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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."
They may be able to crack Sudoku but can they fix the cracks in concrete?
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, welcome our sudoku-solving underlords.
Try this URL instead.
What one fool can do, another can. (Ancient Simian Proverb)
I could probably solve a sudoku with some help from a group of students at the University of Tokyo as well.
This is the article the summary is actually referring to.
They can solve the Times crossword, *then* I'll be impressed.
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!
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
but out of all bacteria that could use used why use one associated with human disease?
That's OK, can we just get some of the cementing bacteria to heal the cracks?
You see? You see? Your stupid minds! Stupid! Stupid!
Hate to break it to you all, but I talked with this team at the conference and their system doesn't work yet. Neat design though!
But you'll never get bacteria to crack The Game of Life.
Since when is a Sudoku puzzle 4 by 4 with 16 cells? I always played the nine by nine version with 81 cells.
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.
You have just proved your intelligence's upper limit matches that of the bacteria.
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
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.
But can they be bred to run Linux?
Table-ized A.I.
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.
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.
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.
"Sudokoli"
But can they play Crysis?
But, what about the carbon footprint ? How much of life supporting medium is required for a given 'computational' bacteria ?
This is all well and good... but what will really impress me is when they figure out how many bacteria are needed to change a light bulb!!
Next up: modified hantavirus that can solve the Rubik's Cube in less than 21 moves.
I should do more puzzles while on the crapper....
Biological computing rears its bacteria laden head every few years. I remember a few years ago a guy with four large vats of a bacterium managed to get them to solve the travelling salesman problem faster than any computer known. Problem was, he couldn't ask them how they did it. Its nice to see its not dead (oh just ignore the pun sparky), just hibernating for a while (ok, pay serious attention to that pun, serious).
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 abiogenetic character depending on which aboveboard it active aural a four-by-four sudoku grid. The bacilli can aswell accurate one of four colours to represent the after amount of their square. As with any sudoku puzzle, a baby amount of the filigree squares are accustomed a amount from the alpha by auspicious the bacilli in these squares to differentiate and yield on one of the four colours web designing company in chandigarh.
Stanislaw Lem has been describing something like that - bacterias communicating in Morse code.
No. shit!
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.
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
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 been some kind of miscommunication. If they had actually created bacteria that solved sudoku, they would have done better in the contest.
Thanks for the link. It had never occurred to me that when I'm being hypnotized, bacteria play sudoku in my brain!
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 done into getting very small objects such as bacteria and DNA molecules to perform computation: they offer the promise of far higher levels of parallelism than are possible with conventional computing devices. Quantum computers as I understand them seem to offer something very close, but not quite the kind of unbounded parallelism that should be offered by a hypothetical NTM, but this is a murky area of research (it involves showing that BQP != NP, which seems about as hard as trying to prove P != NP).
Qu'on me donne six lignes écrites de la main du plus honnête homme, j'y trouverai de quoi le faire pendre.
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!
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)) which can equivalently be defined in terms of polylog-depth poly-size (acyclic) boolean circuits.
Your comments?