> DNA is just a sequence of bits, software is too

That's not the argument being made by DOJ. They're not saying that DNA sequences per se are unpatentable. On the contrary, they agree that man-made DNA sequences are indeed potentially patentable (assuming they're not "obvious" in view of other pre-existing DNA sequences, including for example genes in the wild). The brief argues only that if a DNA sequence occurs in nature, you shouldn't be able to get a patent on the isolated sequence.

That could be kind of tricky. If we want to make custom proteins, for example, the most straightforward way to do it is to build up a protein from bits of naturally-occurring proteins for which we already know the folded structure.

I'll give a more concrete example. Certain zinc finger proteins can bind to particular DNA sequences. By chaining together a few of these units, we can engineer proteins that bind to a particular sequence of DNA and promote or inhibit its transcription into RNA -- obviously a very useful thing to be able to do.

Do these custom zinc finger proteins count as patentable? On the one hand, we're mostly plagiarizing from nature. On the other hand, there are a lot of tough issues to solve in order to get to where we can reliably use these things. Personally, I think the bioengineering challenges are a bigger barrier to competition than a patent could be: if someone set up a company that could sell custom zinc finger arrays at a reasonable price, their expertise would matter a lot more than any patent.

That's where obviousness analysis comes in. It's tough to do in hindsight. That's why courts look to "objective evidence." For example, praise from other researchers, or extensive citation of the published paper, could be indirect evidence of nonobviousness.

(One of my partners at my former law firm told a story about representing a major university in seeking a patent for a biotech invention. It took a number of years for the PTO to do the initial examination of the patent application. The patent examiner perfunctorily rejected the application, asserting that the claimed invention would have been obvious in view of the prior art. My partner responded that in the years that the inventors had been waiting on the PTO to examine the patent application, they had been awarded the Nobel Prize for that very invention. Result: Obviousness rejection withdrawn. Of course, I could well be misremembering, but it nicely illustrates the principle.)

> DNA is just a sequence of bits, software is too.

I don't quite see how that plays into it. You can just as easily dismiss any physical creation as a collection of elements.

Although to be fair, every patented thing can be represented as a sequence of bits.

I disagree.

Sure, you can describe your patented process/machine/etc. with text, which you can in turn represent as a sequence of bits. But there's a difference between the patented thing being described with a series of bits and it actually being a series of bits.

Genes are purely a series of bits. But unless you want to specify the exact place where every atom goes through some crazy coordinates, you can't represent an actual machine as a series of bits--you can just describe it with a series of bits.