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.

[EnderWiggins]

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

Others can call it "aardvarks' for all it matters.

What can you demonstrate?

[Southack]

I can demonstrate that both aided and unaided processes are capable of achieving the same insertion point.

That alone disproves the author's claim of Evolutionary proof, though no doubt you'll flail about pretending the contrary.

[allmendream]

No, the genetic code refers to a specific property of genetic DNA that corresponds to the amino acid sequence of a protein.

The promoter region of a gene, where a protein transcription factor will bind and “read” the gene into messenger RNA does not contain a code for an amino acid sequence and is therefore NOT part of the genetic code.

The introns of a genetic region are spliced out of the messenger RNA, they also do not contain “genetic code”.

The vast majority of our DNA, in fact, doesn't contain any “genetic code”. So your statement that “All DNA is comprised of genetic code” is incorrect and betrays an ignorance of the fundamental basics of biology.

Less than 5% of our genomic DNA contains translatable information in the form of “genetic code”.

[Southack]

Nope. Messenger RNA contains genetic coding, too.

[allmendream]

I did not deny for a second that mRNA contains genetic code.

The only DNA that does contain genetic code is DNA that gets transcribed into mRNA in the context of a gene.

Less than 5% of our genome is DNA in the context of a gene that contains a genetic code.

Thus your statement that “all DNA contains genetic code” betrays a fundamental ignorance of basic biology.

By getting out of my statement that you thought I was in any way denying that mRNA has genetic code, you betray a lack of basic reading comprehension.

[EnderWiggins]

And I can balance a garden rake on my chin.

A demonstration of an alternate explanation to the pattern of ERVs described in the opening paper is the only thing that would be of value to the discussion. The demonstration you offer here is the same one that has already failed several times in this thread.

[Southack]

"The only DNA that does contain genetic code is DNA that gets transcribed into mRNA in the context of a gene. Less than 5% of our genome is DNA in the context of a gene that contains a genetic code." - allmendream

DNA is comprised sugars and bases. The sugars are structural. One presumes that you aren't trying to count the sugars to arrive at your 95% to 5% ratio.

The bases are *all* either genetic code (e.g. for processing) or data (e.g. for the life/program blueprint).

If we only understand 5% of the code/data, we would be foolish to be imperical about the other 95%.

Oooooooh, "junk DNA." One observer's "junk" might be another programmer's comments in the code. Comments that could easily be encrypted, by the way.

[Southack]

You’re still flailing. You lost back when you couldn’t admit to your own self-contradiction, and were destined to lose even before that point when you failed to see the logical fallacy of the author for this thread.

You’re wasting my time.

[allmendream]

The genetic code refers to a specific code that “translates” into an amino acid sequence.

For example, the base triple codon AUG specifies the amino acid Methionine.

The promoter region of a gene has DNA that forms a specific 3-D conformation that will bind to a protein transcription factor. There is no “code” involved, just one 3-D structure binding to a complementary 3-D structure.

There is no doubt that the promoter region of a gene is functional; but there is, quite simply, no “code” involved - certainly not the genetic code.

Less than 5% of our genome contains DNA that is transcribable into mRNA that contains an ACTUAL “genetic code”. Genetic = gene. A gene is a region of DNA that “codes” for a protein. Thus DNA with a “genetic code” is genetic DNA that is translatable into the amino acid sequence of a protein.

Thus your statement that “all DNA contains genetic code” is completely wrong.

[Southack]

"The promoter region of a gene has DNA that forms a specific 3-D conformation that will bind to a protein transcription factor. There is no “code” involved, just one 3-D structure binding to a complementary 3-D structure." -allmendream

Of course there is code involved.

[Southack]

"Thus your statement that “all DNA contains genetic code” is completely wrong." - allmendream

What part of DNA is neither sugar nor base?!

[allmendream]

Not a “code” as the word is used in English, and certainly not the “genetic code” under discussion.

Is there a “code” involved when a Phillips head screwdriver fits a Philips head screw? Or is it just complimentary 3-D shapes?

And your “what part of DNA is neither a sugar or a base” is just idiotic. We are not arguing over what DNA is made of, just what the genetic code is and how much DNA can be translated using the “code” into an amino acid sequence.

Only genetic DNA has DNA that makes sense in the context of a “genetic code” and genetic DNA is less than 5% of the genome.

Thus your “all DNA has genetic code” statement is absolutely wrong and betrays a fundamental ignorance.

[EnderWiggins]

I "lost?" I lost what? Exactly? Did you think we were playing Lacrosse or something? Tiddly-winks perhaps?

You have provided in microcosm a classic example of the transcendent intellectual bankruptcy of the entire "Intelligent Design" movement. The movement consists almost exclusively of people loudly asserting with no evidence that there is an alternative explanation for the origin and diversity of life on earth other than that of Darwinian evolution.

And yet, when pressed on the issue, no such alternatives has ever been forthcoming. ID "scientists" do not publish in refereed scientific journals, they do not do actual scientific research, they do not actually defend any original ideas that derive from their vacuous theorizing.

There is no "there" there.

Of course we all know why... and in this "we" I am being inclusive of both real scientists and ID proponents. This is because ID is not science at all. It is simply "the wedge strategy" of a program of conservative Christian evangelism... or so admit the founders of the movement.

So go ahead and run away, Southack. It is certainly the only option you have left, given that you have been asked almost a half dozen times to put up or shut up and ungraciously chose neither. You have completely and comprehensively failed to provide any alternative whatsoever to the explanation of ERVs and their proof of common ancestry among the primates contained in the paper that inspired this thread.

Your at this point pathetic appeal to "logic" founders on the rocks of evidence. A syllogism can be as logical as all get out, and still be factually false. This is why we do not reason from a vacuum... we reason from the evidence.

By this "we" however, I do not include you and your brethren among the ID cult. I mean only real scientists.

Have a really nice day.

[Southack]

"And your “what part of DNA is neither a sugar or a base” is just idiotic. We are not arguing over what DNA is made of, just what the genetic code is and how much DNA can be translated using the “code” into an amino acid sequence." - allmendream

DNA is comprised of sugars and bases. The bases are all codons; DNA data or code. Data is processed. Code instructs the processing.

You are arguing that there is something else to DNA besides sugars and bases; that some part of DNA is niether code nor data.

[allmendream]

Wow are you ever confused.

All DNA bases are not codons. A “codon” is three RNA bases that CODE for a specific amino acid in the context of a ribosome.

I am not arguing that DNA is anything other than what it is, a long molecular polymer of sugars and bases. That is your own delusion that somehow by saying that all DNA is not a genetic code that SOMEHOW I am arguing about the molecular structure of DNA. That is idiotic and delusional.

A code in language a series of symbols that, using a code “key” can be translated into a different series of symbols that convey meaning.

The DNA in genes (less than 5% of the genome) contains a series of DNA bases organized by threes into “codons”, can be translated by the molecular “key” of a ribosome into sequence of amino acids, the “meaning” of which is to make a functional macro-molecule.

As such there is nothing inherent in the molecular structure of DNA, the bases or sugars, that makes this a code. All bases or sugars are not codes, so why the fixation that if I deny that all DNA contains information translatable through the genetic code that somehow I am denying that DNA is made up of bases and sugars? Obviously you are as unfamiliar with basic logic as you are with basic biology.

The vast majority of our DNA is NOT made up of “genetic code” in that the DNA is NOT organized into codons that specify a specific functional amino acid sequence.

[Southack]

"The vast majority of our DNA is NOT made up of “genetic code” in that the DNA is NOT organized into codons that specify a specific functional amino acid sequence." - allmendream

Too limited. All of the ladder-steps in DNA are code or data (leaving only the sugar structural bonds).

You are wanting to pretend that only amino-acid data counts, but genetic code exists that also controls how that data is processed.

[allmendream]

It is not a code.

And certainly not the genetic code.

The genetic code is a specific thing. DNA gets transcribed into mRNA that is fed into a ribosome. The ribosome is like a little enigma machine, a “key” for the code, that translates the sequence of nucleic acids in RNA into the sequence of amino acids in a functional protein.

If you are suggesting that all DNA function is a “code” then that is an incorrect usage of the word code, and has nothing to do with the “genetic code” (genetic = gene = a section of DNA that codes for a specific protein). A transcription factor binding to the promoter region of a gene is no more a “code” than a Phillips head screwdriver fitting a Phillips head screw involves a “code”.

Is your idiotic statement that “all DNA contains genetic code” your ignorant way of suggesting that all DNA has some FUNCTION? (I remind you that not all function is a “code”) That is quite a bit different than saying that all DNA contains the genetic code, but equally as wrong.

[allmendream]

It might help if you had any idea what you were talking about. Here then, for your further education, is the ACTUAL genetic code. Like any code it converts a string of undecipherable information into a useful string of information; in this case a series of nucleic acids that has no meaning outside of the context of the genetic code, into a sequence of amino acids that form a functional protein. D-r-i-n=k-y-o-u-r-o-v-a-l-t-i-n-e. :)

[Southack]

There is 1 codon that codes a starting-signal in a protein, that is the codon for the amino acid Methionine: AUG, and there are 3 codons that give a stop-signal. The nucleotide sequence of bases between the startcodon and the stopcodon is eventually translated into a protein.

What else do you *think* is in DNA?!

[allmendream]

What else is there beside genetic DNA that contains the genetic code?

Well there is the promoter region where transciption factors bind and recruit RNA polymerase to transcribe the gene into mRNA. The promoter region is NOT translatable via the genetic code into a functional amino acid sequence, thus it does not contain the genetic code.

Introns within the mRNA are spliced out. Most introns, if they were left intact within the mRNA, would introduce stop codons or a frame shift mutation that would render the “message” of the mRNA into gibberish. Introns are NOT translatable via the genetic code into a functional amino acid sequence in a protein, and thus it also does not contain the genetic code.

Short repeat DNA does not contain the genetic code.

Telomereic and Centromeric DNA does not contain the genetic code.

In fact the only DNA that DOES contain the genetic code are those DNA sequences in an “open reading frame” that are transcribable into mRNA that is a CODE for the sequence of amino acids that build a functional protein. As such less than 5% of the genome has information via the genetic code.

Do you even begin to see how ludicrous and ignorant and WRONG your statement that ALL DNA has the genetic code is?

Unless you can “translate” that DNA sequence via the genetic code key I provided into an amino acid sequence that forms a functional protein; it cannot be said to contain the genetic code.