinders come to mind:

"The aim of science is to seek the simplest explanations of complex facts. We are apt to fall into the error of thinking that the facts are simple because simplicity is the goal of our quest. The guiding motto in the life of every natural philosopher should be, 'Seek simplicity, and distrust it.'"

Alfred North Whitehead (1861-1947)

"For every complex problem, there is a solution that's simple, straightforward -- and wrong."

H.L. Mencken (1880-1956)

Dolly: why does your mind boggle? Wouldn't it be better off thinking things through after concerted investigation of the subject?

One more question for you, does your Flagellum article propose a fairly detailed, step-by-step possible evolutionary scenario for the flagellum where: 1) each intermediate confers a functional advantage (or at very least serves some kind of function) 2) the gap between each step can be analyzed probabilistically to gauge if it is reasonably probable or not.

Dolly: why does your mind boggle? Wouldn’t it be better off thinking things through after concerted investigation of the subject?

gregwrld: Dolly: why does your mind boggle? Wouldn't it be better off thinking things through after concerted investigation of the subject?

The mind boggles that gifted men and woman cannot see that randomness and survival of the fittest are inadequate to explain the flagellum self assembling motor. Lets go where the evidence leads.

— Dolly Sheriff

I imagine this is what Halo is referring to when he talks about each intermediate providing some kind of positive benefit.

The mind also boggles that anyone would still use that old "it takes more faith" nonsense.

Lurkers, please notice what Dolly conveniently omitted. That it takes more faith than what?

Frank J: ...please tell us whether you agree ... that the evidence leads at least to: 1. Common ancestry of humans, dogs and dogwoods. 2. A 3-4 billion year history of life on Earth.

Mike Elzinga: It’s like trying to explain modern aircraft design to a cargo cultist.

Frank J: The mind also boggles that anyone would still use that old "it takes more faith" nonsense. Lurkers, please notice what Dolly conveniently omitted. That it takes more faith than what?

Dolly,

Thanks for your prompt reply.

What is that "bankrupt world view" that the "Darwinian explanation" provides, and do the 11,000+ members of Christian clergy that signed that statement adhere to that world view?

What about Schwabe, Senapathy and Goldschmidt, who have offered "naturalistic" explanations that explicitly deny Darwinian evolution (the first 2 denying also common descent)? Do their explanations also provide that "bankrupt world view"?

Nigel D: Questions that Dembski carefully ignores include:
(1) If there is design, why does so much of the evidence indicate incompetent design rather than intelligent design?
(2) By what mechanism does the design come to be actuated?
(3) How are we to determine when, in the ancestry of bacteria, the design event occurred?
(4) Were there many design events or just one? How are we to measure this?
(5) Why can we see no evidence for the existence of a designer (remember that Dembski has asserted that evidence of design does not necessarily implicate the existence of a designer)?
(6) How is design supposed to occur if not through natural processes or a designer?

It is the Darwinian explanation that falls so painfully short of providing satisfying answers. Unfortunately it also provides a bankrupt world-view as well.

Nigel D: Questions that Dembski carefully ignores include:
(1) If there is design, why does so much of the evidence indicate incompetent design rather than intelligent design?
(2) By what mechanism does the design come to be actuated?
(3) How are we to determine when, in the ancestry of bacteria, the design event occurred?
(4) Were there many design events or just one? How are we to measure this?
(5) Why can we see no evidence for the existence of a designer (remember that Dembski has asserted that evidence of design does not necessarily implicate the existence of a designer)?
(6) How is design supposed to occur if not through natural processes or a designer?

Mike Elzinga: Perhaps you could clarify for us just how all of the modern conveniences that science has provided (including that computer you are writing on) have been the result of a “corrupt world-view”.

What would you estimate the statistical chances would be of the human mind developing through the current mainstream understanding of Darwinian Evolution (Straw men aside)?

Dolly,

Not sure I understand the question, but given life (the chances of it arising at least once is unity by definition), the Darwinian explanation provides testable theory for the origin of species, and thus how "the" human brain (or "the" bacterial flagellum) arose. It makes no comment on the "chances" of that, or of the "chances" that life itself would arise.

I know you wish it would explain more detail, but it's the best we have. As you can see from Behe's concession of old life and common descent, and the steady retreat of others from specifying details of potential alternate explanations, even the most militant detractors seem to admit that "between the lines."

Dolly Sheriff: It is the Darwinian explanation that falls so painfully short of providing satisfying answers. Unfortunately it also provides a bankrupt world-view as well.

Mike Elzinga: Rephrase the question slightly. What would you estimate the statistical chances would be of your winning a $100 million lottery (assuming you entered)? What would your estimate be of someone winning that lottery?

Dolly Sheriff: The electron micro- graph of a flagellum looks uncanning-ly like a human designed motor. The mind boggles!

Dolly Sheriff:

Mike Elzinga: Perhaps you could clarify for us just how all of the modern conveniences that science has provided (including that computer you are writing on) have been the result of a “corrupt world-view”.

Mike, I think you are being a little unkind. The majority of scientists that laid down a foundation for the scientific benefits we now enjoy (including my laptop) did not subscribe to a soulless universe.

Dolly Sheriff: The electron micro- graph of a flagellum looks uncanning-ly like a human designed motor. The mind boggles!

Mike, I think you are being a little unkind. The majority of scientists that laid down a foundation for the scientific benefits we now enjoy (including my laptop) did not subscribe to a soulless universe.

Stanton:

Dolly Sheriff: The electron micro- graph of a flagellum looks uncanning-ly like a human designed motor. The mind boggles!

Except that a human-designed motor is not made out of proteins, oils and sugars that have different simultaneous functions, that does not have different parts that function simultaneously in both an aqueous solution and in a colloid suspension, and is not manufactured inside of the vehicle that needs the motor out of the vehicle's own personal resources.

Dolly Sheriff:

Stanton:

Dolly Sheriff: The electron micro- graph of a flagellum looks uncanning-ly like a human designed motor. The mind boggles!

Except that a human-designed motor is not made out of proteins, oils and sugars that have different simultaneous functions, that does not have different parts that function simultaneously in both an aqueous solution and in a colloid suspension, and is not manufactured inside of the vehicle that needs the motor out of the vehicle's own personal resources.

Excellent point Stanton, you're starting to sound like a design theorist!

Dolly,

Others might call me crazy, but you seem far more reasonable than most of the recent anti-evolutionists on this blog, and not just because you answered my usual questions that most others evade, and not just because you accept evolution's conclusions on the age of life and common descent. Most of your questions about world views and odds of this and that happening are answered here.

If you are still unimpressed with the explanatory power of the Darwinian explanation, you might want to check the self-organization concepts such as those by Stuart Kauffman.

IIRC you are also unimpressed with the explanatory power of ID, and if so, rightly so. But you seem to have bought into their propaganda that their strategy will increase critical thinking among students. There's no quick way to convince you otherwise (this might help), but if you read enough, you will know that they are only trying to mislead.

The electron micro- graph of a flagellum looks uncanning-ly like a human designed motor. The mind boggles!

Dolly Sheriff: Excellent point Stanton, you're starting to sound like a design theorist!

The electron micro- graph of a flagellum looks uncanning-ly like a human designed motor. The mind boggles!

Thanks for your kind words Frank. I certainly am not anti-evolution, but I am anti smug Darwinian dogma, that teaches our children not to question the prevailing scientific world view (Darwinism) on how life came about and discourages them from looking for purpose and meaning in the universe.

Dolly Sheriff: Thanks for your kind words Frank. I certainly am not anti-evolution, but I am anti smug Darwinian dogma, that teaches our children not to question the prevailing scientific world view (Darwinism) on how life came about and discourages them from looking for purpose and meaning in the universe.

PvM: what a crock

Dolly Sheriff: Thanks for your kind words Frank. I certainly am not anti-evolution, but I am anti smug Darwinian dogma, that teaches our children not to question the prevailing scientific world view (Darwinism) on how life came about and discourages them from looking for purpose and meaning in the universe.

"It is the Darwinian explanation that falls so painfully short of providing satisfying answers. Unfortunately it also provides a bankrupt world-view as well."

I wonder if the latter isn't the real reason so many otherwise intelligent people are distressed by the theory of evolution? They somehow see it as a world devoid of hope. If true that's sad. Evolution is the history of survival in a harsh environment. How can one not be proud of each and every one of our ancestors, from the simple to the complex,as each was a champion. Each managed to pass on his/her/its DNA to the next generation. I find that view satisfying and uplifting. "There is grandeur in this view of life..." And 'hope' I might add.

Dolly Sheriff: ... the prevailing scientific world view (Darwinism) on how life came about ...

Perhaps you could clarify for us just how all of the modern conveniences that science has provided (including that computer you are writing on) have been the result of a “corrupt world-view”.

Mike, I think you are being a little unkind. The majority of scientists that laid down a foundation for the scientific benefits we now enjoy (including my laptop) did not subscribe to a soulless universe.

Dolly Sheriff: I am anti smug Darwinian dogma, that teaches our children not to question the prevailing scientific world view (Darwinism) on how life came about and discourages them from looking for purpose and meaning in the universe.

Mike those odds are very different to the odds of a self-forming universe like ours. Non creation/ID scientists have estimated odds of 10 to the minus 100 for that… Odds that you will win the above lottery 30 000 times in a row, taking only one ticket each time. Very lucky indeed!.

Thanks for your kind words Frank. I certainly am not anti-evolution, but I am anti smug Darwinian dogma, that teaches our children not to question the prevailing scientific world view (Darwinism) on how life came about and discourages them from looking for purpose and meaning in the universe.

Ravilyn Sanders: WW, Halo and Dolly should realize ID is not just bad science but also bad religion.

Dolly Sheriff: Thanks for your kind words Frank. I certainly am not anti-evolution, but I am anti smug Darwinian dogma, that teaches our children not to question the prevailing scientific world view (Darwinism) on how life came about and discourages them from looking for purpose and meaning in the universe.

Dolly,
First thanks for agreeing with the age of Earth and common descent. That is unlike most Creationists. May be you are an
Old Earth Creationist.

Why don't you follow your own pet theory? That there is a Designer. Then why did He stop after the nano motor? Why not
a micro motor, a milli motor and a regular motor? The biologists
explain why there is no bigger motor than the one found in the bacteria using the theory of evolution. How does the design
theory explain it?

Why did the Designer create diseases? He hates us?

Why did the Designer put our retinas backward facing? The brain
is behind the eye. If the nerves attach to the retinal cells
(the cones and rods) from behind, the wiring would be simpler,
there will be no blind spot, and the detached retina diseases
would be much rarer. And you know what? There are eyes like
that in other animals. Why did the Designer condemn us to
have an eye designed so badly?

If you follow the evidence wherever it leads to, you will
find an Incompetent Designer, or Indifferent Designer, or
Infernal Designer...

In short, the Design theory provides even less satisfying
answer than the theory of evolution.

Mike Elzinga: And just how does the “prevailing scientific world view (Darwinism)” discourage anyone from looking for purpose and meaning in the universe? Why do you even label the "prevailing scientific world view" as "Darwinism"? That, no doubt, is standard-issue propaganda coming from a pulpit in your church. Do you dare question it?

Stacy S.:

Ravilyn Sanders: WW, Halo and Dolly should realize ID is not just bad science but also bad religion.

This article surely must have hit a nerve somewhere :-) Is this an unusual number of trolls for a single thread? Great article Dan!!

Kevin B: From the IDC point of view, this new article is of somewhat of the nature of a puntgun.... :)

Thanks for your kind words Frank. I certainly am not anti-evolution, but I am anti smug Darwinian dogma, that teaches our children not to question the prevailing scientific world view (Darwinism) on how life came about and discourages them from looking for purpose and meaning in the universe.

— Dolly Sheriff

Dan Jones:

Bobby: Dan, find out the NS policy on self-archiving your publications. If they are one of the many scientific publishers that allow it, you can make the article downloadable from your blog and post the link here.

It’s common practice for science writers to sign a writer’s agreement that hands over the rights to the article – the words themselves, as well as the formatted, illustrated, published piece. And so I would be infringing copyright if I posted my articles online for all to see. I’ve noticed that a number of writers, such as Steve Pinker and Carl Zimmer, have their articles online (Pinker has exact replicas of the published pieces, Zimmer the text from his articles), and wondered how this is possible. My best guess is that these prestigious writers can insist on retaining the copyright on their words, and yet they’re names have so much cache that publishers are still happy to get their stuff into print. I could be wrong, but I think that must be what’s going on.

Dolly writes... I certainly am not anti-evolution, but I am anti smug Darwinian dogma, that teaches our children not to question the prevailing scientific world view (Darwinism)

Torbjörn Larsson, OM: Yes, the mind boggles - why would anyone with access to biological and technical research think that micromachinery, whether natural or artificial, are anything like ordinary machinery? [...]Chemical machinery is stochastic. That is, you can never predict exactly when the next "step" (reaction) will happen. Nor are the reactions or small scale mechanical movements completely irreversible; once in a while the machinery will back up. This in no way resemble everyday machinery.

...The electron micrograph provides novices like myself an opportunity to weigh up the similarities of the micro machine with those of the real world, not having to rely on illustrations. Now, my hubby Ben Sheriff likes to fix stuff, and has often reconditioned a motor - I sometimes have to help clean up the mess. The electron micro- graph of a flagellum looks uncanning-ly like a human designed motor. The mind boggles!

— Dolly Sheriff

SteveF: Nigel D:

One more question for you, does your Flagellum article propose a fairly detailed, step-by-step possible evolutionary scenario for the flagellum where: 1) each intermediate confers a functional advantage (or at very least serves some kind of function) 2) the gap between each step can be analyzed probabilistically to gauge if it is reasonably probable or not.

Your questions are impertinent. The article to which this thread refers (back in the original post, if you can scroll up that far) actually makes it clear that feasible paths for flagellum evolution have only very recently been proposed. This does not mean that every step of the way is enumerated, because it is a proposed evolutionary path. All biologists working in evolutionary science understand that there is no point in working out an evolutionary pathway in excessive detail, because for structures that are as old as the flagellum, it is unlikely that the evidence will ever be available to us to tease out every last detail of how it evolved. But, despite what you seem to be implying, it is enough to demonstrate a feasible route, and it is only the creationists who insist on there being more detail available than it is reasonable to expect. I seem to recall that Behe's latest definition involves the nature of the steps in the development of the flagella. He thinks that every step has to be selectable; I imagine this is what Halo is referring to when he talks about each intermediate providing some kind of positive benefit. This is distinct from Behe's ridiculous claim that we have to be able to specify things in forensic detail.

Dolly Sheriff:

gregwrld: Dolly: why does your mind boggle? Wouldn't it be better off thinking things through after concerted investigation of the subject?

The mind boggles that gifted men and woman cannot see that randomness and survival of the fittest are inadequate to explain the flagellum self assembling motor.

Lets go where the evidence leads.

(1) What, to your mind, is the scientific theory of ID?
(2) Do you agree with Michael Behe that the Earth is over 4 billion years old?
(3) Do you agree with Michael Behe that the evidence for universal common descent is overwhelming?
(4) Do you agree with Michael Behe that most biological change is the result of natural selection (he asserts simply that it cannot all be caused by natural selection)?

— Nigel D

I hope a whole generation of young people are inspired by this new field of molecular biology and are eventually able to find explanations that truly satisfy - not explanations that are just so many Darwinian just-so-stories and require way more faith than the average religious person.

— Dolly Sheriff

Dolly Sheriff: Frank I must agree that the evidence does seem to point to a common ancestry and scientific evidence does agree an age of the earth consistent with those estimates. It is the Darwinian explanation that falls so painfully short of providing satisfying answers. Unfortunately it also provides a bankrupt world-view as well.

It is the Darwinian explanation that falls so painfully short of providing satisfying answers.

— Dolly Sheriff

Unfortunately it also provides a bankrupt world-view as well.

What would you estimate the statistical chances would be of the human mind developing through the current mainstream understanding of Darwinian Evolution (Straw men aside)?

— Dolly Sheriff

Stacy S.: Nigel ... she did answer a couple of them - but to Frank.

Dolly Sheriff: Frank I must agree that the evidence does seem to point to a common ancestry and scientific evidence does agree an age of the earth consistent with those estimates. It is the Darwinian explanation that falls so painfully short of providing satisfying answers. Unfortunately it also provides a bankrupt world-view as well.

Some web sites bring up a Delete box, just for the poster.

I am setting a goal of studying more about how biologists go from noting coincidences to glibly asserting common descent.

Thanks Nigel for this excellent proposal of a curriculim for ID/creationist scientists to tackle. Wouldnt it be better if we encourage them to do just that. I think people like Behe and Dembski are at least encouraging youngsters to research these questions and not to only hold on to the theories which dominate the universities.

— Dolly Sheriff exemplifying creo hypocrisy

Dolly Sheriff:

Mike Elzinga: Perhaps you could clarify for us just how all of the modern conveniences that science has provided (including that computer you are writing on) have been the result of a “corrupt world-view”.

Mike, I think you are being a little unkind. The majority of scientists that laid down a foundation for the scientific benefits we now enjoy (including my laptop) did not subscribe to a soulless universe.

The mind boggles that gifted men and woman cannot see that randomness and survival of the fittest are inadequate to explain the flagellum self assembling motor.

I am anti smug ...

Dolly Sheriff:

Mike Elzinga: Rephrase the question slightly. What would you estimate the statistical chances would be of your winning a $100 million lottery (assuming you entered)? What would your estimate be of someone winning that lottery?

Mike those odds are very different to the odds of a self-forming universe like ours. Non creation/ID scientists have estimated odds of 10 to the minus 100 for that... Odds that you will win the above lottery 30 000 times in a row, taking only one ticket each time. Very lucky indeed!

Dolly Sheriff:

Stanton:

Dolly Sheriff: The electron micro- graph of a flagellum looks uncanning-ly like a human designed motor. The mind boggles!

Except that a human-designed motor is not made out of proteins, oils and sugars that have different simultaneous functions, that does not have different parts that function simultaneously in both an aqueous solution and in a colloid suspension, and is not manufactured inside of the vehicle that needs the motor out of the vehicle's own personal resources.

Excellent point Stanton, you're starting to sound like a design theorist!

Dolly Sheriff:

PvM: what a crock

Dolly Sheriff: Thanks for your kind words Frank. I certainly am not anti-evolution, but I am anti smug Darwinian dogma, that teaches our children not to question the prevailing scientific world view (Darwinism) on how life came about and discourages them from looking for purpose and meaning in the universe.

PvM, we are all crocks (earthenware vessels) but some of use believe that we have more inside us than meets the eye or can be seen under a microscope)

R Ward: "It is the Darwinian explanation that falls so painfully short of providing satisfying answers. Unfortunately it also provides a bankrupt world-view as well." I wonder if the latter isn't the real reason so many otherwise intelligent people are distressed by the theory of evolution? They somehow see it as a world devoid of hope. If true that's sad. Evolution is the history of survival in a harsh environment. How can one not be proud of each and every one of our ancestors, from the simple to the complex,as each was a champion. Each managed to pass on his/her/its DNA to the next generation. I find that view satisfying and uplifting. "There is grandeur in this view of life..." And 'hope' I might add.

Is this an unusual number of trolls for a single thread?

— Stacy S.

Nigel D: While your mind is bogglingly, why has it not occurred to you that the resemblance could be either a coincidence, or superficial?

(1) What, to your mind, is the scientific theory of ID?
(2) Do you agree with Michael Behe that the Earth is over 4 billion years old?
(3) Do you agree with Michael Behe that the evidence for universal common descent is overwhelming?
(4) Do you agree with Michael Behe that most biological change is the result of natural selection (he asserts simply that it cannot all be caused by natural selection)?

— Nigel D

Nigel,

Although unlike most anti-evolutionists she has promptly answered questions 2 and 3, I would not hope for much beyond "I don't know" for 1 and 4.

Her promptness at answering 2 and 3 contrasts sharply with the fact that she has not yet commented on either the world views promoted by anti-evolution positions (e.g. it's OK to quote mine), or how they have infinitely more "holes" than evolution.

Sure, she can say "I don't know" to them too (or simply evade them), but that would suggest that she is giving "alternative science" a free pass that she denies mainstream science.

Yes, it is unusual to get more than one or two, but not unheard-of. There was one thread a few months back that included posts from FL, Mats and another regular crackpot (whose online name eludes me for the present).

— Nigel D

What is a troll?

Peter,

See this.

Some raise the suspicion that they are not true creationists, but rather seek to make creationists look silly.

Some raise the suspicion that they are not true creationists, but rather seek to make creationists look silly.

— Frank J

Dolly: It is the Darwinian explanation that falls so painfully short of providing satisfying answers. Unfortunately it also provides a bankrupt world-view as well.

Dolly Sheriff:

Mike Elzinga: Rephrase the question slightly. What would you estimate the statistical chances would be of your winning a $100 million lottery (assuming you entered)? What would your estimate be of someone winning that lottery?

Mike those odds are very different to the odds of a self-forming universe like ours. Non creation/ID scientists have estimated odds of 10 to the minus 100 for that... Odds that you will win the above lottery 30 000 times in a row, taking only one ticket each time. Very lucky indeed!

Nigel,

I just thought of Keith "Evolander" Eaton. I read that he has been doing that routine for over a decade. After a while I just stopped "feeding," but from what I did have the patience to read, I couldn't tell if he wanted creationists to look silly, or was that far gone (either in terms of his personal beliefs, or in a desire to mislead a la the DI).

Dolly Sheriff: Frank I must agree that the evidence does seem to point to a common ancestry and scientific evidence does agree an age of the earth consistent with those estimates. It is the Darwinian explanation that falls so painfully short of providing satisfying answers. Unfortunately it also provides a bankrupt world-view as well.

What the heck is a "bankrupt world-view", anyway?

Henry

Dolly Sheriff seems to think that

Darwinism ... discourages them [children] from looking for purpose and meaning in the universe.

Notice that Dolly gives no evidence to back up this false assertion. It is, in fact, the exact opposite of the truth: If scientists saw no meaning in the universe, then there would be no reason to study it.

Dolly, please read "Why I'm Happy I Evolved" by evolutionary biologist Olivia Judson

http://www.nytimes.com/2006/01/01/opinion/01judson.html

and see if you can still claim that the study of evolution "provides a bankrupt world-view".

http://en.wikipedia.org/wiki/Internet_troll

I suspect that Dolly is not all she appears to be ("just a housewife"?) - she has obviously spent a lot of time constructing her web-site and the caricatures of Dawkins and Darwin etc. with Pinocchio (liars') noses indicate some kind of religious activist commitment to ridicule and belittle evolutionists. (Never mind Dolly, we can take it!).

But her case raises an interesting point - let's suppose for a moment that she is just an ordinary person who is genuinely baffled by evolutionary theory. She would not be alone, as many people find it hard to truly comprehend the vast aeons of time in which evolutionary processes operate. Most people still do not understand that evolution is not just a series of random mutations, and that natural selection is not at all random. People who do not really understand what is meant by 'survival of the fittest' are the ones who will ascribe negative and emotional values to the phrase and by extension to the whole of evolutionary theory. It is such people who form the ID congregation and who are most likely to be misled by snake-oil merchants like Behe and Dembski.

It is extremely difficult to communicate difficult concepts to people with a limited capacity to understand them but are we doing enough to put our case in a way that is easy to understand?

Dolly Sheriff seems to think that Darwinism ... discourages them [children] from looking for purpose and meaning in the universe.

raven: All that is left is to take over the government, tear up the constitution, sneak this mess into children's science classes, and hope for a new Dark Ages.

What was clear to me is that Dolly hasn't done her homework. I mean she hasn't even scratched the surface! She also seeks to draw a philosophy of life from a description of life. These are going to be hard things for her to get passed, but if she starts a serious investigation, maybe she'll get there.
But first she has to understand that saying some invisible being by some unknown method caused some ill-defined biological event to happen is no competition for the TOE as an explanation.

It is such people who form the ID congregation and who are most likely to be misled by snake-oil merchants like Behe and Dembski. It is extremely difficult to communicate difficult concepts to people with a limited capacity to understand them but are we doing enough to put our case in a way that is easy to understand?

Frank J: Nigel, I just thought of Keith "Evolander" Eaton. I read that he has been doing that routine for over a decade. After a while I just stopped "feeding," but from what I did have the patience to read, I couldn't tell if he wanted creationists to look silly, or was that far gone (either in terms of his personal beliefs, or in a desire to mislead a la the DI).

Peter Ridsdale: It is extremely difficult to communicate difficult concepts to people with a limited capacity to understand them but are we doing enough to put our case in a way that is easy to understand?

Are you aware that most AP Bio curricula require high school students to complete 45 - 50 chapters of material in 8 months? If you work that out, I’m guessing it leaves a week or less for evolution, which generally includes not only natural selection, but speciation AND the history of life on earth. Never mind anything that’s been thought of in the last 25 years. I cannot even imagine how little time there is to devote to evolution in introductory classes, since many teachers are working on NCLB or have end of course tests which stress quantity, not quality of material.

Mike Elzinga: I have often thought that fundamentalist churches have long been the refuge of scoundrels and scam artists ...

Mike

I'll grant you part of the textbook problem is based on publishers avoiding controversy, but I will also point out that in 28 years of teaching in the South, I have always had access to textbooks that gave a clear and unapologetic explanation of evolutionary theory (although often the section on human evolution is abridged). So, I'm not willing to accept fundamentalist interference as the only problem, as tempting as it is.

Teach, many thanks for your comments. I find the contributions made here by professionals in the teaching field very interesting.

David B. Benson:

Mike Elzinga: I have often thought that fundamentalist churches have long been the refuge of scoundrels and scam artists ...

Amen! Hallelujah! Pass the plate...

teach: Mike I'll grant you part of the textbook problem is based on publishers avoiding controversy, but I will also point out that in 28 years of teaching in the South, I have always had access to textbooks that gave a clear and unapologetic explanation of evolutionary theory (although often the section on human evolution is abridged). So, I'm not willing to accept fundamentalist interference as the only problem, as tempting as it is.

Unfortunately in Texas, probably 60 % or more of science teachers won't address evolution because of backlash from the fundies. It is skipped completely or left until the last few days when very little can be covered.

I wish I knew how to do those links that are just words

cool Thanks Jon :-)

Mike those odds are very different to the odds of a self-forming universe like ours. Non creation/ID scientists have estimated odds of 10 to the minus 100 for that…

It is the Darwinian explanation that falls so painfully short of providing satisfying answers. Unfortunately it also provides a bankrupt world-view as well.

Dolly;

I'm sorry that you think that the world is an awful place without God.
What has that got to do with the price of chickens in Calcutta?
I think that you have been told, over and over again, that life without God of Christ is worthless.
I love my Godless Universe.
When a big wave kills thousands of people, it is just a big wave, not a judgment.
When a boy survives a plane crash where 150 people die, it isn't a miracle, it's an accident with a survivor.
When something good happens, it is a happy circumstance.
When something bad happens, it is not a reflection on you or your worth.
In a Godless Universe there is no judgment, there is no punishment (I know, you want bad people to suffer beyond the grave, too bad for your thirst for vengeance), there is no uncertainty about your fate after you die.
It is my belief that Christianity makes people insane, as they try to rationalize the obviously incoherent belief system, with all of its holes and contradictions.
The believers latch onto things like evolution as a defining battle; one that, if they win, will PROVE to themselves what they can only half-way bring themselves to believe.
My proof?
Doubt.
Doubt is addressed to an astonishing degree by the churches. They construct systems for stymieing doubt, for cutting it off at it's inception, for PREVENTING it altogether.
Doubt is expressed by Christ, by Mother Teresa, by Popes and Bishops.
Doubt is cruel.
Doubt in God must be terrible.
See, I don't get that.
That's what I like about being soulless.

Mike

We have a branch of our state university system here, but we're not really a college town per se. And don't get me wrong - the campaigns in many states to intimidate teachers to leave out evolution all together are very real, as are the efforts to water down textbooks. I appreciate every Kitzmiller and Aguillera (sp?) that comes along. But I also believe that there are better ways to teach science than the content heavy/standardized test push that we find ourselves stuck with more and more. It is so hard to spend time on meaningful explanations of, say, speciation events or evo devo when teachers know that the end of course test, upon which their school's funding for the next year may well be based, requires a total memorization of the organelles of a cell and won't have a thing on it about Hox genes. Often times, we have to rely on shortcut definitions and explanations because there's no time for anything else.

Of course, once the great majority of my students leave me, they will never, ever again study evolutionary theory in any depth at all - however, they will be constantly faced, in the movie theater, in some churches and by evangelizing neighbors, with criticism of it. High school is our best chance to grab and excite the greatest number of people about science.

But I also believe that there are better ways to teach science than the content heavy/standardized test push that we find ourselves stuck with more and more.

I don't believe arguments have any effect on Dolly. Pantheism is a convenient loophole. But anyway, I read "Understanding the Present" by Brian Appleyard some years ago and found it quite interesting. I suppose googling may provide some clues to what it is about.

As far as I remember, an important point was to show how and why science is not, and should not be used as a provider of solutions to man's' predicament.

Teach,

Thanks indeed for your insights from the "front line" as 'twere. It makes me realise how lucky I was to attend a school with teachers who were both enthusiastic and knowledgeable, and to face an examination system that rewarded depth of knowledge instead of only breadth (although some breadth was necessary also).

Since the introduction of the national curriculum to the UK, I fear that science education is heading in the direction of the "one mile wide, one inch deep" situation that appears to prevail in the US. What was once taught as three subjects (biology, chemistry and physics) is now taught as two (a "double science" GCSE).

So, I’m not willing to accept fundamentalist interference as the only problem, as tempting as it is.

— teach

If you work that out, I’m guessing it leaves a week or less for evolution, which generally includes not only natural selection, but speciation AND the history of life on earth. Never mind anything that’s been thought of in the last 25 years.

— teach

Frank, you remind me of the structure of benzene.

Level 1 is the Kekulé structure (alternating double and single C-C bonds);

At level 2, we were taught that this is not correct and that the electrons are delocalised;

At level 3, we were taught that the molecular orbitals of benzene are such that the Kekulé structure is a very useful approximation.

I also agree that the public in general seems too ready to accept nonsense and distrusts science, which is simply the process of finding out how the universe works.

@Teach - One of the wonderful things about these new standards is that subjects will be able to be taught in more depth.

Frank, you remind me of the structure of benzene. Level 1 is the Kekulé structure (alternating double and single C-C bonds); At level 2, we were taught that this is not correct and that the electrons are delocalised; At level 3, we were taught that the molecular orbitals of benzene are such that the Kekulé structure is a very useful approximation.

— Nigel D

Nigel D said: What was once taught as three subjects (biology, chemistry and physics) is now taught as two (a “double science” GCSE).

PvM: what a crock Dolly Sheriff: Thanks for your kind words Frank. I certainly am not anti-evolution, but I am anti smug Darwinian dogma, that teaches our children not to question the prevailing scientific world view (Darwinism) on how life came about and discourages them from looking for purpose and meaning in the universe.

PvM: what a crock Dolly Sheriff: Thanks for your kind words Frank. I certainly am not anti-evolution, but I am anti smug Darwinian dogma, that teaches our children not to question the prevailing scientific world view (Darwinism) on how life came about and discourages them from looking for purpose and meaning in the universe.

Who are these people who have estimated the probability of the universe existing to be 10^-100? Haven’t they ever looked out the window? Or have you oversimplified what they were calculating?

Since the introduction of the national curriculum to the UK, I fear that science education is heading in the direction of the “one mile wide, one inch deep” situation that appears to prevail in the US. What was once taught as three subjects (biology, chemistry and physics) is now taught as two (a “double science” GCSE).

Mike Elzinga:

Since the introduction of the national curriculum to the UK, I fear that science education is heading in the direction of the “one mile wide, one inch deep” situation that appears to prevail in the US. What was once taught as three subjects (biology, chemistry and physics) is now taught as two (a “double science” GCSE).

Nigel, What has been the pressure behind this in the UK? Where do educational science standards get generated and put into policy?

Mike Elzinga wrote and Peter Ridsdale concurred: Your religious handlers have misinformed you about this.

Please disclose your best guess of the identity of my “religious handler”. I’d like to call him or her.

— William Wallace

Henry J:

Nigel D said: What was once taught as three subjects (biology, chemistry and physics) is now taught as two (a “double science” GCSE).

Which two of them got lumped together? Henry

Dear William

Do you attend a church on a regular basis? Do you have some kind of priest / minister / elder / evangelist or druid?

Who told you that the Bible is the word of God?

If you answer these questions we may have some idea who is pulling your strings, otherwise we're kind of left in the dark.

Glad to see that you are back, but disappointed that you STILL haven't answered the questions.

What happened to Dolly? Halo, Dolly...

I would have thought that a housewife would be used to the heat in the kitchen.

Bill Gascoyne:

Who are these people who have estimated the probability of the universe existing to be 10^-100? Haven’t they ever looked out the window? Or have you oversimplified what they were calculating?

Isn't this sort of like the "bumblebee can't fly" argument? Our calculations show !A, yet we observe A, and we just know that our calculations must be accurate and pertinent, therefore our observation of A must be an illusion or caused by something else. God forbid we should suspect that our calculations/dogma might be wrong.

Frank J:

Frank, you remind me of the structure of benzene. Level 1 is the Kekulé structure (alternating double and single C-C bonds); At level 2, we were taught that this is not correct and that the electrons are delocalised; At level 3, we were taught that the molecular orbitals of benzene are such that the Kekulé structure is a very useful approximation.

— Nigel D

Oh, you must be a member of the Benzenist Orthodoxy. ;-) Actually, your example was my preferred analogy 6-7 years ago, but I figured (not sure if correctly) that more people would relate to PV=nRT.

The addition of more and more “vocational” or “socially relevant” topics to the curriculum has made timetabling a complete nightmare. One of the several consequences is that time that was once available for science has been sacrificed.

The problem of finding good science teachers varies widely throughout the US. Some districts can’t find (attract) good science teachers, therefore science courses are assigned to people who have no qualifications. The school districts in which this happens are usually poor or are dominated by sectarian groups with a political agenda. I have done some educational consulting work with several school districts and I can tell you that the poorer ones are really pathetic. They can’t keep qualified teachers, and the ones they do keep are not able to handle even the most rudimentary concepts in the subjects of math and science. They simply assign “workbook” activities and grade from a teachers manual. They cannot answer student questions, and the students no longer ask.

— Mike Elzinga

Nigel D: Perhaps we should not wonder at how ignorant so many citizens of the USA seem to be. OTOH, we can and should abhor their complacency.

I think, however, that [the use of probability and bumblebee calculations] shows more about how something can be taken out of context than it does about the arrogance of engineers.

— Nigel D

I wasn't sure if the bumblebees-can't-fly claim had ever been made seriously by a competent person or not. It didn't seem likely that somebody willing to think would miss that it's the fixed-wing assumption that causes that conclusion, but one never really knows what somebody might overlook.

Henry

IIRC, the calculations showed that the bumblebee would be dynamically unstable, not that it couldn't get off the ground or anything like that. I had not been aware that the equations were known to be for fixed wing aircraft. I presume the point of doing the calculation at all would be to test the equations (not the bumblebee) to show how rudimentary our understanding of aerodynamics was at the time. Somebody obviously got wind of it and used it to support other conclusions. Can you say, "social Darwinism"?

With regards to the abiogenesis question that William Wallace wouldn't answer way back when in this very long thread - I just came across this interesting snippet from the Rig Veda (x. 129)

"Who knows the truth? Who can tell whence and how arose this universe? The gods are later than its beginning: who knows therefore whence came this creation? Only that god who sees in highest heaven: he only knows whence came this universe, and whether it was made or uncreated. (sic) He only knows, or perhaps he knows not."

It's a bit more sophisticated than the Christian version, isn't it?

At least in the UK (and unless the situation has changed recently or my original understanding was deeply flawed), a person must possess a university degree in a relevant topic to be employed as a teacher at a state-funded school.

Nigel,

Have you been able to reach the “Benzenist Orthodoxy” link in Comment 143,439?

Anyone else have trouble with it? The links work for me, but not being a computer person I’m not sure if they work anywhere else.

Anyway, here are related articles for all to enjoy. When I wrote about “benzenism” I was unaware of ”Intelligent Grappling.” My idea was inspired by ”Godless Linguistics.”

Frank, I can't access it from work not due to some technical incompatability, but due to a very stringent firewall that includes nanny software to prevent accessing sites that are NSFW. I could request access to the site hosting that page, but I would need to state a work-related reason.

Stacy S.:

Nigel D: Perhaps we should not wonder at how ignorant so many citizens of the USA seem to be. OTOH, we can and should abhor their complacency.

Heeeeyyyyy - I resemble that remark! :-) I think we are just selectively ignorant :-)

Nigel (and others),

Hope you can access them at home. I just want to clear up the "propaganda" that ID has not inspired any "research." ;-)

Frank J:

Frank, you remind me of the structure of benzene. Level 1 is the Kekulé structure (alternating double and single C-C bonds); At level 2, we were taught that this is not correct and that the electrons are delocalised; At level 3, we were taught that the molecular orbitals of benzene are such that the Kekulé structure is a very useful approximation.

— Nigel D

Oh, you must be a member of the Benzenist Orthodoxy. ;-) Actually, your example was my preferred analogy 6-7 years ago, but I figured (not sure if correctly) that more people would relate to PV=nRT.

Wouldn't benzenism be a circular argument? ;) :p

Henry J: Wouldn't benzenism be a circular argument? ;) :p

Thanks! :)

The author of the New Scientist essay on the evolution of the flagellum states: "The evolutionary events linking flagella and T3SSs are not clear, but the homology between them is a devastating blow to the claim of irreducible complexity. This requires that a partial flagellum should be of no use whatsoever - but clearly it is."

What is clear here is that the author does not understand the concept of irreducible complexity. Irreducible complexity does not entail that a component of an irreducibly complex system has "no use whatsoever"; it instead entails that the function of the system is lost whenever one component of the system's irreducible core is removed. It should be obvious that irreducible complexity as it is defined by Behe is not refuted by defining it in another way.

By Behe's first definition of "irreducible complexity", it has absolutely nothing to do with whether or not the feature could have evolved.

By his second definition, he defines "irreducible complexity" to mean "it couldn't have evolved", but gives no demonstration that anything fits that definition.

Uh - which definition are we supposed to use? ;)

Henry

Henry: "By (Behe's) second definition, he defines 'irreducible complexity' to mean 'it couldn’t have evolved', but gives no demonstration that anything fits that definition."

Actually, Henry, Behe never defines irreducible complexity to mean "it couldn't have evolved." Use the definition of irreducible complexity that Behe gives, not definitions that are falsely attributed to him by critics who miss the point.

Jim,
Behe's initial definition of IC was removing a part from the system breaks the function. This situation is expected for evolved systems. Ergo the concept of IC (using that definition) has nothing to do with whether or not something could have evolved.

If he gave a later definition that actually addresses an actual issue, what is that definition and what issue does it address? Or are you sticking with the original definition, the one that was already shown to be irrelevant to evolution theory?

Henry

Both Behe and his allies have used several different definitions of "IC" over the years.

The initial one was that "any system lacking a part is by definition nonfunctional." The nonfunctionality was then the reason that the system couldn't evolve gradually, instead it had to come together all at once.

When counterexamples are shown, e.g. a subset of flagellar parts that is not nonfunctional (the nonflagellar T3SS), THEN they switch to the sneaky definition of IC which always boils down to "unevolvable" or "evolution not reconstructed in infinite detail", and then assert that they haven't been refuted by the example, because whatever example is under discussion either (a) evolved and therefore clearly wasn't IC in the first place so it's not a counterexample or (b) didn't evolve because not every point mutation over billions of years has been given, never minded about dozens of peer-reviewed papers testing & confirming the evolutionary hypothesis, as we have with the immune system.

All this switcheroo shows is that a circular argument is irreducibly complex.

Henry: "Behe’s initial definition of IC was removing a part from the system breaks the function. This situation is expected for evolved systems."

Behe's point is precisely the opposite: that we don't expect an evolved system to develop irreducible complexity as it evolves.

Nick: "The initial (definition of irreducible complexity) was that 'any system lacking a part is by definition nonfunctional.'"

That's close, but not quite accurate. The original definition was this: An irreducibly complex system is "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". You should have written: "Any system that loses its function when any one part is removed is by definition irreducibly complex." If you don't think the definition applies to any biological systems, then I have a proposition to make to you: Have the optical nerve removed from your right eye (I'll cover the cost). If you report back to us that you can still see out of the eye, then I'll concede that the concept of irreducible complexity is without merit.

Nick: "When counterexamples are shown, e.g. a subset of flagellar parts that is not nonfunctional (the nonflagellar T3SS), THEN they switch to the sneaky definition of IC which always boils down to 'unevolvable' or 'evolution not reconstructed in infinite detail', and then assert that they haven’t been refuted by the example, because whatever example is under discussion either (a) evolved and therefore clearly wasn’t IC in the first place so it’s not a counterexample or (b) didn’t evolve because not every point mutation over billions of years has been given, never minded about dozens of peer-reviewed papers testing & confirming the evolutionary hypothesis, as we have with the immune system."

Whether or not a component of an irreducibly complex system has a separate (and different) function of its own is irrelevant to the irreducible complexity of the system as a whole. Your argument here is a distortion of the argument from irreducible complexity. One of the best explanations of that argument that I've seen was given by Dembski and Wells in their recently published "The Design of Life." If you don't have the book, you can find their explanation at:

http://groups.yahoo.com/group/OriginsTalk/message/15513

Heh, you just admitted my point. There was nothing in Behe's original definition about a subset of parts being able to retain some other function.

And, as far as I'm concerned, on Behe's original definition, I am happy to agree that such systems -- breakable systems -- exist. It's just that I know how evolution can produce such systems -- primarily cooption of multipart subsystems with different original functions.

"The Design of Life", which I have read, is not where to find the original definitions, that book was published this year and consists of an extended series of obfuscations and redefinitions to hide the fact that Behe lost his original argument.

Behe’s point is precisely the opposite: that we don’t expect an evolved system to develop irreducible complexity as it evolves.

Nick: "Heh, you just admitted my point. There was nothing in Behe’s original definition about a subset of parts being able to retain some other function."

Of course I admitted your point: the point is irrelevant to the argument from irreducible complexity (this is something you should know if you read "The Design of Life," as you claimed). If the parts of an irreducibly complex biological system can perform different functions of their own, that fact has no bearing on the irreducibility of the system as a whole. Let's hear from Behe on this point:

http://www.discovery.org/a/1831

In a recent column in the Wall Street Journal (February 13, 2004, Science Journal, page B1, “Evolution Critics Come Under Fire for Flaws In 'Intelligent Design'”) science writer Sharon Begley repeated some false claims about the concept of irreducible complexity (IC) that have been made by Darwinists, in particular by Kenneth Miller, a professor of biology at Brown University. After giving a serviceable description in her column of why I argue that a mousetrap is IC, Begley added the Darwinist poison pill to the concept. The key misleading assertion in the article is the following: “Moreover, the individual parts of complex structures supposedly serve no function.” In other words, opponents of design want to assert that if the individual parts of a putatively IC structure can be used for anything at all other than their role in the system under consideration, then the system itself is not IC. So, for example, Kenneth Miller has seriously argued that a part of a mousetrap could be used as a paperweight, so not even a mousetrap is IC. Now, anything that has mass could be used as a paperweight. Thus by Miller’s tendentious reasoning any part of any system at all has a separate “function”. Presto! There is no such thing as irreducible complexity.

That’s what often happens when people who are adamantly opposed to an idea publicize their own definitions of its key terms--the terms are manipulated to wage a PR battle. The evident purpose of Miller and others is to make the concept of IC so brittle that it easily crumbles. However, they are building a straw man. I never wrote that individual parts of an IC system couldn’t be used for any other purpose. (That would be silly--who would ever claim that a part of a mousetrap couldn’t be used as a paperweight, or a decoration, or a blunt weapon?) Quite the opposite, I clearly wrote in Darwin’s Black Box that even if the individual parts had their own functions, that still does not account for the irreducible complexity of the system. In fact, it would most likely exacerbate the problem, as I stated when considering whether parts lying around a garage could be used to make a mousetrap without intelligent intervention. (end quote)

Nick: "... I know how evolution can produce (irreducibly complex) systems – primarily cooption of multipart subsystems with different original functions."

I take it you're not a scientist, Nick (neither am I). No scientist would say that he *knows* how an unobserved biological event (such as the origination of an irreducibly complex biological system) occurred. The scientific method is too heavily reliant on inductive reasoning to deliver certainty. But if you think that co-option is the answer, then let's see your explanation of co-option producing an irreducibly complex biological system. Keep in mind that your explanation must show, with sufficient detail to be testable, that:

(1) the parts were available for co-option;
(2) the availability of the parts was synchronized in both time and space;
(3) the availability of the parts was coordinated so that they assembled properly;
(4) the parts had interface-compatibility so they could work together.

Jim, Nick didn't say he knew the exact details of how something happened. He said he knows, as scientists do, how it can happen. However it is possible to make a plausible inference of how did happen sometimes.

Meanwhile, the burden of proof is on you to show that IC can't evolve. Why can't it? C'mon Jim, why?

By the way, degradation of Pentachlorophenol (PCP) evolved easily.

Popcorn time. :)

Jim, I routinely use evolutionary mechanisms (random mutations, recombination, and differential reproduction as a function of fitness) to evolve irreducibly complex artificial agents on my desktop. I know that evolutionary processes can produce irreducibly complex structures, in both of Behe's senses of the phrase. (For the several senses of "irreducible complexity" used by IDists see the ID Encyclopedia.)

"By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning." [emphasis in original][page 39]

"An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional."

"Even if a system is irreducibly complex (and thus cannot have been produced directly), however, one can not definitely rule out the possibility of an indirect, circuitous route. As the complexity of an interacting system increases, though, the likelihood of such an indirect route drops precipitously." (page 40)

"An irreducibly complex biological system, if there is such a thing, would be a powerful challenge to Darwinian evolution." (page 39)

Jim, you have referred to Behe and associates arguing words, claiming for instance that Miller did use their definition exactly right. He probably did use it right, or as right as a shifty thing like a creationist definition can be used, but that's not the point. Miller is showing how the sorts of end points Behe talks about can be reached. He is talking biology and Behe just plays with words.

Rather than the things you refered to, think of Behe at the Dover trial. When word games would not suffice and he had to provide real biology, he hadn't any to offer. What does that tell you?

Jim said: Nick: "Heh, you just admitted my point. There was nothing in Behe's original definition about a subset of parts being able to retain some other function." Of course I admitted your point

the point is irrelevant to the argument from irreducible complexity (this is something you should know if you read "The Design of Life," as you claimed).

The argument from irreducible complexity, in making the logical point that irreducible complexity rules out direct Darwinian pathways, therefore rules out the form of evolution that is best confirmed. Indirect Darwinian pathways, by contrast, are so open-ended that there is no way to test them scientifically unless they are carefully specified - and invariably, when it comes to irreducibly complex systems, they are left unspecified, thus rendering them neither falsifiable nor verifiable. In making its logical point, the argument from irreducible complexity therefore takes logic as far as it can go in limiting the Darwinian mechanism and leaves empirical considerations to close off any remaining loopholes. And since logical inferences are inherently stronger than empirical inferences, the argument from irreducible compexity's refutation of the Darwinian mechanism is as strong and tight as possible. It's not just that certain biological systems are so complex that we can't imagine how they evolved by Darwinian pathways. Rather, we can show conclusively that direct Darwinian pathways are causally inadequate to bring them about and that indirect Darwinian pathways, which have always been more difficult to substantiate, are utterly without empirical support.

The long quote Nick gave from DoL is bunk. Behe didn't really prove that IC can't evolve directly, and indirect (by Behe's terms) evolution is routine and not some mysterious unverifiable thing.

Co-adapted parts are a normal outcome of evolution. How could you stop evolution from producing them? Behe invented the direct/indirect terms, but in real biology they have no use. It is just a quibble to impress the gullible.

If anyone thinks there is a proof that IC can't evolve directly, present it. It will turn out to be quibbling at best.

The long term evolution of most features of life has not been what Behe, or indeed most people, would call direct. And even short term evolution can be indirect in Behe's terms. So it is surprising to read, on page 40, Behe's argument against indirect evolution of IC systems. Here is the crux of it: "Even if a system is irreducibly complex (and thus cannot have been produced directly), however, one can not definitely rule out the possibility of an indirect, circuitous route. As the complexity of an interacting system increases, though, the likelihood of such an indirect route drops precipitously." (page 40) He simply asserts that evolution of irreducible complexity by an indirect route is so improbable as to be virtually out of the question, except in simple cases. He makes no special connection between indirect evolution and IC. He offers no evidence. He just asserts that it is too improbable.

The design inference and irreducible complexity consist of two components: an extensive negative argument against the plausibility of evolutionary explanations, and then a brief attempt at a positive argument relying on an analogy between biological adaptations and human artifacts. Behe's negative argument against stepwise assembly of "irreducible" systems fails because it mistakenly assumes that evolution proceeds only by improvement of an extant function, whereas evolutionary theory extending back to Darwin has always emphasized the importance of changes of function in the origin of complex adaptations (17–22). [...] 17. Darwin, C. (1859) [On the Origin of Species by Means of Natural Selection (Murray, London,). [particularly this part around p. 147] 18. Darwin, C. (1862) On the Various Contrivances by Which British and Foreign Orchids Are Fertilised by Insects, and on the Good Effects of Intercrossing (Murray, London,). (online here, particularly this) 19. Mayr, E. (1960) "The Emergence of Evolutionary Novelties." The Evolution of Life: Its Origin, History and Future ed. Tax, S. (Univ of Chicago Press, Chicago,) Vol 1, pp. 349–380. [Google Scholar] 20. Jacob, F. (1977) Science 196, 1161–1166. [Google Scholar] 21. Ganfornina, MD & Sanchez, D. (1999) "Generation of evolutionary novelty by functional shift." BioEssays 21, 432–439. [Google Scholar] 22. True, JR & Carroll, SB. (2002) "Gene co-option in physiological and morphological evolution." Annu Rev Cell Dev Biol 18, 53–80. [Google Scholar]

Yeah, it's also true that IC does not even block direct evolutionary pathways, for example because of scaffolding, an example of which is the origin of the venus flytrap as described in Pete's IC Demystified.

(still though, cooption is the main explanation for most major functional novelties)

Cripes we should write a post-Kitzmiller IC argument FAQ, this is about the tenth time we've gotten this new revised-revised version of the IC argument.

I'll bid you adios. I'm leaving town in the morning, so I don't have time to continue the thread. I may or may not pick it back up when I return.

I take it you're not a scientist, Nick (neither am I).

No scientist would say that he *knows* how an unobserved biological event (such as the origination of an irreducibly complex biological system) occurred. The scientific method is too heavily reliant on inductive reasoning to deliver certainty.

But if you think that co-option is the answer, then let's see your explanation of co-option producing an irreducibly complex biological system.

Jim said: I'll bid you adios. I'm leaving town in the morning, so I don't have time to continue the thread. I may or may not pick it back up when I return.

Got some time on my hands after all, so...

RBH said: "Jim, I routinely use evolutionary mechanisms (random mutations, recombination, and differential reproduction as a function of fitness) to evolve irreducibly complex artificial agents on my desktop. I know that evolutionary processes can produce irreducibly complex structures, in both of Behe’s senses of the phrase."

Unless you offer some details, RBH, this is unenlightening. What, exactly, are those "complex artificial agents"? If they are artificial rather than living, what relevance do they have to Darwinian evolution? What function(s) do they perform? Do they lose function when any one component is removed? Are they living? What were the precursor "agents"? What were the functions of the systems as they evolved from precursors to final products? What was the selection function: natural selection, or you?

I think you're bluffing.

Pete: "...the burden of proof is on you to show that IC can’t evolve."

That's what the argument from irreducible complexity purports to do (at least, it purports to show that unintelligent material causes can't cause the evolution of IC systems; it takes no issue with the notion that an intelligent cause, or causes, could cause the evolution of IC systems). Personally, I find the argument from irreducible complexity much more persuasive than the largely evidence-free just-so stories told by Darwinists. But even if the argument is wrong, why are Darwinists relieved of the obligation to show that Darwinian mechanisms are capable of generating irreducibly complex biological systems? Can their theory be validated by wishful speculations alone?

Pete: "Behe finds that 'direct' evolution of IC is logically impossible, (but it isn’t really)..."

Actually, Pete, it is a logical impossibility. For the evolution of an IC biological system to be achieved via a direct Darwinian pathway, the function of the system must be maintained throughout its evolution. But since an IC system loses its function whenever any one component is removed, then all possible precursors to the system (in a direct Darwinian pathway) would not have performed that function. If those precursors performed other functions, then the evolution of the IC system must be by an indirect Darwinian pathway (one in which both function and structure evolve).

Pete: "The long term evolution of most features of life has not been what Behe, or indeed most people, would call direct."

You're bluffing: no one actually knows how "most features of life" evolved.

Pete: "(Behe) simply asserts that evolution of irreducible complexity by an indirect route is so improbable as to be virtually out of the question, except in simple cases."

More than that, Behe calls attention to the complete absence of any detailed and testable indirect Darwinian pathways to an irreducibly complex biological system.

Behe: "An irreducibly complex biological system, if there is such a thing, would be a powerful challenge to Darwinian evolution."

Pete: "By now I think you can see that this is hardly the case."

Actually, Pete, I've seen no arguments here that inflict the slightest damage to Behe's argument.

Jim,

Behe accepts that the earth is billions of years old and we humans and the chimpanzees share a common ancestor. Do you
agree with him, since you defend him so vociferously?

Pete: "Jim, you have referred to Behe and associates arguing words, claiming for instance that Miller did use their definition exactly right. He probably did use it right, or as right as a shifty thing like a creationist definition can be used, but that’s not the point. Miller is showing how the sorts of end points Behe talks about can be reached."

Miller redefined IC to mean that a biological system is not irreducibly complex if any of its components perform a function other than the function performed by the system. Thus, Behe's 5-piece mousetrap is not IC because the wooden platform can be used as a paperweight, or the spring can be used as a tie clip (and so on). By redefining IC in that way, Miller constructed a straw man that he could easily tear down. It ought to be obvious that Behe's argument from irreducible complexity is not refuted by arguing against straw men made of it. (By the way, Behe's 5-piece mousetrap was meant solely to illustrate the concept of irreducible complexity; he was not trying to "prove" his argument by way of analogy, something that can't be done.)

Pete: "Rather than the things you refered to, think of Behe at the Dover trial. When word games would not suffice and he had to provide real biology, he hadn’t any to offer. What does that tell you?"

It tells me that you're not accurately representing Behe's testimony, in which he had a great deal to say about "real biology." If you're annoyed by "word games," you should be irked by the word games used by Miller (and by most of Behe's critics here) to "refute" his argument from irreducible complexity.

Nick: "But if you admit all this, and then admit that functional subsystems exist, then you have to concede that Behe’s original argument didn’t work."

No, I don't. If "functional subsystems exist," it does not logically follow that Darwinian mechanisms produced the IC system in question by bringing those functional subsystems together to form an IC system with an entirely different function. All you're saying is that an IC system might evolve by an indirect Darwinian pathway, a point that Behe concedes. But he finds the point entirely unpersuasive (so do I) because there is a complete absence in the biological literature of any detailed, testable indirect Darwinian pathways to IC biological systems. His argument is not refuted by wishful speculations, such as the claim that the bacterial flagellum was produced by co-opting the type III secretory system and other essential proteins. This particular "refutation" of Behe is especially unpersuasive because the best evidence suggests that if anything, the type III secretory system evolved from the flagellum, not the other way around.

Nick: "But this lack of detail/testing excuse is 100% crap. For examine, the adaptive immune system was one of Behe’s irreducibly complex systems which he said couldn’t evolve in a chapter of his 1996 book Darwin’s Black Box. The evolutionary explanation for its origin, the transposon hypothesis, was proposed decades ago and Behe summarily dismissed it in 1996. But in the last 10 years, experiment after experiment has tested and confirmed the transposon model. This is all summarized in this Nature Immunology article."

I read the article, which confirmed Behe's point that Darwinists fail to provide any detailed, testable Darwinian pathways leading to an irreducibly complex biological system. It's no wonder that Darwinists are convinced that their theory has all the answers to the mystery of life's evolution: they set their standard of "proof" so low that the theory will be "confirmed" by virtually any "model".

Nick: "During the Kitzmiller v. Dover case, Behe was on the witness stand and made exactly the kinds of goalpost-moving claims you are making here. His last stand was to appeal to lack of detail & rigor in the evolutionary cooption explanations. So we presented him with a bunch of the recent peer-reviewed scientific literature on the origin of the adaptive immune system. He’d never read most of it, and he still asserted that it wasn’t enough detail for him. And this is where it became clear that Behe doesn’t really care about actually dealing with real science, instead he is just making up excuses to avoid admitting he’s wrong."

I'll let Behe respond to what you've said here. What follows is a portion of his rebuttal to Judge Jones's willfully obtuse decision that ID theory is religion, not science.

http://www.discovery.org/scripts/viewDB/filesDB-download.php?command=download&id=697

From Judge Jones's decision:

"In fact, on cross-examination, Professor Behe was questioned concerning his 1996 claim that science would never find an evolutionary explanation for the immune system. He was presented with fifty eight peer-reviewed publications, nine books, and several immunology textbook chapters about the evolution of the immune system; however, he simply insisted that this was still not sufficient evidence of evolution, and that it was not 'good enough.'"

Behe replies:

1) Although the opinion’s phrasing makes it seem to come from my mouth, the remark about the studies being “not good enough” was the cross-examining attorney’s, not mine.

2) I was given no chance to read them, and at the time considered the dumping of a stack of papers and books on the witness stand to be just a stunt, simply bad courtroom theater. Yet the Court treats it seriously.

3) The Court here speaks of “evidence for evolution”. Throughout the trial I carefully distinguished between the various meanings of the word “evolution”, and I made it abundantly clear that I was challenging Darwin’s proposed mechanism of random mutation coupled to natural selection. Unfortunately, the Court here, as in many other places in its opinion, ignores the distinction between evolution and Darwinism. I said in my testimony that the studies may have been fine as far as they went, but that they certainly did not present detailed, rigorous explanations for the evolution of the immune system by random mutation and natural selection — if they had, that knowledge would be reflected in more recent studies that I had had a chance to read.

4) This is the most blatant example of the Court’s simply accepting the Plaintiffs’ say-so on the state of the science and disregarding the opinions of the defendants’ experts. I strongly suspect the Court did not itself read the “fifty eight peer-reviewed publications, nine books, and several immunology textbook chapters about the evolution of the immune system” and determine from its own expertise that they demonstrated Darwinian claims. How can the Court declare that a stack of publications shows anything at all if the defense expert disputes it and the Court has not itself read and understood them? In my own direct testimony I went through the papers referenced by Professor Miller in his testimony and showed they didn’t even contain the phrase “random mutation”; that is, they assumed Darwinian evolution by random mutation and natural selection was true —they did not even try to demonstrate it. I further showed in particular that several very recent immunology papers cited by Miller were highly speculative, in other words, that there is no current rigorous Darwinian explanation for the immune system. The Court does not mention this testimony. (end quote)

Nick: "Please give us your detailed, testable ID explanation for the origin of the adaptive immune system."

I don't have one. The science of intelligent design is in the business of developing the evidentiary, logical, and mathematical tools needed to make rigorous design inferences in the biosphere. How design might have been actualized is beyond the scope of ID as it is currently construed, although that's certainly a line of research that scientists ought to follow once the case for design musters the financial and institutional support that any scientific research needs. There is a problem inherent in such research, however. That problem is this: the technology of life is so much more sophisticated than human technology that we are ill-equipped to try to explain how the designs that are so evident in life's technological systems were actualized. Perhaps our own technology will someday be sufficiently advanced that we can try, for example, to do reverse engineering on the technological marvels in living organisms. Research of that kind will, of course, never be attempted if biologists remain stuck in the rut of Darwinism.

Jim,

Could you explain to me the difference between Muller's 'Interlocking complexity', which in 1918 he predicted to be a result of evolution, and Behe's 'irreducible complexity' which he claims is an impossible result of evolution? As far as I can make out, Muller's and Behe's first definition are the same.

Presumably you think Muller was mistaken. Please identify where he was in error.

Nick: "If science isn’t knowledge then what is?"

Science is in the business of providing explanations for natural phenomena. If knowledge is understood as the collection of thoughts in our minds that correspond exactly to reality, then the explanations provided by science can never amount to knowledge. Science is too heavily reliant on inductive reasoning to ever claim that its theories have an exact correspondence to reality (surely, as a scientist-in-training, you're familiar with the problem of induction). When you say that you *know* how an IC biological system evolved, all you're really saying is that a Darwinian explanation for the evolution of that system has taken up residence in your mind and that you find the explanation persuasive. The scientific method doesn't empower you to say that you know the explanation to be true. With regard to explaining natural phenomena, science delivers theories. We can store those theories in our minds, making them a kind of knowledge (knowledge that is often useful). But whether those theories provide the kind of knowledge that amounts to an exact correspondence between our thoughts and reality is always an open question. When you say that you *know* how an irreducibly complex biological system evolved, you're speaking not as a scientist, but as a dogmatist. If you want to make a significant mark on science during your career, you'll need to shed yourself of the tendency to say "I know." Scientific progress depends on minds capable of thinking critically about scientific theories, not on minds that presume to "know."

Ravilyn: "Behe accepts that the earth is billions of years old and we humans and the chimpanzees share a common ancestor. Do you agree with him, since you defend him so vociferously?"

I think that the evidence that the earth is billions of years old is quite persuasive. But I think the evidence that humans and chimps share a common ancestor is much less persuasive. The evidence for common descent serves with equal facility as evidence for common design.

Richard: "Could you explain to me the difference between Muller’s ‘Interlocking complexity’, which in 1918 he predicted to be a result of evolution, and Behe’s ‘irreducible complexity’ which he claims is an impossible result of evolution? As far as I can make out, Muller’s and Behe’s first definition are the same. Presumably you think Muller was mistaken. Please identify where he was in error."

Behe doesn't claim that irreducible complexity is "an impossible result of evolution." He instead claims that the evolution of an IC system is, on logical grounds, provably inaccessible to a direct Darwinian pathway. He also claims that the evolution of an IC system via an indirect Darwinian pathway is highly improbable and lacking unambigouous empirical support.

Without getting involved in semantics, I'm willing to concede that Muller's definition and Behe's definition are referring to the same thing. That they disagree about the evolution of such systems by Darwinian means signifies nothing about the merits of their respective views. Simply pointing to scientists who disagree with Behe's argument from irreducible complexity doesn't show that Behe is wrong.

Jim, your first sentence is not actually correct. By that sentence, the statement, "Thor hits the earth with thunderbolts when he is angry" is science. It would be much more accurate to say, "Science is in the business of providing testable, evidence-based explanations (hypotheses) for natural phenomena, and then testing them. After extensive successful testing, these hypotheses may attain the level of certainty that we mean when we call something a theory." In other words, without objective, repeatable evidence, an explanation is not science.

In addition, you are parsing the term "know" in a very narrow sense, and one that to my devious mind looks pretty, well, devious. It appears that you want the level of certainty only given to religion and mathematics. If every time that I drop an apple, it falls, I can say that I "know" that it will fall, based on, yes, inference from previous tests. When a biologist who has researched a topic thoroughly says that they "know" the explanation for a particular phenomenon, they are saying that the evidence (not just for their own particular experiment but for all of the knowledge up to that point) leads to that conclusion. You say,

"whether those theories provide the kind of knowledge that amounts to an exact correspondence between our thoughts and reality is always an open question"

as if that is a weakness of science. On the contrary, that is the strength of science, that scientists are always open to new information and new conclusions. But after a while, the weight of evidence can lead us to say that we "know" the correct answer to a reasonable certainty, and any reasonable person will use the term "know" to mean in that sense. That doesn't mean that scientists are closed to new explanations, just that new explanations have to explain observations to a better level than the old theories before they will be accepted.

GvlGeologist: "Jim, your first sentence is not actually correct. By that sentence, the statement, 'Thor hits the earth with thunderbolts when he is angry' is science. It would be much more accurate to say, 'Science is in the business of providing testable, evidence-based explanations (hypotheses) for natural phenomena, and then testing them. After extensive successful testing, these hypotheses may attain the level of certainty that we mean when we call something a theory.'"

The only quarrel I have with what you've written is that the scientific method never delivers certainty with respect to scientific theories. Because of its heavy reliance on inductive reasoning, science can only deliver probabilities. Thus you should have written: "After extensive testing, we may become quite confident that a theory provides a satisfactory account of the phenomenon in question." Nick seemed to be saying that the scientific method allows us to say that we know that a theory is true, which is not the case.

GvlGeologist: "When a biologist who has researched a topic thoroughly says that they 'know' the explanation for a particular phenomenon, they are saying that the evidence (not just for their own particular experiment but for all of the knowledge up to that point) leads to that conclusion."

Actually, the word "know" has a much stronger meaning than you give it here. Nick wasn't claiming that he knows an explanation for the evolution of IC biological systems, he was instead claiming that he knows how those systems evolved. The former claim is justifiable; the latter is not, no matter how convincing someone might find the evidence for a Darwinian explanation of the origin of IC biological systems. When scientists tell the general public that they know how life attained its current state of diversity and complexity, they are going beyond what science empowers them to say.

GvlGeologist: "...the strength of science... (is) that scientists are always open to new information and new conclusions."

Ideally, that's the case. But as Darwinist blogs like Panda'sThumb and Pharyngula demonstrate beyond dispute, many (if not most) evolutionary biologists are not open to new information if the information leads to a conclusion of design. I think the chief service provided by such blogs is that they expose the regrettably dogmatic condition of evolutionary biology.

Y'know, I'm wondering about this 'irreducible complexity' thing, and why they bother with subsystems like eyes and immune systems and flagella.

The human body couldn't function without a heart, therefore the human body is irreducibly complex, therefore humans didn't evolve, QED.

Any argument explaining to the hard-of-thinking how this is wrong can also be applied to said subsystems.

Not 'half an eye', but 'an early eye-like development that conferred a survival/reproductive advantage'.

...and you know design is real because...?

Or is this where the 'the jury's still out' prevarication comes in? Do you really expect us to believe any level of detailed description and explanation will ever change your mind about evolution, Jim? Who's the real dogmatist?

So Jim -- I guess you don't believe in knowledge then, because all statements about reality are subject to those same constraints.

I hope you enjoy your relativist worldview...but by the way, I don't know that you exist, so why should I bother with this conversation?

If they are artificial rather than living, what relevance do they have to Darwinian evolution?

For the evolution of an IC biological system to be achieved via a direct Darwinian pathway, the function of the system must be maintained throughout its evolution.

By redefining IC in that way, Miller constructed a straw man that he could easily tear down.

Behe doesn’t claim that irreducible complexity is “an impossible result of evolution.”

In The Origin of Species Darwin stated 6: If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. A system which meets Darwin's criterion is one which exhibits irreducible complexity. By irreducible complexity I mean 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.

try figuring out what they mean by ‘genetic information’

Nick: "So Jim – I guess you don’t believe in knowledge then, because all statements about reality are subject to those same constraints."

I never said that I "don't believe in knowledge," Nick. I was drawing a distinction between things we can know and things we can only infer. With regard to the former, a person would be warranted to say (for example), "I know that Jefferson City is the capital of Missouri." But with respect to inferences (which is what the scientific method delivers, with varying degrees of empirical support), a person is entitled to say "I think," or "I believe," or "I am quite confident that this is true," but he is not empowered by the scientific method to say "I know." No matter how well an inference is empirically supported, the inference does not amount to certain knowledge because of the problem of induction. For example, a person would be warranted to say that he thinks that the transposon model of the evolution of the immmune system is a valid model; he would not be warranted in saying that he knows that the immune system evolved (or even that it could have evolved) in that way.

Nick: "I hope you enjoy your relativist worldview..."

I haven't been arguing in support of relativism. I think that truth is either absolute or it's not truth after all. But I have been arguing that we ought not to say "I know" when we're not warranted in saying it. That's why any scientist who says that he knows (for example) how the immune system evolved is speaking as a dogmatist, not as a scientist. A scientist would say that the transposon model is a plausible (to him) explanation for the evolution of the immune system, but that he could be wrong.

Richard: "Given that creationists/IDers routinely equate Darwin’s views with the modern theory of evolution, it seems to me that this is a clear statement that Behe feels that demonstrating irreducible complexity would invalidate the theory of evolution."

I think it's accurate to say that Behe regards irreducible complexity as something that is inaccessible to Darwinian mechanisms, but he doesn't think that IC completely invalidates Darwinian theory. The microevolutionary claims of the theory are well-supported and not in dispute. In my reading of their books, I've not encountered a single design theorist who thinks that Darwinism is an inadequate explanation for microevolution (such as adaptive changes in the beaks of finches, or bacterial adaption to antibiotics, or adaptive changes in the coloration of peppered moths, or the adaptation of insects to insecticides). Design theorists don't think that Darwinism is a completely false theory; they think that it's in incomplete theory - that it fails to adequately account for such things as irreducibly complex biological systems.

Jim -- observations are often wrong. Especially eyewitness observations. Things thought to be observations are changed all of the time in science, when new data comes in.

Explanations that are well-tested, confirmed by multiple independent data sources, etc., actually deserve more confidence. It is especially true that you can get the general big picture from the data with extremely high confidence without knowing every last detail. E.g. the earth is round, it goes around the sun, common ancestry is true, & the rearrangement capacity of the immune system is descended from a transposon.

The transposon-cooption model for the evolution of the immune system has met every standard of good and highly acceptable science. It constitutes "knowledge" as much as anything in science. Your hair-splitting over the term "knowledge" is occurring because you -- and your pet authorities like Behe -- have got nothing else with which to contradict the science on the evolution of the immune system.

I don't care if you believe the standard science. Just admit that you'd never heard of this piece of science before you began this thread, and that you naively bought into the uninformed claims in The Design of Life as if they were authoritative, and that there is actually a lot more to the science than the ID guys led you to believe.

No matter how well an inference is empirically supported, the inference does not amount to certain knowledge because of the problem of induction.

Flint: "...it’s pure wanking sophistry to argue that because we can’t know reality in any absolute sense, we are justified in fabricating anything that suits our preferences."

I agree. If you think that's the point I've been making, you've missed the point.

Flint: "...irreducible complexity was a prediction derived from evolutionary theory, as an unavoidable, inevitable result of evolutionary processes, many decades before Behe 'discovered' that evolution couldn’t do it."

A theory that posits the incremental assembly of complex biological systems via the mechanism of random mutations and natural selection does not predict irreducible complexity. You're bluffing.

Jim: Ravilyn: "Behe accepts that the earth is billions of years old and we humans and the chimpanzees share a common ancestor. Do you agree with him, since you defend him so vociferously?" I think that the evidence that the earth is billions of years old is quite persuasive. But I think the evidence that humans and chimps share a common ancestor is much less persuasive. The evidence for common descent serves with equal facility as evidence for common design.

Jim,

Keep in mind that the parts can change, too.

Consider what happens given a system that does have one or more parts that it could function without:

If the optional part improves the function of the system (benefit exceeds cost), there'd be nothing to unilaterally block spread of mutations that reduce or remove the organism's ability to do without that removable part.

If the optional part doesn't improve the function (benefit equal or below cost), there be nothing to unilaterally block spread of mutations that remove that part.

Given that, it seems to me that over long periods, there'd be a tendency to reduce the number of parts that the organism can do without, either by dropping them or becoming dependent on them.

Henry

A theory that posits the incremental assembly of complex biological systems via the mechanism of random mutations and natural selection does not predict irreducible complexity. You’re bluffing.

But I think the evidence that humans and chimps share a common ancestor is much less persuasive. The evidence for common descent serves with equal facility as evidence for common design.

Is "Jim" Michael Behe?

the scientific method never delivers certainty with respect to scientific theories. Because of its heavy reliance on inductive reasoning, science can only deliver probabilities.

Nick: "Yeah, it’s also true that IC does not even block direct evolutionary pathways, for example because of scaffolding, an example of which is the origin of the venus flytrap as described in Pete’s IC Demystified."

Pete was spinning a just-so story, as he candidly admitted when he said that the venus flytrap "might...have evolved" in the way related in his story. Since he offered no detailed, testable Darwinian pathway, his just-so story provides no confirmation of Darwinian theory. Imagination is not science.

fnxtr: "Do you really expect us to believe any level of detailed description and explanation will ever change your mind about evolution, Jim?"

What do you mean by "evolution"? I think the evidence is quite strong that evolution (meaning biological change over time, or descent with modification) has occurred. I also think the evidence that Darwinian mechanisms can produce microevolution (such as bacteria adapting to antibiotics, or insects adapting to insecticides, or adaptive changes in the beaks of finches, or adaptive changes in the coloration of peppered moths) is fairly persuasive. But I think the evidence that Darwinian mechanisms (primarily random genetic mutations and natural selection) fully account for macroevolution (such as the evolution of humans from fish [by way of amphibians, reptiles, and some unknown mammal], or the evolution of sexual reproduction from asexual reproduction, or the evolution of feathers from scales, or the evolution of color vision from a light-sensitive spot) is quite pathetic.

Darwinist Richard Dawkins aptly noted that the amount of information in even a single eukaryotic cell exceeds the information contained in a complete set of the Encyclopedia Britannica. Molecular geneticist Michael Denton wrote (in "Evolution: A Theory in Crisis") that "the genetic programmes of higher organisms (consist) of something close to a thousand million bits of information, equivalent to the sequence of letters in a small library of one thousand volumes, containing in encoded form countless thousands of intricate algorithms controlling, specifying and ordering the growth and development of billions and billions of cells into the form of a complex organism..." Like Denton, I think the Darwinian proposition that the vast biological "texts" that shape matter into living organisms were "composed" by random genetic mutations and "published" by natural selection is an affront to reason. This is not to say that Darwinism (in the macro sense) is false simply because it's preposterous, but it is to say that we ought to see some rather extraordinary corroborating evidence before we accept the theory. I'd be willing to accept the macroevolutionary claims of Darwinian theory if such evidence were available, but that evidence is most conspicuous by its absence. That's why Darwinists are constantly trying to make the evidence for microevolution serve as evidence for macroevolution. But aside from wishful speculation, there's no reason to think that the Darwinian mechanisms that cause bacteria to adapt to antibiotics are the same mechanisms that brought bacteria into existence in the first place, or that those mechanisms can cause bacteria to evolve into something other than bacteria (butterfies, perhaps).

fnstr: "Who’s the real dogmatist?"

Well, I've considered the claims of Darwinism and found some of those claims (i.e., the microevolutionary claims) to be fairly persuasive (the same is true of ID theorists, who are willing to accept the well-supported claims of Darwinism). But Darwinists tend to dismiss ID theory out-of-hand, characterizing it as religion, or as warmed-over creationism (which science can safely ignore). The question "Is the design that's so evident in living things real rather than apparent?" is a legitimate scientific question. By refusing to even consider it, Darwinists make it unambiguously clear that in their hands, evolutionary biology has devolved into dogmatism.

Nick: "Jim – observations are often wrong. Especially eyewitness observations. Things thought to be observations are changed all of the time in science, when new data comes in. Explanations that are well-tested, confirmed by multiple independent data sources, etc., actually deserve more confidence."

Since explanations are tested by making observations, how can they deserve more confidence than the observations on which they're based? I submit that we are justified in saying that we know that Jefferson City is the capital of Missouri (we can verify that claim of knowledge by visiting the place), but we are not justified in saying that we know that the origin of the immune system can be attributed to Darwinian mechanisms (observing that historical event is impossible).

Nick: "The transposon-cooption model for the evolution of the immune system has met every standard of good and highly acceptable science."

No doubt it does, but since it doesn't actually detail any Darwinian pathways leading to the immune system, it doesn't actually corroborate the hypothesis that the system arose via Darwinian mechanisms. I saw nothing in the article on the transposon model showing the original precursor from which the immune system allegedly evolved, nor did I see any intermediate precursors whose functions were identified and whose emergence could be credibly attributed to random genetic mutations. As Behe has aptly observed, the kind of data provided by the transposon model (i.e., sequence data, comparison of protein sequences, and comparison of gene sequences) "can't speak to the question of whether random mutation and natural selection produced the complex systems that we're talking about."

Nick: "I don’t care if you believe the standard science. Just admit that you’d never heard of this piece of science before you began this thread, and that you naively bought into the uninformed claims in The Design of Life as if they were authoritative, and that there is actually a lot more to the science than the ID guys led you to believe."

Actually, when I go to the references recommended to me by Darwinists, I find that "the ID guys" got it right more often than not.

Ravilyn: "Well, obviously we evilutionists have no credibility in your eyes, but you seem to trust Behe, the guy with a real PhD a real biologist who contradicts us evilutionists. And he agrees that chimps and humans had a common ancestor. It is this guy’s ideas about Irreducible Complexity you have put so much store on. Why are you fighting us here? Why don’t you and Behe trash it out and come to a conclusion?"

I should think you could answer this question for yourself. I don't need to agree with Behe's thoughts on common descent to find his argument from irreducible complexity persuasive. Common descent is merely descriptive, not explanatory. No matter how persuasive the evidence might be for common descent, that evidence tells us nothing about the cause(s) of common descent.

Ravilyn: "These IDiots cant even agree on these two simple basic questions."

And now the name-calling starts. I'm surprised it's taken this long.

Henry: "Keep in mind that the parts can change, too. Consider what happens given a system that does have one or more parts that it could function without: If the optional part improves the function of the system (benefit exceeds cost), there’d be nothing to unilaterally block spread of mutations that reduce or remove the organism’s ability to do without that removable part. If the optional part doesn’t improve the function (benefit equal or below cost), there be nothing to unilaterally block spread of mutations that remove that part.
Given that, it seems to me that over long periods, there’d be a tendency to reduce the number of parts that the organism can do without, either by dropping them or becoming dependent on them."

Perhaps mutation and selection could remove "optional parts," Henry, but you haven't explained the origin of the system with the "optional parts," nor have you said what that system might have been. Wishful speculation is free, but it doesn't serve to confirm the claim that Darwinian mechanisms can produce irreducibly complex biological systems.

So, then, Jim, can you point out to us the research and experiments Behe did in order to come to his conclusion about "Irreducible Complexity"?

Can you explain to us exactly how Behe arrived at the conclusion that the blood-clotting cascade is irreducibly complex when it utilizes the same proteases used in food digestion? Or, can you explain to us why Behe came to the conclusion that the only function of the antibody is to mark a cell for phagocytosis, even though antibodies have been experimentally demonstrated to be able to perform other functions, including initiating apoptosis, causing antigens to agglutinate, binding to a pathogen in order to impair its metabolism, binding to an antigen in order to inactivate it, marking cells to be attacked by natural killer cells (which kill targeted cells by initiating apoptosis), initiating the "membrane attack complex" which causes bacterial cells to lyse?

Richard: "Scientists do not bluff. That is what Creationists/IDers do. (Irreducible complexity) was predicted to be a consequence of evolution by Hermann Muller in 1918 (Genetic variability, twin hybrids and constant hybrids, in a case of balanced lethal factors. Genetics 3: 422-499)."

When Muller spoke of interlocking complexity, he was referring to the functional relatedness of the parts that make up an entire organism, which he referred to as "a complicated machine." No one denies that the liver (for example) has a functional relationship (or interlocking complexity) with the other organs in the human body, or that the human body would soon cease to function if the liver were removed. Muller's "prediction" was nothing more than a prediction that Darwinism had always made, namely, that organisms would tend to become more complex over time as they gradually acquired "parts" that facilitated their survivability. Some of those "parts" might become essential to the organism's survival, but others would be inessential enhancements (or perhaps even "vestigial" organs). These "parts" might develop interlocking complexity, but only removal of the essential parts would lead to the death of the organism (i.e., the functional failure of the "complicated machine").

Behe's concept of irreducible complexity, by contrast, deals with the functional complexity of individual biological systems, such as the immune system, or the vertebrate blood-clotting cascade. His argument is that because those systems cannot be reduced without destroying their functions, there could not be any direct Darwinian pathways to their origin, and that any indirect Darwinian pathways to their origin are so improbable that we ought to see some rather compelling evidence before we attribute them to Darwinian mechanisms - evidence that is conspicuous by its absence. Darwinian theory does not predict that the complex biological systems that are components of living organisms ought to be irreducibly complex. Neither did Muller. He simply predicted that Darwinian evolution could produce systems that become essential to an organism's survival, and that those systems could develop functional relatedness (or interlocking complexity) with other systems in the organism.

Peter: "Is 'Jim' Michael Behe?"

Nope. I'm a retired airline pilot. My formal education was in civil engineering (B.S., cum laude, University of Missouri). From both my education and my career, I gained a profound respect for science, which is why I object so strenuously to the dogmatism of evolutionary biology.

Jim: "The scientific method never delivers certainty with respect to scientific theories. Because of its heavy reliance on inductive reasoning, science can only deliver probabilities.

Torbjörn: "Wrong, wrong and wrong."

So you say, but saying it doesn't make it so.

Torbjörn: "You may use induction to pose theories, but they are tested on their predictions. In no way can you describe a reliance on rejection of falsehoods as a reliance on induction."

How do we test a scientific theory? We make observations (in the field, or in the lab). If those specific observations are, in the main, consistent with a theory, then we generalize that the theory has been "confirmed." That is the essence of induction, a way of reasoning that delivers confidence (or probabilities), not certainty.

Torbjörn: "Your idea of probabilities is confused, and its application to observations more so. Probabilities are observations on ensembles and populations, and is precisely what quantifies certainty as regards observations and theories."

I'd say that your understanding of my point is confused. Certainty need not be quantified; certainty is 100%. But scientists' confidence that a theory is valid does need to be quantified, if not with a specific number ("We are 90% sure that this theory is valid"), at least in general terms ("We are quite confident that this theory is vaid"). The scientific method delivers confidence, not certainty.

Stanton: "So, then, Jim, can you point out to us the research and experiments Behe did in order to come to his conclusion about 'Irreducible Complexity'?"

Read his books, Stanton. I don't have time to do your homework for you.

Many of us have read his books, Jimmy. He has done NO experiments whatsoever to support his claims.

It is a severe indictment of science education in general -- not just creationists -- that people think writing a book constitutes "research and experimentation". Especially one as dishonest, sloppy, and just plain confused as Behe's.

Jim, "research" in science doesn't just mean "reading the work of other, actual, scientists and blathering ignorantly about them in print."

REAL scientists conduct research by performing experiments based on their hypotheses. They go to the bench and do some honest-to-god hands-on work.

This is what biologists have done with evolution for 150+ years.

This is what ID'ers have flatly refused to do in the last two decades.

It doesn't take a scientist to see the severe disparity in results.

What is it with engineers and ID?

"To a man with an axe, everything looks like a tree."

Since he offered no detailed, testable Darwinian pathway, his just-so story provides no confirmation of Darwinian theory.

What do you mean by “evolution”?

Like Denton, I think the Darwinian proposition that the vast biological “texts” that shape matter into living organisms were “composed” by random genetic mutations and “published” by natural selection is an affront to reason.

Jim: Stanton: "So, then, Jim, can you point out to us the research and experiments Behe did in order to come to his conclusion about 'Irreducible Complexity'?" Read his books, Stanton. I don't have time to do your homework for you.

So you say, but saying it doesn’t make it so.

If those specific observations are, in the main, consistent with a theory, then we generalize that the theory has been “confirmed.”

a way of reasoning that delivers confidence (or probabilities), not certainty.

Certainty need not be quantified; certainty is 100%.

minimalist: "REAL scientists conduct research by performing experiments based on their hypotheses. They go to the bench and do some honest-to-god hands-on work. This is what biologists have done with evolution for 150+ years. This is what ID’ers have flatly refused to do in the last two decades."

If ID theorists refuse to do any research, then why did microbiologist/design theorist Scott Minnich do genetic knock-out experiments that demonstrated the irreducibility of the bacterial flagellum? Why do Dembski and Marks do theoretical research in evolutionary informatics? Why has Wells done design-theoretic research on centrioles? Why did Behe and Snokes do research testing the evolution by gene duplication of protein features that require multiple amino acid residues? I think the research done by design theorists would receive wider recognition if they weren't caught on the horns of a dilemma: Mainstream scientific journals won't (for the most part) publish the papers of design theorists because ID is "not science." How do we know that ID is "not science"? Because the papers of design theorists don't get published in mainstream scientific journals. Catch 22.

But since you brought it up, where is the experimental evidence showing that Darwinian mechanisms turned the frog into a prince?

then why did microbiologist/design theorist Scott Minnich do genetic knock-out experiments that demonstrated the irreducibility of the bacterial flagellum?

Mainstream scientific journals won’t (for the most part) publish the papers of design theorists because ID is “not science.” How do we know that ID is “not science”? Because the papers of design theorists don’t get published in mainstream scientific journals.

Why do Dembski and Marks do theoretical research in evolutionary informatics? Why has Wells done design-theoretic research on centrioles? Why did Behe and Snokes do research testing the evolution by gene duplication of protein features that require multiple amino acid residues?

Torbjörn: "The intention is to arrive at a possible pathway derived from the theory to test the prediction that such pathways exist. As it passes the test it is both a testable prediction and a confirmation."

Any evolutionary pathway could be described as a "possible pathway." Simply imagining a Darwinian pathway constitutes neither a test nor a confirmation of Darwinian theory. If imagining possible pathways is all that it takes to confirm Darwinism, then Darwinism is effectively unfalsifiable, which - by Popper's criterion of potential falsifiability - makes Darwinism unscientific.

Torbjörn: "You get it backwards, the information in the 'texts' (fixated allele frequencies) is mainly composed by natural selection as a response to fitness pressures as the populations genome learns about its current environment."

Natural selection can act only on that which already exists. It can't compose (or bring into being) biological information. Indeed, natural selection can't compose or create anything. It can only "publish" (or spread throughout a population's genome) what random mutations "compose." And as Darwinists constantly remind us, random mutations do not do their work in response to any environmental pressures; their work in "composition" is unresponsive to anything but sheer chance. If they "compose" a useful biological text (something that is highly unlikely), they do so by luck.

Torbjörn: "...selection has to sort out the information (narrow the probability distributions)."

Yes, but selection doesn't compose the information that it sorts out, which is the point. Mutations are the only creative part of the Darwinian mechanism of mutation and selection. If that mechanism "composes" novel biological information that leads to a novel adaptation in an organism, it does so by sheer chance. After the accidental creativity of random mutations occurs (assuming that mutations possess such creativity, a highly dubious proposition), natural selection then acts with law-like regularity to "publish" (or perpetuate) the work of random mutations throughout the gene pool. But believing that the blind Darwinian mechanism generated the vast amounts of biological information in complex organisms is like believing that a blind mechanism could write the novel "War and Peace."

Torbjörn: "Btw, speciation...is tested by the fossil record and some cases of direct observation. What is your specific problem with that evidence?"

The fossil record shows the emergence of different species throughout life's history; it doesn't show that the speciation was caused by Darwinian mechanisms. Additionally, the only speciation that has actually been observed is the hybridization of some flowering plants produced by polyploidy (an increase in the number of chromosomes, as you may know). But as evolutionary biologist Douglas Futuyma observed, polyploidy "does not confer major new morphological characteristics...(and) does not cause the evolution of new genera." Also, polyploidy can't produce the splitting and diverging of species that the branching-tree pattern of life posited by Darwinism requires. Most of what you call observed instances of speciation are actually analyses of existing species to test how they might have originated. Those analyses are not the same as actual observation. Contrary to your claim, evolutionary biologist Lynn Margulis (who is no fan of ID) wrote: "Speciation, whether in the remote Galapagos, in the laboratory cages of the drosophilosophers, or in the crowded sediments of the paleontologists, still has never been directly traced."

Jim,

Re "I think the evidence is quite strong that evolution (meaning biological change over time, or descent with modification) has occurred."

Re "That’s why Darwinists are constantly trying to make the evidence for microevolution serve as evidence for macroevolution."

Given the first of those two sentences of yours, I'm not sure why the second one is of concern. Macroevolution is simply change over time, just a lot of it over a long time.

Re "But Darwinists tend to dismiss ID theory out-of-hand, characterizing it as religion, or as warmed-over creationism (which science can safely ignore)."

No, evolutionary biologists reject ID because nobody is as yet used the concept of ID to explain anything. Come up with a consistently observed pattern in the evidence, such that it could be a logical consequence of life (or some aspect of it) being deliberately engineered, and scientists would be quite happy to research the possibilities. The reason for the rejection of ID is that as yet nobody has described a pattern that does that.

Re "Since explanations are tested by making observations, how can they deserve more confidence than the observations on which they’re based?"

By having the observations repeated and verified by lots of different observers who come from a variety of nations, from a variety of religions (or none), and from a variety of cultures. Observations that can't be repeated aren't given much confidence. (for example, consider the cold fusion hypothesis.)

Re "Perhaps mutation and selection could remove “optional parts,” Henry, but you haven’t explained the origin of the system with the “optional parts,” nor have you said what that system might have been. Wishful speculation is free, but it doesn’t serve to confirm the claim that Darwinian mechanisms can produce irreducibly complex biological systems."

The first part of that is commonly referred to as "moving the goalposts".

As for "wishful speculation" - how and why do people think biologists wish for biological traits to have arisen the way the theory implies? Do you think I want to be distantly related to slime mold or digger wasps or tapeworms? I don't. I don't know of any reason to expect anybody else to, either (although one never really knows what other people might want, I guess).

They conclude it because (1) the possibility is implied by current knowledge of biology and genetics, (2) it doesn't require presuming any totally unknown processes (actually I guess that's a paraphrase of (1), (3) nobody's described evidence of any other process that seems likely to produce the effects that are explained by the current theory (such as nested hierarchy, later species being slightly modified copies of predecessors, occasional diversification of earlier species into many later species, general lack of convergence of non-adaptive traits, geographic grouping of related species, lack of apparently copying of features from one clade into isolated species in other clades).

Btw, the conclusion of common ancestry is not directly dependent on the evidence that accumulation of various mutations, plus recombination, plus various selection effects, caused it. But, the evidence is consistent with both of those conclusions and there's lots of ways in which the relevant evidence could have contradicted either or both of them but hasn't even after more than a century of research. That last is a large part of why scientists accept the current theory, maybe the biggest part. Any cause of new species for which the current theory isn't at least a good approximation, would be very unlikely to repeatedly and consistently produce evidence that continues to fit the current theory.

Re "Darwinian theory does not predict that the complex biological systems that are components of living organisms ought to be irreducibly complex."

How would evolutionary biology avoid expecting evolution to produce systems that would break if one part was removed? To avoid it, there would have to be something that would always prevent unnecessary (or not particularly useful) parts from being dropped, or useful parts becoming necessary as the organisms become dependent on them.

Henry

And why do you think that anyone’s sense of “reason”, and your’s in particular, is applicable in scientific validation? Science is decidedly not common sense, any scientist knows that, that is one major reason why it is so hard.

Jim: "If those specific observations are, in the main, consistent with a theory, then we generalize that the theory has been 'confirmed.'"

Torbjörn: "No. You missed the obvious step. If the theory fails an important test it is rejected. A modified or entirely new theory must explain the new evidence."

I wasn't talking about rejecting theories; I was talking about confirming them. Confirmation of a theory requires positive evidence for the theory, meaning that it must pass the important tests with great consistency.

Torbjörn: "Combining testing with methods such as parsimony sharpens this considerably to pick a preferred theory with (in principle) quantifiable remaining uncertainty."

To say that a theory should be preferred on the basis of "quantifiable remaining uncertainty" is to say that the scientific method can give us confidence that the theory is valid, but it can't provide us with certainty that the theory is valid. That's what I said (although in different words).

Torbjörn: "There is no philosophical induction involved (except when proposing theories, which induction excels in), only empirical testing and learning."

I wasn't arguing that "philosophical induction" is involved in confirming scientific theories. I was instead arguing that empirical testing and observations provide specific data that either support or fail to support a theory (it is rare that a theory never encounters any recalcitrant or contradictory evidence). If the collection of specific data is, in the main, consistent with the theory, then we inductively generalize to say that the theory has been confidently "confirmed."

Jim: "...a way of reasoning that delivers confidence (or probabilities), not certainty."

Torbjörn: "is a huge misconstruction."

No, it's not. Inductive reasoning (or induction), which you conveniently clipped in (mis)quoting me, simply cannot deliver certainty in the way that deductive reasoning (or deduction) can. This is not a scientific point, it's a logical point. Because science is so heavily reliant on induction (reasoning from specific data to generally applicable theories), it can deliver confidence that theories are valid, but it can't deliver certainty that theories are valid. While you think you've been disagreeing with me on this point, you've actually been agreeing with me. As you put it, a scientific theory is accepted when "remaining uncertainty" is low. That's essentially just another way of saying the same thing that I've been saying. The bottom line is that the scientific method never delivers ironclad proof or certain confirmation of any of its theories. Thus it never empowers us to say that we *know* that a theory is true; we can only say that we are quite confident that the theory is true. The theory remains open to disconfirmation if new evidence casts doubt on its validity. If this weren't true, it wouldn't be a genuinely scientific theory.

I think that in your haste to disagree with anything I might say, you missed the point of what I was saying about what the scientific method can deliver.

Torbjörn: "Todays amphibians aren’t the evolutionary ancestors of humans. Can you at least put respectable questions?"

I neither claimed nor suggested that today's amphibians are the evolutionary ancestors of humans. Nonetheless, according to Darwinism, if we could trace the human family tree into the distant past, we'd find amphibians among our ancestors. Can't you make at least a token effort to understand the things I write?

Torbjörn: "The interlocking complexity of the bacterial flagellum isn’t a new and disputed subject."

To remind you, this thread was kicked off by an article in New Scientist averring that "(t)he evolutionary events linking flagella and T3SSs are not clear, but the homology between them is a devastating blow to the claim of irreducible complexity." What you say isn't disputed clearly is.

Torbjörn: "If evolution predicts interlocking complexity (Muller, 1930s IIRC), how can it be a unique and testable prediction from ID? The answer is that it can’t."

It can if Muller's "interlocking complexity" and Behe's "irreducible complexity" are referring to different things, which they are. Darwinism may predict that organisms can acquire systems that develop functional interdependence (or "interlocking complexity"), but it doesn't predict molecular systems (such as the bacterial flagellum) that are irreducibly complex.

Torbjörn: "...the papers (of ID theorists), as it were, can’t stand up to scientific scrutiny in the form of peer review."

Darwin never submitted any of his work to the process of peer review before going public with his theories. If peer review is the sine qua non of science, then whatever Darwin thought he was doing, it wasn't science.

minimalist: "(ID theorists) have to resort to made-up proteins and models they can abuse to cook the books."

The proteins in the molecular biological systems that are the primary focus of ID theory are hardly "made-up." But setting that aside, why is the construction of models a suspect scientific procedure in your eyes? After all, Darwinists construct models with great regularity in attempts to validate the claims they make about the creative powers of Darwinian mechanisms. For example, Nick has tried to glaze our eyes over with references to the transposon model, a model that supposedly demonstrates how Darwinian mechanisms might have brought the immune system into being. Were the transposon modelers simply cooking the books? (My answer would be "Yes." I can't find anything in the transposon model that clearly shows how Darwinian mechanisms could have brought the immune system into being. I think that non-scientists like me and scientists who aren't expert in biology are supposed to simply be bowled over by biological technicalities and jargon that give the illusion that the transposon model explains the origin of the immune system. The transposon model does nothing to disabuse me of my belief that the case for the macroevolutionary claims of Darwinism is primarily a sustained bluff.)

Henry: "Macroevolution is simply change over time, just a lot of it over a long time."

Darwinists have persuasively shown that Darwinian mechanisms can produce minor adaptive changes (or microevolution) in organisms, such as the adaptation of bacteria to antibiotics. But what scientific or logical grounds warrant extrapolating from microevolution to the macroevolutionary claim that those same mechanisms can generate biological novelty, such as the origin of bacteria in the first place, or the evolution of bacteria into something other than bacteria (horseflies, perhaps)?

Henry: "...evolutionary biologists reject ID because nobody is as yet used the concept of ID to explain anything."

Needless to say, design theorists would dispute your assertion.

Henry: "Come up with a consistently observed pattern in the evidence, such that it could be a logical consequence of life (or some aspect of it) being deliberately engineered, and scientists would be quite happy to research the possibilities."

You're essentially saying that the case for design must be made before scientists should consider design. If science proceeded on such a basis, science would go nowhere.

Jim: "Perhaps mutation and selection could remove 'optional parts,' Henry, but you haven’t explained the origin of the system with the 'optional parts,' nor have you said what that system might have been. Wishful speculation is free, but it doesn’t serve to confirm the claim that Darwinian mechanisms can produce irreducibly complex biological systems."

Henry: "The first part of that is commonly referred to as 'moving the goalposts'."

Your part is known as avoiding the question.

Henry: "As for 'wishful speculation' - how and why do people think biologists wish for biological traits to have arisen the way the theory implies?"

There are many reasons why people (including biologists) would wish that life is a wholly material phenomenon. An a priori commitment to materialism is one of those reasons (a commitment that Darwinist Richard Lewontin has candidly admitted most evolutionary biologists hold). A desire to be free from ultimate moral accountability is another reason people are attracted to the wholly materialistic account of life offered by Darwinism. As the late Julian Huxley, once a leader among Darwinists, said in a televised interview: "The reason we accepted Darwinism even without proof, is because we didn't want God to interfere with our sexual mores." There's no moral accountability in Darwinism, and a lot of people like it that way.

Henry: "How would evolutionary biology avoid expecting evolution to produce systems that would break if one part was removed?"

In the same way that evolutionary biology expects genomes to acquire "junk" DNA (an expectation that is increasingly being shown to be wrong). Darwinism predicts biological systems that are cobbled together (i.e., systems with dispensable parts), not systems that are tightly integrated and irreducibly complex.

You’re essentially saying that the case for design must be made before scientists should consider design. If science proceeded on such a basis, science would go nowhere.

Darwinism predicts biological systems that are cobbled together (i.e., systems with dispensable parts), not systems that are tightly integrated and irreducibly complex.

The proteins in the molecular biological systems that are the primary focus of ID theory are hardly “made-up.”

(My answer would be “Yes.” I can’t find anything in the transposon model that clearly shows how Darwinian mechanisms could have brought the immune system into being. I think that non-scientists like me and scientists who aren’t expert in biology are supposed to simply be bowled over by biological technicalities and jargon that give the illusion that the transposon model explains the origin of the immune system. The transposon model does nothing to disabuse me of my belief that the case for the macroevolutionary claims of Darwinism is primarily a sustained bluff.)

So, then, Jim, please explain to us how Behe's statement/claim that the vertebrate immune system is irreducibly complex (despite the fact that echinoderms have a very similar, albeit cruder immune system) will help scientists and doctors study and treat the human immune system.

Jim: "You’re essentially saying that the case for design must be made before scientists should consider design. If science proceeded on such a basis, science would go nowhere."

Flint: "Here we have, once again, the conviction that if one does not START by ASSUMING one’s conclusions, how can one ever reach them?"

There's essentially no connection between what I said and the conviction you falsely attribute to me. I neither claimed nor suggested that any scientific line of inquiry should begin by assuming its conclusion. That's pretty much what Henry said, which is why I took issue with him.

Flint: "The idea that scientists should consider what the evidence suggests, rather than consider the evidence in light of foregone conclusions, is simply outside the religious mental model."

This claim is rich with irony. Darwinists routinely interpret the evidence (such as the fossil record) in light of their foregone conclusion that Darwinian evolution fully accounts for life's diversity and complexity. There is, for example, no reason to label a particular fossil specimen an intermediate, transitional form between its presumed evolutionary ancestors (e.g., dinosaurs) and its presumed evolutionary descendants (e.g., birds) unless the evolution from dinosaurs to birds is presupposed. Darwinian theory justifies the identification of intermediate, transitional forms, which in turn justifies Darwinism. The circularity in reasoning is palpable.

Flint: "...evolutionary theory itself predicted, as an inevitable necessity, the development of tightly integreted irreducibly complex structures. And this was pointed out 90 years ago!"

Here's what Muller wrote 90 years ago:

"(I)t is likely that lethals are really among the commonest
forms of mutants, but they would be discovered much more readily if they were dominant in regard to some visible character than if they were completely recessive, and this would cause the proportion of lethals among the dominant mutant factors to appear to be excessively high, when compared with the proportion among the recessives. Most present-day animals are the result of a long process of evolution, in which at least thousands of mutations must have taken place. Each new mutant in turn must have derived its survival value from the effect which it produced upon the 'reaction system' that had been brought into being
by the many previously formed factors in cooperation; thus a complicated machine was gradually built up whose effective working was dependent upon the interlocking action of very numerous different elementary parts or factors, and many of the characters and factors which, when new, were originally merely an asset finally became necessary because other necessary characters and factors had subsequently become
changed so as to be dependent on the former. It must result, in consequence, that a dropping out of, or even a slight change in any one of these parts is very likely to disturb fatally the whole machinery; for this reason we should expect very many, if not most, mutations to result in
lethal factors, and of the rest, the majority should be 'semi-lethal' or at least disadvantageous in the struggle for life, and likely to set wrong any delicately balanced system, such as the reproductive system. Although THIS CONCLUSION (emphasis added) had suggested itself to the writer in 1912 it would manifestly have been very difficult to obtain experimental evidence for it, not only because of the great rarity with which mutations of any sort occur, but more especially because the detection of a lethal mutation, after. it has occurred, requires special breeding tests of the particular flies containing the lethal factor."

Muller was arguing that mutations tend to be lethal because the "elementary parts" of organisms exhibit "interlocking complexity," which he assumed to be the result of Darwinian evolution. Please note, however, that Muller's interlocking complexity refers to the functional interdependence of the parts of the whole organism. If his interlocking complexity is exactly the same as Behe's irreducible complexity, then there should be a clearly identifiable function (not functions) of the organism that is lost if one of those parts is not present in the organism. So, what is the specific function performed by, say, a dog? To say that the function of a dog is to live doesn't provide the kind of functional specificity needed to also say that a dog is an irreducibly complex biological system. Irreducible complexity is defined by reference to the specific function of a biological system; Muller's interlocking complexity is defined by reference to the functional interdependence of an organism's systems. The two are not the same. Darwinism might predict the latter, but it doesn't predict the former.

It should also be noted that the point Muller was making was a conclusion, not a prediction. Hopefully I don't need to point out the difference between the two.

minimalist: "Your entire argument, then, boils down to 'I don’t understand it, so I’ll just go with what makes me feel better.'"

It's no doubt the case that the technical details of the transposon model are fully understandable only to trained biologists, but the fundamental flaw in the model is that it doesn't demonstrate Darwinian evolution; it simply assumes it.
While wading through the eye-glazing technicalities of the transposon model, any alert reader should be able see that the model doesn't actually show what it supposedly shows: that random mutations and natural selection brought the immune system into being step by tiny Darwinian step. The model simply hangs transposons on Darwinian assumptions without actually showing a Darwinian pathway that the evolution of the immune system might have followed.

Jim: The model simply hangs transposons on Darwinian assumptions without actually showing a Darwinian pathway that the evolution of the immune system might have followed.

Then the onus is on you, Jim, to demonstrate exactly how Intelligent Design “theory” can explain this particular phenomenon better than “Darwinian” explanations.

Henry: “…evolutionary biologists reject ID because nobody is as yet used the concept of ID to explain anything.” Needless to say, design theorists would dispute your assertion.

Henry: “Come up with a consistently observed pattern in the evidence, such that it could be a logical consequence of life (or some aspect of it) being deliberately engineered, and scientists would be quite happy to research the possibilities.” You’re essentially saying that the case for design must be made before scientists should consider design. If science proceeded on such a basis, science would go nowhere.

Jim,

Is this to be a version of the "show me every single fossil intermediate in a smooth transition or evolution is false?" type of argument?

Man, look at those goalposts fly!

Behe claimed that the immune system could not have evolved, that it was irreducible -- take one part away and it ceases to function.

Scientists showed that not only is the immune system reducible, but even the proposed precursor could act, at a molecular level, in ways identical to the 'modern' immune system!

The same thing happened with Behe's claims about the bacterial flagellum. He claimed that you could not have a bacterial flagellum without, what, 40-odd components? Only to be proven wrong, time and again, as species were discovered with far fewer components.

In short, as my entire point has been all along (despite your attempt to move the goalposts), is: which model actually advanced the state of knowledge? Which "side" actually rolled up its sleeves and did the dirty work of testing its model?

Science says, "Here's what we know. How can we test it?"

Behe says, "Here's what we know. We shall go no further! HERE THERE BE DRAGONS"

Which, in principle, is the more fruitful approach, do you think?

Darwinists routinely interpret the evidence (such as the fossil record) in light of their foregone conclusion that Darwinian evolution fully accounts for life’s diversity and complexity.

Henry: "Then please describe the pattern of observations that they’ve explained as logical consequence of their premise that life was in some way deliberately engineered."

In a nutshell, ID theorists argue that biological systems that exhibit specified complexity justify design inferences. Examples of such systems include the bacterial flagellum, the blood-clotting cascade, the immune system, and other systems that are irreducibly complex. Other examples include the biomacromolecules that carry and express the complex specified information that shapes the chemicals of life into living organisms.

Jim: "You’re essentially saying that the case for design must be made before scientists should consider design. If science proceeded on such a basis, science would go nowhere."

Henry: "Huh? Of course a scientist has to make a case for a hypothesis before other scientists will accept it."

I wasn't talking about a hypothesis (or theory) being accepted, or confirmed (to the extent that science ever confirms its hypotheses). I was talking about considering a hypothesis (meaning that the hypothesis will receive scientific scrutiny). The case for a hypothesis is closed (if it is closed at all) after extensive research warrants its acceptance, not before. You seemed to be saying that a hypothesis must be shown to be worthy of acceptance before any research begins. Darwin's hypothesis (that random variations and natural selection are the engine of evolution) was widely rejected by his peers, but it has since won widespread acceptance among biologists (which has no bearing on its validity). To say that a hypothesis has been accepted is to say that the case for the hypothesis has been credibly made in the eyes of those who accept it.

In a nutshell, ID theorists argue that biological systems that exhibit specified complexity justify design inferences. Examples of such systems include [...]

You seemed to be saying that a hypothesis must be shown to be worthy of acceptance before any research begins.

Darwinists routinely interpret the evidence (such as the fossil record) in light of their foregone conclusion that Darwinian evolution fully accounts for life’s diversity and complexity.

minimalist: "Is this to be a version of the 'show me every single fossil intermediate in a smooth transition or evolution is false?' type of argument?"

No. The absence of evidence neither confirms nor disconfirms a theory, but the conspicuous absence of any unambiguous intermediate, transitional forms is (as Darwin candidly admitted) a serious problem for Darwinism. The continuum of life posited by Darwinism is not seen in the fossil record, which is instead characterized by (in Gould's words) sudden appearance and stasis. The fossil record argues against Darwinian gradualism more persuasively than it argues for it, which is why Gould and Eldredge developed their theory of punctuated equilibrium. Punk eek is an ingenious solution to the problem with the fossils, but since punk eek also lacks confirmation, it primarily demonstrates how wonderfully adept Darwinists are in rationalizing the failures of their theory. The problem may be with the fossils, but skeptics are entitled to think that the problem is with the theory.

minimalist: "Science says, 'Here’s what we know. How can we test it?' Behe says, 'Here’s what we know. We shall go no further! HERE THERE BE DRAGONS.' Which, in principle, is the more fruitful approach, do you think?"

The scientific approach. The approach you attribute to Behe is bogus. The design hypothesis is every bit as testable and potentially falsifiable as Darwinism. Indeed, it would be much easier to falsify design than it would be to falsify Darwinism. If it could be credibly shown that a biological system that design theory attributes to design was the product of unintelligent material causes, then design theory would be refuted on the grounds that one does not invoke intelligent causes when unintelligent material causes will do. But Darwinists insist that their theory cannot be falsified until every conceivable Darwinian pathway has been shown to be incapable of leading to an irreducibly complex biological system. A demonstration of that kind would require an exhaustive search of all conceptual possibilities, something that can't be done. For every objection to the presumed creative powers of Darwinian mechanisms, Darwinists have a just-so story to fill the gap. Raise a new objection and a new story will be forthcoming. Since the just-so stories never end, Darwinism can't be falsified.

Flint: "It doesn’t take a whole lot of comprehension of science (but it takes *enough*, which is perhaps the problem?) to understand the relationship between theory and evidence."

If the interpretation of the evidence is informed by a theory, then the interpretation of the evidence doesn't serve to confirm the theory. There must be a way to interpret the evidence independently of the theory to avoid reasoning in a circle. If independent interpretations of the evidence can be made, and if those interpretations can be shown to meet the predictions and hypotheses of the theory, then the evidence serves to confirm the theory. But if a theory is used to justify an interpretation of the evidence, then the interpretation of the evidence doesn't justify the theory. For example, if archaeopteryx is interpreted to be an intermediate, transitional form between dinosaurs and birds simply because Darwinism needs (or predicts) intermediate, transitional forms between dinosaurs and birds (and archaeopteryx is a promising candidate), then the labeling of archaeopteryx as an intermediate, transitional form does nothing to confirm Darwinism. That would be a situation where the theory justifies the interpretation, which in turn justifies the theory. Such circularity in reasoning can't confirm anything.

Jim: "Darwinists routinely interpret the evidence (such as the fossil record) in light of their foregone conclusion that Darwinian evolution fully accounts for life’s diversity and complexity."

Flint: "I’ll deal with one deliberate misrepresentation at a time, to avoid the Gish Gallop of mendacity Jim is trying to palm off on us."

I'm deliberating stating things that I believe to be true. I could be wrong, but I'm not lying and I rather resent the accusation that I am. I've noticed that one of the constants in the evo/ID debate is that anyone who argues for ID will almost invariably be accused of lying if he says something that the evolution side of the debate regards as wrong. PZ Myers has developed this supercilious presumption of inerrancy to an art form, which is why I find him so easy to ignore.

By the way, Gish is a creationist, not an ID proponent. Many, if not most, creationists are either lukewarm towards ID theory or actually oppose it because the theory makes no attempt to validate the Genesis account of creation.

So, then, Jim, please explain how does Intelligent Design "theory" present a superior description and explanation of the fossil record than does "Darwinism"?

Also, you have not explained how claiming that the vertebrate immune system is "irreducibly complex" helps scientists and doctors to study it. In fact, you have not explained how "irreducible complexity" is more helpful to Biology, Medicine or Agriculture than "descent with modification." Why is that?

So, then, Jim, please explain how does Intelligent Design “theory” present a superior description and explanation of the fossil record than does “Darwinism”?

No. The absence of evidence neither confirms nor disconfirms a theory, but the conspicuous absence of any unambiguous intermediate, transitional forms is (as Darwin candidly admitted) a serious problem for Darwinism. The continuum of life posited by Darwinism is not seen in the fossil record, which is instead characterized by (in Gould’s words) sudden appearance and stasis. The fossil record argues against Darwinian gradualism more persuasively than it argues for it, which is why Gould and Eldredge developed their theory of punctuated equilibrium.

Since we proposed punctuated equilibria to explain trends, it is infuriating to be quoted again and again by creationists—whether through design or stupidity, I do not know—as admitting that the fossil record includes no transitional forms. Transitional forms are generally lacking at the species level, but they are abundant between larger groups.

The design hypothesis is every bit as testable and potentially falsifiable as Darwinism

Darwin’s hypothesis (that random variations and natural selection are the engine of evolution) was widely rejected by his peers, but it has since won widespread acceptance among biologists (which has no bearing on its validity). To say that a hypothesis has been accepted is to say that the case for the hypothesis has been credibly made in the eyes of those who accept it.

— Jim

Simply imagining a Darwinian pathway constitutes neither a test nor a confirmation of Darwinian theory.

If imagining possible pathways is all that it takes to confirm Darwinism, then Darwinism is effectively unfalsifiable,

It can’t compose (or bring into being) biological information. [...] Yes, but selection doesn’t compose the information that it sorts out, which is the point. [...] believing that the blind Darwinian mechanism generated the vast amounts of biological information in complex organisms

The fossil record shows the emergence of different species throughout life’s history; it doesn’t show that the speciation was caused by Darwinian mechanisms.

I wasn’t talking about rejecting theories; I was talking about confirming them.

but it can’t provide us with certainty that the theory is valid.

If the collection of specific data is, in the main, consistent with the theory, then we inductively generalize to say that the theory has been confidently “confirmed.”

which you conveniently clipped in (mis)quoting me,

I neither claimed nor suggested that today’s amphibians are the evolutionary ancestors of humans.

where is the experimental evidence showing that Darwinian mechanisms turned the frog into a prince?

To remind you, this thread was kicked off by an article in New Scientist

It can if Muller’s “interlocking complexity” and Behe’s “irreducible complexity” are referring to different things, which they are.

Darwin never submitted any of his work to the process of peer review

If the interpretation of the evidence is informed by a theory, then the interpretation of the evidence doesn’t serve to confirm the theory. There must be a way to interpret the evidence independently of the theory to avoid reasoning in a circle. If independent interpretations of the evidence can be made, and if those interpretations can be shown to meet the predictions and hypotheses of the theory, then the evidence serves to confirm the theory.

But if a theory is used to justify an interpretation of the evidence, then the interpretation of the evidence doesn’t justify the theory. For example, if archaeopteryx is interpreted to be an intermediate, transitional form between dinosaurs and birds simply because Darwinism needs (or predicts) intermediate, transitional forms between dinosaurs and birds (and archaeopteryx is a promising candidate), then the labeling of archaeopteryx as an intermediate, transitional form does nothing to confirm Darwinism. That would be a situation where the theory justifies the interpretation, which in turn justifies the theory. Such circularity in reasoning can’t confirm anything.

I wasn’t talking about rejecting theories; I was talking about confirming them. Confirmation of a theory requires positive evidence for the theory, meaning that it must pass the important tests with great consistency.

The absence of evidence neither confirms nor disconfirms a theory, but the conspicuous absence of any unambiguous intermediate, transitional forms is (as Darwin candidly admitted) a serious problem for Darwinism.

For example, if archaeopteryx is interpreted to be an intermediate, transitional form between dinosaurs and birds simply because Darwinism needs (or predicts) intermediate, transitional forms between dinosaurs and birds (and archaeopteryx is a promising candidate), then the labeling of archaeopteryx as an intermediate, transitional form does nothing to confirm Darwinism.

The design hypothesis is every bit as testable and potentially falsifiable as Darwinism. Indeed, it would be much easier to falsify design than it would be to falsify Darwinism. If it could be credibly shown that a biological system that design theory attributes to design was the product of unintelligent material causes, then design theory would be refuted on the grounds that one does not invoke intelligent causes when unintelligent material causes will do.

Jim: "The absence of evidence neither confirms nor disconfirms a theory, but the conspicuous absence of any unambiguous intermediate, transitional forms is (as Darwin candidly admitted) a serious problem for Darwinism. The continuum of life posited by Darwinism is not seen in the fossil record, which is instead characterized by (in Gould’s words) sudden appearance and stasis. The fossil record argues against Darwinian gradualism more persuasively than it argues for it, which is why Gould and Eldredge developed their theory of punctuated equilibrium."

PvM: "Jim, are you interested in exploring your errors? I do not want to waste my time..."

Yet you wasted it trying (without success) to show that I was wrong...

1) With regard to my claim that Darwin saw the absence of any unambiguous, intermediate transitional forms as a problem for his theory:

"In the sixth chapter I enumerated the chief objections which might be justly urged against the views maintained in this volume. Most of them have now been discussed. One, namely, the distinctness of specific forms and their not being blended together by innumerable transitional links, is a very obvious difficulty." - Charles Darwin, "The Origin of Species"

"...the difficulty of assigning any good reason for the absence of vast piles of strata rich in fossils beneath the Cambrian system is very great. It does not seem probable that the most ancient beds have been quite worn away by denudation, or that their fossils have been wholly obliterated by metamorphic action, for if this had been the case we should have found only small remnants of the formations next succeeding them in age, and these would always have existed in a partially metamorphosed condition. But the descriptions which we possess of the Silurian deposits over immense territories in Russia and in North America, do not support the view that the older a formation is the more invariably it has suffered extreme denudation and metamorphism. The case at present must remain inexplicable; and may be truly urged as a valid argument against the views here entertained." - Charles Darwin, "The Origin of Species"

2) With regard to my claim that Gould admitted that the continuum of life posited by Darwinian gradualism is not seen in the fossil record:

"The history of most fossil species includes two features particularly inconsistent with gradualism: 1. Stasis. Most species exhibit no directional change during their tenure on earth. They appear in the fossil record looking much the same as when they disappear; morphological change is usually limited and directionless. 2. Sudden appearance. In any local area, a species does not arise gradually by the steady transformation of its ancestors; it appears all at once and 'fully formed.'" - Stephen J. Gould, "Evolution's Erratic Pace," Natural History, Vol. 86, No. 5, May 1977, p.14

3) With regard to my claim that Gould and Eldredge developed their theory of punctuated equilibrium as a reaction to the failure of the fossil record to exhibit Darwinian gradualism:

"As a neonate in 1972, punctuated equilibrium entered the world in unusual guise. We claimed no new discovery, but only a novel interpretation for the oldest and most robust of palaeontological observations: the geologically instantaneous origination and subsequent stability (often for millions of years) of palaeontological 'morphospecies'. This observation had long been ascribed, by Darwin and others, to the notorious imperfection of the fossil record, and was therefore read in a negative light--as missing information about evolution (defined in standard palaeontological textbooks of the time 9 as continuous anagenetic transformation or populations, or phyletic gradualism).

"In a strictly logical sense, this negative explanation worked and preserved gradualism, then falsely equated with evolution itself, amidst an astonishing lack of evidence for this putative main signal of Darwinism. But think of the practical or heuristic dilemma for working paleontologists: if evolution meant gradualism, and imperfection precluded the observation of such steady change, then scientists could not access the very phenomenon that both motivated their interest and built life's history. As young, committed and ambitious parents, we therefore proposed punctuated equilibrium, hoping to validate our profession's primary data as signal rather than void." - Stephen J. Gould and Niles Eldredge, Nature, Vol. 366, 18 November, 1993

Jim: "The design hypothesis is every bit as testable and potentially falsifiable as Darwinism."

PvM: "if it made any positive predictions, it would be."

If you'd like to familiarize yourself with some of the predictions made by ID theory, go to:

http://www.ideacenter.org/stuff/contentmgr/files/becbd98b35e8e07260d4e8e92784cbbb/miscdocs/thepositivecasefordesign_v3.pdf

PvM: "So tell us what does ID predict about the flagellum...?"

ID theory contends that the flagellum is the product of design. How that design might have been actualized is only one of the many research possibilities that the conclusion of design opens up.

Re: Punctuated equilibria. This concerns only the transitions between closely related species, i.e. evolution within the creationists' version of "microevolution." These are horse-zebra type "within the kind" differences. Punk Eek explains why transitions between closely related species are relatively rare -- basically it applies the standard Neo-Darwinian model of geographically localized speciation to the fossil record and points out that geographically localized speciation will result in punctuations.

There is no such pattern of stasis and lack-of-transitions over bigger transformations. As Gould said in response to creationist quote-mining of him:

"Since we proposed punctuated equilibria to explain trends, it is infuriating to be quoted again and again by creationists -- whether through design or stupidity, I do not know -- as admitting that the fossil record includes no transitional forms. Transitional forms are generally lacking at the species level, but they are abundant between larger groups."

-- "Evolution as Fact and Theory," Hen's Teeth and Horse's Toes: Further Reflections in Natural History, New York: W. W. Norton & Company, 1994, p. 260.

Creationist Kurt Wise knows and admits all of this, including the commonality of transitional fossils over larger transformations. And he's about the only creationist with serious training.

What astounds me is how the larger creationist/ID community is so spectacularly ignorant of the basics of punk eek and what an actual participant like Gould actually said.

Nick (Matzke)): What astounds me is how the larger creationist/ID community is so spectacularly ignorant of the basics of punk eek and what an actual participant like Gould actually said.

Torbjörn: “Let me be clear that I’m discussing evolution here, not Darwin’s old theory.”

The problem here is that when you say you’re discussing “evolution,” it’s hard to know what you mean. That slippery word has numerous connotations, some of which are uncontroversial (such as “biological change over time”) and some of which are hotly disputed (such as “the theory that all organisms have descended from a common ancestor by wholly material means, primarily random genetic mutations acted on by natural selection”).

With regard to “Darwin’s old theory,” his core hypothesis – that evolution (or descent with modification) is caused by natural selection acting on random variations – remains intact. Neo-Darwinism (or the Modern Synthesis) brought random genetic mutations into that core hypothesis to account for random variations (which Darwin failed to explain). Like many biologists (Eldredge, Miller, and Margulis come to mind), I refer to neo-Darwinism (which is the dominant modern theory of evolution) as simply “Darwinism” (I sometimes also refer to it as “Darwinian theory”). That term has the virtue of making it plain that I’m referring to a theory that purports to explain evolution, not to the process of evolution itself (however that process might be caused).

Torbjörn: “I exactly specified what the test meant, it provides the necessary pathways. As you can’t come up with a problem with the test, you must agree.”

I assume you’re still referring to the just-so story about the evolution of the Venus flytrap. If that’s the case, I quite disagree that the story provides sufficient detail to actually constitute a test of Darwinism.

Torbjörn: “The genome is the observer that utilizes the information, not the outsider studying the system.”

I don’t dispute it, but since natural selection does no creative work (it simply acts on that which has already been brought into being), it cannot possibly be the “author” of the biological information that is used (or expressed) by the genome. If the Darwinian mechanism of random mutations and natural selection can “compose” the biological information needed to cause the evolution of complex biological systems, then random mutations are the “author” who “composes” the information and natural selection is the “publisher” who spreads the information throughout the genome. The information content of a sequence (whether it’s a sequence of letters or a sequence of nucleotides) is imparted to the sequence by its “author,” not by its “publisher.” Natural selection will “publish” a new nucleotide sequence “authored” by random mutations only if the information in that sequence brings into being an adaptation that is advantageous to the organism.

Torbjörn: “There is no belief here, the ev program shows how selection increases information and mutation decreases it by measuring the Shannon information directly.”

Shannon information is irrelevant to the evolution of organisms. Shannon information is present in any sequence regardless of whether the sequence conveys a message. But in biology, only sequences of nucleotides that convey messages (or instructions) are of any significance. Any sequence of nucleotides produced by random mutations will bear Shannon information, but only sequences that bear meaningful messages (or instructions) will have any effect on the evolution of organisms.

Jim: “The fossil record shows the emergence of different species throughout life’s history; it doesn’t show that the speciation was caused by Darwinian mechanisms.”

Torbjörn: “This is an answer to an aside after I showed you that your claims aren’t engaging the science. Now you do it again, evolution (already the old Darwinian theory), predicts speciation.”

I fail to see that what I wrote about the fossil record is not “engaging the science.” Nor do I see why the mere fact that Darwinism predicts speciation counts as a point in favor of the theory. Unless it can be shown that Darwinian mechanisms cause speciation, validating the prediction that life will be characterized by numerous species (something that the fossil record credibly does) does very little to confirm Darwinism (which purports to explain how speciation occurs). In 1996, biologists Scott Gilbert, John Opitz, and Rudolf Raff (all of whom accept the core tenets of Darwinism) wrote in the journal Developmental Biology: "Genetics might be adequate for explaining microevolution, but microevolutionary changes in gene frequency were not seen as able to turn a reptile into a mammal or to convert a fish into an amphibian. Microevolution looks at adaptations that concern the survival of the fittest, not the arrival of the fittest. The origin of species – Darwin’s problem – remains unsolved.”

In 2008, Darwin’s problem still remains unsolved.

Torbjörn: "If you have a better theory that does this you must present it."

Actually, it's not necessary to have a replacement theory to take issue with an existing theory. Nonetheless, I think that design theory can do what Darwinism (a theory entirely comitted to unintelligent material causes) cannot do, namely, account for the origin of biological information (which, like all information, is not a material phenomenon).

Torbjörn: "...there is no reasonable doubt that (evolution) is the correct theory."

I think there's considerable doubt that it's the correct theory (at least, in the macro sense), and I don't think that the Darwinian faithful have cornered the market on reason.

I don’t dispute it, but since natural selection does no creative work (it simply acts on that which has already been brought into being), it cannot possibly be the “author” of the biological information that is used (or expressed) by the genome. If the Darwinian mechanism of random mutations and natural selection can “compose” the biological information needed to cause the evolution of complex biological systems, then random mutations are the “author” who “composes” the information and natural selection is the “publisher” who spreads the information throughout the genome.

Shannon information is irrelevant to the evolution of organisms. Shannon information is present in any sequence regardless of whether the sequence conveys a message. But in biology, only sequences of nucleotides that convey messages (or instructions) are of any significance. Any sequence of nucleotides produced by random mutations will bear Shannon information, but only sequences that bear meaningful messages (or instructions) will have any effect on the evolution of organisms.

In 1996, biologists Scott Gilbert, John Opitz, and Rudolf Raff (all of whom accept the core tenets of Darwinism) wrote in the journal Developmental Biology: “Genetics might be adequate for explaining microevolution, but microevolutionary changes in gene frequency were not seen as able to turn a reptile into a mammal or to convert a fish into an amphibian. Microevolution looks at adaptations that concern the survival of the fittest, not the arrival of the fittest. The origin of species – Darwin’s problem – remains unsolved.” In 2008, Darwin’s problem still remains unsolved.

“My research on turtles and my research into evolutionary developmental biology is fully within Darwinian parameters. My gripe has been that neo-Darwinism has supposed that population genetics was the only genetics needed to explain Darwinian evolution. I claim that developmental genetics is also needed. So my research has been to include developmental genetics into the Darwinian mix.” And Douglas L. Erwin (author of [24]) told NCSE, “While the article considers the relationship between micro - and macro- evolution, the Discovery Institute is inaccurate in saying that I am challenging the standard view of evolution. The treatment of macroevolution in that paper is an extension, but by no means a challenge. Further, although more work may be needed to fully understand macroevolutionary events, there is no evidence that requires, or even suggests, a role for so-called ‘intelligent design’.”

— Scott Gilbert

Actually, it’s not necessary to have a replacement theory to take issue with an existing theory. Nonetheless, I think that design theory can do what Darwinism (a theory entirely comitted to unintelligent material causes) cannot do, namely, account for the origin of biological information (which, like all information, is not a material phenomenon).

The problem here is that when you say you’re discussing “evolution,” it’s hard to know what you mean. That slippery word has numerous connotations, some of which are uncontroversial (such as “biological change over time”) and some of which are hotly disputed (such as “the theory that all organisms have descended from a common ancestor by wholly material means, primarily random genetic mutations acted on by natural selection”).

Jim: “I wasn’t talking about rejecting theories; I was talking about confirming them.”

Torbjörn: “Exactly, you missed what constitutes the power in the scientific method, empirical testing and rejection of falsehoods.”

Empirical testing has been at the heart of my comments about the problem of induction. Empirical testing provides specific data; if the specific data is, in the main, consistent with a theory, then scientists can inductively generalize to say that the theory has been confidently confirmed. Certainly falsehoods should be rejected, but that does not obviate the need to provide positive evidence *for* a theory.

Jim: “(The scientific method) can’t provide us with certainty …”

Torbjörn: ”As I already noted and you conveniently try to slip by, certainty is commonly the set difference to uncertainty - you are discussing absolute certainty and absolute Truth. But science is about observable facts and testable theories, and can give certainty beyond reasonable doubt. You should learn about science."

“Reasonable doubt” is a legal concept, not a scientific concept. But setting that aside, you’re saying essentially the same thing that I’ve been saying: that with respect to scientific theories, the scientific method does not deliver the kind of certainty that warrants saying “I know that this theory is true.” At best it only empowers a scientist to say “I am quite confident that this theory is true.” To remind you, this particular thread was kicked off by Nick’s claim that he knows how the immune system could have evolved, a claim that the scientific method does not empower him to make.

Torbjörn: “Claim ‘confirmation’ all what you want, but it doesn’t explain why theories are tested and false theories rejected.”

If theories aren’t tested with an eye towards confirming them (to the extent that the scientific method can deliver confirmation), then why test them at all?

Torbjörn: “Learn about science.”

As much as I enjoy a good debate, there are two kinds of people I generally ignore:

1) Those who resort to name-calling (which is why I pay little or no attention to Stanton).

2) Those who resort to condescension (which is why I’m done with you).

Empirical testing has been at the heart of my comments about the problem of induction. Empirical testing provides specific data; if the specific data is, in the main, consistent with a theory, then scientists can inductively generalize to say that the theory has been confidently confirmed. Certainly falsehoods should be rejected, but that does not obviate the need to provide positive evidence *for* a theory.

Mike: “So how do you establish the Christian bible as the foundation on which the world and the fossil record should be interpreted?”

How did the Bible get into this? There’s nothing in design theory about the Bible. Or about God, for that matter.

Mike: “All the arguments we see from creationists are totally circular; namely, bible says of itself that it is true, therefore it is true. “

Since I’m not a young-earth creationist (which is what the term “creationist” most commonly refers to), I have no interest in debating this point with you, Mike.

Mike: “Do you think that every independent line of evidence is a self-consistent, circular form of reasoning?”

No, but evolutionary biologists indulge in circular reasoning with such regularity that I think they’ve become unaware that they’re doing it. Aside from the circularity involved in labeling intermediate, transitional forms, circular reasoning is also involved in identifying vestigial organs (evolutionary theory “justifies” the claim that an organ is vestigial, which is then used to “justify” evolutionary theory), and in identifying homologous structures (common ancestry is used to “justify” the claim of homology, which is then used to “justify” common ancestry).

Mike: “How does archaeopteryx confirm the Christian bible?”

How did the Bible get into this? If you want to debate a creationist, you’ll need to look elsewhere.

What experiments or other forms of empirical tests have been done to confirm Intelligent Design "theory", Jim?

What experiments did Behe do to confirm that the bacterial and eukaryotic flagella were designed? What experiments did Behe do to confirm that the blood-clotting cascade system and the vertebrate immune system were designed?

Behe never so much as even hinted to any sort of experimental work that lead his conclusions. That is why I asked you in the first place. Perhaps you would like to explain the reason why you have not so much as even given the slightest hint to the sort of experimental work that can be done to confirm Intelligent Design "theory" in any of your posts?

Well Jim, speaking of condescension,

1. You haven't dealt with any of the science of immune system evolution. For example, explain to me why scientists thought there should be a free-living transposon related to the immune system RAG genes, when the only evidence for the existence of such a transposon was the fact that the RAG genes look like a modified transposon. Successful prediction, dramatically successful test.

2. You haven't admitted that you misconstrued Gould's view, and you haven't dealt with the transitional fossils that he and other paleontologists say exist (go here for a primer on those or read Prothero's new book).

Please remind me, why should I take you or your arguments seriously?

Jim: Mike: “Do you think that every independent line of evidence is a self-consistent, circular form of reasoning?” No, but evolutionary biologists indulge in circular reasoning with such regularity that I think they’ve become unaware that they’re doing it. Aside from the circularity involved in labeling intermediate, transitional forms, circular reasoning is also involved in identifying vestigial organs (evolutionary theory “justifies” the claim that an organ is vestigial, which is then used to “justify” evolutionary theory), and in identifying homologous structures (common ancestry is used to “justify” the claim of homology, which is then used to “justify” common ancestry).

Mike: “How does archaeopteryx confirm the Christian bible?” How did the Bible get into this? If you want to debate a creationist, you’ll need to look elsewhere.

And since Darwin, many more unambiguous transitional fossils have been found. So your argument at best is that Darwin lacked the data, something that has been corrected. 2) With regard to my claim that Gould admitted that the continuum of life posited by Darwinian gradualism is not seen in the fossil record: “The history of most fossil species includes two features particularly inconsistent with gradualism: 1. Stasis. Most species exhibit no directional change during their tenure on earth. They appear in the fossil record looking much the same as when they disappear; morphological change is usually limited and directionless. 2. Sudden appearance. In any local area, a species does not arise gradually by the steady transformation of its ancestors; it appears all at once and ‘fully formed.’” - Stephen J. Gould, “Evolution’s Erratic Pace,” Natural History, Vol. 86, No. 5, May 1977, p.14

3) With regard to my claim that Gould and Eldredge developed their theory of punctuated equilibrium as a reaction to the failure of the fossil record to exhibit Darwinian gradualism: “As a neonate in 1972, punctuated equilibrium entered the world in unusual guise. We claimed no new discovery, but only a novel interpretation for the oldest and most robust of palaeontological observations: the geologically instantaneous origination and subsequent stability (often for millions of years) of palaeontological ‘morphospecies’. This observation had long been ascribed, by Darwin and others, to the notorious imperfection of the fossil record, and was therefore read in a negative light–as missing information about evolution (defined in standard palaeontological textbooks of the time 9 as continuous anagenetic transformation or populations, or phyletic gradualism). “In a strictly logical sense, this negative explanation worked and preserved gradualism, then falsely equated with evolution itself, amidst an astonishing lack of evidence for this putative main signal of Darwinism. But think of the practical or heuristic dilemma for working paleontologists: if evolution meant gradualism, and imperfection precluded the observation of such steady change, then scientists could not access the very phenomenon that both motivated their interest and built life’s history. As young, committed and ambitious parents, we therefore proposed punctuated equilibrium, hoping to validate our profession’s primary data as signal rather than void.” - Stephen J. Gould and Niles Eldredge, Nature, Vol. 366, 18 November, 1993

Jim: “The design hypothesis is every bit as testable and potentially falsifiable as Darwinism.” PvM: “if it made any positive predictions, it would be.” If you’d like to familiarize yourself with some of the predictions made by ID theory, go to:

PvM: “So tell us what does ID predict about the flagellum…?” ID theory contends that the flagellum is the product of design. How that design might have been actualized is only one of the many research possibilities that the conclusion of design opens up.

PvM:

Yet you wasted it trying (without success) to show that I was wrong… 1) With regard to my claim that Darwin saw the absence of any unambiguous, intermediate transitional forms as a problem for his theory:

And since Darwin, many more unambiguous transitional fossils have been found. So your argument at best is that Darwin lacked the data, something that has been corrected.

2) With regard to my claim that Gould admitted that the continuum of life posited by Darwinian gradualism is not seen in the fossil record: “The history of most fossil species includes two features particularly inconsistent with gradualism: 1. Stasis. Most species exhibit no directional change during their tenure on earth. They appear in the fossil record looking much the same as when they disappear; morphological change is usually limited and directionless. 2. Sudden appearance. In any local area, a species does not arise gradually by the steady transformation of its ancestors; it appears all at once and ‘fully formed.’” - Stephen J. Gould, “Evolution’s Erratic Pace,” Natural History, Vol. 86, No. 5, May 1977, p.14

Even though Gould does outline both gradual as well as stasis and abrupt changes? You are wrong to claim that Gould stated this. Quote mining statements which appear to support your claim while ignoring quotes that disprove your claim is not a very convincing method of argument.

3) With regard to my claim that Gould and Eldredge developed their theory of punctuated equilibrium as a reaction to the failure of the fossil record to exhibit Darwinian gradualism: “As a neonate in 1972, punctuated equilibrium entered the world in unusual guise. We claimed no new discovery, but only a novel interpretation for the oldest and most robust of palaeontological observations: the geologically instantaneous origination and subsequent stability (often for millions of years) of palaeontological ‘morphospecies’. This observation had long been ascribed, by Darwin and others, to the notorious imperfection of the fossil record, and was therefore read in a negative light–as missing information about evolution (defined in standard palaeontological textbooks of the time 9 as continuous anagenetic transformation or populations, or phyletic gradualism). “In a strictly logical sense, this negative explanation worked and preserved gradualism, then falsely equated with evolution itself, amidst an astonishing lack of evidence for this putative main signal of Darwinism. But think of the practical or heuristic dilemma for working paleontologists: if evolution meant gradualism, and imperfection precluded the observation of such steady change, then scientists could not access the very phenomenon that both motivated their interest and built life’s history. As young, committed and ambitious parents, we therefore proposed punctuated equilibrium, hoping to validate our profession’s primary data as signal rather than void.” - Stephen J. Gould and Niles Eldredge, Nature, Vol. 366, 18 November, 1993

Again you are very selectively quote mining Gould while ignoring what he said

Jim: “The design hypothesis is every bit as testable and potentially falsifiable as Darwinism.” PvM: “if it made any positive predictions, it would be.” If you’d like to familiarize yourself with some of the predictions made by ID theory, go to:

Unless you provide me with some specific examples us to discuss, I reject your claim.

PvM: “So tell us what does ID predict about the flagellum…?” ID theory contends that the flagellum is the product of design. How that design might have been actualized is only one of the many research possibilities that the conclusion of design opens up.

A totally vacuous statement where design is defined as 'we don't know'. So in other words, ID claims that since we do not know how the flagellum arose, we should consider it to be 'designed'. A total abuse of language and logic.

Richard: "If you do not consider Tiktaalik, for example, to be an intermediate, transitional form, what exactly would you consider to be an intermediate, transitional form? What features would it have to enable you to say 'Ah! Here is a transitional.'"

The features of Tiktaalik make it a good candidate to be an intermediate, transitional form between fish and amphibians. Tiktaalik gives every appearance of being morphologically intermediate in some ways between fish and amphibians, but unless one presupposes that amphibians evolved from fish, there's no good reason to label Tiktaalik an intermediate,
transitional form. Frankly, I don't know how intermediate, transitional forms could be identified independent of the assumptions of evolutionary theory, but unless such independent identification can be made, the organisms that are labeled intermediate, transitional forms can't justify
the theory.

Jim: "For example, if archaeopteryx is interpreted to be an intermediate, transitional form between dinosaurs and birds simply because Darwinism needs (or predicts) intermediate, transitional forms between dinosaurs and birds (and archaeopteryx is a promising candidate), then the labeling of
archaeopteryx as an intermediate, transitional form does nothing to confirm Darwinism."

Richard: "That is not the reason that it is considered to be a transitional form and if you knew anything about the species you would know this."

Because Darwinism needs ancestor/descendant relationships, transitional forms can also be called "ancestors." While I readily admit that I'm not an expert in paleontology, Gareth Nelson (American Museum of Natural History) is. In an interview published in the Wall Street Journal , Nelson candidly described what the identification of "ancestors" means in practice:

"We've got to have some ancestors. We'll pick those. Why? Because we know they have to be there, and these are the best candidates. That's by and large the way it has worked. I am not exaggerating."

Richard: "No IDer has ever said that a specific result would refute 'design' as a whole."

Perhaps I should have indicated that I was borrowing from design theorist Wm. Dembski, who wrote (in "The Design Revolution):

"If it could be shown that biological systems that are wonderfully complex, elegant, and integrated - such as the bacterial flagellum - could have been formed by a
gradual Darwinian process (and thus that irreducible complexity is an illusion), then intelligent design would be refuted on the general grounds that one does not invoke intelligent causes when undirected natural causes will do. In that case Occam's razor would finish off intelligent design quite nicely."

Perhaps you should read what ID theorists actually say, rather than the things that are falsely attributed to them on blogs like Pharyngula and The Panda's Thumb.

Jim: The features of Tiktaalik make it a good candidate to be an intermediate, transitional form between fish and amphibians. Tiktaalik gives every appearance of being morphologically intermediate in some ways between fish and amphibians, but unless one presupposes that amphibians evolved from fish, there's no good reason to label Tiktaalik an intermediate, transitional form. Frankly, I don't know how intermediate, transitional forms could be identified independent of the assumptions of evolutionary theory, but unless such independent identification can be made, the organisms that are labeled intermediate, transitional forms can't justify the theory.

Perhaps you should read what ID theorists actually say, rather than the things that are falsely attributed to them on blogs like Pharyngula and The Panda's Thumb.

Jim: "In 1996, biologists Scott Gilbert, John Opitz, and Rudolf Raff (all of whom accept the core tenets of Darwinism) wrote in the journal Developmental Biology: 'Genetics might be adequate for explaining microevolution, but microevolutionary changes in gene frequency were not seen as able to turn a reptile into a mammal or to convert a fish into an amphibian. Microevolution looks at adaptations that concern the survival of the fittest, not the arrival of the fittest. The origin of species – Darwin’s problem – remains unsolved.'"

PvM: "Nice quote mining...What does Gilbert have to say on this topic?"

Your quote mining supported mine (thanks). In your Gilbert quote, he affirms his faith in Darwinism (as I noted), but he also admits that the population genetics embraced by Darwinism fails to adequately explain evolution (in both the micro and macro sense). Hence his own work in developmental genetics to try to solve the problem that he contends Darwinism has not yet solved: the origin of species.

PvM: "Claiming 'it’s all designed' really is not sufficient."

It's also not a claim that design theorists make. For example, in "Darwin's Black Box," Behe wrote:

"Just because we can infer that some biochemical systems were designed does not mean that all subcellular systems were explicitly designed."

Or as Dembski wrote (in "Intelligent Design") in response to Gould's claim that the panda's thumb is an "odd arrangement" that defies attribution to an intelligent designer (who Gould took to be God):

"The design theorist is not committed to every biological structure being designed. Mutation and selection do operate in natural history to adapt organisms to their environments. Perhaps the panda's thumb is such an adaptation."

It would be helpful if you'd respond to things that design theorists actually say, rather than to things you falsely attribute to them.

Nick: "As Gould said in response to creationist quote-mining of him:

"Since we proposed punctuated equilibria to explain trends, it is infuriating to be quoted again and again by creationists – whether through design or stupidity, I do not know – as admitting that the fossil record includes no transitional forms. Transitional forms are generally lacking at the species level, but they are abundant between larger groups."

Indeed, Gould did a lot of backpedaling after writing:

"The extreme rarity of transitional forms in the fossil record persists as the trade secret of paleontology. The evolutionary trees that adorn our textbooks have data only at the tips and nodes of their branches; the rest is inference, however reasonable, not the evidence of fossils."

How did the Bible get into this? There’s nothing in design theory about the Bible. Or about God, for that matter.

How did the Bible get into this? If you want to debate a creationist, you’ll need to look elsewhere.

It would be helpful if you’d respond to things that design theorists actually say, rather than to things you falsely attribute to them.

Jim: "Shannon information is irrelevant to the evolution of organisms. Shannon information is present in any sequence regardless of whether the sequence conveys a message. But in biology, only sequences of nucleotides that convey messages (or instructions) are of any significance. Any sequence of nucleotides produced by random mutations will bear Shannon information, but only sequences that bear meaningful messages (or instructions) will have any effect on the evolution of organisms."

PvM: "Shannon information is an essential concept as Shannon information increases invariably when there are processes of variation and selection. A sequence of nucleotides produced by random mutations will have zero shannon information, contrary to your claim. How familiar are you with Shannon information?"

I know enough about it to know that Shannon information is solely concerned with the improbability or complexity of a string of characters rather than its patterning or significance. A sequence of nucleotides can be chock full of Shannon information, but unless the sequence is chock full of meaningful information, it has no biological significance. Unintelligent causes can easily produce Shannon information, but they are quite ill-equipped to produce meaningful information (such as the information contained in the sequence of letters in this paragraph).

By the way, could you clarify how random mutations can both increase Shannon information and produce zero Shannon information?

PvM: "A totally vacuous claim, which argues without any further evidence that 1. Information is not a ‘material phenomenon’"

“Information is Information, neither matter nor energy. No materialism that fails to take account of this can survive the present day.” - Norbert Weiner, MIT mathematician/information theorist and the "Father of Cybernetics"

PvM: "I can show you how simple Darwinian processes can explain information in the genome."

OK. Do it. Then clear a space on your mantle for the Nobel Prize that awaits you.

PvM: "Are you saying that there is no ‘positive evidence’ for the theory of evolution?"

No, but evolutionary biologists have adduced precious little evidence supporting the macroevolutionary claims of the theory. Where, for example, is the evidence showing that Darwinian mechanisms caused sexual reproduction to evolve from asexual reproduction? Or that Darwinian mechanisms caused eyes capable of color vision to evolve from light-sensitive spots? Or that Darwinian mechanisms caused men to evolve from fish?

“If it could be shown that biological systems that are wonderfully complex, elegant, and integrated - such as the bacterial flagellum - could have been formed by a gradual Darwinian process (and thus that irreducible complexity is an illusion), then intelligent design would be refuted on the general grounds that one does not invoke intelligent causes when undirected natural causes will do. In that case Occam’s razor would finish off intelligent design quite nicely.”

Frankly, I don’t know how intermediate, transitional forms could be identified independent of the assumptions of evolutionary theory, but unless such independent identification can be made, the organisms that are labeled intermediate, transitional forms can’t justify the theory.

PvM: “I can show you how simple Darwinian processes can explain information in the genome.”

OK. Do it. Then clear a space on your mantle for the Nobel Prize that awaits you.

vM: “Are you saying that there is no ‘positive evidence’ for the theory of evolution?” No, but evolutionary biologists have adduced precious little evidence supporting the macroevolutionary claims of the theory. Where, for example, is the evidence showing that Darwinian mechanisms caused sexual reproduction to evolve from asexual reproduction? Or that Darwinian mechanisms caused eyes capable of color vision to evolve from light-sensitive spots? Or that Darwinian mechanisms caused men to evolve from fish?

PvM: “Shannon information is an essential concept as Shannon information increases invariably when there are processes of variation and selection. A sequence of nucleotides produced by random mutations will have zero shannon information, contrary to your claim. How familiar are you with Shannon information?” I know enough about it to know that Shannon information is solely concerned with the improbability or complexity of a string of characters rather than its patterning or significance.

A sequence of nucleotides can be chock full of Shannon information, but unless the sequence is chock full of meaningful information, it has no biological significance. Unintelligent causes can easily produce Shannon information, but they are quite ill-equipped to produce meaningful information (such as the information contained in the sequence of letters in this paragraph).

By the way, could you clarify how random mutations can both increase Shannon information and produce zero Shannon information?

PvM: “A totally vacuous claim, which argues without any further evidence that 1. Information is not a ‘material phenomenon’” “Information is Information, neither matter nor energy. No materialism that fails to take account of this can survive the present day.” - Norbert Weiner, MIT mathematician/information theorist and the “Father of Cybernetics”

PvM: “I can show you how simple Darwinian processes can explain information in the genome.” OK. Do it. Then clear a space on your mantle for the Nobel Prize that awaits you.

For the work others have already done?

Or that Darwinian mechanisms caused men to evolve from fish?

Nick: “As Gould said in response to creationist quote-mining of him: “Since we proposed punctuated equilibria to explain trends, it is infuriating to be quoted again and again by creationists – whether through design or stupidity, I do not know – as admitting that the fossil record includes no transitional forms. Transitional forms are generally lacking at the species level, but they are abundant between larger groups.” Indeed, Gould did a lot of backpedaling after writing: “The extreme rarity of transitional forms in the fossil record persists as the trade secret of paleontology. The evolutionary trees that adorn our textbooks have data only at the tips and nodes of their branches; the rest is inference, however reasonable, not the evidence of fossils.”

Mike: "...who or what is the 'intelligent designer'? Is it natural or supernatural?"

That's something that ID theory can't decide, but as a theist, I think that God is the designer implicated by design theory. ID theorists argue that biological data can justify design inferences, but they also argue that there is no inferential trail leading from the biological data to the identity of the designer. If ID theory is a theistic enterprise committed to proving that God exists, it's not a very promising strategy on the part of ID theorists to repeatedly tell people that ID theory can't deliver such proof.

Mike: "So how do you propose to gain access to the supernatural?"

I don't. Neither do ID theorists, who repeatedly argue that only theology and philosophy (not science) can underwrite the conclusion that God is the designer implicated by design theory. For example, in "The Edge of Evolution," Behe wrote:

"...if one wishes to be academically rigorous, one can't leap directly from design to a transcendent God. To reach a transcendent God, other, nonscientific arguments have to be made - philosophical and theological arguments."

Mike: "Did you follow any of the Dover trial?"

I read Judge Jones' decision and much of the trial's transcript. Judge Jones is not a stupid man, which suggests that he was being willfully obtuse in failing to distinguish ID theory from its theistic implications (a distinction that is quite easily grasped). Big Bang theory is another theory with obvious theistic implications. If Judge Jones were asked to decide the scientific legitimacy of Big Bang theory, consistency in reasoning would require him to declare the theory to be religion, not science.

The most shameful (for Judge Jones) part of Judge Jones' written opinion was the section in which he deemed to decide that ID is religion. That part of his decision was largely copied verbatim from the egregiously misnamed "Findings of Fact" provided to him by the ACLU, demonstrating that the judge was on a mission that he would not allow to be derailed by exercising judicial impartiality in weighing the evidence.

Mike: "ID/Creationists make lots of claims, but never provide evidence for those claims."

I can't speak for creationists, Mike (I don't read their stuff), but I've read some two dozen books by ID theorists, who quite consistently provide evidence for the claims they make. If your education in ID has come from the critics of ID, I have no doubt that you've been seriously misinformed.

Mike: "You say many false things, deliberately."

As I've already said, I consistently write things that I believe to be true. I could be wrong, but I'm not lying (I'd have to know that I'm wrong to be lying).

Mike: "You learned this tactic from Duane Gish."

Actually, I've never read a single thing that Gish has written. I know him only by name.

Mike: "We watch the questions you avoid answering..."

You won't learn anything by doing that. I suspect that many of those questions are asked by posters (like Stanton) whom I ignore. In any event, if all you want to talk about is me, I have no interest in continuing a conversation with you.

I read Judge Jones’ decision and much of the trial’s transcript. Judge Jones is not a stupid man, which suggests that he was being willfully obtuse in failing to distinguish ID theory from its theistic implications (a distinction that is quite easily grasped). Big Bang theory is another theory with obvious theistic implications. If Judge Jones were asked to decide the scientific legitimacy of Big Bang theory, consistency in reasoning would require him to declare the theory to be religion, not science.

— Jim

The most shameful (for Judge Jones) part of Judge Jones’ written opinion was the section in which he deemed to decide that ID is religion. That part of his decision was largely copied verbatim from the egregiously misnamed “Findings of Fact” provided to him by the ACLU, demonstrating that the judge was on a mission that he would not allow to be derailed by exercising judicial impartiality in weighing the evidence.

Jim remind us again, how does ID explain the origin and evolution of the bacterial flagellum?

Or does ID indeed have no scientific content as it is based on an eliminative argument? In other words, ID cannot formulate any positive hypotheses without additional hypotheses. And since ID refuses to make such additional hypotheses, it is doomed to scientific irrelevancy.

Richard: "They used to say that about the mammalian eye, but when a series of gradual steps from a simple light-sensitive patch on a cell to an eye was presented, the argument was dropped."

All that's lacking from that particular just-so story are the molecular details showing how a light-sensitive patch could have evolved into a mammalian eye, which provides vision not simply because of its structure, but because of extraordinarily complex electro-chemical processes.

Richard: "How about just looking and seeing if it either has features typical of two apparently disparate groups or features that are intermediate between the two groups? In the case of Tiktaalik, for example, it has features that are commonly found in fish. It has other features that are commonly found in amphibians."

How about platypus? It has features commonly found in reptiles and features commonly found in mammals. Is there any reason to suppose that platypus is an intermediate, transitional form unless we presuppose that it's evolving into either a fully reptilian or a fully mammalian animal? How can we know that either platypus or Tiktaalik are intermediate, transitional forms rather than curious mosaics?

PvM: “I can show you how simple Darwinian processes can explain information in the genome.”

Jim: "OK. Do it. Then clear a space on your mantle for the Nobel Prize that awaits you."

Richard: "Over at AtBC someone (and I regret I mislaid the author’s name) responded to ‘How is it possible?’ with

HOW IS IT POSSIBLE (Original)

HOW IS IT POSSIBLE HOW IS IT POSSIBLE (Duplication)

HOW IS IT POSSIBLE I SHOW IT POSSIBLE (Translocation)

New information from simple genetic processes. All that is needed now is a little selection in favour of the new version."

That's it? And you find that persuasive? If you could tie some actual biological details to the original, to the duplication, and to the translocation, you might have something. But all your word game shows is that an intelligent agent (you) can alter a meaningful sequence of letters to produce a different meaningful sequence of letters.

PvM: "But you want to know what the evidence is and here I can walk you through some of the fascinating findings of evolutionary science.

1. Asexual to sexual reproduction. First of all, for a while this was seen as a problem for Darwinian theory, since there is a significant ‘cost of sex’. However, science has been slowly uncovering that there are circumstances under which sexual reproduction can be advantageous. An excellent example are snails which reproduce asexually and sexually and are observed to switch when under significant environmental pressure. In other words, under strong environmental pressures, they switch to sexual reproduction. So far so good. Of course, this does not explain HOW sexual reproduction arose, but it shows that there are environmental pressures under which sexual reproduction is advantageous."

That's all very interesting, but none of it constitutes evidence that Darwinian mechanisms (or any other unguided material mechanisms) brought sexual reproduction into being. When we want to know how sexual reproduction originated, we're not enlightened by the fact that sexual reproduction can be advantageous.

PvM: "Remind us again: How does ID explain the origin and maintenance of sexual reproduction?"

So far as I know, ID has not yet developed an explanation for the origin of sexual reproduction. But why should that count against ID and not against Darwinism, which also has no explanation for the origin of sexual reproduction (as you've quite helpfully demonstrated)?

Nick: "Well, now you’re just another creationist hack."

Thanks, Nick. I can't reply to everyone here, so you've quite thoughtfully given me cause to add you to my ignore list.

PvM: "Information can be measured, quantified, observed, destroyed."

True enough, but that doesn't make information a material phenomenon. Take any book from your library. Open it to any page. Is the information on that page reducible to matter? Of course not. It appears to me that you're confusing the medium with the message. Darwinism can explain changes in the medium (primarily, the nucleic acids), but it doesn't explain the origin of the messages.

PvM, Nick, Stanton, Bill,

Thanks for your tireless efforts and clarity here.

PvM: "Perhaps you can explain to us why you believe that the findings of fact, which were based on the trial record were ‘misnamed’?"

Because they were so chock full of factual errors. They would have been more appropriately titled "Findings of Fiction." Additionally, the ACLU's "Findings of Fact," which Judge Jones copied nearly verbatim into his decision, were provided to the judge nearly a month before the trial. If you'd like to acquaint yourself with the factual errors in the ACLU's pretrial report, go to:

http://www.discovery.org/scripts/viewDB/filesDB-download.php?command=download&id=1186

If your education in ID has come from the critics of ID, I have no doubt that you’ve been seriously misinformed.

That’s it? And you find that persuasive? If you could tie some actual biological details to the original, to the duplication, and to the translocation, you might have something. But all your word game shows is that an intelligent agent (you) can alter a meaningful sequence of letters to produce a different meaningful sequence of letters.

Jim: PvM: "Remind us again: How does ID explain the origin and maintenance of sexual reproduction?" So far as I know, ID has not yet developed an explanation for the origin of sexual reproduction. But why should that count against ID and not against Darwinism, which also has no explanation for the origin of sexual reproduction (as you've quite helpfully demonstrated)?

What PvM should have asked: Remind us again: Why aren't ID proponents trying to explain the origin and maintenance of sexual reproduction?

The circularity in reasoning is palpable.

#145987 There are many reasons why people (including biologists) would wish that life is a wholly material phenomenon. An a priori commitment to materialism is one of those reasons (a commitment that Darwinist Richard Lewontin has candidly admitted most evolutionary biologists hold). [...]

No, but evolutionary biologists have adduced precious little evidence supporting the macroevolutionary claims of the theory.

Because they were so chock full of factual errors. They would have been more appropriately titled “Findings of Fiction.” Additionally, the ACLU’s “Findings of Fact,” which Judge Jones copied nearly verbatim into his decision, were provided to the judge nearly a month before the trial. If you’d like to acquaint yourself with the factual errors in the ACLU’s pretrial report, go to:

How about platypus? It has features commonly found in reptiles and features commonly found in mammals.

Is there any reason to suppose that platypus is an intermediate, transitional form unless we presuppose that it’s evolving into either a fully reptilian or a fully mammalian animal?

That’s all very interesting, but none of it constitutes evidence that Darwinian mechanisms (or any other unguided material mechanisms) brought sexual reproduction into being.

Big Bang theory is another theory with obvious theistic implications. If Judge Jones were asked to decide the scientific legitimacy of Big Bang theory, consistency in reasoning would require him to declare the theory to be religion, not science.

That’s all very interesting, but none of it constitutes evidence that Darwinian mechanisms (or any other unguided material mechanisms) brought sexual reproduction into being. When we want to know how sexual reproduction originated, we’re not enlightened by the fact that sexual reproduction can be advantageous. PvM: “Remind us again: How does ID explain the origin and maintenance of sexual reproduction?” So far as I know, ID has not yet developed an explanation for the origin of sexual reproduction. But why should that count against ID and not against Darwinism, which also has no explanation for the origin of sexual reproduction (as you’ve quite helpfully demonstrated)?

How about platypus? It has features commonly found in reptiles and features commonly found in mammals. Is there any reason to suppose that platypus is an intermediate, transitional form unless we presuppose that it’s evolving into either a fully reptilian or a fully mammalian animal?

How can we know that either platypus or Tiktaalik are intermediate, transitional forms rather than curious mosaics?

But all your word game shows is that an intelligent agent (you) can alter a meaningful sequence of letters to produce a different meaningful sequence of letters.

Mike: "I, as most here have done, have read nearly all of the ID and Creationist literature, far more than you have."

If you've read *any* creationist literature, you've read more of it than I have (although I did thumb through a book on creationism handed to me by some Jehovah's Witnesses who had come to our door). But I have read some two dozen books by design proponents. If you (and others here) are equally well-read in the design literature, then the alternative explanations for all the erroneous things you say about it are not flattering to you.

Mike: "Why do you think that ID/Creationists have managed to produce absolutely nothing in the way of scientific results after 40+ years of claims and bullying naive audiences?"

Without conceding the merits of your claim, it should be noted that the science of intelligent design, as practiced by design theorists such as Behe, Dembski, Wells, Minnich, Meyer, Bradley, etc., has only been around for some two decades. Why should anyone expect the theory to have achieved theoretical and evidentiary maturity in such a short period of time, especially since the theory has been met by dogmatic, hostile resistance from mainstream biologists (dogmatism and hostility that blogs like Pharyngula and Panda's Thumb put on prominent display)? When Darwinism had reached the two-decade mark in its history, it still didn't have an explanation for the source of the variations that were (and are) a central part of its evolutionary mechanism. When the modern synthesis (or neo-Darwinism) merged genetics and Darwinism some 70 years ago, the theory acquired a mechanism for variation (i.e., random mutations), but the theory's proponents still haven't shown that random mutations can do all the creative work that they attribute to them.

Jim: "...all your word game shows is that an intelligent agent (you) can alter a meaningful sequence of letters to produce a different meaningful sequence of letters."

Mike: "This is another indication that you don’t get it. It is a simple illustration of simple rules that lead to complex patterns. Patterns develop, evolve, flip and mutate in all kinds of physical systems in Nature, not just living systems. Crystals and snowflakes are built from very simple rules."

Simple rules build ordered patterns, not complex patterns (order and complexity are not the same thing). But even if they could build complex patterns, mere complexity (of even vast proportions) is irrelevant. The patterns in question are the highly aperiodic sequences of nucleotides that carry meaningful biological information (that is to say, sequences bearing complex specified information). There are no simple rules that can build such sequences (at least, no such rules have been discovered). If a blindly operating mechanism (such as random mutations) composes a biologically meaningful sequence of nucleotides, it does so by chance, not by following a simple rule that reliably generates complex sequences that bear meaningful information. Science is entitled to appeal to chance, but that appeal can go only so far before a better explanation ought to be sought. With respect to attributing all of life's diversity and complexity to chance (coupled with the law-like operation of natural selection), evolutionary biologists are straining credulity beyond the breaking point. I've often wondered why the Darwinian faithful regard their credulity as being epistemically superior to the incredulity of skeptics.

It would be interesting to hear you debate this point with the late Pierre-Paul Grasse, the eminent French zoologist and former president of the French Academy of Sciences. Grasse, universally regarded as one of the most learned biologists of the 20th century once wrote:

"Some contemporary biologists, as soon as they observe a mutation, talk about evolution. They are implicitly supporting the following syllogism: mutations are the only evolutionary variations, all living things undergo mutations, therefore all living things evolve. This logical scheme is, however, unacceptable: first, because its major premise is neither obvious nor general; second, because its conclusion does not agree with the facts. No matter how numerous they may be, mutations do not produce any kind of evolution.

"How does the Darwinian mutational interpretation of evolution account for the fact that the species that have been the most stable - some of them for the last hundreds of millions of years - have mutated as much as the others do? Once one has noticed microvariations (on the one hand) and specific stability (on the other), it seems very difficult to conclude that the former (microvariation) comes into play in the evolutionary process.

"Mutations have a very limited 'constructive capacity'; this is why the formation of hair by mutation of reptilian scales seems to be a phenomenon of infinitesimal probability; the formation of mammae by mutations of reptilian integumentary glands is hardly more likely...

"Mutations, in time, occur incoherently. They are not complementary to one another, nor are they cumulative in successive generations toward a given direction. They modify what preexists, but they do so in disorder, no matter how...As soon as some disorder, even slight, appears in an organized being, sickness, then death follow. There is no possible compromise between the phenomenon of life and anarchy.

"The opportune appearance of mutations permitting animals and plants to meet their needs seems hard to believe. Yet the Darwinian theory is even more demanding: a single plant, a single animal would require thousands and thousands of lucky, appropriate events. Thus, miracles would become the rule: events with an infinitesimal probability could not fail to occur...There is no law against day dreaming, but science must not indulge in it."

Jim: "...but evolutionary biologists have adduced precious little evidence supporting the macroevolutionary claims of the theory."

Henry: "1) The fossil record produces branching tree structures, with a nested hierarchy of species at the ends of the branches."

You've run aground at the outset, Henry. The fossil record from the Cambrian era (when most of the major phyla emerged in a geological eyeblind, so to speak) looks nothing like the branching tree pattern predicted by Darwinism. It looks more like a lawn.

Henry (summarizing the rest of his evidence): "Those results are expected if evolution is via accumulation of heritable changes over time, among species that don’t interchange DNA with each other. They are what is directly explained by the current theory."

All of that evidence is quite consistent with descent with modification, but it doesn't establish that random mutations and natural selection produced descent with modification. The evidence for common descent is equally compatible with ID theory, but it offers no more support for ID than it does for the presumed creative abilities of the Darwinian mechanism of mutation and selection. All of the commonalities that suggest evolutionary relationships serve with equal facility to suggest common design relationships. The case is not closed, notwithstanding Darwinist bluster to the contrary.

Jim: "Big Bang theory is another theory with obvious theistic implications. If Judge Jones were asked to decide the scientific legitimacy of Big Bang theory, consistency in reasoning would require him to declare the theory to be religion, not science."

Henry: "Hardly. The Big Bang was based on evidence, starting with the observation that distant objects show a red shift that is generally larger the more distant the object is from us, leading to the conclusion that at some point in the past everything in the observable universe was jammed into a very tiny amount of space."

Quite so. Big Bang theory, just like ID theory, is based on empirical evidence, not on theology or Scripture. But since Big Bang theory contends that nature (i.e., matter, energy, time, and space) did not exist prior to the Big Bang, it implies a cause of the Big Bang that is external to nature (or supernatural). Theists are likely to think that the supernatural cause implicated by Big Bang theory is God. If the theistic implications of ID theory require that students be protected from hearing about it, then the kind of reasoning Judge Jones used in the Dover trial would require students to also be protected from hearing about Big Bang theory.

Jim: You've run aground at the outset, Henry. The fossil record from the Cambrian era (when most of the major phyla emerged in a geological eyeblind, so to speak) looks nothing like the branching tree pattern predicted by Darwinism. It looks more like a lawn.

Henry (summarizing the rest of his evidence): "Those results are expected if evolution is via accumulation of heritable changes over time, among species that don’t interchange DNA with each other. They are what is directly explained by the current theory." All of that evidence is quite consistent with descent with modification, but it doesn't establish that random mutations and natural selection produced descent with modification. The evidence for common descent is equally compatible with ID theory, but it offers no more support for ID than it does for the presumed creative abilities of the Darwinian mechanism of mutation and selection. All of the commonalities that suggest evolutionary relationships serve with equal facility to suggest common design relationships. The case is not closed, notwithstanding Darwinist bluster to the contrary.

Jim: "How about platypus? It has features commonly found in reptiles and features commonly found in mammals. Is there any reason to suppose that platypus is an intermediate, transitional form unless we presuppose that it’s evolving into either a fully reptilian or a fully mammalian animal?"

Richard: "You seem to have a basic misunderstanding of evolution. Organisms do not follow preordained pathways so the platypus is neither evolving into being fully reptilian nor into being fully mammalian (presumably you mean into a placental)."

Read what I wrote again, Richard - this time for understanding. I wasn't arguing that platypus is evolving into being fully reptilian or fully mammalian. I was simply using platypus to illustrate the point that evolution must be presupposed before an organism can be labeled an intermediate, transitional form (not in the sense of being morphologically intermediate, but in the sense of being an evolutionary intermediate).

Jim: Quite so. Big Bang theory, just like ID theory, is based on empirical evidence, not on theology or Scripture.

But since Big Bang theory contends that nature (i.e., matter, energy, time, and space) did not exist prior to the Big Bang, it implies a cause of the Big Bang that is external to nature (or supernatural).

Theists are likely to think that the supernatural cause implicated by Big Bang theory is God. If the theistic implications of ID theory require that students be protected from hearing about it, then the kind of reasoning Judge Jones used in the Dover trial would require students to also be protected from hearing about Big Bang theory.

Simple rules build ordered patterns, not complex patterns

Read what I wrote again, Richard - this time for understanding. I wasn’t arguing that platypus is evolving into being fully reptilian or fully mammalian.

Is there any reason to suppose that platypus is an intermediate, transitional form unless we presuppose that it’s evolving into either a fully reptilian or a fully mammalian animal?

The fossil record from the Cambrian era (when most of the major phyla emerged in a geological eyeblind, so to speak) looks nothing like the branching tree pattern predicted by Darwinism. It looks more like a lawn.

Without conceding the merits of your claim, it should be noted that the science of intelligent design, as practiced by design theorists such as Behe, Dembski, Wells, Minnich, Meyer, Bradley, etc., has only been around for some two decades. Why should anyone expect the theory to have achieved theoretical and evidentiary maturity in such a short period of time, especially since the theory has been met by dogmatic, hostile resistance from mainstream biologists (dogmatism and hostility that blogs like Pharyngula and Panda’s Thumb put on prominent display)?

Simple rules build ordered patterns, not complex patterns (order and complexity are not the same thing). But even if they could build complex patterns, mere complexity (of even vast proportions) is irrelevant. The patterns in question are the highly aperiodic sequences of nucleotides that carry meaningful biological information (that is to say, sequences bearing complex specified information). There are no simple rules that can build such sequences (at least, no such rules have been discovered). If a blindly operating mechanism (such as random mutations) composes a biologically meaningful sequence of nucleotides, it does so by chance, not by following a simple rule that reliably generates complex sequences that bear meaningful information. Science is entitled to appeal to chance, but that appeal can go only so far before a better explanation ought to be sought. With respect to attributing all of life’s diversity and complexity to chance (coupled with the law-like operation of natural selection), evolutionary biologists are straining credulity beyond the breaking point. I’ve often wondered why the Darwinian faithful regard their credulity as being epistemically superior to the incredulity of skeptics.

You’ve run aground at the outset, Henry. The fossil record from the Cambrian era (when most of the major phyla emerged in a geological eyeblind, so to speak) looks nothing like the branching tree pattern predicted by Darwinism.

Quite so. Big Bang theory, just like ID theory, is based on empirical evidence, not on theology or Scripture.

No matter how numerous they may be, mutations do not produce any kind of evolution.

Grassé proposed an evolutionary theory in which living matter contains an undiscovered "internal factor" that compels life to evolve along predetermined lines ...

Having demolished Darwinism, what, then, does Grassé put in its place as an explanation of evolution? This is where Grassé becomes vague and unconvincing. He argues that living matter must contain some ‘internal factors’ that compel life to evolve along predetermined lines. These ‘factors’ are not mystical or magical, they are physical and should be discoverable by science, he reasons, and biologists should make a great effort to discover them. Many Christians will be encouraged by this distinguished biologist’s conclusion that something more than Darwinism is needed to account for the living world. And most of them will find it easier to believe in the creative activity of God, than in Grassé’s elusive ‘internal factors’.

Oh and Jim, remember your statement about science having shown how simple processes of variation and chance can increase the information in the genome as something deserving a Nobel prize?

Have you abandoned your line of arguments that such is impossible now that we have shown the evidence? Do you need more evidence?

You are making a lot of ill informed statements, such as the findings of fact being full of errors, and when it comes to defend your claims, you somehow seem to choke.

I'd love to explore in more depth your claims about information and the genome or the Findings of Fact 'errors'.

Whaddaysay?

Richard: "What do you know of chaos theory? In addition, when you throw in a little random variation situations can quickly become very complex."

I have no quarrel with the point you're making here, Richard. But the point is irrelevant. The ability of unintelligent material mechanisms to produce complexity of even mind-boggling proportions is beyond dispute, but the ability of those mechanisms to produce *specified complexity* (such as the specified complexity exhibited by the sequence of letters in this paragraph) has never been shown, either by observation or by simulation.

Richard: "No biologist does presuppose that (platypus) is evolving into either a fully reptilian or a fully mammalian animal. If you did not intend to suggest that they do, you should have used different wording."

Good grief, Richard. I made it plain from the outset that I was using platypus for the sole purpose of demonstrating that evolution must be presupposed before an organism (either living or fossilized) can be labeled an intermediate, transitional form. It's curious that platypus has both reptilian and mammalian features, but unless we presuppose that there is an evolutionary link between reptiles and mammals, there would be no reason to label platypus an intermediate, transitional form between the two. The same thing is true of fossilized organisms. It simply makes no sense to label organisms intermediate, transitional forms unless evolution is presupposed. But if evolutionary theory informs the labeling (as it does), the labeling doesn't justify the theory. Circular reasoning of that kind can't confirm anything.

Richard: "....as paleontologists study further the Burgess, Ediacaran and Dengying fossils they are finding more and more that are difficult to unequivocally place in one phylum or another, in other words, they are finding intermediate forms."

Oh, come on. Difficulty in assigning fossils to "one phylum or another" hardly signifies that those fossils are intermediate forms (an an evolutionary sense).

Richard: "Finally, if you are not capable of telling us what the theory of intelligent design states, will you please stop referring to ID theorists?"

I've been told that everyone here is already well-versed in ID literature (although the things they say and the questions they ask about ID belie that claim). But since you asked, the core propositions of ID theory are these:

1) Specified complexity (which includes irreducible complexity and complex specified information) is a reliable indicator, or hallmark, of design.

2) Many biological systems (especially at the molecular level) exhibit specified complexity.

3) Unintelligent material mechanisms (such as random mutations and natural selection) do not suffice to explain the origin of biological systems that exhibit specified complexity.

4) Therefore, complex biological systems that exhibit specified complexity are the products of design.

The core hypothesis of Darwinism could be briefly stated in this way: All biological complexity and diversity can be attributed to unintelligent material causes (primarily to random genetic mutations and natural selection).

The core hypothesis of design theory could be briefly stated in this way: Many biological systems defy wholly material explanations and can be attributed to an intelligent cause (or causes).

The purpose of the science of intelligent design (as it is currently construed) is to develop theoretical, evidentiary, logical, and mathematical support for the design hypothesis.

There are three quite legitimate questions that can be asked about any system, biological or otherwise:

1) Was this system designed?

2) How was the design actualized?

3) Who was the designer?

As ID theory is currently construed, it is focused entirely on the first question, but critics keep demanding that it answer all three questions. These critics apparently fail to appreciate that unless the first question can be answered in the affirmative, the other two questions are pointless. But if the first question *can* be answered in the affirmative in a scientifically rigorous way (as ID theorists contend it can), and if that affirmative answer captures the imagination of enough biologists to allow ID to win the institutional and financial support it needs to move into the scientific mainstream, then there could be a great deal of scientific research undertaken to try to answer the second question. But the third question, ID theorists contend, is a question that should be referred to philosophers and theologians.

Mike: "If you are willing to admit that ID has not achieved 'theoretical and evidentiary maturity', why do you suppose so much time, effort and money goes into getting an ID curriculum into public education without going through the vetting processes of scientific peer-review?"

As you no doubt know, Mike, Discovery Institute is the primary institutional home of what has come to be called the ID movement. But as you apparently don't know, DI *opposes* attempts by school boards to mandate the teaching of design theory in the public schools precisely because the theory lacks sufficient theoretical maturity to warrant such a thing (you can verify this for yourself by going to DI's website). DI has no objections, however, to biology teachers teaching ID concepts to their students if they choose to do so. DI, unlike the Darwinian establishment, supports academic freedom.

It should also be noted that Discovery Institute opposed the actions taken by the Dover school board.

Mike: "Panda’s Thumb, the National Center for Science Education, Pharyngula, and other such efforts are clearing houses for exposing the pseudo-science tactics of the Discovery Institute and the thousands of grass-roots religious sects attempting to leverage off ID and Scientific Creationism to get their religious shtick into the classroom."

I'm sure that's how they view their mission, but what they show to those who don't share their commitment to Darwinism is that mainstream evolutionary biology has become utterly dogmatic. They're performing a valuable service by doing that: dogmatism exposed might become dogmatism defeated, an outcome much to be desired by anyone with a genuine respect for science.

PvM: "You are making a lot of ill informed statements, such as the findings of fact being full of errors..."

I was wrong about one thing, PvM: the ACLU's hilariously titled "Findings of Fact" was presented to Judge Jones about a month before he issued his ruling, not a month before the trial (as I had said). Chalk it up to faulty memory. But I was right about two other things: that in the part of his decision where Judge Jones presumed to decide that ID theory is religion, not science, he copied the ACLU's "Findings of Fact" nearly verbatim (so much for weighing the evidence with judicial impartiality); and that the "Findings of Facts" are chock full of errors (I've already given you a reference where you can confirm this for yourself).

If the Discovery Institute is so opposed to letting an immature "science" like Intelligent Design "theory" be taught in schools before it has "matured," then why were they so eager to have it taught in the science curriculum at Dover, Pennsylvania, complete with the incompetently edited "Of Pandas and People"?

Furthermore, if the Discovery Institute is so concerned with maturing Intelligent Design "theory," then, why is it that every single one of the members of the Discovery Institute have done absolutely no experimental work aimed at validating the organization's pet theory since the Discovery Institute's inception?

the ability of those mechanisms to produce *specified complexity* (such as the specified complexity exhibited by the sequence of letters in this paragraph) has never been shown, either by observation or by simulation.

It’s curious that platypus has both reptilian and mammalian features, but unless we presuppose that there is an evolutionary link between reptiles and mammals, there would be no reason to label platypus an intermediate, transitional form between the two. The same thing is true of fossilized organisms. It simply makes no sense to label organisms intermediate, transitional forms unless evolution is presupposed. But if evolutionary theory informs the labeling (as it does), the labeling doesn’t justify the theory. Circular reasoning of that kind can’t confirm anything.

But since you asked, the core propositions of ID theory are these:

The core hypothesis of Darwinism could be briefly stated in this way: All biological complexity and diversity can be attributed to unintelligent material causes (primarily to random genetic mutations and natural selection).

The core hypothesis of design theory could be briefly stated in this way: Many biological systems defy wholly material explanations and can be attributed to an intelligent cause (or causes).

I was wrong about one thing, PvM: the ACLU’s hilariously titled “Findings of Fact” was presented to Judge Jones about a month before he

issued his ruling, not a month before the trial (as I had said). Chalk it up to faulty memory. But I was right about two other things: that in the part of his decision where Judge Jones presumed to decide that ID theory is religion, not science, he copied the ACLU’s “Findings of Fact” nearly verbatim (so much for weighing the evidence with judicial impartiality); and that the “Findings of Facts” are chock full of errors (I’ve already given you a reference where you can confirm this for yourself).

3) Unintelligent material mechanisms (such as random mutations and natural selection) do not suffice to explain the origin of biological systems that exhibit specified complexity.

— Jim

As you no doubt know, Mike, Discovery Institute is the primary institutional home of what has come to be called the ID movement. But as you apparently don’t know, DI *opposes* attempts by school boards to mandate the teaching of design theory in the public schools precisely because the theory lacks sufficient theoretical maturity to warrant such a thing (you can verify this for yourself by going to DI’s website). DI has no objections, however, to biology teachers teaching ID concepts to their students if they choose to do so. DI, unlike the Darwinian establishment, supports academic freedom.

I’m sure that’s how they view their mission, but what they show to those who don’t share their commitment to Darwinism is that mainstream evolutionary biology has become utterly dogmatic. They’re performing a valuable service by doing that: dogmatism exposed might become dogmatism defeated, an outcome much to be desired by anyone with a genuine respect for science.

But I was right about two other things: that in the part of his decision where Judge Jones presumed to decide that ID theory is religion, not science, he copied the ACLU’s “Findings of Fact” nearly verbatim (so much for weighing the evidence with judicial impartiality); and that the “Findings of Facts” are chock full of errors (I’ve already given you a reference where you can confirm this for yourself).

PvM: "Darwinism remains as strong as ever. The answer to this is surprisingly simple: the arguments against Darwinism show more of a level of ignorance rather than a real problem."

The strength of Darwinism (like beauty) is in the eye of the beholder. It would be difficult to sustain the notion that evolutionary biologist Lynn Margulis (the late Carl Sagan's wife) is ignorant of either biology in general or Darwinism in particular, yet she has serious doubts about Darwinism's explanatory power. Margulis, famous for her theory that mitochondria were once independent bacterial cells, describes herself as a "Darwinist," and she is - IF that term is understood to mean someone who accepts that evolution results from random variations acted on by natural selection. But Margulis is not a neo-Darwinist (to remind you, I use the term "Darwinism" as a shorthand way to refer to neo-Darwinism). She is entirely unpersuaded that random mutations can provide the variations needed for evolution to proceed very far (for example, from fish to men). She has said that history will ultimately judge neo-Darwinism as "a minor twentieth-century religious sect within the sprawling religious persuasion of Anglo-Saxon biology."

In her public talks, Margulis frequently asks molecular biologists in the audience to identify a single unambiguous example of a new species being formed by the accumulation of random mutations. No replies have been forthcoming. In 2002 she wrote: "Speciation, whether in the remote Galapagos, in the laboratory cages of the drosophilosophers, or in the crowded sediments of the paleontologists, still has never been directly traced."

Margulis would also take issue with the claims made here that detailed, testable Darwinian pathways to complex biological systems have been identified. She characterizes the empirical solidity of neo-Darwinism in this way:

"Like a sugary snack that temporarily satisfies our appetite but deprives us of more nutritious foods, neo-Darwinism sates intellectual curiosity with abstractions bereft of actual details - whether metabolic, biochemical, ecological, or of natural history."

Echoing Margulis, James Shapiro (a molecular biologist at the University of Chicago) candidly observed that "there are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular systems, only a variety of wishful speculations. It is remarkable that Darwinism is accepted as a satisfactory explanation for such a vast subject - evolution - with so little rigorous examination of how well its basic theses work in illuminating specific instances of biological adaptation or diversity." And in virtually identical language, noted cell biologist Franklin Harold wrote (in "The Way of the Cell") that "(t)here are presently no detailed Darwinian accounts of the evolution of any biochemical or cellular system, only a variety of wishful speculations."

Margulis characterizes the theoretical condition of neo-Darwinism in this way:

"Neo-Darwinism, which insists on (the slow accrual of mutations), is in a complete funk."

You'll no doubt accuse me once more of "quote mining" (which is not an actual argument, as you seemingly think), but if you're going to lay my objections to Darwinism on ignorance, then you also need to show that Margulis, Shapiro, and Harold - along with many other scientists and scholars who have doubts about Darwinism - are all ignoramuses.

PvM: "Since specified complexity is defined as the inability of material mechanisms to explain a system (yet), calling something specified complex is basically an admission of ignorance."

Good grief. Mike said you people are well-versed in design theory, in which case I'll leave it to Mike to provide you with the correct definition of specified complexity. (Note: When I said that one of the core propositions of ID theory is that specified complexity is a reliable indicator of design, that did not constitute a definition of specified complexity. I thought you knew what it was, but I was wrong.)

You’ll no doubt accuse me once more of “quote mining” (which is not an actual argument, as you seemingly think), but if you’re going to lay my objections to Darwinism on ignorance, then you also need to show that Margulis, Shapiro, and Harold - along with many other scientists and scholars who have doubts about Darwinism - are all ignoramuses.

The major steps in evolution involved symbiogenesis, which Margulis described succinctly as “the inheritance of acquired genomes” and more formally in its relationship to symbiosis, “the long-term physical association between members of different types (species).” The problem with neo-Darwinism, Margulis concluded, is that “Random changes in DNA alone do not lead to speciation. Symbiogenesis–the appearance of new behaviors, tissues, organs, organ systems, physiologies, or species as a result of symbiont interaction–is the major source of evolutionary novelty in eukaryotes–animals, plants, and fungi.”

I have no quarrel with the point you’re making here, Richard. But the point is irrelevant. The ability of unintelligent material mechanisms to produce complexity of even mind-boggling proportions is beyond dispute, but the ability of those mechanisms to produce *specified complexity* (such as the specified complexity exhibited by the sequence of letters in this paragraph) has never been shown, either by observation or by simulation.

Mike: "Did you also suppress the memory of the Wedge Document? Have you even read the Wedge Document? Do you know anything about its history? Do you know its primary author? Do you know who wrote the language injected by Rick Santorum into the No-Child-Left-Behind Bill in Congress? Do you know about the activities in Kansas, Florida, Ohio, Texas, and other states? Do you know about the bills introduced into State Legislatures that push ID? Do you know about the graduate student at Ohio State who stacked his committee? We do. And there is much more."

Yes, I've read the Wedge Document. But I really don't have any interest in your paranoia. I've heard it all before. People who have good arguments stick to making good arguments. People who don't have good arguments attack the motives, the intentions, the character, and the intelligence of those with whom they disagree. Any skeptic of Darwinism reading the kind of arguments that Darwinists make against ID will almost instantly perceive that the Darwinian establishment is in full panic.

With that, I'll bid you farewell. It's actually been somewhat pleasurable being here. The insults aren't as pervasive as they are on Pharyngula, but I still haven't found someone who can defend Darwinism without making himself a royal pain in the ass.

One closing comment: This thread began with Nick's claim that ID theorists had shifted from saying that components of an irreducibly complex biological system could not perform any functions of their own to saying that they could. Yet Behe, who developed the concept in "Darwin's Black Box," specifically said that the components of IC systems might serve functions of their own. Nothing has changed, including the refusal of Darwinists to try to understand the arguments that design theorists make.

Good grief. Mike said you people are well-versed in design theory, in which case I’ll leave it to Mike to provide you with the correct definition of specified complexity.

I still haven’t found someone who can defend Darwinism without making himself a royal pain in the ass.

PvM: “Since specified complexity is defined as the inability of material mechanisms to explain a system (yet), calling something specified complex is basically an admission of ignorance.” Good grief. Mike said you people are well-versed in design theory, in which case I’ll leave it to Mike to provide you with the correct definition of specified complexity. (Note: When I said that one of the core propositions of ID theory is that specified complexity is a reliable indicator of design, that did not constitute a definition of specified complexity. I thought you knew what it was, but I was wrong.)

Before I proceed, however, I note that Dembski makes an important concession to his critics. He refuses to make the second assumption noted above. When the EF implies that certain systems are intelligently designed, Dembski does not think it follows that there is some intelligent designer or other. He says that, "even though in practice inferring design is the first step in identifying an intelligent agent, taken by itself design does not require that such an agent be posited. The notion of design that emerges from the design inference must not be confused with intelligent agency" (TDI, 227, my emphasis). Source: Ryan Nichols, The Vacuity of Intelligent Design Theory

I still haven’t found someone who can defend Darwinism without making himself a royal pain in the ass.

— Jim

Mike: Duh; looks complicated to me. Musta been designed. Here; I’ll make up some probability numbers, take the negative logarithm to base 2, and if it is a big enough number, it was intelligently designed by a sectarian god of some sort which we won’t discuss in order to make it look respectable enough to get around Edwards vs. Aguillard.

In fact, that seems quite accurate although it is framed in much more official sounding language of logarithms, specification and No Free Lunches, all of which collapse given the actual evidence. That of course does not prevent Dembski (and Marks) from trying again to shore up a useful mathematical construct. But until ID stops relying on ignorance, and starts proposing its own explanations, it is doomed to remain a scientifically vacuous concept.

And I can easily show that this is the case:

Explain to me how ID explains anything in a non-trivial manner?

With that, I’ll bid you farewell. It’s actually been somewhat pleasurable being here. The insults aren’t as pervasive as they are on Pharyngula, but I still haven’t found someone who can defend Darwinism without making himself a royal pain in the ass.

That of course does not prevent Dembski (and Marks) from trying again to shore up a useful mathematical construct. But until ID stops relying on ignorance, and starts proposing its own explanations, it is doomed to remain a scientifically vacuous concept.

With that, I’ll bid you farewell. It’s actually been somewhat pleasurable being here. The insults aren’t as pervasive as they are on Pharyngula, but I still haven’t found someone who can defend Darwinism without making himself a royal pain in the ass.

Yes, I’ve read the Wedge Document. But I really don’t have any interest in your paranoia. I’ve heard it all before. People who have good arguments stick to making good arguments. People who don’t have good arguments attack the motives, the intentions, the character, and the intelligence of those with whom they disagree. Any skeptic of Darwinism reading the kind of arguments that Darwinists make against ID will almost instantly perceive that the Darwinian establishment is in full panic.

That’s something that ID theory can’t decide, but as a theist, I think that God is the designer implicated by design theory. ID theorists argue that biological data can justify design inferences, but they also argue that there is no inferential trail leading from the biological data to the identity of the designer. If ID theory is a theistic enterprise committed to proving that God exists, it’s not a very promising strategy on the part of ID theorists to repeatedly tell people that ID theory can’t deliver such proof.

If the Discovery Institute is so opposed to letting an immature “science” like Intelligent Design “theory” be taught in schools before it has “matured,” then why were they so eager to have it taught in the science curriculum at Dover, Pennsylvania, complete with the incompetently edited “Of Pandas and People”?

http://www.discovery.org/scripts/viewDB/filesDB-download.php?command=download&id=1372

Discovery Institute...issued a statement on October 6, 2004 opposing the policy under consideration by the Dover board:

"[A] recent news report seemed to suggest that the Center for Science & Culture endorses the adoption of textbook supplements teaching about the scientific theory of intelligent design (ID), which simply holds that certain aspects of the universe and living things can best be explained as the result of an intelligent cause rather
than merely material and purposeless processes like natural selection. Any such suggestion is incorrect."

Despite the lack of support from the Discovery Institute, on October 18, 2004 the board voted to adopt a policy that required discussion of ID in biology classes. Shortly thereafter, the Discovery Institute expressed to the news media its opposition to the adopted policy, and the Institute’s disagreement with the policy was acknowledged in an article published in early November 2004 by the Associated Press. The board later modified its policy to require that an oral disclaimer be read to biology classes. The disclaimer
stated, “Intelligent Design is an explanation of the origin
of life that differs from Darwin’s view” and noted that
“[t]he reference book, 'Of Pandas and People', is available for students who might be interested in gaining an understanding of what Intelligent Design actually involves.”

Discovery Institute…issued a statement on October 6, 2004 opposing the policy under consideration by the Dover board:

And the DI had sent some confusing messages with the release of a book titled "Intelligent Design in Public School Science Curricula: A Legal Guidebook" by David K. DeWolf, Stephen C. Meyer, Mark E. DeForrest

"If you actually read about the Big Bang, you would know that it states that all of the matter in the Universe had once converged at a single point before expanding."

http://www.big-bang-theory.com/

The Big Bang theory is an effort to explain what happened at the very beginning of our universe. Discoveries in astronomy and physics have shown beyond a reasonable doubt that our universe did in fact have a beginning. Prior to that moment there was nothing; during and after that moment there was something: our universe. The big bang theory is an effort to explain what happened during and after that moment.

According to the standard theory, our universe sprang into existence as "singularity" around 13.7 billion years ago. What is a "singularity" and where does it come from? Well, to be honest, we don't know for sure. Singularities are zones which defy our current understanding of physics. They are thought to exist at the core of "black holes." Black holes are areas of intense gravitational pressure. The pressure is thought to be so intense that finite matter is actually squished into infinite density (a mathematical concept which truly boggles the mind). These zones of infinite density are called "singularities." Our universe is thought to have begun as an infinitesimally small, infinitely hot, infinitely dense, something - a singularity. Where did it come from? We don't know. Why did it appear? We don't know.

After its initial appearance, it apparently inflated (the "Big Bang"), expanded and cooled, going from very, very small and very, very hot, to the size and temperature of our current universe. It continues to expand and cool to this day and we are inside of it: incredible creatures living on a unique planet, circling a beautiful star clustered together with several hundred billion other stars in a galaxy soaring through the cosmos, all of which is inside of an expanding universe that began as an infinitesimal singularity which appeared out of nowhere for reasons unknown. This is the Big Bang theory.

There are many misconceptions surrounding the Big Bang theory. For example, we tend to imagine a giant explosion. Experts however say that there was no explosion; there was (and continues to be) an expansion. Rather than imagining a balloon popping and releasing its contents, imagine a balloon expanding: an infinitesimally small balloon expanding to the size of our current universe.

Another misconception is that we tend to image the singularity as a little fireball appearing somewhere in space. According to the many experts however, space didn't exist prior to the Big Bang. Back in the late '60s and early '70s, when men first walked upon the moon, "three British astrophysicists, Steven Hawking, George Ellis, and Roger Penrose turned their attention to the Theory of Relativity and its implications regarding our notions of time. In 1968 and 1970, they published papers in which they extended Einstein's Theory of General Relativity to include measurements of time and space. According to their calculations, time and space had a finite beginning that corresponded to the origin of matter and energy." The singularity didn't appear in space; rather, space began inside of the singularity. Prior to the singularity, nothing existed, not space, time, matter, or energy - nothing. So where and in what did the singularity appear if not in space? We don't know. We don't know where it came from, why it's here, or even where it is. All we really know is that we are inside of it and at one time it didn't exist and neither did we.

Big Bang theory is another theory with obvious theistic implications. If Judge Jones were asked to decide the scientific legitimacy of Big Bang theory, consistency in reasoning would require him to declare the theory to be religion, not science.

— Jim

PvM: And the DI had sent some confusing messages with the release of a book titled "Intelligent Design in Public School Science Curricula: A Legal Guidebook" by David K. DeWolf, Stephen C. Meyer, Mark E. DeForrest

The Big Bang theory is an effort to explain what happened at the very beginning of our universe…

"...why is it that every single one of the members of the Discovery Institute have done absolutely no experimental work aimed at validating the organization’s pet theory since the Discovery Institute’s inception?"

http://www.evolutionnews.org/2006/10/response_to_barbara_forrests_k_7.html

Important Facts Left Out About ID Research

In her Kitzmiller account, Barbara Forrest leaves out information about the scientific research supporting ID, claiming "creationists are executing every phase except producing scientific data to support ID." Ignoring her usage of the "creationist" label, Dr. Forrest's argument mimics that of Judge Jones. Both Dr. Forrest and Judge Jones ignored the testimony provided in the courtroom during the Kitzmiller trial by Scott Minnich about his own experiments which demonstrate the irreducible complexity of the flagellum. Amazingly, Judge Jones then wrote that "ID has not been the subject of testing or research" (pg. 64 of online version).

The best way to refute Judge Jones / Barbara Forrest's claim is to let the reader see the testimony of Scott Minnich. Minnich is a pro-ID microbiologist who testified as follows on the next-to-last-day of the trial about his own research and experimentation into the irreducibly complex nature of the bacterial flagellum:

Q. Do you know employ principles and concepts from intelligent design in your work?

A. I do.

Q. And I'd like for you to explain that further. I know you've prepared several slides to do that.

A. Sure. All right. I work on the bacterial flagellum, understanding the function of the bacterial flagellum for example by exposing cells to mutagenic compounds or agents, and then scoring for cells that have attenuated or lost motility. This is our phenotype. The cells can swim or they can't. We mutagenize the cells, if we hit a gene that's involved in function of the flagellum, they can't swim, which is a scorable phenotype that we use. Reverse engineering is then employed to identify all these genes. We couple this with biochemistry to essentially rebuild the structure and understand what the function of each individual part is. Summary, it is the process more akin to design that propelled biology from a mere descriptive science to an experimental science in terms of employing these techniques.

So it was inoculated right here, and over about twelve hours it's radiated out from that point of inoculant. Here is this same derived from that same parental clone, but we have a transposon, a jumping gene inserted into a rod protein, part of the drive shaft for the flagellum. It can't swim. It's stuck, all right? This one is a mutation in the U joint. Same phenotype. So we collect cells that have been mutagenized, we stick them in soft auger, we can screen a couple of thousand very easily with a few undergraduates, you know, in a day and look for whether or not they can swim.

We have a mutation in a drive shaft protein or the U joint, and they can't swim. Now, to confirm that that's the only part that we've affected, you know, is that we can identify this mutation, clone the gene from the wild type and reintroduce it by mechanism of genetic complementation. So this is, these cells up here are derived from this mutant where we have complemented with a good copy of the gene. One mutation, one part knock out, it can't swim. Put that single gene back in we restore motility. Same thing over here. We put, knock out one part, put a good copy of the gene back in, and they can swim. By definition the system is irreducibly complex. We've done that with all 35 components of the flagellum, and we get the same effect.

(Kitzmiller Transcript of Testimony of Scott Minnich pgs. 99-108, Nov. 3, 2005)

During this testimony, Scott Minnich showed slides in the courtroom documenting his own research experiments, which performed knockout experiments upon the flagellum, and found that the flagellum is irreducibly complex. Minnich produced relevant experimental data which confirmed a prediction made by intelligent design, and he used this research to support intelligent design in the courtroom. Yet Dr. Forrest completely ignored this testimony, as did Judge Jones, who did not even mention it in the Kitzmiller ruling. Given the testimony of an expert witnesses's own personal experiments which was directly presented before him, it is incredible that Judge Jones could write "ID has not been the subject of testing or research."

Dr. Scott Minnich, a microbiologist at the University of Idaho, is a fellow of Discovery Institute's Center for Science & Culture

http://www.discovery.org/csc/fellows.php

FYI

http://www.newworldencyclopedia.org/entry/Intelligent_design

Important Facts Left Out About ID Research

http://en.wikipedia.org/wiki/Evolution_of_flagella

FYI

Among other things, "Truth"Detector, did the scientists who did that experiment create other knockout bacteria that corresponded with all of the other component proteins? To declare that the bacterial flagellum is irreducibly complex after only experimenting with the assessment of a single component protein is not only ignorant hubris, but sloppy science, if science at all. It's like declaring that a car is an irreducibly complex structure because it can not function without all of its sparkplugs. Furthermore, why didn't the Discovery Institute mention this experiment as evidence at the Dover Trial? Why is it Judge Jones' fault that none of the Discovery Institute stars mentioned this experiment? Why didn't this single experiment convince the Templeton Foundation to give the Discovery Institute more grant money? What are the other experiments and research projects the staff of the Discovery Institute working on?

"(I)n judging the nature of the debate over the origin and subsequent diversity of life, there is (an) aspect of litigation that sheds light on why the debate is conducted as it is. A psychology that commonly operates in litigation is that opposing lawyers are primed to reject every statement by the other side - for there is no advantage in considering that the statements might be true. Lawyers are not engaged in a mutual search for the truth. In comparing the writings of the science-trained advocates of intelligent design with the writings of their opponents, I see that psychology occurring again and again on just one side of the debate: the side of the science establishment. That psychology is *not* evident in the work of intelligent design proponents that I have read. The fact that it is missing from their work is one reason why I have come to trust them more than their opponents in this debate. I think that the intelligent design advocates want to talk with me about looking for the truth. In sharp contrast, the science establishment is primarily engaged in using intimidation, ridicule, and innuendo against its critics." - Attorney Edward Sisson (LLD, magna cum laude, Georgetown; BS, environmental design, MIT), describing the kind of argumentation that dominates blogs like the Panda's Thumb and Pharyngula to a tee.

From your copy-and-paste temper tantrum, are we to presume that you are wholly incapable of answering any questions asked of you in your own words, then?

I think that the intelligent design advocates want to talk with me about looking for the truth.

why is it that every single one of the members of the Discovery Institute have done absolutely no experimental work aimed at validating the organization’s pet theory since the Discovery Institute’s inception?”

My working theory: TruthDetector is Larry trying to hide who he is.

That psychology is *not* evident in the work of intelligent design proponents that I have read. The fact that it is missing from their work is one reason why I have come to trust them more than their opponents in this debate. I think that the intelligent design advocates want to talk with me about looking for the truth. In sharp contrast, the science establishment is primarily engaged in using intimidation, ridicule, and innuendo against its critics.” - Attorney Edward Sisson (LLD, magna cum laude, Georgetown; BS, environmental design, MIT), describing the kind of argumentation that dominates blogs like the Panda’s Thumb and Pharyngula to a tee.

My working theory: TruthDetector is Larry trying to hide who he is.

"The Darwinian claim to explain all of evolution is a popular half-truth whose lack of explicative power is compensated for only by the religious ferocity of its rhetoric." - Evolutionary biologist Lynn Margulis, "Acquiring Genomes: A Theory of the Origin of Species"

FYI

http://www.discovery.org/scripts/viewDB/filesDB-download.php?command=download&id=1186

But, she quickly added, “I am definitely a Darwinist though.

Lynn Margulis, Dorion Sagan, Acquiring Genomes: The Theory of the Origins of the Species , pgs 29-30 We agree that very few potential offspring ever survive to reproduce and that populations do change through time, and that therefore natural selection is of critical importance to the evolutionary process. But this Darwinian claim to explain all of evolution is a popular half-truth whose lack of explicative power is compensated for only by the religious ferocity of its rhetoric. Althouth random mutations influenced by the course of evolution, their influence was mainly by loss, alteration, and refinement. One mutation confers resistance to malaria but also makes happy blood cells into the deficient oxygen carriers of sickle cell anemics. Another mutation converts a gorgeous newborn into a cystic fibrosis patient or a victim of early onset diabetes. One mutation causes a flightly red-eyed fruit fly fail to take wing. Never, however, did that one mutation make a wing, a fruit, a woody stem, or a claw appear. Mutations, in summary, tend to induce sickness, death, or deficiencies. No evidence in the vast literation of heredity change shows unambiguous evidence that random mutation itself, even with geographical isolation of populations, leads to speciation. Then how do new species come into being? How do cauliflowers descend from tiny, wild Mediterranean cabbagelike plants, or pigs from wild boars? Darwin's successors have returned to the rugged volcanic islands of the Galapagos, off the coast of Ecuador, to watch evolution in action. Perhaps the most compelling case of nonstop evolutionary change is the work of Professors Peter and Rosemary Grant on exactly those finches that were made famous by Darwin and his successors. The paucity of other birds on these remote outposts and the severity of environmental pressures led, somehow, to rampant and rapid speciation from common avian ancestors. As Jonathan Wiener (1999) describes in his book, The Beak of the Finch, study of variation and the changes in these birds, isolated from the South American mainland for a million years, gives us the best traditional view of how the speciation process should work.

TruthDetector: FYI http://www.discovery.org/scripts/viewDB/filesDB-download.php?command=download&id=1186

FYI

"The horrid doubt always arises whether the convictions of man's mind, which has developed from the mind of the lower animals, are of any value or at all trustworthy. Would anyone trust the conviction of a monkey's mind, if there are any convictions in such a mind?" (Charles Darwin, Letter to W. Graham, July 3rd, 1881, in Darwin, F., ed., "The Life and Letters of Charles Darwin," 1898, Basic Books: New York NY, Vol. I., 1959, reprint, p.285)

"If my mental processes are determined wholly by the motions of atoms in my brain, I have no reason to suppose that my beliefs are true...and hence I have no reason for supposing my brain to be composed of atoms." (J.B.S. Haldane, "Possible Worlds," Chatto & Windus: London, 1927, p.209)

"The idea that one species of organism is, unlike all the others, oriented not just toward its own increased prosperity but toward Truth, is as un-Darwinian as the idea that every human being has a built-in moral compass - a conscience that swings free of both social history and individual luck." (Richard Rorty, "Untruth and Consequences," The New Republic, July 31, 1995, pp. 32-36)

"The Astonishing Hypothesis is that 'You,' your joys and your sorrows, your memories and your ambitions, your sense of personal identity and free will, are in fact no more than the behavior of a vast assembly of nerve cells and their associated molecules." (Francis Crick, "The Astonishing Hypothesis: The Scientific Search for the Soul," Scribner's, 1994, p. 3)

"I am astonished that otherwise intelligent and informed people, including physicians, are reluctant to believe that mind, as part of life, is matter and only matter." (Arthur Kornberg, "The Two Cultures: Chemistry and Biology," Biochemistry 26, 1987, pp. 6888-91)

"On Kornberg's own premises...his astonishment was unjustified. Presumably, one kind of chemical reaction in the brain causes Kornberg to accept materialist reductionism, while another kind of reaction causes those physicians to doubt it." (Phillip Johnson, "Reason in the Balance: The Case Against Naturalism in Science, Law & Education," Intervarsity Press, 1995, p. 65)

"(If the) mind is a product of the irrational (which materialistic-naturalistic evolution claims it is) then how shall I trust my mind when it tells me about Evolution? What makes it impossible that it should be true is not so much the lack of evidence for this or that scene in the drama as the fatal self-contradiction which runs right through it. The Myth (of Evolution) cannot even get going without accepting a good deal from the real sciences. And the real sciences cannot be accepted for a moment unless rational inferences are valid: for every science claims to be a series of inferences from observed facts. It is only by such inferences that you can reach your nebulae and protoplasm and dinosaurs and sub-men and cave-men at all. Unless you start by believing that reality in the remotest space and the remotest time rigidly obeys the laws of logic, you can have no ground for believing in any astronomy, any biology, any palaeontology, any archaeology. To reach the positions held by the real scientists - which are then taken over by the Myth - you must, in fact, treat reason as an absolute. But at the same time the Myth asks me to believe that reason is simply the unforeseen and unintended by-product of a mindless process at one stage of its endless and aimless becoming. The content of the Myth thus knocks from under me the only ground on which I could possibly believe the Myth to be true. If my own mind is a product of the irrational - if what seem my clearest reasonings are only the way in which a creature conditioned as I am is bound to feel - how shall I trust my mind when it tells me about Evolution? They say in effect: 'I will prove that what you call a proof is only the result of mental habits which result from heredity which results from bio-chemistry which results from physics.' But this is the same as saying: 'I will prove that proofs are irrational': more succinctly, 'I will prove that there are no proofs': The fact that some people of scientific education cannot by any effort be taught to see the difficulty, confirms one's suspicion that we here touch a radical disease in their whole style of thought. But the man who does see it, is compelled to reject as mythical the cosmology in which most of us were brought up. That it has embedded in it many true particulars I do not doubt: but in its entirety, it simply will not do. Whatever the real universe may turn out to be like, it can't be like that." (C.S. Lewis,"The Funeral of a Great Myth," in "Christian Reflections," 1967, Hooper, W., ed., Fount: Glasgow UK, Fourth Impression, 1988, pp.117-118)

"Here is a curious case: If Darwin's naturalism is true, there is no way of even establishing its credibility let alone proving it. Confidence in logic is ruled out. Darwin's own theory of human origins must therefore be accepted by an act of faith. One must hold that a brain, a device that came to be through natural selection and chance-sponsored mutations, can actually know a proposition or set of propositions to be true. C.S. Lewis puts the case this way: 'If all that exists is Nature, the great mindless interlocking event, if our own deepest convictions are merely the by-products of an irrational process, then clearly there is not the slightest ground for supposing that our sense of fitness and our consequent faith in uniformity tell us anything about a reality external to ourselves. Our convictions are simply a fact about us - like the colour of our hair. If Naturalism is true we have no reason to trust our conviction that Nature is uniform.' (C.S. Lewis, 'Miracles: A Preliminary Study,' 1947, Fontana: London, 1960, Revised Edition, 1963, reprint, p.109] What we need for such certainty is the existence of some 'Rational Spirit' outside both ourselves and nature from which our own rationality could derive. Theism assumes such a ground; naturalism does not." (J.W. Sire, "The Universe Next Door: A Basic World View Catalog," 1976, InterVarsity Press: Downers Grove IL, Second Edition, 1988, pp.94-95)

"The validity of rational thought, accepted in an utterly non-naturalistic, transcendental (if you will), supernatural sense is the necessary presupposition of all other theorizing. There is simply no sense in beginning with a view of the universe and trying to fit in the clailms of thought at a later stage. By thinking at all we have claimed that our thoughts are more than mere natural events. All other propositions must be fitted in as best they can around that primary claim." (C.S. Lewis, "A Christian Reply to Professor Price," Phoenix Quarterly, vol. 1, No. 1, Autumn 1946)

Questions for discussion:

Modern evolutionary theory (or ToE) reduces the human mind to matter. All thoughts, then, are material events produced by material causes. Material causes do not intend their effects; they merely produce them without reason or understanding. Material causes are therefore irrational.

1) How is it possible to defend ToE with arguments that are the products of irrational material causes (as they must be if ToE is true)?

2) On what grounds could we suppose that arguments for ToE are more trustworthy than arguments against ToE if all arguments are the products of irrational material causes (as they must be if ToE is true)?

3) If ToE is true, how could we possibly know it?

3) If ToE is true, how could we possibly know it?

The problem here is that when you say you’re discussing “evolution,” it’s hard to know what you mean.

the just-so story

A sequence of nucleotides produced by random mutations will have zero shannon information,

Empirical testing has been at the heart of my comments about the problem of induction.

“Reasonable doubt” is a legal concept, not a scientific concept.

resort to condescension

that doesn’t make information a material phenomenon.

Big Bang theory is another theory with obvious theistic implications. If Judge Jones were asked to decide the scientific legitimacy of Big Bang theory, consistency in reasoning would require him to declare the theory to be religion, not science.

it implies a cause of the Big Bang that is external to nature (or supernatural).

halo said: "At any rate, critics of the argument from irreducible complexity look to save Darwinism not by enlisting direct Darwinian pathways to bring about irreducibly complex systems but by enlisting indirect Darwinian pathways to bring them about. In indirect Darwinian pathways, a system evolves not by preserving and enhancing an existing function but by continually transforming its function… How does the argument from irreducible complexity handle indirect Darwinian pathways? Here the point at issue is no longer logical but empirical. The fact is that for irreducibly complex biochemical systems, no indirect Darwinian pathways are known. At best biologists have been able to isolate subsystems of such systems that perform other functions. But any reasonably complicated machine always includes subsystems that perform functions distinct from the original machine. So the mere occurrence or identification of subsystems that could perform some function on their own is no evidence for an indirect Darwinian pathway leading to the system. [[What’s needed is a seamless Darwinian account that’s both detailed and testable of how subsystems undergoing coevolution could gradually transform into an irreducibly complex system.]] No such accounts are available or have so far been forthcoming. Indeed, if such accounts were available, critics of intelligent design would merely need to cite them, and intelligent design would be refuted."

halo said: "This little story teaches several lessons. First, the word jump can be offered as an explanation of how someone crossed a barrier, but the explanation can range from completely convincing to totally inadequate depending on the details (such as how wide the barrier is). Second, [[long journeys can be made much more plausible if they are explained as a series of smaller jumps rather than one great leap]]. And third, in the absence of smaller jumps, it is very difficult to prove right or wrong someone who asserts that stepping stones existed in the past but have disappeared."

Sean said:

halo said: "At any rate, critics of the argument from irreducible complexity look to save Darwinism not by enlisting direct Darwinian pathways to bring about irreducibly complex systems but by enlisting indirect Darwinian pathways to bring them about. In indirect Darwinian pathways, a system evolves not by preserving and enhancing an existing function but by continually transforming its function… How does the argument from irreducible complexity handle indirect Darwinian pathways? Here the point at issue is no longer logical but empirical. The fact is that for irreducibly complex biochemical systems, no indirect Darwinian pathways are known. At best biologists have been able to isolate subsystems of such systems that perform other functions. But any reasonably complicated machine always includes subsystems that perform functions distinct from the original machine. So the mere occurrence or identification of subsystems that could perform some function on their own is no evidence for an indirect Darwinian pathway leading to the system. [[What’s needed is a seamless Darwinian account that’s both detailed and testable of how subsystems undergoing coevolution could gradually transform into an irreducibly complex system.]] No such accounts are available or have so far been forthcoming. Indeed, if such accounts were available, critics of intelligent design would merely need to cite them, and intelligent design would be refuted."

Behe Wrote (c) 1996, 2006, that,

"This little story teaches several lessons. First, the word jump can be offered as an explanation of how someone crossed a barrier, but the explanation can range from completely convincing to totally inadequate depending on the details (such as how wide the barrier is). Second, [[long journeys can be made much more plausible if they are explained as a series of smaller jumps rather than one great leap]]. And third, in the absence of smaller jumps, it is very difficult to prove right or wrong someone who asserts that stepping stones existed in the past but have disappeared."

So Halo, in "[[What’s needed is a [[[seamless]]] Darwinian account that’s both detailed and testable of how subsystems undergoing coevolution could gradually transform into an irreducibly complex system.]]", says that Behe is completely wrong in "[[long journeys can be made [[[much more plausible]]] if they are explained as [[[a series of smaller jumps]]] rather than [[[one great leap]]] ]]" because even filling in more gaps (with new potential DNA code flagellum subcomponents being found and used which makes them available for mutatable DNA material) doesn't reconstruct the seamless mutation history of the now nonexistant past observation data. And even constructing a complete story from evidences and mechanisms in the future, with the best DNA simulation programs of the future, will not provably reconstruct time-history from millions of years ago. So only a time machine is suitable for Halo, and Behe is plain wrong that smaller steps are "much more plausible", as Halo only claims a seamless reconstruction of time and DNA history millions of years ago will suffice for the faithlessness of Creationists in all Science. By the way, since you (Halo) like evidence and concrete things without any faith in an ultimate truth in Science, what do you think is the meaning of the nearly identical DNA chromosomes, architecture, and details between chimpanzees and humans shown in the video? It means something, but what? Mice, amoeba, plants, and bacteria, don't have DNA chromsomes, architecture, and detail code ordering at all like each other or humans and primates, unlike the similarity found between humans and chimpanzees so well show. Or explanation of methods of complexity arising from complexity arising from simplicty naturally described in my blog, section 3? http://www.youtube.com/watch?v=oI29OXqLB8M BLOG: http://lonerubberdragon.blogspot.com/