Testing Intelligent Design Theory?

Originally posted by _ison0922

Hmmm... my back-and-forth with you hasn't actually been able to delve into the realms of support for ID. Thus far, I've spent all my time with you, noting how incredibly uninformed you are, and correcting your inaccurate paraphrasing of my posts.

I meant to do tis the last time I posted, but I'll go ahead and do it here.

I apologize for misquoting you.
I was an accident. Since I didn't make that clear now I want to make that clear.

Originally posted by _ison0922

Originally posted by ME
You didn't include examples of people who failed to get them included.

I further feel the need to point out the logical fallacies that exist in describing NDT as science and IDT as being unscientific, as they two bases for hypotheses appear to be methodologically equivalent.

Well, let's see, for a theory to qualify as a scientific theory it must be:

1)Consistent (internally and externally)
I think ID is pretty consisitant, unless you disagree let's move on.

2)Parsimonious (sparing in proposed entities or explanations, see Occam's Razor)
______________Hmm, well the whole point of intelligent design is that an "intelligence" or higher power of some sort(aliens/god/what have you) must have guilded evolution, as life as we know it couldn't ahve come about by just evolution alone. Or as William Dembski, one of intelligent design's leading proponents, put it "there are natural systems that cannot be adequately explained in terms of undirected natural forces and that exhibit features which in any other circumstance we would attribute to intelligence."

So it is NOT parsimonious.

3)Useful (describes and explains observed phenomena)
I think we can both agree that ID is 'useful'.

4)Empirically testable & falsifiable (see Falsifiability)

AS this is the whole point of this thread, I am interested in any examples of empirical testing of ID.

5)Based upon multiple observations, often in the form of controlled, repeated experiments.

As far as I can tell this just mean that #4 is done repeatably by more than one person.

__________Also I would like point out that due to its failure to adhere to scientific standards, in September 2005 38 Nobel laureates issued a statement saying "intelligent design is fundamentally unscientific; it cannot be tested as scientific theory because its central conclusion is based on belief in the intervention of a supernatural agent."
___________Now even if we got past that, there's another little problem. ID does't meet the criteria for scientific evidence used by most courts, the Daubert Standard. The Daubert Standard governs which evidence can be considered scientific in United States federal courts and most state courts. The four Daubert criteria are:

1)The theoretical underpinnings of the methods must yield testable predictions by means of which the theory could be falsified.
2)The methods should preferably be published in a peer-reviewed journal.
3)There should be a known rate of error that can be used in evaluating the results.
4)The methods should be generally accepted within the relevant scientific community.


________Hmm, lets' see here, when deciding Kitzmiller v. Dover Area School District on December 20, 2005, Judge John E. Jones III ruled that "we have addressed the seminal question of whether ID is science. We have concluded that it is not, and moreover that ID cannot uncouple itself from its creationist, and thus religious, antecedents."

_____________ Sop, the real issue is that the scientific method is based on methodological naturalism and so does not accept supernatural explanations. This becomes the sticking point for Intelligent design and is addressed in "The Wedge" strategy as an axiom of science that must be challenged before Intelligent design could be accepted by the broader scientific community.

Originally posted by _ison0922
I didn't include examples of people's whose work "failed to be included" because it's not relevant. The point of that post was to demonstrate that new and revolutionary ideas are often not accepted by the science community, but later are accepted and become important. ....... Rejected papers are not the issue, the issue is sound scientific ideas that are initially rejected by the science community.......What's your point?

_______My point was simply that their are many rejected papers that don't make ever get accepted by the scientific community. And that just because a paper is rejected doesn't mean that the theory is a valid scientific one. I mean, the intelligent design movement has yet to publish an article in a peer-reviewed scientific journal. Well, there was one. It was written by the Stephen C. Meyer(of the Discovery Institute) and it appeared in the peer-reviewed "Proceedings of the Biological Society of Washington"( the August 2004 issue to be more exact) but was later withdrawn by the publisher because it had circumvented the journal's peer-review standards.

___________This failure to follow the procedures of scientific discourse, and the failure to submit work to the scientific community which withstands scrutiny, is a strong argument against intelligent design being considered valid science. I mean even Dembski has written that perhaps the best reason to be skeptical of his ideas is that intelligent design has yet to establish itself as a thriving scientific research program. In a 2001 interview, Dembski even said that he stopped submitting to peer-reviewed journals because of their slow time-to-print. And because he makes more money publishing books.
_______ Even worse for IDer's such as yourself is Behe has stated that there are no peer reviewed articles by anyone advocating for intelligent design supported by pertinent experiments or calculations which provide detailed rigorous accounts of how intelligent design of any biological system occurred and he has even conceded that there are no peer-reviewed articles supporting his claims of intelligent design or irreducible complexity. No established scientific journal has yet published an intelligent design article. ID, by appealing to a supernatural agent, conflicts with the naturalistic axiom of science.

[Edit: how does one indent a paragraph around here!]

[edit on 27-12-2005 by I_AM_that_I_AM]

Originally posted by mattison0922
but the whole point of ID is that there is higher intelligence guilding Evolution.

There are no statements in IDT that say a higher intelligence is 'guiding evolution.' This is your own spin on the basis of the theory.

REally?
Cause according to Dembski:

But how do we know that nature requires no help from a designing intelligence? Certainly, in special sciences ranging from forensics to archaeology to SETI (the Search for Extraterrestrial Intelligence), appeal to a designing intelligence is indispensable. What's more, within these sciences there are well-developed techniques for identifying intelligence. Essential to all these techniques is the ability to eliminate chance and necessity.

Now how is he Not saying that a "higher inteligence" (or as he put's it a 'designing intelligence') guilded evolution/the developement of life?

.... Thus far abiogenesis theories, have yielded pretty much nothing in terms of elucidating natural laws that would permit the formation of life from simple organic molecules.

A theory of the gaps?
Sorry, try again.

In fact, William Dembski, one of intelligent design's leading proponents, has stated that the fundamental claim of intelligent design is that "there are natural systems that cannot be adequately explained in terms of undirected natural forces and that exhibit features which in any other circumstance we would attribute to intelligence."

While there is some info in the definition you cited, books actually contain descriptions, justifications, examples, and references. It's the logical next step for you.

You mean the like BS Behe put out, Darwin's Black Box?
He couldn't even show ONE IC molecule.

While evolution makes no claim re: a higher power, evolution DOES assume that there is in fact a naturalistic explanation for biological origins.

NOpe, that' Abiogenesis, which at best is a ssub theory underneath ET, not ET itself. Abiogenesis' can end up being proven disproven with out harming ET itself.

ID makes no such assumption. While it is not touted as such, in my own mind, ID theory lacks such a presupposition.

The whole point of ID is tha their is an "inteligent Designer" hence thname Intelligent Design.
What did you think that meant?

Maybe there is a naturalistic explanation for biological origins, and maybe there isn't.

ACcordingot ID their isn't one.

Ummm... that was my point. Everyone is such a skeptic here, and everyone wants to 'Deny Ignorance,' yet this bunch of well informed debunkers is seemingly completely unwilling to open a book and read about the theory they're debunking. Reading a refutation of Dembski is NOT the same as reading Dembski. Getting information off the Talk Origins website is not studying evolutionary theory. If you want to debunk IDT, for crying out loud read an ID book and make some coherent arguments of your own. Not one person who has ever posted in the O & C forum against IDT appears to ever have read, Behe,

See above comments about Darwin's black box.

I regularly call people on this, and NO ONE has ever come back and said, Yes I read Behe, and these points in particular are BS and here's why. The best the debunkers can come up with here is "ID isn't science," and a bunch of linked quotes from people who feel the same as them. [sarcasm]Oh yeah, that's objective[/sarcasm].

Did it ever occur to you that ID isn't science?
Seriously, you seem rather dismissive of people who oppose you views.
I am not talking about reading Darwin or NDTer's stuff.
I amd talking about reading ANTI-ID stuff. There is a difference.

Ummm... yes it does. That's why I ask them what books, articles, etc. about IDT have they read.

What ANTI-ID stuff have you read?
NOT NDT stuff, but ANTI-ID stuff?
[crickets]

I asked if you had any thoughts of your own about this.

So you want thougth's of my own that are somehow NOT original?



[edited quote tags -nygdan]

[edit on 3-1-2006 by Nygdan]

I feel a little weird calling you I_AM, but I can't think of a better contraction, let me know if something works better for you.

Well... it took us a little bit of time, but this is what I was talking about. Good Post, keep it up.

Oh yes, and one more thing... I don't get why you abbreviated my name '_ison0922" am I missing something here. I can enjoy a good laugh too, even at my own expense. What's the punchline?

Originally posted by I_AM_that_I_AM
I meant to do tis the last time I posted, but I'll go ahead and do it here.

I apologize for misquoting you.
I was an accident. Since I didn't make that clear now I want to make that clear.

Apology accepted and appreciated

Now... down to brass tacks.

Originally posted by _ison0922
Well, let's see, for a theory to qualify as a scientific theory it must be:

1)Consistent (internally and externally)
I think ID is pretty consisitant, unless you disagree let's move on.

Okay, I can agree to this.

2)Parsimonious (sparing in proposed entities or explanations, see Occam's Razor)
______________Hmm, well the whole point of intelligent design is that an "intelligence" or higher power of some sort(aliens/god/what have you) must have guilded evolution, as life as we know it couldn't ahve come about by just evolution alone. Or as William Dembski, one of intelligent design's leading proponents, put it "there are natural systems that cannot be adequately explained in terms of undirected natural forces and that exhibit features which in any other circumstance we would attribute to intelligence."

Disagreed. I agree with you about parsimony, ie: Science should be parsimonius. But your definition of ID is confused. It doesn't say that an intelligence must have guided evolution. This is patently false. It does state that certain features of biological systems appear to be to complex to have arrived via natural selection, and I personally agree with this. But my personal opinion isn't entirely germane in this context. However I did feel the need to clarify this definition. ID has no problem with evolution proceeding as is more or less described by mainstream science. Behe pretty much believes in the common descent of apes and man, for example. There is nothing suggesting that any force guided evolution at any point. IDT is an origins theory.

And there are in fact natural systems that don't appear to be the product of any known law. The systems according to Richard Dawkins, exhibit the appearance of design. Furthermore, many of these systems have no reasonable explanation of how they could have come about via natural selection. Examples of such systems include, photosynthesis, electron transport, and all the associated proteins.

So please explain to me how parsimony is employed when something that exhibits the appearance of design, has no reasonable explanation of origins via natural selection, is then assumed to have been created via natural selection. That doesn't sound very parsimonius to me.

IMO, the design inference is much more parsimonius than the inference from natural selection.

4)Empirically testable & falsifiable (see Falsifiability)

AS this is the whole point of this thread, I am interested in any examples of empirical testing of ID.

ID is testable and falsifiable. You can in fact test to see if systems are IC. This is the basis for Doolittle's rebuttals of Behe, and in Matzke's horrific assemblage of a 'paper' on the origins of the bacterial flagellum. If the concept of IC was inherently unfalsifiable, scientists wouldn't waste there time rebutting Behe's claims. Furthermore, I have already described experiments in this thread, that can test for the IC nature of biological systems. Rather than rewrite something I've already written I would simply refer you to these experiments that I've already proposed. So... in conclusion, members of the mainstream scientific community have demonstrated ID's inherent ability to be falsified, I have proposed falsifiable experiments, and so has Behe. So on this point, we are in disagreement.

Mind you, IDT doesn't attempt to prove the designer, but the design. You can eliminate the design hypothesis by demonstrating that something needn't have been designed and could have arisen by natural selection. In this respect IDT is inherently MORE falsifiable than is NDT.

5)Based upon multiple observations, often in the form of controlled, repeated experiments.

As far as I can tell this just mean that #4 is done repeatably by more than one person.

Well, in this case both IDT and NDT fail. There are no experiments that can falsify NDT. NDT is inferred from factual observations, but is not a 'fact' in and of itself. Yes it's true, the ID crowd has not in fact produced any meaningful data thus far, but this is not due to the scientific status of the theory, but due more to the environment and hostility that surround ID. So in terms of being based on repeatable, multiple observations, both NDT and IDT fail this test.

Also I would like point out that due to its failure to adhere to scientific standards, in September 2005 38 Nobel laureates issued a statement saying "intelligent design is fundamentally unscientific; it cannot be tested as scientific theory because its central conclusion is based on belief in the intervention of a supernatural agent."

Thanks again for the current events lesson, but I am aware of the opinions of these people. I thought it was 40 Nobel Laureates though. It appears that this group of individuals is also misinformed about ID, and it's unlikely that they are familiar with the theory on even a cursory level. I won't address the errors that pervade the article in question, just the ones you mention. We've already discussed the testability of IDT; ID IS inherently testable and falsifiable, at least to the degree that NDT is. The theory is NOT based on thei intervention of a 'supernatural' agent, as the designer is not identified. The designer could in fact be a highly evolved extra-terrestrial, and is not limited to a supernatural agent. The point is that these scientists have missed the boat: you don't test for the designer, you infer the designer by testing for the design, big difference. Though, not without a precedent in science, for example SETI, and pretty much the entire field of archaeology are ID based sciences. And yes, I do know that SETI researchers recently came out against ID. If my research money was somehow tied or otherwise linked to the ID movement, I'd probably say something like that too. Research money is hard enough to come by, without being associated by proxy with a bunch of people mainstream science considers to be 'crackpots.'

Now even if we got past that, there's another little problem. ID does't meet the criteria for scientific evidence used by most courts, the Daubert Standard. The Daubert Standard governs which evidence can be considered scientific in United States federal courts and most state courts. The four Daubert criteria are:[deletia]


________Hmm, lets' see here, when deciding Kitzmiller v. Dover Area School District on December 20, 2005, Judge John E. Jones III ruled that "we have addressed the seminal question of whether ID is science. We have concluded that it is not, and moreover that ID cannot uncouple itself from its creationist, and thus religious, antecedents."

Honestly, I couldn't care less what the courts say about science. The courts have never been responsible for defining science, and I don't give them any credibility in this respect now. IMO, this most recent decision in Dover is political and not scientific anyway. But IMO, the findings of the court are irrelevant to the scientific status of the theory. Not trying to start another discussion in this thread, but the courts also stated OJ isn't a murderer.

Sop, the real issue is that the scientific method is based on methodological naturalism and so does not accept supernatural explanations.

I have repeatedly pointed out that ID is perfectly capable of operating within the realm of methodological naturalism. ID has no issue operating within this constraint, which is something that most people are unaware of, and others conveniently ignore when presented to them.

This becomes the sticking point for Intelligent design and is addressed in "The Wedge" strategy as an axiom of science that must be challenged before Intelligent design could be accepted by the broader scientific community.

The Discovery Institute does not = ID. Yes they are pretty much the main think tank devoted to sheltering ID theorists, but they don't have the theory under lock and key. While certain aspects of the Wedge document don't sit well with me as a scientist, I don't see it as being dangerous to science. As long is scientists operate within the realm of methodological naturalism, the metaphysical presuppositions are irrelevant. Newton believed that Gravity with occassional assistance from God helped keep the planets in their orbit. People don't want to hang Newton for his metaphysical presuppositions, why should Behe and Dembski hang, figuratively speaking of course.

My point was simply that their are many rejected papers that don't make ever get accepted by the scientific community.

Yes, I know this. As I mentioned, I've got a bunch of rejected papers. When I say 'a bunch,' I mean four. They weren't rejected because of faulty logic, rather the reviewers wanted to see one additional experiment, or series of experiments. I've since moved on from those projects and probably will never complete the work unfortunately.

And that just because a paper is rejected doesn't mean that the theory is a valid scientific one.

Of course it doesn't. Though peer review is a much different process now, than it was 50 years ago, but this is somewhat peripheral. But papers are often rejected for good reason. Almost every paper is rejected on its first review, so there is nothing abnormal about rejected papers, and it is in fact the norm.

I mean, the intelligent design movement has yet to publish an article in a peer-reviewed scientific journal. Well, there was one. It was written by the Stephen C. Meyer(of the Discovery Institute) and it appeared in the peer-reviewed "Proceedings of the Biological Society of Washington"( the August 2004 issue to be more exact) but was later withdrawn by the publisher because it had circumvented the journal's peer-review standards.

Well, the issue of why it was withdrawn is more complex than that, but again not exactly relevant to our topic, so I won't expand on this aspect. But you are correct, there are no 'ID papers' per se, and Meyer's paper in fact, contains no experimental data. But yes, the ID community hasn't generated much in terms of hard data. But is this a function of the inherent untestable nature of the theory, or the political environment surrounding the theory. I personally believe it's the latter and not the former. BTW, there is another paper published by Behe in Protein Science with ID implications. If you're interested, I can get you a link. The political environment is going to make it tough for IDTist to get anything published in mainstream science journals, but this says nothing about the scientific nature of the theory.

This failure to follow the procedures of scientific discourse, and the failure to submit work to the scientific community which withstands scrutiny, is a strong argument against intelligent design being considered valid science. I mean even Dembski has written that perhaps the best reason to be skeptical of his ideas is that intelligent design has yet to establish itself as a thriving scientific research program. In a 2001 interview, Dembski even said that he stopped submitting to peer-reviewed journals because of their slow time-to-print. And because he makes more money publishing books.

Yes, this was my point above... the environment surrounding IDT will make it extremely difficult to publish the theory or for the theory to gain credibility. The recent efforts to force ID into schools, on top of being totally inappropriate and unprecendented academically, were incredibly damaging to the ID movement.

Even worse for IDer's such as yourself

I am not an "IDer," I am merely supportive of the movement. As I mentioned the failure or success of ID doesn't affect me personally, nor will it change the way I carry out science. I just hate to see things so misrepresented and maligned, especially when I believe they could provide valuable insight.

Behe has stated that there are no peer reviewed articles by anyone advocating for intelligent design supported by pertinent experiments or calculations which provide detailed rigorous accounts of how intelligent design of any biological system occurred and he has even conceded that there are no peer-reviewed articles supporting his claims of intelligent design or irreducible complexity. No established scientific journal has yet published an intelligent design article. ID, by appealing to a supernatural agent, conflicts with the naturalistic axiom of science.

Please document the source of said quotes, specifically:

there are no peer-reviewed articles supporting his claims of intelligent design or irreducible complexity

and

ID, by appealing to a supernatural agent, conflicts with the naturalistic axiom of science.

Originally posted by I_AM_that_I_AM
REally?
Cause according to Dembski:

But how do we know that nature requires no help from a designing intelligence? Certainly, in special sciences ranging from forensics to archaeology to SETI (the Search for Extraterrestrial Intelligence), appeal to a designing intelligence is indispensable. What's more, within these sciences there are well-developed techniques for identifying intelligence. Essential to all these techniques is the ability to eliminate chance and necessity.

This says nothing about a higher intelligence 'guiding evolution.' It does talk about detecting intelligence in systems but says nothing about a higher intelligence 'guiding evolution.' My issue was with 'guiding evolution,' not 'higher intelligence.' IDT says nothing about a higher intelligence 'guiding evolution.'

Now how is he Not saying that a "higher inteligence" (or as he put's it a 'designing intelligence') guilded evolution/the developement of life?

'Guiding evolution' are your words not Dembski's the presence of a higher intelligence is integral to ID; I wouldn't argue that. What IS open for debate and testing is the idea that certain systems are a product of that intelligence.

A theory of the gaps?
Sorry, try again.

Who said anything about 'gaps?' I said abiogenesis have yielded little useful information. ID is simply approaching the problem from a different perspective. It's not filling in the 'gaps' by saying 'God did it.' Its purpose is to explore biological origins, within the realm of methodological naturalism, via a different base of hypothesis formation. It doesn't fill in the 'gaps' with God. It's science, not religion.

In fact, William Dembski, one of intelligent design's leading proponents, has stated that the fundamental claim of intelligent design is that "there are natural systems that cannot be adequately explained in terms of undirected natural forces and that exhibit features which in any other circumstance we would attribute to intelligence."

Yes, like I've said repeatedly, there are no natural laws that can account for certain systems present in biologicals. This isn't some big secret. Why are we coming back to the definition of ID. My issue was never with 'higher intelligence;' it was with 'guiding evolution.' There are no criteria for points when the designer is likely to have intervened, this is what is being tested for: evidence of design, nothing more.

You mean the like BS Behe put out, Darwin's Black Box?
He couldn't even show ONE IC molecule.

You've not actually read DBB have you? Interesting that you're so willing to dismiss something you've not read as BS. Kind of goes against 'denying ignorance' and 'learing for yourself' that you were such a huge proponent of a couple of posts ago.

I am not sure what you mean by "[h]e couldn't even show ONE IC molecule." The book obviously contains descriptions of IC systems including the blood clotting cascades, and flagellum. I would imagine that you are referring the the refutations of Behe's work that exist on the internet. You may not know this, but Doolittle, after his rebutting Behe, actually apologized to Behe, and said he was 'right,' not about IC necessarily, but that his own analysis of second site mutants was in fact flawed. There exists no reasonable explanation of the origin of the bacterial flagellum. And yes, I am aware of Matzke's paper. Go ahead and cite if you want, but there is a reason that paper is on the internet and not in a peer-reviewed journal. Many of the problems lie in his usage of SecIII systems for homology to the flagellum. The SecIII system does maintain homology to the flagellum, but that's because mainstream science believes it's derived from the flagellum, not the other way around. And as an expert on the ATP synthase, I can state the parrallels and homologies he draws between the two systems are pathetic and not even weakly supported.

NOpe, that' Abiogenesis, which at best is a ssub theory underneath ET, not ET itself. Abiogenesis' can end up being proven disproven with out harming ET itself.

I know I am in the minority with respect to this, but I disagree. Abiogenesis only 'evolved' as a result of the theory of common descent. Abiogenesis theories wouldn't be necessary were it not for the theory of common descent. If abiogenesis was disproven the entire theory of common descent would come into question. How could it not? In this way abiogenesis and ET are inextricably linked. I understand it's convenient to separate the issues for the sake of argument, but convenience aside, the two theories are for all intents and purposes, married. Again, if abiogenesis were somehow disproven, which it can't be, then the entire theory of common descent would be in quesiton. Please correct me if I am wrong.

The whole point of ID is tha their is an "inteligent Designer" hence thname Intelligent Design.

What did you think that meant?

My point was ID makes no assumption about systems in general. For example the hemoglobin system is not a good candidate for tests against IC, in all likelihood, the hemoglobin system did evolve in a manner similar to that described by science. The ATP synthase (synthase, not synthetase) is a good candidate for tests of IC, as there is no reasonable mechanism via which it could have arisen. When an IDTist would test this, they would be operating under no assumption, ie: maybe this system was designed, maybe it wasn't. While ID, DOES make the claim that life is too complex to have come about via natural selection, it doesn't necessarily make assumptions about the individual components. That's what it tests for, whether or not a component could have arisen via naturalistic methods. This is what I mean. IDTist's fully acknowledge that NS can produce complex things, not just all complex things, and that's what it looks to elucidate.

ACcordingot ID their isn't one.

Yes, for life itself this is true, there isn't one. Do you know of one that's been kept from science? But they DO want to explore the origins of complex systems. This desire to explore and test hypotheses is specifically why ID isn't a Gap theory.

Ummm... that was my point. Everyone is such a skeptic here, and everyone wants to 'Deny Ignorance,' yet this bunch of well informed debunkers is seemingly completely unwilling to open a book and read about the theory they're debunking. Reading a refutation of Dembski is NOT the same as reading Dembski. Getting information off the Talk Origins website is not studying evolutionary theory. If you want to debunk IDT, for crying out loud read an ID book and make some coherent arguments of your own. Not one person who has ever posted in the O & C forum against IDT appears to ever have read, Behe,

See above comments about Darwin's black box.

Okay, I'll ask again. Have you read DBB?

Did it ever occur to you that ID isn't science?

Sure it has. I pretty much believed that for the first couple of years of my graduate education. That's specifically why I read the stuff... so I could make an informed opinion.

Seriously, you seem rather dismissive of people who oppose you views.

I am not dismissive of people who oppose my views. I am dismissive of people who speak from a position of authority that has no basis in reality. I am dismissive of people who state "ID is unscientific," or "ID is just creationism in disguise," who have obviously not read any IDT. I am dismissive of people who authoratatively argue a position from a point of complete ignorance. Perhaps you can let me know why I shouldn't dismiss these people.

You'll note that I post in pretty much two forums, O & C, because it's my main intellectual hobby, and Science and Technology, because I feel qualified. I don't post in UFO's and cryptozoology as I don't know about these things. I don't see why people feel compelled to comment authoratatively re: things they know nothing about. Perhaps you can fill me in here as well.

I am not talking about reading Darwin or NDTer's stuff.
I amd talking about reading ANTI-ID stuff. There is a difference.

Of course there's a difference. Darwin was obviously in no position to comment on the ID movement, as it didn't exist, at least in its present form.

And yes, I have read anti-ID stuff. I am intimately familiar with much of it.

What ANTI-ID stuff have you read?
NOT NDT stuff, but ANTI-ID stuff?

Did you want the complete list, or just what I can remember off the top of my head? Does this mean that you'll 'fess up about which ID books you've read?

Let's see, off the top of my head anti-ID literature that doesn't include traditional Darwinist or NDT:

Creationism's Trojan Horse

Unintelligent Design

Evolution vs. Creationism

Why intelligent design fails

God, Darwin, and the Devil

Defending Evolution

I am certainly familiar with the entire TO archive, and the NCSE's website

Your turn.

So you want thougth's of my own that are somehow NOT original?

Call them what you will, but do you have any thoughts of your own about ID, original or otherwise?

So... which books supportive of IDT have you read?

[Edit by mattison0922 to elaborate on an idea]

[edit on 27-12-2005 by mattison0922]

I just wanted to add a couple of things.

Firstly, the link to Behe's article in Protein Science. I would also encourage you to read the reply to Behe, as well as Behe's rebuttal to the reply. There may exist a rebuttal of Behe's rebuttal, but to my knowledge one doesn't exist.

Secondly, I was looking over some of my books last night, and I remembered the title of one of the books incorrectly. It was in fact God, the Devil, and Darwin, with the associated subtitle. Sorry, my mistake :

Originally posted by mattison0922
I just wanted to add a couple of things.

Firstly, the link to Behe's article in Protein Science. I would also encourage you to read the reply to Behe, as well as Behe's rebuttal to the reply. There may exist a rebuttal of Behe's rebuttal, but to my knowledge one doesn't exist.

Secondly, I was looking over some of my books last night, and I remembered the title of one of the books incorrectly. It was in fact God, the Devil, and Darwin, with the associated subtitle. Sorry, my mistake

:

1)You can just call me I_AM(i am or I_am or i_am etc...).
2)My names matt, so calling you mattison sounds weird to me.
Maybe it's just me.
Will work on a longer post later....

Originally posted by I_AM_that_I_AM
Will work on a longer post later....

Cool. I had begun to lose faith.

BTW, how in the heck did you go from like 30 ATS pts to more than 1000 in a day?

Hi matt, good discussion here. I was gonna ask these questions in another thread but they seem to fit better here.

So you seem to know the biological and scientific intricacies of the ID hypothesis. I have some simple questions...

(i) what if Flagellum seems irreducible? Does this mean there are no other mechanisms that could have produced this phenomena without reverting to intelligent designers?

(ii) what happens if Flagellum seems readily reducible? What happens to ID then?

cheers.

[edit on 14-1-2006 by melatonin]

[edit on 14-1-2006 by melatonin]

Ok I guess your busy. I'll give my considered opinion for all it's worth, lol. I research in neuroscience and the ID hypothesis reminds me of another pretty vacuous theory - Damasio's 'somatic marker hypothesis'. But forgive me for any misinterpretations, i'd just like an informed comment


As said before IDH is a theory of ORIGINS, therefore it should make some claims about the mechanisms that produce these IC organisms. Just stating in must be due to intelligent design results in a pretty vacuous theory. Otherwise, there will be other parsimonious possibilities that have not been considered (and no matter how improbable, it would be more probable and parsimonious than invoking an intelligent designer, unless you suggest a mechanism).

Behe himself said that there are indirect methods that could result in IC organisms. It could be an existing evolutionary process or maybe some other natural process we do not yet know of, or maybe both.

The notion of IC seems pretty inexplanatory, an IC organism/process shows ID because it is irreducibly complex (tautological?). What is complex, give a definiton so that can measure or predict IC. So, Dembski (sp) suggests that an IC molecule is one that has his suggested probablility of occuring, under his suggested conditions and processes - although, other conditions and processes are possible? Therefore complexity of an organism/process, is actually defined externally. Also, probability tells us that the probability of something existing that actually does exist is p=1 (i.e. it does exist - so a parsimonious explanation may exist).

So if p=1 and we have an apparently IC molecule what does that tell us? Does this mean it is sourced from intelligent design. Well not really, it just means we could well not know of a suitable process that doesn't require intelligent design. so we really need to think about the probablities of the possible pathways to the organism/process - would intelligent design be the most probable, if it defeats the physical laws of the universe then it probably isn't likely (I'm sure creating mass from nothing will be a violation, otherwise it must conform to our physics - well does that mean we need ID?)

Matt, you seem to destroy that guys paper on flagellum and Sec III. Is his suggested pathway completely unprobable? And I dont mean the exact homology etc (I totally trust your judgement on it), just the pathway with some other suitable homologous organism? Also, different pathways to flagellum must exist and have been suggested (indirect maybe). As a biologist (I also have degree in Chem, not bio though ) you must admit that circuitous routes to biochemical processes are very common (doesn't E. Coli have some). It would be more probable that a simple process would develop, however more improbable processes do exist. Also, many ID papers are not published for similar reasons as his, omission, misinterpretation, and just-so claims seem common in ID literature (similar to complaints of ID proponents).

Dolphin's blood coagulation functions fine without one of the components of the apparent IC process? Now this is where the ad nauseum bit of the IC notion comes in - it has been falsified and now Behe says it was never IC - is this going to continue ad nauseum? Why did Behe suggest this process if it is not IC? Simple, there is no independent measure or theoretical basis of IC, if we can't really indicate IC independently, then any complex biochemical process that has not yet been explained, can be deemed IC, until we find it's not. (This is the comparison with Damasio's hypothesis - researchers constantly shoot his possibilities down, but then he moves the goalpost, i.e. its almost unfalsifiable but keeps some busy).

Behe proposes the mousetrap as an analogy for IC. I guess a radio would also be analogous - this study describes the spontaneous evolution of a radio. The researchers used a simulated evolutionary process in which the fitness of an electronic circuit as an oscillator was selected for. Of course, there are criticisms - well whose methodology is perfect?

www.cogs.susx.ac.uk...

Another simulation, avida (Lenski et al, Nature 2003), has modelled origin by NDT, what about schneider's EV? Again, they may not be perfect, but neither was Behe's paper you mention. From what I gather from people who understand these simulations, Trumans rebuttle was not so convincing.

So what about IC=IDH, well accounting for the possibility of other possible mechanisms, it doesn't really it's a pretty big leapfrom IC to a designer. We may be able to falsify each IC organism/process proposed, I would question whether we can falsify IDH itself and that is the issue, unless you give a mechanism outlining the process of design to test, not the result (NDT can). Just because we can't find a mechanism for IC doesn't mean one does not exist. We had to wait a very long time to provide a better explanation than creationist ideas, it may take just as long to completely refute such a vacuous theory as IDH.

And please don't criticise NDT's theoretical shortcomings to justify IDH's, it needs to stand alone. I would suggest that NDT would have difficulty explaining a hominid fossil in the same strata as early dino's and if humans showing closer DNA comparisons to a worms than a chimp. It can be falsified.

Anyway, I see a value in anything that cleans up problems in science, and ID will do that for life-sciences. I understand the problems ID will have for acceptance, a lot of it is due to its poor construction - I know this because a supervisor of mine supports an area of science that is deemed pseudoscience by many (neuro-psychoanalysis).

Cheers and thanks for your time







[edit on 14-1-2006 by melatonin]

[edit on 14-1-2006 by melatonin]

[edit on 14-1-2006 by melatonin]

Originally posted by melatonin
Hi matt, good discussion here. I was gonna ask these questions in another thread but they seem to fit better here.

Thanks. Glad to hear someone is reading and absorbing. My apologies for the delayed response.... we had a party tonight, so I've been pretty much occupato all day.... am pretty drunk now, but will try to answer this question at least. Please forgive my ramblings.

So you seem to know the biological and scientific intricacies of the ID hypothesis. I have some simple questions...

(i) what if Flagellum seems irreducible? Does this mean there are no other mechanisms that could have produced this phenomena without reverting to intelligent designers?

Of course not. It just means we haven't discovered them yet. Certainly the question is open to other hypotheses.

(ii) what happens if Flagellum seems readily reducible? What happens to ID then?

Nothing. The flagellum is removed as an 'icon of Intelligent Design' and the next IC system is explored.

Thanks for reading. Promise to answer your other question sometime tomorrow when sober.

Originally posted by mattison0922

Originally posted by melatonin
Hi matt, good discussion here. I was gonna ask these questions in another thread but they seem to fit better here.

Thanks. Glad to hear someone is reading and absorbing. My apologies for the delayed response.... we had a party tonight, so I've been pretty much occupato all day.... am pretty drunk now, but will try to answer this question at least. Please forgive my ramblings.

So you seem to know the biological and scientific intricacies of the ID hypothesis. I have some simple questions...

(i) what if Flagellum seems irreducible? Does this mean there are no other mechanisms that could have produced this phenomena without reverting to intelligent designers?

Of course not. It just means we haven't discovered them yet. Certainly the question is open to other hypotheses.

(ii) what happens if Flagellum seems readily reducible? What happens to ID then?

Nothing. The flagellum is removed as an 'icon of Intelligent Design' and the next IC system is explored.

Thanks for reading. Promise to answer your other question sometime tomorrow when sober.

Cheers for the response, I hope you didn't have too bad a hangover, lol.

so really if we can't predetermine or predict IC, how can we really test it? How can we really tell if a process/organism is ID'ed, can we really distinguish it from a naturally developed process/organism?

There are many known processes that are improbable and seem IC and have been shown to have natural explainable causes.

You have suggested possible tests for IC but as you admit there are other possibilities that can account for what we see. If we test one, and find it's not IC, then we move to the next, without any other purpose than to find an object that we can see as impossible with current levels of knowledge. So we are really testing evolutionary theories and not ID. Is NDT perfect, most likely not but that doesn't by default suggest ID. Every theory can be refined, even general relativity may need this.

It really does seem to be an argument from incredulity. Flagellum looks very complex, we suggest it is improbable and therefore it is ID and we prefer to ignore all possible mechanisms. If you can't show why and how an IC molecule is ID'ed, it is untestable and unfalsifiable. You already admit that if flagellum is shown to not be IC and can develop by known processes then we move on to the next.

Unless you can really ascertain a mechanism that can be falsified that suggests ID produced IC molecules, the argument of that ID is pure incredulity and not actual science will remain. Otherwise, if we eventually show every possible IC molecule is not so, then we move to a lower level of incredulity (i.e. abiogenesis) and so on ad nauseum until we get to the big bang and say, ID created the universe.

However, saying that, if we see the scientific purpose as being to refine current theories, then I'm all for it - but ID is dead already as a possible scientific theory unless it is refined in itself (and how do we really test it). So what is it's purpose, I suggest it is to simply discredit Darwinian theories.

My interest in this is because of my research into the neuroscience of consciousness (and it's elements). You could say that the mind is ID'ed, I suggest it may be much more complex and improbable than the IC processes that have been suggested (e.g. how are the individual elements of our environment binded into that which we actually perceive, how did empathy develop from simple instinctual processes of emotion). I would suggest natural processes of evolution have created consciousness however improbable this may seem at first glance. I can see ID'ers eventually impinging on our area of research.

Originally posted by melatonin
Ok I guess your busy. I'll give my considered opinion for all it's worth, lol. I research in neuroscience and the ID hypothesis reminds me of another pretty vacuous theory - Damasio's 'somatic marker hypothesis'. But forgive me for any misinterpretations, i'd just like an informed comment

What does your research involve? What's your educational background? I am unfamiliar with this particular hypothesis you mention.

As said before IDH is a theory of ORIGINS, therefore it should make some claims about the mechanisms that produce these IC organisms.

I understand this is a popular belief. I don't see why people put this restraint on ID. The same condition is not applied to gravity. We don't know the mechanism via which gravity operates, but I don't see people lining up to claim that gravity is unscientific because we don't know if it's a wave, or whether the graviton is for real. Obviously science in general is not held to this standard, why should ID be?

Just stating in must be due to intelligent design results in a pretty vacuous theory. Otherwise, there will be other parsimonious possibilities that have not been considered (and no matter how improbable, it would be more probable and parsimonious than invoking an intelligent designer, unless you suggest a mechanism).

Disagreed. Just stating what is due to ID? IDTists don't due this anyway. IDTist's don't say 'We've studied this and determine it to be designed, end of story." There are certain systems that show hallmarks of design, and those that don't. You don't study systems that seem like the could have arisen via natural selection. The hemoglobin system is a good example of this. There does seem to be a relationship between hemoglobin and myoglobin, the system doesn't exhibit signs of irreducible complexity, and is thus not a good candidate to test for design. Please note that this doesn't mean the system wasn't designed, it's just not a good candidate to detect design.

Other systems are different. I'll take my favorite example, photosynthesis. PS exhibits all the signs of being a designed system: Appears to be IC, there's no good explanation for its origins based on natural selection, etc. Mainstread scientists admit that these systems 'appear' designed, and there exists no reasonable mechanism for their origins via NS, how can NS be the most parsimonious assumption. IMO, in the case of things that appear designed and for which there exists no reasonable mechanism of their origins via any other extant theory, the assumption for design is much more parsimonious.

Parsimony is not absolutely related to a mechanism.

Behe himself said that there are indirect methods that could result in IC organisms. It could be an existing evolutionary process or maybe some other natural process we do not yet know of, or maybe both.

Where did Behe say this? This pretty much goes against the whole concept of IC. Where specifically did Behe state this. I'm not familiar with this quote, and I definitely would have taken note of it had I read it.

The notion of IC seems pretty inexplanatory,

Ummmm.... that's because it's not an explanation it's an observation.

an IC organism/process shows ID because it is irreducibly complex (tautological?).

Hmmmm... looks like you're trying to create a circular argument where one doesn't exist. A system may exhibit the hallmarks of ID due to it's IC nature... end of sentence.

What is complex, give a definiton so that can measure or predict IC. So, Dembski (sp) suggests that an IC molecule is one that has his suggested probablility of occuring, under his suggested conditions and processes - although, other conditions and processes are possible? Therefore complexity of an organism/process, is actually defined externally. Also, probability tells us that the probability of something existing that actually does exist is p=1 (i.e. it does exist - so a parsimonious explanation may exist).

Okay... there's definitely some confusion here:

IC as defined by Behe:

A single system composed of several well-matched, interacting parts that contribute to the basic function of the system, wherein the removal of any one of the parts causes the system to effectively cease functioning.

Taken from Darwins Black Box, pg 39

IC as defined by Dembski:

A system performing a given basic function is irreducibly complex if it includes a set of well-matched, mutually interacting, nonarbitrarily individuated parts such that each part in the set is indispensable to maintaining the system's basic, and therefore original, function. The set of these indispensable parts is known as the irreducible core of the system.

Taken from No Free Lunch, pg 285

So in reality, IC has nothing to do with probabilities directly. Perhaps you can read these definitions, and rephrase your question when you have a better understanding of the concept of IC.

So if p=1 and we have an apparently IC molecule what does that tell us? Does this mean it is sourced from intelligent design. Well not really, it just means we could well not know of a suitable process that doesn't require intelligent design. so we really need to think about the probablities of the possible pathways to the organism/process - would intelligent design be the most probable, if it defeats the physical laws of the universe then it probably isn't likely (I'm sure creating mass from nothing will be a violation, otherwise it must conform to our physics - well does that mean we need ID?)

Hmmm... not sure how we got to IDT 'defeating the physical laws of the universe,' it's certainly not postulated in the theory anywhere that I've read. I am also not sure where the 'creating mass from nothing' came from, but if you really have a problem with that, then I suggest you take it up with the physicists researching the singularity and big bang theory as well.

Matt, you seem to destroy that guys paper on flagellum and Sec III. Is his suggested pathway completely unprobable? And I dont mean the exact homology etc (I totally trust your judgement on it), just the pathway with some other suitable homologous organism?

You certainly don't need to take my word for it. Mainstream sciences opinion with respect to the flagellum and SecIII system is that SecIII is derived from the flagellum. The reason is this: flagella are present in pretty much all categories of bacteria.... they pretty much seem to be universal. However the SecIII system is not universal; it is thought to have arisen until much later... after the appearance of metazoans. So... it seems like Matzke is willing to ignore the opinion of mainstream science to prove a point, but expects people to dogmatically believe their assertions about evolution. Matzke is pretty much willing to ignore mainstream sciences opinion about something simply so he can prove IDTists wrong. This paper is a classic case of literature bluffing. He's relying on people not taking the time to chase down his refs. and critically think about his hypothesis.

Also, different pathways to flagellum must exist and have been suggested (indirect maybe).

Must they? Why? Matzke also proposed that the ATP synthase (synthase not synthetase) was related to the flagellum. This is just not true. I can see why he's reaching for it; the ATP synthase is biological rotary motor, with a mechanism vaguely analogous to that of the flagellum, unfortunately, once again his assertions aren't even weakly supported. In fact, he imports the wrong portion of the apparatus to harness proton flux.

As a biologist (I also have degree in Chem, not bio though

) you must admit that circuitous routes to biochemical processes are very common (doesn't E. Coli have some).

Actually, I'm not quite sure what you mean here, so I am going have to ask you rephrase the question. If you know of some these circuitous routes in E. coli please provide an example.

It would be more probable that a simple process would develop, however more improbable processes do exist. Also, many ID papers are not published for similar reasons as his, omission, misinterpretation, and just-so claims seem common in ID literature (similar to complaints of ID proponents).

What? What ID papers aren't published for ommission, misinterpretation, etc? To my knowledge, there are 2 papers published by the ID community, none of which contains any actual data. The community isn't very active currently and very few profs. openly admit to being IDTists. I won't admit it, except for here, to my wife and a very few close friends in science.

Dolphin's blood coagulation functions fine without one of the components of the apparent IC process? Now this is where the ad nauseum bit of the IC notion comes in - it has been falsified and now Behe says it was never IC - is this going to continue ad nauseum?

I am unfamiliar with the Dolphins Blood example. Where did you come across this? I do know that Doolittle refuted Behe's claims of IC blood clotting cascades, then later admitted to Behe that his own analysis of second site mutations was wrong, and in fact apologized to Behe. I would be interested to read this Dolphins Blood example though.

Why did Behe suggest this process if it is not IC? Simple, there is no independent measure or theoretical basis of IC, if we can't really indicate IC independently, then any complex biochemical process that has not yet been explained, can be deemed IC, until we find it's not. (This is the comparison with Damasio's hypothesis - researchers constantly shoot his possibilities down, but then he moves the goalpost, i.e. its almost unfalsifiable but keeps some busy).

There does exist the possibility that Behe is simply mistaken. I know Behe, and he doesn't have some evil agenda... he's not interested in maintaining the idea of IC at all costs, he's a totally reasonable guy who happens to subscribe to a non-traditional view of biological origins.

Behe proposes the mousetrap as an analogy for IC. I guess a radio would also be analogous - this study describes the spontaneous evolution of a radio. The researchers used a simulated evolutionary process in which the fitness of an electronic circuit as an oscillator was selected for. Of course, there are criticisms - well whose methodology is perfect?

www.cogs.susx.ac.uk...

Another simulation, avida (Lenski et al, Nature 2003), has modelled origin by NDT, what about schneider's EV? Again, they may not be perfect, but neither was Behe's paper you mention. From what I gather from people who understand these simulations, Trumans rebuttle was not so convincing.

Unfortunately simulations aren't necessarily applicable in the real world. I am familiar with Lenski's paper, and was not impressed. I could just as easily direct you to Behe's protein science paper. That leaves us with two published articles that pretty much state opposite things.

So what about IC=IDH, well accounting for the possibility of other possible mechanisms, it doesn't really it's a pretty big leapfrom IC to a designer. We may be able to falsify each IC organism/process proposed, I would question whether we can falsify IDH itself and that is the issue,

Why? Darwinism is inherently unfalsifiable, and no one seems to balk at that.

unless you give a mechanism outlining the process of design to test, not the result (NDT can). Just because we can't find a mechanism for IC doesn't mean one does not exist. We had to wait a very long time to provide a better explanation than creationist ideas, it may take just as long to completely refute such a vacuous theory as IDH.

It may take some time, then again, it may never happen. The fact of the matter seems to be that irrespective of anything else, there will always be scientists that infer design from what they observe. Seems like it's always been the case, and may always be. The assumption that things weren't designed is actually reasonably new. Certainly the inference from design is not a new idea, and will likely always be a consideration for some.

And please don't criticise NDT's theoretical shortcomings to justify IDH's, it needs to stand alone. I would suggest that NDT would have difficulty explaining a hominid fossil in the same strata as early dino's and if humans showing closer DNA comparisons to a worms than a chimp. It can be falsified.

Untrue. When out of place artifacts are discovered, they are invariably dismissed as hoaxes, which a good number of them may be. But the fact of the matter is that NDT has always been flexible enough to accomodate pretty much whatever evidence... the molecular clock is reliable for genes, except for the genes it's not, Mutation is random, except when it's directed, you get the idea.

Anyway, I see a value in anything that cleans up problems in science, and ID will do that for life-sciences. I understand the problems ID will have for acceptance, a lot of it is due to its poor construction - I know this because a supervisor of mine supports an area of science that is deemed pseudoscience by many (neuro-psychoanalysis).

Well... now I am totally confused, Do you or do you not see ANY inherent value with hypotheses based from an assumption of design.

Cheers and thanks for your time

Likewise, and thanks for the thought provoking post... I am going to look into this dolphin's blood stuff too. Will post when I find something out.

*Edit* Okay... I looked into this Dolphin Blood thing... could be an issue for the IC of the blood clotting cascade... intriguing indeed... good find will have too look into this in some detail.... this could take me some time.

[edit on 15-1-2006 by mattison0922]

Originally posted by melatonin
Cheers for the response, I hope you didn't have too bad a hangover, lol.

My apologies for that... I really should not have responded... sometimes I think ATS is like crack though... once you start you're just compelled to keep doing it.

so really if we can't predetermine or predict IC, how can we really test it? How can we really tell if a process/organism is ID'ed, can we really distinguish it from a naturally developed process/organism?

I don't think I ever said we can't predict IC... at least not while sober. That's one of my big points, you can predict IC. Please see my other post re: photosynthesis. There are certain systems that fit within the testable framework of an IC systems, and others that wouldn't.

There are many known processes that are improbable and seem IC and have been shown to have natural explainable causes.

Please provide examples of said processes.

You have suggested possible tests for IC but as you admit there are other possibilities that can account for what we see.

Of course. Nothing is going to be definitive in origins science.

If we test one, and find it's not IC, then we move to the next, without any other purpose than to find an object that we can see as impossible with current levels of knowledge.

That 'test one and move onto the next' is admittedly poorly worded and doesn't convey my feelings about how science and research should be performed. I would never have written that statement to convey such an idea when sober... my bad.

So we are really testing evolutionary theories and not ID.

I'm actually on record in this forum as saying that IDT and NDT are more--or-less tested the same way, so I sort of agree with you. I am more likely to word it like: A test for IDT is often also a test for NDT, ie: you can in fact have results that don't support the inference from design.

Is NDT perfect, most likely not but that doesn't by default suggest ID. Every theory can be refined, even general relativity may need this.

I know this is a popular notion... that IDT isn't proven by default, and I agree with this... though it's currently the only origins theory competing philosophically with NDT and abiogenesis. Not that it's proven by default, it's just the one of the only other marginally mainstream theories. Someone posted something called "intervention theory" recently, but it just sounds like IDT to me.

It really does seem to be an argument from incredulity.

I can see how one is inclined to think this, but I disagree.

Flagellum looks very complex, we suggest it is improbable and therefore it is ID and we prefer to ignore all possible mechanisms.

Untrue. I'm sure that Behe would love to be able to get some grant money to actually test his theories. People aren't saying it's IC and throwing up their hands and walking away... they want to study from a different basis of hypothesis... there's nothing wrong with this IMO.

If you can't show why and how an IC molecule is ID'ed, it is untestable and unfalsifiable.

Untrue. You can show that something needn't have been designed and is explainable by natural mechanisms, thus falsifying the IC hypothesis for that system.

You already admit that if flagellum is shown to not be IC and can develop by known processes then we move on to the next.

Again... my bad... Please don't hold me to my drunken ramblings.

Unless you can really ascertain a mechanism that can be falsified that suggests ID produced IC molecules, the argument of that ID is pure incredulity and not actual science will remain. Otherwise, if we eventually show every possible IC molecule is not so, then we move to a lower level of incredulity (i.e. abiogenesis) and so on ad nauseum until we get to the big bang and say, ID created the universe.

However, saying that, if we see the scientific purpose as being to refine current theories, then I'm all for it - but ID is dead already as a possible scientific theory unless it is refined in itself (and how do we really test it). So what is it's purpose, I suggest it is to simply discredit Darwinian theories.

Please refer to previous statements re: falsification/testability, drunken rambling, and the duality of testing IDT/NDT.

Of course my purpose is to advance science. I am a scientist. I certainly don't want to see science and progressed stifled.

[quot]My interest in this is because of my research into the neuroscience of consciousness (and it's elements). You could say that the mind is ID'ed, I suggest it may be much more complex and improbable than the IC processes that have been suggested (e.g. how are the individual elements of our environment binded into that which we actually perceive, how did empathy develop from simple instinctual processes of emotion). I would suggest natural processes of evolution have created consciousness however improbable this may seem at first glance. I can see ID'ers eventually impinging on our area of research.
Impinging? How does someone testing their own hypothesis negatively affect you? It has nothing to do with you. It's their research program, not yours.

Originally posted by mattison0922

Originally posted by melatonin
Ok I guess your busy. I'll give my considered opinion for all it's worth, lol. I research in neuroscience and the ID hypothesis reminds me of another pretty vacuous theory - Damasio's 'somatic marker hypothesis'. But forgive me for any misinterpretations, i'd just like an informed comment

What does your research involve? What's your educational background? I am unfamiliar with this particular hypothesis you mention

I have two firsts - psychology/neuroscience and chemistry – an MSc in clinical neuroscience and am in my last year of my PhD in cognitive neuroscience studying elements of social neuroscience and I help teach 1st yr experimental methodology (I would fail any of my students who came up with a hypothesis like IDH for its inherent methodological flaws, I'm sorry to say).

As said before IDH is a theory of ORIGINS, therefore it should make some claims about the mechanisms that produce these IC organisms.

I understand this is a popular belief. I don't see why people put this restraint on ID. The same condition is not applied to gravity. We don't know the mechanism via which gravity operates, but I don't see people lining up to claim that gravity is unscientific because we don't know if it's a wave, or whether the graviton is for real. Obviously science in general is not held to this standard, why should ID be?

But the theory of relativity does not pertain to origins. It is a description of a natural physical force and makes predictions about how it acts on physical bodies, the notion of gravity may even need refining. ID just seems to say “some systems seem awfully complex, therefore it must have been designed and we’ll ignore the fact that other possibilities exist”. To be useful it should make predictions that can be falsified about origins. It is meant to be an explanation of the origin of life, not a description of certain molecules. Maybe IC does some description and has the possibility of being falsified for a proposed system by actually testing NDT - but IC is not IDH.

Just stating in must be due to intelligent design results in a pretty vacuous theory. Otherwise, there will be other parsimonious possibilities that have not been considered (and no matter how improbable, it would be more probable and parsimonious than invoking an intelligent designer, unless you suggest a mechanism).

Disagreed. Just stating what is due to ID? IDTists don't due this anyway. IDTist's don't say 'We've studied this and determine it to be designed, end of story." There are certain systems that show hallmarks of design, and those that don't. You don't study systems that seem like the could have arisen via natural selection. The hemoglobin system is a good example of this. There does seem to be a relationship between hemoglobin and myoglobin, the system doesn't exhibit signs of irreducible complexity, and is thus not a good candidate to test for design. Please note that this doesn't mean the system wasn't designed, it's just not a good candidate to detect design.

Other systems are different. I'll take my favorite example, photosynthesis. PS exhibits all the signs of being a designed system: Appears to be IC, there's no good explanation for its origins based on natural selection, etc. Mainstread scientists admit that these systems 'appear' designed, and there exists no reasonable mechanism for their origins via NS, how can NS be the most parsimonious assumption. IMO, in the case of things that appear designed and for which there exists no reasonable mechanism of their origins via any other extant theory, the assumption for design is much more parsimonious.

Parsimony is not absolutely related to a mechanism.

But how do you know it is designed? Simply because current knowledge can’t explain it We can’t definitively explain the purpose of dreams but we don’t say ID created them. Mechanism is more important, but when you are invoking a possible supernatural force, parsimony should be. IDH/IC just ignores other possibilities that could happen. I see words like “scaffolding” and ‘function change” bandied about by NDT.

Behe himself said that there are indirect methods that could result in IC organisms. It could be an existing evolutionary process or maybe some other natural process we do not yet know of, or maybe both.

Where did Behe say this? This pretty much goes against the whole concept of IC. Where specifically did Behe state this. I'm not familiar with this quote, and I definitely would have taken note of it had I read it.

I read behe’s book when it first come out, but I sold it on as I was not impressed then. Here is a quote…

"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)

So the appearance of IC does not really invoke ID…

The notion of IC seems pretty inexplanatory,

Ummmm.... that's because it's not an explanation it's an observation.

an IC organism/process shows ID because it is irreducibly complex (tautological?).

Hmmmm... looks like you're trying to create a circular argument where one doesn't exist. A system may exhibit the hallmarks of ID due to it's IC nature... end of sentence.

What is complex, give a definiton so that can measure or predict IC. So, Dembski (sp) suggests that an IC molecule is one that has his suggested probablility of occuring, under his suggested conditions and processes - although, other conditions and processes are possible? Therefore complexity of an organism/process, is actually defined externally. Also, probability tells us that the probability of something existing that actually does exist is p=1 (i.e. it does exist - so a parsimonious explanation may exist).

Okay... there's definitely some confusion here:

IC as defined by Behe:

A single system composed of several well-matched, interacting parts that contribute to the basic function of the system, wherein the removal of any one of the parts causes the system to effectively cease functioning.

Taken from Darwins Black Box, pg 39

IC as defined by Dembski:

A system performing a given basic function is irreducibly complex if it includes a set of well-matched, mutually interacting, nonarbitrarily individuated parts such that each part in the set is indispensable to maintaining the system's basic, and therefore original, function. The set of these indispensable parts is known as the irreducible core of the system.

Taken from No Free Lunch, pg 285

So in reality, IC has nothing to do with probabilities directly. Perhaps you can read these definitions, and rephrase your question when you have a better understanding of the concept of IC.

So if p=1 and we have an apparently IC molecule what does that tell us? Does this mean it is sourced from intelligent design. Well not really, it just means we could well not know of a suitable process that doesn't require intelligent design. so we really need to think about the probablities of the possible pathways to the organism/process - would intelligent design be the most probable, if it defeats the physical laws of the universe then it probably isn't likely (I'm sure creating mass from nothing will be a violation, otherwise it must conform to our physics - well does that mean we need ID?)

Hmmm... not sure how we got to IDT 'defeating the physical laws of the universe,' it's certainly not postulated in the theory anywhere that I've read. I am also not sure where the 'creating mass from nothing' came from, but if you really have a problem with that, then I suggest you take it up with the physicists researching the singularity and big bang theory as well.

Yes, they provide explanation of what an IC molecule would exhibit, Dembski also suggested that an IC system is something that would be beyond his “universal probability bound”, i.e. it would not occur by chance. This is an arbitrary figure of something like 1x10 to the power of 150. This involves his own questionable determination of the situation.

ID is tautological, ID is an IC system that is not reducible. Unless you can show IC molecules that have been designed and show why that is the case. The ‘level of processing’ theory in psychology suggested that memory is determined by the ‘level’ that information is processed at. How do you determine this, by the amount of items remembered at a particular ‘level’. All simple testing suggested this. We defined what the levels were but there was no independent measure of level. Eventually we could use fMRI to measure brain activity, it was found that more brain activity is present at higher LOP’s. So now we have an independent measure. What is IC? - it is a molecule that is irreducibly complex and has been designed. Why? Because we cannot show any other possibility. How do we know it was designed - because it is irreducible complex. Can’t you see the problem, it is very vacuous, it explains nothing. Theories and hypotheses would add to science knowledge, all ID will do is say we don’t really know how this developed so we’ll invoke an intelligent designer.

Matt, you seem to destroy that guys paper on flagellum and Sec III. Is his suggested pathway completely unprobable? And I dont mean the exact homology etc (I totally trust your judgement on it), just the pathway with some other suitable homologous organism?

You certainly don't need to take my word for it. Mainstream sciences opinion with respect to the flagellum and SecIII system is that SecIII is derived from the flagellum. The reason is this: flagella are present in pretty much all categories of bacteria.... they pretty much seem to be universal. However the SecIII system is not universal; it is thought to have arisen until much later... after the appearance of metazoans. So... it seems like Matzke is willing to ignore the opinion of mainstream science to prove a point, but expects people to dogmatically believe their assertions about evolution. Matzke is pretty much willing to ignore mainstream sciences opinion about something simply so he can prove IDTists wrong. This paper is a classic case of literature bluffing. He's relying on people not taking the time to chase down his refs. and critically think about his hypothesis.

Also, different pathways to flagellum must exist and have been suggested (indirect maybe).

Must they? Why? Matzke also proposed that the ATP synthase (synthase not synthetase) was related to the flagellum. This is just not true. I can see why he's reaching for it; the ATP synthase is biological rotary motor, with a mechanism vaguely analogous to that of the flagellum, unfortunately, once again his assertions aren't even weakly supported. In fact, he imports the wrong portion of the apparatus to harness proton flux.

As I said, I’m not supporting Matzke’s paper. I know little molecular biology to even think of this. What I’m suggesting is that so far we can show how a lot of very complex systems have developed through evolution from simpler organisms. Bacteria will have no fossil record, so we have no way of knowing what has existed on the earth before now. If other possible routes to flagellum exist, they must be considered. Remember Behe in 1994 raised the lack of fossil evidence for whales and was quickly rebuffed. He is working from personal incredulity and nothing more. He only accepts NS because the evidence is overwhelming.

As a biologist (I also have degree in Chem, not bio though

) you must admit that circuitous routes to biochemical processes are very common (doesn't E. Coli have some).

Actually, I'm not quite sure what you mean here, so I am going have to ask you rephrase the question. If you know of some these circuitous routes in E. coli please provide an example.

There are many biochemical processes that if we designed them using our intelligence would be much, much simpler than is shown (i.e. a circuitous route developed, suggested indirect methods in the development of function do exist). I’ll try and find some for you - It’s in a paper in a chemical education journal.

It would be more probable that a simple process would develop, however more improbable processes do exist. Also, many ID papers are not published for similar reasons as his, omission, misinterpretation, and just-so claims seem common in ID literature (similar to complaints of ID proponents).

What? What ID papers aren't published for ommission, misinterpretation, etc? To my knowledge, there are 2 papers published by the ID community, none of which contains any actual data. The community isn't very active currently and very few profs. openly admit to being IDTists. I won't admit it, except for here, to my wife and a very few close friends in science.

Sorry, my bad, it was meant to have a semi-colon in, that’s why it said ID literature. What I was trying to say is that a lot of the ID literature (i.e. books and articles) exhibits the same characteristics they accuse opponents of. For example, In his recent paper he makes a theoretical claim, but has also criticized other of using theoretical supposition to support arguments.

Dolphin's blood coagulation functions fine without one of the components of the apparent IC process? Now this is where the ad nauseum bit of the IC notion comes in - it has been falsified and now Behe says it was never IC - is this going to continue ad nauseum?

I am unfamiliar with the Dolphins Blood example. Where did you come across this? I do know that Doolittle refuted Behe's claims of IC blood clotting cascades, then later admitted to Behe that his own analysis of second site mutations was wrong, and in fact apologized to Behe. I would be interested to read this Dolphins Blood example though.

I’ll respond to this below.

Why did Behe suggest this process if it is not IC? Simple, there is no independent measure or theoretical basis of IC, if we can't really indicate IC independently, then any complex biochemical process that has not yet been explained, can be deemed IC, until we find it's not. (This is the comparison with Damasio's hypothesis - researchers constantly shoot his possibilities down, but then he moves the goalpost, i.e. its almost unfalsifiable but keeps some busy).

There does exist the possibility that Behe is simply mistaken. I know Behe, and he doesn't have some evil agenda... he's not interested in maintaining the idea of IC at all costs, he's a totally reasonable guy who happens to subscribe to a non-traditional view of biological origins.

well that’s fine but he is forcing his hypothesis to fit the data. Let the data speak for itself. As you mention before, there is no data, and all there will ever be is “this doesn’t seem to develop by known processes”.

Behe proposes the mousetrap as an analogy for IC. I guess a radio would also be analogous - this study describes the spontaneous evolution of a radio. The researchers used a simulated evolutionary process in which the fitness of an electronic circuit as an oscillator was selected for. Of course, there are criticisms - well whose methodology is perfect?

www.cogs.susx.ac.uk...

Another simulation, avida (Lenski et al, Nature 2003), has modelled origin by NDT, what about schneider's EV? Again, they may not be perfect, but neither was Behe's paper you mention. From what I gather from people who understand these simulations, Trumans rebuttle was not so convincing.

Unfortunately simulations aren't necessarily applicable in the real world. I am familiar with Lenski's paper, and was not impressed. I could just as easily direct you to Behe's protein science paper. That leaves us with two published articles that pretty much state opposite things.

Have you read the radio evolution paper? It’s actually a fine bit of research I feel. The mousetrap analogy is very poor, it doesn’t reproduce, these do and use all the hallmarks of evolution. Some computer simulations are very good at predicting real-world behaviour, even in psychology which is as unpredictable as it gets.

So what about IC=IDH, well accounting for the possibility of other possible mechanisms, it doesn't really it's a pretty big leapfrom IC to a designer. We may be able to falsify each IC organism/process proposed, I would question whether we can falsify IDH itself and that is the issue,

Why? Darwinism is inherently unfalsifiable, and no one seems to balk at that.

IDH should stand on its own, without attempting to fall back on other theories supposed failings.

unless you give a mechanism outlining the process of design to test, not the result (NDT can). Just because we can't find a mechanism for IC doesn't mean one does not exist. We had to wait a very long time to provide a better explanation than creationist ideas, it may take just as long to completely refute such a vacuous theory as IDH.

It may take some time, then again, it may never happen. The fact of the matter seems to be that irrespective of anything else, there will always be scientists that infer design from what they observe. Seems like it's always been the case, and may always be. The assumption that things weren't designed is actually reasonably new. Certainly the inference from design is not a new idea, and will likely always be a consideration for some.

I’m sure they will but science we need to test and observe. Unless we can test there is no science, how do you actually test for IC without resorting to showing NDT cannot explain a certain process at this point in time?

And please don't criticise NDT's theoretical shortcomings to justify IDH's, it needs to stand alone. I would suggest that NDT would have difficulty explaining a hominid fossil in the same strata as early dino's and if humans showing closer DNA comparisons to a worms than a chimp. It can be falsified.

Untrue. When out of place artifacts are discovered, they are invariably dismissed as hoaxes, which a good number of them may be. But the fact of the matter is that NDT has always been flexible enough to accomodate pretty much whatever evidence... the molecular clock is reliable for genes, except for the genes it's not, Mutation is random, except when it's directed, you get the idea.

Maybe it can try but when it gets ridiculous like trying to explain away obvious falsification it will need to be assessed on its merits. How would you explain away humans being shown to be more related by DNA to a worm than a primate? If they tried they would be sneered at. I’m sure after comtinuous retesting they would have to accept the fact it is wrong. However, you think about it, NDT has mountains of converging evidence supporting it. It will not be adjusted just because we cannot yet show how flagellum evolved.

Anyway, I see a value in anything that cleans up problems in science, and ID will do that for life-sciences. I understand the problems ID will have for acceptance, a lot of it is due to its poor construction - I know this because a supervisor of mine supports an area of science that is deemed pseudoscience by many (neuro-psychoanalysis).

Well... now I am totally confused, Do you or do you not see ANY inherent value with hypotheses based from an assumption of design

There is no inherent value in a flawed hypothesis and bad science. It will strengthen NDT not weaken it, if anything.

Cheers and thanks for your time

Likewise, and thanks for the thought provoking post... I am going to look into this dolphin's blood stuff too. Will post when I find something out.

*Edit* Okay... I looked into this Dolphin Blood thing... could be an issue for the IC of the blood clotting cascade... intriguing indeed... good find

will have too look into this in some detail.... this could take me some time.

[edit on 15-1-2006 by mattison0922]

Yep, so Behe has now apparently said the system was not IC. The paper was 30 or so years old. He could not have researched this that well.


Can’t you see that this will never stop until every supposed IC system has been falsified, we cannot test for ID unless we have a theometer. I have no issue with there being a creator, I’m agnostic, I see places for a creator. But it will never be science unless we can somehow test for their presence, it will always rely on the absence of another explanation.


I’ll answer your second post here also…

Originally posted by mattison0922

Originally posted by melatonin
Cheers for the response, I hope you didn't have too bad a hangover, lol.

My apologies for that... I really should not have responded... sometimes I think ATS is like crack though... once you start you're just compelled to keep doing it.

It’s great that there is actual proper science debate on ID here, hope you had a good night though

so really if we can't predetermine or predict IC, how can we really test it? How can we really tell if a process/organism is ID'ed, can we really distinguish it from a naturally developed process/organism?

I don't think I ever said we can't predict IC... at least not while sober. That's one of my big points, you can predict IC. Please see my other post re: photosynthesis. There are certain systems that fit within the testable framework of an IC systems, and others that wouldn't.

But it still falls to the fact that you are not testing IC but the absence of another explanation.

There are many known processes that are improbable and seem IC and have been shown to have natural explainable causes.

Please provide examples of said processes.

You have suggested possible tests for IC but as you admit there are other possibilities that can account for what we see.

Of course. Nothing is going to be definitive in origins science.

Some suggest the bones of the ear as a system that can be considered IC and has evolved by changing function.

But the fact that you are testing for the absence of another explanation will result in ad nauseum science. Its like saying “certain objects on the earth are not under the influence of gravity” and then having to test every single known object, finding a balloon and determining that a balloon is not affected by gravity without looking for another explanation.

If we test one, and find it's not IC, then we move to the next, without any other purpose than to find an object that we can see as impossible with current levels of knowledge.

That 'test one and move onto the next' is admittedly poorly worded and doesn't convey my feelings about how science and research should be performed. I would never have written that statement to convey such an idea when sober... my bad.

Believe me this is what they have in mind. We cannot test IC unless we can really positively show IC and how it is IC, rather than saying “current theories cannot explain this!”. Any system found to not be IC will then be deemed not IC. Unless we can independently predict it, not just use incredulity.

So we are really testing evolutionary theories and not ID.

I'm actually on record in this forum as saying that IDT and NDT are more--or-less tested the same way, so I sort of agree with you. I am more likely to word it like: A test for IDT is often also a test for NDT, ie: you can in fact have results that don't support the inference from design.

Is NDT perfect, most likely not but that doesn't by default suggest ID. Every theory can be refined, even general relativity may need this.

I know this is a popular notion... that IDT isn't proven by default, and I agree with this... though it's currently the only origins theory competing philosophically with NDT and abiogenesis. Not that it's proven by default, it's just the one of the only other marginally mainstream theories. Someone posted something called "intervention theory" recently, but it just sounds like IDT to me.

There is no doubt you are solely testing NDT, I will show you why I think this is the case in another post. You cannot base a hypothesis on the fact an experiment may not support another similar theory. It’s just bad science

It really does seem to be an argument from incredulity.

I can see how one is inclined to think this, but I disagree.

Flagellum looks very complex, we suggest it is improbable and therefore it is ID and we prefer to ignore all possible mechanisms.

Untrue. I'm sure that Behe would love to be able to get some grant money to actually test his theories. People aren't saying it's IC and throwing up their hands and walking away... they want to study from a different basis of hypothesis... there's nothing wrong with this IMO.

If you can't show why and how an IC molecule is ID'ed, it is untestable and unfalsifiable.

Untrue. You can show that something needn't have been designed and is explainable by natural mechanisms, thus falsifying the IC hypothesis for that system.

“for that system” – therefore ID prediction is not possible, it is based on incredulity and nothing else. You are actually testing NDT and not IDH? Matt, you are highlighting exactly the problem - this will continue ad nauseum. You cannot form a falsifiable test for IC by simply trying to falsify another theory.

You already admit that if flagellum is shown to not be IC and can develop by known processes then we move on to the next.

Again... my bad... Please don't hold me to my drunken ramblings.

But you just stated the exact same thing, “falsifying IC for that system”. There is no real basis for IC other than speculation and incredulity (and maybe wishful-thinking)

Unless you can really ascertain a mechanism that can be falsified that suggests ID produced IC molecules, the argument of that ID is pure incredulity and not actual science will remain. Otherwise, if we eventually show every possible IC molecule is not so, then we move to a lower level of incredulity (i.e. abiogenesis) and so on ad nauseum until we get to the big bang and say, ID created the universe.

However, saying that, if we see the scientific purpose as being to refine current theories, then I'm all for it - but ID is dead already as a possible scientific theory unless it is refined in itself (and how do we really test it). So what is it's purpose, I suggest it is to simply discredit Darwinian theories.

Please refer to previous statements re: falsification/testability, drunken rambling, and the duality of testing IDT/NDT.

Of course my purpose is to advance science. I am a scientist. I certainly don't want to see science and progressed stifled.

The only way ID will advance research is by falsifying every single system proposed and supporting NDT and maybe even finding other naturalistic explanations. When will we actually be able to test IC?

My interest in this is because of my research into the neuroscience of consciousness (and it's elements). You could say that the mind is ID'ed, I suggest it may be much more complex and improbable than the IC processes that have been suggested (e.g. how are the individual elements of our environment binded into that which we actually perceive, how did empathy develop from simple instinctual processes of emotion). I would suggest natural processes of evolution have created consciousness however improbable this may seem at first glance. I can see ID'ers eventually impinging on our area of research.

Impinging? How does someone testing their own hypothesis negatively affect you? It has nothing to do with you. It's their research program, not yours.

Because we will have a lot of badly formed hypotheses and it will waste resources in a wild-goose chase for an untestable and unfalsifiable proposition. All this is really doing is testing NDT, it is not testing IDH at all. I have thought about testing the Somatic-marker hypothesis but there is no real point, it's a dead duck (which is pretty much like IDH)


[edit on 15-1-2006 by melatonin]

OK what is good science, what is bad?

a hypothesis is a test about a prediction. We form a hypothesis, suitable method and observe, then we form a conclusion. Although scientists like to think they are testing the experiemntal hypothesis, they are actually trying to falsify and test the null hypothesis, i.e. trying to falsify their experimental hypothesis. This is based on Karl Popper's decriptions of good science and is held in high regard.

Forming hypotheses...

[B]Somatic Marker hypothesis (good science, good hypothesis, vacuous theory)[/B]

experimental: somatic markers aid complex decision-making

null: somatic markers do not aid complex decision-making

Operationalisable variables:

(i) somatic markers - a bodily process due to emotion that is integrated in the brain via experience.

(ii) complex decision-making - making choices under situations of complexity and uncertainty

so we test using a complex decision-making task over time and measure bodily derived emotional responses (skin conductance)

results - we find increased SCR over time before people make bad choices indicating an emotional 'warning' signal derived from visceral processes, these people perform the task well.

conclusion - somatic-markers 'mark' bad choices and guide adaptive decisions.


[B]Intelligent Design (bad science, bad hypothesis, no theory)[/B]

experimental: certain natural systems are are IC

null: certain natural systems are not IC

operationalised concepts:

certain systems - those we cannot show a process for (systems showing features of IC)

IC= behe/dembski defn (systems showing features of IC).

Method: Test a certain system by showing another theory cannot yet explain its mechanism (e.g. remove proteins from flagella throw lots in a test tube with stuff it will need to develop under certain conditions and observe)

Results: no evidence of a flagella like system - i.e. nothing.

conclusion: This system is IC and therefore it is evidence of ID because current theory (or this methodology - which was it?) did not work.

Can you not see the problem? You are looking for the absence of evidence via the null - certain systems are not IC. You have falsified a possible natural mechanism for current levels of knowledge. That is all. You have actually shown nothing but your experiment failed and that method was insufficient. The current methodolgy is unfalsifiable and results in a tautology because both your variables depended on the same concept, if we could independently measure IC then maybe the tautology would not exist. Now we could use Dembski's probability prediction, but I'm sure most (if not all) organisms would fit this and evolutionary mechanisms already exist for them and it would be easily falsified. So with the current approach all you are doing is testing evolutionary theory, the only indication of ID/IC is the lack of evidence, not a single bit of positive evidence.

The problem with most sciences is that they do not teach good methodology, psychology does because it has a history of having to justify its scientific validity and we are very careful about forming hypothesis and methods in such a subjective and unpredictable science.

Possible good ID hypothesis...

experimental: irreducible systems are formed by intelligent design.

null: certain systems are not formed by ID.

operationalised variables:

intelligent design = ?

Irreducible systems = dembski/behe defn.


Earlier you stated how a friend took 6yrs to synthesise a membrane, should he have given up after 2 and done something else because it was obviously ID? It could take 100 years or 100 experiments to find a mechanism for flagella, it may never be discovered and we may only ever have theory. Even then you have no actual evidence of IC or ID. evemn then ID will still not be accepted, not because its based on some supernatural concept, but because it is just plain bad science. this is why mainstream science is sneering at ID'ers. We know that unless you refine this hypothesis, it will not be testable and falsifiable.

You mention "junk" DNA. Why is it junk? Because we haven't shown a possible use for it yet, that is all. It is still no evidence of ID, only the inability of current knowledge to explain it. we only discovered DNA around 1950, do you expect us to explain the function of every gene in that time? Without evolution we may still think that the appendix is "junk" anatomy, now we know otherwise.

If I could show you previously deemed "junk" DNA that now has a function, would you accept this?




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Originally posted by melatonin
OK what is good science, what is bad?

Will address your posts at length tomorrow, but your two most recent posts demonstrate that you are not reading my posts very carefully at all. Your reference to 'junk' DNA is completely confused, and I don't know anyone who synthesized a membrane. You seem to completely misunderstand nearly everything I've posted or are deliberately misquoting me. Thus far, our interaction has been cordial, and I'll assume the former. Please read my posts carefully before rebutting them. I will address your replies at length some time tomorrow.

Originally posted by mattison0922

Originally posted by melatonin
OK what is good science, what is bad?

Will address your posts at length tomorrow, but your two most recent posts demonstrate that you are not reading my posts very carefully at all. Your reference to 'junk' DNA is completely confused, and I don't know anyone who synthesized a membrane. You seem to completely misunderstand nearly everything I've posted or are deliberately misquoting me. Thus far, our interaction has been cordial, and I'll assume the former. Please read my posts carefully before rebutting them. I will address your replies at length some time tomorrow.

OK no problem, I have no other aim but to be cordial

maybe I've seemed a bit abrupt, I've been busy tonight. It's 6.30am here, I've had little sleep and I'm stressed. Sorry if it came across that way

As for the 'junk' DNA business - as you said in the other thread, it is a pity the word was originally used because we do not know the function of a lot of genes. It was also a pity I presented my argument incorrectly, lol... what I should have said is that "if I could present evidence that deleting chunks of DNA has been shown to not affect the organism would that make a difference? - my bad again, I haven't been on good form tonight, just too much time spent on other stressful things and it's not good for thinking about issues that are not my area of speciality, OK, this is the article I was going to raise on this issue...

Nature. 2004 Oct 21;431(7011):988-93. Related Articles, Links

Megabase deletions of gene deserts result in viable mice.

Nobrega MA, Zhu Y, Plajzer-Frick I, Afzal V, Rubin EM.

DOE Joint Genome Institute Walnut Creek, California 94598, USA.

The functional importance of the roughly 98% of mammalian genomes not corresponding to protein coding sequences remains largely undetermined. Here we show that some large-scale deletions of the non-coding DNA referred to as gene deserts can be well tolerated by an organism. We deleted two large non-coding intervals, 1,511 kilobases and 845 kilobases in length, from the mouse genome. Viable mice homozygous for the deletions were generated and were indistinguishable from wild-type littermates with regard to morphology, reproductive fitness, growth, longevity and a variety of parameters assaying general homeostasis. Further detailed analysis of the expression of multiple genes bracketing the deletions revealed only minor expression differences in homozygous deletion and wild-type mice. Together, the two deleted segments harbour 1,243 non-coding sequences conserved between humans and rodents (more than 100 base pairs, 70% identity). Some of the deleted sequences might encode for functions unidentified in our screen; nonetheless, these studies further support the existence of potentially 'disposable DNA' in the genomes of mammals.



So it seems that deleting massive amounts of mouse DNA did not affect phenotype.


Someone mentioned their friend/acquintance studying for a phD, in this thread, which took 10 years, 6 of which was spent on one issue. I guess I should have reread and searched for that statement to be spot on, so little time, so much to do...

As I have said anything that moves science on is good, the problems ID as a hypothesis is going to have is to show some sort of independent evidence. If blood coagulation has already been falsified, computer simulation show the development of IC with no intelligent interaction, possible pathways exist for some IC systems, large scale deletion of DNA does not affect phenotype - I do think you need to actually show why and how an IC system is ID without recourse to negative supporting evidence. Sorry...



Damn, I am messing up, 5 edits, to get where I wanted. I think I need some R&R. As you probably know, thesis writing is not good for a person's sanity

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Okay... I can't sleep with this S*&# hanging out there... got to address it now... like I said.... just like crack... actually Rren said it first, but I think he's right.

Originally posted by melatonin
I have two firsts - psychology/neuroscience and chemistry – an MSc in clinical neuroscience and am in my last year of my PhD in cognitive neuroscience studying elements of social neuroscience and I help teach 1st yr experimental methodology (I would fail any of my students who came up with a hypothesis like IDH for its inherent methodological flaws, I'm sorry to say).

Awesome with respect to the education. Chemistry is my first love also. Sorry to hear about philosophical bias. I generally fail my students when they performance mandates, not based on my personal beliefs.

But the theory of relativity does not pertain to origins.

So only Origins science is limited to this restraint of necessitating a mechanism? Why is that? That one's never come up in my education.

ID just seems to say “some systems seem awfully complex, therefore it must have been designed and we’ll ignore the fact that other possibilities aexist”.

This is patently untrue. It doesn't ignore that other possibilities exist. I've repeatedly pointed this out. Many systems DON"T exhibit any hallmark of design, and needn't have been designed. I can go through a comprehensive list if necessary, but I've repeatedly mentioned the hemoglobin system as one such system. Other systems that appear to have related components etc., argue against the necessity of design. IDT definitely doesn't ignore these other possibilities. If it did, Behe wouldn't acknowledge that man and apes probably do share a common ancestor, etc.

To be useful it should make predictions that can be falsified about origins. It is meant to be an explanation of the origin of life, not a description of certain molecules. Maybe IC does some description and has the possibility of being falsified for a proposed system by actually testing NDT - but IC is not IDH.

I've repeatedly pointed out that IDT is perfectly capable of making predictions. At least on par with NDT. Furthermore, these predictions CAN be falsified. IDT is not a "description of certain molecules..." It's a basis for hypothesis formation in origins science. IDT can be falsified via these very experiments... it's not going to be falsified in one fell swoop, just like NDT isn't going to be falsified in one fell swoop. It's ridiculous to put this restriction on it, which is what your last sentence I quoted does.

But how do you know it is designed?

You don't. That's what IDT tests for, evidence of design, nothing more.

Simply because current knowledge can’t explain it We can’t definitively explain the purpose of dreams but we don’t say ID created them.

Dreams are quite obviously the product of intelligence. IDT isn't invoked when we don't understand how something happens. Though it's not an unreasonable assumption when

1. A system exhibits the appearance of design
   
2. The current stock of extant theories appears to be an inadequate explanation, because there is no evidence to suggest they're part of the explanation
   

When current knowledge doesn't, or isn't adequately explaining things, often a new hypothesis is not an unreasonable place to start.

Mechanism is more important,

Mechanism is important when it's part of the theory.

but when you are invoking a possible supernatural force, parsimony should be. IDH/IC just ignores other possibilities that could happen. I see words like “scaffolding” and ‘function change” bandied about by NDT.

Please see earlier rebuttals about IDT not ignoring other possibilities.

Furthermore, I've already addressed the question of parsimony... multiple times in fact.

Tell me this: A molecular motor system like the ATP synthase, not only appears to be designed, ie: is an IC molecular machine, and is further part of a system that appears to be IC.

Now:

1. Even Dawkins will acknowledge that such molecular machines exhibit the appearance of design.
   
2. There exists no mechanism via NDT by which ATP synthase of Photosynthesis could have arisen.
   
   
   
   1. There are no homologous proteins that ATP synthase is likely to have arisen from.
      
   2. PS proteins also appear to have no ancestor proteins from which they are likely to have arisen.
      

Now again please explain to me how the assumption from NDT is more parsimonious than the assumption from design.

I read behe’s book when it first come out, but I sold it on as I was not impressed then. Here is a quote…

"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)

Hmmm... this seems to refute the notion that ID proponents 'completely ignore' that other possiblities exist. This quote seems to be a direct confirmation from Behe that possibilities other than IDT may exist. Kind of stands in opposition to your earlier assertions.

So the appearance of IC does not really invoke ID.

It's the other competing theory. If NDT can't account for something, it doesn't mean IDT is proven by default, BUT it does mean that another basis for hypothesis is not only reasonable, but perhaps necessary. It would seem that inference from design is the most parsimonious assumption... in the cases like I've described... NO not in all cases, in very specific cases.

Yes, they provide explanation of what an IC molecule would exhibit, Dembski also suggested that an IC system is something that would be beyond his “universal probability bound”, i.e. it would not occur by chance. This is an arbitrary figure of something like 1x10 to the power of 150. This involves his own questionable determination of the situation.

The figure is hardly arbitrary, it's based on the number of particles in the known universe, as a function of the known amount of time, I believe broken down in planck time increments, coupled with some other known constants that I believe are related to rates of reaction and diffusion, etc.

ID is tautological, ID is an IC system that is not reducible.

ID is not tautological. The notion of design is inferred from a variety of things, likely including, but not necessarily limited to the idea of IC. ID is no more of a tautology than is NDT.

Unless you can show IC molecules that have been designed and show why that is the case.

Nothing in origins science can be proven beyond a doubt... that's the nature of the science. So you can't prove that molecules have been designed. You can base hypotheses from this assumption, and test those hypotheses, those tests will either support you hypothesis or they will not.

The ‘level of processing’ theory in psychology suggested that memory is determined by the ‘level’ that information is processed at. How do you determine this, by the amount of items remembered at a particular ‘level’. All simple testing suggested this. We defined what the levels were but there was no independent measure of level. Eventually we could use fMRI to measure brain activity, it was found that more brain activity is present at higher LOP’s. So now we have an independent measure.

This is not origins science.

What is IC? - it is a molecule that is irreducibly complex and has been designed.

Wrong. IC is an assumption based on observation, and evaluation of existing evidence and theories. IC is an assumption that leads to an inference of design. The 'Design Inference' is an alternative basis for hypothesis formation, fully testable and falsifiable, and as you point out apparently subject to some sort of mathematical rigor.

Why? Because we cannot show any other possibility.

No - not because we can't show any other possibility, but because it currently seems to be the most parsimonious assumption.

How do we know it was designed - because it is irreducible complex.

Ummm... no. We DON"T know it was designed, that's what the hypothesis and test are about. Is the inference from design, sometimes the most parsimonious assumption as has been repeatedly described, supported by data or not.

Can’t you see the problem, it is very vacuous, it explains nothing.

Thus far, the problems as I see them appear to be either you don't understand the theory adequately, or are deliberately trying to misrepresent it.

Theories and hypotheses would add to science knowledge, all ID will do is say we don’t really know how this developed so we’ll invoke an intelligent designer.

Okay for the last time. The theory is perfectly capable of generating data and adding to the body of scientific knowledge. I know it's not the knowledge you want it to be, but it does fufill the requirements for which it was conceptualized. Unfortunately, people don't develop ideas to cater to our particular set desires and or metaphysical presuppositions; they do it for their own reasons.

As I said, I’m not supporting Matzke’s paper.

I didn't take it that way... you asked... I answered.

I know little molecular biology to even think of this. What I’m suggesting is that so far we can show how a lot of very complex systems have developed through evolution from simpler organisms.

This is true, and IDT doesn't have an issue with these. Again, this is why Behe accepts things like common descent of apes and man, etc. This is why Michael Denton has changed his particular perspective to something that resembles a hybrid between theistic evolution and IDT... sort of a 'molecular pre-destination.' But other systems not only lack this explanation, but appear exhibit design. One last time: the appearance of design, the lack of evidence to suggest otherwise, and the apparent inability of extant theories to account for the origins of these systems sometimes make design the most parsimonious assumption.

Bacteria will have no fossil record, so we have no way of knowing what has existed on the earth before now.

Untrue. Scientists have found cyanobacterial fossils

Here are some:


In fact they've discovered them in rocks that are like 3.8 bya. The problem with this is that it leaves less than about 300 million years for abiogenesis and the develpment of complex systems like PS., as cyanobacteria posses a fully functional photosynthetic apparatus.

If other possible routes to flagellum exist, they must be considered.

Of course they do, but they don't. Unless you want to get back to Matzke's paper, which has not been accepted by any peer-reviewed science periodical with good reason.

Remember Behe in 1994 raised the lack of fossil evidence for whales and was quickly rebuffed. He is working from personal incredulity and nothing more.

To be honest with you... I was just getting into origins back then... was still a die hard evolutionist back then. But so what? Is Behe somehow obligated to always be correct? Do you ever propose things that turn out to be untrue? So Behe made a mistake, does this mean everything he's ever done is wrong. Behe is a molecular biologist, not a specialist on the evolution of whales... it's not surprising he might not be aware of all the evidence out there. In some cases though, he's correct, the evidence in fact, DOESN'T exist.

He only accepts NS because the evidence is overwhelming.

Gosh, then he should be crucified. Imagine that, accepting overwhelming evidence. Boy... Behe must really be an innovator.

What better reason to accept a theory than overwhelming evidence?

There are many biochemical processes that if we designed them using our intelligence would be much, much simpler than is shown (i.e. a circuitous route developed, suggested indirect methods in the development of function do exist). I’ll try and find some for you - It’s in a paper in a chemical education journal.

Ummm... yeah as soon as you can provide some specifics, we'll discuss.

Sorry, my bad, it was meant to have a semi-colon in, that’s why it said ID literature. What I was trying to say is that a lot of the ID literature (i.e. books and articles) exhibits the same characteristics they accuse opponents of. For example, In his recent paper he makes a theoretical claim, but has also criticized other of using theoretical supposition to support arguments.

I disagree with you here. Let's talk specifics. I don't know who 'he' is, Behe maybe? Please post a specific reference with your specific objection. Thanks.

well that’s fine but he is forcing his hypothesis to fit the data. Let the data speak for itself. As you mention before, there is no data, and all there will ever be is “this doesn’t seem to develop by known processes”.

Which hypotheses is forcing to fit the data. To my knowledge there isn't a mechanism, or any ancestor proteins the flagellum arose from, which data are being forced into his hypothesis or vice versa?

Have you read the radio evolution paper? It’s actually a fine bit of research I feel. The mousetrap analogy is very poor, it doesn’t reproduce, these do and use all the hallmarks of evolution. Some computer simulations are very good at predicting real-world behaviour, even in psychology which is as unpredictable as it gets.

I looked at it today... it seemed reasonably familiar, but I honestly didn't read it.... can't say whether I've read it for sure or not in the past... will look through my archives though.... am on to this dolphin thing now, so it's likely that will be placed on the back burner for the time being.

IDH should stand on its own, without attempting to fall back on other theories supposed failings.

I'm not falling back on other theories supposed failings. I'm pointing out the logical fallacy of saying something can't be scientific because it's not falsifiable, but ignoring that fact for things that are less objectionable to one's particular metaphysical belief system. But I agree with you. There are repeated instances where I am quoted as saying that the validity of IDT should rest on the theories ability to make meaningful contributions to science. It seems like you're reading most of my posting, so you must have come across this.

I’m sure they will but science we need to test and observe. Unless we can test there is no science, how do you actually test for IC without resorting to showing NDT cannot explain a certain process at this point in time?

Okay... so how much longer are you going to ignore the fact that I've proposed testable experiments, Behe, and others have proposed testable experiments. It's not 'resorting,' as I've repeatedly pointed out it serves as a basis for hypothesis formation and test.

it will need to be assessed on its merits.

AGAIN, I agree completely with this.

How would you explain away humans being shown to be more related by DNA to a worm than a primate?

Why would I try to explain it away? That humans and chimps DNA is more similar than humans and worms is a fact. There's no point in trying to say this relationship doesn't exist. The fact of the matter is chimps and humans have similar DNA. There are multiple inferences, including but not limited to common descent that one can attibute that evidence too. It makes sense that their DNA is similar, they are very similar organisms. It would be expected.

I do know how Behe attempts to 'explain away' this evidence: common descent.

If they tried they would be sneered at. I’m sure after comtinuous retesting they would have to accept the fact it is wrong.

They wouldn't try because it's foolish; it's arguing against available evidence. As I've repeatedly pointed out: IDT doesn't argue against much of this evidence you are mentioning. Are you deliberately trying to obscure the conversation by interjecting this irrelevant info?

However, you think about it, NDT has mountains of converging evidence supporting it. It will not be adjusted just because we cannot yet show how flagellum evolved.

Do you think I've not thought about it. For crying out loud, I had evolutionary theory taught to me for pretty much 10 solid years in college and grad school, worked in a few post docs where common descent is of course inferred. I've read pretty much every single book on origins science in existence, I maintain a personal archive containing literally 1000's of mainstream science articles relevant to this topic, I've actively debated the topic from both sides of the issue for multiple years. I'm pretty much willing to guarantee you that I've thought more about this topic than anyone else in this forum. I personally follow most of the major journals... relevant to my field, and try to keep up with info posted by the TalkOrigins archive, Discovery Institute, Talk Design, even the ICR. So... Ummm yeah... I've considered it.

That NDT can't explain some things suggests perhaps other hypotheses should be explored. I limit myself to discussing IDT specifically because no one seems to have problems with things like self organization theories etc.

There is no inherent value in a flawed hypothesis and bad science. It will strengthen NDT not weaken it, if anything.

Obviously I disagree with both your assessment re: bad science and flawed hypotheses, for the reasons described above. I further assert that much of your reasoning seems to demonstrate a clear misunderstanding of much of IDT.

Yep, so Behe has now apparently said the system was not IC. The paper was 30 or so years old. He could not have researched this that well.

Yeah... like I said I am still looking into this... gotta go back and read DBB after I read the articles I looked up today.

Can’t you see that this will never stop until every supposed IC system has been falsified,

Gosh... I'm sorry, but I don't want science to stop. My job depends on science not stopping. If science stops, I am screwed. I would imagine that Behe and Dembski are in the same boat to a certain extent... you too. I say good for them. If somehow molecules were being shown to not be IC, I'd think you'd think that was a good thing.

we cannot test for ID unless we have a theometer.

You can test for design without invoking cliche internet jargon. You can't test for the presence of a supernatural designer without a theometer. And technically IDT isn't limited to supernatural creators.

I have no issue with there being a creator, I’m agnostic, I see places for a creator. But it will never be science unless we can somehow test for their presence, it will always rely on the absence of another explanation.

Testing for evidence of design currently is, and will continue to be science: think SETI and archaeology at least. The absence of other explanations is a perfect reason for a new hypothesis.

It’s great that there is actual proper science debate on ID here, hope you had a good night though

I agree. It's nice to see some other PhD's or at least potential PhD's here. Not that I think everyone need a degree or anything, but it makes it nice to be able to communicate at a high level.

But it still falls to the fact that you are not testing IC but the absence of another explanation.

I don't know why you assume this. Experiments I've proposed specifically test IC.

Some suggest the bones of the ear as a system that can be considered IC and has evolved by changing function.

This is a logical fallacy. If a system can be inferred to have evolved from a 'change of function' then the system, by definition isn't IC.

But the fact that you are testing for the absence of another explanation will result in ad nauseum science.

Okay... one last time, you are not 'testing for the absence of another explanation...' that's an impossibilty.

Its like saying “certain objects on the earth are not under the influence of gravity” and then having to test every single known object, finding a balloon and determining that a balloon is not affected by gravity without looking for another explanation.

It's not like that at all.

Believe me this is what they have in mind.

Ummm... I know this is a conspiracy site, and all, but how do you know what Behe, Dembski, Johnson etc. have in mind?

We cannot test IC unless we can really positively show IC and how it is IC, rather than saying “current theories cannot explain this!”. Any system found to not be IC will then be deemed not IC. Unless we can independently predict it, not just use incredulity.

I cannot address this argument of testing IC again. I've repeatedly pointed out that it is testable. I've proposed experiments, others have proposed experiments, etc. Until your rebuttals re: this issue get more specific, this discussion can't move forward re: this specific subtopic.

There is no doubt you are solely testing NDT, I will show you why I think this is the case in another post. You cannot base a hypothesis on the fact an experiment may not support another similar theory. It’s just bad science

Hmmmm.... no one said anything about basing "a hypothesis on the fact an experiment may not support another similar theory." I certainly never said that. Those words came from your keyboard.

“for that system” – therefore ID prediction is not possible,

What? We were talking about falsifying a particular hypothesis. How did we jump to prediction. We've already covered prediction. ID is perfectly capable of making predictions. I've mentioned a couple in this very thread I believe.

Matt, you are highlighting exactly the problem - this will continue ad nauseum. You cannot form a falsifiable test for IC by simply trying to falsify another theory.

Okay, one last last time. This is NOT what IDT is attempting to do. My suggestion would be to read some of Dembski's stuff, and perhaps re-read DBB. You state you weren't impressed with DBB, but then later state that your knowledge of Molecular Biology is not adequate to address my simple arguments in this thread. How then are you able to decipher and discredit Behe's significantly more complex arguments contained in DBB?

But you just stated the exact same thing, “falsifying IC for that system”. There is no real basis for IC other than speculation and incredulity (and maybe wishful-thinking)

Ummm... those are not the exact same thing. “Falsifying IC for that system” does not translate into a systematic evaluation of every proposted IC system. And even if it does, so what? That's how genome sequencing is done, sequence a critter and move on to the next. Just because you don't agree with this particular assumption doesn't make it wrong or inherently bad science.

The only way ID will advance research is by falsifying every single system proposed and supporting NDT and maybe even finding other naturalistic explanations.

And if this happened, it would be bad why? This of course being your opinion.

Because we will have a lot of badly formed hypotheses and it will waste resources in a wild-goose chase for an untestable and unfalsifiable proposition.

Yeah, well right now, it seems we have a lot of misunderstanding about the basics of IDT and a lot of the same rebuttal repeated over and over again.

Earlier you stated how a friend took 6yrs to synthesise a membrane, should he have given up after 2 and done something else because it was obviously ID?

Okay. My friend took years to crystallize a membrane protein. I brought it up because when he had first taken on the project, no membrane proteins had been crystallized. In fact, many people believed it impossible to crystallize membrane proteins because of their large hydrophobic regions. For the same reason, others believed that if the proteins did crystallize, they would likely not represent the true in vivo structure. The point of my story was the Jim was told his hypothesis was not testable in essence, that his experiment would not work. The point was he had faith in his hypothesis and endured. So of course I don't think he should have given up. Obviously, I fully support him having busted his A#&. In fact, if he had busted just a little harder, he would have won the Nobel Prize in Chemistry in '88... got scooped by a couple of months.

It could take 100 years or 100 experiments to find a mechanism for flagella, it may never be discovered and we may only ever have theory.

We'll never have a theory if we don't try something and start somewhere.

You mention "junk" DNA. Why is it junk?

It's not junk. If you'll note, in any post I've ever mentioned 'junk DNA,' I refer to that as an unfortunate misnomer. I hate that term.

Because we haven't shown a possible use for it yet, that is all.

Please consider the context of things we're discussing. That was exactly my point. In fact the term 'junk DNA' is a product of the Darwinian assumption. The hypotheses from evolution claimed that this DNA was not used, and was a 'remnant of the evolutionary process.' Hence the misnomer 'junk DNA.' Of course junk DNA is now being shown to have critical functions in the cell. This is of course something that the design inference would have predicted. We might have learned the function of 'junk DNA' a decade ago had this erroneous assumption not been made.

It is still no evidence of ID, only the inability of current knowledge to explain it.

Again, please consider the context of my statements. I wasn't saying 'junk DNA proves IDT is true,' I stated that this is an example of the predictive power of IDT, not as being proof of ID. I would encourage you to read my posts more carefully.

we only discovered DNA around 1950, do you expect us to explain the function of every gene in that time?

Untrue. The structure of DNA was solved in the '50's. We've known about DNA for a lot longer than that... the first suggestion that DNA was the hereditary material was in the 20's with the Griffith experiment.
Avery, then Hershey and Chase would expand on the ideas. I think in the 40's and early '50's.

And this isn't about 'explaining the function of every gene,' it's about assessing which theories seem to adequate for addressing origins issues. NDT seems to be adequate in addressing some issues of origins, but certainly not all. Origins science obviously didn't begin with molecular biology, it's been around much longer than that.

Without evolution we may still think that the appendix is "junk" anatomy, now we know otherwise.

Depending on what you're willing to believe there may not be any reason to describe the appendix as vestigal.

If I could show you previously deemed "junk" DNA that now has a function, would you accept this?

Again, I suggest reading my posts more carefully. I fully acknowledge that junk DNA is not junk at all. I've pretty much always said this... I refuse to refer to it as 'junk DNA' in any of my classes.

And again my point was that IDT would predict that 'junk DNA' is not junk by any definition of the word, which we are learning is true.

Originally posted by melatonin

Nature. 2004 Oct 21;431(7011):988-93. Related Articles, Links

Megabase deletions of gene deserts result in viable mice.

Nobrega MA, Zhu Y, Plajzer-Frick I, Afzal V, Rubin EM.

DOE Joint Genome Institute Walnut Creek, California 94598, USA.

The functional importance of the roughly 98% of mammalian genomes not corresponding to protein coding sequences remains largely undetermined. Here we show that some large-scale deletions of the non-coding DNA referred to as gene deserts can be well tolerated by an organism. We deleted two large non-coding intervals, 1,511 kilobases and 845 kilobases in length, from the mouse genome. Viable mice homozygous for the deletions were generated and were indistinguishable from wild-type littermates with regard to morphology, reproductive fitness, growth, longevity and a variety of parameters assaying general homeostasis. Further detailed analysis of the expression of multiple genes bracketing the deletions revealed only minor expression differences in homozygous deletion and wild-type mice. Together, the two deleted segments harbour 1,243 non-coding sequences conserved between humans and rodents (more than 100 base pairs, 70% identity). Some of the deleted sequences might encode for functions unidentified in our screen; nonetheless, these studies further support the existence of potentially 'disposable DNA' in the genomes of mammals.

Okay... some non-coding DNA thus far appears to be dispensible, and other times it seems to be necessary. Because an organism can survive without something doesn't mean that it doesn't have a function. That I've not had my tonsils for more than 30 years perfectly demonstrates this; tonsils have a function, but apparently are dispensable.

As I have said anything that moves science on is good, the problems ID as a hypothesis is going to have is to show some sort of independent evidence. If blood coagulation has already been falsified, computer simulation show the development of IC with no intelligent interaction, possible pathways exist for some IC systems, large scale deletion of DNA does not affect phenotype - I do think you need to actually show why and how an IC system is ID without recourse to negative supporting evidence. Sorry...

No reason to apologize. For the most part, I agree with you. ID should have some sort of data to support its assertions, some sort of falsifiable tests, etc. Where you and I differ is whether or not these things exist. I say they do, or at least in the case of data, they can exist; you say they don't. This is our point of disagreement.

I won't address you somatic cell hypothesis stuff here and now;

Intelligent Design (bad science, bad hypothesis, no theory)[/B]

experimental: certain natural systems are are IC

Ummm... this is NOT an experimental hypothesis

null: certain natural systems are not IC

Based on the above hypothesis, this isn't relevant. Besides this seems a litte bit like a straw man to me. You set up a hypothesis that not only can't be tested experimentally, but is not falsifiable. 'Certain natural systems' is not specific enough for your hypothesis.

Method: Test a certain system by showing another theory cannot yet explain its mechanism

This isn't what you are testing for, especially given the blurb below.

(e.g. remove proteins from flagella throw lots in a test tube with stuff it will need to develop under certain conditions and observe)

This is a drastic oversimplification of anything I've described, and in fact real experiments would be much more structured.

Results: no evidence of a flagella like system - i.e. nothing.

These are not results. No results are not results. Without getting into a lot of the complexity of the experimental design. You could virtually ensure that a working flagella would 'evolve,' it's all about the experimental set up, and refining the conditions by which the flagellum could re-evolve. Certian threshold values for gene homology, including the non-coding elements of genes, could be considered and calculated for... you can actually design some complex experiments that are pretty much guaranteed to generate meaningful data. Just because you can't conceive of these experiments doesn't mean they don't exist.

conclusion: This system is IC and therefore it is evidence of ID because current theory (or this methodology - which was it?) did not work.

Again, you're wrong. You don't base theories off of a lack of results. You need to have meaningful data that can be tested an repeated.

The problem with most sciences is that they do not teach good methodology,

I'm sorry, but my education in methodology is top notch. I've published papers in the Journal of Biological Chemistry, Biochemistry, Plant Pathology, Photosynthesis Research, and several others, and have never been faulted for my methodology.

Possible good ID hypothesis...

experimental: irreducible systems are formed by intelligent design.

Again, this is not an experimental hypothesis. There's nothing testable here.



[edit on 16-1-2006 by mattison0922]

[edit on 16-1-2006 by mattison0922]

Maybe not the exact experimental hypothesis for your experiments but they are the concepts on which the exact findings and conclusions would be based. Of course, when I say decision-making task, it's a bit more complicated than that, the exact perfromance is assessed over block and we are actually testing learning, or more exactly and improvement of learning and an increase in adaptive choice over the course of the experiment, we look for an index of learning. In other words, yes the are not the exact predictions but the are what the theory believes would happen when under examination. The are very simplified.

So what have you suggested (quoted from earlier)...

Behe claims that something like 34 or 40 proteins are necessary and sufficient for the motor (sorry, but motor IS a totally appropriate analogy for this and many biological proteins) to operate; this group of proteins constitutes its Irreducible Core. A very simple test of the IC nature of this motor protein assemblage is to knock out one or two of these proteins from the ICore and see if the bacteria can ‘re-evolve’ just these one or two components of the ICore. In fact, you could tailor your experiment very specifically: You select the simplest protein components for elimination, increasing the chances of the re-evolution event. You could further test the IC core by adding back a proteins that are X% homologous to the original protein, until one day you restore function via NDT or not. And yes, I am aware of the Lac operon experiments.

What I state, which admittedly is in simplified form, seems correct. You are hoping to show that under whatever conditions you determine, that flagellum would not "re-evolve". If a system is IC, then the basis of your hypothesis is "flagella under these conditions will not re-evolve - null: flagella under these conditions will re-evolve" or if we view it as NDT "flagella under these conditions will re-evolve - null: flagella under these conditions will not re-evolve". Of course, as I admitted, that is simplified but that would be your strong conclusion from the data. If someone in my class, suggested that we test a certain system and make a strong conclusion, without proposing an alternative supported by independent evidence, from negative results, I would fail them. It is not preconceived, it is science. You cannot test the IDH however much you like to think you can. You can show that a certain system may be IC, but this does not equate to IDH. Why do you think there is a bias in publishing? Because negative results (and when I say this, I mean opposite to your hypothesis) really don't help us, it could be anything from methodolgy to poor theory, to chance results.

They are ultimately the same inferences but reversed. so a test of IDH is actually a reversed test for NDT. Nothing more. In fact, it doesn't even have any other reason than it looks IDH to even test it. You have no theory but either it isn't NDT because certain factors suggest it's IC, or it is IC because certain factors suggest it.

The problem is that with the middle ear, if you remove a bone function is lost, it fits your IC "prediction". However, we know this is not the case. It changed function over time. The way IDH views NDT is too simplified. You do not know the exact mechanism/conditions that it did evolve under, you can make predictions of what they are but you still do not know. We didn't know how whales evolved from a land mammal, but it did the legs changed function. ID ignores this possibility. Apparently, blood coagulation had "all the hallmarks of design", now it was never IC. If you can't predict what is IC and what is not, then you are doing blind science.

Can you provide a test of IDH that does not rely, in essence, on an attempt at falsifying NDT, therefore leaving the most parsimonious explanation as ID?

2000 years ago we did not know how life even started to evolve, we had the most parsimonious explanation. If we knew for cetain a god existed, then it probably would be the most parsimonious. But we don't. We have since assessed the evidence, now we have a another mechanism, that is in some ways less parsimonious, but predicts what the evidence shows - the data speaks for itself. In certain areas it is not perfect, we do not know the answers. You propose some of these systems as IC, some have since been shown to fit current knowledge, some not. Computer simulations have shown how IC can develop without design - are these perfect? Well of course not, but they can predict. Take the coagulation business - it has been proposed as IC because it looks IC, as you said it is a description. Behe's current knowledge (even though a 30 year old paper existed) could not explain it, it has since been falsified. The only basis of IC is, some systems look IC, we don't know if there is another mechanism, but this is a candidate. If it's falsified, then it wasn't IC, and we'll move to the next. Even combination methods of chemsity have the possibility of eventually proposing, mechanisms and predictions, IC will do no such thing. The only mechanism you have is ID.

What you propose is to fall back on ancient methods of thinking. We are not able to describe the mechanism by which certain systems evolved and therefore the most parsimonious is an "intelligent designer". You stated earlier that mechnanism, can be more important than parsimony. I agreed. You suggest that IDH will provide an alternate mechanism. But you cannot provide one. You have a theory that proposes an intelligent designer, but you are not interested in the concept as any more than a roadblock. Behe described evolution a "darwin's black box", in fact behe has his black box. The IDH hypothesis has no more mechanism than "ID" did it, and as science depends on a description of a system that when viewed in it's IDH state is tautological. You are attempting nothing more than why is an orange, orange? And then proposing "intelligent design" caused it. There is no mechanism, pure description. It has no explanatory power other than "ID" did it. Is that a problem? Well no, of course it could be true - a designer may have come from another planet using their faster than light drive, place some bacteria, they designed in the lab within the physical laws of the universe (unless you are proposing something supernatural and physical laws may be broken), onto our planet. Everything we see today evolved from that one bacteria. Now the question would be "where the aliens designed or did they evolve?". If you suggest that IC systems are designed, then it's a fair assumption, the basis of all life was design. Then we have to think about who desined the designer? And so on, and so forth. It still explains nothing other than ID caused what we see, which has always been the case, but science could not show this and will never be able to, it will only do this by default.

A thought experiment: 500 years from now we have the ability to create in the lab the complete DNA sequence of an organism. Furthermore, we have a species capable of reproducing (we are capable of ID). we design a FTL drive and go to a hospitable planet. We place a series of evolvable basic organsisms (maybe including some type of flagellum) on this planet and observe. Higher forms of life evolves. They get to where we are now with the knowledge we have, they are in a similar situation. How do they solve this problem? They invoke an intelligent designer, and they are correct for life on their planet. Now they need to think about who designed their designer? Of course, as you believe, they could suggest a supernatural force. Does he conform to the physical laws of this universe or did he just appear with a magically developed biogenesis apparatus that must conform to our physical laws, or maybe he uses his divine powers and life just appears out of thin air? Life evolves to where we are today. We eventually develop to proposed level of advancement, but we have invoked an supernatural ID, however, we can also develop life using physical laws of this universe. Was it intelligent design within laws of this universe, or ID from a supernatural source? We are stuck in a bind. The question science should aim to answer is: can life evolve within this universe, under our physical laws, from the simple molecules of universe creation. If we can show that, great, it is possible. If we can't, then we keep trying to attempt this. Is their an ID? Even if we show life evolved, maybe we are the spawn of some alien species and we were ID'ed. But the question remains - can life evolve under the said conditions? If we invoke a supernatural ID'er with powers that are outside of this universe, he can create life with divine powers, he could have done all the things the forms of creationists propose, maybe coming here occassionally, placing a new form of life. Maybe creating all life 6000 years ago and using moses and creating a book which we have today, confusing us with fossil evidence and other signs. Maybe he did what we could do in the future and place the elements of biogenesis on this planet, using some apparatus to use physical laws to produce the needed molecules for biogenesis. But the question still remains - can life evolve from basic molecules in our universe under our physical laws? Otherwise, we fall back on lack of knowledge and the supernatural - Is this science? A big question is - how would be able to differentiate between the ID life we created, and life that we think has evolved? We cannot, the only way is by historical evidence. How do we know the various forms of dog evolved by intellgent selection? because of historical evidence. We already have apparent historical evidence of ID for life on this earth, numerous sources of it, so maybe life here was ID. But the scientific question remains.


You have stated that evolutionary theory is unfasifiable, yet are attemtping to falsify it. I have shown you how evolutionary theory can be falsified. Yet then you fall back on "well we have no problem with evolution". Abiogenesis is falsifiable, we can set up an experiment and we can falsify and then improve method, and then falsify etc. We have a basis for these experiments, we have even produced replicating RNA, we have mechanisms and methods. But IDH is unfalsifiable it has no mechanism but ID which as you said you are not trying to account for, no method to show this but you propose tests of IC as a reverse hypothesis of evolutionary theory. You say negative results are no results...How do you propose to get actual positive results for IC? I would guess by getting negative results for evolutionary theory. If you only have description of certain systems and no mechanism, then even at the moment ID is the most parsimonious answer, it always has been for certain people. But does it help us in science, does it answer the question - can life evolve in this universe from basic molecules?

Maybe there are a few fossils of certain forms of bacteria, I was wrong. Are you suggesting that every bacteria will leave a fingerprint somewhere in the environment? We can't even expect this for backboned species due to the conditions required. You are simply proposing we will test within our current knowledge and if we can't see how this happened, it must be design, that's the most parsimonious answer but we have no mechanism but supernatural ID or an intelligence from elsewhere which may or may not have evolved from basic molecules in this universe- it leads us nowhere but to the questions that science is already trying to answer. If we invoke a supernatural ID, then the question still remains.

Yous seem to believe I have preconceived ideas, yet what I suggest is the case - we can test a certain system to see if current levels of knowledge can see a mechanism by which this system evolved naturally, if not it's IC, therefore ID is most parsimonious. But it still does not answer the question - can life evolve from basic molecules in this universe? Abiogenesis may not have produced a species with replicable DNA yet. If and when it does, can we assume life is only ID or only formed from basic molecules in our universe? No, but we can assume that conditions allow it, that is all. Supernatural explanations will always remain, so will ID from elsewhere.

You suggest it's scientific, I, and many others, suggest it is fundamentally flawed. It does not answer the question we are seeking - can life evolve from basic molecules within the laws of this universe? At the moment the answer is - we don't know, the most parsimonious answer for some is, and always has been and always will be, it was probably ID. the problem is you can never test this hypothesis, no matter how you conceive it. Does it bother me that we cannot test this? Not at all, I still see places for a creator, I just don not believe we can positively test for it, it will always be by default.


[edit on 16-1-2006 by melatonin]

[edit on 16-1-2006 by melatonin]

Originally posted by melatonin
Behe claims that something like 34 or 40 proteins are necessary and sufficient for the motor (sorry, but motor IS a totally appropriate analogy for this and many biological proteins) to operate; this group of proteins constitutes its Irreducible Core. A very simple test of the IC nature of this motor protein assemblage is to knock out one or two of these proteins from the ICore and see if the bacteria can ‘re-evolve’ just these one or two components of the ICore. In fact, you could tailor your experiment very specifically: You select the simplest protein components for elimination, increasing the chances of the re-evolution event. You could further test the IC core by adding back a proteins that are X% homologous to the original protein, until one day you restore function via NDT or not. And yes, I am aware of the Lac operon experiments.

What I state, which admittedly is in simplified form, seems correct. You are hoping to show that under whatever conditions you determine, that flagellum would not "re-evolve". If a system is IC, then the basis of your hypothesis is "flagella under these conditions will not re-evolve - null: flagella under these conditions will re-evolve" or if we view it as NDT "flagella under these conditions will re-evolve - null: flagella under these conditions will not re-evolve". Of course, as I admitted, that is simplified but that would be your strong conclusion from the data. If someone in my class, suggested that we test a certain system and make a strong conclusion, without proposing an alternative supported by independent evidence, from negative results, I would fail them. It is not preconceived, it is science. Why do you think there is a bias in publishing? Because negative results (and when I say this, I mean opposite to your hypothesis) really don't help us, it could be anything from methodolgy to poor theory, to chance results.

Okay, there's some confusion here. This is likely my fault, due to my poorly worded explanation. The experiment doesn't in fact doesn't rely on negative results. The experiments would need to be tailored very specifically to yield useful information. For example, let's say system x is hypothesized to be IC. System X is composed on 10 proteins at it's hypothesized IC core. The experiment is interested in determining the degree and type of variation that permit re-evolution of the ICcore. For example you eliminate protein 1 from this core. You now have a non-functional system x mutant. The first thing to do is establish yourself a control species. This is accomplished quite easily via insertion of extrachromosomal DNA containing the deleted gene(s), but also the deleted genes regulatory apparatus. Thus we now have a 'control' species, wherein system x's function is restored via the previously described insertion. Now we work backwords, by designing genes to insert that have less and less homology to the original insertion. Basically, the idea is to decrease the homolgy and functionality of the gene itself and or it's regulatory regions. As the gene becomes less homologous to the lost gene, the functionality of the protein is likely to decrease (based on the design inference). The data could essentially be quantified a few different ways. You could condsider functionality of the flagella as a function of homology to the original protein of interest. You could further perform "lab evolution" experiments wherein the change in functionality of the protein in question is correlated to the number of generation times the culture has been growing. So the experiment DOESN'T rely on negative results. You can't publish negative results. The experiment is designed to yield useful information about the system being studied; negative results are not useful. But discovering the tolerance for change that these IC systems can handle is useful information. Furthermore, there is every reason to believe such experiments would work. Pretty much everything I've described is very basic molecular biology or biochemistry. There are certain critical factors that need to be considered, choice of IC system, choice of organism, etc. But the experiment absolutely can be designed to yield useful data; the experiment can be set up with the appropriate positive and negative controls. Finally, the data can be quantified in a meaningful way, for which precedents already exist.

They are ultimately the same inferences but reversed. so a test of IDH is actually a reversed test for NDT. Nothing more.

Ummm... yeah, I think that's what I've been saying. IDT and NDT can often be tested with the same experiments.

In fact, it doesn't even have any other reason than it looks IDH to even test it.

The reason to test: AGAIN 1. the systems exhibits hallmarks of design. 2. There exists no evidence to suggest it arose via currently extant theories. So yes, in essence you are correct, there are certain criteria that make the system testable, they are somewhat more rigorous than 'it looks IDH,' but your basic statement is correct.

You have no theory but either it isn't NDT because certain factors suggest it's IC, or it is IC because certain factors suggest it

I don't understand this statement. Yes certain 'factors' suggest something is IC... just like certain 'factors' suggest that things share a common ancestor.

The problem is that with the middle ear, if you remove a bone function is lost, it fits your IC "prediction". However, we know this is not the case. It changed function over time.

Again, I'm not superfamiliar with this example, but we've already discussed this. If there is evidence to suggest that the components of the middle ear evolved via a change of function, then the system by definition is not IC.

The way IDH views NDT is too simplified. You do not know the exact mechanism/conditions that it did evolve under, you can make predictions of what they are but you still do not know. We didn't know how whales evolved from a land mammal, but it did the legs changed function. ID ignores this possibility.

Ummm no it doesn't. It makes perfect note of these possibilities. As I've repeatedly explained to you IDT, does not have an issue with theories of common descent. This is not to say that everyone in the ID community accepts that whales evolved exactly as mainstream science says they did, but IDT specifically acknowledges the evidence for common descent. But just like some in the evolution camp can't decide whether or not Archaeopteryx was a true bird, or just a transition to birds, there may be some dissention within the ranks re: specifics.

Can you provide a test of IDH that does not rely, in essence, on an attempt at falsifying NDT, therefore leaving the most parsimonious explanation as ID?

The test I proposed doesn't rely on falsifying NDT. It seeks to explore the relationship between gene sequence, system functionality, and 'generation times.'

You propose some of these systems as IC, some have since been shown to fit current knowledge, some not.

Which systems alleged to be IC (dolphin blood aside) have been shown to 'fit current knowledge?'

Computer simulations have shown how IC can develop without design - are these perfect?

Computer simulations are inherently tests for design, not random processes like evolution. The very act of 'designing organisms in silico' is in and of itself an act of ID.

Well of course not, but they can predict. Take the coagulation business - it has been proposed as IC because it looks IC, as you said it is a description. Behe's current knowledge (even though a 30 year old paper existed) could not explain it, it has since been falsified.

I'm not convinced of this. Personally, I am still reading the stuff about the clotting cascade, and I'm re-reading Behe's chapter.

Furthermore, computer simulations don't falsify anything. They are capable of supporting or not supporting hypotheses, but with respect to biology, computer simulations are generally referred to as 'fact-free science.'

The only mechanism you have is ID.

ID is not a 'mechanism' in the traditional sense.

What you propose is to fall back on ancient methods of thinking.

Oh yes. I am going to need to break out my rosetta stone to convert ancient molecular biology protocols into modern english. I was astonished to find out that ancient peoples were capable of gene knockouts and knock ins. And those primitive centrifuges... how did they get those slaves to run so fast? It's the ancient spectrophotometers that bug me. You can't use 'em on a rainy day... you can't focus enough sunlight to get through the prism to the detector.

We are not able to describe the mechanism by which certain systems evolved and therefore the most parsimonious is an "intelligent designer".

This is a drastic oversimplification of what I said, and leaves out such critical portions of the explanation as to constitute deliberate misrepresentation of my point. I've repeatedly pointed out, hypotheses from IDT are based on more than just 'we can't describe the mechanism.'

You have a theory that proposes an intelligent designer, but you are not interested in the concept as any more than a roadblock.

That's absurd. I am interested in this as a lot more than a roadblock. I am interested in it as an alternative basis of hypothesis formation. I am unsure what you mean by interested as no more than a roadblock. Please elaborate.

Behe described evolution a "darwin's black box", in fact behe has his black box.

Sounds like a title for a book/article. Why don't you write it? I'll review the molecular stuff for you.

You have stated that evolutionary theory is unfasifiable, yet are attemtping to falsify it.

I am in way attempting to falsify evolutionary theory. How does my belief that IDT can be scientific and contribute meaningfully to science translate to mattison0922 is trying falsify evolutionary theory?

I have shown you how evolutionary theory can be falsified.

Where did you do this?

Yet then you fall back on "well we have no problem with evolution".

I don't fall back on it. Why does it bug you so much that I am willing to accept certain things postulated by evoutionary theory, but unwiling to accept others based on evidence? I'm sorry this is so troubling for you. It's not a fall back, as much as it is the truth.

Abiogenesis is falsifiable, we can set up an experiment and we can falsify and then improve method, and then falsify etc.

You can't falsify the entire theory of abiogenesis. To do so would mean you would have to conclusively show that no pathway exists whereby non-living materials can form living materials. That is an impossibilty. You can falsify certain components of the theory, but you can't falsify abiogenesis.

We have a basis for these experiments, we have even produced replicating RNA, we have mechanisms and methods.

These RNA experiments are a joke. They in no way are an accurate representation of the prebiotic world with respect to concentration of reagents, stereochemical considerations, etc. If you've got some specifics you'd like to discuss, then bring 'em up here. We definitely have not produced replicating RNA. This is an extreme extrapolation of the experimental results that have been observed. I am pretty deep into the thermodynamics of this stuff, especially the thermodynamics of biopolymer formation. Would be more than happy to discuss with you here.

But IDH is unfalsifiable

How many times are you going to ignore that I've repeatedly pointed out that IDT is falsifiable. I've offered specifics, and you keep coming back with the general 'ID isn't falsifiable' meanwhile ignoring anything I point out that contradicts this. You can falisfy the concept of IDT very easily: by demonstrating that systems needn't have been designed. This criteria for falsification is inherently more falsifiable than NDT.

Maybe there are a few fossils of certain forms of bacteria, I was wrong. Are you suggesting that every bacteria will leave a fingerprint somewhere in the environment?

Ummm... no. You said bacteria don't leave fossils. I said they do.

You are simply proposing we will test within our current knowledge and if we can't see how this happened, it must be design,

I proposed nothing of the sort. I never said it must be. I've been very careful about my language. I said experiments can support of not support the inference from design. I didn't say it 'must be design' Please highlight specifically where I said "it must be design" Otherwise I'd really appreciate it if you'd stop misquoting me.

Yous seem to believe I have preconceived ideas,

We all have preconceived ideas. Welcome to humanity.

You suggest it's scientific, I, and many others, suggest it is fundamentally flawed. It does not answer the question we are seeking - can life evolve from basic molecules within the laws of this universe?

I suggest this, and many other suggest this. That IDT is not accepted by mainstream science isn't troubling to me in the least. Most scientists I know are just as misinformed about IDT as the general public.

BTW, it might not provide you with the answer YOU are seeking, but you can't assume that all scientists seek the same knowledge. It's capable of providing researchers with what THEY seek, irrespective of what your opinion is re: what people should seek. Sorry for the lousy wording.

At the moment the answer is - we don't know, the most parsimonious answer for some is, and always has been and always will be, it was probably ID. the problem is you can never test this hypothesis, no matter how you conceive it.

For the last time: YOU CAN TEST FOR THE SUGGESTION OF DESIGN

OK, I found the reference for you Matt. This paper describes many biochemical pathways that are circuitous, and if designed, should be much simpler. Of course, this is not IC. But it shows there is no teleology in the evolutionary process, it just happens and is undirected. Circuitous routes seem a "hallmark" of evolution, yet Behe would like to ignore such possibilities for his IC systems.
Journal of Chemical Education (2004) Evidence from biochemical pathways in favour of unfinished evolution rather than intelligent design. 81, 1051.

Examples...

Case 1: Unnecessary Inversions (2, p 673)
The oxidation of fatty acids with odd numbers of carbon
atoms goes through the sequence:
CO2
propionyl CoA (S )-methylmalonyl CoA
epimerase
(R)-methylmalonyl CoA succinyl CoA
B12
In the epimerase step, the original S configuration at C2 of
the methylmalonate moiety is inverted (racemized) to R. Why
is this extra step, inversion of configuration at one of the chiral
centers of methylmalonyl CoA required? Intelligent design
would either have made the diastereomer with the R configuration
for the methylmalonyl moiety directly, or would
have designed the B12-requiring mutase to accept the diastereomer
with (S)-methylmalonic acid. The answer from the
evolutionary standpoint is that if it works, don’t fix it (at least
not rapidly).

Case 2: Unnecessary Pathways (3)
A somewhat similar stereochemical situation occurs in
the biosynthesis of some plant alkaloids where reticuline, with
one chiral center, is an intermediate. In a complex metabolic
pathway that begins with L-tyrosine, (S )-reticuline is first
formed and is then inverted to (R)-reticuline via an oxidation–
reduction reaction. (S )-Reticuline is the biosynthetic
precursor for berberine, β-narcotine, and so forth. (R )-
reticuline is required for the formation of thebaine, codeine,
morphine, and so forth. Much metabolic manipulation could
have been avoided by using (S )-reticuline for the biosynthesis
of all of these alkaloids.

Case 3: Duplicate Pathways (4–6)
In some cases, there are two separate pathways for formation
of a metabolite in different organisms. Examples include
lysine biosynthesis via the common diaminopimelic
acid route and by the less common α-aminoadipic acid route
(some fungi, Euglena); L-ascorbic acid biosynthesis via D-glucuronic
acid (animals) and via L-galactose (plants); and the
biosynthesis of phenylalanine and tyrosine by the “classical”
route (E. coli, B. subtilis) as well as via arogenic acid
(Cyanobacteria, Euglena). Many other examples could have
been cited. An intelligent designer would probably have been
content with a single pathway in all cases.

Case 4: Unnecessary Waste (2, p 775)
The penultimate step in tryptophan biosynthesis is the
condensation of indole with the 3-carbon amino acid, serine.
But in the previous step, an adequate 3-carbon fragment was
removed as glyceraldehyde 3-phosphate. Indeed, an identical
3-carbon fragment is retained during the biosynthesis of
histidine (ref 2, p 777).

Case 5: Unnecessary Connections (2, p 1022)
DNA is double-stranded; one strand runs in the direction
5´ → 3´ and the other runs in the 3´ → 5´ direction.
When DNA is replicated, one strand is made continuously
in the 5´ → 3´direction, but the other strand is made discontinuously
and in pieces (the Okazaki fragments) but also
in the 5´ → 3´ direction. The pieces then have to be put
together in a complicated way. We would have designed a
system using two polymerase activities: the first using deoxyribonucleotide
5´-triphosphates and the second deoxyribonucleotide
3´-triphosphates. Then both strands could be
made continuously.

I know at times it seems we are talking past each other here, I'm sorry that is the case, I just believe all your experiments will ever do is show that this looks designed, we can't really explain it in other terms, and cause an examination of NDT. As you said, we can never test for an ID mechanism, it will always be description. It really should be conceived as "the principle of irreducible complexity" not a hypothesis of ID, because as you admit, it is untestable. Science will not collapse because of it, but I do wonder of the motivations of many of its proponents. A while back, a long-term member of an ID organisation, who has a faith and is a scientist, left an ID organisation because he deemed they were not interested in science. Behe has previously claimed the lack of evidence for whale evolution, is he really that certian of NS or is it a smokescreen. What is this really all about? In the scientific community, it will force many researchers to focus on proposed IC systems taking resources away from other valid questions; in wider society, the sight of a few failed experiments will raise hopes of ID and discrediting NDT, even though it does no such thing as Behe admits.