mathematical modeling and biologybdeng1/research/... · mathematical modeling and biology bo deng...
TRANSCRIPT
![Page 1: Mathematical Modeling and Biologybdeng1/Research/... · Mathematical Modeling and Biology Bo Deng Introduction Examples of Models Consistency Model Test Mathematical Biology Conclusion](https://reader033.vdocuments.site/reader033/viewer/2022060314/5f0b96957e708231d4313fef/html5/thumbnails/1.jpg)
MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
Mathematical Modeling and Biology
Bo Deng
Department of MathematicsUniversity of Nebraska – Lincoln
March 10, 2016
www.math.unl.edu/∼bdeng11 / 24
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MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
What is modeling?
Mathematical modeling is
to translate nature into mathematics
to be logically consistent
to fit the past and to predict future
to fail against the test of time, i.e. to give way to a bettermodel
2 / 24
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MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
What is modeling?
Mathematical modeling is
to translate nature into mathematics
to be logically consistent
to fit the past and to predict future
to fail against the test of time, i.e. to give way to a bettermodel
2 / 24
![Page 4: Mathematical Modeling and Biologybdeng1/Research/... · Mathematical Modeling and Biology Bo Deng Introduction Examples of Models Consistency Model Test Mathematical Biology Conclusion](https://reader033.vdocuments.site/reader033/viewer/2022060314/5f0b96957e708231d4313fef/html5/thumbnails/4.jpg)
MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
What is modeling?
Mathematical modeling is
to translate nature into mathematics
to be logically consistent
to fit the past and to predict future
to fail against the test of time, i.e. to give way to a bettermodel
2 / 24
![Page 5: Mathematical Modeling and Biologybdeng1/Research/... · Mathematical Modeling and Biology Bo Deng Introduction Examples of Models Consistency Model Test Mathematical Biology Conclusion](https://reader033.vdocuments.site/reader033/viewer/2022060314/5f0b96957e708231d4313fef/html5/thumbnails/5.jpg)
MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
What is modeling?
Mathematical modeling is
to translate nature into mathematics
to be logically consistent
to fit the past and to predict future
to fail against the test of time, i.e. to give way to a bettermodel
2 / 24
![Page 6: Mathematical Modeling and Biologybdeng1/Research/... · Mathematical Modeling and Biology Bo Deng Introduction Examples of Models Consistency Model Test Mathematical Biology Conclusion](https://reader033.vdocuments.site/reader033/viewer/2022060314/5f0b96957e708231d4313fef/html5/thumbnails/6.jpg)
MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
Human history has two periods – before and aftercalculus (1686/1687)
Issac Newton (1642-1727) is the founding father ofmathematical modeling
James Clerk Maxwell (1831-1879), Albert Einstein(1879-1955), Erwin Schrodinger (1887-1961), ClaudeShannon (1916-2001) are some of the luminary disciples
Calculus is the principle language of nature
This century is the century of mathematical biology, whichis to translate Charles Darwin’s (1809-1882) theory intomathematics
3 / 24
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MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
Human history has two periods – before and aftercalculus (1686/1687)
Issac Newton (1642-1727) is the founding father ofmathematical modeling
James Clerk Maxwell (1831-1879), Albert Einstein(1879-1955), Erwin Schrodinger (1887-1961), ClaudeShannon (1916-2001) are some of the luminary disciples
Calculus is the principle language of nature
This century is the century of mathematical biology, whichis to translate Charles Darwin’s (1809-1882) theory intomathematics
3 / 24
![Page 8: Mathematical Modeling and Biologybdeng1/Research/... · Mathematical Modeling and Biology Bo Deng Introduction Examples of Models Consistency Model Test Mathematical Biology Conclusion](https://reader033.vdocuments.site/reader033/viewer/2022060314/5f0b96957e708231d4313fef/html5/thumbnails/8.jpg)
MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
Human history has two periods – before and aftercalculus (1686/1687)
Issac Newton (1642-1727) is the founding father ofmathematical modeling
James Clerk Maxwell (1831-1879), Albert Einstein(1879-1955), Erwin Schrodinger (1887-1961), ClaudeShannon (1916-2001) are some of the luminary disciples
Calculus is the principle language of nature
This century is the century of mathematical biology, whichis to translate Charles Darwin’s (1809-1882) theory intomathematics
3 / 24
![Page 9: Mathematical Modeling and Biologybdeng1/Research/... · Mathematical Modeling and Biology Bo Deng Introduction Examples of Models Consistency Model Test Mathematical Biology Conclusion](https://reader033.vdocuments.site/reader033/viewer/2022060314/5f0b96957e708231d4313fef/html5/thumbnails/9.jpg)
MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
Human history has two periods – before and aftercalculus (1686/1687)
Issac Newton (1642-1727) is the founding father ofmathematical modeling
James Clerk Maxwell (1831-1879), Albert Einstein(1879-1955), Erwin Schrodinger (1887-1961), ClaudeShannon (1916-2001) are some of the luminary disciples
Calculus is the principle language of nature
This century is the century of mathematical biology, whichis to translate Charles Darwin’s (1809-1882) theory intomathematics
3 / 24
![Page 10: Mathematical Modeling and Biologybdeng1/Research/... · Mathematical Modeling and Biology Bo Deng Introduction Examples of Models Consistency Model Test Mathematical Biology Conclusion](https://reader033.vdocuments.site/reader033/viewer/2022060314/5f0b96957e708231d4313fef/html5/thumbnails/10.jpg)
MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
Model as approximation – Newton’s planetarymotion
SunPlanet
~r1~r2
~r
m1~r1 = −Gm1m2
~r1 − ~r2‖~r1 − ~r2‖3
m2~r2 = −Gm1m2~r2 − ~r1‖~r2 − ~r1‖3
~r = ~r1 − ~r2
A few calculus maneuvers lead to
r(θ) =ρ
1 + ε cos θ
with the eccentricity 0 ≤ ε < 1 for elliptic orbits
4 / 24
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MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
Model as approximation – Newton’s planetarymotion
SunPlanet
~r1~r2
~r
m1~r1 = −Gm1m2
~r1 − ~r2‖~r1 − ~r2‖3
m2~r2 = −Gm1m2~r2 − ~r1‖~r2 − ~r1‖3
~r = ~r1 − ~r2
A few calculus maneuvers lead to
r(θ) =ρ
1 + ε cos θ
with the eccentricity 0 ≤ ε < 1 for elliptic orbits4 / 24
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MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
Special Relativity – Einstein’s model of space andtime
One Assumption:
The speed of light is constant for every stationary observer
x
y
v
0 x
y
0
K K
A few calculus maneuvers lead to E = mc2, and more
5 / 24
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MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
Special Relativity – Einstein’s model of space andtime
One Assumption:
The speed of light is constant for every stationary observer
x
y
v
0 x
y
0
K K
A few calculus maneuvers lead to E = mc2, and more
5 / 24
![Page 14: Mathematical Modeling and Biologybdeng1/Research/... · Mathematical Modeling and Biology Bo Deng Introduction Examples of Models Consistency Model Test Mathematical Biology Conclusion](https://reader033.vdocuments.site/reader033/viewer/2022060314/5f0b96957e708231d4313fef/html5/thumbnails/14.jpg)
MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
Special Relativity — Einstein’s model of space andtime
One Assumption:
The speed of light is constant for every stationary observer
x
y
0 x
y
0
Kct
vt
L
[√c2 − v2]t = ct
K
Prediction: Time dilation for K-frame observer
t =L
c√
1− (v/c)2>L
c= t
6 / 24
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MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
Special Relativity — Einstein’s model of space andtime
One Assumption:
The speed of light is constant for every stationary observer
x
y
0 x
y
0
Kct
vt
L
[√c2 − v2]t = ct
K
Prediction: Time dilation for K-frame observer
t =L
c√
1− (v/c)2>L
c= t
6 / 24
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MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
General Relativity — Model of space and time inacceleration
x
y
x
y
c∆t
v0∆t
c∆t
v1∆t
v1 = a∆t+ v0
Prediction: Light beam bendsunder acceleration or near massivebodies
7 / 24
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MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
General Relativity — Model of space and time inacceleration
x
y
x
y
c∆t
v0∆t
c∆t
v1∆t
v1 = a∆t+ v0
Prediction: Light beam bendsunder acceleration or near massivebodies
7 / 24
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MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
Mathematical model need not be mathematical
Gregor Johann Mendel (1822-1884) found the firstmathematical model in biology, leading to the discovery ofgene
Parent Genotype
Offspring
Genotype
mrr×f rr
mrD×f rD
mDD×f D
D
mrr×f rD
or
mrD×f rr
mrr×f D
Dor
mDD×f rr
mrD×f D
Dor
mDD×f rD
z′rr 1 1/4 0 1/2 0 0z′rD 0 1/2 0 1/2 1 1/2z′DD 0 1/4 1 0 0 1/2
8 / 24
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MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
One More Example: Structure of DNA by modeling
Rosalind Franklin and Maurice Wilkins had the data, butJames D. Watson and Francis Crick had the frame ofmind to model the data (1953)
9 / 24
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MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
Another More – Predation in Ecology
The mathematical model was discovered by Crawford Stanley(Buzz) Holling (1930- ) in 1959
Td — average time a predator takes to discover a prey
Tk — average time a predator takes to kill a prey
Td,k = Td + Tk — average time a predator takes todiscovery and kill a prey
Rd =1
Td— rate of discovery, i.e. number of preys a
predator would find in a unit time
Rk =1
Tk— rate of killing, i.e. number of preys a predator
would kill in a unit time
Rd,k =1
Td,k=
1
Td + Tk— rate of discovery and killing
10 / 24
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MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
Another More – Predation in Ecology
The mathematical model was discovered by Crawford Stanley(Buzz) Holling (1930- ) in 1959
Td — average time a predator takes to discover a prey
Tk — average time a predator takes to kill a prey
Td,k = Td + Tk — average time a predator takes todiscovery and kill a prey
Rd =1
Td— rate of discovery, i.e. number of preys a
predator would find in a unit time
Rk =1
Tk— rate of killing, i.e. number of preys a predator
would kill in a unit time
Rd,k =1
Td,k=
1
Td + Tk— rate of discovery and killing
10 / 24
![Page 22: Mathematical Modeling and Biologybdeng1/Research/... · Mathematical Modeling and Biology Bo Deng Introduction Examples of Models Consistency Model Test Mathematical Biology Conclusion](https://reader033.vdocuments.site/reader033/viewer/2022060314/5f0b96957e708231d4313fef/html5/thumbnails/22.jpg)
MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
Another More – Predation in Ecology
The mathematical model was discovered by Crawford Stanley(Buzz) Holling (1930- ) in 1959
Td — average time a predator takes to discover a prey
Tk — average time a predator takes to kill a prey
Td,k = Td + Tk — average time a predator takes todiscovery and kill a prey
Rd =1
Td— rate of discovery, i.e. number of preys a
predator would find in a unit time
Rk =1
Tk— rate of killing, i.e. number of preys a predator
would kill in a unit time
Rd,k =1
Td,k=
1
Td + Tk— rate of discovery and killing
10 / 24
![Page 23: Mathematical Modeling and Biologybdeng1/Research/... · Mathematical Modeling and Biology Bo Deng Introduction Examples of Models Consistency Model Test Mathematical Biology Conclusion](https://reader033.vdocuments.site/reader033/viewer/2022060314/5f0b96957e708231d4313fef/html5/thumbnails/23.jpg)
MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
Another More – Predation in Ecology
The mathematical model was discovered by Crawford Stanley(Buzz) Holling (1930- ) in 1959
Td — average time a predator takes to discover a prey
Tk — average time a predator takes to kill a prey
Td,k = Td + Tk — average time a predator takes todiscovery and kill a prey
Rd =1
Td— rate of discovery, i.e. number of preys a
predator would find in a unit time
Rk =1
Tk— rate of killing, i.e. number of preys a predator
would kill in a unit time
Rd,k =1
Td,k=
1
Td + Tk— rate of discovery and killing
10 / 24
![Page 24: Mathematical Modeling and Biologybdeng1/Research/... · Mathematical Modeling and Biology Bo Deng Introduction Examples of Models Consistency Model Test Mathematical Biology Conclusion](https://reader033.vdocuments.site/reader033/viewer/2022060314/5f0b96957e708231d4313fef/html5/thumbnails/24.jpg)
MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
Model of Predation in Ecology
And Holling’s predation function form:
Rd,k =1
Td + Tk=
1/Td1 + Tk(1/Td)
=Rd
1 + TkRd
Prediction: Assume the discovery rate is proportional tothe prey population X, Rd = aX. Then the Holling TypeII predation rate must saturate as X →∞
limX→∞
Rd,k = limX→∞
aX
1 + TkaX=
1
Tk
X
Rd,k
0
1Tk
11 / 24
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MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
Model of Predation in Ecology
And Holling’s predation function form:
Rd,k =1
Td + Tk=
1/Td1 + Tk(1/Td)
=Rd
1 + TkRd
Prediction: Assume the discovery rate is proportional tothe prey population X, Rd = aX. Then the Holling TypeII predation rate must saturate as X →∞
limX→∞
Rd,k = limX→∞
aX
1 + TkaX=
1
Tk
X
Rd,k
0
1Tk
11 / 24
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MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
Consistency
Not every piece of mathematics can be a physical law ormodel. Logical consistency is the first and necessaryconstraint
Time Invariance Principle (TIP)
A model must has the same functional form for every timeindependent observation
Newtonian mechanics is TIP-consistent:
st
x0
x(s, x0)
x(t+ s, x0) = x(t, x(s, x0))
12 / 24
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MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
Consistency
Not every piece of mathematics can be a physical law ormodel. Logical consistency is the first and necessaryconstraint
Time Invariance Principle (TIP)
A model must has the same functional form for every timeindependent observation
Newtonian mechanics is TIP-consistent:
st
x0
x(s, x0)
x(t+ s, x0) = x(t, x(s, x0))
12 / 24
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MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
Special Relativity is self-consistent
Let P be a point, having K = (x, y, z, t) coordinate in theK-frame and K = (x, y, z, t) coordinate in the K-frame.Then they are exchangeable via a linear transformationdepending the speed v:
K = KL(v)
Let K = (x, y, z, t) be the coordinate of the same point ina K-frame moving at speed u with respect to theK-frame. Then we have
K = KL(u) = KL(v)L(u) = KL(w) with w =u+ v
1 + uvc2
The operation u⊕ v =u+ v
1 + uvc2
for elements u, v ∈ (−c, c)
defines a commutative group
13 / 24
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MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
Special Relativity is self-consistent
Let P be a point, having K = (x, y, z, t) coordinate in theK-frame and K = (x, y, z, t) coordinate in the K-frame.Then they are exchangeable via a linear transformationdepending the speed v:
K = KL(v)
Let K = (x, y, z, t) be the coordinate of the same point ina K-frame moving at speed u with respect to theK-frame. Then we have
K = KL(u) = KL(v)L(u) = KL(w) with w =u+ v
1 + uvc2
The operation u⊕ v =u+ v
1 + uvc2
for elements u, v ∈ (−c, c)
defines a commutative group
13 / 24
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MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
Special Relativity is self-consistent
Let P be a point, having K = (x, y, z, t) coordinate in theK-frame and K = (x, y, z, t) coordinate in the K-frame.Then they are exchangeable via a linear transformationdepending the speed v:
K = KL(v)
Let K = (x, y, z, t) be the coordinate of the same point ina K-frame moving at speed u with respect to theK-frame. Then we have
K = KL(u) = KL(v)L(u) = KL(w) with w =u+ v
1 + uvc2
The operation u⊕ v =u+ v
1 + uvc2
for elements u, v ∈ (−c, c)
defines a commutative group13 / 24
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MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
Holling’s predation model is consistent
Tc — average time to consume a prey
Td,k,c = Td + Tk + Tc — average time to discover, kill,and consume a prey
Then the rate of predation is self-consistent:
Rd,k,c =1
Td,k,c=
1
Td + Tk + Tc
=Rd,k
1 + TcRd,k=
Rd1 + (Tk + Tc)Rd
14 / 24
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MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
Holling’s predation model is consistent
Tc — average time to consume a prey
Td,k,c = Td + Tk + Tc — average time to discover, kill,and consume a prey
Then the rate of predation is self-consistent:
Rd,k,c =1
Td,k,c=
1
Td + Tk + Tc
=Rd,k
1 + TcRd,k=
Rd1 + (Tk + Tc)Rd
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MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
Holling’s predation model is consistent
Tc — average time to consume a prey
Td,k,c = Td + Tk + Tc — average time to discover, kill,and consume a prey
Then the rate of predation is self-consistent:
Rd,k,c =1
Td,k,c=
1
Td + Tk + Tc
=Rd,k
1 + TcRd,k=
Rd1 + (Tk + Tc)Rd
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MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
Pay the TIP, or else
All differential equation models are TIP-consistent
Most mapping models in ecology are TIP-inconsistent
Example: Logistic map
xn+1 = Qλ(xn) = λxn(1− xn)
cannot be a model for which n represents time
The time n+ 2 observation yields a different functionalform:
xn+2 = Qλ(xn+1) = Qλ(Qλ(xn)) 6= Qµ(xn)
for any value µ. Strike one on the logistic map
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MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
Pay the TIP, or else
All differential equation models are TIP-consistent
Most mapping models in ecology are TIP-inconsistent
Example: Logistic map
xn+1 = Qλ(xn) = λxn(1− xn)
cannot be a model for which n represents time
The time n+ 2 observation yields a different functionalform:
xn+2 = Qλ(xn+1) = Qλ(Qλ(xn)) 6= Qµ(xn)
for any value µ. Strike one on the logistic map
15 / 24
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MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
Pay the TIP, or else
All differential equation models are TIP-consistent
Most mapping models in ecology are TIP-inconsistent
Example: Logistic map
xn+1 = Qλ(xn) = λxn(1− xn)
cannot be a model for which n represents time
The time n+ 2 observation yields a different functionalform:
xn+2 = Qλ(xn+1) = Qλ(Qλ(xn)) 6= Qµ(xn)
for any value µ. Strike one on the logistic map
15 / 24
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MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
Pay the TIP, or else
All differential equation models are TIP-consistent
Most mapping models in ecology are TIP-inconsistent
Example: Logistic map
xn+1 = Qλ(xn) = λxn(1− xn)
cannot be a model for which n represents time
The time n+ 2 observation yields a different functionalform:
xn+2 = Qλ(xn+1) = Qλ(Qλ(xn)) 6= Qµ(xn)
for any value µ. Strike one on the logistic map15 / 24
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MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
Model Test – Finding the Best Fit
x1, . . . , xn — Observed states at time t1, . . . , tn for anatural process which are modeled by competing modelsy(t; y0, p) and z(t; z0, q), respectively, with parameter p, q,and initial state y0, z0
Model selection criterion: All else being equal whicheverhas a smaller error is the benchmark model by default:
Ey = min(y0,p)
n∑i=1
[y(ti; y0, p)− xi]2
Ez = min(z0,q)
n∑i=1
[z(ti; z0, q)− xi]2
Any parameter is only meaningful to its model, and itsvalue can only be derived by best-fitting the observed datato the model
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MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
Model Test – Finding the Best Fit
x1, . . . , xn — Observed states at time t1, . . . , tn for anatural process which are modeled by competing modelsy(t; y0, p) and z(t; z0, q), respectively, with parameter p, q,and initial state y0, z0
Model selection criterion: All else being equal whicheverhas a smaller error is the benchmark model by default:
Ey = min(y0,p)
n∑i=1
[y(ti; y0, p)− xi]2
Ez = min(z0,q)
n∑i=1
[z(ti; z0, q)− xi]2
Any parameter is only meaningful to its model, and itsvalue can only be derived by best-fitting the observed datato the model
16 / 24
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MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
Model Test – Finding the Best Fit
x1, . . . , xn — Observed states at time t1, . . . , tn for anatural process which are modeled by competing modelsy(t; y0, p) and z(t; z0, q), respectively, with parameter p, q,and initial state y0, z0
Model selection criterion: All else being equal whicheverhas a smaller error is the benchmark model by default:
Ey = min(y0,p)
n∑i=1
[y(ti; y0, p)− xi]2
Ez = min(z0,q)
n∑i=1
[z(ti; z0, q)− xi]2
Any parameter is only meaningful to its model, and itsvalue can only be derived by best-fitting the observed datato the model
16 / 24
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MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
Model Test – Fit the past, predict the future
Edmond Halley (1656-1742) used Newtonian mechanics topredict the 1758 return of Halley’s Comet, giving thecomet its name
Arthur Eddington (1882-1944) used the total solar eclipseof May 29, 1919 to confirm general relativity’s predictionfor the bending of starlight by the Sun, making Einstein aninstant world celebrity
Gregor Mendel’s Laws of Inheritance (1866) wasrediscovered in 1900, ushering in the science of moderngenetics
Holling’s model of predation is ubiquitous in theoreticalecology
17 / 24
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MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
Model Test – Fit the past, predict the future
Edmond Halley (1656-1742) used Newtonian mechanics topredict the 1758 return of Halley’s Comet, giving thecomet its name
Arthur Eddington (1882-1944) used the total solar eclipseof May 29, 1919 to confirm general relativity’s predictionfor the bending of starlight by the Sun, making Einstein aninstant world celebrity
Gregor Mendel’s Laws of Inheritance (1866) wasrediscovered in 1900, ushering in the science of moderngenetics
Holling’s model of predation is ubiquitous in theoreticalecology
17 / 24
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MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
Model Test – Fit the past, predict the future
Edmond Halley (1656-1742) used Newtonian mechanics topredict the 1758 return of Halley’s Comet, giving thecomet its name
Arthur Eddington (1882-1944) used the total solar eclipseof May 29, 1919 to confirm general relativity’s predictionfor the bending of starlight by the Sun, making Einstein aninstant world celebrity
Gregor Mendel’s Laws of Inheritance (1866) wasrediscovered in 1900, ushering in the science of moderngenetics
Holling’s model of predation is ubiquitous in theoreticalecology
17 / 24
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MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
Model Test – Fit the past, predict the future
Edmond Halley (1656-1742) used Newtonian mechanics topredict the 1758 return of Halley’s Comet, giving thecomet its name
Arthur Eddington (1882-1944) used the total solar eclipseof May 29, 1919 to confirm general relativity’s predictionfor the bending of starlight by the Sun, making Einstein aninstant world celebrity
Gregor Mendel’s Laws of Inheritance (1866) wasrediscovered in 1900, ushering in the science of moderngenetics
Holling’s model of predation is ubiquitous in theoreticalecology
17 / 24
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MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
Mathematical Biology — To Translate Evolution toMathematics
Example: One Life Rule
Every organism lives only once and must die in any finite timein the presence of infinite population density
In math translation: Let xt be the population at time t.Then the per-capita change must satisfy
xt − x0x0
=xtx0− 1 ≥ −1
Lead to
One Life Rule ⇐⇒ limx0→∞
xt − x0x0
= −1
and to the logistic equation
x(t) = rx(t)[1− x(t)/K]
with x(t) = xt, r the max per-capita growth rate, and Kthe carrying capacity
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MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
Mathematical Biology — To Translate Evolution toMathematics
Example: One Life Rule
Every organism lives only once and must die in any finite timein the presence of infinite population density
In math translation: Let xt be the population at time t.Then the per-capita change must satisfy
xt − x0x0
=xtx0− 1 ≥ −1
Lead to
One Life Rule ⇐⇒ limx0→∞
xt − x0x0
= −1
and to the logistic equation
x(t) = rx(t)[1− x(t)/K]
with x(t) = xt, r the max per-capita growth rate, and Kthe carrying capacity
18 / 24
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MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
Mathematical Biology — To Translate Evolution toMathematics
Example: One Life Rule
Every organism lives only once and must die in any finite timein the presence of infinite population density
In math translation: Let xt be the population at time t.Then the per-capita change must satisfy
xt − x0x0
=xtx0− 1 ≥ −1
Lead to
One Life Rule ⇐⇒ limx0→∞
xt − x0x0
= −1
and to the logistic equation
x(t) = rx(t)[1− x(t)/K]
with x(t) = xt, r the max per-capita growth rate, and Kthe carrying capacity
18 / 24
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MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
Footnote: model or no model, generalization orrelativism is often the problem
Strike two on the logistic map x1 = λx0(1− x0):
limx0→∞
x1 − x0x0
= limx0→∞
[λ(1− x0)− 1] = −∞ 6= −1
While the logistic equation, x′(t) = rx(t)(1− x(t)/K),dogged another consistency bullet
limx0→∞
x(t;x0)− x0x0
= limx0→∞
[K
x0 + (K − x0)e−rt− 1
]= −1
There should be no different versions of the same reality,but refined approximations
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MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
Footnote: model or no model, generalization orrelativism is often the problem
Strike two on the logistic map x1 = λx0(1− x0):
limx0→∞
x1 − x0x0
= limx0→∞
[λ(1− x0)− 1] = −∞ 6= −1
While the logistic equation, x′(t) = rx(t)(1− x(t)/K),dogged another consistency bullet
limx0→∞
x(t;x0)− x0x0
= limx0→∞
[K
x0 + (K − x0)e−rt− 1
]= −1
There should be no different versions of the same reality,but refined approximations
19 / 24
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MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
Footnote: model or no model, generalization orrelativism is often the problem
Strike two on the logistic map x1 = λx0(1− x0):
limx0→∞
x1 − x0x0
= limx0→∞
[λ(1− x0)− 1] = −∞ 6= −1
While the logistic equation, x′(t) = rx(t)(1− x(t)/K),dogged another consistency bullet
limx0→∞
x(t;x0)− x0x0
= limx0→∞
[K
x0 + (K − x0)e−rt− 1
]= −1
There should be no different versions of the same reality,but refined approximations
19 / 24
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MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
One More Example: Why DNA is coded in 4 bases?
The AT pair has one weak O-H bond but the GC pair hastwo O-H bonds. Hence, the GC pair takes longer tocomplete binding than the AT pair does
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MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
One More Example: Why DNA is coded in 4 bases?
The AT pair has one weak O-H bond but the GC pair hastwo O-H bonds. Hence, the GC pair takes longer tocomplete binding than the AT pair does
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MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
One More Example: Why DNA is coded in 4 bases?
Start with a conceptual model: DNA replication is acommunication channel
Every communication is characterized by the transmissiondata rate in bits per second, i.e. the information entropyper second
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MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
One More Example: Why DNA is coded in 4 bases?
Start with a conceptual model: DNA replication is acommunication channel
Every communication is characterized by the transmissiondata rate in bits per second, i.e. the information entropyper second
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MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
One More Example: Why DNA is coded in 4 bases?
Start with a conceptual model: DNA replication is acommunication channel
Every communication is characterized by the transmissiondata rate in bits per second, i.e. the information entropyper second
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MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
One More Example: Why DNA is coded in 4 bases?
For 2n paired bases, the replication rate is
R2n =log2(2n)
τ12+τ34+···+τ(2n−1)(2n)
n
in bits per time
If 53 ≤
τGCτAT≤ 2.7, then: max
nR2n = R4
Punch Line: Life is a reality show on your DNA channel
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MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
One More Example: Why DNA is coded in 4 bases?
For 2n paired bases, the replication rate is
R2n =log2(2n)
τ12+τ34+···+τ(2n−1)(2n)
n
in bits per time
If 53 ≤
τGCτAT≤ 2.7, then: max
nR2n = R4
Punch Line: Life is a reality show on your DNA channel
22 / 24
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MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
One More Example: Why DNA is coded in 4 bases?
For 2n paired bases, the replication rate is
R2n =log2(2n)
τ12+τ34+···+τ(2n−1)(2n)
n
in bits per time
If 53 ≤
τGCτAT≤ 2.7, then: max
nR2n = R4
Punch Line: Life is a reality show on your DNA channel22 / 24
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MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
Closing Comments
Mathematics is driven by open problems, but science isdriven by existing solutions
Mathematical modeling is to find the equation to whichnature fits as a solution
Mathematics is to create more hays but modeling is tofind the needle in haystack
Mathematical biology is not to solve mathematicalproblems of models but to find mathematical models forbiological problems
Training to be a mathematical modeler does need to solvemathematical problems of reasonable models.
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MathematicalModeling and
Biology
Bo Deng
Introduction
Examples ofModels
Consistency
Model Test
MathematicalBiology
Conclusion
Mathematical modeling is to construct the picture sothat the consequence of the picture is the picture ofthe consequence.
– Anonymous or by Heinrich Hertz (1857-1894)
24 / 24