Ardi - Ardipithecus ramidus

[ageofknowledge]

What I'm seeing is that evolutionary biologists maintain that the pseudogenes, SINES, LINEs, and endogenous retroviruses shared among humans and the great apes provide persuasive evidence that these primates arose from a common lineage. The crux of this argument rests on the supposition that these classes of noncoding DNA lack function and arose through random biochemical events.

False.

For example, ERVs don't have to be non-coding to still be overwhelming evidence for ape common ancestry. Do you see why?

The key idea is that an ERV drops a DNA sequence into a random place into a chromosome in a germ cell. If that germ cell fertilizes, grows up, goes to college to study evolution, and reproduces, then the ERV has a chance to become fixed in the population. If the population later splits and becomes two species, both species propagate that ERV in the same location!

Elementary my dear Watson. But I'm busy so will reply later. Until then: Peace.

[Byblos]

The point I'm making with the HIV virus is that it can infect both species separately. It's not an impossibility for viruses. It is also possible a few of the retroviruses are likely to infect both humans and apes at the same location.

False. You're just making stuff up.

The chance of "a few of the retroviruses" infecting humans and chimps at the same chromosome and location is essentially zero. A specific retrovirus can and does insert itself at many different chromosome positions, even within the same organism. In gene therapy, retroviruses can be problematic for this very reason; the retroviruses may randomly splice into something critical in the host DNA.

And if just "a few" retroviruses insert at the same place, as you say, then why don't we see in apes (or any other related group of animals for that matter) the same ERV at a different chromosome or position?!

As I said before, the only reasonable conclusion is that the ERVs inserted their DNA before the human and chimp split.

Your last question above makes no sense, especially from your perspective so you might want to rephrase it. Besides, did you even bother reading my posts on probability or the links AoK and I provided and the multitude of questions scientists themselves are raising wrt so-called ERVs?

[Gman]

Your last question above makes no sense, especially from your perspective so you might want to rephrase it. Besides, did you even bother reading my posts on probability or the links AoK and I provided and the multitude of questions scientists themselves are raising wrt so-called ERVs?

Those were some good links for sure guys...

Getting back to Ardi, RTB has come out with some interesting observations on the subject...

Ardi- Hardly evidence for Human Evolution

[DannyM]

Your last question above makes no sense, especially from your perspective so you might want to rephrase it. Besides, did you even bother reading my posts on probability or the links AoK and I provided and the multitude of questions scientists themselves are raising wrt so-called ERVs?

Those were some good links for sure guys...

Getting back to Ardi, RTB has come out with some interesting observations on the subject...

Ardi- Hardly evidence for Human Evolution

Yeah, absolutely. I don't get much time for a browsing usually but just spent a good 20 minuted on the link you just provided and found it very good, Gman.

[touchingcloth]

If humans are higher than chimps...who claims that they are?

Hey, if you can't figure that out, then I don't think I need to be talking with you.
That's like the guy on another thread who was trying to say that "2+2=4" wasn't a fact.

I'm trying to get at what you mean by "higher" or "more evolved".
If you mean by that that humans are more intelligent, then yes, we are more evolved.
If you mean by that that humans are better at climbing trees, then chimps are more evolved.
If you mean by that that humans are more adapted to their envionment than chimps are to theirs, then no, we are not.

[Gman]

If you mean by that that humans are more intelligent, then yes, we are more evolved.

And if we go by this statement we could certainly reason that there are more intelligent humans than other humans in the world too...

You can find a lot of this mentioned in one of Darwin's books called “The Descent of Man."

"At some future period, not very distant as measured by centuries, the civilized races of man will almost certainly exterminate and replace the savage races throughout the world. At the same time the anthropomorphous apes. . . will no doubt be exterminated. The break between man and his nearest allies will then be wider, for it will intervene between man in a more civilized state, as we may hope, even than the Caucasian, and some ape as low as a baboon, instead of as now between the negro or Australian and the gorilla. (Darwin; “The Descent of Man”, 2nd ed. P.178)."

[ageofknowledge]

True Gman but most evolutionists skip right over the portions of evolutionary theory that cannot be normalized with the ideological modern liberal politically correct social order they created. Currently race is taught as a social concept not a biological one using markers such as language. Evolutionists, yea the entire system they built and force upon the world stinks of this type of hypocrisy.

[IgoFan]

Retroviral Gene Vectors Show Clear Target Preferences

Your reference is evidence FOR, not against, common descent.

The study found hundreds of different integration sites for each type of retrovirus targeting the same type of cells in rhesus monkeys.

And the study, including those mentioned below, show that the retrovirus integration site location follows a non-uniform probability distribution function, i.e., retrovirus location is a random variable.

Moreover, nothing in the study says that any retrovirus integration sites were at the same location, which is absolutely necessary for your creationist hypothesis.

In glaring contrast, each given ERV shared between humans and chimps is at the exact same location and on the same corresponding chromosome.

Such evidence is overwhelmingly consistent with the ERVs inserting their DNA into the human and chimp common ancestor. Descendants don't change ERV locations, so if humans and chimps split, we'd expect each ERV to be in the exact same location in both humans and chimps. And lo and behold that's exactly what we find!

And just the tip of the iceberg of references that give measures of the distribution of retrovirus integration site locations: (2008) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2453317, (2005) http://www.virologyj.com/content/2/1/68, (2008) http://genesdev.cshlp.org/content/23/5/633.full, (2006) http://jvi.asm.org/cgi/content/full/80/ ... type=HWFIG, (2005) http://www.nature.com/mt/journal/v11/n1 ... 5153a.html, (2006) http://www.jsbi.org/journal/GIW06/GIW06P093.pdf

[Gman]

Your reference is evidence FOR, not against, common descent.

The study found hundreds of different integration sites for each type of retrovirus targeting the same type of cells in rhesus monkeys.

And the study, including those mentioned below, show that the retrovirus integration site location follows a non-uniform probability distribution function, i.e., retrovirus location is a random variable.

Moreover, nothing in the study says that any retrovirus integration sites were at the same location, which is absolutely necessary for your creationist hypothesis.

In glaring contrast, each given ERV shared between humans and chimps is at the exact same location and on the same corresponding chromosome.

Such evidence is overwhelmingly consistent with the ERVs inserting their DNA into the human and chimp common ancestor. Descendants don't change ERV locations, so if humans and chimps split, we'd expect each ERV to be in the exact same location in both humans and chimps. And lo and behold that's exactly what we find!

And just the tip of the iceberg of references that give measures of the distribution of retrovirus integration site locations: (2008) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2453317, (2005) http://www.virologyj.com/content/2/1/68, (2008) http://genesdev.cshlp.org/content/23/5/633.full, (2006) http://jvi.asm.org/cgi/content/full/80/ ... type=HWFIG, (2005) http://www.nature.com/mt/journal/v11/n1 ... 5153a.html, (2006) http://www.jsbi.org/journal/GIW06/GIW06P093.pdf

Did you read the article? It states.. "surprisingly, MLV targeted one gene—known previously to be involved in spontaneous leukemias and in murine retroviral oncogenesis—seven times, a “highly nonrandom” result suggesting that such insertions may occur far more often than previously thought."

They say that certain retroviral insertions are “highly nonrandom." You are saying that they are random. In your own words you stated "An ERV RANDOMLY inserts its DNA at any of MILLIONS of possible places along the host DNA." Well you are wrong.. If the retrovirus has clear target preferences then it is "possible" that they hit at the same location..

Non-randomness is still not entirely ruled out here even with those sources you quoted.. In fact one of your sources states the following, "These findings contribute to a growing body of evidence indicating that retroviral integration is not random." Growing? Growing but not necessarily exclusive evidence.. In fact the yeast Ty elements may even demonstrate a stricter target site preference.

Again, what you have here is circumstantial evidence. You would have to use a time machine to go back in time to prove your point when it was inserted..

In other words, this is all faith based...

[IgoFan]

[... text of last post omitted ...]

You're still not understanding how an overwhelmingly crucial conclusion from these articles destroys your argument.

Do a million infections of a specific retrovirus. You'll have close to (more likely, exactly) a million different integration sites spread over different chromosomes.

Remember that between humans and chimps, a shared ERV has the exact same integration site on the same chromosome.

But I'll even spot you the spectacularly ridiculous optimistic odds of an exact location match for a specific ERV as 1 in 10, instead of 1 in 1000000. Now, raise that 1 in 10 chance to the power of the number of different shared ERVs between just humans and chimps. Do you see how, as you say, "possible" that is? If that isn't close enough to zero for you, then raise to the power of the number of shared ERVs among all apes. Still not good enough? How about among all mammals?

After seeing the word "non-random", you prematurely stopped reading and understanding, in order to start your end zone dance against evolution.

What is confusing you is that the retrovirus articles talk of "preferential" integration locations. Before DNA analysis became so quick and cheap, scientists initially saw from their few data points that the same retrovirus inserted itself over all the chromosomes, and throughout the length of each chromosome.

Now with vastly more retrovirus insertion location data, scientists (and not creationists, who don't do science) saw that insertion location was not simply a uniform random variable, i.e., insertions were not spread evenly across each possible DNA location on each chromosome. Rather, retrovirus insertions generally tend to land somewhere in the vicinity of very common features, e.g., the start of a gene, a region of high gene density.

But the overall conclusion is still the same. The creationist hypothesis of location-identical ERV insertions happening independently in both humans and chimps is inconceivably improbable. The evolutionary hypothesis of ERV insertions in the human-chimp common ancestor is breathtakingly consistent with the data.

Again, what you have here is circumstantial evidence. You would have to use a time machine to go back in time to prove your point when it was inserted.. In other words, this is all faith based...

Please, I beg you, don't take my word for it. Say this to a scientist or researcher at your local university. Ask her to rate your statement on a scale from 1 to 10, with 10 being "the most inexplicably bizarre as related to science". No need to report back on your results, UNLESS she rates it less than a 15.

[Gman]

We are clearly deviating from Ardipithecus ramidus here..

You're still not understanding how an overwhelmingly crucial conclusion from these articles destroys your argument.

Those articles prove nothing but a certain viewpoint, that's all.. And you still haven't addressed our questions posted by Age and Byblos. Again what you have here are assumptions..

Please answer the following..

To expand a little on AoK's post, here's a list of questions (from this link) scientists need to answer before ERV's can be accepted as such:

How Did ERV Related Elements Insert Themselves into Germ Cells Thousands of Times Without Fatalistic Damage to the Host?

How is it that ERVS are Considered Copies of Disease Producing Exogenous Retroviruses but None Have Been Proven to Directly Cause Disease?

What Made ERV Elements Change From Viral Activities to Cellular Activities and Create New Essential Genes?

How Could ERVS Create a Specie-Specific Regulatory Network that Controls the Expression of Cells in a Collective Manner?

What Made Unrelated ERVS in Unrelated Species Create Almost the Same Gene (Convergent Evolution)?

What Made Two Unrelated ERV LTRS Evolve Independently in Creating the Same Regulatory Roles for the Same Gene (Convergent Evolution)?

What Made ERV LTRS Immediately Turn into Essential Gene Regulators Upon Insertion?

What Made LTRS Acquire Transcription Abilities for Essential Genes?

Where is the Proof that ERV LTRS can “Self-Replicate” and Why Don't We See them Doing it Now?

What made the same erv transcribe differently between supposedly closely related species?

What made the same erv transcribe differently among different cell types within the same organism?

There's a few more but you get the gist, too many questions, too many assumptions.

Do a million infections of a specific retrovirus. You'll have close to (more likely, exactly) a million different integration sites spread over different chromosomes.

Remember that between humans and chimps, a shared ERV has the exact same integration site on the same chromosome.

But also remember that "apes do not have a fused chromosome. The human chromosomal fusion argument focuses on a fusion event that is specific to the human line, and therefore provides a highly limited form of evidence for human / ape common ancestry."

http://www.ideacenter.org/contentmgr/sh ... hp/id/1392

But I'll even spot you the spectacularly ridiculous optimistic odds of an exact location match for a specific ERV as 1 in 10, instead of 1 in 1000000. Now, raise that 1 in 10 chance to the power of the number of different shared ERVs between just humans and chimps. Do you see how, as you say, "possible" that is? If that isn't close enough to zero for you, then raise to the power of the number of shared ERVs among all apes. Still not good enough? How about among all mammals?

Right, so now you have to make up the rules so that you can bend them in your favor… Being is that you have no rules. The fact here is more research is needed to prove these hypothesis and the reason is because we know very little about retroviral DNA. Thus it is still “growing” as your sources say..

After seeing the word "non-random", you prematurely stopped reading and understanding, in order to start your end zone dance against evolution.

And that is exactly what the article stated.. Please stop denying it. Before you keep insinuating how retroviruses are random junk viruses, you seem to forget the fact that when scientific knowledge increases the amount of junk DNA decreases.. There are many genes that were considered pseudo genes however when further research was made these genes turned out to be useful.. This is true in both ERV's and “so called” junk DNA. As an example the ERV's that are only present in mammals are actually essential for reproduction. Others guide a system that helps the mother to accept the embryo or prevent pathogens to infect the placenta. In other words, they perform a specific function in reproduction and are useful to the organism. So it's no wonder why humans and other mammals share ERV's because they reproduce in a similar way..

But not all mammals reproduce this way. Monotremes, as an example, lay eggs. Why? Because they are a different spieces..

What is confusing you is that the retrovirus articles talk of "preferential" integration locations. Before DNA analysis became so quick and cheap, scientists initially saw from their few data points that the same retrovirus inserted itself over all the chromosomes, and throughout the length of each chromosome.

What is confusing you is that you only have a hypothesis.. This is an idea or an assumption.. Hardly a slam dunk for evolution.

Now with vastly more retrovirus insertion location data, scientists (and not creationists, who don't do science)

Oh so only the evolutionary scientists are real scientists? I see.. I think you should also be aware that the public scientific communities are in no way going to admit that Darwinian evolution is unscientific or false. Keep in mind that many of these institutions rely heavily on public funds to operate. No way would they ever admit that evolution was false... They would literally loose their budgets or shoot themselves in the foot. In fact, when they make a supposed scientific claim for Darwinism, they actually get more money or more grants to continue their research...

saw that insertion location was not simply a uniform random variable, i.e., insertions were not spread evenly across each possible DNA location on each chromosome. Rather, retrovirus insertions generally tend to land somewhere in the vicinity of very common features, e.g., the start of a gene, a region of high gene density.

But the overall conclusion is still the same. The creationist hypothesis of location-identical ERV insertions happening independently in both humans and chimps is inconceivably improbable. The evolutionary hypothesis of ERV insertions in the human-chimp common ancestor is breathtakingly consistent with the data.

Do you remember the PtERV? This is one of thew ERV's that was present in chimps and gorillas but not in humans falsifying evolution.. However, it turned out that PtERV prevents chimps and apes from getting HIV. In fact it is hypothesized that some ERV's serve as a natural vaccine against retroviruses or the cure for cancer or HIV and other retroviruses depend on ERV. Again it performs a certain function..

Please, I beg you, don't take my word for it. Say this to a scientist or researcher at your local university. Ask her to rate your statement on a scale from 1 to 10, with 10 being "the most inexplicably bizarre as related to science". No need to report back on your results, UNLESS she rates it less than a 15.

The problem here is that many scientists are evolutionists and since evolution predicts that retroviral “has” to be junk DNA, many scientists assume the research in retroviral DNA is pointless.. They are biased against it. Now some ERV's may not show an apparent function, however, based on the evidence, we can conclude that retroviral DNA is not junk, some ERV's have or had a function that is yet unknown.

More here: http://www.godandscience.org/evolution/ ... hFRivSphWH

The fact that at least some ERV's have a function contradicts the claim of random insertions because proteins like ERV's can only be useful or functional if they are in a specific location of the genome, in other words the insertions where not random.

Look at the link we provided.. It is also a fact that most ERV's do not have an infectious counterpart suggesting that maybe most ERV's did not come from retroviral insertions, but rather that most ERV's had always been part of the genome from the very beginning..

Sorry..

[IgoFan]

Please answer the following..
[... omitted list of questions irrelevant to the current issue ...]

AFTER we resolve the absolutely key issue here, we can pursue your most important question from your list. But I can understand why you want to change the subject. Admitting the scientific evidence about shared ERVs at the same DNA location would be painful.

But I'll even spot you the spectacularly ridiculous optimistic odds of an exact location match for a specific ERV as 1 in 10, instead of 1 in 1000000. Now, raise that 1 in 10 chance to the power of the number of different shared ERVs between just humans and chimps. Do you see how, as you say, "possible" that is? If that isn't close enough to zero for you, then raise to the power of the number of shared ERVs among all apes. Still not good enough? How about among all mammals?

Right, so now you have to make up the rules so that you can bend them in your favor…

To help your argument, I spotted you spectacularly ridiculous optimistic odds for an exact ERV location match. And you're now complaining that I'm bending the rules in my favor?!

For someone with a computer science degree, you have a peculiar understanding of probability.

After seeing the word "non-random", you prematurely stopped reading and understanding, in order to start your end zone dance against evolution.

And that is exactly what the article stated.. Please stop denying it. [...]

I explained in the previous post why the meaning of "non-random" in the science articles doesn't help your effectively zero chance of matching an exact ERV location between humans and chimps.

And because humans and chimps share not one, but about 20 ERVs having the exact same corresponding position in their genomes, the chance of your creationist hypothesis of independent ERV infections "winning the lottery" 20 times is "almost zero" to the 20th power, which is, well, uh, zero.

Still don't understand? Here's a similar explanation from a bonafide popular retrovirus researcher: "You need to remember that where retroviruses insert in a genome is random. Like I've said a hundred times before, yes, some like to insert near active genes, and some like quiet genes, but exactly where a retrovirus inserts-- near which active genes, exactly which nucleotides are up/down stream, is random."

Because this retrovirus researcher writes so well, you MUST read her short fascinating intro to ERVs: http://vwxynot.blogspot.com/2007/06/end ... dence.html

And I have looked at your creationist-written references. None of them (or the underlying real science articles that they regularly misrepresent) says that two independent infections from a specific retrovirus occurring at the exact same DNA location have ever been found in apes or reproduced in a lab. And again for good reason, the probability is very low.

Is the reason that you have not acknowledged the evidence that two independent ERV infections cannot wind up in the same DNA location, that you're smart enough to know that to do so would be a spectacular confirmation for common descent, which beautifully explains how those ERVs are at exactly the same position? And we cannot let any evil evidence like THAT through the door, because who knows what else might come through.

Do you remember the PtERV? This is one of thew ERV's that was present in chimps and gorillas but not in humans falsifying evolution.. However, it turned out that PtERV prevents chimps and apes from getting HIV. In fact it is hypothesized that some ERV's serve as a natural vaccine against retroviruses or the cure for cancer or HIV and other retroviruses depend on ERV. Again it performs a certain function..

PtERVs (or as you say, "thew[sic] ERV's[sic]") are not at the same corresponding chromosome positions between chimps and gorillas. So the PtERVs, which are indeed independent infection events, are not relevant to the issue here, which is shared ERVs at the same corresponding positions.

Oh so only the evolutionary scientists are real scientists? I see..
[... laughable creationist conspiracy theories about the scientific community omitted ...]

The truly sad part is that many creationists incorrectly believe that their faith depends on not understanding evolution.

[touchingcloth]

Is the reason that you have not acknowledged the evidence that two independent ERV infections cannot wind up in the same DNA location, that you're smart enough to know that to do so would be a spectacular confirmation for common descent, which beautifully explains how those ERVs are at exactly the same position? And we cannot let any evil evidence like THAT through the door, because who knows what else might come through.

Sounds like Morton's Demon.

The truly sad part is that many creationists incorrectly believe that their faith depends on not understanding evolution.

My god is so powerful he couldn't possibly have used something as beautiful as evolution.

[jlay]

beautiful?
Is that a scientific term.

[Gman]

AFTER we resolve the absolutely key issue here, we can pursue your most important question from your list. But I can understand why you want to change the subject. Admitting the scientific evidence about shared ERVs at the same DNA location would be painful.

You obviously can't answer the questions... I'm sorry to see that. Admit what? The argument isn't the location, part of the argument here is lumping ERV's into the "junk DNA" category while forgetting the essential beneficial function of some ERVs and the interaction between ERVs and other host DNA sequences. This actually suggests that some retroviruses were created in the cell as part of the host genome. If so, they are in the same spot for a reason or function or they had a function at some time ago but are now dormant. Of course some ERV's are not functional but not all of them according to what you're saying..

To help your argument, I spotted you spectacularly ridiculous optimistic odds for an exact ERV location match. And you're now complaining that I'm bending the rules in my favor?!

Spotted me what? You have nothing to spot. You have nothing to give here because you don't even know what you have....

Again, "The number of ERVs in the human genome is over 100,000 and, depending on the research paper, they account for 1-10% of the DNA in most mammals. If you throw in all the fragmented ERV derivatives, about 50% of human DNA is comprised of ERV elements. Up until now, they have been mostly and erroneously thought of as useless 'junk' DNA that is disease related.

http://www.whoisyourcreator.com/endogen ... ruses.html

The fact here is more research is needed to prove these hypothesis and the reason is because we know very little about retroviral DNA and/or how they insert or when they inserted. Also ERV's need to be in very specific places in order to be functional. Why would they be random? In fact you need ERV's to survive.

For someone with a computer science degree, you have a peculiar understanding of probability.

Oh, I see we are resorting to ad hominem attacks now are we? You don't even have any probabilities here..

I explained in the previous post why the meaning of "non-random" in the science articles doesn't help your effectively zero chance of matching an exact ERV location between humans and chimps.

And because humans and chimps share not one, but about 20 ERVs having the exact same corresponding position in their genomes, the chance of your creationist hypothesis of independent ERV infections "winning the lottery" 20 times is "almost zero" to the 20th power, which is, well, uh, zero.

Again what are you talking about? I don't believe in chance... You have to defend chance not me. That is your belief... I believe it was put there for a purpose, by a creator for both chimps and humans.. Just like chimps have hands and humans have hands. They serve a purpose. For grasping... Do you understand yet?

Still don't understand?

Yes, I understand that you don't understand.. And that this hypothesis is being made "after the fact." Pure speculation..

Here's a similar explanation from a bonafide popular retrovirus researcher: "You need to remember that where retroviruses insert in a genome is random. Like I've said a hundred times before, yes, some like to insert near active genes, and some like quiet genes, but exactly where a retrovirus inserts-- near which active genes, exactly which nucleotides are up/down stream, is random."

Because this retrovirus researcher writes so well, you MUST read her short fascinating intro to ERVs: http://vwxynot.blogspot.com/2007/06/end ... dence.html

This proves what I was saying to you before... This is merely a hypothesis. Even she stated at the end that it was her "hypothesis." Hardly empirical evidence for evolution. Sorry.

And I have looked at your creationist-written references. None of them (or the underlying real science articles that they regularly misrepresent) says that two independent infections from a specific retrovirus occurring at the exact same DNA location have ever been found in apes or reproduced in a lab. And again for good reason, the probability is very low.

Again, where is your evidence that all ERV's are viral insertions? Maybe it's the other way around. Maybe viruses came from ERV's and not ERV's came from viruses. In order to be functional they have to be in the exact same place.

Is the reason that you have not acknowledged the evidence that two independent ERV infections cannot wind up in the same DNA location, that you're smart enough to know that to do so would be a spectacular confirmation for common descent, which beautifully explains how those ERVs are at exactly the same position? And we cannot let any evil evidence like THAT through the door, because who knows what else might come through.

Ad hominem's again? And evil evidence? I'll agree with you that you have an idea. I'll give you that.

So this is it? ERV's, this is the earth shattering evidence for evolution? This is what is preventing you from believing in creation?? Wow..

PtERVs (or as you say, "thew[sic] ERV's[sic]") are not at the same corresponding chromosome positions between chimps and gorillas. So the PtERVs, which are indeed independent infection events, are not relevant to the issue here, which is shared ERVs at the same corresponding positions.

The point being here is that ERV's perform a function and are not as random as you may think..

The truly sad part is that many creationists incorrectly believe that their faith depends on not understanding evolution.

The truly sad part is that many evolutionists incorrectly believe that their faith rests on some sort of empirical evidence.