But as it can be synthesised, that refutes the argument that "if we destroyed it, it would be gone forever"
Yes. While destroying existing stocks would not eradicate the virus forever, it would still help minimize the risks of accidental releases.
1. Why is that viral gene in there?
When you insert a new gene (such as an herbicide resistance gene in Monsanto's Roundup Ready crops) into a plant, you also need to insert a piece of DNA called a promoter that tells the plant to turn the gene on. The scientists who created the GMOs chose to insert the promoter from the cauliflower mosaic virus (CaMV), as it is particularly good at this task and is very well studied. This promoter also happens to include part, but not the entirety, of gene VI from the virus.
* 2. Was it put there by accident or by purpose? * 2(a). If by accident, how, when, what happened? * 2(b). If by purpose, why, and by whom?
As stated above, the fragment of gene VI was placed into the GMOs on purpose. Because fragments of genes are generally inactive, the presence of the gene fragment is not expected to be problematic and showed no evidence of causing problems during the testing of the GMOs. Furthermore, because cauliflower mosaic virus is a naturally occurring virus, the full gene VI can be found in many non-GMO crops (for example, see this 2004 study).
3. How come the American scientists never detected this viral gene? * 3(a). Was it because of incompetence, or was it because the American scientists were not allowed to publish their finding, if they had found it before the Europeans?
These findings were not published before because we already knew that many GMOs contain a fragment of CaMV gene VI. In fact, in the Podevin and du Jardin study, the authors "found" the gene VI fragments by simply querying a database. A more substantial finding would have been if they found evidence that the gene VI fragments are actually made into functional protein (a prerequisite for the gene VI fragment to cause any deleterious effects), but this study did not investigate this issue. Rather, the study simply looked at what proteins might be produced in the worst case scenario and concluded that any possible proteins made from the gene VI fragments are unlikely to be human allergens or toxins. The authors speculate these possible proteins could be harmful to the plant itself, but because many of these GMOs are very productive plants that produce high yields in commercial settings, this possibility seems unlikely.
Sydney Brenner, who won the Nobel Prize in Physiology or Medicine for his work on programmed cell death, wrote a nice essay in the journal Science (subscription required) describing what he saw as a major paradigm shift in the 1950s and 60s that created modern molecular biology. Prior to the discovery of the structure of DNA by Watson and Crick, biologists had been focusing on how DNA and its associated proteins might be carrying out the functions of the cell. The discovery of the structure of DNA, however, fundamentally changed how researchers approached these questions by revealing that DNA is really just carrying information. Brenner writes:
"We can now see exactly what constituted the new paradigm in the life sciences: It was the introduction of the idea of information and its physical embodiment in DNA sequences of four different bases. Thus, although the components of DNA are simple chemicals, the complexity that can be generated by different sequences is enormous. In 1953, biochemists were preoccupied only with questions of matter and energy, but now they had to add information. In the study of protein synthesis, most biochemists were concerned with the source of energy for the synthesis of the peptide bond; a few wrote about the “patternization” problem. For molecular biologists, the problem was how one sequence of four nucleotides encoded another sequence of 20 amino acids."
Indeed, following this paradigm shift, Watson and others quickly worked out the question of how the information encoded in DNA gets read by the cell and their work now forms the central dogma of modern molecular biology. Therefore, Kuhn's concept of paradigm shifts does indeed apply to biology.