Lines of Evidence ( Part 1 : ERVs )

[SteveB28]

I'm an average person. I "get" evolution. I may not understand all of the minutia, and I couldn't tell you how, for example, genome sequencing works, but I understand, at a basic level, how it works, and how we know it worked like that. Because, honestly? Most of the evidence is pretty easy to understand.

Animals reproduce with slight modifications. Over time, these modifications can add up until the animal has changed phenomenally. This is really basic, and the evidence for descent with modification can be seen every time you look at a family photo. It is therefore reasonable to assume that at some point, we shared a common ancestor. However, understandably, some people don't consider this particularly convincing, and demand more evidence.

"Viruses can insert themselves into replicating DNA and thus become part of our genetic code. We can find many insertion sites that are the same between us and chimpanzees, and if we compare insertion sites among all currently living animals, we can find degrees of similarity that match up to what the fossil record would tell us about the tree of life."

That's a bit difficult to wrap your head around, but by no means impossible. The problem is, people who reject evolution keep on saying "that's not good enough, that's not good enough" until the strongest evidence - stuff like ERVs or genetic similarities or the transposons in chromosome 2 - show up, they say "I don't get it, therefore it doesn't count". I'm sorry, but sometimes, things are a little complicated.

Well said young Cadet! Couldn't agree more - and I think it a cowardly retreat from reality when people throw up these pathetic arguments from ignorance.

I did the bulk of my studies in biology more than 60 years ago, yet I find the basic tenets of ERV insertion relatively easy to follow - and contrary to the other 'old bloke' in this discussion, the mathematics are child's play.

- these ancient viruses inserted themselves randomly, or near enough to it.

- there are billions of locations.

- the chances that just one or two would lodge in the same locations over different species is highly unlikely: the chance that thousands would do so coincidentally is almost impossible.

- this pattern is more closely aligned between closely related species.

- ergo, it forms crushingly heavy evidence in favour of common ancestry.

What is so difficult to comprehend?

 

[lewiscalledhimmaster]

Understanding Evolution is easy, understanding the evidence which relates to evolution can be complicated.

'....accept evolution on faith, as they will never understand the science behind it. ....' OWG
'....'sell' the theory knowing that the 'proof' is unintelligible to the average person. ....' OWG
'Understanding evolution isn't a high priority for most people.' OWG

Perhaps I can recommend a tutor?

 

[The Cadet]

And, speaking of which, if I may...

The average person has to accept evolution on faith, as they will never understand the science behind it. How do scientists feel about having to 'sell' the theory knowing that the 'proof' is unintelligible to the average person.

Question. If your doctor tells you "this treatment will help clear up your eczema," do you consider it faith to take that medicine? What if you ask how it works, and he offers you some long, complex spiel about non-steroidal anti-inflammatory drugs, protein receptors, and all kinds of other things you know nothing about - is it his fault that you know nothing about this?

Obviously not. We turn to experts to help explain the things we don't know, and it's not faith when we don't understand what they're saying. Many things in science are phenomenally complex. Your doctor spent 8+ years in med school, plus another 5 years in postgraduate studying to become a practitioner. Do you really think he can boil down his knowledge so easily to someone who just casually walks in and wants to know how it works? This stuff (wow, your profanity filter is possibly the most obnoxious I have ever seen) is difficult and takes real effort. It's not "faith" when we put our trust in legitimate scientific authorities to explain how the world works. It's not their fault when we don't put in the effort needed to understand all of the evidence in the field - especially when, like in the case of evolution, it actually isn't that difficult to wrap your head around.

 

[OldWiseGuy]

I'm an average person. I "get" evolution. I may not understand all of the minutia, and I couldn't tell you how, for example, genome sequencing works, but I understand, at a basic level, how it works, and how we know it worked like that. Because, honestly? Most of the evidence is pretty easy to understand.

So there's lots that you don't understand.

Animals reproduce with slight modifications. Over time, these modifications can add up until the animal has changed phenomenally. This is really basic, and the evidence for descent with modification can be seen every time you look at a family photo. It is therefore reasonable to assume that at some point, we shared a common ancestor. However, understandably, some people don't consider this particularly convincing, and demand more evidence.

When I look at family photos I see similarities, not "phenomenal changes."

"Viruses can insert themselves into replicating DNA and thus become part of our genetic code. We can find many insertion sites that are the same between us and chimpanzees, and if we compare insertion sites among all currently living animals, we can find degrees of similarity that match up to what the fossil record would tell us about the tree of life."

All this tells me is the God made living creatures out of pretty much the same stuff.

That's a bit difficult to wrap your head around, but by no means impossible. The problem is, people who reject evolution keep on saying "that's not good enough, that's not good enough" until the strongest evidence - stuff like ERVs or genetic similarities or the transposons in chromosome 2 - show up, they say "I don't get it, therefore it doesn't count". I'm sorry, but sometimes, things are a little complicated.

I understand (most of) what science has discovered. I just don't accept that it is evidence against special creation.

And what do you mean by the term "stuff"?

 

[OldWiseGuy]

And, speaking of which, if I may...



Question. If your doctor tells you "this treatment will help clear up your eczema," do you consider it faith to take that medicine? What if you ask how it works, and he offers you some long, complex spiel about non-steroidal anti-inflammatory drugs, protein receptors, and all kinds of other things you know nothing about - is it his fault that you know nothing about this?

I agree with and accept this as valid science, but not a case for evolution.

Obviously not. We turn to experts to help explain the things we don't know, and it's not faith when we don't understand what they're saying. Many things in science are phenomenally complex. Your doctor spent 8+ years in med school, plus another 5 years in postgraduate studying to become a practitioner. Do you really think he can boil down his knowledge so easily to someone who just casually walks in and wants to know how it works? This stuff (wow, your profanity filter is possibly the most obnoxious I have ever seen) is difficult and takes real effort. It's not "faith" when we put our trust in legitimate scientific authorities to explain how the world works. It's not their fault when we don't put in the effort needed to understand all of the evidence in the field - especially when, like in the case of evolution, it actually isn't that difficult to wrap your head around.

Evolutionists don't answer my questions. I ask for the time and they tell me the weather. How is one to learn?

 

[Subduction Zone]

Well said young Cadet! Couldn't agree more - and I think it a cowardly retreat from reality when people throw up these pathetic arguments from ignorance.

I did the bulk of my studies in biology more than 60 years ago, yet I find the basic tenets of ERV insertion relatively easy to follow - and contrary to the other 'old bloke' in this discussion, the mathematics are child's play.

- these ancient viruses inserted themselves randomly, or near enough to it.

- there are billions of locations.

- the chances that just one or two would lodge in the same locations over different species is highly unlikely: the chance that thousands would do so coincidentally is almost impossible.

- this pattern is more closely aligned between closely related species.

- ergo, it forms crushingly heavy evidence in favour of common ancestry.

What is so difficult to comprehend?

And one thing that I like about ERV's is that they give the evolution side a valid "odds argument". When ever I see a creationist odd's argument the way to refute it is to show that their basic assumptions are wrong. Once you do that it does not matter how good their math is. At that point they are already at the stage of GIGO.

On the other hand creationists have not been able to refute ERV arguments. Not only do they "look like viruses" to the point where they are obvious to virologists. At least one example of a recent one has been "revived". And we can shown that they do attach randomly and that the same viruses, except for expected mutations, can be found in equivalent positions in the genome of different species. It is the slam dunk for evolution that creationists keep demanding. Yet of course they still reject it. In fact one cannot be a creationist without eventually denying all science.

 

[OldWiseGuy]

".........., understanding the evidence which relates to evolution can be complicated."

Now we're getting somewhere.

 

[The Cadet]

<this was an empty field>

I feel the need to point out that when you quote me like that and insert your comments that way, it makes it kind of a huge pain in the tuchus to respond.

Anyways. Yes, there's lots I don't know. There's a reason that evolutionary biology is essentially its own discipline - the amount of evidence is staggering, and a lot of it is phenomenally complex. The deeper you go into the rabbit-hole, the harder it is to understand. As C0nc0rdance so famously put it:

"Ask a college freshman what a gene is and you'll get a straightforward, 10-second answer. Ask a grad student and they might need 10 minutes. Ask a professor, he might need 45 minutes, a cup of coffee, and a research grant."

The actual discovery of endogenous retroviruses, for example, is beyond me. I have no idea how they search for those in the genome. However, I accept that they can and do based on the evidence available in the peer-reviewed literature. What's more, I know that if I spent the time and energy to look, I could find out. That's the great thing about science.

I personally find the evidence which I do understand highly convincing. DonExodus2 lays it out some of it really impressively in this video, and there are many like it on his channel and around youtube.

And yes, none of it is good evidence against special creation. This is because special creation is unfalsifiable. It doesn't matter what evidence arises, the supernatural cause can always just have made it that way. It's a patently unscientific theory that offers no method of proving it right or wrong.

God made all the stuff more or less the same? Well why did he make certain things more similar to others, and why does this match perfectly with the phylogenetic tree of life that the fossil evidence provides? "Because he made it that way."
Okay, but if God made all the stuff more or less the same, why do some genetically divergent species have incredibly similar structures with fundamentally different genetics (a great example of this is bacterial chemotaxis)? "Because he made it that way."
And if this creator is an all-powerful God, why would he make such obvious engineering mistakes like the Laryngeal nerve of the giraffe or the human blind spot? And if he is the God of the bible, a benevolent creator, why would he create something like HIV or Bubonic Plague? "God works in mysterious ways."

There is no rhyme or reason; regardless of how something actually works, "God just did it that way because of reasons sufficient to him" answers all questions. It also has the side-effect of offering absolutely no explanatory or predictive power ("god did it" neither offers us any real insight into how the world works nor gives us the ability to predict things like the Tiktaalik discovery), which makes it really quite useless.

As for looking at family photos and seeing only minor differences, yeah. Genetic change over a single generation is minor. However, over time, these changes can add up immensely. Thunderf00t may have gone off the deep end recently, but he did produce one of the most brilliant explanations of the micro/macroevolution issue I have ever seen (version 2.0 and the remix, while lacking the brevity of the linked video, go into a lot more detail about it).

 

[sfs]

Most people should be able to grasp the main concepts of evolution and important pieces of evidence with a little work. Assuming they want to grasp them, that is. The math in population genetics can get a little sophisticated (and sometimes quite sophisticated -- is everyone here up on Müntz-Szasz theory?), but you don't have to understand that for most purposes.

 

[The Cadet]

Most people should be able to grasp the main concepts of evolution and important pieces of evidence with a little work. Assuming they want to grasp them, that is. The math in population genetics can get a little sophisticated (and sometimes quite sophisticated -- is everyone here up on Müntz-Szasz theory?), but you don't have to understand that for most purposes.

AUGH! MATH AND PROBABILITY! GET IT OFF ME! GET IT OFF ME!!!

 

[OldWiseGuy]

Most people should be able to grasp the main concepts of evolution and important pieces of evidence with a little work. Assuming they want to grasp them, that is. The math in population genetics can get a little sophisticated (and sometimes quite sophisticated -- is everyone here up on Müntz-Szasz theory?), but you don't have to understand that for most purposes.

I like this.

 

[OldWiseGuy]

And if this creator is an all-powerful God, why would he make such obvious engineering mistakes like the Laryngeal nerve of the giraffe or the human blind spot? And if he is the God of the bible, a benevolent creator, why would he create something like HIV or Bubonic Plague? "God works in mysterious ways."

Has anyone shortened this nerve and studied the results? Does anyone know they have a "blind spot"? I didn't know til I read it somewhere, and I had a dickens of a time finding it. In the end I concluded that it was meaningless. Disease is part of this 'planet of death' the God put us on. Also diseases teach us certain lessons regarding health, sanitation, etc. "A hard lesson is a good lesson."

 

[Justatruthseeker]

I'm an average person. I "get" evolution. I may not understand all of the minutia, and I couldn't tell you how, for example, genome sequencing works, but I understand, at a basic level, how it works, and how we know it worked like that. Because, honestly? Most of the evidence is pretty easy to understand.

Animals reproduce with slight modifications. Over time, these modifications can add up until the animal has changed phenomenally. This is really basic, and the evidence for descent with modification can be seen every time you look at a family photo. It is therefore reasonable to assume that at some point, we shared a common ancestor. However, understandably, some people don't consider this particularly convincing, and demand more evidence.

Except that is not what we observe in the fossil record or real life. We see different breeds springing up in one single breeding session. Such as the Chinook which is from a Husky and Mastiff. There was no gradual mutation building up until the breed changed.

http://en.wikipedia.org/wiki/Chinook_(dog)

"Viruses can insert themselves into replicating DNA and thus become part of our genetic code. We can find many insertion sites that are the same between us and chimpanzees, and if we compare insertion sites among all currently living animals, we can find degrees of similarity that match up to what the fossil record would tell us about the tree of life."

Agreed - it tells us that the tree of life does not reflect actual lines of decent - since those Viruses bring the genetic code from the monkey to the man and vise versa - and is not passed down because they are related through hereditary. That's what those viruses tell us.

http://en.wikipedia.org/wiki/Horizontal_gene_transfer_in_evolution

That's a bit difficult to wrap your head around, but by no means impossible. The problem is, people who reject evolution keep on saying "that's not good enough, that's not good enough" until the strongest evidence - stuff like ERVs or genetic similarities or the transposons in chromosome 2 - show up, they say "I don't get it, therefore it doesn't count". I'm sorry, but sometimes, things are a little complicated.

Nothing difficult about it as soon as the evidence is not ignored in favor of imagination. But it is good enough. It is good enough to falsify everything claimed about hereditary lines of decent. You are confused if you think creationists object to the evidence. We accept Viruses are foreign to the body and bring foreign DNA with them. It is the evolutionists that in answer will begin the round of excuses as to why they ignore the data.

 

[The Cadet]

Has anyone shortened this nerve and studied the results?

No. However, this same nerve is present in most animals. In the giraffe... Well, I'll let RationalWiki explain.

In biological homology, the laryngeal nerve can be spotted in a wide variety of animals, from fish to mammals. The structures around the nerve and the nerve itself are homologous to each other and so evolutionary theory postulates that animals evolve from others by distortions and changes in these structures. In fish, considered to be more evolutionarily primitive, the nerve heads straight from the brain, down to the larynx. However, in mammals, the structure of the head and development of the neck from fish-like organisms cause the recurrent laryngeal nerve to become "trapped" under the aortic arch in the thorax. Given a slow and gradual evolution from the biology of a fish to the biology of a mammal, there is no way for the nerve to magically jump from one side of the aortic arch to the other. And so, in mammals the nerve controlling the larynx first delves deep into the chest cavity and then finally up to the larynx.

This considerable detour is consistent with how embryological development entwines with evolution, but less consistent with the idea that organisms were made as they appear to day, individually by an intelligent designer.

The loooooooooong way round
The giraffe is a mammal known most famously for its long neck. True to biological homology, the recurrent laryngeal nerve of the giraffe also routes via the thorax and under the aortic arch, taking the detour to hilarious degrees. While in humans this is a detour of mere inches, in the giraffe the nerve is around 15 ft long.[1] It has been suggested that this plays a part in why giraffes can only make a limited number of low frequency vocalisations[2] and this may have contributed to the legend that the animal makes no noise at all.

An episode Inside Nature's Giants covering the giraffe demonstrated an extraction of the full nerve from the neck.[3]

As the recurrent laryngeal nerve is common to all tetrapods, it's a reasonable assumption (although still speculative as soft material such as nerve cells do not fossilise) that it was also present in many dinosaurs, and notably the long-necked sauropods. The same can be said for whales, although the dissections to remove such a nerve from a whale would be tricky.[4][5] While the giraffe's RLN is about 5 metres (15 ft) in length, other long-necked animals such as the Supersaurus would have had nerves up to 30 metres (~100 ft) long.​

Regardless of how you slice it, an efficient design would not involve it taking a 5-meter detour. And sure, you can find post-hoc rationalizations for why god would have done it that way - "god works in mysterious ways" really is kind of a catch-all. But that's the problem - even in theory, there is literally no evidence which could possibly contradict the hypothesis. In science, this is a big, big problem. An unfalsifiable idea is simply unscientific.

Does anyone know they have a "blind spot"? I didn't know til I read it somewhere, and I had a dickens of a time finding it. In the end I concluded that it was meaningless.

The human blind spot is the point where the optic nerve connects to the back of the eye, and it is in fact a very real place where you cannot take in light. This is not necessary - there are animals without a blind spot, and it's fairly straightforward to design an eye with no such flaw. Maybe God had his reasons, but I don't care, because you're missing the point entirely.

Disease is part of this 'planet of death' the God put us on. Also diseases teach us certain lessons regarding health, sanitation, etc. "A hard lesson is a good lesson."

Of course they are. Now would you please address the point?

 

[OldWiseGuy]

I'm stuck on the simple stuff. Like the 'evolution' of range of motion of limbs and other appendages. I'm particularly interested in the evolution of bird's flight. Like, how many neural/muscle connections are needed to move the wing over a certain distance? And how were these connections made in the first place? And do birds really 'learn' how to fly, or do they fly when they are 'ready' to fly without any training. How does flapping their wings while in the nest prepare them for aerial maneuvers such as gliding, turning, landing, etc., that they do successfully the first time they're airborne? My questions like this are endless. I'm the kid who keeps asking "Why", until dad runs out of answers and shuts down the conversation.

 

[OldWiseGuy]

The human blind spot is the point where the optic nerve connects to the back of the eye, and it is in fact a very real place where you cannot take in light. This is not necessary - there are animals without a blind spot, and it's fairly straightforward to design an eye with no such flaw. Maybe God had his reasons, but I don't care, because you're missing the point entirely.

I get your point. You wouldn't have designed it that way.

Of course they are. Now would you please address the point

Your point conflicts with mine. Widespread disease indicates that health practices are either unknown or have spun out of control.

 

[The Cadet]

Except that is not what we observe in the fossil record or real life. We see different breeds springing up in one single breeding session. Such as the Chinook which is from a Husky and Mastiff. There was no gradual mutation building up until the breed changed.

http://en.wikipedia.org/wiki/Chinook_(dog)

An inner-species comparison is not particularly relevant to species dynamics. Yes, the Husky and the Mastiff can interbreed. They're both dogs. That has very little to do with speciation events. Then there's punctuated equilibrium, which explains that such evolutionary changes happened quite rapidly, but let's be clear here, we're talking about rapidly in the geologic time scale. Not one or two generations.

Agreed - it tells us that the tree of life does not reflect actual lines of decent - since those Viruses bring the genetic code from the monkey to the man and vise versa - and is not passed down because they are related through hereditary. That's what those viruses tell us.

http://en.wikipedia.org/wiki/Horizontal_gene_transfer_in_evolution

Uh... No. The viruses do not "bring the genetic code from the monkey to man and vice versa". What they do is insert small snippets of their own gene code into the genomes of other creatures. What we can then do is compare these insertion sites in our genome to the same in other animal's genomes. It is technically horizontal gene transfer, but not in the way you think - there is no gene being transfered from monkey to man or vice-versa, it's one gene being inserted by a virus into both. And in the same spot in the genome with both. Oh, and this happened several hundred thousand times, with the vast majority of insertions happening, randomly, at exactly the same locations. Makes sense, I guess? Oh, and if you compare the number of shared ERVs between different species and build a cladogram, it matches the cladogram formed by the fossil record. And the one created by comparative anatomy. And the one from embryology. Fancy that.

Nothing difficult about it as soon as the evidence is not ignored in favor of imagination. But it is good enough. It is good enough to falsify everything claimed about hereditary lines of decent. You are confused if you think creationists object to the evidence. We accept Viruses are foreign to the body and bring foreign DNA with them. It is the evolutionists that in answer will begin the round of excuses as to why they ignore the data.

So, just to be clear, these virus insertion sites, shared throughout the genome in hundreds of thousands of spaces between humans and chimps, are signs not that we shared a common ancestor whose genome was affected by these viruses, but rather signs that these viruses inserted themselves into both species in exactly the same places.

Yeah, I'm sorry, this just doesn't make any sense.

 

[Justatruthseeker]

The human blind spot is the point where the optic nerve connects to the back of the eye

I couldn't agree with you more

Whether its geology or paleontology or astronomy and cosmology.

 

[The Cadet]

I'm stuck on the simple stuff. Like the 'evolution' of range of motion of limbs and other appendages. I'm particularly interested in the evolution of bird's flight. Like, how many neural/muscle connections are needed to move the wing over a certain distance? And how were these connections made in the first place? And do birds really 'learn' how to fly, or do they fly when they are 'ready' to fly without any training. How does flapping their wings while in the nest prepare them for aerial maneuvers such as gliding, turning, landing, etc., that they do successfully the first time they're airborne? My questions like this are endless. I'm the kid who keeps asking "Why", until dad runs out of answers and shuts down the conversation.

I get your point. You wouldn't have designed it that way.

No, that is not my point! My point is that regardless of what is brought up, there is always a perfect excuse. My point is that your hypothesis is unfalsifiable. It makes no falsifiable predictions or statements. It is therefore not science, and above all not useful. This is why supernatural explanations that handwave away all the evidence are ultimately supplanted by naturalistic explanations that not only explain the evidence, but make testable predictions. These naturalistic explanations actually help us understand the world.

 

[Loudmouth]

The average person has to accept evolution on faith, as they will never understand the science behind it. How do scientists feel about having to 'sell' the theory knowing that the 'proof' is unintelligible to the average person.

It can be especially frustrating when the average person you are talking about conflates their inability to understand the evidence with the theory being wrong.

Just today I learned the fully half of the genes of common yeast are interchangeable with human genes. My response was, why not? God made everything basically out of the same stuff.

In this thread, we are talking about ERV's evidencing common ancestry between humans and chimps. Any comments?