Category Archives: Talks

Talk by René Zaragüeta: “Why, Willi, why? Phylogenetics and the dichotomy of trees”Talk by René Zaragüeta: “Why, Willi, why? Phylogenetics and the dichotomy of trees”Talk by René Zaragüeta: “Why, Willi, why? Phylogenetics and the dichotomy of trees”

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Date and time: Monday, April 13th, 11.30 am.

Location: Carlos Santamaría Building, Room B14
Speaker: René Zaragüeta i Bagils (Sorbonne, Paris)
Title: “Why, Willi, why? Phylogenetics and the dichotomy of trees”

Abstract: A cladogram is usually considered as resolved when all its branching points are bifurcations. The question I ask is: Why? Why all phylogenetic methods search dichotomous trees? Is evolution, or speciation, dichotomous? I suggest that Hennig’s principle of dichotomy is theoretically grounded. Cladograms—taxa and their relationships—are the result of a Cartesian analysis, which consists of the decomposition of taxa into homologies, i.e. hypotheses of degree of identity. Now, degree of identity is best represented by a ternary relationship, where two features are more identical to each other than any is to a third one. The foundation of taxa and their relationships upon homologies thus results in an intrinsically dichotomous pattern.

I speculate that the theoretical principle of dichotomy was present in Hennig’s theory. However, somehow, Hennig “forgot” his own arguments and the justification for this part of his theory.

Finally, I draw consequences of the theoretical foundation of dichotomy: if the evolutionary process needs not to be dichotomous, in which way are phylogenetic trees phylogenetic?

Talk by Thomas Reydon: Metaphysics Naturalized? The Case of Classification in the Sciences Talk by Thomas Reydon: Metaphysics Naturalized? The Case of Classification in the Sciences Talk by Thomas Reydon: Metaphysics Naturalized? The Case of Classification in the Sciences

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Date and time: Wednesday March 4th. 11.30 am.
Location: Carlos Santamaría Building, Room A4
Speaker: Thomas Reydon
Title: Metaphysics Naturalized? The Case of Classification in the Sciences

Abstract: While the topic of natural kinds has long been a focus of work in the philosophy of science, as well as in other areas of philosophy, a generally accepted account of natural kinds is still lacking. Moreover, there even is no general agreement about the kind of account that is being searched for, or about the criteria that a good account of natural kinds should meet. In response to these problems, in the philosophy of science (though not in other areas) there is a trend to move away from the metaphysics of kinds and classification and to turn to epistemological issues and questions regarding the use of kinds and classifications in various contexts. This trend fits well with the renewed interest in doing naturalistic philosophy of science and the increasing calls for bringing philosophy of science closer to scientific practice.

However, abandoning the search for a metaphysics of kinds and classifications is too quick. A metaphysical account of kinds is a crucial element of the explanation why some kinds and classifications are used in the sciences with more success than others, and some ways of grouping things turn out not to be useful at all. After all, barring cases of epistemic luck the reason for the epistemic and practical success of kinds and classifications must be that they adequately represent some aspect of the world or other. But problem for naturalistic philosophers wanting to elucidate the metaphysics of scientific kinds and classifications is whether naturalistic and practice-oriented philosophy of science can at all come up with an account of the metaphysics of kinds and classifications, rather than staying with epistemological and practical issues. Metaphysics cannot be read off from either epistemology or practice: simply examining scientific kinds and classifications and the ways in which investigators in the various areas of science employ them will not reveal their underpinnings. Thus, some a priori considerations need to enter into the picture – but a priori metaphysics is suspect from a naturalistic viewpoint.

The challenge for a naturalistic and practice-oriented metaphysics of kinds and classification, then, is to bring a priori considerations into play without rendering the account insufficiently naturalistic. In this talk I addresses this challenge and explore what a thoroughly naturalistic metaphysics of kinds and classifications should look like. I will do this by examining two core notions in the debate on kinds and classification, namely the notions of naturalness and, in particular, normativity.


Talk by Olatz González (UPV-EHU): Visualising Basque Fratriarchy: Enactions and Recognition in the Sport of PelotaTalk by Olatz González (UPV-EHU): Visualising Basque Fratriarchy: Enactions and Recognition in the Sport of PelotaTalk by Olatz González (UPV-EHU): Visualising Basque Fratriarchy: Enactions and Recognition in the Sport of Pelota

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Date: Monday, March 2

Time: 11.30 a.m.

Place: Carlos Santamaría Room B14

Speaker: Olatz González (University of Basque Country)

Abstract: Coming soon

“Toward a phenomenology of plant life” – IAS-Research Talk by Michael Marder“Toward a phenomenology of plant life” – IAS-Research Talk by Michael Marder“Toward a phenomenology of plant life” – IAS-Research Talk by Michael Marder

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Michael Marder, Ikerbasque Research Professor of Philosophy at the University of the Basque Country (Vitoria-Gasteiz) was invited to give an IAS-Research Talk on October the 22nd at 10:15. We recorded his talk and it is now available online at:

“The coevolution theory of the origin of the genetic code and an its extension” – IAS-Research Talk by Massimo Di Giulio“The coevolution theory of the origin of the genetic code and an its extension” – IAS-Research Talk by Massimo Di Giulio“The coevolution theory of the origin of the genetic code and an its extension” – IAS-Research Talk by Massimo Di Giulio

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Dr.Massimo Di Giulio (Laboratory for Molecular Evolution, Institute of Genetics and Biophysics “Adriano Buzzati-Traverso”, CNR, Napoli, Italy) will be giving an IAS-Research Talk entitled “The coevolution theory of  the origin of the genetic code and an its extension” on Friday, June 28th 2013, at 11.30 at the Carlos Santamaria Building Room B14.

Abstract

Background: The coevolution theory of the origin of the genetic code suggests that the genetic code is an imprint of the biosynthetic relationships between amino acids. However, this theory does not seem to attribute a role to the biosynthetic relationships between the earliest amino acids that evolved along the pathways of energetic metabolism. As a result, the coevolution theory is unable to clearly define the very earliest phases of genetic code origin. In order to remove this difficulty, I here suggest an extension of the coevolution theory that attributes a crucial role to the first amino acids that evolved along these biosynthetic pathways and to their biosynthetic relationships, even when defined by the non-amino acid molecules that are their precursors.

Results: It is re-observed that the first amino acids to evolve along these biosynthetic pathways are predominantly those codified by codons of the type GNN, and this observation is found to be statistically significant. Furthermore, the close biosynthetic relationships between the sibling amino acids Ala-Ser, Ser-Gly, Asp-Glu, and Ala-Val are not random in the genetic code table and reinforce the hypothesis that the biosynthetic relationships between these six amino acids played a crucial role in defining the very earliest phases of genetic code origin.

Conclusion: All this leads to the hypothesis that there existed a code, GNS, reflecting the biosynthetic relationships between these six amino acids which, as it defines the very earliest phases of genetic code origin, removes the main difficulty of the coevolution theory. Furthermore, it is here discussed how this code might have naturally led to the code codifying only for the domains of the codons of precursor amino acids, as predicted by the coevolution theory. Finally, the hypothesis here suggested also removes other problems of the coevolution theory, such as the existence for certain pairs of amino acids with an unclear biosynthetic relationship between the precursor and product amino acids and the collocation of Ala between the amino acids Val and Leu belonging to the pyruvate biosynthetic family, which the coevolution theory considered as belonging to different biosyntheses.

On the origin of the tRNA molecule – IAS-Research Talk by Massimo Di GiulioOn the origin of the tRNA molecule – IAS-Research Talk by Massimo Di GiulioOn the origin of the tRNA molecule – IAS-Research Talk by Massimo Di Giulio

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Dr.Massimo Di Giulio (Laboratory for Molecular Evolution, Institute of Genetics and Biophysics “Adriano Buzzati-Traverso”, CNR, Napoli, Italy) will be giving an IAS-Research Talk entitled “On the rigin of the tRNA molecule” on Tuesday, June 11th 2013, at 11.30 at the Carlos Santamaria Building Room B14.

Abstract

A model has been proposed suggesting that the tRNA molecule must have originated by direct duplication of an RNA hairpin structure [Di Giulio, M., 1992. On the origin of the transfer RNA molecule. J. Theor. Biol. 159, 199–214]. A non-monophyletic origin of this molecule has also been theorized [Di Giulio, M., 1999. The non-monophyletic origin of tRNA molecule. J. Theor. Biol. 197, 403–414]. In other words, the tRNA genes evolved only after the evolutionary stage of the last universal common ancestor (LUCA) through the assembly of two minigenes codifying for different RNA hairpin structures, which is what the exon theory of genes suggests when it is applied to the model of tRNA origin. Recent observations strongly corroborate this theorization because it has been found that some tRNA genes are completely separate in two minigenes codifying for the 5’ and 3’ halves of this molecule [Randau, L., et al., 2005a. Nanoarchaeum equitans creates functional tRNAs from separate genes for their 5’ and 3’ halves. Nature 433, 537–541]. It is shown that these tRNA genes codifying for the 5’ and 3’ halves of this molecule are the ancestral form from which the tRNA genes continuously codifying for the complete tRNA molecule are thought to have evolved. This, together with the very existence of completely separate tRNA genes codifying for their 5’ and 3’ halves, proves a non-monophyletic origin for tRNA genes — as a monophyletic origin would exclude the existence of these genes which have, on the contrary, been observed.

Dr.Massimo Di Giulio (Laboratory for Molecular Evolution, Institute of Genetics and Biophysics “Adriano Buzzati-Traverso”, CNR, Napoli, Italy) will be giving an IAS-Research Talk entitled “On the rigin of the tRNA Molecule” on Tuesday, June 11th 2013, at 11.30 at the Carlos Santamaria Building Room B14.

Abstract

A model has been proposed suggesting that the tRNA molecule must have originated by direct duplication of an RNA hairpin structure [Di Giulio, M., 1992. On the origin of the transfer RNA molecule. J. Theor. Biol. 159, 199–214]. A non-monophyletic origin of this molecule has also been theorized [Di Giulio, M., 1999. The non-monophyletic origin of tRNA molecule. J. Theor. Biol. 197, 403–414]. In other words, the tRNA genes evolved only after the evolutionary stage of the last universal common ancestor (LUCA) through the assembly of two minigenes codifying for different RNA hairpin structures, which is what the exon theory of genes suggests when it is applied to the model of tRNA origin. Recent observations strongly corroborate this theorization because it has been found that some tRNA genes are completely separate in two minigenes codifying for the 5’ and 3’ halves of this molecule [Randau, L., et al., 2005a. Nanoarchaeum equitans creates functional tRNAs from separate genes for their 5’ and 3’ halves. Nature 433, 537–541]. It is shown that these tRNA genes codifying for the 5’ and 3’ halves of this molecule are the ancestral form from which the tRNA genes continuously codifying for the complete tRNA molecule are thought to have evolved. This, together with the very existence of completely separate tRNA genes codifying for their 5’ and 3’ halves, proves a non-monophyletic origin for tRNA genes — as a monophyletic origin would exclude the existence of these genes which have, on the contrary, been observed.

Dr.Massimo Di Giulio (Laboratory for Molecular Evolution, Institute of Genetics and Biophysics “Adriano Buzzati-Traverso”, CNR, Napoli, Italy) will be giving an IAS-Research Talk entitled “On the rigin of the tRNA Molecule” on Tuesday, June 11th 2013, at 11.30 at the Carlos Santamaria Building Room B14.

Abstract

A model has been proposed suggesting that the tRNA molecule must have originated by direct duplication of an RNA hairpin structure [Di Giulio, M., 1992. On the origin of the transfer RNA molecule. J. Theor. Biol. 159, 199–214]. A non-monophyletic origin of this molecule has also been theorized [Di Giulio, M., 1999. The non-monophyletic origin of tRNA molecule. J. Theor. Biol. 197, 403–414]. In other words, the tRNA genes evolved only after the evolutionary stage of the last universal common ancestor (LUCA) through the assembly of two minigenes codifying for different RNA hairpin structures, which is what the exon theory of genes suggests when it is applied to the model of tRNA origin. Recent observations strongly corroborate this theorization because it has been found that some tRNA genes are completely separate in two minigenes codifying for the 5’ and 3’ halves of this molecule [Randau, L., et al., 2005a. Nanoarchaeum equitans creates functional tRNAs from separate genes for their 5’ and 3’ halves. Nature 433, 537–541]. It is shown that these tRNA genes codifying for the 5’ and 3’ halves of this molecule are the ancestral form from which the tRNA genes continuously codifying for the complete tRNA molecule are thought to have evolved. This, together with the very existence of completely separate tRNA genes codifying for their 5’ and 3’ halves, proves a non-monophyletic origin for tRNA genes — as a monophyletic origin would exclude the existence of these genes which have, on the contrary, been observed.

The Cognitive Domain of a Glider in the Game of Life – IAS-Research Talk by Randall BeerThe Cognitive Domain of a Glider in the Game of Life – IAS-Research Talk by Randall BeerThe Cognitive Domain of a Glider in the Game of Life – IAS-Research Talk by Randall Beer

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Prof. Randall D. Beer (Cognitive Science Program, School of Informatics and Computing, Indiana University, USA) will be giving an IAS-Research Talk entitled “The Cognitive Domain of a Glider in the Game of Life” on Tuesday the 15th January 2013 at 11.00am at B14 Room at the Carlos Santamaría Building. Prof. Randall D. Beer (Cognitive Science Program, School of Informatics and Computing, Indiana University, USA) will be giving an IAS-Research Talk entitled “The Cognitive Domain of a Glider in the Game of Life” on Tuesday the 15th January 2013 at 11.00am at B14 Room at the Carlos Santamaría Building. Prof. Randall D. Beer (Cognitive Science Program, School of Informatics and Computing, Indiana University, USA) will be giving an IAS-Research Talk entitled “The Cognitive Domain of a Glider in the Game of Life” on Tuesday the 15th January 2013 at 11.00am at B14 Room at the Carlos Santamaría Building. Continue reading →