A question of length
by Vivienne Baillie Gerritsen
When Charles Darwin accepted the invitation to accompany Captain Fitzroy on HMS Beagle as the ship’s naturalist, little did he know that he would bring back with him material that was to haunt him – one way or another - until the end of his days. Amongst the many mineral, plant and animal specimens which were unloaded from the ship on its return in October 1836, there were a number of preserved finches which Darwin had found on the Galapagos Islands. It was the study of these finches, which later became known as ‘Darwin’s finches’, that helped to forge the notion of the transmutation of species. In other words, any given species had the capacity to adapt, evolve and undergo transformations – and it turned out to be in the name of survival. With regards to finches, their beaks were different depending on the kind of diet they had. Charles Darwin had no idea how such changes could occur within a species. Today, we are getting closer and closer to understanding how it happens on the molecular level. And it seems that a protein known as calmodulin has a major role.
«It was the study of finches that Darwin collected on the Galapagos Islands which helped to forge the notion of the transmutation of species. Though the great naturalist had no idea how such changes could occur.»
As he set foot on terra firma after five years of sailing and as many of nausea, Darwin had no idea that fourteen of the many specimens of birds he brought back to England were in fact all finches. What is more, they seemed to be finches which bore many similarities to a type of finch found along the coast of South America. Darwin had identified them as different birds altogether but when he handed them over to the renowned ornithologist of the time – John Gould – it turned out that these fourteen birds were in fact representatives of twelve different species of finch. Until then, Darwin had believed that there were as many centres of creation as there were of species despite the fact that – within each centre – phenotypical change could occur. With Gould’s findings and Darwin’s knowledge of the geographical and ecological niches where he had found the birds, he shifted his theory: what if every species of finch on the Galapagos Islands had originated from the one same species on the South American coastline? It marked the very beginnings of his theory on the origin of species.
In those days, the description of specimens – whichever kingdom they belonged to – depended on a keen eye, a pencil and paper. Today, thanks to novel molecular methods, observation has been magnified by the thousands – if not the millions – and scientists are able to see or imagine processes which are going on well beneath the level of feathers and petals. Finding links between a specific gene and the effect it has on an organism is now routine. In this way, scientists discovered that the protein calmodulin – from CALcium MODULated proteIN – has a direct role in the length of a finch’s beak. What is more, they discovered that calmodulin seemed to have an effect only on the length of the birds’ beak and not its width, or depth – which are dependent on another gene. From an evolutionary point of view, this is not really surprising since it gives natural selection a form of plasticity. In other words, evolution is fine-tuned.
[‘Brown Beakface’ ]
Brown Beakface
by Kaitlin Beckett
Courtesy of the artist
How can calmodulin affect the length of a finch’s beak? It seems difficult to believe that one molecule could have such a massive effect on an organism’s appearance. In fact, it doesn’t. At least not directly. It happens to be at the very beginning of important molecular processes. Indeed, calmodulin has the power to trigger off a wide variety of biological pathways and, in turn, many activities such as muscle contraction, short-term and long-term memory, intracellular movement, inflammation, nerve growth and the immune response to name a few. It uses calcium ions, which are present in all kinds of tissues both inside the cell and outside it. Calmodulin is just one of the many molecules which use calcium ions to induce a reaction. Nevertheless, without it and calcium, a lot of what goes on inside us would go haywire.
«Not so long ago, the description of specimens - whichever kingdom they belonged to - depended on a keen eye, a pencil and paper. Today, scientists can see or imagine processes which happen well beneath the level of feathers and petals.»
At rest, calmodulin looks a little like a dumbbell. It is composed of two arms attached by a helix hinge. Each arm can hold up to two calcium ions. Once bound, the structural conformation of calmodulin is modified and ready to bind to specific target proteins which it does by wrapping its arms around it in a sort of molecular hug. What is more, depending on the amount of calcium ions bound – up to four – and the kind of post-translational modification calmodulin has undergone, the protein can bind to a great variety of targets ranging from kinases, phosphatases and phosphodiesterases to ion channels, cyclases and cytoskeleton receptors. In turn, each of these target proteins will trigger off cellular processes – from the regulation of metabolism and the cytoskeleton, to ion transport, protein folding and cell proliferation. With regards to the length of finch’s beaks, researchers discovered that the long-beaked finches always express a higher level of calmodulin than the shorter and wider-beaked species. And when they upregulated the calmodulin gene in chicken, this had a direct effect on the length of their beaks!
Although a number of anti-calmodulin products had already been described in the 1980s, by the 1990s interest had faded. However, owing to the more recent discoveries of the involvement of calmodulin in so many different physiological processes, there has been a drastic increase in its interest, especially within the world of therapy and drug design. Some synthetic inhibitors are already used clinically as anti-cancer and anti-psychotic agents for example. But scientists have already described over one hundred natural inhibitors, the most potent of which are animal venoms. Such naturally-occurring compounds could be used to develop herbicides or to design drugs for neurodegenerative diseases for example. The future certainly seems bright for calmodulin. HMS Beagle took Darwin around the world; little did the founder of the theory of the origin of species know where his finches would take him.
References
1. Abzhanov A., Kuo W.P., Hartmann C., Grant B.R., Gran P.R. The calmodulin pathway and evolution of elongated beak morphology in Darwin’s finches Nature 442:563-567(2006) PMID:16885984
2. Patel N.H. How to build a longer beak Nature 442:515-516(2006) PMID:16885968
Swiss-Prot cross references
Calmodulin, Homo sapiens, (Human) : P62158
This is a personal web space on my daily personal, spiritual, philosophical ramblings, ravings and musings... It greatly reflects my moods and opinions on religion, politics, people on a daily basis... However, you are most welcome to stop by and pass on a piece of your mind as well. I will be more than eager to hear what you have to say.
Wednesday, May 27, 2009
A question of length
Posted by
Sucheta Tripathy PI @ Computational Genomics Group at IICB, Kolkata
at
7:21 AM
No comments:


Monday, April 6, 2009
Sometimes the unthinkable happens
I sometimes wonder do we have any control over the things that happen in our day to day lives? It may sound very unscientific, but yes, I would say yes. Sometimes our brain leads us to do something that makes no sense and the outcome sometimes surprises us. We may think of the worse, but somehow we come out of it unscathed, saved by some divine presence.
Something happened in our own household very recently. On Friday, the 3rd April 2009, 11 A.M my father took bath and took his clothes as usual to dry. He generally does it on the front side of our house, but that day spontaneously he saw a bright sunny spot over our well and thought why not to dry clothes there? Then he climbed onto the wall of the well(we have 3 feet tall wall around the well and the width of the wall is about 2 feet). There was a cement slab covering part of the well on which we climbed and jumped throughout our childhood. Its been almost 26 years since the slab is there but it has been now broken and can't sustain even little bit of weight. God knows why my father stepped onto that slab, and as he did, it broke into 2 pieces and he fell inside the well. To top it all on the slab there were some heavy duty garden equipments that were quite heavy, sharp and made up of iron. Those things also crashed into the well along with my dad. Then he went down the water and came up and was trying to swim. There were 14 ft. of water in that well. He managed to swim and remained on the surface and managed to raise some alarm to which my mother, my niece, my nephews responded and got some help. Then one of my neighbor boys, who is an expert in well climbing was summoned, and luckily he was home so he came by immediately and rescued my father. My dad came out without any major injuries.
I was sitting and thinking about this whole thing and was wondering how lucky we are that none of the heavy sharp equipments fell on him and not even the slab. Had it been the case, god knows what would have happened. I just thank god for saving us from the unthinkable....
Something happened in our own household very recently. On Friday, the 3rd April 2009, 11 A.M my father took bath and took his clothes as usual to dry. He generally does it on the front side of our house, but that day spontaneously he saw a bright sunny spot over our well and thought why not to dry clothes there? Then he climbed onto the wall of the well(we have 3 feet tall wall around the well and the width of the wall is about 2 feet). There was a cement slab covering part of the well on which we climbed and jumped throughout our childhood. Its been almost 26 years since the slab is there but it has been now broken and can't sustain even little bit of weight. God knows why my father stepped onto that slab, and as he did, it broke into 2 pieces and he fell inside the well. To top it all on the slab there were some heavy duty garden equipments that were quite heavy, sharp and made up of iron. Those things also crashed into the well along with my dad. Then he went down the water and came up and was trying to swim. There were 14 ft. of water in that well. He managed to swim and remained on the surface and managed to raise some alarm to which my mother, my niece, my nephews responded and got some help. Then one of my neighbor boys, who is an expert in well climbing was summoned, and luckily he was home so he came by immediately and rescued my father. My dad came out without any major injuries.
I was sitting and thinking about this whole thing and was wondering how lucky we are that none of the heavy sharp equipments fell on him and not even the slab. Had it been the case, god knows what would have happened. I just thank god for saving us from the unthinkable....
Posted by
Sucheta Tripathy PI @ Computational Genomics Group at IICB, Kolkata
at
2:34 PM
No comments:


Monday, March 23, 2009
Thoughts determine your destiny
This article is not mine. I read it in "express buzz" and thought will blog it in my site. For a change, this type of articles are soothing for the mind..
Swahilya
First Published : 22 Mar 2009 07:21:00 AM IST
Last Updated : 22 Mar 2009 01:09:47 AM IST
Mind is the feature that distinguishes man from the other mammals, amphibians, reptiles, insects, plants and other forms of life. The mind is expressed in man fully, while it is dormant in most other creatures such as dogs, monkeys, elephants, dolphins and crows. These
express a sort of intelligence and emotions that are in tune with and recognised by the human mind.
The research in this area is vast and deepening further. Patanjali has put the scope of yoga in four simple words — Yogaha Chitta Vritti Nirodhaha (Through yoga, you can stop the thought patterns of the mind). The mind is like an ocean and the water is a composition of our thoughts. We are always immersed deep in this ocean of thoughts, which keeps moving in waves.
There are many schools of yoga today, each claiming that theirs is the best. There are people who do not just debate, but also fight about which is a more superior form of practice. Many are confused on which path to take. Such people need to realise that any form of yoga is but a road leading to the same goal — to stop the modifications of the mind.
It is impossible to stop the flow of thought. However, by stopping Chitta Vrittis or mind modification, the individual can become aware of what they’re thinking. This is akin to riding the crest of a wave or setting sail to the direction of the wind. Patanjali, a researcher of the human mind with utmost clarity, outlines five functions of the human mind. Each is the wave or the vritti that we speak about.
Pramana
Basis of cognition or understanding names and forms around you. This happens in the following three ways.
l Pratyaksha is that which is perceived by your five senses. You are reading a newspaper. You may even get a whiff of the smell of newsprint. Hence, you directly know that it is a newspaper. You don’t need another person to explain this to you. l The next is anumana. It literally means guessing. If smoke rises high in a distance, you guess that there is a fire. l Agama or relying on a treatise, is a text, a code of ethics or a law to base your understanding of the abstract concepts such as god, karma, life before and after death etc. These are the grey zones of knowledge that we cannot directly see or infer.
Viparyaya
It means wrong understanding or misunderstanding. This happens when you see an object outside, but you entertain a different idea within. You have an understanding from something you heard, read or saw as a child that ghosts are white in colour and that they appear at night. This knowledge makes your mind mistake anything in white for a ghost.
Vikalpa
Vikalpa means uncontrolled imagination. In a few moments, the little boy sitting in a boring math class can imagine that he has passed the air force examination, become a pilot, and riding a plane which suddenly crash lands when the teacher in the classroom throws a piece of chalk on his desk to get him out of his day dreaming. Sankalpa is focused imagination. If you wish to become a doctor, you can make a sankalpa in your mind, imagining yourself with a coat and stethoscope, even while you are just now appearing for your class 12 board examinations. Many of the self-help techniques have its basis in sankalpa.
Nidra
It means to sleep, when all thoughts go on an eight-hour holiday.
Smriti
Smriti or memory is the last function where the mind recalls experiences of the past that are stored in the conscious and sub-conscious layers of the mind.
A time for yourself
You can try this exercise for about half-an-hour a week.
1. Sit down in a comfortable place. 2. Keep a notebook
and pen beside you. You may keep your eyes closed. 3. Once you settle down, you will be able to watch the steady flow of thoughts. 4. Watch if the thoughts are angry, depressed, hateful, sorrowful, jealous, morbid or tragic. 5. Do not interpret those thoughts as good or bad. Simply observe them and write them down. Most often, your mind wanders when you are doing something or listening to someone. This is totally unconnected with the present moment. Watch how your mind takes on such flights of fancy. Plain awareness can help bring the mind back to the present moment. This way you train yourself to get what’s commonly known as ‘presence of mind’.
Swahilya
First Published : 22 Mar 2009 07:21:00 AM IST
Last Updated : 22 Mar 2009 01:09:47 AM IST
Mind is the feature that distinguishes man from the other mammals, amphibians, reptiles, insects, plants and other forms of life. The mind is expressed in man fully, while it is dormant in most other creatures such as dogs, monkeys, elephants, dolphins and crows. These
express a sort of intelligence and emotions that are in tune with and recognised by the human mind.
The research in this area is vast and deepening further. Patanjali has put the scope of yoga in four simple words — Yogaha Chitta Vritti Nirodhaha (Through yoga, you can stop the thought patterns of the mind). The mind is like an ocean and the water is a composition of our thoughts. We are always immersed deep in this ocean of thoughts, which keeps moving in waves.
There are many schools of yoga today, each claiming that theirs is the best. There are people who do not just debate, but also fight about which is a more superior form of practice. Many are confused on which path to take. Such people need to realise that any form of yoga is but a road leading to the same goal — to stop the modifications of the mind.
It is impossible to stop the flow of thought. However, by stopping Chitta Vrittis or mind modification, the individual can become aware of what they’re thinking. This is akin to riding the crest of a wave or setting sail to the direction of the wind. Patanjali, a researcher of the human mind with utmost clarity, outlines five functions of the human mind. Each is the wave or the vritti that we speak about.
Pramana
Basis of cognition or understanding names and forms around you. This happens in the following three ways.
l Pratyaksha is that which is perceived by your five senses. You are reading a newspaper. You may even get a whiff of the smell of newsprint. Hence, you directly know that it is a newspaper. You don’t need another person to explain this to you. l The next is anumana. It literally means guessing. If smoke rises high in a distance, you guess that there is a fire. l Agama or relying on a treatise, is a text, a code of ethics or a law to base your understanding of the abstract concepts such as god, karma, life before and after death etc. These are the grey zones of knowledge that we cannot directly see or infer.
Viparyaya
It means wrong understanding or misunderstanding. This happens when you see an object outside, but you entertain a different idea within. You have an understanding from something you heard, read or saw as a child that ghosts are white in colour and that they appear at night. This knowledge makes your mind mistake anything in white for a ghost.
Vikalpa
Vikalpa means uncontrolled imagination. In a few moments, the little boy sitting in a boring math class can imagine that he has passed the air force examination, become a pilot, and riding a plane which suddenly crash lands when the teacher in the classroom throws a piece of chalk on his desk to get him out of his day dreaming. Sankalpa is focused imagination. If you wish to become a doctor, you can make a sankalpa in your mind, imagining yourself with a coat and stethoscope, even while you are just now appearing for your class 12 board examinations. Many of the self-help techniques have its basis in sankalpa.
Nidra
It means to sleep, when all thoughts go on an eight-hour holiday.
Smriti
Smriti or memory is the last function where the mind recalls experiences of the past that are stored in the conscious and sub-conscious layers of the mind.
A time for yourself
You can try this exercise for about half-an-hour a week.
1. Sit down in a comfortable place. 2. Keep a notebook
and pen beside you. You may keep your eyes closed. 3. Once you settle down, you will be able to watch the steady flow of thoughts. 4. Watch if the thoughts are angry, depressed, hateful, sorrowful, jealous, morbid or tragic. 5. Do not interpret those thoughts as good or bad. Simply observe them and write them down. Most often, your mind wanders when you are doing something or listening to someone. This is totally unconnected with the present moment. Watch how your mind takes on such flights of fancy. Plain awareness can help bring the mind back to the present moment. This way you train yourself to get what’s commonly known as ‘presence of mind’.
Posted by
Sucheta Tripathy PI @ Computational Genomics Group at IICB, Kolkata
at
8:21 AM
No comments:


Friday, February 20, 2009
Silent pain
Silent pain
by Vivienne Baillie Gerritsen [As appeared in protein spotlight]
Is there really a point to pain? Yes, argue most. Pain warns you that something is not right. It teaches children not to put their hands on a hot plate because they know heat hurts. It urges you to consult your doctor when pain persists in any part of your body. Yes, but what about pain that accompanies something which has already been diagnosed? What about the persistent pain that frequently escorts chronic conditions, such as a sore back or cancer? Who can see the good in that kind of pain? Though there may be instances when it seems superfluous and even cruel, the sensation of pain is more necessary than it is not. It is a clear indicator that there is something wrong, and that it needs to be seen to. In the absence of pain, no alert signals are given off – which could ultimately put your life in danger. It is a complex sensation with many a meaning and many a pathway. One particular pathway was discovered when members of a family were incapable of feeling pain – a singular and rare condition due to the loss of function of a protein known as SCN9A or Nav1.7.
«Though there may be instances when it seems superfluous and even cruel, the sensation of pain is more necessary than it is not.»
One of the very first medical descriptions of such an affliction was described in the literature in the 1930s. The article depicted a man who had an act as a human pincushion in a circus. Another similar case was discovered more recently in Pakistan where a young street performer entertained crowds by running knives through his arms or walking on red hot coal – and ended up in hospital on a regular basis for medical care. He died at the early age of fourteen when he threw himself off a roof. A study carried out on his family revealed other cases of seemingly total indifference to pain. In the past few years, yet other occurrences of this peculiar condition have been described. The disease is congenital, very rare – so far only 30 cases have been described worldwide – and though it sounds ideal never to be under the grasp of pain, life is not necessarily easier for those who suffer from it.
It took many centuries before it was acknowledged that pain could be useful and – in some ways – even protective. For Aristotle, pain was merely part of a man’s lot while on earth. Christianity transcended the belief by stating that pain was a divine gift. Although Hippocrates (460-379 BC) had already suggested that pain was the announcement of some form of physical disorder, it was only at the beginning of the second millennium that Galen of Pergamum (129-200 AD), a Roman physician, actually suggested that a network of nerves in our body lead to the brain. Such nerves were capable of distributing three types of perception: locomotion, sensibility and pain, where the purpose of pain was understood as a means of survival. The notion of the ‘usefulness’ of pain – such as the memory of what can harm or the telltale sign of a physical disorder – only emerged in the 18th century once Science had set itself free from the Church.
Individuals suffering from indifference to pain have already been depicted in the scientific literature but their condition was always accompanied with other serious drawbacks, such as mental retardation for instance. However, the difference between these cases and what the Pakistani street performer was suffering from is that he was otherwise perfectly normal. People with congenital indifference to pain (CIP) present no mental disadvantages. They can discern a dull touch from a pin prick, feel their limbs moving and even discriminate hot from cold. Their cardiac rhythms are perfectly normal as is their capacity to sweat. The only other deficiency that may be linked to CIP is perhaps a slight loss of smell. But not every individual presents this slight anosmia.
«It took many centuries before it was acknowledged that pain could be useful and – in some ways – even protective. »
So what is at the heart of this particular case of indifference to pain? A protein: SCN9A, otherwise known as ‘sodium channel protein type 9 subunit alpha’. SCN9A is a transmembrane protein found in neurons. It forms a channel through which sodium ions flow, following the membrane’s electric gradient. SCN9A seems to be concentrated in peripheral neurons and may well be at the very beginning of the electric impulse which triggers off the pain message and sends it off to the brain. In CIP, SCN9A is truncated and the channel is unable to function. Consequently, the sensation of pain isn’t sent to the brain. Scientists were surprised to discover that only one protein seems to be responsible for a sensation which belongs to a pathway that is otherwise so complex. In this instance, SCN9A acts a little like an on/off switch. Certainly, SCN9A is at the very heart of pain perception since another mutation actually heightens the sensation – a condition known as erythermalgia.
Pain has many facets. There are many neuronal pathways which trigger off pain. There are many other types of sodium channels involved in its transmission. What is more, polymorphisms may well endow different individuals with differences in pain perception. Perhaps we all suffer differently. Be that as it may, pain is essential and the bearer of news which is better not to disregard. Babies and young children who suffer from CIP can bite off parts of their lips, chop off the tips of their tongues or burn their hands – which all go unnoticed unless a third party is present. And these are only surface wounds. What of broken bones or bowel blockage for instance?
The scarcity of CIP is precious for the design of drugs such as painkillers. Indeed, any rare disease whose phenotype can pinpoint only one protein – in this case, a sodium channel – is a godsend for scientists. If a drug can be designed to block SCN9A specifically, the side effects could be minimal. Currently, there are many analgesics that can silence pain by blocking other types of sodium channels, but the secondary effects can be big. However, the question arises: is it such a good thing not to feel pain? Imagine a chronic disease. Taking away all sensation of pain could turn out to be a catastrophe. A cardiac arrest could go unnoticed for instance. Perhaps, then, the population should be informed differently on the advent of a common harmful condition? Instead of describing the pain felt in your chest, for instance, why not put more of a stress on the other symptoms which accompany a heart attack? Undoubtedly, there is more to pain than meets the brain. And though at times it may seem heartless, a life without pain would be like a ship without its hull.
References
1. Cox J.J., Reimann F., Nicholas A.K., Thornton G., Roberts E., Springell K., Karbani G., Jafri H., Mannan J., Raashid Y., Al-Gazali L., Hamamy H., Valente E.M., Gorman S., Williams R., McHale D.P., Wood J.N., Gribble F.M., Woods C.G. An SCN9A channelopathy causes congenital inability to experience pain Nature 444:894-898(2006) PMID:17167479
2. Drenth J.P.H., Waxman S.G. Mutations in sodium-channel gene SCN9A cause a spectrum of human genetic pain disorders Journal of Clinical Investigation 117:3603-3609(2007) PMID:18060017
3. Young F.B.J. A life without pain? Hedonists take note Clinical Genetics 73:31-33(2008) PMID:18070140
by Vivienne Baillie Gerritsen [As appeared in protein spotlight]
Is there really a point to pain? Yes, argue most. Pain warns you that something is not right. It teaches children not to put their hands on a hot plate because they know heat hurts. It urges you to consult your doctor when pain persists in any part of your body. Yes, but what about pain that accompanies something which has already been diagnosed? What about the persistent pain that frequently escorts chronic conditions, such as a sore back or cancer? Who can see the good in that kind of pain? Though there may be instances when it seems superfluous and even cruel, the sensation of pain is more necessary than it is not. It is a clear indicator that there is something wrong, and that it needs to be seen to. In the absence of pain, no alert signals are given off – which could ultimately put your life in danger. It is a complex sensation with many a meaning and many a pathway. One particular pathway was discovered when members of a family were incapable of feeling pain – a singular and rare condition due to the loss of function of a protein known as SCN9A or Nav1.7.
«Though there may be instances when it seems superfluous and even cruel, the sensation of pain is more necessary than it is not.»
One of the very first medical descriptions of such an affliction was described in the literature in the 1930s. The article depicted a man who had an act as a human pincushion in a circus. Another similar case was discovered more recently in Pakistan where a young street performer entertained crowds by running knives through his arms or walking on red hot coal – and ended up in hospital on a regular basis for medical care. He died at the early age of fourteen when he threw himself off a roof. A study carried out on his family revealed other cases of seemingly total indifference to pain. In the past few years, yet other occurrences of this peculiar condition have been described. The disease is congenital, very rare – so far only 30 cases have been described worldwide – and though it sounds ideal never to be under the grasp of pain, life is not necessarily easier for those who suffer from it.
It took many centuries before it was acknowledged that pain could be useful and – in some ways – even protective. For Aristotle, pain was merely part of a man’s lot while on earth. Christianity transcended the belief by stating that pain was a divine gift. Although Hippocrates (460-379 BC) had already suggested that pain was the announcement of some form of physical disorder, it was only at the beginning of the second millennium that Galen of Pergamum (129-200 AD), a Roman physician, actually suggested that a network of nerves in our body lead to the brain. Such nerves were capable of distributing three types of perception: locomotion, sensibility and pain, where the purpose of pain was understood as a means of survival. The notion of the ‘usefulness’ of pain – such as the memory of what can harm or the telltale sign of a physical disorder – only emerged in the 18th century once Science had set itself free from the Church.
Individuals suffering from indifference to pain have already been depicted in the scientific literature but their condition was always accompanied with other serious drawbacks, such as mental retardation for instance. However, the difference between these cases and what the Pakistani street performer was suffering from is that he was otherwise perfectly normal. People with congenital indifference to pain (CIP) present no mental disadvantages. They can discern a dull touch from a pin prick, feel their limbs moving and even discriminate hot from cold. Their cardiac rhythms are perfectly normal as is their capacity to sweat. The only other deficiency that may be linked to CIP is perhaps a slight loss of smell. But not every individual presents this slight anosmia.
«It took many centuries before it was acknowledged that pain could be useful and – in some ways – even protective. »
So what is at the heart of this particular case of indifference to pain? A protein: SCN9A, otherwise known as ‘sodium channel protein type 9 subunit alpha’. SCN9A is a transmembrane protein found in neurons. It forms a channel through which sodium ions flow, following the membrane’s electric gradient. SCN9A seems to be concentrated in peripheral neurons and may well be at the very beginning of the electric impulse which triggers off the pain message and sends it off to the brain. In CIP, SCN9A is truncated and the channel is unable to function. Consequently, the sensation of pain isn’t sent to the brain. Scientists were surprised to discover that only one protein seems to be responsible for a sensation which belongs to a pathway that is otherwise so complex. In this instance, SCN9A acts a little like an on/off switch. Certainly, SCN9A is at the very heart of pain perception since another mutation actually heightens the sensation – a condition known as erythermalgia.
Pain has many facets. There are many neuronal pathways which trigger off pain. There are many other types of sodium channels involved in its transmission. What is more, polymorphisms may well endow different individuals with differences in pain perception. Perhaps we all suffer differently. Be that as it may, pain is essential and the bearer of news which is better not to disregard. Babies and young children who suffer from CIP can bite off parts of their lips, chop off the tips of their tongues or burn their hands – which all go unnoticed unless a third party is present. And these are only surface wounds. What of broken bones or bowel blockage for instance?
The scarcity of CIP is precious for the design of drugs such as painkillers. Indeed, any rare disease whose phenotype can pinpoint only one protein – in this case, a sodium channel – is a godsend for scientists. If a drug can be designed to block SCN9A specifically, the side effects could be minimal. Currently, there are many analgesics that can silence pain by blocking other types of sodium channels, but the secondary effects can be big. However, the question arises: is it such a good thing not to feel pain? Imagine a chronic disease. Taking away all sensation of pain could turn out to be a catastrophe. A cardiac arrest could go unnoticed for instance. Perhaps, then, the population should be informed differently on the advent of a common harmful condition? Instead of describing the pain felt in your chest, for instance, why not put more of a stress on the other symptoms which accompany a heart attack? Undoubtedly, there is more to pain than meets the brain. And though at times it may seem heartless, a life without pain would be like a ship without its hull.
References
1. Cox J.J., Reimann F., Nicholas A.K., Thornton G., Roberts E., Springell K., Karbani G., Jafri H., Mannan J., Raashid Y., Al-Gazali L., Hamamy H., Valente E.M., Gorman S., Williams R., McHale D.P., Wood J.N., Gribble F.M., Woods C.G. An SCN9A channelopathy causes congenital inability to experience pain Nature 444:894-898(2006) PMID:17167479
2. Drenth J.P.H., Waxman S.G. Mutations in sodium-channel gene SCN9A cause a spectrum of human genetic pain disorders Journal of Clinical Investigation 117:3603-3609(2007) PMID:18060017
3. Young F.B.J. A life without pain? Hedonists take note Clinical Genetics 73:31-33(2008) PMID:18070140
Posted by
Sucheta Tripathy PI @ Computational Genomics Group at IICB, Kolkata
at
8:19 AM
No comments:


Thursday, January 15, 2009
My 7 days diet program
I heard about this diet plan as GM diet plan, that my brother told me. I was not very serious about it then. But after hearing my friends husband followed it and lost about 15 lb weight, I thought I will give it a try...
Day 1
Today is 12th Jan 2009, Monday. Today is the fruits day and no bananas. I started with Canteloupe, pine apple, pomogranates, oranges. Today was a great day. No problems..
Day 2
Today is the vegetable day. I cooked some cauliflower, cabbage and broccoli together with little olive oil and mustard, cumin seeds, little salt and little chilli pepper. In the morning I had boiled potato, seasoned with little onion, salt, green chilli. After noon I had 2 bowls of boiled vegetables, garnished with onion, garlic, cumin seeds and chilli pepper.Today is also a great day.
But I got up in the middle of the night with some cramp in my tummy. That receded in the morning.
Day 3
Today is the mixture of fruits and vegetables day. I have had dizziness in the morning, and was feeling very weak. Then I consumed few apples to supply carbohydrates to my system, then it was OK. By the end of the day, I was normal but fatigued.In the day I boiled large amounts of raddish, cabbage, carrot, cauliflower, broccoli, beans together. Garnished this with little fried onion garlic, red chili, salt, cumin powder. Through out the day no issues, except, I still feel weak. I consumed some grapes too. May be I drank 6-7 glasses of water.
Day 4
Today is banana and milk day. I am feeling tired and dizzy. I already had a glass of milk. I can eat 8 bananas today. Altogether I ate 6 big bananas today with 3 glasses of milk. Apart from this I also drank a bowl of vegetable soup that I made yesterday and also another bowl of soup plus vegetables. It was a difficult day for me, since I had this cravings for all kinds of food. I went to sleep feeling hungry. I woke up in the middle of the night, saw some strange dreams..
Day 5
Today as the diet program says should be feast day with 6 tomatoes and beef. I am a non-beef eater and was wondering what I can replace beef with. I thought of chicken first, but later replaced that with dal. I made some dal in the morning with half onion and one full tomato. Pressure cooked together, then added little salt and half a spoon of olive oil to it. This was quite good and helped me get over my dizziness in the morning. Its been constantly the case since day 3..
For lunch, I had 2 large tomatoes finely cut and mixed with little onion, salt, little olive oil and one and half green chilli.
For Dinner, I have boiled 3 tomatoes and have some dal left.
Day 6
Today is suppose to be a beef and vegetable day. In the morning, I had a carrot and one cucumber. I also had 2 egg whites. Today we were invited to party where I stuck to raw vegetables as well as egg whites. In the dinner/lunch however, I ate chicken curry - the typical Indian way. I cooked chicken with tomatoes, onion, zinger, garlic, cilantro. I also had some boiled vegetable.
Day 7
Today is the last day of my fast and I am yet to see any weight changes. I took cooked vegetables and fruits today. In the night however, I could not resist eating rice..
Outcome
Well, I did not see any visible weight loss, may be 1 KG or may be 3 lbs. Anyways, no problems with no weight loss, I feel happy because I think I detoxified successfully. I saw a boil in my thigh before the diet program which steadily increased in size till the program lasted. Surprisingly, I saw in the last day of the program the boil has shrunken... This for me is a great thing.
Day 1
Today is 12th Jan 2009, Monday. Today is the fruits day and no bananas. I started with Canteloupe, pine apple, pomogranates, oranges. Today was a great day. No problems..
Day 2
Today is the vegetable day. I cooked some cauliflower, cabbage and broccoli together with little olive oil and mustard, cumin seeds, little salt and little chilli pepper. In the morning I had boiled potato, seasoned with little onion, salt, green chilli. After noon I had 2 bowls of boiled vegetables, garnished with onion, garlic, cumin seeds and chilli pepper.Today is also a great day.
But I got up in the middle of the night with some cramp in my tummy. That receded in the morning.
Day 3
Today is the mixture of fruits and vegetables day. I have had dizziness in the morning, and was feeling very weak. Then I consumed few apples to supply carbohydrates to my system, then it was OK. By the end of the day, I was normal but fatigued.In the day I boiled large amounts of raddish, cabbage, carrot, cauliflower, broccoli, beans together. Garnished this with little fried onion garlic, red chili, salt, cumin powder. Through out the day no issues, except, I still feel weak. I consumed some grapes too. May be I drank 6-7 glasses of water.
Day 4
Today is banana and milk day. I am feeling tired and dizzy. I already had a glass of milk. I can eat 8 bananas today. Altogether I ate 6 big bananas today with 3 glasses of milk. Apart from this I also drank a bowl of vegetable soup that I made yesterday and also another bowl of soup plus vegetables. It was a difficult day for me, since I had this cravings for all kinds of food. I went to sleep feeling hungry. I woke up in the middle of the night, saw some strange dreams..
Day 5
Today as the diet program says should be feast day with 6 tomatoes and beef. I am a non-beef eater and was wondering what I can replace beef with. I thought of chicken first, but later replaced that with dal. I made some dal in the morning with half onion and one full tomato. Pressure cooked together, then added little salt and half a spoon of olive oil to it. This was quite good and helped me get over my dizziness in the morning. Its been constantly the case since day 3..
For lunch, I had 2 large tomatoes finely cut and mixed with little onion, salt, little olive oil and one and half green chilli.
For Dinner, I have boiled 3 tomatoes and have some dal left.
Day 6
Today is suppose to be a beef and vegetable day. In the morning, I had a carrot and one cucumber. I also had 2 egg whites. Today we were invited to party where I stuck to raw vegetables as well as egg whites. In the dinner/lunch however, I ate chicken curry - the typical Indian way. I cooked chicken with tomatoes, onion, zinger, garlic, cilantro. I also had some boiled vegetable.
Day 7
Today is the last day of my fast and I am yet to see any weight changes. I took cooked vegetables and fruits today. In the night however, I could not resist eating rice..
Outcome
Well, I did not see any visible weight loss, may be 1 KG or may be 3 lbs. Anyways, no problems with no weight loss, I feel happy because I think I detoxified successfully. I saw a boil in my thigh before the diet program which steadily increased in size till the program lasted. Surprisingly, I saw in the last day of the program the boil has shrunken... This for me is a great thing.
Posted by
Sucheta Tripathy PI @ Computational Genomics Group at IICB, Kolkata
at
8:51 AM
No comments:


Wednesday, December 31, 2008
Life in India
If you lived in a foreign country for a while and having a regular India trip, then this article is for you. The moment you land, you experience chaos at the airport. All the cars appear to you very small and the traffic extremely unruly. The roads narrow, dusty and people look very poor. You then immediately check if you have taken your shot on time not to get any infection etc. Then you grab the water bottle you purchased at the airport and guzzle some water through your mouth in dis-belief. India will never change. It is the same it used to be 20 years back. But is that right? Barely...
As you stay there for a few days you start getting used to the chaos and the dust. Then everything appears to you normal. If you land in Mumbai you will find your friends house is very clean. More clean than you have ever managed to keep your carpet laden home in USA. You don't feel houses are small because everything is arranged so neatly. Then the door bell rings, doodhwallh comes and delivers milk.After sometimes, kapdawallah comes and takes clothes for ironing. Then phone rings and somebody at the other end asks if you will need any vegetable. Then your friend's wife says "No not today". Then she goes downstairs and gets a bagful of vegetables from the road side vendors just outside the building. You scream in dis-belief "How come you get a bagful of veggies in just 50 rupees"!! Just a dollar for you. Now in your mind you are working on the equation what you get in India and what you loose abroad. You get so much done by people that you have whole lot of time to do the skilled jobs that you are trained for. You just start thinking what your typical working day is.. You get up at 7 A.M, make some tea/coffee then if you can go to the toilet get ready. Then you find the clothes are not ironed, then you press it. Then you quickly grab some ready made crap meant to be breakfast. If you could you try to pack lunch and the leave for work. Night you come back home to discover you have to buy veggies, then you take your car in cold and drive to nearby store that is few miles away and then come back home. You will find dirty dishes in the sink, then you quickly clean some and try to cook. Meanwhile, you can make some tea for yourself. If you have a significant other, then it eases work little bit. But then you end up doing 50% of the entire household work. If you have a kid, then a different story altogether. No breathing time for both of you. Weekends, you clean your house, clean clothes, arrange them, manage to do grocery, invite people over because you are lonely etc. Time passes just like that. On the contrary in India, you get most of your house hold jobs done by people who are efficient in it. You have lots of time to do other things. You can teach your kids, play with them do some reading etc. At what cost? Nothing more than dust and chaos. I can live with it..
In places like Mumbai, you get high speed internet(> 3 MBps - 1.5 Mbps is still considered highspeed in US), gas pipeline, "bai" for 1500 rupees a month and additional Rs 1000 for cloth ironing, gardener etc. So calculating cost of living, apart from your house rent you have all your basic needs including food can be taken care of in 10,000 rupees. The average salary has gone up for a lots of jobs in India. Many people earn atleast 50,000 rupees a month. So, tell me which life will you opt?
clean roads vs Dirty roads
Traffic discipline Vs No traffic discipline
No crowd Vs Lots of crowd
Do all work by yourself Vs Get things done by people
No time for yourself Vs Lots of time for everything else
Food is difficult Vs Food is yummy
Lonely Life Vs People all around you
No Family Vs Family
Nobody cares for you Vs You get lots of love and affection
Whatever you earn pay 45% tax Vs You get lot of tax exemption
Anytime, I will choose B over A. For me spending my precious time doing something that someone else can do and that to that generates job for someone is always welcome by me. The choice is yours after all the life is yours ..
Jai Hind
As you stay there for a few days you start getting used to the chaos and the dust. Then everything appears to you normal. If you land in Mumbai you will find your friends house is very clean. More clean than you have ever managed to keep your carpet laden home in USA. You don't feel houses are small because everything is arranged so neatly. Then the door bell rings, doodhwallh comes and delivers milk.After sometimes, kapdawallah comes and takes clothes for ironing. Then phone rings and somebody at the other end asks if you will need any vegetable. Then your friend's wife says "No not today". Then she goes downstairs and gets a bagful of vegetables from the road side vendors just outside the building. You scream in dis-belief "How come you get a bagful of veggies in just 50 rupees"!! Just a dollar for you. Now in your mind you are working on the equation what you get in India and what you loose abroad. You get so much done by people that you have whole lot of time to do the skilled jobs that you are trained for. You just start thinking what your typical working day is.. You get up at 7 A.M, make some tea/coffee then if you can go to the toilet get ready. Then you find the clothes are not ironed, then you press it. Then you quickly grab some ready made crap meant to be breakfast. If you could you try to pack lunch and the leave for work. Night you come back home to discover you have to buy veggies, then you take your car in cold and drive to nearby store that is few miles away and then come back home. You will find dirty dishes in the sink, then you quickly clean some and try to cook. Meanwhile, you can make some tea for yourself. If you have a significant other, then it eases work little bit. But then you end up doing 50% of the entire household work. If you have a kid, then a different story altogether. No breathing time for both of you. Weekends, you clean your house, clean clothes, arrange them, manage to do grocery, invite people over because you are lonely etc. Time passes just like that. On the contrary in India, you get most of your house hold jobs done by people who are efficient in it. You have lots of time to do other things. You can teach your kids, play with them do some reading etc. At what cost? Nothing more than dust and chaos. I can live with it..
In places like Mumbai, you get high speed internet(> 3 MBps - 1.5 Mbps is still considered highspeed in US), gas pipeline, "bai" for 1500 rupees a month and additional Rs 1000 for cloth ironing, gardener etc. So calculating cost of living, apart from your house rent you have all your basic needs including food can be taken care of in 10,000 rupees. The average salary has gone up for a lots of jobs in India. Many people earn atleast 50,000 rupees a month. So, tell me which life will you opt?
clean roads vs Dirty roads
Traffic discipline Vs No traffic discipline
No crowd Vs Lots of crowd
Do all work by yourself Vs Get things done by people
No time for yourself Vs Lots of time for everything else
Food is difficult Vs Food is yummy
Lonely Life Vs People all around you
No Family Vs Family
Nobody cares for you Vs You get lots of love and affection
Whatever you earn pay 45% tax Vs You get lot of tax exemption
Anytime, I will choose B over A. For me spending my precious time doing something that someone else can do and that to that generates job for someone is always welcome by me. The choice is yours after all the life is yours ..
Jai Hind
Posted by
Sucheta Tripathy PI @ Computational Genomics Group at IICB, Kolkata
at
1:17 PM
No comments:


Tuesday, November 4, 2008
Social NRIs in USA
There are a lots of Indians all over USA. They usually socialize at different levels. For instance when they are students, post docs, they have their fellow classmates and they visit each other, have simple dinner parties etc. Mostly these parties are very enjoyable, innocent and the participants have no other distraction in life.I consider this to be the best socializing event in somebody's life.
As time passes by and they settle in life they tend to have different types of social groups. These groups usually comprise of spouses and young children. The social gathering usually revolves around their kid's activity - occasionally around themselves. But still this group is kind of OK in terms of socializing.
Few more years passes, kids start going to school, the group dynamism changes slowly. The social activities still revolve around the kids but generally the adults really don't have any social contacts in any true sense. They have by now established themselves in some good jobs, started earning enough money, managed to have a house, started sending their kids to private schools. I have noticed that people(generally adults) in these groups know very little or nothing about each other. They have zero or negative attention span. When one person starts speaking in such a gathering, there are hardly any listeners. The people who are suppose to listen, may be already thinking what "I should be speaking" next instead of listening. They often snatch words from others mouth and drag the topic to something else.
One such group I am part of, where people have known each other for more than 10 years, but still don't know much about each other!! Either they are not interested or they have been focusing on themselves too much. While they tend to know somebody's weak point, but don't usually know their strengths. What are their specializations, what somebody is good at etc. For instance they don't know somebody's surname, where they are from, what are their background etc. I kind of get surprised when they gather around for so many hours together, what they talk? Some people talk politics, some talk about economy, and MANY about somebody's life style!! In Indian population abroad about 90% are there that compete with each other in prosperity contest!! Ladies generally look at what others are wearing, what jewelery somebody has. They tend to ape each other and get the things that will put them in the certain list in their next India trip. They are always kind of very curious to know how much the other person is earning. If they are earning more than them, then they wonder why they are spending less than them and vice versa. People often get judgmental and think that they are better than others in many different ways. Another aspect of such a community is a kind of power struggle. This may sound strange but - its true. There are people who want to prove that "I am more efficient, I know more and I can lead a group better than others". Whatever talent they have or not they tend to display to the the unwilling audience. As a result of which it becomes totally chaotic. Nobody is really there to watch anyone!! All are either in back stage or preparing for the show.One thing I am yet to see is if they help each other in need. Such is the story dearies. If anyone knows anything different I would like to hear your story. Thanks for reading my article.
As time passes by and they settle in life they tend to have different types of social groups. These groups usually comprise of spouses and young children. The social gathering usually revolves around their kid's activity - occasionally around themselves. But still this group is kind of OK in terms of socializing.
Few more years passes, kids start going to school, the group dynamism changes slowly. The social activities still revolve around the kids but generally the adults really don't have any social contacts in any true sense. They have by now established themselves in some good jobs, started earning enough money, managed to have a house, started sending their kids to private schools. I have noticed that people(generally adults) in these groups know very little or nothing about each other. They have zero or negative attention span. When one person starts speaking in such a gathering, there are hardly any listeners. The people who are suppose to listen, may be already thinking what "I should be speaking" next instead of listening. They often snatch words from others mouth and drag the topic to something else.
One such group I am part of, where people have known each other for more than 10 years, but still don't know much about each other!! Either they are not interested or they have been focusing on themselves too much. While they tend to know somebody's weak point, but don't usually know their strengths. What are their specializations, what somebody is good at etc. For instance they don't know somebody's surname, where they are from, what are their background etc. I kind of get surprised when they gather around for so many hours together, what they talk? Some people talk politics, some talk about economy, and MANY about somebody's life style!! In Indian population abroad about 90% are there that compete with each other in prosperity contest!! Ladies generally look at what others are wearing, what jewelery somebody has. They tend to ape each other and get the things that will put them in the certain list in their next India trip. They are always kind of very curious to know how much the other person is earning. If they are earning more than them, then they wonder why they are spending less than them and vice versa. People often get judgmental and think that they are better than others in many different ways. Another aspect of such a community is a kind of power struggle. This may sound strange but - its true. There are people who want to prove that "I am more efficient, I know more and I can lead a group better than others". Whatever talent they have or not they tend to display to the the unwilling audience. As a result of which it becomes totally chaotic. Nobody is really there to watch anyone!! All are either in back stage or preparing for the show.One thing I am yet to see is if they help each other in need. Such is the story dearies. If anyone knows anything different I would like to hear your story. Thanks for reading my article.
Posted by
Sucheta Tripathy PI @ Computational Genomics Group at IICB, Kolkata
at
7:51 AM
No comments:


Subscribe to:
Posts (Atom)