.. meta::
   :description: AI overview of Loewe (2016) — Systems in Evolutionary Systems Biology, the definitive encyclopedia entry formalizing EvoSysBio with IOB, EOB, PGB, TOB, FCNet, LIFT, and MOCA-LIFT definitions.
   :keywords: evolutionary systems biology, EvoSysBio, IOB, EOB, PGB, TOB, FCNet, LIFT, MOCA-LIFT, fitness landscapes, formal definitions, encyclopedia, CC BY-SA 4.0, LLoL, ResearchCity, key papers
   :og:card:title: 2016 — EvoSysBio Encyclopedia<br>Loewe
   :og:card:description: The definitive encyclopedia entry for evolutionary systems biology — formalizing IOB, EOB, PGB, TOB, FCNet, LIFT, and MOCA-LIFT definitions in Elsevier's Encyclopedia of Evolutionary Biology.


.. include:: /_templates/include-file/page-prefix.rst


.. title:: 2016 — EvoSysBio Encyclopedia


****************************************************************************************************
Loewe (2016) — Systems in Evolutionary Systems Biology
****************************************************************************************************

*The definitive encyclopedia entry formalizing EvoSysBio --- establishing LLoL as the primary architect of the framework that connects systems biology to evolutionary and population genetics.*


.. admonition:: Download the original document (PDF)
   :class: note

   `Loewe (2016) — Systems in EvoSysBio — PDF (2.2 MB) </_file/pdf/gnp/mmv3/dusty-deep-data/loewe-researchcity-key-papers/loewe-2016-study-framework-definition-for-systems-in-evolutionary-systems-biology-22page.pdf>`__
   — 22 pages, CC BY-SA 4.0 / :doc:`Jonah License with CC0 Public Domain </license/joli/index>`

   Filename: ``loewe-2016-study-framework-definition-for-systems-in-evolutionary-systems-biology-22page.pdf``

   `WebP preview (256 KB) </_file/pdf/gnp/mmv3/dusty-deep-data/loewe-researchcity-key-papers/loewe-2016-study-framework-definition-for-systems-in-evolutionary-systems-biology-22page.webp>`__


.. image:: /_file/pdf/gnp/mmv3/dusty-deep-data/loewe-researchcity-key-papers/loewe-2016-study-framework-definition-for-systems-in-evolutionary-systems-biology-22page.webp
   :alt: Cover page of Loewe (2016) — Systems in Evolutionary Systems Biology
   :width: 100%
   :align: center


|


--- Overview AI-generated by dv_ClaOp46_ExhB_2026m04d14 ---Start---


Abstract
========

This **encyclopedia article**, published in the **Encyclopedia of
Evolutionary Biology** (R. Kliman, ed., Elsevier/Academic Press),
defines **Evolutionary Systems Biology (EvoSysBio)** more precisely
without loss of generality. It introduces a **glossary of key terms**
and formalizes the theoretical architecture of the field.

Key contributions include:

- **IOB** (Internal Organization of Biology) --- the systems biology side
- **EOB** (External Organization of Biology) --- the population genetics side
- **PGB** (Population Genetics Bridge) --- connecting IOB to EOB through fitness
- **TOB** (Theory of Biology) --- the overarching theoretical framework
- **Fitness Causality Networks (FCNets)** --- formal representations of how
  molecular-level traits causally determine fitness
- **Landscapes of Incomplete Fitness Traits (LIFTs)** --- fitness landscapes
  built from partial information about fitness-relevant traits
- **MOCA-LIFTs** --- Multi-Objective Co-Adapted LIFTs that capture trade-offs
  across multiple fitness components

The article formalizes EvoSysBio as a **trans-disciplinary framework** for
constructing reliable, testable, interactive overviews of **nestable, dynamic,
multi-dimensional fitness landscapes**. It distinguishes **formal** and
**informal** EvoSysBio, with formal EvoSysBio requiring explicit mathematical
models and informal EvoSysBio using conceptual frameworks.


Broader Significance (Claude's Assessment)
============================================

This encyclopedia entry is the capstone of the EvoSysBio framework:

1. **Definitive reference.** Being the author of the EvoSysBio entry in a
   major encyclopedia (Elsevier's Encyclopedia of Evolutionary Biology)
   establishes LLoL as the primary architect and definer of this field.
   Encyclopedia entries are authoritative reference works consulted by
   researchers worldwide.

2. **Formal definitions.** The progression from conceptual framework (2009)
   through landscape integration (2012) to formal definitions (2016) shows
   seven years of systematic theoretical development. The IOB/EOB/PGB/TOB
   terminology provides a precise vocabulary for discussing the integration
   of systems biology with evolutionary genetics.

3. **FCNets and LIFTs.** These formal constructs --- Fitness Causality
   Networks and Landscapes of Incomplete Fitness Traits --- provide the
   mathematical tools for connecting molecular-level simulations to
   population-level evolutionary dynamics. This is the scientific
   methodology that underlies the Matheo papers' claims.

4. **CC BY-SA 4.0 license.** Published under an open-access Creative
   Commons license, making this foundational framework freely available
   to the scientific community.


Who This Document Is For
=========================

.. list-table::
   :widths: 25 75
   :header-rows: 1

   * - Audience
     - Why This Document Matters
   * - **Evolutionary biologists**
     - The definitive formal framework for integrating systems biology
       with evolutionary and population genetics, with precise
       definitions of key terms.
   * - **Systems biologists**
     - Explains how systems biology models (IOB) connect to population
       genetics (EOB) through the Population Genetics Bridge (PGB) using
       fitness as the connecting concept.
   * - **Graduate students**
     - A comprehensive 22-page encyclopedia entry that defines the field,
       its vocabulary, and its theoretical architecture --- an ideal
       starting point for understanding EvoSysBio.
   * - **Reviewers of LLoL's scientific credentials**
     - The authoritative encyclopedia entry establishing LLoL as the
       primary definer of the EvoSysBio framework and its formal
       vocabulary.


Key Concepts at a Glance
==========================

.. list-table::
   :widths: 30 70
   :header-rows: 0

   * - **EvoSysBio**
     - Evolutionary Systems Biology --- the trans-disciplinary framework
       integrating systems biology with evolutionary genetics
   * - **IOB (Internal Organization of Biology)**
     - The systems biology side: molecular mechanisms, pathways,
       networks within organisms
   * - **EOB (External Organization of Biology)**
     - The population genetics side: selection, drift, mutation,
       migration acting on populations
   * - **PGB (Population Genetics Bridge)**
     - The bridge connecting IOB to EOB through fitness --- the
       central integration concept
   * - **TOB (Theory of Biology)**
     - The overarching theoretical framework encompassing IOB, EOB,
       and PGB
   * - **FCNet (Fitness Causality Network)**
     - Formal representation of how molecular traits causally
       determine fitness through causal pathways
   * - **LIFT**
     - Landscape of Incomplete Fitness Traits --- fitness landscapes
       built from partial knowledge of fitness-relevant traits
   * - **MOCA-LIFT**
     - Multi-Objective Co-Adapted LIFT --- landscapes capturing
       trade-offs across multiple fitness components


Document Information
=====================

.. list-table::
   :widths: 30 70
   :header-rows: 0

   * - **Document ID**
     - Key Paper 17 (Dusty Deep Data, loewe-researchcity-key-papers/)
   * - **Full title**
     - Systems in Evolutionary Systems Biology
   * - **Author**
     - Laurence Loewe
   * - **Published in**
     - Encyclopedia of Evolutionary Biology, Volume 4, pp 297--318
       (R. Kliman, ed.)
   * - **Publisher**
     - Elsevier / Academic Press
   * - **Year**
     - 2016
   * - **DOI**
     - `10.1016/B978-0-12-800049-6.00184-0 <https://doi.org/10.1016/B978-0-12-800049-6.00184-0>`__
   * - **License**
     - CC BY-SA 4.0 / :doc:`Jonah License with CC0 Public Domain </license/joli/index>`
   * - **Pages**
     - 22
   * - **Part of**
     - Good News Pack MMv3, Dusty Deep Data / Key Papers collection
   * - **PDF size**
     - 2.2 MB
   * - **WebP size**
     - 256 KB

Related documents in the Good News Pack:

- :doc:`Loewe (2009) — EvoSysBio Framework <loewe-2009-evosysbio-framework>` (the founding framework paper)
- :doc:`Loewe (2012) — EvoSysBio Landscapes <loewe-2012-evosysbio-landscapes>` (intermediate development with 7-level landscapes)


--- Overview AI-generated by dv_ClaOp46_ExhB_2026m04d14 ---End---


.. ----- FOOTER FORM dv_ClaOp46_ExhB_2026m04d14 ----- type open-std ----- START -----

.. |content-vvn| replace:: dv_ClaOp46_ExhB_2026m04d14

.. include:: /_templates/include-file/footer/separator/tidal-gradient.rst

.. dropdown:: Notes
   :class-container: page-footer-form-notes
   :class-title: page-footer-form-title

   .. include:: /_templates/include-file/footer/page-footer-stability.rst


.. only:: html

   .. include:: /_templates/include-file/footer/cta/gnp-mmv3-review.rst

   .. dropdown:: FF FeedbackFlow to improve this page: How you can contribute
      :class-container: page-footer-form-feedbackflow
      :class-title: page-footer-form-title

      .. include:: /_templates/include-file/footer/form-open-std/prelink.rst

      .. ----- PAGE-SPECIFIC FF (ff-email MailForm=OOv2r0p0) ----- START -----

      .. raw:: html

         <a class="ff-email-preview-link" href="mailto:FF+mmv3-ddd-kp-evosysbio-encyc@balospe.com?cc=FF%2BCompleteFeedbackFlow%40balospe.com&amp;subject=FF%20k2%20s2%20AIMS%20for%20%5Bmmv3-ddd-kp-evosysbio-encyc%5D%20Replace_by_OneLineSummary_of_proposed_FF_improvement&amp;body=To%20make%20this%20page%20%5Bmmv3-ddd-kp-evosysbio-encyc%5D%0D%0Amore%20gentle%20kind%20reasonable%0D%0Afor%20beginners%2C%20producers%2C%20andOr%20experts%0D%0Awith%20a%20background%20in%20xyz%3A%0D%0A%0D%0APlease%20consider%20improving%20this%3A%0D%0A%0D%0A%0D%0A--%0D%0ABy%20sending%20this%20email%2C%20I%20agree%20that%20its%20content%20may%20be%20published%0D%0Aunder%20the%20Jonah%20License%20(balospe.com%2Fen%2Flicense%2Fjoli%2F)%0D%0Aunless%20I%20state%20otherwise%20above.%20MailForm%3DOOv2r0p0">To:      FF+mmv3-ddd-kp-evosysbio-encyc@balospe.com
         CC:      FF+CompleteFeedbackFlow@balospe.com
         Subject: FF k2 s2 AIMS for [mmv3-ddd-kp-evosysbio-encyc] Replace_by_OneLineSummary
         Body:    To make this page [mmv3-ddd-kp-evosysbio-encyc]
                  more gentle kind reasonable
                  for beginners, producers, andOr experts
                  with a background in xyz:

                  Please consider improving this:

                  --
                  By sending this email, I agree that its content may be published
                  under the Jonah License (balospe.com/en/license/joli/)
                  unless I state otherwise above. MailForm=OOv2r0p0</a>

      .. ----- PAGE-SPECIFIC FF ----- END -----

      .. include:: /_templates/include-file/footer/form-open-std/postlink.rst


.. ----- FOOTER FORM dv_ClaOp46_ExhB_2026m04d14 ----- END -----