How Do Cells Compute

1
How Do Cells Compute?

• John J. Tyson
• Department of Biological Sciences
• Virginia Bioinformatics Institute

2
Do Cells Compute?
3
Computer
bit string
bit string
N N2
computations
x
decisions
4
Is the cell anInformation Processing System?
IPS
input
output
5
Cell
6
Bacteria
1
lactose metabolizing enzymes
0
0
7
Bacteria
1
lactose metabolizing enzymes
1
0
8
Bacteria
0
lactose metabolizing enzymes
1
1
9
Bacteria
0
lactose metabolizing enzymes
0
0
10
Fission Yeast
7 mm
14 mm
Wild type Mutant
(wee1D)
different set point
size control
11
Fibroblast
cell cycle arrest
repair
Ionizing radiation damages DNA
12
Fibroblast
Programmed Cell Death
13
Is a cell like a computer?
Laptop
Cell
14
in the last 5 years
Cell
Carbon
Carbon
Molecular Systems Biology
Watery
Analog
Parallel
Hard-wired
Sloppy
Self-reproducing
Evolved
15
20 years ago
Cell
Winfree Kauffman Oster Perelson Goldbete
r Segel Glass Mackey Rinzel
Keizer Goodwin, Meinhardt, Odell, Tyson,
Carbon
Carbon
Watery
Analog
Parallel
Hard-wired
Sloppy
Self-reproducing
Evolved
16
How do cells make decisions?
Paul Nurse, Nature (1975)
17
Fission Yeast
Wee1
P
Wee1
CycB
P
Cdc25
P
CycB
cdc25ts
wee1OP
Cdc25
wee1ts
cdc25OP
18
Fission Yeast
Mitosis Cell Division
Wee1
P
MPF
Wee1
CycB
P
DNA synthesis
Cdc25
P
CycB
size
Cdc25
size
19
Size at Division1.0 WT size
20
Wee1
P
Cdc20
ks
Wee1
CycB
P
APC-P
APC
Cdc25
P
Cdc20
CycB
MPF
Cdc25
21
total cyclin
MPF
Cell (2005)
Joe Pomerening
22
How do cells compute?
Switches and Clocks
23
The class of chemical switching networks will be
promising candidates for a possible new
technology of chemical reaction systems.
24
The living cell is Rösslersflüssiges
Automataa miniature, self-reproducing,
water-soluble biochemical computer.
25
DARPA, NIH, McDonnell Foundation