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Author Topic:   Creationist ERV Misinformation
Taq
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Posts: 9852
Joined: 03-06-2009
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(4)
Message 16 of 29 (902435)
11-23-2022 12:17 PM


Bad Reasons to Believe
I went to the Reasons to Believe website and searched their articles with the keywords "endogenous retroviruses". From what I can see, they all discuss the same misinformation already covered earlier in this thread.
You searched for endogenous retroviruses - Reasons to Believe
1. Retroviral insertion is not random enough. That's false. Even in a best case scenario, insertional bias will only produce ~1% shared ERV's.
2. ERV's have function. Only a tiny fraction can be shown to have function, and even if they all had function they would still be smoking gun evidence for common ancestry.
3. PtERV1 is found in chimps and gorillas but not humans or orangutans. They forget to mention that they are not at orthologous positions in the chimp and gorilla genomes.
4. Departures from the expected phylogeny. There are known mechanisms that create these departures, such as ILS. It is expected that we will see a noisy phylogenetic signal if species evolved from a common ancestor. It is the ratio of noise to signal that matters, and they are reticent to even acknowledge the massive and overwhelming phylogenetic signal that sits out way above the noise.
5. Retroviruses can't produce ERVs in the first place. They acknowledge the case of ERVs being produced by an exogenous retrovirus in koalas, but they tell their audience to just ignore it for no apparent reason.
Nothing really original here. Just a rehash of what other creationist authors have written.

  
Taq
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(4)
Message 17 of 29 (902908)
11-28-2022 3:23 PM


ICR = Information Corruption Regime
I ran across an article at ICR that made a claim about ERV's that I had not come across before:
quote:
First, genetic data indicate that these sequences are not millions of years old. Using the comparative tools of evolutionary genetics, secular scientists compared the gene sequences of viruses to their counterparts in animal genomes and found that, at most, the variation in these sequences indicates they can be no more than 50,000 years old.2 So, if these viral-like sequences are not millions of years old, then where did they come from?
[off topic note: the use of "secular scientist" still makes me giggle. What's next? Secular baseball players? Secular dentists?]
That's a bit convoluted, but their claim is pretty clear. They are claiming that ERVs are not older than 50,000 years. To support this claim, they cite:
Molecular Clocks and the Puzzle of RNA Virus Origins
So what does the paper actually say?
quote:
Although the ultimate origins of RNA viruses are uncertain, it seems reasonable to assume that these infectious agents have a long evolutionary history, appearing with, or perhaps before, the first cellular life-forms (38). While the RNA viruses we see today may not date back quite this far, the evidence that some DNA viruses have evolved with their vertebrate hosts over many millions of years (24) makes an equally ancient history for RNA viruses a natural expectation. Yet a very different picture of RNA virus origins is painted if their gene sequences are compared; by using the best estimates for rates of evolutionary change (nucleotide substitution) and assuming an approximate molecular clock (21, 33), it can be inferred that the families of RNA viruses circulating today could only have appeared very recently, probably not more than about 50,000 years ago. Hence, if evolutionary rates are accurate and relatively constant, present-day RNA viruses may have originated more recently than our own species.
Well, that's a very different picture than the one painted by ICR. The scientific paper is saying that currently circulating RNA viruses originated no more than 50,000 years ago. It says nothing about ERVs originating within the last 50,000 years. On top of that, the article clearly states that there are examples of DNA viruses that have evidence for host/virus co-evolution over the last several million years. Strange that they didn't mention that (sarcasm implied). The paper also goes on to explain why comparison of circulating RNA viruses leads to these conclusions.
The rest of the ICR article hits the usual misinformation bullet points, such as some ERVs having function and no examples of extant exogenous retroviruses producing heritable endogenous retroviruses (see Koala Retrovirus [KoRV]).

  
Mahershalalhashbaz
Junior Member (Idle past 329 days)
Posts: 5
Joined: 12-23-2022


Message 18 of 29 (904555)
01-01-2023 3:04 AM
Reply to: Message 4 by Taq
11-16-2022 10:45 AM


Re: The Discovery Institute Spreads Misinformation
quote:
The first example comes from the Discovery Institute.

Do Shared ERVs Support Common Descent?
The Article is in 3 parts if anyone wants to see all of them for full context
Revisiting an Old Chestnut: Retroviruses and Common Descent (Updated)
Do Shared ERVs Support Common Ancestry?
More Points on ERVs

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 Message 4 by Taq, posted 11-16-2022 10:45 AM Taq has replied

Replies to this message:
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Mahershalalhashbaz
Junior Member (Idle past 329 days)
Posts: 5
Joined: 12-23-2022


Message 19 of 29 (904556)
01-01-2023 3:14 AM
Reply to: Message 1 by Taq
11-15-2022 11:39 AM


TAQ:
This means that out of the 203,000 ERV's reported in the human genome only 82 are not shared with chimps at the same base. ​
Are you sure this is a valid method of calculating Orthologous ERV's? I tried to find an independent source and the best I could find was Orthologous endogenous retroviruses exhibit directional selection since the chimp-human split which says "Overall, we identified 336 chimp-human pairs of sequence from a variety of genomic locations".

This message is a reply to:
 Message 1 by Taq, posted 11-15-2022 11:39 AM Taq has replied

Replies to this message:
 Message 20 by Taq, posted 01-03-2023 11:12 AM Mahershalalhashbaz has replied

  
Taq
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Posts: 9852
Joined: 03-06-2009
Member Rating: 4.4


Message 20 of 29 (904624)
01-03-2023 11:12 AM
Reply to: Message 19 by Mahershalalhashbaz
01-01-2023 3:14 AM


Mahershalalhashbaz writes:
Are you sure this is a valid method of calculating Orthologous ERV's?
Yes. ERV's are either orthologous or lineage specific. If they aren't lineage specific then they are orthologous. If only 82 human ERV's are lineage specific then the rest must be orthologous. The 203,000 human ERV's counted by the Human Genome Consortium was done by top scientists, so I see no reason to doubt it.
I tried to find an independent source and the best I could find was Orthologous endogenous retroviruses exhibit directional selection since the chimp-human split which says "Overall, we identified 336 chimp-human pairs of sequence from a variety of genomic locations".
They used several filters to narrow the field down which means they excluded a lot of ERV's from the study. They were looking for more recent insertions that are full length, so right away they are excluding about 90% of ERV's that are solo LTR's. Of the candidates, they further excluded older full length ERV's because they were focused on more recent insertions, as stated in the results section:
quote:
We wanted to see if recently integrated proviruses accumulated mutations more quickly than neighbouring DNA. Our approach was to examine substitutions into ERVs and their neighbouring genomic sequence that lead to differences between human and chimpanzee. To achieve this goal we identified ERVs and their flanking DNA from both species.
Orthologous endogenous retroviruses exhibit directional selection since the chimp-human split - PMC
They were NOT trying to measure the total number of ERV's in the human or chimp genome.

This message is a reply to:
 Message 19 by Mahershalalhashbaz, posted 01-01-2023 3:14 AM Mahershalalhashbaz has replied

Replies to this message:
 Message 22 by Mahershalalhashbaz, posted 01-05-2023 2:17 AM Taq has replied
 Message 24 by sensei, posted 02-15-2023 10:05 PM Taq has replied

  
Taq
Member
Posts: 9852
Joined: 03-06-2009
Member Rating: 4.4


Message 21 of 29 (904625)
01-03-2023 11:15 AM
Reply to: Message 18 by Mahershalalhashbaz
01-01-2023 3:04 AM


Re: The Discovery Institute Spreads Misinformation
Mahershalalhashbaz writes:
The Article is in 3 parts if anyone wants to see all of them for full context
Is there anything you would like to see addressed that hasn't been so far?

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 Message 18 by Mahershalalhashbaz, posted 01-01-2023 3:04 AM Mahershalalhashbaz has not replied

  
Mahershalalhashbaz
Junior Member (Idle past 329 days)
Posts: 5
Joined: 12-23-2022


Message 22 of 29 (904682)
01-05-2023 2:17 AM
Reply to: Message 20 by Taq
01-03-2023 11:12 AM


I think you already covered this in #15.

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 Message 20 by Taq, posted 01-03-2023 11:12 AM Taq has replied

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Taq
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Posts: 9852
Joined: 03-06-2009
Member Rating: 4.4


Message 23 of 29 (904690)
01-05-2023 10:58 AM
Reply to: Message 22 by Mahershalalhashbaz
01-05-2023 2:17 AM


Mahershalalhashbaz writes:
I think you already covered this in #15.
Do you know of any creationist sources whose articles on ERV's are honest and consistent with the scientific literature? I have yet to find one.

This message is a reply to:
 Message 22 by Mahershalalhashbaz, posted 01-05-2023 2:17 AM Mahershalalhashbaz has not replied

  
sensei
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Posts: 467
Joined: 01-24-2023


Message 24 of 29 (906674)
02-15-2023 10:05 PM
Reply to: Message 20 by Taq
01-03-2023 11:12 AM


Do you have similar data on shared ERVs with other mammals or with reptiles or fish?

This message is a reply to:
 Message 20 by Taq, posted 01-03-2023 11:12 AM Taq has replied

Replies to this message:
 Message 25 by Taq, posted 02-16-2023 12:49 PM sensei has replied

  
Taq
Member
Posts: 9852
Joined: 03-06-2009
Member Rating: 4.4


Message 25 of 29 (906728)
02-16-2023 12:49 PM
Reply to: Message 24 by sensei
02-15-2023 10:05 PM


sensei writes:
Do you have similar data on shared ERVs with other mammals or with reptiles or fish?
Over time ERV's will accumulate mutations to the point that they can no longer be compared to one another. This is true for the vast majority of sequence in vertebrate genomes. Over those evolutionary distances (humans to distantly related mammals, reptiles, fish) it is better to compare conserved sequences which tend to be functional sequences. Since the vast majority of ERV's are not functional and accumulate mutations at a rate consistent with neutral drift they fade into the background much faster than functional DNA. There is also the problem of recombination and indels which can make synteny and orthology hard to determine.

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 Message 24 by sensei, posted 02-15-2023 10:05 PM sensei has replied

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sensei
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Posts: 467
Joined: 01-24-2023


Message 26 of 29 (906757)
02-16-2023 2:24 PM
Reply to: Message 25 by Taq
02-16-2023 12:49 PM


Alright, understood. Thanks!

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sensei
Member
Posts: 467
Joined: 01-24-2023


Message 27 of 29 (912847)
10-04-2023 8:36 AM
Reply to: Message 1 by Taq
11-15-2022 11:39 AM


Taq:
In table 2 of the chimp genome paper they report 82 human specific ERV's and 279 chimp specific ERV's.
I don't see these numbers 82 and 279 in table 2. Could you explain to me where or how you got these numbers?
Thanks!

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 Message 1 by Taq, posted 11-15-2022 11:39 AM Taq has not replied

Replies to this message:
 Message 28 by Granny Magda, posted 10-04-2023 10:09 AM sensei has replied

  
Granny Magda
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Posts: 2462
From: UK
Joined: 11-12-2007
Member Rating: 4.1


Message 28 of 29 (912850)
10-04-2023 10:09 AM
Reply to: Message 27 by sensei
10-04-2023 8:36 AM


Hi sensei,
By adding ERV Class 1 to ERV Class 2.
Mutate and Survive

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sensei
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Posts: 467
Joined: 01-24-2023


Message 29 of 29 (912874)
10-05-2023 3:56 AM
Reply to: Message 28 by Granny Magda
10-04-2023 10:09 AM


Ah yes, thank you!

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 Message 28 by Granny Magda, posted 10-04-2023 10:09 AM Granny Magda has not replied

  
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