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Engineering is evolution: a perspective on design processes to engineer biology

Author

Listed:
  • Simeon D. Castle

    (24 Tyndall Avenue)

  • Michiel Stock

    (Ghent University)

  • Thomas E. Gorochowski

    (24 Tyndall Avenue
    Cantock’s Close)

Abstract

Careful consideration of how we approach design is crucial to all areas of biotechnology. However, choosing or developing an effective design methodology is not always easy as biology, unlike most areas of engineering, is able to adapt and evolve. Here, we put forward that design and evolution follow a similar cyclic process and therefore all design methods, including traditional design, directed evolution, and even random trial and error, exist within an evolutionary design spectrum. This contrasts with conventional views that often place these methods at odds and provides a valuable framework for unifying engineering approaches for challenging biological design problems.

Suggested Citation

  • Simeon D. Castle & Michiel Stock & Thomas E. Gorochowski, 2024. "Engineering is evolution: a perspective on design processes to engineer biology," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-48000-1
    DOI: 10.1038/s41467-024-48000-1
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    References listed on IDEAS

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    1. Ilkka Hanski, 1998. "Metapopulation dynamics," Nature, Nature, vol. 396(6706), pages 41-49, November.
    2. R. Z. Moger-Reischer & J. I. Glass & K. S. Wise & L. Sun & D. M. C. Bittencourt & B. K. Lehmkuhl & D. R. Schoolmaster & M. Lynch & J. T. Lennon, 2023. "Evolution of a minimal cell," Nature, Nature, vol. 620(7972), pages 122-127, August.
    3. Niels Klitgord & Daniel Segrè, 2010. "Environments that Induce Synthetic Microbial Ecosystems," PLOS Computational Biology, Public Library of Science, vol. 6(11), pages 1-17, November.
    4. Jeffrey E. Barrick & Dong Su Yu & Sung Ho Yoon & Haeyoung Jeong & Tae Kwang Oh & Dominique Schneider & Richard E. Lenski & Jihyun F. Kim, 2009. "Genome evolution and adaptation in a long-term experiment with Escherichia coli," Nature, Nature, vol. 461(7268), pages 1243-1247, October.
    5. Attila Becskei & Luis Serrano, 2000. "Engineering stability in gene networks by autoregulation," Nature, Nature, vol. 405(6786), pages 590-593, June.
    6. C. Brandon Ogbunugafor, 2023. "Mutations that enhance evolvability may open doors to faster adaptation," Nature Communications, Nature, vol. 14(1), pages 1-3, December.
    7. Behzad D. Karkaria & Alex J. H. Fedorec & Chris P. Barnes, 2021. "Automated design of synthetic microbial communities," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    8. Simeon D. Castle & Claire S. Grierson & Thomas E. Gorochowski, 2021. "Towards an engineering theory of evolution," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    9. R. Z. Moger-Reischer & J. I. Glass & K. S. Wise & L. Sun & D. M. C. Bittencourt & B. K. Lehmkuhl & D. R. Schoolmaster & M. Lynch & J. T. Lennon, 2023. "Publisher Correction: Evolution of a minimal cell," Nature, Nature, vol. 620(7973), pages 18-18, August.
    10. Joseph L. Watson & David Juergens & Nathaniel R. Bennett & Brian L. Trippe & Jason Yim & Helen E. Eisenach & Woody Ahern & Andrew J. Borst & Robert J. Ragotte & Lukas F. Milles & Basile I. M. Wicky & , 2023. "De novo design of protein structure and function with RFdiffusion," Nature, Nature, vol. 620(7976), pages 1089-1100, August.
    11. Joshua Rees-Garbutt & Oliver Chalkley & Sophie Landon & Oliver Purcell & Lucia Marucci & Claire Grierson, 2020. "Designing minimal genomes using whole-cell models," Nature Communications, Nature, vol. 11(1), pages 1-12, December.
    12. Joshua Rees-Garbutt & Oliver Chalkley & Sophie Landon & Oliver Purcell & Lucia Marucci & Claire Grierson, 2020. "Author Correction: Designing minimal genomes using whole-cell models," Nature Communications, Nature, vol. 11(1), pages 1-1, December.
    13. Drew Endy, 2005. "Foundations for engineering biology," Nature, Nature, vol. 438(7067), pages 449-453, November.
    14. Avihu H. Yona & Eric J. Alm & Jeff Gore, 2018. "Random sequences rapidly evolve into de novo promoters," Nature Communications, Nature, vol. 9(1), pages 1-10, December.
    15. Kevin M. Esvelt & Jacob C. Carlson & David R. Liu, 2011. "A system for the continuous directed evolution of biomolecules," Nature, Nature, vol. 472(7344), pages 499-503, April.
    16. Leland H. Hartwell & John J. Hopfield & Stanislas Leibler & Andrew W. Murray, 1999. "From molecular to modular cell biology," Nature, Nature, vol. 402(6761), pages 47-52, December.
    17. Ross D. Jones & Yili Qian & Velia Siciliano & Breanna DiAndreth & Jin Huh & Ron Weiss & Domitilla Del Vecchio, 2020. "An endoribonuclease-based feedforward controller for decoupling resource-limited genetic modules in mammalian cells," Nature Communications, Nature, vol. 11(1), pages 1-16, December.
    18. Michael B. Elowitz & Stanislas Leibler, 2000. "A synthetic oscillatory network of transcriptional regulators," Nature, Nature, vol. 403(6767), pages 335-338, January.
    19. Matthew J. Tarnowski & Thomas E. Gorochowski, 2022. "Massively parallel characterization of engineered transcript isoforms using direct RNA sequencing," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    20. Carolyn N. Bayer & Maja Rennig & Anja K. Ehrmann & Morten H. H. Nørholm, 2021. "A standardized genome architecture for bacterial synthetic biology (SEGA)," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
    21. Timothy S. Gardner & Charles R. Cantor & James J. Collins, 2000. "Construction of a genetic toggle switch in Escherichia coli," Nature, Nature, vol. 403(6767), pages 339-342, January.
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