16 replies to this topic

[iSilurian]

I wanted to just independently get this topic out there, to see, well firstly what people have to say about it, if anything at all.
It is another important evidence for the theory of evolution.

Endogenous retroviruses are essentially, viruses that have their genetic makeup inserted into our DNA. When living things are attacked by these viruses, the genes that contain the DNA of the viruses, depending on what cells they attack within living things, can be passed on to our children. and our children pass it to their children etc etc, just like all DNA is passed on to our progeny. Ok so, now, if you think about, a family tree. That of a kin of people. distant cousins and second cousins and third cousins and second aunts and uncles etc etc, all will be on small distant branches of a family tree. Whereas parents, first brothers and sisters, will be on primary branches.

With that understanding, lets say i am attacked by an ERV. ok so now, my children will have the retroviral signature within them. Now lets say one of my children are attacked by a second ERV. now my grandchildren will have the ERV signature of me, and my children's ERV within them (2 ERV traces total). so my grandchildren will have 2 signatures (1 from me, and 1 from my children), and my children will have 1 signature (from me).  With multiple attacks occuring over time, the later generations of an organism will have more and more Retroviral traces within their DNA.

http://www.st-edmund...ages/image3.jpg


So in the picture above, we can see a family tree.  The parents being on the left while the progeny being on the right.  You have your viruses indicated by an orange color inserting themselves (attacking the grandparent) and all the predecessors containing that marker from the attack. And then again later in time (the children) get attacked again, leaving the grand children (gorilla, chimp, bonobo, and human) with both sets of viruses at current times.

Now, with this said, we can determine the relatedness of living things based on the number of ERV signatures they have within them. For example, i can tell my grandchildren are closer related to my children than they are to me, because they have more ERVs traces in common.  And likewise i can tell that Chimps, bonobos, humans and gorillas are closer related to eachother than tarsiers or gibbons.  And we can make a tree out of this.

Now, some people may say, well maybe the ERVs just happen to match up like our DNA does.  Well, first off there are roughly 30 thousand ERV traces within our DNA.  Thats 30 thousand, that have insterted into very specific base pairs of our genome which number in the millions.  So it would be essentially like throwing 30 thousand darts at a dart board with billions of holes at random.  And then our children identically threw 30 thousand darts and hit the exact same holes in the dart board of billions of holes by pure chance.  The chances of this not demonstrating common descent are essentially non existent.


But heres the kicker, The phylogenetic tree of life that we create based on ERV traces, matches the trees that we create in other fields of science like paleontology.  So, the order and sequence that i find bones in the earth, matches the order and sequence that i find ERVs in living mammals such as ourselves.

It essentially proves common descent between us and the animal kingdom and it proves our relatedness by family and ancestor.

Edited by iSilurian, 18 December 2011 - 08:30 PM.

[Master Chief]

I remember reading this article.  You should have linked the peer reviewed article as reference (so that people don't think that you made it up). I think  you did a good job of explaining it.  

On a different topic, take a look at the article that I posted below:
http://www.scienceda...205102713.htm  

I was taken aback when I read that article (although the thought of this occurring did come to my mind once)

[traderjoe]

The theory of evolution is in completeness compatible with Islam and Islamic thought. We hear very little of how early Muslim thinkers and scientists had developed primitive ideas on the theory of Evolution long before Darwin existed. Al Jahiz for example came up with "the struggle for existence" as the root cause of the origin of new species in his own description for the Natural selection.

Abu Rayhan Biruni, and Naser Din Tusi, for example had actually came up with Lamarckism (precursor to evolution in European schools) long before they existed. Many others had very advanced thinking related to evolution- although this culture of scholastic thinking died down within the Muslim world as soon as the Colonial era took hold of Muslim nations. Ibn Al Haithami, Al Khazini and Al Dinavari were all in line with the idea of transmutation of plants as an idea on their respective books regarding the nature of plant species. There is plenty of information regarding the origin of evolutionary thought and how compatible it is with Islamic ideas of Divine creation.



For example when you see a verse like this:

24:45 "God has created every [living] creature from water. And of them are those that move on their bellies, and of them are those that walk on two legs, and of them are those that walk on four. God creates what He wills. Indeed, God is over all things competent."

You are immediately reminded of charts describing progressive geneology of species that could define evolution of a range of creatures described succinctly (in Arabic prose). Also one of the 99 names of God is Al-Bari (that could be translated as "the shaper" or "the evolver").

Here is a Shia lecture on Evolution Dr. Sayyid Jafar Al-Qazwini:



This is one of the famous lectures on theory of Evolution on man (by Motahari)

http://www.al-islam....-human-evol.htm

(Scroll down to the view of Islam section for more detail on what he thought on Evolution of human beings, whcih  I found to be very interesting)
It is nevertheless very unfortunate that so much of the Muslim world tries so hard to reject this scientific fact.

I am a former Agnostic-Atheist of Sunni background and I accept evolution not only as a scientific fact, but also compatible with my faith in Islam.

[ShiaSoldier@2007]

I may have not understood the concept correctly, so I was just wondering if you could shed some light on the topic. First question is: wouldn't there be variation from animal to animal? Let's say one ape has been infected by more ERVs than another ape, wouldn't this cause variation in the number of provirus infromation (not sure if this is the correct terminology) in the two, if so couldn't the sample which resembles the human sample be coincidentally selected? I was also wondering whether the ERVs affected the exons because this would most likely cause the descendants to have debilitating features, and if natural selection were to run its course, these descendants would die out. This would mean that the presence of alike provirus information in the DNA could be because the animals were present at around the same time, and all the ERV that did not affect vital DNA was only kept. Also is the possibility that other ERVs could have caused point mutations causing stop codons to be inserted in essential parts of the DNA thus rendering important genes useless. This would also mean that provirus information could be present due to its harmless nature and emergence in a similar time period as opposed to presence due to inheritance.

I know it is phrased awkwardly but it has been a long day of homework so my brain is a little wacky right now. Just message me if you want more structured questions.

Jazakallah for your time,

Edited by ShiaSoldier@2007, 18 December 2011 - 11:34 PM.

[comrade]

Endogenous retroviruses? As in the body produces it by itself? Or is it an external thing that then invades a host genome?

What is the difference between this "ERV" and HIV?

Anyways, evolution says nothing about morality. So who cares?

[Master Chief]

comrade, on 18 December 2011 - 11:59 PM, said:

Endogenous retroviruses? As in the body produces it by itself? Or is it an external thing that then invades a host genome?

What is the difference between this "ERV" and HIV?

Anyways, evolution says nothing about morality. So who cares?

If I may attempt to answer your question:
Endogenous retroviruses are sequences in the genome that are considered to be derived from ancient viral infections of germ cell in an animal (which includes humans). These bits are then passed to the next generation. http://en.wikipedia....nous_retrovirus

Human immunodeficiency virus (HIV) is a lentivirus, which is a member of the retrovirus family that attacks Helper T cells, macrophages and dendritic cells and renders a person with no immune system http://en.wikipedia.....org/wiki/HIV  

Hope that answers your question

[comrade]

So these retroviruses incorporate into gametes instead of somatic cells, therby letting it pass through generations.  HIV attacks somatic (non-germ) cells.  I get it now.

[iSilurian]

ShiaSoldier@2007, on 18 December 2011 - 11:33 PM, said:

I may have not understood the concept correctly, so I was just wondering if you could shed some light on the topic. First question is: wouldn't there be variation from animal to animal? Let's say one ape has been infected by more ERVs than another ape, wouldn't this cause variation in the number of provirus infromation (not sure if this is the correct terminology) in the two, if so couldn't the sample which resembles the human sample be coincidentally selected? I was also wondering whether the ERVs affected the exons because this would most likely cause the descendants to have debilitating features, and if natural selection were to run its course, these descendants would die out. This would mean that the presence of alike provirus information in the DNA could be because the animals were present at around the same time, and all the ERV that did not affect vital DNA was only kept. Also is the possibility that other ERVs could have caused point mutations causing stop codons to be inserted in essential parts of the DNA thus rendering important genes useless. This would also mean that provirus information could be present due to its harmless nature and emergence in a similar time period as opposed to presence due to inheritance.

I know it is phrased awkwardly but it has been a long day of homework so my brain is a little wacky right now. Just message me if you want more structured questions.

Jazakallah for your time,

Hmm, ill try to reword it.  I dont quite understand your question.  Ok so, when a man and a women have a child, the child is built by the DNA of the parents.  So, in regards to the topic.  A virus attacks a person.  And the virus basically puts its own genetic material into the DNA of the person being attacked.  So then when that person has a child. The child carries the same DNA that the parent has provided, and that includes the viral DNA that the parent provides.

Ok, so lets say a person is attacked by "virus A", and the person then has 2 children (Bob and George).  Ok now, the 2 children (Bob and George) have the DNA of the parent within them, and the two children have DNA from "virus A" within them as well.  Ok, now lets say Bob is attacked by "Virus B", Ok, now Bobs children will have both "Virus A" and "Virus B" in them.  Because they got Virus A from the grandparent and they got Virus B from their parent.  But George on the other hand did not get attacked and George has kids.  Georges kids only have Virus A within them.

So if we looked at everyones DNA, we could see that Bobs kids were closely related because they all had both Virus A and Virus B DNA within them. And we could also tell that georges kids were related to Bobs kids, because both george and bobs kids all contained Virus A.  So we can judge how closely these organisms are related and we can make a family tree out of it.

Thats a pretty good explanation.  Just look at the diagram.  And imagine along the bottom of the diagram (the X axis), imagine that is time.  present time being on the right and older time in the past, being on the left.  So as time progresses, organisms are infected and their descendents carry the DNA to the next generation.
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Ok, i just reread your first question too.  You said "Let's say one ape has been infected by more ERVs than another ape, wouldn't this cause variation in the number of provirus infromation (not sure if this is the correct terminology) in the two"

Yes, there would be. Meaning, if 1 viruse infected a chimpanzee and 2 infected a bonobo, then the bonobo would have 2 + whatever ones it already had, and the chimp would have 1 plus the ones it already had.

Then you said "if so couldn't the sample which resembles the human sample be coincidentally selected?".  Well the thing is.  The human genome is made of billions of molecules.  When the viruses infect the organism, they slide in 1 spot out of those 3 billion possible spots.  So its a very specific place they slide in.  And thats where they stay.  Also, you can tell the difference between 1 virus from another.  So imagine a dart board with 3 billion spots that darts could fit in. And imagine you have multiple colored darts. And you randomly threw your darts of all colors at the dart board. (the chimp board). And then lets say you did it again at the "bonobo board".  There would be no mistaking the chimp board with the bonobo board.  Unless you managed to somehow throw your darts at the boards in the exact same spots of the 3 billion....you would know the difference between one and the other.

Im trying to understand your question but i dont :/ sorry.  If you reword it maybe ill understand.  I hope ive helped.

Then you said "I was also wondering whether the ERVs affected the exons because this would most likely cause the descendants to have debilitating features. Also is the possibility that other ERVs could have caused point mutations causing stop codons to be inserted in essential parts of the DNA thus rendering important genes useless. This would also mean that provirus information could be present due to its harmless nature and emergence in a similar time period as opposed to presence due to inheritance."

I understand what youre saying, but none of this seems to hold relation to what im talking about.  I dont mean to be rude, but this is all irrelevant. Let me go get some research and stuff and ill return with more info that may bring clarity to what were talking about.  Here check this out.  Maybe im misunderstanding your statement.

http://www.plosone.o...al.pone.0001026

ok here is a video.  He talks about ERVs at about 8 minutes in.



This second video is made by a guy, hes a bit more aggressive against creation concepts, and his videos are more bias, so if you have a problem with listening to atheists rant, you may not want to watch it.  However the video talks about ERVs with more clarity.



Those should help. And if you want research, you can just go to pubmed (http://www.ncbi.nlm.nih.gov/pubmed/) And search for info on ERVs, or ERV-K remnants in particular i believe are shared by related great apes.  Though attempting to read these research papers may not be easy.  Maybe i can find a news article or something more entertainment oriented on it.  Ill return with more.

Edited by iSilurian, 19 December 2011 - 01:10 AM.

[iSilurian]

And ShiaSoldier, just let me know if the explanation was lacking something.  I am not a biologist (though i do know a bit about biology) and therefore i know my words can be a bit shafty in explanation when it comes to the field.  But also, i am interested in the topic and in the finer details.  Being provided questions on the material drives me to do more in depth research, which i usually enjoy.

[comrade]

I do like biology so this is interesting.

But isn't it interesting...
ONE piece of evidence favoring evolution and you are its enthusiastic advocate.
BILLIONS of pieces of evidence for the existence of Allah, and yet you still step back and say "I don't know, and I don't think we'll ever know".

Why so firm to make believe in the first but not the second?

[iSilurian]

comrade, on 20 December 2011 - 08:46 PM, said:

I do like biology so this is interesting.

But isn't it interesting...
ONE piece of evidence favoring evolution and you are its enthusiastic advocate.
BILLIONS of pieces of evidence for the existence of Allah, and yet you still step back and say "I don't know, and I don't think we'll ever know".

Why so firm to make believe in the first but not the second?

One piece?  Well, not only does this essentially prove evolution, but this isnt the only piece of evidence.  The reason i am confident in the material of this topic is because it is something that we can all see with our very own eyes.  It is locked and confirmed in our genes.  Plus, i like science, its what i do.

[comrade]

You trust the five senses exclusively? So in your view nothing can be present without also being apparent to the human eye? That's caveman regressive belief right there.

Again, it's interesting that you're quick to say evolution has been "proved" by a paper on viruses, yet apparently millions of books/scripts/narrations/forum posts are not yet enough to "prove" that God exists.

This seriously blows my mind.

[iSilurian]

comrade, on 20 December 2011 - 11:51 PM, said:

You trust the five senses exclusively? So in your view nothing can be present without also being apparent to the human eye? That's caveman regressive belief right there.

Again, it's interesting that you're quick to say evolution has been "proved" by a paper on viruses, yet apparently millions of books/scripts/narrations/forum posts are not yet enough to "prove" that God exists.

This seriously blows my mind.

Well, trusting the 5 senses is definitely not a bad thing.  And if you trust them, which presumably we all do.  Then this topic will be very revealing in regards to the origins of mankind, which is what it is made for.

[comrade]

I said EXCLUSIVELY.

[iDevonian]

comrade, on 21 December 2011 - 07:23 AM, said:

I said EXCLUSIVELY.

Im not a fan of trusting my emotions.  Often emotions can lead us into trouble, they can lead us into believing things that arent real.

[bolbol]

Most of things we believe to be true are social constructions of reality. Most of science consists of bias, political filtering, intuition, framing, making ambiguity rigid, selectivity etc. The biggest scam in the Western world with regards to science is that it acts as if it can give a clear cut, objective, empirical answers to questions, including the even bolder move to start 'discrediting' Islam. There are a number of cases where this has turned horribly wrong.

Edited by bolbol, 15 January 2012 - 07:54 AM.

[iDevonian]

bolbol, on 15 January 2012 - 07:52 AM, said:

Most of things we believe to be true are social constructions of reality. Most of science consists of bias, political filtering, intuition, framing, making ambiguity rigid, selectivity etc. The biggest scam in the Western world with regards to science is that it acts as if it can give a clear cut, objective, empirical answers to questions, including the even bolder move to start 'discrediting' Islam. There are a number of cases where this has turned horribly wrong.

If you want to try to downsize our science, then do it with legitimate arguments. Also this has nothing to do with Islam, nor have I attempted to even relate it to such, and nor have I attempted to disprove it.

You know, even with my religion stated as an agnostic, I am agnostic simply because I do not have answers/knowledge to religious questions, but that doesnt mean I have anything against Islam.  I would even still be a muslim as I once was, if not for my lack of knowledge of the religion and all that it entails.  So please dont come in here indirectly pointing fingers and trying to criticise what we do.  If you want to come in here talking trash, then bring a real argument.

Edited by iDevonian, 15 January 2012 - 08:08 AM.