---
title: Software As Biology
transition: fade
---

<style>
.quote {
  right:0;
  left:0;
  text-align:center;
  position:absolute;
  top:50%;
  margin:0 48px !important;
  font-size:55px !important;
  -webkit-transform: translate(0, -50%);
}
</style>

{% macro quote(img=None) -%}
{% if img %}
<table style="margin:100px">
<tr>
<td width="200"><img src="{{img}}"></td>
<td width="40"></td>
<td style="font-size:150%"> {{ caller() }} </td>
</tr>
</table>
{% else %}
<div class="quote">{{ caller() }}</div>
{% endif %}
{%- endmacro %}


{% from "deckjs.html" import section with context %}

{% call section('--------------- First Page ----------------------') %}

## <span style="font-size:85%">Software As Biology</span>

### Code Mesh - December 4, 2013
### Garrett Smith @gar1t

<img src="cloudbees.png" style="margin-top:100px" height="250">

{% endcall %}

{% call section('--------------- Opening --------------------------') %}

# A long time ago at Pycon far, far away...

{% endcall %}

{% call section('--------------- Problem --------------------------') %}

## The Problem With Software These Days...

<img src="grumpy.jpg" height="600">

{% endcall %}

{% call section('--------------- Design ---------------------------') %}

# Is <em>Design</em>

{% endcall %}

{% call section('--------------- Disclaimer -----------------------') %}

## Disclaimer: I'm not a real life scientist

<img src="frankenstein.jpg" height="600">

{% endcall %}

{% call section('--------------- Human Brain ----------------------') %}

## Popular Science: The Human Brain

<img src="brain.jpg" height="600">

{% endcall %}

{% call section('--------------- Aliens ---------------------------') %}

## Fantasy vs Reality

<img src="aliens.jpg" height="600">

{% endcall %}

{% call section('--------------- Aliens ---------------------------') %}

## Fantasy vs Reality

<img src="usecase-diagram.png" height="600">

{% endcall %}

{% call section('--------------- Genius ---------------------------') %}

## Genius, Visionary, Creator

<img src="edison.jpg" height="600">

{% endcall %}

{% call section('--------------- 1% / 99% --------------------------') %}

## 1% Inspiration, 99% Perspiration

<img src="edison.jpg" height="600">

{% endcall %}

{% call section('--------------- Valery Quote 1 --------------------') %}

## Paul Valéry

{% call quote('valery-small.jpg') %}
It takes two to invent anything.
{% endcall %}

{% endcall %}

{% call section('--------------- Valery Quote 2 --------------------') %}

## Paul Valéry

{% call quote('valery-small.jpg') %}
The one makes up combinations.
{% endcall %}

{% endcall %}

{% call section('--------------- Valery Quote 3 --------------------') %}

## Paul Valéry

{% call quote('valery-small.jpg') %}
The other chooses, recognizes what he wishes and what is important to him.
{% endcall %}

{% endcall %}

{% call section('--------------- Valery Quote 4 --------------------') %}

## Paul Valéry

{% call quote('valery-small.jpg') %}
<em>Genius</em> is the readiness of the second one to grasp the value of what
has been laid before him and to choose it.
{% endcall %}

{% endcall %}

{% call section('--------------- Finches ---------------------------') %}

## Genius: Natural Selection?

<img src="finches.jpg" height="600">

{% endcall %}

{% call section('--------------- Photosynthesis --------------------') %}

## Genius: Photosynthesis?

<img src="photosynthesis.jpg" height="600">

{% endcall %}

{% call section('--------------- Dark / Light -----------------------') %}

## Two Stages of Photosynthesis

<img src="darklightstages.gif" height="600">

{% endcall %}

{% call section('--------------- Z Scheme ---------------------------') %}

## Light Stage (Z Scheme)

<img src="zscheme.jpg" height="600">

{% endcall %}

{% call section('--------------- Calvin Cycle -----------------------') %}

## Dark Stage (Calvin Cycle)

<img src="calvin.gif" height="600">

{% endcall %}

{% call section('--------------- Titan -----------------------------') %}

## Earth Before Photosynthesis

<img src="titan.jpg" height="600">

{% endcall %}

{% call section('--------------- Mountains --------------------------') %}

## Earth After Photosynthesis

<img src="mountains.jpg" height="600">

{% endcall %}

{% call section('--------------- Cyanobateria -----------------------') %}

## Cyanobacteria Vision Statement

{% call quote('cyanobacteria.jpg') %}

To maintain atmospheric oxygen levels and supply all of the organic compounds
and most of the energy necessary for all life on Earth

{% endcall %}

{% endcall %}

{% call section('--------------- Species ----------------------------') %}

## Genius Everywhere

<img src="species.jpg" height="600">

{% endcall %}

{% call section('--------------- Species-2---------------------------') %}

## Genius Everywhere

<img src="species-2.jpg" height="600">

{% endcall %}

{% call section('--------------- Species-3---------------------------') %}

## Genius Everywhere

<img src="species-3.jpg" height="600">

{% endcall %}

{% call section('--------------- Species-4---------------------------') %}

## Genius Everywhere

<img src="species-4.jpg" height="600">

{% endcall %}

{% call section('--------------- Species-5---------------------------') %}

## Genius Everywhere

<img src="species-5.jpg" height="600">

{% endcall %}

{% call section('--------------- Species-6---------------------------') %}

## Genius Everywhere

<img src="species-6.jpg" height="600">

{% endcall %}

{% call section('--------------- Species-7---------------------------') %}

## Genius Everywhere

<img src="species-7.jpg" height="600">

{% endcall %}

{% call section('--------------- Species-8---------------------------') %}

## Genius Everywhere

<img src="species-8.jpg" height="600">

{% endcall %}

{% call section('--------------- Species-9---------------------------') %}

## Genius Everywhere

<img src="species-9.jpg" height="600">

{% endcall %}

{% call section('--------------- Species-N --------------------------') %}

## Genius Everywhere

<div style="font-size:150%;margin-top:200px;text-align:center">
  Zoom out 23 more times (8.7 million species)</div>

{% endcall %}

{% call section('--------------- Tuna -------------------------------') %}

## Intelligent Design?

<img src="tuna.jpg" height="600">

{% endcall %}

{% call section('--------------- Hintjens ---------------------------') %}

## Pieter Hintjens

{% call quote('hintjens.jpg') %}
Never design anything that's not a precise minimal answer to a problem we can
identify and have to solve.
{% endcall %}

{% endcall %}

{% call section('--------------- RoK --------------------------------') %}

## Richard O'Keefe

{% call quote('rok.jpg') %}
Start with the simplest thing that has a chance of working.
{% endcall %}

{% endcall %}

{% call section('--------------- David Allen ------------------------') %}

## David Allen

{% call quote('allen.jpg') %}
You don't actually do a project; you can only do action steps related to it.
{% endcall %}

{% endcall %}

{% call section('--------------- Me ---------------------------------') %}

## Me on "Drunken Stumble"

{% call quote('smith.jpg') %}
<div>1. Lean
<br><span style="font-size:75%">Vision / Go That-A-Way</span>
</div>
<div style="margin-top:20px">2. Stumble
<br><span style="font-size:75%">Only ever do the next obvious thing</span>
</div>
{% endcall %}

{% endcall %}

{% call section('-------------On Agile ------------------------------') %}

# Sounds Like "Agile"

{% endcall %}

{% call section('------------ On Agile Quote -------------------------') %}

## From *Agile Manifesto*

<div class="quote">
Continuous attention to technical excellence and good design enhances agility
</div>

{% endcall %}

{% call section('------------ On Agile Quote -------------------------') %}

## From *Agile Manifesto*

<div class="quote">
Build projects around motivated individuals
</div>

{% endcall %}

{% call section('------------ On Agile Quote -------------------------') %}

## From *Agile Manifesto*

<div class="quote">
Working software is the primary<br>measure of progress
</div>

{% endcall %}

{% call section('------------- Slow Clap -----------------------------') %}

## Slow Hand Clap for Agile!

<img src="slowclap.gif" height="600">

{% endcall %}

{% call section('--------- What is software as biology? --------------') %}

## Software As Biology

- Focus on the mechanics of solutions
- Understand how nature "solves" problems
- Use knowledge of biology to inform, inspire, or confirm ideas for software
  construction

{% endcall %}

{% call section('------------- Speciation ----------------------------') %}

# Example: Speciation

{% endcall %}

{% call section('------------- Leaps ---------------------------------') %}

## Evolution vs Revolution (Punctuated Equillibrium)

<img src="leaps.jpg" height="600">

{% endcall %}

{% call section('------------ Lizards --------------------------------') %}

## Allopatric Speciation

<img src="speciation.png" height="600">

{% endcall %}

{% call section('------------ Google Maps ----------------------------') %}

# Speciation: Google Maps

{% endcall %}

{% call section('------------ Software Forking / Merging --------------') %}

## Software Release Strategy

<img src="googlemaps-speciation.png" height="600">

{% endcall %}

{% call section('------------ Microscope ------------------------------') %}

## Small vs Large Change

<img src="microscope.jpg" height="600">

{% endcall %}

{% call section('------------ Fisher Quote-1 --------------------------') %}

## R.A. Fisher

{% call quote('fisher.jpg') %}
Any large change will have a very small probability of improving the
adjustment.
{% endcall %}

{% endcall %}

{% call section('------------ Fisher Quote-2 --------------------------') %}

## R.A. Fisher

{% call quote('fisher.jpg') %}
In the case of the smallest change, the chance of improvement should be almost
exactly one half.
{% endcall %}

{% endcall %}

{% call section('-------------Speciation Implications -------------') %}

## Lessons from Speciation

- Revolution is evolution plus time
- Copy freely (split populations)
- Merge (interbreed) or keep separate (speciation)
- Large changes are usually bad

{% endcall %}

{% call section('--------------- Sex ------------------------------') %}

# Example: Sex

{% endcall %}

{% call section('------------- Ubiquitous -------------------------') %}

## Nearly All Complex Life Bangs

<img src="sex.jpg" height="600">

{% endcall %}

{% call section('------------- Michael Jordans --------------------') %}

## Cloning vs Sex

<img src="jordan.jpg" height="600">

{% endcall %}

{% call section('------------- Peacock ----------------------------') %}

## Cost of Sex

<img src="peacock.jpg" height="600">

{% endcall %}

{% call section('------------- Dancer -----------------------------') %}

## Cost of Sex

<img src="dancer.jpg" height="600">

{% endcall %}

{% call section('------------- Dancer -----------------------------') %}

## Cost of Sex

<img src="cats.jpg" height="600">

{% endcall %}

{% call section('------------- Meiosis ----------------------------') %}

## Meiosis / Gene Shuffling

<img src="meiosis.png" height="600">

{% endcall %}

{% call section('------------- Fruit Flies ------------------------') %}

## Sex Combines Mutations

<img src="fruitflies.jpg" height="600">

{% endcall %}

{% call section('------------- Diversity --------------------------') %}

## Sex: Invest In Diversity and Change

<img src="diversity.png" height="600">

{% endcall %}

{% call section('--------------- Sex Implications -----------------') %}

## Lessons from Sex

- Homogeneity wins in the short term but eventually goes extinct
- In the long term, investing in diversity pays
    - Introduce widely ranging technologies
	- Hire for diversity (background, language expertise, experience)
- Must have selectable "individuals"
- Prepare to select beneficial, abandon harmful

{% endcall %}

{% call section('--------------- Death ----------------------------') %}

# Example: Death

{% endcall %}

{% call section('------------- Apoptosis --------------------------') %}

## Apoptosis

<img src="apoptosis.jpg" height="600">

{% endcall %}

{% call section('------------ Cell Death Triggers -----------------') %}

## Triggers for Cell Death

- Blebbing
- Cell shrinkage
- Nuclear fragmentation
- Chromatin condensation
- Chromosomal DNA fragmentation

{% endcall %}

{% call section('------------ Erlang Process Death ----------------') %}

## Programmed Cell Death: Erlang

    :::erlang
	{ok, Value} = do_something().  %% "crash" if not successful

<img src="process-crash.png">

{% endcall %}

{% call section('------------ PCD: System-1 -----------------------') %}

## PCD: System Orientation

<img src="system.png" height="600">

{% endcall %}

{% call section('------------ PCD: System-2 -----------------------') %}

## PCD: System Orientation

<img src="failure.png" height="600">

{% endcall %}

{% call section('--------------- Death Implications ---------------') %}

## Lessons from Death

- Death is *useful* - build for it
    - Process crash
	- Service retirement
	- Project cancelation
- Death requires life
    - Process restart
	- New replacement services
	- Many small projects

{% endcall %}

{% call section('--------------- Coelacanth -----------------------') %}

# Example: Coelacanth

{% endcall %}

{% call section('--------------- Coelacanth -----------------------') %}

## Outdated, Legacy, So 1990s

<img src="coelacanth.jpg" height="600">

{% endcall %}

{% call section('------------ Coelacanth Implications -------------') %}

## Lessons From Coelacanth

- Moral judgements don't apply
- Suitability is sufficient
- Change only when there's pressure to change

{% endcall %}

{% call section('------------ Other Examples ----------------------') %}

## Other Examples?

- **Mitochrondria:** symbiosis can result in significant "leaps" in complexity
- **Junk DNA:** amoeba genome is 220x larger than ours, mostly junk - does
  nature refactor?
- **Adaptive immune system:** learning to detect pathogens - does this
  apply to software testing and monitoring?
- **Nervous System:** message passing, performance, reliability

{% endcall %}

{% call section('------------ Implications ------------------------') %}

## Lessons?

- Without *selection* there can be no progress
    - Independent, small
- Without *variation* there can be no selection
    - Fork code, invest in diversity
- Large change is generally bad

{% endcall %}

{% call section('------------ Whats the point? --------------------') %}

# What's The Point Again?

{% endcall %}

{% call section('------------ UML Diagram -------------------------') %}

## One Model

<img src="class-diagram.png" height="600">

{% endcall %}

{% call section('------------ Ecosystem ---------------------------') %}

## Another Model

<img src="ecosystem.jpg" height="600">

{% endcall %}

{% call section('------------- Reading List------------------------') %}

## Some Good Books

<style>
table.books p {
  font-size:0.8em;
  margin-top:0;
  text-align:center;
}

table.books td {
  padding:10px 30px;
}

table.books img {
  margin-bottom: 10px;
}
</style>

<table class="books">
<tr>
<td>
<img src="selfish-gene.jpg" height="175">
<p class="caption">
<strong>The Selfish Gene</strong><br>
Richard Dawkins</p>
</td>

<td>
<img src="life-ascending.jpg" height="175">
<p class="caption">
<strong>Life Ascending</strong><br>
Nick Lane</p>
</td>

<td>
<img src="dragons-of-eden.jpg" height="175">
<p class="caption">
<strong>Dragons Of Eden</strong><br>
Carl Sagan</p>
</td>

<td>
<img src="tell-tale-brain.jpg" height="175">
<p class="caption">
<strong>The Tell Tale Brain</strong><br>
V.S. Ramachandran</p>
</td>
</tr>

<tr>
<td>
<img src="parasite-rex.jpg" height="175">
<p class="caption">
<strong>Parasite Rex</strong><br>
Carl Zimmer</p>
</td>

<td>
<img src="emergence.jpg" height="175">
<p class="caption">
<strong>Emergence</strong><br>
Steven Johnson</p>
</td>

<td>
<img src="blind-watchmaker.jpg" height="175">
<p class="caption">
<strong>The Blind Watch Maker</strong><br>
Richard Dawkins</p>
</td>

<td>
<img src="machinery-of-life.jpg" height="175">
<p class="caption">
<strong>The Machinery Of Life</strong><br>
David Goodsell</p>
</td>
</tr>

</table>

{% endcall %}

{% call section('------------ Questions ---------------------------') %}

## Are There Any Questions?

<img src="questions.jpg" height="600">

{% endcall %}