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Primate Endogenous Retroviruses Insertions


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#1 Jerome007

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Posted 12 September 2006 - 10:35 PM

Hey everyone. Got a biology question for ya.

It is the I idea that identical Endogenous retrovirus (ERV) insertions across primates prove a common ancestor. I'm not a big biology buff so I wasn't able to find much on this other then a post on another forum. Thoughts?

http://www.christian...es.html&page=23

#2 Fred Williams

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Posted 13 September 2006 - 02:30 PM

Hey everyone. Got a biology question for ya.

It is the I idea that identical Endogenous retrovirus (ERV) insertions across primates prove a common ancestor.  I'm not a big biology buff so I wasn't able to find much on this other then a post on another forum. Thoughts?

http://www.christian...es.html&page=23

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Here's the illusion behind claims like this - they assume the ERVs are functionless. The fact we have found some ERVs to have a function alone refutes this as evidence of common ancestry. Others are highly conserved (can't suffer mutation), which is strong evidence they are important (functional). Just because we do not know what they do in all cases, does not mean they have no function and are some evolutionary leftover. More speculation borne of question begging from our fairytale lover friends. :)

More details can be found here.

Fred

#3 Phaedrus

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Posted 27 September 2006 - 01:01 AM

ERVs are an odd sort of an evidence, the claim is that identical sequences are found in identical places in the Chimp/human genomes. I have not been able to find the publication that gives us the sequence identity, chromosome number and location of the seqeunce. I did find this from a little over a year ago, it is as enigmatic as the Talk Origins arguments that this is some kind of a smoking gun:

"Endogenous retroviruses. Endogenous retroviruses (ERVs) have become all but extinct in the human lineage, with only a single retrovirus (human endogenous retrovirus K (HERV-K)) still active24. HERV-K was found to be active in both lineages, with at least 73 human-specific insertions (7 full length and 66 solo long terminal repeats (LTRs)) and at least 45 chimpanzee-specific insertions (1 full length and 44 solo LTRs). A few other ERV classes persisted in the human genome beyond the human–chimpanzee split, leaving 9 human-specific insertions (all solo LTRs, including five HERV9 elements) before dying out."

(Initial Sequence of the Chimpanzee Genome, Nature Sept 1 2005)

If this is something chimps and humans have in common then why are they spoken of as human and chimpanzee specific. These are known to be the most highly transposable elements in the respective genomes, at what point are the sequences identical because I haven't found any and I have been looking for months.

"Against this background, it was surprising to find that the chimpanzee genome has two active retroviral elements (PtERV1 and PtERV2) that are unlike any older elements in either genome; these must have been introduced by infection of the chimpanzee germ line. The smaller family (PtERV2) has only a few dozen copies, which nonetheless represent multiple (5–8) invasions, because the sequence differences among reconstructed subfamilies are too great (8%) to have arisen by mutation since divergence from human. It is closely related to a baboon endogenous retrovirus (BaEV, 88% ORF2 product identity) and a feline endogenous virus (ECE-1, 86% ORF2 product identity). The larger family (PtERV1) is more homogeneous and has over 200 copies. Whereas older ERVs, like HERV-K, are primarily represented by solo LTRs resulting from LTR–LTR recombination, more than half of the PtERV1 copies are still full length, probably reflecting the young age of the elements. PtERV1-like elements are present in the rhesus monkey, olive baboon and African great apes but not in human, orang-utan or gibbon, suggesting separate germline invasions in these species."

PtERV1 and PtERV2 supposedly happened after the human/chimpanzee split, they give reasons for this. However, the PtERV1 ERV is present in the rhesus monkey, olive baboon and African great apes but not in humans! What is up with that?

I have had evolutionists rant and rave about ERVs but when they are confronted with the actual scientific data they are ready to change the subject. What they will tell you is that this represents some kind of a twin nested hiearchy, which is absurd, you wouldn't use highly transposable elements for something like that. You would use mitochondria dna (mtDNA) which is also refered to as a molecular clock. The molecular clocks are notoriously inaccurate and do not line up with what their paloeontologist brethren are saying. Molecular clocks can be as far out as 10-12 million years for the chimpanzee human split and that varies by a great deal as well.

ERVs are not proof of anything, if you notice there is very little scientific literature even being produced. That is because no one knew they were there until fairly recently and no one quite knows what to make of them, especially evolutionists.

Grace and peace,
Mark

#4 chance

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Posted 27 September 2006 - 01:40 PM

Extract from http://www.pnas.org/...ull/96/18/10254

a.

The genomes of modern humans are riddled with thousands of endogenous retroviruses (HERVs), the proviral remnants of ancient viral infections of the primate lineage.

b.

Most HERVs are non-functional (junk DNA) , selectively neutral loci. This fact, coupled with their sheer abundance in primate genomes, makes HERVs ideal for exploitation as phylogenetic markers.

(my italics)
c.

Retroviruses are unique among RNA viruses in their ability to integrate DNA copies of their genomes into the genome of the infected cell. On occasion, integration takes place in a germ-line cell, giving rise to an endogenous retrovirus (ERV), which can be inherited by the offspring of the infected host, and may eventually become fixed in the gene pool of the host population


Thus, if on a common strand of DNA that is found in chimps and Humans we find this situation:

ABCABCABCABCretroxyzABCABCABC, you can comfortably state that the infection happened when the species were one (although it does not rule out the possibility of an identical infection on the same location).

Where as if you find this:

In humans BCABCABCABCretropqrBC

and this in chimps BCAretroghiBCABCABCBC

you can confidently claim the two infections happened some time after the human and chimp linage split.

#5 Phaedrus

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Posted 03 October 2006 - 03:46 PM

chance,

I am getting kind of curious what your interest in the subject of creation/evolution actually is. I don't know if you are a Christian, scientist, amature philosopher, all of the above, none of the above...etc. I just thought I would ask before we went another round in the ERV catagory. You seem pretty fascinated with the subject, I was wondering what it was that attrachted you to the subject.

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Posted 03 October 2006 - 05:35 PM

chance,

(1) CAN THE EVIDENCE BE EXPLAINED DIFFERENTLY?

are there virus strains that attack several species?

If so, could the evidence for the attacks be with equal validity from either common ancestry as common vulnerability to attack?

(2) IS THE EVIDENCE BASED ON CODING PROBABILITY? IF SO ... IS SUCH EVIDENCE TYPE REALLY RESTRICTED TO "RELATED" FORMS?

Granted, the liklihood of common ancestry could be evidenced by a very improbable DNA string being replicated in purported modern descendants.

... what does that say about improbable coding (e.g. for the eye) appearing in a common form in non-ancestral species with separate "paths" (e.g. eye in a fly, & in eye in human, eye in octopus )?

Doesnt the argument based on improbability actually point away from common descent if it can be found that improbable DNA sequences have a common base function and coding across non-related species? (e.g. we didnt get the vertebrate eye from an octopus ancestor, did we?)

#7 chance

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Posted 03 October 2006 - 08:05 PM

I am getting kind of curious what your interest in the subject of creation/evolution actually is. I don't know if you are a Christian, scientist, amature philosopher, all of the above, none of the above...etc. I just thought I would ask before we went another round in the ERV catagory. You seem pretty fascinated with the subject, I was wondering what it was that attrachted you to the subject.


I am an atheist not a Christian.

Science junky would be a reasonable classification. My background is avionics and logistics in a military environment.

Philosophy, well only at an armchair level, start quoting dead Greek philosophers at me and my eyes will glaze over rather rapidly. :blink: I do appreciate rational discussions however, to which I must say this site is pleasantly populated.

I dabble in the Bible forums mainly to learn.

Re EvC discussions - I do not believe YEC (nor ID) is valid science and come to places such as this in an attempt to demonstrate this.


How about yourself, what are your interests and background re these discussions?

#8 chance

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Posted 04 October 2006 - 01:27 PM

(1) CAN THE EVIDENCE BE EXPLAINED DIFFERENTLY?

are there virus strains that attack several species?

If so, could the evidence for the attacks be with equal validity from either common ancestry as common vulnerability to attack?


I would think such is possible, (sorry I’m no expert in this), But I would expect the scientist can recognise the stuff they are looking at and would think it comparable to “DNA fingerprinting”.

But consider this – If retrovirus infections do reflect ancient attacks, their appearance should match evolution phylogenetic trees, yes? and the more matches that are found increases the support of evolutionary theory.
Now consider the reverse – If evolutionary theory is not true you are basically forced into saying that identical retroviral infections have attacked identical areas of the gnome across species boundaries, every time!



(2) IS THE EVIDENCE BASED ON CODING PROBABILITY? IF SO ... IS SUCH EVIDENCE TYPE REALLY RESTRICTED TO "RELATED" FORMS?

Granted, the liklihood of common ancestry could be evidenced by a very improbable DNA string being replicated in purported modern descendants.

... what does that say about improbable coding (e.g. for the eye) appearing in a common form in non-ancestral species with separate "paths" (e.g. eye in a fly, & in eye in human, eye in octopus )?

Doesnt the argument based on improbability actually point away from common descent if it can be found that improbable DNA sequences have a common base function and coding across non-related species? (e.g. we didnt get the vertebrate eye from an octopus ancestor, did we?)



Haaaaaaaaaaaaayyyy, no fair using improbability arguments against me. :P

The types of events are a however a little different:

Infection - a specific fingerprint in a specific location, assumed to be caused by a single infection. Odds are it has been inherited from a common ancestor.

The eye has evolved (several times) slowly and in a stepwise fashion where at each step selective pressures are involved. Slightly different origins should (do) produce different types of eye.

Arguments that state it’s improbable for ‘X’ to evolve have IMO been either been poorly thought out, contain bad math, poor understanding of evolution, very abbreviated explanation of the math involved, or flawed reasoning (sometimes all of the above) ( generalising from reading such in many forums over a number of years).

#9 Phaedrus

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Posted 06 October 2006 - 05:42 PM

I am an atheist not a Christian.

Science junky would be a reasonable classification. My background is avionics and logistics in a military environment.


Actually I'm an evangelical with an avid interest in Christian apologetics. Currently I am on active duty in Iraq, oddly enough working in logistics. Isn't that ironic, that may well be the one thing we have in common.

Philosophy, well only at an armchair level, start quoting dead Greek philosophers at me and my eyes will glaze over rather rapidly.  :P  I do appreciate rational discussions however, to which I must say this site is pleasantly populated.


Philosophy is an interest of mine as well, I particularly like Plato and Aristotle. A lot of it is deadly dull but sometimes they can seem almost comical as they wrestle with deep and profound questions. Plato in the Republic is asked for all sorts of definitions but when it came to a simple word like 'good' he was lost and felt completely imcompetant to answer it. The average person looks at that and just marvels that anyone would need to ask, much less not be able to answer.

I dabble in the Bible forums mainly to learn.

Re EvC discussions - I do not believe YEC (nor ID) is valid science and come to places such as this in an attempt to demonstrate this.


Historically ID has been considered natural theology which is pretty much a twilight area between science and theology. YEC is actually a logical consequence of the Bible as history and really nothing more then a theological perspective on natural science.

How about yourself, what are your interests and background re these discussions?


I happened upon a discussion about teaching creationism in the public schools, an idea I have never advocated. I agreed with the main contention of the posters that it was a bad idea and mentioned in passing that I was a creationist. I got multiple posts that were really agressive and highly critical. Before it was over I was deep into the creation/evolution controversy. I have learned to enjoy the exchanges and there is never a shortage of people who will engage on the topic at any length.

#10 chance

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Posted 13 November 2006 - 01:40 PM

Hi Phaedrus, I’m back in Australia after a bit of a break.

Phaedrus>
Actually I'm an evangelical with an avid interest in Christian apologetics. Currently I am on active duty in Iraq, oddly enough working in logistics. Isn't that ironic, that may well be the one thing we have in common.


Tis a small world that’s for sure.


chance>
Philosophy, well only at an armchair level, start quoting dead Greek philosophers at me and my eyes will glaze over rather rapidly.    I do appreciate rational discussions however, to which I must say this site is pleasantly populated.

Phaedrus>
Philosophy is an interest of mine as well, I particularly like Plato and Aristotle. A lot of it is deadly dull but sometimes they can seem almost comical as they wrestle with deep and profound questions. Plato in the Republic is asked for all sorts of definitions but when it came to a simple word like 'good' he was lost and felt completely imcompetant to answer it. The average person looks at that and just marvels that anyone would need to ask, much less not be able to answer.


Re good - That’s the difference between a gut feeling and defining things, I can well understand Plato’s hesitance and difficulty in answering what appears to be such a simple answer, life can have so many twists and turns and consequences that it may not have an answer.


chance>
I dabble in the Bible forums mainly to learn.

Re EvC discussions - I do not believe YEC (nor ID) is valid science and come to places such as this in an attempt to demonstrate this.

Phaedrus>
Historically ID has been considered natural theology which is pretty much a twilight area between science and theology. YEC is actually a logical consequence of the Bible as history and really nothing more then a theological perspective on natural science.

(my italics) I would have to agree with this , i.e. if biblical literacy is a ‘given’, YEC cannot be far behind.


chance>
How about yourself, what are your interests and background re these discussions?


Phaedrus>
I happened upon a discussion about teaching creationism in the public schools, an idea I have never advocated. I agreed with the main contention of the posters that it was a bad idea and mentioned in passing that I was a creationist. I got multiple posts that were really agressive and highly critical. Before it was over I was deep into the creation/evolution controversy. I have learned to enjoy the exchanges and there is never a shortage of people who will engage on the topic at any length.


Good for you, Hope you continue to enjoy such.

#11 deadlock

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Posted 19 November 2006 - 06:06 AM

Haaaaaaaaaaaaayyyy, no fair using improbability arguments against me. :lol:

The types of events are a however a little different:

Infection - a specific fingerprint in a specific location, assumed to be caused by a single infection. Odds are it has been inherited from a common ancestor.

The eye has evolved (several times) slowly and in a stepwise fashion where at each step selective pressures are involved.  Slightly different origins should (do) produce different types of eye.


Show me the math proving this way it´s more probable.

Arguments that state it’s improbable for ‘X’ to evolve have IMO been either been poorly thought out, contain bad math, poor understanding of evolution, very abbreviated explanation of the math involved, or flawed reasoning (sometimes all of the above) ( generalising from reading such in many forums over a number of years).

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It seems to me simple rhetorical.Again, show me the math proving what you´re saying

#12 chance

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Posted 19 November 2006 - 02:45 PM

chance>
Haaaaaaaaaaaaayyyy, no fair using improbability arguments against me. 

The types of events are a however a little different:

Infection - a specific fingerprint in a specific location, assumed to be caused by a single infection. Odds are it has been inherited from a common ancestor.

The eye has evolved (several times) slowly and in a stepwise fashion where at each step selective pressures are involved.  Slightly different origins should (do) produce different types of eye.

deadlock>
Show me the math proving this way it´s more probable. movedAgain, show me the math proving what you´re saying


It has been my experience that from the POV of science the ‘math’ has yet to progress (or it may be that I doo not know where to look for it), the main argument is that there are so many variables and unknowns. It has been the YEC population that has attempted to simplify the evolutionary process to some over simplistic spreadsheet equation, that coupled with bad assumptions. But I’ll have another look and see if I can find something that will meet your expectations.


Arguments that state it’s improbable for ‘X’ to evolve have IMO been either been poorly thought out, contain bad math, poor understanding of evolution, very abbreviated explanation of the math involved, or flawed reasoning (sometimes all of the above) ( generalising from reading such in many forums over a number of years).

It seems to me simple rhetorical.


On the contrary, some YEC equations have been constructed with such poor reasoning and contained such obvious mathematical errors, it has been very easy to disprove them (as I have shown on more than one occasion in this forum).

#13 deadlock

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Posted 19 November 2006 - 03:12 PM

On the contrary, some YEC equations have been constructed with such poor reasoning and contained such obvious mathematical errors, it has been very easy to disprove them (as I have shown on more than one occasion in this forum).

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Show to me

#14 Springer

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Posted 19 November 2006 - 06:18 PM

It has been my experience that from the POV of science the ‘math’ has yet to progress (or it may be that I doo not know where to look for it), the main argument is that there are so many variables  and unknowns.  It has been the YEC population that has attempted to simplify the evolutionary process to  some over simplistic spreadsheet equation, that coupled with bad assumptions.  But I’ll have another look and see if I can find something that will meet your expectations.
On the contrary, some YEC equations have been constructed with such poor reasoning and contained such obvious mathematical errors, it has been very easy to disprove them (as I have shown on more than one occasion in this forum).

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Yes, we don't know all of variables. However, there is a lot we do know. We know what the average rate of mutations is in higher organisms. We can estimate generation times and population numbers. Even if you use the most liberal variables in favor of evolution, no one come up with a reasonable model of microevolutionary transformations that conforms to known laws of probability.

In calculating probability, one must remember that proposed mechanisms demonstrate a purposeful progression in one direction. This is why I keep insisting that it's impossible. You seem to think that there's no improbability of a squid and a mammal independently developing the same type of eye. If you're relying on specific mutations that occur on the order of one in 10 billion births, what is the liklihood of sequential mutations in two or more unrelated organisms following the same pathway? Regardless of the model you propose, it will not be possible. The only way for you to justify your position is to use incorrect logic and deny that proposed mechanisms of evolutionary transformation do not follow conventional laws of probability.

#15 Guest_Markster106_*

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Posted 18 March 2008 - 02:25 PM

Here's the illusion behind claims like this - they assume the ERVs are functionless. The fact we have found some ERVs to have a function alone refutes this as evidence of common ancestry. Others are highly conserved (can't suffer mutation), which is strong evidence they are important (functional). Just because we do not know what they do in all cases, does not mean they have no function and are some evolutionary leftover. More speculation borne of question begging from our fairytale lover friends. :)

More details can be found here.

Fred

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just because they have functions doesn't mean they can't have been inserted naturally

so are you saying that God inserted viral DNA into our genomes?

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Posted 19 March 2008 - 05:16 AM

It has been my experience that from the POV of science the ‘math’ has yet to progress (or it may be that I doo not know where to look for it), the main argument is that there are so many variables  and unknowns.  It has been the YEC population that has attempted to simplify the evolutionary process to  some over simplistic spreadsheet equation, that coupled with bad assumptions.  But I’ll have another look and see if I can find something that will meet your expectations.
On the contrary, some YEC equations have been constructed with such poor reasoning and contained such obvious mathematical errors, it has been very easy to disprove them (as I have shown on more than one occasion in this forum).

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are you sure the errors arent youres?




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