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Maxwell's Demon in Biochemical Signal Transduction With Feedback Loop
Maxwell's Demon in Biochemical Signal Transduction With Feedback Loop
Received 2 Jul 2014 | Accepted 12 May 2015 | Published 23 Jun 2015 DOI: 10.1038/ncomms8498 OPEN
Signal transduction in living cells is vital to maintain life itself, where information transfer in
noisy environment plays a significant role. In a rather different context, the recent intensive
research on ‘Maxwell’s demon’—a feedback controller that utilizes information of individual
molecules—have led to a unified theory of information and thermodynamics. Here we
combine these two streams of research, and show that the second law of thermodynamics
with information reveals the fundamental limit of the robustness of signal transduction
against environmental fluctuations. Especially, we find that the degree of robustness is
quantitatively characterized by an informational quantity called transfer entropy. Our
information-thermodynamic approach is applicable to biological communication inside cells,
in which there is no explicit channel coding in contrast to artificial communication. Our result
could open up a novel biophysical approach to understand information processing in living
systems on the basis of the fundamental information–thermodynamics link.
1 Department of Physics, The University of Tokyo, Tokyo 113-0033, Japan. 2 Department of Basic Science, The University of Tokyo, Tokyo 153-8902, Japan.
w Present addresses: Department of Physics, Tokyo Institute of Technology, Tokyo 152-8551, Japan (S.I.); Department of Applied Physics, The University of
Tokyo, Tokyo 113-8656, Japan (T.S.). Correspondence and requests for materials should be addressed to S.I. (email: sosuke@stat.phys.titech.ac.jp).
A
crucial feature of biological signal transduction lies in the Results
fact that it works in noisy environment1–3. To understand Model. The main components of E. coli chemotaxis are the ligand
its mechanism, signal transduction has been modelled as density change l, the kinase activity a and the methylation level
noisy information processing4–11. For example, signal m of the receptor (Fig. 1). A feedback loop exists between a and
transduction of bacterial chemotaxis of Escherichia coli (E. coli) m, which reduces the environmental noise in the signal
has been investigated as a simple model organism for sensory transduction pathway from l to a (ref. 49). Let lt, at and mt be the
adaptation12–16. A crucial ingredient of E. coli chemotaxis is a values of these quantities at time t. They obey stochastic dynamics
feedback loop, which enhances the robustness of the signal due to the noise, and are described by the the following coupled
transduction against environmental noise. Langevin equations7,14,16:
The information transmission inside the feedback loop can be 1 a
quantified by the transfer entropy, which was originally a_ t ¼ ta ½at at ðmt ; lt Þ þ xt ;
1 m ð1Þ
introduced in the context of time series analysis17, and has m _t ¼ tm at þ xt ;
been studied in electrophysiological systems18, chemical where at ðmt ; lt Þ is the stationary value of the kinase activity under
processes19 and artificial sensorimotors20. The transfer entropy the instantaneous values of the methylation level mt and the
is the conditional mutual information representing the directed ligand signal lt. In the case of E. coli chemotaxis, we can
information flow, and gives an upper bound of the redundancy of approximate at ðmt ; lt Þ as amt blt, by linearizing it around the
the channel coding in an artificial communication channel with a steady-state value7,14. xxt (x ¼ a,m) is the white Gaussian noise
feedback loop21; this is a fundamental consequence of Shannon’s 0
with hxxt i ¼ 0 and hxxt xxt0 i ¼ 2Ttx dxx0 dðt t 0 Þ, where h?i
second theorem22,23. However, as there is not any explicit channel describes the ensemble average. Ttx describes the intensity of
coding inside living cells, the role of the transfer entropy in the environmental noise at time t, which is not necessarily
biological communication has not been fully understood. thermal inside cells. The noise intensity Tta characterizes the
The transfer entropy also plays a significant role in thermo- ligand fluctuation. The time constants satisfy tm ta 40, which
dynamics24. Historically, the connection between thermodynamics implies that the relaxation of a to at is much faster than that of m.
and information was first discussed in the thought experiment of The mechanism of adaptation in this model is as follows
‘Maxwell’s demon’ in the nineteenth century25–27, where the (Fig. 2; refs 14,16). Suppose that the system is initially in a
demon is regarded as a feedback controller. In the recent stationary state with lt ¼ 0 and at ¼ at ðmt ; 0Þ ¼ 0 at time t o 0,
progress on this problem in light of modern non-equilibrium and lt suddenly changes from 0 to 1 at time t ¼ 0 as a step
statistical physics28,29, a universal and quantitative theory of function. Then, at rapidly equilibrates to at ðmt ; 1Þ so that the
thermodynamics feedback control has been developed, leading to difference at at becomes small. The difference at at plays an
the field of information thermodynamics24,30–48. Information important role, which characterizes the level of adaptation. Next,
thermodynamics reveals a generalization of the second law of mt gradually changes to satisfy at ðmt ; 1Þ ¼ 0, and thus at returns
thermodynamics, which implies that the entropy production of a to 0, where at at remains small.
target system is bounded by the transfer entropy from the target
system to the outside world24.
In this article, we apply the generalized second law to establish Robustness against environmental noise. We introduce a key
the quantitative relationship between the transfer entropy and the quantity that characterizes the robustness of adaptation, which is
robustness of adaptive signal transduction against noise. We show defined as the difference between the intensity of the ligand noise
a
that the transfer entropy gives the fundamental upper bound of t and the
T mean square error of the level of adaptation
the robustness, elucidating an analogy between information ðat at Þ2 :
thermodynamics and the Shannon’s information theory22,23. We 1 1
numerically studied the information-thermodynamics efficiency Jta :¼ a Tta a ðat at Þ2 : ð2Þ
t t
of the signal transduction of E. coli chemotaxis, and found that
the signal transduction of E. coli chemotaxis is efficient as an The larger Jta is, the more robust the signal transduction is against
information-thermodynamic device, even when it is highly the environmental noise. In the case of thermodynamics, Jta
dissipative as a conventional heat engine. corresponds to the heat absorption in a and characterizes the
Measurement t=0 t ~ m
lt
–CH3 CheB lt = 1
Ligand l
a–t (mt , 1) = 0
m mt
CheA
Methylation level Flagellar motor
Kinase activity a
of receptor lt = 0
: Negative feedback loop at
Feedback
violation of the fluctuation–dissipation theorem28. Since the equation (4) shows the significant role of the feedback loop,
environmental noise is not necessarily thermal in the present implying that the robustness of adaptation can be enhanced
situation, Jta is not exactly the same as the heat, but is a against the environmental noise by the feedback using informa-
biophysical quantity that characterizes the robustness of tion. This is analogous to the central feature of Maxwell’s demon.
adaptation against the environmental noise. To further clarify the meaning of inequality (equation (4)), we
focus on the case of the stationary state. If there was no feedback
Information flow. We here discuss the quantitative definition of loop
between m and a, then the second law reduces to
the transfer entropy17. The transfer entropy from a to m at time t ðat at Þ2 ta Tta , which, as naturally expected, implies that
is defined as the conditional mutual information between at and the fluctuation of the signal transduction is bounded by the
mt þ dt under the condition of mt: intensity of the environmental
noise. In contrast, in the presence
Z of a feedback loop, ðat at Þ2 can be smaller than ta Tta owing to
p½mt þ dt j at ; mt the transfer entropy dIttr in the feedback loop:
dIttr :¼ dmt þ dt dat dmt p½mt þ dt ; at ; mt ln ;
p½mt þ dt j mt
ð3Þ dI tr
at Þ2 ta Tta 1 t ta :
ðat ð5Þ
where p[mt þ dt, at, mt] is the joint probability distribution of dt
(mt þ dt, at, mt), and p[mt þ dt|at, mt] is the probability distribution
of mt þ dt under the condition of (at, mt). The transfer entropy This inequality clarifies the role of the transfer entropy in
characterizes the directed information flow from a to m during an biochemical signal transduction; the transfer entropy
infinitesimal time interval dt (refs 17,50), which quantifies a characterizes an upper bound of the robustness of the signal
causal influence between them51,52. From the non-negativity of transduction in the biochemical network. The equality in
the conditional mutual information23, that of the transfer entropy equation (5) is achieved in the limit of a - 0 and ta/tm - 0
follows: dIttr 0. for the linear case with at ðmt ; lt Þ ¼ amt blt (Supplementary
Note 1). The latter limit means that a relaxes infinitely fast and the
Second law of information thermodynamics. We now consider process is quasi-static (that is, reversible) in terms of a. This is
the second law of information thermodynamics, which char- analogous to the fact that Maxwell’s demon can achieve the
acterizes the entropy change in a subsystem in terms of the maximum thermodynamics gain in reversible processes35.
information flow (Fig. 3). In the case of equation (1), the gen- In general, the information-thermodynamic bound becomes tight
eralized second law is given as follows (see also Methods section): if a and tm/ta are both small. The realistic parameters of the
bacterial chemotaxis are given by a ’ 3 and ta =tm ’ 0:1 (refs
ajm Jta 7,14,16), and therefore the real adaptation process is accompanied
dIttr þ dSt dt: ð4Þ
Tta by a finite amount of information-thermodynamics dissipation.
ajm Our model of chemotaxis has the same mathematical structure
Here, dSt is the conditional Shannon entropy change
ajm as the feedback cooling of a colloidal particle by Maxwell’s
defined
R as dS t :¼ S½at þ dt j mt þ dt S½at j mt with S½at j mt :¼ demon36,38,42,47, where the feedback cooling is analogous to the
dat dmt p½at ; mt ln p½at j mt , which vanishes in the stationary
noise filtering in the sensory adaptation49. This analogy is a
state. The transfer entropy dItr t on the left-hand side of central idea of our study; the information-thermodynamic
inequalities (equation (5) in our case) characterize the
robustness of adaptation as well as the performance of feedback
Conventional thermodynamics
cooling.
Information thermodynamics
a|m Information flow am Numerical result. We consider the second law (equation (4)) in
dSt dIt
tr dSt
non-stationary dynamics, and numerically demonstrate the
power of this inequality. Figure 4 shows Jta dt=Tta and
ajm
info
t :¼ dIttr þ dSt ð6Þ
a a m
Tt Tt Tt
Heat flow Heat flow Heat flow in six different types of dynamics of adaptation, where the ligand
a
–Jt –Jt
a
–Jt
m signal is given by a step function (Fig. 4a), a sinusoidal function
(Fig. 4b), a linear function (Fig. 4c), an exponential decay
Figure 3 | Schematics of information thermodynamics and conventional (Fig. 4d), a square wave (Fig. 4e) and a triangle wave (Fig. 4f).
thermodynamics. A green (blue) circle indicates subsystem a (m) and a These results confirm that info t gives a tight bound of
grey polygonal line indicates their interaction. (a) The second law of Jta , implying that the transfer entropy characterizes the robustness
information thermodynamics characterizes the entropy change in a well. In Fig. 4b,f, the robustness Jta dt=Tta is nearly equal to
subsystem in terms of the information flow between the subsystem and the the information-thermodynamics bound info t when the
ajm
outside world (that is, info
t :¼ dItrt þ dSt Jat dt=Tta ). The information- signal and noise are decreasing or increasing rapidly (for example,
thermodynamics picture concerns the entropy change inside the dashed t ’ 0:008 and t ¼ 0.012 in Fig. 4f).
square that only includes subsystem a. (b) the conventional second law of
thermodynamics states that the entropy change in a subsystem is Conventional second law of thermodynamics. For the purpose
compensated for by the entropy change in the outside world (that is, of comparison, we next consider another upper bound of the
SL m m am a a
t :¼ Jt dt=Tt þ dSt Jt dt=Tt ). The conventional thermodynamics robustness, which is given by the conventional second law of
picture concerns the entropy change inside the dashed square, which thermodynamics without information.
We define the heat
includes the entire systems a and m. As explicitly shown in this paper, absorption by m as Jtm :¼ a2t =ðtm Þ2 , and the Shannon entropy
information thermodynamics gives a tighter bound of the robustness Jat in change in the total system
R as dSamt :¼ S½at þ dt ; mt þ dt S½at ; mt
the biochemical signal transduction of E. coli chemotaxis. with S½at ; mt :¼ dat dmt p½at ; mt ln p½at ; mt , which vanishes
0.02 0.06
0.04
0.035 0.015 0.05
a
a
a
a
Robustness Jt dt / Tt
Robustness Jt dt / Tt
Robustness Jt dt/Tt
0.03
info
info
0.04
info
0.01
, Ξt
, Ξt
, Ξt
0.025
a
a
0.005 0.03
SL
SL
SL
0.02
0 0.02
Bonuds Ξt
Bonuds Ξt
Bonuds Ξt
0.015
–0.005 0.01
0.01
–0.01 0
0.005
–0.015 –0.01
0
–0.005 –0.02 –0.02
0 0.01 0.02 0.03 0.04 0.05 0.06 0 0.01 0.02 0.03 0.04 0.05 0.06 0 0.01 0.02 0.03 0.04 0.05 0.06
Time t Time t Time t
0.012 1 1 0.7 10
0.01 0.01 0.6
Signal lt
Signal lt
8
a
Signal lt
0.8 0.8
Noise Tt
Noise Tt
Noise Tt
0.008 0.005 0.5
0.6 0.6 0.4 6
0.006 0 0.3
0.4 0.4 4
0.004 –0.005 0.2
0.002 0.2 0.2 0.1 2
-0.01
0 0 0 0 0
0 0.01 0.02 0.03 0.04 0.05 0.06 0 0.01 0.02 0.03 0.04 0.05 0.06 0 0.01 0.02 0.03 0.04 0.05 0.06
0.008 0 0.015
a
a
Robustness Jt dt / Tt
Robustness Jt dt / Tt
Robustness Jt dt / Tt
–0.005
info
info
info
0.006 0.01
, Ξt
, Ξt
, Ξt
–0.01
a
a
0.004 0.005
–0.015
SL
SL
SL
Bonuds Ξt
Bonuds Ξt
Bonuds Ξt
–0.02 0
0.002
–0.025 –0.005
0
–0.03
–0.01
–0.002 –0.035
–0.015
–0.004 –0.04
–0.045 –0.02
0 0.01 0.02 0.03 0.04 0.05 0.06 0 0.01 0.02 0.03 0.04 0.05 0.06 0 0.01 0.02 0.03 0.04 0.05 0.06
Time t Time t Time t
0.012 1 0.012 0.1 0.012 1
0.01 0.01
a
a
0.01
Signal lt
Signal lt
Signal lt
0.8 0.08 0.8
Noise Tt
Noise Tt
Noise Tt
0.008 0.6 0.008 0.008 0.6
0.06 0.006
0.006 0.006
0.4 0.04 0.004 0.4
0.004 0.004
0.002 0.2 0.002 0.02 0.002 0.2
0 0 0 0 0 0
0 0.01 0.02 0.03 0.04 0.05 0.06 0 0.01 0.02 0.03 0.04 0.05 0.06 0 0.01 0.02 0.03 0.04 0.05 0.06
Figure 4 | Numerical results of the information-thermodynamics bound on the robustness. We compare the robustness Jat (red line), the information-
thermodynamic bound info t (green line) and the conventional thermodynamic bound SL t (blue line). The initial condition is the stationary state with
at ¼ amt blt , fixed ligand signal blt ¼ 0, and noise intensity Ta ¼ 0.005. We numerically confirmed that SL t t
info
Jat dt=Tta holds for the six transition
processes. These results imply that, for the signal transduction model, the information-thermodynamic bound is tighter than the conventional
thermodynamic bound. The parameters are chosen as ta ¼ 0.02, tm ¼ 0.2, a ¼ 2.7 and Ttm ¼ 0:005 to be consistent with the real parameters of E. coli
bacterial chemotaxis 7,14,16. We discuss the six different types of input signals blt (red solid line) and noises Tta (green dashed line). (a) Step function:
blt ¼ 0.01 and Tta ¼ 0:5 for t 4 0. (b) Sinusoidal function: blt ¼ 0.01 sin(400t) and Tta ¼ 0:5 j sinð400tÞ j þ 0:005 for t 4 0. (c) Linear function:
blt ¼ 10t and Tta ¼ 100t þ 0:005 for t 4 0. (d) Exponential decay: bLt ¼ 0.01[1 exp( 200t)] and Tta ¼ 0:5½1 expð 200tÞ þ 0:005 for t 4 0.
(e) Square wave: blt ¼ 0:01½1 þ bsinð200tÞc and Tta ¼ 0:05½1 þ bsinð200tÞc þ 0:005 for t 4 0, where b . . . c denotes the floor function. (f) Triangle wave:
blt ¼ 0:01j2ð100t b100t þ 0:5cÞj and Tta ¼ 0:5j2ð100t b100t þ 0:5cÞj þ 0:005 for t 4 0.
in the stationary state. We can then show that on the inequalities (equation (8)):
is an upper bound of Jta dt=Tta , as a straightforward consequence of where the second term on the right-hand side is given
the conventional second law of thermodynamics of the total sys- by the ratio between the information-thermodynamic
tem of a and m (refs 28,29). The conventional second law implies dissipation info
t Jta dt=Tta and the entire thermodynamic
that the dissipation in m should compensate for that in a (Fig. 3). dissipation t Jta dt=Tta . This quantity satisfies 0 r w r 1,
SL
Figure 4 shows Jta dt=Tta along with info t and SLt . Remarkably, and w ’ 1 (w ’ 0) means that information-thermodynamic
information-thermodynamic bound info t gives a tighter bound of bound is much tighter (a little tighter) compared with the
Jta than the conventional thermodynamics bound SL t such that conventional thermodynamic bound. We numerically calculated
w in the aforementioned six types of dynamics of adaptation
Jta (Supplementary Figs 1–6). In the case of a linear function
SL info
t t dt; ð8Þ
Tta (Supplementary Fig. 3), we found that w increases in time t and
approaches to w ’ 1. In this case, the signal transduction of
for every non-stationary dynamics shown in Fig. 4. Moreover, we E. coli chemotaxis is highly dissipative as a thermodynamic
can analytically show inequalities (equation (8)) in the stationary engine, but efficient as an information transmission device.
state (Supplementary Note 4).
To compare the information-thermodynamic bound and the Comparison with Shannon’s theory. We here discuss the simi-
conventional thermodynamics one more quantitatively, we larity and the difference between our result and the Shannon’s
introduce an information-thermodynamic figure of merit based information theory (refs 22,23; Fig. 5). The Shannon’s second
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