ten_models.htm

May 18, 1999

About ten models for metabolic/growth regulation in fluctuating environments

What are the different mechanisms by which algae could regulate their metabolic activities and cellular composition in response to a fluctuating environment? How do these models for their regulation compare?

Not all of these models can be justified and the behaviors of some models may overlap.

Different species could be using different underlying logic for response to environmental cues.

model description example
0. No response

cells don't respond to environmental cues very strongly

cells may have constitutive regulation of major components

hypothesized for cyanobacteria in mixed waters
1. dynamic - optimizing

feedback control regulates both the activity of the components and the quantity of the components

this would be the most likely model

STELLA models for this

optimization algorithms such as this can be compared to Shuter's model

1.b oscillations

dynamic models can be made to oscillate

this might be a subset of 1

NADH being produced in glycolysis
2. shift up/shift down

this also is a subset of the dynamic optimization model

simple dynamic models can show this behavior without over-riding genetic parameters

cells have some global regulators that set the region of metabolism, normal gene and enzyme feedback type controls work as well

starvation response
3. differentiation

some unicelluar algae differentiate

in response to fluctuation in environmental cues there would be imposed variability in cell types

diatoms cell size

cyanobacteria (heterocysts, vegetative,

single cell to colony forming transition

4. stochastic or contrarian

cells could have random generators that push individuals to have a particular metabolism that is independent of what the current or past cues would indicate

this would be a good survival mechanism but would have trouble in a competitive environment

C & S strategies are competitive - R strategy may be more designed for survival?

genetic models for transposons
5. weighted response/fuzzy logic

instead of being based on Boolean logic, there could be a weighted response to the logic

fuzzy logic is fundamentally different than weighted Boolean, but that might be difficult to work with in these scenarios

 

 

getting to be like a network response

6. network

the regulation could be based more on the network and connections as a complex system than indicators of flow and feedback

complex systems (such as N-K networks) can display jumps between basins that have major significance in the outcomes but are due to only slight changes in the logic

these systems could be similar to the shift up/shift down, the differentiating cell or the fuzzy logic models

 
7. self-awareness

one of the basic assumptions in reductionist biology is that there is no general sensory mechanism for the current state, that has to be a synthesis of the individual metabolic cues

cells could be programmed to maintain their flux capacity in a certain range, this would lead to the cells having a "goal" rather than converging on an optimum

flux capacity could be detected as some quantity such as the redox potential of intermediates in photosynthesis rather than the amount of NADPH produced

cells divide when they reach a preset size

8. predictive

cells might be able to predict some aspects of their environment

there maybe patterns in the chaos/turbulence that can be detected - although I'm not specifying how this might happen

circadian rythms are a simple example

 

9. fields and gradients

cells might respond to their position in a field or chemical gradient

fields could be set up between algae of the same species (although I don't exactly know how this would happen except for a chemical gradient).

light field

gravity, magnetic, temperature or other field

 

hormones or some indicator chemical triggers switch from single to colonial forms as response to predation

10. cell to cell communication Cells communicate with each other using hormones cAMP and CO2 fixation (Francko abstracts)
11. groups of cells as an individual

connection between cells to form an organism/individual

water column would be made up of distinct individuals (each individual made up of cells that are unconnected in 3D)

only suggestion is that this happens in another dimension (other than 3 dimentional space, such as through string theory)

 

 

I am exploring the use of models in understanding algal physiology in a work-in-progress "three models". This paper focuses more on what we can learn by comparing highly descriptive models, dynamic simulation models, and network models for metabolism. Each model has something to contribute to our understanding.