Why do we get certain diseases, whereas other diseases do not exist?

In this book, Alon, one of the founders of systems biology, builds a foundation for systems medicine.

Starting from basic laws, the book derives why physiological circuits are built the way they are. The circuits have fragilities that explain specific diseases and offer new strategies to treat them.

By the end, the reader will be able to use simple and powerful mathematical models to describe physiological circuits. The book explores, in three parts, hormone circuits, immune circuits, and aging and age-related disease. It culminates in a periodic table of diseases.

Alon writes in a style accessible to a broad range of readers – undergraduates, graduates, or researchers from computational or biological backgrounds. The level of math is friendly and the math can even be bypassed altogether. For instructors and readers who want to go deeper, the book includes dozens of exercises that have been rigorously tested in the classroom

More at: www.taylorfrancis.com

Why information is the unifying principle that allows us to understand the evolution of complexity in nature

More than 150 years after Darwin’s revolutionary On the Origin of Species, we are still attempting to understand and explain the amazing complexity of life. Although we now know how evolution proceeds to build complexity from simple ingredients, quantifying this complexity is still a difficult undertaking. In this book, Christoph Adami offers a new perspective on Darwinian evolution by viewing it through the lens of information theory. This novel theoretical stance sheds light on such matters as how viruses evolve drug resistance, how cells evolve to communicate, and how intelligence evolves. By this account, information emerges as the central unifying principle behind all of biology, allowing us to think about the origin of life—on Earth and elsewhere—in a systematic manner.

Adami, a leader in the field of computational biology, first provides an accessible introduction to the information theory of biomolecules and then shows how to apply these tools to measure information stored in genetic sequences and proteins. After outlining the experimental evidence of the evolution of information in both bacteria and digital organisms, he describes the evolution of robustness in viruses; the cooperation among cells, animals, and people; and the evolution of brains and intelligence. Building on extensive prior work in bacterial and digital evolution, Adami establishes that (expanding on Dobzhansky’s famous remark) nothing in biology makes sense except in the light of information. Understanding that information is the foundation of all life, he argues, allows us to see beyond the particulars of our way of life to glimpse what life might be like in other worlds.

Read the full article at: press.princeton.edu

A Passion for Cooperation is the exciting autobiography of Robert Axelrod, one of the most acclaimed and wide-ranging scientists of the last fifty years. After being recognized by President Kennedy for being a promising young scientist while in high school, Axelrod built a career dedicated to collaborating with business school professors, international relations scholars, political scientists, computer scientists, and even evolutionary biologists and cancer researchers. Fifty years later, he was honored by President Obama with the National Medal of Science for scientific achievement and leadership and his work has been referred to as the gold standard of interdisciplinary research. 

Yet Axelrod’s autobiography is not just an account of his wide-ranging passion for cooperation. It reveals his struggles to overcome failures and experience the joys of gaining new insights into how to achieve cooperation. A Passion for Cooperation recounts Robert Axelrod’s adventures talking with the leader of the organization Hamas, the Prime Minister of Israel, and the Foreign Minister of Syria. Axelrod also shares stories of being hosted in Kazakhstan by senior Soviet retired generals and visiting China with well-connected policy advisors on issues of military aspects of cyber conflict. Through stories of the difficulties and rewards of interdisciplinary collaborations, readers will discover how Axelrod’s academic and practical work have enriched each other and demonstrated that opportunities for cooperation are much greater than generally thought. 

More at: press.umich.edu

Amil Merchant, Simon Batzner, Samuel S. Schoenholz, Muratahan Aykol, Gowoon Cheon & Ekin Dogus Cubuk 
Nature (2023)

Novel functional materials enable fundamental breakthroughs across technological applications from clean energy to information processing1,2,3,4,5,6,7,8,9,10,11. From microchips to batteries and photovoltaics, discovery of inorganic crystals has been bottlenecked by expensive trial-and-error approaches. Concurrently, deep-learning models for language, vision and biology have showcased emergent predictive capabilities with increasing data and computation12,13,14. Here we show that graph networks trained at scale can reach unprecedented levels of generalization, improving the efficiency of materials discovery by an order of magnitude. Building on 48,000 stable crystals identified in continuing studies15,16,17, improved efficiency enables the discovery of 2.2 million structures below the current convex hull, many of which escaped previous human chemical intuition. Our work represents an order-of-magnitude expansion in stable materials known to humanity. Stable discoveries that are on the final convex hull will be made available to screen for technological applications, as we demonstrate for layered materials and solid-electrolyte candidates. Of the stable structures, 736 have already been independently experimentally realized. The scale and diversity of hundreds of millions of first-principles calculations also unlock modelling capabilities for downstream applications, leading in particular to highly accurate and robust learned interatomic potentials that can be used in condensed-phase molecular-dynamics simulations and high-fidelity zero-shot prediction of ionic conductivity.

Read the full article at: www.nature.com

A unique exploration of teleonomy—also known as “evolved purposiveness”—as a major influence in evolution by a broad range of specialists in biology and the philosophy of science.

The evolved purposiveness of living systems, termed “teleonomy” by chronobiologist Colin Pittendrigh, has been both a major outcome and causal factor in the history of life on Earth. Many theorists have appreciated this over the years, going back to Lamarck and even Darwin in the nineteenth century. In the mid-twentieth century, however, the complex, dynamic process of evolution was simplified into the one-way, bottom-up, single gene-centered paradigm widely known as the modern synthesis. In Evolution “On Purpose,” edited by Peter A. Corning, Stuart A. Kauffman, Denis Noble, James A. Shapiro, Richard I. Vane-Wright, and Addy Pross, some twenty theorists attempt to modify this reductive approach by exploring in depth the different ways in which living systems have themselves shaped the course of evolution.

Evolution “On Purpose” puts forward a more inclusive theoretical synthesis that goes far beyond the underlying principles and assumptions of the modern synthesis to accommodate work since the 1950s in molecular genetics, developmental biology, epigenetic inheritance, genomics, multilevel selection, niche construction, physiology, behavior, biosemiotics, chemical reaction theory, and other fields. In the view of the authors, active biological processes are responsible for the direction and the rate of evolution. Essays in this collection grapple with topics from the two-way “read-write” genome to cognition and decision-making in plants to the niche-construction activities of many organisms to the self-making evolution of humankind. As this collection compellingly shows, and as bacterial geneticist James Shapiro emphasizes, “The capacity of living organisms to alter their own heredity is undeniable.”

More at: mitpress.mit.edu