Viruses that prove common descent

[pshun2404]

Yes, I know. See Veritas: ERV FAQ: ERVs are essential in reproduction (syncytin and the formation of the placenta). How can this be? and Veritas: ERV FAQ: ERVs promote the transcription of host DNA. Doesn't this prove they are designed?

It's possible that the 200,000 or so ERVs and elements include some that have been misidentified as being of viral origin, but it's equally possible that other viral elements have not been identified as such due to mutational degradation.

I agree that makes perfect sense.

 

[pshun2404]

ok. so lets take your position that those are a true viral insertions (just for the sake of the argument). again: this claim dont hold water because ervs have a small space in the genome that they can actually insert themself. if those scientists from the encode projects right and about up to 100% of the genome can be functional: we can explain those shared ervs without a common descent.

Read post 158 carefully. You can see Barry allows for SOME wiggle room. The OP however implies these genetic areas (some of which are insertions) demonstrate Common Descent and I believe in one sense they do but the conclusion of it meaning a Universal Common Descent (which Barry probably accepts) is another matter entirely.

The question of Common Descent is predicated on what one means. These ERVs do not prove anything, because perfectly reasonable alternative explanations exist. In other words, all cats today (Felidae; Felines) had common ancestors (maybe a few basic types) and all are but variations of those earlier cats that had the propensity for what happens by natural selection and speciation (the production of variety) and the other view would say at some point the felines branched off from earlier mammalian forms that branched off from reptiles and so on all the way back to single celled organisms.

I do not believe what are now being called ERVs demonstrate, with any assurance, that the latter is the case. I think many people (like Barry) in their best objectivity, already being convinced the latter is true, interpret the evidence through that lense.

 

[pshun2404]

What we really know is that many of the alleged ERVs are SIMILAR (not the same), some are located in different sections of each specie’s respected genomes, and some may not actually be ERVs at all (though many others can be stated to be actual ERVs without any doubt). To obtain a rough estimate (again not exact) microbiologist, Zachery Williams, who researches ERVs at Tufts University, admits we must “guesstimate” (use a line of best guess) from among possibilities.

Carl Zimmer in, “We Are Viral from the Beginning,” The Loom , Discover, June 14, 2012, believes ERVs are sections of the genome that “look like” retroviral invasions. And he tells us “most endogenous retroviruses mutate so much they are reduced to genetic baggage, unable to do anything at all.” However, many sequences identified as ERVs do carry the hallmark signs of being or at least having been virus related insertions. All should accept that as true. The question is then HOW can these be EXPLAINED (and I assure though there is consensus all are not in full agreement), plus we have to be honest and admit some of these have functional purpose in each of the respective genomes compared.

Jonathan P. Stoye, “Koala Retrovirus: A Genome Invasion in Real Time,” Genome Biology 7, no. 11 (2006): 241, doi:10.1186/gb-2006-7-11-241, reveals that ERVs often appear to move around to different places (an EXPLANATION used to deal with the fact that they appear in different places but this does not actually mean they moved around unless we can demonstrate in one place at one point and in another at a later time in the same organism, which we have not observed) which sometimes causes a problem for comparative genomes. Having said that, we KNOW that there are certain ERVS that ARE located in the exact same place across multiple genomes, and YES humans and chimps have the highest correlation of these. That's a fact! What it may indicate is opinion

 

[Barry Desborough]

Read post 158 carefully. You can see Barry allows for SOME wiggle room. The OP however implies these genetic areas (some of which are insertions) demonstrate Common Descent and I believe in one sense they do but the conclusion of it meaning a Universal Common Descent (which Barry probably accepts) is another matter entirely.

The question of Common Descent is predicated on what one means. These ERVs do not prove anything, because perfectly reasonable alternative explanations exist. In other words, all cats today (Felidae; Felines) had common ancestors (maybe a few basic types) and all are but variations of those earlier cats that had the propensity for what happens by natural selection and speciation (the production of variety) and the other view would say at some point the felines branched off from earlier mammalian forms that branched off from reptiles and so on all the way back to single celled organisms.

I do not believe what are now being called ERVs demonstrate, with any assurance, that the latter is the case. I think many people (like Barry) in their best objectivity, already being convinced the latter is true, interpret the evidence through that lense.

The fact that chimps and humans share common ancestry falsifies evolution-denying creationism. That is sufficient to destroy all of it, like a tumbling house of cards.

 

[pshun2404]

The fact that chimps and humans share common ancestry falsifies evolution-denying creationism. That is sufficient to destroy all of it, like a tumbling house of cards.

And I would agree if it were proven true (though I tell you I am not anti-evolution, I just do not agree with everything SOME evolutionists insist these things mean). I have the exact same problem with SOME creationists because they assume somethings true but do not really have evidence. If its true then fine I will adjust but until I can say it has been demonstrated beyond a reasonable doubt then I will continue to ask questions and offer alternative points of view on the same data. In other words I am not anti-creation, I believe in a creator, but I do not agree with everything "creationists" insist these things mean. I believe evolution happens, but I do not agree with everything I am told about it by evolutionists.

Show me who/what the common ancestor for chimps and humans is....

 

[dad]

ok. so lets take your position that those are a true viral insertions (just for the sake of the argument). again: this claim dont hold water because ervs have a small space in the genome that they can actually insert themself. if those scientists from the encode projects right and about up to 100% of the genome can be functional: we can explain those shared ervs without a common descent.

Source?

 

[pshun2404]

Khodosevich, Konstantin; Lebedev, L; Sverdolv, E. (October 2002). "Endogenous retroviruses and human evolution". Comparative and Functional Genomics. 3 (6) AND Kim FJ, Battini JL, Manel N, Sitbon M (2004)."Emergence of vertebrate retroviruses and envelope capture". Virology. 318 (1): 183–91 both show how transposons (movable ERVs) play a vital role in gene expression and regulation.

These are essential genomic functions, therefore in my opinion, we should see these small sequences not as insertions, but as a necessary (not acquired) part of our actual genome.


Cotton, J. (2001). "Retroviruses from retrotransposons". Genome Biology. 2 (2): 6. Tell us, “It appears that the transition from nonviral retrotransposon to retrovirus has occurred independently at least eight times, and the source of the envelope gene responsible for infectious ability can now be traced to a virus in at least four of these instances. This suggests that potentially, any LTR retrotransposon can become a virus through the acquisition of existing viral genes.”

Many believe this means that not all ERVs may have originated as an insertion by a retrovirus but that some may have been the source for the genetic information in the retroviruses they resemble.

 

[pshun2404]

So I guess at this juncture it would be cool to get some feedback on what you each think a retrovirus is.

We know they are not alive, but when they come into contact with living things they act in some ways as if alive. We know each virus contains some small portion of a genome (either a DNA or RNA sequence).

I believe viruses are actually the smallest remnant of previously living disintegrated creatures and they float around freely or exist on surfaces that if they enter your cells can and will contribute this piece if material (which the cell accepts because it is similar to its own information) to be translated and transcribed.

What about you?

 

[Barry Desborough]

Source?

ENCODE Project
They discovered that large parts of the genome, previously unexplored, contained elements that were transcribed. Creationists and ID nuts span that into "there is no junk DNA".

 

[dad]

ENCODE Project
They discovered that large parts of the genome, previously unexplored, contained elements that were transcripted. Creationists and ID nuts span that into "there is no junk DNA".

So that is the small place he was talking about?

 

[Barry Desborough]

Khodosevich, Konstantin; Lebedev, L; Sverdolv, E. (October 2002). "Endogenous retroviruses and human evolution". Comparative and Functional Genomics. 3 (6) AND Kim FJ, Battini JL, Manel N, Sitbon M (2004)."Emergence of vertebrate retroviruses and envelope capture". Virology. 318 (1): 183–91 both show how transposons (movable ERVs) play a vital role in gene expression and regulation.

These are essential genomic functions, therefore in my opinion, we should see these small sequences not as insertions, but as a necessary (not acquired) part of our actual genome.


Cotton, J. (2001). "Retroviruses from retrotransposons". Genome Biology. 2 (2): 6. Tell us, “It appears that the transition from nonviral retrotransposon to retrovirus has occurred independently at least eight times, and the source of the envelope gene responsible for infectious ability can now be traced to a virus in at least four of these instances. This suggests that potentially, any LTR retrotransposon can become a virus through the acquisition of existing viral genes.”

Many believe this means that not all ERVs may have originated as an insertion by a retrovirus but that some may have been the source for the genetic information in the retroviruses they resemble.

Thank you. I'm aware of these papers.

Retroviruses exist in two forms: exogenous retroviruses in the environment and proviruses in the DNA of hosts. ERVs are proviruses that just happen to have gotten into the DNA of host germline cells, and thence, by cell division, into all nuclear cells. Retrovirus' replication cycle involves transitions between these two basic forms - free virions with RNA genomes, and integrated proviral forms with DNA genomes. It is not a huge surprise that even mutated proviruses can, by recombination, assemble what it takes to regenerate the transcripts required to produce an exogenous virus.

The fact that some ERVs include elements that perform essential functions for the host is not evidence that they are not of retroviral origin. See Veritas: ERV FAQ: ERVs do stuff. Doesn't that prove that they didn't originate from retroviruses, but were designed?

 

[Barry Desborough]

So that is the small place he was talking about?

No. He thinks that retroviruses can only integrate in a very limited number of DNA loci. But he has nothing to support this idea.

 

[xianghua]

Source?

An integrated encyclopedia of DNA elements in the human genome : Nature : Nature Research

and they checked a part of all cell types. not all of them. its could be that about 100% of the genome is functional.

 

[Barry Desborough]

An integrated encyclopedia of DNA elements in the human genome : Nature : Nature Research

and they checked a part of all cell types. not all of them. its could be that about 100% of the genome is functional.

"Could be"'s don't count in science. You need evidence. And anyway, the DNA in all (non-mosaic) individual organisms is the same, going from one cell to another.

Also, knock-out mouse experiments show that you can inactivate large swathes of their DNA without any deleterious effects.

See also Why Onions Have More DNA Than You Do

 

[xianghua]

"Could be"'s don't count in science. You need evidence.

here is a good one:

A meta-analysis of the genomic and transcriptomic composition of complex life. - PubMed - NCBI

take a look at figure one.

Also, knock-out mouse experiments show that you can inactivate large swathes of their DNA without any deleterious effects.

true. you can also knock-out many car components without geting any harm to the car. but it doesnt mean that those components are non functional.

 

[Barry Desborough]

here is a good one:

A meta-analysis of the genomic and transcriptomic composition of complex life. - PubMed - NCBI

take a look at figure one.



true. you can also knock-out many car components without geting any harm to the car. but it doesnt mean that those components are non functional.

That ncDNA is largely transcribed does not mean that it is all related to essential functions.

The mouse-car analogy is a poor one. We would all agree that a car is a designed object, and even decoration serves a function - to make the car attractive. Comparing it to a mouse is begging the question that the mouse is designed.

 

[pshun2404]

Thank you. I'm aware of these papers.

Retroviruses exist in two forms: exogenous retroviruses in the environment and proviruses in the DNA of hosts. ERVs are proviruses that just happen to have gotten into the DNA of host germline cells, and thence, by cell division, into all nuclear cells. Retrovirus' replication cycle involves transitions between these two basic forms - free virions with RNA genomes, and integrated proviral forms with DNA genomes. It is not a huge surprise that even mutated proviruses can, by recombination, assemble what it takes to regenerate the transcripts required to produce an exogenous virus.

The fact that some ERVs include elements that perform essential functions for the host is not evidence that they are not of retroviral origin. See Veritas: ERV FAQ: ERVs do stuff. Doesn't that prove that they didn't originate from retroviruses, but were designed?

Again as alleged proof of your point you reference your self...hmmm? And I did not say these segments were designed. What I referred to was that some (SOME) may not be viral insertions at all (opinions can and do vary), but actual parts of the genome that were always present, hence not "insertions"...so because some look as if this fact might be true, it is easy for the die-hards trying to "shape public opinion" (a polite was of saying to engineer or even manipulate) to just explain this potential problem away by applying the presupposed hypothesis, i.e., they were inserted into a shared common ancestor (which may or may not be true and has not been demonstrated or observed).

To show a true "insertion" into the human genome (at least in my opinion..yes I refer to myself but I call this "opinion" or point of view) one first has to demonstrate they were not there, and now they are, which has not been demonstrated save only in a very few.

 

[Barry Desborough]

Again as alleged proof of your point you reference your self...hmmm? And I did not say these segments were designed. What I referred to was that some (SOME) may not be viral insertions at all (opinions can and do vary), but actual parts of the genome that were always present, hence not "insertions"...so because some look as if this fact might be true, it is easy for the die-hards trying to "shape public opinion" (a polite was of saying to engineer or even manipulate) to just explain this potential problem away by applying the presupposed hypothesis, i.e., they were inserted into a shared common ancestor (which may or may not be true and has not been demonstrated or observed).

To show a true "insertion" into the human genome (at least in my opinion..yes I refer to myself but I call this "opinion" or point of view) one first has to demonstrate they were not there, and now they are, which has not been demonstrated save only in a very few.

See Veritas: ERV FAQ: Why do virologists and geneticists think that ERVs come from retroviruses? Isn't that just supposition on their part?

Yes, I am linking to one of my own pages. I produced them to save repeating myself endlessly. Follow the links and you will find the scientific literature that backs it up.

 

[xianghua]

That ncDNA is largely transcribed does not mean that it is all related to essential functions.

the ar ticle isnt about transcription but about a correlation between complexity (in terms of cell types number) and the amount of suppose junk.

The mouse-car analogy is a poor one. We would all agree that a car is a designed object, and even decoration serves a function - to make the car attractive. Comparing it to a mouse is begging the question that the mouse is designed.

so all i need to do is to prove that nature was designed. correct? and in this case do you agree also that the entire argument about ervs will falsified too?.

 

[Barry Desborough]

the ar ticle isnt about transcription but about a correlation between complexity (in terms of cell types number) and the amount of suppose junk.




so all i need to do is to prove that nature was designed. correct? and in this case do you agree also that the entire argument about ervs will falsified too?.

Sequences that differentiate cell types would necessarily need to be transcribed. It's very difficult to see what you think your point is here.

Good luck with proving that nature was designed, but that's irrelevant. Retroviruses and the ERVs they create prove common descent, whether they were designed or not.