Problem-Solving Bacteria Crack Sudoku 86
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."
They May Crack Sudoku ... (Score:2, Redundant)
Wrong link in TFS? (Score:2)
Re:Wrong link in TFS? (Score:4, Funny)
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.
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They may be able to crack Sudoku but can they fix the cracks in concrete? [slashdot.org]
Jeez, didn't you have biology in high school? Sudoku is what the bacteria are doing in their spare time, their day job being repairing concrete.
Next Step (Score:1, Funny)
Now if we can just get the bacteria to watch "Sarah Palin's Alaska", we'll have another 3.4x10^35 registered Republican voters.
I for one... (Score:1, Insightful)
I, for one, welcome our sudoku-solving underlords.
Link (Score:5, Informative)
What's so special? (Score:1, Insightful)
Re:What's so special? (Score:5, Funny)
Real Link (Score:1)
Call me when... (Score:2, Funny)
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Or, you know, a *real* Sudoku. A Sudoku puzzle has 81 squares, not 16.
Re:Call me when... (Score:4, Interesting)
The Wonderful World of Synthetic Biology (Score:2, Informative)
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
I smell a conspiracy! (Score:3, Interesting)
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Unfortunately, most Americans probably cannot spell "Escherichia coli", "bacteria", or even "E. coli" (trouble w/the "E", I'm sure) so the write-in campaign would have failed. Some would deny that the bacteria could have even evolved to be so intelligent. A few would have questioned the bacteria's citi
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That's a low bar.
Why E.coli? (Score:1, Informative)
E. coli is frequently used as a model organism in microbiology studies. 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.
In 1946, Joshua Lederberg and Edward Tatum first described the phenomenon known as bacterial conjugation using E. coli as a model bacterium,[72] and it remains the primary model to study conjugation.[citation needed] E. coli was an integral part of the first experiments to understand phage genetics,[73] and early researchers, such as Seymour Benzer, used E. coli and phage T4 to understand the topography of gene structure.[74] Prior to Benzer's research, it was not known whether the gene was a linear structure, or if it had a branching pattern.
E. coli was one of the first organisms to have its genome sequenced; the complete genome of E. coli K12 was published by Science in 1997.[75]
The long-term evolution experiments using E. coli, begun by Richard Lenski in 1988, have allowed direct observation of major evolutionary shifts in the laboratory.[76] In this experiment, one population of E. coli unexpectedly evolved the ability to aerobically metabolize citrate. This capacity is extremely rare in E. coli. As the inability to grow aerobically is normally used as a diagnostic criterion with which to differentiate E. coli from other, closely related bacteria such as Salmonella, this innovation may mark a speciation event observed in the lab.
By combining nanotechnologies with landscape ecology complex habitat landscapes can be generated with details at the nanoscale.[77] On such synthetic ecosystems evolutionary experiments with E. coli have been performed in order to study the spatial biophysics of adaptation in an island biogeography on-chip.
http://en.wikipedia.org/wiki/Escherichia_coli [wikipedia.org]
but out of all bacteria that could use used why use one associated with human disease?
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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.
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In addition, the pathogenic E. coli have several virulence factors that lab strains don't (ex
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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
Re:Why E.coli? (Score:5, Informative)
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.
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The main reason to chose E. coli is because it handles very well under lab conditions. Easy to culture, very robust.
Sudoku cracked! (Score:2)
That's OK, can we just get some of the cementing bacteria to heal the cracks?
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Four by four? (Score:2, Insightful)
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More like Pseudoku.
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Technically you could have a 1x1 board but there's not much fun in that!
Because there wouldn't be a unique solution.
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Technically you could have a 1x1 board but there's not much fun in that!
Because there wouldn't be a unique solution.
Yes there would.
3x3 sudoku uses the digits from 1-9
2x2 sudoku uses the digits from 1-4
So 1x1 sudoku would use the digits from 1-1. So here is the unique solution to all 1x1 sudoku:
1
There. Now, wasn't that fun?
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While Sodoku is usually played with a 9x9 board, any square number would work. 4x4, 16x16, I've even seen a 25x25 in a Sodoku book before. (Started it, but didn't want to spend that much free time finishing it.) Technically you could have a 1x1 board but there's not much fun in that!
It isn't necessary to have a square number size, it just means that you are forced out of having a puzzle comprising row-, column- and square-based "house"s when you do. Various polyomino forms have been done, from plain rectangular to the the "Squiggly" variety at dailysudoku.co.uk
Being reasonably competent at the various 9x9 forms (I seek puzzles online because the only puzzle I've found in the national press that I can't solve is the supposed- world's hardest [guardian.co.uk] [solution [guardian.co.uk]]), I can't see that there's any grea
sudoku is trivial (Score:2)
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As an aside, 10 ms is about twenty million CPU cycles on a run-of-the-mill PC. So the fact that a handful of bacteria might be designed to solve a problem which takes you 20 million computations is pretty snazzy in my opinion. (The overhead of Python, the OS, your browser, the fact that the bacteria use a smaller sudoku grid etc. don't take away from any of this -- it's
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I wrote a Python script to solve Sudoku puzzles. It takes 10 milliseconds. For a hard game where a guess is required, it takes 20 milliseconds. Interpreted Python. 10 milliseconds. Humans are terrible at this game because they can't remember 89 things at once. But it is really trivial.
I bet you're a real hit at parties.
Is it not in the Debian repositories yet? (Score:1)
sudo: ku: command not found
me@mybox:~$ sudo apt-get install ku
Reading package lists... Done
Building dependency tree
Reading state information... Done
E: Couldn't find package ku
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That codec is not FOSS.
On everyone's mind: (Score:2)
But can they be bred to run Linux?
Generalized Sudoku is NP-complete (Score:4, Interesting)
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.
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Although the meaning does change a bit, you can still apply big-O to a computation on more than one processor. Obviously with exponentially many processors, an NP problem can be solved in polynomial time. On other hand, using O(n^2) (or some other polynomial) bacteria to solve an NP-complete problem in polynomial time would be an interesting result.
But will they publish their results?
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Yes, Big-Oh is relevant: it's turing-simulatable (Score:2)
Would standard big O notation even matter here?
Yes, although we're not saying "This takes O(f(n)) turing machine transitions" nor "This takes O(g(n)) instructions on an abstract pointer machine" nor "This takes O(h(n)) x86 cpu cycles".
In this situation you have a massive number of small processors limited in the data of the problem they have access to, compared to the traditional model of computation with one actor.
I conjecture this to be turing-simulatable with polynomial overhead. If they can do it in polynomial time, so can my turing machine. Which would prove P = NP. Which would be big news.
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The way I've always understood nondeterministic Turing machines is that they are an idealized model of computation where you in essence have unbounded parallelism. If you had very large numbers of processing elements, large enough to grow to the scale required for the problem which you're attempting to solve, then arguably you have what almost amounts to a nondeterministic Turing machine, albeit with a very large, but still finite, bound on parallelism. This is, after all, the reason why research is being
Does that formalize? (Score:2)
The way I've always understood nondeterministic Turing machines is that they are an idealized model of computation where you in essence have unbounded parallelism.
Can you formalise this?
I know you can define NP in two equivalent ways: as the languages of either (1) non-deterministic machines making polynomially many transitions along every computation path; or (2) deterministic polynomial-time machines which verify polynomially sized solution candidates to a given instance.
I'm not sure how parallelism enters the picture. I know of parallelism relating to NC, Nick's Class (see http://en.wikipedia.org/wiki/NC_(complexity) [wikipedia.org]) which can equivalently be defined in terms of
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The Sudoku problem is in general NP-complete [u-tokyo.ac.jp]
.
From their website they are solving a simpler problem:
here we solve a 4x4 grid version. However, expanding on the same principles, our E. coli can theoretically solve larger grids, for example 9x9 grids.
9x9 Sudoku problems that you find in magazines or online are trivial Constraint Satisfaction Problems (CSP) [wikipedia.org]. Trivial CSP solvers can solve thousands of these in one second. By solving such a trivial problem I am not sure that their work can be scaled to more complex variants. Their 4x4 variant is so simple that it can even be solved efficiently by a trivial program which can be written from scratch in a couple of hours. This is in contrast to the genera
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Big deal (Score:2)
crazy (Score:2)
The interesting part of this article (Score:4, Interesting)
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.
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I may have misinterpreted your comment, though. It's mostly the last sentence that makes me
Bacteria, I dub thee.... (Score:1, Funny)
"Sudokoli"
Carbon ? (Score:1)
Next up: hantavirus solves Rubik's Cube (Score:1)
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web designing (Score:1)
Stanislaw Lem "Imaginary magnitude" (Score:1)
Politics (Score:1)
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When they try it with a virus (Score:1)
Bad Article (Score:1)
Outside of this article, there's no indication that these E. coli actually exist. Check the U Tokyo iGem page: http://2010.igem.org/Team:UT-Tokyo/Sudoku_construct [igem.org]
I guess it's difficult since their page keeps talking about 'our E. coli', but we also never see any results from 'their E. coli'. I think they're more hypothetical at this point.
They have an interesting model and system, but nothing on their actual E. coli or their results. Everything is idealized and simulated. I think there must have just b
Bad Headline, replace with... (Score:1)
Japanese university students succeed in creating worlds smallest cyborg thinking-machine robots. Fleshy, squishy micro-borg can now outdo me in Sudoku?!? RUN! FLEE FOR YOUR LIVES!