Endogenous Retroviruses: Why Creationism is Wrong

Loudmouth · #91 20th July 2007, 12:22 PM

Originally Posted by FishFace

No. It's. Not. If it's not in the same place HOW IS IT HOMOLOGOUS?!

Nitpick: Insertions from the same retrovirus are homologous. For example, all of the PtERV1 env genes in apes are homologous. However, they are not orthologous ERV insertions. That is, they are not found at orthologous positions in the genome.

If it wasn't random, they wouldn't form a nested hierarchy - you'd have insertions in the same locus in completely unrelated species. As it happens, this isn't the case.

Nitpick: All species are related. Also, RV insertions are not truly random. They have preferred insertion sites within the genome. However, the number and size of insertion sites is quite large so the argument still works. It is best to say that RV insert randomly among preferred insertion sites.

Uhh... No. Wrong. Just a moment, let me find the fallacy... Here it is, Denying the Antecedent. Identical mutations in identical places indicates a common ancestor. The lack thereof does not indicate not a common ancestor - ESPECIALLY when there already are identical mutations in identical places!

It's a good thing that mark's arguments do not work in court. Imagine if a defendant got off because they found other fingerprints in addition to his on a murder victim. "But your honor, my clients fingerprints were not the only fingerprints on the corpse." Yeah, that works.

FishFace · #92 20th July 2007, 01:15 PM

Originally Posted by Loudmouth

Nitpick: Insertions from the same retrovirus are homologous. For example, all of the PtERV1 env genes in apes are homologous. However, they are not orthologous ERV insertions. That is, they are not found at orthologous positions in the genome.

Point taken. Is this nitpick specific to biological jargon, or did I botch the meaning of homologous in general parlance, too?

Nitpick: All species are related. Also, RV insertions are not truly random. They have preferred insertion sites within the genome. However, the number and size of insertion sites is quite large so the argument still works. It is best to say that RV insert randomly among preferred insertion sites.

Reverse-nitpick: the difference between "select randomly from any of millions of sites" and "select randomly between any of tens of thousands of sites" is not enough for me to not say "randomly"

Nonetheless, point taken

It's a good thing that mark's arguments do not work in court. Imagine if a defendant got off because they found other fingerprints in addition to his on a murder victim. "But your honor, my clients fingerprints were not the only fingerprints on the corpse." Yeah, that works.

Or in parenting cases - "Your honour, my client is obviously the father since these marker genes are identical between my client and the child."
"Objection! These two marker genes are different! By the reverse logic of your case, they mustn't be related!"

Loudmouth · #93 20th July 2007, 05:46 PM

Originally Posted by FishFace

Point taken. Is this nitpick specific to biological jargon, or did I botch the meaning of homologous in general parlance, too?

It's ambiguous. Are you talking about homologous viruses or homologous sequences between primates? Homologous usually refers to sequence while orthologous refers to placement.

This disticntion becomes important when reading the primary lit. Many papers focus on the retrovirus, investigating how the virus mutates over time. In these studies they compare the sequences of homologous viral genes and the placement in the host genome as well. It pays to be careful.

Reverse-nitpick: the difference between "select randomly from any of millions of sites" and "select randomly between any of tens of thousands of sites" is not enough for me to not say "randomly"
Nonetheless, point taken

Again, it's a minor nitpick but to me "random insertion" implies that a virus will randomly insert into any base in the genome. This is not true. Viruses have preferences. Some viruses prefer to insert upstream of gene-rich areas. HIV likes to insert into CpG islands.

Or in parenting cases - "Your honour, my client is obviously the father since these marker genes are identical between my client and the child."
"Objection! These two marker genes are different! By the reverse logic of your case, they mustn't be related!"

Indeed. You would think that when mark uses phrases such as "mutation rate" that he would get it.

Loudmouth · #94 20th July 2007, 05:56 PM

Originally Posted by sfs

It's in the human genome paper: Nature. 2001 Feb 15;409(6822):860-921.

It took a little while to sink in and then I felt stupid. The HG paper lists 200,000 ERV's in three classes. The chimp genome lists a few hundred lineage specific insertions. Soon as the bold part clicked in my head it made sense.

Another interesting paper is this one (April 2007) describing the retrotransposon and ERV content of the recently sequence macaque genome. I especially enjoyed the following illustration:

The red ERV's are old world monkey lineage specific. The blue ERV's can be found in the macaque/human common ancestor.

AuraTwilight · #95 20th July 2007, 05:58 PM

This thread wins so hard.

FishFace · #96 20th July 2007, 09:27 PM

Originally Posted by Loudmouth

It's ambiguous. Are you talking about homologous viruses or homologous sequences between primates? Homologous usually refers to sequence while orthologous refers to placement.

This disticntion becomes important when reading the primary lit. Many papers focus on the retrovirus, investigating how the virus mutates over time. In these studies they compare the sequences of homologous viral genes and the placement in the host genome as well. It pays to be careful.

Received and understood

Again, it's a minor nitpick but to me "random insertion" implies that a virus will randomly insert into any base in the genome. This is not true. Viruses have preferences. Some viruses prefer to insert upstream of gene-rich areas. HIV likes to insert into CpG islands.

Being on this forum is like being back in Biology class, except without having to do the shoddy excuses for practicals (and the inevitable deathly boring write-up)

FishFace · #97 20th July 2007, 09:32 PM

Originally Posted by AuraTwilight

This thread wins so hard.

ERV insertions, human chromosome number 2 and Vitamin C mutations are the three most definite pieces of evidence, in my opinion, that common descent is true. There is simply no way out, if you have understood the argument.

AuraTwilight · #98 21st July 2007, 03:08 AM

ERV insertions, human chromosome number 2 and Vitamin C mutations are the three most definite pieces of evidence, in my opinion, that common descent is true. There is simply no way out, if you have understood the argument.

I know. I was agreeing.

FishFace · #99 21st July 2007, 08:54 AM

Originally Posted by AuraTwilight

I know. I was agreeing.

I know, so was I

shernren · #**100** 21st July 2007, 10:16 AM

Originally Posted by Loudmouth

It took a little while to sink in and then I felt stupid. The HG paper lists 200,000 ERV's in three classes. The chimp genome lists a few hundred lineage specific insertions. Soon as the bold part clicked in my head it made sense.

Another interesting paper is this one (April 2007) describing the retrotransposon and ERV content of the recently sequence macaque genome. I especially enjoyed the following illustration:

The red ERV's are old world monkey lineage specific. The blue ERV's can be found in the macaque/human common ancestor.

Would you mind doing a teeny bit more exposition on this picture? I really don't know what I should be looking out for when I look at it. I don't really do bio any more.