Intelligent Design Investigation

Research Sources

Patterns of Design in Living Systems  •  41 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.

Mitrophanov and Groisman — Positive Feedback in Cellular Control Systems

Author: Alexander Y. Mitrophanov; Eduardo A. Groisman
Positive Feedback in Cellular Control Systems • BioEssays • 2008
Scientific Review Neutral
DOI: 10.1002/bies.20769
Used in this investigation
Evidence
  • Feedback Control in Living Systems — Positive Feedback

Bębenek and Ziuzia-Graczyk — DNA Replication Proofreading

Author: Anna Bębenek; Izabela Ziuzia-Graczyk
Fidelity of DNA Replication—a Matter of Proofreading • Current Genetics • 2018
Scientific Review Neutral
DOI: 10.1007/s00294-018-0820-1
Used in this investigation
Evidence
  • Error Detection and Correction — Proofreading

Hintze and Adami — Evolution of Complex Modular Biological Networks

Author: Arend Hintze; Christoph Adami
Evolution of Complex Modular Biological Networks • PLOS Computational Biology • 2008
Scientific Research Neutral
DOI: 10.1371/journal.pcbi.0040023
Used in this investigation
Evidence
  • Modularity in Biological Systems — Evolution Of Modularity
Explanations
  • Evolution by Natural Selection — Network Evolution
Questions & Objections
  • Does Natural Selection Explain Engineering-Like Organization? — Network Evolution

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
Explanations
  • Engineering Principles as Convergent Solutions — Engineering Biology Comparison
Questions & Objections
  • Are Engineering Comparisons Only Analogies? — Engineering Biology Comparison

Inouye et al. — Trade-Offs in Robustness, Resilience, and Performance

Author: Brian D. Inouye; Berry J. Brosi; Emily H. Le Sage; Manuel T. Lerdau
Trade-offs Among Resilience, Robustness, Stability, and Performance and How We Might Study Them • Integrative and Comparative Biology • 2021
Scientific Review Neutral
DOI: 10.1093/icb/icab178
Used in this investigation
Evidence
  • Trade-Offs, Constraints, and Failure Modes — Performance Robustness Tradeoffs

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
  • Engineering Analogies in Biology — Protein Machines

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 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
  • Hierarchical Organization and Control — Regulatory Hierarchy
Explanations
  • Constraint, Inheritance, and Historical Development — Inherited Regulatory Architecture
Questions & Objections
  • Do Imperfect and Fragile Biological Systems Count Against Design? — Historical Constraint

Ramsay and Woods — Homeostasis and Allostasis in Physiological Regulation

Author: Douglas S. Ramsay; Stephen C. Woods
Clarifying the Roles of Homeostasis and Allostasis in Physiological Regulation • Psychological Review • 2014
Scientific Review Neutral
DOI: 10.1037/a0035942
Used in this investigation
Evidence
  • Homeostasis and Biological Regulation — Physiological Regulation

Hancock et al. — Feedback and Buffering in Cellular Homeostasis

Author: Edward J. Hancock; Jordan Ang; Antonis Papachristodoulou; Guy-Bart Stan
The Interplay between Feedback and Buffering in Cellular Homeostasis • Cell Systems • 2017
Scientific Research Neutral
DOI: 10.1016/j.cels.2017.09.013
Used in this investigation
Evidence
  • Homeostasis and Biological Regulation — Cellular Homeostasis

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
Explanations
  • Purposeful Design — Evolutionary Critique
Questions & Objections
  • Are We Seeing Design Because We Already Expect It? — Evolutionary Critique

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
  • Integration of Multiple Regulatory Networks — Gene Regulatory Networks

Karsenti — Self-Organization in Cell Biology

Author: Eric Karsenti
Self-Organization in Cell Biology: A Brief History • Nature Reviews Molecular Cell Biology • 2008
Scientific Review Neutral
DOI: 10.1038/nrm2357
Used in this investigation
Explanations
  • Self-Organization and Emergent Order — Cellular Self Organization
Questions & Objections
  • Can Self-Organization Produce Order Without Design? — Cellular Self Organization

Billman — Homeostasis as a Central Organizing Principle

Author: George E. Billman
Homeostasis: The Underappreciated and Far Too Often Ignored Central Organizing Principle of Physiology • Frontiers in Physiology • 2020
Scientific Review Neutral
DOI: 10.3389/fphys.2020.00200
Used in this investigation
Evidence
  • Homeostasis and Biological Regulation — Scientific Foundation

Edelman and Gally — Degeneracy and Complexity

Author: Gerald M. Edelman; Joseph A. Gally
Degeneracy and Complexity in Biological Systems • Proceedings of the National Academy of Sciences • 2001
Scientific Review Neutral
DOI: 10.1073/pnas.231499798
Used in this investigation
Evidence
  • Redundancy and Backup Systems — Biological Degeneracy

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
Explanations
  • Evolution by Natural Selection — Adaptation
Questions & Objections
  • Does Natural Selection Explain Engineering-Like Organization? — Adaptation

El-Samad — Biological Feedback Control

Author: Hana El-Samad
Biological Feedback Control—Respect the Loops • Cell Systems • 2021
Scientific Review Neutral
DOI: 10.1016/j.cels.2021.05.004
Used in this investigation
Evidence
  • Feedback Control in Living Systems — Scientific Foundation

Makadia et al. — Intracellular Information Processing

Author: Hirenkumar K. Makadia; James S. Schwaber; Rajanikanth Vadigepalli
Intracellular Information Processing through Encoding and Decoding of Dynamic Signaling Features • PLOS Computational Biology • 2015
Scientific Research Neutral
DOI: 10.1371/journal.pcbi.1004563
Used in this investigation
Evidence
  • Biological Information Processing — Dynamic Information Processing

Kitano — Biological Robustness

Author: Hiroaki Kitano
Biological Robustness • Nature Reviews Genetics • 2004
Scientific Review Neutral
DOI: 10.1038/nrg1471
Used in this investigation
Evidence
  • Robustness Under Perturbation — Scientific Foundation
  • Trade-Offs, Constraints, and Failure Modes — Robustness Fragility Tradeoffs
Explanations
  • Engineering Principles as Convergent Solutions — Robust System Architecture
Questions & Objections
  • Does Natural Selection Explain Engineering-Like Organization? — Robustness And Evolution
  • Are Engineering Comparisons Only Analogies? — Shared Architecture
  • Does Convergent Evolution Explain Repeated Biological Solutions? — Robust Architecture
  • Do Imperfect and Fragile Biological Systems Count Against Design? — Robustness Fragility Tradeoff
  • Are We Seeing Design Because We Already Expect It? — Evolutionary Explanation

Halatek et al. — Self-Organization of Intracellular Patterns

Author: J. Halatek; F. Brauns; E. Frey
Self-Organization Principles of Intracellular Pattern Formation • Philosophical Transactions of the Royal Society B • 2018
Scientific Review Neutral
DOI: 10.1098/rstb.2017.0107
Used in this investigation
Explanations
  • Self-Organization and Emergent Order — Intracellular Pattern Formation
Questions & Objections
  • Can Self-Organization Produce Order Without Design? — Pattern Formation

Papin et al. — Cellular Signalling Networks

Author: Jason A. Papin; Tony Hunter; Bernhard O. Palsson; Shankar Subramaniam
Reconstruction of Cellular Signalling Networks and Analysis of Their Properties • Nature Reviews Molecular Cell Biology • 2005
Scientific Review Neutral
DOI: 10.1038/nrm1570
Used in this investigation
Evidence
  • Biological Information Processing — Signaling Networks
  • Integration of Multiple Regulatory Networks — Signaling Network Integration

Green and Sharpe — Positional Information and Reaction-Diffusion

Author: Jeremy B. A. Green; James Sharpe
Positional Information and Reaction-Diffusion: Two Big Ideas in Developmental Biology Combine • Development • 2015
Scientific Review Neutral
DOI: 10.1242/dev.114991
Used in this investigation
Explanations
  • Self-Organization and Emergent Order — Developmental Pattern Formation
Questions & Objections
  • Can Self-Organization Produce Order Without Design? — Developmental Patterning

Purvis and Lahav — Cellular Information through Signaling Dynamics

Author: Jeremy E. Purvis; Galit Lahav
Encoding and Decoding Cellular Information through Signaling Dynamics • Cell • 2013
Scientific Review Neutral
DOI: 10.1016/j.cell.2013.02.005
Used in this investigation
Evidence
  • Biological Information Processing — Signaling Dynamics

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
  • Trade-Offs, Constraints, and Failure Modes — Evolutionary Constraints
Explanations
  • Evolution by Natural Selection — Selection And Constraint
  • Constraint, Inheritance, and Historical Development — Evolutionary Constraint
Questions & Objections
  • Does Convergent Evolution Explain Repeated Biological Solutions? — Convergent Evolution

Stelling et al. — Robustness of Cellular Functions

Author: Jörg Stelling; Uwe Sauer; Zoltan Szallasi; Francis J. Doyle III; John C. Doyle
Robustness of Cellular Functions • Cell • 2004
Scientific Review Neutral
DOI: 10.1016/j.cell.2004.09.008
Used in this investigation
Evidence
  • Robustness Under Perturbation — Cellular Robustness

Walpole et al. — Multiscale Computational Models

Author: Joseph Walpole; Jason A. Papin; Shayn M. Peirce
Multiscale Computational Models of Complex Biological Systems • Annual Review of Biomedical Engineering • 2013
Scientific Review Neutral
DOI: 10.1146/annurev-bioeng-071811-150104
Used in this investigation
Evidence
  • Hierarchical Organization and Control — Multiscale Integration

Schaffer and Ideker — Multiscale Structure of Biological Systems

Author: Leah V. Schaffer; Trey Ideker
Mapping the Multiscale Structure of Biological Systems • Cell Systems • 2021
Scientific Review Neutral
DOI: 10.1016/j.cels.2021.05.012
Used in this investigation
Evidence
  • Hierarchical Organization and Control — Multiscale Hierarchy

Hartwell et al. — From Molecular to Modular Cell Biology

Author: Leland H. Hartwell; John J. Hopfield; Stanislas Leibler; Andrew W. Murray
From Molecular to Modular Cell Biology • Nature • 1999
Scientific Review Neutral
DOI: 10.1038/35011540
Used in this investigation
Evidence
  • Modularity in Biological Systems — Biological Modularity

Csete and Doyle — Reverse Engineering of Biological Complexity

Author: Marie E. Csete; John C. Doyle
Reverse Engineering of Biological Complexity • Science • 2002
Scientific Review Neutral
DOI: 10.1126/science.1069981
Used in this investigation
Explanations
  • Engineering Principles as Convergent Solutions — Systems Level Convergence
Questions & Objections
  • Are Engineering Comparisons Only Analogies? — Systems Comparison
  • Does Convergent Evolution Explain Repeated Biological Solutions? — Systems Convergence
  • Do Imperfect and Fragile Biological Systems Count Against Design? — Complexity And Failure
  • Are We Seeing Design Because We Already Expect It? — Naturalistic Systems Explanation

Félix and Wagner — Robustness and Evolution

Author: Marie-Anne Félix; Andreas Wagner
Robustness and Evolution: Concepts, Insights and Challenges from a Developmental Model System • Heredity • 2008
Scientific Review Neutral
DOI: 10.1038/sj.hdy.6800915
Used in this investigation
Evidence
  • Robustness Under Perturbation — Evolutionary Robustness

Nowak et al. — Evolution of Genetic Redundancy

Author: Martin A. Nowak; Maarten C. Boerlijst; Jonathan Cooke; John Maynard Smith
Evolution of Genetic Redundancy • Nature • 1997
Scientific Research Neutral
DOI: 10.1038/40618
Used in this investigation
Evidence
  • Redundancy and Backup Systems — Genetic Redundancy

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
Explanations
  • Purposeful Design — Irreducible Complexity

Tenazinha and Vinga — Integrated Biological Networks

Author: Nuno Tenazinha; Susana Vinga
A Survey on Methods for Modeling and Analyzing Integrated Biological Networks • IEEE/ACM Transactions on Computational Biology and Bioinformatics • 2011
Scientific Review Neutral
DOI: 10.1109/TCBB.2010.117
Used in this investigation
Evidence
  • Integration of Multiple Regulatory Networks — Integrated Biological Networks

Somvanshi et al. — Integral Feedback Control in Biological Systems

Author: Pramod R. Somvanshi; Anilkumar K. Patel; Sharad Bhartiya; K. V. Venkatesh
Implementation of Integral Feedback Control in Biological Systems • WIREs Systems Biology and Medicine • 2015
Scientific Review Neutral
DOI: 10.1002/wsbm.1307
Used in this investigation
Evidence
  • Feedback Control in Living Systems — Negative Feedback

Kafri et al. — Responsive Backup Circuits

Author: Ran Kafri; Melissa Levy; Yitzhak Pilpel
The Regulatory Utilization of Genetic Redundancy through Responsive Backup Circuits • Proceedings of the National Academy of Sciences • 2006
Scientific Research Neutral
DOI: 10.1073/pnas.0604883103
Used in this investigation
Evidence
  • Redundancy and Backup Systems — Responsive Backup

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
  • Do Engineering-Like Patterns Indicate Design? — Design Inference
Explanations
  • Purposeful Design — Specified Information

Kunkel and Erie — DNA Mismatch Repair

Author: Thomas A. Kunkel; Dorothy A. Erie
DNA Mismatch Repair • Annual Review of Biochemistry • 2005
Scientific Review Neutral
DOI: 10.1146/annurev.biochem.74.082803.133243
Used in this investigation
Evidence
  • Error Detection and Correction — Mismatch Repair

Kunkel and Bebenek — DNA Replication Fidelity

Author: Thomas A. Kunkel; Katarzyna Bebenek
DNA Replication Fidelity • Annual Review of Biochemistry • 2000
Scientific Review Neutral
DOI: 10.1146/annurev.biochem.69.1.497
Used in this investigation
Evidence
  • Error Detection and Correction — Replication Fidelity

Alon — Network Motifs

Author: Uri Alon
Network Motifs: Theory and Experimental Approaches • Nature Reviews Genetics • 2007
Scientific Review Neutral
DOI: 10.1038/nrg2102
Used in this investigation
Evidence
  • Modularity in Biological Systems — Network Motifs

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
Explanations
  • Constraint, Inheritance, and Historical Development — Historical Contingency
 Sources are gathered from the evidence, explanations, and objections linked to this investigation and are shown once per source.