Evolution and Intelligent Design

[Pierson5]

I am not familiar enough with the body of literature to even guess. I'm not sure. I was merely focusing on this particular citation. Would you agree, however, that much of it is still undiscovered (origins unknown)?

then a fair question here is why are you attempting to discuss this subject?
To agree that much is "still undiscovered" Would presume a working knowlege of every component in order to assert the extent of what is left to be discovered right?

I am attempting to discuss the mostly "known" parts of this system. From previous citations it appears that some of this system is a still a mystery. Neither of us can use the "mystery" parts as evidence for evolution OR Intelligent Design. That's what I'm trying to establish.

So, examining each of these (identified) proteins would be a good start to determine how this system may have come about, correct?

ummm it would appear that so far it's a no. they have examined the proteins intently and still can't understand how they act in concert and much less about how they came to play that part.

Sure, researchers still don't have a complete understanding of how they act. But it appears some of the proteins have been identified as being responsible for these actions. Even if we don't understand the workings of the proteins in detail, maybe we can still try to figure out where they came from?

Are these proteins not performing 3D spatiotemporal control?

Are they performing their part in systematic control or are they the total cause? If you choose total cause then the question regresses to how they get to their positions in space and time. Fortunately, we don't have to worry about infinite regress. lol

I'm not sure I follow. The "total system" would be the collected formation of all the limbs in an organism, correct? So, this "part" of the system (e.g. thumb-pinky) would just be one piece. Each of the pieces (that we know of) function the same way to collectively make up the whole system, correct?

You were referencing the proteins. And the question is do you think the 'proteins' are performing as a part of a greater system or are they acting independantly? and if you think independantly then how do these proteins get to their specific positions to do their part?
Each of the pieces we do know about do not all function the same way. Have you read none of the reference papers I have cited?

I may have oversimplified it. By functioning in "the same way" I meant, they (proteins cited in this publication) are responsible for the formation of limbs. They may go about the formation in different ways, but that's not what I'm arguing. As you mentioned above, we may not understand the intricate details of how the system works, but maybe that's not necessary for determining the origin of the system.

When you say "how they get their positions in space and time," what are you referring to? The limbs, or the proteins responsible for the formation of them?

Proteins... the subject you refered to.

So this would be a pretty good way to test your hypothesis, correct? If we examine these proteins and the research shows they are irreducibly complex or have no evolutionary history, (unlike Behe's flagellum), that would be pretty good evidence for your hypothesis.

Let's see now you are;
hypothesizing that the sun orbits the earth and that there are undefined predictions to support the hypothesis which really doesn't help define anything for me.
And then you assert that daily observations indicate your hypothesis was correct. Hmmmm
So far you are in good company with some ancient peoples because for 1500 yrs or more the observable evidence backed their geocentric theory too.
Now you state some measurements contradict the hypothesis and it is repeatable. nice
In this case it appears that the hypothesis cannot be adjusted to fit the new data so it has no choice but to go into the hypothesis garbage bin. so far it has scientific method written all over it. To bad that the original 'theory' had enough evidence to make it a theory and enough believers to overlook some of the little things that didn't agree with it.

So it looks like you accept that astronomy does, in fact, employ the scientific method. The issue you have with my (oversimplified) example is the theory accepted before this type of experiment (and before the scientific method was popularized) was wrong.

The observable evidence of the sun rising every day was meant to be an example of a prediction. We could have used the stars/other planets revolving around the earth as a prediction supporting the geocentric model. Or, any of these:

Further, every star was on a "stellar" or "celestial" sphere, of which the earth was the center, that rotated each day, using a line through the north and south pole as an axis. The stars closest to the equator appeared to rise and fall the greatest distance, but each star circled back to its rising point each day. The second common notion supporting the geocentric model was that the Earth does not seem to move from the perspective of an Earth bound observer, and that it is solid, stable, and unmoving. In other words, it is completely at rest.

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

You have to remember, this was back in the 16th century. Galileo is considered the father of the scientific method.

The geocentric model held sway into the early modern age, but from the late 16th century onward was gradually superseded by the heliocentric model of Copernicus, Galileo and Kepler. However, the transition between these two theories met much resistance, not only from Christian theologians, who were reluctant to reject a theory that was in agreement with Bible passages (e.g. "Sun, stand you still upon Gibeon", Joshua 10:12 - King James 2000 Bible), but also from those who saw geocentrism as an accepted consensus that could not be subverted by a new, unknown theory.

In today's age, we don't have the pressure of risking our lives to publish new data, or go against the grain. It's actually encouraged. BUT, you need to have the evidence to support your hypothesis.

Theories change to accommodate new evidence. This is nothing new. If the evidence is contradictory (like was shown with the geocentric model) then it is thrown out for a theory that accurately accommodates the new evidence. The theory of gravity is a popular example of a theory changing to accommodate new evidence:

http://en.wikipedia.org/wiki/Gravitatio ... nal_theory

It has been altered a few times. Although, we don't find too many theory of gravity deniers.

[Pierson5]

I am quite aware of indirect testing. This type of testing presupposes the existence of what you are testing for and if you get a result that appears favorable then you infer the existence of what you presupposed. Got it. Know it. And yet you still did not provide any method to test the subjects I have been specifically pointing out at every turn;
How do you test for a single common ancestor of all life?
How do you test to show that mutation is actually random?
How do you test to see if NS can perform what they think it does?
So once again you avoid these specific topics and try to redirect the question at hand to other things.....

As far as the questions you keep proposing.

1. We've gone over the converging lines of evidence for the single common ancestor. You test for these things the same way you use the scientific method in the example I gave for astronomy earlier. Knowing what we know about genetics, germ theory, etc... If we all share a common ancestor, what should we expect to find when we examine other living organisms? If the genetic evidence was all over the place, this would be a problem for this hypothesis and for the ToE.

As opposed to ID. If ID is true, what should we expect to find? Whatever we find, "the designer just made it that way." Is not an acceptable answer and is unfalsifiable/not science.

2. Actually random? As opposed to what? Material causes (e.g. radiation)? Or mutations guided by a designer (e.g. variant of theistic evolution)? I don't think you are arguing for either of these, so I don't see the point of the question.

3. Not sure what you mean specifically about this one.

[timnerk]

I do not see much "conclusive" evidence for a type of macro-evolution. No theories or scientific principles appear to govern the relationship between mutation, selection, and the rise of new species. I'm not here to say it didn't happen. If it did, it really doesn't bother me. I am a Christian, but I do not see this as a problem for doctrine. It seems clear that the earth is really old. It seems clear that things change within limits. What seems muddled is this idea that change on earth appears to have no or few limits according to most evolutionary biologists. The mantra "natural selection, random mutation" becomes a god of it's own with limitless creating power. This seems acceptable to evolutionists, while the suggestion of an actual mind as the arbiter of "limitless creating power" is not acceptable.

There are those who claim to objectively collect evidence and form a conclusion. I believe there are few who actually do this. There are biases on both sides of the isle that are employed when these competing ideas about life are approached. But for the sake of argument I'll say that there are a few who are truly objective. What would the universe tell them about itself. Would they really come to believe in what Darwin said? Or, would they come to believe what Descartes said? It is difficult to answer this question objectively, because once one has made a decision for one side or the other objectivity is blurred on even the sharpest of minds. One starts defending a position, and their reputation and credibility come into play.

I think the idea of internal change is interesting. Not conclusive, but interesting nonetheless. External influence appears to fit some observations. I'm not going to make that case today, but I'll say this: the age of the earth, and evolutionary theory do not lead us to atheism. These things simply may be true or not in the mind of any thinker, yet God may continue or not, to exist. What appears to remain true, is that atheism is the only belief that necessitates atheism. Nothing else necessitates that there is no God, except for atheism itself.

[KBCid]

I am not familiar enough with the body of literature to even guess. I'm not sure. I was merely focusing on this particular citation. Would you agree, however, that much of it is still undiscovered (origins unknown)?

then a fair question here is why are you attempting to discuss this subject?
To agree that much is "still undiscovered" Would presume a working knowlege of every component in order to assert the extent of what is left to be discovered right?

I am attempting to discuss the mostly "known" parts of this system. From previous citations it appears that some of this system is a still a mystery. Neither of us can use the "mystery" parts as evidence for evolution OR Intelligent Design. That's what I'm trying to establish.

Your attempting to discuss a subject that you have not studied in any depth. How do you suppose that such an interaction will end?
From previous citations I have never stated that the system is still a mystery. The system is quite clear to me. The only mystery parts are those that have not been defined yet as part of the implementation for the system.
You can try to establish that 'mystery parts' aren't used as evidence, but you would first have to point to where I assert mystery parts as evidence. If you want to have an intellectual intercourse about this system you need to become familiar with how matter can be spatially and temporally controlled. What are the chances of that happening? the simplicity of the situation here is that I assert the existence of a system and provide the empirical evidences that point to that reality and you simply say I don't see it and claim that it is a mystery that will some day be figured out.

they have examined the proteins intently and still can't understand how they act in concert and much less about how they came to play that part.

Sure, researchers still don't have a complete understanding of how they act. But it appears some of the proteins have been identified as being responsible for these actions. Even if we don't understand the workings of the proteins in detail, maybe we can still try to figure out where they came from?

And researchers are doing just that. So all is well on the research front. However, knowing every nut and bolt of a system is not necessary to know what is required functionally to allow it to work.

You were referencing the proteins. And the question is do you think the 'proteins' are performing as a part of a greater system or are they acting independantly? and if you think independantly then how do these proteins get to their specific positions to do their part?
Each of the pieces we do know about do not all function the same way. Have you read none of the reference papers I have cited?

I may have oversimplified it. By functioning in "the same way" I meant, they (proteins cited in this publication) are responsible for the formation of limbs. They may go about the formation in different ways, but that's not what I'm arguing. As you mentioned above, we may not understand the intricate details of how the system works, but maybe that's not necessary for determining the origin of the system.

There is sufficient understanding to attempt a discussion of origins but origins is only one small aspect of the importance here. The origination point is the hypothetical part. The rest is system mechanics.

When you say "how they get their positions in space and time," what are you referring to? The limbs, or the proteins responsible for the formation of them?

Proteins... the subject you refered to.

So this would be a pretty good way to test your hypothesis, correct? If we examine these proteins and the research shows they are irreducibly complex or have no evolutionary history, (unlike Behe's flagellum), that would be pretty good evidence for your hypothesis.

Your not paying very good attention are you? so far you are the only one implying that proteins may be irreducibly complex or can't have history, both quite illogical with even a cursory understanding of the subject already past in discussion.
What is the difference between a screw and the car it is used in? If we are to discuss the subject then you need to understand the subject or you will keep making erronious statements.
Also lets be clear on the Behe point, His concepts have not been refuted they are believed to have been hypothetically overcome.
Irreducible complexity is a normal part of intelligently designed structures and imagining that such formations can evolve in a stepwise fashion is handwaving without evidence.
I will also point out that the ones doing the imagining of how to overcome the Behe point now have one more thing to explain before they can really overcome his argument. How does the spaciotemporally controlled matter that forms a flagellum change its spatiotemporally controlled position from a previous controlled position elsewhere in the organism (since they assume that multiple parts simply got repurposed). Would you like to try and give that answer a shot?
It would be interesting to actually hear someone try to define how 3 dimensionally controlled and specified arrangements of matter could all converge spatially where they would need to occur and at the times in the actual formation process when they would need to appear in order to build a functional flagellum.
Give it a try see if you can logically explain how such a thing is possible. I would love to delve into how 3 dimensional controlled matter can conceptually be rearranged. We are far beyond 'simple plasm' here but you can't learn if you don't try.

so far it has scientific method written all over it. To bad that the original 'theory' had enough evidence to make it a theory and enough believers to overlook some of the little things that didn't agree with it.

So it looks like you accept that astronomy does, in fact, employ the scientific method. The issue you have with my (oversimplified) example is the theory accepted before this type of experiment (and before the scientific method was popularized) was wrong.

I accept just about anything that comes from the scientific method. If at any time astronomy or geology or any of a number of disciplines produces information in this manner then all is good. However, when it doesn't then I don't accept it.

You have to remember, this was back in the 16th century. Galileo is considered the father of the scientific method.

I know the story quite well. Don't you find it kind of odd that intelligence had to evolve such a concept? I wonder how anyone actually knew anything prior to him since he concieved how to actually know something.

In today's age, we don't have the pressure of risking our lives to publish new data, or go against the grain. It's actually encouraged. BUT, you need to have the evidence to support your hypothesis.

Now we just risk our livelihood.

Theories change to accommodate new evidence. This is nothing new. If the evidence is contradictory (like was shown with the geocentric model) then it is thrown out for a theory that accurately accommodates the new evidence. The theory of gravity is a popular example of a theory changing to accommodate new evidence

Theories are only allowed to change within the philisophical parameters that is imposed on the method. NAturalism is what is currently being imposd therefore a theory can never include intelligent design.

[Pierson5]

I am not familiar enough with the body of literature to even guess. I'm not sure. I was merely focusing on this particular citation. Would you agree, however, that much of it is still undiscovered (origins unknown)?

then a fair question here is why are you attempting to discuss this subject?
To agree that much is "still undiscovered" Would presume a working knowlege of every component in order to assert the extent of what is left to be discovered right?

I am attempting to discuss the mostly "known" parts of this system. From previous citations it appears that some of this system is a still a mystery. Neither of us can use the "mystery" parts as evidence for evolution OR Intelligent Design. That's what I'm trying to establish.

...
You can try to establish that 'mystery parts' aren't used as evidence, but you would first have to point to where I assert mystery parts as evidence. If you want to have an intellectual intercourse about this system you need to become familiar with how matter can be spatially and temporally controlled. What are the chances of that happening? the simplicity of the situation here is that I assert the existence of a system and provide the empirical evidences that point to that reality and you simply say I don't see it and claim that it is a mystery that will some day be figured out.

Every time you ask/cite a question that has not been answered (to my knowledge) by the scientific community and claiming it as evidence for ID. Like the questions you ask below. I'm not sure if you are just trying to point out my ignorance on the subject, or if it's genuinely a question which has yet to be answered. An unanswered question is just that, an unanswered question.

Even in the quote directly below, you state there is still much that is not understood. These are the types of mysteries I'm referring to. Let's focus on what we know, so far, and go from there. I figured a good place to start was the citation we are discussing now.

they have examined the proteins intently and still can't understand how they act in concert and much less about how they came to play that part.

Sure, researchers still don't have a complete understanding of how they act. But it appears some of the proteins have been identified as being responsible for these actions. Even if we don't understand the workings of the proteins in detail, maybe we can still try to figure out where they came from?

And researchers are doing just that. So all is well on the research front. However, knowing every nut and bolt of a system is not necessary to know what is required functionally to allow it to work.

Sure.. I'm not talking about understanding how it functions completely. I'm talking about origins. It appears in this citation, a few proteins have been identified as part of this system. Can we focus on those?

You were referencing the proteins. And the question is do you think the 'proteins' are performing as a part of a greater system or are they acting independantly? and if you think independantly then how do these proteins get to their specific positions to do their part?
Each of the pieces we do know about do not all function the same way. Have you read none of the reference papers I have cited?

I may have oversimplified it. By functioning in "the same way" I meant, they (proteins cited in this publication) are responsible for the formation of limbs. They may go about the formation in different ways, but that's not what I'm arguing. As you mentioned above, we may not understand the intricate details of how the system works, but maybe that's not necessary for determining the origin of the system.

There is sufficient understanding to attempt a discussion of origins but origins is only one small aspect of the importance here. The origination point is the hypothetical part. The rest is system mechanics.

Origins is a small aspect of importance? I disagree. If the origin is from "a designer," that is VERY important. Nobel prize importance. You are claiming this system could have only come about from design. We are discussing origins.

When you say "how they get their positions in space and time," what are you referring to? The limbs, or the proteins responsible for the formation of them?

Proteins... the subject you refered to.

So this would be a pretty good way to test your hypothesis, correct? If we examine these proteins and the research shows they are irreducibly complex or have no evolutionary history, (unlike Behe's flagellum), that would be pretty good evidence for your hypothesis.

..
What is the difference between a screw and the car it is used in? If we are to discuss the subject then you need to understand the subject or you will keep making erronious statements.

Uhhh, Ok... If we use your car example: Lets say we take the screw and determine it has no evolutionary history and was poofed into existence magically. That would be evidence for design and evidence against evolution. Why can't we examine the proteins the same way? I don't understand why you don't think this is a good way to test your hypothesis...

Also lets be clear on the Behe point, His concepts have not been refuted they are believed to have been hypothetically overcome.
Irreducible complexity is a normal part of intelligently designed structures and imagining that such formations can evolve in a stepwise fashion is handwaving without evidence.
I will also point out that the ones doing the imagining of how to overcome the Behe point now have one more thing to explain before they can really overcome his argument. How does the spaciotemporally controlled matter that forms a flagellum change its spatiotemporally controlled position from a previous controlled position elsewhere in the organism (since they assume that multiple parts simply got repurposed). Would you like to try and give that answer a shot?
It would be interesting to actually hear someone try to define how 3 dimensionally controlled and specified arrangements of matter could all converge spatially where they would need to occur and at the times in the actual formation process when they would need to appear in order to build a functional flagellum.
Give it a try see if you can logically explain how such a thing is possible. I would love to delve into how 3 dimensional controlled matter can conceptually be rearranged. We are far beyond 'simple plasm' here but you can't learn if you don't try.

Here are the questions I was talking about earlier, if my first statement was confusing. If you have any problem with the data published regarding the flagellum, here you go: http://www.talkdesign.org/faqs/flagellum.html#update

Email the authors if you believe they are in error.

You have to remember, this was back in the 16th century. Galileo is considered the father of the scientific method.

I know the story quite well. Don't you find it kind of odd that intelligence had to evolve such a concept? I wonder how anyone actually knew anything prior to him since he concieved how to actually know something.

I don't find it odd at all. There were references to the scientific method in philosophy over the years, but, I would say, Galileo really perfected it. Superstition was a much more popular method of "knowing" prior to 16th century.

In today's age, we don't have the pressure of risking our lives to publish new data, or go against the grain. It's actually encouraged. BUT, you need to have the evidence to support your hypothesis.

Now we just risk our livelihood.

Ok...

Theories change to accommodate new evidence. This is nothing new. If the evidence is contradictory (like was shown with the geocentric model) then it is thrown out for a theory that accurately accommodates the new evidence. The theory of gravity is a popular example of a theory changing to accommodate new evidence

Theories are only allowed to change within the philisophical parameters that is imposed on the method. NAturalism is what is currently being imposd therefore a theory can never include intelligent design.

This again... You were so adamant earlier that the designer is not identified. Why the need to invoke the supernatural? Read through the Dover transcripts if you believe we should include the supernatural in the scientific method. I don't want to get into this again. Behe thought the same thing, and in court he admitted astrology would then fall into the category of "science."

[KBCid]

I am quite aware of indirect testing. This type of testing presupposes the existence of what you are testing for and if you get a result that appears favorable then you infer the existence of what you presupposed. Got it. Know it. And yet you still did not provide any method to test the subjects I have been specifically pointing out at every turn;
How do you test for a single common ancestor of all life?
How do you test to show that mutation is actually random?
How do you test to see if NS can perform what they think it does?
So once again you avoid these specific topics and try to redirect the question at hand to other things.....

As far as the questions you keep proposing. 1. We've gone over the converging lines of evidence for the single common ancestor.

No we have not.

You test for these things the same way you use the scientific method in the example I gave for astronomy earlier. Knowing what we know about genetics, germ theory, etc...

generalisations sound good but this is not an actual answer

If we all share a common ancestor, what should we expect to find when we examine other living organisms?

Isn't that the question needing a testable answer? If 'p' then 'x'. If our hypothetical 'single' common ancestor ever existed then all of the

systems that come from it would hypothetically exhibit what? What evidence should we expect to see in a test of a decendant that could 'only' be explainable by a single common ancestor concept?

Found: The Oldest Animal Ever on Planet Earth
Otavia antiqua could be the earliest human ancestor, predating the previous earliest known animal by tens of millions of years.
Our earliest evolutionary ancestor may have been found in the form of microscopic sponge-like organisms recently discovered inside extremely ancient African rocks. If that turns out to be so, it would displace animal life’s previous earliest known ancestor (unremarkably, another sponge-like “metazoan”) by predating it by perhaps 100 million years.
Otavia is thought to have lived in calm, shallow waters and fed on the bacteria and algae that was fairly abundant there.
Otavia didn’t evolve much, but perhaps it didn’t need to. The record shows that if the researchers are right, Otavia weathered at least two “snowball Earths,”
http://www.popsci.com/science/article/2 ... anet-earth

Things that make you go hmmmm. IF otavia didn't evolve much then how did we get here from there?
What experimental evidence did the researchers see that would lead them to think this could be the 'single common ancestor'?
Would it be the fact that this is the oldest organism found so far.
I would also question the point about what it ate. If it was eating bacteria and algae then how would it be the first common ancestor of all life?
isn't algae and bacteria living? What did it eat until its decendants mutated into the living forms of bacteria and algae that it could eat?
Well of course the answer would that that evolved too.
Isn't science wonderful?

If the genetic evidence was all over the place, this would be a problem for this hypothesis and for the ToE.

What specific genetic evidence is only explainable by a single common ancestor?

As opposed to ID. If ID is true, what should we expect to find? Whatever we find, "the designer just made it that way." Is not an

acceptable answer and is unfalsifiable/not science.

I don't believe I have ever heard an ID person state that. This ID person asserts that designed things exhibit specifiable types of information.

Now let me rephrase your strawman argument from the ID perspective;
If evolution is true, what should we expect to find? Whatever we find, "it just evolved that way" Is not an acceptable answer and is unfalsifiable/not science.

Ask anyone and they can confirm that every single thing scientists observe in life they attribute to evolution. Even in the case of things that are conceptually unrelated it is still considered evolution... convergent evolution... Yup the eye evolved multiple times. Flight evolved multiple times. If that doesn't explain things right then we can always assert Parallel evolution in which case the environment forced it to evolve that way.
How has any of this been tested by scientific method?

2. Actually random? As opposed to what? Material causes (e.g. radiation)? Or mutations guided by a designer (e.g. variant of theistic evolution)? I don't think you are arguing for either of these, so I don't see the point of the question.

What would logically be apposed to random? I know this is a tough question but give it a try. I would recommend you understand what random means prior to trying to determine what would be apposed to it;

random
1. Having no specific pattern, purpose, or objective
3. Of or relating to an event in which all outcomes are equally likely, as in the testing of a blood sample for the presence of a substance.
http://www.thefreedictionary.com/random

In biology
The modern evolutionary synthesis ascribes the observed diversity of life to natural selection, in which some random genetic mutations are retained

in the gene pool
http://en.wikipedia.org/wiki/Randomness#In_biology

Do you see the point yet?

3. Not sure what you mean specifically about this one.

Natural selection results in the reduction of genetic variation through the elimination of maladapted individuals and consequently of the mutations that caused the maladaptation.
http://en.wikipedia.org/wiki/Natural_se ... _synthesis

Isn't it strange that the same questions being asked repeatedly have never actually been answered by two respondents referring to them.

How 'artful dodgers' answer questions without answering them
How can some people answer a question without answering it, yet satisfy their listeners? A new study has explored this skill of 'artful dodging' and how to better detect it.
close attention to the relevance of speakers' answers with regard to the questions, or if the text of the correct question was visible to the listeners as the speaker responded. The ability to recognise a dodge more than doubled, from 39% without the text to 88% with the text.
"Still, our results suggest that in many cases, dodges cause sought-after and relevant information to go unspoken, with little awareness and few
consequences," added the authors. The study has been published online in the Journal of Experimental Psychology: Applied.
http://www.dnaindia.com/scitech/report_ ... em_1540385

[Ivellious]

Found: The Oldest Animal Ever on Planet Earth
Otavia antiqua could be the earliest human ancestor, predating the previous earliest known animal by tens of millions of years.
Our earliest evolutionary ancestor may have been found in the form of microscopic sponge-like organisms recently discovered inside extremely ancient African rocks. If that turns out to be so, it would displace animal life’s previous earliest known ancestor (unremarkably, another sponge-like “metazoan”) by predating it by perhaps 100 million years.
Otavia is thought to have lived in calm, shallow waters and fed on the bacteria and algae that was fairly abundant there.
Otavia didn’t evolve much, but perhaps it didn’t need to. The record shows that if the researchers are right, Otavia weathered at least two “snowball Earths,”
http://www.popsci.com/science/article/2 ... anet-earth

Things that make you go hmmmm. IF otavia didn't evolve much then how did we get here from there?
What experimental evidence did the researchers see that would lead them to think this could be the 'single common ancestor'?
Would it be the fact that this is the oldest organism found so far.
I would also question the point about what it ate. If it was eating bacteria and algae then how would it be the first common ancestor of all life?
isn't algae and bacteria living? What did it eat until its decendants mutated into the living forms of bacteria and algae that it could eat?
Well of course the answer would that that evolved too.
Isn't science wonderful?

This a bizarre and really poorly written/researched article, to say the least. Hardly any information is given, and once again we have a case of a journalist who misuses terminology and makes confusing statements that sound fine, but upon further inspection are just wrong.

If I understand the article correctly, I think what they are trying to say is that this organism is the oldest known relative of all animals. KBC, your lack of understanding of evolution and biology in general might lead you to believe that there is a discrepancy in evolutionary theory when they say that other organisms existed alongside octavia...But in fact octavia could have been the first multi-celled animal species on Earth (which would have evolved from bacteria). Algae is a plant, and therefore no animals would have evolved from it. Just like we have bacteria today, it is expected that the bacteria that evolved into octavia would still be around (as well as millions of other varieties of bacteria).

Also, your question about "why if octavia didn't evolve much did other animals develop" is also based on a lack of evolutionary understanding. Again, just because a species evolves from another does not mean that the predecessor species must die off in the process. For instance, it would seem as though octavia could have lived over a large amount of coastline. If natural selection gave rise to new variants of octavia in one part of the Earth due to a changing landscape or other environmental factors, this would have no effect on the survival of octavia a thousand miles away. Octavia might have thrived in a certain region for millions of years without any problem, but that doesn't mean evolution of octavia populations could not have occurred at all in other places.

[KBCid]

You can try to establish that 'mystery parts' aren't used as evidence, but you would first have to point to where I assert mystery parts as evidence. If you want to have an intellectual intercourse about this system you need to become familiar with how matter can be spatially and temporally controlled. What are the chances of that happening? the simplicity of the situation here is that I assert the existence of a system and provide the empirical evidences that point to that reality and you simply say I don't see it and claim that it is a mystery that will some day be figured out.

Every time you ask/cite a question that has not been answered (to my knowledge) by the scientific community and claiming it as evidence for ID. Like the questions you ask below. I'm not sure if you are just trying to point out my ignorance on the subject, or if it's genuinely a question which has yet to be answered. An unanswered question is just that, an unanswered question.

Setting up another strawman argument? What Does the observation of a 3D spatiotemporal control system have to do with ID? How could it possibly be evidence for ID?
The fact is that spatiotemporal control systems have been investigated quite well... there is no need to be ignorant about the subject simply because one scientific discipline hasn't studied it. Mine is not an argument from ignorance. You are free to study the subject at any time and no I won't hold your hand and lead you around to every citation on the subject.

Even in the quote directly below, you state there is still much that is not understood. These are the types of mysteries I'm referring to. Let's focus on what we know, so far, and go from there. I figured a good place to start was the citation we are discussing now.

they have examined the proteins intently and still can't understand how they act in concert and much less about how they came to play that part.

There is much you don't understand and is a mystery to you. This doen't mean that it is actually a mystery to everyone. This is the logic of "if I don't know it then its a mystery to everyone". Good luck with that one.

Sure, researchers still don't have a complete understanding of how they act. But it appears some of the proteins have been identified as being responsible for these actions. Even if we don't understand the workings of the proteins in detail, maybe we can still try to figure out where they came from?

And researchers are doing just that. So all is well on the research front. However, knowing every nut and bolt of a system is not necessary to know what is required functionally to allow it to work.

Sure.. I'm not talking about understanding how it functions completely. I'm talking about origins. It appears in this citation, a few proteins have been identified as part of this system. Can we focus on those?

If you aren't concerned about understanding how the system functions then what is there to discuss?
You want to try and discern the origin of the proteins that take part in the positioning process? I have a simple answer for you "they were transcribed and translated from the genome. Are you getting any further understanding about the system from that?

Spatiotemporal chemical dynamics in living cells: From information trafficking to cell physiology
Molecular sciences, including molecular biology, genomics, proteomics, and crystallography, have now described life in unprecedented depth and breadth. Yet these descriptions have not improved significantly the rate of drug discovery. Themolecular defect in sickle cell anemia was discovered nearly a half-century ago, yet in 50 years what treatments has this knowledge yielded?
The defects in oncogenes were found in the 1970s, and those in cystic fibrosis and Duchenne muscular dystrophy were discovered in the 1980s, but we have yet to see significant improvements in clinical care. Whatever scientific insights might have been gained, molecular science has not yielded sufficient insight to provide better care for patients.
So what have we missed? By so thoroughly embracing structural reductionism, we have learned a great deal about the system’s parts without really understanding how the system works. For example, a list of the capacitors, resistors, and the other functional parts found in a television set are not sufficient to deduce how a television works. As the parts list of the human genome is much longer than that of a television set, and the behavior of its components more subtle, it is not surprising that molecular biology has not yielded the anticipated cornucopia of new drugs. Living cells require networks of enzymes and receptors with large numbers of feedback loops under conditions held far from thermodynamic equilibrium. Therefore, the properties of individual isolated components can never adequately model the dynamic chemical processes that underlie cell functions. The part cannot explain the whole; to understand how all of the parts of a cell work in concert, the parts must be studied in their cell biological context at a time-scale relevant to the physico-chemical processes under study.
...the processes underlying cell behavior more closely resemble the decision making processes of a computer than the dynamics of a stirred
chemical reactor.
http://www.sownar.com/silvercluster/Spa ... iology.pdf

There is sufficient understanding to attempt a discussion of origins but origins is only one small aspect of the importance here. The origination point is the hypothetical part. The rest is system mechanics.

Origins is a small aspect of importance? I disagree. If the origin is from "a designer," that is VERY important. Nobel prize importance. You are claiming this system could have only come about from design. We are discussing origins.

If we are to discuss origins then it requires that we determine causes and effects.
The effect is the control of matter both spatially and temporally
Now you assert what you know that is capable of causing it.
This is how science works form a question then propose an answer and then test it. Simple stuff.

What is the difference between a screw and the car it is used in? If we are to discuss the subject then you need to understand the subject or you will keep making erronious statements.

Uhhh, Ok... If we use your car example: Lets say we take the screw and determine it has no evolutionary history and was poofed into existence magically. That would be evidence for design and evidence against evolution. Why can't we examine the proteins the same way? I don't understand why you don't think this is a good way to test your hypothesis...

How did you determine it has no evolutionary history?
It is obviously not a logical way to test the theory since the system in question reproduces 3 dimensional form. I would further point out that you cannot tell a manufactured / intelligently designed protein from any other type of proposed formation process.

Craig Venter creates synthetic life form
The new organism is based on an existing bacterium that causes mastitis in goats, but at its core is an entirely synthetic genome that was constructed from chemicals in the laboratory.
The single-celled organism has four "watermarks" written into its DNA to identify it as synthetic and help trace its descendants back to their creator, should they go astray.
http://www.guardian.co.uk/science/2010/ ... -life-form

This is why current intelligent designers had to put a watermark in the coding "to identify it as synthetic". So far your conceptual method is batting zero for the possibility of gaining knowlege.

Also lets be clear on the Behe point, His concepts have not been refuted they are believed to have been hypothetically overcome.
Irreducible complexity is a normal part of intelligently designed structures and imagining that such formations can evolve in a stepwise fashion is handwaving without evidence.
I will also point out that the ones doing the imagining of how to overcome the Behe point now have one more thing to explain before they can really overcome his argument. How does the spaciotemporally controlled matter that forms a flagellum change its spatiotemporally controlled position from a previous controlled position elsewhere in the organism (since they assume that multiple parts simply got repurposed). Would you like to try and give that answer a shot?
It would be interesting to actually hear someone try to define how 3 dimensionally controlled and specified arrangements of matter could all converge spatially where they would need to occur and at the times in the actual formation process when they would need to appear in order to build a functional flagellum.
Give it a try see if you can logically explain how such a thing is possible. I would love to delve into how 3 dimensional controlled matter can conceptually be rearranged. We are far beyond 'simple plasm' here but you can't learn if you don't try.

Here are the questions I was talking about earlier, if my first statement was confusing. If you have any problem with the data published regarding the flagellum, here you go: http://www.talkdesign.org/faqs/flagellum.html#update. Email the authors if you believe they are in error.

I have no problem with what they published. Hoewever, they are silent on this the point I just made. So if you believe they have adressed it then clip the part that works for you and we can discuss it.

I know the story quite well. Don't you find it kind of odd that intelligence had to evolve such a concept? I wonder how anyone actually knew anything prior to him since he concieved how to actually know something.

I don't find it odd at all. There were references to the scientific method in philosophy over the years, but, I would say, Galileo really perfected it. Superstition was a much more popular method of "knowing" prior to 16th century.

Superstition is still a popular method of "knowing". Doesn't mean that some people have not always discerned things in a more scientific way.

Theories are only allowed to change within the philisophical parameters that is imposed on the method. NAturalism is what is currently being imposd therefore a theory can never include intelligent design.

This again... You were so adamant earlier that the designer is not identified. Why the need to invoke the supernatural? Read through the Dover transcripts if you believe we should include the supernatural in the scientific method. I don't want to get into this again. Behe thought the same thing, and in court he admitted astrology would then fall into the category of "science."

What is supernatural about intelligence? are you supernatural? how does intelligence equate to supernatural?
Then define how naturalism can be tested by scientific method.

[KBCid]

...Otavia antiqua could be the earliest human ancestor...
Isn't science wonderful?

This a bizarre and really poorly written/researched article, to say the least. Hardly any information is given, and once again we have a case of a journalist who misuses terminology and makes confusing statements that sound fine, but upon further inspection are just wrong.

We can believe you based on your historic observations.

If I understand the article correctly, I think what they are trying to say is that this organism is the oldest known relative of all animals.

They were in fact saying just that. Which nullifies the statement "Our earliest evolutionary ancestor" since it would have to be just another in a line from the earliest ancestor of all life. If evolutionary hypothesis is logically followed through then all lineages trace their ancestry to one organism that was the "earliest evolutionary ancestor".

KBC, your lack of understanding of evolution and biology in general might lead you to believe that there is a discrepancy in evolutionary theory when they say that other organisms existed alongside octavia...But in fact octavia could have been the first multi-celled animal species on Earth (which would have evolved from bacteria). Algae is a plant, and therefore no animals would have evolved from it. Just like we have bacteria today, it is expected that the bacteria that evolved into octavia would still be around (as well as millions of other varieties of bacteria).

The discrepancy I was pointing out was the word play on "Our earliest evolutionary ancestor" since the earliest would be the single common ancestor of life. Of course this is only obvious if you noticed the discrepancy too.

Also, your question about "why if octavia didn't evolve much did other animals develop" is also based on a lack of evolutionary understanding.

It was a rhetorical question. The hidden question was "how could it be worded as the earliest human ancestor if it was not alone".

Of course a good point to ponder here is that if it was just another step in the chain and it was the result of a small stepwise change then why don't we see its ancestors as fossils? Or do you think that maybe this is the step from single to multicellularity?
If so how would you rationalise its ability to repeat the organization of its new 3 dimensional macro architecture?
Let me reword that; How do cells become 3 dimensionally arranged into functional forms and reproduce that arrangement?
One small step for single cells and one gigantic leap in spatiotemporal control of matter. It just evolved...

[sandy_mcd]

NAturalism is what is currently being imposd therefore a theory can never include intelligent design.

Science (and even naturalism) is capable of detecting design.
1) Design by an alien intelligence could be detectable and is consistent with both. Perhaps we could find remnants of their machines, maybe even still functional which would let us design living things.
2) Design by a supernatural entity might be detectable. For example, if some scientist discovered that our chromosomes had little tags which spelled out our parents names in their native tongues, that would be pretty good evidence for a supernatural designer.
So it is false to say the intelligent design can't be included.
But noting (as has been known for years) that some sort of complex spatiotemporal control of development is necessary does not constitute scientific evidence of either natural or supernatural intelligent design.

[Pierson5]

You can try to establish that 'mystery parts' aren't used as evidence, but you would first have to point to where I assert mystery parts as evidence. If you want to have an intellectual intercourse about this system you need to become familiar with how matter can be spatially and temporally controlled. What are the chances of that happening? the simplicity of the situation here is that I assert the existence of a system and provide the empirical evidences that point to that reality and you simply say I don't see it and claim that it is a mystery that will some day be figured out.

Every time you ask/cite a question that has not been answered (to my knowledge) by the scientific community and claiming it as evidence for ID. Like the questions you ask below. I'm not sure if you are just trying to point out my ignorance on the subject, or if it's genuinely a question which has yet to be answered. An unanswered question is just that, an unanswered question.

Setting up another strawman argument? What Does the observation of a 3D spatiotemporal control system have to do with ID? How could it possibly be evidence for ID?
The fact is that spatiotemporal control systems have been investigated quite well... there is no need to be ignorant about the subject simply because one scientific discipline hasn't studied it. Mine is not an argument from ignorance. You are free to study the subject at any time and no I won't hold your hand and lead you around to every citation on the subject.

How is it a strawman? There are many things unknown about this system. You ask a few questions. I will admit I don't know the details about how this system functions. If your questions have answers, provide the citation after the question. If not, I don't see the point of asking a specific science question about your system that has yet to be answered by the scientific community. What is your point? Here is an unanswered question?

http://embryo.asu.edu/view/embryo:125126

Today those who study morphogenesis are asking many questions and trying to determine, for example, how tissues form from populations of cells, how tissues construct organs, how organs grow, how growth is coordinated, how migrating cells are oriented, and how polarity is achieved. The problem of morphogenesis is recognized by many to be one of the most elusive questions of development as it is intertwined with questions of regulation and how the organism functions as a whole.

I'm not asking you to teach me about the subject. I'm asking for the citation or research being done that concludes this is the product of biological design. You have posted many citations about how the system functions/works, but not one of them concludes that the system could not have come about through evolutionary processes, or is the product of biological design. Not a single one.

Even in the quote directly below, you state there is still much that is not understood. These are the types of mysteries I'm referring to. Let's focus on what we know, so far, and go from there. I figured a good place to start was the citation we are discussing now.

they have examined the proteins intently and still can't understand how they act in concert and much less about how they came to play that part.

There is much you don't understand and is a mystery to you. This doen't mean that it is actually a mystery to everyone. This is the logic of "if I don't know it then its a mystery to everyone". Good luck with that one.

See the citation above. I have never claimed that "I don't know, therefore nobody does." I'm merely going off of what I have read from other citations, like the one above.

Sure, researchers still don't have a complete understanding of how they act. But it appears some of the proteins have been identified as being responsible for these actions. Even if we don't understand the workings of the proteins in detail, maybe we can still try to figure out where they came from?

And researchers are doing just that. So all is well on the research front. However, knowing every nut and bolt of a system is not necessary to know what is required functionally to allow it to work.

Sure.. I'm not talking about understanding how it functions completely. I'm talking about origins. It appears in this citation, a few proteins have been identified as part of this system. Can we focus on those?

If you aren't concerned about understanding how the system functions then what is there to discuss?
You want to try and discern the origin of the proteins that take part in the positioning process? I have a simple answer for you "they were transcribed and translated from the genome. Are you getting any further understanding about the system from that?

I'm not trying to "understand the system." I'm trying to understand how you come to your conclusion. The ORIGIN of the system. I'm sure you will agree with me that we don't have to understand how something functions/is built to understand where it originated.

So these proteins obviously take part in this system. You say they were translated from the genome. Could they have come about through evolutionary processes?

Spatiotemporal chemical dynamics in living cells: From information trafficking to cell physiology
Molecular sciences, including molecular biology, genomics, proteomics, and crystallography, have now described life in unprecedented depth and breadth. Yet these descriptions have not improved significantly the rate of drug discovery. Themolecular defect in sickle cell anemia was discovered nearly a half-century ago, yet in 50 years what treatments has this knowledge yielded?
The defects in oncogenes were found in the 1970s, and those in cystic fibrosis and Duchenne muscular dystrophy were discovered in the 1980s, but we have yet to see significant improvements in clinical care. Whatever scientific insights might have been gained, molecular science has not yielded sufficient insight to provide better care for patients.
So what have we missed? By so thoroughly embracing structural reductionism, we have learned a great deal about the system’s parts without really understanding how the system works. For example, a list of the capacitors, resistors, and the other functional parts found in a television set are not sufficient to deduce how a television works. As the parts list of the human genome is much longer than that of a television set, and the behavior of its components more subtle, it is not surprising that molecular biology has not yielded the anticipated cornucopia of new drugs. Living cells require networks of enzymes and receptors with large numbers of feedback loops under conditions held far from thermodynamic equilibrium. Therefore, the properties of individual isolated components can never adequately model the dynamic chemical processes that underlie cell functions. The part cannot explain the whole; to understand how all of the parts of a cell work in concert, the parts must be studied in their cell biological context at a time-scale relevant to the physico-chemical processes under study.
...the processes underlying cell behavior more closely resemble the decision making processes of a computer than the dynamics of a stirred
chemical reactor.
http://www.sownar.com/silvercluster/Spa ... iology.pdf

And? Their goal is to understand the system and create new drugs. I am trying to determine the origin of the system, not how the system works. You have said and shown, many times, you understand how the system functions. But, you are going one step further and claiming to have the answer and evidence of the origin (biological design). That's what we are discussing.

There is sufficient understanding to attempt a discussion of origins but origins is only one small aspect of the importance here. The origination point is the hypothetical part. The rest is system mechanics.

Origins is a small aspect of importance? I disagree. If the origin is from "a designer," that is VERY important. Nobel prize importance. You are claiming this system could have only come about from design. We are discussing origins.

If we are to discuss origins then it requires that we determine causes and effects.
The effect is the control of matter both spatially and temporally
Now you assert what you know that is capable of causing it.
This is how science works form a question then propose an answer and then test it. Simple stuff.

Going off of your citation, researches have identified the cause of a few parts of the system. The proteins we are discussing. The proteins are CAUSING the formation of the limbs to form (EFFECT). Let's take this cause, research it, and see where it came from. If it evolved, we should find evidence of that, if it did not evolve, we should find evidence for IC.

What is the difference between a screw and the car it is used in? If we are to discuss the subject then you need to understand the subject or you will keep making erronious statements.

Uhhh, Ok... If we use your car example: Lets say we take the screw and determine it has no evolutionary history and was poofed into existence magically. That would be evidence for design and evidence against evolution. Why can't we examine the proteins the same way? I don't understand why you don't think this is a good way to test your hypothesis...

How did you determine it has no evolutionary history?
It is obviously not a logical way to test the theory since the system in question reproduces 3 dimensional form. I would further point out that you cannot tell a manufactured / intelligently designed protein from any other type of proposed formation process.

Obviously I'm not an evolutionary biologist. You are involved in academia, propose your question to a professor in the biology department. You are free to study the subject at any time and no I won't hold your hand and lead you around to every citation on the subject.

Why don't we take a look at what other researchers have concluded. If they conclude the system came about through evolutionary history, then you can contact them and voice your concerns about the methods they used to determine it. If they conclude it is not possible to come about through evolution (IC), then there you go, evidence for your side.

Also lets be clear on the Behe point, His concepts have not been refuted they are believed to have been hypothetically overcome.
Irreducible complexity is a normal part of intelligently designed structures and imagining that such formations can evolve in a stepwise fashion is handwaving without evidence.
I will also point out that the ones doing the imagining of how to overcome the Behe point now have one more thing to explain before they can really overcome his argument. How does the spaciotemporally controlled matter that forms a flagellum change its spatiotemporally controlled position from a previous controlled position elsewhere in the organism (since they assume that multiple parts simply got repurposed). Would you like to try and give that answer a shot?
It would be interesting to actually hear someone try to define how 3 dimensionally controlled and specified arrangements of matter could all converge spatially where they would need to occur and at the times in the actual formation process when they would need to appear in order to build a functional flagellum.
Give it a try see if you can logically explain how such a thing is possible. I would love to delve into how 3 dimensional controlled matter can conceptually be rearranged. We are far beyond 'simple plasm' here but you can't learn if you don't try.

Here are the questions I was talking about earlier, if my first statement was confusing. If you have any problem with the data published regarding the flagellum, here you go: http://www.talkdesign.org/faqs/flagellum.html#update. Email the authors if you believe they are in error.

I have no problem with what they published. Hoewever, they are silent on this the point I just made. So if you believe they have adressed it then clip the part that works for you and we can discuss it.

You have no problem with what they published? The paper and citations are on the evolution of the flagellum. This is the exact opposite of the conclusion you are coming to. Again, you are proposing a question

How does the spaciotemporally controlled matter that forms a flagellum change its spatiotemporally controlled position from a previous controlled position elsewhere in the organism (since they assume that multiple parts simply got repurposed).

Why don't you go ahead and email the authors your concern. Their conclusion is obviously wrong in your eyes. I'll say again, we don't need to understand the intricate details of how something works to have an understanding of how it originated.

I know the story quite well. Don't you find it kind of odd that intelligence had to evolve such a concept? I wonder how anyone actually knew anything prior to him since he concieved how to actually know something.

I don't find it odd at all. There were references to the scientific method in philosophy over the years, but, I would say, Galileo really perfected it. Superstition was a much more popular method of "knowing" prior to 16th century.

Superstition is still a popular method of "knowing". Doesn't mean that some people have not always discerned things in a more scientific way.

Of course not. But the scientific way of thinking wasn't really popularized until much later.

Theories are only allowed to change within the philisophical parameters that is imposed on the method. NAturalism is what is currently being imposd therefore a theory can never include intelligent design.

This again... You were so adamant earlier that the designer is not identified. Why the need to invoke the supernatural? Read through the Dover transcripts if you believe we should include the supernatural in the scientific method. I don't want to get into this again. Behe thought the same thing, and in court he admitted astrology would then fall into the category of "science."

What is supernatural about intelligence? are you supernatural? how does intelligence equate to supernatural?
Then define how naturalism can be tested by scientific method.

As Sandy pointed out, the method does a pretty good job of detecting intelligence now. You have provided your own examples earlier in this thread of researchers determining if something was designed or not, so I think you'll agree. If not, why don't you give us an example of an experiment using a better method than the scientific method to determine what you are proposing. Testing naturalism with the scientific method has nothing to do with this. As I've pointed out SEVERAL times, not everyone who accepts evolution is a naturalist. Miller - Catholic, Dr. Robbert T. Bakker - Minister.

[KBCid]

You can try to establish that 'mystery parts' aren't used as evidence, but you would first have to point to where I assert mystery parts as evidence. If you want to have an intellectual intercourse about this system you need to become familiar with how matter can be spatially and temporally controlled. What are the chances of that happening? the simplicity of the situation here is that I assert the existence of a system and provide the empirical evidences that point to that reality and you simply say I don't see it and claim that it is a mystery that will some day be figured out.

Every time you ask/cite a question that has not been answered (to my knowledge) by the scientific community and claiming it as evidence for ID. Like the questions you ask below. I'm not sure if you are just trying to point out my ignorance on the subject, or if it's genuinely a question which has yet to be answered. An unanswered question is just that, an unanswered question.

Setting up another strawman argument? What Does the observation of a 3D spatiotemporal control system have to do with ID? How could it possibly be evidence for ID?
The fact is that spatiotemporal control systems have been investigated quite well... there is no need to be ignorant about the subject simply
because one scientific discipline hasn't studied it. Mine is not an argument from ignorance. You are free to study the subject at any time and no I won't hold your hand and lead you around to every citation on the subject.

How is it a strawman?

When you assert that I am pointing to mystery parts as evidence for ID. Spatiotemporal control of matter is not a mystery.

There are many things unknown about this system.

No there are not.

You ask a few questions. I will admit I don't know the details about how this system functions.

You are quite correct. 'YOU' don't understand it.

If your questions have answers, provide the citation after the question. If not, I don't see the point of asking a specific science question about your system that has yet to be answered by the scientific community. What is your point? Here is an unanswered question?

Intelligent life has been spatiotemporally controlling matter since before recorded history. You are part of that group. Do you require a scientist to explain to you how you perform that action? If you need someone to explain how this works to you and you are already one of the few intelligent agencies that performs the very action you are questioning then the question is begged for how it could be explained to you.

I'm not asking you to teach me about the subject. I'm asking for the citation or research being done that concludes this is the product of biological design.

I am not making the assertion "this is the product of biological design"

You have posted many citations about how the system functions/works, but not one of them concludes that the system could not have come about through evolutionary processes, or is the product of biological design. Not a single one.

Because the only answer currently allowed is natural causes which they can't show has the capability of forming such a system which is why they simply consider it an unknown or a mystery that they hope will one day be solved. By philosophically limiting the range of possible answers allowed there will always be unsolvable mysteries that will conceptually someday be answered.

There is much you don't understand and is a mystery to you. This doen't mean that it is actually a mystery to everyone. This is the logic of "if I don't know it then its a mystery to everyone". Good luck with that one.

See the citation above. I have never claimed that "I don't know, therefore nobody does." I'm merely going off of what I have read from other citations, like the one above.

To which we can continue with the same rationale that "if the people I trust to know an answer don't currently know it then no one knows it".

If you aren't concerned about understanding how the system functions then what is there to discuss?
You want to try and discern the origin of the proteins that take part in the positioning process? I have a simple answer for you "they were transcribed and translated from the genome. Are you getting any further understanding about the system from that?

I'm not trying to "understand the system." I'm trying to understand how you come to your conclusion. The ORIGIN of the system.

.

Then why propose studying the proteins to get a clue to origins if all you want is to know how I form conclusions? I form conclusions based on scientific understanding and logic.
I conclude that the spatiotemporal system of controlling matter is necessary for the replication of living forms and that it could not evolve since it is irreducibly complex. Pretty simple. Have stated this numerous times. What part do you fail to comprehend.

I'm sure you will agree with me that we don't have to understand how something functions/is built to understand where it originated.

I'm sure I don't agree. Understanding how the components of crystaline structures function / are built allows for the understanding of 'how' their structures can possibly originate and logically infer 'where' they could originate. In the living system we have investigated the components and it has been determined that there is no natural tendency for cells or their components to become arranged in a particular pattern so one must look beyond the individual parts to discern sytematic control. In order to understand where something could come from you would have to know causes and effects. What cause have you observed that makes matter operate in a spatiotemporally ordered way?.

So these proteins obviously take part in this system. You say they were translated from the genome. Could they have come about through evolutionary processes?

What evolutionary process was available prior to a replication system? This is precisely why you can't discern the origin of a system by analyzing a single component. This is also where your failure to comprehend the system being discussed causes you to keep asking erronious questions such as this. The fact is that the protein components are controlled in time and space just as they help do their part in the control of other structural formations. They are components that are controlled systematically. read the following again;

Spatiotemporal chemical dynamics in living cells: From information trafficking to cell physiology
Molecular sciences, including molecular biology, genomics, proteomics, and crystallography, have now described life in unprecedented depth and breadth. Yet these descriptions have not improved significantly the rate of drug discovery.
So what have we missed? By so thoroughly embracing structural reductionism, we have learned a great deal about the system’s parts without really understanding how the system works. For example, a list of the capacitors, resistors, and the other functional parts found in a television set are not sufficient to deduce how a television works. As the parts list of the human genome is much longer than that of a television set, and the behavior of its components more subtle, it is not surprising that molecular biology has not yielded the anticipated cornucopia of new drugs. Living cells require networks of enzymes and receptors with large numbers of feedback loops under conditions held far from thermodynamic equilibrium. Therefore, the properties of individual isolated components can never adequately model the dynamic chemical processes that underlie cell functions. The part cannot explain the whole; to understand how all of the parts of a cell work in concert, the parts must be studied in their cell biological context at a time-scale relevant to the physico-chemical processes under study.
...the processes underlying cell behavior more closely resemble the decision making processes of a computer than the dynamics of a stirred
chemical reactor.
http://www.sownar.com/silvercluster/Spa ... iology.pdf

And? Their goal is to understand the system and create new drugs. I am trying to determine the origin of the system, not how the system works. You have said and shown, many times, you understand how the system functions. But, you are going one step further and claiming to have the answer and evidence of the origin (biological design). That's what we are discussing.

If you wish to understand the origin of something you must first understand cause and effect. Until you realise that you can't comprehend a cause until you comprehend the effect then you will be in a constant state of ignorance for both understandings.

If we are to discuss origins then it requires that we determine causes and effects.
The effect is the control of matter both spatially and temporally
Now you assert what you know that is capable of causing it.
This is how science works form a question then propose an answer and then test it. Simple stuff.

Going off of your citation, researches have identified the cause of a few parts of the system. The proteins we are discussing.

No they have not identified the cause yet. They have found components that take part in an action.

The proteins are CAUSING the formation of the limbs to form (EFFECT). Let's take this cause, research it, and see where it came from. If it evolved, we should find evidence of that, if it did not evolve, we should find evidence for IC.

The proteins take part in CAUSING the formation of the limbs to help produce the EFFECT. The proteins have been researched and they all come from DNA transcription and translation and that is the end of the line for what can be determined for their part in the system. In order to determine their cause now requires the explanation for the origin of DNA. So how does DNA keep originating in every descendant? How did your DNA originate? Was it a chance occurance? All of these questions require a logical explanation that you can't discern by the observable evidence of a component performing an action.

How did you determine it has no evolutionary history?
It is obviously not a logical way to test the theory since the system in question reproduces 3 dimensional form. I would further point out that you cannot tell a manufactured / intelligently designed protein from any other type of proposed formation process.

Obviously I'm not an evolutionary biologist. You are involved in academia, propose your question to a professor in the biology department. You are free to study the subject at any time and no I won't hold your hand and lead you around to every citation on the subject.

Then why are you attempting to discuss this subject? My questions have been posed. I don't need to study the subject to gain understanding as I have already done that and I didn't need any handholding to do it.

Why don't we take a look at what other researchers have concluded. If they conclude the system came about through evolutionary history, then you can contact them and voice your concerns about the methods they used to determine it. If they conclude it is not possible to come about through evolution (IC), then there you go, evidence for your side.

We have taken a look and in every case they conclude that they don't know... refer to what has already been cited. I have also cited material from other researchers that have dealt with similar subjects that conclude a requirment for design. So your position is not based on what others have said it is based on a foundational assumption of what you believe is possible and you only accept input from others who hold the same belief.

I have no problem with what they published. Hoewever, they are silent on this the point I just made. So if you believe they have adressed it then clip the part that works for you and we can discuss it.

You have no problem with what they published? The paper and citations are on the evolution of the flagellum. This is the exact opposite of the conclusion you are coming to. Again, you are proposing a question

Their conclusion is based on a hypothetical possibility not an empirical answer. Their conclusion is based soley on their own hypothetical possibility that has not adressed the spatiotemporal control system so their conclusion is based on an argument from ignorance. I will restate this so pay attention;

How does the spaciotemporally controlled matter that forms a flagellum change its spatiotemporally controlled position from a previous controlled position elsewhere in the organism (since they assume that multiple parts simply got repurposed). Would you like to try and give that answer a shot?
When you can show that 'they' have adressed this point then we can include their hypothetical assumptions for review. Till then you and they are handwaving.

How does the spaciotemporally controlled matter that forms a flagellum change its spatiotemporally controlled position from a previous controlled position elsewhere in the organism (since they assume that multiple parts simply got repurposed).

Why don't you go ahead and email the authors your concern. Their conclusion is obviously wrong in your eyes. I'll say again, we don't need to understand the intricate details of how something works to have an understanding of how it originated.

I have sent my paper to numerous places on the evo side and so far no reply.
You can say things a million times... it doesn't make it true and as near as I can tell you are neither a biologist or an engineer so how would you know what is required to determine origins of anything. Maybe you should cite a paper that defines what is required to to make an origins determination since it is likely that you didn't write your own.

Theories are only allowed to change within the philisophical parameters that is imposed on the method. Naturalism is what is currently being imposed therefore a theory can never include intelligent design.

This again... You were so adamant earlier that the designer is not identified. Why the need to invoke the supernatural? Read through the Dover transcripts if you believe we should include the supernatural in the scientific method. I don't want to get into this again. Behe thought the same thing, and in court he admitted astrology would then fall into the category of "science."

What is supernatural about intelligence? are you supernatural? how does intelligence equate to supernatural?
Then define how naturalism can be tested by scientific method.

As Sandy pointed out, the method does a pretty good job of detecting intelligence now.

This does not answer why intelligence = supernatural to you. I am certainly not inferring that intelligence is supernatural.

You have provided your own examples earlier in this thread of researchers determining if something was designed or not, so I think you'll agree. If not, why don't you give us an example of an experiment using a better method than the scientific method to determine what you are proposing.

My proposition is that intelligence can be tested and that it can leave telltale signatures of its having acted that are discernable.

Testing naturalism with the scientific method has nothing to do with this. As I've pointed out SEVERAL times, not everyone who accepts evolution is a naturalist. Miller - Catholic, Dr. Robbert T. Bakker - Minister.

Naturalism is the only accepted philosophy used to explain how things came to exist. If you can't or won't test it then what makes it scientific?
There are a number of people who participate in the field of study who hold differing beliefs however, this doesn't eliminate the fact that they can't submit a paper based on their beliefs as apposed to others who do believe in naturalism that can submit papers based on that belief.

[KBCid]

NAturalism is what is currently being imposd therefore a theory can never include intelligent design.

Science (and even naturalism) is capable of detecting design.

Really what is their criteria?

1) Design by an alien intelligence could be detectable and is consistent with both. Perhaps we could find remnants of their machines, maybe even still functional which would let us design living things.

What if living things are the machines that were left behind?

2) Design by a supernatural entity might be detectable. For example, if some scientist discovered that our chromosomes had little tags which spelled out our parents names in their native tongues, that would be pretty good evidence for a supernatural designer.
So it is false to say the intelligent design can't be included.

Then try submitting a paper that is friendly to ID and see how that turns out. Remember they consider ID untestable. So how can design be both detectable according to you and untestable according to mainstream science? In the science I use if you can detect something then it is testable.

But noting (as has been known for years) that some sort of complex spatiotemporal control of development is necessary does not constitute scientific evidence of either natural or supernatural intelligent design.

Then you know of a way that natural causes can form such a control system? and why does design have to = supernatural? If some other intelligent agent found the things we sent to mars does that make us supernatural too?
the old strawman supernatural ploy... it just never gets old for them and they never explain why they use it.

[snorider]

Evolution is a theory, so is gravity.
It's a theory that has survived many tenacious tests by many institutions over a long period of time.

There is a reason why creationism is not taught in schools.
http://en.wikipedia.org/wiki/Kitzmiller ... l_District
http://video.google.com/videoplay?docid ... 2613200911

[KBCid]

Evolution is a theory, so is gravity. It's a theory that has survived many tenacious tests by many institutions over a long period of time.

The geocentric theory lasted for 15 centuries so length of time is no rationale for correctness.
Fallacy: Appeal to Tradition
Appeal to Tradition is a fallacy that occurs when it is assumed that something is better or correct simply because it is older, traditional, or "always has been done."
http://www.nizkor.org/features/fallacie ... ition.html

There is a reason why creationism is not taught in schools.

So why isn't ID taught? remember this thread is Evolution and intelligent design