chemodiversity/vortrag/vortrag.md

---
title: Chemodiversity
subtitle: A short overview of this project
author: Stefan Dresselhaus
license: BSD
affiliation: Theoretic Biology Group<br>
             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`{.haskell}** consists of

- a **`Genome`{.haskell}**, a simple list of genes
  - Triple of `(Enzyme, Quantity, Activation)`{.haskell}
  - without order or locality (i.e. interference of neighboring genes)
  - `Quantity`{.haskell} is just an optimization (=Int) to group identical
    `Activation`{.haskell}s
  - `Activation`{.haskell} is a float $\in [0..1]$ to regulate the activity of
    the `Enzyme`{.haskell} genetically
- an `absorbNutrients`{.haskell}-Function to simulate various effects when
  absorbing nutrients out of the environment, depending on the environment (i.e.
  *can* use informations about chemistry, predators, etc.)
  - Not used in our simulation, as we only have `PPM`{.haskell} as "nutrient"
    and we take everything given to us.

Metabolism simulation
---------------------

Creation of compounds from the given resources is an iterative process:

- First of all we create a conversion Matrix $\Delta_c$ with corresponding
  startvector $s_0$.
- We now iterate $s_i = (\mathbb{1} + \Delta_c) \cdot s_{i-1}$ for a fixed number of times
  (currently: $100$) to simulate the metabolism^[2]^.  

  ::: footer :::
  ^[2]^: Thats a 'lie', we calculate $(\mathbb{1} + \Delta_c)^{100}$ efficiently via
  `lapack`-internals
  :::

- Entries in the matrix come from the `Genome`{.haskell}: an `Enzyme`{.haskell} which
  converts $i$ to $j$ with quantity $q$ and activity $a$ yield
  $$\begin{eqnarray*}
  \Delta_c[i,j] &\mathrel{+}=& q\cdot a,\\
  \Delta_c[j,i] &\mathrel{+}=& q\cdot a, \\
  \Delta_c[i,i] &\mathrel{-}=& q\cdot a, \\
  \Delta_c[j,j] &\mathrel{-}=& q\cdot a
  \end{eqnarray*}.$$
  - This makes the Enzyme-reaction invertible as both ways get treated equally.

Metabolism-example
------------------

- Given a simple Metabolism with $1$ nutrient (first row/column) and $2$ Enzymes
  in sequence, we have given $\Delta_c$ wtih corresponding startvector $s_0$:
  $$\Delta_c = 0.01 \cdot \begin{pmatrix}
  -1 & 1  & 0 \\
   1  & -2 & 1 \\
   0  & 1  & -1 \\
  \end{pmatrix}, s_0 = \begin{pmatrix}\text{PPM:} & 3 \\ \text{Compound1:} & 0 \\ \text{Compound2:} & 0\end{pmatrix}.$$

- In the simulation this yields us
  $$s_{100} \approx \begin{pmatrix}\text{PPM:} & 1 \\ \text{Compound1:} & 1 \\ \text{Compound2:} & 1\end{pmatrix},$$
  which is the expected outcome for an equilibrium.


Assumptions for metabolism simulation
-------------------------------------

- All Enzymes are there from the beginning
- All Enzyme-reactions are reversible without loss
- static conversion-matrix for fast calculations (unsuited, if i.e. enzymes
  depend on catalysts)
- One genetic enzyme corresponds to (infinitely) many real (proportional weaker)
  enzymes in the plant, which get controlled via the "activation" parameter

Fitness
-------

- We handle fitness as $\text{survival-probability} \in [0..1]$ and model each
  detrimental effect as probability which get multiplied together.
- To calculate the fitness of an individual we take three distinct effects into
consideration:
  - Static costs of enzymes
    - Creating enzymes weakens the primary cycle and thus possibly beneficial
      traits (growth, attraction of beneficial organisms, ...)
      $$F_s := \text{static_cost_factor} \cdot \sum_i q_i \cdot a_i \quad | \quad (e_i,q_i, a_i) \in \text{Genome}$$
    - limits the amount of dormant enzymes
  - Cost of active enzymes
    - Cost of using up nutrients
      $$F_e := \text{active_cost_factor} \cdot \frac{\text{Nutrients used}}{\text{Nutrients available}}$$
  - Deterrence of attackers $F_d$ (next slide)

Attacker
--------

- Predators are modeled after [Svennungsen et al. (2007)](http://doi.org/10.1098/rspb.2007.0456)
- Each predator has an expected number of attacks $P_a$, that are
  poisson-distributed with impact $P_i$.
- Plants can defend themselves via
  - toxins that the predator is affected by with impact-probability $D_t(P_i)$
  - herd-immunity via effects like automimicry: $D_{pop} = \mathbb{E}[D_t(P_i)]$
- All this yields the formula:

  $$F_d := 1 - e^{- (D_{pop} \cdot P_a) (1-D_t(P_i))}$$

- The attacker-model is only valid for many reasonable assumptions
  - equilibrium population dynamics
  - equal dense population
  - which individual to attack is independently chosen
  - etc. (Details in the paper linked above)

Haploid mating
--------------

- We hold the population-size fixed at $100$
- Each plant has a reproduction-probability of
  $$p(\textrm{reproduction}) = \frac{\textrm{plant-fitness}}{\textrm{total fitness in population}}$$
  yielding a fitness-weighted distribution from that $100$ new offspring are
  drawn
- in inheritance each gene of the parent goes through different steps (with
  given default-values)^[3]^

  ::::: footer
  ^[3]^: in case of quantity $q > 1$ the process is repeated $q$ times
  independently.
  ::::

  - **mutation**: with $p_{mut} = 0.01$ another random enzyme is produced, but
    activation kept
  - **duplication**: with $p_{dup} = 0.05$ the gene gets duplicated (quantity $+1$)
  - **deletion**: with $p_{del} = p_{dup}$ the gene get deleted (or quantity $-1$)
  - **addition**: with $p_{add} = 0.005$ an additional gene producing a random
    enzyme with activation $0.5$ gets added as mutation from genes we do not
    track (i.e. primary cycle)
  - **activation-noise**: activation is changed by $c_{noise} = \pm 0.01$ drawn from
    a uniform distribution, clamped to $[0..1]$

:::: notes
- Default values **not** motivated in any way!
- finding out how these values influence is core!
::::

--------------------------------------------------------------------------------

Simulations
-----------

- Overall question: What parameters are necessary for chemodiversity?
  - How can we see chemodiversity?
  - We define an Enzyme $E$ as divers, if the average of this Enzyme in the
    population stays below $0.5$, so $E_i \in E_{div} \text{iff.} \mathbb{E}[E_i] < 0.5$
  - We can then count the number of diverse Enzymes per plant $E_{d,p_i} =
    |\left\lbrace E_i | E_i \in E_{div}, E_{i,p_i} > 0.5,  \right\rbrace|$
- To get an insight into how this behaves we observe several other parameters
  every generation:
  - Fitness $\in [0..1]$
  - Number of different compounds created
  - Amount of compounds created
  - Number of Plants theoretically resistant to predator $i$ (i.e. **can** produce
    a toxin to defend themselves, albeit not to $100\%$.

Simulations (cont.)
-------------------

- General setup of the simulation:
  - All using the example-environment shown before
    - 27 different compounds, 1 Nutrient (simulating the primary metabolism)
    - 7 of 27 compounds are toxic
    - at least 3 compounds are needed for total immunity
    - 4 predators
  - Duration of 2000 generations
- Different setups tested:
  - Behavior of predators (`AlwaysAttack`{.haskell}, `AttackRandom`{.haskell}, `AttackInterval Int`{.haskell})
  - varying $\text{static_enzyme_cost}$ from $0.0$ to $0.20$ in steps of $0.02$
    - effectively limits the amount of maximal enzymes to $\frac{1}{\text{static_enzyme_cost}}$
  - varying $\text{nutrient_impact}$ from $0.0$ to $1.0$ in steps of $0.1$
    - makes toxins less/more costly to produce


--------------------------------------------------------------------------------

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

--------------------------------------------------------------------------------

Effect of Predator-Behavior onto chemodiversity
----------------------------------------

![Graph](img/attackRate_E_d_mu_vs_C_mu.png)

Effect of static enzyme cost
----------------------------

![Graph](img/staticCost_Fitness_vs_num_compounds.png)

Effect of static enzyme cost (cont.)
------------------------------------

![Graph](img/staticCost_Fitness_vs_e_d_mu.png)

Effect of static enzyme cost (cont.)
------------------------------------

![Graph](img/staticCost_e_d_mu_vs_num_compounds.png)

Effect of nutrient-impact
-------------------------

![Graph](img/nutrientCost_Fitness_vs_num_compounds.png)

Effect of nutrient-impact (cont.)
---------------------------------

![Graph](img/nutrientCost_Fitness_vs_e_d_mu.png)

Effect of nutrient-impact (cont.)
---------------------------------

![Graph](img/nutrientCost_e_d_mu_vs_num_compounds.png)