Developmental memory capacity, robustness and attractor basins in gene networks
Developmental memory capacity is a property of gene networks studied by Szilágyi and colleagues in 2020. A network must return neighbouring embryonic states to the same adult state, so the neighbourhood lies inside one basin of attraction8. Manu and colleagues (2009) tied buffered, discrete responses to attractors and basin boundaries56. Earlier physiologists used buffering for chemical stability13.
- Earliest held
- 1915, Bayliss, W. M.
- Most discussed in
- Structures of Respiratory Supercomplex…, 2019
- In the library
- 213 passages in 84 works
- Rewritten
- 2026-10-25
Buffers in physiology
Bayliss (1915) reported that Fernbach and Hubert compared bicarbonates, phosphates and amino acids to tampons that soak up excess ions. He found the English word buffer poorly descriptive, since a railway buffer does not absorb the engine as these substances absorb ions1. Loeb (1916) cited Henderson's view that buffers in sea water and blood form part of the fitness of the environment2. Haldane (1917) granted that the body holds so much buffer that considerable acid or alkali could be added without measurable change. He still held that exact regulation of blood reaction is indispensable3. Hill (1926) argued that muscle must contain a more effective buffer, analogous to haemoglobin4.
Canalization and attractors
Manu and colleagues (2009) analysed the gap gene system of Drosophila. They wrote that a discrete and buffered response to perturbations marks a canalized developmental system. Waddington, they noted, explained these two properties by postulating favoured stable trajectories called chreods5. From a model based on gene expression data, they concluded that multistable dynamical systems show both properties. Attractors damp small perturbations, and discontinuous boundaries between basins give a discrete response to larger ones6. They concluded that the trajectory of the gap gene system is a chreod5.
Basins in bioelectric memory
Law and Levin (2015) modelled resting potential bistability in amphibia. In their models, voltages started in the physiological range converged on one of two locally stable voltages. The basins of attraction for the two voltages were disconnected along the voltage axis. Starting from hyperpolarization to -140 mV, the system evolved to the higher-voltage memory7. The same vocabulary of stable states and basins is applied here to membrane voltage rather than gene expression.
Measured robustness
Szilágyi, Szabó, Santos and Szathmáry (2020) required a developmental process to be robust against stochastic perturbations of the embryonic state and of the gene interaction matrix. Neighbouring embryonic states must fall in the basin of the matching adult state8. They tested recovery under increasing perturbation. The network was very robust to changes in the embryonic state and moderately robust to additive perturbations. Robustness was limited when interactions were eliminated9. They traced a sharp difference between evolutionary and analytic models in that last case to peculiarities of the evolutionary process9.
A railway buffer does not absorb the engine itself, as the substances referred to absorb ions.
Bayliss, W. M., 1915 · Principles of General Physiology · open at passage 907Instead of saying that the organisms are adapted to the medium, L. Henderson has pointed out the fitness of the environment for the development of organisms
Loeb, J., 1916 · The Organism as a Whole, from a Physicochemical Viewpoint · open at passage 482the blood, and the body as a whole, are so full of so-called buffer substances that a considerable amount of acid or alkali might be added without any measur- able disturbance of the blood alkalinity being produced.
Haldane, J. S., 1917 · Organism and Environment as Illustrated by the Physiology of Breathing · open at passage 75It is necessary to suppose that some more effective buffer, something analogous to the haemoglobin of blood, is present in muscle
Hill, A. V., 1926 · Muscular Activity · open at passage 98A discrete [6],[7] and buffered response to perturbations is the hallmark of a canalized developmental system.
Manu, Surkova S, Spirov AV, Gursky VV, Janssens H, Kim AR…, 2009 · Canalization of gene expression and domain shifts in the Drosophila blastoderm… · open at passage 40Small perturbations are damped because of phase space volume contraction driven by attractors. A discrete response to larger perturbations is a consequence of the discontinuous boundaries between the basins of attraction
Manu, Surkova S, Spirov AV, Gursky VV, Janssens H, Kim AR…, 2009 · Canalization of gene expression and domain shifts in the Drosophila blastoderm… · open at passage 40voltages initialized in the physiological range converge on one of two locally stable voltages. The basins of attraction for these stable voltages are however, disconnected (in V)
Law R, Levin M, 2015 · Bioelectric memory: modeling resting potential bistability in amphibian embryos… · open at passage 29It requires that the neighborhood (according to a given metric) of the embryonic states must also be in the basin of their corresponding adult states.
Szilágyi A, Szabó P, Santos M, Szathmáry E, 2020 · Phenotypes to remember: Evolutionary developmental memory capacity and… · open at passage 27The system is very robust against perturbations regarding the embryonic state, it is moderately robust against additive perturbations and has limited robustness against eliminated interactions
Szilágyi A, Szabó P, Santos M, Szathmáry E, 2020 · Phenotypes to remember: Evolutionary developmental memory capacity and… · open at passage 27