## Bacterial Computer Solves Hamiltonian Path Problem 135 135

Rob writes

*"A team of US scientists has engineered bacteria that can solve complex mathematical problems faster than anything made from silicon. The research, published today in the Journal of Biological Engineering (abstract and provisional PDF), proves that bacteria can be used to solve a puzzle known as the Hamiltonian Path Problem, a special case of the traveling salesman problem. The researchers say that this proof-of-concept experiment demonstrates that bacterial computing is a new way to address NP-complete problems using the inherent advantages of genetic systems."*
## the possibilities! (Score:5, Insightful)

## Misleading (Score:1, Insightful)

I think this is quite misleading since the effort to genetically modify the bacteria is not included in the quantification of how fast the computation is being completed. If programmers are allowed to spend enough time to prepare input data for the fastest possible calculation, it may be just as fast or faster than the bacteria. Even if this is not the case, the overhead of preparing the bacteria should not be ignored.

## So? (Score:5, Insightful)

At best, this seems to be a novel form of analog computer. [wikipedia.org] They have their uses, but calling them "faster than silicon" is very misleading; a soap bubble can solve the mean surface problem [wikipedia.org] but I won't be replacing my Core 2 with one.

## Re:the possibilities! (Score:2, Insightful)

The advantage? Self-replication. Bacteria are crafted, made to do what they do naturally (replicate to populations of millions or more), and then create answers as a by-product of that replication. This has serious possibilities for streamlining any massive iterative function. Essentially, a biological computer grows to meet the problem at hand, unlike static circuits that must slowly work their way through a potentially massive set of answers. The technology isn't even in its infancy yet, but it's yet another field of development with mind-blowing potential.

## Re:this still does not prove p == np (Score:1, Insightful)

The reductions we already have work.

But this still doesn't say anything about P or NP, because those are defined with Turing machines, not soap bubbles.

## Hamiltonian path != traveling salesman (Score:3, Insightful)

I would be more impressed if they found the shortest path on an undirected graph with variable length edges.

## parallel computations only half the battle (Score:4, Insightful)

Hmm. Deja vu here. DNA was used to solve this exact problem:

http://www.jyi.org/volumes/volume8/issue2/features/srivastava.html [jyi.org]

It should be noted, however, that even though the DNA would be able to compute the routes in a massively parallel fashion, you still would have to search all the solutions to identify the shortest one, so that kind of defeats the purpose of it. Unless the DNA or the bacteria could compute all the results _and_ identify the correct and optimal answer, then as far as we are concerned the problem is still gotta be close to NP complete (IE strands of DNA to check go up exponentially with problem size). Sounds like these bacteria change color, so maybe that helps reduce the size of the answer set.

## Re:So? (Score:3, Insightful)

We don't know these bacteria can't be fooled, either. That's not the point, anyway: An analog computer may be useful. But it will solve the problem by "brute force", taking advantage of the massive parallelism inherent in the real world in the form of molecules or bacteria. It may solve the problem "quickly" in our perception, but it's far from efficient in polynomial time, and it doesn't help in terms of P = NP.

And like any analog computer, these bacteria need to be carefully designed to solve a specific problem. Which makes them utterly unsuited for the everyday tasks we perform on digital computers using general-purpose CPUs.

## Re:Summary is overrated (Score:4, Insightful)

## This is incredibly underwhelming (Score:3, Insightful)

## Re:parallel computations only half the battle (Score:1, Insightful)

Now I remember why I still read slashdot. Despite all the "frist post", "hot grits", "in soviet russia", "goatse" and whatever other random bollocks goes on here, you still get real geeks, making real news, posting real insightful comments.

Thanks Andrew for taking the time to read and post here..

It sounds like incredibly interesting work, particularly so for me as a software engineer with a wife who works in the biomed industry. Congrats on the paper!

Also, with reference to the gp post, I thought that the previous (DNA) version of the algorithm was using something like gel electrophoresis to sort the resulting DNA fragments by size (making it relatively easy to find the shortest path).. ??