Mathematical biology

@book{eden1967inadequacies2,
    author = "Eden, M",
    title = "Inadequacies of neo-Darwinian evolution as a scientific theory, in Moorehead, P. S., and Kaplan, M. M., eds., Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution",
    year = "1967",
    publisher = "Philadelphia, Pa., Wistar Institute Press, p. 5-19",
    note = "talkorigins\_source = {true}; raw\_reference = {Eden, M., 1967, Inadequacies of neo-Darwinian evolution as a scientific theory, in Moorehead, P. S., and Kaplan, M. M., eds., Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution: Philadelphia, Pa., Wistar Institute Press, p. 5-19.}"
}

@techreport{wright1967comments4,
    author = "Wright, S",
    title = "Comments on the Preliminary Working Papers of Eden and Waddington, in Moorehead, P. S., and Kaplan, M. M., eds., Mathematical Challenges to the Neo-Darwinian Theory of Evolution, 5 of Wistar Institute Symposium",
    year = "1967",
    howpublished = "Philadelphia, Wistar Institute, p. 117-120",
    note = "talkorigins\_source = {true}; raw\_reference = {Wright, S., 1967, Comments on the Preliminary Working Papers of Eden and Waddington, in Moorehead, P. S., and Kaplan, M. M., eds., Mathematical Challenges to the Neo-Darwinian Theory of Evolution, 5 of Wistar Institute Symposium: Philadelphia, Wistar Institute, p. 117-120.}"
}

@article{gale1968mathematical,
    author = "GALE, J",
    title = "Mathematical challenges to the Neo-Darwinian interpretation of evolution Edited by P. S. Moorhead and M. M. Kaplan. Pp xi + 140. The Wistar Institute Press, Philadelphia. 1967. $5",
    year = "1968",
    journal = "Endeavour",
    url = "https://doi.org/10.1016/0160-9327(68)90113-0",
    doi = "10.1016/0160-9327(68)90113-0",
    number = "101",
    openalex = "W1965607512",
    pages = "103",
    volume = "27"
}

@article{hamilton1969review,
    author = "Hamilton, John M.",
    title = "Review: Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution, by Paul S. Moorhead and Martin M. Kaplan",
    year = "1969",
    journal = "The American Biology Teacher",
    url = "https://doi.org/10.2307/4442469",
    doi = "10.2307/4442469",
    number = "3",
    pages = "186-187",
    volume = "31"
}

@techreport{easton1973a1,
    author = "Easton, T. A",
    title = "A note on the mathematics of microsphere division",
    year = "1973",
    howpublished = "Bulletin of Mathematical Biology, v. 35, p. 259-262",
    note = "talkorigins\_source = {true}; raw\_reference = {Easton, T. A., 1973, A note on the mathematics of microsphere division: Bulletin of Mathematical Biology, v. 35, p. 259-262.}"
}

@misc{spotila1973a3,
    author = "Spotila, J. R. et al",
    title = "A mathematical model for body temperatures of large reptiles",
    year = "1973",
    howpublished = "Implications for dinosaur ecology: American Naturalist, v. 107, p. 391-404",
    note = "talkorigins\_source = {true}; raw\_reference = {Spotila, J. R. et al., 1973, A mathematical model for body temperatures of large reptiles: Implications for dinosaur ecology: American Naturalist, v. 107, p. 391-404.}"
}

@incollection{kostitzin1978mathematical,
    author = "Kostitzin, V. A.",
    title = "Mathematical Biology: Chapter 15 Evolution",
    year = "1978",
    booktitle = "Lecture Notes in Biomathematics",
    url = "https://doi.org/10.1007/978-3-642-50151-7\_18",
    doi = "10.1007/978-3-642-50151-7\_18",
    openalex = "W987053169",
    pages = "413-423"
}

@incollection{rechenberg1984the,
    author = "Rechenberg, Ingo",
    title = "The Evolution Strategy. A Mathematical Model of Darwinian Evolution",
    year = "1984",
    booktitle = "Springer Series in Synergetics",
    url = "https://doi.org/10.1007/978-3-642-69540-7\_13",
    doi = "10.1007/978-3-642-69540-7\_13",
    openalex = "W23797105",
    pages = "122-132",
    references = "doi101002fedr4910860506, doi1010160378475482901173, doi1023072581158, openalexw1514875444"
}

Abstract This annual series gets off to a shaky start. Three of the articles promised in the pre‐publication leaflet miss Volume 1, and there is no editorial or introduction whatever. Despite the distinguished editors, two of eight papers have the wrong titles on the contents page; figure lay‐out is poor, (e.g. p. 44); the six figures on p. 53 have one unbroken caption running for 20 lines on two pages, and are referred to in the text in reverse order; the index is inadequate, e.g. “Natural selection, 52” (it is mentioned elsewhere); and I found six spelling errors. For a slim volume priced at NZ$l00, someone should be ashamed.

@article{doi10108003036758198610418172,
    author = "Flux, John E. C.",
    title = "Oxford Surveys in Evolutionary Biology, edited by R.Dawkins and M.Ridley. Oxford University Press; Volume 1, pp. 222; Volume 2, pp. 243; 1984, 1985. NZ$100 (approx.) each.",
    year = "1986",
    journal = "Journal of the Royal Society of New Zealand",
    abstract = "Abstract This annual series gets off to a shaky start. Three of the articles promised in the pre‐publication leaflet miss Volume 1, and there is no editorial or introduction whatever. Despite the distinguished editors, two of eight papers have the wrong titles on the contents page; figure lay‐out is poor, (e.g. p. 44); the six figures on p. 53 have one unbroken caption running for 20 lines on two pages, and are referred to in the text in reverse order; the index is inadequate, e.g. “Natural selection, 52” (it is mentioned elsewhere); and I found six spelling errors. For a slim volume priced at NZ$l00, someone should be ashamed.",
    url = "https://doi.org/10.1080/03036758.1986.10418172",
    doi = "10.1080/03036758.1986.10418172",
    openalex = "W2079542219"
}

Darwinian Evolution. Anthony Flew. New Brunswick, NJ: Transaction Publishers, 1997.150 pp.

@article{bowler1998darwinian,
    author = "Bowler, Peter J.",
    title = "Darwinian Evolution",
    year = "1998",
    journal = "American Anthropologist",
    abstract = "Darwinian Evolution. Anthony Flew. New Brunswick, NJ: Transaction Publishers, 1997.150 pp.",
    url = "https://doi.org/10.1525/aa.1998.100.3.806",
    doi = "10.1525/aa.1998.100.3.806",
    number = "3",
    openalex = "W4230133078",
    pages = "806-807",
    volume = "100"
}

@article{doi101016jenvsoft201409013,
    author = "Maier, Holger R. and Kapelan, Zoran and Kasprzyk, Joseph and Kollat, Joshua B. and Matott, L. Shawn and da Conceição Cunha, Maria and Dandy, Graeme C. and Gibbs, Matthew S. and Keedwell, Edward and Marchi, Angela and Ostfeld, Avi and Savić, Dragan and Solomatine, Dimitri and Vrugt, Jasper A. and Zecchin, Aaron C. and Minsker, Barbara and Barbour, Emily and Kuczera, G. and Pasha, Fayzul and Castelletti, Andrea and Giuliani, Matteo and Reed, Patrick M.",
    title = "Evolutionary algorithms and other metaheuristics in water resources: Current status, research challenges and future directions",
    year = "2014",
    journal = "Environmental Modelling \& Software",
    url = "https://doi.org/10.1016/j.envsoft.2014.09.013",
    doi = "10.1016/j.envsoft.2014.09.013",
    openalex = "W2108750696",
    references = "doi101016jpaerosci200502001, doi1010292011wr011527, doi101061ascewr194354520000053, doi10108003052159508941193"
}

The amino acid sequence of a protein affects both its structure and its function. Thus, the ability to modify the sequence, and hence the structure and activity, of individual proteins in a systematic way, opens up many opportunities, both scientifically and (as we focus on here) for exploitation in biocatalysis. Modern methods of synthetic biology, whereby increasingly large sequences of DNA can be synthesised de novo, allow an unprecedented ability to engineer proteins with novel functions. However, the number of possible proteins is far too large to test individually, so we need means for navigating the 'search space' of possible protein sequences efficiently and reliably in order to find desirable activities and other properties. Enzymologists distinguish binding (Kd) and catalytic (kcat) steps. In a similar way, judicious strategies have blended design (for binding, specificity and active site modelling) with the more empirical methods of classical directed evolution (DE) for improving kcat (where natural evolution rarely seeks the highest values), especially with regard to residues distant from the active site and where the functional linkages underpinning enzyme dynamics are both unknown and hard to predict. Epistasis (where the 'best' amino acid at one site depends on that or those at others) is a notable feature of directed evolution. The aim of this review is to highlight some of the approaches that are being developed to allow us to use directed evolution to improve enzyme properties, often dramatically. We note that directed evolution differs in a number of ways from natural evolution, including in particular the available mechanisms and the likely selection pressures. Thus, we stress the opportunities afforded by techniques that enable one to map sequence to (structure and) activity in silico, as an effective means of modelling and exploring protein landscapes. Because known landscapes may be assessed and reasoned about as a whole, simultaneously, this offers opportunities for protein improvement not readily available to natural evolution on rapid timescales. Intelligent landscape navigation, informed by sequence-activity relationships and coupled to the emerging methods of synthetic biology, offers scope for the development of novel biocatalysts that are both highly active and robust.

@article{doi101039c4cs00351a,
    author = "Currin, Andrew and Swainston, Neil and Day, Philip J. and Kell, Douglas B.",
    title = "Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently",
    year = "2014",
    journal = "Chemical Society Reviews",
    abstract = "The amino acid sequence of a protein affects both its structure and its function. Thus, the ability to modify the sequence, and hence the structure and activity, of individual proteins in a systematic way, opens up many opportunities, both scientifically and (as we focus on here) for exploitation in biocatalysis. Modern methods of synthetic biology, whereby increasingly large sequences of DNA can be synthesised de novo, allow an unprecedented ability to engineer proteins with novel functions. However, the number of possible proteins is far too large to test individually, so we need means for navigating the 'search space' of possible protein sequences efficiently and reliably in order to find desirable activities and other properties. Enzymologists distinguish binding (Kd) and catalytic (kcat) steps. In a similar way, judicious strategies have blended design (for binding, specificity and active site modelling) with the more empirical methods of classical directed evolution (DE) for improving kcat (where natural evolution rarely seeks the highest values), especially with regard to residues distant from the active site and where the functional linkages underpinning enzyme dynamics are both unknown and hard to predict. Epistasis (where the 'best' amino acid at one site depends on that or those at others) is a notable feature of directed evolution. The aim of this review is to highlight some of the approaches that are being developed to allow us to use directed evolution to improve enzyme properties, often dramatically. We note that directed evolution differs in a number of ways from natural evolution, including in particular the available mechanisms and the likely selection pressures. Thus, we stress the opportunities afforded by techniques that enable one to map sequence to (structure and) activity in silico, as an effective means of modelling and exploring protein landscapes. Because known landscapes may be assessed and reasoned about as a whole, simultaneously, this offers opportunities for protein improvement not readily available to natural evolution on rapid timescales. Intelligent landscape navigation, informed by sequence-activity relationships and coupled to the emerging methods of synthetic biology, offers scope for the development of novel biocatalysts that are both highly active and robust.",
    url = "https://doi.org/10.1039/c4cs00351a",
    doi = "10.1039/c4cs00351a",
    openalex = "W2160719116",
    references = "doi101007bfb0015249, doi101038nrg3744"
}

@book{flew2018darwinian,
    author = "Flew, Antony",
    title = "Darwinian Evolution",
    year = "2018",
    url = "https://doi.org/10.4324/9781351312844",
    doi = "10.4324/9781351312844",
    openalex = "W4234260069"
}

@incollection{crossref2021darwinian,
    title = "Darwinian Evolution",
    year = "2021",
    booktitle = "A Philosopher Looks at Human Beings",
    url = "https://doi.org/10.1017/9781108907057.004",
    doi = "10.1017/9781108907057.004",
    openalex = "W4249678390",
    pages = "48-74"
}