Knots in Yoga

Knots in Yoga



Key Terms

  • Granthies or Knots
  • Bandha or Locks
  • Chakra or Energy Centers
  • Nadis
  • Kundalini shakti
  • Tantra
  • Yoga
  • Knots
  • Triplicity
  • Tribhang
  • Trefoil Knot
  • Dhumra Linga, Bana Linga, Itara Linga
  • Brahma, Vishnu, Rudra Knots
  • Tamas, Rajas, Sattva Gunas

3 Granthi in Kundalini Yoga


In Kundalini Yoga, it is said that there are three Granthi can be responsible for preventing prana from rising up through Sushumna Nadi. This Granthi three knots prevent one’s full potential from Kundalini rising energy. These three knots are Brahma Granthi, Vishnu Granthi and Rudra Granthi. They also relate to the Prakritis three Gunas (Tamas, Rajas and Sattva).

Some yogis in yoga see Granthi as a bamboo tree, where each segment is a barrier or barrier to the increase in kundalini energy.

The chakras in the psycho-physical human body at the dormant state form complex intertwined structures, called Granthi, or knots, as they are “link” matter and spirit, enhancing the sense of ego. There are three main granthis in the human body, which make the trinity of Brahma, Vishnu, and Shiva respectively, and they are called Brahma Granthi, Vishnu Granthi and Rudra Granthi.
In any practice to achieve success in the process of Kundalini awakening it is important to open these psychic knots. However, it is quite difficult because of granthi inextricably connected with all that we are accustomed to thinking of our personality, our habits, qualities, desires.

Three granthis together constitute the unconscious complexes (samskara) woven by illusion, and the weight and rigidity of the past is strong opposition to the passage of spiritual power.

The three Granthi are :

  1. Brahma granthi. it covers the area of Mulahara and Svadhisthan chakras. Some call it the perineal knot. It relates to the Tamas Guna (Mulahara and Svadhishthana) the universal destructive power.
    In both the Jabal and the Yogashikha Upanishad state that this granthi is located in the Muladhard chakra. However, most tantric scriptures place it in the Manipura chakra.
  2. Vishnu granthi (doing and prana). It covers the area between Manipura, Anahata and Vishuddi chakras. Sometimes it is known as the navel knot. It relates to the Rajas Guna (Manipura and Anahata) – the universal power of motion and activity.
    Vishnu granthi is said to be located in the area of Anahata chakra (the heart center), which is also the seat of prana. The heart is also the major knot chakra. So, to take the Kundalini Shakti into the passage of the Sushumna through Anahata chakra is also not very easy.
  3. Rudra granthi (Jnana, true knowledge). It covers the areas of Ajna and Sahasrara chakras. It is also known as the forehead knot. Unlike the other five chakras, the Ajna chakra is not connected to the spinal cord. So, the Rudra granthi is blocking the flow of prana beyond the sixth chakra between the eyebrows, Ajna chakra, upwards toward Sahasrara. It relates to the Sattva Guna (Vishuddha and Ajna), the universal creative power.

The Brahma granthi separates the first two chakras (Mulahra and Suadhisthana chakras) from the Manipura chakra. The sympathetic chain is continuous, however, at the upper level of the splanchnic nerves, the presynaptic system changes to the post-synaptic system. So, one can say the Vishnu Granthi is between the Manipura and the Anahata chakras.

Brahma Granthi is the first major block that sadhaka need to transcend. This granthi keeps a person under the illusion of the material benefits, physical pleasures, lethargy, ignorance, and uncertainty.
Among all the most powerful is an illusion of physical pleasure. This granthi plays an important role because it is responsible for the material man’s thinking. It creates a kind of attraction in the nature of the human mind.

Brahma granthi is covered by the essence it produces. This essence is called as “Kledam”. It is colorless and smells as a lotus flower. It is like a mixture of ‘Kapha’ which covers the entrance of Sushumna and also lubricates the Nadi connected. This lubrication helps the pulses of Nadi.

This Kledam is a thick mixture and thickens when we get older if we don’t practice yoga. With the power of Yoga can penetrate this barrier and go up through Sushumna through each barrier.

In short, anatomically the Granthis exist due to either the change of systems from sympathetic to parasympathetic, the separation of Vagus nerve from the Sacral nerve, or the changes from presynaptic fibers to postsynaptic fibers.

The philosophy of Kundalini Yoga is associated with the flow of energy in the channels called Ida and Pingala, (the female and male channels of the astral body, comparable to the sensory and motor nerves of the physical body) and its criss-cross centers in the spinal canal called Sushumna Nadi called chakras.

The three major intersections in the central Sushumna Nadi are at Muladhara (pelvic region), Anahata (chest region) and Ajna chakras (between the eyebrows) are interpreted as Granthi because the exchange energies of physical and mental levels occur at these three places and named after the Trinity.

Granthi means a knotted area which prevents the free flow of energy (Prana) from rising upwards. The concept and explanations related to granthi is a vague term that deals with very internal issues of undoing it and hard to give a figurative expression in a stone medium because they are levels of awareness where the power of Maya, ignorance, and attachment to material things are especially strong.

According to ancient spiritual science, every human has a gross physical body, the subtle astral body, and mind as its counterpart which is linked to each other. Though mind resides and interacts in the physical body, it cannot be given proof for its structure nor location in the body, but the mind influences the astral body also. The energy for the physical body is through external aids, but, energy for the astral body is dependent on the calm state of mind which can be achieved by getting out of the worldly entanglements termed as granthi.

The Ida and Pingala Nadi that are like spirals of opposite poles of the central axis intertwine and unlock while passing through the seven chakras. Psychic knots of granthis are like protective blockages for the gradual change in awareness and open only with the purification of mind and balance between the two Nadi. The purpose of granthis is to block the sudden upward flow of prana, are like circuit breakers to protect the overload that may occur to the practitioner in case of a spontaneous ascension. The display of ‘granthis’ is associated with the ‘Trinity’ as the three main deities (Tri Murti).

They are visualized like psychic knots or obstacles on the path of the awakened kundalini, (The power of awareness) which is difficult to pass through for every human, as it brings about a change in personality. Each aspirant must transcend these barriers to make a clear passageway for the ascending kundalini. In tantra based sculptures, the two major components Nadi, Ida and Pingala of kundalini as are pictured in anthropomorphic form as male and female human figures and crisscross is indicated as in contact or the hand positioned in the specific region of chakra.

In sculptural representations of this topic, the figures, since it is related to mind, the core of ‘Chitta’, are usually presented in a nude form, as the bare body represents the unadorned form of mind. In symbolic representations, they are like male and female snakes coiling at three places. The psychic Knots of granthi is depicted in the symbolized form as the Shiva Linga symbol. Different temples use different motifs to convey this topic in sculptures. The two sculptural representations are:

  • Symbolic representation of granthi, through the Linga and snakes.
  • Representation of grant in the human body in a personified form.

Kundalini yoga, a classification under tantra yoga is the form of subtle energy that flows in tubular channels called Nadis towards the conductor. The conductor is nothing but the nerve energy in the physical body that is encased in the spinal canal and called Sushumna. The intersections are recognized as chakras, seven in number, where the two nadi crisscross. At every chakra, a perfect balance and harmony must be established between the two Ida, Pingala Nadi or otherwise the energy of kundalini cannot progress to higher levels in the central channel of Sushumna.

In sculptural representations of tantra yoga depictions, the mind was projected as the female deity and prana as the male deity. Some sculptures depict the two male and female figures to be in contact at three or five regions like the foot, knee, genital place (Muladhara), heart (Anahata) and the tip of the nose (that is connected to Ajna chakra). Some schools recognize the chakras to be sixteen starting from foot, knee, palm, and so on. The contact at the foot and knee is suggestive of the lower points from which the Ida and Pingala (Female and male Nadi) arise and proceed. The contact at the foot is suggestive of the initial phase of activating the Ida and Pingala Nadi.

To clear Brahma granthi is to establish in totality, clearing Vishnu granthi is perceiving the existence of universal life principle and to clear Rudra granthi is to attain a non-duality of realization of oneness and universal awareness.


Brahma Granthi

Brahma Granthi at Muladhara chakra is represented by the Dhumra Lingam. Dhum means smoky. The linga is represented smoky and ill-defined (some Lingas made of Sphatika – a crystalline form of quartz stone) as a Symbol of the physical world. It is also called Svayambhu linga- the self-created linga. It signifies the establishment of life principles in totality.

Brahma granthi functions in the base region of the Muladhara chakra at the genital area and hence a display of organs. It implies the entanglement with physical pleasures, material objects, and excessive selfishness or a sense of fear. It also implies the ensnaring power of tamas – negativity, lethargy, and ignorance. Such negative qualities act as hindrances and stop the serpent power kundalini from awakening. Once this blockage is removed from the energy instincts of the deep rootedness with worldly affairs, the realm of consciousness gets awakened and the trapped serpent power energy is released. The kundalini or primal energy is thus able to rise beyond Muladhara and Swadhisthana without bogged down by the attractions to which our consciousness is hooked. On breaking open the Brahma granthi, the practitioner feels relaxed and enjoys bliss arising from the void.

The figures related to the granthis are nude because they are related to the state of mind ‘Chitta’ and personal. Muladhara relates to, Ajna chakra as the starting and release points of prana, which is indicated in the sculptures as contact points. Muladhara has a direct link to Ajna chakra – situated in midbrain but indicated as above the nose, between the eyebrows. The subtle energy of these two Ida-Pingala currents crosses over to connect with the right and left hemispheres of the brain.

Brahma granthi is the manifest force of the energy of life and creation, depicted in sculptures as the pleasure of touch. It is known as blockage of Brahma because it holds the consciousness at the level related to physical dimensions like sensuality or procreation. Once this blockage is overcome, the consciousness of deep rootedness to worldly pleasures is released. The kundalini can rise above, crossing this knot.

Vishnu Granthi

Vishnu Granthi in Anahata chakra (between Manipura and Ajna chakra) is represented as Bana Linga. The linga is depicted red or gold-colored as a Symbol of the subtle world. Clearing Vishnu knot is to perceive the existence of universal life principles.

The contact at the chest is the second stage of awareness at Vishnu granthi – to detach from emotions related to bondage. Vishnu granthi operates in the region of the Anahata chakra in the heart region. It is associated with the bondage of emotional attachment and attachment to people and inner psychic visions. It relates to the qualities of rajas – the tendency towards passion, ambition, bondage and assertiveness, individual ego and power. Once the blockage at Vishnu granthi is removed, the practitioner feels great bliss. The sustenance energy undergoes a change from the localized centers of the physical level to the universal level which means the energies of the body become harmonious with the energies of the cosmos. The interaction between the individual personality and the cosmos begins to happen naturally & spontaneously, enhancing the quality of compassion.

The position of placement of chakra wheel as balls suggests that she is activating the Ida and Pingala in legs as well as in hand with the acupressure or chakra ball. It also gives a hint that opening out of Vishnu granthi is not a spontaneous act. It begins from the hand and leg Nadi, followed by the opening of Brahma granthi at Muladhara. In the right hand, as she is holding the ball, highlighting the thumb as the starting point of Nadi in hands. Activating the center of hands and feet is beneficial to health.

The freedom from the knotty – worldly problems and the freedom from knotty congestion in her meridians that restricts the flow of bioenergy at her mental and physical levels – are viewed as obstacles, the root cause for problems and indicated as the cloth around the breasts called ‘kanchuka’ with a knot. Philosophically, clearing the knot of kanchuka means liberation – freedom from ignorance, bondage, commitments due to obligations of bondage, power are the obstacles project as knotty problems in life. The aspirant is constantly advised to dissociate from all limitations and identify oneself with all the pervading, blissful, non-duality spirit of the Brahman.

Rudra Granthi

Rudra Granthi in Ajna chakra is called Itara or Itakhya Linga. The linga is black, well defined with a very consolidated outline. Here, in Ajna, the awareness of ‘what I am’ is more sharply defined and various capacities are being awakened. The Dhumra and Bana Linga are depicted in lotus petals and only Itara linga is well defined. It signifies a state of non-duality. Clearing of Rudra granthi promotes spiritual vision. Awareness goes at the transpersonal level with super consciousness.

The loving gaze was used as a simile in tantra based sculptures to explain the abstract concept that mind (female) and prana (male) are harmonizing and mind is coming under the control of prana, in other words, mind is one with the object concentrated upon enjoying supreme bliss and super consciousness called ‘samadhi’.

The third contact at nose tip is related to crossing the hurdle of Rudra granthi – restraining from the thoughts of pride that comes sometimes from service to others or as the knower of knowledge. The pride prevents one from uniting with all with a non-dual thought. The three granthis when crossed, open the doors of Sahasrara chakra promoting spiritual vision and super consciousness. The Ida Pingala Nadi first intersect at the base of the spine and ends at the third eye center indicated at the apex of the nose. At the third eye center, these two currents cross over to connect with the right and left hemispheres of the brain.

The nose of the two male and female figures touch to symbolize the revitalization of memory and concentration of intuitive knowledge or cognition. Physiologically, the nasal nerves of olfactory bulb travel directly to the limbic area of the brain which controls the unconscious intuition of memory and sexuality. It functions in the region of Ajna chakra governing the Ajna and Sahasrara chakras. It represents the transformation of an existing form, idea or concept into the universal aspect. It is associated with the attainment of siddhis, a psychic phenomenon but still attached to and the concept of self as the power. In a psychological perspective, though serving others is a completely satisfactory way to spend one’s life at this stage, this service could create resentment against others, and view them as lesser beings as the pride of acquiring knowledge sometimes gains an upper hand. One must surrender the sense of individual ego and transcend duality to make further spiritual progress and then complete the circle by bringing that consciousness into compassionate actions.

With awareness, yoga practitioners ascend towards the Sahasrara chakra where the final merging of the individual Soul or Atman with the universal cosmic soul takes place to achieve the realization of oneness.

Awakening of Kundalini Shakti

Rshi Patanjali said “it is very difficult to walk on this Yoga path (Kundalini) like walking in the eyes of a knife that is very sharp, wrong or slipped a little too wounded” also walked to meet Him like doing a masterpiece project, all obstacles and obstacles we must be able to overcome only with determination. , disciplined and diligent practice.

So far we leave Him to approach him is something that requires extra energy. The energy that drives the realization of the Yoga goal is Kundalini Energy. Energy is power, power, shakti, power or whatever the term all of this already exists within us and also outside ourselves. Enormous energy that lies dormant in the form of a 3.5-circle snake with his head facing down around Linga swayambhu Siwa.

If the Kundalini energy is able to be raised, this energy will push someone to reach his life goal or his Yoga goals. The increase in Kundalini’s energy will cleanse every chakra that is passed then activate the chakras and various Siddhas will be felt even though it is still only a moment. The increase in Kundalini will be very helpful, especially to increase self-awareness and the vitality of the body is also increased, for example, to help self-healing or even become a healer.

But what needs to be considered is not only the benefits that are very useful, but also how we deal with every problem caused by the rise in Kundalini. Because the increase in kundalini will clean and open the knot chakra because kundalini is only limited to energy so this energy will play just breaking down, so we need to know the knowledge and directing techniques so that nothing happens that is desired. Many spiritual aspirants have fallen ill because of Him without realizing that the cause is Kundalini (kundalini syndrome).

Everyone has this Energy hidden in our body. Kundalini energy is very large energy like nuclear energy in the body. It can be imagined how much energy is in our bodies if this energy we are able to generate. To generate Kundalini energy you need sufficient knowledge, especially regarding the Main Chakra. In addition to this knowledge, a guide who really knows about the awakening of Kundalini or a spiritual teacher is very much needed.

Kundalini is the mother who protects us, the mother of the universe is often referred to as Mrs. Durga (Hyang Nini Bagawati), Mrs. Gayatri and Mrs. Saraswati. To awaken this Sakti Energy there are various ways and with certain training.

If the awakening of Kundalini towards this negative direction will have unfavorable consequences, there are several things that are affected that can hurt the physical body, this can be really real or will change the nature, emotions, behavior, and others towards the negative.

Kundalini is more commonly interpreted as a scroll, a power is in “Kunda” which is a quadratic place or mandala (Muladhara chakra), encircling the “Linga” three half circles that are above the “Yoni” Kundalini in the form of a snake resides in the cakra Muladhara and in in Muladhara there is linga and yoni this is where Kundalini as a power of silence. Kundalini is also known by various names including Mrs. Durga, Mother at times, Mrs. Bhuta, Mother Universe, Mrs. Bagawati and so on, all Mother’s names are Himself. She is also referred to as Ibu Prana, the inner Power of the Mother or latent energy whatever the name refers to her. I offer my devotion to the Great Mother … Energy Mother …

The negative polarities will flow towards the positive polarity, and the positive polarity is in the fontanel in Sahasrara Cakra where the Supreme Lord is located. Passive Shiva who is silent but whose vibrations spread to meet nature. Single Shiva (Eka) and many (various) at the same time. Shiva who lives in Sahasrara means that the vibrations of his silence dwell in each person’s Sahasrara. He sits in his favorite siddhasana, he whose body is bright as the reflection of sunlight on a snow mountain, whose hair is neatly woven, which flows holy Ganga water, surrounded by beautiful crescent moons, wears snakes as His necklace, blue-necked, body covered with weed, His two hands lifted up to give blessings and deliver from all fears, adorned with tiger skins as His garments, who sat on a lotus of thousands of golden leaves, whose smiles emit vibrations of peace.

The awakening of the Kundalini energy flow is determined by our level of consciousness, or in other words, we process it, we are the controller.

The thing to consider is that energy is still energy, He will follow our own consciousness, follow our mindset if we think towards virtue

Purification of Karma through 3 Granthi

In each bulkhead, vertebrae are stored with positive and negative karma as long as humans life. Every action or result of mental karma will be placed according to the place that caused it.

For example karma as a result of:

  • Material things, rough emotions, supernatural powers, magic, etc. are stored at the bottom (Muladhara).
  • Desires, desires and low egos are stored in Swadistana.
  • Subtle emotions, dynamism, strength, etc. are stored in the central node of the Manipura chakra (Stomach).
  • Feelings, love, envy, sadness, happiness, will be stored in the heart’s central node (Anahata),
  • The ego is more subtle, including the highest ego that wants to reach God stored in the Wisudhi chakra.
  • Mental instability, ignorance, wisdom, weigh and decide right and wrong, good and bad, mental balance, are stored in Ajna before heading for Enlightenment (in the Sahasrara chakra), … etc … according to the causes of chakra activeness and its consequences.

The two way of Oneness and Karma Melting through this method (granthi) :

  1. From top  (Sahasrara chakra) heading down through Sushumna. The meeting was in the deepest depth of Ajna. While experiencing calm, it will release fluid from the pineal gland, producing a form of fluid / Tirta Amritha which then drips into Sushumna, penetrates and removes impurities in each segment.
    This method is considered safer, and the risk is minimal. Although safe, it does not mean without obstacles and mental obstacles that need to be overcome. The effect is cold and some even feel like ice water flowing in each segment to the lower end until it merges with the power of Kundalini (Shiva-Shakti).
  2. From bottom (Muladhara chakra) by awakening the power of Kundalini. This Kundalini fire breaks through and increases the burning of karma in each of its ascension paths until it experiences unification in Sahasrara (Shiva-Shakti).
    In every process of ascension ranging from the most subtle (the heat) to the magma fire, the perpetrator will experience many obstacles to significant changes in mental effects and the temptation to get siddhi.

Being aware of every moment of attitudes and mental changes or the like is very necessary to get to the next level, as well as efforts to unleash the power of the siddhis obtained. Giving up the siddhi that is obtained does not mean that it will disappear when the higher attainments all of the things below will also be followed and controlled (included).

Both unity from above and taking the road from the bottom produced “Amritha / Tirta Kundalini”. The effect of this will result in peace, calm, silence, towards Samadhi.

In Bali, this meaning is also poured into the song Wargasari Down the Tirta so sublime … etc. Where this is the way from above (Requesting) the union of Shiva and Durga / Shakti (Kundalini).

In Kanda pat he the power that results in the purification of Tirta seeps through the bamboo cavities, arteries and the like depending on the experience he sees,

This result is also a Tirta “wiping out” (negative melting) released through saliva (vaguely inserted in a glass of water for Tirta by some Balinese healers). While some possessed (kerauhan) he came out through a kind of mucus through the nose when possessed.

Untying the Knots That Bind Us








March, 2015

The Sanskrit word granthi means “knot” or “doubt” and also means “an especially difficult knot to untie.” People in India wearing a sari or dhoti cloth will form a small pouch to hold money, and close it by knotting the fabric – this tightly knotted purse is called a granthi. Granthi in spiritual practice are psychological or psychic barriers to total freedom. Granthi prevent prana from moving freely up sushumna nadi. Granthi bind the soul; they lock us to our misperception of reality (avidya) and self (asmita). They hold us to our preferences (raga and dvesha) and root us in fear of death (abhinivesha). Knowledge (jnana) is a key component to transcend fear, and together with action (karma) they give wings to our spiritual desires – the rise of Kundalini.

The hathayoga methods for untying these knots are the bandhas, or energy locks. By focusing the pranas in Sushumna Nadi the bandhas increase the potency of the rising Kundalini allowing us to transcend normal restrictions of thinking and acting.

Brahma Granthi is located at the base of the spine between Muladhara Chakraand Svadhisthana Chakra where primitive brain functioning like the “fight or flight reflexes” guarantee survival. Fear of death, anxiety about food, shelter or clothing, or general lack of grounding, all manifest as Brahma Granthi. When you experience fear in an asana like handstand or split, and the fear itself prevents success, this is Brahma Granthi. Lack of spare time can be part of this knot. When your bills and rent payment keep you at work and away from yoga, that is Brahma Granthi.

Mula (Root) Bandha is the first consolidation of Prana and Apana, piercing Brahma Granthi. Vitality, thought, breath, and speech are joined in pursuit of truth. This root lock can be applied all the time transforming every thing we do into a holy act.

Vishnu Granthi knots energy between Manipura Chakra and Anahata Chakra. This Granthi is a knot of individual ego and power. Our clinging to ego, self-cherishing and the quest for personal power can slow spiritual success. Fear of being ignored or of loosing prestige may plague our spiritual growth. This is a knot of power and manipulation, but it is also the knot of accumulation. Accumulation of power, possessions, and fame, all tie us to this level of consciousness. In order to transcend this level of consciousness we must “give up the love of power, for the power of love!” The degree of vulnerability that we show in life – the ability to put our façade aside and challenge our own status quo, unties Vishnu Granthi.

Uddiyana (Flying up) Bandha is the second consolidation of Prana, Apana, and Samana vayus.

Applied together with Mula Bandha, this lock pierces Vishnu Granthi. The individual is able to transcend individuality. The whole abdomen is drawn in and up – symbolizing the renunciation of accumulation and concentration of energy upward toward Anahata Chakra.

Rudra granthi is knotted between the Anahata and Ajña chakras. The attractiveness of heart centered action and the experience of serving others can distract the yogi who desires to “Be Love” – not just experience it. Serving others is a completely satisfactory way to spend your life, but this service could become your cross to bear, where you hold resentment against others, and view them as lesser beings. We must strive to transcend otherness and experience the “oneness of being” in the highest levels of consciousness, and then complete the circle by bringing that consciousness into our compassionate actions. When we are free from the illusion of otherness our actions emerge spontaneously from Love. Jalandhara Bandha enables this leap of consciousness.

The consummate consolidation of prana is Jalandhara Bandha (Cloud Catching Lock or Net Lock – for the network of nadis in the neck) when Prana, Apana, Samana and Udana vayu in Sushumna Nadi loosen Rudra Granthi, and the veil of separation is lifted.

Teaching Tips

  • The yoga practices reveal where we are stopped by granthi, psychological knots, and give us tools for negotiating and loosening those limitations. The granthi are pierced through asana, meditation, pranayama, samyama, virtuous acts, purification of diet, good intention, yama and niyama, mudra, and through nada techniques like chanting and mantra.
  • Practice each bandha separately.
    • Mula: This bandha can be applied while breathing and moving freely.
      The two parts of this lock are a) contraction of the interior of the perineal body on men, or the vaginal walls for women, and b) the area from the pubic bone to navel draws inward and upward slightly.
    • Uddiyana: The diaphragm moves toward the throat drawing the entire abdomen in and up. This lock is only practiced on exhale retention when breathing is not possible and movement is internalized.
    • Jalandhara: Can be applied after inhale or exhale, bringing chest to chin. The spine should stay relatively straight and the chin should rest in the cleft between the clavicle bones.
  • Teach all bandha applied simultaneously in Mahamudra. See Hathayogapradipika Chapter 3, Verses 10-13
  • Investigate the psychological barriers to freedom that are embodied in the granthi, from fear of death and anxiety about survival (Muladhara,) to the accumulation of power and prestige (Manipura,) to the “feel good” effect of helping others, rather than serving others (Anahata.)
  • Teach about the Pranamaya Kosha and it’s component vayus. Asana practice most directly affects the Pranamaya Kosha and consolidates the energy of consciousness into a force of enlightenment.

In Bhagavad Gita 7.1 there is a reference to granthi as doubt, and refuge of the Lord as freedom from that doubt. In Srimad-Bhagavatam 1.2.17-21, bhakti-yoga severs the granthi (hard knot) of material affection and enables one to come at once to the stage of asamsayam-samagram.

The Bandhas and the Granthis


Bandhas are inner body locks that engage both the physical and the energetic body. They provide inner support during asana practice, stimulate the flow of prana and help to release the granthis, which can be understood as energy blockages or psychological knots.

By combining the action of opposing muscles, the bandhas can be activated. Their use during asana practice increases strength, stability and mental focus. Their use during pranayama intensifies its cleansing effect by directing agni or the internal fire to burn the waste matter that has settled and blocks the flow of energy.

Often referred to as locks, the bandhas help to balance two important energies within the body: the prana vayu and apana vayu. If prana is associated with drawing in that which nourishes us, apana is associated with letting go of that which is potentially toxic. Prana is connected to the inhalation and apana to the exhalation. The meeting of these two opposing energies at the base of the spine awakens the Kundalini energy.

There are three main bandhas: Jalandhara, Uddiyana and Mula bandha. Activating all three of these bandhas at the same time is referred to as Mahabandha or main lock.

The Bandhas


The Bandhas

Jalandhara Bandha: the throat lock. Jalandhara bandha can be applied by contracting the front muscles in the neck when tucking the chin towards the sternum. This bandha is naturally activated in some asanas like Sarvangasana (Shoulder Stand) or Halasa (Plough Pose). It is subtly activated during Ujjayi pranayama in which the glottis (the area where the vocal cords are located) is gently contracted.
This bandha focuses the mind on the fifth or throat chakra and contains the upward-flowing movement of prana past the throat. It also seals off the downward movement of “nectar” from the sahasrara or crown chakra, which is said to preserve youth and vitality.

Uddiyana Bandha: the abdominal lock. Uddiyana bandha is applied by contracting the upper abdominal muscles (just below the solar plexus). This bandha is naturally activated after each exhalation when the lungs are emptied and the diaphragm rises. During asana practice it is especially useful to apply this bandha to support the lumbar region in back bends. When used together with Mula bandha, it strengthens the abdominal muscles. While performing asanas it is not possible to fully engage this bandha as it would constrain breathing. This bandha focuses the mind on the third chakra and directs prana up towards the sixth chakra.

Mula Bandha: the root lock. Mula bandha is applied by contracting the pelvic floor and elevating the inner organs in this region like the bladder and genitals. Other groups of muscles, like the upper leg adductors (by slightly pressing the knees together), can intensify this bhanda. If engaged during asana practice it is said to “provide an extra lift, which is especially useful when jumping”. This bandha focuses the mind on the first chakra, and directs prana from the pelvic region upwards, providing energy to the whole body and stopping it from flowing downwards out of the body.

Activating the bandhas can also help to unblock the three granthisor knots that prevent prana from freely circulating within the Sushuma nadi. These knots can block the chakras and keep us tied to negative attitudes and emotions, preventing us from fully experiencing the richness of life.

The Granthi

The Granthi


The Bramha or Vital Granthi is associated with the first three chakras (root, sacrum and solar plexus). This granthi blocks us by feeding our attachment to physical comfort, material wealth and accumulation. It can be unblocked by activating Mula bhanda. To regulate the energy in these vital chakras and granthi, Patanjali recommends self discipline.

The Vishnu or Love Granthi is associated with the fourth and fifth chakras (heart and throat). This granthi blocks us by feeding our attachment to emotional excitement, self-centeredness and lack of receptivity to others’ needs. It can be unblocked by activating Uddyiana bandha. To boost the energy of the love chakras and granthi, Patanjali recommends devotion and commitment.

The Rudra or Light Granthi is associated with the last two chakras (third eye and crown of the head). This granthi blocks us by feeding our attachment to our opinions, prejudices, fantasies and intellectual pride. It can be unblocked by activating Jalandhara bandha. To dissolve pride and “dark” mental patterns, Patanjali recommends self-knowledge.



Please see my related posts

Knot Theory and Recursion: Louis H. Kauffman

Interconnected Pythagorean Triples using Central Squares Theory

The Great Chain of Being

Indra’s Net: On Interconnectedness





Key Sources of Resources


Untying the Knots That Bind Us

Truth, Beauty, and Goodness

Truth, Beauty, and Goodness

Its beauty which brings one closer to truth and goodness.

Truth, Beauty, and Goodness

Key Terms

  • Fundamental Triplicity
  • Satyam Shivam Sundram
  • Sat Chit Ananda
  • Truth Beauty Goodness
  • Platonic Triad
  • Socratic Trinity
  • Ken Wilber AQAL Model
  • Victor Cousin
  • Charles Sanders Peirce
  • Semiotics
  • I – You – We – It

From Awakening Wonder:

A Classical Guide to TRUTH, GOODNESS & BEAUTY

The True, the Good, and the Beautiful

It is in this civilizational context that we first encounter the emergence of the cosmic values known as the True, the Good, and the Beautiful. The Greek term aletheia (“truth”) literally means “nonconcealment,” the negation of lethein, “to elude notice, to be unseen.”9 Aletheia thus connotes a sense of disclosure: “truth in the sense of the unhiddenness . . . and disclosedness of the state of affairs which exhibits itself and is therefore perceived in its actuality.”10 The term agathos (“good”) as an adjective connoted “the significance or excellence of a thing or person” and was eventually developed by philosophers to designate the goal, purpose, or meaning of existence.11 Likewise, kalos (“beauty”) is generally rendered as “beautiful,” “healthy,” “excellent,” “strong,” or “good.”12 It is during the fifth century BC that we find two of the three terms used together. For example, kalos is first used together with agathos in a political or social context: the kaloi and agathoi are leading citizens who embody the virtues of the polis, the Greek city-state. Indeed, the synonymity of the terms contracted into a single word, kalokagathia.

Plato and the “Socratic Trinity”

However, it is not until the writings of Plato that these three terms converge into mutually interpreting concepts, in what has been termed the “Socratic trinity” or “Platonic triad.” Though Plato did not provide a systematic treatment of Truth, Goodness, and Beauty, it is not coincidental that the first clear presentation of the True, the Good, and the Beautiful historically comes from a fifteenth-century commentary on Plato’s Philebus by the Italian humanist scholar Marsilio Ficino.13

Truth, Goodness, and Beauty for Plato were divine concepts; they make up what he called the eidon, the eternal transcendent world of the ideas or forms. This Socratic trinity is the eternal source of life in which the totality of our cosmos participates as an eikon, a temporal, finite image or icon of the eternal transcendent world of the Ideas or Forms. For Plato, the universe is very much alive, or at least inextricably bound up with divine activity, and is thereby considered an object of veneration. In the Timaeus, the world is animated by a rational soul, which is the macrocosmic basis for the microcosmic human soul.14 Humans, as microcosmic replications of the larger macrocosmic world, are composed of tripartite souls that loosely correspond to the Socratic trinity: logos, thymos or ethos, and eros or epithymetes. The logos involves our rational capacities; the thymos or ethos involves our emotional, ethical, or moral capacities; and the epithymetes or eros involves our desires and aesthetic capacities.15 And it is through the tripartite soul that was forged in the world of the forms before our birth and embodiment (Plato held more or less to a doctrine of reincarnation) that the individual human can mirror, reflect, or image the virtues of the True, the Good, and the Beautiful, and thus exemplify and participate in divine life.

Now, for Plato, the dilemma is that we as tripartite souls already possess a knowledge of the virtues, literally the divine order of the eternal ideas or forms—the imprint—of the True, the Good, and the Beautiful, but this knowledge has been forgotten as the result of our birth and embodiment. As he made clear in his Meno, knowledge does not derive from inductive or deductive processes or an investigation into the nature of things, but rather knowledge is a recollection, what Plato termed anamnesis, a recovery of Truth insofar as our souls have experienced it prior to our embodiment.16 So the key here is that knowledge needs to be awakened. And it is philosophia, the love of wisdom, that seeks to recover human perception of the True, the Good, and the Beautiful so as to restore the human soul to its participation in divine life. This pursuit of Truth in the Phaedrus and Gorgias, of Goodness in the Republic, and of Beauty in Diotima’s speech in the Symposium, in effect reorients the human person to the divine world of the eternal and immutable, and thereby effects a harmonious relationship with the cosmos, which itself participates in divine life.

The Platonic Conception of Truth, Goodness, and Beauty

The precise relationship between the True, the Good, and the Beautiful in Plato is very difficult to determine, largely because these concepts are not treated systematically but rather are spread out among his works. But we can map out a broad, general model for how they work together in relation to the tripartite soul.

For Plato, the Good is not simply a thing or a value; the Good is universal priority in which all true things participate and from which they exist. In book VII of the Republic, Plato considered the Good to be the universal principle, the self-sufficient source of all being and the irreducible essence of reality:

[I]n the region of the known the last thing to be seen and hardly seen is the idea of Good, and that when seen it must needs point us to the conclusion that this is indeed the cause for all things of all that is right and beautiful, giving birth in the visible world to light, and the author of light and itself in the intelligible world being the authentic course of truth and reason.17

For Plato, the Good is not simply a thing or a value; the Good is universal priority in which all true things participate and from which they exist. The Good is “beyond being” and is thus the foundation of all hypotheses which requires no hypothesis; that Idea from which all Ideas emerge and on which they depend.18 According to his allegory of the cave in book VII of the Republic, the Good is to the world of Ideas much like what the sun is to our perceptible, physical world. As such, the Good, the divine source of life, is in itself unknowable, being the essence, the light, by which all things are known and perceived. The Good itself must thus be revealed; it must be communicated to the human mind by means of aletheia or “Truth.”19 Drawing from the allegory of the cave, we might say that Truth is the splendor of the Good that can be perceived by the soul.20 For Plato, Truth involves understanding how all things in our world, all particulars, participate in and derive their nature from the Good.21 Thus, concomitant with its etymology, it is the nature of Truth to reveal or disclose reality, the priority of the Good, to the human mind or logos.

However, the Good is not merely revealed to the mind through Truth. A desire, an eros, is awakened for the Good within the human soul through kalos or “Beauty.” In Diotima’s speech in the Symposium, Beauty is the object of eros or love.22 And it is here that Plato revealed the means by which the soul encounters the True and the Good. In awakening eros, Plato’s conception of Beauty becomes inextricably linked with Grecian physics, in that eros constitutes the law of attraction. Empedocles had envisioned the cosmos as a whole and all the particulars within it, including humans, as directed by eros and eris, literally “desire” and “strife,” which served as the opposing forces of attraction and repulsion. In accordance with Greco-Roman physics, this love, this desire awakened through Beauty, serves the indispensable role of momentum or motivation in intellectual, moral, and spiritual pursuits. This is why we associate Beauty with “attraction”; through Beauty we are drawn to the True and the Good. By awakening eros within us, Beauty provides us with the allure, the momentum, the gravitational pull toward the True and the Good and thus unites us with the divine source of life:

When a man has been thus far tutored in the lore of love, passing from view to view of beautiful things, in the right and regular ascent, suddenly he will have revealed to him, as he draws to the close of his dealings in love, a wondrous vision, beautiful in its nature; and this, Socrates, is the final object of all those previous toils. . . . Beginning from obvious beauties he must for the sake of that highest Beauty be ever climbing aloft, as one the rungs of a ladder, from one to two, and from two to all beautiful bodies; from personal Beauty he proceeds to beautiful observances, from observance to beautiful learning, and from learning at last to that particular study which is concerned with the beautiful itself and that alone; so that in the end he comes to know the very essence of Beauty.23

The important point here is that Beauty, because of its divine nature, is always linked with the True and the Good. In order for something to be truly beautiful, it must by definition draw one to the True and the Good. When eros or love is amputated from Truth and Goodness, say in the case of pornography, it is no longer love but rather lust or epithymia.24 The Greeks alluded to this differentiation in the mythologies of the Muses and the Sirens: the Muses are the daughters of Zeus who inspire Beauty and Truth, while the Sirens are water nymphs who lure sailors to their deaths through their bewitching songs. So we see here a highly ethical significance to this encounter with the True, the Good, and the Beautiful. Because Beauty communicates the True and the Good through its radiance, the awakening of eros always involves the awakening of arête—the classical virtues (wisdom, moderation, justice, and courage)—which occurs when the logos, thymos, and epithymetes or eros constituting the tripartite human soul reflect the balance or harmony of the cosmos.25 Thus Plato saw an inextricable link between virtue and a true knowledge of the world.

The important point here is that Beauty, because of its divine nature, is always linked with the True and the Good. In order for something to be truly beautiful, it must by definition draw one to the True and the Good.

Encountering Truth, Goodness, and Beauty through Paideia

For Plato, the educational project of paideia involves teaching students to repudiate what deserves repudiation and to love what is in fact lovely and deserving of our desires.26 This involves what amounts to be a three-stage process.

First, there is the need to realize there is in fact a problem, that one is in fact ignorant and incapable of accounting for reality. This admission of personal impoverishment, what the Greeks called aporia and the Latins called pietas, is the rationale for the Socratic Dialogue; Socrates was able to impart wisdom only when his interlocutor admits ignorance and perplexity.

Second, this intellectual and spiritual vacuousness, this virtue of humility, can then be filled—and filled not merely with facts but with a recollection of the knowledge of the world as it relates to that which is eternally True, Good, and Beautiful. This stage involves a twofold purification by which students cultivate a detachment from false things and an attachment to true things. The twofold purification consists of a moral and an intellectual purification. Moral purification involves the practice of the virtues, which in effect distances the soul from the confines and temptations of the body. Intellectual purification, or theoria, involves contemplation of the True, the Good, and the Beautiful, particularly in mathematics, where students are able see the reality that lies beyond appearances. Thus, all subjects in an educational curriculum serve as lenses through which the True, the Good, and the Beautiful can be encountered. Gymnastics cultivate the virtue of enkrateia or self-mastery; music and poetry provide the chief means by which the rhythm and harmony of the cosmos can be communicated through the body and sunk deeply into the recesses of the soul.27

Third, there is ultimate theoria, the union of the soul with the True, the Good, and the Beautiful, a beatific vision that one simply cannot experience while embodied. One experiences this vision only at death.28


Truth, Goodness, and Beauty emerge historically in a world very much removed from our own. This world was characterized by cosmic piety, the sense that the universe was alive with divine presence and thus obligated all people born into the world to live a particular kind of life, one that oriented the self into a harmonious relationship with the world and others. This obligation was lived out in the life of the polis, the city-state, which served as the civic center for communion between men and the gods. In order to foster a harmonious relationship with the cosmos and city, the Greek educational project called paideia sought to instill within students a love for the cosmic values: Truth, Goodness, and Beauty. As particularly developed in the work of Plato, these values served as the harmonious model for cultivating a comparable harmony in one’s own soul, which one then lived out in harmony with one’s fellow man, and thus exemplified and perpetuated the cosmic harmony that sustained the world.

The educational project of paideia involves teaching students to repudiate what deserves repudiation and to love what is in fact lovely and deserving of our desires.

Plato’s philosophy provides us with the cosmic, anthropological, and civic frames of reference for the emergence of a distinctly Christian development of the True, the Good, and the Beautiful, and it is to this Christian reappropriation that we now turn.

Please see my related posts:

Truth, Beauty, and Goodness: Integral Theory of Ken Wilber

Cyber-Semiotics: Why Information is not enough

The Great Chain of Being

Indra’s Net: On Interconnectedness

On Holons and Holarchy

Interconnected Pythagorean Triples using Central Squares Theory

Shapes and Patterns in Nature

Consciousness of Cosmos: A Fractal, Recursive, Holographic Universe

Integral Philosophy of the Rg Veda: Four Dimensional Man

Meta Integral Theories: Integral Theory, Critical Realism, and Complex Thought

Myth of Invariance: Sound, Music, and Recurrent Events and Structures

Mind, Consciousness and Quantum Entanglement

Understanding Rasa: Yoga of Nine Emotions

Geometry of Consciousness

Key Sources of Research:

Lectures on the true, the beautiful, and the good

Victor Cousin

Translation by O. W. Wight

Click to access cousin.PDF

Awakening Wonder:

A Classical Guide to TRUTH, GOODNESS & BEAUTY

Stephen R. Turley, PhD

Click to access prod059505_smpl0.pdf


Click to access SeeNoEvil_Chapter3.pdf



John Levi Martin

Click to access The%20Birth%20of%20the%20True,%20the%20Good,%20and%20the%20Beautiful.pdf

Beauty as a transcendental in the thought of Joseph Ratzinger

John Jang

University of Notre Dame Australia

Quotes by Victor Cousin

What is Code Biology?

What is Code Biology?




Key Terms

  • Code Biology
  • Biosemiotics
  • Charles Sanders Peirce
  • Genetic Code
  • Musical Harmony
  • Symmetry
  • Jay Kappraff
  • Gary Adamson
  • Pythagorean Triples
  • Harmonic Laws
  • Numbers
  • Geometry
  • Matrices
  • Self, Culture, Nature
  • I, We, It, Its
  • Sergey V. Petoukhov
  • Codes
  • Meaning
  • Value
  • Marcello Barbieri
  • RNA, DNA, Proteins, Cells
  • Code Semiotics
  • Ferdinand D Saussure


What is Code Biology?

Codes and conventions are the basis of our social life and from time immemorial have divided the world of culture from the world of nature. The rules of grammar, the laws of government, the precepts of religion, the value of money, the rules of chess etc., are all human conventions that are profoundly different from the laws of physics and chemistry, and this has led to the conclusion that there is an unbridgeable gap between nature and culture. Nature is governed by objective immutable laws, whereas culture is produced by the mutable conventions of the human mind.

In this millennia-old framework, the discovery of the genetic code, in the early 1960s, came as a bolt from the blue, but strangely enough it did not bring down the barrier between nature and culture. On the contrary, a protective belt was quickly built around the old divide with an argument that effectively emptied the discovery of all its revolutionary potential. The argument that the genetic code is not a real code because its rules are the result of chemical affinities between codons and amino acids and are therefore determined by chemistry. This is the ‘Stereochemical theory’, an idea first proposed by George Gamow in 1954, and re-proposed ever since in many different forms (Pelc and Welton 1966; Dunnil 1966; Melcher 1974; Shimizu 1982; Yarus 1988, 1998; Yarus, Caporaso and Knight 2005). More than fifty years of research have not produced any evidence in favour of this theory and yet the idea is still circulating, apparently because of the possibility that stereochemical interactions might have been important at some early stages of evolution (Koonin and Novozhilov 2009). The deep reason is probably the persistent belief that the genetic code must have been a product of chemistry and cannot possibly be a real code. But what is a real code?

The starting point is the idea that a code is a set of rules that establish a correspondence, or a mapping, between the objects of two independent worlds (Barbieri 2003). The Morse code, for example, is a mapping between the letters of the alphabet and groups of dots and dashes. The highway code is a correspondence between street signals and driving behaviours (a red light means ‘stop’, a green light means ‘go’, and so on).

What is essential in all codes is that the coding rules, although completely compatible with the laws of physics and chemistry, are not dictated by these laws. In this sense they are arbitrary, and the number of arbitrary relationships between two independent worlds is potentially unlimited. In the Morse code, for example, any letter of the alphabet could be associated with countless combinations of dots and dashes, which means that a specific link between them can be realized only by selecting a small number of rules. And this is precisely what a code is: a small set of arbitrary rules selected from a potentially unlimited number in order to ensure a specific correspondence between two independent worlds.

This definition allows us to make experimental tests because organic codes are relationships between two worlds of organic molecules and are necessarily implemented by a third type of molecules, called adaptors, that build a bridge between them. The adaptors are required because there is no necessary link between the two worlds, and a fixed set of adaptors is required in order to guarantee the specificity of the correspondence. The adaptors, in short, are the molecular fingerprints of the codes, and their presence in a biological process is a sure sign that that process is based on a code.

This gives us an objective criterion for discovering organic codes and their existence is no longer a matter of speculation. It is, first and foremost, an experimental problem. More precisely, we can prove that an organic code exists, if we find three things: (1) two independents worlds of molecules, (2) a set of adaptors that create a mapping between them, and (3) the demonstration that the mapping is arbitrary because its rules can be changed, at least in principle, in countless different ways.


Two outstanding examples

The genetic code

In protein synthesis, a sequence of nucleotides is translated into a sequence of amino acids, and the bridge between them is realized by a third type of molecules, called transfer-RNAs, that act as adaptors and perform two distinct operations: at one site they recognize groups of three nucleotides, called codons, and at another site they receive amino acids from enzymes called aminoacyl-tRNA-synthetases. The key point is that there is no deterministic link between codons and amino acids since it has been shown that any codon can be associated with any amino acid (Schimmel 1987; Schimmel et al. 1993). Hou and Schimmel (1988), for example, introduced two extra nucleotides in a tRNA and found that that the resulting tRNA was carrying a different amino acid. This proved that the number of possible connections between codons and amino acids is potentially unlimited, and only the selection of a small set of adaptors can ensure a specific mapping. This is the genetic code: a fixed set of rules between nucleic acids and amino acids that are implemented by adaptors. In protein synthesis, in conclusion, we find all the three essential components of a code: (1) two independents worlds of molecules (nucleotides and amino acids), (2) a set of adaptors that create a mapping between them, and (3) the proof that the mapping is arbitrary because its rules can be changed.


The signal transduction codes

Signal transduction is the process by which cells transform the signals from the environment, called first messengers, into internal signals, called second messengers. First and second messengers belong to two independent worlds because there are literally hundreds of first messengers (hormones, growth factors, neurotransmitters, etc.) but only four great families of second messengers (cyclic AMP, calcium ions, diacylglycerol and inositol trisphosphate) (Alberts et al. 2007). The crucial point is that the molecules that perform signal transduction are true adaptors. They consists of three subunits: a receptor for the first messengers, an amplifier for the second messengers, and a mediator in between (Berridge 1985). This allows the transduction complex to perform two independent recognition processes, one for the first messenger and the other for the second messenger. Laboratory experiments have proved that any first messenger can be associated with any second messenger, which means that there is a potentially unlimited number of arbitrary connections between them. In signal transduction, in short, we find all the three essential components of a code: (1) two independents worlds of molecules (first messengers and second messengers), (2) a set of adaptors that create a mapping between them, and (3) the proof that the mapping is arbitrary because its rules can be changed (Barbieri 2003).


A world of organic codes

In addition to the genetic code and the signal transduction codes, a wide variety of new organic codes have come to light in recent years. Among them: the sequence codes (Trifonov 1987, 1989, 1999), the Hox code (Paul Hunt et al. 1991; Kessel and Gruss 1991), the adhesive code (Redies and Takeichi 1996; Shapiro and Colman 1999), the splicing codes (Barbieri 2003; Fu 2004; Matlin et al. 2005; Pertea et al. 2007; Wang and Burge 2008; Barash et al. 2010; Dhir et al. 2010), the signal transduction codes (Barbieri 2003), the histone code (Strahl and Allis 2000; Jenuwein and Allis 2001; Turner 2000, 2002, 2007; Kühn and Hofmeyr 2014), the sugar code (Gabius 2000, 2009), the compartment codes (Barbieri 2003), the cytoskeleton codes (Barbieri 2003; Gimona 2008), the transcriptional code (Jessell 2000; Marquard and Pfaff 2001; Ruiz i Altaba et al. 2003; Flames et al. 2007), the neural code (Nicolelis and Ribeiro 2006; Nicolelis 2011), a neural code for taste (Di Lorenzo 2000; Hallock and Di Lorenzo 2006), an odorant receptor code(Dudai 1999; Ray et al. 2006), a space code in the hippocampus (O’Keefe and Burgess 1996, 2005; Hafting et al. 2005; Brandon and Hasselmo 2009; Papoutsi et al. 2009), the apoptosis code (Basañez and Hardwick 2008; Füllgrabe et al. 2010), the tubulin code (Verhey and Gaertig 2007), the nuclear signalling code (Maraldi 2008), the injective organic codes (De Beule et al. 2011), the molecular codes (Görlich et al. 2011; Görlich and Dittrich 2013), the ubiquitin code (Komander and Rape 2012), the bioelectric code (Tseng and Levin 2013; Levin 2014), the acoustic codes (Farina and Pieretti 2014), the glycomic code (Buckeridge and De Souza 2014; Tavares and Buckeridge 2015) and the Redox code (Jones and Sies 2015).

The living world, in short, is literally teeming with organic codes, and yet so far their discoveries have only circulated in small circles and have not attracted the attention of the scientific community at large.


Code Biology

Code Biology is the study of all codes of life with the standard methods of science. The genetic code and the codes of culture have been known for a long time and represent the historical foundation of Code Biology. What is really new in this field is the study of all codes that came after the genetic code and before the codes of culture. The existence of these codes is an experimental fact – let us never forget this – but also more than that. It is one of those facts that have extraordinary theoretical implications.

The first is the role that the organic codes had in the history of life. The genetic code was a precondition for the origin of the first cells, the signal transduction codes divided the descendants of the common ancestor into the primary kingdoms of Archaea, Bacteria and Eukarya, the splicing codes were instrumental to the origin of the nucleus, the histone code provided the rules of chromatin, and the cytoskeleton codes allowed the Eukarya to perform internal movements, including those of mitosis and meiosis (Barbieri 2003, 2015). The greatest events of macroevolution, in other words, were associated with the appearance of new organic codes, and this gives us a completely new understanding of the history of life.

The second great implication is the fact that the organic codes have been highly conserved in evolution, which means that they are the great invariants of life, the sole entities that have been perpetuated while everything else has been changed. Code Biology, in short, is uncovering a new history of life and bringing to light new fundamental concepts. It truly is a new science, the exploration of a vast and still largely unexplored dimension of the living world, the real new frontier of biology.



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Pertea M, Mount SM, Salzberg SL (2007) A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana. BMC Bioinformatics, 8, 159.

Ray A, van der Goes van Naters W, Shiraiwa T and Carlson JR (2006) Mechanisms of Odor Receptor Gene Choice in Drosophila. Neuron, 53, 353-369.

Redies C and Takeichi M (1996) Cadherine in the developing central nervous system: an adhesive code for segmental and functional subdivisions. Developmental Biology, 180, 413-423.

Ruiz i Altaba A, Nguien V and Palma V (2003) The emergent design of the neural tube: prepattern, SHH morphogen and GLI code.Current Opinion in Genetics & Development, 13, 513–521.

Schimmel P (1987) Aminoacyl tRNA synthetases: General scheme of structure-function relationship in the polypeptides and recognition of tRNAs. Ann. Rev. Biochem., 56, 125-158.

Schimmel P, Giegé R, Moras D and Yokoyama S (1993) An operational RNA code for amino acids and possible relationship to genetic code. Proceedings of the National Academy of Sciences USA, 90, 8763-8768.

Shapiro L and Colman DR (1999) The Diversity of Cadherins and Implications for a Synaptic Adhesive Code in the CNS. Neuron, 23, 427-430.

Shimizu M (1982) Molecular basis for the genetic code. J. Mol. Evol., 18, 297-303.

Strahl BD and Allis D (2000) The language of covalent histone modifications. Nature, 403, 41-45.

Tavares EQP and Buckeridge MS (2015) Do plant cells have a code? Plant Science, 241, 286-294.

Trifonov EN (1987) Translation framing code and frame-monitoring mechanism as suggested by the analysis of mRNA and 16s rRNA nucleotide sequence. Journal of Molecular Biology, 194, 643-652.

Trifonov EN (1989) The multiple codes of nucleotide sequences. Bulletin of Mathematical Biology, 51: 417-432.

Trifonov EN (1999) Elucidating Sequence Codes: Three Codes for Evolution. Annals of the New York Academy of Sciences, 870, 330-338.

Tseng AS and Levin M (2013) Cracking the bioelectric code. Probing endogenous ionic controls of pattern formation. Communicative & Integrative Biology, 6(1), 1–8.

Turner BM (2000) Histone acetylation and an epigenetic code. BioEssays, 22, 836–845.

Turner BM (2002) Cellular memory and the Histone Code. Cell, 111, 285-291.

Turner BM (2007) Defining an epigenetic code. Nature Cell Biology, 9, 2-6.

Verhey KJ and Gaertig J (2007) The Tubulin Code. Cell Cycle, 6 (17), 2152-2160.

Wang Z and Burge C (2008) Splicing regulation: from a part list of regulatory elements to an integrated splicing code. RNA, 14, 802-813.

Yarus M (1988) A specific amino acid binding site composed of RNA. Science, 240, 1751-1758.

Yarus M (1998) Amino acids as RNA ligands: a direct-RNA-template theory for the code’s origin. J. Mol. Evol.,47(1), 109–117.

Yarus M, Caporaso JG, and Knight R (2005) Origins of the Genetic Code: The Escaped Triplet Theory. Annual Review of Biochemistry, 74,179-198.



The classical theories of the genetic code claimed that its coding rules were determined by chemistry—either by stereochemical affinities or by metabolic reactions—but the experimental evidence has revealed a totally different reality: it has shown that any codon can be associated with any amino acid, thus proving that there is no necessary link between them. The rules of the genetic code, in other words, obey the laws of physics and chemistry but are not determined by them. They are arbitrary, or conventional, rules. The result is that the genetic code is not a metaphorical entity, as implied by the classical theories, but a real code, because it is precisely the presence of arbitrary rules that divides a code from all other natural processes. In the past 20 years, furthermore, various independent discoveries have shown that many other organic codes exist in living systems, which means that the genetic code has not been an isolated case in the history of life. These experimental facts have one outstanding theoretical implication: they imply that in addition to the concept of information we must introduce in biology the concept of meaning, because we cannot have codes without meaning or meaning without codes. The problem is that at present we have two different theoretical frameworks for that purpose: one is Code Biology, where meaning is the result of coding, and the other is Peircean biosemiotics, where meaning is the result of interpretation. Recently, however, a third party has entered the scene, and it has been proposed that Robert Rosen’s relational biology can provide a bridge between Code Biology and Peircean biosemiotics.



Please see my related posts

Semiotics, Bio-Semiotics and Cyber Semiotics

Autocatalysis, Autopoiesis and Relational Biology

Geometry of Consciousness

Mind, Consciousness and Quantum Entanglement



Key Sources of Research:


Code Biology


What is Code Biology?

Marcello Barbieri

Code Biology, Peircean Biosemiotics, and Rosen’s Relational Biology

Marcello Barbieri




Why Biosemiotics? An Introduction to Our View on the Biology of Life Itself

Kalevi Kull, Claus Emmeche and Jesper Hoffmeyer





Eliseo Fernández

Click to access PRfinal.pdf




What Does it Take to Produce Interpretation? Informational, Peircean and Code-Semiotic Views on Biosemiotics

Søren Brier & Cliff Joslyn

Naturalizing semiotics: The triadic sign of Charles Sanders Peirce as a systems property





Arran Gare





Jay Kappraff

Gary W. Adamson


Click to access report0809-12.pdf



The genetic code, 8-dimensional hypercomplex numbers and dyadic shifts


Sergey V. Petoukhov


Click to access 1102.3596.pdf




A Fresh Look at Number

Jay Kappraff

Gary Adomson

Click to access bridges2000-255.pdf





G. Darvas, A.A. Koblyakov, S.V.Petoukhov, I.V.Stepanian






On the Semio-Mathematical Nature of Codes

Yair Neuman & Ophir Nave

Click to access On-the-Semio-Mathematical-Nature-of-Codes.pdf




Miloje M. Rakočević


Click to access 0610044.pdf




Genetic Code Table: A note on the three splittings into amino acid classes

Miloje M. Rakočević


Click to access 0903.4110.pdf





Miloje M. Rakočević


Click to access 0703011.pdf




Tidjani Négadi


Click to access 1305.5103.pdf




Genetic Code as a Coherent System

Miloje Rakočević


Click to access Genetic-Code-as-a-Coherent-System.pdf





Miloje M. Rakočević


Click to access A-New-Genetic-Code-Table.pdf




Harmonically Guided Evolution

Richard Merrick


Click to access a084ad5ca081cf5ac00c82c77d5857795745.pdf




Golden and Harmonic Mean in the Genetic Code

Miloje M. Rakočević

Click to access 35c07d4f0e09a12acc2d6822a16407a14ccd.pdf


Cyber-Semiotics: Why Information is not enough

Cyber-Semiotics: Why Information is not enough


CyberSemiotics is a framework developed by Prof. Soren Brier.  He is from Copenhagen Business School, Denmark.



From Cybersemiotics: a semiotic-systemic transdisciplinary approach

Since the critique of the logical positivists’ unity of science for being too reductionist to be transdisciplinary, most scientists have abandoned this model. But other candidates have emerged. The first was evolutionary system science and cybernetics, which was instrumental in producing the new information science supporting the development of cognitive science, with computation as the central process. But the new info-computational transdisciplinary framework still lacks a phenomenological and hermeneutical foundation just as system science and cybernetics did. Peircean semiotics has this foundation and includes a theory of information and has a transdisciplinary scope, but lacks the self-organization theory developed in autopoiesis theory, which Luhmann uses in his new communicatively based system theory. Cybersemiotics integrates Peirce and Luhmann’s paradigms into a new transdisciplinary framework encompassing the theory of mind as embodied, extended, enacted and embedded.


From Can Cybersemiotics Solve the Problem of Informational Transdisciplinarity?

A transdisciplinary theory for cognition and communication has at least been described from the following paradigms

  • An objective information processing view or info-mechanicism;
  • A social constructivist view;
  • A systemic cybernetic view of self-organization;
  • Semiotic paradigms of experience and interpretation (phenomenological and hermeneutical aspects) including biosemiotic going into animal, plant, bacterial and cellular living systems. They all have their transdisciplinary shortcomings.

A transdisciplinary framework called Cybersemiotics that
integrate phenomenological and hermeneutical aspect in Peircean semiotic logic with cybernetic and systemic autopoietic emergentist process-informational view, is suggested.


From Cybersemiotics: A New Foundation for Transdisciplinary Theory of Information, Cognition, Meaningful Communication and the Interaction Between Nature and Culture

Cybersemiotics constructs a non-reductionist framework in order to integrate third person knowledge from the exact sciences and the life sciences with first person knowledge described as the qualities of feeling in humanities and second person intersubjective knowledge of the partly linguistic communicative interactions, on which the social and cultural aspects of reality are based. The modern view of the universe as made through evolution in irreversible time, forces us to view man as a product of evolution and therefore an observer from inside the universe. This changes the way we conceptualize the problem and the role of consciousness in nature and culture. The theory of evolution forces us to conceive the natural and social sciences as well as the humanities together in one theoretical framework of unrestricted or absolute naturalism, where consciousness as well as culture is part of nature. But the theories of the phenomenological life world and the hermeneutics of the meaning of communication seem to defy classical scientific explanations. The humanities therefore send another insight the opposite way down the evolutionary ladder, with questions like: What is the role of consciousness, signs and meaning in the development of our knowledge about evolution?

Phenomenology and hermeneutics show the sciences that their prerequisites are embodied living conscious beings imbued with meaningful language and with a culture. One can see the world view that emerges from the work of the sciences as a reconstruction back into time of our present ecological and evolutionary self understanding as semiotic intersubjective conscious cultural and historical creatures, but unable to handle the aspects of meaning and conscious awareness and therefore leaving it out of the story. Cybersemiotics proposes to solve the dualistic paradox by starting in the middle with semiotic cognition and communication as a basic sort of reality in which all our knowledge is created and then suggests that knowledge develops into four aspects of human reality: Our surrounding nature described by the physical and chemical natural sciences, our corporality described by the life sciences such as biology and medicine, our inner world of subjective experience described by phenomenologically based investigations and our social world described by the social sciences. I call this alternative model to the positivistic hierarchy the cybersemiotic star. The article explains the new understanding of Wissenschaft that emerges from Peirce’s and Luhmann’s conceptions.




Please see my related posts:

Meta Integral Theories: Integral Theory, Critical Realism, and Complex Thought

Socio-Cybernetics and Constructivist Approaches

Truth, Beauty, and Goodness: Integral Theory of Ken Wilber

Semiotics, Bio-Semiotics and Cyber Semiotics

Society as Communication: Social Systems Theory of Niklas Luhmann

Autocatalysis, Autopoiesis and Relational Biology

Systems View of Life: A Synthesis by Fritjof Capra

Systems and Organizational Cybernetics





Key Sources of Research:



Soren Brierøren-brier



A New Foundation for Transdisciplinary Theory of Information, Cognition, Meaningful Communication and the Interaction Between Nature and Culture

Søren Brier


Click to access cf50ffc5edbc110ccd08279d6d8b513bfbe2.pdf

A transdisciplinary and evolutionary framework encompassing information with meaningful cognition and communication through second order cybernetics and Peircean semiotics

Soren Brier





Why information is not enough!

A Trans-Disciplinary Approach to Information, Cognition and Communication Studies, Through an Integration of Niklas Luhmann’s Communication Theory with C. S. Peirce’s Semiotics.


Click to access luhmann02.pdf




A Festschrift honoring Professor Søren Brier on the Occasion of his 60th Birthday


Click to access 9788770719964.pdf




Cybersemiotics: a semiotic-systemic transdisciplinary approach

Studia Kulturoznawcze nr 1 (7), 247-265 2015


Click to access Studia_Kulturoznawcze-r2015-t-n1_(7)-s247-265.pdf





The Paradigm of Peircean Biosemiotics

Soren Brier

Click to access Brier_2008_peircean_biosemiotics.pdf




Levels of Cybersemiotics: Possible ontologies of signification

Soren Brier

Click to access 2_Brier_v1_2.pdf




Cybersemiotics: An Evolutionary World View Going Beyond Entropy and Information into the Question of Meaning

Søren Brier





Soren Brier


Click to access Brier%20P26.pdf




Cybersemiotics: A New Foundation for Transdisciplinary Theory of Information, Cognition, Meaning, Communication and Consciousness

Soren Brier

Click to access 798.pdf



Cybersemiotics: A Semiotic-systemic Transdisciplinary Approach


Søren Brier


Click to access s_ren_brier_cybersemiotics_a_semiotic_systemic_publishersversion.pdf



The riddle of the Sphinx answered: On how C. S. Peirce’s transdisciplinary semiotic philosophy of knowing links science and spirituality


Søren Brier


Click to access Brier_Peirce.pdf


Cybersemiotics and the Question of Knowledge


Soren Brier


Habit as a Connecting Nature, Mind and Culture in
C.S. Peirce’s Semiotic Pragmaticism †

Søren Brier

How Peircean semiotic philosophy connects Western science with Eastern emptiness ontology

Cybersemiotics and the reasoning powers of the universe: philosophy of information in a semiotic-systemic transdisciplinary approach

Soren Brier

Cybersemiotics: An Evolutionary World View Going Beyond Entropy and Information into the Question of Meaning

Søren Brier

 Cybersemiotic Pragmaticism and Constructivism

Søren Brier


Click to access 3b1ab5c1eda273c1d4a5f4974c63df847ede.pdf

Cognitive Semiotics


Click to access Zlatev2012-Paris1.pdf


Meta Integral Theories: Integral Theory, Critical Realism, and Complex Thought

Meta Integral Theories: Integral Theory, Critical Realism, and Complex Thought


Three Meta Integral Theories:

  • Integral Theory (Ken Wilber)
  • Critical Realism (Roy Bhaskar)
  • Complex Thought (Edgar Morin)


Please see review papers for each of the theory in the references below.

These are the best meta theories in my opinion.

Ken Wiber, Roy Bhaskar, and Edgar Morin have created ideas worth reading about.


Keynote Address by Sean Esbjorn-Hargens



Keynote Address by Sean Esbjorn-Hargens



Keynote Address by Sean Esbjorn-Hargens




Keynote Address by Sean Esbjorn-Hargens




I also suggest Cyber Semiotics a book by Soren Brier.


Please see my related posts:

Semiotics, Bio-Semiotics and Cyber Semiotics

Truth, Beauty, and Goodness: Integral Theory of Ken Wilber

Systems View of Life: A Synthesis by Fritjof Capra




Key Sources of Research:



Overview of Integral Theory

Click to access Integral_Theory_Overview.pdf



Critical Realism

Click to access Critical%20Realism_REVISED.pdf



Ken Wilber on Critical Realism

Click to access Critical%20Realism_Revisited-1.pdf

Complex Thought

Click to access Complex_Thought_FINAL.pdf


Metatheory for the Twenty-First Century: Critical Realism and Integral Theory in Dialog

edited by Roy Bhaskar, Sean Esbjörn-Hargens, Nicholas Hedlund, Mervyn Hartwig

2017 published by Routledge




Keynote Address by Sean Esbjorn-Hargens

ITC 2013

Click to access Esbjorn-Hargens%27%20ITC%202013%20Keynote.pdf

Ontological and Epistemic Considerations for Integral Philosophy

Nicholas H. Hedlund-de Witt

Click to access Hedlund-de%20Witt_Nick_ITC2013.pdf




A Complex Integral Realist Perspective: Towards A New Axial Vision

By Paul Marshall

© 2017 – Routledge

Situating Critical Realism Philosophically

Ruth Groff

Department of Political Science St. Louis University

Click to access GROFF.pdf




Sean Esbjorn-Hargens discusses integrative thinking and the new leadership

June 2017 Podcast




The Future of Leadership for Conscious Capitalism

By: Barrett C. Brown



Edgar Morin



Integral Theory (Ken Wilber)




From the Concept of System to the Paradigm of Complexity

Edgar Morin
Translated by Sean Kelly

Click to access morin-paradigm-of-complexity.pdf




Integral Meta-Theory – The What and Why

Zak Stein



Sophia Speaks: An Integral Grammar of Philosophy

By Bruce Alderman

Click to access Alderman_ITC2013.pdf




The Variety of Integral Ecologies: Kosmopolitan Complexity and the New Realisms

Sean Kelly

Adam Robbert

Sam Mickey

Click to access Mickey%20%26%20Robbert%20%26%20Kelly_ITC2013.pdf


Metatheory for the Anthropocene: Emancipatory Praxis For Planetary Flourishing (Routledge Studies in Critical Realism (Routledge Critical Realism))

Nicholas Hedlund (Editor), Sean Esbjörn-Hargens (Editor)




Meta Integral Foundation




Toward an Integrative Theory of Higher Education: Connecting Lines of Inquiry from Morin’s Complex Thought, Bhaskar’s Critical Realism, and Wilber’s Integral Theory

Gary P. Hampson and Matthew Rich-Tolsma




INTRODUCTION: On the Deep Need for Integrative Metatheory in the 21st-Century

Nicholas Hedlund
Sean Esbjörn-Hargens
Mervyn Hartwig
Roy Bhaskar




Situating the Mapmaker: An Imminent Critique of Wilber’s Cartography of the
Transphysical Worlds

Prepared by Nicholas Hedlund-de Witt, M.A.

Professor Eric Weiss

California Institute of Integral Studies

Spring 2011

Semiotics, Bio-Semiotics and Cyber Semiotics

Semiotics, Bio-Semiotics, and Cyber Semiotics


From The Biosemiotic Approach in Biology: Theoretical Bases and Applied Models

Biosemiotics is a growing field that investigates semiotic processes in the living realm in an attempt to combine the findings of the biological sciences and semiotics. Semiotic processes are more or less what biologists have typically referred to as “signals,” “codes,” and “information pro- cessing” in biosystems, but these processes are here understood under the more general notion of semiosis, that is, the production, action, and interpretation of signs. Thus, biosemiotics can be seen as biology interpreted as a study of living sign systems—which also means that semiosis or sign process can be seen as the very nature of life itself. In other words, biosemiotics is a field of research investigating semiotic processes (meaning, signification, communication, and habit formation in living systems) and the physicochemical preconditions for sign action and interpretation.

To treat biosemiotics as biology interpreted as sign systems study is to emphasize an important intertheoretical relation between biology as we know it (as a field of inquiry) and semiotics (the study of signs). Biosemiotics offers a way of understanding life in which it is considered not just from the perspectives of physics and chemistry, but also from a view of living systems that stresses the role of signs conveyed and inter- preted by other signs in a variety of ways, including by means of molecules. In this sense, biosemiotics takes for granted and preserves the complexity of living processes as revealed by the existing fields of biology, from molecular biology to brain science and behavioral studies. However, biosemiotics attempts to bring together separate findings of the various disciplines of biology (including evolutionary biology) into a sign- theoretical perspective concerning the central phenomena of the living world, from the ribosome to the ecosystem and from the beginnings of life to its ultimate meanings. From this perspective, no positivist (i.e., theory-reductionist) form of unification is implied, but simply a broader approach to life processes in general, paying attention to the location of biology between the psychological (the humanities) and the physical (natural) sciences.

Furthermore, by incorporating new concepts, models, and theories from biology into the study of signs, biosemiotics attempts to shed new light on some of the unsolved questions within the general study of sign processes (semiotics), such as the question about the origins of signification in the universe (e.g., Hoffmeyer 1996), and the major thresholds in the levels and evolution of semiosis (Sebeok 1997; Deacon 1997; Kull 2000; Nöth 2000). Here, signification (and sign action) is understood in a broad sense, that is, not simply as the transfer of information, but also as the generation of the very content and meaning of that information in all living sign producers and sign receivers.

Sign processes are thus taken as real: they are governed by regularities (habits, or natural rules) that can be discovered and explained. They are intrinsic in living nature, but we can access them—not directly, but indirectly through other sign processes (e.g., scientific measurements and qualitative distinction methods)—even though the human representation and understanding of these processes in the construction of explanations is built up as a separate scientific sign system distinct from the organisms’ own sign processes.

One of the central characteristics of living systems is the highly organized character of their physical and chemical processes, partly based upon informational and molecular properties of what has been described in the 1960s as the genetic code (or, more precisely, organic codes). Distinguished biologists, such as Ernst Mayr (1982), have seen these informational aspects as one of the emergent features of life, namely, as a set of processes that distinguishes life from everything else in the physical world, except perhaps human-made computers. However, while the informational teleology of computer programs are derived, qua being designed by humans to achieve specific goals, the teleology and informational characteristics of organisms are intrinsic, qua having evolved naturally, through adaptational and evolutionary processes. The reductionist and mechanistic tradition in biology (and philosophy of biology) has seen such processes as being purely physical and having to do with only efficient causation. Biosemiotics is an attempt to use the concepts of semiotics in the sense employed by Charles Sanders Peirce to answer questions about the biological emergence of meaning, intentionality, and a psychological world (CP 5:484).  Indeed, these are questions that are hard to answer within a purely mechanistic and reductionist framework.


From The Biosemiotic Approach in Biology: Theoretical Bases and Applied Models

The term “biosemiotic” was first used by F. S. Rothschild in 1962, but Thomas Sebeok has done much to popularize the term and the field.  Apart from Charles Peirce (1939–1914) and Charles Morris (1901– 1979), early pioneers of biosemiotics were Jakob von Uexküll (1864– 1944), Heini Hediger (1908–1992), and Giorgio Prodi (1928–1987), and the founding fathers were Thomas Sebeok (1920–2001) and Thure von Uexküll (1908–2004). After 2000, an institutionalization of biosemiotics can be noticed: since 2001, annual international meetings of biosemioticians have been taking place (initially organized by the Copenhagen and Tartu groups); in 2004, the International Society for Biosemiotic Studies was established (with Jesper Hoffmeyer as its first president; see Favareau 2005); the specialized publications Journal of Biosemiotics (Nova Science) and Biosemiotics (Springer) have appeared; several collections of papers have characterized the scope and recent projects in biosemiotics, such as a special issue of Semiotica 127 (1/4) (1999), Sign Systems Studies 30 (1) (2002), Sebeok and Umiker-Sebeok 1992, Witzany 2007, and Barbieri 2007.

Also, from the 1960s to the 1990s, the semiotic approach in biology was developed in various branches:

a. Zoosemiotics, the semiotics of animal behavior and communication

b. Cellular and molecular semiotics, the study of organic codes and protolinguistic features of cellular processes

c. Phytosemiotics, or sign processes in plant life

d. Endosemiotics, or sign processes in the organism’s body

e. Semiotics in neurobiology

f. Origins of semiosis and semiotic thresholds


From Cybersemiotics: A New Foundation for Transdisciplinary Theory of Information, Cognition, Meaningful Communication and the Interaction Between Nature and Culture


Cybersemiotics constructs a non-reductionist framework in order to integrate third person knowledge from the exact sciences and the life sciences with first person knowledge described as the qualities of feeling in humanities and second person intersubjective knowledge of the partly linguistic communicative interactions, on which the social and cultural aspects of reality are based. The modern view of the universe as made through evolution in irreversible time, forces us to view man as a product of evolution and therefore an observer from inside the universe. This changes the way we conceptualize the problem and the role of consciousness in nature and culture. The theory of evolution forces us to conceive the natural and social sciences as well as the humanities together in one theoretical framework of unrestricted or absolute naturalism, where consciousness as well as culture is part of nature. But the theories of the phenomenological life world and the hermeneutics of the meaning of communication seem to defy classical scientific explanations. The humanities therefore send another insight the opposite way down the evolutionary ladder, with questions like: What is the role of consciousness, signs and meaning in the development of our knowledge about evolution? Phenomenology and hermeneutics show the sciences that their prerequisites are embodied living conscious beings imbued with meaningful language and with a culture. One can see the world view that emerges from the work of the sciences as a reconstruction back into time of our present ecological and evolutionary self- understanding as semiotic intersubjective conscious cultural and historical creatures, but unable to handle the aspects of meaning and conscious awareness and therefore leaving it out of the story. Cybersemiotics proposes to solve the dualistic paradox by starting in the middle with semiotic cognition and communication as a basic sort of reality in which all our knowledge is created and then suggests that knowledge develops into four aspects of human reality: Our surrounding nature described by the physical and chemical natural sciences, our corporality described by the life sciences such as biology and medicine, our inner world of subjective experience described by phenomenologically based investigations and our social world described by the social sciences. I call this alternative model to the positivistic hierarchy the cybersemiotic star. The article explains the new understanding of Wissenschaft that emerges from Peirce’s and Luhmann’s conceptions.


Key People:

  • Thomas Sebeok
  • L M Rocha
  • Jesper Hoffmeyer
  • Charles Sanders  Pierce
  • Soren Brier
  • Marcello Barbieri
  • Howard Pattee
  • Jakob von Uexküll
  • Stanley Salthe
  • Claus Emmeche
  • M. Florkin
  • Kalevi Kull
  • Donald Favareau
  • Umberto Eco
  • Koichiro Matsuno
  • Thure von Uexküll
  • Gregory Bateson


Key Sources of Research:


A Short History of Biosemiotics

Marcello Barbieri

Click to access Marcello%20Barbieri%20(2009)%20A%20Short%20History%20of%20Biosemiotics.pdf



The Biosemiotic Approach in Biology : Theoretical Bases and Applied Models

Jo ã o Queiroz, Claus Emmeche, Kalevi Kull, and Charbel El-Hani



Irreducible and complementary semiotic forms

Howard Pattee


Click to access irreducible_and_complementary_semiotic_howard_pattee.pdf



Howard Pattee;jsessionid=0E1C125F151B5165F839E8FAC5411A00?doi=


Essential Readings in Biosemiotics: Anthology and Commentary

D. Favareau,

Essential Readings in Biosemiotics, Biosemiotics 3,

Springer Science+Business Media B.V. 2010



Introduction: An Evolutionary History of Biosemiotics

Donald Favareau

Essential Readings in Biosemiotics, Biosemiotics 3


Click to access Lesson_13_Favareau_History_biosemiotics.pdf



Introduction to Biosemiotics: The New Biological Synthesis

edited by Marcello Barbieri


A New Foundation for Transdisciplinary Theory of Information, Cognition, Meaningful Communication and the Interaction Between Nature and Culture

Søren Brier


Click to access Brier,%20Cybersemiotics,%20Vol.%209,%20No.%202.pdf



Levels of Cybersemiotics: Possible ontologies of signification

Søren Brier


Click to access 2_Brier_v1_2.pdf


Design and Information in Biology: From Molecules to Systems

By J. A. Bryant


Cognitive Biology: Dealing with Information from Bacteria to Minds

By Gennaro Auletta


The cell as the smallest DNA-based molecular computer

Sungchul Ji


Click to access The_cell_as_the_smallest_DNA_based_molecular_computer.pdf


Semiotics Web page of Umberto Eco


Biosemiotics in the twentieth century: A view from biology



Click to access semi.1999.127.385.pdf


Biosemiotics: a new understanding of life

Marcello Barbieri


Click to access Bar08.pdf


What Does it Take to Produce Interpretation? Informational, Peircean and Code-Semiotic Views on Biosemiotics

Søren Brier & Cliff Joslyn

Click to access 02e7e529745b2b7e66000000.pdf


Spencer-Brown, G. (1972).

Laws of Form

New York: Crown Publishers


The Paradigm of Peircean Biosemiotics

Søren Brier

Click to access Brier_2008_peircean_biosemiotics.pdf




Click to access BiosemBiophys.pdf


Biosemiotic Questions

Kalevi Kull & Claus Emmeche & Donald Favareau

Click to access a4414fbb4bdca11561d08cb4de0a0d6c.pdf


Autocatalysis, Autopoiesis and Relational Biology

AutoCatalysis, Autopoiesis, and Relational Biology



The term autopoiesis is often encountered in the systems literature and is generally interpreted loosely as concerned with self-organizing systems and life. While this is partially true, the concept is actually very detailed and particular, and its implications are very far-reaching. This is not always fully appreciated, not least because of the difficulty of the original papers. Auto­poiesis was coined by Humberto Maturana and Francisco Varela to describe the nature of living as opposed to nonliving systems – it is thus an explanation of the nature of life. This, in itself, is an important enough subject and their theory has far-reaching implications for biology. They went further, however, and also developed fundamental ideas about the nervous system, perception, language, and cognition in general. These, too, have very significant impli­cations, not least for methodologies concerned with taking action within human activity systems, the design of systems in general and computer systems in particular, and for cognitive science and artificial intelligence.


Autopoiesis is a concept developed by Humberto Maturana and Francisco Varela in order to analyze the nature of living systems. It takes into account the circular organization of metabolism and it redefines the concepts of structure and organization.

Any system can be decomposed into processes and components, which interact through processes to generate other components. The definition of an Autopoietic system considers that “it is organized as a bounded network of processes of production, transformation and destruction of components that produces the components which: a)through their interactions and transformations continuously regenerate and realize the network of processes (relations) that produced them and b)constitute it (the machine) as a concrete entity in the space in which they (the components) exist by specifying the topological domain of its realization as such a network”.


From Autopoietic and (M,R) systems



In 1972, in the middle of a cataclysmic political turmoil, two Chilean biologists introduced the concept of Autopoietic systems6 (‘‘auto’’=self and ‘‘poiesis’’= generating or producing) as a theoretical construction on the nature of living systems centering on two main notions: the circular organization of metabolism and a redefinition of the systemic concepts of structure and organization. Maturana and Varela’s starting point was that any system can be decomposed into processes and components. Components interact through processes to generate other components.

The notion of circular organization is given in Autopoiesis, and it is immediately clarified in the theory by the very definition of an Autopoietic system:

‘‘an Autopoietic system is organized as a bounded network of processes of production, transformation and destruction of components which:

  1. (i)  through their interactions and transformations continuously regenerate and realize the network of processes that produced them
  2. (ii)  constitute the system as a concrete entity in the space in which the components exist by specifying the topological realization of the system as such a network’’ (Varela et al., 1974; Maturana and Varela, 1975, 1980).

In an Autopoietic system, the result of any given process is the production of components that eventually would be transformed by other processes in the network into the components of the first process. This property, termed operational closure, is an organizational property that perfectly coexists with the fact that living systems are, from a physical point of view, energetically and materially open systems. The molecules that enter the system determine the system’s organization, which generates pathways whose operation produces molecular structures that determine the physical system and the system’s organization (Fig. 7) (Fleischaker, 1990). Thus an Autopoietic system does not have inputs or outputs, instead it creates a web of molecular processes that result in the maintenance of the autopoietic organization. Because an Autopoietic system’s internal dynamics are self-determined, there is no need to refer any operational (or organizational) aspect to the outside. Thus the environment does not inform, instruct or otherwise define the internal dynamics, it only perturbs the system’s dynamics. This does not mean that an Autopoietic system is completely independent from its medium. Instead it means that the system specifies its own internal states and the domain of its changes. In this context, external events act as perturbations that only trigger internal changes. But the magnitude and direction of these changes are defined by the internal dynamics of the system and not by the external perturbations (Maturana and Mpodozis, 2000).


The second clause demands that an Autopoietic system has ‘‘sufficiently complex’’ dynamics to self- produce the boundaries that separate the systems from the ‘‘non-system’’. This apparently trivial clause has profound implications as it touches upon the problem of autonomy and also serves to weed out from the Autopoietic forest some pure formal systems. Thus Autopoietic systems are not simple relational devices that connect components with components via complex graphs. Autopoietic systems must conform to an important topological property: their boundary (in the space where their components exist) is actively produced by the network of processes that define the system’s identity. This property of Autopoietic systems couples a purely relational property (operational closure) with a topological property and it demands that an Autopoietic system must be an autonomous unity, topographically and functionally segregated from its medium, but yet dependent from this medium (Weber, 2001). In the realm of molecules, the coupling of these two conditions necessarily implies that the minimal metabolism must be rather more complex than the spatial coupling of a direct chemical reaction with its reverse reaction.


From Autopoietic and (M,R) systems


Relational Biology

In the 1930s, Nicolas Rashevsky, a physicist by training, championed the biophysical approach to understanding living systems. Rashevsky and his stu- dents created a systematic theoretical effort that consisted of applying theories from physics to explain biological phenomena like cell division and neural processing (Rashevsky, 1938). Around 1950, Rashevsky became convinced that his intense and novel ‘‘bio- physical’’ approach was fundamentally limited for understanding living systems as a whole. He realized that his previous work had dealt only with bit parts of the phenomena of living systems, without considering their peculiar organization. Thus, Rashevsky coined the term Metric Biology to refer to all aspects where a reductionist approach to biology was valid and the term Relational Biology to aspects that depended on the organization of living systems rather than the matter found inside them (Rashevsky, 1954).

In 1958–1959, as a graduate student of Nicolas Rashevsky, Robert Rosen published three papers (Rosen, 1958a, b, 1959) that were a rigorous attempt to formalize the intuitive notions of relational biology. His formalism (known as (M,R) systems) used mathematical language based on a modern and abstract branch of mathematics (Theory of Categories (Eilenberg and MacLane, 1945)). Since not many biologists are well-enough versed in algebraic theory to evaluate its utility, (M,R) systems has not had the wide impact it may deserve. Despite the limited audience Rosen could capture with his ideas, Rosen continued to develop the theory of (M,R) systems and the use of the theory of categories in Biology for 40 years until his death in 1998.

(M R) Systems 

Metabolism-repair systems ((M,R)) were introduced by Robert Rosen as an abstract representation of cell metabolic activity. The representation was obtained in the context of Relational Biology, which means that organization prevails over the physico- chemical structure of the components involved. This fact was determinant for algebraically formalizing (M,R) systems using the theory of categories.

Two elements are considered in the construction of (M,R) systems: the metabolic activity (M) and the repair functions (R) acting on the unities of the metabolic process.

The metabolic system M is considered as an input-output system. In the categorical representation, inputs and outputs are the objects of the category and the processes connecting these elements are represented by the arrows of the category.


From Autocatalytic Sets: From the Origin of Life to the Economy


Autocatalytic Sets

The framework was originally developed in the context of a chemical reaction system, which can be described formally as a set (collection) of molecules; possible chemical reactions between these molecules; and, additionally, catalysts. A catalyst is a molecule that significantly increases the rate at which a chemical reaction happens, without being consumed in that reaction. In this context, catalysts can be viewed as providing functionality, because they determine which reactions happen at high enough rates to be relevant. In fact, without catalysts, life would most likely not be possible at all, because the chemical reactions vital for life would not happen fast enough, and they would not be synchronized with one another. Finally, we assume that there are small numbers of molecules, called the food set, that are assumed to be freely available from the environment. This reflects the notion that at least certain types of molecules (e.g., water, hydrogen, nitrogen, carbon dioxide, iron) would have been around on the early Earth, before the origin of life, and could be used freely as chemical building blocks.


Given such a chemical reaction system, a subset of its chemical reactions, together with the molecules involved in them, is called an autocatalytic set if (a) every reaction in the subset is catalyzed by at least one molecule from this subset and (b) every molecule in the subset can be produced from the food set by a series of reactions from this subset only. This two-part definition formally captures the idea of a functionally closed (part a) and self-sustaining (part b) system. The molecules mutually help (through catalysis) in each others’ production, and the set as a whole can be built up and maintained (through these mutually catalyzed reactions) from a steady supply of food molecules.


Stuart Kauffman (1971) was one of the first scientists to introduce this notion of autocatalytic sets. He subsequently constructed a simple mathematical model of chemical reaction systems to argue that such autocatalytic sets will arise spontaneously (Kauffman 1986, 1993). In his model (known as the binary polymer model), molecules are represented by simple bit strings (sequences of zeros and ones) of maximum length n. The chemical reactions consist of either gluing two bit strings together into a larger one (e.g., 000 + 11 → 00011), or cutting one bit string into two smaller ones (e.g., 010101 → 01 + 0101). The molecules (bit strings) are then assigned randomly, with a given probability, p, as catalysts for the possible reactions. In other words, there is a probability, p, that an arbitrary molecule will catalyze an arbitrary reaction. By changing the values of the parameters n and p and randomly generating the catalysis assignments, different instances of the model can be created.


Kauffman then developed a mathematical argument to show that, in his binary polymer model, given a fixed value for the probability of catalysis, p, and a large enough value for the maximum molecule length, n, the existence of autocatalytic sets is basically inevitable. However, this argument was later criticized (Lifson 1997) because it implies an exponential increase in the (average) level of catalysis. In other words, every time the maximum length n of the molecules (bit strings) in the model is increased by one, each molecule will end up catalyzing about twice as many reactions as before. This will indeed eventually lead to the existence of autocatalytic sets (for large enough n), but at a chemically unrealistically high level of catalysis. Furthermore, this notion of autocatalytic sets was also criticized for lacking evolvability (Vasas et al. 2010). In Kauffman’s argument, an autocatalytic set will appear as one “giant connected component” in the chemical reaction network. This, however, implies that there is no room for change, growth, or adaptation— in other words, no possibility for the autocatalytic set to evolve.


Key Ideas and Concepts:

  • Relational Biology
  • System Biology
  • Biosemiotics
  • Anticipation
  • Autopoiesis
  • Social Autopoiesis
  • MR systems
  • Self Reference
  • Mathematical Biology
  • Theoretical Biology
  • Socio-Cybernetics
  • Cyber Semiotics
  • Autocatalysis
  • Hyper Recursive/Incursive Automata


Each of these Idea needs a separate post.  Can not do justice to them all here.  Will try to write future posts expanding these ideas.

Autopoiesis, Autocatalysis, and Relational biology have been extended into other areas of inquiry.  Autopoiesis has been extended into Social systems theory through work of Niklas Luhmann.  Other researchers have extended it into organizational theory for firms.  Relational Biology has also extended into Futures research using concept of biology of Anticipation.


Key People:

  • Robert Rosen
  • Niklas Luhmann
  • Humburto Maturana
  • F Varela
  • Roberto Poli
  • Nicholas Rashevsky
  • John Kineman
  • M Nadin
  • A H Louie
  • Dirk Baecker
  • Soren Brier
  • Stuart Kaufman
  • Daniel Dubois
  • Donald C. Mikulecky
  • Milan Zeleny
  • Tibor Ganti


Key Sources of Research:


A relational theory of biological systems

Robert Rosen


Anticipatory Systems

Robert Rosen


A relational theory of biological systems II

Robert Rosen


The representation of biological systems from the standpoint of the theory of categories

Robert Rosen


Robert Rosen’s anticipatory systems

A.H. Louie


Click to access 09e4150cdd961e4a87000000.pdf


A Critical Evaluation of Luhmann’s Theory of Social Systems



Click to access quad50.pdf


Systems biology: The reincarnation of systems theory applied in biology?

Olaf Wolkenhauer

Date received (in revised form): 5th June 2001

Click to access 258.full.pdf





Click to access Zeleny%201977%20Formal.pdf



Dr. John Jay Kineman, Ph.D


The Dawn of Mathematical Biology


Daniel Sander Hoffmann


Click to access 1511.01455.pdf


Modeling Living Systems

Peter Andras


Click to access PAmodlivECAL2009.pdf


theory of organismic sets and mathematical relations


Click to access 41184.pdf


Tracing organizing principles:

Learning from the history of systems biology


Click to access Green%26Wolkenhauer.pdf



Eliseo Fernández

Click to access biosemiotics_and_the_relational_turn_in_biology.pdf


Autopoietic and (M,R) systems

Juan Carlos Letelier, Gonzalo Mar!ın, Jorge Mpodozis

Click to access Autop.Rosen.pdf






Click to access louie-mr-2006.pdf


Some Thoughts on A. H. Louie’s ‘‘More Than Life Itself: A Reflection on Formal Systems and Biology’’

Claudio Gutie ́rrez • Sebastia ́n Jaramillo • Jorge Soto-Andrade


Click to access thoughts-Louie.pdf


Relational Models of Social Systems


Click to access seidman.PDF


A Unified Approach to Biological and Social Organisms

N. Rashevsky


Essays on More Than Life Itself

A. H. Louie

Click to access essaysOnMoreThanLifeItself.pdf



Rosen’s (M,R) system in process algebra

Derek Gatherer1,3* and Vashti Galpin2

Click to access 1752-0509-7-128.pdf



The reflection of life: functional entailment and imminence in relational biology,

by A. H. Louie,

Springer, New York, NY, 2013, xxxii + 243 pp., ISBN 978-1-4614-6927-8

Click to access quo_vadis_relational_biology.pdf


Even more than life itself: beyond complexity

Donald C. Mikulecky


Click to access beyondcomplexityrev8310.pdf


Rosen R (1991)

 Life itself: a comprehensive inquiry into the nature, origin, and fabrication of life.

Columbia University Press, New York


Rosen R (2000)

Essays on life itself.

Columbia University Press, New York


Prolegomena: What Speaks in Favorof an Inquiry into Anticipatory Processes?

Mihai Nadin

Click to access edit_prolegomena.pdf



Eliseo Fernández

Click to access PRfinal.pdf


An Introduction to the Ontology of Anticipation

Roberto Poli

Click to access read_Poli-An-Introduction-to-the-Ontology-of-Anticipation.pdf


Autopoiesis 40 years Later. A Review and a Reformulation

Pablo Razeto-Barry

Click to access Autopoiesis_40_years_later_2012%20-%20Razeto-Barry_1.pdf


The mathematical biophysics of Nicolas Rashevsky

Paul Cull

Click to access rashevsky.pdf


The spread of hierarchical cycles

A.H. Louiea* and Roberto Poli


Louie, A.H.,


More than life itself: a synthetic continuation in relational biology.


Catalysis at the Origin of Life Viewed in the Light of the (M,R)-Systems of Robert Rosen

Athel Cornish-Bowden* and María Luz Cμrdenas



Click to access Bolzano09.pdf


Luhmann, Niklas.

“Insistence on systems theory: Perspectives from Germany-An essay.”

Social Forces (1983): 987-998.

Click to access LuhmannSystems.pdf


Luhmann N. (1986)

The autopoiesis of social systems.

In: Geyer F. & van der Zouwen J. (eds.) Sociocybernetic paradoxes. Sage, London: 172–192.



Gotthard Bechmann and Nico Stehr


Click to access luhmann_02.pdf


Luhmann, N.

“Essays on Self Reference.




Mingers J. (2002)

Can social systems be autopoietic? Assessing Luhmann’s social theory.

Sociological Review 50(2): 278–299.


Mingers J. (1989)

An Introduction to Autopoiesis – Implications and Applications.

Systems Practice 2(2): 159–180.



Maturana H. R. (1980)

Autopoiesis: Reproduction, heredity and evolution.

In: Zeleny M. (ed.) Autopoiesis, dissipative structures and spontaneous social orders, AAAS Selected Symposium 55 (AAAS National Annual Meeting, Houston TX, 3–8 January 1979). Westview Press, Boulder CO: 45–79







Click to access 1207.pdf


Varela F. J. (1980)

Describing the logic of the living. The adequacy and limitations of the idea of autopoiesis.

In: Zeleny M. (ed.) Autopoiesis: A theory of living organization. North-Holland, New York: 36–48



What Is Autopoiesis?

Milan Zeleny

Click to access 1194.pdf


Autopoiesis, a Theory of Living Organizations

Milan Zeleny


Maturana H. R. (1980)

Man and society.

In: Benseler F., Hejl P. M. & Köck W. K. (eds.) Autopoiesis, communication, and society: The theory of autopoietic systems in the social sciences


Order through fluctuation: Self-organization and social system

Ilya Prigogine

In Erich Jantsch (ed.), Evolution and Consciousness: Human Systems in Transition. Reading Ma: Addison-Wesley 93–130 (1976)


Maturana H. R. (1981)


In: Zeleny M. (ed.) Autopoiesis: A theory of the living organization. Westview Press, Boulder CO: 21–33.


Maturana H. R. (2002)
Autopoiesis, structural coupling and cognition: A history of these and other notions in the biology of cognition.
Cybernetics & Human Knowing 9(3–4): 5–34.



Pier Luigi Luisi

Autopoiesis: a review and a reappraisal

Click to access luisi_autopoiesis.pdf


From autopoiesis to neurophenomenology:
Francisco Varela’s exploration of the biophysics of being


Click to access art05.pdf


Life and mind: From autopoiesis to neurophenomenology. A tribute to Francisco Varela


Click to access Thompson,%20Evan%20-%20Life%20and%20Mind%20From%20autopoiesis%20to%20neurophenomenology.pdf


Autopoiesis, Communication, and Society: The Theory of Autopoietic Systems in the Social Sciences

Frank Benseler, Peter M. Hejl & Wolfram K. Köck


Boden M. (2000)

Autopoiesis and life.

Cognitive Science Quarterly 1: 117–145.


Systems Typologies in the Light of Autopoiesis: A Reconceptualization of Boulding’s Hierarchy, and a Typology of Self-Referential Systems

John Mingers


Click to access 550181e60cf24cee39f79f7c.pdf


The Problems of Social Autopoiesis

John Mingers

Click to access 004635379d4ef9f5b7000000.pdf


Varela F. J. (1996)

The early days of autopoiesis: Heinz and Chile.

Systems Research 13(3): 407–417


Uribe R. B. (1981)

Modeling autopoiesis.

In: Zeleny M. (ed.) Autopoiesis: A theory of living organization. Elsevier North Holland, New York: 49–62.


Some Remarks on Autocatalysis and Autopoiesis

Barry McMullin



Category Theoretical Distinction between Autopoiesis and (M,R) Systems

Tatsuya Nomura

Click to access 00b7d518a427671ea9000000.pdf


Smith J. D. (2014)

Self-concept: Autopoiesis as the Basis for a Conceptual Framework.

Systems Research and Behavioral Science 31(1): 32–46.


Fleischaker G. R. (1992)

Questions concerning the ontology of autopoiesis and the limits of its utility.

International Journal of General Systems, 21(2): 131–141.


Villalobos M. & Ward D. (2015)

Living systems: Autopoiesis, autonomy and enaction.

Philosophy & Technology 28(2): 225–239.


A Calculus for Autopoiesis

Dirk Baecker

June 1, 2012


The Sciences of Complexity and “Origins of Order”

Stuart A. Kauffman



Approaches to the Origin of Life on Earth

Stuart A. Kauffman



The phase transition in random catalytic sets


Rudolf Hanel, Stuart A. Kauffman, and Stefan Thurner



Click to access 0504776.pdf


Origins of Order in Dynamical Models



Click to access Origins_of-Order_review.pdf


On emergence, agency, and organization


Click to access 557065ab08ae7d0f5f900e19.pdf


 Autocatalytic Sets: From the Origin of Life to the Economy

Wim Hordijk


Autocatalysis, Information and Coding

Peter R. Willis


Click to access 00-01-003.pdf


Autocatalytic sets and boundaries

Wim Hordijk and Mike Steel*~hmac=6760deec426b5c9098efc365d7e9f047b20e06f02e1216aca77226e764abda13


Catalysis at the Origin of Life Viewed in the Light of the (M,R)-Systems of Robert Rosen

Athel Cornish-Bowden and María Luz Cμrdenas


Click to access Bolzano09.pdf


Closure to efficient causation, computability and artificial life

Mar ́ıa Luz Ca ́rdenasa,∗ Juan-Carlos Letelierb, Claudio Gutie ́rrezc, Athel Cornish-Bowdena and Jorge Soto-Andrade


Autopoietic and (M,R) systems

Juan Carlos Letelier*, Gonzalo Mar!ın, Jorge Mpodozis


Click to access autopoietic_mr.pdf



J. C. Letelier(1) and A. N. Zaretzky


Click to access AutopoiesisandMRsystems.pdf



Economics And The Collectively Autocatalytic Structure Of The Real Economy

November 21, 201112:28 PM ET





Click to access autocatalyticreplication.pdf