Popular Science

Here is a set of posts that I penned down towards a better understanding of a few science subjects by the general public - also termed as "popular science" posts:

The Art and Science of Music

“Heard Melodies are sweet, but those unheard sweeter” - Keats.

The dictionary definition of music is an arrangement of sounds that is exciting or pleasant to listen to. It has to be noted that word exciting or pleasant is not well-defined :). To elucidate, like any form of art , music is also very subjective and the appreciation of a form of music differs from person to person. However, there are some combinations of sounds , that are common in all forms of music that would excite everyone irrespective of whether they have been tuned to it or not.

For instance, to a newborn, the mother’s voice is music since it soothes the child. For infants, the chirping of birds, (it could be a crow or a nightingale) may be musical. For toddlers, the rhythmic clapping of hands, feet and a synchronised group “Hurray” may be musical. Hence the logic of teaching kids several aspects of the world through rhymes and jingles. There is probably no one in this world who could be termed non-musical. It is the choice of the rhythms and the patterns that they are used to (or rather the brain is trained to appreciate) that varies in individuals.

To an advanced audience, music can be considered as the combination of pitches(frequencies) and rhythm (permutations) . In an orchestra, all instruments (including the vocal cords in singing) have to obey certain ground rules of common pitch and rhythm. The harmonics produced by the excitation of stringed instruments (like violin, guitar, veena, cello), the vibrations produced by percussion instruments like drums, tabla, mridangam and the wind instruments like flute, trumpet, trombone (as well as the vocal cord) are played in synchrony to bring about harmony. It is as if the artists communicate with each other in musical language.

Did you know that music is one of the few faculties that require both the left and the right hemispheres co-ordination of the brain? Most logical operations require the left lobe while the creative faculties require the right lobe. What is the art and science in music that makes the brain do this ? More on these are to follow in the next posts.

The Frequencies in Music

As all of us would know, a song can be decomposed into several notes, each of which is a frequency. There are seven notes that are used are building blocks for any tune - Do, Re, Me, Far, So, La, Te. ( Remember the evergreen ‘The Sound of Music’ song by Julie Andrews’). In the Oriental world, we call these the ‘sapthaswaras’ - Sa,Re, Ga, Ma, Pa, Da, Ne . Each of these swaras is but a vibration at a frequency that is higher as compared to the previous swara.

All the seven swaras constitute an octave. The shift of all the seven swaras by 7 by one octave means one is shifting the base frequencies by 7 frequency windows. The average human voice can naturally be trained to sing upto 2 octaves, while some gifted singers like Freddie Mercury could sing upto 4 octaves.

The base frequency of the lowest note (Sa) is considered as the constant denominator for all instruments in an orchestra. To be more specific, if the lower Sa (Do) is sung or played in an instrument at 55 Hz, the Re (Re) is played at 60 Hz. Ga may be played at 70Hz and so on. When a person sings, they tune their vocal cords to sing at the base frequency of one of the well established frequencies notated as A, A#, B, B#, C, C#, D, D#, E, F, F#, G, G# . This base frequency is also called as the “Shruthi” in the Carnatic and Hindustani world. The violins, guitars, and all other instruments also adjust the tensions in their strings to match the scale of the singer. Any slight deviations from the base frequency would lead to cacophony in an orchestra.

For instance, let us try to understand how an instrument like violin is played from the frequency perspective. The 4-stringed violin is considered to have originated from the Western world , though there is some evidence in the form of sculptures in Indian temples indicating that the instrument was played in ancient India as well. The bow (which was originally made using a pony’s tail hair) was used to excite a string of certain thickness producing sound that matched one of the frequencies above (A, A# etc). The tension of the string was controlled by screws to change the vibrating base frequency. To play the other notes on the violin, the fingers were placed at appropriate positions to change the harmonics of the vibrating string. Any incorrect positioning of the fingers lead to “abaswara” or “wrong notes”.

Humans vary in perceiving the tonal frequencies (as opposed to perceiving loudness). To reiterate, loudness and tone are not the same measures, in fact most cases, they are the opposite of each other. However, it is possible for the ear(and the brain) to train to differentiate the tonal differences in music, with time.

The Rhythm in Music

The notion of rhythm is closely associated with the conception of time. We call something rhythmic when it repeats regularly in time - it could repeat hourly or daily or annually or even every once in a while. For instance, our heart beats follows the sinus rhythms and beats approximately 72 times once a minute. The moon, sun, and all organisms follow rhythmic patterns regularly. Interatomic particles are also known to vibrate at specific frequencies.

In music, rhythms are normally achieved by percussion instruments - vibration of a layer of material on a wooden surface - mridangam or the tabla or the drums, excited either by the finger or the mallets. In Carnatic and Hindustani music, the rhythms are connected to what is called the taal or tala. A certain amount of time can be split into specific number of equal intervals - the no. of intervals specifying the beats in the tala. The Aadi taal has 8 beats per taal and is one of the most popular talas in Indian music. The choice of a taal for a particular song depends on the notes and the nature of the song. When a musician composes a song and is left with say 5 intervals remaining in a taal, she could either make it a 1-1-1-1-1 or 2-2-1 or a 1-2-2 or 2-1-2 or even a 3-1-1 or a 4-1 combination. What she chooses to do is upto her creativity within the scope of the song’s lyrics and the nature of the raga (We will understand more of the raga in the next part).

The percussionist understands the beats in a cycle of a taal and plays the instrument accordingly - complementing the vocalist/string instrumentalist. For instance a 3 beat interval would sound like a ta - ki - tha , ta-ki-tha, while a 4 beat interval would sound like ta-ka-di-mi in the mridangam or tabla. Variations brought about in the song in its natural course would involve a change in the rhythm.

More often than not, the vocalist moves to a faster rhythm in the middle of the song - to showcase her acumen and to bring about some josh, in which case she may switch to 16 syllables per taal (instead of 8 ) in case of aid taal for instance . Noting this variation at the critical time is important for the other musicians to pace their pace exactly then. Any deviations in the rhythm will also sound unpleasant in an orchestra. It is very important for a musician to stick to the rhythm inspite of the longer or shorter syllables of the song (that may span 1.5 or 2 or 4 beats instead of 1 in some cases) . This requires a lot of multi-tasking for the brain to distinguish the song’s rhythm from the percussionist rhythm and may take years of training. It is also important to note that it is the rhythms that complement dancing when performed in parallel with music

What are Raagas?

We had touched upon the notes or the sapthaswaras in an earlier post - Do Re Me Fa So La Te or Sa Re Ga Ma Pa Da Ni (notated as S R2 G2 M P D2 N2). The definition of a raaga in the Indian Carnatic/HIndustanai context is a unique combination of all or a subset of these notes which acts as a superset of notes for the composition. For instance, the raaga Mohana in Carnatic (equivalent to Bhupali in Hindustani) has only 5 notes - S R2 G2 P D2 in its ascent and S D2 P G2 R2 in descent. No composition of Mohana will have other notes like Ma or Ni. This raaga is considered to be a Janya (derivative) of the Sankarabharanam raaga (Bilawal in Hindustani) which has all 7 notes.

In Western music, the nearest equivalent to a raaga is a scale. The Major scale corresponds to Sankarabharanam or the Bilawal raaga. However there are no janya ragas that have only a subset of the 7 notes in Western music. A keen observer would note that there have been numbers added to the R, G, D, N in the notations in the Indian form. Indeed there are more than 7 notes in the Indian form of music - R1, R2, G1, G2, M1. M2. D1. D2, N1, N2. Only S, P are constant and do not have alter egos. All ragas might have only one version of the chala swaras (i.e.) R, G, D, N in most cases.

The concept of ragas makes the composition of music more specific. The composer has to limit the notes to only what the raaga allows in its ascent/descent (also called as aarohana, avarohana) . If one thinks about why that was done, there could be several answers - the most obvious one being that a specific raaga incites a particular emotion in the listener. For instance, the raaga Mohana or Bhupali induces feelings of happiness and cheer, why ragas like Saveri (S R1, G3, M1,P, D1 - S, N2,D1,P,M1,G2,R1) induces devotion. The fact that even a minor shift of the frequency in a single note from R1 to R2 has the ability to change the emotion of the listener from cheer to deep feelings of penance, is a tribute to the composer and the structure of the music itself.

Did you also know that certain raagas are played/sung during certain times of the day, particularly in the royal courts in olden days - Bhupali (Mohana) is played in the morning, while Brindavana Saraang is played in the afternoons. Shankarabharanam is typically played in the evening while khamaj (harikhamboji) in the nights. Also it is interesting to note that the etymology (name derivation) of each raaga has a science and story to it. Shankarabharanam translates to ‘a jewel for Shiva(sankar)’ and was originally composed by Ravana, the king of Lanka, who also happens to be a great musician and Shiva devotee.

What is Epigenetics?

We all know that our DNA defines us. It distinguishes one species (like rat) from another (humans) and is also responsible for specific variations in an individual. No two individuals (except monozygotic or identical twins) carry the same genetic code. Any changes in the genetic code cause mutations, which may be either beneficial (leading to evolution) or harmful (leading to diseases).

While all the cells of the body have the same genetic code, why do the skin cells behave differently from the brain cells or the cells in the eyes ? It is because only a certain set of genes are switched on in each type of cells. The switching on and off is controlled by a variety of biological factors collectively termed as EPIGENETICS . These are the changes that control gene expressions (switching on/off )without altering the genetic code. In other words, DNA may be the blueprint, but the actual building is constructed using the epigenetic factors.

I will not go into the biochemical details of the epigenetic factors in these posts. It suffices to know that they are also inherited like the genome and at the same time, respond to environmental , diet and physical changes in an organism. Most of the diseases including cardio vascular diseases and cancer are largely caused by epigenetic irregularities (also partly by mutations ) .

So what are the factors that influence the epigenetic changes in an organism? Circadian rhythms (sleep cycles), food, drugs , physical activity and the chemicals in the environment are a few but not all the factors. We shall explore some of these in the later posts.

Circadian Rhythms

Circadian rhythms or the biological clock can broadly refer to the set of changes that the body goes through, from the molecular level of the DNA to the organism's macro level, in a 24 hour cycle in tune with the external factors like light, food timings etc. At the spiritual level one can think of circadian rhythms as the cycles that the human beings undergo biologically , being a part of the larger creation ,synchronising with the Nature's cycles like day-night cycle or the seasons.

Have you ever wondered why you might be waking up around the same time everyday in the morning, unless your sleep or physical activity/stress levels in the previous day was perturbed ? That is because the various tissues in the body have a peripheral clock controlling the cellular mechanisms in a cycle. These peripheral clocks are controlled by a master clock in the brain which responds to a light stimulus amongst other things.

The body tunes its metabolism and repair cycles depending on one's food and sleep timings. At the cellular level , this manifests as the time for transcription or cell division. There are several epigenetic factors that work in a feedback loop in sync with the brain's clock to maintain this cycle at the cellular level. There are some Clock Controlled Genes (CCG) in the body that work in a circadian manner in about 24 hour cycle. These genes are heavily influenced by the epigenetic modifiers that are the result of the external stimulus to the brain's clock. When this is disrupted beyond repair, the body ends up with diseases like uncontrolled cell division (aka cancer) or cardio vascular diseases or hormonal imbalances (ranging from diabetes to infertility).

So what can we do to maintain or help the body's biological clock : Sleep and eat ON TIME. Intense physical activity should be preferably done during the same time every day. Sleep patterns are the most important factor in the circadian rhythm cycle. Sleeping should also be preferably done in a dark environment.

Epigenetics and Stress

Stress can be defined as any stimulus that challenges the body physically or psychologically. It can be acute or chronic and includes a wide range of events like compulsive overexercise to fear of social defeat. There are various hormones released as stress response in the body that affect the functioning of the brain, particularly influencing the faculties of memory, synapsis (learning , unlearning) as well as cognitive functions, some of which are beneficial in the short term. For instance, a prey has to run on seeing a predator without thinking much or face death. This is also called the FFF response - Fright, Fight or Flight response. However chronic (long term) stress has been associated with illnesses in the individual.

Recent studies have highlighted how long term stress can have heritable changes to one's psyche and physiology through epigenetic modifications and gene expressions in the brain. There is a network formed by hypothalamus (brain) and the pituitary gland (in the brain) and the adrenal gland(kidney) called the HPA axis. When exposed to a threatening stimulus (stress), corticosteroids and similar hormones are produced . They affect the expression of certain genes in the above network through factors such as sirtuin. At the cellular level, sirtuin helps regulate the metabolism (for cells to produce oxygen through glucose). Sirtuins can be considered as the guardians of genomic stability. Chronic stress affects their epigenetic functioning, causing the body to fail at various levels, starting from the central nervous system to reproduction.

It is important to understand that the changes caused by chronic stress are on the epigenome and therefore, inherited through generations of cells as well as passed from parents to offspring. Pre-natal stress has been associated with health issues in the newborns for similar reasons.

One cannot live without stress in this era, we can only learn to live with it by handling it better. There are several mechanisms like deep breathing (producing more oxygen to the cells in the body and influencing sirtuin and other epigenetic factors), right attitude and a relatively simpler life that can aid us to help our bodies in tackling chronic stress.

Autophagy

When the body is not fed externally for more than 12 hours approximately, a process called autophagy sets in. "Auto" means self and "phagy" means to eat, in Greek. The process by which cells eats themselves or rather kill their components and recycle them for renewal is called autophagy. This is an essential mechanism for clearing out debris and harmful proteins from the cells. This process also helps in releasing energy for the cells for further repair. One can think of autophagy as recycling at the cellular level.

Autophagy has several important roles to play in the maintenance of a healthy body. Particularly removing the waste products from the brain cells is important as the neurons exist for the whole lifetime and therefore crucial for preventing neurodegenerative diseases like Alzheimer's or Parkinson's. Autophagy is also an important factor in suppressing the development of cancer. It also helps in production of newer cells , slowing down the ageing process.

Stress , food, sleep patterns and a few other environmental factors influence the smooth functioning of autophagy in the body. The genes controlling autophagy are epigenetically regulated by these factors. Too less or too much of autophagy disrupt the bodies natural cleaning mechanisms and lead to auto immune or infectious diseases or even cancer. Infact some of the anti cancer drugs target regulation of autophagy mechanisms.

So what can we do to help autophagy thrive at the right balance in the body? Eat in the day and sleep in the night :) . Intermittent fasting (for 12-14 hours) is known to have benefits for the same reason. I would also like to add that different cultures of the world observe days of fasting as traditional practices (like today is Ekadeshi - a day of fasting in the Hindu culture). Similarly other cultures around the world have recommended periods of fasting which may be beneficial for the body, if observed correctly.

Cryptography

Cryptography literally translated from Greek means "the art of creating and solving codes - or encoding and decoding". Here, by codes, we refer to secret messages that cannot be easily read by the layman. The earliest known forms of cryptography dates back to the Egyptians who used hieroglyphics in between their messages.

Secret codes were very important in monarchies and in the political scenarios. An interesting story is about how Mary, Queen of Scots tried to used substitution ciphers(where a symbol was used to substitute a letter) to plot against her cousin, Elizabeth I . Her coded letters sent to her co-conspirators were captured by Queen Elizabeth's henchmen and Mary's guilt and life depended on if the strength of the secret code. Unfortunately it was broken and she was hung by her cousin's orders. It goes to prove that the code was not strong enough and could be broken by an expert with brute force methods.

There are also instances in history where secret messages were encoded in scalp of messengers who would wait till they grew their hair and then cross territories. Upon reaching the desired destination, they would shave their heads again to reveal the messages. This kind of cryptography is rudimentary and relies only on the faith and skill of the messenger

During World War II, the Enigma machine was employed by the Nazis to send messages to all their military units in a coded manner. As much as the Allied forces intercepted these messages , they could not be broken for several months because of the complexity of the numbers and the possibilities. It took the genius of Britain's most famous mathematicians and Alan Turing to finally break it and call it on the Nazis.

In the modern era, cryptography exists everywhere. In the HTTPS connection, S stands for SSL , which forms the basis of a secret communication. As simple as SSL sounds, the math behind it is very simple and relies on the complexity of prime numbers. There are hackers everywhere trying to steal passwords and break encryption protocols of banks. The stronger their codes are, the lesser the chances of breaking them.

So next time you type your password, remember that a lot is done at the backend to store and retrieve it correctly.There is a lot more to our passwords than what meets the eyes.

Accidents in Science

Most of the important strides in science have happened because there were some unforeseen mishaps that led to unexpected breakthroughs. One such important discovery was the invention of the first antibiotics - Penicillin by Alexendar Fleming, a Scottish researcher. Dr. Fleming was often considered to be careless as a lab technician. In the year 1928, he had his culture plate of Staphylococcus growing in his lab uncovered when we went on a 2-week vacation . Upon return he found that there were many zones that were free of Staphylococcus and those were the areas occupied by a green mold (fungus) called Penicillium notatum. He isolated the mold and on further experimentation discovered that the mold prevented the growth of the bacteria even upon extreme dilute amounts. This led to the invention of the first antibiotics and he was awarded the Nobel Prize for Medicine in 1945. Can we imagine a world without antibiotics today ?

In the 18th century, Edward Jenner was credited with the invention of the first smallpox vaccine. He had observed that milkmaids do not contract smallpox as much as the others in the community. He later realized it is because they develop cowpox, a relatively milder form of the infection from cows which seemed to protect them from the deadlier version of smallpox. He isolated the pus from a cow's udder and injected it to a 8 year old boy and later exposed him to the smallpox virus. The boy had a mild cowpox infection and recovered but surprisingly did not develop smallpox. This is credited as the first vaccination in history that we know.

The way vaccines work are by injecting a milder form of the microbe that belongs to the same family as the deadlier version into the body. The immune system of the body responds by producing antibody combinations that try to target the virus. One of the combinations of the antibodies works against the milder version and the person develops immunity against the family of viruses. When the person is exposed to a deadlier version of the virus, the immune system's memory reproduces the same antibodies before the microbes multiply in the body, thereby suppressing the infection. Today, we have a host of vaccines for different diseases. They are vastly effective but the individual effect depends on the exact antigen and the antibody (the immune system's orchestration and memory). So that is where a healthy immune system is considered to be beneficial.

Fast forward to the 21st century, the CRISPR - cas technique was invented by two women being awarded the Nobel this year. Historically, this is the first year , the Nobel was awarded to only women scientists without a male co-scientist. CRISPR is a repetitive DNA sequence found in bacteria that have been previously attacked by viruses (bacteriophages). Later it was discovered that bacteria use these CRISPR segments to discover viral DNA and use cas enxyme to cut and disable the viral DNA . This was initially discovered by a group of scientists around 1990. In 2012, the female duo of Jennifer Doudna and Emmanuelle Charpentier showed how to use this natural bacterial defence mechanism to edit genes. This became a very inexpensive genetic engineering tool that can cure many diseases caused by faults in DNA , including cancer.

Numbers in Nature

Most of you would be familiar with Fibonacci numbers - the sequence of numbers obtained by adding the previous 2 consecutive numbers - 0,1,1,2,3,5,8,13,21…… This sequence is obtained by adding the numbers as (0,1,(1+1),(1+2),(2+3),(3+5),(5+8)….Mathematically this sequence is enigmatic as the ratio between any 2 numbers (for larger numbers) in this sequence tends to become around 1.618 (also known as Golden Ratio). It is interesting to note that the petals of flowers would be one of the Fibonacci numbers . This is also true for spiralled artifacts such as the no. of spirals in a pinecone. Again, the arrangement of leaves in a plant would follow this Fibonacci sequence. Apparently nature was aware of this golden ratio, when it designed its beautiful objets d’art.

The credit for the discovery of the Fibonacci numbers is given to Fibonacci in Italy in the 13th century. He discovered the pattern using a hypothetical puzzle of breeding rabbits. However about 100 years earlier, the Indian mathematician Hemachandra had discovered this sequence by computing the ways in which Sanskrit poetry could be composed. Infact, the golden ratio is the basis of the construction of the pyramids in Egypt which insinuates that ancient Egyptians were also aware of this sequence and ratio.

Coming back to nature, it is considered that the human body is designed as per the Fibonacci spiral. The position of the eyes, the ratio of the length of the of the eyeline to the nose, the ears or even the length of the palms to the torso are all mathematically related by the golden ratio. This was well observed by Leonardo da Vinci when he drew his famous portrait of the “Vitruvian Man” - a human inscribed within a circle.

Another ratio that is all too familiar is pi (3.14…). This is the irrational number that is the ratio of the circumference of a circle to its diameter. (Think of a pi when you eat a pizza next time) . It has been discovered that pi plays a major role in the patterns found in nature - like the stripes of a zebra or the spots of a leopard. Pi is also known to play a major role in the cell division timings and sleep-wake cycle of all organisms in nature.

Math and Science exists all around us, we just have to open our eyes to it.