Intelligent Design Investigation

Research Sources

Biological Innovation and Evolutionary Mechanisms  •  31 unique sources
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These are the research sources used in this investigation. A source is listed once even when it supports several evidence records, explanations, or objections. The entries below also show where each source is used so that the research trail can be followed.

Eyre-Walker and Keightley — Fitness Effects of New Mutations

Author: Adam Eyre-Walker; Peter D. Keightley
The Distribution of Fitness Effects of New Mutations • Nature Reviews Genetics • 2007
Scientific Review Neutral
DOI: 10.1038/nrg2146
Used in this investigation
Evidence
  • Mutation and Genetic Variation — Scientific Foundation

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
Evidence
  • Changes in Protein Function — Experimental Evidence
Explanations
  • Modification of Existing Biological Systems — Protein Function

Carvunis et al. — Proto-Genes and De Novo Gene Birth

Author: Anne-Ruxandra Carvunis; Thomas Rolland; Ilan Wapinski; Michael A. Calderwood; Muhammed A. Yildirim; Nicolas Simonis; Benoit Charloteaux; César A. Hidalgo; Justin Barbette; Balaji Santhanam; Gloria A. Brar; Jonathan S. Weissman; Aviv Regev; Nicolas Thierry-Mieg; Michael E. Cusick; Marc Vidal
Proto-Genes and De Novo Gene Birth • Nature • 2012
Scientific Research Neutral
DOI: 10.1038/nature11184
Used in this investigation
Evidence
  • The Origin of New Genes — De Novo Gene Birth
Explanations
  • The Origin of Biological Novelty — De Novo Gene Birth
  • Intelligent Design and the Limits Question — Demonstrated Novelty
Questions & Objections
  • Isn't This Just Microevolution? — De Novo Gene Birth
  • Does De Novo Gene Birth Answer the Information Question? — De Novo Gene Birth
  • Is Intelligent Design Just an Argument from What Science Has Not Yet Explained? — Demonstrated Novelty

Martin and Orgogozo — Loci of Repeated Evolution

Author: Arnaud Martin; Virginie Orgogozo
The Loci of Repeated Evolution: A Catalog of Genetic Hotspots of Phenotypic Variation • Evolution • 2013
Scientific Research Neutral
DOI: 10.1111/evo.12081
Used in this investigation
Evidence
  • Convergence and Repeated Solutions — Repeated Genetic Change

Prud'homme et al. — Emerging Principles of Regulatory Evolution

Author: Benjamin Prud'homme; Nicolas Gompel; Sean B. Carroll
Emerging Principles of Regulatory Evolution • Proceedings of the National Academy of Sciences • 2007
Scientific Review Neutral
DOI: 10.1073/pnas.0700488104
Used in this investigation
Evidence
  • Changes in Gene Regulation — Regulatory Mechanisms

Stern — Genetic Causes of Convergent Evolution

Author: David L. Stern
The Genetic Causes of Convergent Evolution • Nature Reviews Genetics • 2013
Scientific Review Neutral
DOI: 10.1038/nrg3483
Used in this investigation
Evidence
  • Convergence and Repeated Solutions — Genetic Convergence

Angelini and Kaufman — Developmental Genetics and Arthropod Body Plans

Author: David R. Angelini; Thomas C. Kaufman
Comparative Developmental Genetics and the Evolution of Arthropod Body Plans • Annual Review of Genetics • 2005
Scientific Review Neutral
DOI: 10.1146/annurev.genet.39.073003.112310
Used in this investigation
Evidence
  • Developmental Change and Body Plans — Comparative Evidence

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
  • The Origin of Biological Novelty — Evolutionary Novelty
  • From Observed Change to Major Innovation — Evolutionary Novelty
  • Intelligent Design and the Limits Question — Scope Of Explanation
Questions & Objections
  • Is Intelligent Design Just an Argument from What Science Has Not Yet Explained? — Scope Of Explanation

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

Davidson and Erwin — Gene Regulatory Networks and Animal Body Plans

Author: Eric H. Davidson; Douglas H. Erwin
Gene Regulatory Networks and the Evolution of Animal Body Plans • Science • 2006
Scientific Research Neutral
DOI: 10.1126/science.1113832
Used in this investigation
Evidence
  • Developmental Change and Body Plans — Gene Regulatory Networks
Explanations
  • From Observed Change to Major Innovation — Gene Regulatory Networks

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
Questions & Objections
  • Haven't Experiments Demonstrated Major Evolutionary Innovation? — Metabolic Refinement

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
Evidence
  • Gene Duplication and New Functions — Scientific Foundation
Explanations
  • Modification of Existing Biological Systems — Gene Duplication
  • Intelligent Design and the Limits Question — Demonstrated Mechanism
Questions & Objections
  • Does Gene Duplication Create New Information? — Gene Duplication
  • Is Intelligent Design Just an Argument from What Science Has Not Yet Explained? — Demonstrated Mechanism

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
Evidence
  • Changes in Gene Regulation — Scientific Foundation
Explanations
  • Modification of Existing Biological Systems — Regulatory Change

Orr — The Genetic Theory of Adaptation

Author: H. Allen Orr
The Genetic Theory of Adaptation: A Brief History • Nature Reviews Genetics • 2005
Scientific Review Neutral
DOI: 10.1038/nrg1523
Used in this investigation
Evidence
  • Natural Selection and Adaptation — Scientific Foundation

Innan and Kondrashov — Evolution of Gene Duplications

Author: Hideki Innan; Fyodor Kondrashov
The Evolution of Gene Duplications: Classifying and Distinguishing Between Models • Nature Reviews Genetics • 2010
Scientific Review Neutral
DOI: 10.1038/nrg2689
Used in this investigation
Evidence
  • Gene Duplication and New Functions — Evolutionary Models
Questions & Objections
  • Does Gene Duplication Create New Information? — Duplication Models

Hoekstra and Coyne — The Locus of Evolution

Author: Hopi E. Hoekstra; Jerry A. Coyne
The Locus of Evolution: Evo Devo and the Genetics of Adaptation • Evolution • 2007
Scientific Review Neutral
DOI: 10.1111/j.1558-5646.2007.00105.x
Used in this investigation
Evidence
  • Changes in Gene Regulation — Scientific Qualification

Bridgham et al. — Evolution of Hormone-Receptor Complexity

Author: Jamie T. Bridgham; Sean M. Carroll; Joseph W. Thornton
Evolution of Hormone-Receptor Complexity by Molecular Exploitation • Science • 2006
Scientific Research Neutral
DOI: 10.1126/science.1123348
Used in this investigation
Evidence
  • Changes in Protein Function — Ancestral Reconstruction

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
Evidence
  • Mutation and Genetic Variation — Experimental Evidence
  • Natural Selection and Adaptation — Experimental Evidence
  • Experimental Evolution — Scientific Foundation
Explanations
  • Known Evolutionary Mechanisms — Experimental Evidence

Feder et al. — Geographic Mode of Speciation and Genomic Divergence

Author: Jeffrey L. Feder; Samuel M. Flaxman; Scott P. Egan; Aaron A. Comeault; Patrik Nosil
Geographic Mode of Speciation and Genomic Divergence • Annual Review of Ecology, Evolution, and Systematics • 2013
Scientific Review Neutral
DOI: 10.1146/annurev-ecolsys-110512-135825
Used in this investigation
Evidence
  • Speciation and Reproductive Isolation — Genomic Divergence
Questions & Objections
  • Does Speciation Demonstrate Large-Scale Evolution? — Genomic Divergence

Näsvall et al. — Real-Time Evolution of New Genes

Author: Joakim Näsvall; Lei Sun; John R. Roth; Dan I. Andersson
Real-Time Evolution of New Genes by Innovation, Amplification, and Divergence • Science • 2012
Scientific Research Neutral
DOI: 10.1126/science.1226521
Used in this investigation
Evidence
  • Gene Duplication and New Functions — Experimental Evidence
Questions & Objections
  • Isn't This Just Microevolution? — Experimental Innovation
  • Does Gene Duplication Create New Information? — Experimental Evidence

Losos — Convergence, Adaptation, and Constraint

Author: Jonathan B. Losos
Convergence, Adaptation, and Constraint • Evolution • 2011
Scientific Review Neutral
DOI: 10.1111/j.1558-5646.2011.01289.x
Used in this investigation
Evidence
  • Convergence and Repeated Solutions — Scientific Foundation

Zhao et al. — De Novo Genes

Author: Li Zhao; Nicolas Svetec; David J. Begun
De Novo Genes • Annual Review of Genetics • 2024
Scientific Review Neutral
DOI: 10.1146/annurev-genet-111523-102413
Used in this investigation
Evidence
  • The Origin of New Genes — Scientific Review
Questions & Objections
  • Does De Novo Gene Birth Answer the Information Question? — Scientific Review

Yuan et al. — Laboratory-Directed Protein Evolution

Author: Ling Yuan; Itzhak Kurek; James English; Robert Keenan
Laboratory-Directed Protein Evolution • Microbiology and Molecular Biology Reviews • 2005
Scientific Review Neutral
DOI: 10.1128/MMBR.69.3.373-392.2005
Used in this investigation
Evidence
  • Changes in Protein Function — Scientific Foundation

Long et al. — The Origin of New Genes

Author: Manyuan Long; Esther Betrán; Kevin Thornton; Wen Wang
The Origin of New Genes: Glimpses from the Young and Old • Nature Reviews Genetics • 2003
Scientific Review Neutral
DOI: 10.1038/nrg1204
Used in this investigation
Evidence
  • The Origin of New Genes — Scientific Foundation
Explanations
  • The Origin of Biological Novelty — New Gene Origin
Questions & Objections
  • Does De Novo Gene Birth Answer the Information Question? — New Gene Origin

Nosil and Schluter — Genes Underlying Speciation

Author: Patrik Nosil; Dolph Schluter
The Genes Underlying the Process of Speciation • Trends in Ecology & Evolution • 2011
Scientific Review Neutral
DOI: 10.1016/j.tree.2011.01.001
Used in this investigation
Evidence
  • Speciation and Reproductive Isolation — Genetic Mechanisms
Questions & Objections
  • Does Speciation Demonstrate Large-Scale Evolution? — Genetic Mechanisms

Lenski and Travisano — 10,000-Generation Evolution Experiment

Author: Richard E. Lenski; Michael Travisano
Dynamics of Adaptation and Diversification: A 10,000-Generation Experiment with Bacterial Populations • Proceedings of the National Academy of Sciences • 1994
Scientific Research Neutral
DOI: 10.1073/pnas.91.15.6808
Used in this investigation
Evidence
  • Experimental Evolution — Experimental Evidence
Explanations
  • Known Evolutionary Mechanisms — Experimental Evidence

Raff — Evo-Devo and the Evolution of Development

Author: Rudolf A. Raff
Evo-Devo: The Evolution of a New Discipline • Nature Reviews Genetics • 2000
Scientific Review Neutral
DOI: 10.1038/35049594
Used in this investigation
Evidence
  • Developmental Change and Body Plans — Scientific Foundation
Explanations
  • From Observed Change to Major Innovation — Developmental Evolution

Rice and Hostert — Laboratory Experiments on Speciation

Author: William R. Rice; Ellen E. Hostert
Laboratory Experiments on Speciation: What Have We Learned in 40 Years? • Evolution • 1993
Scientific Review Neutral
DOI: 10.1111/j.1558-5646.1993.tb01257.x
Used in this investigation
Evidence
  • Speciation and Reproductive Isolation — Experimental Evidence
Questions & Objections
  • Isn't This Just Microevolution? — Speciation
  • Does Speciation Demonstrate Large-Scale Evolution? — Experimental Evidence

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
  • Known Evolutionary Mechanisms — Experimental Innovation
Questions & Objections
  • Haven't Experiments Demonstrated Major Evolutionary Innovation? — Experimental Evidence

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
Questions & Objections
  • Haven't Experiments Demonstrated Major Evolutionary Innovation? — Genetic Mechanism
 Sources are gathered from the evidence, explanations, and objections linked to this investigation and are shown once per source.