If I understand the situation correctly, it seems fairly similar to the status quo with drugs, for better or worse. You can't patent chemicals naturally occurring in plants that have medicinal uses, but you can patent synthetic versions of the same drug.

I think you do understand it correctly, but I find it very disturbing. The difference between these two situations is night and day: the complete synthesis of naturally occurring small molecules is unique each time, and can require dozens of PhD-level chemists and a decade or more to complete, if it's even possible. It requires a huge amount of invention, and a huge amount of discovery.

Making cDNA is a standard kit, on order from any number of vendors, and is a standard molecular biology technique.

So basically, the Supreme Court, or at least Justice Clarence Thomas, is completely clueless.

So, I have a background in chemistry and molecular biology and I take the exact opposite opinion - there's no categorical difference between the total synthesis and PCR. There are total syntheses that are straightforward - and the synthesis of most commercial drugs are usually very straightforward (for obvious economical reasons). And (rarely) you can have dastardly PCR reactions that refuse to work except under highly fine-tuned conditions that for long periods of time unexplainably work in the hands of only one researcher.

Ease is not the question by which a patent is judged. When you do a PCR reaction, introns or not, you are creating a NEW molecule that didn't exist before. Period. If the judges are claiming that the "information content" is what counts, then that goes against the molecule-patenting precedent - it's really the "molecular identity" which should count.

Now, my preference is to not allow patenting - at all - but to be consistent with the existing patenting landscape, they should have allowed the myriad patents (except for the "method" of comparing a patient sequence with the reference sequence) to pass.

>but to be consistent with the existing patenting landscape, they should have allowed the myriad patents (except for the "method" of comparing a patient sequence with the reference sequence) to pass.

You are completely right that the biological molecules could be considered identical to small chemical molecules, and that trivial chemical manufacturing steps could be patented; I do not do synthesis but all the synthetic organic chemists I know are pursuing incredibly complex and difficult procedures that are not on the same playing field as any PCR reaction, and I did not know that simple and straightforward techniques could be patented (which would seem to be counter to the "person skilled in the art" bar that's commonly used for patents, but I am not a synthetic chemist).

However, and I may be completely out of line, I think that the most important thing with patent law is to go for maximum utility as opposed to maximum consistency. Patent law is legal invention intended to maximize innovation and advancement, there is no underlying need for consistency in different realms. The biological and chemical realms have completely different monetization strategies, and it would make sense for the IP realms to be different, just as there are completely different standards for patents of composition, methods and systems. If somebody is using cDNA of a particular gene as a therapy and selling that compound, I could see that being patentable. However, I can't see patents of cDNA for diagnostic purposes being patentable; there the cDNA patent blocks any innovation on the interesting part, the analysis of information.

a method patent generally should not be "simple and straighforward" (but there are always things like "patent on a method to swing on a swing"). But molecule patents are not method patents.

Furthermore, what constitutes a "trivial chemical manufacturing step" is not really appropriate for a legal decision. Even if step 12 in the synthesis is obvious, is it trivial to decide to use a 500 L batch fed reactor with piping radius X, with a copper pipe, and chiller unit Z for step 12? But in the molecule patents, the steps to synthesis are not necessarily relevant. All that is claimed is the structure of the molecule.

"all the synthetic organic chemists I know are pursuing incredibly complex and difficult procedures"

Keep in mind that the pursuit of complex and difficult procedures (or, really, the molecules that lead to them) is the essential purpose of synthetic organic chemistry in academia, and industrial chemistry is a very, very different beast. Those easy reactions that you learned in your intro ochem class textbook (SNs, Es, Aryl substitutions, halogenations, nitrations, carbonyl chemistry...) it's really those reactions that dominate industrial chemistry - for several reasons - they don't require exotic conditions (extreme cold, extreme hot) - they aren't super exothermic - that's a huge problem when you scale to 500 L you don't want your reaction chamber to turn into a bomb - they have been around for decades so optimization techniques are well characterized - they have been around for decades so regulatory approval is simpler.

But all of this is moot, because the patenting of a molecule doesn't generally hing on the process.

Consider - if you had a Drexler-like nanomachine that could 3d-print a molecular structure on demand, such that chemistry would essentially become "kit-ified" in the same way that molecular biology is, should then chemical patents then be invalidated?

"Patent law is legal invention intended to maximize innovation and advancement, there is no underlying need for consistency in different realms. The biological and chemical realms have completely different monetization strategies, and it would make sense for the IP realms to be different, just as there are completely different standards for patents of composition, methods and systems."

That is generally supposed to be for congress to decide, not the courts.

Well, I wouldn't say that...cDNA patents are like saying "You can't copyright that public domain book in .doc format but if you make it a PDF you can". cDNA is no different than post-transcriptional mRNAs that have already been processed to remove introns (Which is part of the "unnatural" claim) in terms of the data stored; cDNA and mRNA are just two different storage mediums. Albeit they have some different biological consequences but thats nothing special as far as patents should be concerned

In Europe you can secure a copyright on a photograph of a work in the public domain (e.g. a Rembrandt). Provided that you've kept the source away from cameras, you can enforce your copyright on the grounds that any instance of "your" image were either copied illegally, or created illegally.

The same does not hold true in the US, thanks to Bridgman Art Library vs. Corel

"Bridgeman Art Library v. Corel Corp., 36 F. Supp. 2d 191 (S.D.N.Y. 1999), was a decision by the United States District Court for the Southern District of New York, which ruled that exact photographic copies of public domain images could not be protected by copyright in the United States because the copies lack originality. Even if accurate reproductions require a great deal of skill, experience and effort, the key element for copyrightability under U.S. law is that copyrighted material must show sufficient originality."

http://en.wikipedia.org/wiki/Bridgeman_Art_Library_v._Corel_....

Of course, this is one ruling by one court. It could be challenged. In the meantime, it looks like the SCOTUS has taken the view that copies can be yours, even if the original isn't.

The practical difference is that the originals are in the genetic makeup of billions and circulating freely, whereas notable paintings tend to be unique and tightly controlled.

So I'm not super familiar with drug patent laws - can those synthetic version and naturally occurring version be identical (as in chemically) or does the natural one need to be subtly different (e.g. extra methyl group, or whatever)?

I'm not sure if this answers your question:

If an algae produces molecule A, one can determine its structure and (in theory) synthesize it in a lab. Both will be structurally identical. Of course, if the chemist wants to add X or Y moieties to the original algal molecule, he can. One could also determine the source of a certain molecule (bio vs. lab) by looking at the different isotopes in each molecule.

(In theory because some syntheses are practically extremely difficult.)

depends on the patent. Usually a drug patent will claim "molecule scaffold with substitutents X can be {list of substituents}, Y can be {list of substitutents}". Then they will claim a very broad list substituents. It may not always be enforceable, if you can claim that your derivative substituent is "non-obvious" but most people won't bother because the litgation will be a PITA.