5D Library

Preface: The Brain That Talks to Itself

5D Library › The Default Mode Network, the Entropic Brain and Neural Oscillations · 中文

Preface: The Brain That Talks to Itself

Note

Legal and medical notice. Please read before anything else. This book is a review of published research in computational neuroscience, pharmacology and cognitive science, with mathematical models. It is not medical advice and not legal advice. Chapter 3 discusses psilocybin and related tryptamines. In Malaysia, psilocybin and psilocin are listed in the First Schedule of the Dangerous Drugs Act 1952; in China, in most other countries and under the United Nations Convention on Psychotropic Substances of 1971 they are strictly controlled. Possessing, producing, supplying or using them is a serious offence in those places, and they carry real medical and psychiatric risks. This book does not advise, encourage or describe how anyone might obtain or use any controlled substance, and gives no doses. Clinical studies of these substances are reviewed only to understand, in the language of computational neuroscience, how the 5-HT2A receptor and the default mode network work, and so to make the case for the entirely legal practices of attention in Chapters 4 and 8. Anyone with a mental-health condition, a history of psychosis, seizures, heart disease, or who is pregnant, should speak to a doctor before beginning any intensive practice, including long meditation retreats.

When nothing is asked of it, the brain does not go quiet. In the late 1990s, researchers comparing brain scans taken during tasks with scans taken at rest noticed that a particular set of regions was consistently more active at rest and switched down whenever a task began. Marcus Raichle and his colleagues called it the brain’s “default mode” (Raichle et al. 2001). These regions, centred on the medial prefrontal cortex and the posterior cingulate cortex, turned out to be busiest when we think about ourselves, remember the past, imagine the future and let our minds wander.

This book is about that network, and about the rhythms and molecules that change it. It asks why a brain at rest spends almost as much energy as a brain at work; how billions of neurons fall into step, and what the mathematics of coupled oscillators says about that; what the receptor for serotonin known as 5-HT2A does, and why research on substances that act on it has shaped the scientific idea of an “entropic brain”; how meditation reaches some of the same networks without any substance; what the pineal gland actually does, and what the tiny calcite crystals found in it are and are not; and what light and sound flicker at 40 Hz, and “binaural beats”, have and have not been shown to do. It reads these questions beside the Diamond Sūtra, the Platform Sūtra and the Daoist Secret of the Golden Flower, and ends with a four-week sitting log and a pre-registered experiment that uses nothing but breath and sound.

What this book is and is not

This is a book of models and reviews. Each chapter states an established piece of neuroscience, physics or pharmacology and runs it in a short Python program so that the reader can change the numbers and see what happens. Unless a source is given, the numbers in the programs are illustrative; they show how an argument works, not measurements of any brain. Where the book proposes how a model applies, it says so in a hypothesis box, with the result that would show it to be wrong.

How to read the boxes

As in the other books of the 5D Library, different kinds of statement are kept apart.

Evidence

Evidence boxes report published findings, with their sources.

Calculation

Calculation boxes give formulas and short Python programs. Every program runs as printed with a standard Python 3 installation and nothing else, and its output is shown underneath it.

Hypothesis · not established

Hypothesis boxes hold the author’s ideas. They are labelled “not established”, and they say what result would show them to be wrong.

Source text

Source text boxes quote the classical texts, with the author’s translation.

Note

Note boxes give cautions and explain choices.

The plan of the book

  1. The default mode network and the cost of a self. The brain’s energy budget at rest, the hubs of the default network, and a graph-theory model of what happens when a hub is removed.
  2. Neural oscillations and the Kuramoto model. The brain’s rhythms from delta to gamma, and a simulation of coupled oscillators that shows synchrony appearing suddenly at a critical coupling strength.
  3. The 5-HT2A receptor and the entropic brain. Receptor binding by the Hill–Langmuir equation, Lempel–Ziv complexity and entropy, and a review of the imaging and clinical studies, with their risks and limits.
  4. Meditation and the default network. The imaging evidence on experienced meditators, a model of mind-wandering and noticing, and why trained attention differs in stability and safety from a pharmacological change.
  5. The pineal gland. From Descartes’ speculation to the biochemistry of melatonin and its suppression by light, and the physics of the calcite microcrystals found in the gland.
  6. Entrainment. Forty-hertz light and sound stimulation, from mice to the first human studies, and the mathematics and the evidence on binaural beats.
  7. The classics of mind. The Diamond Sūtra, the Platform Sūtra and the Secret of the Golden Flower, read beside the shift from a narrative self to present-moment awareness.
  8. Practice and a pre-registered experiment. A four-week log of daily sitting and mind-wandering catches, and a randomised crossover trial comparing breath-focused listening with binaural beats.

This edition

This is version 1.0.0, the first complete edition: a preface and eight chapters, in Chinese and English. Corrections, and references the author has missed, are welcome through the 5D Library website.

Disclosure

The author and his group operate websites on singing (vocal.guru and singingasia.com, where the author teaches a listening method discussed in Chapter 4), on frequency and resonance (sacredcubit.com and tensorcoil.com) and on health topics (ketohackers.com and nadplusnadplus.com), and so have a commercial interest in some of the subjects of this book. The book does not promote any product, course or supplement. All the code and the study protocol are published openly for anyone to check.

References

Raichle, Marcus E., Ann Mary MacLeod, Abraham Z. Snyder, William J. Powers, Debra A. Gusnard, and Gordon L. Shulman. 2001. “A Default Mode of Brain Function.” Proceedings of the National Academy of Sciences 98 (2): 676–82.

Fan, Y. (2026). The Default Mode Network, the Entropic Brain and Neural Oscillations: 5-HT2A Receptor Kinetics, Pineal Calcite Microcrystals and the Computational Neuroscience of Meditative Attention [默认模式网络、熵脑与神经振荡] (Version 1.0.0). 5D Library. https://doi.org/10.5281/zenodo.23697320 · Licensed under Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0).