Is all TRUTH scientifically knowable?

[Scott J]

UT, I would argue that there was never a time when conditions were so ideal for our moment in history. Therefore, nothing is arbitrary- not our distance from the sun, relation to the stars, degree of gravitational decay, degree of atmospheric decay, etc. It is all as it needs to be at this moment. If it were different then it would defy God's plan for man as of now.

So in other words, whether this represents billions of years of 10K, God has necessitated that things be as they are... it is not arbitrary but rather a divine choice that neither of us is equipped to fathom.

 

[Scott J]

BTW UT, I would still like your answer to my question.

 

[UTEOTW]

"Please name the effects of the supposed new, beneficial, HIGHER capabilities arising from this supposed new information.

I virus that damages a gene is not an example of increasing information. At best it is lateral, at worst it is detrimental."

Well the case of the viral gene that was inserted during an infection and then in later generations mutated became a gene important to the devolpment of the placenta during reproduction. So it was not a case of a virus damaging a gene.

"The fly mutation you mentioned... would that have yielded an advantage or disadvantage to the fly in natural selection? The second set of wings were useless. The net result would be that this mutation would have been de-selected which serves to disprove rather than proving macroevolution."

Not sure what you are talking about here with the two sets of wings. The fruit fly mutation that we previously discussed was a new gene used by the sperm of the fly. The mutation was so advantageous that it swept through the lab's population of flys very quickly all on its own. I would suppose that it would have had the same result in a wild population also.

"Yes. I believe so. I believe that diseases like AIDS are examples of our progressive weakening coupled with the opportunity provided by deviant sexual behavior."

AIDS has nothing to do with whether we are weakening as a species. It happened too suddenly. You would have to suppose that from one generation to the next that our immune system was uniformly damaged or something similar.

"For someone without billions of dollars in resources to have people "prove" my contentions, I don't think you have done all that well at shooting my major suggestions down."

Your "alternatives" really are not specific enough to shoot holes in. Nothing concrete. Nothing evidentiary.

I would love to have a comprehensive theory from you that winds all the various lines of evidence into a single consistent explanation instead of the ad hoc explanations we get now. A theory with evidence that specifically supports that theory. One with specific lines of evidence that would falsify the theory. One that made specific predictions about what else we should find as we research.

And since YEers generally lump all science into a catchall of "evolution" then we would need similar details for things such as astronomy and geology.

"It shows change. I didn't say that man had lost all ability to adapt."

You were pretty clear that you though the direction of change would always be harmful. "Man will continue to grow weaker on the whole as his genome decays- more disease, more detrimental mutations."

You also were clear that there could not be beneficial change. "I know that is what the theory "proposes". I simply have seen no observed/experimental proof that it works that way. The "missing link" so to speak is the upward development. I have not argued against speciation... but speciation by the processes we actually observe. Animals use the genetic abilities inherited from their parents to adapt... not to evolve into a higher species. The evidence supports lateral change or descent (a net loss of information) not accumulation."

But now when beneficial change is shown, you then change to allow for adaptation. You have to choose one or the other. Things can adapt or they cannot.

"But you do feel the need to invoke naturalism for every historical event concerning creation?"

I do where God's creation indicates that it is the correct way of viewing it.

"Must something be "true" to be scientific? Can something be "false" and be science?

If it turns out that God created the world by means other than evolution (which I hope you at least admit as a possibility considering the attributes claimed for Him in the Bible), will that mean that evolution was not valid science all along?"

I am still not entirely sure what you are asking, but I'll take a stab in the dark.

There are theories that are later shown to have either been mistaken or to have been flawed. The "aether" is a good example. So there are examples of of theories that were in science that were later found to not be true. So, no, it does get it right the first time every time.

While it is certainly possible that God used means other than long periods of change to create what we see, what we know of the world and the universe right now strongly suggests that He did use such processes to create. It is also entirely possible that we may find contradictory information in the future that will indicate something else. But that is not the case now. If it is in the future, then theories will be modified accordingly. Most scientists are not out to ptomote an agenda. They simply want the truth. If the data moves that truth in a new direction, I feel confident that most will move that way in time.

 

[Phillip]

Originally posted by UTEOTW:
"A) Either you KNOW God is real and you accept Jesus as your Lord and Savior and include the room for God's supernatural ability in the science you observe"

I think I have been clear. I go for A but I refuse to go for it in arbitrary ways. You can simply say it is all supernatural but that means a lot of what we see was done for very arbitrary means. I, personally, don't accept that.

Thank you UTEOTW, I did not see this post. I appreciate the answer.

 

[UTEOTW]

"The component mechanisms you claim for macroevolution are mostly falsifiable but not the composite explanation you would like to blend them into."

After thinking about it, this is something I wanted to come back to. I am not completely sure that we are talking about the same thing here, but since it is the various lines of evidence that I have presented as best being explained by evolution and because these are the items that I have also been giving you specific examples of what would falsify them, I think we are talking about the same thing.

Now there are a number of such things that I have used. The twin nested heirarchy. Genetic vestiges. Developmental. Pseudogenes. Morphological vestiges. And so on. These are the things that are best explained by evolution. When you ask for evidence of evolution, these are the things I try to present. When you claim that evolution is not falsifiable, these are the things that I will give you examples of how to falsify them.

I do not think it can be divorced as you tried to do. If the pieces are falsifiable, then the whole is too. If evolution is the tie that binds all the pieces together best, then it is most likely the true explanation. Especially in the absence of a more parsimonious explanation.

Let's explain.

Let's just return to one of my favorites. Retroviral inserts. I like this one because it gets away from any hint of common designer argument because this involves viral DNA that has been fused during infections. This is a process that we can observe today quite readily. (HIV is a widely studied retrovirus, for one example.) It is also an example of how arbitrary the design would have to be to include such items in a young earth scenario. We can tell that the sequences are not useful because of the pattern of mutation. Useful code tends to have mutations mainly in the third position of each three base codon because changes here are often silent. Changes to the other two positions are much more likely to cause change in function.

To refresh, when a retrovirus infects a host, it can insert part of its DNA into the genome of the host's cells. In rare cases, this insertion will happen in a reproductive cell which is then later used for reproduction. If this happens, then the viral DNA becomes a part of the genome of the offspring. Occasionally, such a sequence will become fixed into the entire population.

Now, not every insert is shared among all apes. This alone allows for the reconstruction of trees based on which species have which inserts. This provides a convenient place for you to falsify evolution. For example. if you could show that humans and baboons shared a few inserts at exactly the same locations which were missing in chimps and gorillas, you could make a strong case against the current theory. On the other hand, any other proposed theory must explain why the species shared these particular inserts in these particular locations. But which inserts are shared is not even the point I want to stress.

So let's look at another side of this. Let's take just the shared inserts. For each shared insert, you can look at how mutations have accumulated in each sequence. By matching up where the sequences from different species show the same mutations and where they show different mutations, you can construct trees of how they are related. This become powerful evidence when you do this for many different sequences and come up with the same patterns. Especially when these patterns match the pattern of which sequences are shared to begin with. Especially when the patterns match those from other types of genetics. Especially when all of these match the patterns from the fossil record.

Common descent explains these shared patterns of mutation very well. This again provides a means to falsify evolution. For example, if you could show that contrary to prediction that these patterns were often contradictory or that they often do not nest in ways consistent with other data. In addition, any competing theory must explain this pattern of mutation.

On another thread, someone suggested that perhaps all of the apes swapped infections while on the ark and that furthermore some of the insertions could have been transferred by other infectious agents. This explanation could tell us why the same insertions are shared but not the locations and not the mutations in the insertions.

No other theory can adequately explain the data collect from endogenous retroviral inserts. This line of evidence by itself is enough to establish evolution as a viable theory in the absence of any other data. Abd this is just a very small slice of the evidence from just this line. And all of the retroviral data is puny compared to the data from the other lines.

Now, for further reading, I suggest that you read the following paper. It shows how these techniques are applied to twelve specific inserts. It mentions some important things, such as the markers surrounding the inserts that allow you to know they are in the same location.

http://www.pnas.org/cgi/content/full/96/18/10254

A figure in the paper gives the trees produced from the twelve sequences. See how similar they are? This would not be the case if they were all inserted recently and mutated in separate lines. This would not be the case if the inserted sequences were later swapped. This would not be the case if they served some unknown purpose. This data is only explainablee by common descent. Any other proposed alternative must be able to explain it in detail. Not just an ad hoc, general statement. You have yet to propose an alternative that accounts for such things in such detail.

http://www.pnas.org/content/vol96/issue18/images/large/pq1892815002.jpeg

 

[Scott J]

Now there are a number of such things that I have used. The twin nested heirarchy. Genetic vestiges. Developmental. Pseudogenes. Morphological vestiges. And so on. These are the things that are best explained by evolution. When you ask for evidence of evolution, these are the things I try to present. When you claim that evolution is not falsifiable, these are the things that I will give you examples of how to falsify them.

I do not dispute that these things have been explained in terms of evolution... what I dispute is that evolution is necessary to make a rational explanation of these things.

I believe that evolution's assumption of naturalism puts unwarranted limitation on possible causes.

 

[Scott J]

Let's just return to one of my favorites. Retroviral inserts. I like this one because it gets away from any hint of common designer argument because this involves viral DNA that has been fused during infections. This is a process that we can observe today quite readily. (HIV is a widely studied retrovirus, for one example.) It is also an example of how arbitrary the design would have to be to include such items in a young earth scenario. We can tell that the sequences are not useful because of the pattern of mutation. Useful code tends to have mutations mainly in the third position of each three base codon because changes here are often silent. Changes to the other two positions are much more likely to cause change in function.

To refresh, when a retrovirus infects a host, it can insert part of its DNA into the genome of the host's cells. In rare cases, this insertion will happen in a reproductive cell which is then later used for reproduction. If this happens, then the viral DNA becomes a part of the genome of the offspring. Occasionally, such a sequence will become fixed into the entire population.

Now, not every insert is shared among all apes. This alone allows for the reconstruction of trees based on which species have which inserts. This provides a convenient place for you to falsify evolution. For example. if you could show that humans and baboons shared a few inserts at exactly the same locations which were missing in chimps and gorillas, you could make a strong case against the current theory. On the other hand, any other proposed theory must explain why the species shared these particular inserts in these particular locations. But which inserts are shared is not even the point I want to stress.

This example fails on several points.

First, HIV provides a very good example of how two or more different species can acquire a retrovirus in a way that does not point to a common ancestor. Now assuming that this was a non-lethal retrovirus, I think it is likely that some of the species would assimulate the mutation in a similar way while others would assimulate it in different ways through successive generations.

Second, the insert does not lead to useful information that will likely lead to the formation of some complex biological system. At best you have a lateral change. At worst you have a species that is weaker because of this.

Third, it does not follow that a retrovirus would ever produce the kind of genetic modification needed for macroevolution. An organism so damaged by these inserts would not move to greater functionality... it would most likely cease to function at all.

Fourth, this case again is a speculative explanation. Not an observation. Not a reproducable experiment.

Fifth, retroviruses can never represent a cause for early evolution... they themselves had to have evolved some time later.

Sixth, retroviruses are resisted and any changes produced by such a mechanism would most likely not be favored/allowed unless it was completely benign. Changes in structure or function are not benign.

Seventh, retroviruses are coded and have specific functionality. An intelligently designed machine that can effect the coding of an intelligently designed machine is a relatively small leap. A chance organism coded by luck of the draw effecting the coding of another chance organism coded by luck is a huge leap.

 

[UTEOTW]

I think you missed the whole point.

I was not trying to explain mechanisms of how it happened. I was explaining clues that lead to letting us know it did happen. Most of your response has to do with "information" which is a case of building and knocking down a straw man.

The point was to show how shared insertions in the same locations with specific patterns of mutation lead to a conclusion of common descent.

YOu straw man failed to address any of this. Maybe why some organisms would exposed to the same viruses. But no reason why they should have nearly identical sets of infections that result in the very same inserts being added in the very same genetic locations. Furthermore, why the pattern of accumulated mutations since the insertions should so very strongly correlate to the same trees. And why the trees from theses methods should so strongly correlate to trees from other methods.

There is no hint of an alternative that explains these details. And that is what we must have. Another process that generates this specific type of data.

There is no such process that has been proposed.

 

[Scott J]

Originally posted by UTEOTW:
I think you missed the whole point.

I was not trying to explain mechanisms of how it happened. I was explaining clues that lead to letting us know it did happen. Most of your response has to do with "information" which is a case of building and knocking down a straw man.

I don't think so UT.

You don't "know" it "did" happen. The clues at best say it could have happened. The "information" aspect of this isn't a straw man... it is the main contended issue.

Do viruses infect? Yes. Do those viruses sometimes result in damage that is replicated and passed on? Apparently that may be the case. You need much more than this however to prove that man evolved from amoeba.

The point was to show how shared insertions in the same locations with specific patterns of mutation lead to a conclusion of common descent.

That's fine and dandy. I accept that as being within the realm of possibility but because of my belief that overall the evidence does point toward design as well as direct statements by scripture- I remain skeptical of that conclusion.

Like I mentioned, HIV gives yields a refutation of your explanation. HIV has infected several species without the benefit of a common ancestor that carried the disease.

Maybe why some organisms would exposed to the same viruses. But no reason why they should have nearly identical sets of infections that result in the very same inserts being added in the very same genetic locations.

What do we actually "know" is common about this scenario? The retrovirus. I find it more likely that the retrovirus had a novel capability to leave the insert in certain locations favorable to that process than that the insert points to a common ancestor.

Furthermore, why the pattern of accumulated mutations since the insertions should so very strongly correlate to the same trees.

Maybe because the trees were customized to fit the finding? What do you mean "strongly correlate"? For what you assert to be true, it must exactly correlate.

There is no hint of an alternative that explains these details.

I just gave you one. Life forms with similar DNA by design are infected by retroviruses with a novel capability to leave inserts at favorable sites.

There is no such process that has been proposed.

Have you actually proposed this to a biochemist or such that is a creation/ID proponent?

I haven't researched it... but before I go expert hunting (should I find the time) I want to understand on what basis you claim that no alternative has been proposed.

 

[UTEOTW]

"You don't "know" it "did" happen. The clues at best say it could have happened."

I explained that. A virus infected an ancestor of ours. The virus inserted a part of its genome into a cell that was later used for reproduction. The insertion was then part of that offspring's genome and later got fixed into the whole population. We can tell by the genetic markers. This was covered in the paper I referenced.

"Do viruses infect? Yes. Do those viruses sometimes result in damage that is replicated and passed on? "

Yes, and it is the pattern how how it was passed on that is key here.

"I accept that as being within the realm of possibility but because of my belief that overall the evidence does point toward design as well as direct statements by scripture- I remain skeptical of that conclusion."

These insertions are not covered by design. They are products of infection.

"Like I mentioned, HIV gives yields a refutation of your explanation. HIV has infected several species without the benefit of a common ancestor that carried the disease."

Then perhaps you can point me to where HIV has resulted in the insertion of the same genetic sequence across several species in the SAME LOCATION in each species and in a nested heirarchy of mutations in those species consistent with other lines of evidence. That is what it would take for HIV to refute my claims. Not just that it can infect, not just that in can infect multiple species, not just that it inserts it DNA.

It is, however, an example of such a process we can study today to be more certain that our claims about the past our accurate.

"What do we actually "know" is common about this scenario? The retrovirus. I find it more likely that the retrovirus had a novel capability to leave the insert in certain locations favorable to that process than that the insert points to a common ancestor."

Did you read the paper? This was covered specifically.

The mechanisms of insertion and they have been observed to be random. So this eliminates your possibility of the various virii being prone to only insert in one specific location. For more read

Varmus, H. E. & Swanstrom, R. (1984) in RNA Tumor Viruses, eds. Weiss, R., Teich, N. M., Varmus, H. E. & Coffin, J. M. (Cold Spring Harbor Lab. Press, Plainview, NY), pp. 369-512.

and

Brown, P. O. (1997) in Retroviruses, eds. Coffin, J. M., Hughes, S. H. & Varmus, H. E. (Cold Spring Harbor Laboratory Press, Plainview, NY).

"Maybe because the trees were customized to fit the finding? What do you mean "strongly correlate"? For what you assert to be true, it must exactly correlate."

No, this is more of a mathematical analysis. Statistics. It is called bootstrap analysis. It does not depend on prior assumptions or on customizing the results to fit some preconceived notion.

You can disagree with what the trees mean but you have no basis to disagree on the trees them selves. If you disagree with what they mean then it is up to you to provide the alternate, better explanation.

"I just gave you one. Life forms with similar DNA by design are infected by retroviruses with a novel capability to leave inserts at favorable sites."

Nope. Insertions are observed to be random.

"Have you actually proposed this to a biochemist or such that is a creation/ID proponent?

I haven't researched it... but before I go expert hunting (should I find the time) I want to understand on what basis you claim that no alternative has been proposed."

Let me rephrase the statement.

Though I have read young earth material quite a bit, I have found no explanation for the retroviral inserts that accounts for both the same insertions, the same locations for the insertions and for the pattern of mutations in the insertions.

Your attempts at explanation above fail the test of being consistent with observations. You claim that the insertion tend to infect the same place without presenting evidence of such while I have presented evidence that they are truly random. You have only denied the phylogenic trees without giving a reason while they are wrong and ignoring the math that gives the trees straight from the data itself. (Read that as NOT from forcing it to a preconceived notion.) You made only ad hoc attempts with no supporting data and in disagreement with the actual observations.

I repeat my previous assertion. There is no other parsimonious explanation for all aspects of the data. The retroviral inserts themselves are powerful evidence for the common descent of man with the other apes.

I'll re-link the paper for you here. It is good reading and you may want to spend some time with the references at the end. I suggest Google Scholar. ( http://scholar.google.com/ )

http://www.pnas.org/cgi/content/full/96/18/10254

 

[UTEOTW]

The above may require a bit of work on your part.

In the mean time, could you define what you mean by "information" and what kinds of things you would accept as evidence that information does increase and / or that mutations can be beneficial?

It would greatly help to have a better idea of what you mean by these things.

[ January 31, 2005, 09:02 PM: Message edited by: UTEOTW ]

 

[Scott J]

The mechanisms of insertion and they have been observed to be random. So this eliminates your possibility of the various virii being prone to only insert in one specific location.

I am operating on your information primarily and trusting you to be accurate and consistent.

Earlier you said that this effect always happened at a particular pair. Now you are saying it is random. Please reconcile these two assertions for me.

I have only novice understanding of genetics but either I misunderstood or you seem to have contradicted your own evidence.

By the way, if these are indeed random then that adds even more weight to my contention that it is no evidence whatsoever of a common ancestor. The virus and its ability to leave a persistent insert is the constant. It is simply able to infect more than one species.

Other questions: Are all members of a species infected with this way? If not, what has been the observations of the pair that would have otherwise been subject to infection?

Other than reproducing part of the virus' code, is there any novel ability, system, or protein being produced due to the infection? Has this actually resulted in a net increase in usable information or is this simply an infection genetically passed by reproduction?

 

[Scott J]

Though I have read young earth material quite a bit, I have found no explanation for the retroviral inserts that accounts for both the same insertions, the same locations for the insertions and for the pattern of mutations in the insertions.

....You claim that the insertion tend to infect the same place without presenting evidence of such while I have presented evidence that they are truly random.

To be... or not to be... random.

Please reconcile these two statements.

 

[UTEOTW]

OK. The location of the inserts at the time of insertion is random. Once inserted and fixed into the gene pool, they are always found at the same location in the various species and within a species.

There is a line in the paper I referenced for you that states that because the locations of insertions are known to be random, that when you find two species that have the same insert in the same location the only possible explanation is that they share a common ancestor. YOu had suggested that perhaps separate infections in separate species led to the same insertions. I countered that the observations are that the insertions happen at random locations so when two species show the same location for the same insert, this indicates a SINGLE insertion event.

"Other questions: Are all members of a species infected with this way? If not, what has been the observations of the pair that would have otherwise been subject to infection?"

These inserts are only useful for such tracing when the insertion gets fixed into a population. From what I understand, all humans share almost all of the same insertions. I seem to recall one insertion that has been found only in a specific human population. So it occurred since our last common ancestor. Other genetic sequences are also known to only be present in certain populations.

It is rather rare for the insertion to happen in a cell later used for reproduction, so there should be little expectation of finding variety of insertions in a population. And as far as I know, this is true.

The inserts under consideration are those that have both been in a reproductive cell that was later used and that then became fixed into the population.

 

[Scott J]

Originally posted by UTEOTW:
OK. The location of the inserts at the time of insertion is random. Once inserted and fixed into the gene pool, they are always found at the same location in the various species and within a species.

Which goes back to my contention about the common theme being the virus not a common ancestor. Insertions are random but they only "stick" in a certain location. This does not necessarily point back to a common ancestor but rather to a range of species infected at random points with the same virus. A virus that has the ability to leave behind a permanent marker at a specific location. Perhaps the location is simply hospitable to the insert... like a blind spot in genetic proofreading.

that when you find two species that have the same insert in the same location the only possible explanation is that they share a common ancestor.

That does not follow UT. If these inserts are being made randomly but require special conditions to become persistent then you would expect the cell to purge them at every other place.

I countered that the observations are that the insertions happen at random locations so when two species show the same location for the same insert, this indicates a SINGLE insertion event.

But that is not necessarily true. What we see is a shared weakness, not a shared ancestor.

BTW, I would consider this genetic bad news, not good news. It cannot be a good thing that an organism passes part of a virus on to its offspring in such a way. At best, you are talking about a species that is now weaker due to wasting energy to replicate useless material. At worst, you are describing a species that has become less durable.

"Other questions: Are all members of a species infected with this way? If not, what has been the observations of the pair that would have otherwise been subject to infection?"

These inserts are only useful for such tracing when the insertion gets fixed into a population. From what I understand, all humans share almost all of the same insertions.

I would expect that all members of a species would not possess the trait for two reasons related to my idea of common descent.

First, I believe that this is a mechanism by which descendents of a rich genome could acquire mutations that prevented them from moving back up stream so to speak- Not the only mechanism, but one.

Second, I would expect even benign but useless materials would be disfavored over time. The mutated gene and its insert would progressively disappear- amounting to a permanent loss of genetic variability if not function.

The inserts under consideration are those that have both been in a reproductive cell that was later used and that then became fixed into the population.

In what way was function changed? How does the location of the insert appear in members of a species that do not have the insert? Is the insert static or does it change over time?

 

[UTEOTW]

"Which goes back to my contention about the common theme being the virus not a common ancestor. Insertions are random but they only "stick" in a certain location. This does not necessarily point back to a common ancestor but rather to a range of species infected at random points with the same virus. A virus that has the ability to leave behind a permanent marker at a specific location. Perhaps the location is simply hospitable to the insert... like a blind spot in genetic proofreading."

No, no. That was the point of the two references.

Let's try a slightly different approach.

When the virus enters a given cell, it may attempt to insert its DNA into that of the host. (Now, I am not a virologists so I cannot say whether it attemps this in every cell or just some though I would suspect every cell.) If the attempt is successful, then the DNA becomes a part of the genome of that cell. I will make the assumption here that the purpose is to have host cell crank out copies of a protein the virus needs.

Now, where that insertion happens is random. But, once successful, it is stuck in that one spot not to be removed. Each insertion in each cell would happen at a different location because the location is random.

Though the location is random, once inserted it is stuck at that spot. Now, if a sperm cell or egg cell (or more specifically the germ line cell that eventually makes the particular egg or sperm) is infected, this randomly inserted bit of viral DNA will be passed on to the offspring. Every cell in the offspring will have this insert and at the same location and will pass it on to its offspring.

It is only the ability to leave behind a marker that the virus possesses. It does not have the ability to leave that marker at a particular spot. The randomness of the location of insertion has been demonstrated. Since it is part of the genome now, the host also does not try and remove it. The subject of removal was also covered in the paper I linked for you. It is very rare for a mutation to remove the insert once it is there. And when it does happen, there are genetic markers that still remain that show where the insert was.

There is no reason for the location to be more or less hospitable to this DNA sequence than to any other non-coding sequence. It is simply there.

"That does not follow UT. If these inserts are being made randomly but require special conditions to become persistent then you would expect the cell to purge them at every other place."

Not really. The cell has no way to know what piece of genetic junk to purge. It just sits there.

The only special condition for it to become persistent is for it to be in a cell that is later used for reproduction. This will make it persistent in the offspring. For the entire population, it must happen that through sexual reproduction eventually all of the members of the population have the gene. It is then fixed into the population.

"But that is not necessarily true. What we see is a shared weakness, not a shared ancestor."

No, it really is a shared insertion. Again, because of the randomness of it all and the incredible size of the genome, only a shared insertion explains the connection. This is bolstered by the pattern of mutations after the lines of ancestors split into different species.

"BTW, I would consider this genetic bad news, not good news. It cannot be a good thing that an organism passes part of a virus on to its offspring in such a way. At best, you are talking about a species that is now weaker due to wasting energy to replicate useless material. At worst, you are describing a species that has become less durable."

Not really. It is junk that is not expressed. About the only drain is having to have a few extra nucleotides around to reproduce the sequence when the cell divides. Otherwise it just sits there.

In addition, there are examples of these sequences mutating and becoming a useful gene for the organism.

"First, I believe that this is a mechanism by which descendents of a rich genome could acquire mutations that prevented them from moving back up stream so to speak- Not the only mechanism, but one."

The sequences are not expressed and do not interfere with the other activities of the cell. They neither hinder nor help.

"Second, I would expect even benign but useless materials would be disfavored over time. The mutated gene and its insert would progressively disappear- amounting to a permanent loss of genetic variability if not function."

Well, partially right. Since they are useless, they are not conserved. Mainly they just accumulate random mutations. This is what allows us to trace ancestry through the inserts. It would be rare for a deletion mutation to snip just this particular sequence. (As stated above, this scenario is covered in the paper.)

"In what way was function changed? How does the location of the insert appear in members of a species that do not have the insert? Is the insert static or does it change over time?"

No function was changed. They appear in the whole population just because of the randomness of sexual reproduction. Most likely, a beneficial mutation not connected to the insertion in any way comes along. As this beneificial trait sweeps through the population due to selection (Called a selective sweep. I have previously linked you to an example.) other genes get carried along for the ride. Some of these can be such inserts.

Now remember, this is very rare. You are only talking about a number on the order of magnitude of a dozen such inserts specific to the apes. This is over about 10 million years or so of evolution. So it is a rare occurance indeed.

Even in individuals, it is very rare for such an insert to be passed on. We know this because the human population shares these inserts almost exactly. If it were common, then different people would have a different combination of inserts.

The insert is static in the sense that it does not move. It is dynamic in the sense that random mutation can accumulate very easily because the sequence is not useful and is therefore not conserved. But, again, it is these changes that allow us to use math to build the relationship trees.

 

[Scott J]

Not really. It is junk that is not expressed. About the only drain is having to have a few extra nucleotides around to reproduce the sequence when the cell divides. Otherwise it just sits there.

So in other words, this phenomenon that we have wasted a great deal of time discussing has nothing at all to contribute to macroevolution?

 

[Scott J]

BTW, none of what you posted adds up to common ancestory as a necessity and I still do not think you have successful dismissed the possibility of common design as opposed to common ancestory.

You have asserted that only common ancestory explains the insert but the reasoning you have posted does not result in that level of certainty.

 

[Phillip]

Then again, we are going back to the place we started. Scientific research eliminates the variable of a supernatural God. Is that a correct equation to be using, especially when dealing with the creation which is documented by God's Word?

 

[UTEOTW]

"So in other words, this phenomenon that we have wasted a great deal of time discussing has nothing at all to contribute to macroevolution?"

It is strong evidence that it happened. You do not accept the mechanisms when presented so it seems that maybe we should focus solely on some of the evidence for it for a while. Any alternate ideas must be able to explain the details of our observations. There is, as yet, no parsimonious explanation for the details outside of common descent.

"BTW, none of what you posted adds up to common ancestory as a necessity and I still do not think you have successful dismissed the possibility of common design as opposed to common ancestory."

I disagree.

First off the shared insertions themselves in the same locations are really a fairly tight case. One that can be considered to be beyond a reasonable doubt. That there are numerous such shared insertions is an even tighter case. Quoting the paper I referenced for you.

Endogenous retrovirus loci provide no less than three sources of phylogenetic signal, which can be used in complementary fashion to obtain much more information than simple distance estimates of homologous sequences. First, the distribution of provirus-containing loci among taxa dates the insertion. Given the size of vertebrate genomes (>1 × 109 bp) and the random nature of retroviral integration (22, 23), multiple integrations (and subsequent fixation) of ERV loci at precisely the same location are highly unlikely (24). Therefore, an ERV locus shared by two or more species is descended from a single integration event and is proof that the species share a common ancestor into whose germ line the original integration took place (14).

In case you are wondering waht the text says are the other two...

Second, as with other sequence-based phylogenetic analyses, mutations in a provirus that have accumulated since the divergence of the species provide an estimate of the genetic distance between the species. Because, for any given provirus, it is highly unlikely that there will be selection for or against any specific sequence, it is safe to assume that the rate of accumulation of mutations approximates the rate of their occurrence, with appropriate corrections for reversion. Analysis of closely related proviruses integrated at different sites should also reveal regional differences in mutation rates.

Third, sequence divergence between the LTRs at the ends of a given provirus provides an important and unique source of phylogenetic information. The LTRs are created during reverse transcription to regenerate cis-acting elements required for integration and transcription. Because of the mechanism of reverse transcription, the two LTRs must be identical at the time of integration, even if they differed in the precursor provirus (Fig. 1A). Over time, they will diverge in sequence because of substitutions, insertions, and deletions acquired during cellular DNA replication.

Common design is ruled out because these are functionless bits of junk. You can tell they are functionless by the mutations. First, if they were useful, then the sequences would be more conserved by selective pressures. Second, if they were useful, there would be a disparity in which positions had substitutions because the changes to the third letter of each codon tends to be silent while changes to the other two positions are more significant.

A common design that littered the genomes with random bits of viral DNA would be a sloppy design indeed.

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"Then again, we are going back to the place we started. Scientific research eliminates the variable of a supernatural God. Is that a correct equation to be using, especially when dealing with the creation which is documented by God's Word? "

I am not denying that God could have done this if He so desired.

Are you suggesting that He littered the genomes of organisms with bits of mutated DNA from viruses that apparently never actually infected their hosts and in a pattern that is only consistent with common descent? For what purpose?

This is my problem with such reasoning. Sure, you can inject a supernatural explanation wherever you find no other way to refute something. But it requires an arbitrary and capricious use of the supernatural both by you and by God. There is no purpose for putting these random bits of viral DNA in there. But they can tell us about how God created. You just choose not to accept it and without even a plausible alterante explanation.