What if a company makes and patents a cDNA that is later found to also exist naturally?
Have we sequenced every variant of every species?
Case in point, Monsato make GM crops that resist herbicides. What if the parts they are patenting, have analouges in some other plant in the wild?
Monsanto is, in part, doing exactly what you suggested. The genetic element that grants their crops resistance to glyphosate (Round-Up) was discovered in microbes growing in waste runoff containing glyphosate. The patent is on the plants that have been transformed / engineered to contain this naturally occurring resistance gene in their genome and express it to garner resistance to the herbicide.
The cDNA argument is much worse to ludicrous. The only thing one could imagine is patentable surrounding the issue of cDNA is the technique involved in its generation, but that ship has sailed long ago. The entire process of generating cDNA is by using materials all found in nature. The RNA template that is used to generate cDNA in these cases of naturally occurring genes is obviously naturally occurring* and the technology to even create cDNA in the first place is using a naturally occurring enzyme, reverse transcriptase (found in retroviruses like HIV to catalyze the conversion of their genomic RNA to DNA). Because all these elements exist in the natural world, it is certainly possible in say HIV infected humans that random gene mRNA molecules have been converted to cDNA, thus negating the argument of generating something that does not exist in the natural world. More importantly, the only facet of this whole process of generating cDNA that is artificial is placing the materials in a tube together, NOT inventing any novel chemicals or enzymes to catalyze the process!
* In cells, mRNA molecules are heavily modified, sections spliced out, nucleotides edited, the 5' end capped, the 3' end poly-adenylated, so with the arguments placed forth concerning cDNA, one can imagine in vitro transcription of a gene creates an RNA molecule that doesn't exist in nature and can therefore be patented. Ridiculous, right?