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Supreme Court: Natural Isolated DNA Not Patentable, Synthetic DNA Is [pdf]

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Re: Supreme Court: Natural Isolated DNA Not Patentable, Synthetic DNA Is [pdf]

#111

Post by bdg »

albertzeyer wrote: post #58

Isn't all synthetic DNA based on natural DNA?

No. Natural DNA occurs in nature, much like a the alignment of magnetic fields may occur in some metals. Synthetic DNA has been designed by someone who sat down and said "Okay, today we're going to write DNA, it's sequence will be ACGTTTGACGTACGTTCAGTG....." and we're going to mix our newly designed gene into a larger natural DNA strand and this synthetic gene inside of the DNA will make this tree glow a very slight yellow-tinge, then we're going to sell that on kickstarter. http://www.kickstarter.com/projects/antonyevans/glowing-plan... (the only reason they're using a larger DNA strand is a full strand might cost in the range of $100b-$1t presently)

This is not the same as what's been done more frequently for the last long while which was dissecting existing genes from other DNA strands (lets say gene XYZ from a starfish) and introducing it into a bacteria.

Also, this doesn't mean I agree with the new law. I think this motion is even more nonsensical than software patents we face today, and has already handed off all the wonderful innovations that the synthetic biology revolution has to offer to a nation who's pumping loads of cash into this sector: China.

Re: Supreme Court: Natural Isolated DNA Not Patentable, Synthetic DNA Is [pdf]

#112

Post by daughart »

dnautics wrote: post #99
daughart wrote: post #85

Earlier quoted context omitted.

This decision affirms a previous decision that synthetic modifications to DNA sequences are patented - regardless of whether they have introns. You see, the ruling suggests that the act of creating a new synthetic, modified DNA molecule (in this case without introns) is patent-able. (Not a comment on your opinion about patents, only the part about patentability relying on introns.)

can you link to this previous decision?

"In Chakrabarty, scientists added four plasmids to a bacte- rium, which enabled it to break down various components of crude oil. 447 U. S., at 305, and n. 1. The Court held that the modified bacterium was patentable." Diamond v. Chakrabarty, 447 U. S. 303, 309 (1980), If I am reading this correctly.

EDIT: Sorry I re-read my original comment - I meant "synthetic modifications", not necessarily only to DNA, but to natural products in general.

Re: Supreme Court: Natural Isolated DNA Not Patentable, Synthetic DNA Is [pdf]

#113

Post by daughart »

tocomment wrote: post #90
daughart wrote: post #87

Earlier quoted context omitted.

It absolutely should mean this. Maybe 23andme can be something more than a toy.

What are some examples of exciting new SNPs they could test for? Besides BRCA.

A quick Google search for "patented disease alleles" suggests Crohn's disease, some forms of kidney disease, diabetes, and many more!

Re: Supreme Court: Natural Isolated DNA Not Patentable, Synthetic DNA Is [pdf]

#114

Post by niels_olson »

What if your life is saved from the debilitating effects of an enzyme deficiency by a virally-delivered sequence which also infects your spermatocytes (1)? And that sequence is passed to your child?

(1) http://en.wikipedia.org/wiki/Testicular_immunology#The_effec...

Re: Supreme Court: Natural Isolated DNA Not Patentable, Synthetic DNA Is [pdf]

#115

Post by daughart »

dnautics wrote: post #98
daughart wrote: post #83

This sets the stage for a simple way to overturn any cDNA patent. Somewhere in the body of any person infected with a retrovirus such as HIV exists a completely natural molecule of BRCA1 cDNA.

I'm pretty sure prior art doesn't work that way.

Isn't the standard here whether or not these molecules exist in nature? Honest question.

Re: Supreme Court: Natural Isolated DNA Not Patentable, Synthetic DNA Is [pdf]

#116

Post by daughart »

alsocasey wrote: post #106
daughart wrote: post #78

Earlier quoted context omitted.

From what I understand, Myriad's test involved synthesis of cDNA (which we scientists refer to as "complementary DNA", not "composite DNA" as SCOTUS does). This is still covered by the patent. However, any test based on sequencing the genomic DNA, for example, would not violate Myriad's patent. Genomic sequencing of these genes was previously a violation of the patent. This is definitely a step forward. In the long r…

The issue is that a hypothetical diagnostic attempting to sequence this region would likely be pre-processed with a PCR to facilitate sequencing of only the region of interest... this necessarily involves a cDNA step. You could sequence the whole genome at higher depth, but this would be more expensive. Edit: My mistake, the patent covers the reverse transcription step exclusively, not the act of transcription in gen…

PCR is not covered by the patent, only reverse transcription of the processed RNA molecule to cDNA. There are many flavors of genomic PCR that are fine under this interpretation, including a rapid SNP-detecting digital qPCR.

Re: Supreme Court: Natural Isolated DNA Not Patentable, Synthetic DNA Is [pdf]

#118

Post by daughart »

shmerl wrote: post #94
daughart wrote: post #81

Earlier quoted context omitted.

Really? Say goodbye to the promise of synthetic biology then!

You can say goodbye to it if that will be patentable. Someone will patent all combinations - and goodbye.

I suspect you are a troll, but I will respond anyway...

Sequence space is very large. There are only a total of 8 million US patents. There are 16 million 12-base-pair nucleotide sequences. To patent the sequence space of a functional product and regulatory region would require more patents than there are molecules in the universe.

Also to patent something you have to show use.

Re: Supreme Court: Natural Isolated DNA Not Patentable, Synthetic DNA Is [pdf]

#119

Post by nsxwolf »

joshmlewis wrote: post #70
michael_miller wrote: post #61

Earlier quoted context omitted.

I know you meant well with your comment, but in general, it's best to avoid well-actually comments. This is one of Hacker School's core rules; they elaborate on why it's a good idea to avoid these types of comments at https://www.hackerschool.com/manual .

What you linked to wasn't the HN 'manual'? In the actual guidelines found here: http://ycombinator.com/newsguidelines.html it doesn't say anything about well actually comments. It says be smart in your discussions and don't just get opinionated, it says to present facts and actually address the thing that you're arguing over. I believe having proper arguments and discussions is one of the core things HN is about. It…

This is also such a terrific "well-actually" I'm glad he broke this non-existant rule. It is absolutely maddening to hear people misinterpret the 3/5ths rule, and I'm convinced basically no one in this country understands it.

Re: Supreme Court: Natural Isolated DNA Not Patentable, Synthetic DNA Is [pdf]

#120

Post by daughart »

ryusage wrote: post #109
daughart wrote: post #88

Earlier quoted context omitted.

What I'm referring to is not only synthesis (artificially generating), but design and engineering. This is substantively different than natural products, in that they are truly invented.

The problem I have with it is that, in all cases, any synthetic DNA could exist in nature. We can't even verify with 100% certainty that any given sequence doesn't already exist in nature. If it doesn't exist already, it could in the future, naturally, through evolution.

As I pointed out to shmerl above, sequence space is very large, and in general sparsely populated. A functional gene product and regulatory sequence is often thousands of base pairs. 4^1000 = 10^600. There are only 10^80 molecules in the universe. So if you have done truly de novo design, you can be pretty sure it doesn't exist somewhere else by random chance.

That being said, I think that even if you take a natural gene and modify it meaningfully - that should be patent-able. For instance, if you take an enzyme and engineer a version that doesn't degrade as readily, or has much better activity, that should be patent-able, don't you think?

EDIT: There's a good deal of prior art regarding numbers. As for patenting molecules, we allow that all the time... drugs, compounds, etc. Because they are discovered as I describe above.

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