The Villain of CRISPR • Hacker News Board

Re: The Villain of CRISPR

#51

Post by wavefunction » Mon, Jan 25, 2016, 5:46 PM UTC

jedberg wrote: post #34

daughart wrote: post #32

Earlier quoted context omitted.

It will take millions of dollars of research to turn this basic bioengineering technique into an approved (safe and effective) human therapy. How do you motivate investors to fund this research without the safety net of a patent to protect that investment from free-loaders?

The way it was done before patents -- government funded research institutions whose only motivation was to provide scientific breakthroughs so they could continue to receive government funding.

That's a very cynical and inaccurate appraisal of "The Time Before Patents."

Most scientific breakthroughs throughout history were pursued due to simple curiosity or necessity, precisely because without an international framework of patent law "patents" and the pursuit of technology as intellectual property directly for financial gain was impossible.

The British for example attempted to control physical access to textile IP but Samuel Slater[1] memorized as much as he could and "exported it" along with himself to the Americas to reap a fortune.

[1]https://en.wikipedia.org/wiki/Samuel_Slater

Re: The Villain of CRISPR

#52

Post by jedberg » Mon, Jan 25, 2016, 5:48 PM UTC

daughart wrote: post #46

jedberg wrote: post #34

Earlier quoted context omitted.

The way it was done before patents -- government funded research institutions whose only motivation was to provide scientific breakthroughs so they could continue to receive government funding.

There's a huge gap between the scientific breakthrough and the work needed to create a safe and effective therapy. It's not academically interesting, and academic scientists won't do it. It's optimization, not discovery. And what about the cost of the clinical trial, which could be $500m? Government funded research institutions will continue to provide BREAKTHROUGHS to receive funding.

> And what about the cost of the clinical trial, which could be $500m?

That's an interesting one, because that cost is entirely caused by the government. The government could for example fund clinical trials, since they're the ones who are interested in it's results (as is by extension the public).

As for the rest, if the science were freely available without a patent from the scientists, companies could still spend money making it a therapy and making a profit by doing it better and more efficiently than their competitors, and they could still get a patent on their work.

We're talking about making the science patent free, not the product.

Re: The Villain of CRISPR

#53

Post by nonbel » Mon, Jan 25, 2016, 5:50 PM UTC

cowsandmilk wrote: post #45

nonbel wrote: post #31

Earlier quoted context omitted.

Please link to one/some of the papers you are referring to. From what I have seen, they always detect edits in the controls or fail to report enough information to say either way, eg: "Although rare (∼1–2%), edits were detected with Cas9-only control treatment, including at the predicted CXCR4 cut site, potentially indicating trace amounts of experimental contamination of the Cas9 RNPs." http://www.pnas.org/content/1…

What other controls do you expect to see? Dataset S1 seems complete to me. There is a similar background level of indels both at the CXCR4 site and off-target 1 and off-target 2 sites. The experiment increases indels at the CXCR4 site, but not at the off-target sites.

The proportion of HDR (ie HindIII reads only) without the template. What percent of cells will randomly mutate to get HindIII recognition sites?

Also, seeing what happens using template only would be good. We would expect low baseline levels of HDR to occur right? I it is plausible few out of 10^5 or 10^6 cells will require repair at that locus even without any Cas9.

Re: The Villain of CRISPR

#54

Post by nonbel » Mon, Jan 25, 2016, 5:53 PM UTC

daughart wrote: post #48

nonbel wrote: post #44

Earlier quoted context omitted.

Start with 10^6 cells. Say 0.1% (1 in 1000) are already mutants at that site. Then add something that kills 100% the non-mutants and you will be left with 10^3 mutants without any gene editing. Say it kills 50% of the non-mutants and renders the rest quiescent due to DNA damage (not dividing), then you are left with 10^3 mutants and 5 x 10^5 non-mutants at time t0. After eg 7 divisions you will have 10^3 x 2^7 = 1.28…

No pre-existing cells have the mutation at the site you're trying to engineer. It just doesn't happen. Otherwise selection alone would be good enough. But mice cells don't have that much intrinsic variation. Plus a lot of time they're inserting whole genes or larger payloads. The statistical probability of that arising from chance is zero.

>"No pre-existing cells have the mutation at the site you're trying to engineer. It just doesn't happen."

Not in any paper on CRISPR I have read, in fact just the opposite: there are always low levels of mutants found in the controls (eg Schumann et al 2015 linked below). Please link to the papers that have lead you to make this claim.

Re: The Villain of CRISPR

#55

Post by akiselev » Mon, Jan 25, 2016, 6:03 PM UTC

daughart wrote: post #32

junto wrote: post #20

I hate the fact that breakthroughs like this are patentable. People need to follow Alexander Flemings lead: The pharmacist Sir Alexander Fleming is revered not just because of his discovery of penicillin – the antibiotic that has saved millions of lives – but also due to his efforts to ensure that it was freely available to as much of the world’s population as possible. Fleming could have become a hugely wealthy man…

It will take millions of dollars of research to turn this basic bioengineering technique into an approved (safe and effective) human therapy. How do you motivate investors to fund this research without the safety net of a patent to protect that investment from free-loaders?

How about the way we do it now, with patents on devices, therapies, and drugs that are approved by the FDA instead of on the techniques used to develop them? There is even a way to extend the patent life of these developments to account for the amount of time it takes to receive government approval with a maximum term of 14 years after approval [1]. Patenting such a fundamental technique as CRISPR will only set back research for more than a decade and prevent most investors from funding further research while giving companies a huge headstart if they are located outside of the USPTO's jurisdiction.

[1] http://www.fda.gov/Drugs/DevelopmentApprovalProcess/SmallBus...

Re: The Villain of CRISPR

#56

Post by biehl » Mon, Jan 25, 2016, 6:03 PM UTC

jedberg wrote: post #52

daughart wrote: post #46

Earlier quoted context omitted.

There's a huge gap between the scientific breakthrough and the work needed to create a safe and effective therapy. It's not academically interesting, and academic scientists won't do it. It's optimization, not discovery. And what about the cost of the clinical trial, which could be $500m? Government funded research institutions will continue to provide BREAKTHROUGHS to receive funding.

> And what about the cost of the clinical trial, which could be $500m? That's an interesting one, because that cost is entirely caused by the government. The government could for example fund clinical trials, since they're the ones who are interested in it's results (as is by extension the public). As for the rest, if the science were freely available without a patent from the scientists, companies could still spend…

Exactly. An evaluation of the efficiency of "buying" clinical trials with patents would be very interesting.

Re: The Villain of CRISPR

#57

Post by nonbel » Mon, Jan 25, 2016, 6:09 PM UTC

jimrandomh wrote: post #40

nonbel wrote: post #15

I have never seen a paper on CRISPR that can distinguish between selecting pre-existing mutants and actually modifying genes. I have read probably a dozen or so at this point, and it is amazing that they always fail to address this either in citations or actual data. At first I thought it was an honest mistake, but now it would not surprise me if some of the main players know that their experiments with CRISPR have b…

The papers I've looked at sequence and measure the on-target mutation rate, and don't have any steps in them that would select for mutants (because that would ruin the measurement). Where do you propose the selection for mutants would be happening? Unless I'm misunderstanding something about how the experiments are done, your theory would require many groups to be independently committing scientific fraud, which is v…

No fraud is necessary, just sloppy interpretation of data.

Staying with Schuman et al (2015) linked in this thread, they start with 2.5 x 10^5 cells and end up with 5 x 10^4 to 2 x 10^5 three to four days later. Why are there fewer cells even without accounting for any division? Because the treatment is toxic. This is reported in many papers.

I don't know what the proliferation rate is like for the cells in the conditions of that study, but apparently up to 7 divisions in 4 days is considered plausible for T-cells: http://www.ncbi.nlm.nih.gov/pubmed/17367338

Re: The Villain of CRISPR

#58

Post by daughart » Mon, Jan 25, 2016, 6:20 PM UTC

nonbel wrote: post #54

daughart wrote: post #48

Earlier quoted context omitted.

No pre-existing cells have the mutation at the site you're trying to engineer. It just doesn't happen. Otherwise selection alone would be good enough. But mice cells don't have that much intrinsic variation. Plus a lot of time they're inserting whole genes or larger payloads. The statistical probability of that arising from chance is zero.

>"No pre-existing cells have the mutation at the site you're trying to engineer. It just doesn't happen." Not in any paper on CRISPR I have read, in fact just the opposite: there are always low levels of mutants found in the controls (eg Schumann et al 2015 linked below). Please link to the papers that have lead you to make this claim.

That is far more easily explained by contamination, which, as you mention, is actually how they explain it in papers.

Re: The Villain of CRISPR

#59

Post by nonbel » Mon, Jan 25, 2016, 6:32 PM UTC

daughart wrote: post #58

nonbel wrote: post #54

Earlier quoted context omitted.

>"No pre-existing cells have the mutation at the site you're trying to engineer. It just doesn't happen." Not in any paper on CRISPR I have read, in fact just the opposite: there are always low levels of mutants found in the controls (eg Schumann et al 2015 linked below). Please link to the papers that have lead you to make this claim.

That is far more easily explained by contamination, which, as you mention, is actually how they explain it in papers.

Here is another (supplementary table 2). https://www.ncbi.nlm.nih.gov/pubmed/26121415

I can keep going, but would prefer you bring references of your own so I cannot be accused of cherry picking.

Re: The Villain of CRISPR

#60

Post by eggie » Mon, Jan 25, 2016, 6:39 PM UTC

KasianFranks wrote: post #12

A Nobel Prize is now at stake. Lifespan, disease and the human race is at stake. The internal scientific politicking on both sides is classic. "by going into depth about the contributions of early CRISPR pioneers, Lander is able to almost literally write Doudna and Charpentier (and, for that matter, genome-editing pioneer George Church, whose CRISPR work has also been largely ignored) out of this history. They are me…

> Lifespan, disease and the human race is at stake.

CRISPR is just one tiny replaceable part of any therapy-driving genome editing technique. The frenzy around it overstates its importance.

Cas9 is significant as the first RNA-guided nuclease that we learned how to manipulate, but there are probably many more in nature. Hopefully we will be able to construct our own in short order.

We have had very high quality programmable nucleases for a long time. Nucleases are not the principal expense in genome engineering. Further, if you want to be sure that the cuts you make are correct and on-target you might want to take the time to use another system than Cas9/tracRNA.

However, dCas9 (disabled Cas'es) and friends are amazingly novel, in that they allow us to make huge libraries of targeted DNA binding complexes that don't cut DNA, but let us pull particular things to particular places in the genome. This is an incredible boon to certain research threads. For example, see http://www.sciencedirect.com/science/article/pii/S0092867413...