Origin Stories: DNA Transposition

I find the entire concept of genetic code fascinating. I’ve taken a few biology classes over the years, and every time we discussed DNA, I marveled at how something could simultaneously be so simple yet so complex. Thus, I had wanted for a long time to make a puzzle that relied on DNA.  I knew the opportunity for that puzzle had arrived in the summer of 2010, when I learned of the topic for one of the Volume 18 issues of Imagine: Biotechnology. The second puzzle was subsequently created in 2013, for the Frontiers in Medicine issue.

In the earliest brainstorming phases of creating a brand new type of puzzle, I usually start by writing down all the ideas that I have. No matter if they become part of the puzzle or not, I just want to make note of everything in my head, so that later thoughts or avenues I pursue don’t cloud my original ideas. Sometimes, those original ideas are changed significantly by the time the final puzzle is produced. (Sometimes the original ideas don’t produce anything of value whatsoever!) Remarkably, for the DNA transposition puzzles, much of my original ideas appear unchanged in the final puzzle.


Notes from July 22, 2010:

Going back to mazes with structure and rules1, the puzzle contains a set of connected paths. What governs which paths you can take at any intersection is a token that changes. (Instead of keeping track of this in the physical space, like in the Cell Wall Transport System puzzles, this puzzle uses an external item, more like the subway token puzzles2.)

You have a bit of DNA. Some intersections do nothing, but some rearrange bits of the DNA according to order. For example,

rearrange

would move the first bit to between the third and fourth (making it the new third). So GATC would become ATGC.

Different paths have different restrictions. For example, a path could only let pass bits of DNA that have the sequence “GA”. The original piece of DNA could pass through this, but not the new rearranged piece (as it does not have “GA”).


The crucial idea of a “token” that you carried through the puzzle was essentially what made this puzzle different from my previous puzzles, and helped to clarify the instructions to others. The “intersections” became the bubbles in the final puzzle, while the “paths” became the connecting tubes. The diagram is meant to be an iconic representation of the prototypical chemistry lab apparatus.

dnat.Puzzle00

The instructions took several passes, with the assistance of a few biologists called in by myself or my editor, adjusting the vocabulary to best fit what was happening in the puzzle. For example, I initially used the word translocation, which I found out typically refers to moving whole parts of a chromosome. Transposition is more appropriate when moving a shorter sequence or, in this case, individual nucleotides. Also, using the term DNA isn’t appropriate here, since DNA refers to the entire molecule, not a short sequence of nucleotides. The instructions therefore use the term genetic material, even though DNA is retained in the name of the puzzle.

The design of the puzzle took a while to finalize.  I needed to visually communicate how each bubble transformed the genetic material.

bubbles

Early attempts directly translated what I had in my notes, using numbers to show the rearrangement of nucleotides. These needed to be large to clearly display the numbers, but were too large and too cluttered for the rest of the puzzle. Thankfully, I hit upon the idea of completely eliminating the numbers and letting greyscale boxes denote the positions of the nucleotides.

This type of puzzle necessitates charting all possible paths through the problem space in order to ensure the designated solution is the shortest. In other words, every pairing of position and genetic token that is possible by moving through the puzzle must be examined. Because of the cyclical nature of the puzzle (repetitively rearranging the nucleotides and moving back to the same physical position in the puzzle), loops are possible (moving around the puzzle and returning to the same location with the same order of nucleotides). This challenge of representing a problem space with these loops was resolved by using one-way arrows.

dnat.Solution00PS
Problem space for example DNA Transposition puzzle, shown above

Moving up each arrow loops back to a position that could have been achieved using fewer moves (sometimes utilizing a very different path through the puzzle), while the most direct solution is highlighted in blue.

  1. I now call these hybrid puzzles.
  2. The subway token puzzles were originally written for an educational psychology class on creativity I took in graduate school. I later created a set of those puzzles for the 5th and 6th grade Math Meet, an annual event for local school children hosted by the University of Wisconsin–Madison math department.