One of the most influential entities in today's world is the social media influencer. The all-pervading nature of social media has greatly impacted not just the youth but people across different sociodemographic groups. Therefore, it is impossible to ignore the influence of social media. To attain salvation, one can spread the lord's message through social media to make the best possible use of this influence.
You must have one or more of the following attributes to be an influencer.
Wealth (Example: Ratan Tata used his wealth to positively influence various spheres of society.)
Strength (Example: Manoj Kumar Chopra)
Fame (Example: LeBron James has fewer followers than Virat Kohli)
Knowledge (Example: The mathematician Srinivasan Ramanujan)
Beauty (Example: Angelina Jolie)
Renunciation (Example: Yogi Adityanath)
Although these influencers wield large influence, this influence is not permanent. With time, wealth, strength, fame, knowledge, beauty and renunciates will be forgotten. We may remember only a small fraction of the influencers of the yesteryears. As more time passes, very few will be remembered. The supreme lord Krishan is the supreme influencer with all six attributes. Hence, his influence is very powerful and lasts for long periods. In the Bhagavad Gita, the supreme lord describes in Chapter 4 that he had imparted the supreme secret to the Sun God and his lineage. However, this knowledge was lost over time. The relevant verses are provided below:
BG 4.1: The Supreme Lord Shree Krishna said: I taught this eternal science of Yog to the Sun God, Vivasvan, who passed it on to Manu; and Manu, in turn, instructed it to Ikshvaku.
BG 4.2: O subduer of enemies, the saintly kings thus received this science of Yog in a continuous tradition. But with the long passage of time, it was lost to the world.
BG 4.3: The same ancient knowledge of Yog, which is the supreme secret, I am today revealing unto you, because you are My friend as well as My devotee, who can understand this transcendental wisdom.
Even the supreme influencer needs to provide knowledge in a form understandable to the people of the current age. Social media influencers can greatly impact society by passing on the spiritual knowledge of the Supreme lord Krishna.
Chapter 11: With 55 verses or shlokas, the eleventh chapter is one of three chapters with more than 50 verses. The other chapters are chapter-2 and 18. and it describes the opulence of Lord Bhagavan Sri Krishna.
Krishna, the Supreme Personality of Godhead (Shloka 5-8,32-34, 47-49, 52-55): 20 Shlokas
Arjuna (Shloka 1-4,15-31, 36-46, 51): 32 Shlokas
Sanjaya (Shloka 9,35, 50): 3 Shlokas
Brief Summary: In this chapter, Arjuna requests Lord Krishna to show his cosmic form/universal form. Lord Krishna blessed Arjuna with divine eyes so that he could see the universal form. Lord Krishna demonstrated (showed) the universal form as follows:
The universal form (Biology):
Unlimited mouths
Unlimited eyes
Unlimited wonderful vision
Celestial ornaments
Many divine weapons
Celestial garlands and garments
Divine scent
Body with many arms, bellies, mouths and eyes, limitless
Terrible teeth
Glowing eyes
The universal form (Physics): Radiance of thousand suns, Sun & moon are eyes, blazing fire from the mouth
The universal form (Spiritual): Lord Shiva, Bramha and different sages
Demigods and sages feared the terrific manifestation of the Universal form and surrendered. Everybody looked on in wonder. Even Arjuna was bewildered and amazed, lost his steadiness of the mind. Arjuna could see the heads of sons of Dhrtarastra and their allies smashed between the teeth of the lord. Lord Krishna said except for Pandavas, everyone in the war field will be destroyed; it is already destined, and Arjuna is just an instrument. He guided Arjuna to follow the divine plan. Arjuna once again offered obeisance with folded hands. Arjuna describes the benevolent and fearful aspects of the Lord as the cause of all causes and limitless.
Arjuna apologised for the offences he committed, considering the Lord to be his friend. Just as a father forgives his son, friend, another friend, husband, and wife, Krishna also tolerates our mistakes. Therefore, Arjuna requests the lord to bestow grace on him. Subsequently, Arjuna requested the lord to be gracious and return to the four-armed form.
Four-armed form:
Helmet head
Club, Wheel, Conch and Lotus flower in hand
Krishna had not shown his universal form to anyone else as it required divine eyes. No one can see Lord Krishna's universal form in the material world even after studying the Vedas, performing sacrifices and charity, and performing pious activities and penances. As per Arjuna's request, the lord displayed his four-armed form and, subsequently, the two-armed form. Arjuna's mind composure could be restored by seeing the lord in a human-like form. Even demigods cherish the opportunity to see the universal form. Only through undivided devotional service can one understand Lord Krishna.
In the final verse, Lord Krishna assures liberation for the following:
One who engages in pure devotional service
One who is detached from the results of fruitive activities
The number of genomes that are becoming available is increasing at a very fast pace (exponentially?). One of the early analyses that bioinformaticians focussed on was the discovery of genome-wide patterns such as gene density and its correlates and genetic diversity and its determinants. Identifying such patterns and verifying the reliability of the observed pattern is one of the first steps. Once such patterns are known, trying to decipher the processes underlying these patterns would be an important next step.
Moving from Patterns to Processes would also involve the development of a strong theory that can make testable predictions. Once such a theory is available, it is possible to simulate scenarios and evaluate the theory. A well-grounded theory would be required to progress the scientific understanding of a field.
The study by Teekas et al. examined a specific type of genetic region known as low complexity regions (LCRs) in the DNA of tetrapods, a group that includes amphibians, reptiles, birds, and mammals. LCRs are sequences in DNA
that are made up of repetitive or simple sequences of nucleotides (the building
blocks of DNA). These regions are interesting because they can change rapidly
and might help organisms adapt to their environments.
The Role of LCRs in Evolution and
Adaptation
LCRs can be a source of new traits and functions in organisms. The length
and composition of LCRs are influenced by two main factors: mutation and
natural selection. Mutation can change the DNA sequence randomly, sometimes
leading to longer or shorter LCRs. For instance, mutations such as replication
slippage (where the DNA copying process makes mistakes) can cause variations in
LCR length. High levels of guanine (G) and cytosine (C) nucleotides, known as
high %GC content, also contribute to these changes.
On the other hand, natural selection can favour certain variations that
are beneficial for survival and reproduction. The interplay between these
mutations and selection pressures determines the specific characteristics of
LCRs in different organisms.
Key Findings
Location and
Function of Positively Selected Sites (PSS):
Positively
selected sites (PSS) are parts of genes that have undergone selection
because they provide some advantage.
PSS and LCRs
are often found at the ends of genes in tetrapods.
PSS at the
center of genes tend to be involved in defense mechanisms, such as the
immune response, while PSS at the ends of genes are associated with more
general functions.
Characteristics
of LCR-Containing Genes:
Genes with
LCRs in tetrapods tend to have a higher %GC content.
These genes
show a lower ratio of non-synonymous to synonymous substitutions (ω or
dN/dS), indicating strong purifying selection. Purifying selection
removes harmful mutations, ensuring the gene remains functional.
Despite the
rapid functional diversity that LCRs can provide, they are subject to
intense purifying selection to maintain beneficial traits.
Purity and
Position of LCRs:
LCRs are
commonly found in genes but are less pure, meaning they have more
variation.
As the purity
of LCRs increases (i.e., they become more uniform), they tend to be
located in specific parts of the gene, suggesting their evolutionary role
depends on their composition.
Supporting the Robustness of the
Patterns
The robustness of these patterns was supported through several methods:
Consistency
Across Data Sets:
The
researchers observed these patterns across multiple tetrapod species,
ensuring that the findings were not limited to a single group or dataset.
Statistical
Analysis:
They used
statistical methods to test whether the patterns were significant and not
due to random chance. This included analyzing the %GC content and ω
ratios to confirm their observations.
Replication and
Validation:
The findings
were validated by comparing different gene regions and across different
species to ensure that the patterns were consistent and reproducible.
Understanding Underlying Processes
By identifying these patterns, the researchers gained insights into the
underlying biological processes:
Mutation and
Selection Dynamics:
The study
highlighted how mutations create variability in LCRs and how natural
selection shapes these variations to enhance adaptability and function.
Functional
Roles of Gene Regions:
The
position-specific roles of PSS within genes revealed how different parts
of a gene can evolve to serve distinct functions, such as defence
mechanisms or general cellular processes.
Evolutionary
Strategies:
The variation
in %GC content and ω ratios between LCR-containing and non-LCR-containing
genes illustrated different evolutionary strategies. LCRs contribute to
rapid adaptation while being tightly controlled by purifying selection to
prevent harmful mutations.
Building a Theoretical Framework
With the increasing availability of genomes, bioinformaticians can now
analyze large datasets to discover genome-wide patterns, such as gene density
and genetic diversity. Identifying and verifying the reliability of these
patterns is a crucial first step. Once reliable patterns are known, the next
step is understanding the underlying processes.
In this study, the researchers' findings contribute to building a
theoretical framework for understanding genetic diversity and adaptation:
Model
Development:
The identified
patterns can be used to develop models that explain how LCRs evolve and
contribute to functional diversity in genes. These models can help
predict how genes adapt to environmental pressures.
Integration of
Mechanisms:
By integrating
the roles of mutation and selection, the framework can explain how
genetic diversity is generated and maintained in different species.
Predictive and
Explanatory Power:
A robust
theoretical framework can predict new evolutionary trends and explain
observed patterns in genetic data. For instance, it can help predict
which genes might evolve rapidly in response to new environmental
challenges.
Guiding Future
Research:
The framework
can guide future research by highlighting key areas for investigation,
such as the specific mechanisms by which LCRs influence gene function and
adaptation.
Moving from patterns to processes involves developing a strong theory
to make testable predictions. Once such a theory is available, scientists
can simulate scenarios and evaluate the theory's validity. A well-grounded
theory is essential for advancing the scientific understanding of a field, as
it provides a structured way to interpret data and predict future observations.
Conclusion
This
study sheds light on the complex dynamics of low-complexity regions in the DNA
of tetrapods. By revealing how these regions are influenced by mutation and
selection and how they contribute to functional diversity and adaptation, the
researchers have laid the groundwork for a theoretical framework to
enhance our understanding of genetic evolution. The robustness of the findings,
supported by rigorous statistical analysis and validation across multiple
species, ensures that the patterns identified are reliable and meaningful. This
framework will be invaluable for future studies exploring genetic diversity and
the evolutionary processes that shape life on Earth.
* This blogpost is generated using chatGPT
We talked about how Open Science is changing the way science is done and the important role of the Royal Society in facilitating this. The terms Open and Science have come together to form a new coalition championed by those disillusioned by the academic research culture. For instance, Rachael Ainsworth discusses how the "Research Culture is Broken, and Open Science can Fix It".
Rachael Ainsworth is not the Royal Society. So it's not just established, well-known societies; even an individual with passion and dedication can advocate for open science. However, the world is the way it is, and it takes power, prestige, prominence in science and the credibility of a society to be heard. Michael Nielsen is somewhere in between the Royal Society and Rachael Ainsworth and describes himself as somebody who "helped pioneer...the modern open science movement". He uses interesting anecdotes involving important people to highlight the challenges of doing Open Science.
We are also moving from a text-dominated communication medium to a video-dominated medium. Given the buzz currently surrounding Open Science, it seems reasonable that the study by Teekas and group be published in Open Biology: A fast, open-access Royal Society journal publishing high-impact biology at the molecular and cellular level. Of course, the manuscript spent over a year on bioRxiv and had seen multiple journals before making its way to the pre-print server in July 2023. Here is a brief timeline:
Chapter 10: With 42 verses or shlokas, the tenth chapter is one of the lengthier chapters, and it describes the opulence of Lord Bhagavan Sri Krishna.
Krishna, the Supreme Personality of Godhead (Shloka 1-11,19-42): 35 Shlokas
Arjuna (Shloka 12,18): 7 Shlokas
Brief Summary: Initially, the lord explains his opulence to Arjuna by stating that he is the source of demigods and is unborn. All the qualities, good and bad are created by him (Intelligence, freedom from doubt, happiness and distress, fame and infamy, fear and fearlessness, etc.). Four great sages were followed by seven great sages, and the manus came from Krishna's mind. He is the source of the spiritual and material world.
The inquisitive Arjun further requests the lord to explain his mystical powers. In response, lord Krishna says his opulence is limitless, yet he will highlight the prominent aspects.
Supersoul- seated in the heart of all entities.
Aditya's: Vishnu
Lights: Sun
Stars: Moon
Maruts: Marichi
Vedas: Sama Veda
Demigods: Indra
Senses: Mind
Living beings: Consciousness
Rudras: Shiva
Yaksha: Rakshas
Lord of wealth
Vasu: Fire
Mountains: Meru
Chief: Brahaspati
Generals: Karthikeya
Bodies of water: Ocean
Sages: Brigu
Vibrations: Trancendental Om
Sacrifice: Chanting of holy names (Japa)
Immovable things: Himalaya
Trees: Banyan
Sages among the demigods: Narad
Gandarva: Chitarta
Perfect beings: Kapila
Horse: Uccahsrava
Lordly elephants: Iravat
Men: Monarch
Weapons: Thunderbolt
Cows: Surabhi
Procreation: Kandarpa, the god of love
Serpents: Vasuki
Nagas: Ananta
Aquatics: Varuna
Dispensers of justice: Yama
Demons: Prahalada
Beast: Lion
Birds: Garuda
Purifier: wind
Wielders of weapons: Rama
Fish: Shark
River: Ganga
Conclusive truth
Letters: A
Inexhaustible: Time
Creators: Bramha
Women: Fame, fortune, fine speech, memory, intelligence, steadfastness, patience
Hymns: Brahatsama
Months: Margashira
Seasons: Spring
Splendour, Victory, Adventure
Strong: Strength
Splendid: splendour
Pandavas: Arjuna
Sages: Vyasa
Great Thinkers: Usana
Descendants of Vrisni: Vasudeva
Culprits: Punishment
Victorious: Morality
Wise: Wisdom
Generating seed
No end of the lord's divine manifestations. Only a few are described here.
More than a hundred or Hundreds of journals have disappeared from the internet. Journals provide a record of scholarly work and are supposed to last for posterity. The by-line says that researchers have identified dozens of open-access or OA journals that went offline in the two decades spanning 2000-2020, and hundreds more could be at risk. Notably, the articles published by these OA journals have also vanished without any trace. These are not just articles published by "predatory journals" but even those published by journals associated with a "scholarly society or a research institution". Journals have sophisticated systems to back up and archive the scholarly record. The LOCKSS (Lots of Copies Keep Stuff Safe) Program launched by Stanford Libraries in 1999 is a pioneer in such efforts that have emerged over the years.
Each of these options exists on the internet. For instance,
A record of which journals have archived their content on which repositories is available at the Keepers Registry. Recently, we published an article about "Hundreds of independent midsize deletions mediate DNA loss in wild relatives of Red Jungle Fowl" in the journal Animal Gene (previously known as Agri gene). Soon after the article appeared online, the journal announced, "This journal will be closed after December 31, 2023. Authors are invited to submit their manuscripts to Gene Reports or Gene." While not associated with any society, the journal published by Elsevier can be considered an honest-to-god, non-predatory journal. Nonetheless, it will stop publishing articles at the end of this year. Our article may be the last or one of the last five articles to be published by this journal. One could even argue we killed this journal as our paper marked the end of this journal.
With the ISSN of 2352-4065 and the title "Animal Gene." the journal is preserved on both the CLOCKSS Archive and Portico. Moreover, the pre-print of the manuscript was posted on bioRxiv before it was submitted to the journal. Given the availability of such multiple backups, it would appear our precious manuscript will survive the end of the world.
It is almost the end of November; it is the month in which JA was born. JA was the granddaughter of John Child Hannyngton and Kunhi Kurumbi Kuruvai. So, it is possible to say that JA was 1/4th British. In recent years, we have seen more articles written about JA and her work from Indian and British authors. After her return to India following the invitation by the then PM, JA worked at various places in India. During this period, the paper titled "Further studies in Saccharum-zea hybrid I. Mitotic studies" was published by JA in Heredity volume 28, pages 141–142 (1972). It has been five decades since this article was published. In this entire time, the article is cited ~5 times. A genomic view of this work would be interesting and will probably happen at some point.
Being second at anything generally means you have lost the race. However, if you are the second-highest mountain on Earth, it is still a pretty astounding place to be. Mount K2, also popular as Savage Mountain, excels at killing people and is probably one of the most deadly mountains to climb. At a height of over 8600 meters, K2 has very little flora and fauna. Peafowl are most definitely not part of K2 native fauna. So why does the blog post have a title claiming the sacred peafowl has made its way to Mount K2?
If you have seen the first episode of Season 4 of the TV series Madam Secretary (which follows the fictional life of a woman US secretary of state), you will know it is called the "News Cycle". The TV show features a fictional US secretary of state but is based on various current affairs spanning the TV series's time frame (2014-2019). In this episode, the secretary meets the Assistant Vice-Minister of Foreign Affairs for Timor-Leste (located in Southeast Asia) to make a political point. Unfortunately, the minister suddenly and inexplicably dies during the meeting. Before the secretary and her team figure out what is happening, a blogger (much more popular than the current one) suggests the secretary killed the Assistant Vice-Minister. The blog/website is a fringe website called "Champion of Facts". Soon, the story starts trending on social media (erstwhile Twitter). The secretary appears on a pre-scheduled news show to discuss serious policy issues, only to be sidetracked by the anchor to address these rumours bolstered by the secretary's political opponents. The secretary responds with "...this is obvious crackpot theorizing, which quite possibly is the work of a disinformation campaign by a foreign power. What Senator Morejon is doing by legitimizing this baseless story, it's not just immoral and unethical. It undermines the stability of democratic government."
She continues:
"Reliable information is the bedrock of any institution, be it science, government or private enterprise. If citizens can't tell the difference between fact and fiction, then the entire project of civilisation turns to dust."
Soon, a crowd gathers outside the TV studio, chanting, "Murderer!! Murderer!!". "Lock her up!" Deja Vu?
The words of Supreme Court Justice Louis Brandeis from over a century ago: “Sunlight is said to be the best of disinfectants.” are echoed by Nadine, the secretary's chief of staff. Following this, the secretary and her team race to reveal the truth behind the murder of the Assistant Vice-Minister of Foreign Affairs. The episode ends with the USA and China cooperating with each other to bring down the actual murderers. However, the citizens still have a tough time believing the secretary is not a murderer.
Now, coming back to peafowl, the most consequential population genomic research regarding green peafowl was published two years ago by the journal Proceedings of the Royal Society B. In this article titled "Population genomic, climatic and anthropogenic evidence suggest the role of human forces in endangerment of green peafowl (Pavo muticus)" the authors demonstrate the effect human forces have had in the endangerment of the green peafowl. As with other journals of the Royal Society, the reviewer's comments are made public upon publication of the article.
The first reviewer makes several comments with the following really crucial points:
Line 120: There is good north-south sampling, but the western populations were not sampled, so
parts of the range were not included.
Line 238: The term iconic is used in several places, and while the Indian peafowl might be
considered iconic (well-recognized worldwide), the green peafowl is much less known in many
parts of the world, so it may not really be iconic.
However, neither of the reviewers had any concerns regarding the analysis of population structure, mostly about limited sampling across the range. The second main result is "(b) Lack of population structure". Using 790 898 putatively unlinked and neutral loci from the total 22 unrelated modern samples of the green peafowl, the authors found no signals of stratification among the sampled individuals, with the lowest CV error at K = 1. This analysis is done to justify pooling the samples into one single run of the demography inference software SMC++. The statement is, "Therefore, we pooled these samples in the subsequent demographic inference."
The discussion section has a sub-section titled "(c) Conservation implications". One of the take-home messages is, "Fortunately, this study predicted that extensive climatically suitable habitats remain in both continental Southeast Asia and Java Island for this endangered bird."
The study suggests the possibility of population recovery through active conservation intervention by:
restrictions on hunting
habitat conservation
re-introductions
Although the article's main message is to suggest the role of human forces in the decline of the peafowl populations, it has various unsaid/underappreciated implications. First, the identification of a K of 1 for the widespread sampling, including "11 from southwest China, seven from Thailand, one from Cambodia and the remaining 12 seized by Chinese customs with a probable origin of Vietnam. We also resequenced six museum specimens stored in Kunming Natural History Museum of Zoology and collected from southwest China during 1956–1976, a period with relatively abundant green peafowls." This suggests a lack of sub-structure within the species.
Interestingly, another study re-sequenced 14+1 (used for de novo assembly) additional green peafowl and generated a "Chromosome-Level Genome Assembly of the Green Peafowl (Pavo muticus) ". This adds up to a dataset of 38+15=53 green peafowl genomes. All 15 re-sequenced samples from this second study are from individuals in captivity. These high-quality published datasets provide a fairly reasonable dataset for further analysis and inference. The pre-print by Patil et al., 2023 does just that. By investigating the genetic structure among the samples using PCA, structure analysis, phylogenetic tree building, coalescent split time estimation and demographic history reconstruction, it is claimed that at least three distinct populations can be identified among the green peafowl sampled by these two studies. This would somewhat contradict the earlier paper's result "(b) Lack of population structure". However, the whole sample set analysed by Patil et al., 2023 is much larger than those available in the initial study. It would appear that increasing sample size helped identify the population structure within the green peafowl. Identifying this population structure is not the only major result of the manuscript of Patil et al., 2023. Another notable result is the identification of a putative inter-species hybrid peafowl individual with genetic ancestry of both the blue and green peafowl species. The paper claims the presence of such hybrids may have implications for maintaining captive populations.
Genomics is no rocket science but has many of the same jingoistic stereotypes. The sequencing and assembly of the giant panda genome by scientists from BGI has political symbolism, as this species has appeared on the Gold Panda coins issued by the People's Republic of China. The video below about Zambia's space program, led by Edward Makuka Nkoloso, also paints a picture of the surprising links between nationalism and scientific progress. If nothing else, the term Afronaut and its widespread use in literary work would not have happened without Nkoloso. It would not be an exaggeration to say that Makuka Nkoloso inspires many.
Given the strong emotions surrounding the space program, the moon landing by Americans in July 1969 was claimed to have been faked. A crazy conspiracy theory to support this claim began circulating soon after the moon mission. Using "evidence" such as the flag is flapping, the shadows not parallel to each other, the Van Allen belt would have killed the astronauts, etc., the conspiracy theorists try to ground their claims in some sort of logic. Another less well-known conspiracy theory associated with the moon landing is the claim of ancient ruins of a once glorious civilisation that thrived on the moon. Many other conspiracy theories have been spawned over the decades since the initial moon landing. A 60-minute Australia episode explores these two conspiracy theories and has real scientists debunk each of the "logical arguments" made by the conspiracy nuts. This documentary also features an interview with a NASA scientist who says that these claims have largely been ignored as responding to them would give more credence to conspiracies.
Mittal et al., 2019 claimed that the results in Figure 3C of a paper published in 2017 in the highly reputed journal Science Advances were not supported by data (see Supplementary Figure S3 in the Mittal paper). However, the repute of the SA paper has garnered over 100 citations post-2019 and continues to grow. In contrast, the SR paper claiming the results are not supported has less than 20 citations, most of which are potential self-citations. Now, are these claims as crazy as the moon landing conspiracy theories? Opinions of people tend to have a greater influence on how human society acts rather than facts. After all, Derek Lowe, the popular blogger and chemist, goes on to call Scientific Reports (in not so many words) a fake research publishing predatory machine in his blog "In the pipeline".
Interestingly, Derek Lowe's blog is published on the same website, www.science.org, as the journal Science Advances. Based on this, it is logical for any sane person to form an opinion that the article published by a predatory machine cannot be trusted when it is criticising the actual incarnation of integrity. Hence, it is unsurprising that "Predatory-journal papers have little scientific impact". By extension, authors who publish in predatory journals are gullible entities whose results can never be trusted. Why do we believe things that aren't true? Philip Fernbach has a TEDx talk that answers this question. He argues, "Understanding is contagious". This contagious understanding, paired with ignorance, can lead to us believing in things that aren't true.
After constructive and quality-improving reviews of the Patil et al., 2023pre-print, the manuscript is finally published in a real, honest-to-God, non-predatory journal (Conservation Genetics). The title still remains "Conservation implications of diverse demographic histories: the case study of green peafowl (Pavo muticus, Linnaeus 1766)". Interestingly, this is the first paper on any peafowl to be published by this journal. Will this suffer the same fate of ignorance, or will it stimulate more work on the diversity within green peafowl is something that only time will tell.
