Human Evolution: Endogenous Retroviruses prove that humans and chimps share a common ancestor.

Gene ^ | 2000 Apr 18 | Lebedev, Y. B. et. al.

[EnderWiggins]

Endogenous retroviruses are the remnant DNA of a past viral infection. Retroviruses (like the AIDS virus or HTLV1, which causes a form of leukemia) make a copy of their own viral DNA and insert it into their host's DNA. This is how they take over the cellular machinery of a cell and use it to manufacture new copies of the virus.

Sometimes, the cell that get’s infected by such a virus is an immature egg cell in the ovary of a female animal. Such cells can be stored in a state of suspended animation or dormancy for as much as 50 years before they complete meiosis and become mature egg cells ready to be fertilized. Because they are dormant gene expression is suppressed and the infection cannot take over the cell and kill it. If that egg later matures and is fertilized, the newborn organism will have that endogenous retrovirus in every one of its cells, and so will all of its descendants.

Every viral infection is unique. The complete genome of an animal is so huge, and the insertion point of a virus’s DNA is so random that it is statistically impossible for any two individuals to have the same exact endogenous retrovirus in the same exact spot on the genome unless they both inherited it from a common ancestor who had the original infection. And the infection of a germ cell is so rare that ERVs make up only somewhere between 1% and 8% of the entire human genome.

If two humans have the same identical ERV, it is proof that they are descended from a common ancestor. And if two different species have the identical ERV, it is proof that they too are descended from a common ancestor. In humans, there are about 30,000 different ERVS embedded in each person's DNA. Except for those later duplicated by a duplication mutation, all of them record unique infections of a single ancestral individual. Now here is where it gets really interesting.

There are at least seven different known instances of shared ERVs between chimps and humans... i.e. ERVs which are the identical viral DNA inserted into the identical spot of the genome. 100% of all chimps and 100% of all humans have these same ERVs. This is only possible if 100% of all chimps and all humans are descended from the single individual that had these original infections.

They are proof that humans and chimps share a common ancestor.

In a 2000 paper published in the journal Gene researchers identified ERVS shared by different primates and used them to assemble a family tree of monkeys apes and humans. Yes... we share ERVs with these lower primates as well. Here is what it looked like:





Figure 4.4.1. Human endogenous retrovirus K (HERV-K) insertions
in identical chromosomal locations in various primates
(Reprinted from Lebedev et al. 2000)


The arrows show the relative insertion times of the viral DNA into the host genome (determined using the “genetic clock” of accumulated later point mutations). All branches to the right carry that ERV - a reflection of the fact that once a retrovirus has inserted into the germ-line DNA of a given organism, it will be inherited by all descendants of that organism.

Reference: Lebedev, Y. B., Belonovitch, O. S., Zybrova, N. V, Khil, P. P., Kurdyukov, S. G., Vinogradova, T. V., Hunsmann, G., and Sverdlov, E. D. (2000) "Differences in HERV-K LTR insertions in orthologous loci of humans and great apes." Gene 247: 265-277.

[Southack]

"I need to go back on one point... there is another possible explanation that conforms with intelligent design... but it requires a designer who is also being deliberately deceptive. I for one do not believe that God is liar." - EnderWiggins

Logic doesn't care what you believe.

[wolf78]

Since when do apes have a conscience?

Fallacy of illicit minor

[EnderWiggins]

You really seem to have a very dismal opinion of God. If you want to portray him as mediocre programmer reusing broken code to save a buck, I will not stop you.

I choose to have a higher opinion of his design skills.

[EnderWiggins]

Am I to understand that you are asserting that logically, God is a liar?

Because it's difficult to come up with an alternative interpretation of that comment.

[Southack]

"You really seem to have a very dismal opinion of God. If you want to portray him as mediocre programmer reusing broken code to save a buck, I will not stop you. I choose to have a higher opinion of his design skills." - EnderWiggins

Opinion and logic are not synonyms.

My original post destroyed the claim that ERVs were proof of Evolution ... by showing that routine lab work inserts ERVs into DNA today by design, not by Evolution. Thus, there is a non-Evolutionary option...which means that Evolution was not proven (please, no sophomoric rants that nothing is really provable, let's not devolve to that level).

I used logic. You used opinion. One is scientific, the other is debatable.

[EnderWiggins]

"My original post destroyed the claim that ERVs were proof of Evolution ... by showing that routine lab work inserts ERVs into DNA today by design, not by Evolution."

Again... your "routine lab work" absolutely fails to account for the ERVs as found in the primate family tree. It does not explain the independent but mutually reinforcing data sets they provide. The first being their relative age, the second being their distribution.

Neither are explained by design since the accumulation of point mutations demonstrate that they were acquired tens of thousand, hundreds of thousands and millions of years apart. They do not reflect a single or even several closely spaced events of design... but multiple millions of years over which the insertions were periodically made. I would be fascinated in a "design rationale" for that fact.

And second... the pattern of distribution does not reflect the sort of purposeful reuse found in things designed by humans. I'd love for you to try and assemble a phylogenetic tree for the products of human engineering that would have no exceptions in the distribution of technology that leaped across clades falsifying the pattern of descent with modification. It cannot be done. I assure you (as an engineer myself) I have made the effort. If you can demonstrate otherwise...have at it.

Even accepting your portrayal of God as a mediocre software engineer constrained by budgets or time (a very weird idea that you seem to have no problem with) there is no possible way of assembling a tree of phylogenetic descent for computer programs... even operating systems like Windows. The code instead reflects the contagious technology of actual design, and not the nested similarities created by descent with modification and characteristic of biological organisms.

Does code get reused? Of course. Might even bits of broken code be retained? I imagine it is possible, although it would still be, by definition, bad design. Again, I speak as an engineer, and as a person who has managed teams of engineers. But does code get reused in a patter that perfectly mimics descent with modification?

Not on this planet.

Your alternative seems to have missed these details. And they are the only important part of the proof. Odd that. But in final review, your alternative is not an "non-Evolutionary option at all," it is essentially an appeal to divine conspiracy.

I know you have a high regard of your own command of logic. I can only point out that logic, even of the most refined and sublime sort is of little use if it fails to address the issues at hand.

[firebrand]

The story of Adam and Eve is not “silly.” It bears at least as much contemplation as looking at the chimps in the zoo. Calling it silly is sinking to the level of the anti-science crowd.

[Southack]

"Again... your "routine lab work" absolutely fails to account for the ERVs as found in the primate family tree. It does not explain the independent but mutually reinforcing data sets they provide. The first being their relative age, the second being their distribution."

Incorrect. ERVs are just genetic code. That code gets inserted into the same place and then later re-used is common for software designers.

What would be *correct* to postulate would be that one program was coded before another. The evidence at hand would support that statement.

What is *incorrect* to postulate is that only un-aided processes such as Evolution could explain the ERV code insertion points in different programs over a vast time-period...because we can see identical code being re-used by Intelligent processes in modern software design.

Thus, un-aided processes and aided processes both offer potential, reasonable, demonstrable solutions.

Ergo, one can't claim that *only* un-aided processes were involved. Modern software lab evidence shows that aided processes have done the insertion in question, so aided processes must be included as a potential cause.

QED

[EnderWiggins]

"Incorrect. ERVs are just genetic code. That code gets inserted into the same place and then later re-used is common for software designers."

Ah.... I'm sorry. I assumed that you knew what ERVs were. I was wrong.

ERVs are not "just genetic code." In fact, they do not code for anything at all.

So their insertion "in the same place" or "reuse" is pointless... at least from the perspective of intelligent design. Once again your analogy with software engineering proves to be a bad one.

"What would be *correct* to postulate would be that one program was coded before another. The evidence at hand would support that statement."

It is fascinating that you would label as "correct" a postulate that fails to account for any of the actual features seen in the ERVs under consideration.

That postulation is actually a continuation of your ad hoc characterization of the designer as deliberately deceptive. It requires that the sequence in which that coding took place exactly mimicked descent with modification over multiple millions of years... something again for which I'd love to see a reasonable design rationale.

It also fails completely to account for the accumulation of point mutations at all, and they are the diagnostic feature allowing us to temporally sequence the ERVs. It is another feature you fail to account for with any sort of design rationale.

It also fails (yet again) to show any genuine analogy with the intelligent design of humans, as even when humans code "one program after another" and reuse code, the final design is a mosaic of new code, old code and borrowed code that repeatedly and dramatically violates the pattern demanded by genealogical descent.

How is it that you imagine for a second that your "alternative explanation" is an alternative at all, when it explains none of the facts that are so neatly and comprehensively accounted for by the naturalistic explanation?

"Thus, un-aided processes and aided processes both offer potential, reasonable, demonstrable solutions."

That would only be true if both processes actually explained the phenomenon. But in this case only the un-aided process explains any of it.

As is common in creationist attempts to explain away powerful evidence for which you actually have no naturalistic alternative, you have again resorted to a first step of "magic," augmented by deliberate deception on the part of the magician. It is a wonderful unfalsifiable (hence patently unscientific) explanation completely on par with "The universe is only 30 seconds old, and all of us were magically created a half minute ago complete with false memories of a past that never took place, libraries full of false history books, a vast geologic column recording events that actually never occured, and a fictional multi billion year record of fake cosmic events coded into starlight created in flight."

That assertion is essentially no different from your "alternative" posed here. It may be satisfying to you... it may even be true. But it is not science.

Now... if you are eventually able to use your august command of "logic" to come up with an alternative explanation for ERVs that actually explains them, I'm all ears and promise to be impressed.

To this point... not so much.

[Southack]

"ERVs are not "just genetic code." In fact, they do not code for anything at all." - EnderWiggins

LOL! More of your fairy tales, I see. You are completely incorrect, however.

All DNA is comprised of genetic code, even ERVs.

Ta taa. Come back after you've passed basic Biology.

[Southack]

"So their insertion "in the same place" or "reuse" is pointless... at least from the perspective of intelligent design. Once again your analogy with software engineering proves to be a bad one." - EnderWiggins

Nonsense! Oh, if someone had such a small mind that they were unaware of how public keys were inserted into encrypted data, perhaps they could make simpletonian claims such as "ERVs aren't genetic code" or "insertion in the same place is pointless," but to any educated cryptographer or software programmer, such statements would be laughable.

I'm laughing.

...at you...

[Southack]

"That would only be true if both processes actually explained the phenomenon. But in this case only the un-aided process explains any of it." - EnderWiggins

Sigh. Incorrect again, I see.

Ender, unaided processes aren't magic. Aided processes can always accomplish the same thing. You are making the same error that the original author of the article for this thread made by assuming that only an unaided process can accomplish some specific feat.

[EnderWiggins]

Laugh away. You have no choice to laugh since you seem to be unable to argue the point.

Your “alternative explanation” must first actually be an explanation before it can be considered an alternative. You’ve been offered several opportunities at this point to actually offer one.

The silence has been deafening.

The closest you have come to making a point is to identify DNA as a code. That’s good... but we figured that out almost 60 years ago. You have accounted for exactly none of the features of ERVs that prove them to be exactly what they are.

So... again, until such time as you actually provide an alternative explanation that accounts for the features of the ERVs that I have covered several times now, I leave you to your laughter. Us folks with “small minds” have real science to do.

[EnderWiggins]

You continue to miss the point entirely. It is not that aided processes cannot cannot accomplish some of the same things that unaided processes can. It is that only one process actually explains this specific phenomenon. You have certainly not proposed an alternative. Except of course the "dishonest magician" which we both know is not science.

[Southack]

"It is not that aided processes cannot cannot accomplish some of the same things that unaided processes can. It is that only one process actually explains this specific phenomenon." - EnderWiggins

That's incorrect. First of all, you argued, and the author of the article for this thread implied (by saying that ERV insertion point commonality "proved" Evolution) that an unaided process was the only explanation. And that's wrong.

An aided process can insert ERVs into the same place as can an unaided process.

Second, aided processes such as software self-modification, software viri modifying an OS, genetic lab work deliberately inserting ERVs into DNA, and cryptologists inserting the public half of a key into an encrypted data segment are *all* processes that yield the same insertion point result.

Which is to say, you're just as wrong, and clueless, as the author of the article. Neither of you have shown the slightest education about cryptography, and neither of you have demonstrated any knowledge of modern genetic lab work.

Now stubborness and obtuseness...that you've both got in spades. You clearly talk more than you listen, and think less than you espouse.

Go back and try again.

[EnderWiggins]

”That's incorrect. First of all, you argued, and the author of the article for this thread implied (by saying that ERV insertion point commonality "proved" Evolution) that an unaided process was the only explanation. And that's wrong.”

And yet, even after all your posts on the subject, the unaided process described by the article still actually does remain “the only explanation.” For that to change you have to actually provide us with an alternate explanation... and you have yet to do so. There is no need to again recount the specific details of the ERVs, their ages and their distribution other than to point out that your facile attempt at another explanation fails to address any of them.

”An aided process can insert ERVs into the same place as can an unaided process.”

Sure they could. But what would lead you to believe that an alternative to that single feature of these ERVs is an alternative explanation to the phenomenon of ERVs?

The paper is not about how a single ERV came to exist in multiple organisms in the identical spot in the genome... it is about the pattern and distribution of multiple ERVs across an entire mammalian order.

”Second, aided processes such as software self-modification, software viri modifying an OS, genetic lab work deliberately inserting ERVs into DNA, and cryptologists inserting the public half of a key into an encrypted data segment are *all* processes that yield the same insertion point result.”

As you struggle to overcome my simple observation that you have failed abysmally to provide an alternative explanation for ERVs, you dig yourself deeper. Need I remind you about the first rule of holes?”

At least this time you have made a feeble attempt to explain a single feature of the ERVs... the appearance of ERVs in the same location on the genome in multiple species. Let’s see how you did.

First off, discussion of encryption keys is an irrelevant red herring, since the DNA code is no more encrypted than any ordinarily alphabet. We all understand the design rational for such encryption in software, but there is no biological analog. It would be like appealing to nuclear reactors when trying to explain the deep diving of whales.

Second, self modifying software is actually (once set up) an unaided process that actually concedes the ability of genetic information to evolve on its own without intelligent guidance. The entire process was created in acknowledgment of the power of “natural selection” and is the attempt of software engineers to use nature as a model. Letting no irony go unsmelted... the one good analogy you provide is one that supports your opponent‘s position.

Third, software viruses (note the correct plural form) modifying an OS fails at least two different ways to provide a good analogy. A) It represents an active somatic infection which endogenous retroviruses are not. ERVs (as we have covered several times in spite of your quibbling) are not active infections at all. B) It does not resemble in any way the somatic infections of real retroviruses. Engineered retroviruses are designed to insert themselves at a specific place in the host code because that is necessary to their function. As a result, they are useless to distinguish between individual events of infection. Were ERVs the result of the same or a similar process, they could not possible exist in a pattern that mimics perfectly descent with modification. They would (again) leap across clades and destroy any pattern of genealogical descent.

And finally, labwork in which human beings deliberately modify genes are yet another perfect example of how the only intelligent designer that we have actual experience with creates a pattern of technology that does not resemble the natural biological pattern in the least. Since human designers do not have the same deceptive intent of the “lying magician” that you ultimately require for your “alternative” to be true, they make no attempt to mimic the nested pattern of progressively degraded ERVs that nature has provided us. Thus, no such pattern exists.

Now... you have attempted with little success to offer an alternate explanation to a single feature of the phenomenon we are discussing, but an actual alternative to the phenomenon itself is not even attempted.

”Which is to say, you're just as wrong, and clueless, as the author of the article. Neither of you have shown the slightest education about cryptography, and neither of you have demonstrated any knowledge of modern genetic lab work.”

Your myopia here becomes easier to understand as our discussion progresses. You actually do not understand the paper discussed in this thread at all. You certainly do not understand ERVs and the phenomenon that requires explanation. The school of red herring that populate your argument appear to all be honest. What I mean by that is you don’t even realize they are red herring because you do not understand the phenomenon in the first place.

I am growing more and more to enjoy your accusations of my ignorance. It certainly is your only fallback for covering up the complete failure on your part to provide an actual alternative to the paper that commenced this thread.

[Southack]

And yet, even after all your posts on the subject, the unaided process described by the article still actually does remain “the only explanation.” ... ”An aided process can insert ERVs into the same place as can an unaided process.” Sure they could." - EnderWiggins

You appear to be unable to see the contradiction in your own admissions and claims, but there it is, for one, above in claiming that there is "only one" process that can explain it, and then admitting that yet another process can explain it.

Logic 101 eludes you.

[Southack]

"First off, discussion of encryption keys is an irrelevant red herring, since the DNA code is no more encrypted than any ordinarily alphabet. We all understand the design rational for such encryption in software, but there is no biological analog." - EnderWiggins

What you call indecypherable "junk DNA," others call "encrypted comments in code."

[Southack]

"Second, self modifying software is actually (once set up) an unaided process that actually concedes the ability of genetic information to evolve on its own without intelligent guidance." -EnderWiggins

You're finally getting warmer, but still not quite there yet.

[EnderWiggins]

Your equivocation does not equal my contradiction.

Until such time as somebody comes up with an alternate explanation, it is a simple statement of fact there is only one explanation for the phenomenon.

You certainly have yet to offer one... in spite of how many posts? I’ve lost count. There certainly might be unknown explanations out there somewhere... but none at this point can even be termed “hypothetical.”

Logic 101 you say?

http://www.fallacyfiles.org/equivoqu.html