A scientific exploration of mind at all scales of the universe
Hepatitis D virus, also called hepatitis delta virus, is one of the strangest human viruses. Its genome is a tiny circular single-stranded RNA of only about 1,700 nucleotides, and it produces essentially one protein in two forms—the small and large hepatitis delta antigens. It does not encode its own enzyme to copy its RNA as most RNA viruses do. It doesn’t produce its own envelope proteins or…
From a Primitive Energy Sensor to the Master Guardian of Cellular Energy Long before animals, plants, or the first eukaryotic cells existed, bacteria and archaea already decided the best to use their energy. Every cell continuously judged whether enough ATP was available to build new molecules, or whether scarce resources demanded conservation and repair instead. Early life responded to energy…
Increasing Intelligence of mTOR: From a Primitive Survival Kinase to the Master Integrator of Complex Life The story of mTOR shows that biology builds increasingly intelligent molecules not by inventing entirely new molecules, but by continuously expanding the information-processing abilities of existing ones. Today, mTOR (mechanistic Target of Rapamycin) is near the top of the regulatory…
Adenosine is in perpetual motion. The aromatic adenine ring continually redistributes its electrons, creating changing electrostatic landscapes that influence how it interacts with neighboring molecules. The ribose sugar flexes between slightly different conformations, altering the molecule's three-dimensional geometry. The bond connecting the base to the sugar rotates, allowing adenosine to…
RNA is a structural molecule whose three-dimensional architecture stores biological information, interacts with cellular proteins, catalyzes chemical reactions, and coordinates an infectious life cycle. It carries out these actions through precise three-dimensional structures capable of recognizing and binding other molecules with high specificity. What is less widely appreciated is that RNA…
For most of scientific history, light was viewed primarily as a source of energy. Plants used it to power photosynthesis, animals used it for vision, and sunlight warmed the Earth. Modern biology has revealed that light is one of nature's richest information systems—connected to all other biological information systems. Every day, every organism on Earth continuously reads an enormous vocabulary…
The most fundamental distinction between life and non-life on Earth is not metabolism, reproduction, or even DNA—it is the capacity to harvest, transform, and respond to light energy. Every living system depends, directly or indirectly, on the ability of certain molecules to absorb photons and undergo electronic transitions that enable chemistry otherwise forbidden by ordinary energy. Light is…
A viroid is smaller than a virus. It is a strand of RNA with 246 to 467 nucleotides in length. It is single-stranded, with extensive self-bonding between bases and forms into a fluctuating rod-like or branched structure. It does not produce proteins, has no capsid or membrane, and hijacks cell enzymes to copy itself with a circular rolling mechanism. Thus far, viroids are only found in plants.…
If mind exists throughout all of nature, then how would it manifest in the realm of atoms? Would atoms have desires, goals, and plans? What would be their behaviors and personalities? Because their electronic structures are so different, each atom in living matter behaves in remarkably consistent, and different, ways. Therefore it is not difficult to describe them as having distinct personalities.…
The first signals from bacteria communicating to fellow comrades were discovered in the 1960s. It took 60 years of research to realize the intelligence of bacteria. The first virus signal was discovered in 2017 and in the nine years since then a vast amount of information has been discovered about virus communication. Much of the research has been in phage viruses––viruses that interact with and…
Adenine––The First Intelligent Molecule Life did not begin with cells, organs, brains, or nervous systems. Some molecules possessed such extraordinary chemical and physical properties that they repeatedly became the foundation for increasingly complex intelligent biological systems. Among them, one molecule stands out above all others—adenine. Perhaps the reason adenine was the first truly…
In 1972, a British pharmacologist named Geoffrey Burnstock published a paper proposing that ATP is released from nerve terminals and acts as a neurotransmitter. The scientific establishment's response was a dismissal. The objections were that as the universal energy currency of all living cells, ATP was too ubiquitous to serve as a signal among neurons––it was everywhere, inside everything. That…
For more than a century, neuroscience has been built around a neuron-centered worldview. The heroes of this story are familiar neurotransmitters: dopamine, serotonin, norepinephrine, acetylcholine, glutamate, and GABA. Textbooks describe neurons communicating across synapses in brain circuits using these specialized chemical messengers. The vast ‘connectome’ network of axons and dendrites was…
For more than a century, biology has largely viewed cellular communication as a chemical process. This chemical view has been very helpful in describing a large number of cellular signaling pathways. However, modern cell biology increasingly reveals a deeper reality. Cells are not simply bags of chemicals. They are highly organized information-processing systems operating across many scales…
When most people imagine a living cell, they picture a microscopic bag of organic materials. In fact, as described in prior posts, a cell is a vast, organized society whose members constantly communicate, cooperate, negotiate, compete, and adapt to changing conditions. At the center of this society lies a remarkable transportation system: an immense network of molecular tracks, scaffolds, motors,…
Dynein is a vastly more complex motor than kinesin. It walks along microtubules carrying vesicles, RNA granules, mitochondria, signaling complexes, and even large full chromosomes. It moves the entire cell nucleus during immune cell movement and manages the extraordinarily complex choreography of chromosome separation during cell division. It is a motor with awareness of what each situation…
Kinesin is an individual cellular motor made of just four protein chains that senses, navigates, makes decisions, and walks with two feet, step by step like a human. It picks up a variety of cargo, such as vesicles, mitochondria, molecular complexes, or messenger RNA and walks, one deliberate step at a time, along a highway of protein cables toward a precise destination. Walking upright on two…
Many of the cell’s most important functions occur through the actions of a huge, dynamic, complex scaffold that extends throughout the cell. It consists of tracks along which molecular motors walk and carry necessary cargo everywhere in the cell. This scaffold is not made like rigid, passive railroad tracks, but tracks that grow, shrink, and bend—precisely organized, but dynamic and instantly…
Since DNA’s discovery, molecular biology had operated on reassuring assumptions: every protein folds into one precise, stable shape; shape determines its function; and shape is determined by a sequence of amino acids produced by a sequence of DNA letters. It was a clean idea. The holy grail of bioscience for decades was finding the shapes of proteins and the DNA codes that determine that shape. It…
Water is the medium that makes life possible. Water is so ordinary that we rarely think of it as doing anything. But inside a living cell, water is not a passive background—it is an active participant in nearly every molecular event and every cellular structure. The water molecule has a peculiar geometry. One oxygen atom pulls so strongly on two hydrogen atoms that it ends up slightly negative,…