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AMPK and The Increasing Intelligence of Molecules
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 availability, but it did so through many separate, local biochemical sensors rather
jonlieff
6 days ago13 min read


mTOR’s Emergence as the Master Cellular Regulator
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 hierarchy of virtually every human cell. It decides whether cells should grow or shrink,
jonlieff
Jul 266 min read


The Dance of Adenosine, AMP, ATP, and RNA
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 present different molecular surfaces to enzymes, receptors, and RNA. Around it, layer
jonlieff
Jul 253 min read


Infectious RNA Dancing Structures: Highly Concentrated Biological Information
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 achieves this wide range of interactions not despite its constant movement, but becau
jonlieff
Jul 237 min read


The Language of Light
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 carried by photons. From bacteria living deep in the oceans to giant sequoias, fu
jonlieff
Jul 225 min read


Light As Biological Information
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 life's most versatile form of information, regulation, and chemical power. At the m
jonlieff
Jul 206 min read


A Strand of RNA with Only 250 Nucleotides Has a Complex Lifestyle
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. Also, they can contain ribozymes, which are RNA regions that are able to accuratel
jonlieff
Jul 196 min read


What If Atoms Can Think…
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. These personalities arise from the fundamental laws of quantum mechanics—th
jonlieff
Jul 186 min read


Complex Virus Communication
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 inhabit bacteria. It is clear now that phage viruses are not making decisions ba
jonlieff
Jul 156 min read


Is This How Life Began?
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 intelligent molecule is the remarkable number of ways it can interact with its surround
jonlieff
Jul 46 min read


A Communication System for All Cells
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 skepticism delayed a medical revolution by two decades. Burnstock continued wor

Jon Lieff
Jul 25 min read


ATP and Adenosine—Fundamental Cellular Communication Signals
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 believed to determine mental events. Neurons were viewed as the only true informatio

Jon Lieff
Jun 225 min read
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