The simplest, simplest definition of evilution: Change over time.
Your children are different from you. You are different from your parents. Your parents are different from their parents. And so on and so on and so on.
But if Person A is older than you and has different DNA, that doesnt automatically mean Person A is one of your parents. If Person B is younger than you and has different DNA, that doesnt automatically mean Person B is your child.
You might think the above statement is obvious, but that is precisely the faulty reasoning used in a previous publication on XMTV/MLV-like/whatever viruses in Chronic Fatigue Syndrome, according to a recent publication in Advances in Virology (this journal creeps me out. i dont know why it exists. which probably means it will have an impact factor of 29 in a year).
Lo et al published sequences of MLV-like viruses they found in archived samples, modern samples, and fresh samples from some individual patients. The sequences were different! Hurray! Evidence that MLV-somethings are infecting humans!
… Not so fast.
Simply having differences between sequences does not make a quasispecies shifting in response to immune selective pressure. The differences have to make sense. The fresh sequences are related to the newish sequences which are related to the old sequences. A phylogenetic tree of the sequences should look like this:
The youngest samples are different but related to the middle-aged sequences, which are different from but related to the old sequences.
Thats not what Lo et al found. They found something like this:
YAY! Differences! Well, no. The ‘differences’ between the sequences was not evolution. Their data was contamination, and they were just detecting different mouse ERVs at each time-point. When you add ERVs into the phylogenetic tree, ‘MLV-like viruses’ were not evolving. They were climbing up and down a tree of ERVs.
When someone in Coffins lab purposefully contaminated reactions by putting vanishingly small quantities of mouse DNA into PCR reactions (1/100th of a cell), they got the exact same ‘tree’ as Lo et al.
There is more to evilution than ‘change over time’. You can make any number of mistakes and find ‘change’ where there is none. There has to be a relatedness, and that relatedness has to make sense.
The most likely explanation for Lo et als data is that they found mouse ERVs over and over, not that they found retroviruses in patients that just happened to evolve along ERV lines.
Occams razor takes a slice of the XMRV–> human pathogen hypothesis.