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  Topic: Evolution of the horse; a problem for Darwinism?, For Daniel Smith to present his argument< Next Oldest | Next Newest >  
oldmanintheskydidntdoit



Posts: 4999
Joined: July 2006

(Permalink) Posted: Oct. 07 2007,06:25   

Quote (Daniel Smith @ Oct. 07 2007,05:59)
I think similar levels of detail can be found in the earth's various systems in regards to their near perfect fitness for life.  Also, the cosmos, the sun, the moon, all these things are so arranged and physical properties so ordered as to be perfect for life on this planet as well.  Certainly atomic principles and the composition of matter and energy are also remarkable.  The properties of water, carbon, oxygen, hydrogen, light, gravity, etc. are all things which appear to behave as if planned out in advance for the purpose of life on this planet.  I can't think of anything that just appears to be random.  Can you?

So I guess my example would be to compare a human laboratory - where man provides a controlled environment for certain lifeforms to reside - to the earth and its environment.

Well, what about the rest of the known universe. In the entire volume of the known universe this planet hosts the only known lifeforms.

Therefore the composition of "matter and energy" may seem remarkable to you for hosting life as we know it, but to me it seems more remarkable that this same matter and energy configuration appears to only host that life at one particular locus. Why would that be, if that configuration is explicitly designed to foster life as we know it?
More remarkable is the lack of ET then the finding of it here, if indeed our particular solar system is designed and the rules are designed, why not the planet next door? Why is Mars not thriving? It's very earth like, at least as good as we're gonna get anytime soon in person. Hollywood are already there!

If it was all planned out in advance, why for only 1 planet in the known universe?

We've started to identify details about extrasolar planets now. Photos even.

What does your theory say about life elsewhere in the universe? Predicts it? Y/N?

I suppose what I'm really asking Daniel, is do you consider the entire known universe intelligently designed for the purpose of hosting life on this planet?

I mean, if the solar system is designed, why stop there?

If it is designed, then why did it appear to end there?

--------------
I also mentioned that He'd have to give me a thorough explanation as to *why* I must "eat human babies".
FTK

if there are even critical flaws in Gauger’s work, the evo mat narrative cannot stand
Gordon Mullings

  
Reciprocating Bill



Posts: 4265
Joined: Oct. 2006

(Permalink) Posted: Oct. 07 2007,08:14   

Quote (Daniel Smith @ Oct. 07 2007,06:17)
Also, when people say that science cannot investigate God or the supernatural, that's not entirely correct.  Science can (and does) investigate claims of supernatural activity - so long as the supernatural activity is supposed to have affected the physical world...

This passage is correct, and also encapsulates the challenge you have set for yourself. I'll sharpen my earlier statement to reflect your comment: "The existence of God is not amenable to scientific investigation, because God can do anything, in any order, at any time, outside the constraints of natural law, and hence no empirical test can be devised to verify God's existence. However, specific claims regarding God's actions in the physical world can be put to empirical test."

One source of assertions regarding God's actions has been the Bible, which makes very specific, testable claims about the world as God created it (e.g. the age of the earth) and his actions within the world (creation of animals and human beings ex nihilo a few thousand years ago; a subsequent world wide flood). One reason why friction has arisen between those who are inclined to Biblical literalism and the advances of the natural sciences is that many Biblical claims about the actions of God CAN be tested, have been tested, and have been found to be obviously false.

However, you are not drawing from Biblical claims about God's actions (although I gather you once did). Your claims are much more sophisticated, and concern the origination of the astounding complexity we observe in the biological world. You don't find current theory about the origination of such complexity believable (for reasons you are happy to enumerate). You claim, instead, that the emergence of biological complexity was accomplished by an all knowing God.

Here you've already gone much beyond the claims of the intelligent design movement generally, as represented by Behe, Dembski, Meyer etc.  They have carefully avoided publicly speculating about the identity and nature of the designer, and have repeatedly declined to make any claims whatsoever regarding the designer's characteristics, modes of action, etc. Because they have been unwilling to propose a model of the design or of the designer, and claim they are solely interested in design detection, that brand of ID has been utterly incapable of generating unique testable predictions about future empirical findings, and fails to rise to the level of a an empirical science.

You've identified the designer. God is the designer. You've also offered some speculations about the manner in which he originated design: he did it by means of "front-loading" information into the genome or genomes of one or more early organisms, front-loading that reflected foreknowledge of the history of the world in all of its detail, as I described above. You see the outcome of that designer's actions in nature - "I find complex intricate systems analogous (but far superior) to power plants, factories with automated assembly lines, communication networks, super highway systems, waste management (with recycling!), and on and on."

OK, now a careful distinction: "Complex intricate systems analogous (but far superior) to power plants, factories with automated assembly lines, communication networks, super highway systems, waste management" are the phenomena that (you say) still demand explanation. Your explanation is that these complex systems were designed by an all knowing God. I think you can see that it would be circular to then point to those self-same "complex intricate systems" as proof that your explanation for their existence is correct - those complex systems that so amaze us all are the very phenomena that call for explanation in the first place. Poring over and expressing amazement at biological complexity, even if that complexity has been elucidated by science, is not itself a scientific activity.  

Rather, to rise to the level of a scientific assertion, your model must make testable empirical predictions that uniquely "put your theory at risk." That is, you must formulate predictions regarding future empirical findings that, if disconfirmed, indicate that the model from which those predictions arose must be modified or discarded. Because you have already asserted that the designer is an omnipotent, all knowing God, you have put yourself in the position of having to make specific predictions regarding God's actions in the world, predictions with power to put your model at risk of disconfirmation.

I think you will agree that this is a problem. It is inherent in the definition of any "God" of sufficient capability to set the entire universe into motion that there are no limitations upon his activities. As I stated earlier, God can do anything, anywhere, anytime, without constraint of the laws of physics. He even specified the laws of physics themselves. Given that, any empirical finding regarding his proposed actions in the world would appear to be compatible with the God hypothesis. Hence it falls to YOU, as you formulate your model of the origins of biological complexity in a scientific manner, to make statements about God's characteristics of sufficient specificity to predict future empirical findings regarding his actions in the world. These assertions must limit God's scope in some way, either based upon constraints (God can do this, but he can't do that) or upon other more intentional characteristics (God would do this, but wouldn't do that). It falls to you to do this before making the relevant observations, in such a way that subsequent disconfirmation would prompt you to conclude, "God does not have the characteristics I proposed."

That's a tall order. In a some respects you've already made some such assertions, although you haven't described how they arise from a specific model of God, or how to test them. Nevertheless, since front-loading is an action in the world, it is potentially testable. I could easily generate some unique testable predictions regarding future empirical findings that arise from front-loading. However, because I find front-loading implausible for reasons I have already described and believe such tests are likely to be a waste of time, it falls to YOU to devise unique empirical predictions that put your theory at risk and then conduct the relevant tests. Ideally, your predictions would put your assertions about God's actions in the world, and hence his characteristics, at risk, as well.

You've got your work cut out for you.

--------------
Myth: Something that never was true, and always will be.

"The truth will set you free. But not until it is finished with you."
- David Foster Wallace

"Here’s a clue. Snarky banalities are not a substitute for saying something intelligent. Write that down."
- Barry Arrington

  
JAM



Posts: 517
Joined: July 2007

(Permalink) Posted: Oct. 07 2007,13:27   

Quote (Daniel Smith @ Oct. 07 2007,05:46)
I think that I need to clarify my position before we can decide how best to test it.

I feel a breeze.
Quote
When I say "functional sequences" I mean functional as in "used within the cell".

That works for me.
Quote
By this definition, I'd say that anything that is transcribed would qualify as functional - since the cellular machinery is going through the trouble of transcribing it.

That is a prediction of an intelligent design hypothesis, but MET (non-Darwinian) predicts that there will be loads of RNA that has no function.
Quote
So this would include protein coding sequences as well as ncRNA sequences, and anything else that's transcribed.

But if we find anything that's transcribed but not functional, your hypothesis is dead, correct?
Quote
I also must clarify that I do actually believe that all functional sequences (as I've defined them) are evolutionarily constrained.  It's just that I don't think you can find functionality or constraint by comparing sequences to other lineages (since I posit that there are no truly neutral sites).

What if some sites have far greater rates of change over time, Daniel?

What sequences are used for forensic DNA analysis?
Quote
If comparing to other lineages, the function must first be known and then the entire sequence that provides that function compared.

Not a problem.
Quote
However, the only true test of constraint is comparison to ancestral DNA within the same lineage.

Oh-oh...it looks like I'm going to have to retract my retraction. Your prediction:
Quote
there are many functional sequences that are different (even radically so) amongst related lineages - this due to their being of designed, not mutational, origin.

makes clear predictions about the relationships between modern sequences. No ancestral sequences are required.

  
jeannot



Posts: 1201
Joined: Jan. 2006

(Permalink) Posted: Oct. 07 2007,13:47   

Quote
there are many functional sequences that are different (even radically so) amongst related lineages - this due to their being of designed, not mutational, origin.

That's unclear. How will you know that differences are not the result of mutations? Drift, positive selection and negative selection can lead to different level of divergence between regions.
And what to you mean by "being of designed origin"? Do new genes appear (from God knows where) instantaneously in a lineage? Or were they front loaded in the first cell?

  
Daniel Smith



Posts: 970
Joined: Sep. 2007

(Permalink) Posted: Oct. 08 2007,02:18   

Quote (JAM @ Oct. 07 2007,13:27)
           
Quote (Daniel Smith @ Oct. 07 2007,05:46)
I think that I need to clarify my position before we can decide how best to test it.

I feel a breeze.
             
Quote
When I say "functional sequences" I mean functional as in "used within the cell".

That works for me.
             
Quote
By this definition, I'd say that anything that is transcribed would qualify as functional - since the cellular machinery is going through the trouble of transcribing it.

That is a prediction of an intelligent design hypothesis, but MET (non-Darwinian) predicts that there will be loads of RNA that has no function.

Then this is what we need to test.
             
Quote

             
Quote
So this would include protein coding sequences as well as ncRNA sequences, and anything else that's transcribed.

But if we find anything that's transcribed but not functional, your hypothesis is dead, correct?

As for my hypothesis being "dead" if we find anything that conflicts with what I've predicted:  I don't really think that's fair since scientists are constantly finding things they don't expect and simply adjust their hypotheses to fit the evidence when they do.  I will not therefore totally abandon my hypothesis if the results are different, I will simply adjust it (unless the results completely shoot it out of the water).
             
Quote

             
Quote
I also must clarify that I do actually believe that all functional sequences (as I've defined them) are evolutionarily constrained.  It's just that I don't think you can find functionality or constraint by comparing sequences to other lineages (since I posit that there are no truly neutral sites).

What if some sites have far greater rates of change over time, Daniel?

This is precisely the issue.  How do we know the rate if it turns out that there are no neutral sites?  We must first determine that these sites are truly neutral and are actually accumulating mutations.
             
Quote


What sequences are used for forensic DNA analysis?

That's a tough question, and I'm not sure I know the best answer for that.
             
Quote

             
Quote
If comparing to other lineages, the function must first be known and then the entire sequence that provides that function compared.

Not a problem.
             
Quote
However, the only true test of constraint is comparison to ancestral DNA within the same lineage.

Oh-oh...it looks like I'm going to have to retract my retraction. Your prediction:              
Quote
there are many functional sequences that are different (even radically so) amongst related lineages - this due to their being of designed, not mutational, origin.

makes clear predictions about the relationships between modern sequences. No ancestral sequences are required.

I'm not backing off my original prediction, but I think certain terms mean different things to both of us, so I'm just trying to clarify.

I believe that most (if not all) sequences in a genome are functional and therefore resistive to mutation (constrained).  This means there are no neutral sites that are accumulating mutations.

I also believe that macroevolution (when it happens) is not the result of accumulating mutations but is rather; saltational - that is - it creates new types that may have sequences that are radically different from the sequences from which they diverged (hence my earlier prediction).

Therefore, this is what I expect:

1.  Sequence comparisons between related lineages will result in a mixture of like and unlike functional sequences.  

2.  Sequence comparisons within the same lineage will show evolutionary constraint across the board - even in what are presently considered neutral sites.

3.  What are presently considered neutral sites will be found to be "instructional" - that is, they will carry the instructions that tell the various proteins, RNA and enzymes where to go, when to go and what to do when they get there.

Now, the third prediction is more of a guess, but I think it makes sense.  We know about sequences that code for proteins, and we know about sequences that regulate them, but we don't know how a certain protein "knows" where to go, what to do and when to do it.  My guess is that these instructions are carried in what are presently considered neutral sites and - for that reason - these sites resist mutations just like all other evolutionarily constrained sites.

I hope that's clearer.

--------------
"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright

"The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

  
Daniel Smith



Posts: 970
Joined: Sep. 2007

(Permalink) Posted: Oct. 08 2007,02:34   

Quote (oldmanintheskydidntdoit @ Oct. 07 2007,06:25)
 
Quote (Daniel Smith @ Oct. 07 2007,05:59)
I think similar levels of detail can be found in the earth's various systems in regards to their near perfect fitness for life.  Also, the cosmos, the sun, the moon, all these things are so arranged and physical properties so ordered as to be perfect for life on this planet as well.  Certainly atomic principles and the composition of matter and energy are also remarkable.  The properties of water, carbon, oxygen, hydrogen, light, gravity, etc. are all things which appear to behave as if planned out in advance for the purpose of life on this planet.  I can't think of anything that just appears to be random.  Can you?

So I guess my example would be to compare a human laboratory - where man provides a controlled environment for certain lifeforms to reside - to the earth and its environment.

Well, what about the rest of the known universe. In the entire volume of the known universe this planet hosts the only known lifeforms.

Therefore the composition of "matter and energy" may seem remarkable to you for hosting life as we know it, but to me it seems more remarkable that this same matter and energy configuration appears to only host that life at one particular locus. Why would that be, if that configuration is explicitly designed to foster life as we know it?
More remarkable is the lack of ET then the finding of it here, if indeed our particular solar system is designed and the rules are designed, why not the planet next door? Why is Mars not thriving? It's very earth like, at least as good as we're gonna get anytime soon in person. Hollywood are already there!

If it was all planned out in advance, why for only 1 planet in the known universe?

We've started to identify details about extrasolar planets now. Photos even.

What does your theory say about life elsewhere in the universe? Predicts it? Y/N?

I suppose what I'm really asking Daniel, is do you consider the entire known universe intelligently designed for the purpose of hosting life on this planet?

I mean, if the solar system is designed, why stop there?

If it is designed, then why did it appear to end there?

I know it sounds like a cop-out but all designers make choices that many of us don't understand.  If we cannot directly ask a designer why they made certain choices, the best we can hope for is to examine their designs and try to make an educated guess based on what we observe.  

I can't do any more than guess as to "why" God did what he did, but my best guess is that he made life rare in the universe so that; as we delve more deeply into it's intricacies, we might become more keenly aware of the delicate and highly improbable balances required for it's mere existence and might be more deeply in awe of the mind that created - not only life - but the very conditions in which it thrives.

As for there being other lifeforms on other planets; we've already covered that in this thread and I made a couple predictions:

1.  That we won't find other planets with life on them.

and (to cover my butt),

2.  If we do find life elsewhere it will be remarkably similar to life on earth.

--------------
"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright

"The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

  
oldmanintheskydidntdoit



Posts: 4999
Joined: July 2006

(Permalink) Posted: Oct. 08 2007,02:57   

Quote (Daniel Smith @ Oct. 08 2007,02:34)
I know it sounds like a cop-out but all designers make choices that many of us don't understand.  If we cannot directly ask a designer why they made certain choices, the best we can hope for is to examine their designs and try to make an educated guess based on what we observe.

Then please make an educated guess as to the reason for the huge variety of beetle species.

--------------
I also mentioned that He'd have to give me a thorough explanation as to *why* I must "eat human babies".
FTK

if there are even critical flaws in Gauger’s work, the evo mat narrative cannot stand
Gordon Mullings

  
oldmanintheskydidntdoit



Posts: 4999
Joined: July 2006

(Permalink) Posted: Oct. 08 2007,02:59   

Quote (Daniel Smith @ Oct. 08 2007,02:34)
1.  That we won't find other planets with life on them.

So, as far as you are concerned the entire universe is here for your benefit?

That's some monstrous ego you've got going on there!

--------------
I also mentioned that He'd have to give me a thorough explanation as to *why* I must "eat human babies".
FTK

if there are even critical flaws in Gauger’s work, the evo mat narrative cannot stand
Gordon Mullings

  
Daniel Smith



Posts: 970
Joined: Sep. 2007

(Permalink) Posted: Oct. 08 2007,03:22   

Quote (Reciprocating Bill @ Oct. 07 2007,08:14)
         
Quote (Daniel Smith @ Oct. 07 2007,06:17)
Also, when people say that science cannot investigate God or the supernatural, that's not entirely correct.  Science can (and does) investigate claims of supernatural activity - so long as the supernatural activity is supposed to have affected the physical world...

This passage is correct, and also encapsulates the challenge you have set for yourself. I'll sharpen my earlier statement to reflect your comment: "The existence of God is not amenable to scientific investigation, because God can do anything, in any order, at any time, outside the constraints of natural law, and hence no empirical test can be devised to verify God's existence. However, specific claims regarding God's actions in the physical world can be put to empirical test."

One source of assertions regarding God's actions has been the Bible, which makes very specific, testable claims about the world as God created it (e.g. the age of the earth) and his actions within the world (creation of animals and human beings ex nihilo a few thousand years ago; a subsequent world wide flood). One reason why friction has arisen between those who are inclined to Biblical literalism and the advances of the natural sciences is that many Biblical claims about the actions of God CAN be tested, have been tested, and have been found to be obviously false.  
I am not as quick to abandon biblical claims as you might think, since many biblical claims have not been proven false.  For instance the biblical claims about death and disease, war and poverty, human childbirth, even weeds, all still hold true today.  But that's another subject.          
Quote


However, you are not drawing from Biblical claims about God's actions (although I gather you once did). Your claims are much more sophisticated, and concern the origination of the astounding complexity we observe in the biological world. You don't find current theory about the origination of such complexity believable (for reasons you are happy to enumerate). You claim, instead, that the emergence of biological complexity was accomplished by an all knowing God.

Here you've already gone much beyond the claims of the intelligent design movement generally, as represented by Behe, Dembski, Meyer etc.  They have carefully avoided publicly speculating about the identity and nature of the designer, and have repeatedly declined to make any claims whatsoever regarding the designer's characteristics, modes of action, etc. Because they have been unwilling to propose a model of the design or of the designer, and claim they are solely interested in design detection, that brand of ID has been utterly incapable of generating unique testable predictions about future empirical findings, and fails to rise to the level of a an empirical science.
I can't speak for them but I suspect their reluctance is due to the fact that they are trying to make their theory fit into the realm of naturalistic science - and thus they feel they can't identify the designer as God.
I feel differently.  I feel that we can speculate about how the "mind of God" has affected the physical universe and make testable predictions based on those speculations.          
Quote


You've identified the designer. God is the designer. You've also offered some speculations about the manner in which he originated design: he did it by means of "front-loading" information into the genome or genomes of one or more early organisms, front-loading that reflected foreknowledge of the history of the world in all of its detail, as I described above. You see the outcome of that designer's actions in nature - "I find complex intricate systems analogous (but far superior) to power plants, factories with automated assembly lines, communication networks, super highway systems, waste management (with recycling!), and on and on."

OK, now a careful distinction: "Complex intricate systems analogous (but far superior) to power plants, factories with automated assembly lines, communication networks, super highway systems, waste management" are the phenomena that (you say) still demand explanation.
Yes that's true.      
Quote
Your explanation is that these complex systems were designed by an all knowing God.
Yes that's true also, but I went beyond that - since I first pointed out their analogous qualities with known designs - thereby establishing the precedent of the designer/design as a workable, observable explanation for such systems.      
Quote
I think you can see that it would be circular to then point to those self-same "complex intricate systems" as proof that your explanation for their existence is correct - those complex systems that so amaze us all are the very phenomena that call for explanation in the first place. Poring over and expressing amazement at biological complexity, even if that complexity has been elucidated by science, is not itself a scientific activity.  
That's true, but I've done more than that:  I've suggested a source - an all knowing God that (as you say) "can do anything, in any order, at any time, outside the constraints of natural law", and I hope to show that the evidence actually requires such a being.
I believe that any unbiased look at all the requirements for life on this planet will lead any honest person to rule out chance as a cause.  We are then left with only non-random causes.  My argument is that - once we get to that point - if we examine the delicate balances that exist in nature, and all the intricate complexities of the literally trillions of systems involved in life, a mind of infinite intelligence is the only logical, non-random cause for all of this.      
Quote


Rather, to rise to the level of a scientific assertion, your model must make testable empirical predictions that uniquely "put your theory at risk." That is, you must formulate predictions regarding future empirical findings that, if disconfirmed, indicate that the model from which those predictions arose must be modified or discarded. Because you have already asserted that the designer is an omnipotent, all knowing God, you have put yourself in the position of having to make specific predictions regarding God's actions in the world, predictions with power to put your model at risk of disconfirmation.

I think you will agree that this is a problem. It is inherent in the definition of any "God" of sufficient capability to set the entire universe into motion that there are no limitations upon his activities. As I stated earlier, God can do anything, anywhere, anytime, without constraint of the laws of physics. He even specified the laws of physics themselves. Given that, any empirical finding regarding his proposed actions in the world would appear to be compatible with the God hypothesis. Hence it falls to YOU, as you formulate your model of the origins of biological complexity in a scientific manner, to make statements about God's characteristics of sufficient specificity to predict future empirical findings regarding his actions in the world. These assertions must limit God's scope in some way, either based upon constraints (God can do this, but he can't do that) or upon other more intentional characteristics (God would do this, but wouldn't do that). It falls to you to do this before making the relevant observations, in such a way that subsequent disconfirmation would prompt you to conclude, "God does not have the characteristics I proposed."

That's a tall order. In a some respects you've already made some such assertions, although you haven't described how they arise from a specific model of God, or how to test them. Nevertheless, since front-loading is an action in the world, it is potentially testable. I could easily generate some unique testable predictions regarding future empirical findings that arise from front-loading. However, because I find front-loading implausible for reasons I have already described and believe such tests are likely to be a waste of time, it falls to YOU to devise unique empirical predictions that put your theory at risk and then conduct the relevant tests. Ideally, your predictions would put your assertions about God's actions in the world, and hence his characteristics, at risk, as well.

You've got your work cut out for you.

You are right - and I'm feeling the pressure!

--------------
"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright

"The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

  
Daniel Smith



Posts: 970
Joined: Sep. 2007

(Permalink) Posted: Oct. 08 2007,03:23   

Quote (oldmanintheskydidntdoit @ Oct. 08 2007,02:57)
Quote (Daniel Smith @ Oct. 08 2007,02:34)
I know it sounds like a cop-out but all designers make choices that many of us don't understand.  If we cannot directly ask a designer why they made certain choices, the best we can hope for is to examine their designs and try to make an educated guess based on what we observe.

Then please make an educated guess as to the reason for the huge variety of beetle species.

God likes beetles?

--------------
"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright

"The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

  
Daniel Smith



Posts: 970
Joined: Sep. 2007

(Permalink) Posted: Oct. 08 2007,03:32   

Quote (jeannot @ Oct. 07 2007,13:47)
 
Quote
there are many functional sequences that are different (even radically so) amongst related lineages - this due to their being of designed, not mutational, origin.

That's unclear. How will you know that differences are not the result of mutations? Drift, positive selection and negative selection can lead to different level of divergence between regions.
And what to you mean by "being of designed origin"? Do new genes appear (from God knows where) instantaneously in a lineage? Or were they front loaded in the first cell?

Good questions.
The only fool-proof way to know if differences in sequences are the result of mutations is to study sequences for long periods of time within the same lineage and see if certain areas drift or are changed due to selection.  We can ascertain differences between lineages, but we can't be sure of the mechanism that produced the differences.
As for new genes.  I'd say that at least the template for them was front loaded into the root of every lineage - whether that means one common ancestor or many.

I suspect that that is one of the reasons the entire genome is transcribed - to error check and keep intact these templates.  Another guess.

--------------
"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright

"The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

  
oldmanintheskydidntdoit



Posts: 4999
Joined: July 2006

(Permalink) Posted: Oct. 08 2007,04:11   

Quote (Daniel Smith @ Oct. 08 2007,03:23)
Quote (oldmanintheskydidntdoit @ Oct. 08 2007,02:57)
Quote (Daniel Smith @ Oct. 08 2007,02:34)
I know it sounds like a cop-out but all designers make choices that many of us don't understand.  If we cannot directly ask a designer why they made certain choices, the best we can hope for is to examine their designs and try to make an educated guess based on what we observe.

Then please make an educated guess as to the reason for the huge variety of beetle species.

God likes beetles?

That's what you call an "educated guess"?

--------------
I also mentioned that He'd have to give me a thorough explanation as to *why* I must "eat human babies".
FTK

if there are even critical flaws in Gauger’s work, the evo mat narrative cannot stand
Gordon Mullings

  
oldmanintheskydidntdoit



Posts: 4999
Joined: July 2006

(Permalink) Posted: Oct. 08 2007,04:12   

Quote (Daniel Smith @ Oct. 08 2007,03:22)

Quote
My argument is that - once we get to that point - if we examine the delicate balances that exist in nature, and all the intricate complexities of the literally trillions of systems involved in life, a mind of infinite intelligence is the only logical, non-random cause for all of this.      


What's the purpose of AIDS?

--------------
I also mentioned that He'd have to give me a thorough explanation as to *why* I must "eat human babies".
FTK

if there are even critical flaws in Gauger’s work, the evo mat narrative cannot stand
Gordon Mullings

  
Daniel Smith



Posts: 970
Joined: Sep. 2007

(Permalink) Posted: Oct. 08 2007,04:27   

Quote (mitschlag @ Oct. 07 2007,06:09)
You are the scientist, DS.  You are responsible for devising the test.

Well, I'm not a scientist, but I think I've got an idea for a test:

Take two members of the same species that have been geographically and reproductively isolated for a long period of time (the longer the better), sequence their genomes and compare them.

My prediction is that the coding and non-coding sequences (basically all sequences) will show an equal amount of evolutionary constraint.

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"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright

"The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

  
Reciprocating Bill



Posts: 4265
Joined: Oct. 2006

(Permalink) Posted: Oct. 08 2007,06:51   

Quote (Daniel Smith @ Oct. 08 2007,04:23)
Quote (oldmanintheskydidntdoit @ Oct. 08 2007,02:57)
Quote (Daniel Smith @ Oct. 08 2007,02:34)
I know it sounds like a cop-out but all designers make choices that many of us don't understand.  If we cannot directly ask a designer why they made certain choices, the best we can hope for is to examine their designs and try to make an educated guess based on what we observe.

Then please make an educated guess as to the reason for the huge variety of beetle species.

God likes beetles?

Indeed. "The Creator, if He exists, has an inordinate fondness for beetles".

- Haldane

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Myth: Something that never was true, and always will be.

"The truth will set you free. But not until it is finished with you."
- David Foster Wallace

"Here’s a clue. Snarky banalities are not a substitute for saying something intelligent. Write that down."
- Barry Arrington

  
Steverino



Posts: 411
Joined: Oct. 2005

(Permalink) Posted: Oct. 08 2007,06:59   

"I know it sounds like a cop-out but all designers make choices that many of us don't understand.  If we cannot directly ask a designer why they made certain choices, the best we can hope for is to examine their designs and try to make an educated guess based on what we observe.  "

While it may not be a cop out, it's BULLSHIT.  It's based on the premise that when we see gaps of information, you feel that God should be included in the discussion until proven otherwise.

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- Born right the first time.
- Asking questions is NOT the same as providing answers.
- It's all fun and games until the flying monkeys show up!

   
mitschlag



Posts: 236
Joined: Sep. 2006

(Permalink) Posted: Oct. 08 2007,07:02   

Quote (Daniel Smith @ Oct. 08 2007,04:27)
 
Quote (mitschlag @ Oct. 07 2007,06:09)
You are the scientist, DS.  You are responsible for devising the test.

Well, I'm not a scientist, but I think I've got an idea for a test:

Take two members of the same species that have been geographically and reproductively isolated for a long period of time (the longer the better), sequence their genomes and compare them.

My prediction is that the coding and non-coding sequences (basically all sequences) will show an equal amount of evolutionary constraint.

Please define "evolutionary constraint."

Predict the expected results that would falsify your hypothesis.

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"You can establish any “rule” you like if you start with the rule and then interpret the evidence accordingly." - George Gaylord Simpson (1902-1984)

  
Reciprocating Bill



Posts: 4265
Joined: Oct. 2006

(Permalink) Posted: Oct. 08 2007,07:19   

Quote (Daniel Smith @ Oct. 08 2007,04:22)
 
Quote (Reciprocating Bill @ Oct. 07 2007,08:14)
...Hence it falls to YOU, as you formulate your model of the origins of biological complexity in a scientific manner, to make statements about God's characteristics of sufficient specificity to predict future empirical findings regarding his actions in the world. These assertions must limit God's scope in some way, either based upon constraints (God can do this, but he can't do that) or upon other more intentional characteristics (God would do this, but wouldn't do that). It falls to you to do this before making the relevant observations, in such a way that subsequent disconfirmation would prompt you to conclude, "God does not have the characteristics I proposed."

...

You've got your work cut out for you.

You are right - and I'm feeling the pressure!

Just be clear that arguments that originate with speculation about God's characteristics, and the way those characteristics are reflected in the world, are theological arguments, not scientific arguments.  If you endeavor to actually do some science based on theological assertions, I've got some equipment you'll need:

1) Hammer.

2) Box of nails.

3) Tree.

4) Jello.

Now, get to work.

--------------
Myth: Something that never was true, and always will be.

"The truth will set you free. But not until it is finished with you."
- David Foster Wallace

"Here’s a clue. Snarky banalities are not a substitute for saying something intelligent. Write that down."
- Barry Arrington

  
Wesley R. Elsberry



Posts: 4991
Joined: May 2002

(Permalink) Posted: Oct. 08 2007,07:49   

Quote

My prediction is that the coding and non-coding sequences (basically all sequences) will show an equal amount of evolutionary constraint.


So, why does the term "linkage disequilibrium" seem to get used by geneticists? Wouldn't your prediction mean that we should see the same degree of linkage disequilibrium everywhere we look? If not, what consequences do you think your "prediction" actually has?

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"You can't teach an old dogma new tricks." - Dorothy Parker

    
Patashu



Posts: 6
Joined: Oct. 2007

(Permalink) Posted: Oct. 08 2007,10:46   

Daniel Smith,

Why do four extra kinds of quarks and leptons exist, despite their existence in the universe not effecting the way carbon-based life runs? If the universe is fine-tuned for life, why add in something entirely arbitary? And remember, a perfect god cannot do anything imperfect.

Secondly, how do we know the universe is fine tuned for us? Given that 74% of the universe is dark energy, would it not be a safe bet to assume that the universe was fine tuned to produce as much dark energy as possible?

  
jeannot



Posts: 1201
Joined: Jan. 2006

(Permalink) Posted: Oct. 08 2007,12:17   

Quote (Daniel Smith @ Oct. 08 2007,04:27)
My prediction is that the coding and non-coding sequences (basically all sequences) will show an equal amount of evolutionary constraint.

Based on your intuition?
Why would that be an evidence for design (assuming you have a clear notion of "evolutionary constraint")?
Please explain.

  
JAM



Posts: 517
Joined: July 2007

(Permalink) Posted: Oct. 08 2007,13:01   

[quote=Daniel Smith,Oct. 08 2007,02:18]     [quote=JAM,Oct. 07 2007,13:27]                   [quote=Daniel Smith,Oct. 07 2007,05:46]By this definition, I'd say that anything that is transcribed would qualify as functional - since the cellular machinery is going through the trouble of transcribing it.[/quote]
That is a prediction of an intelligent design hypothesis, but MET (non-Darwinian) predicts that there will be loads of RNA that has no function.[/quote]
Then this is what we need to test.[/quote]
OK, what do you propose? How about "knocking out" regions using the technology whose developers won the Nobel Prize today?
 [quote]    
Quote
 
Quote
So this would include protein coding sequences as well as ncRNA sequences, and anything else that's transcribed.

But if we find anything that's transcribed but not functional, your hypothesis is dead, correct?

As for my hypothesis being "dead" if we find anything that conflicts with what I've predicted:  I don't really think that's fair since scientists are constantly finding things they don't expect and simply adjust their hypotheses to fit the evidence when they do.[/quote]
That's only true for hypotheses that have a track record. Yours doesn't. I've trashed many hypotheses that I've endorsed in previous publications, for example.
 
Quote
I will not therefore totally abandon my hypothesis if the results are different, I will simply adjust it (unless the results completely shoot it out of the water).

It's your ethical responsibility to state the results that would completely shoot it out of the water.
 
Quote
 
Quote
 
Quote
I also must clarify that I do actually believe that all functional sequences (as I've defined them) are evolutionarily constrained.  It's just that I don't think you can find functionality or constraint by comparing sequences to other lineages (since I posit that there are no truly neutral sites).

What if some sites have far greater rates of change over time, Daniel?

This is precisely the issue.  How do we know the rate if it turns out that there are no neutral sites?

Easily and empirically. We know the mutation rate in the absence of selection. If the rate of change over time is the same as the mutation rate, the only rational inference is the absence of selection. If it is less than the mutation rate, we infer selection.
[quote]
Quote
We must first determine that these sites are truly neutral and are actually accumulating mutations.
                     
Quote


What sequences are used for forensic DNA analysis?

That's a tough question, and I'm not sure I know the best answer for that.

I'm not asking for the "best answer," I'm simply asking for an answer. Certain sequences are used for forensic DNA analysis. What are their characteristics? How polymorphic are they?
Quote
Quote
Quote
If comparing to other lineages, the function must first be known and then the entire sequence that provides that function compared.

Not a problem.
                     
Quote
However, the only true test of constraint is comparison to ancestral DNA within the same lineage.

Oh-oh...it looks like I'm going to have to retract my retraction. Your prediction:                      
Quote
there are many functional sequences that are different (even radically so) amongst related lineages - this due to their being of designed, not mutational, origin.

makes clear predictions about the relationships between modern sequences. No ancestral sequences are required.

I'm not backing off my original prediction, but I think certain terms mean different things to both of us, so I'm just trying to clarify.

Good. Please define "lineage" for starters. Are mice and humans in the same or in different lineages?
Quote
I believe that most (if not all) sequences in a genome are functional and therefore resistive to mutation (constrained).  This means there are no neutral sites that are accumulating mutations.

And the evidence shows that you are wrong.
Quote
I also believe that macroevolution (when it happens) is not the result of accumulating mutations but is rather; saltational - that is - it creates new types that may have sequences that are radically different from the sequences from which they diverged (hence my earlier prediction).

Interesting. Of the ~30,000 protein-encoding genes in the mouse and human genomes, how many do you believe/predict are absent in mouse and present in human, and vice versa?

Quote
Therefore, this is what I expect:

1.  Sequence comparisons between related lineages will result in a mixture of like and unlike functional sequences.
 

I need a rigorous definition of "lineage" before pursuing this one.

Quote
2.  Sequence comparisons within the same lineage will show evolutionary constraint across the board - even in what are presently considered neutral sites.

This is trivially easy to do online. Are you interested or afraid to do so?
Quote
3.  What are presently considered neutral sites will be found to be "instructional" - that is, they will carry the instructions that tell the various proteins, RNA and enzymes where to go, when to go and what to do when they get there.

a) How does that relate to today's Nobel Prize?

b) How about classical genetics--do any homozygous normal inversions exist? If so, doesn't that mean that the sequences disrupted by both breakpoints have no function?

Quote
Now, the third prediction is more of a guess, but I think it makes sense.  We know about sequences that code for proteins, and we know about sequences that regulate them, but we don't know how a certain protein "knows" where to go, what to do and when to do it.

We know a lot about that, Daniel. In fact, it's what I've been working on for the last 16 years, since mouse genetics dumped me into the field.

I'll give you a taste--nothing about the mechanisms involved suggests intelligent design.

Quote
My guess is that these instructions are carried in what are presently considered neutral sites and - for that reason - these sites resist mutations just like all other evolutionarily constrained sites.

I hope that's clearer.

Except for your definition of "lineage," yes. As an introduction to how proteins "know" where to go, you might want to Google "signal sequence" and "nuclear import."

Those are the simple signals intrinsic to the protein. What I study is an order of magnitude or two more complex, fluid, and fuzzy.

  
Henry J



Posts: 5786
Joined: Mar. 2005

(Permalink) Posted: Oct. 09 2007,15:59   

Is there a limit on nesting of quotes? I don't see any apparent syntax errors in that last note, but some of the quotes didn't take for some reason.

Henry

  
JAM



Posts: 517
Joined: July 2007

(Permalink) Posted: Oct. 09 2007,16:20   

Quote (Henry J @ Oct. 09 2007,15:59)
Is there a limit on nesting of quotes? I don't see any apparent syntax errors in that last note, but some of the quotes didn't take for some reason.

Henry

I don't understand it either.

  
C.J.O'Brien



Posts: 395
Joined: Aug. 2005

(Permalink) Posted: Oct. 09 2007,17:12   

Quote
So when I examine the evidence, is that what I find?  Yes, that is exactly what I find.  I find complex intricate systems analogous (but far superior) to power plants, factories with automated assembly lines, communication networks, super highway systems, waste management (with recycling!), and on and on.

Bob O'H already made this point, but at some length.
For concision: None of that is evidence in the scientific sense. It's a restatement of the question in explicitly teleological terms. To consider this evidence (the result of empirical investigation beyond a cursory glance) is to beg the question.

When you actually get in depth and look at some of that cellular machinery, Daniel, you'll see that it does not resemble at all the products of a rational design process. It rather resembles a Rube Goldberg-type cobbled-together mess eerily similar to the sorts of engineering solutions arrived at by evolutionary algorithms.

Most concise: Analogies are not evidence.

If everybody could understand and accept this basic fact of epistemology, Creationism in all its forms would die a long-overdue and merciful death.

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The is the beauty of being me- anything that any man does I can understand.
--Joe G

  
JAM



Posts: 517
Joined: July 2007

(Permalink) Posted: Oct. 09 2007,18:19   

Quote (C.J.O'Brien @ Oct. 09 2007,17:12)
Quote
So when I examine the evidence, is that what I find?  Yes, that is exactly what I find.  I find complex intricate systems analogous (but far superior) to power plants, factories with automated assembly lines, communication networks, super highway systems, waste management (with recycling!), and on and on.

Bob O'H already made this point, but at some length.
For concision: None of that is evidence in the scientific sense. It's a restatement of the question in explicitly teleological terms. To consider this evidence (the result of empirical investigation beyond a cursory glance) is to beg the question.

Not only that, but most of it is false.

If our superhighway systems were anything like the cell's, trucks crashing into each other (combining their cargos), useless detours, and multiple tractors on the same cargo trailer pulling in different directions would play an integral role in every journey.

If human-designed waste management systems were designed analogously to the cell's, we'd have 20% raw sewage in our drinking water and call it delicious.

The amazing thing is that when you work in these fields, you see massive teleological biases among the scientists, so that extra data are required to overcome these analogies.

  
Daniel Smith



Posts: 970
Joined: Sep. 2007

(Permalink) Posted: Oct. 09 2007,21:27   

Quote (Steverino @ Oct. 08 2007,06:59)
While it may not be a cop out, it's BULLSHIT.  It's based on the premise that when we see gaps of information, you feel that God should be included in the discussion until proven otherwise.

No, I'm actually giving God credit for everything - not just the gaps.  You might want to go back and catch up on the previous 10 pages before you jump in and post.

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"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright

"The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

  
Henry J



Posts: 5786
Joined: Mar. 2005

(Permalink) Posted: Oct. 09 2007,21:38   

Quote
1.  That we won't find other planets with life on them.

and (to cover my butt),

2.  If we do find life elsewhere it will be remarkably similar to life on earth.  


Seems like either of those would be consistent with current theory. If the density of life-bearing planets is such that no others are within telescope range, it could be a really long time before humans find any.

It seems at least possible that amino acid chains might be the most effective (or at least most reachable) form of organic molecule, and DNA (or something much like it) might be most likely form of hereditary trait "memory". Otoh there might be other chains that work, but could be a while before we discover them.

Henry

  
Daniel Smith



Posts: 970
Joined: Sep. 2007

(Permalink) Posted: Oct. 10 2007,02:25   

Quote (Henry J @ Oct. 09 2007,15:59)
Is there a limit on nesting of quotes? I don't see any apparent syntax errors in that last note, but some of the quotes didn't take for some reason.

Henry

There seems to be.  I had the same trouble with an earlier reply and could only rectify it by eliminating some quotes.

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"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright

"The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

  
Daniel Smith



Posts: 970
Joined: Sep. 2007

(Permalink) Posted: Oct. 10 2007,02:30   

Quote (mitschlag @ Oct. 08 2007,07:02)
   
Quote (Daniel Smith @ Oct. 08 2007,04:27)
Take two members of the same species that have been geographically and reproductively isolated for a long period of time (the longer the better), sequence their genomes and compare them.

My prediction is that the coding and non-coding sequences (basically all sequences) will show an equal amount of evolutionary constraint.

Please define "evolutionary constraint."

Predict the expected results that would falsify your hypothesis.

I am using the term "evolutionary constraint" to mean a sequence that resists or rejects mutations.
As I understand it, this is the common usage of the term.

The results that would falsify my hypothesis would be if the coding sequences showed evolutionary constraint while the non-coding sequences didn't.

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"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright

"The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

  
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