From 6795c93f99ebb15a01f4d6bf05c9855d179cb874 Mon Sep 17 00:00:00 2001 From: Stefan Dresselhaus Date: Mon, 25 Jun 2018 21:59:56 +0200 Subject: [PATCH] started vortrag & deps, added results of simulation --- .gitmodules | 9 + MathJax | 1 + environment2.json | 2 +- reveal.js-menu | 1 + reveal.js-plugins | 1 + simulations/attackRate/always/1.log | 2002 +++++++++++++++++ simulations/attackRate/always/10.log | 2002 +++++++++++++++++ simulations/attackRate/always/2.log | 2002 +++++++++++++++++ simulations/attackRate/always/3.log | 2002 +++++++++++++++++ simulations/attackRate/always/4.log | 2002 +++++++++++++++++ simulations/attackRate/always/5.log | 2002 +++++++++++++++++ simulations/attackRate/always/6.log | 2002 +++++++++++++++++ simulations/attackRate/always/7.log | 2002 +++++++++++++++++ simulations/attackRate/always/8.log | 2002 +++++++++++++++++ simulations/attackRate/always/9.log | 2002 +++++++++++++++++ .../attackRate/always/environment.json | 1 + 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vortrag/MathJax | 1 + vortrag/chemodiversity.html | 413 ++++ vortrag/css/solarized_plus.css | 650 ++++++ vortrag/img/compound_example.neato | 6 + vortrag/img/compound_example.png | Bin 0 -> 7379 bytes vortrag/img/environment.tree.png | Bin 0 -> 228136 bytes vortrag/img/enzyme_example.neato | 6 + vortrag/img/enzyme_example.png | Bin 0 -> 8840 bytes vortrag/img/predator_example.neato | 8 + vortrag/img/predator_example.png | Bin 0 -> 16052 bytes vortrag/js/zoom.js | 155 ++ vortrag/make-code-footnotesize.tex | 1 + vortrag/reveal.js | 1 + vortrag/reveal.js-menu | 1 + vortrag/reveal.js-plugins | 1 + vortrag/template.html | 211 ++ vortrag/vortrag.md | 255 +++ 299 files changed, 137776 insertions(+), 1 deletion(-) create mode 160000 MathJax create mode 160000 reveal.js-menu create mode 160000 reveal.js-plugins create mode 100644 simulations/attackRate/always/1.log create mode 100644 simulations/attackRate/always/10.log create mode 100644 simulations/attackRate/always/2.log create mode 100644 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b/simulations/attackRate/interval10/environment.json new file mode 100644 index 0000000..dc44d1b --- /dev/null +++ b/simulations/attackRate/interval10/environment.json @@ -0,0 +1 @@ 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+ -1 + ], + [ + { + "contents": 19, + "tag": "GenericCompound" + }, + 1 + ] + ] + }, + { + "dominance": null, + "enzymeName": "GenericCompound 17 -> GenericCompound 25", + "substrateRequirements": [], + "synthesis": [ + [ + { + "contents": 17, + "tag": "GenericCompound" + }, + -1 + ], + [ + { + "contents": 25, + "tag": "GenericCompound" + }, + 1 + ] + ] + }, + { + "dominance": null, + "enzymeName": "GenericCompound 19 -> GenericCompound 20", + "substrateRequirements": [], + "synthesis": [ + [ + { + "contents": 19, + "tag": "GenericCompound" + }, + -1 + ], + [ + { + "contents": 20, + "tag": "GenericCompound" + }, + 1 + ] + ] + }, + { + "dominance": null, + "enzymeName": "GenericCompound 20 -> GenericCompound 21", + "substrateRequirements": [], + "synthesis": [ + [ + { + "contents": 20, + "tag": "GenericCompound" + }, + -1 + ], + [ + { + "contents": 21, + "tag": "GenericCompound" + }, + 1 + ] + ] + }, + { + "dominance": null, + "enzymeName": "GenericCompound 25 -> GenericCompound 26", + "substrateRequirements": [], + "synthesis": [ + [ + { + "contents": 25, + "tag": "GenericCompound" + }, + -1 + ], + [ + { + "contents": 26, + "tag": "GenericCompound" + }, + 1 + ] + ] + }, + { + "dominance": null, + "enzymeName": "GenericCompound 25 -> GenericCompound 27", + "substrateRequirements": [], + "synthesis": [ + [ + { + "contents": 25, + "tag": "GenericCompound" + }, + -1 + ], + [ + { + "contents": 27, + "tag": "GenericCompound" + }, + 1 + ] + ] + } + ], + "predators": [ + [ + { + "fitnessImpact": 0.4901681711436634, + "irresistance": [ + { + "contents": 26, + "tag": "GenericCompound" + } + ], + "numAttacks": 1 + }, + 0.4031670022489978 + ], + [ + { + "fitnessImpact": 0.1531084617953737, + "irresistance": [ + { + "contents": 26, + "tag": "GenericCompound" + }, + { + "contents": 27, + "tag": "GenericCompound" + } + ], + "numAttacks": 1 + }, + 0.73479241706388593 + ], + [ + { + "fitnessImpact": 0.2531084617953737, + "irresistance": [ + { + "contents": 6, + "tag": "GenericCompound" + }, + { + "contents": 7, + "tag": "GenericCompound" + } + ], + "numAttacks": 1 + }, + 0.53479241706388593 + ], + [ + { + "fitnessImpact": 0.3531084617953737, + "irresistance": [ + { + "contents": 12, + "tag": "GenericCompound" + }, + { + "contents": 16, + "tag": "GenericCompound" + } + ], + "numAttacks": 1 + }, + 0.63479241706388593 + ] + ], + "settings": { + "automimicry": false, + "logEveryNIterations": 10, + "numPlants": 100, + "predatorBehaviour": { + "contents": 10, + "tag": "AlwaysAttack" + } + , "mutationRate": 0.01 + , "deletionDuplicationRate": 0.05 + , "geneAddRate": 0.005 + , "activationNoiseIntensity": 0.01 + , "staticEnzymeCost":0.20 + , "nutrientImpact": 0.2 + }, + "soil": [ + [ + [], + 20 + ] + ], + "toxicCompounds": [ + [ + { + "contents": 6, + "tag": "GenericCompound" + }, + 0.5 + ], + [ + { + "contents": 7, + "tag": "GenericCompound" + }, + 1 + ], + [ + { + "contents": 12, + "tag": "GenericCompound" + }, + 0.25 + ], + [ + { + "contents": 15, + "tag": "GenericCompound" + }, + 0.5 + ], + [ + { + "contents": 16, + "tag": "GenericCompound" + }, + 1 + ], + [ + { + "contents": 26, + "tag": "GenericCompound" + }, + 0.5 + ], + [ + { + "contents": 27, + "tag": "GenericCompound" + }, + 1 + ] + ] +} diff --git a/vortrag/Makefile b/vortrag/Makefile new file mode 100644 index 0000000..a1b5e82 --- /dev/null +++ b/vortrag/Makefile @@ -0,0 +1,16 @@ +.PHONY: pdf + +INPUT = vortrag.md + +all: slides + +slides: $(INPUT) + pandoc -f markdown+smart+emoji -t revealjs \ + --template ./template.html \ + --incremental \ + --indented-code-classes=haskell \ + --section-divs \ + -o chemodiversity.html $(INPUT) + +serve: chemodiversity.html + python3 -m http.server 8080 diff --git a/vortrag/MathJax b/vortrag/MathJax new file mode 120000 index 0000000..5feef14 --- /dev/null +++ b/vortrag/MathJax @@ -0,0 +1 @@ +../MathJax/ \ No newline at end of file diff --git a/vortrag/chemodiversity.html b/vortrag/chemodiversity.html new file mode 100644 index 0000000..4f63a73 --- /dev/null +++ b/vortrag/chemodiversity.html @@ -0,0 +1,413 @@ + + + + + + + + + Chemodiversity: A short overview of this project + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + +
+
Chemodiversity
+
A short overview of this project
+
Stefan Dresselhaus
+
Theoretic Biology Group
Bielefeld University
+
+ + + + + + +
+ +
+

What is chemodiversity?

+
    +
  • It was observed, that many plants seem to produce many compounds with no obvious purpose
    • +
  • Using resources to produce such compounds (instead of i.e. growing) should yield a fitness-disadvantage
    • +
  • one expects evolution to eliminate such behavior
    • +
+
+
+

Question: Why is this behavior observed?

+
    +
  • Are these compounds necessary for some unresearched reason? +
      +
    • unknown environmental effects?
      • +
    • unknown intermediate products for necessary defenses?
      • +
    • speculative diversity because they could be useful after genetic mutations?
      • +
    • +
+
+
+

Screening Hypothesis

+
    +
  • First suggested by Jones & Firn (1991)
    • +
  • new (random) compounds are rarely biologically active
    • +
  • plants have a higher chance finding an active compound if they diversify
    • +
  • many (inactive) compounds are sustained for a while because they may be precursors to biologically active substances
    • +
+
+

There are indications for and against this hypothesis by various groups.

+
+
+
+
+

Setting up a simulation

+
+

If you wish to make apple pie from scratch, you must first create the universe
+- Carl Sagan

+
+
+
+ +
+

Defining Chemistry

+
    +
  • First of all we define the chemistry of our environment, so we know all possible interactions and can manipulate them at will.
    • +
  • We differentiate between Substrate and Products: +
      +
    • Substrate can just be used (i.e. real substrates if the whole metabolism should be simulated, PPM[1] in our simplified case)
      • +
    • Products are nodes in our chemistry environment.
      • +
    • +

  • In Code:

    +
    data Compound = Substrate Nutrient
    
+
                  | Produced Component
    
+
                  | GenericCompound Int
    +
    +

    [1]: plants primary metabolism

    +
    • +
+
+
+

Usage in the current Model

+
    +
  • The Model used for evaluation just has one Substrate:
    +PPM with a fixed Amount to account for effects of sucking primary-metabolism-products out of the primary metabolic cycle
    • +
  • This is used to simulate i.e. worse growth, fertility and other things affecting the fitness of a plant.
    • +
  • We are not using named Compounds, but restrict to generic Compound 1, Compound 2 …
    • +
  • Not done, but worth exploring: +
      +
    • Take a “real-world” snapshot of Nutrients and Compounds and recreate them
      • +
    • See if the simulation follows the real world
      • +
    • +
+
+
+

Defining a Metabolism

+
    +
  • We define Enzymes as +
      +
    • having a recipe for a chemical reaction
      • +
    • are reversible
      • +
    • may have dependencies on catalysts to be present
      • +
    • may have higher dominance over other enzymes with the same reaction
      • +
    • +
  • Input can be Substrate and/or Products
    • +
  • Outputs can only be Products
    • +
  • ⇒ This makes them to Edges in a graph combining the chemical compounds
    • +
+
+
+

Usage in the current Model

+
    +
  • Enzymes all +
      +
    • only map 1 input to 1 Output with a production rate of 1 per Enzyme
      +(i.e. -1 Compound 2 -> +1 Compound 5)
      • +
    • are equally dominant
      • +
    • need no catalysts
      • +
    • +
+
+
+

Defining Predators

+
    +
  • Predators consist of +
      +
    • a list of Compounds that can kill them
      • +
    • a fitness impact ([0..1]) as the probability of killing the plant
      • +
    • an expected number of attacks per generation
      • +
    • a probability ([0..1]) of appearing in a single generation
      • +
    • +
  • Predator need not necessary be biologically motivated +
      +
    • i.e. rare, nearly devastating attacks (floods, droughts, …) with realistic probabilities
      • +
    • +
+
+
+

Example Environment

+
+
+
    +
  • The complete environment now consists of +
      +
    • Compounds:
      +
      • +
    • Enzymes:
      +
      • +
    • Predators:
      +
      • +
    • +
+
+
+Our default test-environment
Our default test-environment
+
+

Additional rules:

+
    +
  • Every “subtree” from the marked PPM is treated as a separate species (fungi, animals, …)
    +⇒ Every predator can only be affected by toxins in the same part of the tree
    • +
  • Trees can be automatically generated in a decent manner to search for environmens where specific effects may arise
    • +
+
+
+ +
+
+
+ +
+

Plants

+

A plant consists of …

+
+
+

Metabolism simulation

+

Compounds are created foo..

+
+
+

Fitness

+
    +
  • Static costs of enzymes
    • +
  • Cost of active enzymes
    • +
+
+
+

Attacker

+
    +
  • Rate of attack ~> Paper, Formulas
    • +
  • Defenses +
      +
    • single plant
      • +
    • automimicry
      • +
    • +
+
+
+

Haploid mating

+
    +
  • fixed population-size (100)
    • +
  • $p(\textrm{reproduction}) = \frac{\textrm{plant-fitness}}{\textrm{total fitness in population}}$
    • +
  • Gene +
      +
    • mutation
      • +
    • duplication
      • +
    • deletion
      • +
    • addition
      • +
    • activation-noise
      • +
    • +
+
+
+
+ +
+

Simulations

+

Parameters tested

+
    +
  • x
    • +
  • y
    • +
  • z
    • +
+
+
+
+

Results

+
+

It doesn’t matter how beautiful your theory is, it doesn’t matter how smart you are. If it doesn’t agree with experiment, it’s wrong.
+- Richard P. Feynman

+
+
+
+ +
+ + +
+
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Outline

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+
+ + + + + + + + + + + diff --git a/vortrag/vortrag.md b/vortrag/vortrag.md new file mode 100644 index 0000000..66af79f --- /dev/null +++ b/vortrag/vortrag.md @@ -0,0 +1,255 @@ +--- +title: Chemodiversity +subtitle: A short overview of this project +author: Stefan Dresselhaus +license: BSD +affiliation: Theoretic Biology Group
+ Bielefeld University +abstract: Attempt to find indications for chemodiversity in the plant secondary metabolism according to the screening hypothesis +date: \today + +papersize: a4 +fontsize: 10pt +documentclass: scrartcl + +margin: 0.2 +slideNumber: true +... + + +What is chemodiversity? +----------------------- + +- It was observed, that many plants seem to produce many compounds with no + obvious purpose +- Using resources to produce such compounds (instead of i.e. growing) should + yield a fitness-disadvantage +- one expects evolution to eliminate such behavior + +Question: Why is this behavior observed? +-------------------------------- + +- Are these compounds necessary for some unresearched reason? + - unknown environmental effects? + - unknown intermediate products for necessary defenses? + - speculative diversity because they could be useful after genetic mutations? + +Screening Hypothesis +-------------------- + +- First suggested by Jones & Firn ([1991](https://doi.org/10.1098/rstb.1991.0077)) +- new (random) compounds are rarely biologically active +- plants have a higher chance finding an active compound if they diversify +- many (inactive) compounds are sustained for a while because they may be + precursors to biologically active substances + +. . . + +There are indications for and against this hypothesis by [various groups](https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.12526#nph12526-bib-0093). + + +-------------------------------------------------------------------------------- + +Setting up a simulation +======================= + +>If you wish to make apple pie from scratch, you must first create the universe +> - Carl Sagan + +-------------------------------------------------------------------------------- + +Defining Chemistry +------------------ + +- First of all we define the chemistry of our environment, so we know all possible +interactions and can manipulate them at will. +- We differentiate between **`Substrate`{.haskell}** and + **`Products`{.haskell}**: + - **`Substrate`{.haskell +}** can just be used (i.e. real substrates if the whole metabolism + should be simulated, **`PPM`{.haskell}**^[1]^ in our simplified case) + - **`Products`{.haskell +}** are nodes in our chemistry environment. +- In Code: + ```haskell + data Compound = Substrate Nutrient + | Produced Component + | GenericCompound Int + ``` +::: footer +^[1]^: plants primary metabolism +::: + + +Usage in the current Model +-------------------------- + +- The Model used for evaluation just has one `Substrate`{.haskell}: + `PPM`{.haskell} with a fixed Amount to account for effects of sucking + primary-metabolism-products out of the primary metabolic cycle +- This is used to simulate i.e. worse growth, fertility and other things + affecting the fitness of a plant. +- We are not using named Compounds, but restrict to generic `Compound + 1`{.haskell}, + `Compound 2`{.haskell} ... +- Not done, but worth exploring: + - Take a "real-world" snapshot of Nutrients and Compounds and recreate them + - See if the simulation follows the real world + + +Defining a Metabolism +--------------------- + +- We define **`Enzyme`{.haskell}s** as + - having a recipe for a chemical reaction + - are reversible + - may have dependencies on catalysts to be present + - may have higher dominance over other enzymes with the same reaction + +- Input can be `Substrate`{.haskell} and/or `Products`{.haskell} +- Outputs can only be `Products`{.haskell} +- $\Rightarrow$ This makes them to Edges in a graph combining the chemical + compounds + +Usage in the current Model +-------------------------- + +- `Enzyme`{.haskell}s all + - only map `1`{.haskell} input to `1`{.haskell} Output with a production rate of `1`{.haskell} per `Enzyme`{.haskell} + (i.e. `-1 Compound 2 -> +1 Compound 5`{.haskell}) + - are equally dominant + - need no catalysts + +Defining Predators +------------------ + +- **`Predator`{.haskell}s** consist of + - a list of `Compound`{.haskell}s that can kill them + - a fitness impact ($[0..1]$) as the probability of killing the plant + - an expected number of attacks per generation + - a probability ($[0..1]$) of appearing in a single generation +- `Predator`{.haskell} need not necessary be biologically motivated + - i.e. rare, nearly devastating attacks (floods, droughts, ...) with realistic + probabilities + +Example Environment +------------------- + +:::::::::::::: {.columns} + +::: {.column width=37%} + +- The complete environment now consists of + - `Compound`{.haskell}s: + ![](img/compound_example.png){style="vertical-align:middle"} + - `Enzyme`{.haskell}s: + ![](img/enzyme_example.png){style="vertical-align:middle"} + - `Predator`{.haskell}s: + ![](img/predator_example.png){style="vertical-align:middle"} + +::: + +::: {.column width=63% .fragment} + +![Our default test-environment](img/environment.tree.png){width=75%} + +Additional rules: + +- Every "subtree" from the marked `PPM`{.haskell} is treated as a separate + species (fungi, animals, ...) + $\Rightarrow$ Every predator can only be affected by toxins in the same part of the tree +- Trees can be automatically generated in a decent manner to search for + environmens where specific effects may arise +::: + +:::::::::::::: + +::::: notes ::::: + +CTRL+Click for zoom! + +- All starts at PPM (Plant Primary Metabolism) +- Red = Toxic +- Blue = Predators + +:::: + +-------------------------------------------------------------------------------- + +Plants +------ + +A plant consists of +... + + +Metabolism simulation +--------------------- + +Compounds are created foo.. + + +Fitness +------- + +- Static costs of enzymes +- Cost of active enzymes + + +Attacker +-------- + +- Rate of attack ~> Paper, Formulas +- Defenses + - single plant + - automimicry + +Haploid mating +-------------- + +- fixed population-size (100) +- $p(\textrm{reproduction}) = \frac{\textrm{plant-fitness}}{\textrm{total fitness in population}}$ +- Gene + - mutation + - duplication + - deletion + - addition + - activation-noise + +-------------------------------------------------------------------------------- + +Simulations +----------- + +Parameters tested + +- x +- y +- z + +-------------------------------------------------------------------------------- + +Results +======= + +>It doesn't matter how beautiful your theory is, it doesn't matter how smart you are. If it doesn't agree with experiment, it's wrong. +> - Richard P. Feynman + +-------------------------------------------------------------------------------- + + + + + + + + + + + + + + + + +

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