First off, I am a math guy, not a science guy. I have never pursued a grant for anything evolution related, so don't complain at me about it. Don't whine at a fireman for making a mediocre cop. And pay bloody attention to what you reply to, my post was about the issue (whether or not junk DNA being useless) also appearing in computer science.
Second, major logic fallacy and incorrect use of basic terms right off the bat
What's with the "junk" theorizing about "junk" being "not necessarily junk" for evolution
That is not a theory, not even close. Burden of proof by default lies on a positive claim (the post I replied to), and what I wrote is a negation of that, and an acceptable statement.
And the "junk" assumption that the "junk" need be explained in terms of evolutionary dependence on "junk"
Again, why complain at me about this? I neither wrote nor implied any such thing.
1) Because a virus put it there. I'm no expert on the matter, but from my knowledge genetic engineering is usually done by isolating a desirable gene, replicating it in bacteria (or virus), then having a virus with the gene insert it into the target cell. Which then develops to a full blown organism with the new gene, hopefully. Of course, it's possible that the virus could have put other junk in there. I would like to point out that detecting viral DNA in any organism is by itself no cause for alarm. Hell, our own genomes are chalked full of garbage that viruses put there. Since that garbage doesn't really affect our survival or ability to reproduce, it hasn't been 'weeded' out. Same with plants.
2)That is unknown, though unlikely on purpose. For one thing, genetic modification isn't an exact science. It is possible that the gene in question had nothing to do with a lab; Monsanto's crops come from controlled strains. As we know quite well, if there's a big genetic change in a population when it's bottlenecking, it could easily spread throughout the entire population, and retroviruses are capable of (and often do) inserting extra sequences in the genome. It probably was accidental lab contamination, or a bad reverse transcription that added more than the scientists expected.
3) Now this is getting closer to the disciple I study and work for. First off, there is no table of contents in a cell that tells you what genes are present. And there is no label on a gene that says what it is, what it does, or even if it does something useful. Now, to put it into perspective, maize (corn) has about ~32,000 genes. All full of nothing but A's, C's, T's, and G's. So it's not something you can tell a couple interns to read through and report back if something doesn't look right. So this is a job for computer programs. That can run for up to days to finish. And require trained workers to both know to look for it, as well as actually look for it. Hence stuff like this is *very* *very* *VERY* easy to slip under the radar.
Not that I'm saying Monsanto is a nice hippy company with the well-being of society as its bottom line.