New Neuron Activation Level puzzles posted! https://t.co/xAZXleC8BR
— Tim Boester (@knossosgames) October 22, 2016
Enjoy these two neuron-based puzzles. More updates coming…
It was an active summer here at Knossos Games HQ, with two warm-weather themed updates (Park Trails and Park Cleanup Logic puzzle). But the big news was that Tim moved to Chicago to start his new job as the Director of the Mathematical Sciences Learning Center at the University of Illinois at Chicago.
As always, the Knossos Games summer hiatus was spent preparing updates and puzzles for the magazine and website (as well as packing and unpacking a lot of boxes!). As I’ve commented before, several things are always going on at once, and the summer was spent writing puzzles, preparing site updates, and generally getting things organized. There are a lot of exciting updates coming!
An ongoing catalogue of Knossos Games website issues and minor updates.
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Fixed a bug I discovered in the old version of the Categories listing (from the Version 6 section of the site) that occurred when I updated the Greek Temple puzzles in April. That listing is not regularly updated, but is maintained to support the Version 6 section of the website.
Unfortunately, the Park Trails puzzle wasn’t completely finished in time for June 4 as planned. The solution page was later updated to include a detailed solution and the photo on the instruction page was updated to fix a resolution problem (using the standard trick of having a higher resolution image, in this case 800 x 600, displayed at a lower resolution, 400 x 300).
On April 29, they reported that Universal Uclick, the syndicator of the puzzles, confirmed the allegations that the crossword puzzle themes had been copied from those found in the New York Times.
But the editor of the crosswords, Timothy Parker, would only be placed on a three-month leave, which led to an uproar in the puzzlemaking community.
Then on May 10, FiveThirtyEight reported that Parker was out as USA Today’s crossword puzzle editor, although they would retain Universal Uclick’s services, albeit with a new puzzle editor.
Note: this entry contains minor spoilers about the solutions to the two DNA Transposition puzzles. Go solve them first!
Back when the first DNA Transposition puzzle was printed in Imagine, we were concerned that readers would not completely understand how to solve the puzzle given the abbreviated instructions printed in the available space. In situations like this, the website comes in handy: we can post detailed instructions and examples and print a link in the magazine in case readers want more information. So that’s what we did, but I never got around to posting the actual puzzle (or the second one) until now.
Regardless, I discovered and fixed a few flaws in the original graphics before posting this update. Most of my attention focused on the solution graphics, both the path through the apparatus and the tree diagram showing the problem space. Finding the appropriate way to show a path that loops and doubles back on itself in a single diagram was tricky. I found that creating template path pieces worked best – these could be assembled then merged together to form one seamless, semi-transparent path.
Representing loops in the problem space diagrams presented a similar challenge. I first charted out each problem space on paper, then created a digital version that could be rearranged so that loop connections would be close together (or as close together as possible). Several alignment issues were also corrected in the problem space diagrams.
Compounding all of this in the second puzzle was, in addition to an intended (shortest) solution, an additional solution that merited attention. This meant creating multiple solution path graphics, all of which needed to share the same visual language, and creating a single problem space chart that could highlight each solution separately while still being compact and coherent overall.
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,
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.
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.
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.
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.
An ongoing catalogue of Knossos Games website issues and minor updates.
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The big update for this month was the DNA Transposition puzzles. While the instructions had been posted when the first puzzle appeared in Imagine, neither the first nor second puzzle had ever been posted to the website before.