200,000 ERVs...

[peteos]

The nested hierarchy pattern of genetics including ERV's and psedugenes is what pushed me over the edge into accepting common descent.

In the recent debate between Loudmouth and Mark Kennedy, Loudmouth makes the assertion that we share 200,000 ERVs with chimps (in the same location). Instead of Mark suggested this does not imply common descent, he challenges that this fact is even true. He suggests that we located 200,000 ERVs in humans but never compared them to the chimp genome. Loudmouth asserts we did, by pointing to the Chimp genome paper, which lists lineage specific ERVs, and by deduction we can subtract this number from the total ERVs in chimps and get those that are shared. Mark does not seem to challenge this point in his conclusion.

First off, these are the best disagreements. I hate talking past each other on what evidence might mean. I like it when one side agrees that if such evidence did exist, it would indeed support such and such a conclusion. That way we can go out and measure it and confirm or falsify the theory. That is what is so powerful about common descent to me, there are millions of opportunities to falsify common descent by breaking the nested hierarchy pattern, or seeing a vastly different hierarchy between morphology, fossils, biogeography, and genetics.

So which is it. Is there a paper that directly states that human and chimp ERVs were compared and 200,000 of them were shared? Does it say this in the chimp genome paper text? (I am not a scientist and am not going to read that whole thing). Does this evidence that is undeniably supportive of common descent, and of which convinced me of its reality, actually true?

 

[Loudmouth]

In the recent debate between Loudmouth and Mark Kennedy, Loudmouth makes the assertion that we share 200,000 ERVs with chimps (in the same location).

If I could, I suggest we stick with the terms I used before so things don't get confused. Instead of "shared ERV's" I think it is better to call them orthologous ERV's. Chimps and humans both have ERV-K insertions but not all of them are orthologous (i.e. found at the same spot in the genome).

But yes, you are right. This is an easy test given the fact that both the chimp and human genomes are publically available at http://www.ncbi.nlm.nih.gov/sites/entrez?db=Genome&itool=toolbar

It's very time consuming, but if you understand how to use the DNA analysis tools it is rather simple to find the proposed orthologous ERV's in each genome and do a clustalW or bl2seq comparison of the flanking DNA. Even better, we can look at lineage specific ERV's and find the pre-insertion site in the other genome.

Would anyone be interested in this, or in doing the analysis. I could do a few, but it is time consuming. I know that sfs could do it in his sleep, but he's not around a whole lot.

Instead of Mark suggested this does not imply common descent, he challenges that this fact is even true. He suggests that we located 200,000 ERVs in humans but never compared them to the chimp genome. Loudmouth asserts we did, by pointing to the Chimp genome paper, which lists lineage specific ERVs, and by deduction we can subtract this number from the total ERVs in chimps and get those that are shared. Mark does not seem to challenge this point in his conclusion.

Even worse, he digs his grave even deeper. He accuses me of ignoring the other 4% of the genome that is comprised of retroviral related sequence. What he doesn't realize is that this adds hundreds of thousands of orthologous features that he can not explain except through common ancestry. If MK shows up in this thread I would be happy to throw in the solo LTR's and MaLTR's. Heck, we could also include the hundreds of thousands of orthologous retrotransponsons if he wants.

What went flying over MK's head is that common ancestry is evidenced by the placement of these sequences in the genome, not what percentage of each genome is made up of these sequences. This lack of understanding on MK's part is made even more obvious by the fact that he put forward non-orthologous PtERV's and CERV's as refutations of my argument.

 

[Loudmouth]

There are also cruder methods for testing whether or not ERV's are truly orthologous. One method is to digest DNA with a restriction enzyme and then probe the digested DNA with a radioactive or tagged probe, which is called a Southern blot.

Here is a rundown on how this method works. Restriction enzymes are DNAses (enzymes that break down DNA) that cleave DNA at specific sequences. For example, the restriction enzyme PstI cleaves DNA whenever it sees the following 6 base sequence:

5'-C T G C A^G-3'
3'-G^A C G T C-5'

The "^" mark the spots where the restriction enzyme cuts the DNA. As you can guess, the DNA sequence CTGCAG and it's complementary seqeunce GACGTC do not occur every 10 bases or so in any genome. However, a 6 bases is short enough that any 6 base sequence should show up regularly in a large genome. The distance between each PstI site will be somewhat random so when you digest genomic DNA you will get a whole range of DNA fragments lengths.

The first step in this method is to harvest genomic DNA and incubate it with a restriction enzyme such as PstI. Once the enzyme has done it's work you separate the fragments using gel electrophoresis. This step separates the fragments according to their length because larger fragments have a tougher time moving through the gel than smaller fragments. If you were to view total DNA on the gel you would see some banding but the overall patern would be a smear.

The next step involves transferring the DNA from the gel to a thin membrane. This process preserves the sorting done in the gel electrophoresis step and has the added benefit of exposing the DNA because it is now tethered to a membrane surface instead of embedded in a gel.

The next step is to probe the DNA fragments. In a Southern blot you probe the DNA fragmentson the membrane with your DNA sequence of interest which is tagged with a radioactive element such as 32P or with a chemilumniscent molecule such as DIG. When the membrane and probe are heated it separates the two complementary strands of DNA. When the membrane is cooled the probe anneals to the DNA fragment that has the complementary sequence of DNA. Because the probe is tagged you should have some bands that light up and others that don't.

When this method is done with human, chimp, orangutan, and squirrel monkey genomic DNA using a probe specific to an ERV sequence (the pol gene from the ERV-9 family) you are able to light up genomic DNA fragments containing ERV specific DNA. If humans and chimps share a recent common ancestor then they should also share many of the same sites that are recognized by restriction enzymes, such as that 6 base sequence that PstI recongizes. Therefore, the more closely two species are related the more closely their banding patterns should match. Even more, if these two species share an orthologous ERV then this ERV should be found in the same DNA fragment after digestion. Therefore, if chimps and humans share thousands of ERV's we should see very similar banding patterns when digested DNA is probed with sequences specific to an ERV. Guess what? This is exactly what we see. Even more, the orangutan carries the same ERV's but in different sized fragments which denotes loss or a gain in some of the PstI sites. Compare this to squirrel monkeys which only have a few insertions total compared to those shared by the three apes.

This method does not allow me to say that these ERV's have inserted at the same spot down to the same base. However, the overall pattern is too much to ignore, at least for me. If these ERV's were non-orthologous then there is no reason that we should see the same DNA fragments of approximately the same size light up, but they do.

Reference for illustration: http://vir.sgmjournals.org/cgi/content/abstract/77/8/1631

 

[mark kennedy]

The nested hierarchy pattern of genetics including ERV's and psedugenes is what pushed me over the edge into accepting common descent.

In the recent debate between Loudmouth and Mark Kennedy, Loudmouth makes the assertion that we share 200,000 ERVs with chimps (in the same location). Instead of Mark suggested this does not imply common descent, he challenges that this fact is even true. He suggests that we located 200,000 ERVs in humans but never compared them to the chimp genome. Loudmouth asserts we did, by pointing to the Chimp genome paper, which lists lineage specific ERVs, and by deduction we can subtract this number from the total ERVs in chimps and get those that are shared. Mark does not seem to challenge this point in his conclusion.

First off, these are the best disagreements. I hate talking past each other on what evidence might mean. I like it when one side agrees that if such evidence did exist, it would indeed support such and such a conclusion. That way we can go out and measure it and confirm or falsify the theory. That is what is so powerful about common descent to me, there are millions of opportunities to falsify common descent by breaking the nested hierarchy pattern, or seeing a vastly different hierarchy between morphology, fossils, biogeography, and genetics.

So which is it. Is there a paper that directly states that human and chimp ERVs were compared and 200,000 of them were shared? Does it say this in the chimp genome paper text? (I am not a scientist and am not going to read that whole thing). Does this evidence that is undeniably supportive of common descent, and of which convinced me of its reality, actually true?

The Human Genome Project did report that, but that was an early estimation based on the best evidence available. Things have become clearer over the years, for instance, ERVs make up 8% of the human genome not 4%. Did you realize that the largest group of ERVs in the Chimpanzee Genome does not have ortholouges in the Human Genome?

Mammalian genomic sequence is littered with various classes of endogenous retroviruses that have populated genomes during the course of evolution . In the case of humans, approximately 8.3% of the genome sequence consists of long terminal repeat (LTR) and endogenous retrovirus elements classified into more than 100 separate repeat families and subfamilies...

A total of 95.8% of these sites were non-orthologous when compared between species. ​

This is a more current report:

"We report here that the chimpanzee genome contains at least 42 separate families of endogenous retroviruses, nine of which were not previously identified. All but two (CERV 1/PTERV1 and CERV 2) of the 42 families of chimpanzee endogenous retroviruses were found to have orthologs in humans. Molecular analysis (PCR and Southern hybridization) of CERV 2 elements demonstrates that this family is present in chimpanzee, bonobo, gorilla and old-world monkeys but absent in human, orangutan and new-world monkeys. A survey of endogenous retroviral positional variation between chimpanzees and humans determined that approximately 7% of all chimpanzee-human INDEL variation is associated with endogenous retroviral sequences." (Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses, Genome Biol. 2006 )​

Finally, the most abundant family of ERVs in the Chimpanzee do not have ortholouges in the human genome:

With more than 100 members, CERV 1/PTERV1 is one of the most abundant families of endogenous retroviruses in the chimpanzee genome. CERV 1/PTERV1 elements range in size from 5 to 8.8 kb in length, are bordered by inverted terminal repeats (TG and CA) and are characterized by 4 bp TSDs...Phylogenetic analysis of the LTRs from full-length elements of CERV 1/PTERV1 members indicated that this family of LTRs can be grouped into at least two subfamilies (bootstrap value of 99; Figure 3). The age of each subfamily was estimated by calculating the average of the pairwise distances between all sequences in a given subfamily. The estimated ages of the two subfamilies are 5 MY and 7.8 MY, respectively, suggesting that at least one subfamily was present in the lineage prior to the time chimpanzees and humans diverged from a common ancestor (about 6 MYA). This conclusion, however, is inconsistent with the fact that no CERV 1/PTERV1 orthologues were detected in the sequenced human genome. (Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses) Bolded mine​

This is not as cut and dried as evolutionists are telling you. We do well to explore the evidence ourselves and come to an informed conclusion.

Grace and peace,
Mark

 

[[serious]]

let me give a comparison. If you want to check for plagerism, one of the best things to look for is errors that are shared between the two works. Say I'm writing code and I for some reason toss 17 spaces between the end of a line and a semicolon. Now, this doesn't break the program, but it is an odd way to format the the code. Now, if another program pops up with the same 17 spaces before a semicolon and in the same code, chances are someone copied my work. It doesn't really matter if there are ten other places that the code is formated oddly.

This is what we have with ERVs. Bunches and bunches of cases where the same mistake happens in the same spot. We can thus conclude that both were copied from the same original (last common ancestor) Does it matter that more mistakes were made since? not at all.

As a note, this happened back in college. another student turned in a program remarkably close to mine and a bunch of spaces between the end of a line and a semicolon served as proof that it was a cut and paste job. The other kid almost got kicked out for stealing my work.

EDIT: Mark Kennedy, Which side was that last post supposed to argue for? everything there seems to directly support common descent.

 

[mark kennedy]

let me give a comparison. If you want to check for plagerism, one of the best things to look for is errors that are shared between the two works. Say I'm writing code and I for some reason toss 17 spaces between the end of a line and a semicolon. Now, this doesn't break the program, but it is an odd way to format the the code. Now, if another program pops up with the same 17 spaces before a semicolon and in the same code, chances are someone copied my work. It doesn't really matter if there are ten other places that the code is formated oddly.

This is what we have with ERVs. Bunches and bunches of cases where the same mistake happens in the same spot. We can thus conclude that both were copied from the same original (last common ancestor) Does it matter that more mistakes were made since? not at all.

As a note, this happened back in college. another student turned in a program remarkably close to mine and a bunch of spaces between the end of a line and a semicolon served as proof that it was a cut and paste job. The other kid almost got kicked out for stealing my work.

EDIT: Mark Kennedy, Which side was that last post supposed to argue for? everything there seems to directly support common descent.

I'm a creationist but I thought that was obvious. Loudmouth and I had a formal debate on the subject and in the peanut gallery he invited me to post to this thread. The point of the previous post was that the most abundant family of ERVs in the chimpanzee genome were integrated after the split. LM's facts are fishy at best, for one thing the 200,000 ERVs are based on the initial sequence of the human genome. The facts are outdated and as science progresses we do well to track the changes.

ERVs are not a valid proof of common ancestry. What they are is evidence of independent lineage. Take another look at the previous post and I'll check the thread for a while to see your response.

 

[Loudmouth]

The Human Genome Project did report that, but that was an early estimation based on the best evidence available. Things have become clearer over the years, for instance, ERVs make up 8% of the human genome not 4%. Did you realize that the largest group of ERVs in the Chimpanzee Genome does not have ortholouges in the Human Genome?

Read the paper again, Mark. ERV's make up about 4% and retroviral related sequences make up 8%.

In the case of humans, approximately 8.3% of the genome sequence consists of long terminal repeat (LTR) and endogenous retrovirus elements classified into more than 100 separate repeat families and subfamilies...

And there you go Mark. See how they differentiate between solo LTR's and ERV's? Why can't you do the same?

pic deleted
A total of 95.8% of these sites were non-orthologous when compared between species.

Between what species? What is the comparison? I have already shown, in spades, that nearly all of the 200,000 human ERV's can be found in chimps at orthologous positions. Do you disagree?
This is a more current report:

Finally, the most abundant family of ERVs in the Chimpanzee do not have ortholouges in the human genome:

Chimp PtERV's do not have orthologs in ANY SPECIES. Why is that Mark?

This is not as cut and dried as evolutionists are telling you. We do well to explore the evidence ourselves and come to an informed conclusion.

Grace and peace,
Mark

One thing is cut and dried. Chimps and humans share nearly 200,000 orthologous ERV's. Do you agree or disagree?

 

[Loudmouth]

LM's facts are fishy at best, for one thing the 200,000 ERVs are based on the initial sequence of the human genome. The facts are outdated and as science progresses we do well to track the changes.

Are you saying that the human genome project is already outdated? What does this mean?

ERVs are not a valid proof of common ancestry. What they are is evidence of independent lineage.

How so? Greater than 99% of human ERV's can be found at orthologous positions in the chimp genome. How in the world does this evidence independent insertion?

 

[mark kennedy]

Read the paper again, Mark. ERV's make up about 4% and retroviral related sequences make up 8%.

That's not the point, the most abundant family of ERVs in the chimpanzee genome were independently acquired.

And there you go Mark. See how they differentiate between solo LTR's and ERV's? Why can't you do the same?

You are making this sweeping generality that virtually all of the 200,000 ERVs are identical. That's absurd.

Between what species? What is the comparison? I have already shown, in spades, that nearly all of the 200,000 human ERV's can be found in chimps at orthologous positions. Do you disagree?
This is a more current report:


Chimp PtERV's do not have orthologs in ANY SPECIES. Why is that Mark?

Your begging the question of proof here. The HGP while a landmark publication is none the less outdated. As a matter of fact they simply identified the ERVs in the human genome. There was no comparison to chimpanzee ERVs until the Chimpanzee genome was sequenced. You are still pushing this argument and frankly, I think you are going down a blind alley.

What is even more important you dodged the primary point. The most abundant family of ERVs is evidence of independent lineage. Splitting hairs won't change that and TOE is littered with false positives. This is just one of them.

One thing is cut and dried. Chimps and humans share nearly 200,000 orthologous ERV's. Do you agree or disagree?

I understand that 95% of the comparative sequences are the same. As time goes by and the research continues the profound differences are being revealed. I strongly disagree, in fact I have elaborated on this at length.

 

[[serious]]

I'm a creationist but I thought that was obvious. Loudmouth and I had a formal debate on the subject and in the peanut gallery he invited me to post to this thread. The point of the previous post was that the most abundant family of ERVs in the chimpanzee genome were integrated after the split. LM's facts are fishy at best, for one thing the 200,000 ERVs are based on the initial sequence of the human genome. The facts are outdated and as science progresses we do well to track the changes.

ERVs are not a valid proof of common ancestry. What they are is evidence of independent lineage. Take another look at the previous post and I'll check the thread for a while to see your response.

took another look at it and I see your argument a bit better now. What explanation do you have for the ERVs that are orthologous? How would you explain ERVs forming a nested hierarchy when we sort by them?

 

[Atheuz]

It's hilarious to see a Creationist attempt to debunk Science using inaccurate evidence, but once you start applying real scientific evidence to his view on the origin of life and origin of species everything becomes void and null.

GJ Mark Kennedy... bhahahha.

 

[mark kennedy]

took another look at it and I see your argument a bit better now. What explanation do you have for the ERVs that are orthologous? How would you explain ERVs forming a nested hierarchy when we sort by them?

The same one I have for orthologous in general, horizontal transmission:

Endogenous retroviruses may arise within genomes by at least two different mechanisms: retrotransposition from a pre-existing endogenous retrovirus (intraspecific transmission) or infection and integration via an exogenous source virus (horizontal transmission). Many cross-species transmissions have been documented and frequently manifest themselves as inconsistencies in the presumed phylogeny of closely related species.( Lineage-Specific Expansions of Retroviral Insertions within the Genomes of African Great Apes but Not Humans and Orangutans. PLoS Biol )​

The evidence from the ERVs argue strongly for independent lineage.

 

[mark kennedy]

It's hilarious to see a Creationist attempt to debunk Science using inaccurate evidence, but once you start applying real scientific evidence to his view on the origin of life and origin of species everything becomes void and null.

GJ Mark Kennedy... bhahahha.

It's actually the inaccuracies of evolutionists that convinced me they were inherently disingenuous. Not everything in TOE is suspect, as natural science it works just fine. As an a priori assumption of universal common descent it is hopelessly flawed and I think most evolutionists secretly know this. I say that based on the many false positives they propagate shamelessly.

dantose, how do you explain this?

A total of 95.8% of these sites were non-orthologous when compared between species. ​

"We report here that the chimpanzee genome contains at least 42 separate families of endogenous retroviruses, nine of which were not previously identified. All but two (CERV 1/PTERV1 and CERV 2) of the 42 families of chimpanzee endogenous retroviruses were found to have orthologs in humans. Molecular analysis (PCR and Southern hybridization) of CERV 2 elements demonstrates that this family is present in chimpanzee, bonobo, gorilla and old-world monkeys but absent in human, orangutan and new-world monkeys. A survey of endogenous retroviral positional variation between chimpanzees and humans determined that approximately 7% of all chimpanzee-human INDEL variation is associated with endogenous retroviral sequences." (Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses, Genome Biol. 2006 )​

The most abundant family of ERVs in the Chimpanzee do not have ortholouges in the human genome:

With more than 100 members, CERV 1/PTERV1 is one of the most abundant families of endogenous retroviruses in the chimpanzee genome. CERV 1/PTERV1 elements range in size from 5 to 8.8 kb in length, are bordered by inverted terminal repeats (TG and CA) and are characterized by 4 bp TSDs...Phylogenetic analysis of the LTRs from full-length elements of CERV 1/PTERV1 members indicated that this family of LTRs can be grouped into at least two subfamilies (bootstrap value of 99; Figure 3). The age of each subfamily was estimated by calculating the average of the pairwise distances between all sequences in a given subfamily. The estimated ages of the two subfamilies are 5 MY and 7.8 MY, respectively, suggesting that at least one subfamily was present in the lineage prior to the time chimpanzees and humans diverged from a common ancestor (about 6 MYA). This conclusion, however, is inconsistent with the fact that no CERV 1/PTERV1 orthologues were detected in the sequenced human genome. (Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses) Bolded mine​

 

[Loudmouth]

That's not the point, the most abundant family of ERVs in the chimpanzee genome were independently acquired.

How many PtERV's are their in the chimp genome? About 350? How many human ERV's are found at orthologous positions in the chimp genome? 200,000. Your "most abundant" is lacking in the extreme.

You are making this sweeping generality that virtually all of the 200,000 ERVs are identical. That's absurd.

Then how many are there?

Your begging the question of proof here. The HGP while a landmark publication is none the less outdated. As a matter of fact they simply identified the ERVs in the human genome. There was no comparison to chimpanzee ERVs until the Chimpanzee genome was sequenced.

There were comparisons. One of those comparisons is found in post #3. The paper I reference is from 1996, before the HGP was even done. It clearly indicates that there are orthologous ERV's.

You are still pushing this argument and frankly, I think you are going down a blind alley.

How so? Please show me where I mesed up. The HGP paper lists 200,000 ERV's. The CGP lists 400 chimp specific ERV's and about 100 human specific ERV's. What method did they use to determine which ERV's are specific?

What is even more important you dodged the primary point. The most abundant family of ERVs is evidence of independent lineage. Splitting hairs won't change that and TOE is littered with false positives. This is just one of them.

No one is arguing that the chimp lineage independently acquired ERV's. This is expected. Humans and chimps diverged a few million years ago so this is expected. What is also expected is that humans and chimps should share ERV's at orthologous positions IF THEY SHARE A COMMON ANCESTOR. Of the 200,400 ERV's in the chimp genome 200,000 can be found in the human genome at orthologous positions. This is evidence for common ancestry.

 

[Loudmouth]

The evidence from the ERVs argue strongly for independent lineage.

How do 200,000 ortholgous ERV's shared between humans and chimps evidence independent acquisition of these ERV's? I'm a bit confused here.

 

[mark kennedy]

How many PtERV's are their in the chimp genome? About 350? How many human ERV's are found at orthologous positions in the chimp genome? 200,000. Your "most abundant" is lacking in the extreme.

You have assumed that and never supported it with the actual evidence. You take your 200,000 orthologue statistic from the HGP that never compared them. It's absurd.

Then how many are there?

I have quoted, cited and linked the source material. The most abundant families of ERVs in the Chimpanzee Genome have rare ortholouges in the Human Genome and you know it.

There were comparisons. One of those comparisons is found in post #3. The paper I reference is from 1996, before the HGP was even done. It clearly indicates that there are orthologous ERV's.

I didn't say there weren't, just that your 200,000 ortholouge ERV thesis is false.

How so? Please show me where I mesed up. The HGP paper lists 200,000 ERV's. The CGP lists 400 chimp specific ERV's and about 100 human specific ERV's. What method did they use to determine which ERV's are specific?

Let me ask you this, how many genes did they report in that paper? How many do they report now?

No one is arguing that the chimp lineage independently acquired ERV's. This is expected. Humans and chimps diverged a few million years ago so this is expected. What is also expected is that humans and chimps should share ERV's at orthologous positions IF THEY SHARE A COMMON ANCESTOR. Of the 200,400 ERV's in the chimp genome 200,000 can be found in the human genome at orthologous positions. This is evidence for common ancestry.

No it's not, particularly when the most abundant families are acquired independently. You guys like to emphasize the similarities are such convincing evidence but never admit the inverse logic is intuitively obvious.

Thanks LM, it was fun but I'm kind of busy right now. I have to move the family before I go back. Your in my prayers.

Grace and peace,
Mark

 

[[serious]]

The same one I have for orthologous in general, horizontal transmission:

Endogenous retroviruses may arise within genomes by at least two different mechanisms: retrotransposition from a pre-existing endogenous retrovirus (intraspecific transmission) or infection and integration via an exogenous source virus (horizontal transmission). Many cross-species transmissions have been documented and frequently manifest themselves as inconsistencies in the presumed phylogeny of closely related species.( Lineage-Specific Expansions of Retroviral Insertions within the Genomes of African Great Apes but Not Humans and Orangutans. PLoS Biol )​

The evidence from the ERVs argue strongly for independent lineage.

Are you arguning that all th ERVs just happened to result from the uniform infection of identical viruses in the exact same spot on the genome that just happened to form the predicted nested hierarchy? I got to be honest here, that explanation is rather inadequate.

 

[RichardT]

no CERV 1/PTERV1 orthologues were detected in the sequenced human genome.

Nice find MK.

 

[RichardT]

Your begging the question of proof here. The HGP while a landmark publication is none the less outdated. As a matter of fact they simply identified the ERVs in the human genome. There was no comparison to chimpanzee ERVs until the Chimpanzee genome was sequenced. You are still pushing this argument and frankly, I think you are going down a blind alley.

Is this for real? That's extremely dishonest of them if you ask me.

 

[RichardT]

as natural science it works just fine

You should read Jerry Bergman's "Darwinism and the Deterioration of the Genome", he shows that mutations, the needed mechanism for "new information" (Gitt approach, which is an actual relevant approach for Creation and Evolution) is fatally flawed.

http://www.trueorigin.org/mutations01.asp