Are ERVs evidence for common ancestry

[Elliot_Mudd]

The talk origins article is outdated anyway now isn’t it? The number of shared ERVs is around 100,000, at least that’s the figure I found.

[T_aquaticus]

@Elliot_Mudd

The number of shared ERVs is around 100,000, at least that’s the figure I found.

It is around 203,000 as of the human and chimp genome papers (2001 and 2005 respectively). The tables from those papers can be found in one of my posts just a little ways up in the thread.

[Dan_Eastwood]

Good to see you @T_aquaticus

[Elliot_Mudd]

Right ok. I know the Talk Origins article that said there were just 7 shared is outdated, but still seems odd that even back then they’d only located 7 matching, whereas now we’ve located over 200,000.

[Elliot_Mudd]

Yeah I’d read about the repeats being evidence of an insertion, but I thought that would also be consistent with the claim in the creation.com website that agrees that these insertions only “resemble” viruses:

“Next, the RNase enzyme removes the RNA part, and the remaining single-stranded DNA forms a circular molecule. This circular single-stranded DNA serves as a template for the synthesis of a second DNA strand. The double-stranded DNA copy can now be put back in the genome with the help of the integrase enzyme. The position where this happens is determined by repetitive DNA sequences flanking the ERV element and/or by the sequence specificity of the endonuclease (integrase). Alternatively, the RNA molecule can be packed in a capsule consisting of three proteins, which are specified by the gag gene, and the whole thing looks very much like a virus. Why this packaging is necessary is unclear, but it may prevent the RNA molecule from docking to the wrong places in the cell. On the other hand, the protein-coated viral-like particles may contain biologically active molecules which have to be protected and/or delivered to the right places. In other words, we are dealing with a subcellular transport system.”

The author seems thinks what we are calling an ERVs aren’t ERV but “looks very much like” viruses, and also have “repetitive DNA sequences flanking the ERV element”. So if the author is correct and these insertions are “subcellular transport systems” that look like viruses but are not viruses, then wouldn’t the repeats be consistent with both his view and the view that they really are ERVS.

[Faizal_Ali]

@Elliot_Mudd

Right ok. I know the Talk Origins article that said there were just 7 shared is outdated, but still seems odd that even back then they’d only located 7 matching, whereas now we’ve located over 200,000.

I wonder if the completion of the Human and Chimpanzee Genome Projects is a factor.

[T_aquaticus]

@Elliot_Mudd

Yeah I’d read about the repeats being evidence of an insertion, but I thought that would also be consistent with the claim in the creation.com website that agrees that these insertions only “resemble” viruses:

I’m not sure why you would think that, but it simply isn’t true. It is the opposite of true. There is no reason why those repeats should be there if the ERV’s were not the result of retroviral insertion.

@Elliot_Mudd

“Next, the RNase enzyme removes the RNA part, and the remaining single-stranded DNA forms a circular molecule. This circular single-stranded DNA serves as a template for the synthesis of a second DNA strand. The double-stranded DNA copy can now be put back in the genome with the help of the integrase enzyme. The position where this happens is determined by repetitive DNA sequences flanking the ERV element and/or by the sequence specificity of the endonuclease (integrase).

That’s also false. Retroviruses insert all over the place in the genome, not just in one spot. For example, the bars in the figure below are the 22 autosomal chromosomes and the X sex chromosome. The dots on the bars are insertions of three retroviruses (HIV, MLV, and ASLV). They insert all over the place.

Retroviral DNA integration: ASLV, HIV, and MLV show distinct target site...

The preferences that do exist are for very general features, like transcription units which make up about half of the human genome.

@Elliot_Mudd

Alternatively, the RNA molecule can be packed in a capsule consisting of three proteins, which are specified by the gag gene, and the whole thing looks very much like a virus . Why this packaging is necessary is unclear, but it may prevent the RNA molecule from docking to the wrong places in the cell. On the other hand, the protein-coated viral-like particles may contain biologically active molecules which have to be protected and/or delivered to the right places. In other words, we are dealing with a subcellular transport system.”

We can observe retroviruses producing new ERV’s. The excuses made by the creationists in these articles is a bit like a defense attorney claiming that the swirls of oil just look like fingerprints, but actually aren’t.

[T_aquaticus]

@Elliot_Mudd

I know the Talk Origins article that said there were just 7 shared is outdated,

They only highlighted 7 examples. They never said that there were only 7 shared ERV’s across the whole genome.

There are at least seven different known instances of common retrogene insertions between chimps and humans, and this number is sure to grow as both these organism’s genomes are sequenced (Bonner et al . 1982; Dangel et al . 1995; Svensson et al . 1995; Kjellman et al . 1999; Lebedev et al . 2000; Sverdlov 2000).
29+ Evidences for Macroevolution: Part 4

[Elliot_Mudd]

@T_aquaticus

They only highlighted 7 examples. They never said that there were only 7 shared ERV’s across the whole genome.

Ah right, got that.

@T_aquaticus

The excuses made by the creationists in these articles is a bit like a defense attorney claiming that the swirls of oil just look like fingerprints, but actually aren’t.

Right, so their saying that what we are claim are ancient ERV insertions because they look the same as viral insertions we see today and can observe in the lab, are actually not ERVs, but just look like them.

The author mentions a paper in cell:

“In 2018, two publications addressing this possibility appeared simultaneously in Cell”

To be honest this part went over my head. As you mentioned previously the creationist author thinking that the ERV is really something else is like saying
something else is like a defense attorney claiming that the swirls of oil just look like fingerprints, but actually aren’t. What is the paper in Cell really saying, I’ve looked and it’s going over my head unfortunately.

[T_aquaticus]

@Elliot_Mudd

The author mentions a paper in cell:

“In 2018, two publications addressing this possibility appeared simultaneously in Cell ”

To be honest this part went over my head .

The papers discuss how viral insertions can evolve to take on new functions in the host genome. This in no way puts the viral origin of ERV’s in doubt.

[Elliot_Mudd]

@T_aquaticus

The papers discuss how viral insertions can evolve to take on new functions in the host genome.

Right. So it’s saying that a some ERVS have taken on functions in the genome? Not that they all have? It’s a few specific example where a few out of thousands of insertion has been found to have a function, most of which are functionless?

So in other words we know it’s a viral insertion because the sequence is very close to other known viruses, far closer than anything else. This insertion has then taken on a new function in the genome. That’s all it’s saying.

[thoughtful (Valerie (non-scientist))]

@Elliot_Mudd

It’s a few specific example where a few out of thousands of insertion has been found to have a function, most of which are functionless?

@Elliot_Mudd if you don’t know, you might want to find out how much we/scientists/humanity know about the function (or not) of ERVs, even the entire human genome and how that’s changed over the last few decades. You might be surprised as I was. Most here aren’t going to readily admit what we don’t know and what’s been believed to be true in the past.

[T_aquaticus]

@Elliot_Mudd

So it’s saying that a some ERVS have taken on functions in the genome? Not that they all have?

It is true that only a relative handful of ERV’s have any apparent function, but the purpose of the paper was not to survey all ERV’s and determine how many had function. Instead, they focused in on just one (or a few) ERV’s to determine what function they may have.

On a more general note, the viral genes are already functional when they insert into the genome. They form proteins that fold into stable structures and they will have a variety of basic functions like catalytic activity, DNA/RNA binding, and protein to protein binding. They will also have very strong gene promoters. So its not like it is an insertion of random, inert DNA sequence that starts out with no function. Quite the opposite. Therefore, it isn’t surprising to see alterations of these sequences resulting in new functions that may benefit the host.

@Elliot_Mudd

So in other words we know it’s a viral insertion because the sequence is very close to other known viruses, far closer than anything else. This insertion has then taken on a new function in the genome. That’s all it’s saying.

Yes, sort of. The paper describes the insertions as retrotransposons containing a gag-like gene. Transposons are “jumping genes” that copy themselves and then reinsert into the genome to make more copies of themselves. They are similar to retroviruses in this sense, and some even carry genes that were originally part of viral genomes. However, they aren’t entirely the same as direct retroviral insertions (i.e. provirus or ERV).

The ORF of darc1 is mostly represented by the remnant of a Gypsy-superfamily of transposons (Fig. 2U), specifically dArc1 has strong similarities to the GAG region of a Gypsy-like transposon.
Retrovirus-like Gag Protein Arc1 Binds RNA and Traffics across Synaptic Boutons - PubMed

[CrisprCAS9]

@thoughtful

and how that’s changed over the last few decades.

It’s changed to support the notion that most of the genome isn’t doing anything relevant.

[Michael_Okoko]

@thoughtful

@Elliot_Mudd if you don’t know, you might want to find out how much we/scientists/humanity know about the function (or not) of ERVs

That’s easy. Go read the primary literature on ERVs.

@thoughtful

even the entire human genome and how that’s changed over the last few decades

Again that’s easy. Just the read the primary literature on the human genome.

@thoughtful

Most here aren’t going to readily admit what we don’t know and what’s been believed to be true in the past.

Evidence, please, that the scientists on this forum are intentionally withholding information on what ideas have been abandoned or revised?

Your tone reeks of conspiratorial thinking and its surprising that it is coming from you.

[Faizal_Ali]

@thoughtful

Most here aren’t going to readily admit what we don’t know and what’s been believed to be true in the past.

That’s uncalled for. The scientifically informed people here have been nothing but forthright and honest in their attempts to educate you on matters regarding which you admit you know very little. A little appreciation on your part might be in order?

[Rumraket (Mikkel R.)]

@thoughtful

Most here aren’t going to readily admit what we don’t know and what’s been believed to be true in the past.

From what did you extract that conclusion?

[John_Harshman]

@thoughtful

Most here aren’t going to readily admit what we don’t know and what’s been believed to be true in the past.

Do you even realize when you’re attacking the integrity of the scientists who post here? In this case, it’s your knowledge of science and its history that seems to be faulty.

[T_aquaticus]

@thoughtful

@Elliot_Mudd if you don’t know, you might want to find out how much we/scientists/humanity know about the function (or not) of ERVs, even the entire human genome and how that’s changed over the last few decades.

Why don’t you share what you think has changed.

[Elliot_Mudd]

@T_aquaticus

Yes, sort of. The paper describes the insertions as retrotransposons containing a gag-like gene. Transposons are “jumping genes” that copy themselves and then reinsert into the genome to make more copies of themselves. They are similar to retroviruses in this sense, and some even carry genes that were originally part of viral genomes. However, they aren’t entirely the same as direct retroviral insertions (i.e. provirus or ERV).

Thanks. So you mean the paper that creation.com cites when discussing ERVs isn’t actually specificity about ERVs?

Let me see if I’ve got this right:
It’s actually irrelevant if an ERV is shown to have a function. It’s still evidence for common ancestry because after the ERV has been inserted it can later evolve a new function. For example a broken mouse trap can still be used as a tie clip, or a door wedge. Its obviously still a mouse trap that’s being used for a new purpose. So the ERV is clearly an ERV insertion (we know this because the DNA sequence is more like know viruses than anything else), but it’s taken on a new function.

So the creationist claim that if the ERV (“junk DNA”) is shown to have a function then it’s no longer evidence for common ancestry is wrong as it’s like saying the broken mousetrap that’s being used as a tie clip was never meant to be mousetrap, but it just happens to look like a mousetrap?