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Jim And Penny Caldwell's Archaeological Findings:


BlackCat

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BC, did you see the 2nd example after the irreducibly complex bridge? 

 

 

 http://www.talkdesign.org/faqs/icdmyst/ICDmyst.html#how2eatpcp

 

 

Swimming Systems

We come now to what have become the very most important purported examples of IC in nature: swimming systems. These are flexible projections that microbes use to move themselves through fluids. The three main types of microbes, bacteria, archaea, and single celled eukaryotes, use different swimming structures, and there are major differences between species of each type. Some bacteria even manage to swim without flagella, including little understood Synechococcus (17) and much better understood Spiroplasma melliferum (18). Of course microbial motion is not limited to swimming. They also have ways to move along surfaces and maneuver in sand and ooze. Bardy et al. review almost all of the known ways bacteria and archaea move (19).

Swimming systems depend on what are called molecular motors, a favorite topic of molecular biologists. Those who are curious about molecular motors may start here (20). Brownian ratchets, fascinating in their own right (21), are one of the energy sources for these tiny motors.

From a biological perspective, the function of an organism is to live and grow enough to reproduce. The function of any part of the organism is to contribute to this in any ways whatsoever. Appendages can help a cell in various ways such as sensing the environment, finding food or mates or communicating with other cells. It helps if the appendage can move about. This in turn will move the cell a little. (Think of waving your arm under water). In an environment where swimming is advantageous, it is not surprising that the ability to swim would evolve. Never the less, as the evolution of vertebrate systems like the clotting cascade and the immune system has become better understood, ID proponents have come to rely more and more on swimming systems, especially the bacterial flagellum, as the real evidence for Design in nature.

 

>

 

 

The Bacterial Flagellum

Here it is -- the number one argument for design in nature. ID advocates have even made a movie called Bacterial Flagella: A Paradigm for Design. It is on sale at the ARN web site (30) and briefly discussed in talk.origins (31). Behe said recently:

Bacterial flagella are many, diverse, and complicated. Behe concludes that any bacterial flagellum is composed of at least three parts: a paddle, a rotor, and a motor, and so with swimming as the specified function must be IC (page 72). Even at this crude level, the ICness of a flagellum is not so clear. The problem is that there are additional parts to a complete flagellum. For instance, there are proteins at the base that react to external stimuli and turn the motor on and off, and in some flagella cause it to change directions. And there are other proteins that are arranged in rings where the flagellum passes through the cell membrane."If [biologist Jerry] Coyne demonstrated that the [bacterial] flagellum, (which requires approximately forty gene products) could be produced by selection, I would be rather foolish to then assert that the blood clotting system (which consists of about twenty proteins) required intelligent design". (32)

But the more interesting question is: could a flagellum be IC with proteins, not paddles etc. as parts? Remember, IC is supposed to be the biochemical challenge to evolution. We've already seen that it isn't such a challenge after all, but so much has been made of the purported ICness of the flagellum that one should be well informed on the subject just to be more interesting at parties smile.png. In order to decide, one must first choose a flagellum. Even within a single bacteria species, different strains may have different proteins and different numbers of proteins in their flagella. Even a single rod-shaped bacterium may have quite different flagella at its ends and around its sides. Next, discover and list all the proteins in that particular flagellum. This requires deciding just where it begins, and one's decision about this may depend on the exact function one has in mind for 'the' flagellum. Then comes the hard part: proving that every last protein is required for the function. Oddly, ID proponents show no interest in doing any of this work, not even picking a particular flagellum of a particular bacterium to start on. It is as if just asserting the ICness of 'the' flagellum gives them full satisfaction.

What's the answer? Is any flagellum IC with proteins as parts or not? As this would depend on arbitrary criteria, scientists have not pursued this question as such. But quite a bit has been learned about various flagella. It is clear that all of them absolutely require a good many of their proteins in order to function as swimming systems. But not one is yet known to require every last protein, and some are known not to (193334). Could a flagellum be IC with proteins as parts? Sure. As we have seen in the much simpler case of hemoglobin, proteins can evolve to become codependent. There may be a perfectly IC flagellum out there just waiting to be discovered.

Even so, it wouldn't be the simplest swimming system. As the diagram shows, a bacterial flagellum is much more complex than an archaeal one. This is in part because it is built from, in fact secreted by what is called a type three secretion system (TTSS). This is a complicated thing in itself. It is a tiny tube which starts below the cell wall and sticks out through it, and serves as a conduit for protein export. The flagellar TTSS (there are other kinds) specializes in secreting the rest of a flagellum. The TTSS base counts as part of the flagellum, and is itself about as complex as an archaeal flagellum.

Since it is more complicated than is required for swimming alone, you might suspect that a bacterial flagellum has other functions. You would be right. These other functions vary from bacterium to bacterium and from situation to situation, and scientists have only recently been able to observe them. First, some flagella also export proteins, including ones that cause sickness (35). This is not too surprising since that's what the other TTSS's are known for.

But spirochetes, the spiral shaped bacteria, use flagella in a way one wouldn't expect. Their flagella don't stick out, yet are used for swimming, burrowing, and maintaining the cell's shape. Flagella are grown at both ends and extend toward the middle under the outer membrane. The flagella maintain the cell's spiral shape, and by rotating can create a moving wave along the cell, causing the cell to move in the opposite direction (19).

It is not easy to observe the behavior of individual bacteria in the wild. Just recently though, Danish researchers noticed some unusual behavior by bacteria living on low oxygen marine sediments. To see exactly what the bacteria were doing, they recreated the ecosystem in the laboratory. Who would have thought that some bacteria, shaped like slightly bowed rods, would tether themselves to the sediment with a mucus stalk secreted from the center and then use flagella at both ends to move like a propeller? But that's what these bacteria do. They create a tiny current, refreshing the water around them much faster than diffusion alone could do it (36).

Bacteria can move across surfaces in organized swarms, and quickly colonize a new food source such as your own much larger cells. When swarming, they often grow more flagella than usual and make cell-to-cell contacts with these flagella (37). Some bacteria also use their flagella to hang on to our cells as they try to break in and eat the cell contents (38).

This brings us to the dark side of design. Flagella participate in the cause of quite a few bacterial diseases, including diarrhea (38), ulcers and urinary tract infections (39). If the Designer is directly responsible for flagella then he is implicated as a cause of human diseases. Diarrhea is no joke; it is a leading cause of infant death in some parts of the world. To make matters worse, one can hardly give the Designer credit for flagella without also crediting him with TTSS's in general (40). This puts the Designer solidly behind Bubonic plague (4142) and many other diseases (43). Happily, science makes such beliefs unnecessary.

Swimming systems provide a good illustration of how (not) to think about evolution. Behe argues that evolution can't produce them because they are IC (a dubious claim and not an obstacle to evolution as we have seen). He buttresses this by arguing that is quite improbable that a swimming system good enough to be useful would appear all at once. And it wouldn't evolve slowly, he supposes, because until it became an effective swimming system, there would be nothing for natural selection to select. However, he envisions a part that sticks out, but that has no use at all other than swimming - and at first it can't even do that. But parts that stick out can have a number of functions, and bacterial flagella clearly have several. If there is another reason for it to be there, the sticking out part can gradually evolve more abilities. This involves change of function, or indirect evolution as Behe calls it. He dismisses this possibility, calling it improbable. A closer look shows the opposite.

 

The whole article is a good read, but I just zeroed in on the parts specific to the flagellum motor argument. 

Hey Josh- no I've not read this.  There was a link which bamboozled me with the technical stuff, hence why I emailed the Discovery Institute to ask if anyone had refuted the models put forward as possible evolutionary pathways.  I'm just about to serve dinner, so I'll have a good read of this, and will come back to you later.... :)

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I've had a quick read through and this is a very interesting article.   Some of the articles I've recently read in the last few weeks seem to be at odds with some points being made in this article, and so now I need to re-check my 'facts' before I comment.  I've had a glass of wine with my dinner and so my head is a bit fuzzy now.  So I shall dig deeper into this article over the week and come back to you Josh. smile.png

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Hey Josh- no I've not read this.  There was a link which bamboozled me with the technical stuff, hence why I emailed the Discovery Institute to ask if anyone had refuted the models put forward as possible evolutionary pathways.  I'm just about to serve dinner, so I'll have a good read of this, and will come back to you later.... smile.png

 

I would bet that they send you a reply with pseudo-scientific quotes from physicists and lawyers who, upon further research, will turn out to be Biblical creationists, and that they send you nothing from chemists, biochemists, biologists, or evolutionary biologists.

 

EDIT: except they might include one quote from Michael Behe, whose points were soundly debunked in the Dover trial. But he hasn't actually published any ID/IC papers himself, anyway.

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BlackCat, do you believe that humans were "intelligently designed?"

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Hey Josh- no I've not read this.  There was a link which bamboozled me with the technical stuff, hence why I emailed the Discovery Institute to ask if anyone had refuted the models put forward as possible evolutionary pathways.  I'm just about to serve dinner, so I'll have a good read of this, and will come back to you later.... smile.png

 

I would bet that they send you a reply with pseudo-scientific quotes from physicists and lawyers who, upon further research, will turn out to be Biblical creationists, and that they send you nothing from chemists, biochemists, biologists, or evolutionary biologists.

 

EDIT: except they might include one quote from Michael Behe, whose points were soundly debunked in the Dover trial. But he hasn't actually published any ID/IC papers himself, anyway.

 

I found this list of articles, some of which are peer-reviewed papers.  I noticed Michael Behe's name a few times in the list:  http://www.discovery.org/a/2640

 

It would seem his most recent paper was in 2010.  The subject of the paper may not be ID or IC directly, but from the short description, you can see that Behe is addressing a subject that is supported by the 'theory' of ID.   That list contains some interesting subjects that all seem to be about ID/IC whether directly or indirectly.  Here's an interesting point regarding a paper he had published in 2004:  ''In 2004, Behe published a paper with David Snoke, in the scientific journal Protein Science that uses a simple mathematical model to simulate the rate of evolution of proteins by point mutation,[28] which he states supports irreducible complexity, based on the calculation of the probability of mutations required for evolution to succeed. However, the paper does not mention intelligent design nor irreducible complexity, which were removed, according to Behe, at the behest of the reviewers. Nevertheless, The Discovery Institute lists it as one of the "Peer-Reviewed & Peer-Edited Scientific Publications Supporting the Theory of Intelligent Design".  http://en.wikipedia.org/wiki/Michael_Behe 

 

Do I believe humans are intelligently designed?  Up until recently I wouldn't have hesitated to shout 'yes'.  Now, I'm cautious.  Am I attributing 'mind' or 'intention' to the design we see in nature?  I used to attribute 'mind' ie the mind of God, now I'm not sure.  The subjects raised in those papers, will no doubt fuel scientific research that can only be good, as Akheia mentioned above.   

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Oh BC, I read through the first link and I have to say that this is just plain horrible. Trying to deny the human and ape connection is such a red flag. We're a classification of ape right now (well covered in AronRa's video about falsehoods of creationism). It's not as if there's any question at all that we arose from great apes because we're still great apes as I type this post. We are great apes, like it or not. I understand that you're going through a transition and exC is just the place for that sort of thing. I went through it and I'm sure many others participating had to go through it in their owns ways too. I had to go from full on believing the six day creation myth, special creation of all species, denying the big bang ever happened, denying evolution of any type, to finally seeing through to the BS involved in trying to deny these things. I had the most fundamental upbringing so the changes I've experienced has been radical. 

 

The more I read about it the more I can see the deception at work in the ID / IC camp. This is not very different than the Caldwell thing. And there's also another genre of BB theory denial and it includes atheists who disagree with the BB too. I've looked into that as well. And you'll find very similar claims aimed at poking holes in the standard model cosmology. They'll pick apart the interpretation of red shift in favor of a non-expanding interpretation. The Plasma Physics and Electric Universe camp suppose an infinite universe going back to something like the steady state model. And It's confusing because the atheists see it as a slap in the face to Genesis (with an infinitely old universe instead of a 6,000 year old one) and the Bible while some creationists have tried to align with it just because they're anti-Big Bang and want to try and twist anything anti-Big Bang in their favor. I've seen apologetic videos trying make use of the Electric Universe as if it's can be used in favor of creationism.

 

If you're interested we can dissect the anti-Big Bang movement coming from both atheists and creationists, which I'm sure BAA can lend a helpful hand in because it's addressed to cosmological issues. You can compare that to the ID / IC movement with it's domination of theists with a sprinkling of atheist thought and catch a lot of similar patterns that we're seeing between the two movements. 

 

Non-theistic anti-Big Bang, Plasma / Electric Universe: 

 

 

Here's another series called "The Big Bang Never Happened."

 

http://www.youtube.com/watch?v=1yTfRy0LTD0

 

And altogether what you find with every topic we've discussed in this thread so far is:

 

A ) Pseudo-Archaeology mainly led by creationists. 

 

B ) Pseudo-Biology mainly led by creationists.

 

C ) Pseudo-Cosmology mainly led by creationists. 

 

​Each have varieties of atheists involved who may have different ideas about interpretation than the creationists do, but all in all the whole genre is pseudo-scientific regardless of who you find involved with it or what their credentials happen to be. I think it may be revealing for you to step back and survey all three areas and see how similar they are to one another and how searching for atheists or non-creationists involved in each category doesn't really do any of these issues much justice in the end.

 

I think it's probably best to just keep to the standard models until they've been officially over turned by something powerful enough to over turn any of them. I like being aware of what's out there for sure, but all in all these competitive ideas need a lot more power to ever hope of over turning the accepted mainstream models of archaeology, biology, and cosmology.

 

And I just don't see anything remotely close to that kind of power coming from the minority camps in question that we've been reading about so far. They're all consistently out of sync with the simplest explanations and none have greater predictive power than the accepted models for each category. I would think that truth has a power of it's own accord and will always rise to the top. Traditionally it always has. The earth isn't flat, so the flat earth was necessarily over turned. The sun doesn't orbit the earth. Truth prevailed again.

 

If the universe is not expanding, then the power against the standard model should become overwhelming.

 

If gradual evolution and natural selection didn't and don't happen, then the evidence should be overwhelming.

 

If the Exodus did happen, once again the evidence should be overwhelming.

 

And yet this isn't the case for any of the above. 

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I'm still here, guys!  (Just taking a bit of a back seat, as BC and I have agreed to do.)

 

But if you want any help with the anti-Big Bang pseudoscience, then just holler. 

I'm currently maintaining a holding pattern...

Keeping myself up to date with this thread, but waiting on BC to get back to me when she's ready.

 

Thanks,

 

BAA.

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Oh BC, I read through the first link and I have to say that this is just plain horrible. Trying to deny the human and ape connection is such a red flag. We're a classification of ape right now (well covered in AronRa's video about falsehoods of creationism). It's not as if there's any question at all that we arose from great apes because we're still great apes as I type this post. We are great apes, like it or not.

I don't know if they're all trying to deny the human and ape connection.  In the Wiki link of Behe, it states under the heading 'Darwin's Black Box' that Behe does accept common descent.  The articles that are listed, seem to be dealing with bone fide issues within the fields of molecular biology, chemistry, mathematics, etc  that 'seem' to pose a problem for evolution.  I don't see anything wrong with that.   

 

I understand that you're going through a transition and exC is just the place for that sort of thing. I went through it and I'm sure many others participating had to go through it in their owns ways too. I had to go from full on believing the six day creation myth, special creation of all species, denying the big bang ever happened, denying evolution of any type, to finally seeing through to the BS involved in trying to deny these things. I had the most fundamental upbringing so the changes I've experienced has been radical. 

I was an old earth creationist that embraced science whilst trying to make sense of the Bible.  Now I'm trying to make sense of this 'design' issue which is far more satisfying. 

 

The more I read about it the more I can see the deception at work in the ID / IC camp. This is not very different than the Caldwell thing. And there's also another genre of BB theory denial and it includes atheists who disagree with the BB too. I've looked into that as well. And you'll find very similar claims aimed at poking holes in the standard model cosmology. They'll pick apart the interpretation of red shift in favor of a non-expanding interpretation. The Plasma Physics and Electric Universe camp suppose an infinite universe going back to something like the steady state model. And It's confusing because the atheists see it as a slap in the face to Genesis (with an infinitely old universe instead of a 6,000 year old one) and the Bible while some creationists have tried to align with it just because they're anti-Big Bang and want to try and twist anything anti-Big Bang in their favor. I've seen apologetic videos trying make use of the Electric Universe as if it's can be used in favor of creationism.

 

If you're interested we can dissect the anti-Big Bang movement coming from both atheists and creationists, which I'm sure BAA can lend a helpful hand in because it's addressed to cosmological issues. You can compare that to the ID / IC movement with it's domination of theists with a sprinkling of atheist thought and catch a lot of similar patterns that we're seeing between the two movements. 

From what I have studied and learnt about ID and it's champions, I don't believe they are out to deceive people.   I've looked a bit into the 'theory' that the Big Bang didn't happen, but alas, it's all too technical for me, and so I'm happy to leave it to them to figure it out.  I don't begrudge them their ideas or theories.  The more it is studied, the more the truth will out surely.  The same with the ID issue.  The more the tests and research is done, the bigger the overall picture will become and the truth will emerge.   

 

Non-theistic anti-Big Bang, Plasma / Electric Universe: 

 

 

Here's another series called "The Big Bang Never Happened."

 

http://www.youtube.com/watch?v=1yTfRy0LTD0

 

And altogether what you find with every topic we've discussed in this thread so far is:

 

A ) Pseudo-Archaeology mainly led by creationists. 

 

B ) Pseudo-Biology mainly led by creationists.

 

C ) Pseudo-Cosmology mainly led by creationists. 

 

​Each have varieties of atheists involved who may have different ideas about interpretation than the creationists do, but all in all the whole genre is pseudo-scientific regardless of who you find involved with it or what their credentials happen to be. I think it may be revealing for you to step back and survey all three areas and see how similar they are to one another and how searching for atheists or non-creationists involved in each category doesn't really do any of these issues much justice in the end.

 

I think it's probably best to just keep to the standard models until they've been officially over turned by something powerful enough to over turn any of them. I like being aware of what's out there for sure, but all in all these competitive ideas need a lot more power to ever hope of over turning the accepted mainstream models of archaeology, biology, and cosmology.

 

 

And I just don't see anything remotely close to that kind of power coming from the minority camps in question that we've been reading about so far. They're all consistently out of sync with the simplest explanations and none have greater predictive power than the accepted models for each category. I would think that truth has a power of it's own accord and will always rise to the top. Traditionally it always has. The earth isn't flat, so the flat earth was necessarily over turned. The sun doesn't orbit the earth. Truth prevailed again.

 

If the universe is not expanding, then the power against the standard model should become overwhelming.

 

If gradual evolution and natural selection didn't and don't happen, then the evidence should be overwhelming. ID doesn't assume that evolution and natural selection isn't happening, but it seems to be challenging how we define evolution and natural selection as an unguided process.  Is evolution/natural selection only part of the process?  The papers Iisted in the link seem to be dealing with issues that challenge the 'undirected' aspect of evolution or the extent to which evolution can evolve systems. 

 

If the Exodus did happen, once again the evidence should be overwhelming. 

 

And yet this isn't the case for any of the above. 

I suppose it's hard to have any power when you're in the minority and are presenting something that attacks the accepted model.  

 

 

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BC, did you see the 2nd example after the irreducibly complex bridge? 

 

 

 http://www.talkdesign.org/faqs/icdmyst/ICDmyst.html#how2eatpcp

 

 

Swimming Systems

We come now to what have become the very most important purported examples of IC in nature: swimming systems. These are flexible projections that microbes use to move themselves through fluids. The three main types of microbes, bacteria, archaea, and single celled eukaryotes, use different swimming structures, and there are major differences between species of each type. Some bacteria even manage to swim without flagella, including little understood Synechococcus (17) and much better understood Spiroplasma melliferum (18). Of course microbial motion is not limited to swimming. They also have ways to move along surfaces and maneuver in sand and ooze. Bardy et al. review almost all of the known ways bacteria and archaea move (19).

Swimming systems depend on what are called molecular motors, a favorite topic of molecular biologists. Those who are curious about molecular motors may start here (20). Brownian ratchets, fascinating in their own right (21), are one of the energy sources for these tiny motors.

From a biological perspective, the function of an organism is to live and grow enough to reproduce. The function of any part of the organism is to contribute to this in any ways whatsoever. Appendages can help a cell in various ways such as sensing the environment, finding food or mates or communicating with other cells. It helps if the appendage can move about. This in turn will move the cell a little. (Think of waving your arm under water). In an environment where swimming is advantageous, it is not surprising that the ability to swim would evolve. Never the less, as the evolution of vertebrate systems like the clotting cascade and the immune system has become better understood, ID proponents have come to rely more and more on swimming systems, especially the bacterial flagellum, as the real evidence for Design in nature.

 

>

 

The Bacterial Flagellum

Here it is -- the number one argument for design in nature. ID advocates have even made a movie called Bacterial Flagella: A Paradigm for Design. It is on sale at the ARN web site (30) and briefly discussed in talk.origins (31). Behe said recently:

Bacterial flagella are many, diverse, and complicated. Behe concludes that any bacterial flagellum is composed of at least three parts: a paddle, a rotor, and a motor, and so with swimming as the specified function must be IC (page 72). Even at this crude level, the ICness of a flagellum is not so clear. The problem is that there are additional parts to a complete flagellum. For instance, there are proteins at the base that react to external stimuli and turn the motor on and off, and in some flagella cause it to change directions. And there are other proteins that are arranged in rings where the flagellum passes through the cell membrane."If [biologist Jerry] Coyne demonstrated that the [bacterial] flagellum, (which requires approximately forty gene products) could be produced by selection, I would be rather foolish to then assert that the blood clotting system (which consists of about twenty proteins) required intelligent design". (32)

But the more interesting question is: could a flagellum be IC with proteins, not paddles etc. as parts? Remember, IC is supposed to be the biochemical challenge to evolution. We've already seen that it isn't such a challenge after all, but so much has been made of the purported ICness of the flagellum that one should be well informed on the subject just to be more interesting at parties smile.png. In order to decide, one must first choose a flagellum. Even within a single bacteria species, different strains may have different proteins and different numbers of proteins in their flagella. Even a single rod-shaped bacterium may have quite different flagella at its ends and around its sides. Next, discover and list all the proteins in that particular flagellum. This requires deciding just where it begins, and one's decision about this may depend on the exact function one has in mind for 'the' flagellum. Then comes the hard part: proving that every last protein is required for the function. Oddly, ID proponents show no interest in doing any of this work, not even picking a particular flagellum of a particular bacterium to start on. It is as if just asserting the ICness of 'the' flagellum gives them full satisfaction.

What's the answer? Is any flagellum IC with proteins as parts or not? As this would depend on arbitrary criteria, scientists have not pursued this question as such. But quite a bit has been learned about various flagella. It is clear that all of them absolutely require a good many of their proteins in order to function as swimming systems. But not one is yet known to require every last protein, and some are known not to (193334). Could a flagellum be IC with proteins as parts? Sure. As we have seen in the much simpler case of hemoglobin, proteins can evolve to become codependent. There may be a perfectly IC flagellum out there just waiting to be discovered.

Even so, it wouldn't be the simplest swimming system. As the diagram shows, a bacterial flagellum is much more complex than an archaeal one. This is in part because it is built from, in fact secreted by what is called a type three secretion system (TTSS). This is a complicated thing in itself. It is a tiny tube which starts below the cell wall and sticks out through it, and serves as a conduit for protein export. The flagellar TTSS (there are other kinds) specializes in secreting the rest of a flagellum. The TTSS base counts as part of the flagellum, and is itself about as complex as an archaeal flagellum.

Since it is more complicated than is required for swimming alone, you might suspect that a bacterial flagellum has other functions. You would be right. These other functions vary from bacterium to bacterium and from situation to situation, and scientists have only recently been able to observe them. First, some flagella also export proteins, including ones that cause sickness (35). This is not too surprising since that's what the other TTSS's are known for.

But spirochetes, the spiral shaped bacteria, use flagella in a way one wouldn't expect. Their flagella don't stick out, yet are used for swimming, burrowing, and maintaining the cell's shape. Flagella are grown at both ends and extend toward the middle under the outer membrane. The flagella maintain the cell's spiral shape, and by rotating can create a moving wave along the cell, causing the cell to move in the opposite direction (19).

It is not easy to observe the behavior of individual bacteria in the wild. Just recently though, Danish researchers noticed some unusual behavior by bacteria living on low oxygen marine sediments. To see exactly what the bacteria were doing, they recreated the ecosystem in the laboratory. Who would have thought that some bacteria, shaped like slightly bowed rods, would tether themselves to the sediment with a mucus stalk secreted from the center and then use flagella at both ends to move like a propeller? But that's what these bacteria do. They create a tiny current, refreshing the water around them much faster than diffusion alone could do it (36).

Bacteria can move across surfaces in organized swarms, and quickly colonize a new food source such as your own much larger cells. When swarming, they often grow more flagella than usual and make cell-to-cell contacts with these flagella (37). Some bacteria also use their flagella to hang on to our cells as they try to break in and eat the cell contents (38).

This brings us to the dark side of design. Flagella participate in the cause of quite a few bacterial diseases, including diarrhea (38), ulcers and urinary tract infections (39). If the Designer is directly responsible for flagella then he is implicated as a cause of human diseases. Diarrhea is no joke; it is a leading cause of infant death in some parts of the world. To make matters worse, one can hardly give the Designer credit for flagella without also crediting him with TTSS's in general (40). This puts the Designer solidly behind Bubonic plague (4142) and many other diseases (43). Happily, science makes such beliefs unnecessary.

Swimming systems provide a good illustration of how (not) to think about evolution. Behe argues that evolution can't produce them because they are IC (a dubious claim and not an obstacle to evolution as we have seen). He buttresses this by arguing that is quite improbable that a swimming system good enough to be useful would appear all at once. And it wouldn't evolve slowly, he supposes, because until it became an effective swimming system, there would be nothing for natural selection to select. However, he envisions a part that sticks out, but that has no use at all other than swimming - and at first it can't even do that. But parts that stick out can have a number of functions, and bacterial flagella clearly have several. If there is another reason for it to be there, the sticking out part can gradually evolve more abilities. This involves change of function, or indirect evolution as Behe calls it. He dismisses this possibility, calling it improbable. A closer look shows the opposite.

 

The whole article is a good read, but I just zeroed in on the parts specific to the flagellum motor argument. 

 

Even if there is awareness in the micro world, that only seems to point towards a means by which gradual evolution works. The natural selection would be tied into awareness on micro levels. It might explain why everything looks so much like a nice little factory and so on on these micro levels. But what it doesn't seem to do is lend a hand to special creation. There's no evidence of special creation, not even the flagellum motor. All of the evidence keeps pointing back to gradual evolution.

 

That doesn't knock consciousness out of the picture entirely, it just shows how consciousness would have to operate through trial and error to make ever increasing better use of things. And since it's in everything (presumably), it then applies even to the dark side such as disease. The disease problem doesn't make any sense with respect to an advanced designing intelligence like God. That isn't how nature seems to work. God - or something like it which is a fully developed consciousness - is supposed to distinguish good from bad while consciousness ingrained into nature itself doesn't do that at all. It's in everything. Nothing is good or bad for that type of consciousness. It's just a driving force towards the perpetuation of all varieties of existence. There's no reason to assume that it wouldn't work through disease any more than anything else in existence. It's just this bubbling urge towards the perpetuation of existence and the ability for existence to experience itself on various levels, including from the subatomic to the very macro (refer back to the primacy of consciousness argument for details). 

 

None of this deeper mystical and metaphysical thinking on consciousness as more fundamental than space and matter seems to detract from or counter biological evolution as science has come to understand it. There's really no reason to take off trying to refute science unless you already have the preconceived idea that an external God created all living things via special creation fully functional in present form. And this is something that ought to be made known throughout the spiritual community for those who do not view God as something external and "other." Darwinian evolution is not a threat to the deeper seated mystical views. It need not be treated as one either. Because in the process of trying to refute graduation evolution and natural selection we find all variety of error and a path essentially leading further and further away from truth, rather than closer to it. I think the driving force behind all of this ID and IC is the wrongly supposed idea that it takes away from consciousness and awareness when it really doesn't. It just shows that whatever consciousness may turn out to be, it doesn't start out extremely "intelligent." Rather it has to struggle and work hard to achieve greater levels of intelligence. 

agggghhhh-  I've just lost my post.  I've just been going through the article in red to address some points.   That's an hour wasted.  Wendytwitch.gif

The article states:  'Then comes the hard part: proving that every last protein is required for the function. Oddly, ID proponents show no interest in doing any of this work, not even picking a particular flagellum of a particular bacterium to start on. It is as if just asserting the ICness of 'the' flagellum gives them full satisfaction.'

 

The article is dated 2003 and hence a lot more research has been done.  This short article discusses the research work Scott Minnich has done, so he has done 'the hard part': 

 

http://www.evolutionnews.org/2010/01/spinning_tales_about_the_bacte031141.html   It's an interesting article and also touches on the type III SS.   For more information on the type III SS and the problems with it being a precursor, this article is more indepth:

 

http://www.scribd.com/doc/106728402/The-Bacterial-Flagellum

It is very technical and so if you scroll down to heading 6, it discusses the type III.  It's also a very up to date article regarding what we know about the flagellum.

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I'm still here, guys!  (Just taking a bit of a back seat, as BC and I have agreed to do.)

 

But if you want any help with the anti-Big Bang pseudoscience, then just holler. 

I'm currently maintaining a holding pattern...

Keeping myself up to date with this thread, but waiting on BC to get back to me when she's ready.

 

Thanks,

 

BAA.

Hey BAA- Let's present each other's positions as you suggested.  You go first (when you're ready) , and then I'll have a better idea how to do it. happydance.gif

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The paper on the flagellum is little more than an advanced book report. It offers no unique research of its own or experimental findings made by the author. Also, the bits where the author asserts that the flagellum could only have been created by design have no footnotes; the author just throws up his arms and says, "It must have been designed, I tell you! I can't see how else it could have happened!"

 

That's not science. That's just his opinion. And that is why these intelligent design "papers" are never published in respected peer-reviewed journals, and can only be found in the equivalent of blogs.

 

The only people papers like this speak to are people that are already convinced by intelligent design arguments, and people who are unaware enough of how science operates to say, "Hey, this is really technical with lots of references! This must be legit!"

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It's saying something when creationists even get non-theists to question established science.

 

BC, minority-view scientists have trouble finding acceptance for a reason. People sometimes do have whackjob ideas that turn out to be right, like Tesla and Einstein weren't fully accepted once upon a time. But their IDEAS stood. They predicted things that science turned out to find were true. Nothing denied their findings. And so their findings, as alarming as they were sometimes, became mainstream. We're still finding new stuff that sounds just totally out-there, but that's how science works: she comes up with new stuff that scares the shit out of us all the time, and we use established procedures to figure out if it's true or not. Like when someone thought he'd found a particle that goes faster than light. Remember that? NOBODY condemned him, did they? They just re-measured, that's all. If he'd really found one, it would have thumbed its nose at a hundred years of us thinking we knew something that turned out not to be the case. But nobody freaked out. It'd have just made us work harder to understand what happened.

 

BUT THAT IS NOT WHAT IS GOING ON WITH CREATIONISM.

 

No reputable scientist supports creationism. Not because he's terrified of being found not to be in lockstep with the regime, but because reputable scientists know that creationism is bullshit. The scientist who actually proved creationism right--even a little tiny bit--would get a freakin' Nobel Prize in his field. Scientists don't scurry in fear from stuff that looks whackadoodle. But creationism's ideas do not predict. They do not build upon established science. They either cannot be tested, or when tested turn out not to be true. The accepted model has a century and a half of evidence supporting it, and not a single experiment that successfully dismantles any part of it. So normal science considers creationism, which criticizes that model without actually providing a shred of evidence against it, whackadoodle.

 

You're letting a persecution complex and martyr wish cloud your vision. There's a reason that creationists get attacked, and it has nothing whatsoever to do with everybody being all scared in their booties of their superior Romulan weaponry. Nobody's engaging with their ideas because their ideas are balderdash.

 

The problem is that you don't understand what happens when something actually noteworthy contradicts a reigning model of science, because you don't see it happen often. If you did read more about that end of things, you'd know that creationism's critics aren't acting like this because they're terrified of it being true. They're acting like this because they know, 100% flat-out completely totally with no reservations whatsoever that nothing creationists claim could possibly be true ever. Creationists take that contempt and turn it into a self-fulfilling prophecy. Oh, mainstream science doesn't give them time of day? Well, OBVIOUSLY they wouldn't! They're SCARED!

 

Do you see how Christians do the exact same thing to non-Christians? Well OBVIOUSLY we don't want to turn to Jesus! We just want to SIN!

 

Pfft.

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The paper on the flagellum is little more than an advanced book report. It offers no research of its own. Also, the bits where the author asserts that the flagellum could only have been created by design have no footnotes; the author just throws up his arms and says, "It must have been designed, I tell you! I can't see how else it could have happened!"

 

That's not science.

 

So a scientist can't use other people's research to compile an article?  I don't mind that the author is convinced that the design inferrence is real.  I am not fully convinced but can see that the research that has been done so far, (of which he cites) gives cause to sit up and take notice of this design inference.   

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The paper on the flagellum is little more than an advanced book report. It offers no research of its own. Also, the bits where the author asserts that the flagellum could only have been created by design have no footnotes; the author just throws up his arms and says, "It must have been designed, I tell you! I can't see how else it could have happened!"

 

That's not science.

 

So a scientist can't use other people's research to compile an article?  

 

They can't call it their own finding if they do so, no. A scientific paper needs to advance the knowledge of the field or industry in some way. Such as, "Our team found that..." "Our experiments showed that..." "Our trials indicated..." Not, "Hey, here's a bunch of facts that others have found out about the flagellum. I think it had to have been intelligently designed!" Do you not see the difference?

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The paper on the flagellum is little more than an advanced book report. It offers no research of its own. Also, the bits where the author asserts that the flagellum could only have been created by design have no footnotes; the author just throws up his arms and says, "It must have been designed, I tell you! I can't see how else it could have happened!"

 

That's not science.

 

So a scientist can't use other people's research to compile an article?  

 

They can't call it their own finding if they do so, no. A scientific paper needs to advance the knowledge of the field or industry in some way. Such as, "Our team found that..." "Our experiments showed that..." "Our trials indicated..." Not, "Hey, here's a bunch of facts that others have found out about the flagellum. I think it had to have been intelligently designed!" Do you not see the difference?

Where is he calling it his own finding?  He is offering the theory of ID to account for the biological stuff that he goes into detail with.   You seem to be nitpicking and trying to find fault where there really is none.

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Ok, I'm diving into further reading starting with your first link:

 

Truth or Dare: Why does Dr. Miller promote an improper way of testing for irreducible complexity and misconstrue Behe's theories as prohibiting the use of sub-parts in other systems? Has Dr. Miller actually provided anything close to a complete evolutionary pathway for the origin of the flagellum? Has anyone done this? How does Miller's evidence refute Scott Minnich's genetic knockout experiments which show the flagellum is irreducibly complex with respect to its complement of about 35 genes?

 

First of all, why not ask whether any one from the ID camp has provided any type of pathway for the origin of the flagellum? 

 

Furthermore the evolutionary chart that I posted earlier proposes this very thing. The author of the above may not be aware of it. There's several stages suggested in order to get to the current state of motility. And I don't see the type III issue from the Dover trial as making or breaking any of this either, which seems a bit of a strawman the way the ID is trying to present it. For me, getting down to the truth is worthwhile. So I'll continue reading and check out the second link.

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Now I'm thinking that you're failing to see the difference between a peer reviewed scientific paper, of the kind that is published in Nature or Science, and an article, like you would find in Scientific American or Discover.

 

Scientific papers present unique findings of the authors and whoever they were working with that help to prove (or disprove!) a hypothesis. While the paper may (and usually does) include footnotes to relevant work done by other scientists in the field, it is never just a compilation of others' work. To be published in Nature or Science, the work must report the result of work done by the authors themselves through experiment or measurement. It must provide new information that has been discovered by the authors. While such papers may include the authors' opinions, in order to pass peer review, the data in the paper must support these opinions directly. A scientific paper is structured as follows:

  1. We wanted to find out if X is true.
  2. We hypothesized that if X is true, that the following criteria (a, b, c) would also be true
  3. We set up an experiment/took measurements of the things we thought should prove X
  4. We now list the experimental findings and measurements, as well as the methodology behind them
  5. We found that the experimental results/measured data did/did not support our hypothesis

The paper is then sent through peer review (which is a review by someone who is reputable within the field of the paper in question; engineers and physicists do not review papers about microbiology, or vice versa). Contrary to what non-scientists believe, this is not a friendly process. A good peer review process will tear a paper to pieces. Where did these number come from? How did you measure X? What equipment did you use to find Y? How did you make the leap from A to B? What was the margin of error, and why? If the research/result still stands after this process, then the paper is published. Many papers fail this process.

 

The "paper" you linked to about the flagellum is an article. It lists out a bunch of facts, and then includes some editorializing by the author. This is not an example of a peer reviewed scientific paper, and it doesn't actually prove anything.

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Now I'm thinking that you're failing to see the difference between a peer reviewed scientific paper, of the kind that is published in Nature or Science, and an article, like you would find in Scientific American or Discover.

Scientific papers present unique findings of the authors and whoever they were working with that help to prove (or disprove!) a hypothesis. While the paper may (and usually does) include footnotes to relevant work done by other scientists in the field, it is never just a compilation of others' work. To be published in Nature or Science, the work must report the result of work done by the authors themselves through experiment or measurement. It must provide new information that has been discovered by the authors. While such papers may include the authors' opinions, in order to pass peer review, the data in the paper must support these opinions directly. A scientific paper is structured as follows:

  1. We wanted to find out if X is true.
  2. We hypothesized that if X is true, that the following criteria (a, b, c) would also be true
  3. We set up an experiment/took measurements of the things we thought should prove X
  4. We now list the experimental findings and measurements, as well as the methodology behind them
  5. We found that the experimental results/measured data did/did not support our hypothesis

The paper is then sent through peer review (which is a review by someone who is reputable within the field of the paper in question; engineers and physicists do not review papers about microbiology, or vice versa). Contrary to what non-scientists believe, this is not a friendly process. A good peer review process will tear a paper to pieces. Where did these number come from? How did you measure X? What equipment did you use to find Y? How did you make the leap from A to B? What was the margin of error, and why? If the research/result still stands after this process, then the paper is published. Many papers fail this process.

 

The "paper" you linked to about the flagellum is an article. It lists out a bunch of facts, and then includes some editorializing by the author. This is not an example of a peer reviewed scientific paper, and it doesn't actually prove anything.

 

I didn't link to a 'paper'.   I linked to an article, as I clearly stated.  You are the one that called it a paper.  I linked to it, mainly to provide some information regarding the Type III SS.   I know it's not a peer- reviewed paper. It's an article that had the relevant information regarding the Type  III.  

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It's saying something when creationists even get non-theists to question established science.

 

BC, minority-view scientists have trouble finding acceptance for a reason. People sometimes do have whackjob ideas that turn out to be right, like Tesla and Einstein weren't fully accepted once upon a time. But their IDEAS stood. They predicted things that science turned out to find were true. Nothing denied their findings. And so their findings, as alarming as they were sometimes, became mainstream. We're still finding new stuff that sounds just totally out-there, but that's how science works: she comes up with new stuff that scares the shit out of us all the time, and we use established procedures to figure out if it's true or not. Like when someone thought he'd found a particle that goes faster than light. Remember that? NOBODY condemned him, did they? They just re-measured, that's all. If he'd really found one, it would have thumbed its nose at a hundred years of us thinking we knew something that turned out not to be the case. But nobody freaked out. It'd have just made us work harder to understand what happened.

 

BUT THAT IS NOT WHAT IS GOING ON WITH CREATIONISM.

 

No reputable scientist supports creationism. Not because he's terrified of being found not to be in lockstep with the regime, but because reputable scientists know that creationism is bullshit. The scientist who actually proved creationism right--even a little tiny bit--would get a freakin' Nobel Prize in his field. Scientists don't scurry in fear from stuff that looks whackadoodle. But creationism's ideas do not predict. They do not build upon established science. They either cannot be tested, or when tested turn out not to be true. The accepted model has a century and a half of evidence supporting it, and not a single experiment that successfully dismantles any part of it. So normal science considers creationism, which criticizes that model without actually providing a shred of evidence against it, whackadoodle.

 

You're letting a persecution complex and martyr wish cloud your vision. There's a reason that creationists get attacked, and it has nothing whatsoever to do with everybody being all scared in their booties of their superior Romulan weaponry. Nobody's engaging with their ideas because their ideas are balderdash.

 

The problem is that you don't understand what happens when something actually noteworthy contradicts a reigning model of science, because you don't see it happen often. If you did read more about that end of things, you'd know that creationism's critics aren't acting like this because they're terrified of it being true. They're acting like this because they know, 100% flat-out completely totally with no reservations whatsoever that nothing creationists claim could possibly be true ever. Creationists take that contempt and turn it into a self-fulfilling prophecy. Oh, mainstream science doesn't give them time of day? Well, OBVIOUSLY they wouldn't! They're SCARED!

 

Do you see how Christians do the exact same thing to non-Christians? Well OBVIOUSLY we don't want to turn to Jesus! We just want to SIN!

 

Pfft.

 

Akheia, I understand your concerns.  Not everyone who is interested in ID is a creationist, or concludes that ID equals creationism.   Can't we put that to one side, whilst we discuss the science?  It's the science that will make or break ID. :)

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Ok, I'm diving into further reading starting with your first link:

 

Truth or Dare: Why does Dr. Miller promote an improper way of testing for irreducible complexity and misconstrue Behe's theories as prohibiting the use of sub-parts in other systems? Has Dr. Miller actually provided anything close to a complete evolutionary pathway for the origin of the flagellum? Has anyone done this? How does Miller's evidence refute Scott Minnich's genetic knockout experiments which show the flagellum is irreducibly complex with respect to its complement of about 35 genes?

 

First of all, why not ask whether any one from the ID camp has provided any type of pathway for the origin of the flagellum? 

 

Furthermore the evolutionary chart that I posted earlier proposes this very thing. The author of the above may not be aware of it. There's several stages suggested in order to get to the current state of motility. And I don't see the type III issue from the Dover trial as making or breaking any of this either, which seems a bit of a strawman the way the ID is trying to present it. For me, getting down to the truth is worthwhile. So I'll continue reading and check out the second link.

 

I emailed the Discovery Institute last week, to ask if any one had refuted that model in the evolutionary chart.  I'll let you know if/when I get a reply.  If I don't hear from them, I'll email a few biologists at the other ID sites.  I'll also pose your first question.  It's a good question. :)

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Okay, I'm all caught up now. I said it before, I'll say it again: Occam's Razor. I think I'll add the Argument From Ignorance fallacy to that too. That's when you say you can't prove it didn't so it did. I could say that this morning an electric green magic sky eel came through my kitchen window, and we had coffee together. He was wearing a spiffy top hat and bow tie. You can't prove it didn't happen, so it totally did. This kind of argument is ludicrous: that's not offering proof, that's short-circuiting an argument with lack of proof, rather than finding your own. This is, by definition, the antithesis of science. "There's got to be a creator or intelligent designer, and you can't prove otherwise" isn't proof OF one. And that's what you have to do. Prove it DID. Bring me the head of Nessie and I'll believe there's a serpent in the Loch.

 

We have proof FOR evolution, though. There's a theory that birds developed flight by their early maniraptoran ancestors using feathers on their forearms to help them get up steep slopes (wing assisted incline running, or WAIR hypothesis). How to test? If this is true, then it might be supported by this ability being preserved in existing birds from all over the bird family tree, and even before they learn to fly properly, as a reflex. (Stuff that is in your genetic past might be preserved, if just because natural selection fails to eliminate it. Heck, human babies have a lot of fun reflexes. An infant will try to swim in water, but an older child will fail to try. We lose this ability, and have to be taught to swim as a cultural thing later. Our other relatives, the great apes, don't swim naturally, either. This is why a moat with water is an effective barrier against a gorilla.) This can be tested. And,

Just one piece of evidence. Fun fact: some living birds still have legit CLAWS on what's left of their fingers. (They're mostly covered in fluff, so it's hard to tell, most of the time.) Birds as distantly related as ostriches and the famous hoatzin have claws on their wings. The hoatzin is most famous for it, because they have them as babies, when
before their feathers grow in, and because they use them to climb around. Chickens still have the genes to grow teeth, and, when they do, it's pointy ones like archosaurs. We don't just use DNA to test to see who's the baby-daddy on reality TV. We can see who's related, among all life on Earth. Sure, we share 98% of our genes with chimps, but also 57% with cabbage.

 

I'll leave it to others to debate the specifics, but I do have one thing that's been gnawing at my brain (ha ha). I think one reason that scientists don't explain themselves better is that people are squeamish about hurting other people. Beliefs are considered intensely private things, and we believe people have a right to theirs. I don't want to get up in anyone's face and say: you're wrong about everything, the cake is a lie. It's none of my business. I only debate the issue if it comes up, and/or someone gets in MY face about it. I see how this jitteryness is hurting education, though, and I think maybe science should push harder to be heard. I think everyone's tried to make scientific objections to ID clear, so I'll try another tack: maybe it's an emotional attachment. Forget the scientific evidence, for this or that, for just a moment:

 

I didn't pull any punches here. I don't want to hurt anyone of delicate sensibilities.
Besides, I'm not gonna lie: the idea of a "creator" that would dabble in things like the guinea worm or polio or entire genera of mind-control fungus or the parasitic wasps, scares me rigid. Nature's not exactly benevolent. Given some of the things we see, I'm not really sure how people think the idea of a creator is comforting, in any realistic way. Lots, and lots, and lots of creatures make their way in life by (to humans) hideously amoral ways. Things that cannibalize their siblings in the womb, or obligate siblicide, or the

(Warning: that link is graphic.) the whole lifecycle of the male anglerfish (<= this webcomic link has some spicy language, but it is accurate, actually. Horrifyingly.)

 

I just don't get how anyone could find the creator or intelligent designer of all kinds of creatures that HAVE to make their way in life by torturing other living things an emotionally comforting idea. Good gravy. I'm sure that if every last guinea worm dropped dead tomorrow, nobody would cry.

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ID is 100% creationism, BC. There's no reason for me to accept such a strange request as to not call it what it most assuredly is. "Design" came from creationism, used the same definitions and terminology, was made up by the same fundie groups, and even to this day is dominated by fundie interests. At the Dover trial, evidence was introduced proving without any doubt whatsoever that ID is completely, totally, irrefutably creationism. Remember the cut-and-paste hackjob?

 

If you're a non-theist and interested in creationism, you're like the black guy admitted to the whites-only country club: a curious anomaly among the sea of white faces. They might welcome you in one way because your presence validates some of their lunacy, but follow the politics, follow the money: non-theists are most certainly not their core audience or fanbase.

 

Instead of emailing creationist talking heads, most of whom do not hold degrees in biology and almost none of whom appear in any peer-reviewed journals, why don't you email actual real biologists? Or read biology sites or books about actual biology? A few pages back I linked to a botanical group's statement about creationism. You should not need to prop yourself up with creationist screeds if the science holds up. That's where the Dover school board fell down: in assessing creationism's worthiness as real science, they did not consult any actual, you know, scientists.

 

You're right: it's science that makes or breaks creationism's claims. And creationism has ZERO. NONE. NADA. Not a single peer-reviewed independent introduction of any new knowledge or truth into the human experience.

 

It really sounds like you're straining hard to find something, ANYthing, that props up this last religious holdover in your head. I can understand that. I was the same way about the death penalty.

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I didn't link to a 'paper'.   I linked to an article, as I clearly stated.  You are the one that called it a paper.  I linked to it, mainly to provide some information regarding the Type III SS.   I know it's not a peer- reviewed paper. It's an article that had the relevant information regarding the Type  III.  

 

Except it's not relevant, really. It's the same thing as me saying that invisible faeries designed the Honda Accord, and then providing a detailed parts list for the car, with the sentence "I think it's obvious that invisible faeries designed it" tacked on the end. It's a distraction. It doesn't show any evidence of purposeful design or a designer. You're so hung up on the intricacies of this one thing that you think can prove your case, you're losing sight of the fact that no one can provide anything that actually shows the evidence you're looking for.

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What Akheia said.

 

(Oooh. I feel vaguely sick. I probably shouldn't be doing this over lunch...  ezhappydead.gif )

I guess, as a chaser to that parasites thing, everything doesn't have to be all grim and hopeless without someone engineering all life on Earth (I imagine it would be grimmer WITH, for reasons outlined above). I mean, by definition, we're all winners! Life's tough, scrappy stuff.

The human animal is so cool!

.
There's wonder, not horror, in life on Earth without a designer, because, without one, you can take things as they are, without worrying about their morality. Example, Bald Eagles (Haliaeetus leucocephalus): there's
(pretty brutal); yet
(wow!).
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I'm still here, guys!  (Just taking a bit of a back seat, as BC and I have agreed to do.)

 

But if you want any help with the anti-Big Bang pseudoscience, then just holler. 

I'm currently maintaining a holding pattern...

Keeping myself up to date with this thread, but waiting on BC to get back to me when she's ready.

 

Thanks,

 

BAA.

Hey BAA- Let's present each other's positions as you suggested.  You go first (when you're ready) , and then I'll have a better idea how to do it. happydance.gif

 

Ok BC.

 

Possibly sometime later in the week.  Catch you then.

 

Bye!

 

 

BAA.

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