LIVING COMPUTERS!

(At least very basic computations run by bacteria)

Shunzaburo KidaBiomedical Engineering

April 2010 BME 482

Overview

Definition of computer Design of experiment Future Outlook Results Conclusion

Computer

As defined by www.merriam-webster.com, a computer is a “programmable object that can store, retrieve, and process data.”

Conventional computers (silicon-based) run through possible solutions one at a time, excluding multi-cores

In this journal they utilize Escherichia coli (E. Coli) to execute DNA-based computations along with a protein (Hin) taken from salmonella bacteria

This system of using organic living cells allows for millions of solutions being run at once since each baterium acts as a single computer

Design of Experiment

The special bacteria is designed to run a very simple program of “The Burnt Pancake Problem”

This outline consists of two pancakes of different sizes each with a burnt side.

Flip so largest is on bottom Flip again until burnt sides are down 8 total possible ways of executing

DNA is flipped around until a required order is established for a gene to be activated, which releases a resistance to an antibiotic

Hin Protein

The Hin protein from salmonella acts as the “spatula”

Hin cuts the specific pieces of DNA and shuffles them around (flipping the pancakes), and then reattaches

Also acts as an on/off switch for another protein production if the proper sequence of DNA is achieved

If incorrect resistance to applied antibiotic is dispersed and bacteria dies

Results

Bacterial colonies that created a resistance to tetracycline had accomplished The Burnt Pancake Problem

This can be checked by examining the specific DNA coding

At established time intervals reflects the minimal number of flips required to complete the task

Hin complex was able to flip single “pancakes” of varying size, adjacent segments,and sort multiple segments all at once

Future Outlook

The same group conducted another study using the same E.coli and applied it to another mathematical problem.

This new problem is called the Hamiltonian Path Problem taking in 3 cities as a goal

In past, bacteria was programmed to form patterns, shapes, and colors – using this to perhaps create distinct tissues

Overtime hopefully bacterial computers become more advanced and can process more complex problems

Pros

Can compute millions of scenarios all at once due to each bacterium acting as a single computer

Once identified, solution can be reproduced cheaply

Over an increased time the bacterial computer will increase in power due to the fact that bacteria reproduces

In vitro DNA inversion takes place rapidly (<1 minute)

Cons

Not easy to program problems Will not in near future replace conventional

silicon based computers Currently can only solve simple problems Hin protein can't be fully controlled so random

shuffling is used to fulfill task

Hamiltonian Path Problem

Conclusion

Hin/hix DNA recombination can solve a two adjacent segment inversion system in vivo

Hin/hix complexes were used to regulate inversion efficiency since in vitro DNA inversion was observed as too rapid to detect proper calculations

The hin complex used indicates that this system when recoded could be utilized to compute more complex pancake stacks

This study could be used to observe the synthetic genome rearrangement that have occurred in nature

References

Aron, Jacob. "Bacteria Make Computers Look like Pocket Calculators." Science Blog. Science Blog, 24 July 2009. Web. 15 Apr. 2010. <http://www.guardian.co.uk/science/blog/2009/jul/24/bacteria-computer>.

Bland, Eric. "Discovery News: Bacteria-Run Computer Solves Math Puzzle." Discovery Channel : Science, History, Space, Tech, Sharks, News. 28 May 2008. Web. 15 Apr. 2010. <http://dsc.discovery.com/news/2008/05/28/bacteria-computer-02.html>.

"Computer - Definition and More from the Free Merriam-Webster Dictionary." Dictionary and Thesaurus - Merriam-Webster Online. Web. 15 Apr. 2010. <http://www.merriam-webster.com/dictionary/computer>.

Haynes, Karmella A. "Engineering Bacteria to Solve the Burnt Pancake Problem." Journal of Biological Engineering. 20 May 2008. Web. 15 Apr. 2010. <http://www.jbioleng.org/content/2/1/8>.

Nelson, Bryn. "Living Computers Solve Complex Math Puzzle - Frontiers- Msnbc.com." Breaking News, Weather, Business, Health, Entertainment, Sports, Politics, Travel, Science, Technology, Local, US & World News- Msnbc.com. 2 June 2008. Web. 15 Apr. 2010. <http://www.msnbc.msn.com/id/24880713/ns/technology_and_science-innovation/page/2/>.

Quick, Darren. "First Living Computer Used for Flipping Pancakes." Gizmag Emerging Technology Magazine. 21 May 2008. Web. 15 Apr. 2010. <http://www.gizmag.com/first-living-computer-used-for-flipping-pancakes/9352/>.