"While I don't have time to get into this now (just about to leave on vacation)..."
It will be here when you get back.
"...I would ask what assumptions have been made here.
For example, have all the genes been taken into consideration, or just the ones which code for proteins? Since it has been discovered that DNA formerly thought to be junk actually performs functions such as gene activation, this is important."
I would encourage you to examine the evidence for yourself. If you can find specific mistakes, please point them out. More than likely, we can see where you are going. You will dispute the interpretation of the data. This is where the fun comes in. If you wish to challenge the assumption and the interpretations, then you will need to provide those better YE interpretations that never seem to materialize.
But there are a number of things which you will need to take into consideration as you formulate your alternative explanations. One of the first things mentioned is how most genes can be categorized into one of a small number of families based on similar sequences. This is an area where two things become important. One is that theoretical studies have shown that there are generally a very large number of potential proteins will be suited for a potential function. Second, while survival of the fittest is the catch phrase, often it is really survival of the barely adequate. Genes that are very similar perform different functions dispite the fact that there is very likely other proteins that could form each function much better. An alternate explanation would need to explain why an intelligently designed organism would use suboptimally designed sequences that are similar to one another rather that properly designing each individual gene for its intended purpose. On a related note, one reference I dug up yesterday but that I did not use (perhaps I'll look it up again later) notes that there are only a very small percentage of the possible protein folding arrangements actually used out of those which are possible. It would seem that an intelligently design organism would use everything available rather than using only a small subset. OTOH, it would be expected based on what we know of evolutionary mechanisms for folding patterns and gene sequences to be highly conserved towards that which has worked before.
Another aspect you would have to contend with is the evidence for actual duplication. For instance, at least one reference traced a whole series of duplication of the same gene by showing how particular segments in both introns and exons were repeated. In another case, a retroposon was inserted and over tens of millions of years it mutated until it became useful with lineage branches along the way providing means of determining when certain changes to the gene occurred. YOu would need to explain the presence of this particular pattern in the genome.
As far as your last part, I think that if you read through you will see that both coding and non-coding regions have been used to trace what happened. I'll agree that there have been discoveries in recent years that some parts that were formerly thought of as "junk" have been found to have regulatory purposes if you will acknowledge that much of it really is junk. I have told you several times in the past of methods that can be used to test whether a particular segment actually serves a purpose. Those which are useful will show a diverent pattern of mutation compared to those which are not useful, mainly in the distribution of mutations between the first, second and third positions of each codon. In material that is not useful, the mutations will be equally spread and in those that are useful, the mutations will be much more predominant in the third position. There should also be different rates of muation in selectively conserved sequences and mere junk.
"Also, the paper noted that some of the genes already contained nitralese genes - how do we know this information isn't ALREADY present?"
You say "the." Did you read them all? I cannot even find that term when searching my posts on this thread. Could you link to the post that you mean?
"Next, there is a lot of mention of plasmid DNA rather than nuclear DNA. How do we know these aren't designed to dynamicly adapt under pressure and then disable when the plasmids are de-activated in the abcense of pressure (such as in the case of the nylon eating bacteria)."
I am not sure what you are reading but I cannot find any mention of plasmid DNA on either page of this thread. Could you link to the post which you are talking about. I can find discusion of specific chromosomes, however.
But I still do not know why that even matters. DNA that serves a purpose serves a purpose whether it is nuclear or in plasmids. Adaptation is still adaptation. It is confusing why you should try and separate the two. In any case, the evidence for why it is believed that these genes evolved is presented. You are free to present a theory which better explains all aspects of the observations.
You might also want to explain your nylon bug assertion a bit better. If I remember correctly, it was a frameshift and several point mutations that led to the ability to digest nylon. I am not sure how that fits into whay you are saying.
Finally, you seem to be willing to accept the idea that plasmid DNA is adaptable, why not the whole genetic code? I personally think, and have posted this in the past, that the arrangement of the three letter codons and the differences that arise from changes to each position seems to indicate that the genetic code itself is optimized to adapt.
"Seems pretty unsubstantial to me."
Then you should have no trouble coming up with a better theory. But you did not seem to think the information challenege a few months ago would be very dificult, either, until you actually tried it. You declared victory without ever explaining why any of the examples were not examples of new "information."
It will be here when you get back.
"...I would ask what assumptions have been made here.
For example, have all the genes been taken into consideration, or just the ones which code for proteins? Since it has been discovered that DNA formerly thought to be junk actually performs functions such as gene activation, this is important."
I would encourage you to examine the evidence for yourself. If you can find specific mistakes, please point them out. More than likely, we can see where you are going. You will dispute the interpretation of the data. This is where the fun comes in. If you wish to challenge the assumption and the interpretations, then you will need to provide those better YE interpretations that never seem to materialize.
But there are a number of things which you will need to take into consideration as you formulate your alternative explanations. One of the first things mentioned is how most genes can be categorized into one of a small number of families based on similar sequences. This is an area where two things become important. One is that theoretical studies have shown that there are generally a very large number of potential proteins will be suited for a potential function. Second, while survival of the fittest is the catch phrase, often it is really survival of the barely adequate. Genes that are very similar perform different functions dispite the fact that there is very likely other proteins that could form each function much better. An alternate explanation would need to explain why an intelligently designed organism would use suboptimally designed sequences that are similar to one another rather that properly designing each individual gene for its intended purpose. On a related note, one reference I dug up yesterday but that I did not use (perhaps I'll look it up again later) notes that there are only a very small percentage of the possible protein folding arrangements actually used out of those which are possible. It would seem that an intelligently design organism would use everything available rather than using only a small subset. OTOH, it would be expected based on what we know of evolutionary mechanisms for folding patterns and gene sequences to be highly conserved towards that which has worked before.
Another aspect you would have to contend with is the evidence for actual duplication. For instance, at least one reference traced a whole series of duplication of the same gene by showing how particular segments in both introns and exons were repeated. In another case, a retroposon was inserted and over tens of millions of years it mutated until it became useful with lineage branches along the way providing means of determining when certain changes to the gene occurred. YOu would need to explain the presence of this particular pattern in the genome.
As far as your last part, I think that if you read through you will see that both coding and non-coding regions have been used to trace what happened. I'll agree that there have been discoveries in recent years that some parts that were formerly thought of as "junk" have been found to have regulatory purposes if you will acknowledge that much of it really is junk. I have told you several times in the past of methods that can be used to test whether a particular segment actually serves a purpose. Those which are useful will show a diverent pattern of mutation compared to those which are not useful, mainly in the distribution of mutations between the first, second and third positions of each codon. In material that is not useful, the mutations will be equally spread and in those that are useful, the mutations will be much more predominant in the third position. There should also be different rates of muation in selectively conserved sequences and mere junk.
"Also, the paper noted that some of the genes already contained nitralese genes - how do we know this information isn't ALREADY present?"
You say "the." Did you read them all? I cannot even find that term when searching my posts on this thread. Could you link to the post that you mean?
"Next, there is a lot of mention of plasmid DNA rather than nuclear DNA. How do we know these aren't designed to dynamicly adapt under pressure and then disable when the plasmids are de-activated in the abcense of pressure (such as in the case of the nylon eating bacteria)."
I am not sure what you are reading but I cannot find any mention of plasmid DNA on either page of this thread. Could you link to the post which you are talking about. I can find discusion of specific chromosomes, however.
But I still do not know why that even matters. DNA that serves a purpose serves a purpose whether it is nuclear or in plasmids. Adaptation is still adaptation. It is confusing why you should try and separate the two. In any case, the evidence for why it is believed that these genes evolved is presented. You are free to present a theory which better explains all aspects of the observations.
You might also want to explain your nylon bug assertion a bit better. If I remember correctly, it was a frameshift and several point mutations that led to the ability to digest nylon. I am not sure how that fits into whay you are saying.
Finally, you seem to be willing to accept the idea that plasmid DNA is adaptable, why not the whole genetic code? I personally think, and have posted this in the past, that the arrangement of the three letter codons and the differences that arise from changes to each position seems to indicate that the genetic code itself is optimized to adapt.
"Seems pretty unsubstantial to me."
Then you should have no trouble coming up with a better theory. But you did not seem to think the information challenege a few months ago would be very dificult, either, until you actually tried it. You declared victory without ever explaining why any of the examples were not examples of new "information."
