111 lines
3.8 KiB
Plaintext
111 lines
3.8 KiB
Plaintext
---
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title: Sketch for simulating chemodiversity
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author: Stefan Dresselhaus
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date: 2018-09-21
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format: markdown+lhs
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...
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= (rough) sketch components responsible for chemodiversity
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== Genes
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- define which enzymes are produced in which quantities
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- list in fig. 1 in [1]
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- can be scaled down/inactivated (i.e. when predators leave for generations)
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- easy to ramp up production as long as the genes are still there
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- plants can survive without problems with inactive PSM-cycles when no
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adversaries are present.
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=== Inheritance & Mutation
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- via whole-genome and local-genome duplication
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- copies accumulate mutations that lead to neofunctionalization
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- e.g. subtle differences in terpene synthases can yield vastly different products
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- i.e. these changes can appear easily
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- need to classify products by "chemical distance" for simulation
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- **TODO**: Map/Markov-Chain of mutations that may occur here?
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=== Evolutional strategies
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- "Bet-hedging": reduce variations of fitness over time
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- **TODO**: understand
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- different effects of intra-cohort-variation vs. inter-cohort-variation
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- Plants with inactive PSM can survive if predators are deterred by other
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individuals due to automimicry-effect which *could* foster wider genetic
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variance
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- the more of those individuals are present in a population, the less their
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overall fitness becomes.
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- **TODO**: fitness must also be able to depend on relative appearance of
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adversarial traits in the population
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- Keyword: Frequency-dependent-selection (FDS)
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== Pathways to produce chemical compounds
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- 40k+ compounds just stem from compounds of the calvin-cycle taking the
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MEP-pathway or from the krebs-cycle taking the MVA-pathway
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- both yield the same intermediate product that forms the basis.
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- 10k+ compounds are amino-acid-derivatives
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- Chapter VI in [1] exemplary describes 4 complete different pathways that yield
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compounds.
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- similar compounds/pathways should be found in the simulation
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=== Consequences of producing compounds
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- taking away parts of the calvin/krebs cycle puts pressure on those
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- **TODO**: find out what they do and on what they depend.
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- **TODO**: where do amino-acids come from? How much impact has the diversion of
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these components?
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== Maintaining chemical diversity
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=== + screening hypothesis
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- many PSM found have no *known* biological activity
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- plants "keep them around" in case another mutation needs them to produce
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something "useful"
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- creating things without use increase the need for photosynthesis and/or
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nutrient uptake.
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=== - screening hypothesis
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- it is suggested that local abiotic & biotic selection pressures are the main
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driver
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- inactive molecules are not maintained long
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- it was observed that some plants "rediscovered" some compounds in their
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evolution suggesting they got rid of them when no pressure to maintain them
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was applied
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==== questions resulting from this that should be answered in the simulation
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- details in chapter VIII of [1]
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- how quick can lost diversity be restored?
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- how expensive is it to keep producing many inactive substances while also
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producing active deterrents? Does this lead to a single point-of-failure due
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to overspecialisation? What must be done to prevent this?
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- strong selection pressure *should* decrease quantity of compounds due to
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costs, but plants do not seem to care.
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- is this diversity needed in presence of multiple different adversaries?
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- does the simulation specialize when only presented with one adversary?
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What about adaptive adversaries?
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- adaptation in the qualitative & quantitative evolution in response to
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changed pressure? (i.e. those who cannot adapt quick enough die?)
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= Scenario
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== Plants
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> data Foo = Bar
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== Enzymes
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== Herbivores
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== Environment
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== Fitness
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== Mating & Creation of diversity
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