Robot Wars (Is Intelligent Design bad for science?)

[Gman]

(Post edit: ha ha G, your post just beat mine).

Just barely...

Good input.

And we have more here too from our website.

Can Intelligent Design (ID) be a Testable, Scientific Theory?

[touchingcloth]

That's not true at all. Like Gman always points out, ID is used in many scientific disciplines (archeology, anthropology, forensics, SETI, etc). Why is it that only when it comes to biology it's unscientific?

I think the crux of it is that SETI, archaeology et al use design hypotheses in a manner akin to the watchmaker analogy; that is we recognise the hallmarks of human design in tools and communications, so we should be able to recognise them as such in ancient/alien civilizations if they share similarities with their human equivalents. So for an alien civilization that means if we detect, for example, what appears to be signals modulated onto a carrier wave then it would be reasonable to assume it was sent by an intelligent species. The flipside to that however is that SETI is essentially blind to any communications that are sent in a truly alien manner, using methods/particles/forces/dimensions that we are potentially totally unaware of.

I think that's one way in which ID crosses the threshold of being unscientific; going from the assumption that we can recognise design if it bears the hallmarks of things we know are designed (reasonable) to the assumption that we are able to recognise design in any form it may take (unreasonable).

[touchingcloth]

But true scientific hypothesis must be falsifiable. Can ID be falsifiable? ID is actually quite open to falsification. If we use evolution to falsify ID, all a scientist needs to do is take a bacterium without a flagellum or knock the genes out within the bacterium flagellum, then go to a lab and try to grow the bug for a long time to see if it produces anything resembling a flagellum. If it produces a flagellum, then ID would be proven false on the general grounds that the scientist didn't invoke intelligent causes when purely natural causes would suffice. But let's turn that around, how do we falsify the contention that natural selection produced the bacterium flagellum?

This kind of thing has been done - I'm can't recall which piece of research it was off the top of my head but it essentially went like this:
- Take some cells that feed mainly on a particular food source - glucose, say.
- Remove or otherwise alter the genes for glucose digestion so that the next generation of cells are unable to feed on it
- Breed a number of lines of the impaired cells, and allow each line to propogate for a number of generations in a glucose-rich environment.
The outcome was that some or all of the lines of cells regained the ability to digest glucose, and in manners different from each other and from the original culture (that which had its genome altered).

Similar things have been observed but in a "bottom-down" manner, that is seeing a trait that wasn't present in previous generations emerge in later ones (as opposed to altering genes and waiting for a trait to re-emerge); for example the ability to metabolize citrate seen in Lenski's experiments, and to metabolize nylon in "wild" bacteria.

My point is that none of the above falsifies the ID hypothesis; it may weight things totally or partially against certain flavours of designers, but we can certainly conceive of a designer capable crafting DNA such that it was able to handle such situations.

A question for you all more out of curiosity that anything else - do you believe that the evolution of, say, flagella, or of apes to men is in impossible in principle, or that it just hasn't happened in practice? That is to say, do you think that god created everything pretty much as we see it, but that potentially species could go on to evolve?
To lay this out more orderly:
- All the information needed to turn a single cell into a creature is held in nothing more than the sequence of nucleotides in that cell's DNA (you probably all agree here)
- DNA can mutate in a number of different ways, and mutations are carried forward throughout generations (you probably all agree here, too)
- Mutations can be responsible for new protein sequences, sometimes manifesting itself in the phenotype (I'm guessing you all agree here as well)
In light of that I can think of a few possible outcomes - feel free to say if you agree with any of them, or to suggest more:
a) DNA physically cannot mutate enough to change one species into another - something in DNA itself impedes such mutation
b) DNA physically cannot mutate enough to change one species into another - some factor external to DNA impedes such mutation
c) DNA could, in principle, mutate enough to change one species into another - it just hasn't ever happened
d) DNA could, in principle, mutate enough to change one species into another - but some factor prevents it from doing so

[ageofknowledge]

Rock em Sock em Robot Wars

[Byblos]

That's not true at all. Like Gman always points out, ID is used in many scientific disciplines (archeology, anthropology, forensics, SETI, etc). Why is it that only when it comes to biology it's unscientific?

I think the crux of it is that SETI, archaeology et al use design hypotheses in a manner akin to the watchmaker analogy; that is we recognise the hallmarks of human design in tools and communications, so we should be able to recognise them as such in ancient/alien civilizations if they share similarities with their human equivalents. So for an alien civilization that means if we detect, for example, what appears to be signals modulated onto a carrier wave then it would be reasonable to assume it was sent by an intelligent species. The flipside to that however is that SETI is essentially blind to any communications that are sent in a truly alien manner, using methods/particles/forces/dimensions that we are potentially totally unaware of.

I think that's one way in which ID crosses the threshold of being unscientific; going from the assumption that we can recognise design if it bears the hallmarks of things we know are designed (reasonable) to the assumption that we are able to recognise design in any form it may take (unreasonable).

And who exactly defines what is reasonable and what isn't? If you're not familiar with William Dembsky's work on design probability (he wrote a book called The Design Revolution), he argues that design can be detected by virtue of 2 things: small probability and specification. When we look at the faces on Mount Rushmore, we can conclude with virtual certainty we're not looking at rock erosion because 1) the probability is low, and more importantly, 2) because we can compare the images to similar known images. SETI receives indecipherable radio signals all the time (or at least what is perceived as indecipherable). But if one day SETI receives a radio signal containing a list of the first 1,000 prime numbers what do you think their reaction would be? Similarly, when we look at a bacterial flagellum, we again recognize the low probability of its assembly with naturalistic means (and co-option certainly doesn't answer that if you were going to go there), and more importantly we compare the complex structure to a similar mechanical structure we built ourselves. If you're in a desert and you spot an intricate sand design you might conclude someone made it or maybe by chance a sandstorm created it and that's a reasonable assumption. But if you come across a full functional engine would it still be reasonable to assume a sandstorm produced it? Science tells us that the most logical explanations are usually the simplest ones. What would be the simplest explanation for a functional engine in the desert? Someone made it and brought it there. Who that someone is and what the purpose is certainly still in the realm of science to discover so this fear of darwinian evolutionists claiming that ID will stop scientific discovery is completely unreasonable, unfounded, and plain false. Just because ID invokes a designer doesn't mean the search for who the designer is and what their purpose was needs to stop, on the contrary.

But true scientific hypothesis must be falsifiable. Can ID be falsifiable? ID is actually quite open to falsification. If we use evolution to falsify ID, all a scientist needs to do is take a bacterium without a flagellum or knock the genes out within the bacterium flagellum, then go to a lab and try to grow the bug for a long time to see if it produces anything resembling a flagellum. If it produces a flagellum, then ID would be proven false on the general grounds that the scientist didn't invoke intelligent causes when purely natural causes would suffice. But let's turn that around, how do we falsify the contention that natural selection produced the bacterium flagellum?

This kind of thing has been done - I'm can't recall which piece of research it was off the top of my head but it essentially went like this:
- Take some cells that feed mainly on a particular food source - glucose, say.
- Remove or otherwise alter the genes for glucose digestion so that the next generation of cells are unable to feed on it
- Breed a number of lines of the impaired cells, and allow each line to propogate for a number of generations in a glucose-rich environment.
The outcome was that some or all of the lines of cells regained the ability to digest glucose, and in manners different from each other and from the original culture (that which had its genome altered).

Similar things have been observed but in a "bottom-down" manner, that is seeing a trait that wasn't present in previous generations emerge in later ones (as opposed to altering genes and waiting for a trait to re-emerge); for example the ability to metabolize citrate seen in Lenski's experiments, and to metabolize nylon in "wild" bacteria.

My point is that none of the above falsifies the ID hypothesis; it may weight things totally or partially against certain flavours of designers, but we can certainly conceive of a designer capable crafting DNA such that it was able to handle such situations.

A question for you all more out of curiosity that anything else - do you believe that the evolution of, say, flagella, or of apes to men is in impossible in principle, or that it just hasn't happened in practice? That is to say, do you think that god created everything pretty much as we see it, but that potentially species could go on to evolve?
To lay this out more orderly:
- All the information needed to turn a single cell into a creature is held in nothing more than the sequence of nucleotides in that cell's DNA (you probably all agree here)
- DNA can mutate in a number of different ways, and mutations are carried forward throughout generations (you probably all agree here, too)
- Mutations can be responsible for new protein sequences, sometimes manifesting itself in the phenotype (I'm guessing you all agree here as well)
In light of that I can think of a few possible outcomes - feel free to say if you agree with any of them, or to suggest more:
a) DNA physically cannot mutate enough to change one species into another - something in DNA itself impedes such mutation
b) DNA physically cannot mutate enough to change one species into another - some factor external to DNA impedes such mutation
c) DNA could, in principle, mutate enough to change one species into another - it just hasn't ever happened
d) DNA could, in principle, mutate enough to change one species into another - but some factor prevents it from doing so

For me personally, although I am a creationist, I've entertained theistic evolution as a possibility so even macro-evolution does not threaten my theology in any way. However (and that's a capital HOWEVER), I see no evidence of inter-speciation, only speculation, wishful thinking, and reverse engineering with a priori assumptions. I see no evidence that mutation creates new traits that are beneficial (I hope you're not going to invoke the extra chromosome in Downs as an example here). I do see evidence that enough mutations, coupled with natural selection/adaptation can and do create enough changes for a sub-species to become somewhat different than its origin species. But reverse the process and those differences will disappear.

[touchingcloth]

SETI receives indecipherable radio signals all the time (or at least what is perceived as indecipherable). But if one day SETI receives a radio signal containing a list of the first 1,000 prime numbers what do you think their reaction would be?

My point with SETI is that we might not even get to the stage of unravelling a radio signal, due to it being encoded in a manner that we are totally unfamiliar with. If ET is out there he might not even be using radio waves, or any waves that we know of, to contact us.

Similarly, when we look at a bacterial flagellum, we again recognize the low probability of its assembly with naturalistic means (and co-option certainly doesn't answer that if you were going to go there), and more importantly we compare the complex structure to a similar mechanical structure we built ourselves.

Dembski has a point when he states that for something like a flagellum to appear by chance is of a very, very low order of probability. The same is true of just about any part of a body or cell; fingers, eyes, brains, gametes, are all improbable. The argument that there is no way that the flagellum in particular could have arisen by chance (chance in this situation meaning, I assume, in a single mutation), therefore it was designed rests fully on the assumption that the flagellum stands on its own as a structure and has no possible antecedents that could have been of use to bacteria.

I see no evidence that mutation creates new traits that are beneficial (I hope you're not going to invoke the extra chromosome in Downs as an example here). I do see evidence that enough mutations, coupled with natural selection/adaptation can and do create enough changes for a sub-species to become somewhat different than its origin species. But reverse the process and those differences will disappear.

Would you not call the ability to digest citrate a beneficial trait?

[Byblos]

SETI receives indecipherable radio signals all the time (or at least what is perceived as indecipherable). But if one day SETI receives a radio signal containing a list of the first 1,000 prime numbers what do you think their reaction would be?

My point with SETI is that we might not even get to the stage of unravelling a radio signal, due to it being encoded in a manner that we are totally unfamiliar with. If ET is out there he might not even be using radio waves, or any waves that we know of, to contact us.

Is it your contention then that we ought to stop SETI research? We can only work with whatever technology we have. But the point is clear, if we receive a structured signal the most likely source is intelligence. That is all ID assumes.

Similarly, when we look at a bacterial flagellum, we again recognize the low probability of its assembly with naturalistic means (and co-option certainly doesn't answer that if you were going to go there), and more importantly we compare the complex structure to a similar mechanical structure we built ourselves.

Dembski has a point when he states that for something like a flagellum to appear by chance is of a very, very low order of probability. The same is true of just about any part of a body or cell; fingers, eyes, brains, gametes, are all improbable. The argument that there is no way that the flagellum in particular could have arisen by chance (chance in this situation meaning, I assume, in a single mutation), therefore it was designed rests fully on the assumption that the flagellum stands on its own as a structure and has no possible antecedents that could have been of use to bacteria.

Somehow I knew you were going to invoke the co-option argument. We can examine that if you wish. Perhaps then you can explain how out of 40 protein structures involved in the flagellum, only 10 can be considered co-opters, namely the the type III secretory ones. While those structures do play a different role, as you know it is one that's detrimental to the living organism (if I'm not mistaken their function is to attract viruses). So we have about 10 structures that serve a purpose non-beneficial to the organism, and 30 that serve absolutely no function at all. In order for natural selection to assemble these into a flagellum, it would not only have to know before hand which ones to assemble and gradually assemble them into intermediate forms (because that's how natural selection works, right?) but also have the exact blueprint in which to do it (sequence is extremely important) and the proper timing to do it in (equally as important). To borrow an argument used recently, the probability of that happening by chance is zero. It is not unreasonable to conclude design.

I see no evidence that mutation creates new traits that are beneficial (I hope you're not going to invoke the extra chromosome in Downs as an example here). I do see evidence that enough mutations, coupled with natural selection/adaptation can and do create enough changes for a sub-species to become somewhat different than its origin species. But reverse the process and those differences will disappear.

Would you not call the ability to digest citrate a beneficial trait?

If you had told me the digestion process was replaced by some other nutrient absorption mechanism I would say yes, that's a new and beneficial trait. But the ability to digest one acid over another? Come on.

[zoegirl]

I remember that article, in fact I bookmarked because in that experiment it took the bacteria close to 10000 generations to accumulate simply one beneficial mutation. 10,000 generations...and in a relatively simple organism, and then you have to add multiple mutations to create a working system. Call me a skeptic, but those odds ?

[Byblos]

I remember that article, in fact I bookmarked because in that experiment it took the bacteria close to 10000 generations to accumulate simply one beneficial mutation. 10,000 generations...and in a relatively simple organism, and then you have to add multiple mutations to create a working system. Call me a skeptic, but those odds ?

To call it a beneficial mutation is highly suspect at that. It's more like a case of adaptation than it is of gaining a new and beneficial trait.

[touchingcloth]

Somehow I knew you were going to invoke the co-option argument. We can examine that if you wish. Perhaps then you can explain how out of 40 protein structures involved in the flagellum, only 10 can be considered co-opters, namely the the type III secretory ones. While those structures do play a different role, as you know it is one that's detrimental to the living organism (if I'm not mistaken their function is to attract viruses). So we have about 10 structures that serve a purpose non-beneficial to the organism, and 30 that serve absolutely no function at all. In order for natural selection to assemble these into a flagellum, it would not only have to know before hand which ones to assemble and gradually assemble them into intermediate forms (because that's how natural selection works, right?) but also have the exact blueprint in which to do it (sequence is extremely important) and the proper timing to do it in (equally as important). To borrow an argument used recently, the probability of that happening by chance is zero. It is not unreasonable to conclude design.

I think you're confused there - the type III system is detrimental to other living organisms, not the bacteria itself. How did you arrive at the figure of 30 proteins serving no purpose at all? Most of the proteins essential (i.e. common between most/all flavours of flagella) have homologues in other structures in bacteria.
That isn't to say that the flagella wasn't designed, but to say that it is irreducibly complex is a stretch.

If you had told me the digestion process was replaced by some other nutrient absorption mechanism I would say yes, that's a new and beneficial trait. But the ability to digest one acid over another? Come on.

[/quote]
You've confused gastronomy with chemistry somewhat. The bacteria didn't all of a sudden decide to start munching on citrate rather than glucose (an acid and a sugar btw, not 2 different acids), but gained the ability to chemically break down and utilise citrate. The population of these bacteria soared in comparison to their isolated cousin populations. So that's a new trait, that's beneficial.

[touchingcloth]

I remember that article, in fact I bookmarked because in that experiment it took the bacteria close to 10000 generations to accumulate simply one beneficial mutation. 10,000 generations...and in a relatively simple organism, and then you have to add multiple mutations to create a working system. Call me a skeptic, but those odds ?

The population of bacteria was small (infinitesimal even) as compared to the total population of bacteria on earth. Other mutations and adaptations were observed prior to the citrate mutation, but that mutation was the shocking and unexpected one. It's worth noting that the bacteria were in quite a constrained environment, just sugar, water, citrate and whatever the test tubes were made out of. That a bacteria could mutate to exploit an extra, previously useless, resource, is quite remarkable.
The ability to digest citrate was a 2 step process - 2 separate mutations were needed to compliment each other. The researchers showed that once the first mutation had occurred the bacteria were quite likely to eventually gain the ability to digest citrate (i.e. if you went back to a post first mutation, pre second mutation bacteria population and left them to it, then the ability to digest citrate was shown to emerge in those populations).

It's worth remembering that bacteria are asexual. Unlike sexual organisms they are limited to the genes of their direct ancestors only, unlike us sexual organisms who are free to produce offspring whose genes are a combination of our own and any fertile member of the opposite sex. Bacteria don't have this gene-swapping ability so it is all the more remarkable when a new trait completely dominates vs individuals without that trait.

[Byblos]

Somehow I knew you were going to invoke the co-option argument. We can examine that if you wish. Perhaps then you can explain how out of 40 protein structures involved in the flagellum, only 10 can be considered co-opters, namely the the type III secretory ones. While those structures do play a different role, as you know it is one that's detrimental to the living organism (if I'm not mistaken their function is to attract viruses). So we have about 10 structures that serve a purpose non-beneficial to the organism, and 30 that serve absolutely no function at all. In order for natural selection to assemble these into a flagellum, it would not only have to know before hand which ones to assemble and gradually assemble them into intermediate forms (because that's how natural selection works, right?) but also have the exact blueprint in which to do it (sequence is extremely important) and the proper timing to do it in (equally as important). To borrow an argument used recently, the probability of that happening by chance is zero. It is not unreasonable to conclude design.

I think you're confused there - the type III system is detrimental to other living organisms, not the bacteria itself. How did you arrive at the figure of 30 proteins serving no purpose at all? Most of the proteins essential (i.e. common between most/all flavours of flagella) have homologues in other structures in bacteria.
That isn't to say that the flagella wasn't designed, but to say that it is irreducibly complex is a stretch.

I must have missed this part.

Did you look at the link you provided? Some of the proteins' homologies are listed as none and others are listed as yet unkown.

If you had told me the digestion process was replaced by some other nutrient absorption mechanism I would say yes, that's a new and beneficial trait. But the ability to digest one acid over another? Come on.

You've confused gastronomy with chemistry somewhat. The bacteria didn't all of a sudden decide to start munching on citrate rather than glucose (an acid and a sugar btw, not 2 different acids), but gained the ability to chemically break down and utilise citrate. The population of these bacteria soared in comparison to their isolated cousin populations. So that's a new trait, that's beneficial.

Yes, an acid and a sugar (my point was that it was still a digestive mechanism). In any case, how did they gain this ability to break down citrate? Is the exact pathway by which they gained this new ability known? Was this pathway not there with sugars and all of a sudden it was created out of necessity to process citrate? Or was it there all along and was activated to adapt to a new environment?

[touchingcloth]

Yes, an acid and a sugar (my point was that it was still a digestive mechanism). In any case, how did they gain this ability to break down citrate? Is the exact pathway by which they gained this new ability known? Was this pathway not there with sugars and all of a sudden it was created out of necessity to process citrate? Or was it there all along and was activated to adapt to a new environment?

The ability wasn't there all along (see above reply to zoegirl) but depended on 2 separate mutations. At first this wasn't known, but the researchers hypothesised that due to the mutation rate it was unlikely that it had developed as a single mutation. So they went back, generation by generation, and found a point at which later generations were likely to develop the ability to digest citrate, and earlier generations were not.
There was no necessity to process citrate - the citrate was there all along and individuals weren't punished for not being able to utilise it. But the potential remained for any bacteria that could process it to experience runaway success in terms of how well their offspring propagated.

[Byblos]

Yes, an acid and a sugar (my point was that it was still a digestive mechanism). In any case, how did they gain this ability to break down citrate? Is the exact pathway by which they gained this new ability known? Was this pathway not there with sugars and all of a sudden it was created out of necessity to process citrate? Or was it there all along and was activated to adapt to a new environment?

The ability wasn't there all along (see above reply to zoegirl) but depended on 2 separate mutations. At first this wasn't known, but the researchers hypothesised that due to the mutation rate it was unlikely that it had developed as a single mutation. So they went back, generation by generation, and found a point at which later generations were likely to develop the ability to digest citrate, and earlier generations were not.
There was no necessity to process citrate - the citrate was there all along and individuals weren't punished for not being able to utilise it. But the potential remained for any bacteria that could process it to experience runaway success in terms of how well their offspring propagated.

This doesn't mean that the pathway (the mechanism) wasn't there and only activated with the presence of citrate. Did their DNA structure change in any way? That's the key question I would think.

[touchingcloth]

This doesn't mean that the pathway (the mechanism) wasn't there and only activated with the presence of citrate. Did their DNA structure change in any way? That's the key question I would think.

That's what a mutation is.
12 lines were taken from a single colony of bacteria. If the ability was there but latent (just add citrate) then any of the 12 lines, and any generation of those lines would be able to go on to digest citrate. As it happens only one line has this ability, and even then only after a certain generation.