La ansiedad metodológica como búsqueda de objetividad: la construcción de filogenias moleculares

Edna Suárez, Víctor Hugo Anaya

Resumen


“Methodological anxiety” as searching for objectivity: the construction of molecular phylogenies

Starting on the second half of the 1960’s, a lasting discussion on the advantages of molecular over morphological characters in the constructruction of phylogenies has taken place. This discussion gave way to what we have characterized as a methodological anxiety that has guided the ongoing search for more objective methods and representations in the field. The aforementioned search is embodied in the form or normative principles that include the quantification of evidence, the use of statistical inference tools, the commitment to make explicit the criteria used during its evaluation and the automatization of tools using computers, data bases and the advances in bioinformatics. The practices of objectivity in this field are highly contextualized.

 

Key words: Objectivity, subjectivity, molecular phylogenies, quantification, automatization, methodological problems, evolutionary patterns, classification, statistical inference, evidence evaluation.

 


Texto completo:

PDF

Referencias


Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., y Walter, P. (2002), Molecular Biology of the Cell (4th ed.) London, UK: Garland Science.

Altschul, S. F. (1991), “Amino acid substitution matrices from information theoretic perspective,” J. Mol. Biol. 219: 555-565.

Aronson, J.D. (2002), “’Molecules and monkeys: George Gaylord Simpson and the challenge of molecular evolution,” History and Philosophy of the Life Sciences 24: 441-465.

Beatty, J. (1990), “Evolutionary anti-reductionism: Historical reflections,” Biology and Philosophy 5: 199-210.

Bishop, M.J., y Thompson, E.A. (1986), “Maximum likelihood alignment of DNA sequences,” J. Mol. Biol. 190: 159-165.

Bolton, E. y Britten, R. (1961), Yearly Report to the Carnegie Institution of Washington. Brinkman, F. S. L., y Leipe, D. D. (2001), “Phylogenetic analysis,” in A. D. Baxenasis & B. F. F. Ouellete (Eds.), Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins (2a ed.). New York: J. Wiley & Sons.

Brudno, M., Malde, S., Poliakov, A., Do, C.B. Couronne, O., Dubchak, I., Batzoglou, S. (2003), “Glocal alignment: finding rearrangements during alignment,” Bioinformatics 19 (Suppl. 1): i54-i62.

Daston, L. y Galison, P. (1992), “The image of objectivity,” Representations 40: 81-128.

Daston, L. y Galison, P. (2007), Objectivity. Brooklyn, N.Y: Zone Books.

Dayhoff, M.O., Schwartz, R.M., Orcutt, B.C. (1978), “A model of evolutionary change in proteins,” in Dayhoff, M.O. y Schwartz, R.M. (Eds.), Atlas of Protein Sequence and Structure 5: 345-352.

Dietrich, M.R. (1998), “Paradox and persuasion: Negotiating the place of molecular evolution within evolutionary biology,” Journal of the History of Biology 31: 85-111.

Doolittle, W.F. (1999a), “Phylogenetic classification and the universal tree,” Science 284 (5423): 2124-2129.

Doolittle, W.F. (1999b), “Lateral genomics,” TIG 15(12): M5-M8.

Efron, B. (1979), “Bootstrap methods: Another look at the jackknife,” The Annals of Statistics 7(1): 1–26.

Felsenstein, J. (1985), “Confidence limits on phylogenies: An approach using the bootstrap,” Evolution 39(4): 783-791.

Felsenstein, J. (2004), Inferring Phylogenies. USA: Sinauer Press.

Felsenstein, J., Sawyer, S., Kochin, R. (1982), “An efficient method for matching nucleic acid sequences,” Nucleic Acids Research 10(1): 133-139.

Feng, D.F., Johnson, M.S., Doolittle, R.F. (1985), “Aligning amino acid sequences; Comparison of commonly used methods,” J. Mol. Biol. 21: 112-125.

Fitch, W. (1966), “The relation between frequencies of amino acids and ordered trinucleotides,” J. Mol. Biol. 16: 1-8.

Fitch, W. (1970), “Distinguishing homologous from analogous proteins,” Syst. Zool. 19, 99-113.

Fitch, W. (1971), “Toward defining the course of evolution: minimum change for a specific tree topology,” Syst. Zool. 20(4): 406-416.

Fitch, W. (1988), “This Weeks Citation Classic,” Current Contents 27: 16.

Fitch, W. (2000), “Homology, a personal view on some of the problems,” TIG 16(5): 227-231.

Fitch, W. M., y Margoliash, E. (1967), “Construction of phylogenetic trees,” Science 155(3760): 279-284.

Fitch, W., y Smith, T. (1983), “Optimal sequence alignments,” PNAS 80: 13821386.

Gigerenzer, G., Z. Swijtink, T. Porter, L. Daston, J. Beatty y Kruger., L. (1989), The Empire of Chance: How Probability Changed Science and Everyday Life. Cambridge: Cambridge University Press.

Goodman, M. (1960), “On the emergence of intraspecific differences in the protein antigens of human beings,” The American naturalist 94(875): 153-166.

Goodman, M. (1996), “Epilogue: A personal account of the origins of a new paradigm,” Molecular Phylogenetics and Evolution 5(1): 269–285.

Hagen, J. (2001), “The introduction of computers into systematic research in the United States during the 1960’s,” Studies in the History and Philosophy of Biological and Biomedical Sciences 32: 291-314.

Hagen, J. (2003), “The statistical frame of mind in systematic biology from quantitative zoology to biometry,” Journal of the History of Biology 36: 353-384.

Henikoff, S., y Henikoff, J.G.(1992), “Amino acid substitution matrices from protein blocks,” PNAS 89:10915-10919.

Hull, D. L. (1988), Science as a Process. Chicago: The University of Chicago Press.

Huynen, M., Berend, S., Bork P. (1999), “Lateral gene transfer, genome surveys, and the phylogeny of prokaryotes,” Science 286: 1443a.

Jones, D.T., Taylor W.R., Thornton, J.M. (1992), “The rapid generation of mutation data matrices from protein sequences,” Comp. Appli. Biosci. 8: 275-282.

Jukes, T.H., y Cantor, C.R. (1969), “Evolution of protein molecules,” in H.N. Munro (ed). Mammalian Protein Metabolism (Vol. 3). New York and London: Academic Press.

Lewontin, R. (1974), The Genetic Basis of Evolutionary Change. NY: Columbia University Press.

Kimura, M. (1980), “A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences,” Journal of Molecular Evolution 16: 111–120.

Li, W.-H. (1993), “Unbiased estimation of the rates of synonymous and non synonymous substitution,” J. Mol. Evol. 36: 96-99.

Li, W.-H, Wu C.-I., Luo, C.C. (1985), “A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes,” Mol. Biol. Evol. 2(2): 150-174.

Li, W.-H., y Graur D. (1991), Fundamentals of Molecular Biology, USA: Sinauer Associats, INC.

Margoliash, E. (1963), “Primary structure and evolution of cytochrome C,” PNAS 50(4): 672-679.

Margulis, L. (1981), Symbiosis in Cell Evolution: Microbial Communities in the Archean and Proterozoic Eons. New York: W.H. Freeman and Company.

McLachlan, A.D. (1972), “Repeating sequences and gene duplication in proteins,” J. Mol. Biol. 64: 17-437.

Müller, T., y Vingron, M. (2000), “Modeling amino acid replacement,” J. Comput. Biol. 7(6): 761-776.

Müller, T., Spang, R., Vingron, M. (2002), “Estimating amino acid substitution models: A comparison of Dayhoff’s Estimator, the resolvent approach and a maximum likelihood method,” J. Biol. Evol. 19(1): 8-13.

Needleman, S., y Wunsch, C. (1970), “A general method applicable to the search for similarities in the amino acid sequence of two proteins,” J Mol Biol. 48(3): 443-53.

Nei, M., y Gojobori, T. (1986), “Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions,” Mol. Biol. Evol. 3(5): 418-426.

November, Joseph, A. (2006), “Digitalizing life: The introduction of computers to biology and medicine,”. Unpublished PhD Dissertation. Princeton University.

O’Malley, M.A. and Boucher, Y. (2005), “Paradigm change in evolutionary microbiology,” Stud. Hist. Phil. Biol. & Biomed. Sci. 36:183-208.

Porter, T. M. (1995), Trust in Numbers. The Pursuit of Objectivity in Science and Public Life. New Jersey: Princeton University Press.

Sagan, L. (1967), “On the origin of mitosing cells,” J. Theoretical Biology 14(3) S: 255-274.

Schejter, A., & Agassi, J. (1981), “Molecular phylogenetics: Biological parsimony and methodological extravagance,” in J. Agassi & R. S. Cohen (Eds.), Scientific Philosophy Today. Dordrecht: D. Reidel Publishing Company, pp. 333–356.

Schwartz, R.M., y Dayhoff, M.O. (1978), “Origins of prokaryotes, Eukaryotes, Mitochondria and Chloroplasts,” Science 199 (4327): 395-403.

Simpson, G.G. (1944), Tempo and Mode in Evolution. New York: Columbia University Press.

Simpson, G.G. (1964), “The meaning of taxonomic statements,” in Sherwood L. Washburn (Ed.) Classification and Human Evolution. London: Methuen and Co. Ltd.

Simpson, G. G. y Roe, A. (1939), Quantitative Zoology. New York: Mac Graw Hill. Smith, T. F. (1990), “The history of the genetic sequence databases,” Genomics 6: 701-707.

Sober, E. (1988), Reconstructing the Past, Parsimony, Evolution and Inference. Boston: MIT Press.

Suárez, E. (1996), El origen de disciplinas como integración de tradiciones científicas: El caso de la evolución molecular. Tesis doctoral no publicada. México: Universidad Nacional Autónoma de México.

Suárez, E. (2007) “The rhetoric of informational molecules. Authority and promises in the early days of molecular evolution,” Science in Context 20(4): 649-677.

Thorne J.L., Kishino, H., Flesenstein, J. (1991) “An evolutionary model for maximum likelihood alignment of DNA sequences,” J. Mol .Biol. 33: 114-124.

Winter, P.W., Walsh K.A., Neurat, H. (1968), “Homology applied to proteins,” Science 168 (3861): 1433.

Woese C.R. y Fox, G.E. (1977), “Phylogenetic structure of the prokaryotic domain: The primary kingdoms,” PNAS 74(11): 5088-5090.

Zuckerkandl, E. (1964), “Perspectives in Molecular Anthropology,” in Sherwood l. Washburn (Ed.) Classification and Human Evolution. London: Methuen and Co. Limited.

Zuckerkandl, E., y Pauling, L. (1962), “Molecular disease, evolution and genic heterogeneity,” in Kasha, M y Pullman, B (Eds.) Horizons in Biochemistry: Albert Szent-Gyöyi Dedicatory Volume. NY, USA: Academic Press.

Zuckerkandl, E. y Pauling, L. (1965a), “Molecules as documents of evolutionary history,” Journal of Theoretical Biology 8: 357-366.

Zuckerkandl, E. y Pauling, L. (1965b), “Evolutionary divergence and convergence in proteins,” in Vernon, B. y Vogel, H. (Eds.), Evolving Genes and Proteins. New York: Academic Press.


Enlaces refback

  • No hay ningún enlace refback.


Revista semestral editada por el Centro de Estudios Filosóficos, Políticos
y Sociales Vicente Lombardo Toledano
de la Secretaría de Educación Pública,
la Universidad Autónoma Metropolitana-Iztapalapa y Edicions UIB de la Universitat de les Illes Balears.

Lombardo Toledano 51, Col. Ex-Hda. Guadalupe Chimalistac,
Del. Alvaro Obregón, C.P. 01050, México, D.F.
Tels. (5255) 5661-4679 y 5661-4987
Fax: (5255) 5661-1787