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Endogenous Retroviruses: Evidence for Human Evolution

Asyncritus

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Are you challenging the claim that retroviruses exist? If so, I would love to see your evidence. Don't forget the red portion of the opening post.

If someone wants to challenge this argument, they must present observable evidence and a testable hypothesis.

The idea that humans evolved from chimpanzees or related species, is so absurd that it hardly deserves wasting thinking time upon.

The idea that a broken chromosome could possibly account for the immense gulf that exists between humans and chimpanzees (I'm thinking particularly of the intellectual gulf) is simply laughable.

Your point, however is about the ERVs, the alleged remnants of viral infection and whatnot in the dim and distant past, and which are now relics, evidence of the alleged transition from chimp to human.

As has been shown, and is even now being shown, those alleged relics are nothing of the sort - but have important uses in the genome. I here append a quotation regarding the alleged uselessness of the ERVs.

Perhaps you would like to comment on the evidence adduced.

I acknowledge the source of this article in: The Journal of Creation Research

Large scale function for ‘endogenous retroviruses’

by Shaun Doyle

Endogenous retroviruses (ERVs) are some of the most cited evidences for evolution. They are part of the suite of ‘junk DNA’ that supposedly comprised the vast majority of our DNA. ERVs are said to be parasitic retroviral DNA sequences that infected our genome long ago and have stayed there ever since. These short DNA strands are found throughout the human genome, and make up about 5% of the DNA,(1) or about 10% of the total amount of DNA that is classified as transposable elements (i.e. 50%).(2)

However, the term ‘endogenous retrovirus’ is a bit of a misnomer. There are numerous instances where small transposable elements thought to be endogenous retroviruses have been found to have functions, which invalidates the ‘random retrovirus insertion’ claim. For instance, studies of embryo development in mice suggest that transposable elements (of which ERVs are a subset) control embryo development. Transposable elements seem to be involved in controlling the sequence and level of gene expression during development, by moving to/from the sites of gene control.(3)

Moreover, researchers have recently identified an important function for a large proportion of the human genome that has been labelled as ERVs. They act as promoters, starting transcription at alternative starting points, which enables different RNA transcripts to be formed from the same DNA sequence.

‘We report the existence of 51,197 ERV-derived promoter sequences that initiate transcription within the human genome, including 1,743 cases where transcription is initiated from ERV sequences that are located in gene proximal promoter or 5’ untranslated regions (UTRs).’(4)

And,

‘Our analysis revealed that retroviral sequences in the human genome encode tens-of-thousands of active promoters; transcribed ERV sequences correspond to 1.16% of the human genome sequence and PET tags that capture transcripts initiated from ERVs cover 22.4% of the genome.’(5)

Moreover, researchers have recently identified an important function for a large proportion of the human genome that has been labelled as ERVs.

So we’re not just talking about a small scale phenomenon. These ERVs aid transcription in over one fifth of the human genome! ‘These data illustrate the potential of retroviral sequences to regulate human transcription on a large scale consistent with a substantial effect of ERVs on the function and evolution of the human genome.’(3) This again debunks the idea that 98% of the human genome is junk, and it makes the inserted evolutionary spin look like a tacked-on nod to the evolutionary establishment. These results support the conclusions of the ENCODE project, which found that at least 93% of DNA was transcribed into RNA.

Evolutionists have used shared mistakes in ‘junk DNA’ as ‘proof’ that humans and chimps have a common ancestor. However, if the similar sequences are functional, which they are progressively proving to be, their argument evaporates.

It seems that evolutionist Dr John Mattick, director of the Institute for Molecular Bioscience at the University of Queensland, Brisbane, Australia, was spot on in his assessment of the gravity of the ‘junk DNA’ error:

‘The failure to recognize the full implications of this—particularly the possibility that the intervening noncoding sequences may be transmitting parallel information … may well go down as one of the biggest mistakes in the history of molecular biology.’(6)

Both biblical creationists(7) and ID proponents (8) predicted that transposable elements, such as ‘endogenous retroviruses’, would have a function. In 2000, creationist molecular biologist Linda Walkup proposed that God could have created transposable elements to facilitate variation (adaptation) within biblical kinds.(7)

If the ‘junk DNA’ is not junk, then it puts a big spanner in the work of molecular taxonomists, who assumed that ‘junk DNA’ was free to mutate at random, unconstrained by the requirements of functionality. As Williams points out:

‘The molecular taxonomists, who have been drawing up evolutionary histories (“phylogenies”) for nearly every kind of life, are going to have to undo all their years of “junk DNA”-based historical reconstructions and wait for the full implications to emerge before they try again.’(9)

References

1. Conley, A.B., Piriyapongsa, J. and Jordan, I.K., Retroviral promoters in the human genome, Bioinformatics 24(14):1563–1567, 2008. Return to text.
2. Thornburg, B.G., Gotea V. and Makałowski W., Transposable elements as a significant source of transcription regulating signals, Gene 365:104–110, 2006. Return to text.
3. Batten, D., No joy for junkies, Journal of Creation (TJ) 19(1):3, 2006;
4. Conley et al., ref 1, p. 1563. Return to text.
5. Conley et al., ref 1, p. 1566. Return to text.
6. Mattick, J., cited in: Gibbs, W.W., The unseen genome: gems among the junk, Scientific American 289(5):26–33, November 2003; pp. 29–30.
7. Walkup, L., ‘Junk’ DNA: evolutionary discards or God’s tools?, Journal of Creation (Technical Journal) 14(2):18–30, 2000;
8. Luskin, C., ‘Large Scale’ function for endogenous retroviruses: Intelligent Design prediction fulfilled while another Darwinist argument bites the dust, Discovery Institute, 21 August 2008,
9. Williams, A., Astonishing DNA complexity demolishes neo-Darwinism, Journal of Creation 21(3):111–118, 2007; p. 113.
 
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Loudmouth

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However, the term ‘endogenous retrovirus’ is a bit of a misnomer. There are numerous instances where small transposable elements thought to be endogenous retroviruses have been found to have functions, which invalidates the ‘random retrovirus insertion’ claim.

Nowhere did I make the claim that ERV's evidence common ancestry because ERV's have no function. Nowhere did I make the claim that all ERV's are junk DNA. None of the arguments put forth require ERV's to be non-functional. "Random retrovirus insertion" is not a synonym for junk DNA, and it never has been.

What creationists continually ignore is that it is the origin of ERV's that make them useful genetic markers. That origin is retroviral insertion.
 
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Loudmouth

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Moving on to the next set of observations and evidence . . .

One important word that I want to define ahead of time so the rest of the post is clear:

Orthologous: this indicates that two genes or DNA sequences are found at the same location in the genomes of two species.

Now that we have established what ERV's are, how retroviruses behave, and the pattern of retroviral insertion, we can move on to how they are used as genetic markers, and how they evidence common ancestry.

I will start with a simple analogy that will hopefully make sense once we get to the genetic evidence. Take two people and two unabridged Oxford dictionaries. Give a dictionary to each person and tell them to go to different rooms. Ask them to put on a blindfold, thumb through the dictionary, and randomly pick a 50 words from the dictionary, recording which words they randomly chose. Compare the results from each person.

What will you find? You will find that they did not choose the same words. If they did choose the same word out of tens of thousands, then it was a stroke of luck. The chances of two independent blind picks of words being the same is extremely unlikely. At the same time, you may find that they may tend to pick words towards the middle of the page, and towards the middle of the dictionary. However, these "hotspots" contain thousands of words, so the chances of landing on the same one is still very unlikely. What are the chances that out of 10,000 randomly picked words that 9,000 of them would be the same? Those odds are so vanishingly small that they can be ignored.

The same applies to ERV's. Retroviruses insert randomly into genomes in the same way that a blindfolded person randomly chooses a word in the analogy above. They may have hotspots such as trascriptional units, but those hotspots cover millions or even billions of bases in the genome.

If humans and other species do NOT share a common ancestor, then we would not expect these ERV's to occur at the same base (i.e. orthologous) in each genome with any sort of regularity. The chances of two independent random insertions happening at the same base is very small just as the chances of our two people picking the same word are very small. As one paper puts it:

First, the distribution of provirus-containing loci among taxa dates the insertion. Given the size of vertebrate genomes (>1 × 10^9 bp) and the random nature of retroviral integration (22, 23), multiple integrations (and subsequent fixation) of ERV loci at precisely the same location are highly unlikely (24). Therefore, an ERV locus shared by two or more species is descended from a single integration event and is proof that the species share a common ancestor into whose germ line the original integration took place (14).
Constructing primate phylogenies from ancient retrovirus sequences

As mentioned in the opening post, the human genome contains just over 200,000 ERV's. That's 200,000 retroviral insertions, or 200,000 word picks in our analogy. The chimp genome paper was published 4 years after the human genome paper, and guess what? They found the ERV's in the chimp genome and compared them to the ERV's in the human genome. What did they find?

They found that out of the over 200,000 ERV's in the human genome, less than 100 were NOT found at an orthologous position. They found that over 99% of the ERV's found in the human genome were at the same position in the chimp genome. Here is the table from the chimp genome paper with the ERV's split into class I and II:

nature04072-t2.jpg


The lineage specific insertions are the non-orthologous ERV's, the ERV's not found at the same location in each genome. If humans and chimps do not share a common ancestor, then these numbers should be in the hundreds of thousands. They aren't. They are in the hundreds. Only a relative handful of ERV's in the chimp and human genomes are not found at the same position in each genome.

This is smoking gun proof of common ancestry.
 
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BL2KTN

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Remember what I said, Loudmouth? Nine pages, not a single rebuttal using specifics by creationists. The very few who have posted in the thread have denied on off-topic grounds or using generalities that ignore all the evidence you have provided.

They absolutely will not discuss the information. Confirmation bias every single time.
 
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Loudmouth

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Remember what I said, Loudmouth? Nine pages, not a single rebuttal using specifics by creationists. The very few who have posted in the thread have denied on off-topic grounds or using generalities that ignore all the evidence you have provided.

They absolutely will not discuss the information. Confirmation bias every single time.

Agreed. I actually miss mark kennedy in these discussions. He at least stayed on topic and understood a little bit of what was presented.
 
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BL2KTN

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Loudmouth said:
Agreed. I actually miss mark kennedy in these discussions. He at least stayed on topic and understood a little bit of what was presented.

I don't know... when I would show he was wrong because he didn't know Hebrew (I took it in college), the result tended to be a threat of banning me.
 
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JacksBratt

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Cover eyes. Plant fingers firmly in ears. Repeat, "LALALALALA".

Creationism 101.


Proverbs 3:5King James Version (KJV)

5 Trust in the Lord with all thine heart; and lean not unto thine own understanding.
 
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BL2KTN

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Yes, when information explicitly contradicts the bible... trust Yahweh according to papers written in the Bronze Age by unknown scribes who say they knew Yahweh (the son of El in Canaanite religion). The sky is a hard dome with waters above it because the bible says so!
 
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C

crazyforgod1212

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Wow, a religion that tells its followers to stop thinking. I can see how that can produce more converts.

The Bible doesn't tell us to stop thinking, it tells us HOW to think, and it allows us to see through the empty lies of evolutionism.

You've provided no evidence, here. Only guesses and suppositions made by the Godfearing.
 
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bhsmte

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Although I had my doubts, I was hoping that you would actually address the evidence with some sort of substantive rebuttal. Instead you did what others predicted.

So, what kind of example are you setting for young Christians when you are:
1. Name calling
2. Hurling accusations of lying without evidence of intent.
3. Misrepresenting the position of another poster.
4. Misrepresenting the definition of words.
5. Refusing to discuss the evidence that you asked for.

You are fooling no one by making assertions that are not related to the topic at hand and using those assertions as an excuse to avoid answering the questions concerning the evidence provided.

If you are a teacher in your church and you are the provider of the case against evolution, it is a sad state of affairs for your brand of creationism. What would you do if a young person in your class brought up ERV's in the way that Loudmouth did....yell at them...throw rocks....accuse them of being an antichrist?

Maybe you don't allow questions. Perhaps you feel that your God cannot withstand questions on certain subjects.

Here is the thing though, this poster's main concern is protecting their own belief and if they end up looking foolish in the process, it really doesn't matter, because protecting the belief at all costs, is of paramount importance.
 
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Loudmouth

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The Bible doesn't tell us to stop thinking, it tells us HOW to think, and it allows us to see through the empty lies of evolutionism.

Then show me the lies that I have supposedly told.

You've provided no evidence, here. Only guesses and suppositions made by the Godfearing.

Show me the guesses. Be specific.
 
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Loudmouth

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The truth is available for all those who are willing to look.

Do Shared ERVs Support Common Ancestry? - Evolution News & Views

Praise the Lord!

Let's see how it stacks up. From your page:

"Out of tens of thousands of ERV elements in the human genome, roughly how many are known to occupy the same sites in humans and chimpanzees? According to this Talk-Origins article, at least seven. Let's call it less than a dozen. Given the sheer number of these retroviruses in our genome (literally tens of thousands), and accounting for the evidence of integration preferences and site biases which I have documented above, what are the odds of finding a handful of ERV elements which have independently inserted themselves into the same locus?"

They try to assert that there are less than a dozen ortholgous ERV's shared by humans and chimps. That is a flat out lie. As I have shown, we share nearly 200,000 orthologous ERV's.

Your lying creationist site is a massive failure.

There are at least 2 other massive lies in that piece. Want me to go over those, too?
 
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