First, disclaimer. I work for a large multinational involved in this field (i.e. biotech), ergo I do have a certain POV.
Having said that, I have a passing familiarity with the issue, having worked on the patent side of things. However, my knowledge is several years old now.
To start, one has to realize that the way the US patent system works is a bit odd. (a) approval of the patent is not a final decision, rather it simply means you meet the minimium hurdles. The American system depends on competitors challenging patents which are no good, i.e. were not in fact non-obvious, not in fact original etc. Ergo obtaining a patent is only the first step. (b) You next have to defend your patent. To my knowledge this is the step in which all biotech gene patents are in. Also, again to my now somewhat dated knowledge, all have failed so far. That is all have been overturned.
Next, I would hazard the opinion that early examiners were not in fact properly prepared and a number of gene patents were granted which did not in fact meet the minimium standards. To an extent I do think it is fair to say that initial over-broad, in fact unsupportable patents have seen valuable resources go to litigation as opposed to other areas. But the American system does encourage that.
I believe it is fair to say that complaints all around have resulted in the US Patent Department upgrading the examiners working with biotech applications. That is they’re hiring more people with biological training (whereas before we had some folks trained in engineering examining applications, not entirely inappropriate given that most applications are methadological and not on the very gene itself: e.g. gene guns and the like.).
I frankly think that, regardless of corporate position, naturally occuring sequences should not be patented, even when one describes their function. That simply does not rise to the level of patentability. (ARL has hit the nail on the head with the Newton analogy) What does is finding mechanisms to alter or modify the same.
In any case, I think it is fair to say that the legal status of all this remains very, very murky and I believe the current EU position excludes the idea of patenting genes per se.