Course Review: Basic Neurobiology/Neuroscience at NCBS Bangalore

Basic Neurobiology course offered at NCBS Bangalore consists of 4 modules of around 6 lectures each, plus a couple of labs on electrical models of cells. Each lecture is around 90 minutes. Usually there are three lectures a week but sometimes two lectures and a tutorial or lab-session is also organized. The TA support is rather limited in this course and quality depends mainly on the motivation of TA.

Module 1 is taken by Upinder Bhalla. It is mainly about cellular biophysics, and computation. Major topics covered were: neurons as electrical entities, passive properties and cable theory, active properties and Hodgkin-Huxley equations. And tutorial sessions have Hodgin-Huxley experiments conducted in-silico using MOOSE simulator; and a electrical-circuit based demonstration of cable-theory/passive properties. This module consists of many assignment and quizzes :-).

Module 2 is taken by Shona Chatterjee. It mainly about synaptic transmission in invertebrate and vertebrate nervous systems; snaptic plasticity in the mammalian brain; and basic concepts in neuroanatomy. The lab session has demonstration of Golgi-staining or mouse-brain. There is usually one quiz and no assignments. Quiz may have any sort of tangentially related questions: such as root-word of “Syanpse” in Latin, and name of X who discovered Y.

Module 3 belongs to Vatsala Thirumalai. She taught small circuits. CPG were central to her lectures. The effects of neuromodulators on rhythmic activities of these small circuits were discussed. This module have assignments.
Sanjay Sane took module 4. It was about comparative neurobiology and ethology. He discussed nervous system — their forms and functions — across animal kingdom.  Sensing and neuronal circuitry involved in sensing was one of the core themes. This module have some assigned reading and paper presentation: no pop-quizzes or assignments though he believes in taking written exams.


Arithmetic and marriage

Few days ago, I read a newspaper story; on suspecting that bridegrooms is illiterate, the bride put him under a arithmetic test: “how much is 15 + 6?”. And when the answer was 17, she called off the marriage! And few childhood memories cropped up.

When I was a kid, my father asked me once: “how much is left when you subtract 2.75 out of 4.25?”. He was pleased when I answered it correctly, “You’ll get married”, he said, “if you pass high-school, you can get a scooter in dowry as well”.

Well, it is well known that in traditional Indian system of marriage, popularly known as arranged marriage, would-be- bride and groom need not meet each other before marriage. Though this has been changing (at least in my village and neighborhood). My father and mother did not meet each other, but my brothers and their wives surely did. When marriages are arranged, the family of bride usually hunts for groom. They use their social network to figure out the opening (if some family is planning to get their son married). They would visit the potential groom’s house and meet his father, and also would-be groom if he is available.

If both party agree that marriage is possible (between the family, never mind the young would be couple) then what is discussed next is all important “dowry”. Various things are said about dowry. Dowry — in most cases — is an instrument to buy status. The bride family has to pay much larger sum if the status of groom is higher than the bride. If the girl is earning and have a stable job, the dowry may not be needed or demand is relaxed. If the bride family is not able or willing to pay sufficient dowry then they prefer to marry their daughters into a family of same or lower status. The rule of thumb about dowry is: “it is a payment for status”. And who has known an Indian who is not status conscious?

When I was a kid, government jobs were most prestigious; and less you work in your job, better it was, and if you can manage some outside income (taking bribes) along with your salary then you are the man. If you had such a job, you can demand very high amount of dowry (plus a car). Next was land-ownership which has lost much of sheen these days; and followed by small businesses and other petty clerk jobs.

The land-owning farmers need not any formal education, even though there was respect for it. There was no pressure on a farmer’s kid to do well in school. Only thing he needs to know is simple math: how much he spends and how much he earns. This much would enable him to deal in local market. Surely, he is not sending his wife to buy vegetables in markets?

During these family meeting for fixing marriages, lying was (and still is) the norm. The groom family will lie as much it can about land and education of would-be-groom. An illiterate would be classified as high-school and 1 hectare of land will be presented as 5. If they demanded to see the land-holding papers or the mark-sheets, the fake one would be arranged. The bride family is also from the same culture, they know what is going on. They will inquiry about the land on their own and some disgruntled enemy in the village will tell the truth about land-holding; and for education there was math test.

The mathematics test was the most feared one. The would-be-groom was trained by best school students in the night before the bridge family interviewed him. I remember training one. He was promised a scooter if he passed the interview. He cared little about money in dowry, that would go to his dad anyway. But loosing scooter, no sir no! There was little chance of getting a scooter after failure in interview from anyone else. That guy showed remarkable interest in mathematics that night but failed nonetheless. He managed to get scooter anyway, by convincing bride-family that scooter is for her own good. How she will travel to her remote village? In tempo and horse-cart?

The questions asked were mostly about fractions: how much is left if you have Rs. 3.50 and pay Rs. 2.75?  Mind you, this question is trickier than its sounds. People use traditional fractional names for 3.50 and 2.75; they are not easy to remember. But those were old days when people spent money in fractions. These days, government has stopped minting coins less the 0.50, and you can’t get anything in 0.50 anyway. Being a practical woman, this bride asked him much simpler integer arithmetics; yet our elementary education system did not disappointed her. The finance minister should definitely rethink his budget cuts in primary education. If he thinks primary education is not necessary, he should consider raising the budget allocation anyway. Sure none of his or his colleagues children’s children ever going to go to government school. If not for the sake of overall future of country; at least for the sake of dowry — the birth right of every Indian bridegroom who has some status in this society.

Nothing is more simpler than integer arithmetics; and when our would-be bridegrooms start failing even these tests, we must be ashamed of our primary education system in which our track record in nothing less than a scandal.

Thinking about Languages

“Don’t you see that the whole aim of Newspeak is to narrow the range of thought? In the end we shall make thoughtcrime literally impossible, because there will be no words in which to express it. Every concept that can ever be needed will be expressed by exactly one word, with its meaning rigidly defined and all its subsidiary meanings rubbed out and forgotten.” – 1984, George Orwell

It is hard to imagine how one can learn without some form of thinking available at one’s disposal. If learning is the gift of life, then some form of thinking must be fundamental to all living beings. Thinking is processing, it will not be too much of exaggeration to suggest that thinking is a form of computation. But given the flexibility of this definition, even a small electrical circuit can be classified as thoughtful. For the purpose of this essay, let just say that all thoughts are computations but not all computations are thoughts.

For animals with linguistic capabilities, I’d suggest that main purpose of language is to compress lot of information. Some essential components of compressed information is retained as meaning which is associated with a symbol. Language can be defined as a collection of sequences formed by these symbols and can be used in two ways:
• Decompress the symbols and extract information for self to understand one’s environment.
• Send the symbols across for others to interpret (communication).

We restrict ourselves with the former because in case of the later, the individual might use language for various other tasks – obscuring the information for the purpose of confusing and tricking others for one’s advantage, not always unknowingly. This would not be an easy situation to analyze. When one is dealing with language to understand one’s own environment, perhaps the task of analysis for a person is much easier.

Much depends on the way society singles out certain activities and assign values to them. Needless to say, thinking associated with activities which are assigned high values by the society are going to be valued highly. Here lies the trap. Any language which provides any advantage for a highly values skill over some other language is going to be valued more. Perhaps it not hard to confuse the suitability of a language for a particular task with ability to think about that particular task.

How to neutralize the social content or value system of observer? Designing an experiment to overcome this seems to be a challenging task. Not merely because the designer of experiment himself has a value system to bias him but also because one can only express the experiment in a language itself. If something can not be overcome, it can be bypassed. To avoid this difficulty, we can definitely compare and contrast a complex and sophisticated language with the most primitive one.

Honeybees do pretty well (even perhaps better in some activities) as far as very basic life related functions are concerned. They can communicate the location of food accurately and reproduction effectively without having to evolve a language as complex as ours. On the other hand, if they were to cheat each other of food and sex, they would need a more complex language which allows more compression of information, ambiguous association of meaning with symbols, in which producing confusion and trickery is easier. Some higher primates have the faculty of building basic block of language – suffixing and prefixing sounds to create compound sound. And they are known to use it for various purposes: to get a head-start in competition as well as for cooperation. Yet they have not constructed a complex language, perhaps they are yet to realize that other do have thoughts and the best way to influence thoughts is to use language. It is hard to see how languages makes us better or worse at thinking as such. And even if they do, it would be nearly impossible to quantify such difference.

On the other hand, the idea that languages influence the way we think may be right if only we are willing to set the context. We need to ask us what kind of activity it impinges upon. Does Sankrit allows one to think in more modular way – composition of bigger sentences from smaller sentences is easier? Or German allows us to think more structurally? Music is also a form of language. We can compare Indian classical music with Western classical music. The former is hardly ever written down, instructions are transmitted orally from teacher to pupil. The Western music is almost always written therefore also extremely structured. In Western classical music, it is extremely easy to put a band of musician together and play a piece of music as complex as opera. With Indian classical music, one can hardly imagine putting up a something as complex as opera. There is simply no way to synchronize artists. Having nice structure allows one to create, play and disseminate music easily. On the flip side, you will never hear an entirely different version of Mozart as often as you might hear a raga sung differently. One can enumerate advantages and disadvantages of both musical systems. But it does not address the question if Indian or Western musical languages have certain advantages when it comes to create music as such. If a society put a high premium on team work then Western musical language is the winner, if a society value individual virtuosity more, then the advantage lies with Indian classical tradition.

In nutshell, language is a social category, it is not a neurological category. It might some some neuronal basis which we are yet to discover. It influences and get influenced by culture and traditions. And plays an important role in its own social context. It probably also modifies neuronal pathways, as any repeated activity would do. Some languages are perhaps better suited for expressing and accomplishing some tasks while others are good at others. To say more than that, one would need much more precise definitions of both thought and language.

To end, a good analogy would be of computer languages. Most of them are known to be Turing complete i.e. any program written in one can be written in any other. Using any of them does not limit our capabilities of programming as such. Yet there are problems which are are easy to program in one language are hard in other. Hardware are easy to control in imperative languages, while modularity is easy to achieve in functional framework. And choice depends on what you value more rather than the power they posses.

Course review: Randomness in Biology

Randomness in Biology” is a graduate level course offered at NCBS Bangalore by Dr. Mukund Thattai.

This course follows — in spirit — Handbook of Stochastic Methods: For Physics, Chemistry, and the Natural Sciences by Gardiner and Stochastic Processes in Physics and Chemistry by Van Kampen. It offers a bag full of stochastic tools to biologists for modeling and describing experiments and hypothesis. The course is not intended to be mathematically rigorous but remains very faithful to the spirit of rigor. The instructor strikes the balance between rigor and intuition really well.

The crux of course focused on different types of Random Walk: discrete-time discrete-step, discrete-time continuous-step, and continuous-time and continuous steps; and on Master equations which can describe almost all of the chemistry. Stochastic differential equations along with Fokker-Plank equations were introduced. We did simulations using Langevin equations and Gillespie algorithms.

The assignments were pleasant to solve and they required good knowledge of some language: matlab, mathematica, python etc.

The instructor is full of energy and knows his subject very well. His capacity to switch gears and find connections is breathtaking. He quickly grasps questions asked, and explain the fundamentals very well. Moreover — what is more important — he is not at all lazy when it comes to work out derivations and equations. It is just pleasing to see him in action.

The classroom Safeda, named after a mango variety, deserves as much praise as the instructor for its spacious white-board. To sum up, it is a great course for anyone with graduate level of mathematics. For an engineer who had little exposure to stochastic processes, it was a joyful and enlightening experience, which the instructor did not ruin by setting up unreasonably stupid and routine examinations.

वो आँखे

टखनों पर रखे अपने सर को
रोकते अपने कापते हाथो को,
उस अँधेरे कमरे में
वो आँखे
देख रही है, प्रकाश की वो शिखा
जो जल रही है उस केरोसीन से
जो घर में अब नहीं है बचा।

वेदना तो भी दया आती नहीं ,
देखकर उसकी दशा।
जो जी रही है केवल
मृत्यु के इंतज़ार में।

वो आँखे
शांत है उतनी ही जितना
शांत है जीवन उसका,
चेहरे पर भाव उसके
धूमिल हो चुके है, ऐसे ही
धूमिल जैसे उसके जीवन की याद है.

वो आँखे
झपकती है निरंतर
पर झपकती हो शायद कभी ही
आँखों से पानी गिराने के लिए।

वो आँखे
सोचती है कुछ नहीं, कल के बारें में
व्यस्त रहती है वो सदा
आज मे.

वो आँखे
जो कभी मिली होंगी कुछ आँखों से,
और जो कभी
दिखाती होंगी मघुर सपने
भविष्य की कामनाओं के।

शायद वो आँखे व्यस्त है
खोजती उन्ही यादो को
जो खो गयी है स्मर्तियो में
भूत की मार से।
और ढकी है, चिन्ताओ के परदे से
वर्तमान की।

A trip to Nellyampathy

Last week we went to Kerala for a wedding. The place of wedding was near to Palakkad. Palkkad can be a good base for further trekking. It has many lodges and costly hotels (whichever you prefer). From here, one can take a bus to Nelliampathi village. It takes approximately 2.5 hours to reach the village. Last bus from the village to Palakkad is at 5:30 pm; so plan accordingly. There is small eating place at the bus-stop which is pretty good, and they don’t over-charge you for anything.

Photo Credit: Anushree N

The hike through tea plantation was awesome. tea You can also take jeep from the village to go into the reserved forest. Inside the forest, you are not suppose to walk on foot; but we did for a little while anyway ;-). intothewild jkeep If you are visiting during monsoon (July – December), do carry rain-jacket and extra socks; extra of almost everything drench-able. And heed my warning about leaches and rarely appearing scorpion. leach rain scorpion

बचपन याद आता है

मुझे बचपन याद आता है।
सुबह सवेरे उठना और नहाना
मंदिर में जाना और जल चढाना।
पाठशाला का रास्ता,
किताबे और बस्ता।
मेले में गुब्बारे जलेबी पर मचलना,
नहाना नहर में और इमली पर चढ़ना।

खरबूजों का खेत अकसर सताता है।
मुझे बचपन याद आता है।

जुते खेतो में बिचरना,
फिसलकर मेड से गिरना,
भैय्या से झगड़ना, ओर
अपने कुत्ते से लड़ना।
मुझे अब भी हँसाता है।
मुझे बचपन याद आता है।

घड़ी भर का रूठना,
और फिर हस जाना
दादी के साथ ताश की बाज़ी
और मम्मी का मनाना

शहतूत के पेड़ की टहनी
क्रिकेट का बल्ला
गिनती और पहाड़े
स्कूल का हो हल्ला

मासूम सा चेहरा, अभी भी भाता है
मुझे बचपन याद आता है।