2019 · Nature
Genetic compensation triggered by mutant mRNA degradation
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. The worse layer decides.
How the verdict is decided
The verdict grades both layers: the paradigm this study assumes, and how the study was carried out inside it. Both must be scientific for the whole thing to be scientific. A clean method inside an unscientific paradigm is unscientific. An unscientific method inside a better paradigm is unscientific. A split on either layer is mixed. The worse layer decides.
1·Study methodology
Did this study test its claim with methods that are independent, falsifiable, and non-circular?
UNSCIENTIFIC
This study claims that when mutations produce RNA that gets broken down, the breakdown triggers nearby genes with similar sequences to make more RNA, protecting the organism from the mutation's effects. All three tests fail.
Independently Verifiable
Fail
The PCR machine produced fluorescence curves and the model told them those curves meant specific genes were upregulated, but a stranger sees curves, not transcriptional adaptation.
Falsifiable
Fail
The study offered a comparison between allele types that could theoretically show no difference, but the field has absorbers for any negative: gene-dependent mechanisms, technical sensitivity, or additional pathways.
Non-Circular
Fail
The primers were designed from reference sequences built by the DNA model, and those same primers detected the expression changes the model now claims as evidence.
Why
They took zebrafish embryos and mouse cells and used CRISPR tools designed from known genomic sequences to create mutations in specific genes. They extracted RNA using chemical solutions and reverse-transcribed it. PCR machines produced fluorescence curves, and the model told them those curves meant particular genes were expressed at certain levels. They compared expression between alleles that produce mutant RNA and alleles that produce none. Sequencing machines produced flashes of light, and software aligned those signals to a reference genome assembled using the same model. They used BLAST to find sequence similarity between genes, searching against that same reference. They called the upregulation of similar genes transcriptional adaptation. The fish were sorted into groups by genotyping PCR, which assumes the model to decide which fish carry which mutation. At no point did anyone see a gene being upregulated or RNA being degraded. They saw curves and reads on screens, and the model told them what the signals meant.
2·Paradigm · Genomics / DNA Model
Does the framework this study assumes pass the three tests?
UNSCIENTIFIC
Independently Verifiable
Fail
Nobody has seen DNA, let alone read a code in it; the sequencer produces flashes of light and the model tells them those flashes are genes.
Falsifiable
Fail
If a CRISPR cut fails to produce an expected change, nobody concludes the DNA model is wrong; they conclude the guide was poorly designed or the gene is redundant.
Non-Circular
Fail
The reference genome was assembled using the DNA model, the primers were designed from that assembly, and the detection confirms what the assembly already named.
Why
The DNA model says that sequences of chemical letters inside cells carry instructions for building organisms. Nobody has seen DNA, let alone read a code in it. The sequencer produces flashes of light and the model tells them those flashes are genes. The PCR machine produces a fluorescence curve and the model tells them that curve means a gene is expressed. When a CRISPR cut fails to produce an expected phenotype, nobody concludes the model is wrong. They conclude the guide RNA was poorly designed, the gene is redundant, or additional mechanisms are involved. The reference genome was assembled using the model. The primers were designed from that assembly. The detection confirms what the assembly already named. The model treats a fluorescence signal as a gene being expressed rather than asking what physically happened to the cells. Suppressing or boosting a signal is not the same as understanding what damaged the organism or how it responds.
From the study
RNA was isolated using TRIzol and at least 500 ng RNA was used for reverse transcription using the Maxima First Strand cDNA synthesis kit (Thermo).
Fold changes were calculated using the ΔΔCt method.
The reads were mapped versus the mm10 version of the mouse genome with STAR 2.4.2a using only unique alignments to exclude reads with unclear placing.
Genes were defined to be similar to the mutated gene when a partial match was identified inside the target gene body or its promoter region