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Daniel Smith



Posts: 970
Joined: Sep. 2007

(Permalink) Posted: Nov. 16 2007,19:01   

Quote (oldmanintheskydidntdoit @ Nov. 16 2007,18:55)
Quote (Daniel Smith @ Nov. 16 2007,18:50)
One thing I find interesting here is that most of you have shown no interest in any of the various papers I've cited from the ENCODE project.

These papers clearly show a multi-layered, overlapping, multi-directional "coding" scheme within the human genome.  (I put "coding" in quotes since most of the genome "codes" for things other than proteins and so is currently classified as "non-coding").

They also show quite clearly that most of the human genome is transcribed and functional.

These scientists are suggesting that a re-defining of the most basic term in genetics - the gene - is necessary.

I'll ask again:  When did any of your various theories or hypotheses predict such a complex interwoven tapestry within our genome (or any other)?
And...
Is that why none of you want to talk about it?  Does it cause difficulties for you?

yeah yeah, we know, god did it. what further is there to discuss?

No, the "ENCyclopedia Of DNA Elements Consortium" did it.

Have you read any of it?

--------------
"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

  
mitschlag



Posts: 235
Joined: Sep. 2006

(Permalink) Posted: Nov. 17 2007,07:25   

Quote (Daniel Smith @ Nov. 16 2007,18:50)
One thing I find interesting here is that most of you have shown no interest in any of the various papers I've cited from the ENCODE project.

These papers clearly show a multi-layered, overlapping, multi-directional "coding" scheme within the human genome.  (I put "coding" in quotes since most of the genome "codes" for things other than proteins and so is currently classified as "non-coding").

They also show quite clearly that most of the human genome is transcribed and functional.

These scientists are suggesting that a re-defining of the most basic term in genetics - the gene - is necessary.

I'll ask again:  When did any of your various theories or hypotheses predict such a complex interwoven tapestry within our genome (or any other)?
And...
Is that why none of you want to talk about it?  Does it cause difficulties for you?

One thing I find interesting is that when he can't provide answers to standing questions, Daniel changes the subject.

It's not that we are afraid to talk about it.  We just don't see it as being a problem.  And especially not as evidence for a Designer.

Why should we be shocked to learn something new?   That's the way it goes in science, in which empirical data trump previous belief.  And the pace of discovery keeps accelerating.

So it is irrelevant whether anyone predicted or did not predict new findings.  The excitement is in learning new things and in overthrowing the existent paradigm...whenever possible.

You might understand better if you would read The Structure of Scientific Revolutions.

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

  
JAM



Posts: 503
Joined: July 2007

(Permalink) Posted: Nov. 17 2007,10:30   

Quote (Daniel Smith @ Nov. 16 2007,18:50)
One thing I find interesting here is that most of you have shown no interest in any of the various papers I've cited from the ENCODE project.
These papers clearly show a multi-layered, overlapping, multi-directional "coding" scheme within the human genome.

Why would the human genome be so different from the Drosophila genome?

And if it's a scheme, why don't you understand it? And if it supports your hypothesis, why didn't you predict it?


Quote
(I put "coding" in quotes since most of the genome "codes" for things other than proteins and so is currently classified as "non-coding").

You don't know what you're talking about. Given that, how can you ethically reach the conclusion that we don't know what we are talking about?
Quote
They also show quite clearly that most of the human genome is transcribed and functional.

Now you're just lying. You haven't shown that transcription necessarily implies function. I already asked you to make a prediction about the relationship between the time transcription of an essential gene begins and the time at which the null mutant has a phenotype, but you ran away.
Quote
These scientists are suggesting that a re-defining of the most basic term in genetics - the gene - is necessary.

So what? That does absolutely nothing to support a design hypothesis.
Quote
I'll ask again:  When did any of your various theories or hypotheses predict such a complex interwoven tapestry within our genome (or any other)?

1) MET makes clear, testable predictions about the mechanisms by which the messy, fuzzy nature of our genome came about.
2) As for any other, similar phenomena were shown in the Drosophila bithorax complex FIVE YEARS AGO. Therefore, we predicted similar complexity in the human genome.
Quote
And...
Is that why none of you want to talk about it?  Does it cause difficulties for you?

It doesn't address any of your predictions--it's just the same ol' post hoc spin to try and conceal the fact that you are dishonest, because you won't change or abandon your hypothesis when its predictions are shown to be false.

Bearing false witness is a sin in my Bible, Daniel.

  
JAM



Posts: 503
Joined: July 2007

(Permalink) Posted: Nov. 17 2007,13:31   

Quote (Daniel Smith @ Nov. 15 2007,15:39)
Quote (JAM @ Nov. 13 2007,11:00)
   
Quote (Daniel Smith @ Nov. 11 2007,14:58)
I began that discussion with a severely limited knowledge of genetics - only knowing that there were genes (which I assumed to be regions that only coded for proteins) and non-coding regions between them (which I assumed to be what-is-commonly-referred-to-as "junk DNA").  With this limited knowledge, I made several predictions indicating what I'd expect to find molecularly - including increasing complexity and overlapping and embedded codes.

I don't see how the fact that you didn't know that introns were within genes and are non-coding preserves your hypothesis against the inescapable fact that introns, whether one looks within species, between races, between species within a genus, between genuses within a family (which met YOUR definition of "within a lineage"), or between phyla, diverge more than exons.

It seems to me that your saltational hypothesis still makes an utterly false prediction.
       
Quote
...I feel vindicated in my own mind by what I've found.

I will probably never convince you or anyone else on this board of design, but I'm more fully convinced now than I was when I came here.

Good! Then you'll have no problem explaining how your hypothesis treats non-coding regions within genes completely differently from non-coding regions outside genes.

Let me just say this:

I am still not convinced that the evidence you showed me from VISTA contradicts my hypothesis.

What should convince you, assuming that you were an honest person, was that your prediction was dead wrong. This is why we have the scientific method.
Quote
Until I know what VISTA does and how it does it, I'll have to reserve judgment on it.

It takes you right down to the sequences themselves, Dan. What more is there to know?
Quote
You are convinced (based on VISTA) that I am wrong.

No, I know from decades of professional experience that you are wrong. I merely chose VISTA as a way to present the evidence.
Quote
That's fine - I very well may be wrong!  After all, I'm trying to guess what God was thinking when he designed life.  I'll probably be wrong more than I'm right.

You already know that you are wrong. That's why you are afraid to pursue the predictions you made in your last response to me.

Do you predict that whales will be missing a hind-leg gene? Do you predict that monkeys have a tail gene that humans lack? Both of these stream from your guess as to what God was thinking when he designed, but you are afraid to pursue it, because you have no real faith. This is why ID is first and foremost bad theology.
Quote
All I'm saying is, I'm not seeing what you're seeing (yet at least).
Have you considered opening your eyes to what God Himself has written in the book of nature?
Quote
 I have a lot less knowledge in this area than you so I'm not able to just look at a chart of colors and immediately know what they all represent and how they confirm or falsify my predictions.
 
So how do you explain why you believe your bottom line more than mine, given your lack of knowledge?
Quote
Please be patient with me and please stop accusing me of lying whenever I make ignorant statements!

Then please don't pretend to know things that you don't know. That's lying.

  
oldmanintheskydidntdoit



Posts: 4999
Joined: July 2006

(Permalink) Posted: Nov. 17 2007,19:10   

Quote (Daniel Smith @ Nov. 16 2007,19:01)
Quote (oldmanintheskydidntdoit @ Nov. 16 2007,18:55)
 
Quote (Daniel Smith @ Nov. 16 2007,18:50)
One thing I find interesting here is that most of you have shown no interest in any of the various papers I've cited from the ENCODE project.

These papers clearly show a multi-layered, overlapping, multi-directional "coding" scheme within the human genome.  (I put "coding" in quotes since most of the genome "codes" for things other than proteins and so is currently classified as "non-coding").

They also show quite clearly that most of the human genome is transcribed and functional.

These scientists are suggesting that a re-defining of the most basic term in genetics - the gene - is necessary.

I'll ask again:  When did any of your various theories or hypotheses predict such a complex interwoven tapestry within our genome (or any other)?
And...
Is that why none of you want to talk about it?  Does it cause difficulties for you?

yeah yeah, we know, god did it. what further is there to discuss?

No, the "ENCyclopedia Of DNA Elements Consortium" did it.

Have you read any of it?

all of it.

--------------
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

  
Lou FCD



Posts: 5379
Joined: Jan. 2006

(Permalink) Posted: Nov. 18 2007,06:09   



   
Quote
Urinal at The Fire, by highstrungloner @ Flickr


There's been a bit of clean up, Find it here.

--------------
Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
I think I might love you. Don't tell Deadman -Wolfhound

Work-friendly photography
NSFW photography

   
oldmanintheskydidntdoit



Posts: 4999
Joined: July 2006

(Permalink) Posted: Nov. 18 2007,10:46   

Quote (Daniel Smith @ Nov. 16 2007,18:50)
One thing I find interesting here is that most of you have shown no interest in any of the various papers I've cited from the ENCODE project.

These papers clearly show a multi-layered, overlapping, multi-directional "coding" scheme within the human genome.  (I put "coding" in quotes since most of the genome "codes" for things other than proteins and so is currently classified as "non-coding").

They also show quite clearly that most of the human genome is transcribed and functional.

These scientists are suggesting that a re-defining of the most basic term in genetics - the gene - is necessary.

I'll ask again:  When did any of your various theories or hypotheses predict such a complex interwoven tapestry within our genome (or any other)?
And...
Is that why none of you want to talk about it?  Does it cause difficulties for you?

Very well Daniel. We can't have you thinking that "darwinists" are scared of your layman point of view. I'm a lay person here too.

And as such, here are my questions (conditions, if you like, for further discussion to take place. I'm not a moderator here but I won't bother to engage  again if you don't make a reasonable attempt to answer. Most other people it seems have stopped bothering already).

1) Could you please show me the specific prediction that "darwinism" makes that specifies that multi-layered, overlapping, multi-directional "coding" schemes within the human genome should not exist?

2) Could you please show me the specific prediction that "darwinism" makes that  most of the human genome should not be transcribed and functional.

3) Could you please show me the specific prediction that "darwinism" makes that predicts such a complex interwoven tapestry within our genome (or any other) cannot exist?

Quote
Is that why none of you want to talk about it?  Does it cause difficulties for you?


I suspect you are confusing "scientists were surprised at what they found" with "scientists found something that they  predicted was impossible" or suchlike.

What is it exactly that you want to talk about? So what if scientists are suggesting redefining the gene. How does that in any what whatsoever support the idea that a deity was necessary at any stage along the way. In fact, lets make that question four.

4) How does redefining the gene suggest a supernatural intervention was required? Specifically?

--------------
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

  
VMartin



Posts: 525
Joined: Nov. 2006

(Permalink) Posted: Nov. 18 2007,12:47   

JAM

 
Quote

So if one is intelligently designing a spacing mechanism, why in heaven's name (literally) would one use tandem repeats, which expand and contract (via recombination) at ridiculously high frequencies? Wouldn't unique sequence be the far more intelligent choice?


As a layman I dont know what you and Daniel are meaning by "tandem repeats". Are those repeats  "tandem duplication" or pure "repeated sequences"?

In the second case I don't see how how the difference in the structure of repeated sequences between different species proves Daniel theory by saltus as wrong. It may  have been induced by some unknown mechanism during John Davison's chromosome rearrangements, no? As far as I know repeated sequences by two sisters species are sometimes very different. But they are also different from those of the ancestor species.

This phenomenon is very hard to explain without special mechanism that after speciation causes parallel differentiation of repeated sequences in all locuses of genome. There must be obviously also some process of homogenization of repeated sequences. These repeated sequences are often identical in new species and have sometimes hundered thousands copies.  

So there must be process of  differentiation of repeated sequences in daughter species from mother species and at the same time homogenization of all these repeated sequences to new ones.

Wouldn't be it more simple to assume that such  repeated sequences are for each new species created de novo by saltus?

If the phenomenon is to be explained by molecular drive as I have read elsewhere it would mean that by such process (molecular drive) would be affected many individuals of population simultaneously. It would assume some kind of synchronized evolution of repeated sequences.

Generalizing molecular drive to all genome we are dealing with synchronized evolution, something proposed by Leo Berg (with which John Davison disagree btw).

--------------
I could not answer, but should maintain my ground.-
Charles Darwin

  
Daniel Smith



Posts: 970
Joined: Sep. 2007

(Permalink) Posted: Nov. 18 2007,15:08   

Quote (JAM @ Nov. 17 2007,10:30)
1) MET makes clear, testable predictions about the mechanisms by which the messy, fuzzy nature of our genome came about.

As far as I can see, the only thing messy or fuzzy about our genome is our understanding of it.

--------------
"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: Nov. 18 2007,15:10   

Quote (oldmanintheskydidntdoit @ Nov. 17 2007,19:10)
 
Quote (Daniel Smith @ Nov. 16 2007,18:50)

No, the "ENCyclopedia Of DNA Elements Consortium" did it.

Have you read any of it?

all of it.

All 29 papers?

--------------
"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

  
JAM



Posts: 503
Joined: July 2007

(Permalink) Posted: Nov. 18 2007,15:30   

Quote (Daniel Smith @ Nov. 18 2007,15:08)
Quote (JAM @ Nov. 17 2007,10:30)
1) MET makes clear, testable predictions about the mechanisms by which the messy, fuzzy nature of our genome came about.

As far as I can see, the only thing messy or fuzzy about our genome is our understanding of it.

Mine's a helluvalot less fuzzy than yours. May I take it that you conceded all of the other points in choosing a one-liner? I'm particularly interested in your answers to these questions:

A) Do you predict that whales will be missing a hind-leg gene? Do you predict that monkeys have a tail gene that humans lack? Both of these stream from your guess as to what God was thinking when he designed, but you are afraid to pursue it, because you have no real faith (Note that this relates to the fuzziness that you lack the integrity to address).

B) I have a gene, and both mice and humans homozygous for the null allele die shortly after birth (with essentially the same phenotype). Since according to you, transcription implies function, when I look at transcription of that gene, will it be turned on:
1) right before the age of death in the null mutants,
2) right before or at the time at which mutants can be distinguished from wild-type individuals, or
3) more than a month before 1 or 2?

C) Why is it that you are so breathtakingly arrogant that you believe that God causes millions of children to suffer and die as a lesson to people like you, but getting you to make predictions is like pulling teeth?

  
Henry J



Posts: 4112
Joined: Mar. 2005

(Permalink) Posted: Nov. 18 2007,18:14   

Quote
Wouldn't be it more simple to assume that such repeated sequences are for each new species created de novo by saltus?


Wouldn't the simplest assumption be that a series of repeats was caused by a duplication type mutation? If so, that could occur independently in closely related species. (In which case it would presumably be repetitions of a different sequence, in a different location of the genome.)

Henry

  
Daniel Smith



Posts: 970
Joined: Sep. 2007

(Permalink) Posted: Nov. 18 2007,18:35   

Quote (oldmanintheskydidntdoit @ Nov. 18 2007,10:46)
   
Quote (Daniel Smith @ Nov. 16 2007,18:50)
One thing I find interesting here is that most of you have shown no interest in any of the various papers I've cited from the ENCODE project.

These papers clearly show a multi-layered, overlapping, multi-directional "coding" scheme within the human genome.  (I put "coding" in quotes since most of the genome "codes" for things other than proteins and so is currently classified as "non-coding").

They also show quite clearly that most of the human genome is transcribed and functional.

These scientists are suggesting that a re-defining of the most basic term in genetics - the gene - is necessary.

I'll ask again:  When did any of your various theories or hypotheses predict such a complex interwoven tapestry within our genome (or any other)?
And...
Is that why none of you want to talk about it?  Does it cause difficulties for you?

Very well Daniel. We can't have you thinking that "darwinists" are scared of your layman point of view. I'm a lay person here too.

And as such, here are my questions (conditions, if you like, for further discussion to take place. I'm not a moderator here but I won't bother to engage  again if you don't make a reasonable attempt to answer. Most other people it seems have stopped bothering already).

1) Could you please show me the specific prediction that "darwinism" makes that specifies that multi-layered, overlapping, multi-directional "coding" schemes within the human genome should not exist?

2) Could you please show me the specific prediction that "darwinism" makes that  most of the human genome should not be transcribed and functional.

3) Could you please show me the specific prediction that "darwinism" makes that predicts such a complex interwoven tapestry within our genome (or any other) cannot exist?

     
Quote
Is that why none of you want to talk about it?  Does it cause difficulties for you?


I suspect you are confusing "scientists were surprised at what they found" with "scientists found something that they  predicted was impossible" or suchlike.

What is it exactly that you want to talk about? So what if scientists are suggesting redefining the gene. How does that in any what whatsoever support the idea that a deity was necessary at any stage along the way. In fact, lets make that question four.

4) How does redefining the gene suggest a supernatural intervention was required? Specifically?

First, I'm not aware of any predictions "darwinism" has made about these types of things so I'll have to give you my take on what "darwinism" might predict:

If I understand it correctly, the modern evolutionary theory hypothesizes that morphological change has occurred as a result of millions of years of accumulated mutations within the genomes of organisms.  These random mutations mostly accumulate in non-coding / non-functional areas within the genome.  They will thus eventually create a new genetic sequence or modify an existing functional sequence to the point that a new or improved feature is developed.  That feature then becomes fixed in the genome due to selection.  Of course, there's a whole lot more to it than that, and many others here will no doubt chime in with their take on the mechanisms of evolution, but that's my "nutshell" version.

Now, if that's the case, then we should see some evidence in every genome of millions of years of these accumulated random mutations in non-functional (and functional) areas of the genome.  

What would you expect to see and how does it compare to what we do see?

Of course, if there are no (or very few) non-functional areas in the genome (as I believe), then there would be no place for random mutations to accumulate.  I think what we are actually observing and discovering about genomes is more in line with this approach.

Which brings me to your last question:
At some point; after we realize that whole genomes are functional; after we've discovered bewildering complexity within them; and after we've pretty much eliminated random causes for such things; we have to explore the possibility that intelligence was involved in the design of such a system.  I predict science will some day soon arrive at that point.

--------------
"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: Nov. 18 2007,18:43   

Quote (VMartin @ Nov. 18 2007,12:47)
JAM

       
Quote

So if one is intelligently designing a spacing mechanism, why in heaven's name (literally) would one use tandem repeats, which expand and contract (via recombination) at ridiculously high frequencies? Wouldn't unique sequence be the far more intelligent choice?


As a layman I dont know what you and Daniel are meaning by "tandem repeats". Are those repeats  "tandem duplication" or pure "repeated sequences"?

In the second case I don't see how how the difference in the structure of repeated sequences between different species proves Daniel theory by saltus as wrong. It may  have been induced by some unknown mechanism during John Davison's chromosome rearrangements, no? As far as I know repeated sequences by two sisters species are sometimes very different. But they are also different from those of the ancestor species.

This phenomenon is very hard to explain without special mechanism that after speciation causes parallel differentiation of repeated sequences in all locuses of genome. There must be obviously also some process of homogenization of repeated sequences. These repeated sequences are often identical in new species and have sometimes hundered thousands copies.  

So there must be process of  differentiation of repeated sequences in daughter species from mother species and at the same time homogenization of all these repeated sequences to new ones.

Wouldn't be it more simple to assume that such  repeated sequences are for each new species created de novo by saltus?

If the phenomenon is to be explained by molecular drive as I have read elsewhere it would mean that by such process (molecular drive) would be affected many individuals of population simultaneously. It would assume some kind of synchronized evolution of repeated sequences.

Generalizing molecular drive to all genome we are dealing with synchronized evolution, something proposed by Leo Berg (with which John Davison disagree btw).

Very astute observations Martin.  

I've often wondered "Why repeats?", "Why not random 'gibberish'?"

It seems to me that millions of years of accumulated random mutations in non-functional areas would have to result in random base pairs - as opposed to repeat sequences.

But then again, I don't understand the logic behind the theory of evolution anywhere near as well as the rest of them say they do.

--------------
"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: Nov. 18 2007,19:19   

Quote (JAM @ Nov. 18 2007,15:30)
           
Quote (Daniel Smith @ Nov. 18 2007,15:08)
             
Quote (JAM @ Nov. 17 2007,10:30)
1) MET makes clear, testable predictions about the mechanisms by which the messy, fuzzy nature of our genome came about.

As far as I can see, the only thing messy or fuzzy about our genome is our understanding of it.

Mine's a helluvalot less fuzzy than yours. May I take it that you conceded all of the other points in choosing a one-liner?

No.            
Quote
I'm particularly interested in your answers to these questions:

A) Do you predict that whales will be missing a hind-leg gene?
Not necessarily - though I predict it will be suppressed as to it's full development.  IOW, the non-coding "support cast" for that gene will be markedly different from animals that have fully developed hind legs.            
Quote
Do you predict that monkeys have a tail gene that humans lack?
No.  I predict that their "tail gene(s)" (at least the protein coding parts) may be similar to ours, but all their various regulatory and support elements will be markedly different from ours.  Theirs will have much more activity and development in these non-coding areas - possibly evidenced by a markedly higher level of histone activity.  Ours will be suppressed.      
Quote
Both of these stream from your guess as to what God was thinking when he designed, but you are afraid to pursue it, because you have no real faith (Note that this relates to the fuzziness that you lack the integrity to address).
Why does every response from you have to be so peppered with accusations?  It gets tiring after awhile.  I feel like I'm answering you not so much because I have to defend my positions, but rather because I have to defend my character.        
Quote
B) I have a gene, and both mice and humans homozygous for the null allele die shortly after birth (with essentially the same phenotype). Since according to you, transcription implies function, when I look at transcription of that gene, will it be turned on:
1) right before the age of death in the null mutants,
2) right before or at the time at which mutants can be distinguished from wild-type individuals, or
3) more than a month before 1 or 2?
I'm not sure what you mean by "when I look at transcription of that gene, will it be turned on".  Do you mean "will transcription of that gene be turned on", or will "the gene itself be turned on"?  
Because I think transcription of the gene will always be happening,  but as to when exactly the gene gets turned on, I have no clue.      
Quote


C) Why is it that you are so breathtakingly arrogant that you believe that God causes millions of children to suffer and die as a lesson to people like you, but getting you to make predictions is like pulling teeth?

The suffering of these children (and everything else that happens in life) is a lesson for us all - not just for "people like me".

--------------
"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

  
stevestory



Posts: 9021
Joined: Oct. 2005

(Permalink) Posted: Nov. 18 2007,19:33   

Quote (Daniel Smith @ Nov. 18 2007,20:19)
I'm not sure what you mean by "when I look at transcription of that gene, will it be turned on".  Do you mean "will transcription of that gene be turned on", or will "the gene itself be turned on"?  
Because I think transcription of the gene will always be happening,  but as to when exactly the gene gets turned on, I have no clue.

Dan, we will send you some intro biology textbooks, if you want to learn about biology. You don't understand the basic terminology and concepts. If you're interested in learning, send a PM to Lou FCD or Albatrossity with a mailing address and we will send you some freshman-level textbooks to start with.

   
Arden Chatfield



Posts: 6657
Joined: Jan. 2006

(Permalink) Posted: Nov. 18 2007,21:47   

Quote (Daniel Smith @ Nov. 18 2007,18:43)
Quote (VMartin @ Nov. 18 2007,12:47)
JAM

       
Quote

So if one is intelligently designing a spacing mechanism, why in heaven's name (literally) would one use tandem repeats, which expand and contract (via recombination) at ridiculously high frequencies? Wouldn't unique sequence be the far more intelligent choice?


As a layman I dont know what you and Daniel are meaning by "tandem repeats". Are those repeats  "tandem duplication" or pure "repeated sequences"?

In the second case I don't see how how the difference in the structure of repeated sequences between different species proves Daniel theory by saltus as wrong. It may  have been induced by some unknown mechanism during John Davison's chromosome rearrangements, no? As far as I know repeated sequences by two sisters species are sometimes very different. But they are also different from those of the ancestor species.

This phenomenon is very hard to explain without special mechanism that after speciation causes parallel differentiation of repeated sequences in all locuses of genome. There must be obviously also some process of homogenization of repeated sequences. These repeated sequences are often identical in new species and have sometimes hundered thousands copies.  

So there must be process of  differentiation of repeated sequences in daughter species from mother species and at the same time homogenization of all these repeated sequences to new ones.

Wouldn't be it more simple to assume that such  repeated sequences are for each new species created de novo by saltus?

If the phenomenon is to be explained by molecular drive as I have read elsewhere it would mean that by such process (molecular drive) would be affected many individuals of population simultaneously. It would assume some kind of synchronized evolution of repeated sequences.

Generalizing molecular drive to all genome we are dealing with synchronized evolution, something proposed by Leo Berg (with which John Davison disagree btw).

Very astute observations Martin.  

VMartin has also stated that "if a reptile hatched a bird there is no ancestor in common view." Is that astute, too?

--------------
"Rich is just mad because he thought all titties had fur on them until last week when a shorn transvestite ruined his childhood dreams by jumping out of a spider man cake and man boobing him in the face lips." - Erasmus

  
Henry J



Posts: 4112
Joined: Mar. 2005

(Permalink) Posted: Nov. 18 2007,22:37   

Quote
VMartin has also stated that "if a reptile hatched a bird there is no ancestor in common view." Is that astute, too?


Of course, cladistically speaking, birds are reptiles. ;)

Henry

  
VMartin



Posts: 525
Joined: Nov. 2006

(Permalink) Posted: Nov. 18 2007,23:50   

Quote (stevestory @ Nov. 18 2007,19:33)
           
Quote (Daniel Smith @ Nov. 18 2007,20:19)
I'm not sure what you mean by "when I look at transcription of that gene, will it be turned on".  Do you mean "will transcription of that gene be turned on", or will "the gene itself be turned on"?  
Because I think transcription of the gene will always be happening,  but as to when exactly the gene gets turned on, I have no clue.

Dan, we will send you some intro biology textbooks, if you want to learn about biology. You don't understand the basic terminology and concepts. If you're interested in learning, send a PM to Lou FCD or Albatrossity with a mailing address and we will send you some freshman-level textbooks to start with.

Maybe you can describe the mechanism of gradual homologization of repeated sequences in new species which everybody know about from "intro biolology text books" and which is different from the molecular drive? Otherwise I am afraid that you are as great expert in the evolutionary biology as Erasmus is an "expert" in the problem of aposematism at another thread.

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I could not answer, but should maintain my ground.-
Charles Darwin

  
Arden Chatfield



Posts: 6657
Joined: Jan. 2006

(Permalink) Posted: Nov. 19 2007,00:18   

Quote (VMartin @ Nov. 18 2007,23:50)
Quote (stevestory @ Nov. 18 2007,19:33)
             
Quote (Daniel Smith @ Nov. 18 2007,20:19)
I'm not sure what you mean by "when I look at transcription of that gene, will it be turned on".  Do you mean "will transcription of that gene be turned on", or will "the gene itself be turned on"?  
Because I think transcription of the gene will always be happening,  but as to when exactly the gene gets turned on, I have no clue.

Dan, we will send you some intro biology textbooks, if you want to learn about biology. You don't understand the basic terminology and concepts. If you're interested in learning, send a PM to Lou FCD or Albatrossity with a mailing address and we will send you some freshman-level textbooks to start with.

Maybe you can describe the mechanism of gradual homologization of repeated sequences in new species which everybody know about from "intro biolology text books" and which is different from the molecular drive? Otherwise I am afraid that you are as great expert in the evolutionary biology as Erasmus is an "expert" in the problem of aposematism at another thread.

What exactly are you an expert in, 'Martin'?

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"Rich is just mad because he thought all titties had fur on them until last week when a shorn transvestite ruined his childhood dreams by jumping out of a spider man cake and man boobing him in the face lips." - Erasmus

  
JAM



Posts: 503
Joined: July 2007

(Permalink) Posted: Nov. 19 2007,00:38   

[quote=Daniel Smith,Nov. 18 2007,19:19]  [quote=JAM,Nov. 18 2007,15:30]                
Quote (Daniel Smith @ Nov. 18 2007,15:08)
                 
Quote (JAM @ Nov. 17 2007,10:30)
1) MET makes clear, testable predictions about the mechanisms by which the messy, fuzzy nature of our genome came about.

As far as I can see, the only thing messy or fuzzy about our genome is our understanding of it.

Mine's a helluvalot less fuzzy than yours. May I take it that you conceded all of the other points in choosing a one-liner?[/quote]
No.[/quote]
Then maybe you should respond.
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I'm particularly interested in your answers to these questions:
A) Do you predict that whales will be missing a hind-leg gene?
Not necessarily - though I predict it will be suppressed as to it's full development.

Genes don't "develop." Organisms and organs do.
Please define "it" in this context. Does your hypothesis predict that there will be anything that we humans could call a "hind-leg gene" based on analogies with our own designs?
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IOW, the non-coding "support cast" for that gene will be markedly different from animals that have fully developed hind legs.

Please define "markedly" in this context. It's important.
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Do you predict that monkeys have a tail gene that humans lack?
No.  I predict that their "tail gene(s)" (at least the protein coding parts) may be similar to ours, but all their various regulatory and support elements will be markedly different from ours.

Does your hypothesis predict that there will be anything that we humans could call a "tail gene" based on analogies with our own designs?  
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Theirs will have much more activity and development

Again, the term "development" is gibberish in this context, and "activity" means transcriptional activity in this context. Is that what you mean?
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in these non-coding areas - possibly evidenced by a markedly higher level of histone activity.

What do you mean by "histone activity"? Again, it's important.
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Ours will be suppressed.

Our what, exactly? It has to be measurable. Please provide units.
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Both of these stream from your guess as to what God was thinking when he designed, but you are afraid to pursue it, because you have no real faith (Note that this relates to the fuzziness that you lack the integrity to address).
Why does every response from you have to be so peppered with accusations?

Sit down and take a deep breath. Think, as a Christian, for a moment about what YOU are accusing me and the other scientists of doing here. YOU are accusing US of gross incompetence, and in direct contradiction of clear Biblical guidance, you have made this accusation on the basis of nothing but hearsay.
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It gets tiring after awhile.

Put yourself in my shoes, Dan. I've spent most of my life doing biology, and you come along. Would you describe your claims as humble ones?
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I feel like I'm answering you not so much because I have to defend my positions, but rather because I have to defend my character.

What sort of character makes grandiose claims without evidence, and then discounts the evidence?
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B) I have a gene, and both mice and humans homozygous for the null allele die shortly after birth (with essentially the same phenotype). Since according to you, transcription implies function, when I look at transcription of that gene, will it be turned on:
1) right before the age of death in the null mutants,
2) right before or at the time at which mutants can be distinguished from wild-type individuals, or
3) more than a month before 1 or 2?
I'm not sure what you mean by "when I look at transcription of that gene, will it be turned on".  Do you mean "will transcription of that gene be turned on", or will "the gene itself be turned on"?

The former.
Quote
Because I think transcription of the gene will always be happening,

Why would you think that? WTF do transcription factors do?
 
Quote
 but as to when exactly the gene gets turned on, I have no clue.

Why not? Wouldn't an intelligent designer design it so transcription was turned on when (and where) it was needed, and not before or in other tissues?
Quote
Quote
C) Why is it that you are so breathtakingly arrogant that you believe that God causes millions of children to suffer and die as a lesson to people like you, but getting you to make predictions is like pulling teeth?

The suffering of these children (and everything else that happens in life) is a lesson for us all - not just for "people like me".

I'm sorry, but I don't see what the children who suffer and die are learning. Why shouldn't you and your children be suffering and dying?

  
IanBrown_101



Posts: 927
Joined: April 2007

(Permalink) Posted: Nov. 19 2007,07:35   

Quote (JAM @ Nov. 19 2007,06:38)
Quote
The suffering of these children (and everything else that happens in life) is a lesson for us all - not just for "people like me".

I'm sorry, but I don't see what the children who suffer and die are learning. Why shouldn't you and your children be suffering and dying?

Because their life will be bad anyway, so it's a mercy.

By this logic we should commit multiple genocides in Africa to end their suffering.

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I'm not the fastest or the baddest or the fatest.

You NEVER seem to address the fact that the grand majority of people supporting Darwinism in these on line forums and blogs are atheists. That doesn't seem to bother you guys in the least. - FtK

Roddenberry is my God.

   
Richard Simons



Posts: 425
Joined: Oct. 2006

(Permalink) Posted: Nov. 19 2007,08:17   

Quote
The suffering of these children (and everything else that happens in life) is a lesson for us all - not just for "people like me".

Only if you are aware of it. In which case, wouldn't it be more instructive if it happened in the developed world where communications are so much better, rather than in Third World villages where TV cameras rarely penetrate?

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All sweeping statements are wrong.

  
Erasmus, FCD



Posts: 6349
Joined: June 2007

(Permalink) Posted: Nov. 19 2007,08:36   

I suppose that 'being an expert' in something is sufficiently attained when you know enough about something to point out the flaws in another's reasoning.  like the guts of 80,000 birds being a controlled experiment, or something.

now, i don't know enough about molecular drives and it seems that what daniel is predicting is not very different, at least from the root concepts, from the evolutionary explanation.  

minus the assumption of saltation, which if my contention is above is correct is thus a non-parsimonious explanation. co-opting predictions post hoc is certainly a hallmark of crankery.  gene copy number varies within populations so i don't see what someone's point is...

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You're obviously illiterate as hell. Peach, bro.-FtK

Finding something hard to believe based on the evidence, is science.-JoeG

the odds of getting some loathsome taint are low-- Gordon E Mullings Manjack Heights Montserrat

I work on molecular systems with pathway charts and such.-Giggles

  
Henry J



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(Permalink) Posted: Nov. 20 2007,11:26   

If saltation doesn't work, try pepper-ation...  :p

  
Daniel Smith



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Joined: Sep. 2007

(Permalink) Posted: Nov. 20 2007,18:58   

Quote (Richard Simons @ Nov. 19 2007,08:17)
 
Quote
The suffering of these children (and everything else that happens in life) is a lesson for us all - not just for "people like me".

Only if you are aware of it. In which case, wouldn't it be more instructive if it happened in the developed world where communications are so much better, rather than in Third World villages where TV cameras rarely penetrate?

You know, my wife just lost her mother after years and years of progressive debilitation due to complications of diabetes.  We watched a healthy, beautiful woman disintegrate before our eyes.  When she died, at the young age of 65, she looked like she was 90.  This happened in the most developed nation on earth, with the best medical care available.  Suffering is not restricted to 3rd world countries - nor is it restricted to children.  We all see it.

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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: Nov. 20 2007,19:20   

Quote (mitschlag @ Nov. 17 2007,07:25)
One thing I find interesting is that when he can't provide answers to standing questions, Daniel changes the subject.

Some of you get on me for not answering every question thrown at me here.  You make it out that, if I don't answer your questions, it's because I'm "running away", or "avoiding real questions", or "changing the subject", (even though I'm only one man and there are many of you, firing many questions at me).

I started out talking about the fossil record, Schindewolf, Berg and natural selection, yet most of you wanted to "change the subject" to molecular evidence.

I asked about the multi-layered complexity of the human genome and most of you dismissed it with a shrug of the shoulders as if it was "old news".

I brought up the "histone code" but - no comments.

And, no one even tried to answer this question I posted:        
Quote (Daniel Smith @ Nov. 10 2007,11:29)

In the human genome, what percentage of genomic sequence would you say is likely to be transcribed as nuclear primary transcripts?


So.  Are you all running away? (Or does that only apply to me?)

--------------
"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

  
mitschlag



Posts: 235
Joined: Sep. 2006

(Permalink) Posted: Nov. 21 2007,06:42   

Quote (Daniel Smith @ Nov. 20 2007,19:20)
And, no one even tried to answer this question I posted:              
Quote (Daniel Smith @ Nov. 10 2007,11:29)

In the human genome, what percentage of genomic sequence would you say is likely to be transcribed as nuclear primary transcripts?

So.  Are you all running away? (Or does that only apply to me?)

But, but, but hasn't a start in obtaining data that answer your question been obtained by the ENCODE Project?

And hasn't this just been discussed (e.g. JAM Nov. 17 2007,10:30, among others)?

Looks to me like the ball is in your court to make whatever you want to make out of the data.

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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)

  
mitschlag



Posts: 235
Joined: Sep. 2006

(Permalink) Posted: Nov. 21 2007,07:19   

In case memories need to be refreshed, here is Figure 4 of Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project


Three different technologies (integrated annotation from GENCODE, RACE-array experiments (RxFrags) and PET tags) were used to assess the presence of a nucleotide in a primary transcript. Use of these technologies provided the opportunity to have multiple observations of each finding. The proportion of genomic bases detected in the ENCODE regions associated with each of the following scenarios is depicted: detected by all three technologies, by two of the three technologies, by one technology but with multiple observations, and by one technology with only one observation. Also indicated are genomic bases without any detectable coverage of primary transcripts.

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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)

  
JAM



Posts: 503
Joined: July 2007

(Permalink) Posted: Nov. 21 2007,11:05   

Quote (JAM @ Nov. 17 2007,10:30)
 
Quote (Daniel Smith @ Nov. 16 2007,18:50)
One thing I find interesting here is that most of you have shown no interest in any of the various papers I've cited from the ENCODE project.
These papers clearly show a multi-layered, overlapping, multi-directional "coding" scheme within the human genome.

Why would the human genome be so different from the Drosophila genome?

And if it's a scheme, why don't you understand it? And if it supports your hypothesis, why didn't you predict it?


 
Quote
(I put "coding" in quotes since most of the genome "codes" for things other than proteins and so is currently classified as "non-coding").

You don't know what you're talking about. Given that, how can you ethically reach the conclusion that we don't know what we are talking about?
 
Quote
They also show quite clearly that most of the human genome is transcribed and functional.

Now you're just lying. You haven't shown that transcription necessarily implies function. I already asked you to make a prediction about the relationship between the time transcription of an essential gene begins and the time at which the null mutant has a phenotype, but you ran away.
 
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These scientists are suggesting that a re-defining of the most basic term in genetics - the gene - is necessary.

So what? That does absolutely nothing to support a design hypothesis.
 
Quote
I'll ask again:  When did any of your various theories or hypotheses predict such a complex interwoven tapestry within our genome (or any other)?

1) MET makes clear, testable predictions about the mechanisms by which the messy, fuzzy nature of our genome came about.
2) As for any other, similar phenomena were shown in the Drosophila bithorax complex FIVE YEARS AGO. Therefore, we predicted similar complexity in the human genome.
 
Quote
And...
Is that why none of you want to talk about it?  Does it cause difficulties for you?

It doesn't address any of your predictions--it's just the same ol' post hoc spin to try and conceal the fact that you are dishonest, because you won't change or abandon your hypothesis when its predictions are shown to be false.

Bearing false witness is a sin in my Bible, Daniel.

Daniel, by what twisted logic do you describe this post as running away?

YOU are the one running away.

Also, please convey my deepest sympathies to your wife on the loss of her mother, but let's realize that her death is not relevant to your theologically twisted claim that God is causing children to be poor and dying of malaria just to teach people like you and me a lesson.

Do you not realize that your position implicitly claims that you are much more important in God's sight than those millions of children? If God's goal was to teach you a lesson (because you are so special), wouldn't the lesson be far more effective if he caused YOUR OWN child (or wife or mother) to die of malaria?

  
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