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Do you have examples of all those four kinds of rights being applied to RNA/DNA molecules (or any other molecules for that matter) by actual biochemical companies, or is it just a hypothetical situation?

While from a superficial observation all those rights may seem to cover the same "thing", they are designed to cover only certain aspects of the product in question. In an ideal case, those aspects are not supposed to overlap each other. For instance, the Swedish Trademark Act excludes the physical form of the product from trademark protection if that form is due to the very nature of the product or is required for it to serve its intended purpose. A similar exclusion can be found in the Swedish Designs Protection Act. The proper function of a product, if there is one, is instead meant to be covered by patent rights, if such have been awarded.

Also, I wouldn't regard a chemical molecule a good example of something that could be protected by design rights. According to the (Swedish) law, any design must remain "visible" during normal use of the product; you can't protect the inside of a combustion engine in this fashion unless you make it out of glass or some other transparent material so that the engine operator or driver can enjoy its appearance. The form of a molecule is invisible to humans unless you use an electron microscope or similar device all the time.

You can of course use the shape of the molecule as the basis for a trademark, but then you would typically add some non-essential design elements to make that trademark unique to your product line. I doubt an enlarged three-dimensional model of the actual molecule would be acceptable as a trademark, but a two-dimensional rendering from a particular angle could perhaps be.

Copyright: Well, maybe, but if there is one and only one molecular structure that would serve the intended purpose, then I would say there is no room for artistic creativity. You won't be entitled to copyright to the written representation of some numerical constant of nature merely because you decide to express it using a base nobody considered before, like 17. DNA molecules happen to allow for some variation in code to produce the very same proteins, but then you would have a non-functional aspect separate from the functional one, thus allowing you to encode quotes from Shakespeare using the extra bits available. If those bits are neither read by humans or used in some chemical process, what's the point of trying to assert exclusive rights to them? They don't matter.