Tag: Philosophy and Biology Seminar

Uri Alon (Weinzmann Institute of Science), Title TBA

Uri Alon is Professor, Department of Molecular Cell Biology, Weizmann Institute, Israel. His lab studies biological circuits using a combined experimental and theoretical approach, aiming to uncover general underlying principles that govern their functioning and evolution.
The talk will be virtual and will be given by Zoom. (Please contact Thomas Pradeu for the link).

Steven Frank (Univ. of California Irvine, USA), Title TBA

Steven Frank is Donald Bren Professor & Distinguished Professor, Ecology & Evolutionary Biology
School of Biological Sciences at University of California Irvine (USA)
His main research interests concern evolutionary genetics and host-parasite interactions.
URL: stevefrank.org
Academic Distinctions
Fellow, American Academy of Arts and Sciences, Elected 2012
Fellow, American Association for the Advancement of Science, Elected 2009
John Simon Guggenheim Fellowship, 1995
Theodosius Dobzhansky Prize, Society for the Study of Evolution, 1988
Young Investigator Prize, American Society of Naturalists, 1986

Sarah-Maria Fendt (Professor of Oncology, KU Leuven, Belgium), Nutrient dependencies of metastasis formation

Sarah-Maria Fendt is since 2013 a Principal Investigator at the VIB Center for Cancer Biology and Professor of Oncology at KU Leuven, Belgium. Sarah’s lab is specifically interested in elucidating general regulatory principles in metabolism, and understanding cancer metabolism during metastasis formation as well as during altered whole body physiology. To perform novel research in her fields of interest her group exploits their expertise in metabolomics and fluxomics. The research of Sarah’s lab is currently funded by multiple (inter)national grants and industry, which include an ERC consolidator grant. Sarah received several awards such as the EMBO Gold Medal.
This talk will be given by Zoom. (Please contact Thomas Pradeu for the link).
Metastasis formation is the leading cause of death in cancer patients. We find that metabolic rewiring is a liability of metastasizing cancer cells. For example, we discovered that extracellular remodeling of the metastatic niche, a process essential to metastasis formation, requires a transcriptional- independent regulation via the metabolites. Moreover, we provide knowledge on intratumor heterogeneity of metabolism and its role in metastasis formation. Specifically, we discovered that heterogeneity in the metabolic enzyme phosphoglycerate dehydrogenase (PHGDH) predicts in cancer patients the risk for metastasis formation. Strikingly, loss of PHGDH protein expression drives early dissemination of cancer cells due to a novel mechanism leading to the posttranslational modification of cell surface integrins. More recently, we have investigated the nutrient dependencies of metastasis and find a strong organ specific pattern. Thus, we study the metabolism of metastasizing cancer cells with the goal to define novel therapeutic strategies.

Tyler Brunet (University of Exeter, UK), Constructive Neutral Evolution and its Close Relatives 

Tyler Brunet (University of Exeter, UK) is a Leverhulme Postdoctoral fellow working with John Dupré at Egenis. He is a reformed biologist who turned to philosophy of biology. Among several other topics, he works on constructive neutral evolution (CNE).
Constructive Neutral Evolution (CNE) is a theory for explaining the origin and maintenance of complexity in biological systems without the necessary input of adaptive Evolution by Natural Selection (ENS). CNE was originally developed to explain a few comparatively obscure cases of complexity in molecular biology, including spliceosomal splicing, trypansomal  gene editing, scrambled genes in ciliates, and duplicate gene retention. However, since its conception, CNE has been extended and applied to a number of other cases – both novel molecular cases, and cases at cellular, organismal and ecological levels of organization. At the same time, CNE is not the only theory for explaining biological complexity that differs from ENS. For example, prior to the coinage of CNE the theory of Generative Entrenchment (GE) was also used to explain complexity without reliance on ENS alone; many authors in molecular evolution have since deployed a related, similar theory, here called Contingency and Entrenchment (CE). This talk will define and examine cases of CNE, using examples from molecular, cell and organismal biology, then compare it to other theories of complexity. I present CNE as a more general theory of the evolution of complexity which, alongside traditional adaptive explanations employing ENS, can account for a wide range of complex structures and relationships in biology.
Tyler’s publications:
Brunet TDP (2022). Higher level constructive neutral evolution. Biology & Philosophy, 37(4). Abstract. DOI.
Erasmus A, Brunet TDP (2022). Interpretability and Unification. Philosophy & Technology, 35(2). DOI.
Brunet TDP (2021). Local causation. Synthese, 199(3-4), 10885-10908. Abstract. DOI.
Brunet TDP, Doolittle WF, Bielawski JP (2021). The role of purifying selection in the origin and maintenance of complex function. Studies in History and Philosophy of Science Part A, 87, 125-135. DOI.
Brunet TDP, Fisher E (2020). Reasoning Continuously: a Formal Construction of Continuous Proofs. Studia Logica, 108(6), 1145-1160. Abstract. DOI.
Erasmus A, Brunet TDP, Fisher E (2020). What is Interpretability?. Philosophy & Technology, 34(4), 833-862. Abstract. DOI.
Brunet TDP (2019). On Purpose. ISIS, 110(3), 580-581. Author URL. DOI.
Brunet TDP, Doolittle WF (2018). The generality of Constructive Neutral Evolution. Biology & Philosophy, 33(1-2). DOI.
Doolittle WF, Brunet TDP (2017). On causal roles and selected effects: our genome is mostly junk. BMC BIOLOGY, 15 Author URL. DOI.
Inkpen SA, Douglas GM, Brunet TDP, Leuschen K, Doolittle WF, Langille MGI (2017). The coupling of taxonomy and function in microbiomes. BIOLOGY & PHILOSOPHY, 32(6), 1225-1243. Author URL. DOI.
Brunet TDP (2016). Aims and methods of biosteganography. JOURNAL OF BIOTECHNOLOGY, 226, 56-64. Author URL. DOI.
Doolittle WF, Brunet TDP (2016). What is the Tree of Life?. PLOS GENETICS, 12(4). Author URL. DOI.
Brunet TDP, Doolittle WF (2015). Multilevel Selection Theory and the Evolutionary Functions of Transposable Elements. GENOME BIOLOGY AND EVOLUTION, 7(8), 2445-2457. Author URL. DOI.
Doolittle WF, Brunet TDP, Linquist S, Gregory TR (2014). Distinguishing between “Function” and “Effect” in Genome Biology. GENOME BIOLOGY AND EVOLUTION, 6(5), 1234-1237. Author URL. DOI.
Brunet TDP, Doolittle WF (2014). Getting “function” right. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 111(33), E3365-E3365. Author URL. DOI.

Deborah Gordon (Professor of Biology, Stanford University, USA), The ecology of collective behavior

Deborah Gordon is Professor of Biology at University of Stanford (USA).
Deborah Gordon is a world-leading specialist of ant colonies and collective behaviors. With her group, she uses ant colonies to investigate systems that operate without central control, and explore analogies with other systems, such as the internet, the immune system, and the brain. She is interested in collective behavior, which can take many forms, such as emergence, self-organization, superorganism, quorum sensing, artificial intelligence, and dynamical networks.
Collective behavior operates without central control, using local interactions among participants to allow groups to respond to changing conditions. It is widespread in nature, not only producing the coordinated movement of bird flocks or fish schools, but also regulating activity in natural systems from cells, as in cancer metastasis or embryonic development, to the social groups of many vertebrates. An ecological perspective on collective behavior examines how collective behavior adjusts to changing environments. Ant colonies function collectively, and the enormous diversity of more than 14K species of ants, in different habitats, provides opportunities to look for general ecological patterns. The collective foraging behavior of harvester ants in the desert adjusts activity to manage water loss, while the trail networks of turtle ants in the canopy of the  tropical forest adjust to rapidly changing resources and vegetation. These examples suggests how systems with similar dynamics in their surroundings have evolved to show similar dynamics in the regulation of collective behavior. An ecological perspective can contribute to new insights in medical research.
See here Deborah Gordon’s TED talk: “What ants teach us about the brain, cancer and the Internet”

Publications of Deborah Gordon.

Ned Block (Silver Professor of Philosophy and Psychology, New York University, USA), Perception is non-conceptual

Ned Block is Silver Professor in the Departments of Philosophy, Psychology and Center for Neural Science at New York University (NYU), NY, USA.

This talk will argue that the reason that perception is fundamentally different from cognition is that perception is non-conceptual whereas cognition is conceptual.  I will review evidence that infants between the ages of 6 and 11 months can see colors but cannot accomplish even the simplest kinds of cognition involving colors.  Children of the same ages can see shapes and also exhibit cognition with shape concepts.  I will argue that the upshot is that color perception of these infants is non-conceptual and that one can extrapolate from this finding to all of perception.

David Bilder (Univ. Berkeley, USA), Ancient origins of tumor-host interactions: insights from the Drosophila model

The Bilder Lab (University of Berkeley, USA) studies the molecules and mechanisms that govern the polarity, growth, and morphogenesis of epithelia, the fundamental tissue of all animals and the major constituent of human organs. They also use Drosophila cancer models as a simple system to understand both how epithelial organization prevents tumor formation and how tumors actually kill their hosts.
Example of recent work:
Bilder et al., Tumour-host interactions through the lens of Drosophila, Nature Reviews Cancer (2021)
There is a large gap between the deep understanding of mechanisms driving tumour growth and the reasons why patients ultimately die of cancer. It is now appreciated that interactions between the tumour and surrounding non-tumour (sometimes referred to as host) cells play critical roles in mortality as well as tumour progression, but much remains unknown about the underlying molecular mechanisms, especially those that act beyond the tumour microenvironment. Drosophila has a track record of high-impact discoveries about cell-autonomous growth regulation, and is well suited to now probe mysteries of tumour – host interactions. Here, we review current knowledge about how fly tumours interact with microenvironmental stroma, circulating innate immune cells and distant organs to influence disease progression. We also discuss reciprocal regulation between tumours and host physiology, with a particular focus on paraneoplasias. The fly’s simplicity along with the ability to study lethality directly provide an opportunity to shed new light on how cancer actually kills.

John Dupré (Egenis, University of Exeter, UK), What are viruses? Parasites, processes, parts or all of the above?

John Dupré is Professor of Philosophy of science at the University of Exeter (UK), with a main focus on philosophy of biology. He is the Director of Egenis, the Centre for the Study of Life Sciences.

People still often think that viruses are tiny little things that cause disease by parasitizing larger organisms. Here I argue that viruses are not things, but processes, and while some do, of course, cause serious disease, many or even most may be important positive contributors to larger biological systems. Finally, returning to the mistaken characterization of viruses as things rather than processes, I show how this erroneous reification may have seriously harmful consequences for research.

Stephen M. Downes (Utah), An Early History of the Heritability Coefficient Applied to Humans (1918–1960)

Stephen M. Downes is a Full Professor in the Philosophy Department at the University of Utah (USA). Most of his work is in philosophy of science with special focus on philosophy of biology, philosophy of social science and models and modeling across the sciences. He is also an Adjunct Professor in the School of Biological Sciences at the University of Utah, and a member of the PhilInBioMed network.
Detailed CV.

An Early History of the Heritability Coefficient Applied to Humans (1918–1960)

Stephen M. Downes (in collaboration with Eric Turkheimer)
(See full paper here)
Fisher’s 1918 paper accomplished two distinct goals: unifying discrete Mendelian genetics with continuous biometric phe- notypes and quantifying the variance components of variation in complex human characteristics. The former contributed to the foundation of modern quantitative genetics; the latter was adopted by social scientists interested in the pursuit of Gal- tonian nature-nurture questions about the biological and social origins of human behavior, especially human intelligence. This historical divergence has produced competing notions of the estimation of variance ratios referred to as heritability. Jay Lush showed that they could be applied to selective breeding on the farm, while the early twin geneticists used them as a descriptive statistic to describe the degree of genetic determination in complex human traits. Here we trace the early history (1918 to 1960) of the heritability coefficient now used by social scientists.
Behavior genetics · Heritability · Heritability coefficient · Human behavior genetics

Elliott Sober (Madison): “Natural selection, random mutations and gradualism: Fisher, Kimura, and connecting the dots”

Elliott Sober is Hans Reichenbach Professor and William F. Vilas Research Professor in the Department of Philosophy at University of Wisconsin–Madison, USA. He is one of the founders of the field of philosophy of biology, a major philosopher “in” science, and a specialist of evolutionary biology. He is also a member of the PhilInBioMed Scientific Committee.
Evolutionary gradualism, the randomness of mutations, and the hypothesis that natural selection exerts a pervasive influence on evolutionary outcomes are pair-wise logically independent.  Can the claims about selection and mutation be used to formulate an argument for gradualism?  In his Genetical Theory of Natural Selection, R.A. Fisher made an important start at this project in his famous “geometric argument” about the fitness consequences of random mutations that have different sizes of phenotypic effect.  Kimura’s theory of how the probability of fixation depends on both the selection coefficient and the effective population size shows that Fisher’s argument for gradualism was mistaken.  Here we analyze Fisher’s argument and explain how Kimura’s theory leads to a conclusion that Fisher did not anticipate. We identify a fallacy that reasoning about fitness differences and their consequences for evolution should avoid.  We distinguish forward-directed from backward-directed versions of gradualism.  The backward-directed thesis may be correct, but the forward-directed thesis is not.