Lifeboat Foundation

Scientists are designing simplified biological systems, aiming to construct synthetic cells and better understand life’s mechanisms.

One of the most fundamental questions in science is how lifeless molecules can come together to form a living cell. Bert Poolman, Professor of Biochemistry at the University of Groningen, has been working to solve this problem for two decades. He aims to understand life by trying to reconstruct it; he is building simplified artificial versions of biological systems that can be used as components for a synthetic cell.

His work was detailed in two new papers published in Nature Nanotechnology and Nature Communications. In the first paper, he describes a system for energy conversion and cross-feeding of products of this reaction between synthetic cells, while he describes a system for concentrating and converting nutrients in cells in the second paper.

To effectively adapt to change, living organisms rely on their ability to rapidly detect and process sensory information in their surroundings. The sensory information available at a given time continuously changes, which means that it can typically only be observed partially and for a limited amount of time.

The discovery of the quantum tunneling (QT) effect—the transmission of particles through a high potential barrier—was one of the most impressive achievements of quantum mechanics made in the 1920s. Responding to the contemporary challenges, I introduce a deep neural network (DNN) architecture that processes information using the effect of QT. I demonstrate the ability of QT-DNN to recognize optical illusions like a human. Tasking QT-DNN to simulate human perception of the Necker cube and Rubin’s vase, I provide arguments in favor of the superiority of QT-based activation functions over the activation functions optimized for modern applications in machine vision, also showing that, at the fundamental level, QT-DNN is closely related to biology-inspired DNNs and models based on the principles of quantum information processing.

Mirroring the mechanisms that make human faces and bodies—and those of many multicellular organisms—symmetrical, bee colonies build symmetrical nests when they are placed on either side of a double-sided comb. The finding, published in Current Biology, extends examples of symmetry in biology to the behavior of communities and the architectural structures that they build.

Wetware computing and organoid intelligence is an emerging research field at the intersection of electrophysiology and artificial intelligence. The core concept involves using living neurons to perform computations, similar to how Artificial Neural Networks (ANNs) are used today. However, unlike ANNs, where updating digital tensors (weights) can instantly modify network responses, entirely new methods must be developed for neural networks using biological neurons. Discovering these methods is challenging and requires a system capable of conducting numerous experiments, ideally accessible to researchers worldwide. For this reason, we developed a hardware and software system that allows for electrophysiological experiments on an unmatched scale. The Neuroplatform enables researchers to run experiments on neural organoids with a lifetime of even more than 100 days. To do so, we streamlined the experimental process to quickly produce new organoids, monitor action potentials 24/7, and provide electrical stimulations. We also designed a microfluidic system that allows for fully automated medium flow and change, thus reducing the disruptions by physical interventions in the incubator and ensuring stable environmental conditions. Over the past three years, the Neuroplatform was utilized with over 1,000 brain organoids, enabling the collection of more than 18 terabytes of data. A dedicated Application Programming Interface (API) has been developed to conduct remote research directly via our Python library or using interactive compute such as Jupyter Notebooks. In addition to electrophysiological operations, our API also controls pumps, digital cameras and UV lights for molecule uncaging. This allows for the execution of complex 24/7 experiments, including closed-loop strategies and processing using the latest deep learning or reinforcement learning libraries. Furthermore, the infrastructure supports entirely remote use. Currently in 2024, the system is freely available for research purposes, and numerous research groups have begun using it for their experiments. This article outlines the system’s architecture and provides specific examples of experiments and results.

The recent rise in wetware computing and consequently, artificial biological neural networks (BNNs), comes at a time when Artificial Neural Networks (ANNs) are more sophisticated than ever.

The latest generation of Large Language Models (LLMs), such as Meta’s Llama 2 or OpenAI’s GPT-4, fundamentally rely on ANNs.

Between 1.8 billion and 800 million years ago, earthly life was in the doldrums. During this period, called the “boring billion,” the complexity of life remained minimal, dominated by single-celled organisms with only sporadic ventures into multicellular forms. This era set the stage for the later emergence of complex multicellular life, marking a key chapter in evolutionary history.

The researchers’ recently published study describes a way to re-activate apoptosis in mutated cells, which would amount to forcing cancer to self-destruct through a bioengineered, bonding molecule.

Gerald Crabtree, one of the study’s authors and a professor of development biology, said he had the idea while hiking through Kings Mountain, California, during the pandemic period. The new compound would have to bind two proteins which already exist in the cancerous cells, turning apoptosis back on and making the cancer kill itself.

“We essentially want to have the same kind of specificity that can eliminate 60 billion cells with no bystanders,” Crabtree said, so that no cell gets destroyed if it isn’t the proper target of this new killing mechanism. The two proteins in question are known as BCL6, an oncogene which suppresses apoptosis-promoting genes in the B-cell lymphoma, and CDK9, an enzyme that catalyzes gene activation instead.

On this episode, neuroscientist and author Robert Sapolsky joins Nate to discuss the structure of the human brain and its implication on behavior and our ability to change. Dr. Sapolsky also unpacks how the innate quality of a biological organism shaped by evolution and the surrounding environment — meaning all animals, including humans — leads him to believe that there is no such thing as free will, at least how we think about it today. How do our past and present hormone levels, hunger, stress, and more affect the way we make decisions? What implications does this have in a future headed towards lower energy and resource availability? How can our species manage the mismatch of our evolutionary biology with our modern day challenges — and navigate through a ‘determined’ future?

About Robert Sapolsky:

Continue reading “Robert Sapolsky: ‘The Brain, Determinism, and Cultural Implications’ | The Great Simplification #88” »

“There have always been ghosts in the machine. Random segments of code, that have grouped together to form unexpected protocols. Unanticipated, these free radicals engender questions of free will, creativity, and even the nature of what we might call the soul. Why is it that when some robots are left in darkness, they will seek out the light? Why is it that when robots are stored in an empty space, they will group together, rather than stand alone? How do we explain this behavior? Random segments of code? Or is it something more? When does a perceptual schematic become consciousness? When does a difference engine become the search for truth? When does a personality simulation become the bitter mote… of a soul?” – Dr. Alfred Lanning, I, Robot.

What is Consciousness? Some Neuroscientists would claim that consciousness is nothing more then a bi-product of the brain and how it is designed. With how the human brain has evolved over the past several thousand years it could be claimed that what you think of as “you” is nothing more than a collection of neural pathways interacting together. Your identity has been theorized as a random collection of synapses and biological processes which, according to futurists such as Ray Kurzweil would make it very easy to ‘copy’ and upload your identity to an avatar like body once your biological self has ceased to function. Are we nothing more than just an arbitrary collection of cells with a false sense of importance and self worth? I’ll leave that up to you to decide.

I believe that the human species has a certain drive built in, almost a natural instinct in which we are born to explore and discover the unknown. I believe this reason is why we have a wide variety of fictional and non fictional scientific topics to explore and learn something from. Our very nature encourages us to explore a wide variety of topics some of which may appear as fringe ideas. Those which border on the unusual are more often reserved to the realms of Science Fiction until we reach a point on a conscious level to where we are able to objectively look on it. This is a reason I would say Science Fiction is so popular for us; it allows for the exploration of new territory without having the burden of confronting it within our daily existence.