This bibliography gathers publications over many years from a variety of researchers exploring topics of agency, directionality, and function (among others) with a special emphasis on CASP members. It began with work from teams within the initial Agency, Directionality and Function project and continues to be populated with papers and articles from diverse researchers looking to further develop and expand ways of working interdisciplinarily on the complex theme of teleology.
Included in the bibliography are entries for publications and books that many scholars involved in the Agency, Directionality and Function project recommended as foundational texts in their field of study. We welcome suggestions for additions to the bibliography from CASP members.
Function and Teleology
Wright, L. (1976). >Teleological Explanations: An Etiological Analysis of Goals and Functions. Berkeley: University of California Press.
Zammito, J. (2006). “Teleology then and now: The question of Kant’s relevance for contemporary controversies over function in biology.” Studies in History and Philosophy of Biological and Biomedical Sciences 37(4):748–770.
Zammito, J. (2018). The Gestation of German Biology: Philosophy and Physiology from Stahl to Schelling. Chicago: University of Chicago Press.
Genomics
Álvarez-Carretero, S., Kapli, P., & Yang, Z. (2023). Beginner’s Guide on the Use of PAML to Detect Positive Selection. Molecular Biology and Evolution, 40(4), msad041.
Álvarez-Carretero, S., Kapli, P., & Yang, Z. (2023). Beginner’s Guide on the Use of PAML to Detect Positive Selection. Molecular Biology and Evolution, 40(4), msad041.
Au, E. H., Fauci, C., Luo, Y., Mangan, R. J., Snellings, D. A., Shoben, C. R., Weaver, S., Simpson, S. K., & Lowe, C. B. (2023). Gonomics: uniting high performance and readability for genomics with Go. Bioinformatics, 39(8), btad516.
Davín, A. A., Schrempf, D., Williams, T. A., Hugenholtz, P., & Szöllősi, G. J. (2022). Relative Time Inference Using Lateral Gene Transfers. In H. Luo (Ed.), Environmental Microbial Evolution (Vol. 2569, pp. 75–94). Springer US. https://doi.org/10.1007/978-1-0716-2691-7_4
Gehlert, F. O., Nickel, L., Vakirlis, N., Hammerschmidt, K., Vargas Gebauer, H. I., Kießling, C., Kupczok, A., & Schmitz, R. A. (2023). Active in vivo translocation of the Methanosarcina mazei Gö1 Casposon. Nucleic Acids Research, 51(13), 6927–6943.
Gomez-Garrido, J., Cruz, F., Alioto, T. S., Feiner, N., Uller, T., Gut, M., Sanchez Escudero, I., Tavecchia, G., Rotger, A., Otalora Acevedo, K. E., & Baldo, L. (2023). Chromosome-level genome assembly of Lilford’s wall lizard, Podarcis lilfordi (Günther, 1874) from the Balearic Islands (Spain). DNA Research, 30(3), dsad008.
Juravel, K., Porras, L., Höhna, S., Pisani, D., & Wörheide, G. (2023). Exploring genome gene content and morphological analysis to test recalcitrant nodes in the animal phylogeny. PLOS ONE, 18(3), e0282444.
Lin, H., Moody, E. R. R., Williams, T. A., & Moreau, J. (2023). On the Origin and Evolution of Microbial Mercury Methylation. Genome Biology and Evolution, 15(4).
Livnat, A., & Melamed, D. (2023). Evolutionary honing in and mutational replacement: how long-term directed mutational responses to specific environmental pressures are possible. Theory in Biosciences, 142(2), 87–105.
Sarkar S. GWASs and polygenic scores inherit all the old problems of heritability estimates. Behavioral and Brain Sciences. 2023;46:e227.
Valach, M., Moreira, S., Petitjean, C., Benz, C., Butenko, A., Flegontova, O., Nenarokova, A., Prokopchuk, G., Batstone, T., Lapébie, P., Lemogo, L., Sarrasin, M., Stretenowich, P., Tripathi, P., Yazaki, E., Nara, T., Henrissat, B., Lang, B. F., Gray, M. W., … Burger, G. (2023). Recent expansion of metabolic versatility in Diplonema papillatum, the model species of a highly speciose group of marine eukaryotes. BMC Biology, 21(1), 99.
Williams, S. E., Back, C. R., Best, E., Mantell, J., Stach, J. E. M., Williams, T. A., Race, P. R., & Curnow, P. (2023). Discovery and biosynthetic assessment of “Streptomyces ortus” sp. nov. isolated from a deep-sea sponge. Microbial Genomics, 9(5).
Yazdi, H. P., Olito, C., Kawakami, T., Unneberg, P., Schou, M. F., Cloete, S. W. P., Hansson, B., & Cornwallis, C. K. (2023). The evolutionary maintenance of ancient recombining sex chromosomes in the ostrich. PLOS Genetics, 19(6), e1010801.
History of Life and the Fossil Record
Alroy, J., M. Aberhan, D.J. Bottjer, M. Foote, F.T. Fürsich, P.J. Harries, A.J.W. Hendy, S.M. Holland, L.C. Ivany, W. Kiessling, M.A. Kosnik, C.R. Marshall, A.J. McGowan, A.I. Miller, T.D. Olszewski, M.E. Patzkowsky, S.E. Peters, L. Villier, P.J. Wagner, N. Bonuso, P.S. Borkow, B. Brenneis, M.E. Clapham, L.M. Fall, C.A. Ferguson, V.L. Hanson, A.Z. Krug, K.M. Layou, E.H. Leckey, S. Nürnberg, C.M. Powers, J.A. Sessa, C. Simpson, A. Tomašových, C.C. Visaggi. (2008). “Phanerozoic trends in the global diversity of marine invertebrates.” Science 321:97–100.
Arellano-Nava, B., Halloran, P. R., Boulton, C. A., Scourse, J., Butler, P. G., Reynolds, D. J., & Lenton, T. M. (2022). Destabilisation of the Subpolar North Atlantic prior to the Little Ice Age. Nature Communications, 13(1), 5008.
Armstrong McKay, D. I., Staal, A., Abrams, J. F., Winkelmann, R., Sakschewski, B., Loriani, S., Fetzer, I., Cornell, S. E., Rockström, J., & Lenton, T. M. (2022). Exceeding 1.5°C global warming could trigger multiple climate tipping points. Science, 377(6611), eabn7950.
Ba, Q., Hei, Y., Dighe, A., Li, W., Maziarz, J., Pak, I., Wang, S., Wagner, G. P., & Liu, Y. (2022). Proteotype coevolution and quantitative diversity across 11 mammalian species. Science Advances, 8(36), eabn0756.
Ba, Q., Hei, Y., Dighe, A., Li, W., Maziarz, J., Pak, I., Wang, S., Wagner, G. P., & Liu, Y. (2022). Proteotype coevolution and quantitative diversity across 11 mammalian species. Science Advances, 8(36), eabn0756.
Berry, W.B.N. (1987). Growth of a Prehistorical Time Scale: Based on Organic Evolution. New York: Blackwell Scientific Publications.
Bokulich, A. (2018). “Using models to correct data: palaeodiversity and the fossil record.” Synthese. https://doi.org/10.1007/s11229-018-1820-x.
Borges, D. G. F., Carvalho, D. S., Bomfim, G. C., Ramos, P. I. P., Brzozowski, J., Góes-Neto, A., F. S. Andrade, R., & El-Hani, C. (2023). On the origin of mitochondria: a multilayer network approach. PeerJ, 11, e14571.
Bowler, P.J. (1976). Fossils and Progress: Paleontology and the Idea of Progressive Evolution in the Nineteenth Century. Science History Publications.