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…

Creativity in Biology and Computing

No one has been able to define creativity, which is not surprising as it can existing in many different forms – just as there are many ‘art forms’. Creativity encompasses everything from inventing disruptive technologies to painting ‘Guernica’. 

A number of people have tried to categorize creativity e.g (K Lunke 2016, James C. Kaufman and Ronald Beghetto (2007)

However a ‘silo’ approach to creativity, suggesting that individuals can be creative in some ways, but not others, may be based on ‘cultural norms’.  Such an approach to creativity may present barriers to further development including the development of creative machine intelligence.

Here, I will explore whether different forms of creativity might align with each other.

Read More…

Biological Spintronic Semiconductors: Frontiers


Spintronics is an emerging field of basic and applied research in physics and engineering.  Spintronics, meaning “spin transport electronics”, exploits the intrinsic spin of electrons, in addition to their electronic charge, in solid-state devices like sensors.

Spintronic devices make use of spin properties instead of, or in addition to electron charge to carry information, thereby offering opportunities for novel micro‐ and nano‐electronic devices. These devices are expected to become the ideal memory media for computing and main operating media for future quantum computing..  In spintronics the spin of an electron is controlled by an external magnetic field and polarize the electrons. These polarized electrons are used to control the electric current. The goal of spintronics is to develop a semiconductor that can manipulate the magnetism of an electron…  External magnetic fields can be applied so that the spins are aligned (all up or all down), allowing a new way to store binary data in the form of one’s (all spins up) and zeroes (all spins down).

Biological materials are being investigated in spintronics as in the face of continued miniaturization of components and circuitry in microelectronics, conventional semiconductor microelectronics is rapidly approaching its useful miniaturization limits… For an alternative approach…. biological molecules are known to self‐assemble with nanometer scale resolution and possess some unique qualities that might be crucial for nanoscale fabrication.  A Fakhar 2008.

Biological Semiconductors

The concept of biological semiconductors has been around for some years (e.g A V Vannikov 1970. Bioelectrical signals play critical roles in many biological processes such as energy harvesting, rapid communications and inter/intra cellular synchronisation.  Specific examples include photosynthesis, vision, carbohydrate metabolism, neurophysiology, wound healing, tissue regeneration and embryonic development.

Biological semiconductors already identified include melanin and peptides. Charge transport has also been found in a variety of naturally-derived small molecule, semiconducting biological compounds including carotenoids (produced by plants and bacteria), which offer protection against oxidative species, pigmentation, and light harvesting for photosynthesis. M Mukovich 2012.  

The Giese Group, examined electron transfer along a series of polypeptides and demonstrated that the existence of central aromatic acids can serve as stepping stones to support the electron hopping mechanism. W Sun 2016.  It has been noted that ‘assuming an electron or hole in a polypeptide is located on any peptide group, then if the life of this state is comparable with the period of interpeptide vibrations, the distances between all the bonds in the peptide group are changed and stabilised in this state.  Furthermore, in the neighbourhood of this peptide group, the distances between neighbouring peptitdes also becomes different, which changes the probability of transfer from group to group.  It is observed that the proposed mechanism for this is extremely similar to the mechanism of the motion of a polaron in an oxide semiconductor’. L I. Boguslavskii – 2013.

Spintronics, Spin Chemistry and Quantum Biology 

Spin chemistry is an older field of science than spintronics.  It has been drawn upon by those attempting to explain room temperature quantum mechanical effects in photosynthesis and (possibly) magnetoreception (N Lambert 2013).

Very recently it has been recognised that the fields of spin chemistry and spintronics  are working on very similar areas of science and there is a strong argument for drawing the two fields together.

 J Matysik (2017)  has provided an initial ontology that describes the similarities and differences  between the findings of each field.  It might also be useful to turn this into a semantic web ontology to assist in research, and also connect in other fields including quantum biology, and broader biology.  It is important that there is more communication between chemistry, physics and biology around spin in biological materials.

There are various theories relating to quantum biology, but it is hoped that with the drawing together of scientific disciplines, the exact mechanisms will become clearer.

Quantum Biology as Biological Spintronic Semiconductors.

There are several evidenced examples in biology of processes which involve ultra-fast electron transfer, singlet and triplet spin mechanisms and quantum coherence (taking place at room temperature).

  1. Evidence of the solid state photo-CIDNP effect, singlet and triplet states, ultra-fast electron transfer, and quantum coherence in photosynthesis.
  2. Evidence of the solid state photo-CIDNP effect, singlet and triplet states and ultra-fast electron transfer in some flavoproteins.  In addition there are widely explored scientific theories of cryptochrome (a flavoprotein) and/or magnetite triggering a quantum mechanical effect during ‘magnetoreception’.

Manifestations of quantum coherence in different solid state systems include semiconductor confined systems, magnetic systems, crystals and superconductors. Ultrafast electron transfer and charge separation is possible in semiconductors A Ayzner 2015, S Gélinas 2014.

Read More…

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 […]

Is the Coupling of Circadian Rhythms and Metabolism/Redox Regulating Morphogenesis

Self Organisation Far from Equilibrium

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).  Also see J England 2015 on ‘dissipative adaptation in driven self-assembly’.

Dissipative processes are present in biology.  It is asked whether these could be contributing to morphogenesis.

Stochastic reaction-diffusion simulations have been successfully used in a number of biological applications. Formation of skin patterns and the biochemical processes in living cells (like gene regulatory networks), the cell cycle, circadian rhythms, signal transduction in E Coli chemotaxis, MAPK pathway, oscillations of Min proteins in cell division, and intracellular calcium dynamics are examples of processes mathematically modelled by reaction and reaction-diffusion systems. T Vejchodsky 2013, J Eliaš – ‎2014A Zakharov 2014T Hinze 2011. Read More…

The evolutionary importance of iron sulphur flavoproteins

Iron Sulphur Flavoproteins.

This posting explores how evolution may have brought together flavoproteins and iron-sulphur clusters (as co-factors) to optimise a range of functions – including in sequence. Iron-sulfur clusters rank with biological prosthetic groups, such as hemes and flavins in pervasive occurrence and multiplicity of function.

There has been the tendency in research to explore each of the functions of flavoproteins and iron sulphur clusters separately, but such functions can also combine to support a cycle.

It is proposed that adaptation of multiple functions into a cycle may have emerged through an adaptive evolutionary response – initially to the Great Oxidation Event, and then through endosymbiosis.  Perhaps this even offered the basis for the evolution of photosynthesis and respiration in an oxygen rich environment.

As electron transfer proteins they would enable long range electron transfer (which is used in photosynthesis, respiration, catalytic events). Electron transfer proteins contain redox-active prosthetic groups or “redox sites” where oxidation/reduction occurs. The most common redox sites contain metals such as hemes, iron-sulfur clusters, and copper centers but also include flavins, reducible disulfides, and quinones.  

Electron transfer (ET) is a very simple chemical process but closely governs the life on Earth. In nature, an immediate transfer of the electron(s) in photosynthetic reaction center converts light from the Sun to the forms of chemical energy and is stored in glucose or other types of organic compounds, ultimately supplying “food” for living creatures. In a class of blue-light receptor called cryptochrome found ubiquitously in plants and in animals, the process of ET is pivotal to generate the 24-hour life cycle of circadian rhythm and endogenously informs the body organism “time to sleep”. Furthermore, the ET reaction is also involved in repairing photo-damaged DNA and prevents some diseases like skin cancer. The role of ET in biology serves as an energy transmission and evolves the life using Sun power. Ting-fang He 2011. 

Read More…

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…

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 implication for those who are interested in the concept of the holobiont – which suggests that microbes could have a key role to play in evolution.

Microbes Can Influence Host Gene Expression. 

Recent research suggests that microbe have some influence on the circadian rhythms of their hosts.

The bacterial bioluminescence (from the bacteria ‘Vibrio fischeri’) regulates expression of a host cryptochrome gene in the squid-vibrio symbiosis. This finding that bacteria can directly influence the transcription of a gene encoding a protein implicated in the entrainment of circadian rhythms provided the first evidence for the role of bacterial symbionts in influencing, and perhaps driving, peripheral circadian rhythms in the host. In mammals, biological rhythms of the intestinal epithelium and the associated mucosal immune system regulate such diverse processes as lipid trafficking and the immune response to pathogens. EAC Heath-Heckman 2013.

C A Thaiss et al 2016 found that the intestinal microbiota undergoes diurnal compositional and functional oscillations that affect metabolic homeostasis. And that the rhythmic biogeography and metabolome of the intestinal microbiota regulates the temporal organization and functional outcome of host transcriptional and epigenetic programs.

Microbes can partially disable Hnf4a in mice and zebrafish and perhaps obstruct its protective role (throughout evolution, Hnf4a appears to protect against microbial contributions to inflammatory bowel diseases). When Hnf4a is fully disabled, microbes stimulate patterns of gene expression in animals that are associated with inflammatory bowel diseases. Similar effects in zebrafish and mice suggests that this is a common feature of host-microbe interactions that might have existed in our common (vertebrate) ancestors. J M Davidson et al 2017 

The integral liver transcription factor, hepatocyte nuclear factor 4 alpha (HNF4a) is a key target for circadian and glucocorticoid-mediated orchestration of liver gene expression. Thus, glucocorticoids, as well as body temperature, are likely to be key synchronizers of the liver clock, acting through transcriptional cascades involving mPer2 and other regulators. Key liver-specific proteins, such as the glucocorticoid-responsive HNF4a, likely play roles in local synchronization and circadian transcriptional programming. A B Reddy 2007.

In mice gut microbial colonization influences rhythmic signalling events in the ileal epithelium downstream of toll-like receptors (TLRs). This, in turn, regulates the organization of molecular clock activity and glucocorticoid production in the intestine.. A Mukherji 2013. Glucocorticoids in turn play a key role in circadian cell cycle rhythms. T Dickmeis 2007.

Nearly all aspects of digestion and detoxication – from gastric emptying time to fat processing and xenobiotic degradation by the liver – are under circadian control (Dallmann et al., 2014). Read More…