The New Retrovirus Thread

[joshua 1 9]

Does Collin's believe in a common ancestor?

Yes he does:

In your book, you say religion and science can coexist in one person's mind. This has been a struggle for some people, especially in terms of evolution. How do you reconcile evolution and the Bible?

As someone who's had the privilege of leading the human genome project, I've had the opportunity to study our own DNA instruction book at a level of detail that was never really possible before.

It's also now been possible to compare our DNA with that of many other species. The evidence supporting the idea that all living things are descended from a common ancestor is truly overwhelming.

http://www.beliefnet.com/News/Scien...-Threatened-By-Our-Scientific-Adventures.aspx

Don't stop there, Collins is clearly Theistic Evolution when He says that God used the mechanism of evolution to achieve His goal. God had a plan to create creatures with whom he could have fellowship.

"But I have no difficulty putting that together with what I believe as a Christian because I believe that God had a plan to create creatures with whom he could have fellowship, in whom he could inspire [the] moral law, in whom he could infuse the soul, and who he would give free will as a gift for us to make decisions about our own behavior, a gift which we oftentimes utilize to do the wrong thing.


I believe God used the mechanism of evolution to achieve that goal. And while that may seem to us who are limited by this axis of time as a very long, drawn-out process, it wasn't long and drawn-out to God. And it wasn't random to God.

[He] had the plan all along of how that would turn out. There was no ambiguity about that."


Read more at http://www.beliefnet.com/News/Scien...cientific-Adventures.aspx#EUboAD8dulXaI0FE.99

 

[Jimmy D]

Don't stop there, Collins is clearly Theistic Evolution when He says that God used the mechanism of evolution to achieve His goal. God had a plan to create creatures with whom he could have fellowship.

"But I have no difficulty putting that together with what I believe as a Christian because I believe that God had a plan to create creatures with whom he could have fellowship, in whom he could inspire [the] moral law, in whom he could infuse the soul, and who he would give free will as a gift for us to make decisions about our own behavior, a gift which we oftentimes utilize to do the wrong thing.


I believe God used the mechanism of evolution to achieve that goal. And while that may seem to us who are limited by this axis of time as a very long, drawn-out process, it wasn't long and drawn-out to God. And it wasn't random to God.

[He] had the plan all along of how that would turn out. There was no ambiguity about that."


Read more at http://www.beliefnet.com/News/Scien...cientific-Adventures.aspx#EUboAD8dulXaI0FE.99

We are aware of Francis Collins religious views. I thought you denied the Theory of Evolution and common descent as it is commonly accepted, if not why have you been arguing against it? Unless you've changed your views of course....

It's a red herring anyway, what has this got to do with the OP?

 

[Loudmouth]

That's audacious and amazing.

It is. Not sure what the methods and protocols are like these days, but it probably wasn't that much fun stitching together a few thousand base pair genome. It took the Venter research team 15 years and $40 million to create a 1 million base pair synthetic bacterial genome, which was pretty cool.

 

[Loudmouth]

You seem to be missing the point: "But what if ERVs do perform important genetic functions?"

Then they perform important genetic functions. That doesn't put their origin as a retroviral insertion in question.

Even theistic evolutionist Francis Collins acknowledges that genetic similarity "alone does not, of course, prove a common ancestor" because a designer could have "used successful design principles over and over again." (The Language of God, pg. 134.)"

This Francis Collins?

"Outside of a time machine, Darwin could hardly have imagined a more powerful data set than comparative genomics to confirm his theory."--Dr. Francis Collins, "Faith and the Human Genome"

 

[Loudmouth]

• “‘It’s a radical concept, one that a lot of scientists aren’t very happy with,’ said Francis S. Collins, director of the National Human Genome Research Institute. ‘But the scientific community is going to have to rethink what genes are, what they do and don’t do, and how the genome’s functional elements have evolved.’
  ‘I think we’re all pretty awed by what we’re seeing,’ Collins said. ‘It amounts to a scientific revolution.’
  For half a century, the core concept in biology has been that every cell carries within its nucleus a full set of DNA, including genes. Each gene, in turn, holds coded instructions for assembling a particular protein, the stuff that keeps organisms chugging along.
  As a result, genes were assigned an almost divine role in biological ‘dogma,’ thought to govern not only such physical characteristics as eye color or hair texture, but even much more complicated characteristics, such as behavior or psychology. Genes were assigned blame for illness. Genes were credited for robust health. Genes were said to be the source of the mutations that underlay evolution.
  But the picture now emerging is more complicated, one in which illness, health, and evolutionary change appear to be the work of almost fantastical coordination between genes and swaths of DNA previously written off as junk.
  ‘If the surprising amount of RNA transcribed from genomic ‘junk’ proves to be a powerful regulator of genes, understanding it will be critical in the fight against genetic disease, medical researchers predict. A big push is underway, for example, to develop so-called ‘RNA interference’ drugs, designed to turn off gene activity by mimicking the effects of RNA.’
  ‘For medicine, it could be good news if disease is mainly caused by ‘regulators’ ” in the genome, not mutations in genes themselves,’ said Lander. ‘It suggests that [cures] might be a matter of tweaking the controls – turning them up here, dialing them down there. Nothing about the gene is broken, but the dial may be powered up too high or turned low.’”
  http://www.boston.com/news/globe/health_science/articles/2007/09/
  24/dna_unraveled/?page=4

Topic?

 

[joshua 1 9]

That doesn't put their origin as a retroviral insertion in question.

We need to cut to the chase here. Is your point that somehow retro-viral insertion is evidence for common ancestor because Collins does not argue against that at all. He just believes God had a plan from the beginning of the Universe.

"If God is real, and I believe he is, then he is outside of nature. He is, therefore, not limited by the laws of nature in the way that we are. He's not limited by time. In the very moment of that flash in which the universe was created, an unimaginable burst of energy, God also had the plan of how that would coalesce into stars and galaxies, planets, and how life would arrive on a small planet near the outer rim of a spiral galaxy. And ultimately, over hundreds of millions of years, give rise to creatures with intelligence and in whom he could infuse this search for him and this knowledge of good and evil. And all of that happened in his mind in the blink of an eye. While it may seem to us that this whole process has the risk of randomness and, therefore, an unpredictable outcome, that was not the case for God."

Read more at http://www.beliefnet.com/News/Scien...tific-Adventures.aspx?p=2#ojbll7ygjZ9YbLqj.99

 

[Loudmouth]

We need to cut to the chase here. Is your point that somehow retro-viral insertion is evidence for common ancestor because Collins does not argue against that at all.

Didn't you read the opening post?

My argument is that retroviral insertions evidence common ancestry because they are found at the exact same locations in both the human and chimp genome.

Perhaps you could address the actual argument?

Also, Collins agrees with me.

"I mentioned the ancient repeats we share with mice in the same location showing no conceivable evidence of function, diverging at a constant rate just as predicted by neutral evolution. One could only conclude that this is compelling evidence of a common ancestor or else that God has placed these functionless DNA fossils in the genome of all living organisms in order to test our faith. I do not find that second alternative very credible. After all God is the greatest scientist. Would he play this kind of game?"--Dr. Francis Collins, "Faith and the Human Genome"

The "repeats" that Collins is talking about are transposable elements which are closely related to ERV's.

 

[In situ]

You seem to be missing the point:

Quite fascinating that you would make this remark even after been told you are OT.

It is evidenced by your comment in post #26 that you do not understand the argument in the OP:

"We need to cut to the chase here. Is your point that somehow retro-viral insertion is evidence for common ancestor."

But I am not surprised you do not understand, since no YEC I ever meet have been able to show any sing of actually understanding what nesting is all about. Because when they do understand what nesting is about they stop being YEC's...



(Hint: nesting is the evidence that makes common ancestor an observed fact).

 

[joshua 1 9]

My argument is that retroviral insertions evidence common ancestry because they are found at the exact same locations in both the human and chimp genome.

As you know the argument against your retrovirus "evidence" is that: "The selection of target sites for integration of retroviral DNA is central to the biology of retroviruses and the application of retroviral vectors to gene therapy."

"Recent studies have shown that human immunodeficiency virus (HIV) and murine leukemia virus (MLV) favor integration near different chromosomal features."

http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.0020060

 

[In situ]

As it turns out, the human genome contains 208,000 ERVs

It sums up to 203 thousand for me (class I, II and III). What did i miss?

 

[In situ]

As you know the argument against your retrovirus "evidence" is

I did not know there was an argument against ERV, but I do know there are a lot of nonsense claims, based on ignorance, made by YEC's.

(Did you actual read the OP - because Loudmouth addressed this "argument" in the OP - repeating the same YEC nonsense does not make it less nonsense).

 

[Loudmouth]

As you know the argument against your retrovirus "evidence" is that: "The selection of target sites for integration of retroviral DNA is central to the biology of retroviruses and the application of retroviral vectors to gene therapy."

"Recent studies have shown that human immunodeficiency virus (HIV) and murine leukemia virus (MLV) favor integration near different chromosomal features."

http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.0020060

"For HIV the frequency of integration in transcription units ranged from 75% to 80%, while the frequency for MLV was 61% and for ASLV was 57%. For comparison, about 45% of the human genome is composed of transcription units (using the Acembly gene definition)."
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC509299/

The chromosomal features you speak of make up nearly half of the 3 billion base genome. That's 1.5 billion bases where these viruses could insert, and then they only insert 80% of the time for some of them. Other retroviruses show no such preference.

So, the chances of finding a single insertion at the same base even with this preference for insertion sites is 1 in 1.5 billion.

 

[Loudmouth]

It sums up to 203 thousand for me (class I, II and III). What did i miss?

You missed nothing. What you did see was a mathematical error on my part. Thanks for pointing it out.

 

[joshua 1 9]

they don’t insert at just one base. They insert all over the place.

Your not reading the research, the retros are VERY exacting in where they insert themselves. You are still stuck in the mucky mire of random events that are not random at all. So you are creating a very slippery slope for yourself.

P53 become an important "master gene regulator". This study offers an explanation for how regulatory networks of genes evolved. The advent of gene regulatory networks allowed for greater control over gene expression in higher vertebrates. With tightly controlled variations in gene expression, species that had very similar genetic codes--for instance, humans and chimpanzees--could nevertheless exhibit striking differences.

https://www.sciencedaily.com/releases/2007/11/071114121359.htm

 

[Loudmouth]

Your not reading the research, the retros are VERY exacting in where they insert themselves.

I read the research. It doesn't say that every single insertion happens at the same base. It says that HIV tends to insert into transcription units, and transcription units make up nearly half of the genome.

Did you read the opening post? Try reading it again. There is a big figure showing how a single retrovirus inserted all over the human genome.

 

[joshua 1 9]

I read the research. It doesn't say that every single insertion happens at the same base. It says that HIV tends to insert into transcription units, and transcription units make up nearly half of the genome.

The reason for the study is because retros are so exact in their insertion, which you continue to want to deny. They are doing the research because we need a very exact and precise delivery system in our war against disease.

They are finding that some "retrovirus" are actually regulators and could be one of the mechanisms of evolution.

 

[Loudmouth]

The reason for the study is because retros are so exact in their insertion, which you continue to want to deny.

The study showed that they aren't exact. They insert all over the genome.

So why can ERVs be used as genetic markers, and a test for common ancestry? As stated earlier, part of the viral life cycle is insertion into the host genome. The human haploid genome is around 3 billion bases, as is the genome of other ape species. That’s 3 billion possible places where these retroviruses can insert. When viruses insert into the genome, they don’t insert at just one base. They insert all over the place. In this study, scientists infected cells with three different retroviruses: MLV, HIV, and ASLV. After infection, they mapped where the viruses inserted into the host genome. Below is map of where those viruses inserted, broken down in the 23 human autosomal chromosomes and the X chromosome.

Relationship between Integration Sites and Transcriptional Intensity in the Human Genome

The human chromosomes are shown numbered. HIV integration sites from all datasets in Table 1 are shown as blue “lollipops”; MLV integration sites are shown in lavender; and ASLV integration sites are shown in green. Transcriptional activity is shown by the red shading on each of the chromosomes (derived from quantification of nonnormalized EST libraries, see text). Centromeres, which are mostly unsequenced, are shown as grey rectangles.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC509299/

As everyone can see, the viruses inserted all over the place, into all chromosomes.

They are finding that what is called "retrovirus" are actually regulators and could be one of the mechanisms of evolution.

Since the LTR's of the viral genome are very strong promoters, this isn't unexpected at all. This would be a case of the viral genome having the exact same function before and after insertion.

 

[In situ]

The reason for the study is because retros are so exact in their insertion, which you continue to want to deny.

The OP has a picture of the distribution of the insert sites of the ERV. This is was what we call data, or evidence, and what we base our conclusions on - we do not first assume a conclusion and then try to validate it, but first we look at the evidence and then ask our self, what does this mean.

Now, look at the evidence and ask yourself if the evidence says "exact and precise " or does the evidence say "scattered all over the place"?

Notice, I am not telling you that this or that is the case, I am only asking you to look at the evidence yourself and tell me what you see and what the evidence tells you - I am asking you to make your own conclusion based on the evidence.

They are doing the research because we need a very exact and precise delivery system in our war against disease.

What is a delivery system evidence for? Is it evidence for a delivery system or is it evidence which refute common common ancestor with chimpanzee?

They are finding that some "retrovirus" are actually regulators and could be one of the mechanisms of evolution.

What is a function with ERVs evidence for? Is it evidence that ERVs have a function or is it evidence which refute common common ancestor with chimpanzee?

 

[In situ]

As everyone can see, the viruses inserted all over the place, into all chromosomes.

Yes, but this is evidence that contradicts an assumed YEC conclusion and therefore it is not scientific evidence - remember the 1st tenet of YEC: all science and evidence must agree with the YEC bible interpretation otherwise it is not science or evidence but only a evolutionistic denial that "God did it!".

which you continue to want to deny

Case closed. YEC wins! (again)

 

[In situ]

Centromeres ... are shown as grey rectangles.

To me it looks like the the grey area in chr 13, 14, 15, 21 and 22 is the entire short arm of the chromosome in question.