Sciber

Long-range Collective Quantum Coherence in Tryptophan Mega-Networks of Biological Architectures

noreply@blogger.com (Unknown) — Tue, 24 Mar 2026 10:30:00 +0000

"An empirical-based study has found significant photophysical and photochemical effects in mega-networks of tryptophan in biological architectures resulting from quantum optical enhancement during collective coherence, long-range resonance and synchronization. Contrary to what used to be the common sentiment among experts that the biological system was too wet, noisy, and warm for non-trivial quantum effects like collective coherence, the observed superradiance and long-range interactivity even in the ambient thermal environment of the cell disprove such naïve perspectives (naïve because they were not taking into full account the unique structural / geometric organizational properties of cellular proteins and were based on very simplistic purviews of cellular organization), and is now one of many such findings that demonstrate the robustness of non-trivial quantum effects in the biological system. The findings have wide-ranging implications and are important because collective quantum optical effects in tryptophan mega-networks may underlie key cellular orchestration and signaling processes, like potentially ultrafast information transfer in neuronal axons, which have highly ordered core microtubule filamentary bundles." Full discussion by William Brown. Also news articles at EurekaAlert and PopularMechanics.

See relevant research at:

Babcock NS, Montes-Cabrera G, Oberhofer KE, Chergui M, Celardo GL, Kurian P. [2024] "Ultraviolet Superradiance from Mega-Networks of Tryptophan in Biological Architectures". J Phys Chem B. 128(17):4035-4046. doi: 10.1021/acs.jpcb.3c07936. PMID: 38641327; PMCID: PMC11075083.

Philip Kurian [2025]. "Computational capacity of life in relation to the universe".Sci. Adv.11,eadt4623(2025).DOI:10.1126/sciadv.adt4623

Modeling systems

noreply@blogger.com (Unknown) — Tue, 03 Mar 2026 22:30:00 +0000

Pi the Movie

Fibonacci Sequence

Fibonacci numbers in Nature. The Romanesco Vegetable.
Do Plants Know Math? by PBS NOVA
Fibonacci Spiral Demo.
Fibonacci Music

The magic of Fibonacci numbers by Arthur Benjamin

Peter Hilton (1923-2010) discusses intriguing number tricks that can be explained by analysing the properties of Fibonacci numbers and the related Lucas numbers. The explanations themselves benefit from further explanations which, in their turn, lead to further discoveries. Recorded at Imperial College London during the 1996 London Mathematical Society Popular Lecture series.

D'Arcy Thompson

In retrospect: On Growth and Form by Phillip Ball.
D'Arcy Thompson's Affine Fish Transformations @ Wolfram
S.J. Gould. [1971] "D'Arcy Thompson and the Science of Form". New Literary History, 2 (2): 229-258
W. Arthur [2006]. "D'Arcy Thompson and the theory of transformations".Nature Reviews Genetics 7, 401-406.
Geometry of Growth and Form: Commentary on D'Arcy Thompson
Java applet for shell sketching

Patterns of Life – D’Arcy Thompson, Structuralism and the Shape of Life

Treasures of the Library 5. D'Arcy Thompson, On growth and form

Mathematics of Soft Cells.

BLOOMS: Strobe Animated Sculptures Invented by John Edmark from Charlie Nordstrom on Vimeo. "This series of 3D printed sculptures was designed in such a way that the appendages match Fibonacci's Sequence, a mathematical sequence that manifests naturally in objects like sunflowers and pinecones. When the sculptures are spun at just the right frequency under a strobe light, a rather magical effect occurs: the sculptures seem to be animated or alive!"

protowriting on bones

noreply@blogger.com (Unknown) — Sat, 28 Feb 2026 20:51:00 +0000

Geometric shapes on 40,000-year-old bone and ivory suggest early European Homo sapiens long possessed cognitive tools for language. See news article @ Science and full article @ PNAS.

Advances on cracking Antikythera Mechanism

noreply@blogger.com (Unknown) — Wed, 04 Feb 2026 17:31:00 +0000

"Freeth and colleagues at University College London (UCL) believe they have finally cracked the puzzle using 3D computer modelling. They have recreated the entire front panel, and now hope to build a full-scale replica of the Antikythera using modern materials". News article at BBC News, full article at Scientific Reports.

From Bones to Turing Machines

noreply@blogger.com (Unknown) — Wed, 28 Jan 2026 00:30:00 +0000

The Lebombo Bone and Other Ancient Mathematical Objects
African Binary code

The Ishango Bone

Turing Machine Simulator
Turing Machine Simulator 2
Turing Machine Simulator 3 (Java)

A Turing Machine Overview
BTW, my thoughts on the recent Turing Biopic and a related news article.

Some resources about the Abacus
The Abacus in Various Number Systems
Demo (The Chinese Abacus)
Mechanical Calculators
The Pascaline

The Antikythera Mechanism

The Antikythera Mechanism
NOVA: Ancient Computer

Another video of the Antikythera Mechanism

Babbage, Lovelace and the Analytical Engine
The Difference Engine
The Analytical Engine
9 Neat Facts About the World's First Computer Programmer, Ada Lovelace
Ada Lovelace and the Analytical Engine
Helping Ada Lovelace with her Homework: Classroom Exercises from a Victorian Calculus Course

It Started Digital Wheels Turning

Cool implementation of Babbage's Difference Engine using LEGO! Photos, description of adder and carry propagation logic, mechanical issues, etc. at: By Andy Carol

Von Neumann's Computer Archicture
Von Neumann, J. (1945). “First draft of a report on the EDVAC". Moore School of Electrical Engineering, University of Pennsylvania. DOI: 10.5479/sil.538961.39088011475779.
John von Neumann and the “Report on the EDVAC” from An An Illustrated History of Computers.
Dyson, George. Turing's cathedral: the origins of the digital universe. Pantheon, 2012.

The Manchester Baby (1948)

MESM 1950 (Kyiv)

Module 1 - From Borges to Shannon

noreply@blogger.com (Unknown) — Tue, 27 Jan 2026 20:10:00 +0000

Some pointers to the Jorge Luis Borges stories we discussed in class.

The Library of Babel
The Garden of Forking Paths
Interview with Jorge Luis Borges Borges' biography.

Information Basics
"The heart of his theory is a simple but very general model of communication: A transmitter encodes information into a signal, which is corrupted by noise and then decoded by the receiver. Despite its simplicity, Shannon’s model incorporates two key insights: isolating the information and noise sources from the communication system to be designed, and modeling both of these sources probabilistically. He imagined the information source generating one of many possible messages to communicate, each of which had a certain probability. The probabilistic noise added further randomness for the receiver to disentangle." Full article @ Quanta Magazine.

Predicting Entropy Game Demo. Refining the Estimated Entropy of English by Shannon Game Simulation. Shannon's calculations of entropy of English.
Prediction and Entropy of Languages Wolfram Demo
An experimental estimation of the entropy of English, in 50 lines of Python code
Letter frequency in English
Word and Letter Frequency in English
Entropy of English. .
Text Mechanic - Text Manipulation Tools
Shuffle Letters and Narakeet.
Using Information Theory to Solve Wordle.

1952 – “Theseus” Maze-Solving Mouse @ cyberneticzoo.com

Claude Shannon Demonstrating Theseus

Complexity science could be the key to understanding our place in the universe with David Krakauer

noreply@blogger.com (Unknown) — Mon, 08 Dec 2025 21:23:00 +0000

What is life? What is intelligence? What is… complexity? Neil deGrasse Tyson and co-hosts Chuck Nice and Gary O’Reilly learn how complexity science, chaos theory, and emergence could be the key to understanding our place in the universe with David Krakauer, president of the Santa Fe Institute and professor in complex systems.
If chemistry is universal, could music be? We dive into what makes something “universal,” why Mars is inhabited by robots, and how cities, economies, and societies exhibit emergent behaviors. We explore the roots of complexity science, from steam engines to organisms, and how early thinkers laid the groundwork for studying order in chaos.
What does it mean to call something “emergent”? We break down the definition of emergence, chaos theory, and its relationship to math, physics, biology, economics, and psychology. We discuss humans as individual particles and when the unpredictable becomes predictable. How do we get order out of disorder? We break down how intelligence isn’t just about answers, it’s about understanding. We examine AI, fake knowledge vs. real problem-solving, and whether life itself is a computational process.

The silicon cell

noreply@blogger.com (Unknown) — Sun, 23 Nov 2025 18:27:00 +0000

AI cell models could transform biomedicine—if they work as promised. "This level of detail came at a computational cost—simulating just 20 minutes of a cell’s life required 8 to 10 hours of processing time with high-level GPUs.[...] To their surprise, the simpler methods outclassed the two foundation models in tasks such as classifying cells, the researchers revealed earlier this year in Genome Biology. Even with fine-tuning, some AI cell models still fall short." Full News article @ Science.

Colossus, electronic analog

noreply@blogger.com (Unknown) — Mon, 08 Sep 2025 19:30:00 +0000

"Let us not imagine, however, that Colossus was a programmable, general-purpose computer in the modern sense. It could logically combine two data streams – one on tape, one generated from ring counters – and count the number of 1s encountered, and that was all. Much of the “programming” of Colossus was actually carried out on paper, with operators executing decision trees prepared by analysts." From, The Electronic Computers, Part 2: Colossus.

Mathematicians discover new class of shape seen throughout nature

noreply@blogger.com (Unknown) — Wed, 25 Sep 2024 22:27:00 +0000

‘Soft cells’ — shapes with rounded corners and pointed tips that fit together on a plane — feature in onions, molluscs and more. Full article @ Nature.

What Would the Father of Cybernetics Think About A.I. Today?

noreply@blogger.com (Unknown) — Sat, 20 Apr 2024 22:04:00 +0000

Norbert Wiener's legacy by Seth Lloyd. I reread "Human Use of Human Beings" last year and agree with most, though Wiener was correct about authoritarianism: Whether bottom-up or top-down, we are controlled and not as free as we could given what cybernetics gave us. Still, true that he would be happy that we are still alive!

How mathematics built the modern world

noreply@blogger.com (Unknown) — Fri, 17 Nov 2023 20:18:00 +0000

"Mathematics was the cornerstone of the Industrial Revolution. A new paradigm of measurement and calculation, more than scientific discovery, built industry, modernity, and the world we inhabit today." Full article by Bo Malmberg and Hannes Malmberg @ worksinprogress

Neural-inspired NorthPole energy-efficient computing chip

noreply@blogger.com (Unknown) — Mon, 23 Oct 2023 11:05:00 +0000

"The amount of data humans process and send around the globe on a daily basis is astonishing. However, the energy cost involved is high, and there is a strong need for designing energy-efficient devices. Modha et al. describe a chip with a neural inspired architecture, called NorthPole, that achieves substantially higher performance, energy efficiency, and area efficiency compared with other comparable architectures (see the Perspective by Iyer and Roychowdhury). A key feature of this chip is the recognition that for almost all kinds of computing, access to memory plays as important a role as logic processing. Unlike analog in-memory computing, this purely digital system has the option of tailoring the bit precision as needed, which allows for optimization of the power usage". Full Article @ Science.

How Claude Shannon Invented the Future

noreply@blogger.com (Unknown) — Wed, 23 Aug 2023 22:08:00 +0000

"The heart of his theory is a simple but very general model of communication: A transmitter encodes information into a signal, which is corrupted by noise and then decoded by the receiver. Despite its simplicity, Shannon’s model incorporates two key insights: isolating the information and noise sources from the communication system to be designed, and modeling both of these sources probabilistically. He imagined the information source generating one of many possible messages to communicate, each of which had a certain probability. The probabilistic noise added further randomness for the receiver to disentangle." Full article @ Quanta Magazine.

The role of complexity for digital twins of cities

noreply@blogger.com (Unknown) — Mon, 08 May 2023 22:47:00 +0000

"We argue that theories and methods drawn from #complexity science are urgently needed to guide the development and use of digital twins for cities. [...]. This is the foundation for a new approach that treats cities not as large machines or logistic systems but as mutually interwoven self-organizing phenomena, which evolve, to an extent, like living systems." Full paper @ Nature Computational Science.

A Relational Macrostate Theory Guides Artificial Intelligence to Learn Macro and Design Micro

noreply@blogger.com (Unknown) — Wed, 16 Nov 2022 13:35:00 +0000

"a general theory for how macroscopic properties emerge from conservation of symmetries in the mapping between observations, we provide a machine learning framework that allows a unified approach to identifying macrostates in systems from the simple to complex, and allows the design of new examples consistent with a given macroscopic property." Full article @ Arxiv.

Accumulation and maintenance of information in evolution

noreply@blogger.com (Unknown) — Tue, 06 Sep 2022 19:44:00 +0000

Cool work using information theory to establish upper bounds on information maintenance on organism populations. They "prove a general bound on the rate at which information can accumulate per generation, [finding] that both accumulation and maintenance of information are most efficient (require the least fitness variation per bit) when individual loci experience weak selection. This is relevant for selection on traits influenced by many small-effect loci—a common genetic architecture according to genome-wide association studies." Full paper @ PNAS.

Complexity science and networks in 20 min

noreply@blogger.com (Unknown) — Tue, 06 Sep 2022 18:55:00 +0000

An introduction video to the history and ideas of complexity science and networks in 20 min by Petter Holme.

What Data Can't Do

noreply@blogger.com (Unknown) — Mon, 22 Mar 2021 17:29:00 +0000

"if more data isn’t always the answer, maybe we need instead to reassess our relationship with predictions—to accept that there are inevitable limits on what numbers can offer, and to stop expecting mathematical models on their own to carry us through times of uncertainty." Full article at the New Yorker.

A few things you should know about complex systems

noreply@blogger.com (Unknown) — Mon, 15 Feb 2021 17:16:00 +0000

"Complexity science, also called complex systems science, studies how a large collection of components – locally interacting with each other at small scales – can spontaneously self-organize to exhibit non-trivial global structures and behaviors at larger scales, often without external intervention, central authorities or leaders. The properties of the collection may not be understood or predicted from the full knowledge of its constituents alone. Such a collection is called a complex system and it requires new mathematical frameworks and scientific methodologies for its investigation." A very nice explanation of key concepts with acompanying simulations.

The Hard Lessons of Modeling the Coronavirus Pandemic

noreply@blogger.com (Unknown) — Mon, 15 Feb 2021 17:07:00 +0000

"In the fight against COVID-19, disease modelers have struggled against misunderstanding and misuse of their work. They have also come to realize how unready the state of modeling was for this pandemic." Full article @ Quanta Magazine.

Michael Goldhaber, Simon and the attention economy

noreply@blogger.com (Unknown) — Mon, 08 Feb 2021 13:16:00 +0000

"Most of this came to him in the mid-1980s, when Mr. Goldhaber, a former theoretical physicist, had a revelation. He was obsessed at the time with what he felt was an information glut — that there was simply more access to news, opinion and forms of entertainment than one could handle. His epiphany was this: One of the most finite resources in the world is human attention. To describe its scarcity, he latched onto what was then an obscure term, coined by a psychologist, Herbert A. Simon: 'the attention economy.'" Full article @ NY times.

To Understand This Era, You Need to Think in Systems

noreply@blogger.com (Unknown) — Wed, 03 Feb 2021 11:44:00 +0000

Even though Zeynep Tufekci is a bit dismissive of the existence of complex systems science as a discipline and even departments, this is a great podcast on the Ezra Klein series.

modelling Covid, Interdisciplinarity, and Complexity

noreply@blogger.com (Unknown) — Mon, 04 Jan 2021 14:40:00 +0000

"The pandemic has created a tragic ‘natural experiment’ - a once-in-a-century jolt that could produce unexpected insights. As well as modelling the spread of disease, researchers have had to track the dynamics of social behaviour. Because of modern digital footprints, they have been able to do this in more detail than ever, providing unique insights into how individuals and communities respond to outbreaks. These behavioural changes, whether driven by explicit government policies or local awareness of infection risk, have in turn had complex social, economic and health impacts. Untangling such effects will no doubt be the subject of research far into the future." Full news article @TheGuardian.

molecular collectives that regulate genes

noreply@blogger.com (Unknown) — Fri, 11 Dec 2020 10:43:00 +0000

Cells use condensed ‘blobs’ to collect the molecules involved in regulating genes, sort of "network fluids with viscoelastic properties". Opens very interesting theoretical possibilities for stochastic information processing in eukaryotes. Full article @ chemistryworld.com.