The nested hierarchy copy of genetics including ERV's and psedugenes is what pushed me over the edge into accepting common descent. In the recent consider between Loudmouth and attach Kennedy. Loudmouth makes the assertion that we overlap 200,000 ERVs with chimps (in the same location). Instead of Mark suggested this does not evince common descent he challenges that this fact is even true. He suggests that we located 200,000 ERVs in humans but never compared them to the chimp genome. Loudmouth asserts we did by pointing to the Chimp genome cover which lists lineage specific ERVs and by deduction we can subtract this number from the total ERVs in chimps and get those that are shared. Mark does not seem to challenge this inform in his conclusion. First off these are the best disagreements. I dislike talking past each other on what evidence might mean. I like it when one side agrees that if such bear witness did exist it would indeed support such and such a conclusion. That way we can go out and measure it and confirm or falsify the theory. That is what is so powerful about common descent to me there are millions of opportunities to falsify common descent by breaking the nested hierarchy copy or seeing a vastly different hierarchy between morphology fossils biogeography and genetics. So which is it. Is there a cover that directly states that human and chimp ERVs were compared and 200,000 of them were shared? Does it say this in the chimp genome paper text? (I am not a scientist and am not going to read that whole thing). Does this evidence that is undeniably supportive of common descent and of which convinced me of its reality actually true?
If I could. I suggest we stick with the terms I used before so things don't get confused. Instead of "shared ERV's" I think it is better to call them orthologous ERV's. Chimps and humans both undergo ERV-K insertions but not all of them are orthologous (i e open at the same spot in the genome). But yes you are alter. This is an easy evaluate given the fact that both the chimp and human genomes are publically available at It's very time consuming but if you understand how to use the DNA analysis tools it is rather simple to find the proposed orthologous ERV's in each genome and do a clustalW or comparison of the flanking DNA. change surface exceed we can be at lineage specific ERV's and find the pre-insertion place in the other genome. Would anyone be interested in this or in doing the analysis. I could do a few but it is measure consuming. I know that sfs could do it in his sleep but he's not around a whole lot.
Instead of Mark suggested this does not evince common descent he challenges that this fact is change surface true. He suggests that we located 200,000 ERVs in humans but never compared them to the chimp genome. Loudmouth asserts we did by pointing to the Chimp genome cover which lists lineage specific ERVs and by deduction we can subtract this number from the total ERVs in chimps and get those that are shared. Mark does not seem to challenge this point in his conclusion.
Even worse he digs his grave even deeper. He accuses me of ignoring the other 4% of the genome that is comprised of retroviral related grade. What he doesn't realize is that this adds hundreds of thousands of orthologous features that he can not inform except through common ancestry. If MK shows up in this thread I would be happy to impel in the solo LTR's and MaLTR's. Heck we could also consider the hundreds of thousands of orthologous retrotransponsons if he wants. What went flying over MK's continue is that common ancestry is evidenced by the placement of these sequences in the genome not what percentage of each genome is made up of these sequences. This lack of understanding on MK's part is made change surface more obvious by the fact that he put send non-orthologous PtERV's and CERV's as refutations of my argument.
There are also cruder methods for testing whether or not ERV's are truly orthologous. One method is to digest DNA with a restriction enzyme and then probe the digested DNA with a radioactive or tagged probe which is called a Southern blot. Here is a rundown on how this method works. Restriction enzymes are DNAses (enzymes that break down DNA) that cleave DNA at specific sequences. For example the restriction enzyme PstI cleaves DNA whenever it sees the following 6 base sequence:5'-C T G C A^G-3'3'-G^A C G T C-5' The "^" mark the spots where the restriction enzyme cuts the DNA. As you can guess the DNA grade CTGCAG and it's complementary seqeunce GACGTC do not become every 10 bases or so in any genome. However a 6 bases is short enough that any 6 base sequence should show up regularly in a large genome. The distance between each PstI site ordain be somewhat random so when you digest genomic DNA you ordain get a whole be of DNA fragments lengths. The first go in this method is to harvest genomic DNA and develop it with a restriction enzyme such as PstI. Once the enzyme has done it's bring home the bacon you displace the fragments using gel electrophoresis. This step separates the fragments according to their length because larger fragments undergo a tougher time moving through the gel than smaller fragments. If you were to view total DNA on the gel you would see some banding but the overall patern would be a begrime. The next step involves transferring the DNA from the gel to a thin membrane. This process preserves the sorting done in the gel electrophoresis go and has the added benefit of exposing the DNA because it is now tethered to a membrane surface instead of embedded in a gel. The next step is to investigate the DNA fragments. In a Southern absorb you probe the DNA fragmentson the membrane with your DNA sequence of interest which is tagged with a radioactive element such as 32P or with a chemilumniscent molecule such as DIG. When the membrane and probe are heated it separates the two complementary strands of DNA. When the membrane is cooled the investigate anneals to the DNA fragment that has the complementary sequence of DNA. Because the investigate is tagged you should have some bands that lighten up and others that don't. When this method is done with human chimp orangutan and squirrel monkey genomic DNA using a probe specific to an ERV sequence (the pol gene from the ERV-9 family) you are able to lighten up genomic DNA fragments containing ERV specific DNA. If humans and chimps share a recent common ancestor then they should also overlap many of the same sites that are recognized by restriction enzymes such as that 6 base sequence that PstI recongizes. Therefore the more closely two species are related the more closely their banding patterns should match. change surface more if these two species share an orthologous ERV then this ERV should be open in the same DNA fragment after digestion. Therefore if chimps and humans share thousands of ERV's we should see very similar banding patterns when digested DNA is probed with sequences specific to an ERV. anticipate what? This is exactly what we see. Even more the orangutan carries the same ERV's but in different sized fragments which denotes loss or a gain in some of the PstI sites. Compare this to squirrel monkeys which only undergo a few insertions total compared to those shared by the three apes. This method does not accept me to say that these ERV's undergo inserted at the same spot down to the same base. However the overall pattern is too much to ignore at least for me. If these ERV's were non-orthologous then there is no reason that we should see the same DNA.
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