Talk by Laura Nuño de la Rosa: “Computing evo-devo. Mapping the dynamics and conceptual structure of the evolvability research front”Talk by Laura Nuño de la Rosa: “Computing evo-devo. Mapping the dynamics and conceptual structure of the evolvability research front”Talk by Laura Nuño de la Rosa: “Computing evo-devo. Mapping the dynamics and conceptual structure of the evolvability research front”

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Date and time: July 2, Thursday,11.30 am.

Location: Carlos Santamaría Building, Room B14

Speaker: Laura Nuño de la Rosa

Title: Computing evo-devo. Mapping the dynamics and conceptual structure of the evolvability research front

Abstract: Although evolutionary developmental biology is widely seen as a well established discipline, there is still no agreement on the impact of the introduction of development into the general structure of evolutionary theory. It has recently been argued that philosophy of biology should shift the emphasis from theories to epistemic goals in evolutionary biology, and particularly in evo-devo (Brigandt 2010; Love 2010). In this view, the identity of evo-devo as a discipline does not lay in being a theory, but derives from the pursuit of specific epistemic goals, such as the explanation of evolvability, evolutionary novelty or homology. On the other hand, the development of big data–based approaches and computational analytical methods is revolutionizing the field of the history  of science (Laubichler, Maienschein, and Renn 2013).  In this paper, I will apply these two new approaches to the history and philosophy of science to the study of evolvability, a research topic which is usually taken to be a cornerstone of evo-devo and, more generally, of an Extended Evolutionary Synthesis (Pigliucci 2008).

The plan of the paper is as follows. First, I introduce the methods used to map the research front of evolvability. I have used CiteSpace, an application for visualizing and analyzing trends and patterns in scientific literature which applies co-citation analysis to identify scientific specialities (Chen 2006). Second, I depict the general dynamics and conceptual structure of the evolvability research front and analyse each of the clusters the network is divided in with the aim of answering to the following questions: What is the conceptual structure of the research front of evolvability? Which are the interdisciplinary relationships structuring this research front? How did the research front on evolvability get started? What are the main intellectual turning points along its evolution, and what are the most active areas of research? Finally, I examine the main conceptual tensions among the existing definitions of evolvability. I argue that evolvability sets up ‘trading zones’ (Galison 1999) in scientific research that make possible interdisciplinary exchanges.

References

Brigandt, I. 2010. “Beyond Reduction and Pluralism: Toward an Epistemology of Explanatory Integration in Biology.” Erkenntnis 73 (3): 295–311.

Chen, C. 2006. “CiteSpace II: Detecting and Visualizing Emerging Trends and Transient Patterns in Scientific Literature.” Journal of the American Society for Information Science and Technology 57 (3): 359–77.

Galison, P. 1999. “Trading Zone: Coordinating Action and Belief.” The Science Studies Reader, 137–60.

Laubichler, M. D., J. Maienschein, and J. Renn. 2013. “Computational Perspectives in the History of Science: To the Memory of Peter Damerow.” Isis 104 (1): 119–30.

Love, A. C. 2010. “Rethinking the Structure of Evolutionary Theory for an Extended Synthesis.” In Evolution – the Extended Synthesis, edited by M. Pigliucci and G. B. Müller, 403–41. The MIT Press.

Pigliucci, M. 2008. “Opinion – Is Evolvability Evolvable?” NATURE REVIEWS GENETICS 9 (1): 75–82.

Date and time: July 2, Thursday,11.30 am.

Location: Carlos Santamaría Building, Room B14

Speaker: Laura Nuño de la Rosa

Title: Computing evo-devo. Mapping the dynamics and conceptual structure of the evolvability research front

Abstract: Although evolutionary developmental biology is widely seen as a well established discipline, there is still no agreement on the impact of the introduction of development into the general structure of evolutionary theory. It has recently been argued that philosophy of biology should shift the emphasis from theories to epistemic goals in evolutionary biology, and particularly in evo-devo (Brigandt 2010; Love 2010). In this view, the identity of evo-devo as a discipline does not lay in being a theory, but derives from the pursuit of specific epistemic goals, such as the explanation of evolvability, evolutionary novelty or homology. On the other hand, the development of big data–based approaches and computational analytical methods is revolutionizing the field of the history  of science (Laubichler, Maienschein, and Renn 2013).  In this paper, I will apply these two new approaches to the history and philosophy of science to the study of evolvability, a research topic which is usually taken to be a cornerstone of evo-devo and, more generally, of an Extended Evolutionary Synthesis (Pigliucci 2008).

The plan of the paper is as follows. First, I introduce the methods used to map the research front of evolvability. I have used CiteSpace, an application for visualizing and analyzing trends and patterns in scientific literature which applies co-citation analysis to identify scientific specialities (Chen 2006). Second, I depict the general dynamics and conceptual structure of the evolvability research front and analyse each of the clusters the network is divided in with the aim of answering to the following questions: What is the conceptual structure of the research front of evolvability? Which are the interdisciplinary relationships structuring this research front? How did the research front on evolvability get started? What are the main intellectual turning points along its evolution, and what are the most active areas of research? Finally, I examine the main conceptual tensions among the existing definitions of evolvability. I argue that evolvability sets up ‘trading zones’ (Galison 1999) in scientific research that make possible interdisciplinary exchanges.

References

Brigandt, I. 2010. “Beyond Reduction and Pluralism: Toward an Epistemology of Explanatory Integration in Biology.” Erkenntnis 73 (3): 295–311.

Chen, C. 2006. “CiteSpace II: Detecting and Visualizing Emerging Trends and Transient Patterns in Scientific Literature.” Journal of the American Society for Information Science and Technology 57 (3): 359–77.

Galison, P. 1999. “Trading Zone: Coordinating Action and Belief.” The Science Studies Reader, 137–60.

Laubichler, M. D., J. Maienschein, and J. Renn. 2013. “Computational Perspectives in the History of Science: To the Memory of Peter Damerow.” Isis 104 (1): 119–30.

Love, A. C. 2010. “Rethinking the Structure of Evolutionary Theory for an Extended Synthesis.” In Evolution – the Extended Synthesis, edited by M. Pigliucci and G. B. Müller, 403–41. The MIT Press.

Pigliucci, M. 2008. “Opinion – Is Evolvability Evolvable?” NATURE REVIEWS GENETICS 9 (1): 75–82.

Date and time: July 2, Thursday,11.30 am.

Location: Carlos Santamaría Building, Room B14

Speaker: Laura Nuño de la Rosa

Title: Computing evo-devo. Mapping the dynamics and conceptual structure of the evolvability research front

Abstract: Although evolutionary developmental biology is widely seen as a well established discipline, there is still no agreement on the impact of the introduction of development into the general structure of evolutionary theory. It has recently been argued that philosophy of biology should shift the emphasis from theories to epistemic goals in evolutionary biology, and particularly in evo-devo (Brigandt 2010; Love 2010). In this view, the identity of evo-devo as a discipline does not lay in being a theory, but derives from the pursuit of specific epistemic goals, such as the explanation of evolvability, evolutionary novelty or homology. On the other hand, the development of big data–based approaches and computational analytical methods is revolutionizing the field of the history  of science (Laubichler, Maienschein, and Renn 2013).  In this paper, I will apply these two new approaches to the history and philosophy of science to the study of evolvability, a research topic which is usually taken to be a cornerstone of evo-devo and, more generally, of an Extended Evolutionary Synthesis (Pigliucci 2008).

The plan of the paper is as follows. First, I introduce the methods used to map the research front of evolvability. I have used CiteSpace, an application for visualizing and analyzing trends and patterns in scientific literature which applies co-citation analysis to identify scientific specialities (Chen 2006). Second, I depict the general dynamics and conceptual structure of the evolvability research front and analyse each of the clusters the network is divided in with the aim of answering to the following questions: What is the conceptual structure of the research front of evolvability? Which are the interdisciplinary relationships structuring this research front? How did the research front on evolvability get started? What are the main intellectual turning points along its evolution, and what are the most active areas of research? Finally, I examine the main conceptual tensions among the existing definitions of evolvability. I argue that evolvability sets up ‘trading zones’ (Galison 1999) in scientific research that make possible interdisciplinary exchanges.

References

Brigandt, I. 2010. “Beyond Reduction and Pluralism: Toward an Epistemology of Explanatory Integration in Biology.” Erkenntnis 73 (3): 295–311.

Chen, C. 2006. “CiteSpace II: Detecting and Visualizing Emerging Trends and Transient Patterns in Scientific Literature.” Journal of the American Society for Information Science and Technology 57 (3): 359–77.

Galison, P. 1999. “Trading Zone: Coordinating Action and Belief.” The Science Studies Reader, 137–60.

Laubichler, M. D., J. Maienschein, and J. Renn. 2013. “Computational Perspectives in the History of Science: To the Memory of Peter Damerow.” Isis 104 (1): 119–30.

Love, A. C. 2010. “Rethinking the Structure of Evolutionary Theory for an Extended Synthesis.” In Evolution – the Extended Synthesis, edited by M. Pigliucci and G. B. Müller, 403–41. The MIT Press.

Pigliucci, M. 2008. “Opinion – Is Evolvability Evolvable?” NATURE REVIEWS GENETICS 9 (1): 75–82.

Talk by James diFrisco: “Individuality and the Limits of Biological Functionalism”Talk by James diFrisco: “Individuality and the Limits of Biological Functionalism”Talk by James diFrisco: “Individuality and the Limits of Biological Functionalism”

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Date and time: Monday, June 8, 11.30 am.

Location: Carlos Santamaría Building, Room B14

Speaker: James diFrisco (KU Leuven / Universidad Católica de Lovaina)

Title: Individuality and the Limits of Biological Functionalism

Abstract: According to ordinary intuition, living individuals and organisms are the same thing. Many of our moral and legal practices are connected to organism-based conceptions of individuality. For example, we grant rights to animal organisms rather than to their cells conceived as individuals, and assign moral responsibility to persons in a group rather than to the group as an individual—usually. Developments in biology, however, have indicated that familiar organisms are just one case of individuality among others, such as genes, cells, colonies, groups, species, and even ecosystems. It has therefore become a genuine problem to explain what it is in general that makes something a biological individual.

My project takes its point of departure from the inadequacy of the evolutionary explanation currently on offer, in which being an individual just means being a unit of selection. Instead of opposing this by recourse to more physiological explanations of individuality, however, I suggest it will be more illuminating to place both within a more general framework. I propose to do this by introducing two new elements to the debate: a (1) process-based and (2) hierarchical view of individuality. The first ensures that individuality receives a deeper explanation as a product of fundamental biological processes; the second, that different individuals are explained in terms of processes at different levels—whether they be physiological, evolutionary, or otherwise.

International Workshop on Levels of organization, causality & top-down relationsInternational Workshop on Levels of organization, causality & top-down relationsInternational Workshop on Levels of organization, causality & top-down relations

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International Workshop on Levels of organization, causality & top-down relations
June 4th, 2015
with
William Bechtel (U. California, San Diego): 
Top-down causation without levels 
and
  • Nicole Perret (IEA Nantes): Biological circularity and causality from a Kantian perspective
  • María Cerezo (U. Murcia): Causal dispositionalism in gene expression: the case of alternative splicing
  • Jon Umerez (UPV/EHU): A defense of inter-level causation
  • Leonardo Bich (UPV/EHU): Biological regulation: a theoretical model and its implications
  • Arantza Etxeberria (UPV/EHU): Biological organization & medical normativity

Venue: Faculty of Philosophy, Room 2.6

Time: 9.30 – 18.00

(download full program here)

PROGRAM

9:30: Alvaro Moreno: Brief Presentation

9:40-11:00: William Bechtel: Top-down causation without levels

11:00-11:30 Coffee break (at the cafeteria)

11:30- 12:15: Nicole Perret: Biological circularity and causality from a Kantian perspective

12:15 – 13:00: María Cerezo: Causal dispositionalism in gene expression: the case of alternative splicing

13:00-14:45 Lunch

14:45-15:30: Jon Umerez: A defense of inter-level causation

15:30-16:15: Leonardo Bich: Biological regulation: a theoretical model and its implications

16:15-16-30 Break

16:30-17:15: Arantza Etxeberria: Biological organization & medical normativity

IAS-Research Seminar by Nei de Freitas Nunes-Neto: “Functionality and regulation in ecological and social-ecological systems” IAS-Research Seminar by Nei de Freitas Nunes-Neto: “Functionality and regulation in ecological and social-ecological systems”IAS-Research Seminar by Nei de Freitas Nunes-Neto: “Functionality and regulation in ecological and social-ecological systems”

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Date and time: Monday, May 11, 11.30 am.

Location: Carlos Santamaría Building, Room B14

Speaker: Nei de Freitas Nunes-Neto (Federal University of Bahia, Brazil)

Title: Functionality and regulation in ecological and social-ecological systems 

Abstract: In this talk, I will focus on functionality and regulation of ecological and social-ecological systems, presenting an overview of the work I’m developing along this year at IAS-Research Group. The talk will be composed of two main parts. First of all, I’ll present the organizational approach of ecological functions developed in a previous work, and a possible reformulation of it, pointing to some relevant issues, such as the distinction between primary and non-primary functions and the complex relationships between different closures of constraints associated to a given ecosystem. And, second, based on the previous discussion, I’ll discuss the topic of regulation in ecological and social-ecological systems. Along the presentation, I’ll use examples of ecological or social-ecological systems (based on the following keystone species: a bromeliad, a wild bee and a dung beetle) to illustrate the general ideas.

Talk by Sara Diani: “Complex systems and clinical medicine: do they have fitting points?”Talk by Sara Diani: “Complex systems and clinical medicine: do they have fitting points?”Talk by Sara Diani: “Complex systems and clinical medicine: do they have fitting points?”

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Date and time: Friday, May 8, 11.30 am.

Location: Carlos Santamaría Building, Room B14

Speaker: Sara Diani (Lahnhöhe Zentrum, Lahnstein, Germany)

Title: Complex systems and clinical medicine: do they have fitting points?

Abstract: In the clinical practice we approach diseases with a linear logic, not a complex one, focusing us on a little part of the organism, ignoring what happens in the other compartments. Anytime we try to treat a disease, we make several attempts because we don’t have a unifying and logical model that can help us to define a rational method. Our empiricism would need a consequent rational analysis of it, in order to properly analyze the results.

In other words, except for the studies done by the philosophers of medicine, we do not use a clear model of what is health and what is disease. To this aim the connection between philosophical and theoretical systemic approach to our body and its reactions, the science of complex systems, the study about networks and the “field discipline” in physics, and finally the clinical practice has been here explored.

A new model of interaction between body, environment and disease, by using the latest theories of physics and biology, and the concept of heuristic learning (based on the event and error) is proposed. The disease is triggered by environmental information (except for the genetic ones), and it is an active process, performed through the individual characteristics. Through heuristic learning the system develops its own “best response” to the information in that moment. This will follow the rules of the live organism: to maintain low entropy, the best order possible, and to use the least energy.

This idea has a central role in defining and treating the diseases.

The ratio between medical and biological paradigms with a systemic and holistic perspective could allow us to revolutionize the cures for the patient, to do more effective research to understand deeply the results with the final goal of a new, higher and wider level of medicine.

Date and time: Friday, May 8, 11.30 am.

Location: Carlos Santamaría Building, Room B14

Speaker: Sara Diani (Lahnhöhe Zentrum, Lahnstein, Germany)

Title: Complex systems and clinical medicine: do they have fitting points?

Abstract: In the clinical practice we approach diseases with a linear logic, not a complex one, focusing us on a little part of the organism, ignoring what happens in the other compartments. Anytime we try to treat a disease, we make several attempts because we don’t have a unifying and logical model that can help us to define a rational method. Our empiricism would need a consequent rational analysis of it, in order to properly analyze the results.

In other words, except for the studies done by the philosophers of medicine, we do not use a clear model of what is health and what is disease. To this aim the connection between philosophical and theoretical systemic approach to our body and its reactions, the science of complex systems, the study about networks and the “field discipline” in physics, and finally the clinical practice has been here explored.

A new model of interaction between body, environment and disease, by using the latest theories of physics and biology, and the concept of heuristic learning (based on the event and error) is proposed. The disease is triggered by environmental information (except for the genetic ones), and it is an active process, performed through the individual characteristics. Through heuristic learning the system develops its own “best response” to the information in that moment. This will follow the rules of the live organism: to maintain low entropy, the best order possible, and to use the least energy.

This idea has a central role in defining and treating the diseases.

The ratio between medical and biological paradigms with a systemic and holistic perspective could allow us to revolutionize the cures for the patient, to do more effective research to understand deeply the results with the final goal of a new, higher and wider level of medicine.

Date and time: Friday, May 8, 11.30 am.

Location: Carlos Santamaría Building, Room B14

Speaker: Sara Diani (Lahnhöhe Zentrum, Lahnstein, Germany)

Title: Complex systems and clinical medicine: do they have fitting points?

Abstract: In the clinical practice we approach diseases with a linear logic, not a complex one, focusing us on a little part of the organism, ignoring what happens in the other compartments. Anytime we try to treat a disease, we make several attempts because we don’t have a unifying and logical model that can help us to define a rational method. Our empiricism would need a consequent rational analysis of it, in order to properly analyze the results.

In other words, except for the studies done by the philosophers of medicine, we do not use a clear model of what is health and what is disease. To this aim the connection between philosophical and theoretical systemic approach to our body and its reactions, the science of complex systems, the study about networks and the “field discipline” in physics, and finally the clinical practice has been here explored.

A new model of interaction between body, environment and disease, by using the latest theories of physics and biology, and the concept of heuristic learning (based on the event and error) is proposed. The disease is triggered by environmental information (except for the genetic ones), and it is an active process, performed through the individual characteristics. Through heuristic learning the system develops its own “best response” to the information in that moment. This will follow the rules of the live organism: to maintain low entropy, the best order possible, and to use the least energy.

This idea has a central role in defining and treating the diseases.

The ratio between medical and biological paradigms with a systemic and holistic perspective could allow us to revolutionize the cures for the patient, to do more effective research to understand deeply the results with the final goal of a new, higher and wider level of medicine.

Talk by Marcella Faria: CELL-MATRIX ADHESION COMPLEXES AND THEIR DYNAMIC ASSEMBLY: THE POETICS OF CELL ATTACHMENTTalk by Marcella Faria: CELL-MATRIX ADHESION COMPLEXES AND THEIR DYNAMIC ASSEMBLY: THE POETICS OF CELL ATTACHMENTTalk by Marcella Faria: CELL-MATRIX ADHESION COMPLEXES AND THEIR DYNAMIC ASSEMBLY: THE POETICS OF CELL ATTACHMENT

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Date and time: Monday, April 27th, 11.30 am.

Location: Carlos Santamaría Building, Room B14

Speaker: Marcella Faria, Center For Applied Toxinology ,São Paulo
Title: CELL-MATRIX ADHESION COMPLEXES AND THEIR DYNAMIC ASSEMBLY: THE POETICS OF CELL ATTACHMENT

Abstract: Cell-matrix adhesion complexes (CMACs) are regions responsible for cellular attachment to the extracellular matrix (ECM), they are mainly composed by integrins, α/β heterodimers that bind selectively different ECM components through their extracellular domains acting as receptors for this class of molecules. Upon ECM binding the cytoplasmic tails of integrins will interact with a wide range of recruited factors that regulate integrin clustering in the cell membrane; and also activate signaling pathways that will provide a physical linkage between activated integrins and the microfilament system to be remodeled during cell migration. Ultimately CMACs work as functional protein networks that dynamically connect the ECM to filamentous Actin, controlling cell migration precisely through the continual rearrangement of both ECM adhesion, and Actin polymerization. In the present work we shall examine some attempts to conceptualize “cell migration” as an emergent process developed in the recent specialized literature; they introduce the notions of hierarchic organization into levels i.e. molecular, sub-cellular and cellular and describe an informational flow of increasing complexity versus decreasing number of entities, between these levels. We shall discuss few examples of CMACs remodeling in particular physiological and pathological conditions to argue that cell migration is a process that is also organized into semiotic dimensions. Our approach will not come as an alternative to the systems biology conceptualization initially presented but as a complementary view. Beyond the syntactic level – here illustrated as specific recognition of discrete ECM protein sequences by distinct integrin heterodimers – we shall reach the semantic and pragmatic levels by bringing into light the dynamics of some “word games”, i.e. Lewis Carroll’s doublets; and magic squares. In such poetic games the synthetic transformations subjected by the words have to deal with semantic rules, but are ultimately dictated by meaning, as concrete pragmatic constrains. We will emphasize the integration of synthetics, semantics and pragmatics also for the CMACs continuous remodeling through cell migration.

 

Workshop with Alfred Tauber: on Identity and AutonomyWorkshop with Alfred Tauber: on Identity and AutonomyWorkshop with Alfred Tauber: on Identity and Autonomy

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International Workshop on Autonomy and Identity in the Biomedical Sciences

April 24th, 2015

with

Alfred I. Tauber (Boston University): 

Autonomy versus Dignity: The Search for Philosophical Foundations 

and

  • Argyris Arnellos (KLI): Constitutive self-determination in the transition from uni- to multi-cellularity
  • Antonio Casado (UPV/EHU): Patient autonomy: narrative or episodic?
  • Alvaro Moreno (UPV/EHU): Agency and multicellular identity

Venue: Carlos Santamaría Building, Room A4

Organizers: Antonio Casado and Jon Umerez (UPV/EHU)