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,

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

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

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

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

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

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 simultaneously. Within every cell, billions of molecules continuously exchange infor

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, signaling complexes, organelles, and regulatory molecules that continuously exch

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 requires. Dynein is enormous. Including its essential additional dynactin complex, i

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 legs is rare in nature—humans, ostriches, penguins, kangaroos, and a few others—e

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 responsive. The tracks stretch from the cell's center outward like spokes, providing

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 is very difficult to determine the shapes of any protein from the sequence of a

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, while the two hydrogens are left slightly positive, which results in four partial

Most people picture molecules as rigid, locked-together structures — like tiny pieces of stone. But the molecules inside every living cell are something far more remarkable: they hold together loosely and temporarily on purpose. The strongest molecular bonds—called covalent bonds—share electrons so firmly that breaking them requires a serious chemical event. These strong bonds produce the stable structures of large molecules like DNA, RNA, lipids, and proteins. When the DNA/R

Alternative splicing of messenger RNA has been shown to be critical for the development of the human brain. The ability to make many new and complex proteins allowed the development of the enormous molecular complexity in different neurons and in different regions. For some reason, in evolution humans developed the ability to use alternative splicing much more than other species. This ability is most prominent in the brain. This post updates the most recent understanding of h

Some think viruses are not alive. It is, therefore, very surprising that they can evade elaborate cellular mechanisms used to find and destroy them. Search and destroy mechanisms of the cell and counter attacks from viruses are very complex. Cells use many sensors to find DNA and RNA that is not where it is supposed to be. When found, other mechanisms are triggered to get rid of it. Major cellular tools are pattern recognition receptors with enormous numbers of variations all

Only a very small percentage of the world’s microbes have been discovered, and even less of the much more plentiful and diverse viruses. So, it is not surprising that many dramatic new viruses have recently been found that alter our understanding of evolution. The giant Pandora viruses and many new unique ocean phages have brought forth questions about the validity of the current three-limbed diagram of the tree of life (archaea, bacteria, eukarya). With viruses and virus lik

50% of the human genome consists of jumping genes or mobile genetic elements. The 8% of human DNA from retroviruses has been vital to human evolution, such as determining the human placenta, epigenetic changes in the brain and digestive enzymes. An epigenetic immune system in the nucleus battles the jumping genes for control of the cell and control of evolution. Jumping genes, being large strands of DNA with specific functions, are much more likely to be the drivers of evol

The regulation of DNA is fantastically complex with many different layers: changing 3D shapes of the chromatin and loops of DNA; regional differences in nuclear DNA; large numbers of different epigenetic tags on DNA nucleotides and protective protein histone molecules; complex DNA repair mechanisms and alternative messenger RNA splicing; hundreds of thousands of transcription factors; and many different kinds of small and large RNAs that influence every aspect of the process.

A previous post noted how microbes can help cancers in all stages of their development. Now, it has been found that the one-time microbe now the mitochondria is also vital for cancer to start, to grow, to survive and to metastasize. These microbes and the mitochondria use back and forth communication to help cancers in many ways. This post describes the recent research about mitochondria and its vital relationship to cancer. Mitochondria Joined Forces With Our Cells Two billi