Systems And Networks In Biology Flashcards
Why, in light of the gene-centric view, is it still important for us to study the phenotype?
- knowing the genome does not give much insight into organism or behaviour
- gives contextual utility to ecological analysis
What is a non-equilibrium dynamical system?
- based on principles of non-equilibrium thermodynamics
- constrains and drives organisation
What are the components of a non-equilibrium dynamical system?
- Self-organisation
- Self-assembly
- Energy
Describe self-assembly
- physical association of molecules into an equilibrium structure
- properties at the larger scale are defined by properties of the subunit
Describe self-organisation
- non-equilibrium systems that dissipate energy to achieve a dynamic steady state
- higher (system) level organisation is not explicitly specified by rules
- robust - can recover from severe perturbation of the system
How does dynamic self-organisation arise ?
Spontaneously emerges from a series of (non-linear) local interactions
What is dynamic self-organisation a type of?
Spatio-temporal order
What is the central dogma of molecular biology
The detailed residue-residue transfer of sequential information
Why is the central dogma wrong?
A linear, causal chain does not illustrate the complex network of system interactions across multiple scales that show emergent behaviour
What is the genome?
Protein-gene interactions
What is the proteome?
Protein-protein interactions?
What is metabolism?
Biochemical reactions
Describe a complex system
- Typically has many interacting components
- Non-linear interactions (and feedback loops)
- Emergent properties
Give examples of emergent properties
- spontaneous order
- adaptation
Describe emergent behaviour
a property of a system that is not apparent from its component parts in isolation
How does emergent behaviour arise
Interactions between the components of when operating together in a system
Examples of complex systems:
- Collective behaviour
- Evolution and adaptation
- Game theory
- Networks
- Nonlinear dynamics
- Pattern formation
- Systems theory
What do complex systems consist of?
- Complexity
- Emergence
- Energy
- Self-assembly
- Self-organisation
What was Van Valen’s fitness theory?
- fitness is expansive energy
- natural selection, at any level or time scale, maximises the expected amount of expansive energy
Absolute fitness is defined as
Control of trophic energy level (reduced carbon)
What is the pro of Van Valen’s fitness definition?
- can be applied to all organisms
- avoids issues with individuals, clonality, body size, indeterminate growth or expansion
What are Dynamic Energy Budget models?
The application of Van Valen’s fitness theory at an ecosystem level
What is an experimental approach to investigating a complex system?
- mating in yeast under starvation (the shmoos)
- abstracted network representations
How do we use mating in yeast under starvation to investigate complex systems ?
- analysing gene expression patterns using a DNA microarray
- red = upregulated after pheromone
- green = downregulated
- apply probes to array to measure red/green ratio
- cluster analysis of gene behaviour through gene transcripts
- repeat transcript analysis in different mutant backgrounds with predictions
How are green fluorescently labelled probes made
From cDNA library of normal cells
How are red fluorescently labelled probes made
From cDNA library of cells treated with mating pheromone
Results of starved yeast mating investigation
- > 200 transcripts increased in abundance
- > 200 decrease in abundance
- 383 genes changed by >3 fold
Describe abstract network representations
- Abstract representations of nodes and (directed) edges
- node degree distributions
- metabolic flux networks
- signal transduction networks
- physical transport networks
- food webs
List abstracted network representations
- Basic unit
- Motifs
- Modules
- Transcriptional regulatory network
Give example of abstracted network representation motifs
- SIM
- MIM
- FFL
Give an example of a scale-free abstracted network representation
- Yeast metabolism
- metabolic networks for organisms of all 3 domains of life
The phenotype operates as
Interconnected networks across multiple levels
What are phenotypes
Non-equilibrium systems maintained by continuous energy flows
Network theory provides
One framework to explore high-level concepts across multiple domains
What does non-equilibrium mean?
Requires constant energy input
Give an example of a non-equilibrium system
Us!
Give an example of a self-organising system
- Microtubules
- nucleoli
- lipid-lipid phase
Give an example of a non-linear interaction
Enhancers/repressors binding to the promoter regions
What does the word ‘complicated’ imply?
Predictability
Described starved yeast
Conflict between cell division and shmoo formation pathways
