ERV homology argument and comparative genomics

[mark kennedy]

Loundmouth and I had a formal debate that was focused on a very interesting homology argument. ERVs are a significant part of the human genome and the argument LM was making is that the human ERVs are vitually identical to those of Chimpanzees. When taking a closer look at the latest research I found this to be nothing more then yet another failed homology argument.

mark kennedy v. Loudmouth: Do chimps and humans share a common ancestor?

I even had a chance to have a rather brief exchange with LMs source but the discussion quickly dissipated after he started repeating his argument, rather then defending it. Since some time in the 60s evolutionists have made the arguments that 'I can't find any differences' when comparing DNA sequences of Chimpanzees and Humans. The same argument is being made with regards to ERVs except that now, we know that there are hundreds of millions of differences in the respective genomes known as indels (insertions and deletions) which are really just huge sequences that are different.

By far, the biggest and most significant difference regarding Human vs. Chimpanzee ERVs are the ERV class I. These PTERVs (Pan Troglodyte ERVs) is the single largest and most abundant class of ERVs in the Chimpanzee genome. There is one problem with it, there are virtually none in the human genome.

If the proposed null hypothesis for genetics is valid then common descent has been falsified.

this process is rare and fairly random, so finding retrogenes in identical chromosomal positions of two different species indicates common ancestry. (Prediction 4.5: Molecular evidence - Endogenous retroviruses)​

(Initial Sequence of the Chimpanzee Genome, Nature 2005)​

Ok, fair enough but does this proposal allow for the inverse logic as a null hypothesis? With more than 100 members, CERV 1/PTERV1 is one of the most abundant families of endogenous retroviruses in the chimpanzee genome. (Genome Biol. 2006). They can be found in African great apes but not in humans. What is more the ERV virus is nearly extinct in the human genome with only a couple that actually work. The only thing that ERVs are proof of is the lengths evolutionists will go to to conflate and confuse the evidence.

Look at the comparison of the ERV class I and tell me something. If commonality is proof for common descent, are differences evidence for creation?

I have brought this up a dozen times and evolutionists simply beg the question of proof. They insist that since they are there it must be a small subset of ERVs but this is completely contrary to the facts. It was not predicted for by the common descent model yet the model is never questioned:

Against this background, it was surprising to find that the chimpanzee genome has two active retroviral elements (PtERV1 and PtERV2) that are unlike any older elements in either genome; these must have been introduced by infection of the chimpanzee germ line. The smaller family (PtERV2) has only a few dozen copies, which nonetheless represent multiple (approx5–8) invasions, because the sequence differences among reconstructed subfamilies are too great (approx8%) to have arisen by mutation since divergence from human. (Initial Sequence of the Chimpanzee Genome, Nature 2005)​

The best way to win an argument with an evolutionist is to learn the actual facts. Evolutionists did a major victory dance when the ERV evidence first started being explored and they did the same thing when comparative genomics was on the rise. The commonality has been grossly overstated and when confronted with these facts evolutionists become indignant and repeat the same tired homology arguments.

There is no null hypothesis for Darwinism, it never allows for or even considers, the inverse logic. When you insist that the evidence is unconvincing your being incredulous which is an academically polite way of saying your ignorant. Either you assume universal common descent or you are assumed to be ignorant. That's not science, it's supposition.

I know exactly what to expect from this thread, there will be a poster who knows nothing of the material and will make personal attacks on me throughout the discussion. Evolutionists love to have these guys around so that when the benign scientist type makes his or her appearance they can blind side the creationist with someone else keeping them busy.

I'm not posting this to invite an endless string of biting personal remarks, nor will I treat them as anything else. LM wanted a chance to go over the material again and answer what I consider a slam dunk refutation of yet another deeply flawed homology argument. I post mostly in the Origins Theology forums because I really don't have time for a protracted debate that is going to go in circles anyway, focused almost exclusively on fallacious arguments. I do like to make exceptions when I find a topic that interests me.

One very important question needs to be addressed or the thread will become yet another personal attack, doomed to be buried in the stacks. Is the inverse logic to an homology argument intuitively obvious? More to the point, if things in common are valid arguments for common descent then are differences valid arguments for special, independent creation?

I'll leave you all to your own devices to address the matter at hand and I'll check back from time to time to see if anything substantive emerges.

Grace and peace,
Mark

 

[NailsII]

Look at the comparison of the ERV class I and tell me something. If commonality is proof for common descent, are differences evidence for creation?

If we were created then I wouldn't expect to see the ERV pattern that we do see - because if we were created, there would be no pattern in the ERVs.
Specifically, that there are similarities (or homologies if you prefer) in the non-coding sequences of Pans and Homo DNA.
If we didn't share a commonancestor with chimps and bonobos, you would expect to see virtually no common elements. This is a world apart from what we observe, which is similar sequences with some genetic degredation due to mutation etc.

If you are correct with your assertion that evolution has been falsified by DNA evidence, then DNA fingerprinting is also useless and has no place in the criminal justice system.

Paternity tests based on DNA would also be less than satisfactory.

That is the whole point.

 

[mark kennedy]

If we were created then I wouldn't expect to see the ERV pattern that we do see - because if we were created, there would be no pattern in the ERVs.

What pattern, the largest and most abundant family of ERVs in the Chimpanzee genome being absent in the Human genome?

Specifically, that there are similarities (or homologies if you prefer) in the non-coding sequences of Pans and Homo DNA.
If we didn't share a commonancestor with chimps and bonobos, you would expect to see virtually no common elements. This is a world apart from what we observe, which is similar sequences with some genetic degredation due to mutation etc.

Which loosely translated means you won't talk about the obvious differences. If it's exactly what was expected then why were they so surprised by PTERVs? Why would there be no trace in the human genome and such an abundance in African apes?

If you are correct with your assertion that evolution has been falsified by DNA evidence, then DNA fingerprinting is also useless and has no place in the criminal justice system.

When did I ever say 'evolution'? That's absurd! I said common descent, try to get it right next time. Now if you want to define 'evolution' as common descent you have abandoned natural science in favor of the a priori assumption of universal common descent you have to identify the transcendent principle and define 'evolution'.

If you did you would be the first.

Paternity tests based on DNA would also be less than satisfactory

.

What do you think they compare in paternity tests and what does that have to do with ERVs?

That is the whole point.

Then you don't have a point. You claim it's exactly what you would expect to see without identifying a single prediction regarding ERVs. You have further assumed that 8% of the human genome is the result of gernline invasions. You have also failed to answer the central question.

If differences are a valid evidence of common decent are differences valid evidence for creation?

Just answer the first question, try reading the argument and the requisite research literature and stop begging the question of proof on your hands and knees.

Have a nice day?
Mark

 

[USincognito]

The best way to win an argument with an evolutionist is to learn the actual facts.

Is the second best way to start the same thread over and over as if the discussion hadn't happened before?

 

[mark kennedy]

Is the second best way to start the same thread over and over as if the discussion hadn't happened before?

You never read the OP did you? Just like you probably didn't read any of the requisite scientific literature. LM asked me to post this because when he wanted to discuss a post I made in the Origins Theology forum. Your not going to answer the question either because you are not required to acknowledge the inverse logic, have a null hypothesis or even read what your responding to. All you have to do is post pedantic one liners.

Yea, we've discussed it all before, LM couldn't get his facts straight and not one of you knew enough to help him out. Yea, it's going to happen again and your going to throw out the first fallacious attack just to get the ball rolling. That's nice....

Have a nice day
Mark

 

[Promethean]

If you are correct with your assertion that evolution has been falsified by DNA evidence, then DNA fingerprinting is also useless and has no place in the criminal justice system.

Paternity tests based on DNA would also be less than satisfactory.

That is the whole point.

Indeed. Perhaps this is a crafty attempt of creationists trying to avoid paying child support.

 

[USincognito]

You never read the OP did you?

I read it, well scan it these days, every time you post it.

 

[Guy1]

So far your point seems to be "There are differences- therefore goddidit." I won't comment because, quite frankly, I'm not yet qualified to do so. But if you don't mind my asking; what are your qualifications?

 

[USincognito]

The problem with Mark's argument is that he considers

Homo
ACGTERV1ACGTERV2ACGTACGTACGT

Pan
ACGTERV1ACGTERV2ACGTACGTACGT

Gorilla
ACGTERV1ACGTACGTACGTACGT

to be the same as

Homo
ACGTERV3ACGTACGTACGTACGT

Pan
ACGTACGTACGTACGTERV4ACGT

ACGTACGTERV4ACGTACGTACGT

He can't seem to grasp how important orthologous locations are.

 

[Blayz]

The best way to win an argument with an evolutionist is to learn the actual facts.

Yeah facts collected by evolutionists.

Go get your own facts Mark. Stop misunderstanding ours.

At the very least, please please please learn what "null hypothesis" means.

 

[NailsII]

What pattern, the largest and most abundant family of ERVs in the Chimpanzee genome being absent in the Human genome?

After an estimated 6 million years of genetic seperation there are going to be differences - the entire structure of our Chromosome 2 is witness to that fact (which is a fact that I have never lnown a creationist to have an answer for).
Based on this one observtion, are you suggesting that the thousands of other ERVs found in the Pans & Homo genome are irrelevant?

Which loosely translated means you won't talk about the obvious differences. If it's exactly what was expected then why were they so surprised by PTERVs? Why would there be no trace in the human genome and such an abundance in African apes?

I think you have misunderstood what I was trying to say, so I will try to clarify.
If evolution is true, and we share a common ancestor with chimps, then we would expect to find genetic similarities between us - and we do.
We share around 95-98% of our genome with chimps.
Based on this, you would also expect a non-coding gene sequence, which can mutate randomly with no survival risk to the individual, to vary throughout species according to the length of time they have been seperated genetically.
ERVs are a measure of this, but it also works for functioning genes but they tend to be more highly conserved and the rate of change differs from gene to gene.
Specific ERVs such as Pan troglodytes Endogenous Retrovirus-1 may not be directly predicted and may be described as a suprise when found, this does not mean that is is counter to evolutionary theory.
However, the key point that you seem to have missed is that if there is a whole batch of ERVs in chimps and not in humans then we need an explanation. Either humans have somehow lost these genes (which seems unlikely) or the retorviral insertion happened after the two lineages split.

I would be happy to talk to yuou about the differences, however this would require a lot of research on my part as it is out of my field.
I am a biochemist by definition, but I work in food science, and I have no expertise in DNA analysis.

When did I ever say 'evolution'? That's absurd! I said common descent, try to get it right next time. Now if you want to define 'evolution' as common descent you have abandoned natural science in favor of the a priori assumption of universal common descent you have to identify the transcendent principle and define 'evolution'.

If you did you would be the first.

Evolution is the change in allele frequency in a given population over time.
Common descent is the theory that all life on this planet shares a single, common ancestor.
I don't see a distinction between common descent and universal common descent, but you obviously do.
As common descent requires evolution, I don't think I have committed a sin by interchanging these terms - but you obviously disagree.

What do you think they compare in paternity tests and what does that have to do with ERVs?

DNA fingerprinting was done by using an enzyme to break DNA chains at a specific point, and this was then subjected to gel electrophoresis to seprate out the different strnads - and gave the 'bar code' style diagram that we are all failiar with.
More sophisticated techniques are used nowadays, but the basic principle is the same.
The theory behind this technique is that the closer related yo are to someone, the more homologous your DNA sequences ill be. This is specific to the non-coding sequences, as all humans will share around 99% of their DNA.
Can you see why this is analagous to ERVs?

Then you don't have a point. You claim it's exactly what you would expect to see without identifying a single prediction regarding ERVs. You have further assumed that 8% of the human genome is the result of gernline invasions. You have also failed to answer the central question.

I'm sorry, but there is no assumption that 8% of the human genome is the result of an ancient RNA virus reverse-transcripting its genome into our germ cells DNA - this is an observable fact - otherwise there would be no discussion on ERV's, right?

If differences are a valid evidence of common decent are differences valid evidence for creation?

What would you expect to see if creation were true?
Remember how you looked at the scientific position - you formulated a hypothesis, and a null hypothesis, and lookek at the evidence.
For creation science to be taken seriously, this is the thing it must start doing.
you have a fantastic opportunity to start here, I think you are a well read and intelligent human being, so please feel free to have a go.

Just answer the first question, try reading the argument and the requisite research literature and stop begging the question of proof on your hands and knees.

I don't need to be on my hands and knees, the proof doesn't require begging for as it is regularly read in scientific literature, and if you posed a serious question I would be more than willing to answer it.

You are a clever man, but I think you have made a few mistakes when looking at the evidence due to your a priori assumptions of a supernatural deity being involved.
Nothing personal, I just think that you are trying to overcomplicate the position.

DNa differences between populations are a measure of their separation, ERVs are just specifics which tell us about our evolutionary history.
Until a better explanation comes along, I see no reason to think that this is anything but an observable fact.

 

[mark kennedy]

So far your point seems to be "There are differences- therefore goddidit." I won't comment because, quite frankly, I'm not yet qualified to do so. But if you don't mind my asking; what are your qualifications?

Oh ok, so there are things in common so 'goddidn'tdoit' is a much better explanation.

 

[mark kennedy]

The problem with Mark's argument is that he considers

Homo
ACGTACGTERV2ACGTACGTACGT

Pan
ACGTPtERVACGTERV2ACGTACGTACGT

Gorilla
ACGTPtERVACGTACGTACGTACGT

That is how the facts line up

to be the same as

Homo
ACGTERV3ACGTACGTACGTACGT

Pan
ACGTACGTACGTACGTERV4ACGT

ACGTACGTERV4ACGTACGTACGT

He can't seem to grasp how important orthologous locations are.

You don't seem to appreciate the inverse logic of your argument.

 

[Elendur]

Oh ok, so there are things in common so 'goddidn'tdoit' is a much better explanation.

Why force an explanation? It's honest, and valid, to answer "I don't know" if there's insufficient evidence.

Edit: Whoops, wrong thread sorry about that.

Edit 2: Meh, why not use space if I wasted it:

More to the point, if things in common are valid arguments for common descent then are differences valid arguments for special, independent creation?

I think it's an oversimplification to say that, it would be evidence against common descent but not necessarily evidence for "special, independent creation".
That would entirely depend what you would expect to see if that hypothesis was correct (you know, every hypothesis/theory has to stand on its own).

 

[USincognito]

You don't seem to appreciate the inverse logic of your argument.

Really? That's all you've got to me deflating the balloon of your entire "argument"?

I point out that you simply don't understand why orthology of ERVs is important and all you can do is still pathetically appeal to your false and misapplied "null hypothesis" argument?

Mark, the game has been up for years now. The fact that there are ERVs found in Chimps and Gorillas, but not in humans is not the problem. As my simplistic graphic pointed out, they're not found in orthologous regions. The problem for Creationists is explaining why ERVs are found in orthologous regions in humans and chimps, and then in humans chimps and gorillas and then in humans, chimps, gorillas, orangutans, etc. etc. Why do the orthologous ERVs form a nested hierarchy?

That's what you keep ignoring as if it hasn't been pointed out to you hundreds of times over the last 5 years.

 

[mark kennedy]

After an estimated 6 million years of genetic seperation there are going to be differences - the entire structure of our Chromosome 2 is witness to that fact (which is a fact that I have never lnown a creationist to have an answer for).

How do you know it was 6 million years ago? Where are the chimpanzee ancestors in the fossil record since the split? I have never seen an evolutionist even try a substantive answer for that one.

Based on this one observtion, are you suggesting that the thousands of other ERVs found in the Pans & Homo genome are irrelevant?

Nonsense.

I think you have misunderstood what I was trying to say, so I will try to clarify.

I understood fine, I think your the one who is misunderstanding.

If evolution is true,

Of course you mean common descent.

and we share a common ancestor with chimps, then we would expect to find genetic similarities between us - and we do.

So we expect what we have in common with Chimpanzees, but the differences we explain away.

We share around 95-98% of our genome with chimps.

The commonality of the DNA is 96% at best and that does not take into account chromosomal rearrangements.

Based on this, you would also expect a non-coding gene sequence, which can mutate randomly with no survival risk to the individual, to vary throughout species according to the length of time they have been seperated genetically.

Then explain this, 'PtERV1-like elements are present in the rhesus monkey, olive baboon and African great apes but not in human, orang-utan or gibbon'

ERVs are a measure of this, but it also works for functioning genes but they tend to be more highly conserved and the rate of change differs from gene to gene.
Specific ERVs such as Pan troglodytes Endogenous Retrovirus-1 may not be directly predicted and may be described as a suprise when found, this does not mean that is is counter to evolutionary theory.

What did I tell you? I'm not arguing against evolutionary theory, just common descent. That's a key point you missed.

However, the key point that you seem to have missed is that if there is a whole batch of ERVs in chimps and not in humans then we need an explanation. Either humans have somehow lost these genes (which seems unlikely) or the retorviral insertion happened after the two lineages split.

What if the Gorilla has more in common genetically with the Chimpanzee then Humans? How does that fit into your theory.

I would be happy to talk to yuou about the differences, however this would require a lot of research on my part as it is out of my field.
I am a biochemist by definition, but I work in food science, and I have no expertise in DNA analysis.

I would be delighted to learn more about biochemistry. What kind of online reading would you recommend?

Evolution is the change in allele frequency in a given population over time.

Thank you, notice how that is different from common ancestry?

Common descent is the theory that all life on this planet shares a single, common ancestor.

So you are aware of it and BTW, evolution isn't a theory, it's a phenomenon. At least the way you just defined it. Common descent isn't a theory either since there is no null hypothesis. It's really just a model the data is organized within.

I don't see a distinction between common descent and universal common descent, but you obviously do.

They differ only with regard to scope. Universal common descent is transcendent, common descent is species, genus...etc, specific.

As common descent requires evolution, I don't think I have committed a sin by interchanging these terms - but you obviously disagree.

Not a sin, an error. There's a big moral difference.

DNA fingerprinting was done by using an enzyme to break DNA chains at a specific point, and this was then subjected to gel electrophoresis to seprate out the different strnads - and gave the 'bar code' style diagram that we are all failiar with.
More sophisticated techniques are used nowadays, but the basic principle is the same.
The theory behind this technique is that the closer related yo are to someone, the more homologous your DNA sequences ill be. This is specific to the non-coding sequences, as all humans will share around 99% of their DNA.
Can you see why this is analagous to ERVs?

Sure, it makes a lot of since to use ERVs are markers.

I'm sorry, but there is no assumption that 8% of the human genome is the result of an ancient RNA virus reverse-transcripting its genome into our germ cells DNA - this is an observable fact - otherwise there would be no discussion on ERV's, right?

ERVs being added to the germline is observable, that doesn't represent undeniable proof that 8% of the human genome is the result of them.

What would you expect to see if creation were true?

The same phenomenon repeated throughout human history. If you mean the biochemistry then I would expect the mutation rate to be within a safe parameter to explain the differences.

Remember how you looked at the scientific position - you formulated a hypothesis, and a null hypothesis, and lookek at the evidence.

Actually Darwin proposed a null hypothesis for natural selection, remember what it was?

For creation science to be taken seriously, this is the thing it must start doing.

I have and I do.

you have a fantastic opportunity to start here, I think you are a well read and intelligent human being, so please feel free to have a go.
I don't need to be on my hands and knees, the proof doesn't require begging for as it is regularly read in scientific literature, and if you posed a serious question I would be more than willing to answer it.

I could come up with any number of hypothesis, the formal way scientists do inductive science seems to suggest them. There's one problem with that though:

"The number of rational hypotheses that can explain any given phenomenon is infinite."...The law is completely nihilistic. It is a catastrophic logical disproof of the general validity of all scientific method!. About this Einstein had said, "Evolution has shown that at any given moment out of all conceivable constructions a single one has always proved itself absolutely superior to the rest," ... to Phædrus... To state that would annihilate the most basic presumption of all science! Through...theories and hypotheses, it is science itself that is leading mankind from single absolute truths to multiple, indeterminate, relative ones...Scientifically produced antiscience...chaos.

(Zen and the Art of Motorcycle Maintanance)​

You are a clever man, but I think you have made a few mistakes when looking at the evidence due to your a priori assumptions of a supernatural deity being involved.

Obviously I consider rejecting God's supernatural activities in creation a priori a mistake as well.

Nothing personal, I just think that you are trying to overcomplicate the position.

No, I'm just waiting on LM to make his comments. He is the one who asked me to post this here. We have discussed this previously but he can't post to the Origins Theology forum.

DNa differences between populations are a measure of their separation, ERVs are just specifics which tell us about our evolutionary history.
Until a better explanation comes along, I see no reason to think that this is anything but an observable fact.

So common descent must be assumed and the inverse logic is never allowed. Got it.

 

[mark kennedy]

Why force an explanation? It's honest, and valid, to answer "I don't know" if there's insufficient evidence.

How about you follow the evidence where it leads?

I think it's an oversimplification to say that, it would be evidence against common descent but not necessarily evidence for "special, independent creation".

What if there was an organ that had neither the time nor the means to have evolved?

That would entirely depend what you would expect to see if that hypothesis was correct (you know, every hypothesis/theory has to stand on its own).

A valid hypothesis would have to be.

 

[Guy1]

Oh ok, so there are things in common so 'goddidn'tdoit' is a much better explanation.

That's a strawman you've cooked up in your head. Not even an atheist such as myself is saying that. Theistic evolutionists believe the entire process is being guided by a higher power. This is, of course, an absurd concept to me; because it's indistinguishable from a non-guided evolutionary process.

In summation: My position isn't "giddidn'tdoit." It's "I struggle to think of anything that could be more irrelevant." That's my position on theism in general actually. If it's indistinguishable from any number of much more reasonable, substantiated answers, I don't see why I or anyone else should care.

 

[Elendur]

How about you follow the evidence where it leads?

That's what I'm trying to do but honestly, the natural world is less interesting than the mathematical.

What if there was an organ that had neither the time nor the means to have evolved?

That would be interesting, if it existed I would say that it's a contender for falsifying the common ancestor theory. I would have to add that to show that it had neither the time nor the means to evolve would be hard though.

 

[metherion]

Actually, since chimpanzee fossils have been brought up, here's something for you:
First Chimp Fossils Found; Humans Were Neighbors

Relevant quote:

Modern chimpanzees live primarily in forests in western Africa, far from the arid Rift Valley site where these first fossils emerged.

But the valley's geology, along with the presence of water-loving species like the hippopotamus and the crocodile, suggest the fossil chimp and hominins experienced a lush, more wooded environment than what's present today.

While stories about new discoveries might make fossils seem routine for those who know how to look for them, fossil finds are actually quite rare.

Most animal bones aren't preserved when the creature dies, McBrearty says. The animal has to be buried and its bones replaced by minerals in order to form fossils.

Forest creatures of any species, including chimpanzees, are especially tough to track down in the fossil record. When a forest dweller dies, scavengers and invertebrates quickly step in. Within weeks the entire animal often disappears.

Forest soils are often acidic, making quick work of remains that haven't been destroyed by other creatures.

In contrast, the Rift Valley in eastern Africa provides suitable conditions for preserving fossils, McBrearty says. Here, lakes and streams deposit sediment that erodes off the highlands, burying potential fossils in the valley below.

The valley is also prone to earthquakes that expose the fossils for researchers on the hunt.

Also,

or that many of the apes lived in wooded habitats where their remains were less likely to fossilize in acidic soils.

from New Ape Fossils Found in Africa - ScienceNOW

And then

Like coelacanths, chimps have had few opportunities to enter the fossil record: they have a limited geographic range, and they live in tropical forests, where the acidic soil usually destroys bones within a few years.

from Ghost lineages

So, right there, three separate sites giving the same explanation.

Makes a lot more sense than there being some international evolutionist conspiracy to relabel all chimpanzee bones as human fossils in all museums, dig sites, et cetera.

Metherion