Viruses that prove common descent

[pshun2404]

Now it is generally accepted, as Rational Wiki puts it, that “If two organisms share the same ERV, in the same location, with the same inactivation mutations, then they almost certainly share them due to common inheritance and not two separate infections.” But I have to disagree. This is an assumption!

Their use of the phrase “not two separate infections” IMO is deceptive, because the same infection, in two similar species during the exact time frame, would produce the exact same results that we observe, and therefore it would not be necessary that they be two “separate” infections at all (they are implying this is a claim that has been made, though I searched and could not find it...if one of you do please post a reference or a link) and would thus NOT imply an assumption of common descent.

In my humble opinion, because researchers seek these alleged ERVs out to form or prove phylogenetic trees, lineal relationship is already a pre-supposed conclusion before they assume or seek (which biases the interpretation).

Madalina Barbulescu in, “A HERV-K Provirus in Chimpanzees, Bonobos, and Gorillas, but Not Humans,” Current Biology 11 (May 2001): 779–83, doi:10.1016/S0960-9822(01)00227-5, tells us that some of the ERVs found in chimps, bonobos, and gorillas, are not present in humans and many in humans are not found in any of the others (also see Chris T. Yohn et al., “Lineage-Specific Expansions of Retroviral Insertions within the Genomes of African Great Apes but Not Humans and Orangutans,” PLoS Biology 3, April 2005: e110, 10.1371/journal.pbio).

In light of this, Molecular Biologist, Dr. Anjeanette Roberts believes “the longer I think about ERVs and viral origins, and as I observe scientific reports identifying various critical functions associated with ERVs and other repetitive genomic elements, I believe it may be profitable for driving scientific inquiry to question some of the underlying assumptions that support ERVs as inarguable signs of common descent.”

A study done by Catriona M. Macfarlane and Richard M. Badge, (“Genome-Wide Amplification of Proviral Sequences Reveals New Polymorphic HERV-K(HML-2) Proviruses in Humans and Chimpanzees that are Absent from Genome Assemblies,” Retrovirology 12 (April 2015): id. 35, doi:10.1186/s12977-015-0162-8) implies we may need to re-think the time element generally assumed because mounting evidence indicates a much more recent insertion event for humans than for chimps at many shared ERV insertion sites previously thought to confirm common ancestry.

So from this, simple logic tells us that IF that is true in those samples they examined, THEN it could also be true in other cases (which means the evidence used in these sites no longer can be said to indicate descent). Same insertion, in the same place, yet at two different times, to two different creatures (possibly not related except via taxonomic convention).

So I could also ask (rhetorical, no need to answer), “Does this really prove Common Descent or is that possibility already assumed?” Or even “Perhaps these allegedly similar genomes show a sort of biochemical preference as to where such materials would be placed?” Hmmm? If this case were true, maybe the genome plays a role in selecting which ones may be useful.

 

[Speedwell]

So I could also ask (rhetorical, no need to answer), “Does this really prove Common Descent or is that possibility already assumed?”

False dichtomy. It is consistent with common descent. It might also be consistent with some form of special creation or other, but there is no theoretical model for special creation so who can tell?

 

[dad]

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

Can YOU rule that out?

 

[dad]

False dichtomy. It is consistent with common descent. It might also be consistent with some form of special creation or other, but there is no theoretical model for special creation so who can tell?

So it may be one way or the other. If there was creation, by the way, it was quite special.

 

[dad]

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.

Or used to be functional.

The question seems to be how the ervs got there. How would just being functional mean they got there a certain way?

 

[pshun2404]

False dichtomy. It is consistent with common descent. It might also be consistent with some form of special creation or other, but there is no theoretical model for special creation so who can tell?

Proud of you for even admitting this. Not many here have that level of intellectual integrity. Since "NO one can tell" for sure, the idea should not be presented as the truth.

 

[Speedwell]

Proud of you for even admitting this. Not many here have that level of intellectual integrity. Since "NO one can tell" for sure, the idea should not be presented as the truth.

You understand, that there is always an implicit uncertainty in scientific statements which is taken for granted. The only people who assert that they are being presented as "The Truth" are creationists--who have a "Truth" of their own. To the rest of us it is nothing more than the best science has come up with so far, and nothing more.

 

[pshun2404]

You understand, that there is always an implicit uncertainty in scientific statements which is taken for granted. The only people who assert that they are being presented as "The Truth" are creationists--who have a "Truth" of their own. To the rest of us it is nothing more than the best science has come up with so far, and nothing more.

Oh how I wish that was how it would be taught in public schools everywhere! And please, you cannot be so naive as to suggest you do not know things like this issue are presented as if they are the truth. "Creationists" (as you would define them) are not chosen to partake in curriculum development, only those who accept this view. Do I really have to quote a bunch of textbooks? I have a few right here!

In reality it is only "the best science has come up with so far, and nothing more." That should be made clear right from the start, and then re-emphasized at each juncture.

 

[pshun2404]

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".

Absurd! Of course there is. But huge areas previously claimed to be so by modern Darwinians have function and therefore they were incorrect. Now instead of revamping the theory to fit the data they are misrepresenting the Encode Team (a consortium of 450 world class scientists from a variety of disciplines) and spinning the media with statements like they improperly call these "functions" and other such nonsense. Plus most all those peer reviewed articles I have cited so far are no part of Encode (though I applaud their work and their honesty in the face of such shameful hypothesis driven muck racking).

 

[Speedwell]

Oh how I wish that was how it would be taught in public schools everywhere! And please, you cannot be so naive as to suggest you do not know things like this issue are presented as if they are the truth. "Creationists" (as you would define them) are not chosen to partake in curriculum development, only those who accept this view. Do I really have to quote a bunch of textbooks? I have a few right here!

In reality it is only "the best science has come up with so far, and nothing more." That should be made clear right from the start, and then re-emphasized at each juncture.

Yes, textbooks not written by scientists for biology classes taught by PE coaches in their extra period. If you want to argue that science is badly taught in the public schools, I'll be right beside you. But creationism has no place in the science curriculum of the public schools. The primary purpose of such basic public school science classes is to teach what science is, how scientists reach their conclusions. For example, scientists have concluded, with all of the provisos thereunto appertaining, that the universe is 13 some billion years old. Whether there is a God or not who brought it into being doesn't come into it one way or the other. Similarly, scientists have concluded that life diversifies through biological evolution and most probably from a single common ancestor. That's what science has concluded, right or wrong, and whether there is a God or not doesn't come into it one way or another. The purpose of HS science classes is primarily to teach students what science is, how it works. That is important for them to know, whether they intend to accept it, or confront it for religious reasons.

In reality it is only "the best science has come up with so far, and nothing more." That should be made clear right from the start, and then re-emphasized at each juncture.

It is, in well-conducted science classes. That's where I learned it.

 

[pshun2404]

Yes, textbooks not written by scientists for biology classes taught by PE coaches in their extra period. If you want to argue that science is badly taught in the public schools, I'll be right beside you. But creationism has no place in the science curriculum of the public schools. The primary purpose of such basic public school science classes is to teach what science is, how scientists reach their conclusions. For example, scientists have concluded, with all of the provisos thereunto appertaining, that the universe is 13 some billion years old. Whether there is a God or not who brought it into being doesn't come into it one way or the other. Similarly, scientists have concluded that life diversifies through biological evolution and most probably from a single common ancestor. That's what science has concluded, right or wrong, and whether there is a God or not doesn't come into it one way or another. The purpose of HS science classes is primarily to teach students what science is, how it works. That is important for them to know, whether they intend to accept it, or confront it for religious reasons.It is, in well-conducted science classes. That's where I learned it.

Indeed! That's where I first learned it as well. And I do agree that "creationism has no place in the science curriculum of the public schools", but evidence and arguments for and against should be taught. This statement "scientists have concluded that life diversifies through biological evolution and most probably from a single common ancestor" is fine also if they could include the "most probably" and not assume it as an assumed fact. When they teach it that way over and over and over...the students begin yo believe it as if it has been proven.

 

[Speedwell]

Indeed! That's where I first learned it as well. And I do agree that "creationism has no place in the science curriculum of the public schools", but evidence and arguments for and against should be taught. This statement "scientists have concluded that life diversifies through biological evolution and most probably from a single common ancestor" is fine also if they could include the "most probably" and not assume it as an assumed fact. When they teach it that way over and over and over...the students begin yo believe it as if it has been proven.

Where are these schools which teach it "over and over?" On the other hand, it is certainly closer to being a fact than biblical creationism, whose adherents are the ones mostly complaining about it.

 

[pshun2404]

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".

I know we are told that “our common ancestor” (allegedly 14 million years ago) acquired these ERVs. But in the opinion of many, if ERVs still have function in the genome then that premise falls apart. Now we have found that in fact they do (not all but many).

Those that do have function still perform those functions. For example, out of 240,000 the Encode project has determined that at least 51,195 of them are intimately associated with initiating transcription in the human genome, 1743 in the UTRs (the untranslated areas of the genome). In fact their effect at p53 (a master gene regulator) helps the body fight cancer and without their help we would all get cancer and die. This alleged ERV is a necessary part of the genome not some viral insertion. If it was not a part of US the human race would have dies out epochs ago.

Therefore these section/sequences were essential to the continuation of the human species since the very beginning of humanity. They are and have always been an essential part of who we are. Which means that as much as this may shake the hypothesis, they were never “acquired” in the human genome, but an essential part of it.

In fact W. W. Gibbs in Scientific American’s “The unseen Genome: Gems among the Junk” (289(5) 26-33, Nov. 2003, pp 29-30 he cites Mattick of demonstrating that “The failure to recognize the full implications of this...may well go down in history as one of the biggest mistakes in Molecular Biology.” Because so many ERVs are currently functional, it is highly unlikely that they were inserted millions of years ago by some retro-viruses.

Then there is the process of apoptosis (which kills infected cells) which is largely ignored or not being taken into consideration. Part of this function is designed to kill infected cells. If these were viral infections the apoptosis process would have killed ERV infected cells centuries ago. It would have killed them in individuals and not been in existence long enough to have become a permanent part of ALL our species sex cells. Normally just the T-cells alone would have automatically eliminated them. They do this all the time (even now while we speak) in order to prevent virus infected cells from spreading the infection. This indicates (totally scientifically) that much of what have been labelled ERVs are actually not from retroviruses at all.

If ERVs ARE retroviral insertions why would harmful virus infected reproductive cells be selected as more fit in a natural selection process? These important questions are not even being asked, let alone answered.

 

[pshun2404]

Where are these schools which teach it "over and over?" On the other hand, it is certainly closer to being a fact than biblical creationism, whose adherents are the ones mostly complaining about it.

I was taught this is the explanation for life in grades 5,6,7,8,9, and so on, right on into College Bio 101 and Zoo...we recapped later in Genetics and in Biochem...and if you went to public school you were more than likely taught it there as well...

UCA is not closer to the truth than a Biblical Creation...neither of them has been demonstrated...both rest solely on circumstantial evidence and belief.

 

[Barry Desborough]

Now it is generally accepted, as Rational Wiki puts it, that “If two organisms share the same ERV, in the same location, with the same inactivation mutations, then they almost certainly share them due to common inheritance and not two separate infections.” But I have to disagree. This is an assumption!

A conclusion from the evidence is not an assumption.

Their use of the phrase “not two separate infections” IMO is deceptive, because the same infection, in two similar species during the exact time frame, would produce the exact same results that we observe, and therefore it would not be necessary that they be two “separate” infections at all (they are implying this is a claim that has been made, though I searched and could not find it...if one of you do please post a reference or a link) and would thus NOT imply an assumption of common descent.

No. You are missing the point by several miles. Separate integrations to precisely corresponding DNA loci will be extremely rare. All but a couple of hundred integrations out of some 200,000 to corresponding loci via separate infection is beyond the bounds of credibility.

In my humble opinion, because researchers seek these alleged ERVs out to form or prove phylogenetic trees, lineal relationship is already a pre-supposed conclusion before they assume or seek (which biases the interpretation).

No. They confirm phylogenies already established by other means. What an incredible coincidence!

Madalina Barbulescu in, “A HERV-K Provirus in Chimpanzees, Bonobos, and Gorillas, but Not Humans,” Current Biology 11 (May 2001): 779–83, doi:10.1016/S0960-9822(01)00227-5, tells us that some of the ERVs found in chimps, bonobos, and gorillas, are not present in humans and many in humans are not found in any of the others (also see Chris T. Yohn et al., “Lineage-Specific Expansions of Retroviral Insertions within the Genomes of African Great Apes but Not Humans and Orangutans,” PLoS Biology 3, April 2005: e110, 10.1371/journal.pbio).

Read up on incomplete lineage sorting. There is already material on this in my FAQ. Veritas: ERV FAQ: What if we find an ERV in a common location in chimpanzees and gorillas, but not in humans?

In light of this, Molecular Biologist, Dr. Anjeanette Roberts believes “the longer I think about ERVs and viral origins, and as I observe scientific reports identifying various critical functions associated with ERVs and other repetitive genomic elements, I believe it may be profitable for driving scientific inquiry to question some of the underlying assumptions that support ERVs as inarguable signs of common descent.”

She's not the only one who doesn't understand incomplete lineage sorting.

A study done by Catriona M. Macfarlane and Richard M. Badge, (“Genome-Wide Amplification of Proviral Sequences Reveals New Polymorphic HERV-K(HML-2) Proviruses in Humans and Chimpanzees that are Absent from Genome Assemblies,” Retrovirology 12 (April 2015): id. 35, doi:10.1186/s12977-015-0162-8) implies we may need to re-think the time element generally assumed because mounting evidence indicates a much more recent insertion event for humans than for chimps at many shared ERV insertion sites previously thought to confirm common ancestry.

A gullible reader will assume that you are quoting from the paper. But you are not. You don't seem to understand what 'polymorphism' means. An ERV may be either present or not present at a specific locus. This is an example of genetic polymorphism.

So from this, simple logic tells us that IF that is true in those samples they examined, THEN it could also be true in other cases (which means the evidence used in these sites no longer can be said to indicate descent). Same insertion, in the same place, yet at two different times, to two different creatures (possibly not related except via taxonomic convention).
/

Show me exactly where this is reported.

So I could also ask (rhetorical, no need to answer), “Does this really prove Common Descent or is that possibility already assumed?” Or even “Perhaps these allegedly similar genomes show a sort of biochemical preference as to where such materials would be placed?” Hmmm? If this case were true, maybe the genome plays a role in selecting which ones may be useful.

You can have an answer anyway. For the umpteenth time, integrase cannot target specific DNA loci. That 200,000 ERV elements can end up in precisely corresponding loci in the genomes of two unrelated species by coincidence is beyond the bounds of sane credibility. Veritas: ERV FAQ: Don't retroviruses target particular locations in the DNA? Doesn't this explain corresponding ERVs?

 

[Barry Desborough]

The editor won't let me finish. On your last "rhetorical" point,
You can have an answer anyway. For the umpteenth time, integrase cannot target specific DNA loci. That 200,000 ERV elements can end up in precisely corresponding loci in the genomes of two unrelated species by coincidence is beyond the bounds of sane credibility. Veritas: ERV FAQ: Don't retroviruses target particular locations in the DNA? Doesn't this explain corresponding ERVs?

 

[Barry Desborough]

I know we are told that “our common ancestor” (allegedly 14 million years ago) acquired these ERVs. But in the opinion of many, if ERVs still have function in the genome then that premise falls apart. Now we have found that in fact they do (not all but many).

Those that do have function still perform those functions. For example, out of 240,000 the Encode project has determined that at least 51,195 of them are intimately associated with initiating transcription in the human genome, 1743 in the UTRs (the untranslated areas of the genome). In fact their effect at p53 (a master gene regulator) helps the body fight cancer and without their help we would all get cancer and die. This alleged ERV is a necessary part of the genome not some viral insertion. If it was not a part of US the human race would have dies out epochs ago.

Therefore these section/sequences were essential to the continuation of the human species since the very beginning of humanity. They are and have always been an essential part of who we are. Which means that as much as this may shake the hypothesis, they were never “acquired” in the human genome, but an essential part of it.

In fact W. W. Gibbs in Scientific American’s “The unseen Genome: Gems among the Junk” (289(5) 26-33, Nov. 2003, pp 29-30 he cites Mattick of demonstrating that “The failure to recognize the full implications of this...may well go down in history as one of the biggest mistakes in Molecular Biology.” Because so many ERVs are currently functional, it is highly unlikely that they were inserted millions of years ago by some retro-viruses.

Then there is the process of apoptosis (which kills infected cells) which is largely ignored or not being taken into consideration. Part of this function is designed to kill infected cells. If these were viral infections the apoptosis process would have killed ERV infected cells centuries ago. It would have killed them in individuals and not been in existence long enough to have become a permanent part of ALL our species sex cells. Normally just the T-cells alone would have automatically eliminated them. They do this all the time (even now while we speak) in order to prevent virus infected cells from spreading the infection. This indicates (totally scientifically) that much of what have been labelled ERVs are actually not from retroviruses at all.

If ERVs ARE retroviral insertions why would harmful virus infected reproductive cells be selected as more fit in a natural selection process? These important questions are not even being asked, let alone answered.

Veritas: ERV FAQ: ERVs do stuff. Doesn't that prove that they didn't originate from retroviruses, but were designed?
Veritas: ERV FAQ: How could ERVs survive programmed cell death (apoptosis)?
Veritas: ERV FAQ: How could a species survive a massive invasion of retroviruses into it's genome?

 

[Speedwell]

I was taught this is the explanation for life in grades 5,6,7,8,9, and so on, right on into College Bio 101 and Zoo...we recapped later in Genetics and in Biochem...and if you went to public school you were more than likely taught it there as well...

UCA is not closer to the truth than a Biblical Creation...neither of them has been demonstrated...both rest solely on circumstantial evidence and belief.

Biblical Creationism rests on no evidence whatever.

 

[pshun2404]

A conclusion from the evidence is not an assumption.


No. You are missing the point by several miles. Separate integrations to precisely corresponding DNA loci will be extremely rare. All but a couple of hundred integrations out of some 200,000 to corresponding loci via separate infection is beyond the bounds of credibility.


No. They confirm phylogenies already established by other means. What an incredible coincidence!


Read up on incomplete lineage sorting. There is already material on this in my FAQ. Veritas: ERV FAQ: What if we find an ERV in a common location in chimpanzees and gorillas, but not in humans?


She's not the only one who doesn't understand incomplete lineage sorting.


A gullible reader will assume that you are quoting from the paper. But you are not. You don't seem to understand what 'polymorphism' means. An ERV may be either present or not present at a specific locus. This is an example of genetic polymorphism.

You are a riot! When you declare "A conclusion from the evidence is not an assumption" is not really honest in an of itself, when the conclusion is based on interpretation of the evidence, and the basis of this evidence does not take all of it into account and include that which appears contrary. A solid more viable conclusion would include it all (for and against the hypothesis). Take it all into account and then forgetting the presupposed hypothesis form a conclusion based on all of it for and against.

 

[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 MANY transposons (movable alleged ERVs), not all, 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 ERVs but as a necessary (not acquired) part of our actual genome.

To declare them as “insertions” (and please do not insult me by claiming I do not understand what this means as I accept many as insertions without question), we would have to show them to not be there at one stage of our existence, and then there at a later stage. But since no one can actually show that to be the case, they are forced to default to the narrative attached claiming them as being a inserted in the also unproven alleged UCA from 14 mya (an additional assumption).

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 simply have been genetic information similar to that in the retroviruses they resemble.

Such conclusions, also based on evidence, if not an assumption (their opinion or interpretation of the evidence), would need to be accepted (according to your logic), but they do not agree with the former conclusion you imply I must accept.