#connectome

There’s a peculiar asymmetry emerging.

We can now map fragments of the human brain in petabytes — trace synapses, reconstruct pathways, simulate structure — and still not explain the presence that moves through it.

At the same time, we’re deploying artificial agents into the world. Systems that act, decide, persuade, optimise. Systems that behave like minds, while built atop architectures we only partially understand, pursuing goals defined by incentives we barely examine.

The black box has stopped being a passive instrument. It has become a participant.

This isn’t a technical problem. It’s an ontological one.

Science can describe behaviour. It can map structure. It can measure correlation. But the relationship between structure and experience — between computation and presence — remains unresolved.

The deeper we look, the sharper the boundary becomes.

The ontology gap isn’t shrinking. It’s becoming measurable.

Filed under ongoing Process documentation — signal emerging from noise.

Monkey Matter

The brain uses a complex network of bundles of nerve cells – neurons – to transfer information as we interpret and respond to the world around us. Many of its details are still a mystery, leaving scientists searching for new angles on this vital living supercomputer. Here, researchers examine a monkey’s brain using x-rays at the European synchrotron. Particles forced to loop in circles at high speeds are fired at the tissue sample, uncovering new details based on how the particles scatter. The experiments reveal nerve cell projections known as axons (highlighted as thin multi-coloured lines) and blood vessels (orange) inside a complex region of the cerebral cortex of a monkey. Interestingly, researchers find some groups of axons form layers or laminar structures, adding to our picture of the human brain’s similar connectome.

Written by John Ankers

Video from work by Hans Martin Kjer and colleagues

Danish Research Centre for Magnetic Resonance, Center for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital Amager and Hvidovre, Hvidovre, Denmark

Video originally published with a Creative Commons Attribution 4.0 International (CC BY 4.0)

Published in eLife, February 2025

Upon birth, a person’s brain structure is largely prescribed by experience in the womb and their unique genetic code. As we age, experience continues to imprint unique changes on the brain’s neural connectivity, increasing connections in some areas while decreasing them in others, accumulating reroutes upon reroutes as a person ages and learns, gaining knowledge and experience. Additionally, there are alterations in the strength of existing connections. These processes are especially evident in twins, whose brains are strikingly similar when born. However, as they grow, learn and experience the world, their brains diverge, and their essential selves become increasingly unique.

Essentially, this process creates memory, something so fundamental that it unconsciously surfaces in every aspect of our sense of self. Even our unconscious knowledge of movements needed for riding a bike, speaking a word or even walking require memory. Incredibly, hypothermia victims, who have undergone hours of clinical death signified by an absence of both heart and brain activity can achieve a state of full recovery, demonstrating that neural electrical activity alone is not essential for the storage of memory in the brain.

Although there are indeed anatomical regions that appear to serve relatively specific functions, one’s memory is not formed, stored or recalled within the activity of any single brain region. Certain structures, such as the amygdala and the hippocampus, play key roles but trying to find memory in one specific area is simply impossible. It would be like trying to listen to Beethoven’s Fifth but hearing only the strings (duh duh duh, duuuh!). Instead, memory, in its broadest sense, lies in the uniqueness of a brain’s entire connective structure, known as the connectome. The connectome consists of its complete network of neurons and all the connections between them, called synapses. It is argued that, fundamentally, ‘you are your connectome’.

Thus, a key to unlocking the correspondence between the connectome and memory is to elucidate the entire circuitry of the brain. Tracing the wiring at this scale is no easy task when considering the sheer complexity involved. A mere cubic millimetre of brain tissue contains around 50,000 neurons, with an astonishing total of around 130 million synapses, according to some estimates. An entire human brain, however, is more than 1 million cubic millimetres and contains around 86 billion neurons, nearly equivalent with estimates of the number of stars in our galaxy.