2013 · Nature
Multiplex genome engineering using CRISPR/Cas9 systems
Verdict
UNSCIENTIFIC
Neither the paradigm nor the study inside it passes. The verdict is unscientific.
1·Study methodology · inside the paradigm
UNSCIENTIFIC
Does not follow the scientific method within Genomics / DNA Model.
2·Paradigm · Genomics / DNA Model
UNSCIENTIFIC
Fails the tests. This decides the verdict.
How the verdict is decided
The verdict grades the whole picture: the paradigm this study assumes, and how the study was carried out inside it. A study can follow the scientific method rigorously and still be unscientific, because rigor inside a paradigm only shows the conclusion was reached carefully. It cannot verify the premise the paradigm rests on. So the paradigm decides the verdict. The study’s own score is kept because it shows how the conclusion was built.
1·Study methodology
Did this study test its claim with methods that are independent, falsifiable, and non-circular?
UNSCIENTIFIC
The paper sells the idea that short RNA molecules can direct a nuclease to cut what they call endogenous genomic loci in mammalian cells, enabling programmable editing of what they call the genome. All three tests fail.
Independently Verifiable
Fail
The paper never shows a genomic cut outside a protocol where guide RNAs were built from a reference sequence that already assumes the DNA model.
Falsifiable
Fail
No result in this design could have killed the claim, because a failed cut would be absorbed as a poorly designed guide or low transfection efficiency.
Non-Circular
Fail
The guide RNAs were designed from reference sequences and the cut was confirmed by sequencing, so the tool was built to find what the model already named.
Why
The authors designed guide RNAs from computationally assembled reference sequences, loaded them into cells with Cas9, and then used sequencing to confirm that cleavage occurred at the addresses the model predicted. A fluorescent reporter and loss-of-function phenotypes appeared downstream of constructs built entirely from the DNA model. The visible phenotypes are not independent observations because the guide RNA that produced them was directed by a sequence that presupposes the genome model. The confirmation instrument, sequencing, is the same model running its own process and reporting the output as evidence. If no phenotype appeared, the authors would blame the guide design or transfection conditions, not the premise that DNA is a hereditary code being edited. Every link in the chain, from reference sequence to guide design to sequencing confirmation, depends on the model the paper claims to validate. That is a closed loop. The study never steps outside that loop.
2·Paradigm · Genomics / DNA Model
Does the framework this study assumes pass the three tests?
UNSCIENTIFIC
Independently Verifiable
Fail
What they call a genome has never been observed functioning as a hereditary code inside a living cell using an instrument that does not presuppose the model, and this paper is no exception.
Falsifiable
Fail
If a CRISPR cut fails to produce a phenotype, nobody concludes the DNA model is wrong; they blame the guide RNA, and this paper follows that escape pattern exactly.
Non-Circular
Fail
The reference sequences used to design the guides were computationally assembled from extracted material using the DNA model, and the sequencing used to confirm the cut presupposes the same model.
Why
The Genomics / DNA Model paradigm claims that DNA functions as a hereditary code inside living cells. What they call DNA has never been observed performing that role with an instrument that does not already assume the model. This paper inherits that failure completely. The authors built guide RNAs from reference sequences that were computationally assembled using the DNA model, directed those guides to addresses the model named, and then used sequencing, a model-dependent readout, to confirm the cut. The fluorescent phenotype is downstream of a circular tool. Downstream of circular is still circular. The paradigm absorbs every failure as a technical issue: a failed cut means the guide was wrong, not that the model is wrong. Missing heritability and epigenetic complexity absorb every gap. The terrain distinction applies here as well. The allopathic model that wraps around genomics treats the cell as a machine whose code can be rewritten, ignoring that cellular behavior is a response to the terrain the cell lives in. Suppressing a function or forcing a fluorescent signal is not the same as understanding why the cell behaves as it does.
From the paper
Guide RNAs were designed from the reference sequence of each target locus.
Cleavage at the named genomic address was assayed by sequencing of the target locus and by loss-of-function or fluorescent reporter phenotypes.
Cas9 nucleases can be directed by short RNAs to induce precise cleavage at endogenous genomic loci in human and mouse cells.
Source
Multiplex genome engineering using CRISPR/Cas9 systems
Cong, L; Ran, FA; Cox, D; Lin, S; Barretto, R; Habib, N; Hsu, PD; Wu, X; Jiang, W; Marraffini, LA; Zhang, F
2013 · Nature
Scored from full text · Rubric 1.0