How Microbes Influence Evolution

Associations between microbes and health have been made by researchers for a number of decades, but the question has remained by what mechanism are microbes influencing human health?

A new field of chronobiomics is emerging that may provide an answer this question through researching the associations between microbes and biorhythms. The extent to which large microbial populations, are affected by and/or entrain biorhythms is still being explored, but evidence suggests strong links.

This could also have implications for those who are interested in the concept of the holobiont which suggests that microbes have a key role to play in evolution. Read More…

A Combined Clock and Compass

In animals with magnetoreception, there may be the possibility that cryptochrome (with its connection to both a navigation strategy, and circadian rhythms) may be supporting in an integrated sense of time and place through a system that combined together a clock and compass. Evidence of such a system has been indicated in various species and this is explored further in this posting. Read More…

Collective Behaviours

What is a swarm?

When we think of a swarm, we usually think of swarms of insects, but the term swarm can be applied to different species (e.g herds, flocks, schools, societies (e.g I Couzin. ), and even different scales (e.g gluons, quarks, electrons, particles, cells, organisms, stars, etc).

These ideas are already being explored by a number of scientists, particularly in the field of artificial intelligence where swarm behaviours are used to explore collective behaviour/self organisation.

There are swarming behaviour and growth at various scales, including at cellular level. In their natural environments, cells often undertake complex collective behaviors in response to environmental and population cues. Thus, understanding how cells behave in the wild requires characterizing not only the behavior of isolated cells but also how environmental signals combine with cell-to-cell communication (such as quorum sensing and autocrine signaling to give rise to observed behaviors at the population level). Doing so requires us to examine how the cooperative behaviors of cell colonies differ from those of isolated cells and conversely, how the properties of single cells generate and explain the observed communal behavior. P Mehta 2010.

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Biological Clocks, Reaction-Diffusion, Self Organisation and Quantum Biology


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. Under certain circumstances, entropy producing processes are able to organise themselves in the presence of noise, in a way that so called dissipative structures are formed (Prigogine and Lefever 1975, and Nicolis and Prigogine 1977).  G Bodifee 1986.

Dissipation-driven adaptation has already been explored by a number of well known scientists i.e I Progogine, R Lefever and G Nicolis 1975, M Eigen 1971.  J England 2013, 2014, 2015.

This post seeks to describe a self organising dissipative system which supports biomass/information processing.

Read More…

Superconductivity and the Self Organisation of the 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.

In some materials, the strong electron-electron correlations to other degrees of freedom with the complex many body quantum system lead to new, emergent properties that are controlled by a competition of fluctuation effects, characterised by phase transitions at critical temperature, where correlations lead to coordination with a macroscopic region – resulting in the breaking of a symmetry of the system.

Below the transition temperature, a new broken-symmetry ground state is found, which can possess a variety of novel, emergent properties that are macroscopically observed.  In condensed-matter physics, the complex interaction of many degrees of freedom, such as electrons, ions and spins leads to the formation of properties such as superconductivity, magnetism, charge density waves and orbitally ordered states.

Phase transitions can have a wide variety of important implications including the formation of topological defects , or it may even trigger a period of exponential expansion.

In current physics, from a theoretical perspective, insights from black hole physics and string theory indicate that our ‘macroscopic’ notions of spacetime and gravity are emergent from an underlying microscopic description in which they have no a priori meaning. Read More…

Reaction Diffusion and Self Organisation of the Brain


Interactions between biochemical and mechanobiological activity and feedback loops

It is proposed that the formation and workings of the brain are influenced by an interplay between oscillatory biochemical (reaction-diffusion) and mechanobiological activity (including in response to external stresses), feedback loops, and stochastic resonance.

This relationship between biochemistry and mechanobiology has already been explored in other areas of science.  Waves in the BZ reaction in gels cause deformation, which in turn affects the spiral wave dynamics. Furthermore, a ‘‘chain reaction’’ of spiral wave births and deaths can result from an externally controlled deformation of a medium A. V. Panfilov 2005.  A Adamatsky (2010) describes a propagating excitation wave front inducing an associated mechanical wave of contraction.  Oscillatory dynamics have been found in organs e.g deformation can create spiral waves, and this has been explored in cardiac dynamics. Louis D. Weise et al 2011A. V. Panfilov 2005.

These types of interactions in biology can resemble “chicken or an egg” relationships, as a simple chain of cause and effect is not apparent.  In this paper, it is suggested that this relationship is taking place within a dissipative clock system linking circadian rhythms and cell cycles/oscillations and redox/the metabolism and using positive and negative feedback.  Circadian clocks do not operate in isolation, but rather are mutually dependent upon intrinsically rhythmic cytosolic signals (cAMP, Ca2+, kinases) such as that the cell as a whole has a resonant structure tuned to 24 hour operations. (Hastings et al 2008 in C Colwell 2015).

A fuller range of biological rhythms are explored by Goldbeter 2007.

Biological Rhythms –  (Goldbeter 2007). Period
Neural rhythms 0.001 s to 10 s
Cardiac rhythms 1 s
Calcium Oscillations Sec to min
Biochemical oscillations 30 s to 20 min
Miotic Oscillator 10 min to 24 h
Hormonal rhythms 10 min to 3-5 h (24 h)
Circadian rhythms 24 h
Ovarian cycle 28 days (human)
Annual Rhythms 1 year
Rhythm in ecology and epidemiology years
Segmentation Clock 90 mins
Biological Regulations Examples of Associated Cellular Rhythms
Ion Channel Neural and Cardiac rhythms
Transport Ca2+ oscillations
Gene expression Circadian rhythms, segmentation clock.

Under certain circumstances, entropy producing processes are able to organise themselves in the presence of noise, in a way that so called dissipative structures are formed (Prigogine and Lefever 1975, and Nicolis and Prigogine 1977).  Necessary conditions for the occurance of dissipative structure are that the system is open , that it is in a state far from equilibrium and that non linear processes occur within the system.  In these  conditions, internal small fluctuations may be amplified non linearly by a flow of mass and energy from the surroundings.  The system is then removed irreversibly from its initial state, in particular from any homogeneous or unorganised state that is characteristic for equilibrium conditions.  Therefore the new state is characterised by a more organised internal distribution of matter, energy and process rates.  G Bodifee 1986Goldbeter 2007.

Read More…

Quantum Consciousness Supported by Semiconduction and Superconduction


Manifestations of quantum coherence can be found in different solid state systems including semiconductor confined magnetic systems, crystals and superconductors.

PJ  Hore (2016) has pointed out that 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. 

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. Eukaryotic riboflavin-binding proteins typically bind riboflavin between the aromatic residues of mostly tryptophan- and tyrosine-built triads of stacked aromatic rings…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, including in flavins, with suggestions that a redox doping type mechanism may be in operation (also see Orf 2015 and 2016 

These ideas are further explored in another posting – click here to find out more.  This includes evidence of solid state photo-CIDNP and its involvement in ultra-fast electron transfer, singlet and triplet states and quantum coherence within biology (and therefore at high temperatures).


J Kirschvink (Caltech) claims to have found evidence of magnetoreception in human beings (June 2016).

He has used a Faraday cage to demonstrate that human brains can be influenced by magnetic fields.  When the magnetic field is rotating counterclockwise, there’s a drop in participants’ alpha waves. The suppression of α waves, in the EEG world, is associated with brain processing: a set of neurons were firing in response to the magnetic field, the only changing variable.

Kirschvink’s experiments found that when magnetic field is rotating counterclockwise, there’s a drop in participants’ alpha waves.  Existing research suggests there is a mutual relationship between gamma and alpha oscillations in the visual cortex.  K Hepp (ed P Blanchard and J Frohlich 2015).

Currently the sample size is very small (24 participants) and the results need to be peer reviewed for publishing, but it will be interesting to see further information on this in the future.

The mechanism behind such magnetoreception is unknown, however recently it has been found that a polymer-like protein, dubbed MagR (Drosophila CG8198)  forms a complex with a photosensitive protein called Cryptochrome (Cry).  The MagR/Cry protein complex, the researchers found, has a permanent magnetic moment, which means that it spontaneously aligns in the direction of external magnetic fields. This is the only known protein complex that has a permanent magnetic moment. Cry likely regulates the magnetic moment of the rod-shaped complex, while the iron-sulfur clusters in the MagR protein are probably what give rise to the permanent magnetic polarity of the structure. S Qin – ‎2016.

In transgenic C Elegans, expressing this magnetoreceptor in myo-3-specific muscle cells or mec-4-specific neurons, application of an external magnetic field triggered muscle contraction and withdrawal behaviour of the worms, indicative of magnet-dependent activation of muscle cells and touch receptor neurons. It was also found that the magnetoreceptor could evoke membrane depolrisation and action potentials, generate calcium influx, and trigger neuronal activity in both HEK-293 cells and cultured primary hippocampal neurons when activated by a remote magnetic field. The magnetogenetic control of neuronal activity could be dependent on the direction of the magnetic field and exhibits on-response and off-response patterns for external magnetic fields applied. The group also screened other species’ genomes and showed variants of both proteins were highly conserved across several animals, including pigeons, monarch butterflies, whales and even humans. X Long 2016

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 such findings have been contradicted in other studies.   H Kabuto et al 2001 demonstrated that no ROS generation nor lipid peroxidation could be detected in brain homogenates of exposed mice. Interestingly, they observed a slight decrease in oxidative damage in mice exposed to static field (2–4 mT). S R Balind 2014  also found extremely low frequency magnetic field (50 Hz, 0.5 mT) reduces oxidative stress in the brains of gerbils.  ELF-EMF exposure, in the form of transcranial magnetic stimulation (60-Hz, 0.7 mT) applied to rats for 2 hr twice daily, can prove neuroprotective. Extremely low-frequency EMF can mitigate oxidative damage, elevate neurotrophic protein levels in brain and ameliorate behavioral deficits in rats (I Tunez 2006, I Tasset 2010 and 2013 found that EMFs activated the antioxidant pathway Nrf2 in a Huntington’s disease-like rat mode), Extremely low-frequency electromagnetic fields land   as well as potentially augment neurogenesis. Such studies reiterate that the level and timing of exposure are critical factors impacting outcome measures. M Reale 2014.  

A V Chervakov 2015 has recently explored possible mechanisms underlying the therapeutic effects of transcranial magnetic stimulation. Read More…