IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v15y2024i1d10.1038_s41467-024-48000-1.html
   My bibliography  Save this article

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
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-024-48000-1
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-024-48000-1?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. 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.
    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. "Publisher Correction: Evolution of a minimal cell," Nature, Nature, vol. 620(7973), pages 18-18, August.
    3. 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.
    4. Ilkka Hanski, 1998. "Metapopulation dynamics," Nature, Nature, vol. 396(6706), pages 41-49, November.
    5. 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.
    6. 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.
    7. 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.
    8. Michael B. Elowitz & Stanislas Leibler, 2000. "A synthetic oscillatory network of transcriptional regulators," Nature, Nature, vol. 403(6767), pages 335-338, January.
    9. 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.
    10. 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.
    11. 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.
    12. 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.
    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. 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.
    16. C. Brandon Ogbunugafor, 2023. "Mutations that enhance evolvability may open doors to faster adaptation," Nature Communications, Nature, vol. 14(1), pages 1-3, December.
    17. 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.
    18. 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.
    19. 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.
    20. Attila Becskei & Luis Serrano, 2000. "Engineering stability in gene networks by autoregulation," Nature, Nature, vol. 405(6786), pages 590-593, June.
    21. 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.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Avraham E Mayo & Yaakov Setty & Seagull Shavit & Alon Zaslaver & Uri Alon, 2006. "Plasticity of the cis-Regulatory Input Function of a Gene," PLOS Biology, Public Library of Science, vol. 4(4), pages 1-1, March.
    2. Chen Jia & Ramon Grima, 2024. "Holimap: an accurate and efficient method for solving stochastic gene network dynamics," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    3. T. Ochiai & J. C. Nacher, 2007. "Stochastic analysis of autoregulatory gene expression dynamics," Mathematical and Computer Modelling of Dynamical Systems, Taylor & Francis Journals, vol. 14(4), pages 377-388, November.
    4. Tobias May & Lee Eccleston & Sabrina Herrmann & Hansjörg Hauser & Jorge Goncalves & Dagmar Wirth, 2008. "Bimodal and Hysteretic Expression in Mammalian Cells from a Synthetic Gene Circuit," PLOS ONE, Public Library of Science, vol. 3(6), pages 1-7, June.
    5. Alex J. H. Fedorec & Neythen J. Treloar & Ke Yan Wen & Linda Dekker & Qing Hsuan Ong & Gabija Jurkeviciute & Enbo Lyu & Jack W. Rutter & Kathleen J. Y. Zhang & Luca Rosa & Alexey Zaikin & Chris P. Bar, 2024. "Emergent digital bio-computation through spatial diffusion and engineered bacteria," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    6. Zhou, Peipei & Cai, Shuiming & Liu, Zengrong & Chen, Luonan & Wang, Ruiqi, 2013. "Coupling switches and oscillators as a means to shape cellular signals in biomolecular systems," Chaos, Solitons & Fractals, Elsevier, vol. 50(C), pages 115-126.
    7. Duncan Ingram & Guy-Bart Stan, 2023. "Modelling genetic stability in engineered cell populations," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    8. Stefano Ciliberti & Olivier C Martin & Andreas Wagner, 2007. "Robustness Can Evolve Gradually in Complex Regulatory Gene Networks with Varying Topology," PLOS Computational Biology, Public Library of Science, vol. 3(2), pages 1-10, February.
    9. Andras Gyorgy, 2023. "Competition and evolutionary selection among core regulatory motifs in gene expression control," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    10. Weiyue Ji & Handuo Shi & Haoqian Zhang & Rui Sun & Jingyi Xi & Dingqiao Wen & Jingchen Feng & Yiwei Chen & Xiao Qin & Yanrong Ma & Wenhan Luo & Linna Deng & Hanchi Lin & Ruofan Yu & Qi Ouyang, 2013. "A Formalized Design Process for Bacterial Consortia That Perform Logic Computing," PLOS ONE, Public Library of Science, vol. 8(2), pages 1-9, February.
    11. Thomas B. Kepler & Timothy C. Elston, 2001. "Stochasticity in Transcriptional Regulation: Origins, Consequences and Mathematical Representations," Working Papers 01-06-033, Santa Fe Institute.
    12. Luis Mier-y-Terán-Romero & Mary Silber & Vassily Hatzimanikatis, 2010. "The Origins of Time-Delay in Template Biopolymerization Processes," PLOS Computational Biology, Public Library of Science, vol. 6(4), pages 1-15, April.
    13. Ashty S. Karim & Dylan M. Brown & Chloé M. Archuleta & Sharisse Grannan & Ludmilla Aristilde & Yogesh Goyal & Josh N. Leonard & Niall M. Mangan & Arthur Prindle & Gabriel J. Rocklin & Keith J. Tyo & L, 2024. "Deconstructing synthetic biology across scales: a conceptual approach for training synthetic biologists," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    14. Mario A Marchisio & Jörg Stelling, 2011. "Automatic Design of Digital Synthetic Gene Circuits," PLOS Computational Biology, Public Library of Science, vol. 7(2), pages 1-13, February.
    15. Tai-Yin Chiu & Hui-Ju K Chiang & Ruei-Yang Huang & Jie-Hong R Jiang & François Fages, 2015. "Synthesizing Configurable Biochemical Implementation of Linear Systems from Their Transfer Function Specifications," PLOS ONE, Public Library of Science, vol. 10(9), pages 1-27, September.
    16. Liu, Xian & Wang, Jinzhi & Huang, Lin, 2007. "Global synchronization for a class of dynamical complex networks," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 386(1), pages 543-556.
    17. Evgeni V Nikolaev & Eduardo D Sontag, 2016. "Quorum-Sensing Synchronization of Synthetic Toggle Switches: A Design Based on Monotone Dynamical Systems Theory," PLOS Computational Biology, Public Library of Science, vol. 12(4), pages 1-33, April.
    18. Zomorrodi, Ali R. & Maranas, Costas D., 2014. "Coarse-grained optimization-driven design and piecewise linear modeling of synthetic genetic circuits," European Journal of Operational Research, Elsevier, vol. 237(2), pages 665-676.
    19. Keun-Young Kim & Jin Wang, 2007. "Potential Energy Landscape and Robustness of a Gene Regulatory Network: Toggle Switch," PLOS Computational Biology, Public Library of Science, vol. 3(3), pages 1-13, March.
    20. Liu, Xian & Wang, Jinzhi & Huang, Lin, 2007. "Stabilization of a class of dynamical complex networks based on decentralized control," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 383(2), pages 733-744.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-48000-1. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.