Aharoni et al. — Evolvability of Promiscuous Protein Functions
Author:
Amir Aharoni; Leonid Gaidukov; Olga Khersonsky; Stephen McQ Gould; Cintia Roodveldt; Dan S. Tawfik
The 'Evolvability' of Promiscuous Protein Functions • Nature Genetics • 2005
Scientific Research
Neutral
DOI:
10.1038/ng1482
Used in this investigation
Questions & Objections
-
Can Natural Processes Produce Apparent Design?
—
Protein Evolvability
Foley and Driscoll — Whole Planet Coupling
Author:
Bradford J. Foley; Peter E. Driscoll
Whole Planet Coupling Between Climate, Mantle, and Core: Implications for Rocky Planet Evolution • Geochemistry, Geophysics, Geosystems, Vol. 17 • 2016
Scientific Review
Neutral
DOI:
10.1002/2015GC006210
Used in this investigation
Evidence
-
The Combined Requirements for Complex Life
—
Whole Planet System
Carter — Anthropic Principle in Cosmology
Author:
Brandon Carter
Large Number Coincidences and the Anthropic Principle in Cosmology • Confrontation of Cosmological Theories with Observational Data, IAU Symposium No. 63 • 1974
Conference Paper
Neutral
DOI:
10.1017/S0074180900235638
Used in this investigation
Explanations
-
Chance, Necessity, and Selection Effects
—
Anthropic Selection
Calcott et al. — Engineering and Biology
Author:
Brett Calcott; Arnon Levy; Mark L. Siegal; Orkun S. Soyer; Andreas Wagner
Engineering and Biology: Counsel for a Continued Relationship • Biological Theory • 2015
Scientific Analysis
Neutral
DOI:
10.1007/s13752-014-0198-3
Used in this investigation
Evidence
-
Do Engineering-Like Patterns Indicate Design?
—
Engineering Biology Comparison
Alberts — The Cell as a Collection of Protein Machines
Author:
Bruce Alberts
The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists • Cell • 1998
Scientific Review
Neutral
DOI:
10.1016/S0092-8674(00)80922-8
Used in this investigation
Evidence
-
Molecular Machines in the Cell
—
Scientific Foundation
-
Engineering Analogies in Biology
—
Protein Machines
Alberts et al. — From RNA to Protein
Author:
Bruce Alberts; Alexander Johnson; Julian Lewis; Martin Raff; Keith Roberts; Peter Walter
From RNA to Protein • Molecular Biology of the Cell, 4th edition • 2002
Scientific Reference
Neutral
Used in this investigation
Evidence
-
Biological Information as an Integrated System
—
Scientific Foundation
Alberts et al. — Structure and Function of DNA
Author:
Bruce Alberts; Alexander Johnson; Julian Lewis; Martin Raff; Keith Roberts; Peter Walter
The Structure and Function of DNA • Molecular Biology of the Cell, 4th edition • 2002
Scientific Reference
Neutral
Used in this investigation
Evidence
-
Functional Information in DNA Sequences
—
Sequence Foundation
Woese et al. — Aminoacyl-tRNA Synthetases and the Genetic Code
Author:
Carl R. Woese; Gary J. Olsen; Michael Ibba; Dieter Söll
Aminoacyl-tRNA Synthetases, the Genetic Code, and the Evolutionary Process • Microbiology and Molecular Biology Reviews • 2000
Scientific Review
Neutral
DOI:
10.1128/MMBR.64.1.202-236.2000
Used in this investigation
Evidence
-
Biological Information as an Integrated System
—
System Integration
SEP — Teleological Arguments and Inference to the Best Explanation
Author:
Del Ratzsch; Jeffrey Koperski
Teleological Arguments for God's Existence • Stanford Encyclopedia of Philosophy • 2023
Philosophical Review
Neutral
Used in this investigation
Explanations
-
Inference to the Best Explanation
—
Inference Framework
-
The Cumulative Case for Design
—
Cumulative Inference
Questions & Objections
-
Who Designed the Designer?
—
Philosophical Analysis
-
Even If There Is Design, Why Think the Designer Is God?
—
Designer Identity
Del Vecchio and Sontag — Engineering Principles in Biomolecular Systems
Author:
Domitilla Del Vecchio; Eduardo D. Sontag
Engineering Principles in Bio-Molecular Systems: From Retroactivity to Modularity • European Journal of Control • 2009
Scientific Research
Neutral
DOI:
10.3166/ejc.15.389-397
Used in this investigation
Evidence
-
Engineering Analogies in Biology
—
Engineering Principles
Erwin — Evolutionary Dynamics of Gene Regulation
Author:
Douglas H. Erwin
Evolutionary Dynamics of Gene Regulation • Current Topics in Developmental Biology • 2020
Scientific Review
Neutral
DOI:
10.1016/bs.ctdb.2020.02.006
Used in this investigation
Evidence
-
From Observed Change to Major Innovation
—
Regulatory Evolution
Erwin — Evolutionary Novelty and Innovation
Author:
Douglas H. Erwin
A Conceptual Framework of Evolutionary Novelty and Innovation • Biological Reviews • 2021
Scientific Review
Neutral
DOI:
10.1111/brv.12643
Used in this investigation
Evidence
-
From Observed Change to Major Innovation
—
Evolutionary Novelty
Explanations
-
Natural Processes as the Complete Explanation
—
Evolutionary Novelty
Questions & Objections
-
Does Evolution Remove the Need for Design?
—
Evolutionary Novelty
Erwin and Davidson — Evolution of Hierarchical Gene Regulatory Networks
Author:
Douglas H. Erwin; Eric H. Davidson
The Evolution of Hierarchical Gene Regulatory Networks • Nature Reviews Genetics • 2009
Scientific Review
Neutral
DOI:
10.1038/nrg2499
Used in this investigation
Evidence
-
From Observed Change to Major Innovation
—
Developmental Networks
Sober — What Is Wrong with Intelligent Design?
Author:
Elliott Sober
What Is Wrong with Intelligent Design? • Quarterly Review of Biology • 2007
Philosophical Analysis
Critical Of Design
DOI:
10.1086/511656
Used in this investigation
Explanations
-
Inference to the Best Explanation
—
Critical Analysis
Questions & Objections
-
Is Intelligent Design Just an Argument from Ignorance?
—
Critical Analysis
-
Is Intelligent Design Testable?
—
Testability
-
Who Designed the Designer?
—
Critical Analysis
Sober — Observation Selection and Fine-Tuning
Author:
Elliott Sober
Absence of Evidence and Evidence of Absence: Evidential Transitivity in Connection with Fossils, Fishing, Fine-Tuning, and Firing Squads • Philosophical Studies, Vol. 143, No. 1 • 2009
Journal Article
Critical Of Design Argument
DOI:
10.1007/s11098-008-9315-0
Used in this investigation
Explanations
-
Chance, Necessity, and Selection Effects
—
Selection Effects
Zuckerkandl — Intelligent Design and Biological Complexity
Author:
Emile Zuckerkandl
Intelligent Design and Biological Complexity • Gene • 2006
Scientific Review
Critical Of Design
DOI:
10.1016/j.gene.2006.03.025
Used in this investigation
Evidence
-
Do Engineering-Like Patterns Indicate Design?
—
Evolutionary Critique
ENCODE Consortium — Expanded Encyclopaedias of DNA Elements
Author:
ENCODE Project Consortium; Jill E. Moore; Michael J. Purcaro; et al.
Expanded Encyclopaedias of DNA Elements in the Human and Mouse Genomes • Nature • 2020
Journal Article
Neutral
DOI:
10.1038/s41586-020-2493-4
Used in this investigation
Evidence
-
Functional Information in DNA Sequences
—
Scientific Foundation
Quandt et al. — Fine-Tuning Citrate Metabolic Innovation
Author:
Erik M. Quandt; Jimmy Gollihar; Zachary D. Blount; Andrew D. Ellington; George Georgiou; Jeffrey E. Barrick
Fine-Tuning Citrate Synthase Flux Potentiates and Refines Metabolic Innovation in the Lenski Evolution Experiment • eLife • 2015
Scientific Research
Neutral
DOI:
10.7554/eLife.09696
Used in this investigation
Evidence
-
The Lenski Citrate Innovation
—
Metabolic Refinement
Koonin and Novozhilov — Origin and Evolution of the Genetic Code
Author:
Eugene V. Koonin; Artem S. Novozhilov
Origin and Evolution of the Genetic Code: The Universal Enigma • 2009
Scientific Review
Neutral
Used in this investigation
Evidence
-
The Origin of Biological Information
—
Scientific Foundation
Koonin and Novozhilov — Universal Genetic Code
Author:
Eugene V. Koonin; Artem S. Novozhilov
Origin and Evolution of the Universal Genetic Code • 2017
Scientific Review
Neutral
Used in this investigation
Evidence
-
The Origin of Biological Information
—
Evolutionary Model
Chevance and Hughes — Coordinating Flagellar Assembly
Author:
Fabienne F. V. Chevance; Kelly T. Hughes
Coordinating Assembly of a Bacterial Macromolecular Machine • Nature Reviews Microbiology • 2008
Scientific Review
Neutral
DOI:
10.1038/nrmicro1887
Used in this investigation
Evidence
-
Molecular Machines in the Cell
—
Specific Example
Adams — Alternate Universes and Fundamental Constants
Author:
Fred C. Adams
Constraints on Alternate Universes: Stars and Habitable Planets with Different Fundamental Constants • Journal of Cosmology and Astroparticle Physics, 2016(02), 042 • 2016
Journal Article
Neutral
DOI:
10.1088/1475-7516/2016/02/042
Used in this investigation
Explanations
-
Chance, Necessity, and Selection Effects
—
Physical Parameter Space
Conant and Wolfe — How Duplicated Genes Find New Functions
Author:
Gavin C. Conant; Kenneth H. Wolfe
Turning a Hobby into a Job: How Duplicated Genes Find New Functions • Nature Reviews Genetics • 2008
Scientific Review
Neutral
DOI:
10.1038/nrg2482
Used in this investigation
Questions & Objections
-
Can Natural Processes Produce Apparent Design?
—
Gene Duplication
Fox — Origin and Evolution of the Ribosome
Author:
George E. Fox
Origin and Evolution of the Ribosome • Cold Spring Harbor Perspectives in Biology • 2010
Scientific Review
Neutral
DOI:
10.1101/cshperspect.a003483
Used in this investigation
Evidence
-
Biological Information as an Integrated System
—
Ribosome Context
Wray — Evolutionary Significance of Cis-Regulatory Mutations
Author:
Gregory A. Wray
The Evolutionary Significance of Cis-Regulatory Mutations • Nature Reviews Genetics • 2007
Scientific Review
Neutral
DOI:
10.1038/nrg2063
Used in this investigation
Questions & Objections
-
Can Natural Processes Produce Apparent Design?
—
Regulatory Evolution
Schrum et al. — The Origins of Cellular Life
Author:
Jason P. Schrum; Ting F. Zhu; Jack W. Szostak
The Origins of Cellular Life • 2010
Scientific Review
Neutral
Used in this investigation
Evidence
-
From Chemistry to an Evolvable Living System
—
Scientific Foundation
Richards — Fine-Tuning Parameters
Author:
Jay W. Richards
List of Fine-Tuning Parameters • Discovery Institute • 2015
Id Source
Supports Design
Used in this investigation
Evidence
-
The Cosmological Constant
—
Design Reference
Barrick and Lenski — Genome Dynamics During Experimental Evolution
Author:
Jeffrey E. Barrick; Richard E. Lenski
Genome Dynamics During Experimental Evolution • Nature Reviews Genetics • 2013
Scientific Review
Neutral
DOI:
10.1038/nrg3564
Used in this investigation
Explanations
-
Natural Processes as the Complete Explanation
—
Experimental Evidence
Questions & Objections
-
Does Evolution Remove the Need for Design?
—
Experimental Evidence
Martin — The Cosmological Constant Problem
Author:
Jérôme Martin
Everything You Always Wanted to Know About the Cosmological Constant Problem (But Were Afraid to Ask) • Comptes Rendus Physique, Vol. 13, Nos. 6-7 • 2012
Scientific Review
Neutral
DOI:
10.1016/j.crhy.2012.04.008
Used in this investigation
Evidence
-
The Cosmological Constant
—
Qualification
Sutherland — Studies on the Origin of Life
Author:
John D. Sutherland
Studies on the Origin of Life — The End of the Beginning • 2017
Scientific Review
Neutral
Used in this investigation
Evidence
-
From Chemistry to an Evolvable Living System
—
Chemical Integration
Barnes — Fine-Tuning for Intelligent Life
Author:
Luke A. Barnes
The Fine-Tuning of the Universe for Intelligent Life • Publications of the Astronomical Society of Australia, Vol. 29, No. 4 • 2012
Scientific Review
Neutral
DOI:
10.1071/AS12015
Used in this investigation
Explanations
-
The Cumulative Case for Design
—
Cosmic Fine Tuning
Pallen and Matzke — Evolutionary Origin of Bacterial Flagella
Author:
Mark J. Pallen; Nicholas J. Matzke
From The Origin of Species to the Origin of Bacterial Flagella • Nature Reviews Microbiology • 2006
Scientific Review
Supports Evolutionary Explanation
DOI:
10.1038/nrmicro1493
Used in this investigation
Evidence
-
Can Molecular Machines Be Built Step by Step?
—
Evolutionary Response
Behe — Darwin's Black Box and Irreducible Complexity
Author:
Michael J. Behe
Darwin's Black Box: The Biochemical Challenge to Evolution • Free Press • 1996
Book
Supports Design
Used in this investigation
Evidence
-
Can Molecular Machines Be Built Step by Step?
—
Design Argument
National Academies — Multiparameter Habitability Assessment
Author:
National Academies of Sciences, Engineering, and Medicine
An Astrobiology Strategy for the Search for Life in the Universe • The National Academies Press • 2019
Scientific Review
Neutral
DOI:
10.17226/25252
Used in this investigation
Evidence
-
The Combined Requirements for Complex Life
—
Scientific Foundation
Explanations
-
The Cumulative Case for Design
—
Planetary Habitability
National Academies — Dynamic Habitability
Author:
National Academies of Sciences, Engineering, and Medicine
Origins, Worlds, and Life: A Decadal Strategy for Planetary Science and Astrobiology 2023-2032 • The National Academies Press • 2023
Scientific Review
Neutral
DOI:
10.17226/26522
Used in this investigation
Evidence
-
The Combined Requirements for Complex Life
—
Dynamic Habitability
Adamski et al. — From Self-Replication to Replicator Systems
Author:
Paul Adamski; Marcel Eleveld; Ankush Sood; Ádám Kun; András Szilágyi; Tamás Czárán; Eörs Szathmáry; Sijbren Otto
From Self-Replication to Replicator Systems en Route to de Novo Life • 2020
Scientific Review
Neutral
Used in this investigation
Evidence
-
From Chemistry to an Evolvable Living System
—
Integrated System
Kopparapu, Wolf and Meadows — Characterizing Exoplanet Habitability
Author:
Ravi Kumar Kopparapu; Eric T. Wolf; Victoria S. Meadows
Characterizing Exoplanet Habitability • Planetary Astrobiology • 2020
Scientific Review
Neutral
DOI:
10.2458/azu_uapress_9780816540068-ch17
Used in this investigation
Evidence
-
The Combined Requirements for Complex Life
—
Broader Context
Liu and Ochman — Stepwise Formation of the Bacterial Flagellar System
Author:
Renyi Liu; Howard Ochman
Stepwise Formation of the Bacterial Flagellar System • Proceedings of the National Academy of Sciences • 2007
Scientific Research
Supports Evolutionary Explanation
DOI:
10.1073/pnas.0700266104
Used in this investigation
Evidence
-
Can Molecular Machines Be Built Step by Step?
—
Evolutionary Reconstruction
Pennock — Creationism and Intelligent Design
Author:
Robert T. Pennock
Creationism and Intelligent Design • Annual Review of Genomics and Human Genetics • 2003
Scientific Review
Critical Of Design
DOI:
10.1146/annurev.genom.4.070802.110400
Used in this investigation
Questions & Objections
-
Is Intelligent Design Testable?
—
Critical Scientific Assessment
-
Even If There Is Design, Why Think the Designer Is God?
—
Critical Context
Collins — The Fine-Tuning Design Argument
Author:
Robin Collins
The Fine-Tuning Design Argument • Discovery Institute • 1998
Id Source
Supports Design
Used in this investigation
Evidence
-
The Cosmological Constant
—
Design Interpretation
Carroll — The Cosmological Constant
Author:
Sean M. Carroll
The Cosmological Constant • Living Reviews in Relativity, Vol. 4, Article 1 • 2001
Scientific Review
Neutral
DOI:
10.12942/lrr-2001-1
Used in this investigation
Evidence
-
The Cosmological Constant
—
Scientific Review
Abby and Rocha — Evolution of Type III Secretion from the Flagellum
Author:
Sophie S. Abby; Eduardo P. C. Rocha
The Non-Flagellar Type III Secretion System Evolved from the Bacterial Flagellum and Diversified into Host-Cell Adapted Systems • PLoS Genetics • 2012
Scientific Research
Supports Evolutionary Explanation
DOI:
10.1371/journal.pgen.1002983
Used in this investigation
Evidence
-
Can Molecular Machines Be Built Step by Step?
—
Comparative Evidence
Meyer — Evidence for Design in Physics and Biology
Author:
Stephen C. Meyer
Evidence for Design in Physics and Biology: From the Origin of the Universe to the Origin of Life • Proceedings of the Wethersfield Institute • 2003
Id Source
Supports Design
Used in this investigation
Explanations
-
Inference to the Best Explanation
—
Causal Adequacy
-
Intelligent Causation as an Explanation
—
Positive Design Inference
Questions & Objections
-
Is Intelligent Design Just an Argument from Ignorance?
—
Positive Design Inference
-
Even If There Is Design, Why Think the Designer Is God?
—
Limits Of Design Inference
Meyer — Scientific Status of Intelligent Design
Author:
Stephen C. Meyer
The Scientific Status of Intelligent Design • Stephen C. Meyer • 2005
Id Source
Supports Design
Used in this investigation
Questions & Objections
-
Is Intelligent Design Testable?
—
Design Scientific Status
Meyer — Philosophical Defense of Intelligent Design
Author:
Stephen C. Meyer
A Scientific History and Philosophical Defense of the Theory of Intelligent Design • Stephen C. Meyer • 2008
Id Source
Supports Design
Used in this investigation
Explanations
-
Intelligent Causation as an Explanation
—
Causal Adequacy
Questions & Objections
-
Who Designed the Designer?
—
Causal Explanation
Meyer — Signature in the Cell
Author:
Stephen C. Meyer
Signature in the Cell: DNA and the Evidence for Intelligent Design • 2009
Id Source
Supports Design
Used in this investigation
Evidence
-
The Origin of Biological Information
—
Design Interpretation
-
From Chemistry to an Evolvable Living System
—
Design Interpretation
-
Biological Information as an Integrated System
—
Design Interpretation
-
Do Engineering-Like Patterns Indicate Design?
—
Design Inference
Meyer — Answering the Argument from Ignorance Objection
Author:
Stephen C. Meyer
Denying the Signature • Stephen C. Meyer • 2017
Id Source
Supports Design
Used in this investigation
Explanations
-
Intelligent Causation as an Explanation
—
Positive Evidence
Questions & Objections
-
Is Intelligent Design Just an Argument from Ignorance?
—
Design Response
Weinberg — Anthropic Bound on the Cosmological Constant
Author:
Steven Weinberg
Anthropic Bound on the Cosmological Constant • Physical Review Letters, Vol. 59, No. 22 • 1987
Journal Article
Neutral
DOI:
10.1103/PhysRevLett.59.2607
Used in this investigation
Evidence
-
The Cosmological Constant
—
Life Permitting Constraint
Weinberg — The Cosmological Constant Problem
Author:
Steven Weinberg
The Cosmological Constant Problem • Reviews of Modern Physics, Vol. 61, No. 1 • 1989
Scientific Review
Neutral
DOI:
10.1103/RevModPhys.61.1
Used in this investigation
Evidence
-
The Cosmological Constant
—
Scientific Foundation
Wolf and Koonin — Origin of Translation and the Genetic Code
Author:
Yuri I. Wolf; Eugene V. Koonin
On the Origin of the Translation System and the Genetic Code in the RNA World by Means of Natural Selection, Exaptation, and Subfunctionalization • Biology Direct • 2007
Scientific Paper
Neutral
DOI:
10.1186/1745-6150-2-14
Used in this investigation
Evidence
-
Biological Information as an Integrated System
—
Origin Model
Lazebnik — Can a Biologist Fix a Radio?
Author:
Yuri Lazebnik
Can a Biologist Fix a Radio?—Or, What I Learned While Studying Apoptosis • Cancer Cell • 2002
Scientific Commentary
Neutral
DOI:
10.1016/S1535-6108(02)00133-2
Used in this investigation
Evidence
-
Engineering Analogies in Biology
—
Engineering Methodology
Blount et al. — Historical Contingency and Citrate Innovation
Author:
Zachary D. Blount; Christina Z. Borland; Richard E. Lenski
Historical Contingency and the Evolution of a Key Innovation in an Experimental Population of Escherichia coli • Proceedings of the National Academy of Sciences • 2008
Scientific Research
Neutral
DOI:
10.1073/pnas.0803151105
Used in this investigation
Evidence
-
The Lenski Citrate Innovation
—
Experimental Evidence
Explanations
-
Natural Processes as the Complete Explanation
—
Experimental Innovation
Questions & Objections
-
Does Evolution Remove the Need for Design?
—
Experimental Innovation
Blount et al. — Genomic Analysis of Citrate Innovation
Author:
Zachary D. Blount; Jeffrey E. Barrick; Carla J. Davidson; Richard E. Lenski
Genomic Analysis of a Key Innovation in an Experimental Escherichia coli Population • Nature • 2012
Scientific Research
Neutral
DOI:
10.1038/nature11514
Used in this investigation
Evidence
-
The Lenski Citrate Innovation
—
Genetic Mechanism
