A question of ERVs

mark kennedy · Dec 16, 2018

pshun2404 said:
See I warned everyone and there it is...yeah I will put him on my ignore list as well.

I've had my run ins with him before, just finally tired of it.

46AND2 · Dec 16, 2018

pshun2404 said:
I never read this article and did not even know it existed. Are you claiming I plagiarized two or three paragraphs from here and did not cite this site? I read the article you linked and could not find the alleged example...and why would I have to hide that I am an OWC? I've never denied that!

Can you cut and paste the several paragraphs you cite from your article and post them here? Thanks...I will wait.

Here you go...

pshun2404 said:
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.”

.

pshun2404 · Dec 16, 2018

46AND2 said:
Here you go...

Sorry that does not appear in USCogs article anywhere. Secondly, quotation is not plagiarism.

46AND2 · Dec 16, 2018

pshun2404 said:
Sorry that does not appear in USCogs article anywhere. Secondly, quotation is not plagiarism.

4th paragraph. And yes, uncited quotations are plagiarism.

pshun2404 · Dec 16, 2018

46AND2 said:
4th paragraph. And yes, uncited quotations are plagiarism.

I stand corrected...what she said IS also found in this article (though far from several paragraphs). All the quotations I referred to are the work of reputable scientists (even Roberts), not my words or my work, but if plagiarism includes actual "Quotes" where the actual author is being cited as the source, then I guess I am guilty of that. I apologize and will be sure not to do this again. That does not invalidate her opinion just my quote (which was her not me).

46AND2 · Dec 16, 2018

mark kennedy said:
That's when they are the most vulnerable:

Given the hierarchical, step-wise logic or "architecture" of animal development, early stages such as cleavage and gastrulation lay the groundwork for all that follows. Body plan structures in the adult, for example, trace their cellular lineage to these early stages. Thus, if macroevolution is going to occur, it must begin in early development. Yet it is precisely here, in early development, that organisms are least tolerant of mutations. (Homology, a Concept in Crisis)

For @pshun2404 's benefit. This is another form of plagiarism. The quote that Mark provided here is not found in the source he cited.

This is something you (pshun2404) also did in that same post #29:

pshun2404 said:
Furthermore, 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 shared ERV insertion sites previously thought to confirm common ancestry.”

The quote at the end of this paragraph is not found in the paper you cited by Macfarlane and Badge.

mark kennedy · Dec 16, 2018

46AND2 said:
For @pshun2404 's benefit. This is another form of plagiarism. The quote that Mark provided here is not found in the source he cited.

Yes it is, it's the caption for figure 4.

This is something you also did in that same post #29:

The quote at the end of this paragraph is not found in the paper you cited by Macfarlane and Badge.

I don't know what your talking about there.

46AND2 · Dec 16, 2018

mark kennedy said:
Yes it is, it's the caption for figure 4.

Ah. That's why the find function didn't locate it...figures and captions were not embedded in the article, but rather separate links.

My apologies.

mark kennedy · Dec 16, 2018

46AND2 said:
Ah. That's why the find function didn't locate it...figures and captions were not embedded in the article, but rather separate links.

My apologies.

I guess I could have noted it, understandable that you would be confused under the circumstances.

46AND2 · Dec 17, 2018

pshun2404 said:
Also, nested hierarchies are a humanly devised convention of convenience (to group items by similar qualities or characteristics does not demonstrate lineage). The lineal assumptions are not actual truth.

Let me give you another example whereby we see a specific pattern which common ancestry requires, and is easily falsifiable since MANY other possibilities COULD have been observed:

This paper describes a pattern of similarities (and differences) within the olfactory genes of Orangutans, Gorillas, Chimps, and humans, that is consistent with the theory that Orangutans branched off first, Gorillas next, and finally Chimps and Humans.

As you can see from the image (provided by Biologos--Note that the Gorilla unique mutation number in the Biologos article appears to be in error, as the paper identifies 5 instead of 6):

There are 6 mutations which we share with all three other species.

There are 9 that we share with Chimpanzee and Gorilla

And 12 which we share with Chimps.

It is important to note that the mutations identified silence the expression of the gene in which they are contained (not to worry, there are more than 1000 of them, hence our ability to still smell).

There are no mutations which are shared with just chimps and orangutans (a diversion from the nested hierarchy). There are none which are shared with just gorilla and human (diversion). Same with Chimp and gorilla, human and orangutan, and gorilla and orangutan.

Clearly, the pattern doesn't have to exist, as any one of the combinations in my previous paragraph COULD be observed. But they aren't.

And the pattern matches exactly the pattern found with ERVs.

So I ask you, how do you explain this shared pattern between broken olfactory genes and ERVs, without common ancestry? Because, not only does common ancestry explain it beautifully, it is the required result for common ancestry to be true.

mark kennedy · Dec 17, 2018

46AND2 said:
Let me give you another example whereby we see a specific pattern which common ancestry requires, and is easily falsifiable since MANY other possibilities COULD have been observed:

This paper describes a pattern of similarities (and differences) within the olfactory genes of Orangutans, Gorillas, Chimps, and humans, that is consistent with the theory that Orangutans branched off first, Gorillas next, and finally Chimps and Humans.

As you can see from the image (provided by Biologos--Note that the Gorilla unique mutation number in the Biologos article appears to be in error, as the paper identifies 5 instead of 6):

There are 6 mutations which we share with all three other species.

There are 9 that we share with only Chimpanzee and Gorilla

And 12 which we share with only Chimps.

It is important to note that the mutations identified silence the expression of the gene in which they are contained (not to worry, there are more than 1000 of them, hence our ability to still smell).

There are no mutations which are shared with just chimps and orangutans (a diversion from the nested hierarchy). There are none which are shared with just gorilla and human (diversion). Same with Chimp and gorilla, human and orangutan, and gorilla and orangutan.

Clearly, the pattern doesn't have to exist, as any one of the combinations in my previous paragraph COULD be observed. But they aren't.

And the pattern matches exactly the pattern found with ERVs.

So I ask you, how do you explain this shared pattern between broken olfactory genes and ERVs without common ancestry? Because, not only does common ancestry explain it beautifully, it is the required result for common ancestry to be true.

You make a big deal about 6, 9 and then 12 mutation spots and claim there are hundreds. It's a farce, as many times as I have searched this one out I've never seen it hold up to close scrutiny. The absurdity of the assumption that ERVs are the result of germline invasions is on it's face, ridiculous for starters. Then we are told that some 8% of our genome is the result of germline invasions with no answer for how our ancestors survived the deleterious effects that would have necessarily resulted.

Clearly and obviously the worst homology argument ever but you guys eat it up. I would think fossils and comparative genomics would be a lot more appealing instead of these obscure and convoluted arguments about common mutations in worthless protein coding reading frames. Then there is the fact that 7% of the divergence due to indels is in the ERVs, so it raises a question. If things in common are an argument for common descent, then isn't the inverse logic intuitively obvious, that things different are an argument against common descent?

46AND2 · Dec 17, 2018

mark kennedy said:
You make a big deal about 6, 9 and then 12 mutation spots and claim there are hundreds. It's a farce, as many times as I have searched this one out I've never seen it hold up to close scrutiny. The absurdity of the assumption that ERVs are the result of germline invasions is on it's face, ridiculous for starters. Then we are told that some 8% of our genome is the result of germline invasions with no answer for how our ancestors survived the deleterious effects that would have necessarily resulted.

Clearly and obviously the worst homology argument ever but you guys eat it up. I would think fossils and comparative genomics would be a lot more appealing instead of these obscure and convoluted arguments about common mutations in worthless protein coding reading frames. Then there is the fact that 7% of the divergence due to indels is in the ERVs, so it raises a question. If things in common are an argument for common descent, then isn't the inverse logic intuitively obvious, that things different are an argument against common descent?

So, no explanation for the pattern, then? Didn't think so.

If things in common are an argument for common descent, then isn't the inverse logic intuitively obvious, that things different are an argument against common descent?

No. As I have told you before.

Its about similarities AND differences, and the pattern they create. For example: With the PtERVs that don't fit the nested hierarchy. In order for that observation to fit common ancestry, they should be located at non-orthologous locations. And they are. It is the orthologous ERVs which create the nested hierarchy, because those are the ones passed down through inheritance. The DIFFERENT locations of the PtERVs ALSO supports common ancestry because, as expected, they don't fit the nested hierarchy.

Let me know when you want to actually try to give a better explanation for the pattern.

46AND2 · Dec 17, 2018

mark kennedy said:
You make a big deal about 6, 9 and then 12 mutation spots and claim there are hundreds.

What are you talking about? I think you must have misread. Again.

xianghua · Dec 17, 2018

pshun2404 said:
Precisely! Most critics of this view will just blow the study off as too long to read (Why would they? It throws yet another monkey wrench into the generally accepted mantra just as some of the other studies mentioned).

although i do need to give a credit to some id sources. but as far as i remember i indeed read the whole paper.

xianghua · Dec 17, 2018

46AND2 said:
The apes which have these insertions have them at different parts of their genomes.

not according to the authors:

"24 sites mapped to similar regions of the human reference genome (approximately 160 kb) and could not be definitively resolved as orthologous or non-orthologous"

so basically they arent sure if these ervs are indeed orthologous or not. and you dont know it either. but the real point here is the fact that these ervs are almost in identical position among primates. this fact alone falsify the claim about nested hierarchy, since there is no real difference between identical site and slmost identical one.

46AND2 said:
This indicates that they were obtained by separate events in each of the species, and not passed down through common ancestry (they would be in the same location if due to ancestry).

are you sure about that? because even among chimp and human there is about 4% difference. it means that any gene isnt in the same location between chimp and human. so according to this criteria any gene between human and chimp isnt orthologous.

tas8831 · Dec 17, 2018

THIS is the real reason the autodidact put me on ignore...

tas8831 said:
Wow...

All those decades of study (to include a whopping 5 years studying the art of brainwashing) and you still are lost in the woods...

OK....

Ummm....

OK - let's see.

From the abstract of the Yohn paper:

"We unambiguously map 287 retroviral integration sites and determine that approximately 95.8% of the insertions occur at non-orthologous regions between closely related species. Phylogenetic analysis of the endogenous retrovirus reveals that the gorilla and chimpanzee elements share a monophyletic origin with a subset of the Old World monkey retroviral elements, but that the average sequence divergence exceeds neutral expectation for a strictly nuclear inherited DNA molecule. Within the chimpanzee, there is a significant integration bias against genes, with only 14 of these insertions mapping within intronic regions. Six out of ten of these genes, for which there are expression data, show significant differences in transcript expression between human and chimpanzee. Our data are consistent with a retroviral infection that bombarded the genomes of chimpanzees and gorillas independently and concurrently, 3–4 million years ago. We speculate on the potential impact of such recent events on the evolution of humans and great apes."

And the Barbulescu paper:

"They also show that HERV-K replicated as a virus and reinfected the germline of the common ancestor of the four modern species during the period of time when the lineages were separating and demonstrate the utility of using HERV-K to trace human evolution."

Will you never learn that 1. getting ideas for forum posts from YEC websites is a bad idea and 2. argument via Googling key words and looking for quotes while ignoring context makes you look silly?

Walls of text cannot hide your errors.

tas8831 · Dec 17, 2018

pshun2404 said:
I never read this article and did not even know it existed. Are you claiming I plagiarized two or three paragraphs from here and did not cite this site? I read the article you linked and could not find the alleged example...and why would I have to hide that I am an OWC? I've never denied that!

Can you cut and paste the several paragraphs you cite from your article and post them here? Thanks...I will wait.

Yeah, he did this when I caught him plagiarizing a page listing some information on specific genes, too - claimed he never read it, despite the fact that his post had the exact same spacing and dashes... same phrases in the same order... the exact same mistakes as the original...etc...

Weird how so many supposed Christians will so readily lie to try to cover their other acts of dishonesty.

46AND2 · Dec 17, 2018

xianghua said:
not according to the authors:

"24 sites mapped to similar regions of the human reference genome (approximately 160 kb) and could not be definitively resolved as orthologous or non-orthologous"

so basically they arent sure if these ervs are indeed orthologous or not. and you dont know it either. but the real point here is the fact that these ervs are almost in identical position among primates. this fact alone falsify the claim about nested hierarchy, since there is no real difference between identical site and slmost identical one.

The method they used to compare the ERVs only has a resolution of 100,000 base pairs (out of 3 billion).

275 of 287 ERVs were not even within 100,000 base pairs of each other...that is unambiguously non-orthologous. So yes, I do know it...and you would, too, if you actually understood what you were reading.

There absolutely is a difference between "almost identical" and "identical." One of them means that they share the same spot, and the other means they don't. Duh. Oh, just a hint, the papers which found the actual orthologous ERVs did not use this same BAC method, and discovered that the ERVs are unambiguously found at the same sites.

are you sure about that? because even among chimp and human there is about 4% difference. it means that any gene isnt in the same location between chimp and human. so according to this criteria any gene between human and chimp isnt orthologous.

Yes, I am sure about that. Because when they found the ERVs in each of the respective genomes, they compared the flanking sequences on either side of the ERVs in both genomes, which indicates that they are inserted at the same spot.

46AND2 · Dec 17, 2018

xianghua said:
although i do need to give a credit to some id sources. but as far as i remember i indeed read the whole paper.

No you didn't. Your argument stems entirely from your ID sources (as always). Cause the answer to your questions of me were right in that paper for you to read.

That, or you are just incapable of understanding the paper. In which case, you shouldn't be making an argument about it in the first place.

46AND2 · Dec 17, 2018

tas8831 said:
Yeah, he did this when I caught him plagiarizing a page listing some information on specific genes, too - claimed he never read it, despite the fact that his post had the exact same spacing and dashes... same phrases in the same order... the exact same mistakes as the original...etc...

Weird how so many supposed Christians will so readily lie to try to cover their other acts of dishonesty.

To be fair, he's just copy/pasting apologists who are, in turn, copy/pasting other apologists, and so on until you get back to the first apologist, who for some reason didn't copy/paste the original scientific paper (to manipulate data?), and instead inserted their own mistakes.

But, I do find it humorous that he admits to not checking sources.

A question of ERVs

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