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Biotech

Problem-Solving Bacteria Crack Sudoku 86

Posted by samzenpus
from the and-your-bacteria-just-stink dept.
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."
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Problem-Solving Bacteria Crack Sudoku

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  • They may be able to crack Sudoku but can they fix the cracks in concrete? [slashdot.org]
    • 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? On another site, I would ascribe this to a foolish error, but I'm sure the editors at Slashdot would never allow such a mistake to happen.
    • 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)

    by Anonymous Coward

    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)

    by drcheap (1897540)

    I, for one, welcome our sudoku-solving underlords.

  • Link (Score:5, Informative)

    by PatPending (953482) on Wednesday November 17, 2010 @08:35PM (#34263220)
    Try this [igem.org] URL instead.
  • What's so special? (Score:1, Insightful)

    by iviv66 (1146639)
    I could probably solve a sudoku with some help from a group of students at the University of Tokyo as well.
  • This [newscientist.com] is the article the summary is actually referring to.
  • They can solve the Times crossword, *then* I'll be impressed.
    • by julesh (229690)

      Or, you know, a *real* Sudoku. A Sudoku puzzle has 81 squares, not 16.

      • Re:Call me when... (Score:4, Interesting)

        by delinear (991444) on Thursday November 18, 2010 @05:41AM (#34266178)
        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.
  • by Anonymous Coward

    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

  • by kheldan (1460303) on Wednesday November 17, 2010 @08:44PM (#34263310) Journal
    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!
    • 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!

      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

    • showing much more intelligence and logical-thought ability than anyone else on the ticket

      That's a low bar.

  • Why E.coli? (Score:1, Informative)

    by John Saffran (1763678)
    From wiki it seems that it's widely used for genetic experiments:

    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?

    • Re: (Score:3, Insightful)

      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.

      • In fact, having a robust normal microbiota is associated with health and commensal E. coli (like those from which typical lab strains are derived) are part of that. They hang out, digest materials you wouldn't, make some vitamins, keep your immune system up to snuff (these interactions are essentially 'expected' by your system), and most importantly take up space and nutrients that potential pathogens could use.

        In addition, the pathogenic E. coli have several virulence factors that lab strains don't (ex
    • Re: (Score:2, Informative)

      by genomancer (588755)

      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)

      by atmtarzy (1267802) <ndnjones3@gmai l . c om> on Wednesday November 17, 2010 @09:27PM (#34263610)

      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.

      • by Thing 1 (178996)
        "The K-12 dude. You make a gnarly run like that and girls will get sterile just looking at you."
    • Re: (Score:2, Funny)

      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!
    • E. coli as such is not associated with human disease but rather a normal part of the intestinal flora. There are certain pathogenic strains, but those are in the minority. E. coli count is used for determining water quality, for example, because the presence of E. coli points to the presence of shit, not because of a pathogenic nature of the bacterium.

      The main reason to chose E. coli is because it handles very well under lab conditions. Easy to culture, very robust.

  • That's OK, can we just get some of the cementing bacteria to heal the cracks?

  • Four by four? (Score:2, Insightful)

    by TurtleBay (1942166)
    Since when is a Sudoku puzzle 4 by 4 with 16 cells? I always played the nine by nine version with 81 cells.
    • Re: (Score:3, Insightful)

      More like Pseudoku.

    • Re: (Score:2, Informative)

      by Garth Smith (1720052)
      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!
      • by Dthief (1700318)
        what about 1x1
      • by somejeff (825047)
        50% of trials were a success with binary sudoku! http://www.xkcd.com/74/ [xkcd.com]
      • by tehcyder (746570)

        Technically you could have a 1x1 board but there's not much fun in that!

        Because there wouldn't be a unique solution.

        • 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?

      • by etwills (471396)

        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

  • 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.
    • No one is claiming sudoku isn't computationally easy; it's the fact that bacteria are being used to solve problems mathematical in nature.

      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
    • Re: (Score:1, Troll)

      by tehcyder (746570)

      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.

  • me@mybox:~$ sudo ku
    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
  • But can they be bred to run Linux?

  • by dido (9125) <dido@impe r i u m .ph> on Wednesday November 17, 2010 @10:03PM (#34263894)

    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.

    • by Mask (87752)

      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

      • There are 288 [wikipedia.org] distinct 4x4 Sudoku puzzles (each grid is 2x2; the usual 9x9 case has 3x3 grids). There are ~4 billion 16-square grids of numbers 1-4, so these can be found easily with completely naive methods. A few hours is probably too generous :).
  • Compared to the tricks bacteria pull off to get past your immune system, a little Sudoku is child's play.
  • Seems a lot easier to just use a pencil.
  • by shadow_slicer (607649) on Wednesday November 17, 2010 @10:47PM (#34264320)

    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.

    • Why is that frightening? Every in vivo molecular bio lab has hundreds (thousands?) of 'unique' bacterial strains, particularly E. coli. They are less viable in your system than the billions of bacteria hanging out on your skin (some of which are probably Staph. aureus) right now. In addition, they're usually derivatives of E. coli K12. Similar E. coli are in your colon right now, being nice, normal microbiota.

      I may have misinterpreted your comment, though. It's mostly the last sentence that makes me
  • by Anonymous Coward

    "Sudokoli"

  • But, what about the carbon footprint ? How much of life supporting medium is required for a given 'computational' bacteria ?
  • Next up: modified hantavirus that can solve the Rubik's Cube in less than 21 moves.
  • The address of sudoku has advance to the prokaryotic world. A ache of Escherichia coli bacilli can now break the argumentation puzzles “ with some advice from a accumulation of acceptance at the University of Tokyo, Japan. "Because sudoku has simple rules, we acquainted that maybe bacilli could break it for us, as continued as we advised a ambit for them to follow," says aggregation baton Ryo Taniuchi. The aggregation activate with 16 types of E. coli, anniversary antecedents assigned a audible abio
  • Stanislaw Lem has been describing something like that [amazon.com] - bacterias communicating in Morse code.
  • Now... Sudoku, next... Congress!
  • The virus that ends up wiping out humanity will have been engineered to solve the NYTimes crossword puzzle.
  • 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

  • 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!

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