Problem-Solving Bacteria Crack Sudoku

techbeat writes "A strain of Escherichia coli bacteria can now solve logic puzzles – with some help from a group of students at the University of Tokyo, Japan, reports New Scientist. The team began with 16 types of E. coli, each colony assigned a distinct genetic identity depending on which square it occupied within a four-by-four sudoku grid.The bacteria can also express one of four colors to represent the numerical value of their square. As with any sudoku puzzle, a small number of the grid squares are given a value from the beginning by encouraging the bacteria in these squares to differentiate and take on one of the four colors. The Tokyo team's sudoku-solving bacteria competed in the International Genetically Engineered Machine competition at the Massachusetts Institute of Technology last week."

I smell a conspiracy!

[kheldan]

It is my contention that this scientific breakthrough has been intentionally hushed-up by politicians from both sides of the aisle so that it wouldn't be released before elections just a few weeks ago. Why, even here in California, this remarkable bacteria, showing much more intelligence and logical-thought ability than anyone else on the ticket, would have been a write-in landslide victory for governor!

Generalized Sudoku is NP-complete

[dido]

The Sudoku problem is in general NP-complete [u-tokyo.ac.jp]

. If they can get the bacteria to solve a puzzle in the most general form efficiently, they might be on to something big. I have the feeling though it may turn out to be just as effective as Leonard Adleman's (the A in RSA) attempts at solving Hamiltonian Cycles and other NP-complete problems with DNA-based computing: incredibly promising, but running into practical issues as the problems grow from the trivial to the interesting.

The interesting part of this article

[shadow_slicer]

The interesting part of this article (to me) is not that they made bacteria solve sudoku. What I find interesting is how they solved it:

1) Unlike most sudoku solvers, which use a centralized algorithm. The bacteria use a distributed algorithm: Each individual bacteria cell only knows the contents of cells in their row or column. It's actually a lot more complicated than this though, since there are many bacteria cells for each sudoku square and cells only respond to the first signal they hear from a given position. Given enough bacteria (or time to grow them), the bacteria could brute force a solution (though there appear to be some inherent heuristics that would make a solution probable without the bacteria differentiating into all possible types).

2) The way logic is implemented. They use, what they call a 4C3 leak-switch. This basically is a piece of RNA that codes for 4 different proteins. This piece of RNA can only be transcribed to proteins when there is only one protein left. When the signal is received from another cell, it removes the part of the RNA corresponding to that protein.

3) The communication infrastructure. The bacteria communicate by releasing simple viruses (coded for using the 4C3 leak-switch). These viruses are specialized to only infect bacteria in a certain row or column. When the viruses infect a bacteria they remove the part of the RNA in the 4C3 leak-switch. The viruses are specialized to only infect cells in the corresponding row or column.

The amount of biological power employed in this case is actually rather frightening. This requires the creation of (at least) 16 unique viruses and 16 unique bacteria. Specific receptors for the viruses to bind to the bacteria must have been designed and the protein for both the virus coat and payload transcription need to be tweaked and introduced to the bacteria. A sufficient quantity of each bacteria must have been created.

Re:Call me when...

[delinear]

Taniuchi does say in this article [newscientist.com] "By expanding these principles, 81 types of bacteria could solve a full nine-by-nine grid" - the number of squares that can be solved seems to be entirely dependent on the number of bacteria types, and they were working with 16 types. I don't know how easy it would be to expand that to 81 types (I don't know what differentiates a bacteria "type" or how many variants are commonly available, etc). I assume there was some reason they didn't go with 81 types right away, but maybe it was just time limitations and the maths is solid enough that you can reasonably extrapolate up from a small sample.