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Researcher hopes to program cell
[Original message from MIT]
By Deborah Halber
MIT artificial intelligence researcher Thomas F. Knight wants to be ab
le to program a living cell the way he would program a computer.
A senior research scientist in electrical engineering and computer sci
ence, Dr. Knight doesn't think this idea is far-fetched. From an engin
eering standpoint, he said, living cells are already amazing machines.
They reproduce themselves, are energy-efficient and waste-efficient,
can process chemicals, and can sense stimuli such as light, heat and a
cidity. They can move and fluoresce. Their DNA stores and replicates o
ne megabit of information. "This is way, way, way denser than any form
of silicon technology," he noted. Research and industry already are t
rying to take advantage of some of these features by employing biologi
cal tools to manufacture non-biological devices.
Dr. Knight is working to develop novel computing structures from livin
g biological cells. He spoke to a group of alumni/ae inventors and ent
repreneurs, venture capitalists, business leaders, and Institute facul
ty and staff at the Resource Development-sponsored Technology Breakfas
t Series on October 25.
"A natural cell is already doing computation," he said. "They already
figure out where the food is and what environment they are in, and ada
pt their behavior to those environments. The whole trick is to learn f
rom what the natural world is providing, take those techniques and tur
n them to our own purposes."
Those purposes may be monitoring glucose levels in diabetics, growing
crops that you can inform about a coming drought, or instructing flowe
rs to count the days until Valentine's Day so they bloom on the right
day.
DNA already is "digital" -- the bases that make up the genetic code ar
e four distinct entities.
"If we want to build digital behavior in living cells, we can replicat
e ones and zeroes as the presence or absence of specific DNA binding p
roteins," Dr. Knight said. The binding protein would be used to contro
l which genes are expressed or inhibited, creating outputs of one or z
ero.
Using this method, researchers can design a "NAND" gate. A logic gate
equivalent to an "AND" gate followed by a "NOT" gate, NAND gates are i
mportant because all Boolean logic operations can be built out of them
. With these components, "we now have a universal mechanism able to cr
eate any kind of computational mechanism," he said. "It's all downhill
from here."
To find a cell that he can manipulate in this manner, Dr. Knight is wo
rking on finding and then tailoring the simplest living system possibl
e. He has identified a plant and insect pathogen that may be the ideal
candidate. The simplest bacterium known, it has only 454 genes, compa
red with the thousands owned by its more complex cousin, E. coli. Rese
archers have shown that it may be possible to pare those down to aroun
d 293 essential genes.
While there is still much ground that needs to be covered before resea
rchers can completely fabricate, design and control a living cell, "30
0 is a doable number," Dr. Knight said. From an engineering viewpoint,
this is not an intractable system."
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