Evolution Goes (Retro)Viral

[Occams Barber]

Evidence for evolution tends to be based on a range of research findings rather than a single wham-bam knockout factoid. For many Creationists fossils are the basis for anti-evolutionary arguments and they may not be aware of the strength of genetics in confirming evolution/common ancestry.

In my opinion, the strongest single argument for common ancestry is the existence of Endogenous Retroviruses (ERVs) in cross species DNA. Unfortunately, this can be a tedious, hard-to-follow explanation using concepts unfamiliar to most of us.

I recently came across the ‘Stated Clearly’ YouTube explanation for ERVs which does an excellent job of explaining the link between common ancestry and ERVs in plain, non-technical English with animations. I pirated the video text to put together a written version of how ERVs effectively ‘prove’ common ancestry (see below).

For those of you who prefer Talking Pictures, the YouTube version is tacked in under the text.

OB

ERVs & Common Ancestry

Several decades ago, judgements about the ancestry of species (like humans and chimpanzees) were based largely on fossil comparisons. The discovery of genes and DNA created completely new and different ways of determining these relationships through genetic comparisons.

One method involves the analysis of Endogenous Retrovirus (ERV) DNA shared between species.

A retrovirus is basically a string of RNA which penetrates a cell, converts into DNA and inserts itself, at random, directly into the cell’s DNA chain. Once inserted, the retrovirus DNA is duplicated, as part of the cell DNA, every time the cell duplicates itself.

If an infected cell happens to be a sperm or egg cell involved in fertilisation, that cell’s DNA, including the inserted ERV, will become a permanent part of every cell in the newly created offspring. Given enough time the changed DNA will spread through the entire population and all of its descendants. A retrovirus permanently implanted into a species DNA is known as an Endogenous retrovirus. The human genome contains thousands of ERV segments from a number of different ERVs dating back millions of years.


In 2003 the chimp genome was described and found to be almost the same as human DNA. Chimp DNA also included its own ERVs. This raised immediate questions:

Do chimps and humans share the same ERVs located in the same DNA locations?

If true could this be mere coincidence?

ERV’s insert themselves into DNA at random and there are at least 10 million potential insertion locations in the human genome. The odds for the same virus, inserted in the exact same location, in both chimps and humans, being coincidental is less than 1 in 10 million.

The odds of this coincidentally happening twelve times are one in 10 million multiplied by itself twelve times – a figure bigger than the total number of atoms in the observable Universe.

To check on the possibility of common ERVs, scientists searched chimp DNA for ERVs commonly found in human DNA.

They found 205 instances of the same ERV implanted in the same location in both chimps and humans. The odds that this is a coincidence amount to an impossible one in 5.88 x 10^1418 (588 followed by 1416 zeros).

​

Odds this high amount to certainty. Beyond any reasonable doubt, chimps and humans are descended from a common ancestor.

OB

DNA Evidence That Humans & Chimps Share A Common Ancestor: Endogenous Retroviruses - YouTube

 

[AV1611VET]

74

 

[Occams Barber]

74

Your allegorically metaphorical argument is far too clever for silly me to understand.

Try explaining in plain English.

OB

 

[essentialsaltes]

In my opinion, the strongest single argument for common ancestry is the existence of Endogenous Retroviruses (ERVs) in cross species DNA. Unfortunately, this can be a tedious, hard-to-follow explanation using concepts unfamiliar to most of us.

Someone here wanted it explained as to a 5-year-old, so I obliged as best I could.

 

[Occams Barber]

Someone here wanted it explained as to a 5-year-old, so I obliged as best I could.

LOL - I scanned the thread. Given the childlike level of evolutionary 'knowledge' among your interlocuters I think you got your post just right. By comparison my post reads like a PhD dissertation.

PS . There are a few lost-but-not-forgotten Creationist characters in that thread. It made me feel old.

OB

 

[AV1611VET]

PS . There are a few lost-but-not-forgotten Creationist characters in that thread. It made me feel old.

I miss dad, Split Rock, Thaumaturgy, JohnR7, Hitch Slap, et alii.

 

[USincognito]

LOL - I scanned the thread. Given the childlike level of evolutionary 'knowledge' among your interlocuters I think you got your post just right. By comparison my post reads like a PhD dissertation.

PS . There are a few lost-but-not-forgotten Creationist characters in that thread. It made me feel old.

OB

Loudmouth and I joined in 2003. How do you think I feel?

 

[Occams Barber]

Loudmouth and I joined in 2003. How do you think I feel?

I suppose you must feel quite ancient and musty.

I have written to CF Management to remind them that you will soon be eligible for the CF Combination Gold Watch & Hearing Trumpet in recognition of 20 years of faithful service.

As a Supporter you will also be eligible to use the complementary Zimmer frame when entering the building.

OB

 

[KhlulHloo]

"I miss dad, Split Rock, Thaumaturgy, JohnR7, Hitch Slap, et alii."

Awww. you don't miss me as well?

I was the one atheist who completely agreed with why your God "rested" on the seventh day and the actual point that was made by Him doing that. That was "back in the day", wasn't it?

I also miss dad, he was incredibly funny! I mean, seriously, that whole "physics were different before The Fall" and his whole "Diamond Core of the Earth" thing was so incredibly out there, I thought he was one of those who were purposefully engaging in Poe's Law.

Wasn't JohnR7 a Calvanist? Or am I remembering incorrectly?

Thaumaturgy was fun, Split Rock was fun to engage with, even during ALL the times I disagreed with them...I think I went away before Hitch Slap came on board.

I'm not sure if I'm going to be back on a regular basis on these forums, but I do remember our debates.

And honestly, back before the Forum Rules became as they are today, you and I never got into "yelling matches" back then.

I disagreed with almost everything you said, but we always were civil and friendly to each other.

Long one short (too late!), we had some spirited and very civil debates.

But yea, dad was really "out there" even for a creationist, in my humble opinion

Have a great day, and always keep that "What? Me worry?" attitude

 

[AV1611VET]

TYVM, KhlulHloo, for the very kind words!

Here's an "oldie but goodie" that Split Rock made up for dad and me:

Two creationists take a Commercial flight

AV1611VET: How do we know that the flight crew knows how to fly this plane?

Flight Attendant: They are trained experts and have been doing this for many years.

Dad: All because they are so-called experts doesnt mean they can ignore Gods Word.

Flight Attendant: What does Gods Word have to do with flying an airplane?

AV1611VET: I use my Boolean Standards to show that flying is against The Inerrant Word of God and The Documentation.

Flight Attendant: Are you talking about The Bible? Where does The Bible say that?

AV1611VET: Thinking themselves to be wise they became fools.

Flight Attendant: What does that have to do with flying?

AV1611VET: Homo sapiens means Wise Man, doesnt it? Since the flight crew are Wise Men they are really fools and God will show them they are fools by crashing the plane.

Flight Attendant: What???

Dad: How do these Ivory Tower so-called experts know they can fly this plane between here and the destination? What if the atmosphere between here and the destination is in a different state?

Flight Attendant: Different State?? What do you mean??

Dad: A different state. Like it was before The Split.

Flight Attendant: What Split?

Dad: During the time of Peleg. To think differently, is anti-Bible hogwash and a fantasy!

Flight Attendant: What are you talking about?

Dad: You cannot prove that the space-time state between here and there is not different can you?

Flight Attendant: No, but we have never had any problem flying this route before..

Dad: Ha! You just ASSUME there is no difference now, because you assume the past is the key to the present. That is an Anti-God Lie, and thinking only within the box.. I refuse to accept it!!!

Flight Attendant Please, both of you take your seats!

AV1611VET: You just cant wait to ridicule me, even though I accept 95% of your science!

Dad: I just discovered that human flight is impossible! Amazing!!

Flight Attendant: Please, take your seats so we can take off! I promise it is safe!

AV1611VET: Oh yeah.. just like Thalidomide was a Wonder Drug before it was Plutoed!

Flight Attendant: Thalidomide?

AV1611VET: Sure, Thaldomide proves that your science changes with the flavor of the week!

Dad: Prove with your so called science that the state between here and there is the same! You cant!!!! Human flight is an anti-Bible lie! Amazing!

Flight Attendant: Get off this plane!!!

 

[CoreyD]

Evidence for evolution tends to be based on a range of research findings rather than a single wham-bam knockout factoid. For many Creationists fossils are the basis for anti-evolutionary arguments and they may not be aware of the strength of genetics in confirming evolution/common ancestry.

In my opinion, the strongest single argument for common ancestry is the existence of Endogenous Retroviruses (ERVs) in cross species DNA. Unfortunately, this can be a tedious, hard-to-follow explanation using concepts unfamiliar to most of us.

I recently came across the ‘Stated Clearly’ YouTube explanation for ERVs which does an excellent job of explaining the link between common ancestry and ERVs in plain, non-technical English with animations. I pirated the video text to put together a written version of how ERVs effectively ‘prove’ common ancestry (see below).

For those of you who prefer Talking Pictures, the YouTube version is tacked in under the text.

OB

ERVs & Common Ancestry

Several decades ago, judgements about the ancestry of species (like humans and chimpanzees) were based largely on fossil comparisons. The discovery of genes and DNA created completely new and different ways of determining these relationships through genetic comparisons.

One method involves the analysis of Endogenous Retrovirus (ERV) DNA shared between species.

A retrovirus is basically a string of RNA which penetrates a cell, converts into DNA and inserts itself, at random, directly into the cell’s DNA chain. Once inserted, the retrovirus DNA is duplicated, as part of the cell DNA, every time the cell duplicates itself.

If an infected cell happens to be a sperm or egg cell involved in fertilisation, that cell’s DNA, including the inserted ERV, will become a permanent part of every cell in the newly created offspring. Given enough time the changed DNA will spread through the entire population and all of its descendants. A retrovirus permanently implanted into a species DNA is known as an Endogenous retrovirus. The human genome contains thousands of ERV segments from a number of different ERVs dating back millions of years.


In 2003 the chimp genome was described and found to be almost the same as human DNA. Chimp DNA also included its own ERVs. This raised immediate questions:

Do chimps and humans share the same ERVs located in the same DNA locations?

If true could this be mere coincidence?

ERV’s insert themselves into DNA at random and there are at least 10 million potential insertion locations in the human genome. The odds for the same virus, inserted in the exact same location, in both chimps and humans, being coincidental is less than 1 in 10 million.

The odds of this coincidentally happening twelve times are one in 10 million multiplied by itself twelve times – a figure bigger than the total number of atoms in the observable Universe.

To check on the possibility of common ERVs, scientists searched chimp DNA for ERVs commonly found in human DNA.

They found 205 instances of the same ERV implanted in the same location in both chimps and humans. The odds that this is a coincidence amount to an impossible one in 5.88 x 10^1418 (588 followed by 1416 zeros).

​

Odds this high amount to certainty. Beyond any reasonable doubt, chimps and humans are descended from a common ancestor.

OB

DNA Evidence That Humans & Chimps Share A Common Ancestor: Endogenous Retroviruses - YouTube

True, many believe they can say with certainty, that what they believe is true, but aren't ERVs like fossils?
Can HGT play a role in ERVs being present in the DNA of species? Is it an easy task to determine what role HGT played in this?

For example, I was reading this article, which says -
Detection of HGT and the mechanisms responsible and enabling it, is hence of prime importance.Existing algorithms rely on a strong phylogenetic signal distinguishing the transferred sequence from its recipient genome. Closely related species pose an even greater challenge as most genes are very similar and therefore, the phylogenetic signal is weak anyhow. Notwithstanding, the importance of detecting HGT between such organisms is extremely high for the role of HGT in the emergence of new highly virulent strains.

Lower false positive they say, but is the possibility there for some doubt, and uncertainty?

 

[Occams Barber]

True, many believe they can say with certainty, that what they believe is true, but aren't ERVs like fossils?
Can HGT play a role in ERVs being present in the DNA of species? Is it an easy task to determine what role HGT played in this?

For example, I was reading this article, which says -
Detection of HGT and the mechanisms responsible and enabling it, is hence of prime importance.Existing algorithms rely on a strong phylogenetic signal distinguishing the transferred sequence from its recipient genome. Closely related species pose an even greater challenge as most genes are very similar and therefore, the phylogenetic signal is weak anyhow. Notwithstanding, the importance of detecting HGT between such organisms is extremely high for the role of HGT in the emergence of new highly virulent strains.

Lower false positive they say, but is the possibility there for some doubt, and uncertainty?

Horizontal Gene Transfer (HGT) is associated with lifeforms based on prokaryotic cells like those in bacteria and archaea. Plants and animals are eukaryotes.

From your linked article (my bolding):

HGT is a crucial factor in prokaryotic evolution and is a significant source for genomic novelty resulting in antibiotic resistance or the outbreak of virulent strains.​

​

OB

 

[CoreyD]

Horizontal Gene Transfer (HGT) is associated with lifeforms based on prokaryotic cells like those in bacteria and archaea. Plants and animals are eukaryotes.

From your linked article (my bolding):

HGT is a crucial factor in prokaryotic evolution and is a significant source for genomic novelty resulting in antibiotic resistance or the outbreak of virulent strains.​

​

OB

HGT in eukaryotes has been overshadowed by its prevalence in bacterial genomes, but a large number of cases involving eukaryotes have nevertheless been described. Its impact is variable from lineage to lineage, and many of the lineages that are most affected by HGT are the least studied at the genomic level (for example, protists), so the importance of HGT will probably increase as databases expand.

https://www.cell.com/trends/genetics/fulltext/S0168-9525(20)30206-7

 

[Occams Barber]

HGT in eukaryotes has been overshadowed by its prevalence in bacterial genomes, but a large number of cases involving eukaryotes have nevertheless been described. Its impact is variable from lineage to lineage, and many of the lineages that are most affected by HGT are the least studied at the genomic level (for example, protists), so the importance of HGT will probably increase as databases expand.

https://www.cell.com/trends/genetics/fulltext/S0168-9525(20)30206-7

Sorry about the delay in replying. I've been away from my PC for a couple of days and your reply got buried in the backlog.

After reading your last post, and doing a little research, I have to concede that HGT does happen in eukaryotes, including mammals. I think I based my answer on old, information or lousy memory. Either way you are correct and I made the mistake of failing to check my info.

That leaves us with your issue of whether HGT is an alternative explanation for chimp/human ERV commonality. The short answer is I don't know enough about what is transferred, the process(es) or frequency of eukaryotic HGT. It seems to me unlikely that HGT would produce a result which was consistent with ERV transmission but, since unlikely doesn't mean impossible, I'm going to plead ignorance.

OB

 

[Presbyterian Continuist]

Evidence for evolution tends to be based on a range of research findings rather than a single wham-bam knockout factoid. For many Creationists fossils are the basis for anti-evolutionary arguments and they may not be aware of the strength of genetics in confirming evolution/common ancestry.

In my opinion, the strongest single argument for common ancestry is the existence of Endogenous Retroviruses (ERVs) in cross species DNA. Unfortunately, this can be a tedious, hard-to-follow explanation using concepts unfamiliar to most of us.

I recently came across the ‘Stated Clearly’ YouTube explanation for ERVs which does an excellent job of explaining the link between common ancestry and ERVs in plain, non-technical English with animations. I pirated the video text to put together a written version of how ERVs effectively ‘prove’ common ancestry (see below).

For those of you who prefer Talking Pictures, the YouTube version is tacked in under the text.

OB

ERVs & Common Ancestry

Several decades ago, judgements about the ancestry of species (like humans and chimpanzees) were based largely on fossil comparisons. The discovery of genes and DNA created completely new and different ways of determining these relationships through genetic comparisons.

One method involves the analysis of Endogenous Retrovirus (ERV) DNA shared between species.

A retrovirus is basically a string of RNA which penetrates a cell, converts into DNA and inserts itself, at random, directly into the cell’s DNA chain. Once inserted, the retrovirus DNA is duplicated, as part of the cell DNA, every time the cell duplicates itself.

If an infected cell happens to be a sperm or egg cell involved in fertilisation, that cell’s DNA, including the inserted ERV, will become a permanent part of every cell in the newly created offspring. Given enough time the changed DNA will spread through the entire population and all of its descendants. A retrovirus permanently implanted into a species DNA is known as an Endogenous retrovirus. The human genome contains thousands of ERV segments from a number of different ERVs dating back millions of years.


In 2003 the chimp genome was described and found to be almost the same as human DNA. Chimp DNA also included its own ERVs. This raised immediate questions:

Do chimps and humans share the same ERVs located in the same DNA locations?

If true could this be mere coincidence?

ERV’s insert themselves into DNA at random and there are at least 10 million potential insertion locations in the human genome. The odds for the same virus, inserted in the exact same location, in both chimps and humans, being coincidental is less than 1 in 10 million.

The odds of this coincidentally happening twelve times are one in 10 million multiplied by itself twelve times – a figure bigger than the total number of atoms in the observable Universe.

To check on the possibility of common ERVs, scientists searched chimp DNA for ERVs commonly found in human DNA.

They found 205 instances of the same ERV implanted in the same location in both chimps and humans. The odds that this is a coincidence amount to an impossible one in 5.88 x 10^1418 (588 followed by 1416 zeros).

​

Odds this high amount to certainty. Beyond any reasonable doubt, chimps and humans are descended from a common ancestor.

OB

DNA Evidence That Humans & Chimps Share A Common Ancestor: Endogenous Retroviruses - YouTube

The problem with the view that chimps and humans are descended from a common ancestor is that although there are similarities between the two, there are major differences which make that impossible. Actually, there is a particular plant that has more similarities to human DNA than chimps, so it could be argued that the particular species of plant and humans could have come from a common ancestor. Also, the DNA in the brains of rodents, is nearly the same as humans, and that is why rats and mice are excellent subjects for medical testing because the results seen in them can be applied to humans as well.

The difference between chimps and humans is chimps have no idea of symbolism or of spirituality. There is no record of chimps inventing anything or making any technological advances. There is no way that a chimp could be genetically engineered to think and behave like a human being. Although many animals have souls in order to relate to human, examples being dogs, cats, and cattle, they don't have a spirit where they can relate to God. It is interesting to note that animals that have not been abused by humans are more friendly to humans than those abused. This enables a person to have a pet lion, tiger, bear or cheetah. But lions being hunted in the wild, will run away or attack as soon as they see a human with a weapon, because they know that humans will abuse them, and so the flight or fight instinct takes hold of them.

On the 6th day of creation, after Adam had named the animals, and had a lot of good interaction with them, he was still lonely because he could only interact them them on a limited basis. He needed another human, like himself. This problem was solved by God creating Eve to be his companion.

More and more geneticists are coming to the conclusion, as a result of their research, that the human race descended from just two people, male and female, and not from a pre-existing population.

 

[Occams Barber]

The problem with the view that chimps and humans are descended from a common ancestor is that although there are similarities between the two, there are major differences which make that impossible.

It's the combination of similarities and differences which supports the idea of common ancestry, which is verified by genetics.

Actually, there is a particular plant that has more similarities to human DNA than chimps, so it could be argued that the particular species of plant and humans could have come from a common ancestor.

Humans share a common ancestor with ALL plants and animals. It's known as LUCA = Last Universal Common Ancestor.

Believe it or not - you are distantly related to a banana.

Also, the DNA in the brains of rodents, is nearly the same as humans, and that is why rats and mice are excellent subjects for medical testing because the results seen in them can be applied to humans as well.

Once again, these similarities support the idea that rodents and humans share a common ancestor.

There is no record of chimps inventing anything or making any technological advances. There is no way that a chimp could be genetically engineered to think and behave like a human being.

Chimps are known to have created simple tools including sticks modified to extract termites from termite mounds and stones used to crack tough seeds or fruit open. Chimps also have (limited) access to language and have been taught to communicate with humans using symbols or sign language.

No one is claiming that chimps can be "genetically engineered to think and behave like a human being".

Although many animals have souls in order to relate to human, examples being dogs, cats, and cattle, they don't have a spirit where they can relate to God.

A soul is a religious concept which is not relevant to the study of evolution, which is a science topic.

It is interesting to note that animals that have not been abused by humans are more friendly to humans than those abused. This enables a person to have a pet lion, tiger, bear or cheetah. But lions being hunted in the wild, will run away or attack as soon as they see a human with a weapon, because they know that humans will abuse them, and so the flight or fight instinct takes hold of them.

Animals can learn - just like humans. (I think pet lions are probably a bit risky unless you own a circus)

More and more geneticists are coming to the conclusion, as a result of their research, that the human race descended from just two people, male and female, and not from a pre-existing population.

I've been keeping a casual eye on evolution research for 60 odd years, and this is news to me. If anything, genetic research has confirmed and expanded Darwin's original ideas about evolution. This whole thread is about an aspect of genetic research (ERVs) which confirms evolution.

OB

 

[essentialsaltes]

Actually, there is a particular plant that has more similarities to human DNA than chimps

Across the entire genome? What plant is that?

More and more geneticists are coming to the conclusion, as a result of their research, that the human race descended from just two people

Two people living at the same time? Can you name one of these geneticists?

 

[Presbyterian Continuist]

Across the entire genome? What plant is that?

Two people living at the same time? Can you name one of these geneticists?

More discoveries and developments in science is showing that science is proving the Bible right. Many scientists are saying that mankind descended genetically from an original male and female, just as the Bible says.

 

[Estrid]

More discoveries and developments in science is showing that science is proving the Bible right. Many

Any chance you'd care to share your source
for these extraordinary "facts"?

 

[Occams Barber]

More discoveries and developments in science is showing that science is proving the Bible right. Many scientists are saying that mankind descended genetically from an original male and female, just as the Bible says.

I'm going to take a wild guess that you've heard the terms "Mitochondrial Eve" and "Y Chromosome Adam" and you've misunderstood both terms.

Mitochondrial Eve is not the original female. She is defined as:

the most recent woman from whom all living humans descend in an unbroken line purely through their mothers and through the mothers of those mothers, back until all lines converge on one woman.​

Y Chromosome Adam is similar for males. This Eve and Adam lived at different times in different places
and they lived among other males and females. They are not the original male and female.

This is the Wikipedia explanation;

Mitochondrial Eve - Wikipedia

en.wikipedia.org

This is from the Smithsonian;

No, a Mitochondrial 'Eve' Is Not the First Female in a Species

The latest story about a sperm whale “Eve” shows how people misunderstand the evolutionary term. Fear not: We can clarify

www.smithsonianmag.com

OB