Why do we need to find and quantify distinctive features of a lineage?

Lineage-specific genes, or LSG's have received a great deal of attention in genomic studies of evolution. However, the challenge involved in assembling and annotating genomes has meant that getting accurate numbers and definitive lists has proved difficult. Nonetheless, it has been shown that "Many, but not all, lineage-specific genes can be explained by homology detection failure." Several well-known examples of lineage-specific genes have been the focus of detailed study. For instance, the loss of several functionally related genes in the yeast baker's yeast Saccharomyces cerevisiae has been linked to the loss of corresponding phenotypes. Conclusively establishing the reasons for lineage-specific genes is also troublesome. LSG's can be inferred due to loss, rapid sequence divergence, duplication of genes, or other evolutionary events. Ruling out various possibilities and disentangling the cause and effect is not always possible.

Apart from LSG's, other lineage-specific changes have been noted in cis-regulatory elements, changes in interaction partners, etc. What is the contribution of these different lineage-specific changes? Which changes have had a large role in phenotypic evolution? Are these changes correlated, and if so, in what ways? These kinds of questions regarding the relevance and implications of lineage-specific changes (LSCs) can be answered when the changes can be quantified with confidence by ruling out various bioinformatics artifacts. Once we have answers to these questions, we may begin to understand the evolution of genetic changes from a different perspective. 

Lineage-specific accumulation of repeats in genomes has also been studied, although mostly in non-genic regions. For instance, in a comparison of plant genomes, Patil et al. identified large differences in the repeat content of closely related species. Do similar changes occur in protein repeats? How rampant are such changes genome-wide? These are intriguing questions, especially when it is known that some genes have rapid changes in protein repeat content. Among the various genes that are worthy of study (GWoS), immune genes occupy the prime place. Hence, it is no wonder that Teekas et al. do a comprehensive study of protein repeat evolution in immune genes. In their article titled "Lineage-specific protein repeat expansions and contractions reveal malleable regions of immune genes," they screen the annotated genomes of vertebrates for orthologs that contain protein repeats. Having identified orthologous repeats in orthologous genes, they quantify the expansion or contraction of repeats. Since these sorts of changes in repeat length seem to have a phylogenetic signal, they use PIC (Phylogenetically Independent Contrasts) to identify changes that are most distinctive in specific lineages. What if any of these changes have functional consequences will have to be seen. This approach developed by Teekas et al. opens the door for large scales identification of candidate proteins that may have "tuning knobs" of evolution. On the other hand, if these changes in repeat length have no consequence whatsoever, they reveal the regions of immune genes that are plastic to such changes.

Kantara, Dhanta Kathe: the legend of the forest

It is very rare that a Kannada movie that does not fit into a traditional genre becomes a huge hit, not just in Karnataka but across India. This is even more remarkable when the movie is not a high-budget star-studded enterprise. A folk story about the legend of the enchanted forest does have great appeal when combined with great visuals of the forest and the traditional "Bhoota Kola" dance. Although never actually stated, the movie is about the Western Ghats of India. If any forest in the world is enchanted, the Western Ghats would be the first place one would think of. As a biodiversity hotspot, the forests of the Western Ghats hold many marvelous treasures that remain hidden from humankind. 

We sequenced the genome of the Mesua Ferrea tree last year to investigate the demographic history of several forest trees. This year, we follow that up with the genome of the Wild Jack (Ayani) or Artocarpus hirsutus. Generating the genomes of forest plants by itself will not bring out the magic and lore hidden in their base pairs. Rather, interesting insights that could help us understand the adaptation of these trees to their unique habitat and how this has been achieved through changes in the genome would be of great value not only for commercial exploitation but also to sustain the forests and their diversity. In the pre-print, Patil et al. present the newly generated genome of the Wild Jack and compare its genome with that of two other species of the genus Artocarpus. By doing such comparative genomic analysis, various changes to gene sequences, as well as the complement of genes, are identified. Interestingly, it is found that the repeat content has changed drastically in the closely related commonly cultivated species Artocarpus heterophyllus (Jackfruit). Subsequently, the effect of these repeats on demographic inference is also investigated and builds upon previous work on Populus and human genomes. Nonetheless, the role of habitat is found to be more pronounced than that of repeats or the region of the genome used for the analysis. What other secrets does the enchanted forest hold? Will we ever be able to explore this forest further and what impact this will have on the forest itself are questions for tomorrow. 

Akṣhar Brahma Yog: The Yog of the Eternal God/ Immutable Consciousness or Attaining the Supreme

Chapter 8: With 28 verses or shlokas, the eighth chapter is of intermediate length (i.e.,<5%) and is mostly a monologue by Lord Bhagavan Sri Krishna, except for the first two Shlokas.

Arjuna (Shloka 2): 2 shloka

Krishna, the Supreme Personality of Godhead (Shloka 3-28): 26 shlokas

Brief Summary: In this chapter, Arjuna asks several questions, which are subsequently answered by Lord Bhagavan Sri Krishna, the supreme personality of Godhead.

Arjuna's questions are:

1. What is brahman?
2. What is the self (adhyatma)?
3. What are fruitive activities (karma)?
4. What is this material manifestation (adhibhuta)? 
5. What are the demigods (Adhidaiva)? 
6. How does the Lord of sacrifice (adhiyajna) live in the body? and in which part does he live?
7. How can those engaged in devotional service know you at the time of death?

The lord's answers are as follows:

1. Brahman: The Supreme Indestructible Entity
2. Adhyatma: one’s own self
3. Karma: fruitive activities. i.e., actions that pertain to the material personality of living beings and their development
4. Adhibhūta: the constantly changing material manifestation 
5. Adhidaiva: the universal form of the lord, which includes all the demigods
6. Adhiyajna: I, the supreme lord represented as the super soul, in the heart of every embodied being
7. Those beings who quit their body remembering Lord Sri Krishna attains Moksha. However, those engaged in other contemplations at the time of their death attain that same consciousness. Hence, with practice, one should acquire the skill of remembering the Lord at all times.

Spiritual planets can also be attained by Yogic practices. The Vedic scholars practice celibacy, chant Omkara, and remain detached from all sensual engagements. Those yogis who constantly think of me with exclusive devotion can attain me easily. These great souls who have attained me never return to this world filled with misery as they are immune to rebirth. 

All the material planets, including the Bramha planet, are subject to misery and rebirth. Only upon attaining the Lord's abode is one freed from re-birth. The time calculations are different for different planets. For instance, one day on the Bramha planet equals four yugas rotating thousand times for a human. Hence, in one Bramha day, many living entities come into being and culminate at night, and the same cycle continues. 

If one leaves the body at the auspicious time given in the Vedic literature, even accidentally will escape from the cycle of birth and death. However, for the devotees, there are no such limitations. 

Devotional service is equivalent to:

1. Studying the Vedas
2. Performing sacrifices
3. Undergoing austerities
4. Giving charity
5. Pursuing philosophical or fruitive activities

Favorite Shlokas:

Shloka 1-2:

kiṁ tad brahma kim adhyātmaṁ kiṁ karma puruṣhottama

adhibhūtaṁ cha kiṁ proktam adhidaivaṁ kim uchyate

adhiyajñaḥ kathaṁ ko ’tra dehe ’smin madhusūdana

prayāṇa-kāle cha kathaṁ jñeyo ’si niyatātmabhiḥ

Shloka 5:

anta-kāle cha mām eva smaran muktvā kalevaram

yaḥ prayāti sa mad-bhāvaṁ yāti nāstyatra sanśhayaḥ

Jñāna Vijñāna Yog: Yog through the Realization of Divine Knowledge

Chapter 7: With 30 verses or shlokas, the seventh chapter is of intermediate length (i.e.,<5%) and includes a monologue by Lord Bhagavan Sri Krishna.

Krishna, the Supreme Personality of Godhead (Shloka 1-30): 30 shlokas

Brief Summary: In this chapter, the Supreme Personality of Godhead Shree Krishna fully reveals the knowledge and wisdom after knowing that nothing else remains to be known in this world.

Among a thousand --> hardly one/few strive(s) for perfection--> Among those who have perfection, hardly one person truly knows the lord. 

Two types of energy in the lord through which all living beings are manifested:

1. Material/inferior energy= sum of (Earth, water, fire, air, space, mind, intellect, and ego).
2. Superior/soul energy= consists of embodied souls that form the basis of life in this world.

Lord Sree Krishna, the Supreme Personality of the Godhead, is analogous to the thread which holds all the beads together. Hence, the lord is the source of the entire creation into whom everything dissolves. The lord is also

1. the taste of water
2. radiance of the sun and the moon
3. sacred syllable Om in Vedic mantras
4. sound in ether
5. ability in humans
6. pure fragrance of the earth
7. brilliance in fire
8. life-force in all beings
9. penance of the ascetics
10. eternal seed of all beings
11. the intellect of the intelligent
12. the splendor of the glorious
13. the strength (devoid of desire and passion) of the strong
14. sexual activity not conflicting with virtue or scriptural injunctions

Three material states of existence/modes of Maya: goodness (sattva), passion (rajas) & ignorance (tamas).

Only by surrendering to the lord can one overcome Maya. 

Four kinds of people that don't surrender to me:

1. Those ignorant of the knowledge.
2. Those who are lazy follow their lower nature though capable of knowing me.
3. Those with deluded intellect.
4. Those with a demonic nature.

Four kinds of pious people engage in my devotion:

1. The distressed.
2. The seekers after knowledge (inquisitive).
3. The seekers of worldly possessions.
4. Those who are situated in knowledge/ seek absolute truth. (Dearest to the Lord)

We tend to pray to different deities (demigods) to fulfill our material desires as per our nature. Even these desires are taken care of due to Lord Krishna's benediction. The different deities can be considered different parts of the Lord's body.  However, the results obtained by praying to demigods are transient. The ultimate goal can be achieved by surrendering to Krishna. 

Lord Krishna has absolute knowledge of the past, present, and future.  Those who strive for liberation from the cycles of birth and death by surrendering to me realize the divine and achieve Krishna consciousness.  

Favorite Shlokas:

Shloka 7:

mattaḥ parataraṁ nānyat kiñchid asti dhanañjaya

mayi sarvam idaṁ protaṁ sūtre maṇi-gaṇā iva

Shloka 17:

teṣhāṁ jñānī nitya-yukta eka-bhaktir viśhiṣhyate

priyo hi jñānino ’tyartham ahaṁ sa cha mama priyaḥ

The ecology of influenza - role of gene loss in natural disease reservoirs

The CDC defines a reservoir of an infectious agent "as the habitat in which the agent normally lives, grows, and multiplies." When the infectious agent spills over from such a reservoir species into other susceptible species, the pathogen experiences strong selective constraints in the new host. This new environment may then select for a more potent pathogen that can spread in the new host or even across other vertebrate species. The brilliant Robert G Webster describes a lifetime of knowledge he has accumulated on this spill-over process in his talk "Influenza: Lessons learned from Pandemic H1N1" at Columbia University. This talk, now more than a decade old, has some interesting discussion at the end that, in hindsight, now after the covid pandemic looks intriguing. 

The most interesting part of the talk for me is when he talks about birds. First, he mentions that shorebirds (Charadriiformes) such as the Ruddy Turnstone (Arenaria interpres), Semipalmated Sandpiper (Calidris pusilla), Sanderling (Calidris alba), European herring gull (Larus argentatus), laughing gull (Leucophaeus atricilla), and Red knot (Calidris canutus) and waterfowl (Anseriformes) species such as mallard or wild duck (Anas platyrhynchos) and pintail or northern pintail (Anas acuta) are some of the migratory birds that are monitored for influenza in North America. The second time he mentions birds is when he explains the difference between Ducks and Chicken and how the RIG-I gene is lost in chickens. RIG-I is an immune sensor that activates the production of interferon-Beta. A more detailed talk that focuses on the loss of this gene and how the discovery was made is explained by Katherine Magor of the University of Alberta in her talk titled "How ducks survive the flu; the secrets of the reservoir host." 

It has been more than a decade since the paper describing the lack of RIG-I in chicken and "Association of RIG-I with innate immunity of ducks to influenza" has been published. In this decade, it has been established that the "Loss of RIG-I leads to a functional replacement with MDA5 in the Chinese tree shrew". Although a paper (from fish immunologist Chris Secombes) looking at the "Origin and evolution of the RIG-I like RNA helicase gene family" claimed that "Unlike RIG-I, whose presence in chicken and some fish species is uncertain..", it did not conclusively establish the lack of RIG-I in chicken. Limitations in genome assembly quality and availability of large genomic datasets can be blamed for these uncertainties. Notably, the paper by Secombes also investigates the origin of RIG-I and related genes through gene fusion, domain duplication, and deletion and follows in the line of a previous paper titled "Evolution of MDA-5/RIG-I-dependent innate immunity: Independent evolution by domain grafting".

The birth and death of the genes from the terminal complement pathway are surprisingly similar to the history of the RIG-I-like RNA helicase gene family. Domain fusion events are involved in the birth of both gene families at the boundary of invertebrates and vertebrates, both RIG-I and C9 are lost in Galliform birds but are present in Anseriform birds and both are involved in the immune response. Finally, our manuscript dealing with the Birth and Death in the Terminal Complement Pathway is published.

 

Dhyān Yog: The Yog of Meditation also known as the Atma-Samyama Yoga

Chapter 6: With 47 verses or shlokas, the sixth chapter is of the same length as the first chapter. 

Arjuna (Shloka 33-34, 37-39): 5 shlokas

Krishna, the Supreme Personality of Godhead (Shloka 1-32, 35-36, 40-47): 42 shlokas

Brief Summary: In this chapter, the lord explains the Dhyan Yog aspect as a continuation of his answer to prince Arjuna in the previous chapter.

Sanyāsīs=yogis=who perform prescribed duties without desiring the results of their actions, is free from feelings of possessiveness, lives in seclusion, and engage the body, mind, and self in a relationship with the supreme.

Shloka 5-6: The mind can be your friend if you have conquered it, but it can also be your worst enemy if you have failed to conquer your mind. 

Free from Dualities: Cold and heat, Joy and sorrow, honor and dishonor, happiness and distress

For the satisfied yogi who is in KC, 

• Shloka 8: Dirt=stones=gold
• Shloka 9: Well-wishers=friends=foe=pious=sinners=affectionate=benefactors=envious=neutral =mediators. Notably, this shloka lacks a purport. 

Shloka 11-12 are very specific in detail regarding the pre-requisites for meditation. The specifics are:

1. Should be performed in a sacred/secluded place. A list of sacred places is mentioned in the purport and includes Prayag, Mathura, Brindavan, Rishikesh, and Haridwar.
2. Kusha/Kusa grass (Desmostachya bipinnata) should be covered with deerskin and a soft cloth to prepare a seat.
3. The seat should be at optimum height, i.e., neither too high nor too low.

Shloka 13-14: The sitting position requires the alignment of the body, neck, and head in a straight line. One should focus on the tip of the nose and meditate upon the divine within the heart.

Yoga is not a mere physical exercise, rather it is a means to attain the abode of the lord (AOL). The importance of proper sleep and a healthy diet are explained concerning becoming a perfect yogi. Discipline in the lifestyle can mitigate all material pains, one has to follow the correct schedule for habits of eating, sleeping, recreation, and work in day-to-day life.

The flickering nature of the mind can be controlled by the practice of yoga which can lead to the attainment of trance or "samadhi.". In the stage of samadhi, the person is engrossed in self and attains the highest form of happiness, and is unaffected by the miseries of the material world. 

Arjuna questions the knowledge imparted by Lord Krishna regarding yoga as impractical and unendurable. Characters of the mind described by the prince Arjuna:

• Restless
• Turbulent
• Strong
• Obstinate
• More difficult to control than the wind

Lord: practice & detachment. Possible for those who have learned to control the mind.

Arjuna further enquires what happens to the unsuccessful yogi who cannot reach his goal due to an unsteady mind. Would such a person miss out on both material enjoyment and spiritual success? 

The lord reassures Arjuna as follows:

• Those who strive for KC are never overcome by evil.
• Unsuccessful yogi attains the abode of the virtuous (AOV) upon death. After dwelling in AOV for many ages, such a yogi is reborn in the family of pious and prosperous people.
• Else, if a yogi has developed dispassion through long practice of yoga, such a yogi is reborn in the family endowed with divine wisdom.
• Following rebirth, the yogi strives for liberation with even greater earnestness by reawakening the wisdom of past lives. 

Shloka 46: yogi > tapasvī (ascetic) ; yogi > jñānī (a person of learning); yogi > karmī (ritualistic performer)

The results of spiritual practices are accumulated and passed to the next birth. Hence, even the unsuccessful yogi is making progress and eventually attains liberation. In the last shloka, lord Krishna highlighted the importance of surrendering oneself to the divine with utmost faith and love becoming the highest yogi.

Favorite Shlokas:

Shloka 5:

uddhared ātmanātmānaṁ nātmānam avasādayet

ātmaiva hyātmano bandhur ātmaiva ripur ātmanaḥ

Shloka 16:

nātyaśhnatastu yogo ’sti na chaikāntam anaśhnataḥ

na chāti-svapna-śhīlasya jāgrato naiva chārjuna

Karm Sanyās Yoga: The Yog of Renunciation

Chapter 5: With 29 verses or shlokas, the fifth chapter is one of the shorter chapters. 

Arjuna (Shloka 1): 1 shloka

Krishna, the Supreme Personality of Godhead (Shloka 2-29): 28 shlokas

Brief Summary: In this chapter, Lord Krishna responds to prince Arjun's question about whether the path of renunciation of action or working with devotion is better.

The Lord reassures the prince that both paths lead to the supreme goal. Yet, he notes that working with devotion is easier/better than the renunciation of action. Then the lord proceeds to explain that both renunciation of action and devotional action are the same. The Krishna conscious person is a pure soul who controls his mind and senses, being dear to everyone. 

Shloka 10 mentions the analogy of "Padma-patram iva āmbhasā" (which means like water on a lotus leaf) to reiterate that those who perform actions by abandoning all attachments are unaffected by sin just like a lotus leaf which remains untouched by water. The 13th shloka refers to the human body as a city of 9 gates in which the soul resides happily through self-control and detachment.

Shloka 5.18: For the truly learned, Brahmin=cow=elephant=dog=dog eater as the same consciousness resides in all.  

Krishna conscious person (KCP),

1. Has equanimity (i.e., neither rejoices upon success nor laments upon failure or unpleasantness) of mind. The famous poet Hari Vansh Rai Bachan is credited with saying "Man ka ho to acha, na ho to aur bi acha.".This means that if things happen according to your wishes it is good, it is even better if they don't. The sense of equanimity and the importance of surrendering to the divine is exemplified by this statement.
2. Knows the divinity within all beings.
3. Enjoys unlimited happiness.
4. Is free from fear, anger and material desires.
5. Is self-realised and self-disciplined
6. Conquer the cycle of birth and death in this very life.

Shlokas 27-28 emphasise the role of meditation for the liberation of the soul, with the help of breath control. Meditation can also be attained by concentrating between the eyebrows thereby liberating us from desires, fear and anger. 

Favourite Shlokas:

Shloka 10:

brahmaṇyādhāya karmāṇi saṅgaṁ tyaktvā karoti yaḥ

lipyate na sa pāpena padma-patram ivāmbhasā

Sholkas 27-28: 

sparśhān kṛitvā bahir bāhyānśh chakṣhuśh chaivāntare bhruvoḥ

prāṇāpānau samau kṛitvā nāsābhyantara-chāriṇau

yatendriya-mano-buddhir munir mokṣha-parāyaṇaḥ

vigatechchhā-bhaya-krodho yaḥ sadā mukta eva saḥ

Escape from MAC's TCP

Understanding the mysteries of birth and death is a complicated affair that has preoccupied mankind from time immemorial. Escaping from the miseries inherent in the cycle of birth and death has been propounded as the ultimate goal of life in eastern religions. Nirvana or liberation from the "beginningless cycle of repeated birth, mundane existence, and dying again" is something that countless spiritual seekers aspire to attain. Attaining liberation requires the utmost faith and effort and is never available to those who doubt everything. In fact, the Bhagavat Gita goes so far as to say, "sanśhayātmā vinaśhyati." in chapter-4.40. Hence, the doubting soul has happiness neither in this world nor in the next.

Yet, one can have a doubting soul that fails to understand this sublime transcendental knowledge. Escaping from something simpler may be possible for such doomed souls. A recent pre-print by Sharma et al. focuses on the escape from the MAC (Membrane Attack Complex) encoded by the TCP (Terminal Complement Pathway). In their manuscript titled "Birth and Death in Terminal Complement Pathway," Sharma et al. investigate the emergence of the terminal component pathway in early vertebrates using sequence similarity analysis, comparison of exon length, phase, and domain order. Starting with "Four possible scenarios for the birth of the terminal complement pathway (TCP)," the authors evaluate each scenario against available data to find the most supported aspects. As part of their investigation, the "Status of terminal complement pathway (TCP) components" is identified in representative species from various vertebrate clades. Their research discovered that the complement C9 gene has been duplicated in several species of the order Squamata and potentially degraded in Galliform birds.

The complement C9 of chicken and other Galliform birds has escaped MAC's TCP. Death does not mean liberation. So how do we know that C9 is liberated and not simply dead? Sharma et al. find that the chicken repeat 1 (CR1) element is inserted at the C9 locus in the intronic regions and in the middle of exons. The presence of CR1 elements within the exons disrupts the coding frame and will continue to do so until it is removed. Hence, the re-birth of the C9 gene would require a careful excision of the CR1 elements to reestablish the reading frame. Based on the relatively special type of gene death seen in C9, one could argue a scenario of liberation. But how permanent is liberation? Can a liberated soul be again condemned to a cycle of birth and death? 

Does the soul merge with god after liberation, or does it just become part of a cosmic soul distinct from god? Liberation is even more challenging to understand than birth and death as it remains a primarily theoretical concept for us mere mortals. Nonetheless, C9 is dead; long live the TCP!

Transcendental Knowledge: Jnana Karm Sanyas Yog

Chapter 4: With 42 verses or shlokas, the fourth chapter is similar in length to the first and third chapters. 

Arjuna (Shloka 4): 1 shloka

Krishna, the Supreme Personality of Godhead (Shloka 1-3;5-42): 41 shlokas

Brief Summary: In this chapter, Lord Krishna highlights that knowledge of the Bhagavad Gita has been transferred in disciplic succession since time immemorial :

Lord Krishna--> Sun God --> Manu--> Ikhshvaku

However, this succession was broken over time due to reasons not mentioned in the original text. Hence, the Lord restored this transcendental knowledge through his devotee and dear friend Arjuna. In this chapter's only shloka attributed to Arjuna, he has raised a doubt that the Sun god is from a much older period, then how Lord Krishna could have preached the Gita to him? 

The rest of the Shlokas involve a detailed answer from lord Krishna to this question. Lord Krishna emphasized that all souls are transcendental and have existed for many lifetimes. The only difference is that the memory of souls is limited to the present life due to limited sense perception. However, lord Krishna remembers everything. 

Two Shlokas (7 & 8) made famous by the television series Mahabaratha are part of this chapter. The interpretation of these two shlokas is that whenever irreligion becomes predominant, the lord himself appears on this planet to re-establish principles of religion. The concept of moksha is again explained in the subsequent shlokas. Moksha, or liberation from the endless cycles of birth and death, is the ultimate aim of life and can be attained by total surrender to the divine. Freedom from attachment, fear, anger, and fruitive activities will pave the path towards liberation. We cannot please Krishna with our fruitive efforts. 

• Distinguishing between Action, Inaction, and Forbidden action is complex and requires subtlety.
• Abandoning proprietorship over our own possessions. 

One of the most commonly recited Shlokas before consumption of food in India is Shloka 24, which states, "For those who are completely absorbed in God-consciousness, the oblation is Brahman, the ladle with which it is offered is Brahman, the act of offering is Brahman, and the sacrificial fire is also Brahman. Such persons, who view everything as God, easily attain Him." 

i.e., oblation==ladle==act of offering==sacrificial fire==Brahman

Those who are interested in self-realization offer various types of oblations, such as:

1. functions of all the senses, the vital force [breath]
2. material possessions, practice the yoga of eightfold mysticism
3. study the Vedas for the advancement of transcendental knowledge
4. practice breath control (pranayama)

Hence, sacrifice of one form or the other is required for spiritual attainment. Another essential aspect of spiritual life is the guidance of a spiritual master (guru/self-realized soul). The realization of transcendental knowledge can lead to the liberation of even sinners. 

Favorite Shlokas:

Shloka 7:

yada yada hi dharmasya

glanir bhavati bharata

abhyutthanam adharmasya

tadatmanam srjamy aham

Shloka 8:

paritranaya sadhunam

vinasaya ca duskrtam

dharma-samsthapanarthaya

sambhavami yuge yuge

Shloka 24:

brahmarpanam brahma havir

brahmagnau brahmana hutam

brahmaiva tena gantavyam

brahma-karma-samadhina

Karma Yoga: The Yog of Action

Chapter 3: With 43 verses or shlokas, the third chapter is similar in length to the first chapter. Having finished 3 chapters, we will be using the "The Holy Geeta"  Commentary by Swami Chinmayananda as supplementary reading material. This version of the Gita is published by the Chinmaya Mission.

• Arjuna (Shloka 1-2;36): 3 sholkas
• Krishna, the Supreme Personality of Godhead (Shloka 3-35;37-43): 40 shlokas

Brief Summary: In this chapter, Arjuna asks the Lord why he is being asked to fight this horrible war if the path of knowledge is better than action. Arjuna asks the Lord to clarify which is the path to the greatest good and dispel the confusion created in chapter-2. The rest of the chapter explains action and its practice. 

First, Lord Krishna explains that in this world, two paths exist. One is the path of knowledge and the other is the path of action. Mere renunciation or abstinence from work does not lead one to freedom from action. Restraining the senses while the mind wanders the material world is hypocrisy. On the other hand, controlling the mind and engaging in work without attachment is the superior path. Performing the duties that are assigned to you is better than inaction. All work binds you to the world, except that which is done as Yajna or sacrifice. 

All living entities depend on food for sustenance. Food is the result of rains that occur due to the performance of Yajna or sacrifice. This sacrifice is a result of duties prescribed by the Vedas. Similarly, the lord also has to perform certain actions without which the world would be destroyed. The shloka 30 focuses on the total surrender of our desires to Krishna with no expectations of profit or ownership. By performing duties with no attachment to the results, one becomes free from bondage.

Shlokas 33 and 34 give an overview of the conscious (both controllable and uncontrollable) and subconscious (uncontrollable)  mind. It can be described at 3 levels, Samskara, raga/dvesha, and karma. The samskara is from the subconscious level and is beyond our control. Similarly, Karma despite being in the conscious is uncontrollable as we become conscious of it only after it has taken place. For example, we can regret an action/emotion after it has passed. However, it would be too late by then to control it. The secret gap between the layers of Samskara and karma is the raga/dvesha which is controllable and conscious. Raga/dvesha refers to our likes/dislikes which are the foundation of our actions. Katha Upanishad mentions that in every stage of our life, we make decisions based on Shreyas and preyas. Shreyas is a consequence that produces lasting benefit and Preyas provides immediate pleasure.

You can see this video in which Swami Sarvapriyananda explains this in detail.

Arjuna asks an interesting question in the 36th verse, why does one feel compelled to perform sinful acts against their will? 

The lord explains that this is merely lust that gets transformed to wrath upon contact with the material world. Only by overcoming lust (which happens to be a formidable enemy) can one know that the soul is superior to the intellect. 

 i.e., Body< Senses< Mind< Intellect< Soul 

Favorite Shlokas:

Shloka 14:

annad bhavanti bhutani

parjanyad anna-sambhavah

yajnad bhavati parjanyo

yajnah karma-samudbhavah

Shloka 27:

prakrteh kriyamanani

gunaih karmani sarvasah

ahankara-vimudhatma

kartaham iti manyate

Shloka 38: 

dhūmenāvriyate vahnir yathādarśho malena cha

yatholbenāvṛito garbhas tathā tenedam āvṛitam

Sānkhya Yoga: The Yog of Analytical Knowledge

Disclaimer: All details are with regards to the book Bhagavad Gita As it is by his divine grace A.C. Bhaktivedanta Swami Prabhupada founder-Acarya of the International Society for Krishna Consciousness.  However, the summary, views expressed and errors in the interpretation and understanding are the authors' own opinions. The goal of this write-up is to serve as class notes for the author in the upcoming exams.

Chapter 2: With 72 shlokas the second chapter "Sānkhya Yoga" is the second-longest chapter and is considered to present the gist of the entire Bhagavad Gita. The chapter is simply referred to as "Contents of the Gita Summarized" in the version of as-it-is. The use of the heading "Sankhya" leads to speculation about its link to the Sankhya philosophy. 

• Sanjaya (Shloka 1; 9-10): 3 shlokas
• Arjuna (Shloka 4-8; 54): 6 sholkas
• Krishna, the Supreme Personality of Godhead (Shloka 2-3;11-53; 55-72): 63 shlokas

Brief Summary: In this chapter, Lord Krishna answers the questions raised by Arjuna in chapter-1 and tries to convince him that fighting the war by overcoming his apprehensions is the correct path. Arjun completely surrenders to his friend and accepts Krishna as his mentor seeking his guidance. The lord justifies the killing of the kuru army by explaining the eternity of the soul and the need for compliance with one's duty. Lord Krishna preaches that one's mind should remain steady irrespective of the favorable or adverse circumstances. As the seasons change in nature in the same way perception of our circumstances changes throughout our life. The wise man is not bewildered by such changes (happiness or distress, loss or gain, victory or defeat, death) and remains unfazed. According to Vedanta, such a person of a steady mind is eligible for liberation (i.e., attainment of moksha or escape from the cycle of birth and death).

In this chapter, the shlokas can be categorized under Karma yoga (duty), Gyan yoga (knowledge), and Bhakti yoga (surrender). These three aspects of yoga are further explained in greater detail in subsequent chapters. 

1) The eternity of the soul has been described in several shlokas in different ways to drive home the main message.  For example, 

• Change of clothes==change of the body for the soul
• Young age, old age, and death for the body ---> In the same way the soul also changes the body

 2) In order to attain liberation: 

• One should not be indulged in sense pleasures (desires).
• Keep the mind free from attachment, fear, anger, and lust.
• Not be disturbed by the incessant flow of desires.
• Be always involved in devotional service of the lord

3) Guidance on the performance of duties 

• Action without expectation of results. This chapter contains the most popular shloka of the Bhagavad Gita which every Indian has probably heard either through movies or everyday proclamations states that "One should perform their duties diligently with detachment and not focusing on the results of their actions". (Shloka 47)
• The shloka 48 states that one should perform his/her duties equipoise abandoning all attachment to success or failure. Such equanimity is described as yoga in the scriptures.
• The various characteristics of a person with a steady mind are described at the end of chapter-2.

Salient observations:

1. In Shloka 23, it is given that the soul is eternal. It can not be destroyed by weapons, fire, water, or wind.
2. In Shloka 58, the tortoise withdrawing its limbs into its shell is compared to a person withdrawing his senses from the material world.
3. Shloka 48 states that one can perform his duties with a balanced state of mind irrespective of attachment with success and failure. (Yoga definition).

Favorite Shlokas:

Shloka 13:

dehino 'smin yathä dehe

kaumäraà yauvanaà jarä

tathä dehäntara-präptir

dhéras tatra na muhyati

Shloka 47:

karmaṇy-evādhikāras te mā phaleṣhu kadāchana

mā karma-phala-hetur bhūr mā te saṅgo ’stvakarmaṇi

Shloka 63:

krodhād bhavati sammohaḥ sammohāt smṛiti-vibhramaḥ

smṛiti-bhranśhād buddhi-nāśho buddhi-nāśhāt praṇaśhyati

Shloka 70:

āpūryamāṇam achala-pratiṣhṭhaṁ

samudram āpaḥ praviśhanti yadvat

tadvat kāmā yaṁ praviśhanti sarve

sa śhāntim āpnoti na kāma-kāmī

 

Arjuna's Vishada Yoga: Prince Arjuna's anguish

Disclaimer: All details are with regards to the book Bhagavad Gita As it is by his divine grace A.C. Bhaktivedanta Swami Prabhupada founder-Acarya of the International Society for Krishna Consciousness.  However, the summary, views expressed and errors in the interpretation and understanding are the authors' own opinions. The goal of this write-up is to serve as class notes for the author in the upcoming exams.

Chapter 1: With 46 shlokas (in contrast to 47 in other versions), the first chapter "Arjuna's Vishada Yoga" is of intermediate length and sets the stage for the chapters that follow. 

• Dhritrashtra (Shloka 1): 1 sholka
• Sanjaya (Shloka 2-20; 24-27; 46): 24 shlokas
• Arjuna (Shloka 21-23; 28-45): 21 sholkas

Brief Summary: In this chapter, the Kurukshetra battlefield is described by Sanjaya, (the counselor of king Dhritrashtra) in response to the request of the blind king Dhritrashtra. With the help of the special power given to Sanjaya by his guru Vyasa, he was able to envision the battlefield from Dhritrashtra's room. This chapter deals with the apprehensions of the Pandava prince Arjuna in waging a war against his cousins the Kauravas despite his proficiency as a warrior (being a Kshatriya). Sometimes we are also very indecisive and are not wanting to take up new challenges despite being skilled and capable. Our mind has a tendency to underestimate our abilities and comes up with numerous reasons for not performing a particular task. The mind tends to remain in its comfort zone. This chapter highlights this aspect of the human mind. 

Salient observations:

1. The warriors on the side of the Pandavas included Yuyudhana (i.e., Satyaki), Virata, Drupada (i.e., Yajnasena), Dhristaketu, Chekitana, and the King of Kashi, Purujit, Kuntibhoja, Saibya, Yudhamanyu, Uttamauja, sons of Draupadi and the son of Subhadra with Bhima as their General. (Shlokas 4-6)
2. With Bhishma as their General, the Kauravas had great warriors like Drona, Karna, Kripa, Ashwathama, Vikarna, and son of Somadatta (i.e., Bhurishrava). (Shloka 8)
3. The battle cry signifying the beginning of the war is characterized by the blowing of various musical instruments which was started by Bhishma. The description of conch shells blown by various warriors is given in detail with conch shell names of the 5 Pandava princes and Lord Krishna (Lord Krishna: Panchajanya; Arjuna: Devadatta; Bhima: Paundra; King Yudhisthira: Anantavijaya; Nakula: Sughosa; Sahadeva: Manipushaka). (Shlokas 12-19)
4. In Shloka 12 it is mentioned that Bheeshma roared like a lion. In Shloka 14 it is described that Arjuna's chariots were drawn by white horses. 
5. Having seen the combatants in both the armies prince Arjuna refuses to fight and provides the following reasons for his refusal (this observation is inspired by writings of DiscoverSuperSoul):

D: Discontentment (inability to enjoy victory): Shlokas 32-35 

I: Indecision: (confusion regarding the correct path): Sholkas from chapter 2

C: Compassion (attachment towards his own kinsmen): Shloka 31

E: End of the dynasty (and the consequences thereof): Shlokas 39-43

F: Fear of accruing sin (karmic consequences of sin): Shlokas 36-38

          

We provide the mnemonic of DICE-F (remember as DICE Failure) to remember the reasons given by Arjuna. The entire war is the consequence of gambling with dice and Yudhiṣṭhira's failure.

Favorite Shlokas:

Sholka 10:

aparyaptam tad asmakam balam bhismabhiraksitam

paryaptam tv idam etesam balam bhimabhiraksitam

Sholkas 28-29:

drstvemam sva-janam krsna yuyutsum samupasthitam

sidanti mama gatrani mukham ca parisusyati

vepathus ca sarire me roma-harsas ca jayate

gandivam sramsate hastat tvak caiva paridahyate

Sholka 44:

aho bata mahat papam kartum vyavasita vayam

yad rajya-sukha-lobhena hantum sva-janam udyatah

Our Doubts:

1. Why are the conch shells described in such great detail? What is the significance of these sounds?
2. Should one perform his duties diligently even if it is going to cause suffering for others?

Names of Arjuna and Krishna:

Arjuna:

1. Gudakesha
2. Partha
3. Kaunteya
4. Dhananjaya
5. Kapi-dhvajah

Krishna:

1. Hrishikesha
2. Madhava
3. Janardhana
4. Varshneya
5. Achyuta
6. Keshava
7. Madhusudhana

Bhagwad Geeta in numbers - a speculative commentary

The data in this table is compiled from the resources available online and corresponds to the version of the Bhagwad Geeta that has 700 shlokas/slokas.

Chapter	Title	Total	Krishna	Arjuna	Sanjaya	Dhritrashtra	Percentage_by_chapter	Cumulative percentage
1	Arjuna_s_Vishada_Yoga	47	0	21	25	1	6.71	6.71
2	Sankhya_Yoga	72	63	6	3	0	10.29	17.00
3	Karma_Yoga	43	40	3	0	0	6.14	23.14
4	Jnana-Karma-Sanyasa_Yoga	42	41	1	0	0	6.00	29.14
5	Karma-Sanyasa_Yoga	29	28	1	0	0	4.14	33.29
6	Atma-Samyama_Yoga	47	42	5	0	0	6.71	40.00
7	Jnana-Vijnana_Yoga	30	30	0	0	0	4.29	44.29
8	Aksara-ParaBrahma_Yoga	28	26	2	0	0	4.00	48.29
9	Raja-Vidya-Raja-Guhya_Yoga	34	34	0	0	0	4.86	53.14
10	Vibhuti_Yoga	42	27	7	8	0	6.00	59.14
11	Viswarupa-Darsana_Yoga	55	22	33	0	0	7.86	67.00
12	Bhakti_Yoga	20	19	1	0	0	2.86	69.86
13	Ksetra-Ksetrajna-Vibhaga_Yoga	34	34	0	0	0	4.86	74.71
14	Gunatraya-Vibhaga_Yoga	27	26	1	0	0	3.86	78.57
15	Purushottama_Yoga	20	20	0	0	0	2.86	81.43
16	Daivasura-Sampad-Vibhaga_Yoga	24	24	0	0	0	3.43	84.86
17	Shraddhatraya-Vibhaga_Yoga	28	27	1	0	0	4.00	88.86
18	Moksha-Sanyasa_Yoga	78	71	2	5	0	11.14	100.00
Total	Bhagwad_Geeta	700	574	84	41	1
	Percentage_by_character		82.00	12.00	5.86	0.14

The table given above provides the count of slokas in each of the chapters of Bhagwad Geeta. Details of the number of slokas are further separated by the characters attributed to these slokas. In addition to the actual numbers, the values are also summarised as sums, percentages, and cumulative percentages to help with the speculative commentary given below.

Commentary:

1. The Bhagwad Geeta has been described as "a dialogue between Pandava prince Arjuna and his guide and charioteer Krishna, the Supreme Personality of Godhead". However, these numbers help highlight the fact that in addition to Krishna and Arjuna, the text contains two more characters (i.e., Sanjaya and Dhritrashtra).
2. It should be noted that Dhritrashtra appears only in the first chapter. The first shloka of the first chapter to be precise. Although his counselor Sanjaya appears in four chapters (the first two, chapter 10, and the last chapter), the actual number of shlokas attributed to the kuru king Dhritrashtra is only 1. It looks almost as if the character of Dhritrashtra was forgotten. Even the sporadic appearance of Sanjaya at the beginning middle and end seems a bit surprising. Is it possible that these two characters were added to the Bhagwad Geeta at a later date?
3. Although the Bhagwad Geeta is considered a "dialogue", the percentage of shlokas attributed to each character shows that the bulk of the shlokas (82%) is coming from the lord Krishna and only 12% is from Arjuna. Even Sanjaya with his observer status has almost 6% of slokas. In fact, five chapters (i.e., 7, 9, 13, 15, and 16) are monologues with only the lord Bhagavan Krishna speaking. Even the other chapters are strongly skewed with the lord Bagvan Krishna speaking more than 90% of the time in eight chapters (i.e., 3, 4, 5, 8, 12, 14, 17, and 18) and more than 85% in another two chapters (i.e., 2 and 6). Only chapters 10 and 11 seem more balanced with the lord contributing ~64% and 40% respectively. Chapter-1 again stands out with 0% contribution from the supreme personality of godhead.
4. Half the shlokas are completed by the time we reach the 9th of the 18 chapters. Overall, the content is rather evenly distributed across the 18 chapters with the exception of chapters 2 and 18 which contribute more than 10% each. 

Several luminaries have written commentaries or Bhashya's on the interpretation of the Gita. Apparently writing a commentary on the god's song was considered a requirement for scholastic advance in the ancient world. However, it is unclear to me how many of these commentaries were written without anticipation of results.