alife.html

<h1>Artificial life: resources &amp; links</h1>

<time datetime="2022-07-31">Created: 2022-07-31<br/>Last updated: 2022-07-31</time>

<p>These are some projects &amp; articles related to that I have found interesting. I intend to update it as I find more. I hope this list can be valuable to anyone interested in learning more about artificial life.</p>

<h2>Projects</h2>

<table>
  <thead>
    <th>Year</th>
    <th>Name</th>
    <th>Description</th>
  </thead>
  <tr>
    <td>1984</td>
    <td>Langton's Loops</td>
    <td>
      Cellular automaton with a simple loop-shaped replicator. Often adapted.
      <br/>
      <a href="https://en.wikipedia.org/wiki/Langton's_loops">Wikipedia</a>
    </td>
  </tr>
  <tr>
    <td>1984</td>
    <td>Core War</td>
    <td>
      Game involving interacting programs, often self-replicating ones.
      <br/>
      <a href="https://en.wikipedia.org/wiki/Core_War">Wikipedia</a>
    </td>
  </tr>
  <tr>
    <td>1991</td>
    <td>Tierra</td>
    <td>
      Studying evolution using programs living in linear memory.
      <br/>
      <a href="https://en.wikipedia.org/wiki/Tierra_(computer_simulation)">Wikipedia</a>
      <br/>
      <a href="https://www.youtube.com/watch?v=Wl5rRGVD0QI">YouTube: Project Tierra</a>
      <br/>
      <a href="https://github.com/bioerrorlog/Tierra">Source code</a>
    </td>
  </tr>
  <tr>
    <td>1993</td>
    <td>Avida</td>
    <td>
      Inspired by Tierra, studies evolution of programs living in linear memory.
      <br/>
      <a href="https://en.wikipedia.org/wiki/Avida">Wikipedia</a>
    </td>
  </tr>
  <tr>
    <td>2015</td>
    <td>Lenia</td>
    <td>
      Cellular automaton with continuous cell values.
      <br/>
      <a href="https://chakazul.github.io/lenia.html">Home page</a>
      <br/>
      <a href="https://github.com/Chakazul/Lenia">Source code</a>
    </td>
  </tr>
  <tr>
    <td>2016</td>
    <td>SALIS</td>
    <td>
      Inspired by Tierra, studies evolution of programs living in linear memory.
      <br/>
      <a href="https://youtube.com/user/nlno88">YouTube channel with videos explaining the simulation</a>
    </td>
  </tr>
  <tr>
    <td>2016*</td>
    <td>Alien</td>
    <td>
      Particle simulation in continuous space.
      <br/>
      * May have been around <a href="https://link.springer.com/article/10.1007/s00287-007-0205-1">since 2008</a> or earlier?
      <br/>
      <a href="https://alien-project.org/">Home page</a>
      <br/>
      <a href="https://github.com/chrxh/alien">Source code</a>
    </td>
  </tr>
  <tr>
    <td>2019</td>
    <td>Myco</td>
    <td>
      Inspired by SALIS, studies evolution of programs living in 2D memory.
      <br/>
      <a href="https://www.youtube.com/watch?v=zoA1G7jY02U">YouTube: Myco: An Artificial Life Experiment</a>
      <br/>
      <a href="https://github.com/Reconcyl/myco">Source code</a>
    </td>
  </tr>
  <tr>
    <td>2020</td>
    <td>Broth</td>
    <td>
      Particle simulation in continuous space, with behavior governed by internal programs within control particles.
      <br/>
      <a href="https://www.ellahoeppner.com/broth-an-attempt-at-simulating-artificial-life/">Introduction</a>
      <br/>
      <a href="https://github.com/Ella-Hoeppner/broth">Source code</a>
    </td>
  </tr>

</table>

<h2>Inspiration</h2>

<p>Sources of inspiration for artificial life, and more generally, the study of biology from a computational perspective:</p>

<table>
  <thead>
    <th>Year</th>
    <th>Link</th>
  </thead>
  <tr>
    <td>2017</td>
    <td><a href="https://berthub.eu/dna/">DNA: Bert Hubert</a></td>
  </tr>
  <tr>
    <td>2017</td>
    <td><a href="https://www.oreilly.com/radar/open-endedness-the-last-grand-challenge-youve-never-heard-of/">Open-endedness: The last grand challenge you've never heard of</a> by James Somers</td>
  </tr>
  <tr>
    <td>2020</td>
    <td><a href="https://www.youtube.com/watch?v=2hf9yN-oBV4">YouTube: I Grew Real Spider Silk Using Yeast</a> (hand-coding DNA)</td>
  </tr>
  <tr>
    <td>2020</td>
    <td><a href="https://berthub.eu/articles/posts/reverse-engineering-source-code-of-the-biontech-pfizer-vaccine/">Reverse Engineering the source code of the BioNTech/Pfizer SARS-CoV-2 Vaccine</a></td>
  </tr>
  <tr>
    <td>2020</td>
    <td><a href="https://jsomers.net/i-should-have-loved-biology/">"I should have loved biology"</a> by James Somers</td>
  </tr>
</table>

<h2>Videos</h2>

<ul>
  <li><a href="https://www.youtube.com/watch?v=VrTM6wYl4Us">Self-reproducing cells in an artificial chemistry</a></li>
  <li><a href="https://www.youtube.com/watch?v=5IpK5meen28">Emergence of self-reproducing evoloops from empty space</a></li>
  <li><a href="https://www.youtube.com/watch?v=NjMb-JeI45I">Real Time Genesis</a></li>
  <li><a href="https://www.youtube.com/watch?v=xqdVHXkGCAw">How to Create Life</a></li>
  <li><a href="https://www.youtube.com/watch?v=p5DPF5S8lZ4">Artificial Chemistry - multiple divisions</a></li>
  <li><a href="https://www.youtube.com/watch?v=J5yE8Si8rMM">Nanopond artificial life system</a></li>
  <li><a href="https://www.youtube.com/watch?v=ZYFFRY7EjrI">Paul Dworkin on evolvable LISP-like instruction chemistries at Grey Thumb Boston</a></li>
  <li><a href="https://www.youtube.com/watch?v=6kJwfq9GUUg">Kyle Harrington on Artificial Embryology at Grey Thumb Boston September 8th 2008</a></li>
  <li><a href="https://www.youtube.com/watch?v=oDKgc5fx0gU">Brian Peltonen on ant simulation and virtual ecosystems at Grey Thumb Boston</a></li>
  <li><a href="https://www.youtube.com/user/DaveAckley/videos">Dave Ackley</a> (channel)</li>
  <li><a href="https://www.youtube.com/watch?v=inxIAPKa5RM&list=PLTgOEHhJanuNe5no_0F6wx_at5Ig7F1l-&index=5">OEE3 Session 1 Discussion</a> (playlist)</li>
</ul>

<h2>Articles</h2>

<table>
  <thead>
    <th>Year</th>
    <th>Link</th>
  </thead>
  <tr>
    <td>1994</td>
    <td><a href="http://life.ou.edu/pubs/oji/ojihtml.html">Evolution, Complexity, Entropy, and Artificial Reality</a></td>
  </tr>
  <tr>
    <td>2002</td>
    <td><a href="https://arxiv.org/pdf/nlin/0210027.pdf">Open-Ended Artifical Evolution</a></td>
  </tr>
  <tr>
    <td>2004</td>
    <td><a href="http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.595.3445&rep=rep1&type=pdf">A Functional Self-Reproducing Cell in a Two-Dimensional Artificial Chemistry</a></td>
  </tr>
  <tr>
    <td>2004</td>
    <td><a href="http://www.tim-taylor.com/papers/rboe/">Redrawing the Boundary between Organism and Environment</a></td>
  </tr>
  <tr>
    <td>2006</td>
    <td><a href="https://www.mitpressjournals.org/doi/pdf/10.1162/artl.2006.12.4.461">Spatial-Pattern-Induced Evolution of a Self-Replicating Loop Network</a></td>
  </tr>
  <tr>
    <td>2007</td>
    <td><a href="https://github.com/timhutton/squirm3">Evolvable Self-Reproducing Cells in a Two-Dimensional Artificial Chemistry</a></td>
  </tr>
  <tr>
    <td>2011</td>
    <td><a href="https://www.cs.bham.ac.uk/research/projects/cogaff/misc/m-m-overview.html">The Meta-Morphogenesis Project</a></td>
  </tr>
  <tr>
    <td>2012</td>
    <td><a href="https://www.mitpressjournals.org/doi/pdf/10.1162/978-0-262-31050-5-ch059">Energy-based Artificial Chemistry Simulator</a></td>
  </tr>
  <tr>
    <td>&lt;2015</td>
    <td><a href="https://chemlambda.github.io/index.html">Chemlambda</a></td>
  </tr>
  <tr>
    <td>2014</td>
    <td><a href="https://arxiv.org/pdf/1710.06055.pdf">Evolution in Virtual Worlds</a></td>
  </tr>
  <tr>
    <td>2018</td>
    <td><a href="https://www.mitpressjournals.org/doi/pdf/10.1162/isal_a_00018">Seeking Open-Ended Evolution in Swarm Chemistry II: Analyzing Long-Term Dynamics via Automated Object Harvesting</a></td>
  </tr>
  <tr>
    <td>2018</td>
    <td><a href="https://arxiv.org/pdf/1806.06628.pdf">Cardinality Leap for Open-Ended Evolution: Theoretical Considerations and Demonstration by "Hash Chemistry"</a></td>
  </tr>
  <tr>
    <td>2021</td>
    <td><a href="https://arxiv.org/abs/2103.08406">Increased Complexity and Fitness of Artificial Cells that Reproduce Using Spatially Distributed Asynchronous Parallel Processes</a></td>
  </tr>
  <tr>
    <td>2021</td>
    <td><a href="https://web.archive.org/web/20210427073515/http://www.elsi.jp/en/news_events/highlights/2021/species_formed_prior_origin_life">Species could have formed prior to the origin of life</a> (archive.org link)</td>
  </tr>
</table>

<h2>More Resources</h2>

<ul>
  <li><a href="https://cell-auto.com/">cell-auto.com</a>: More links to information about cellular automata &amp; artificial life</li>
  <li><a href="https://www.reddit.com/r/alife">Artificial life subreddit</a></li>
  <li><a href="https://mitpress.mit.edu/books/artificial-chemistries">Artificial Chemistries</a> (Banzhaf &amp; Yamamoto): book that includes discussion about the origin of life &amp; the creation of artificial life</li>
</ul>