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Where is the evidence for Evolution?

Envisage
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6/18/2014 4:28:05 PM
Posted: 2 years ago
At 6/18/2014 4:17:10 PM, GarretKadeDupre wrote:
I'd like to see the single best evidence for Universal Common Descent.

At 6/18/2014 4:17:10 PM, GarretKadeDupre wrote:
I'd like to see the single best evidence for Universal Common Descent.

Genetic sequencing.

Which shows verbatim sections of DNA being identical, including endogenous reteroviral infections and pseudo genes.

Over multiple genes and infections, plot all species with the same infections in the same family/clades and do that for all genes shared.

What you get is a philogenetic tree (family tree) which maps onto trees you can build off any gene with variations, or with anatomical trees.

An observation which is not easily explained by any other process known other than common ancestry, and yes that includes the ad hoc 'common designer' explanation.
GarretKadeDupre
Posts: 2,023
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6/18/2014 4:40:22 PM
Posted: 2 years ago
At 6/18/2014 4:28:05 PM, Envisage wrote:
At 6/18/2014 4:17:10 PM, GarretKadeDupre wrote:
I'd like to see the single best evidence for Universal Common Descent.

At 6/18/2014 4:17:10 PM, GarretKadeDupre wrote:
I'd like to see the single best evidence for Universal Common Descent.

Genetic sequencing.

Which shows verbatim sections of DNA being identical, including endogenous reteroviral infections and pseudo genes.

Over multiple genes and infections, plot all species with the same infections in the same family/clades and do that for all genes shared.

What you get is a philogenetic tree (family tree) which maps onto trees you can build off any gene with variations, or with anatomical trees.

An observation which is not easily explained by any other process known other than common ancestry, and yes that includes the ad hoc 'common designer' explanation.

A key assumption here is that endogenous retroviral infections even exist. Can you demonstrate to me that they do? Yes, I know the sequences are *called* ERVs, but I want you to show that it's an accurate label. For example, cite me an observation of an ERV introducing itself into an organism's DNA and getting passed down to it's offspring.
Proof that people witnessed living dinosaurs:
http://www.debate.org...
Burzmali
Posts: 1,310
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6/18/2014 4:47:13 PM
Posted: 2 years ago
At 6/18/2014 4:40:22 PM, GarretKadeDupre wrote:
At 6/18/2014 4:28:05 PM, Envisage wrote:
At 6/18/2014 4:17:10 PM, GarretKadeDupre wrote:
I'd like to see the single best evidence for Universal Common Descent.

At 6/18/2014 4:17:10 PM, GarretKadeDupre wrote:
I'd like to see the single best evidence for Universal Common Descent.

Genetic sequencing.

Which shows verbatim sections of DNA being identical, including endogenous reteroviral infections and pseudo genes.

Over multiple genes and infections, plot all species with the same infections in the same family/clades and do that for all genes shared.

What you get is a philogenetic tree (family tree) which maps onto trees you can build off any gene with variations, or with anatomical trees.

An observation which is not easily explained by any other process known other than common ancestry, and yes that includes the ad hoc 'common designer' explanation.

A key assumption here is that endogenous retroviral infections even exist. Can you demonstrate to me that they do? Yes, I know the sequences are *called* ERVs, but I want you to show that it's an accurate label. For example, cite me an observation of an ERV introducing itself into an organism's DNA and getting passed down to it's offspring.

Do you want an "outside of the lab" example, or will you accept an example where researchers deliberately infected an organism and the ERV was passed down to its offspring?
Envisage
Posts: 3,646
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6/18/2014 5:01:27 PM
Posted: 2 years ago
At 6/18/2014 4:40:22 PM, GarretKadeDupre wrote:
At 6/18/2014 4:28:05 PM, Envisage wrote:
At 6/18/2014 4:17:10 PM, GarretKadeDupre wrote:
I'd like to see the single best evidence for Universal Common Descent.

At 6/18/2014 4:17:10 PM, GarretKadeDupre wrote:
I'd like to see the single best evidence for Universal Common Descent.

Genetic sequencing.

Which shows verbatim sections of DNA being identical, including endogenous reteroviral infections and pseudo genes.

Over multiple genes and infections, plot all species with the same infections in the same family/clades and do that for all genes shared.

What you get is a philogenetic tree (family tree) which maps onto trees you can build off any gene with variations, or with anatomical trees.

An observation which is not easily explained by any other process known other than common ancestry, and yes that includes the ad hoc 'common designer' explanation.

A key assumption here is that endogenous retroviral infections even exist. Can you demonstrate to me that they do? Yes, I know the sequences are *called* ERVs, but I want you to show that it's an accurate label. For example, cite me an observation of an ERV introducing itself into an organism's DNA and getting passed down to it's offspring.

It doesn't actually matter if it's an ERV or not, several of the sequences do map onto ERV's verbatim except for the part which allows the 'inserted gene' to actually code for it.

What we have are specific sequence of genetic code, in a very specific place in the genome, which you will find in the same specific place in closely related species, but completely absent once the putative 'parent tree link' is passed.

There are dozens of such sequences, and with those sequences you get a philogenetic tree, which as I stated, is not readily explained by any other process other than common ancestry.

The same applies to pseudogenes, for example. Where the branch with the defunct genes will show exactly the same pattern you see by plotting the endogenous reteroviruses.

You also get exactly the same tree by looking at the same (highly conserved) gene (such as cytochrome 45) and looking for the mutation rate between species, exactly the same tree emerges, with mutations occurring in specific locations/ways. Once again, not readily explained by any other process other than common ancestry.
GarretKadeDupre
Posts: 2,023
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6/18/2014 5:23:11 PM
Posted: 2 years ago
At 6/18/2014 5:01:27 PM, Envisage wrote:
At 6/18/2014 4:40:22 PM, GarretKadeDupre wrote:
At 6/18/2014 4:28:05 PM, Envisage wrote:
At 6/18/2014 4:17:10 PM, GarretKadeDupre wrote:
I'd like to see the single best evidence for Universal Common Descent.

At 6/18/2014 4:17:10 PM, GarretKadeDupre wrote:
I'd like to see the single best evidence for Universal Common Descent.

Genetic sequencing.

Which shows verbatim sections of DNA being identical, including endogenous reteroviral infections and pseudo genes.

Over multiple genes and infections, plot all species with the same infections in the same family/clades and do that for all genes shared.

What you get is a philogenetic tree (family tree) which maps onto trees you can build off any gene with variations, or with anatomical trees.

An observation which is not easily explained by any other process known other than common ancestry, and yes that includes the ad hoc 'common designer' explanation.

A key assumption here is that endogenous retroviral infections even exist. Can you demonstrate to me that they do? Yes, I know the sequences are *called* ERVs, but I want you to show that it's an accurate label. For example, cite me an observation of an ERV introducing itself into an organism's DNA and getting passed down to it's offspring.

It doesn't actually matter if it's an ERV or not, several of the sequences do map onto ERV's verbatim except for the part which allows the 'inserted gene' to actually code for it.

What we have are specific sequence of genetic code, in a very specific place in the genome, which you will find in the same specific place in closely related species, but completely absent once the putative 'parent tree link' is passed.

There are dozens of such sequences, and with those sequences you get a philogenetic tree, which as I stated, is not readily explained by any other process other than common ancestry.

The same applies to pseudogenes, for example. Where the branch with the defunct genes will show exactly the same pattern you see by plotting the endogenous reteroviruses.

You also get exactly the same tree by looking at the same (highly conserved) gene (such as cytochrome 45) and looking for the mutation rate between species, exactly the same tree emerges, with mutations occurring in specific locations/ways. Once again, not readily explained by any other process other than common ancestry.

For your argument to hold, do you agree that the phylogenetic tree must be consistent with the morphological tree?
Proof that people witnessed living dinosaurs:
http://www.debate.org...
Envisage
Posts: 3,646
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6/18/2014 5:34:45 PM
Posted: 2 years ago
At 6/18/2014 5:23:11 PM, GarretKadeDupre wrote:
At 6/18/2014 5:01:27 PM, Envisage wrote:
At 6/18/2014 4:40:22 PM, GarretKadeDupre wrote:
At 6/18/2014 4:28:05 PM, Envisage wrote:
At 6/18/2014 4:17:10 PM, GarretKadeDupre wrote:
I'd like to see the single best evidence for Universal Common Descent.

At 6/18/2014 4:17:10 PM, GarretKadeDupre wrote:
I'd like to see the single best evidence for Universal Common Descent.

Genetic sequencing.

Which shows verbatim sections of DNA being identical, including endogenous reteroviral infections and pseudo genes.

Over multiple genes and infections, plot all species with the same infections in the same family/clades and do that for all genes shared.

What you get is a philogenetic tree (family tree) which maps onto trees you can build off any gene with variations, or with anatomical trees.

An observation which is not easily explained by any other process known other than common ancestry, and yes that includes the ad hoc 'common designer' explanation.

A key assumption here is that endogenous retroviral infections even exist. Can you demonstrate to me that they do? Yes, I know the sequences are *called* ERVs, but I want you to show that it's an accurate label. For example, cite me an observation of an ERV introducing itself into an organism's DNA and getting passed down to it's offspring.

It doesn't actually matter if it's an ERV or not, several of the sequences do map onto ERV's verbatim except for the part which allows the 'inserted gene' to actually code for it.

What we have are specific sequence of genetic code, in a very specific place in the genome, which you will find in the same specific place in closely related species, but completely absent once the putative 'parent tree link' is passed.

There are dozens of such sequences, and with those sequences you get a philogenetic tree, which as I stated, is not readily explained by any other process other than common ancestry.

The same applies to pseudogenes, for example. Where the branch with the defunct genes will show exactly the same pattern you see by plotting the endogenous reteroviruses.

You also get exactly the same tree by looking at the same (highly conserved) gene (such as cytochrome 45) and looking for the mutation rate between species, exactly the same tree emerges, with mutations occurring in specific locations/ways. Once again, not readily explained by any other process other than common ancestry.

For your argument to hold, do you agree that the phylogenetic tree must be consistent with the morphological tree?

Largely so, yes. Although I would expect the philogenetic trees to be substantially more accurate and precise than the morphological one, as morphology comes from a culmination of not necessarily specific genes.

In English, the same macroscopic trait can arise from different gene instructions, just like you can prove Pythagoras in two+ ways, whereas the philogenetic trees actually look at the blueprints themselves.
HumbleThinker1
Posts: 144
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6/18/2014 6:06:57 PM
Posted: 2 years ago
At 6/18/2014 4:17:10 PM, GarretKadeDupre wrote:
I'd like to see the single best evidence for Universal Common Descent.

The universal genetic code. And not only its very existence, but that scientists utilized evolution to predict it before it was discovered.

"In fact, in 1963"three years before the code was finally solved"Hinegardner and Engelberg published a paper in Science formally explaining the evolutionary rationale for why the code must be universal (or nearly so) if universal common descent were true, since most mutations in the code would likely be lethal to all living things. Note that, although these early researchers predicted a universal genetic code based on common descent, they also predicted that minor variations could likely be found. Hinegardner and Engelberg allowed for some variation in the genetic code, and predicted how such variation should be distributed if found:

'... if different codes do exist they should be associated with major taxonomic groups such as phyla or kingdoms that have their roots far in the past.' (Hinegardner and Engelberg 1963)

Similarly, before alternate codes were found, Francis Crick and Leslie Orgel expressed surprise that minor variants of the code had not been observed yet:

'It is a little surprising that organisms with somewhat different codes do not coexist.' (Crick and Orgel 1973, p. 344)

Crick and Orgel were correct in their surprise, and today we know of about a dozen minor variants of the standard, universal genetic code (see the grey, red, and green codons in Figure 1.1.1). As Hinegardner and Engelberg predicted, the minor variations in the standard genetic code are indeed associated with major taxonomic groups (vertebrates vs. plants vs. single-celled ciliates, etc.)...

In the absence of the theory of common descent, it is quite possible that every species could have a very different genetic code, specific to it only, since there are 1.4 x 1070 informationally equivalent genetic codes, all of which use the same codons and amino acids as the standard genetic code (Yockey 1992). This possibility could be extremely useful for organisms, as it would preclude interspecific viral infections. However, this has not been observed, and the theory of common descent effectively prohibits such an observation." From http://www.talkorigins.org...
HumbleThinker1
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6/18/2014 6:28:05 PM
Posted: 2 years ago
At 6/18/2014 4:28:05 PM, Envisage wrote:
Which shows verbatim sections of DNA being identical, including endogenous reteroviral infections and pseudo genes.

A great example of this is the nested hierarchy created by the GULO (vitamin c) psuedogene between primates. A good write up can be found here http://www.evolutionarymodel.com...

Essentially, scientists have compared many sections, base for base, of the broken gene between many primate species, including human, and a species of rat that has a fully functional GULOP gene, which most species of rat do have. When compared, the shared and unique mutations perfectly create a nested hierarchy that is consistent with evolutionary predictions. In other words, the closest related species (ie. humans and chimps) have the most shared mutations and the least unique mutations, while the more distant species (ie. humans and macaque) share fewer mutations and have more unique mutations between them. And the entire primate lineage shares 19 individual mutations.

That each primate would independently get these 19 mutations when given the myriad number of unique mutations that could have occurred is statistically impossible (aka astronomically unlikely).
Mhykiel
Posts: 5,987
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6/18/2014 6:32:35 PM
Posted: 2 years ago
At 6/18/2014 5:34:45 PM, Envisage wrote:
At 6/18/2014 5:23:11 PM, GarretKadeDupre wrote:
At 6/18/2014 5:01:27 PM, Envisage wrote:
At 6/18/2014 4:40:22 PM, GarretKadeDupre wrote:
At 6/18/2014 4:28:05 PM, Envisage wrote:
At 6/18/2014 4:17:10 PM, GarretKadeDupre wrote:
I'd like to see the single best evidence for Universal Common Descent.

At 6/18/2014 4:17:10 PM, GarretKadeDupre wrote:
I'd like to see the single best evidence for Universal Common Descent.

Genetic sequencing.

Which shows verbatim sections of DNA being identical, including endogenous reteroviral infections and pseudo genes.

Over multiple genes and infections, plot all species with the same infections in the same family/clades and do that for all genes shared.

What you get is a philogenetic tree (family tree) which maps onto trees you can build off any gene with variations, or with anatomical trees.

An observation which is not easily explained by any other process known other than common ancestry, and yes that includes the ad hoc 'common designer' explanation.

A key assumption here is that endogenous retroviral infections even exist. Can you demonstrate to me that they do? Yes, I know the sequences are *called* ERVs, but I want you to show that it's an accurate label. For example, cite me an observation of an ERV introducing itself into an organism's DNA and getting passed down to it's offspring.

It doesn't actually matter if it's an ERV or not, several of the sequences do map onto ERV's verbatim except for the part which allows the 'inserted gene' to actually code for it.

What we have are specific sequence of genetic code, in a very specific place in the genome, which you will find in the same specific place in closely related species, but completely absent once the putative 'parent tree link' is passed.

There are dozens of such sequences, and with those sequences you get a philogenetic tree, which as I stated, is not readily explained by any other process other than common ancestry.

The same applies to pseudogenes, for example. Where the branch with the defunct genes will show exactly the same pattern you see by plotting the endogenous reteroviruses.

You also get exactly the same tree by looking at the same (highly conserved) gene (such as cytochrome 45) and looking for the mutation rate between species, exactly the same tree emerges, with mutations occurring in specific locations/ways. Once again, not readily explained by any other process other than common ancestry.

For your argument to hold, do you agree that the phylogenetic tree must be consistent with the morphological tree?

Largely so, yes. Although I would expect the philogenetic trees to be substantially more accurate and precise than the morphological one, as morphology comes from a culmination of not necessarily specific genes.

In English, the same macroscopic trait can arise from different gene instructions, just like you can prove Pythagoras in two+ ways, whereas the philogenetic trees actually look at the blueprints themselves.

ERVs does not discount a design hypothesis.

ERVs are not passed down to all offspring.

The Exogenous Retroviruses that injects the information into DNA by reverse transcription, may also cause the same ERV in unrelated organisms.

NO ONE has any genetic information older than 700,000 years old, That is one horse. A phylogenetic tree by ERV lineage can not accurately extend past this point nor is it reliable at 700,000 years because it is only one organism.

The remainder of the tree is constructed from hypothesis for genetic drift and averaged mutation rate.

This is then compared to the morphological tree and adjusted to match the morphological tree by a few statistical deviations.
Envisage
Posts: 3,646
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6/18/2014 6:50:50 PM
Posted: 2 years ago
At 6/18/2014 6:32:35 PM, Mhykiel wrote:
At 6/18/2014 5:34:45 PM, Envisage wrote:
At 6/18/2014 5:23:11 PM, GarretKadeDupre wrote:
At 6/18/2014 5:01:27 PM, Envisage wrote:
At 6/18/2014 4:40:22 PM, GarretKadeDupre wrote:
At 6/18/2014 4:28:05 PM, Envisage wrote:
At 6/18/2014 4:17:10 PM, GarretKadeDupre wrote:
I'd like to see the single best evidence for Universal Common Descent.

At 6/18/2014 4:17:10 PM, GarretKadeDupre wrote:
I'd like to see the single best evidence for Universal Common Descent.

Genetic sequencing.

Which shows verbatim sections of DNA being identical, including endogenous reteroviral infections and pseudo genes.

Over multiple genes and infections, plot all species with the same infections in the same family/clades and do that for all genes shared.

What you get is a philogenetic tree (family tree) which maps onto trees you can build off any gene with variations, or with anatomical trees.

An observation which is not easily explained by any other process known other than common ancestry, and yes that includes the ad hoc 'common designer' explanation.

A key assumption here is that endogenous retroviral infections even exist. Can you demonstrate to me that they do? Yes, I know the sequences are *called* ERVs, but I want you to show that it's an accurate label. For example, cite me an observation of an ERV introducing itself into an organism's DNA and getting passed down to it's offspring.

It doesn't actually matter if it's an ERV or not, several of the sequences do map onto ERV's verbatim except for the part which allows the 'inserted gene' to actually code for it.

What we have are specific sequence of genetic code, in a very specific place in the genome, which you will find in the same specific place in closely related species, but completely absent once the putative 'parent tree link' is passed.

There are dozens of such sequences, and with those sequences you get a philogenetic tree, which as I stated, is not readily explained by any other process other than common ancestry.

The same applies to pseudogenes, for example. Where the branch with the defunct genes will show exactly the same pattern you see by plotting the endogenous reteroviruses.

You also get exactly the same tree by looking at the same (highly conserved) gene (such as cytochrome 45) and looking for the mutation rate between species, exactly the same tree emerges, with mutations occurring in specific locations/ways. Once again, not readily explained by any other process other than common ancestry.

For your argument to hold, do you agree that the phylogenetic tree must be consistent with the morphological tree?

Largely so, yes. Although I would expect the philogenetic trees to be substantially more accurate and precise than the morphological one, as morphology comes from a culmination of not necessarily specific genes.

In English, the same macroscopic trait can arise from different gene instructions, just like you can prove Pythagoras in two+ ways, whereas the philogenetic trees actually look at the blueprints themselves.

ERVs does not discount a design hypothesis.

Any design hypothesis that accounts for these are just choc full of ad hoc explanations. There is absolutely no reason why species would have their genomes designed in this specific way, with the ERV's falling in the precise positions and phylogenetic locations (the fact we can even make a tree with them in the first place, which would be impossible if random/designed).

ERVs are not passed down to all offspring.

Actually they are if an ERV is established in a population. You need to look at populations and not individuals. That is like saying the genetic code for myoglobin is not passed to all offspring otherwise, which is just absurd.

The Exogenous Retroviruses that injects the information into DNA by reverse transcription, may also cause the same ERV in unrelated organisms.

Not in exactly the same location, with exactly the same verbatim strand of DNA. Remember just how large the genome is (3 billion base pairs), the chances of this happening with all these conditions are absurdly small.

NO ONE has any genetic information older than 700,000 years old, That is one horse. A phylogenetic tree by ERV lineage can not accurately extend past this point nor is it reliable at 700,000 years because it is only one organism.

The remainder of the tree is constructed from hypothesis for genetic drift and averaged mutation rate.

This is then compared to the morphological tree and adjusted to match the morphological tree by a few statistical deviations.

Show me your source on this crap.
Mhykiel
Posts: 5,987
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6/18/2014 8:09:39 PM
Posted: 2 years ago
At 6/18/2014 6:50:50 PM, Envisage wrote:
At 6/18/2014 6:32:35 PM, Mhykiel wrote:
At 6/18/2014 5:34:45 PM, Envisage wrote:
At 6/18/2014 5:23:11 PM, GarretKadeDupre wrote:
At 6/18/2014 5:01:27 PM, Envisage wrote:
At 6/18/2014 4:40:22 PM, GarretKadeDupre wrote:
At 6/18/2014 4:28:05 PM, Envisage wrote:
At 6/18/2014 4:17:10 PM, GarretKadeDupre wrote:
I'd like to see the single best evidence for Universal Common Descent.

At 6/18/2014 4:17:10 PM, GarretKadeDupre wrote:
I'd like to see the single best evidence for Universal Common Descent.

Genetic sequencing.

Which shows verbatim sections of DNA being identical, including endogenous reteroviral infections and pseudo genes.

Over multiple genes and infections, plot all species with the same infections in the same family/clades and do that for all genes shared.

What you get is a philogenetic tree (family tree) which maps onto trees you can build off any gene with variations, or with anatomical trees.

An observation which is not easily explained by any other process known other than common ancestry, and yes that includes the ad hoc 'common designer' explanation.

A key assumption here is that endogenous retroviral infections even exist. Can you demonstrate to me that they do? Yes, I know the sequences are *called* ERVs, but I want you to show that it's an accurate label. For example, cite me an observation of an ERV introducing itself into an organism's DNA and getting passed down to it's offspring.

It doesn't actually matter if it's an ERV or not, several of the sequences do map onto ERV's verbatim except for the part which allows the 'inserted gene' to actually code for it.

What we have are specific sequence of genetic code, in a very specific place in the genome, which you will find in the same specific place in closely related species, but completely absent once the putative 'parent tree link' is passed.

There are dozens of such sequences, and with those sequences you get a philogenetic tree, which as I stated, is not readily explained by any other process other than common ancestry.

The same applies to pseudogenes, for example. Where the branch with the defunct genes will show exactly the same pattern you see by plotting the endogenous reteroviruses.

You also get exactly the same tree by looking at the same (highly conserved) gene (such as cytochrome 45) and looking for the mutation rate between species, exactly the same tree emerges, with mutations occurring in specific locations/ways. Once again, not readily explained by any other process other than common ancestry.

For your argument to hold, do you agree that the phylogenetic tree must be consistent with the morphological tree?

Largely so, yes. Although I would expect the philogenetic trees to be substantially more accurate and precise than the morphological one, as morphology comes from a culmination of not necessarily specific genes.

In English, the same macroscopic trait can arise from different gene instructions, just like you can prove Pythagoras in two+ ways, whereas the philogenetic trees actually look at the blueprints themselves.

ERVs does not discount a design hypothesis.

Any design hypothesis that accounts for these are just choc full of ad hoc explanations. There is absolutely no reason why species would have their genomes designed in this specific way, with the ERV's falling in the precise positions and phylogenetic locations (the fact we can even make a tree with them in the first place, which would be impossible if random/designed).

Bare assertion. Retroviruses are not living. A design hypothesis that accounts for their presence to transmit information for survival purposes is just one in accordance with Design+ERV.

And common design already accounts for exact genetic information seen in different species. There are 4 letters that make up DNA. And as you said 3 billion pairs. So it is possible that a sequence of 200 letters is exactly the same as another sequence of 200 letters that never arose from retrovirus transcription.

In fact is the identification of ERV's objective or just looking for similar small 100 letter sequences? The Latter http://rstb.royalsocietypublishing.org...


ERVs are not passed down to all offspring.

Actually they are if an ERV is established in a population. You need to look at populations and not individuals. That is like saying the genetic code for myoglobin is not passed to all offspring otherwise, which is just absurd.

IF established. But they are not always established. And I am correct they are not always passed on to offspring from the original organism.

The Exogenous Retroviruses that injects the information into DNA by reverse transcription, may also cause the same ERV in unrelated organisms.

Not in exactly the same location, with exactly the same verbatim strand of DNA. Remember just how large the genome is (3 billion base pairs), the chances of this happening with all these conditions are absurdly small.

Many mutations happen to a ERV sequence and the sequence shifts through Loci.

http://www.ncbi.nlm.nih.gov...

ERV found in baboon and cat. Instead of saying baboon and cat were related the scientist said there was an extended infection shared between the 2 species. http://www.ncbi.nlm.nih.gov...


NO ONE has any genetic information older than 700,000 years old, That is one horse. A phylogenetic tree by ERV lineage can not accurately extend past this point nor is it reliable at 700,000 years because it is only one organism.


Oldest DNA: http://news.nationalgeographic.com...

Now think about what is being said here. The phylogenetic tree you speak of is based on ERV's found in DNA.

DNA does not last forever. So when you read somewhere that an ERV is from 25 million years ago, it is by estimation and not because they found some 25 million year old specimen that has the ERV in it.

The remainder of the tree is constructed from hypothesis for genetic drift and averaged mutation rate.


How is the ERV estimated to be 25 million years olf if it is not found in any 25 million year old fossil? By what I said an estimate based on mutation rates of the species and average genetic drift. http://www.ncbi.nlm.nih.gov...

This is then compared to the morphological tree and adjusted to match the morphological tree by a few statistical deviations.


http://www.uccs.edu...

Model selection for phylogenetic trees : http://www.annualreviews.org...

http://bioinformatics.bio.uu.nl... Notice: "Systematic detection and subsequent exclusion of products of horizontal gene transfer" I Highly encourage everyone to read how the most accepted tree was created.

Identification and removal of Horizontal Gene Transferred sequences were done manually.

Genetic sequences do not denote speciation. The genetic information space of all life is extremely noisy. The way this is "fixed" is comparing the construction to the taxonomy based tree.

Show me your source on this crap.

No look it up. DNA doesn't last for millions of years so how can an accurate 4 family tree be created from Genetic Information? It can't without hypothetical predictions, formulas,
Burzmali
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6/18/2014 8:35:56 PM
Posted: 2 years ago
At 6/18/2014 8:09:39 PM, Mhykiel wrote:
In fact is the identification of ERV's objective or just looking for similar small 100 letter sequences? The Latter http://rstb.royalsocietypublishing.org...

What are you talking about with this? The smallest sequence I see in there is 600 bp. Where do you see, at that link, that they're looking for similar small 100 bp sequences?
Mhykiel
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6/18/2014 8:37:43 PM
Posted: 2 years ago
Most algorithms for phylogenetic reconstruction attempt to reverse a given model of evolution... Unfortunately, the sequence length for a single gene appears to be bounded in nature, to a few thousand base pairs; and attempts to obtain longer sequences by concatenating the sequences of several genes tend to exacerbate difficulties with alignments and of course give rise to the gene tree vs. species tree problem.
Mhykiel
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6/18/2014 8:53:44 PM
Posted: 2 years ago
At 6/18/2014 8:35:56 PM, Burzmali wrote:
At 6/18/2014 8:09:39 PM, Mhykiel wrote:
In fact is the identification of ERV's objective or just looking for similar small 100 letter sequences? The Latter http://rstb.royalsocietypublishing.org...

What are you talking about with this? The smallest sequence I see in there is 600 bp. Where do you see, at that link, that they're looking for similar small 100 bp sequences?

And the entire rest of my post is made null and void by this one contention. Well you are wrong the smallest was 450 bp not 600 bp.
Mhykiel
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6/18/2014 9:00:45 PM
Posted: 2 years ago
At 6/18/2014 8:53:44 PM, Mhykiel wrote:
At 6/18/2014 8:35:56 PM, Burzmali wrote:
At 6/18/2014 8:09:39 PM, Mhykiel wrote:
In fact is the identification of ERV's objective or just looking for similar small 100 letter sequences? The Latter http://rstb.royalsocietypublishing.org...

What are you talking about with this? The smallest sequence I see in there is 600 bp. Where do you see, at that link, that they're looking for similar small 100 bp sequences?

* edited*

And what the entire rest of my post is made null and void by this one contention? I was merely backing up what I said to Envisage that thinks ERV analysis can be done objectively on animals older than 700,000 years.

Well you are wrong the smallest was 400 bp not 600 bp.
Mhykiel
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6/18/2014 9:03:30 PM
Posted: 2 years ago
Nothing in ERV genetic analysis Excludes Intelligent Design.

Because it most certainly does not definitely suggest a Common Descent of Life.
Burzmali
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6/18/2014 9:14:56 PM
Posted: 2 years ago
At 6/18/2014 8:53:44 PM, Mhykiel wrote:
At 6/18/2014 8:35:56 PM, Burzmali wrote:
At 6/18/2014 8:09:39 PM, Mhykiel wrote:
In fact is the identification of ERV's objective or just looking for similar small 100 letter sequences? The Latter http://rstb.royalsocietypublishing.org...

What are you talking about with this? The smallest sequence I see in there is 600 bp. Where do you see, at that link, that they're looking for similar small 100 bp sequences?

And the entire rest of my post is made null and void by this one contention. Well you are wrong the smallest was 450 bp not 600 bp.

No, the smallest was 600. The one time they mention a 450 bp region, they're talking about an insertion that was a difference in the homology of ERV-L in one clade. But to know what the smallest region that was analyzed was, you'd have to actually read the article and determine the size yourself by subtracting the start from the end points, rather than just looking for a number that fits whatever (incorrect) point you're trying to make.

I'm not saying the rest of your post was made null by this, but this is at least the third time I've personally seen you be wrong about your own source or about a principle of evolution and genetics. It's very difficult to take someone's criticism seriously when they're constantly making these kinds of simple mistakes.
Mhykiel
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6/18/2014 9:35:03 PM
Posted: 2 years ago
At 6/18/2014 9:14:56 PM, Burzmali wrote:
At 6/18/2014 8:53:44 PM, Mhykiel wrote:
At 6/18/2014 8:35:56 PM, Burzmali wrote:
At 6/18/2014 8:09:39 PM, Mhykiel wrote:
In fact is the identification of ERV's objective or just looking for similar small 100 letter sequences? The Latter http://rstb.royalsocietypublishing.org...

What are you talking about with this? The smallest sequence I see in there is 600 bp. Where do you see, at that link, that they're looking for similar small 100 bp sequences?

And the entire rest of my post is made null and void by this one contention. Well you are wrong the smallest was 450 bp not 600 bp.

No, the smallest was 600. The one time they mention a 450 bp region, they're talking about an insertion that was a difference in the homology of ERV-L in one clade. But to know what the smallest region that was analyzed was, you'd have to actually read the article and determine the size yourself by subtracting the start from the end points, rather than just looking for a number that fits whatever (incorrect) point you're trying to make.

I'm not saying the rest of your post was made null by this, but this is at least the third time I've personally seen you be wrong about your own source or about a principle of evolution and genetics. It's very difficult to take someone's criticism seriously when they're constantly making these kinds of simple mistakes.

Now that I know you are on the case I will make sure to use exact numbers. My main goal was to give a general appreciation of what ERV analysis can and can't do.

Horizontal Gene Transfer happens. So 2 unrelated organisms can share similar sequences.

There are no samples of genetic material millions of years old. So any Phylogenetic Trees expressing the speciation of animals earlier than that is not based on genetic evidence. But assumed from calculating back from animals thought to be related.

Thought to be related through morphological study and not genetic.

There question of a common descent of all life is unanswerable by genetics. Which is why it is being replaced with a vague fog for most rooted trees.

So intelligently design is not defeated by the genetic evidence. And the trees crafted make a lot more assumptions and hypothetical values then Envisage suggests.

Facts neither of you have addressed.
Burzmali
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6/18/2014 10:51:10 PM
Posted: 2 years ago
At 6/18/2014 9:35:03 PM, Mhykiel wrote:
At 6/18/2014 9:14:56 PM, Burzmali wrote:
At 6/18/2014 8:53:44 PM, Mhykiel wrote:
At 6/18/2014 8:35:56 PM, Burzmali wrote:
At 6/18/2014 8:09:39 PM, Mhykiel wrote:
In fact is the identification of ERV's objective or just looking for similar small 100 letter sequences? The Latter http://rstb.royalsocietypublishing.org...

What are you talking about with this? The smallest sequence I see in there is 600 bp. Where do you see, at that link, that they're looking for similar small 100 bp sequences?

And the entire rest of my post is made null and void by this one contention. Well you are wrong the smallest was 450 bp not 600 bp.

No, the smallest was 600. The one time they mention a 450 bp region, they're talking about an insertion that was a difference in the homology of ERV-L in one clade. But to know what the smallest region that was analyzed was, you'd have to actually read the article and determine the size yourself by subtracting the start from the end points, rather than just looking for a number that fits whatever (incorrect) point you're trying to make.

I'm not saying the rest of your post was made null by this, but this is at least the third time I've personally seen you be wrong about your own source or about a principle of evolution and genetics. It's very difficult to take someone's criticism seriously when they're constantly making these kinds of simple mistakes.

Now that I know you are on the case I will make sure to use exact numbers. My main goal was to give a general appreciation of what ERV analysis can and can't do.

Horizontal Gene Transfer happens. So 2 unrelated organisms can share similar sequences.

Certainly prokaryotes can easily share similar sequences. But it is unheard of (as far as I know) for horizontal gene transfer to happen between two animals. For that to occur, a virus capable of infecting two allegedly unrelated species would have to pick up a gene from one and infect the germ cells of the other. Infection of germ cells is pretty rare to begin with, as is the acquisition of complete genes by viruses from animal hosts. It's also rare for retroviruses to be capable of infecting species that aren't closely related. For instance, dogs aren't in danger of being infected by the feline leukemia virus. Anyway, horizontal gene transfer is why phylogenetic trees are constructed from analysis of numerous genes and ERV sequences. There is an outside chance that homology of a single gene could be the result of horizontal gene transfer. But homology of a dozen, in multiple animals? That's effectively impossible.

There are no samples of genetic material millions of years old. So any Phylogenetic Trees expressing the speciation of animals earlier than that is not based on genetic evidence. But assumed from calculating back from animals thought to be related.

Thought to be related through morphological study and not genetic.

There question of a common descent of all life is unanswerable by genetics. Which is why it is being replaced with a vague fog for most rooted trees.

So intelligently design is not defeated by the genetic evidence. And the trees crafted make a lot more assumptions and hypothetical values then Envisage suggests.

Facts neither of you have addressed.

The odds of a single ERV appearing at the same point in our genome as it does in a chimpanzee's genome, through independent infection, is about 1:3,000,000,000 (since they usually insert randomly). There are tens of thousands of ERVs in both genomes, and only ~30 of ours are unique to us. As we look at species that we are more distantly related to, the number of shared ERVs drops in accordance with that relationship. The same happens with comparisons of other species. We don't need ancient DNA to determine these relationships among existing animals.

I don't understand how people can argue against that as evidence of common descent.
Mhykiel
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6/18/2014 11:38:46 PM
Posted: 2 years ago
At 6/18/2014 10:51:10 PM, Burzmali wrote:
At 6/18/2014 9:35:03 PM, Mhykiel wrote:
At 6/18/2014 9:14:56 PM, Burzmali wrote:
At 6/18/2014 8:53:44 PM, Mhykiel wrote:
At 6/18/2014 8:35:56 PM, Burzmali wrote:
At 6/18/2014 8:09:39 PM, Mhykiel wrote:
In fact is the identification of ERV's objective or just looking for similar small 100 letter sequences? The Latter http://rstb.royalsocietypublishing.org...

What are you talking about with this? The smallest sequence I see in there is 600 bp. Where do you see, at that link, that they're looking for similar small 100 bp sequences?

And the entire rest of my post is made null and void by this one contention. Well you are wrong the smallest was 450 bp not 600 bp.

No, the smallest was 600. The one time they mention a 450 bp region, they're talking about an insertion that was a difference in the homology of ERV-L in one clade. But to know what the smallest region that was analyzed was, you'd have to actually read the article and determine the size yourself by subtracting the start from the end points, rather than just looking for a number that fits whatever (incorrect) point you're trying to make.

I'm not saying the rest of your post was made null by this, but this is at least the third time I've personally seen you be wrong about your own source or about a principle of evolution and genetics. It's very difficult to take someone's criticism seriously when they're constantly making these kinds of simple mistakes.

Now that I know you are on the case I will make sure to use exact numbers. My main goal was to give a general appreciation of what ERV analysis can and can't do.

Horizontal Gene Transfer happens. So 2 unrelated organisms can share similar sequences.

Certainly prokaryotes can easily share similar sequences. But it is unheard of (as far as I know) for horizontal gene transfer to happen between two animals. For that to occur, a virus capable of infecting two allegedly unrelated species would have to pick up a gene from one and infect the germ cells of the other. Infection of germ cells is pretty rare to begin with, as is the acquisition of complete genes by viruses from animal hosts. It's also rare for retroviruses to be capable of infecting species that aren't closely related. For instance, dogs aren't in danger of being infected by the feline leukemia virus. Anyway, horizontal gene transfer is why phylogenetic trees are constructed from analysis of numerous genes and ERV sequences. There is an outside chance that homology of a single gene could be the result of horizontal gene transfer. But homology of a dozen, in multiple animals? That's effectively impossible.


Insects and mammals
http://www.mobilednajournal.com...

Plant and Insect
http://online.sfsu.edu...

HGT is facilitated by Host-parasite relationships. Do you have anything to suggest HGT is so rare?

There are no samples of genetic material millions of years old. So any Phylogenetic Trees expressing the speciation of animals earlier than that is not based on genetic evidence. But assumed from calculating back from animals thought to be related.

Thought to be related through morphological study and not genetic.

There question of a common descent of all life is unanswerable by genetics. Which is why it is being replaced with a vague fog for most rooted trees.

So intelligently design is not defeated by the genetic evidence. And the trees crafted make a lot more assumptions and hypothetical values then Envisage suggests.

Facts neither of you have addressed.

The odds of a single ERV appearing at the same point in our genome as it does in a chimpanzee's genome, through independent infection, is about 1:3,000,000,000 (since they usually insert randomly). There are tens of thousands of ERVs in both genomes, and only ~30 of ours are unique to us. As we look at species that we are more distantly related to, the number of shared ERVs drops in accordance with that relationship. The same happens with comparisons of other species. We don't need ancient DNA to determine these relationships among existing animals.


ERVs are not inserted randomly. The prefer locations.

http://www.ncbi.nlm.nih.gov...
http://www.plosbiology.org...

I don't understand how people can argue against that as evidence of common descent.

I think the descendents of a canine are common descent to a canine. I'm not arguing there is no common descent.

There are ERVs in chimpanzee and gorillas not in humans. explained by 2 separate insertion events, one in gorillas, one in chimps. And the ERV is absent in humans by recombination. Another ERV is present in old world monkeys and African apes but not humans.

There are so many mechanisms to how a sequence gets put into a genome in the location of the genome, you can practically write any kind of story you want.
Burzmali
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6/19/2014 12:17:41 AM
Posted: 2 years ago
At 6/18/2014 11:38:46 PM, Mhykiel wrote:
At 6/18/2014 10:51:10 PM, Burzmali wrote:
At 6/18/2014 9:35:03 PM, Mhykiel wrote:
At 6/18/2014 9:14:56 PM, Burzmali wrote:
At 6/18/2014 8:53:44 PM, Mhykiel wrote:
At 6/18/2014 8:35:56 PM, Burzmali wrote:
At 6/18/2014 8:09:39 PM, Mhykiel wrote:
In fact is the identification of ERV's objective or just looking for similar small 100 letter sequences? The Latter http://rstb.royalsocietypublishing.org...

What are you talking about with this? The smallest sequence I see in there is 600 bp. Where do you see, at that link, that they're looking for similar small 100 bp sequences?

And the entire rest of my post is made null and void by this one contention. Well you are wrong the smallest was 450 bp not 600 bp.

No, the smallest was 600. The one time they mention a 450 bp region, they're talking about an insertion that was a difference in the homology of ERV-L in one clade. But to know what the smallest region that was analyzed was, you'd have to actually read the article and determine the size yourself by subtracting the start from the end points, rather than just looking for a number that fits whatever (incorrect) point you're trying to make.

I'm not saying the rest of your post was made null by this, but this is at least the third time I've personally seen you be wrong about your own source or about a principle of evolution and genetics. It's very difficult to take someone's criticism seriously when they're constantly making these kinds of simple mistakes.

Now that I know you are on the case I will make sure to use exact numbers. My main goal was to give a general appreciation of what ERV analysis can and can't do.

Horizontal Gene Transfer happens. So 2 unrelated organisms can share similar sequences.

Certainly prokaryotes can easily share similar sequences. But it is unheard of (as far as I know) for horizontal gene transfer to happen between two animals. For that to occur, a virus capable of infecting two allegedly unrelated species would have to pick up a gene from one and infect the germ cells of the other. Infection of germ cells is pretty rare to begin with, as is the acquisition of complete genes by viruses from animal hosts. It's also rare for retroviruses to be capable of infecting species that aren't closely related. For instance, dogs aren't in danger of being infected by the feline leukemia virus. Anyway, horizontal gene transfer is why phylogenetic trees are constructed from analysis of numerous genes and ERV sequences. There is an outside chance that homology of a single gene could be the result of horizontal gene transfer. But homology of a dozen, in multiple animals? That's effectively impossible.


Insects and mammals
http://www.mobilednajournal.com...

Plant and Insect
http://online.sfsu.edu...

HGT is facilitated by Host-parasite relationships. Do you have anything to suggest HGT is so rare?

Can you please quote the part in your second link that states some observation of transfer from plants to insects? What I saw in there was from plants to bacteria in insects. And it isn't substantiated by any clear observation. I accept that it is possible, even likely, but I don't see much indication that it has or even could happen between plants and insects.

Anyway, I admit that I don't know enough about horizontal gene transfer in mutlicellular orgaisms to say with as much certainty that it's so rare. The fact that you were able to come up with one clear example, while I couldn't even find one after about 20 minutes of searching, seems to indicate it's pretty rare. By all means, though, if you want to cite your single example as evidence that the many thousands of shared ERVs between species are bunk, then I can't do much to disabuse you of that. William of Ockham will probably be spinning in his grave.

There are no samples of genetic material millions of years old. So any Phylogenetic Trees expressing the speciation of animals earlier than that is not based on genetic evidence. But assumed from calculating back from animals thought to be related.

Thought to be related through morphological study and not genetic.

There question of a common descent of all life is unanswerable by genetics. Which is why it is being replaced with a vague fog for most rooted trees.

So intelligently design is not defeated by the genetic evidence. And the trees crafted make a lot more assumptions and hypothetical values then Envisage suggests.

Facts neither of you have addressed.

The odds of a single ERV appearing at the same point in our genome as it does in a chimpanzee's genome, through independent infection, is about 1:3,000,000,000 (since they usually insert randomly). There are tens of thousands of ERVs in both genomes, and only ~30 of ours are unique to us. As we look at species that we are more distantly related to, the number of shared ERVs drops in accordance with that relationship. The same happens with comparisons of other species. We don't need ancient DNA to determine these relationships among existing animals.


ERVs are not inserted randomly. The prefer locations.

http://www.ncbi.nlm.nih.gov...
http://www.plosbiology.org...

Do you have a link to the full text of the first article? The random insertion of provirus DNA has been thought to be true for a long time. I can believe that it isn't actually random, but it would be nice to know what the actual number is. Even if we assume that there are 2000 different places that each retrovirus might integrate, that would put the chances of us sharing ERVs at the same points in our genome as chimps at 1:2000^100,000+.

I don't understand how people can argue against that as evidence of common descent.

I think the descendents of a canine are common descent to a canine. I'm not arguing there is no common descent.

There are ERVs in chimpanzee and gorillas not in humans. explained by 2 separate insertion events, one in gorillas, one in chimps. And the ERV is absent in humans by recombination. Another ERV is present in old world monkeys and African apes but not humans.

There are so many mechanisms to how a sequence gets put into a genome in the location of the genome, you can practically write any kind of story you want.

Do you have links to these ERVs that you're talking about? Forgive me, but your track record on interpreting scientific papers isn't so hot.
Mhykiel
Posts: 5,987
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6/19/2014 1:22:07 AM
Posted: 2 years ago
At 6/19/2014 12:17:41 AM, Burzmali wrote:
At 6/18/2014 11:38:46 PM, Mhykiel wrote:
At 6/18/2014 10:51:10 PM, Burzmali wrote:
At 6/18/2014 9:35:03 PM, Mhykiel wrote:
At 6/18/2014 9:14:56 PM, Burzmali wrote:
At 6/18/2014 8:53:44 PM, Mhykiel wrote:
At 6/18/2014 8:35:56 PM, Burzmali wrote:
At 6/18/2014 8:09:39 PM, Mhykiel wrote:
I'm not saying the rest of your post was made null by this, but this is at least the third time I've personally seen you be wrong about your own source or about a principle of evolution and genetics. It's very difficult to take someone's criticism seriously when they're constantly making these kinds of simple mistakes.

Now that I know you are on the case I will make sure to use exact numbers. My main goal was to give a general appreciation of what ERV analysis can and can't do.

Horizontal Gene Transfer happens. So 2 unrelated organisms can share similar sequences.

Certainly prokaryotes can easily share similar sequences. But it is unheard of (as far as I know) for horizontal gene transfer to happen between two animals. For that to occur, a virus capable of infecting two allegedly unrelated species would have to pick up a gene from one and infect the germ cells of the other. Infection of germ cells is pretty rare to begin with, as is the acquisition of complete genes by viruses from animal hosts. It's also rare for retroviruses to be capable of infecting species that aren't closely related. For instance, dogs aren't in danger of being infected by the feline leukemia virus. Anyway, horizontal gene transfer is why phylogenetic trees are constructed from analysis of numerous genes and ERV sequences. There is an outside chance that homology of a single gene could be the result of horizontal gene transfer. But homology of a dozen, in multiple animals? That's effectively impossible.


Insects and mammals
http://www.mobilednajournal.com...

Plant and Insect
http://online.sfsu.edu...

HGT is facilitated by Host-parasite relationships. Do you have anything to suggest HGT is so rare?

Can you please quote the part in your second link that states some observation of transfer from plants to insects? What I saw in there was from plants to bacteria in insects. And it isn't substantiated by any clear observation. I accept that it is possible, even likely, but I don't see much indication that it has or even could happen between plants and insects.


It reads on to make a case that the trans-genetic material could be established in the host organism. Possible by this find in a coffee beetle, http://www.nature.com...

Plants
http://link.springer.com...
http://www.biomedcentral.com...
http://aem.asm.org...
Artificial HGT in plants
http://www.sciencedaily.com...

Mammal
http://www.sciencedaily.com...
http://www.pnas.org...
http://www.scielo.br...

Anyway, I admit that I don't know enough about horizontal gene transfer in mutlicellular orgaisms to say with as much certainty that it's so rare. The fact that you were able to come up with one clear example, while I couldn't even find one after about 20 minutes of searching, seems to indicate it's pretty rare. By all means, though, if you want to cite your single example as evidence that the many thousands of shared ERVs between species are bunk, then I can't do much to disabuse you of that. William of Ockham will probably be spinning in his grave.


Seems to happen with hosts and shared parasites or gut bacteria. So we do become what we eat. Genetically.

I don't know how 20 minutes you could not find anything. Try using search terms like non-Mendelian Inheritance, Lateral Gene Transfer, Horizontal gene Transfer, Endogenous Retrotransposons, Transposon Mutagenesis or just Retrotransposons

<snip>

The odds of a single ERV appearing at the same point in our genome as it does in a chimpanzee's genome, through independent infection, is about 1:3,000,000,000 (since they usually insert randomly). There are tens of thousands of ERVs in both genomes, and only ~30 of ours are unique to us. As we look at species that we are more distantly related to, the number of shared ERVs drops in accordance with that relationship. The same happens with comparisons of other species. We don't need ancient DNA to determine these relationships among existing animals.


ERVs are not inserted randomly. The prefer locations.

http://www.ncbi.nlm.nih.gov...
http://www.plosbiology.org...

Do you have a link to the full text of the first article? The random insertion of provirus DNA has been thought to be true for a long time. I can believe that it isn't actually random, but it would be nice to know what the actual number is. Even if we assume that there are 2000 different places that each retrovirus might integrate, that would put the chances of us sharing ERVs at the same points in our genome as chimps at 1:2000^100,000+.


First Article text: http://www.aidsreviews.com...

http://www.sciencedirect.com...
http://www.plosbiology.org...
http://nar.oxfordjournals.org...

I don't understand how people can argue against that as evidence of common descent.

I think the descendents of a canine are common descent to a canine. I'm not arguing there is no common descent.

There are ERVs in chimpanzee and gorillas not in humans. explained by 2 separate insertion events, one in gorillas, one in chimps. And the ERV is absent in humans by recombination. Another ERV is present in old world monkeys and African apes but not humans.

There are so many mechanisms to how a sequence gets put into a genome in the location of the genome, you can practically write any kind of story you want.

Do you have links to these ERVs that you're talking about? Forgive me, but your track record on interpreting scientific papers isn't so hot.

PTERV1 Apes, chimpanzees, monkeys Not humans or orangutangs
http://www.ncbi.nlm.nih.gov...

HERV-K chimps, gorillas, but not humans.
http://www.sciencedirect.com...

I skim the references I give most the time. I remember some fact and I do a quick search for details I can remember and skim for a citation.

Probably not the most accurate means. But I doubt Envisage even took 5 minutes to research the construction of phylogenetic trees to see who was correct.

That is a good example of what I am talking about. I know that the trees can not be purely constructed on similar sequences past 700,000 (it was off the top off my head that I remembered that being the oldest genome sequenced and it was a horse.) I knew the splits in branches were calculated my mutation rates and drift. And I knew that tree construction relied on algorithms built based on the initial morphologically created tree.

In response I get told It all was crap. With barely an effort to correct himself. So no I did not take an hour proof reading all my sources. Maybe he can admit his mistake later.
Such
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6/19/2014 1:51:17 AM
Posted: 2 years ago
At 6/18/2014 4:17:10 PM, GarretKadeDupre wrote:
I'd like to see the single best evidence for Universal Common Descent.

I wanted to answer this yesterday, but I couldn't come up with a good way to interpret what you meant, or what anyone means, but "universal common descent."

Are you asking for irrefutable evidence that all life came from a single animal? You aren't going to get it -- there is no currently accepted theory of evolution that suggests that.

Are you asking for irrefutable evidence that all flora and fauna on this planet derived from a single cell? Once again, there is no theory that supports this notion.

Evolution proposes that there were conditions in which elements came together in such a way that they began to exhibit lifelike characteristics. One of these characteristics was evolution, and this increased their complexity until you have the complexity (and diversity) that you see today.

Can we start from there, or are there discrepancies with that?
Mhykiel
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6/19/2014 2:32:37 AM
Posted: 2 years ago
At 6/19/2014 1:51:17 AM, Such wrote:
At 6/18/2014 4:17:10 PM, GarretKadeDupre wrote:
I'd like to see the single best evidence for Universal Common Descent.

I wanted to answer this yesterday, but I couldn't come up with a good way to interpret what you meant, or what anyone means, but "universal common descent."

Are you asking for irrefutable evidence that all life came from a single animal? You aren't going to get it -- there is no currently accepted theory of evolution that suggests that.

Are you asking for irrefutable evidence that all flora and fauna on this planet derived from a single cell? Once again, there is no theory that supports this notion.

Evolution proposes that there were conditions in which elements came together in such a way that they began to exhibit lifelike characteristics. One of these characteristics was evolution, and this increased their complexity until you have the complexity (and diversity) that you see today.

Can we start from there, or are there discrepancies with that?

This is what the Universal Common Descent looks like: http://www.texscience.org...
Such
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6/19/2014 3:34:18 AM
Posted: 2 years ago
At 6/19/2014 2:32:37 AM, Mhykiel wrote:
At 6/19/2014 1:51:17 AM, Such wrote:
At 6/18/2014 4:17:10 PM, GarretKadeDupre wrote:
I'd like to see the single best evidence for Universal Common Descent.

I wanted to answer this yesterday, but I couldn't come up with a good way to interpret what you meant, or what anyone means, but "universal common descent."

Are you asking for irrefutable evidence that all life came from a single animal? You aren't going to get it -- there is no currently accepted theory of evolution that suggests that.

Are you asking for irrefutable evidence that all flora and fauna on this planet derived from a single cell? Once again, there is no theory that supports this notion.

Evolution proposes that there were conditions in which elements came together in such a way that they began to exhibit lifelike characteristics. One of these characteristics was evolution, and this increased their complexity until you have the complexity (and diversity) that you see today.

Can we start from there, or are there discrepancies with that?

This is what the Universal Common Descent looks like: http://www.texscience.org...

Okay, so, yeah. That's about right.

So, that leads to my next question -- I've posted a video on several of these innumerable threads asking this same question. GKD, have you not seen this video? It's a presentation by a molecular biologist detailing experiments that led to conditions mirroring theoretical descriptions of primordial ooze.

Wouldn't that suffice?
Envisage
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6/19/2014 4:11:54 AM
Posted: 2 years ago
At 6/18/2014 8:09:39 PM, Mhykiel wrote:
At 6/18/2014 6:50:50 PM, Envisage wrote:
At 6/18/2014 6:32:35 PM, Mhykiel wrote:
At 6/18/2014 5:34:45 PM, Envisage wrote:
At 6/18/2014 5:23:11 PM, GarretKadeDupre wrote:
At 6/18/2014 5:01:27 PM, Envisage wrote:
At 6/18/2014 4:40:22 PM, GarretKadeDupre wrote:
At 6/18/2014 4:28:05 PM, Envisage wrote:
At 6/18/2014 4:17:10 PM, GarretKadeDupre wrote:
I'd like to see the single best evidence for Universal Common Descent.


For your argument to hold, do you agree that the phylogenetic tree must be consistent with the morphological tree?

Largely so, yes. Although I would expect the philogenetic trees to be substantially more accurate and precise than the morphological one, as morphology comes from a culmination of not necessarily specific genes.

In English, the same macroscopic trait can arise from different gene instructions, just like you can prove Pythagoras in two+ ways, whereas the philogenetic trees actually look at the blueprints themselves.

ERVs does not discount a design hypothesis.

Any design hypothesis that accounts for these are just choc full of ad hoc explanations. There is absolutely no reason why species would have their genomes designed in this specific way, with the ERV's falling in the precise positions and phylogenetic locations (the fact we can even make a tree with them in the first place, which would be impossible if random/designed).

Bare assertion. Retroviruses are not living. A design hypothesis that accounts for their presence to transmit information for survival purposes is just one in accordance with Design+ERV.

This is ad hoc reasoning made with zero evidence. And considering these sequences make up a large chunk (up to 5% of our DNA), this claim seems prima facie frivolous.

And common design already accounts for exact genetic information seen in different species. There are 4 letters that make up DNA. And as you said 3 billion pairs. So it is possible that a sequence of 200 letters is exactly the same as another sequence of 200 letters that never arose from retrovirus transcription.

You are ignoring my point.

These sequences are could exactly as written, in EXACTLY the same locations in the DNA. It is not enough to say by chance these sequences could repeat (the odds against this are stupidly small anyway), it's like reading two different books and finding on page 54 of both of then the exact same paragraph word for word.

Again there is absolutely no reason why a common designer would do it this way. The real killer is that you can make a philogenetic tree with these sequences, by looking at which organisms posses certain ones, and which ones don't.

This would be virtually IMPOSSIBLE without common ancestry.

In fact is the identification of ERV's objective or just looking for similar small 100 letter sequences? The Latter http://rstb.royalsocietypublishing.org...



ERVs are not passed down to all offspring.

Actually they are if an ERV is established in a population. You need to look at populations and not individuals. That is like saying the genetic code for myoglobin is not passed to all offspring otherwise, which is just absurd.

IF established. But they are not always established. And I am correct they are not always passed on to offspring from the original organism.

But some do become established. And that's what we look at today. You do know that large human populations possess a common erv strange that some humans do not? That is an example of an erv that is not yet/might not ever established.

The Exogenous Retroviruses that injects the information into DNA by reverse transcription, may also cause the same ERV in unrelated organisms.

Not in exactly the same location, with exactly the same verbatim strand of DNA. Remember just how large the genome is (3 billion base pairs), the chances of this happening with all these conditions are absurdly small.

Many mutations happen to a ERV sequence and the sequence shifts through Loci.

http://www.ncbi.nlm.nih.gov...

ERV found in baboon and cat. Instead of saying baboon and cat were related the scientist said there was an extended infection shared between the 2 species. http://www.ncbi.nlm.nih.gov...

Ignores the point I made. The chances if this happening otherwise are absurd. And we have many examples of them. Note it doesn't actually matter if it's an erv or not, any specific sequence of DNA does the job if it is suddenly inserted.


NO ONE has any genetic information older than 700,000 years old, That is one horse. A phylogenetic tree by ERV lineage can not accurately extend past this point nor is it reliable at 700,000 years because it is only one organism.


Oldest DNA: http://news.nationalgeographic.com...

Now think about what is being said here. The phylogenetic tree you speak of is based on ERV's found in DNA.

DNA does not last forever. So when you read somewhere that an ERV is from 25 million years ago, it is by estimation and not because they found some 25 million year old specimen that has the ERV in it.

Oh, I thought you were talking about something else. I never made the claim we were looking at ancient DNA, looking at today's DNA is enough to establish common ancestry.

Would have been cool to clone a dinosaur though. Might still be possible.

The remainder of the tree is constructed from hypothesis for genetic drift and averaged mutation rate.


How is the ERV estimated to be 25 million years olf if it is not found in any 25 million year old fossil? By what I said an estimate based on mutation rates of the species and average genetic drift. http://www.ncbi.nlm.nih.gov...

This is then compared to the morphological tree and adjusted to match the morphological tree by a few statistical deviations.


http://www.uccs.edu...

Model selection for phylogenetic trees : http://www.annualreviews.org...

http://bioinformatics.bio.uu.nl... Notice: "Systematic detection and subsequent exclusion of products of horizontal gene transfer" I Highly encourage everyone to read how the most accepted tree was created.

Identification and removal of Horizontal Gene Transferred sequences were done manually.

Genetic sequences do not denote speciation. The genetic information space of all life is extremely noisy. The way this is "fixed" is comparing the construction to the taxonomy based tree.

Show me your source on this crap.

No look it up. DNA doesn't last for mi
Envisage
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6/19/2014 4:12:48 AM
Posted: 2 years ago
Also we can do a debate on this if you want. I haven't done an evolution debate in ages, not since with Gade
Mhykiel
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6/19/2014 5:05:10 AM
Posted: 2 years ago
At 6/19/2014 4:11:54 AM, Envisage wrote:
At 6/18/2014 8:09:39 PM, Mhykiel wrote:
At 6/18/2014 6:50:50 PM, Envisage wrote:
At 6/18/2014 6:32:35 PM, Mhykiel wrote:
At 6/18/2014 5:34:45 PM, Envisage wrote:
At 6/18/2014 5:23:11 PM, GarretKadeDupre wrote:
At 6/18/2014 5:01:27 PM, Envisage wrote:
At 6/18/2014 4:40:22 PM, GarretKadeDupre wrote:
At 6/18/2014 4:28:05 PM, Envisage wrote:
At 6/18/2014 4:17:10 PM, GarretKadeDupre wrote:
I'd like to see the single best evidence for Universal Common Descent.

This is ad hoc reasoning made with zero evidence. And considering these sequences make up a large chunk (up to 5% of our DNA), this claim seems prima facie frivolous.

ERVs do not exclude the possibility of life being intelligently designed. A common ancestor to life is impossible to discern from HGT and ERVs.

Even inside an evolutionary view, Mutation alone is insufficient. Horizontal Gene Transmission, hybridization, etc.. make a more compelling complete picture for evolution. But again the models derived from ERV have their limitations. They do not discount an intelligent source for life. Only a view that begins with No non-human intelligence, derives such a conclusion.


And common design already accounts for exact genetic information seen in different species. There are 4 letters that make up DNA. And as you said 3 billion pairs. So it is possible that a sequence of 200 letters is exactly the same as another sequence of 200 letters that never arose from retrovirus transcription.

You are ignoring my point.

These sequences are could exactly as written, in EXACTLY the same locations in the DNA. It is not enough to say by chance these sequences could repeat (the odds against this are stupidly small anyway), it's like reading two different books and finding on page 54 of both of then the exact same paragraph word for word.


That's because that is not accurate. The sequences are not exactly the same. They are similar. A sequence of 500bp in 3 different species will have 3 different insertions and deletions. These gaps are skipped over when identifying ERVs.

The locations are not completely random. If you bother to scroll up I gave I think 4 links to the contrary.

I more appropriate analogy is finding between 20 science textbooks similar (75% match) paragraphs that describe the electromagnetic spectrum.

Again there is absolutely no reason why a common designer would do it this way. The real killer is that you can make a philogenetic tree with these sequences, by looking at which organisms posses certain ones, and which ones don't.

I refer you again to: http://bioinformatics.bio.uu.nl...

Where you can see that organism with certain ERVs were deemed non-related despite the sharing of the ERV. These were described as independent insertions of an ERV. I believe earlier I gave a link to one such ERV example shared between cats and baboons.


This would be virtually IMPOSSIBLE without common ancestry.

Some common ancestry does occur. Impossible? certainly not. Lateral or Horizontal Gene transmission can account for non-related species acquiring new genetic information from shared parasites, food sources, and other vectors. Add in intermittent hybridization and you can have a whole bag of similar sequences across species and genus.


In fact is the identification of ERV's objective or just looking for similar small 100 letter sequences? The Latter http://rstb.royalsocietypublishing.org...




ERVs are not passed down to all offspring.

Actually they are if an ERV is established in a population. You need to look at populations and not individuals. That is like saying the genetic code for myoglobin is not passed to all offspring otherwise, which is just absurd.

IF established. But they are not always established. And I am correct they are not always passed on to offspring from the original organism.

But some do become established. And that's what we look at today. You do know that large human populations possess a common erv strange that some humans do not? That is an example of an erv that is not yet/might not ever established.

Are you aware there are ERVs established in chimpanzees and gorillas not present in humans or orangutangs? http://jgv.sgmjournals.org... I don't think is even the same link I gave earlier but it is the same ERV

Even established is not safe. And it is suspected the ERV is present in Gorillas and chimps by 2 different injection periods.

The Exogenous Retroviruses that injects the information into DNA by reverse transcription, may also cause the same ERV in unrelated organisms.

Not in exactly the same location, with exactly the same verbatim strand of DNA. Remember just how large the genome is (3 billion base pairs), the chances of this happening with all these conditions are absurdly small.

Many mutations happen to a ERV sequence and the sequence shifts through Loci.

http://www.ncbi.nlm.nih.gov...

ERV found in baboon and cat. Instead of saying baboon and cat were related the scientist said there was an extended infection shared between the 2 species. http://www.ncbi.nlm.nih.gov...

Ignores the point I made. The chances if this happening otherwise are absurd. And we have many examples of them. Note it doesn't actually matter if it's an erv or not, any specific sequence of DNA does the job if it is suddenly inserted.

They are not exact character for character transcriptions into the exact same loci. And when they are injected chances are they are inserted in preferential spots.



NO ONE has any genetic information older than 700,000 years old, That is one horse. A phylogenetic tree by ERV lineage can not accurately extend past this point nor is it reliable at 700,000 years because it is only one organism.


Oldest DNA: http://news.nationalgeographic.com...

Now think about what is being said here. The phylogenetic tree you speak of is based on ERV's found in DNA.

DNA does not last forever. So when you read somewhere that an ERV is from 25 million years ago, it is by estimation and not because they found some 25 million year old specimen that has the ERV in it.

Oh, I thought you were talking about something else. I never made the claim we were looking at ancient DNA, looking at today's DNA is enough to establish common ancestry.

So you think an accurate phylogenetic tree can be made from ERVs that show the branching off of say Dinosaur and bird?

As I said earlier, the back tracking of such splits for non extant animals is by using techniques of mutation rates (which differ between animals and can change in a population depending on other factors), average of genetic drift, and comparison to other trees, especially a morphological or body-plan decided upon tree.


Would have been cool to clone a dinosaur though. Might still be possible.

If birds did not lose a lot of genetic material from there earlier ancestors, a feathered dinosaur cold have been reverse grown from the bird DNA. Bird DNA in some species still have the information to make teeth.

Maybe you have seen this stuff: http://www.ted.com...

http://www.oeb.harvard.edu...