Transcript Journal of Biological Engineering

LIVING COMPUTERS!
(At least very basic computations run by
bacteria)
Shunzaburo Kida
Biomedical Engineering
April 2010 BME 482
Overview

Definition of computer

Design of experiment

Future Outlook

Results

Conclusion
Computer
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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

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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

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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
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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



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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
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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

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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
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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/bacteriacomputer>.
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.merriamwebster.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-usedfor-flipping-pancakes/9352/>.