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Comment by daughart | Hacker News Reader

It's not clear to me what you are saying. Cas9/CRISPR unambiguously cuts the genome at a target site determined by the guide RNA sequence. In the presence of a DNA oligo with partial complementarity to the cut site, the DNA repair mechanism will sometimes incorporate the "payload" oligo, causing the genetic locus to be engineered from one sequence to another, predetermined sequence.

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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 x 10^5 mutants, corresponding to 25% of the total.

It depends on the initial number of cells, initial proportion of mutants, division rates, and toxicity. I have also noted that the initial number of cells is usually reported without any uncertainty, which makes me think those numbers may be rather unreliable.

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.

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.

I'm assuming you're trolling so I will stop responding. CRISPR isn't my field and I'm not going to dig into supplements to disprove your theory, which is that CRISPR is not real somehow? I work in the Church lab. I know tens of researchers personally who use this technology. I am confident that CRISPR is real. However, attempting to prove this to you is a waste of my time.

Why would you assume someone providing references that contradict your unreferenced claims is trolling? I am not trolling. Also, I am not claiming that the usual mechanism proposed to explain this data is wrong, only that the published data is just as consistent with a selection mechanism. AFAICT, no one knows either way.

Please link to the data that you believe contradicts my proposed mechanism.

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