For Humanity
Everything here is free, with no signup. Three parts: the mechanism, what it opens up, and the experiment that tests it. These are live documents and they change as we learn.
What we found
DNA read as a machine rather than as a text. The same control grammar appears in bacteriophages and in the human genome.
The Absolute Syntax
A conserved repeat and reverse-transcriptase architecture in jumbo Staphylococcus phages. The mechanism, the coupling math, and a comparative analysis of SA1 and MarsHill.
Human Frontier ART
Applying the phage grammar to the human genome. Retroelement regulation on chromosome 21, stated with its own limits.
What it would make possible
Forty applications across the two papers, each written twice: once in technical terms and once in plain English.
The Absolute Syntax: Use Cases
Twenty applications of the phage brake grammar, each one explained in plain English. Ten open to anyone, ten held.
Human Frontier ART: Use Cases
From diagnostics to gene-therapy architecture, in plain English. What the human findings would make possible if they hold.
The experiment
The model predicts that a specific 12-nucleotide sequence halts reverse transcriptase mid-copy, and that a scrambled version of the same bases does not. These four documents specify that experiment: the sequences, the protocol, the controls and the enzyme.
How the four fit together
Read 1 for the mechanism and the coordinates. Order the four sequences in 3. Run the procedure in 2 with an off-the-shelf enzyme from 4, which needs no gene synthesis. One day of bench work once the sequences arrive.
The control carries the design. It holds the same five A and seven T bases as the consensus motif and matches its nearest-neighbour melting temperature to three decimal places, so a difference in pausing cannot be attributed to composition or to melting. It is screened on both strands against the LINE-1 insertion consensus, the σ70 −10 element, the TATA-box core and the polyadenylation signals. Selection criteria are in 3.
Technical Brief
The mechanism behind the 12-nucleotide AT motif, its genomic coordinates, and the enrichment reported at p = 0.065 rather than rounded up. Ends with a section on what the package does and does not establish.
Bench Protocol
A primer-extension assay testing whether the motif arrests reverse transcriptase. Reagents, timings, the controls that make a result interpretable, and how to read the gel.
Oligo Package
Four sequences, ready to order. The consensus template and a control matched to a melting-temperature difference of 0.000 degrees, screened on both strands against known regulatory and insertion motifs.
Construct Specification
The reverse transcriptase to express, with accession, coordinates and full protein sequence. Includes a commercial-enzyme pilot that needs no gene synthesis and is interpretable whichever way it comes out.