Archive | Uncategorized RSS for this section

BioCybernetics: A Biological Clock System

Many articles on biocybernetics focus on a single system in the organism. This may be because a biological entity is thought as being too complex to be considered in its entirety.

But many system properties are only understandable when the cooperation of its parts are considered.

Cybernetics is meant to be concerned with those properties of systems that are independent of their concrete material or components. The only way to abstract a system’s physical aspects or components while still preserving its essential structure and functions is to consider relations: how do the components differ from or connect to each other? How does the one transform into the other?… Cybernetics, is interested in processes where an effect feeds back into its very cause.. Read More…

Advertisements

Good Timing: The Synchronisation of Neural Networks in Computing and Implications for Neurology

A symbiotic relationship now exists between the study of neural networking in computing, and neurology.  Artificial neural networks were originally inspired by neuroscience, although major developments have been guided by insights into the mathematics of efficient optimization, rather than neuroscientific findings.  A H Marblestone 2016.  Now neurology is looking towards the development of neural networks to increase our understanding of how the brain works.  There is the possibility that  the two fields will increasingly merge – with particular recognition of the importance of bio-physics in the study of intelligence.

For a long time, the accepted model of memory formation was linear. Short term memories were thought to directly transform into long term memory in a classical, mechanistic fashion. But this model has been challenged.

The new model emerging is complex and non-linear.  The brain is starting to be seen as ‘more than the sum of its parts’ – analogous to a parallel computer (with many interconnected networks), artificial neural networks/deep learning, or a ‘network of networks (such as the Internet), with all the problems (cascading failures) and solutions (built in redundancy) that are associated with such a model.

Modern neuroscience is going through a renaissance of its own – moving away from mechanistic views of the brain, to focus on connectivity.  It recognises some networks may be particularly important for such connectivity e.g the default mode network – which is effected in various neurological conditions such as Alzheimer’s, as well as altered states of consciousness such as meditation and psychedelic drug use.
Read More…

Circadian Rhythms and Ageing

Intraterrestrial life extends down at least 5 km and animals are found even in the deepest oceans. The biosphere is, therefore, dominated by dark, largely “arrhythmic” habitats, and in terms of biomass, most of life on earth resides in places isolated from the direct effects of the sun…studies of species that live away from the sun […]

Multi-model Oscillation Based Connectivity Theory Applied to the Integration of Sensory Data

1. Global Clock Synchronisation 

In computing many emerging sensor network applications require that the sensors in the network agree on the time. A global clock in a sensor system will help process and analyze the data correctly and predict future system behavior. For example, in the vehicle tracking application, each sensor may know the time when a vehicle is approaching. By matching the sensor location and sensing time, the sensor system may predict the vehicle moving direction and speed. Without a global agreement on time, the data from different sensors cannot be matched up. Other applications that need global clock synchronization include environment monitoring (for example, temperature), navigation guidance, and any other application that requires the coordination of locally sensed data and mobility.  Q Li 2004.

In these systems various approaches have been taken to temperature compensation  e.g Q Li 2004. S Chauhan 2012.   J M Castillo-Secilla 2013. 

A similar approach could potentially be taken to synchronising biosensors. A Prindle 2015T Danino 2009. J Hasty 2008,  J V Selinger 2003,

This posting considers whether a similar mechanism to global clock sychronisation could be connecting together biological sensors, and supporting temperature compensation.

Another posting on this site explores how this could also support the operational of neural networks. Read More…

Attempting Transdisciplinary Research

Over recent years, the field of “systems biology” has been emerging.  It is throwing light on areas that have long been a mystery.  But how should systems biology develop into a mature discipline? Read More…

Draft: The Emergent Universe and Superconductivity

An Emergent Universe

New states can arise from far from equilibrium, possessing an extraordinary degree of order, whereby trillions of molecules coordinate their actions in space and time.  Prigogine coined the term “dissipative structures” to describe them, since they result from the exchange of matter and energy between system and environment, together with the production of entropy (dissipation) by the system.  

The complex and mutually dependent processes leading to the formation of structures, collectively called “self organisation”…in such a universe, irreversible non-equilibrium thermodynamics allows for the possibility of self organisation leading to structures ranging from planets and galaxies to cells and organisations.  R Highfield and P Coveney 2015.

According to Masser (2006), it would be appropriate to represent the Big Bang not as a single event, but as an on-going process of gradual formation out of chaos.  In other words the evolution of the universe is a continuous self-organisation process that has led to its currently observed structure with a host of galaxies, galaxy clusters and planetary systems.

One indication of such emergence could be seen through patterns known to be generated by self organisation. Read More…

Draft 2: Quantum Coherence and Neurology

Quantum Coherence in Biology.

There is direct evidence for the presence of quantum coherence over appreciable length scales and timescales in the FMO pigment protein complex of the green sulphur bacteria.

It has also been theorised that magnetoreception (triggered by cryptocrhome or magnetite) is utilising quantum mechanical effects.   N Lambert – ‎2012.

The question has remained, how are such quantum effects generated?

One possibility is that the solid state photo-CIDNP effect, singlet and triplet states, ultra-fast electron transfer, and quantum coherence found in photosynthesis (and theorised in magnetorception). During charge separation in biology, triplet states can react with molecular oxygen generating destructive singlet oxygen. The triplet product yield in bacteria and plants is observed to be reduced by weak magnetic fields.  This effect is due to ‘solid-state photochemically induced dynamic nuclear polarization (photo-CIDNP), which is an efficient method of creating non-equilibrium polarization of nuclear spins by using chemical reactions, which have radical pairs as intermediates. A Marais – ‎2016

This process bares a strong resemblance to spintronic semiconductors.  And Certain organic semiconductors (OLEDs) exhibit magnetoelectroluminescence or magnetoconductance, the mechanism of which shares essentially identical physics with radical pairs in biology – specifically singlet and triplet states generated during magnetoreception. PJ Hore (2016).

Biological materials implicated in quantum biology are similar in structure to organic semiconductors. Organic molecules that serve as chromophores (of which flavins such as cryptochrome, are examples) consist of extended conjugated π-systems (the same structure as organic semiconductors) – which allow electronic excitation by sunlight and provide photochemical reactivity. …..Ultrafast electron transfer mechanisms from an aromatic moiety to a photoexcited flavin are not only observed for riboflavin-binding proteins but for other flavoproteins, like for BLUF (blue light sensing using FAD) domains, cryptochromes, and DNA photolyases. H Staudt 2011.  And in biology, evidence has been found that the existence of central aromatic acids can serve as stepping stones to support an electron hopping mechanism W Sun 2016.   J R Winkler 2015

This has implications for consciousness.  For “if nuclear spin resonance is found to have an impact on the spin-dependent electron transport due to the hyperfine interaction, ultimately the opposite process may become possible: storing electronic spin information in the nuclear spin.”   J Matysik (2017). It is already known that cryptochrome plays a role in animal memory. CK Mulder 2016 , A Malik 2015.

More information on possible biological spintronic semiconductors is  available on this site – click here to find out more.

Is there evidence of similar effects in human beings?

J Kirschvink (Caltech) claims to have found evidence of magnetoreception in human beings (June 2016). A V Chervakov 2015 has recently explored possible mechanisms underlying the therapeutic effects of transcranial magnetic stimulation, and suggested magnetoreception may be implicated.

Evidence of reduced triplet product yield in brain tissue following exposure to magnetic fields would be required to demonstrate that the solid state photo CIDNP state effect was present in the brain.

A number of papers have proposed that oxidative stress could be caused by electro-magnetic fields e.g ELF-EMFs exposure (50 Hz, 0.1–1.0 mT) was shown to significantly affect antioxidant enzymatic capacity in both young and aged rat brains (S Falcone 2008).  However other studies suggest that magnetic fields could decrease oxidative stress and damage in rats and gerbils.  H Kabuto et al 2001 ,S R Balind 2014, I Tunez 2006, I Tasset 2010, 2013. Such studies show that the level and timing of exposure are critical factors impacting outcome measures. M Reale 2014.  

Read More…