I want to tell the story of a beautiful phenomenon in biology. In some sense it’s the prototype of much of the activity of life. The phenomenon is the way in which an individual cell of E. coli forages for nutrients. This process, known as “chemotaxis”—the “chemo-” for chemical and the “taxis” from the Greek τάξις, for tactics—is intelligence in one of its most elemental forms. An individual E. coli has no brain, obviously, and is even many orders of magnitude simpler than a human cell, and yet already it possesses something like a sense of smell, drive, even a memory. Chemotaxis recasts E. coli not as some aimless gut-pest but rather as an exquisitely sophisticated physical computer.
The cognitive cell: bacterial behavior reconsidered
Research on how bacteria adapt to changing environments underlies the contemporary biological understanding of signal transduction, and signal transduction provides the foundation of the information-processing approach that is the hallmark of the ‘cognitive revolution,’ which began in the mid-20th century. Yet cognitive scientists largely remain oblivious to research into microbial behavior that might provide insights into problems in their own domains, while microbiologists seem equally unaware of the potential importance of their work to understanding cognitive capacities in multicellular organisms, including vertebrates. Evidence in bacteria for capacities encompassed by the concept of cognition is reviewed. Parallels exist not only at the heuristic level of functional analogue, but also at the level of molecular mechanism, evolution and ecology, which is where fruitful cross-fertilization among disciplines might be found.
Principles of Minimal Cognition: Casting Cognition as Sensorimotor Coordination
Within the cognitive sciences, cognition tends to be interpreted from an anthropocentric perspective, involving a stringent set of human capabilities. Instead, we suggest that cognition is better explicated as a much more general biological phenomenon, allowing the lower bound of cognition to extend much further down the phylogenetic scale. We argue that elementary forms of cognition can already be witnessed in prokaryotes possessing a functional sensorimotor analogue of the nervous system. Building on a case-study of the Escherichia coli bacterium and its sensorimotor system, the TCST-system, we home in on the characteristics of minimal cognition, and distinguish it from more basic forms of ontogenetic adaptation. In our view, minimal cognition requires an embodiment consisting of a sensorimotor coupling mechanism that subsumes an autopoietic organization; this forms the basis of the growing consensus that the core of cognition revolves around sensorimotor coupling. We discuss the relevance of our interpretation of minimal cognition for the study of cognition in general
Steering yourself by the bootstraps: how cells create their own gradients for chemotaxis
Chemotaxis, where cell movement is steered by chemical gradients, is a widespread and essential way of organising cell behaviour. But where do the instructions come from – who makes gradients, and how are they controlled? We discuss the emerging concept that chemotactic cells often create attractant gradients at the same time as responding to them. This self-guidance is more robust, works across greater distances, and is more informative about the local environment than passive responses. Several mechanisms can establish autonomous gradients.
Cellosophical Explorations #2 - Cellosophy
Bacterial Chemotaxis as a model system
Cognition without brains? Learning and memory in microorganisms
Memory and learning are cognitive abilities typically associated with animals that possess a complex nervous system. Interestingly, recent studies suggest that microorganisms might also display learning-like behaviours. However, a factor limiting progress in this field is the lack of shared, microbe-specific frameworks that allow microbiologists to easily compare discoveries with concepts developed in cognitive sciences. In this review, we aim to bridge this gap by providing a conceptual overview of the definitional requirements for memory and learning to classify microbial behaviours and capabilities. Additionally, we identify and address problems that cause conceptual ambiguity in the microbial cognition literature, thereby facilitating more productive debates on the topic. Finally, we provide a novel perspective on how microbes might ‘learn’ from each other.
All living cells are cognitive
All living cells sense and respond to changes in external or internal conditions. Without that cognitive capacity, they could not obtain nutrition essential for growth, survive inevitable ecological changes, or correct accidents in the complex processes of reproduction. Wherever examined, even the smallest living cells (prokaryotes) display sophisticated regulatory networks establishing appropriate adaptations to stress conditions that maximize the probability of survival. Supposedly "simple" prokaryotic organisms also display remarkable capabilities for intercellular signalling and multicellular coordination. These observations indicate that all living cells are cognitive.
Functional Information: Towards Synthesis of Biosemiotics and Cybernetics
Biosemiotics and cybernetics are closely related, yet they are separated by the boundary between life and non-life: biosemiotics is focused on living organisms, whereas cybernetics is applied mostly to non-living artificial devices. However, both classes of systems are agents that perform functions necessary for reaching their goals. I propose to shift the focus of biosemiotics from living organisms to agents in general, which all belong to a pragmasphere or functional universe. Agents should be considered in the context of their hierarchy and origin because their semiosis can be inherited or induced by higher-level agents. To preserve and disseminate their functions, agents use functional information - a set of signs that encode and control their functions. It includes stable memory signs, transient messengers, and natural signs. The origin and evolution of functional information is discussed in terms of transitions between vegetative, animal, and social levels of semiosis, defined by Kull. Vegetative semiosis differs substantially from higher levels of semiosis, because signs are recognized and interpreted via direct code-based matching and are not associated with ideal representations of objects. Thus, I consider a separate classification of signs at the vegetative level that includes proto-icons, proto-indexes, and proto-symbols. Animal and social semiosis are based on classification, and modeling of objects, which represent the knowledge of agents about their body (Innenwelt) and environment (Umwelt).
How Life Works: A User’s Guide to the New Biology
“Bold and intriguing.”—Wall Street Journal • “Penetrating. . . . Provocative and profound.”—Publishers Weekly (starred review) • “Offers plenty of food for thought.”—Kirkus Reviews (starred review) “Ball’s marvelous book is both wide-ranging and deep. . . . I could not put it down.”—Siddhartha Mukherjee, author of The Song of the Cell and the Pulitzer Prize–winning The Emperor of All Maladies A new, cutting-edge vision of biology that revises our understanding of what life itself is, how to enhance it, and what possibilities it offers. Biology is undergoing a quiet but profound transformation. Several aspects of the standard picture of how life works—the idea of the genome as a blueprint, of genes as instructions for building an organism, of proteins as precisely tailored molecular machines, of cells as entities with fixed identities, and more—have been exposed as incomplete, misleading, or wrong. In How Life Works, Philip Ball explores the new biology, revealing life to be a far richer, more ingenious affair than we had guessed. Ball explains that there is no unique place to look for an answer to this question: life is a system of many levels—genes, proteins, cells, tissues, and body modules such as the immune system and the nervous system—each with its own rules and principles. How Life Works explains how these levels operate, interface, and work together (most of the time). With this knowledge come new possibilities. Today we can redesign and reconfigure living systems, tissues, and organisms. We can reprogram cells, for instance, to carry out new tasks and grow into structures not seen in the natural world. As we discover the conditions that dictate the forms into which cells organize themselves, our ability to guide and select the outcomes becomes ever more extraordinary. Some researchers believe that ultimately we will be able to regenerate limbs and organs, and perhaps even create new life forms that evolution has never imagined. Incorporating the latest research and insights, How Life Works is a sweeping journey into this new frontier of the life sciences, a realm that will reshape our understanding of life as we know it.
The sentient cell: the cellular foundations of consciousness
"All species, extant and extinct, from the simplest unicellular prokaryotes to humans, have an existential consciousness. Without sentience, the first cells that emerged some 4 billion years ago would have been evolutionary dead-ends, unable to survive in the chaotic, dangerous environment in which life first appeared and evolved. In this book, Arthur Reber's theory, the Cellular Basis of Consciousness (CBC), is outlined and distinguished from those models that argue that minds could be instantiated on artificial entities and those that maintain consciousness requires a nervous system. The CBC framework takes a novel approach to classic topics such as the origin-of-life, philosophy of mind, the role of genes, the impact of cognition, and how biological information is processed by all species. It also calls for a rethinking of a variety of issues including the moral implications of the sentient capacities of all species, how welfare concerns need to be expanded beyond where they currently are, and critically, how all life is intertwined in a coordinated cognitive ecology. The Sentient Cell explores this revolutionary model, which updates the standard neo-Darwinian framework within which current approaches operate and examines the underlying biomolecular features that are the likely candidates for the "invention" of consciousness and outline their role in cellular life." --
Design in The Age of Biology: Shifting From a Mechanical-Object Ethos to an Organic-Systems Ethos
In the early twentieth century, our understanding of physics changed rapidly; now, our understanding of biology is undergoing a similar rapid change.
What Physical ‘Life Force’ Turns Biology’s Wheels? | Quanta Magazine
The bacterial flagellar motor is finally understood after 50 years. In its workings, columnist Natalie Wolchover finds the essence of life.
A Cell So Minimal That It Challenges Definitions of Life | Quanta Magazine
The newly described microbe represents a world of parasitic, intercellular biodiversity only beginning to be revealed by genome sequencing.
Learning Outside the Brain: Integrating Cognitive Science and Systems Biology
Learning is commonplace in organisms such as ourselves and even in organisms as far distant as the bee and the octopus. Such learning is implemented by brains, or neuronal networks, and has been extensively studied within ethology, psychology, cognitive science, and neuroscience. Whether learning also takes place in nonneuronal settings has remained a matter of sustained controversy, too often dominated by ideological views. In this survey, I will explain how learning can be rigorously interpreted as a form of information processing and then explore the evidence for whether learning also takes place in organismal contexts outside the brain, such as physiology, development, and individual cells. I will try to explain why it is important to build bridges in this way between cognitive science and systems biology, why concepts and methods from various branches of engineering may be helpful in this task, and what the eventual impact may be on how we think about the organism.
A Complex Hierarchy of Avoidance Behaviors in a Single-Cell Eukaryote
Dexter et al. replicate the disputed, century-old observations of Jennings, confirming by video microscopy and statistical analysis that the single-cell ciliate Stentor roeseli exhibits a hierarchy of avoidance behaviors. They show further that each organism’s decision between contracting and detaching resembles a fair coin toss.
A Drive to Survive
Since 2005, Karl Friston's proposal that the principle of free energy minimization underpins the purposive behavior of living agents has evolved through thou...
Controlled Mold
A blog about fermentation, engineering, and cell-ag. We run wild experiments on microbes and try to eat them, all with the help of computers and math.