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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."
Try this URL instead.
What one fool can do, another can. (Ancient Simian Proverb)
Slashdot, I applaud your enthusiasm about synthetic biology and the iGEM competition. For all you interested folks out there, check out 2010.igem.org for information about the competition, and take a look at all the awesome wikis made by teams who competed. Also check out the results page at ung.igem.org/Results?year=2010.
-From your friendly 2010 iGEM competition participant
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!
Are YOU using the TOOL, or is the TOOL using YOU? Think about it!
Since when is a Sudoku puzzle 4 by 4 with 16 cells? I always played the nine by nine version with 81 cells.
but out of all bacteria that could use used why use one associated with human disease?
How many bacteria can you think of that are not associated with some human disease? Even the yeast that we use to make beer (and bread) can be a disease agent under the right (or wrong) circumstances.
That said, for each bacterium you can name that is associated with disease, the same has numerous strains that don't harm humans. The E Coli used in the lab is not the same strain that is found in cattle feces.
Damn_registrars has no butt-hole. Damn_registrars has no use for a butt-hole.
Disease and biological study are sort of a circular dependency.
E.coli is one of the best biological test organisms because we've studied it so much. We understand most of its genetics, reproductive behavior, control signals, metabolism, etc... in part because it's fairly simple, but also precisely because it causes disease so it has been studied a lot in the past. It's also not very pathenogenic compared to most organisms... anything out of control is dangerous but it grows slowly and needs a lot from its environment so it's easy to keep in check.
The same holds true for a lot of "model organisms" (species that biologists can mess with without too many moral complications, like E.coli and fruit flies). S.aureus ("Staph") and Y.pestis (the plague) are horrific little bugs if they go unchecked in the wild... but they have a lot to teach us and if we can learn how to stop them we stand to gain a lot. Soo they're among the most studied species out there. Same goes for S.cerevisiea... baker's yeast :).
G
Cultivated strains (e.g. E. coli K12) are well-adapted to the laboratory environment, and, unlike wild type strains, have lost their ability to thrive in the intestine. Many lab strains lose their ability to form biofilms.[70][71] These features protect wild type strains from antibodies and other chemical attacks, but require a large expenditure of energy and material resources.
Basically the E. coli K12 gets totally owned by our immune system, as in before it has a chance to cause much damage, as in it doesn't make us sick, as in it is not "associated with human disease". In an abstract sense, saying, "K12 is 'associated with human disease' because O157:H7 is (and probably others are) associated with human disease," is very much like saying, "garden snakes/<insert relatively harmless snake> are associated with human death because black mambos/king cobras/<insert other deadly snake> is associated with human death." More colloquially put, "OMG it's a snake! It's going to kill me!" and "OMG it's E. coli! It's going to make me sick!" have the same logical flaws.
Not only that, but I wouldn't trust E. Coli bacteria for ANY solutions because they're usually full of shit ..er.. I mean they're usually on shit....no! I mean ....ah fuck it!
RIP America
July 4, 1776 - September 11, 2001
The fact that you're comparing your abilities to that of bacteria worries me.
If it rhymes it must be true.
The Sudoku problem is in general NP-complete
. 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.
Qu'on me donne six lignes écrites de la main du plus honnête homme, j'y trouverai de quoi le faire pendre.
When I clicked on the first link, I got a preview "article" titled "Sign in to read: brain asymmetry eases hypnotic trance". What relation does this have to the summary?
Once you're in an asymmetric hypnotic trance /. seems much easier to understand.
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.
Taniuchi does say in this article "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.