The reason they could opt for a more information-dense bit is because of the physics of the reading head. When the head sticks to a -1, it contorts in a predictable way. When it sticks to a section deemed +1, it contorts the opposite way. For 0, no contortion.
Then, if you shine light at the molecular machine while it reads, each of the three contortions will twist that light in a unique way. The scientists were able to follow along with how the head was changing its shape by reading this light. They used a process called circular dichroism spectroscopy to determine the shape of the ratchet as it
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