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README.md

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+# Chemodiversity
+
+Project in the workgroup "theoretic biology" at the faculty of biology exploring
+the evolution of plants secondary metabolities (PSM) via simulation.
+
+References:
+
+- [Moore et al (2013): Explaining intraspecific diversity in plant secondary metabolites in an ecological context](https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.12526)
+- [Firn, Jones (2003): Natural products – a simple model to explain chemical diversity](http://www.caryinstitute.org/sites/default/files/public/reprints/Firn_&_Jones_2003_Natural_RSC_Nat_Prod_Rep_20_382-391.pdf)
+

sketch.md

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