Recently, a paper in Nature on building neural networks with DNA-based switches caught my attention.[1] The authors, Kevin Cherry and Lulu Qian, developed an interesting system that uses DNA base pairing to implement a trainable neural network. However, for me, what was even more interesting was a story hidden in the Methods section and Supplementary Information.

How can DNA learn?

As I discussed on this blog back in 2023, DNA base pairing can be used to perform computations. Back then, I was writing about relatively simple computational systems, for example ones that could add two 6-bit numbers. These were built of logic gates, like an AND gate that releases a piece of single stranded DNA only when two other “input” strands are present.

The current paper goes far and beyond this. The authors came up with a clever system of making DNA logic gates that don’t interfere with each [...]

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Outline:

(00:36) How can DNA learn?

(03:20) How did the authors learn from DNA?

(08:07) What can we learn from this story?

The original text contained 3 footnotes which were omitted from this narration.

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First published:
September 9th, 2025

Source:
https://www.lesswrong.com/posts/dbkAw25xbgN6ENERA/a-profile-in-courage-on-dna-computation-and-escaping-a-local

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Narrated by TYPE III AUDIO.

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Images from the article:

Diagram showing three steps: toehold binding, branch migration, and strand dissociation.

The image shows two design diagrams comparing inhibited weight, activator, and label configurations. The diagrams illustrate different layouts and components, with Design 1 showing a simpler arrangement compared to Design 2's more complex structure with additional elements and connections.

The key components shown in both designs include:
- Inhibited weight (W*i,j)
- Activator (Act i,j)
- Inhibited activator
- Label sections
- Various nodes and connections marked with symbols like Tj, Xi, U, B

Design 2 introduces additional elements and more intricate pathways compared to Design 1, with both designs using color-coding (blue and red) to distinguish different parts of the system.

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“A profile in courage: On DNA computation and escaping a local maximum” by Metacelsus

LessWrong (30+ Karma)