how do cells compute? john j. tyson department of biological sciences virginia bioinformatics...
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How Do Cells Compute?
John J. TysonDepartment of Biological Sciences
Virginia Bioinformatics Institute
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Do Cells Compute?
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Computer
bit string bit string
N N2
x x
01
00
10
11
1
0
1
0
either A or Bbut not both
computations
decisions
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Is the cell anInformation Processing System?
IPSinput output
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Cellnutrients
repellants
damage
hormones
heat shock
growth & division
movement
geneexpression
death
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BacteriaGlucose
Lactose
1
0
glucosemetabolizing
enzymes
1
lactosemetabolizing
enzymes
0
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BacteriaGlucose
Lactose
lactosemetabolizing
enzymes
1
1 0
glucosemetabolizing
enzymes
1
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BacteriaGlucose
Lactose
lactosemetabolizing
enzymes
0
1 1
glucosemetabolizing
enzymes
1
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BacteriaGlucose
Lactose
lactosemetabolizing
enzymes
0
0 0
glucosemetabolizing
enzymes
1
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Fission Yeast
14 m
7 m
Wild type Mutant (wee1)
“size control” different “set point”
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Fibroblast
Ionizing radiationdamages DNA
cell cycle arrest
repair
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Fibroblast
ProgrammedCell Death
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Is a cell like a computer?
Laptop Cell
Solid state Watery
Programmable Hard-wired
Precise Sloppy
Digital Analog
Sequential Parallel
Manufactured Self-reproducing
Designed Evolved
Silicon CarbonSilicon Carbon
DGaD LoDD
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…in the last 5 years
“Molecular Systems Biology”
CellCarbon
Watery
Hard-wired
Sloppy
Analog
Parallel
Self-reproducing
Evolved
Carbon
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20 years ago…
Winfree & Kauffman
Oster & Perelson
Goldbeter & Segel
Glass & Mackey
Rinzel & Keizer
Goodwin, Meinhardt, Odell, Tyson, …
CellCarbon
Watery
Hard-wired
Sloppy
Analog
Parallel
Self-reproducing
Evolved
Carbon
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How do cells make decisions?
WT
cdc
wee
Paul Nurse, Nature (1975)
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Fission Yeast
P Wee1
Wee1P
Cdc25
CycB
CycB
Cdc25
MPFMitosis Promoting Factor
++P
WT
cdc
wee
cdc25ts
wee1ts
wee1OP
cdc25OP
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Fission Yeast
P Wee1
Wee1P
Cdc25
CycB
CycB
Cdc25
mass/ DNA
0 1 2
Cdc2/Cdc13
10-3
10-2
10-1
100
S/G2
M
size
MP
F
size
SN14m
wee1OPwee1
P++
DNA synthesis
Mitosis & Cell Division
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0.01 0.1 1 10 100 1000 10000
1
10
100
1000
0.4
3.0
WT
Cdc25 activity (%)
Wee
1 ac
tivity
(%
) cdc
cut
wee
quantized
Size at Division1.0 = WT size
wee1ts
wee1OP
cdc25OP
cdc25ts
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P
Cdc25
Wee1
Wee1P
Cdc25
CycB
PCdc20
Cdc20
APC-PAPC
CycB
0
0.5
1
0 1 2
MP
F
total cyclin
ks
MPF
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Joe Pomerening
Cell (2005)
MPF
total cyclin
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How do cells compute?
Switches and Clocks
ks
MPF
mass/ DNA
0 1 2
Cdc2/Cdc13
10-3
10-2
10-1
100
S/G2
M
size
MP
F
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The class of chemical switching networks will be promising
candidates for a possible new technology of chemical reaction
systems.
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nutrients
repellants
damage
hormones
heat shock
growth & division
movement
geneexpression
death
The living cell is Rössler’s“flüssiges Automata”:
a miniature, self-reproducing, water-soluble biochemical
computer.
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$$: DARPA, NIH, McDonnell Foundation