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Perceptron theory · the wet body · molecular

The perceptron in DNA

No wires, no light, no chip — a test tube. Encode the weights as the amount of each DNA strand in solution; the multiply happens because two strands meet at a rate proportional to the product of their concentrations; the sum happens because many reactions pour into one output species. The threshold is a real molecule that soaks up signal until a level is crossed. It is slow as syrup and runs once — but every molecule is a processor, and it computes inside a drop of water.
weights = strand concentrations  ·  multiply = mass action k[A][B]  ·  sum = a shared output strand  ·  threshold = a seesaw gate
✓ STRONG

Strand displacement & seesaw gates. The primitives are built and characterised — Qian & Winfree's seesaw gates made working DNA logic and a 4-neuron Hopfield net in a tube (2011).

◐ MIDDLING

DNA neural nets. Cherry & Qian (2018) classified handwritten digits in solution — real, but hours-slow, one-shot, and hard to reset or scale.

◔ FRONTIER

Practical / in-vivo molecular computers. Reusable, fast, in-cell DNA computation — open. Today it's a beautiful proof, not a workhorse.

I · The multiply is a collision

Two strands — an input and a weight — drift in solution. They react only when they bump into each other, and the rate of bumping is set by the law of mass action: rate = k · [input] · [weight] A product of concentrations is a multiply, done by diffusion. Turn the weight strand up and the same input produces more output: a tunable synapse made of nucleotides.

input + weight strands collide → output accumulates at rate k[A][B]
reaction rate ∝ [A]·[B]
0.00
output produced (the product)
multiply= mass action [A][B]weight= a strand amountspeed= minutes to hours

II · The threshold is a seesaw

Summing is easy — many reactions feed one output strand and its concentration adds them up. The hard part, the nonlinearity, is a real trick: a threshold strand that greedily consumes signal until it's used up, after which the output restores sharply. The result is a sigmoid in chemistry — below the threshold, almost nothing; above it, a clean ON. That seesaw gate is a DNA neuron.

the seesaw restoration curve · ● is your operating point · below threshold ≈ OFF, above ≈ ON (a molecular sigmoid)
0.50
restored output
OFF
fires above threshold

III · Learns, and cascades for depth

Set the weight concentrations and the molecular neuron learns AND/OR; one gate is one cut, so XOR needs a second layer of gates fed by the first's restored output — depth, in cascaded reactions. The gift is parallelism and place: the computation happens everywhere in the volume at once, in the same medium as biology.

target:
press train
the gift= massively parallel, in solutionthe cost= slow (hrs), one-shotthe dream= compute inside a cell

Honest place in the family: DNA won't out-run silicon at anything you'd time with a clock. Its case is where it runs — in a droplet, in tissue, in the body — doing a small classification with no hardware at all. A real perceptron you could, in principle, swallow.

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