Gene Regulation Instructions - System Modeling 5
Level of biological organization linking cell level division and population level evolution
Biology levels and genetics
Modeling 5: Gene Regulation
System Modeling 5: Gene Regulation Instructions
System Modeling 5: Gene Regulation
An example of why it's so critical to understand where the boundaries are when considering a system. (developed from Eric Wolstenholme's Archetype examples by Gene Bellinger)
YouTube Video
Hospital Early Discharge Boundaries
Go to Gene Bellinger's insight version with video link This common archetype of systems that include relapse or recidivism allows exploration of the unintended effects of increasing upstream capacity and swamping downstream capacity. The increase in the relapse rate eventually returns to swamp upstream capacity as well. A social welfare example, based on a TANF case study, from How Small System Dynamics Models Can Help the Policy Process. N. Ghaffarzadegan, J. Lyneis, GP Richardson. System Dynamics Review 27,1 (2011) 22-44 abstract Conference version here
Swamping Insight
This is a stock-flow consistent model, namely the simplest (SIM) model with government money. I have added imports and exports and an exchange rate which has an influence on consumption demand via real disposable income and real foreign demand.
Godley/Lavoie (2006), chapter 3
(I had to change the equation for consumption demand. The disposable income now enters with a time lag of one period. Otherwise the model would be recursive and would not work in Insight Maker. Thanks to Gene for support.)designed by Dirk Ehnts (blog)
SIM model, open economy version
From Fig 1.1 p11 Pigliucci M and Muller GB (2010) Evolution: The Extended Synthesis. This is a shift in emphasis from statistical correlation to mechanistic causation (p12), including the conditions for the origin and innovation of traits (p13). It overcomes the gradualism, externalism and gene centrism of the Modern Synthesis. Non-gradual change is a property of complex dynamical systems. EvoDevo processes generate particular forms of change rather than others.Genes are followers in the evolutionary process that capture the emergent interactions among environment, development and inheritance into genetic-epigenetic circuits, which are passed to and elaborated on in subsequent generations (p14).
Evolution extended synthesis
SM5: Gene Regulation Instructions
Gemini AI interactions Jan2026 on community disorder and wellbeing using Gene Bellinger's prompts after discussion with Kurt Kreuger on Community networks (and network within a population ABM) See also social marketing and community wellbeing search insights
From community disorder to wellbeing
Small Intestine example from Progress in Biophysics & Molecular Biology Special Issue 2016 From the century of the genome to the century of the organism: New theoretical approaches paper on organization. Compare with Bogdanov (click tag)
Biology Principles of Organization and Variation 1
Abstract
High altitude environments challenge the physiology of
mammals mainly due to hypoxic conditions. As a response to this, many mammals
show molecular adaptations e.g. by mutations in the genes encoding the hemoglobins.
This can result in an increase O2 affinity (and thereby a
leftshifted O2 dissociation curve) which will enhance the pulmonary
loading of O2. However, the shift can also hamper the O2 unloading
process to the metabolic tissue. To elucidate this trade-off between loading and
unloading a numerical computer model was made in the program Insigt maker based
on the organism, deer mouse (
Peromyscus
maniculatus). The numerical solution was calculated by the Runge-Kutta
method. A time step (dt) of 0.00001 was chosen, as the results were independent
of dt at this value. This was tested by investigating the residual values of an
interval of dt around 0.00001. The model showed how the trade-off is expressed
at different altitudes and how the degree of advantages/disadvantages varies.
Based on the model it can be suggested that the trade-off is beneficial, when
the hypoxia is severe at high altitude. This is consistent with previously
findings.
Model af O2 transport under hypoxi
This is a stock-flow consistent model, namely a modified version of the simplest (PC) model with money and boonds.
Godley/Lavoie (2006), chapter 4
(I had to change the equation for consumption demand. The disposable income now enters with a time lag of one period. Otherwise the model would be recursive and would not work in Insight Maker. Thanks to Gene for support.)designed by Dirk Ehnts (blog)
PC model
Regulación de la expresión en múltiples niveles de un gen hipotético de oxidoreductasa. Parametros; H2O2: moleculas iniciales de H2O2; Tasa Oxidativa: velocidad a la que la celula produce nuevo H2O2, Mutación TR1 y ProtS: Activa las mutaciones en estos genes (ver panel de información); miARN: activa la regulación por miARNs.
Proyecto Molecular
WIP based mostly on Jan
Toporowski
2013 vol 1 and
2018 vol 2 books on Michal Kalecki: An Intellectual Biography
Layout Consistent with David Wheat MacroEconomic model CLD Insight by Gene Bellinger
Kalecki economic thought
copied from: Gene Bellinger (Success to the Successful Archetype | Insight Maker)
Success to the successful archetype represents two reinforcing structures which may be in a delicate balance though as soon as one gains a small advantage the resource allocation favors the more successful and the result is then rapidly skewed in the direction of the more successful. See also
Archetypes.
Success to the Successful Archetype
copied from: Gene Bellinger (Shifting the Burden Archetype | Insight Maker)
A shifting the burden structure occurs when there are different ways to address a situation. With one approach being easier, faster, and requiring fewer resources, which do you think gets pursued? The problem is that taking the easier path ensures one will have to take the easier path repeatedly, and makes it harder to pursue the long-term better solution. See also
Archetypes.
Shifting the Burden Archetype