Evolution



Biological adaptation by mutation, natural selection and random diffusion.

Analogies and disanalogies between tooth-and-claw natural selection, and our statistical learning methods. Stochastic process models of gene and population dynamics.

See also geometry of fitness landscapes, cooperation.

I would like to better understand:

Jon Carlos Baez, Fisher’s fundamental theorem is an interesting dissection of SDEs and evolution.

Ruben Bolling, How to draw Doug

Connection with mathematical optimisation

Nisheeth Vishnoi, Nature, Dynamical Systems and Optimization:

The language of dynamical systems is the preferred choice of scientists to model a wide variety of phenomena in nature. The reason is that, often, it is easy to locally observe or understand what happens to a system in one time-step. Could we then piece this local information together to make deductions about the global behavior of these dynamical systems? The hope is to understand some of nature’s algorithms and, in this quest, unveil new algorithmic techniques. In this first of a series of posts, we give a gentle introduction to dynamical systems and explain what it means to view them from the point of view of optimization.

Nisheeth Vishnoi, Markov Chains Through the Lens of Dynamical Systems: The Case of Evolution:

In this post, we will see the main technical ideas in the analysis of the mixing time of evolutionary Markov chains introduced in a previous post. We start by introducing the notion of the expected motion of a stochastic process or a Markov chain. In the case of a finite population evolutionary Markov chain, the expected motion turns out to be a dynamical system which corresponds to the infinite population evolutionary dynamics with the same parameters. Surprisingly, we show that the limit sets of this dynamical system govern the mixing time of the Markov chain. In particular, if the underlying dynamical system has a unique stable fixed point (as in asexual evolution), then the mixing is fast and in the case of multiple stable fixed points (as in sexual evolution), the mixing is slow. Our viewpoint connects evolutionary Markov chains, nature’s algorithms, with stochastic descent methods, popular in machine learning and optimization, and the readers interested in the latter might benefit from our techniques.

Evolution of cooperation

See evolution of cooperation.

Directed evolution

Not that great as an algorithm in silico, but amazing in actual chemistry and biology: What is directed evolution and why did it win the chemistry Nobel prize?

Packer and Liu (2015);Wang et al. (2021);Wu et al. (2019)

Extended Evolutionary Synthesis

The extended evolutionary synthesis (EES) is new a way to think about and understand evolutionary phenomena that differs from the conception that has dominated evolutionary thinking since the 1930s (i.e., the modern synthesis). The EES does not replace traditional thinking, but rather can be deployed alongside it to stimulate research in evolutionary biology.

The extended evolutionary synthesis emphasizes two key unifying concepts that feature in progressive readings of some sections of the evolutionary biology literature — constructive development and reciprocal causation

Perhaps this is where the memes went?

Chickens and group selection

TODO: find a deeper explanation than Chickens and Group Selection (Hester et al. 1996; Muir 1996).

Genetic programming

See genetic programming.

To read

References

Acevedo, Miguel A., Forrest P. Dillemuth, Andrew J. Flick, Matthew J. Faldyn, and Bret D. Elderd. 2019. Virulence-Driven Trade-Offs in Disease Transmission: A Meta-Analysis*.” Evolution 73 (4): 636–47.
Aldous, David J. 1999. Deterministic and Stochastic Models for Coalescence (Aggregation and Coagulation): A Review of the Mean-Field Theory for Probabilists.” Bernoulli 5 (1): 3–48.
Altenberg, Lee. 2012. Resolvent Positive Linear Operators Exhibit the Reduction Phenomenon.” Proceedings of the National Academy of Sciences 109 (10): 3705–10.
———. 2013. Implications of the Reduction Principle for Cosmological Natural Selection.” arXiv:1302.1293 [Gr-Qc, q-Bio], February.
Altenberg, Lee, and Marcus W. Feldman. 1987. Selection, Generalized Transmission and the Evolution of Modifier Genes. I. The Reduction Principle.” Genetics 117 (3): 559–72.
Axelrod, Robert, and William D. Hamilton. 1981. The Evolution of Cooperation.” Science, New Series, 211 (4489): 1390–96.
Baez, John C. 2011. Renyi Entropy and Free Energy,” February.
Bar-Yam, Yaneer. 1999. Formalizing the Gene Centered View of Evolution.” Advances in Complex Systems 2: 277.
Beerenwinkel, Niko, Lior Pachter, Bernd Sturmfels, Santiago Elena, and Richard E Lenski. 2007. Analysis of Epistatic Interactions and Fitness Landscapes Using a New Geometric Approach.” BMC Evolutionary Biology 7 (1): 60.
Beinhocker, Eric D. 2007. Origin of Wealth: Evolution, Complexity, and the Radical Remaking of Economics. Harvard Business Press.
Beinhocker, Eric D. 2011. Evolution as Computation: Integrating Self-Organization with Generalized Darwinism.” Journal of Institutional Economics 7 (Special Issue 03): 393–423.
Bergman, Aviv, and Marcus W. Feldman. 1992. Recombination Dynamics and the Fitness Landscape.” Physica D: Nonlinear Phenomena 56 (1): 57–67.
Bowles, Samuel. 2001. Individual Interactions, Group Conflicts, and the Evolution of Preferences.” Social Dynamics 155: 190.
———. 2004. Microeconomics: Behavior, Institutions, and Evolution. Princeton University Press.
Bowles, Samuel, and Herbert Gintis. 2004. The Evolution of Strong Reciprocity: Cooperation in Heterogeneous Populations.” Theoretical Population Biology 65 (1): 17–28.
Boyd, Robert, and Peter J Richerson. 1988. Culture and the Evolutionary Process. Chicago: University of Chicago Press.
———. 1999. “Complex Societies: The Evolutionary Origins of a Crude Superorganism.” Human Nature 10: 253.
Boyd, Robert, and Peter J. Richerson. 1990. Group Selection Among Alternative Evolutionarily Stable Strategies.” Journal of Theoretical Biology 145 (3): 331–42.
———. 1992. Punishment Allows the Evolution of Cooperation (or Anything Else) in Sizable Groups.” Ethology and Sociobiology 13 (3): 171–95.
Ehrlich, Paul R, and Simon A Levin. 2005. “The Evolution of Norms.” PloS Biology 3: –194.
Feldman, M. W., and U. Liberman. 1986. An Evolutionary Reduction Principle for Genetic Modifiers.” Proceedings of the National Academy of Sciences 83 (13): 4824–27.
Fitch, W. Tecumseh. 2006. The Biology and Evolution of Music: A Comparative Perspective.” Cognition 100 (1): 173–215.
Gottlieb, Anthony. n.d. It Ain’t Necessarily So.” The New Yorker.
Gould, S J, and N Eldredge. 1977. Punctuated Equilibria: The Tempo and Mode of Evolution Reconsidered.” Paleobiology 3 (2): 115–51.
Gould, S. J., R. C. Lewontin, J. Maynard Smith, and Robin Holliday. 1979. The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme.” Proceedings of the Royal Society of London. Series B. Biological Sciences 205 (1161): 581–98.
Harper, Marc. 2009. The Replicator Equation as an Inference Dynamic,” November.
Hasson, Uri, Samuel A. Nastase, and Ariel Goldstein. 2020. Direct Fit to Nature: An Evolutionary Perspective on Biological and Artificial Neural Networks.” Neuron 105 (3): 416–34.
Hester, Patricia Y., W.M. Muir, J.V. Craig, and J.L. Albright. 1996. Group Selection for Adaptation to Multiple-Hen Cages: Production Traits During Heat and Cold Exposures , Poultry Science 75 (11): 1308–14.
Hetzer, Moritz, and Didier Sornette. 2013a. The Co-Evolution of Fairness Preferences and Costly Punishment.” PLoS ONE 8 (3): e54308.
———. 2013b. An Evolutionary Model of Cooperation, Fairness and Altruistic Punishment in Public Good Games.” PLoS ONE 8 (11): e77041.
Hofbauer, Josef, and Karl Sigmund. 2003. Evolutionary Game Dynamics.” Bulletin of the American Mathematical Society 40 (4): 479–519.
Hug, Laura A., Brett J. Baker, Karthik Anantharaman, Christopher T. Brown, Alexander J. Probst, Cindy J. Castelle, Cristina N. Butterfield, et al. 2016. A new view of the tree of life.” Nature Microbiology 1 (April): 16048.
Judson, Olivia P. 2017. The Energy Expansions of Evolution.” Nature Ecology & Evolution 1 (April): 0138.
Kauffman, Stuart A. 1993. The Origins of Order: Self-Organization and Selection in Evolution. Oxford University Press.
Kauffman, Stuart A, and Sonke Johnsen. 1991. Coevolution to the Edge of Chaos: Coupled Fitness Landscapes, Poised States, and Coevolutionary Avalanches*.” Journal of Theoretical Biology 149: 467–505.
Kaznatcheev, Artem. 2020. Evolution Is Exponentially More Powerful with Frequency-Dependent Selection.” bioRxiv, May, 2020.05.03.075069.
Kirby, Simon. 1998. Learning, Bottlenecks and the Evolution of Recursive Syntax.” In.
Le, Stephen, and Robert Boyd. 2007. “Evolutionary Dynamics of the Continuous Iterated Prisoner’s Dilemma.” Journal of Theoretical Biology 245: 258–67.
Lenski, Richard E, Charles Ofria, Robert T Pennock, Christoph Adami, Richard E Lenski, Charles Ofria, Robert T Pennock, and Christoph Adami. 2003. The Evolutionary Origin of Complex Features.” Nature 423 (6936): 139.
Liberman, Uri, and Marcus W. Feldman. 1986. Modifiers of Mutation Rate: A General Reduction Principle.” Theoretical Population Biology 30 (1): 125–42.
McAvoy, Alex. 2015. Stochastic Selection Processes.” arXiv:1511.05390 [q-Bio], November.
McGee, Ryan Seamus, Olivia Kosterlitz, Artem Kaznatcheev, Benjamin Kerr, and Carl T. Bergstrom. 2022. The Cost of Information Acquisition by Natural Selection.” bioRxiv.
Mühlenbein, H, and T Mahnig. 2003. “Evolutionary Algorithms and the Boltzmann Distribution.” Foundations of Genetic Algorithms 7: 525–56.
Muir, W. M. 1996. Group selection for adaptation to multiple-hen cages: selection program and direct responses.” Poultry Science 75 (4): 447–58.
Nowak, Martin A, and DAvid C Krakauer. 1999. “The Evolution of Language.” Proceedings of the National Academy of Sciences of the United States of America 96 (14): 8028.
Nowak, Martin A, Corina E Tarnita, and Edward O Wilson. 2010. “The Evolution of Eusociality.” Nature 466: 1057–62.
Østman, Bjørn, Arend Hintze, and Christoph Adami. 2012. Impact of Epistasis and Pleiotropy on Evolutionary Adaptation.” Proceedings of the Royal Society of London. Series B: Biological Sciences 279 (1727): 247–56.
Packer, Michael S., and David R. Liu. 2015. Methods for the Directed Evolution of Proteins.” Nature Reviews Genetics 16 (7): 379–94.
Plotkin, Joshua B, and Martin A Nowak. 2000. Language Evolution and Information Theory.” Journal of Theoretical Biology 205: 147–59.
Richerson, Peter J, Robert T Boyd, and Joseph Henrich. 2003. “Cultural Evolution of Human Cooperation.” Genetic and Cultural Evolution of Cooperation, 357.
Riolo, Rick L, Michael D Cohen, and Robert Axelrod. 2001. Evolution of Cooperation Without Reciprocity.” Nature 414 (6862): 441.
Schmidt, Michael D, and Hod Lipson. 2008. Coevolution of Fitness Predictors.” IEEE Transactions on Evolutionary Computation 12: 736–49.
Schuster, Peter. 2010. Mathematical Modeling of Evolution. Solved and Open Problems.” Theory in Biosciences, 1–19.
Sciences, National Academy of. 2020. Correction for Wu Et Al., Machine Learning-Assisted Directed Protein Evolution with Combinatorial Libraries.” Proceedings of the National Academy of Sciences 117 (1): 788–89.
Sethi, Rajiv, and Somanathan. 1996. The Evolution of Social Norms in Common Property Resource Use.” The American Economic Review 86: 766–88.
Shalizi, Cosma Rohilla. 2009. Dynamics of Bayesian Updating with Dependent Data and Misspecified Models.” Electronic Journal of Statistics 3: 1039–74.
Sinervo, B., and C. M. Lively. 1996. The Rock–Paper–Scissors Game and the Evolution of Alternative Male Strategies.” Nature 380 (6571): 240.
Skinner, B F. 1986. “The Evolution of Verbal Behavior.” J Exp Anal Behav 45: 115–22.
Smith, John Maynard. 1980. “The Theory of Games and the Evolution of Animal Conflicts.” Journal of Theoretical Biology 47: 209–21.
Smith, Subrena E. 2020. Is Evolutionary Psychology Possible? Biological Theory 15 (1): 39–49.
Solé, Ricard V, Bernat Corominas-Murtra, Sergi Valverde, and Luc Steels. 2010. Language Networks: Their Structure, Function, and Evolution.” Complexity 15: 20–26.
Solé, Ricard V, José M Montoya, and Douglas H Erwin. 2002. Recovery After Mass Extinction: Evolutionary Assembly in Large-Scale Biosphere Dynamics.” Philosophical Transactions of the Royal Society B: Biological Sciences 357: 697–707.
Solé, Ricard V., Sergi Valverde, Marti Rosas Casals, Stuart A. Kauffman, Doyne Farmer, and Niles Eldredge. 2013. The Evolutionary Ecology of Technological Innovations.” Complexity 18 (4): 15–27.
Stadler, Bärbel M R, and Peter F Stadler. 2004. “The Topology of Evolutionary Biology.” In Modeling in Molecular Biology, edited by G Ciobanu and Grzegorz Rozenberg, 267–86. Springer Verlag.
Stadler, Bärbel M R, Peter F Stadler, Günter P Wagner, and Walter Fontana. 2001. The Topology of the Possible: Formal Spaces Underlying Patterns of Evolutionary Change.” Journal of Theoretical Biology 213 (2): 241–74.
Stadler, Peter F. 2002. “Fitness Landscapes.” In Biological Evolution and Statistical Physics, 187–207. Springer Verlag.
Tamariz, Monica, T. Mark Ellison, Dale J. Barr, and Nicolas Fay. 2014. Cultural Selection Drives the Evolution of Human Communication Systems.” Proceedings of the Royal Society B: Biological Sciences 281 (1788): 20140488.
Tsoukas, Haridimos. 1993. Organizations as Soap Bubbles: An Evolutionary Perspective on Organization Design.” Systemic Practice and Action Research V6: 501–15.
Vanchurin, Vitaly, Yuri I. Wolf, Mikhail Katsnelson, and Eugene V. Koonin. 2021. Towards a Theory of Evolution as Multilevel Learning.” Cold Spring Harbor Laboratory.
Wagner, Andreas. 2003. Risk Management in Biological Evolution.” Journal of Theoretical Biology 225: 45–57.
Wagner, Günter P, and Lee Altenberg. 1996. “Complex Adaptations and the Evolution of Evolvability.” Evolution.
Wang, Yajie, Pu Xue, Mingfeng Cao, Tianhao Yu, Stephan T. Lane, and Huimin Zhao. 2021. Directed Evolution: Methodologies and Applications.” Chemical Reviews 121 (20): 12384–444.
Wilke, Claus O, Christopher Ronnewinkel, and Thomas Martinetz. 2001. Dynamic Fitness Landscapes in Molecular Evolution.” Physics Reports 349 (5): 395–446.
Wolpert, David H, and William G Macready. 2005. Coevolutionary Free Lunches.” IEEE Transactions on Evolutionary Computation 9 (6): 721–35.
Wu, Zachary, S. B. Jennifer Kan, Russell D. Lewis, Bruce J. Wittmann, and Frances H. Arnold. 2019. Machine Learning-Assisted Directed Protein Evolution with Combinatorial Libraries.” Proceedings of the National Academy of Sciences 116 (18): 8852–58.
Yule, G. Udny. 1925. A Mathematical Theory of Evolution, Based on the Conclusions of Dr. J. C. Willis, F.R.S. Philosophical Transactions of the Royal Society of London. Series B, Containing Papers of a Biological Character 213 (402-410): 21–87.
Zhaxybayeva, Olga, and J. Peter Gogarten. 2004. Cladogenesis, coalescence and the evolution of the three domains of life.” Trends in genetics: TIG 20 (4): 182–87.

No comments yet. Why not leave one?

GitHub-flavored Markdown & a sane subset of HTML is supported.