What Would You Conclude? (ERVs & Human-Chimpanzee Common Ancestry)

Are ERVs (Endogenous Retroviruses) evidence for evolution that humans and chimpanzees are related and have a common ancestor?  Consider the facts and you decide.

Summary of Facts:

1.  Some viruses (we'll call them ERVs) insert their genetic material into the genomes of organisms in random places and this genetic material can be inherited. [Analogy: Imagine an ERV is like a food stain on a random page of a book]

2.  In humans, there are >100,000 such places in our genome where genetic material from these ERVs has been randomly inserted.  [Analogy: Imagine you get a book that has over 100,000 random stains of different shapes and sizes on different pages]

3.  Over 99.9% of these >100,000 ERVs are also found in the chimpanzee genome in the same, corresponding locations. [Analogy: Imagine a friend gets a copy of the book and when you compare you discover that it, too, has >100,000 random stains, and 99.9% of these stains are in the same, corresponding places as your book]

What Would You Conclude? (What is the best explanation of the facts?)

A.  Independent Ancestry: The human and chimpanzees genomes independently acquired >100,000 bits of viral genetic material in the same corresponding locations by luck. [Analogy: The two books independently acquired almost all of these >100,000 stains in the same places by luck]

B.  Common Ancestry: 99.9% of these >100,000 ERVs are found in the same, corresponding places in the human genome and chimpanzee genome because humans and chimpanzees are related and have a common ancestor that already had 99.9% of these >100,000 ERVs in the places where they're found. [Analogy: The two books have >100,000 food stains nearly all in the same place because they are photocopies of a third book that already had 99.9% of these stains in the locations where they're found]

Personally, I'd have to go with "B. Common Ancestry."  It's the most parsimonious explanation of the facts.  The alternative is simply too improbable to believe, but perhaps others disagree.  Feel free to weigh-in.

(*Note the argument that these ERV similarities in humans and chimpanzees are due to separate creation "according to a common design" doesn't work, because again, it is *foreign* genetic material put into genomes by viruses during viral infections and thus, could not be part of any original creation)

I'm convinced but then I'm one of the converted. I've no doubt that some creationists will try to pick holes in your argument & will never be convinced.

I suspect you're right.  No evidence is ever enough for those who have already predetermined what the answer *must* be.  And this was just the beginning.  ERVs actually provide several layers of evidence.  Here's a good treatment of the subject along with a more in depth version that also counters a number of creationists "arguments."

Endogenous-retroviruses-in-your-genome-show-common-ancestry-with-primates

Three Layers of Endogenous Retroviral Evidence for the Evolution Model

Why should anyone assume it is because they share the same ancestry, you think this can only be the only possible explanation? Design sharing similar features are ruled out automatically as a possibility how? Interesting that you should submit that it is improbable for 'the alternative'; exactly how many alternatives do you believe there are, and how did you do the math?

Excellent questions TMuse.   If you re-read the OP you'll see that common ancestry is not an assumption, but a conclusion that we reason to as the best explanation of the facts. 

Also below, I have copied and pasted my post to you on ERVs that I gave to you in the "Mathematical Challenges" thread.  As you'll remember, my post included some probability calculations for you and also explained why the "design sharing similar features" argument doesn't work and doesn't apply to ERVs (which I, similarly, also explained above in post#2 of this thread).  Below at the end, you'll also see the two links I gave you before that provide even more detail and technical information that should be sufficient to answer any additional questions that you have.  But feel free to let me know if you still have more questions:

https://www.chess.com/clubs/forum/view/mathematical-challenges-to-darwins-theory-of-evolution?page=6#comment-48819734

TruthMuse 

*That article was also but one example of the evidence that humans and other primates share a common ancestor, but it is hardly the only one.  

*A significant amount of additional evidence for human and non-human primate common ancestry also exists, such as the powerful evidence from endogenous retroviruses (ERVs):

(1) We have over 100,000 places in the human genome where ERV genetic material is found--distinctive DNA from different viruses that were inserted into our DNA in quasi-random locations during viral attacks/infections at different times in the past.  All of these ERVs are found in all humans in the same locations of the genome, with only one ERV exception that is not found in all humans (indicating that this one exception became fixed in the human population after humans had already originated as a species)

(2) However, 99.9% of these ERVs are also found in the chimpanzee genome at the same corresponding locations (or "loci")

(3) Each specific type of ERV has on average about 10,000 different locations in the genome where the viral DNA could be inserted, so the odds that a given virus would just so happen by sheer random "dumb" luck to independently insert DNA in the same location in the human genome and separately in the corresponding location in the chimpanzee genome is thus on average 1 chance in 10,000 or 0.01%.  The odds of such a "dumb" luck event happening twice is the probability of the events multipled: 1/(10,000)^2 = 0.00001 x 0.00001 = 0.00000001 or 0.00001%.  The odds, then, of such a freak coincidence occurring 100,000 times is 1/(10,000)^100,000, which is such an immensely improbable occurrence that dwarfs the results of the first study I posted.

(4) In short, it is statistically impossible that the 99.9% ERV correlation between human and chimpanzee genomes is the result of independent occurrence.  Such incredible correspondence only makes sense if chimpanzees and humans inherited these specific ERV insertions from a shared common ancestor.

(5) It also doesn't make sense to argue that all these similarities are just the result of an intelligent designer using a common design, because ERVs comprise distinctive, foreign viral DNA that is inserted during viral infections, and thus, are not part of any original design but would have to come after the fact after any original creation (separate or otherwise) of humans and chimpanzees.

(6) But wait, there's more: rigorous mathematical studies of the mutation rate within these segments of viral DNA allow us to construct timelines of when the different ERVs were inserted and the results are not only NON-random but exhibit hierarchies and nested hierarchies that correspond to phylogenetic evolutionary trees (*where for example, the primates most different from humans show the greatest disparity/genetic divergence while the primates closest to humans--chimpanzees---show the least and often not only have the same ERVs in the same locations in the genome but also the same mutations in the same ERV; again, providing powerful evidence of shared common ancestry.

Here's a good intro to the subject along with a more technical treatment:

Endogenous-retroviruses-in-your-genome-show-common-ancestry-with-primates

Three Layers of Endogenous Retroviral Evidence for the Evolution Model

I fail to see a difference between what is assumed is a factual statement, from one reached by a conclusion. I think that is more like a distinction without a difference, in my opinion. What if our best explanation isn't reflecting reality, wouldn't our then best conclusions lead us down an error-prone path? I have not looked too deep into this yet but will come back after I read it all. Thank you for your time in presenting this.

TMuse wrote:

I fail to see a difference between what is assumed is a factual statement If you're going to claim that the 3 facts aren't true facts, then the burden of proof is on you to demonstrate it.  Can you? from one reached by a conclusion. I think that is more like a distinction without a difference, in my opinion. What if our best explanation isn't reflecting reality, wouldn't our then best conclusions lead us down an error-prone path? "What if's" are hypothetical speculations.  Do you have actual evidence that common ancestry is not the best explanation of the ERVs?  If so, then by all means present it.  If not, then common ancestry remains the best explanation of the evidence.  I have not looked too deep into this yet but will come back after I read it all. Thank you for your time in presenting this Sure, it is an interesting topic.

*Earlier you seemed to suggest that there are other possibe conclusions.  Let's brainstorm all possible conclusions we can come up with to explain >100,000 stains in the same places in two separate books:

A.  The two books independently acquired >100,000 stains in the same places by luck.

B.  One book already had all these stains and the second book is a copy of it, or, similarly, both books are copies of an third book that already had these stains.

C.....?

D.....?

*Any other explanations?  Are we missing anything that can be added to the list of possibilities?

Something I never understood about ERVs.

ERVs are viruses, which insert themselves into the chromosome, right? And act as genes?

My question is about proportion.

Are viruses like thousands of times larger than a gene? Even having their very own complete genome?

To me, this sounds like stuffing a semi-truck into a glove box.

"So, are you discrediting the conclusions because humans drew them, and humans are error-prone because we can’t possibly know the truth about everything?"

I'm not discrediting anything, merely pointing out it is difficult to know anything with certainty. I had three main issues in the lab I worked while troubleshooting a problem; I worked with the mechanical team that kept the equipment up and running within specifications, the class team that wrote the code for the programs, and the engineers that wrote instructions for the experiments. Any issue's root cause could have happened because of hardware or software. Looking at the data, even getting what we would call good results doesn't mean everything is correct! Something still could be going on we are unaware of that is giving us a false impression; if we are not careful, we can also make a lousy foundational assumption.

Certainty in anything is often elusive but we can usually make statements regarding the confidence we have in something being the case.

Imagine reading some text online in which you notice some word is spelt idiosynchratically? For example, a redundant spelling of the word shown is 'shewn'. You might not think much about this until you come across another article months later, in which the (anonymous) author also uses shewn.

Wouldn't you feel justified in suspecting that they both originated from some common source?

Now imagine that there were thousands of such idiosynchratic miss-spellings in both texts. What degree of confidence would you have that both had a common origin? Of course you could never have complete certainty but that needn't stop us placing the needle very close to 100% confidence.

So you don’t trust the results because the scientists could have come up with them erroneously? One can make this argument for pretty much anything scientific. Until you find evidence supporting your statement, the argument is merely an automatic default against any scientific finding.

Thank you for the reply, B Pawn.

@TruthMuse

I feel like @stephen_33 and @PyriteDragon have made valid points but curious to hear your take

I am in the midst of an end of quarter craziness right now, so my responses will be slow. Forgive me for not being swift in my responses. I have not read anything yet.

At the heart of this, in my opinion, is the assumption that there are only two alternative causes that seem a bit overly simplistic to me. A common design could play a factor; adding more to the minimal sample size of choices besides chimpanzee and humans may reveal this isn't as specified as this study suggests as well. If it is or isn't more common among other species, that suggests what?

More to come.

With respect to assumptions, conclusions, and all of the facts in terms we all understand here. I didn't make this up first but I want to use it. When we calculate, creating the perfect plan in a chess game, we do so based upon our conclusions looking at all of the pieces. Then many times, the person we are playing, ruins our perfect plan, by making all the wrong moves. In biology or anything else very vast with causes and effects, all the data isn't always visible to us, or we may not understand something enough. When our perfect plans fail in chess, even with everything right in front of us, I fail to see how we can be really sure about events in the distant past when not everything is clear.