Tanja Gesell

From Santa Fe Institute Events Wiki

My name is Tanja Gesell and I am a PhD student at the Vienna Biocenter and of the Bioinformatics Integration Network Austria (GEN-AU). At the moment, I am finishing my PhD in Bioinformatics. I already have degrees in Biology and Fine Art. I first heard about the Santa Fe Institute during my art studies and it sparked my fascination for the origin of order and origin of life.

A little more about me


In my free time, I like to indulge in my interest in old and modern art (e.g. Giotto, Pierro della Francesca, Mike Kelly, Barnet Newman, Ad Reinhard) and watch old and new movies (e.g. Godard, Bunuel, Kubrick, Tarkowski). I am looking forward to working with you, as well as joining in discussions about structure, models, complexity, perceptions and all .... simply with a drink in the evenings in Santa Fe.

Thanks to the organizers for giving me the opportunity to come to Santa Fe.

I am looking forward to meeting you all!

1. What are your main interests?

I am interested in questions relating to the origin, creation and the development of our knowledge and the origin of life and order. Originally, I focused on the biology of the brain, animal behavior, and morphological evolution. I then studied Fine Art with seminars in philosophy, which focused me on the development of methods and methodology. During my PhD sudies in Bioinformatics, I have enjoyed the clear definitions of signs, e.g. {A,C,G,T} for DNA. Given this well-defined alphabet, I am interested in the mechanisms of explanations: How can we define structure? What are the dynamics of evolution? How and why does the structure change? What is the Origin of order and Origin of Life ?

It is interesting for me to learn how we explore our own inner beings in the context of science and map our own perceptions into general scientific rules in an attempt to represent them. Or let's say: Fine Art in the adge of natural scientific epistemology.

2. What sorts of expertise can you bring to the group?

I am most experienced in working with Monte Carlo Simulations, complex sequence evolution models, patterns of evolution and RNA molecules. Additionally, I am experienced in the field of fine art.

In particular, I have worked on aspects of a phylogenetic definition of structure based on neighborhood systems of RNA structural features. The simulation approach that I developed provides a general framework for sequence evolution with site-specific interactions along a phylogentic tree and can be applied to other interactions within biological sequences, and certainly to other sequences of various disciplines. It is possible to extend that to other different discrete characters and site-specific interaction patterns. (The program is written in C. Moreover, I have some experience in R and a little bit in mathematica.) Furthermore, I can bring a definition of structure into the discussion, which consists of three aspects: the substitution matrix, a neighborhood system and the phylogenetic tree. The substitution matrix specifies the evolutionary dynamics of nucleotide evolution. However, the matrix is influenced by the neighborhood system that defines the interactions among sites in a DNA sequence. The phylogenetic tree introduces an additional dependency pattern in the observed sequences.

3. What do you hope to get out of the CSSS?

I would like to gain more insight into other fields of complex behavior in mathematical, physical, living, and, now especially, social systems and brain behavior, as well as some basic knowledge about computational linguistics, information theory and logic. Meeting people who are interested in similar questions and setting up research collaboration with them would be a major bonus. As well as learning technical and mathematical skills (e.g. the tutorial about eigenvalues), I really want to have discussions about structure with people from other fields. I want to get inside scientists' brains, learn more about the different behavior and positions of different people. How are they doing science?

4. Do you have any possible projects in mind for the CSSS?

I already found some possible projects of yours that are very interesting (e.g. study the dynamics of HIV transmission in southern Africa, protein modularity, a fuzzy cognitive map from a causal description of a system, group phenomena by a network model, ...) and here is a suggestion of another possible project in my mind:

A Critique of Structure Definitions (or let's say: A Critique of Structure in Use)

In a first view it seems obvious what a structure is. Recently, there has been a lot of literature, e.g. in poststructuralist theory (Deleuze, Barthes, Levy-Strauss etc.). However, it seems that there is a lack of a clear, general definition. Based on the work of Oswald Wiener, it seems that the Church-Turing thesis could be an appropriate framework to try to eluciate the definition of structure. So far, I have looked at molecular structures based on RNA features (see above) and have written a program to show pictures and animations illustrating possible ways to model sequence evolution, as well as discussing the importance of a definition of structure from a phylogenetic viewpoint. Straigthforward, I consider different existing definitions of RNA structure, for example single minimum free energy, consensus structure or abstract shapes. How can we define structure in various disciplines (e.g. in physics, linguistics, philosophy, information theory, brain behaviour, social systems, or urban systems) and can we map that into a general definition? In addition, it would be great if we could come up with a general framework, animations and illustrations doing this. I would be happy to work together and discuss ideas about this with people from different fields.