Viruses that prove common descent

[TagliatelliMonster]

so such a robot can evolve naturally and therefore a robot isnt evidence for design according to this logic.

That doesn't sound like an answer to my question.
You are welcome to try again:

How does a robot made from organic components differ from a natural system made from organic components?

 

[TagliatelliMonster]

Which you subscribe to depends on your base assumption.

My base assumption is that things that are supported by evidence and which are testable, are more believable then those things that aren't.

This assumption leads me to accept ERV's as quite knock-down evidence of common descent.

If you do not assume viruses arose before mammalian life then you could propose the origin of retroviruses came from existing genomic sequences.

And if you assume that pigs can fly into space and beyond, you could propose that pigs landed on the moon before humans.

But I don't see how that would be particularly helpfull for anything.

 

[Barry Desborough]

Oops. Post mix-up. Sorry.

 

[xianghua]

Even if life was designed by some undesigned designer, the evidence from ERVs still stands.

how actually? if chimp and human are the product of desing and not a common descent- we dont need to believe in the erv argument.

I asked you to address the evidence that ERVs are of retroviral origin. You ignored the request. You ignored the evidence. You are not the only one to studiously ignore it. But here's another chance. What follows is a copy and paste of a page from my FAQ. Let's see if you or anyone else has what it takes to address this evidence. I very much doubt it, but here's your chance to put your money where your mouth is.

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Much material in this page has been lifted from Abbie Smith.Hope you don't mind Abbie,

Every detail of every full ERV is replete with complex and subtle details attesting to its origin in retroviruses. ERVs have the same structure as retroviral integrations. This is some -10 kilobases of genes specific to the retroviral replication cycle. All retroviruses and complete ERVs include genes we call gag, pol and env. The function of these genes will be gone into in detail in the following notes. In addition, several other features common to retroviral integrations and ERVs only make sense in terms of the requirements of the retroviral replication cycle.

"The gag gene encodes for ‘Gag’ the giant protein, which gets chopped into several smaller proteins, Matrix, Capsid, and Nucleocapsid (and sometimes a few more tiny ones, depending on the retrovirus)."

"Matrix is the structural protein just inside the envelope (the membrane the virus stole from its host cell). It has ‘outside’ functions (targeting the virus assembly to the right kind of cell membrane, keeping the outside protein env, in order) and ‘inside’ functions (targeting the reverse transcribed DNA to the new host cell nucleus). Jack of all trades protein, like lots of retroviral proteins. They run a tight ship."

"Capsid forms the viral ‘core’. Normally when you think of a ‘virus’, you think of this shape, an icosahedron. Retroviral ‘cores’ really look more like a cylinder-cone-thingie, like the bottom pic here. That particular pic is also worth a second look– More protein cuts to Capsid need to take place after a baby virus buds off from its host cell to make an immature virus mature. Blocking this maturation step is what the next family of anti-HIV-1 retrovirals do. *thumbs up*"

"Nucleocapsid is a structural protein that wraps up the retroviral genome to make sure its packaged properly into the Capsid."

Pol codes for all the enzymes a retrovirus needs:"

"Protease– Chomps big proteins into all the little functional proteins, like we saw with Gag getting chomped into Matrix/Capsid/Nucleocapsid. The name ‘protease’ can be a little confusing because all organisms have ‘proteases‘, but only the protease that the retrovirus carries with it is the ‘right‘ protease to cleave in all the ‘right’ spots to get all the ‘right’ proteins in the end. Instead of giving retroviral proteases a special name, they just named it ‘Protease’. heh. Protease inhibitors are a great target for anti-retrovirals."

"Reverse Transcriptase– Another target for anti-retrovirals. Though the process of reverse transcription can be found in you and I (coooool), retroviruses need to carry an enzyme with them to convert viral RNA into DNA on demand. This process not only requires converting an RNA genome into a DNA genome, but also:"

"RNase H– The RT enzyme has (at least) two active sites. One performs the process of reverse transcription. Another active site has RNase activity (chops up RNA, specifically, RNA Hybridized with DNA haha!). RNase H chews up the old RNA template after a single strand of DNA has been made, so the single strand of DNA can be made into double stranded DNA, and subsequently inserted into the host cells genome. This might make more sense if you see this animation. *might* The process of reverse transcription is rather absurd."

"Integrase– Host cells don't come packed with the necessary biochemical machinery to move DNA out of the cytoplasm into the nucleus, to be inserted into the host DNA. So once again, retroviruses need to bring an enzyme capable of performing those activities. Integrase should be a perfect target for antiretrovirals… But we havent figured any out yet…"

Env. See http://scienceblogs.com/erv/2008/07/17/intro-to-ervs-envy-my-env/

LTRs. See this page. RNA polymerase's normal function is to convert nuclear DNA into messenger RNA that makes for proteins. It does not normally make RNA that 'codes" for promoters. Our bodies have no need for them. But retroviruses need their promoters to be converted back to RNA for when the replication cycle begins again. Long terminal repeats (LTRs) cause the RNA polymerase to produce them by a complicated "hack". The point is, that LTRs basic and original function is a part of the replication process of retroviruses. They cannot be part of any supposed original "design" of our genomes. That would not make any sense.

See Veritas: ERV FAQ: ERVs promote the transcription of host DNA. Doesn't this prove they are designed? and http://scienceblogs.com/erv/2009/07/16/intro-to-ervs-ltr-gator

Retroviruses exhibit the distinctive viral codon bias.

The Phoenix virus was resurrected from the multiple instances of an ERV which is to be found in each human cell. Each instance is a 'failed' retrovirus, but when a 'majority vote' for each base was taken, the resulting DNA produced, "viral particles that disclose all of the structural and functional properties of a bona-fide retrovirus, can infect mammalian, including human, cells, and integrate with the exact signature of the presently found endogenous HERV-K progeny." See also The "Phoenix Virus": an explanation of an experiment.

A retrovirus has been caught in the act of becoming endogenized: See The koala retrovirus KoRV and The Koala's Tale.

Retroviruses leave a telltale trace of integration in the form of a repeated host sequence either side of the integrated provirus. This is also evident in ERVs. From Virology Blog: Retroviral Integration and the XMRV Provirus, "The image below shows some of the characteristic features of retroviral integration. A the top is the unintegrated linear DNA of avian sarcoma/leukosis virus produced by reverse transcription. Upon completion of integration, two base pairs (AA•TT) are lost from both termini, and a 6-bp target site in host DNA (pink) is duplicated on either side of the proviral DNA. This target site varies in length from 4 to 6 bp among different retroviruses. The proviral DNA (middle) ends with the conserved 5′-T G…C A-3′ sequence. The provirus serves as a template for the production of the viral RNA genome (bottom)."

again: do you have a specific point that we cant explain under the design model? its a fact that all the genes for a virus are also exist in the host. so its also possible that an erv created from the host genome. and we have evidence that about 25% of the viral genome was made from host genome. you also cant explain how the virus survive in the first place without an host. those two facts alone point against the insertion idea. and even if those a real viral insertions- there are only few places in the genome that a virus can insert into the genome and also be fixed in the population.

 

[xianghua]

That doesn't sound like an answer to my question.
You are welcome to try again:

How does a robot made from organic components differ from a natural system made from organic components?

from phisical prespective its not. so you believe that a robot dont need a design?

 

[Barry Desborough]

how actually? if chimp and human are the product of desing and not a common descent- we dont need to believe in the erv argument.

Still ignoring the evidence, I see. Keep it up. I love documenting you creationists and your studied ignorance.

I think you have seen this before. It's something else for you to ignore.

Veritas: ERV FAQ: But how can you rule out design as an explanation?

If anyone thinks that ERVs are designed for a purpose or for several purposes, they must have answers to the following.

a) What is reverse transcriptase designed to do?
b) What is integrase designed to do?
c) Why were ERVs designed with a viral codon bias?
d) What is the design purpose of re-transcribable promoters?
e) What were the HERVs that generated the consensus sequence that generated Phoenix designed for?
f) What is the design purpose of both exogenous and endogenous KoRV?
g) If chimps and humans have commonly located ERVs, what is the design purpose of giving these common ERVs common disabling mutations?
h) What is the design purpose of giving some people HERVs and not others?
i) What is the design purpose of creating different syncytins in different placental lineages?

 

[Barry Desborough]

from phisical prespective its not. so you believe that a robot dont need a design?

I asked you to start your own thread about this. Please show some manners and comply.

 

[dad]

I have a tree in my garden. I think that it wasn't there yesterday. Can you prove that I'm mistaken?/

ERVs don't come from under your nose or garden. Is there some thread where you can pretend there is some relation to the origins debate and ERVs? Sorry, but you have no carte blanche to ignore the evidences anymore. I have evidence that you cannot show how ERVs transferred from chimp to man in the past near the supposed split. That evidence is that you obviously not only have NO evidence but fail to address the issues. In a thread where there is a pretense of connecting ERVs to the theory of evolution of man, you must do more than try to hide and turn out the lights.

 

[dad]

ERV FAQ: Why do virologists and geneticists think that ERVs come from retroviruses? Isn't that just supposition on their part?.

Because they purposely use a very limited data set and method to determine where things came from. When doing so leads to outright anti bible anti creation stories and claims, that is called wickedness.

 

[Barry Desborough]

ERVs don't come from under your nose or garden. Is there some thread where you can pretend there is some relation to the origins debate and ERVs? Sorry, but you have no carte blanche to ignore the evidences anymore. I have evidence that you cannot show how ERVs transferred from chimp to man in the past near the supposed split. That evidence is that you obviously not only have NO evidence but fail to address the issues. In a thread where there is a pretense of connecting ERVs to the theory of evolution of man, you must do more than try to hide and turn out the lights.

 

[Barry Desborough]

Because they purposely use a very limited data set and method to determine where things came from. When doing so leads to outright anti bible anti creation stories and claims, that is called wickedness.

Limited data sets like whole genome surveys? Yeah. Gotcha.

 

[TagliatelliMonster]

from phisical prespective its not

Then how can you tell the difference?

so you believe that a robot dont need a design?

I didn't say that. Obviously, a ROBOT needs a designer by very definition of what a robot is.

But clearly, you are trying to insinuate with this that we living things are somehow robots or analogous to it at least...

So I'ld just like to jump to the end of your argument if you don't mind, so that we don't waste time on your attempt to trap me with word games.

See, this is why I asked you how a "robot" made from organic components would be different from a natural system made from organic components.

You just admitted that there would be no difference.

So there you go... if you are unable to tell the difference between "designed life" and "natural life" - then how on earth could you ever claim that life needs to be designed???

 

[TagliatelliMonster]

I asked you to start your own thread about this. Please show some manners and comply.

Sorry, I missed that.

Now I feel guilty for driving my response to that nonsense home...

 

[pshun2404]

It's all supposition, trust me.

Hang on, you almost have the right idea here. In the time of Noah the mutations had not had time to accumulate so it meant bigger gene pools. Now once things have speciated there are bottlenecks, adaptive evolution isn't going to happen on that scale. Now as far as the ERVs, infection in the germline is pretty rare and certainly nothing heritable has been documented. Once again, that kind of transfer still happens but on the scale they are talking about, forget it.

There is every indication that this isn't something subject to change over time. God provided for the passing of heritable traits, known in science as the laws of inheritance. It's as simple as this, they take an occasional mutation with a beneficial effect or a mutation in roughly the same place in two genomes and that's supposed to be proof. The far weightier matter regarding the three fold expansion of the human brain from that of apes they ignore.

Probably weren't, the living systems of the time probably had pristine genomes that accumulated mutations over time.

Look at it realistically, what do you expect from people who have never really known anything but the natural order. If you remember right, the gospel was made clear to you not by your own powers of perception but because God made himself known to you by some means. That's how I remember my conversion, so I understand people who do not deviate from naturalistic reasoning, it's all they have ever known.

Grace and peace,
Mark

Very well put Mark. Especially your concluding paragraph. As man thinks in his heart so is he.

Has everyone experienced the spiritual nature of reality? No! But that does not mean the others haven't. Have all heard from God? NO! But that does not mean these also haven't. Have all seen or experienced a manifestation of or from God? No! But that does not mean none have. The things of the Spirit can only be discerned spiritually they are foolishness to the natural man. One of your many good posts....thanks.

 

[Barry Desborough]

Very well put Mark. Especially your concluding paragraph. As man thinks in his heart so is he.

Has everyone experienced the spiritual nature of reality? No! But that does not mean the others haven't. Have all heard from God? NO! But that does not mean these also haven't. Have all seen or experienced a manifestation of or from God? No! But that does not mean none have. The things of the Spirit can only be discerned spiritually they are foolishness to the natural man. One of your many good posts....thanks.

Utterly devoid of evidence and irrelevant to the topic. Yes, very well put.

 

[Barry Desborough]

Sorry, I missed that.

Now I feel guilty for driving my response to that nonsense home...

It's how these people operate. They have no sensible response to the facts and the logic, so they attempt to distract from it. Don't feel too bad.

 

[dad]

Limited data sets like whole genome surveys? Yeah. Gotcha.

Limited data like whether there WAS ANY genome like we know it today in the days of Noah.

 

[JDD_III]

My base assumption is that things that are supported by evidence and which are testable, are more believable then those things that aren't.

This assumption leads me to accept ERV's as quite knock-down evidence of common descent.



And if you assume that pigs can fly into space and beyond, you could propose that pigs landed on the moon before humans.

But I don't see how that would be particularly helpfull for anything.

The difference is you can test whether pigs fly but you cannot test what the chimp and human genome was like 7mya.

And given this is a forum debating creation and evolution, you have to at least accept that we are debating evidence interpretation thus to start with base assumptions that prove your point is illogical in such a setting and circular. So you have to consider the alternative approach.

You are saying ERVs provide evidence for common descent. Yes, they do, based on assuming certain things (which by the nature of this forum are not a given otherwise this forum should just shut down now and lets all leave).

I'm asking you to consider, what if these sequences were already in existence on day 1 of design. What if viruses did not exist in day 1 of design. What if they arose somehow after? What if it was the result of a type of genetic deterioration? Given they are jumping genes, they possess features that mean they could be "infective" in nature. So what if viruses actually arose from such sequences?

After all, we are debating the Christian account of creation versus evolution therefore if you are going to assume the former, it is only fair to play through the scenario that God created humans and other mammals with good genomes and the Fall caused those genomes to go wrong. And it is fair to assume that viruses did not exist prior to the fall.

In fact, ERVs are rather strange for evolution - evolution can randomly master the existence of complex organs such as an eye, but cannot get rid of waste sequences such as ERVs which happen to stay in the genome? Further, many important functions are being found for ERV sequences and continue to be so.

So again I ask, can you hypothesise a situation where what we see as ERVs now were once functional in a less deteriorated original genomic blueprint in multiple organisms, much like homologous proteins across species?

And, for reference, read this paper if you want an explanation from this end around:
http://creation.com/images/pdfs/tj/j27_3/j27_3_105-112.pdf

Best,
J

 

[Barry Desborough]

Limited data like whether there WAS ANY genome like we know it today in the days of Noah.

Why don't you get a professional lobotomy? (Or have you already had one?)

 

[Barry Desborough]

The difference is you can test whether pigs fly but you cannot test what the chimp and human genome was like 7mya.

And given this is a forum debating creation and evolution, you have to at least accept that we are debating evidence interpretation thus to start with base assumptions that prove your point is illogical in such a setting and circular. So you have to consider the alternative approach.

You are saying ERVs provide evidence for common descent. Yes, they do, based on assuming certain things (which by the nature of this forum are not a given otherwise this forum should just shut down now and lets all leave).

I'm asking you to consider, what if these sequences were already in existence on day 1 of design. What if viruses did not exist in day 1 of design. What if they arose somehow after? What if it was the result of a type of genetic deterioration? Given they are jumping genes, they possess features that mean they could be "infective" in nature. So what if viruses actually arose from such sequences?

After all, we are debating the Christian account of creation versus evolution therefore if you are going to assume the former, it is only fair to play through the scenario that God created humans and other mammals with good genomes and the Fall caused those genomes to go wrong. And it is fair to assume that viruses did not exist prior to the fall.

In fact, ERVs are rather strange for evolution - evolution can randomly master the existence of complex organs such as an eye, but cannot get rid of waste sequences such as ERVs which happen to stay in the genome? Further, many important functions are being found for ERV sequences and continue to be so.

So again I ask, can you hypothesise a situation where what we see as ERVs now were once functional in a less deteriorated original genomic blueprint in multiple organisms, much like homologous proteins across species?

And, for reference, read this paper if you want an explanation from this end around:
http://creation.com/images/pdfs/tj/j27_3/j27_3_105-112.pdf

Best,
J

1) Peer Terborg has posted several times to my blog. He is insane. Please see his comments and my responses.

2) You confuse creationism with Christianity. Please don't do that. creationism is a sub-sect in Christianity, Islam and Judaism. To try to equate creationism with Christianity is dishonest.

3) You say that the case for common descent from ERVs depends on "assumptions", but you fail to specify what you think they are. What do you think they are?

4) Do you think you can answer questions a) to i) here? Give them your best shot. Veritas: ERV FAQ: But how can you rule out design as an explanation?

5) Any assertions you want to make need to be supported by evidence. "It could be" is of little interest. Anything could be, but there is no reason to think it may be true without evidence.