A picture of Newton's telescope.
You can find the link to the documentary here ... PBS link.
It is also available on Netflix Instant.
Friday, September 21, 2012
Monday, September 17, 2012
I would recommend visiting just for this one exhibition.
Soul Kitchen
Saturday, April 21, 2012
My current view on working in biology - post in progress
The question of what is biophysics, physical biology, theoretical biology or just "a physicist in biology" is one that comes up when my colleagues and I are taking some time away from working on a particular problem. I am of the opinion that while we are working on a particular problem we tend not to concern ourselves with these manner of questions. My intellectual superiors appear to be from a school of thought where one is guided by a subtle and unspoken combination of intuition and pragmatism while solving a problem. I rarely see them consciously going down a path that they believe will reveal deep insights into biology of the kind that some people believe that we have in the physical sciences. They solve problems and hope to learn as much as they can by focusing on one particular system at a time. What are they guided by?
Arguably the manner in which physics and biology have progressed in the last 200-300 years is very different. To say biology is a younger field is already assuming that biology has to catch up with physics, that its history will be the same as physics with a time delay. I don't know if this is true. While it is important to have direction it is also imperative that we look at new phenomena with new eyes and not impose the concepts and formalisms that we carry around to too great an extent. It is in attempting to tread this fine line between being inspired by our past successes in science while being open to new insights that is so exciting for many of my friends and myself.
It certainly is clear that within recent years the emphasis on quantitative biology with a slightly more theoretical emphasis (and I mean slight) is in vogue. But it isn't the first time biological work has been conducted by physicists. So what is this new revolution? I am not certain I can answer this question, but it appears that the last 30-40 years gave us unprecedented insights into the microscopics of biology. Our understanding and control of core genetic and cell biological processes is one of the first things that strikes the physicist that wanders into the wrong section of the library or Arxiv. While impressed, we are also struck by how different this feeling is when compared to our sense of awe that we feel when studying physics. One of my favorite quotes comes from Einstein: The eternal mystery of the world is its comprehensibility. I don't think anyone could claim to have this sense of mystery after sitting in on a developmental or cell biology course. And so, I believe that it is this that is driving us in the field. Atleast it is what is driving me. And to repeat, I do not believe that the sciences will repeat themselves. Indeed, it seems ridiculous since biological matter is made of physical matter. Our hope is to have new insight into very different kinds of questions. I will now outline a non-exhaustive list of a few that I think are exciting and worth pursuing.
That being said, and I think scientist trained as biologist recognize this fact as well, an emphasis on quantitative experiments is essential. One could recount several instances in history where great leaps forward in our understanding were a consequence of arduous quantitative experimentation. My perspecitve is again not historical. Being quantitative is the most straightforward way of communicating results and hence central to progress. Being quantitative is the most straightforward way of debunking an idea, or putting forth a new one.
How is information such as shape and size encoded in the pseudo digital and linear blue print of the genome? This is the subject that I work on currently. I spend my time thinking about how tissues pattern and mold themselves. This molding isn't an abstract concept. The embryo generates limbs, fingers, etc etc. and it does so by moving things around. As a physicist, in particular, a mechanician, I have some basic understanding of how to think about dynamics. The way an embryo does this is by regulating its force generating machinery, its cytoskeleton. Furthermore, while each cell receives "instruction" from its genetic map it must also incorporate information it is getting from its surroundings, other cells for example. A cell in isolation does something, and can do something, very different from closely packed cells. The blue print must endow the cell with an ability to incorporate all this information and execute a plan that molds a desired form. And so, my current goal is to understand the regulation of the cytoskeleton and the effects of cellular interactions that leads to changes in tissue shape and architecture based on an understanding of mechanics.
What kind of answer am I looking for? I believe this is an important question. When Newton was challenged that his universal law of gravitation failed to provide any reason as to its causal nature, his response was "it should suffice that I have told you how things move". Nonetheless, that question lingered and led to other breakthroughs in our understanding. Eventually I would like an understanding in terms of where, or how, spatial information, like shape, is encoded in the genome. Eventually I would like to understand how the biological blue print that we all carry around in every cell of our body knows to make a human and not a zebra, despite both of us being constructed from the same stuff. The question of design is fascinating to me.
Now for something completely different. While fossils provide evidence that life originated relatively soon after the formation of this planet we still have little understanding of what the "origin of life" involved? Said again, the questions of design and origin are still wide open an manifestly not downstream of the fundamental physical laws and models that we have for the "dead" stuff. I have no idea how to go about thinking about this. Indeed, I don't believe I have even succeeded in posing a question here. While it may seem like a cope out, I believe what will constitute an advance in our understanding here would be a precise scientific question that guides a line of research. That being said, I have by reservations. The question of the origin of life isn't based on an empirical fact. Its based on a very anthropomorphic idea that we are somehow different to dead things. I claim that this is not a scientific observation. I hope it is not interpreted as cowardice and a sign of defeat that I resort to Newton's response that it should suffice (atleast for now perhaps) to describe "how" life is. I certainly don't intend to dissolve this field, but I have little scientific evidence to base any optimism on.
Two other questions that stand out and perhaps ought to be directions of inquiry are related to neuroscience and evolution. I will focus on the former since I am not certain how to talk about the latter. One can again phrase the question of neuroscience in terms of information. Whether we talk about organisms with central nervous systems (brains) or not, it is apparent that behavioral and sensory computations are done within the nervous system. Other theorists might phrase their reasons for studying the nervous system differently, personally I would like to empirically understand how it works. If we were given a circuit that we knew nothing about we would go about probing it using voltmeters and other such devices. Eventually we might even have an understanding of what it is computing. Is it a CPU in a washing machine or a gps navigator? A similar, perhaps a little pedestrian, point of view will, I believe, lead to insights in neuroscience. This doesn't imply an advocacy for mapping out every neuron and every connection. It simply means to wed yourself to the question of figuring out how it works and not wedding yourself to a tool.
Do I believe that we will find fundamental principles? I don't know. Clearly we all aim to, and try to, work on systems that we believe will provide insight into a broad class of behaviours. Echoing Darwin, otherwise we might as well climb into a pit and start counting pebbles and recording their shapes and sizes. It is this strange blend of Aristotelian rationalism and Baconian empiricism that we must tread without resorting to dogmatism. We simply don't know whether some "deep" underlying principles will appear in the same way that they have in fundamental physics. Regardless, we can make progress. We can try to do science and reduce the number of facts that constitute an understanding of the world.
Arguably the manner in which physics and biology have progressed in the last 200-300 years is very different. To say biology is a younger field is already assuming that biology has to catch up with physics, that its history will be the same as physics with a time delay. I don't know if this is true. While it is important to have direction it is also imperative that we look at new phenomena with new eyes and not impose the concepts and formalisms that we carry around to too great an extent. It is in attempting to tread this fine line between being inspired by our past successes in science while being open to new insights that is so exciting for many of my friends and myself.
It certainly is clear that within recent years the emphasis on quantitative biology with a slightly more theoretical emphasis (and I mean slight) is in vogue. But it isn't the first time biological work has been conducted by physicists. So what is this new revolution? I am not certain I can answer this question, but it appears that the last 30-40 years gave us unprecedented insights into the microscopics of biology. Our understanding and control of core genetic and cell biological processes is one of the first things that strikes the physicist that wanders into the wrong section of the library or Arxiv. While impressed, we are also struck by how different this feeling is when compared to our sense of awe that we feel when studying physics. One of my favorite quotes comes from Einstein: The eternal mystery of the world is its comprehensibility. I don't think anyone could claim to have this sense of mystery after sitting in on a developmental or cell biology course. And so, I believe that it is this that is driving us in the field. Atleast it is what is driving me. And to repeat, I do not believe that the sciences will repeat themselves. Indeed, it seems ridiculous since biological matter is made of physical matter. Our hope is to have new insight into very different kinds of questions. I will now outline a non-exhaustive list of a few that I think are exciting and worth pursuing.
That being said, and I think scientist trained as biologist recognize this fact as well, an emphasis on quantitative experiments is essential. One could recount several instances in history where great leaps forward in our understanding were a consequence of arduous quantitative experimentation. My perspecitve is again not historical. Being quantitative is the most straightforward way of communicating results and hence central to progress. Being quantitative is the most straightforward way of debunking an idea, or putting forth a new one.
So what do I believe a theo
How is information such as shape and size encoded in the pseudo digital and linear blue print of the genome? This is the subject that I work on currently. I spend my time thinking about how tissues pattern and mold themselves. This molding isn't an abstract concept. The embryo generates limbs, fingers, etc etc. and it does so by moving things around. As a physicist, in particular, a mechanician, I have some basic understanding of how to think about dynamics. The way an embryo does this is by regulating its force generating machinery, its cytoskeleton. Furthermore, while each cell receives "instruction" from its genetic map it must also incorporate information it is getting from its surroundings, other cells for example. A cell in isolation does something, and can do something, very different from closely packed cells. The blue print must endow the cell with an ability to incorporate all this information and execute a plan that molds a desired form. And so, my current goal is to understand the regulation of the cytoskeleton and the effects of cellular interactions that leads to changes in tissue shape and architecture based on an understanding of mechanics.
What kind of answer am I looking for? I believe this is an important question. When Newton was challenged that his universal law of gravitation failed to provide any reason as to its causal nature, his response was "it should suffice that I have told you how things move". Nonetheless, that question lingered and led to other breakthroughs in our understanding. Eventually I would like an understanding in terms of where, or how, spatial information, like shape, is encoded in the genome. Eventually I would like to understand how the biological blue print that we all carry around in every cell of our body knows to make a human and not a zebra, despite both of us being constructed from the same stuff. The question of design is fascinating to me.
Now for something completely different. While fossils provide evidence that life originated relatively soon after the formation of this planet we still have little understanding of what the "origin of life" involved? Said again, the questions of design and origin are still wide open an manifestly not downstream of the fundamental physical laws and models that we have for the "dead" stuff. I have no idea how to go about thinking about this. Indeed, I don't believe I have even succeeded in posing a question here. While it may seem like a cope out, I believe what will constitute an advance in our understanding here would be a precise scientific question that guides a line of research. That being said, I have by reservations. The question of the origin of life isn't based on an empirical fact. Its based on a very anthropomorphic idea that we are somehow different to dead things. I claim that this is not a scientific observation. I hope it is not interpreted as cowardice and a sign of defeat that I resort to Newton's response that it should suffice (atleast for now perhaps) to describe "how" life is. I certainly don't intend to dissolve this field, but I have little scientific evidence to base any optimism on.
Two other questions that stand out and perhaps ought to be directions of inquiry are related to neuroscience and evolution. I will focus on the former since I am not certain how to talk about the latter. One can again phrase the question of neuroscience in terms of information. Whether we talk about organisms with central nervous systems (brains) or not, it is apparent that behavioral and sensory computations are done within the nervous system. Other theorists might phrase their reasons for studying the nervous system differently, personally I would like to empirically understand how it works. If we were given a circuit that we knew nothing about we would go about probing it using voltmeters and other such devices. Eventually we might even have an understanding of what it is computing. Is it a CPU in a washing machine or a gps navigator? A similar, perhaps a little pedestrian, point of view will, I believe, lead to insights in neuroscience. This doesn't imply an advocacy for mapping out every neuron and every connection. It simply means to wed yourself to the question of figuring out how it works and not wedding yourself to a tool.
Do I believe that we will find fundamental principles? I don't know. Clearly we all aim to, and try to, work on systems that we believe will provide insight into a broad class of behaviours. Echoing Darwin, otherwise we might as well climb into a pit and start counting pebbles and recording their shapes and sizes. It is this strange blend of Aristotelian rationalism and Baconian empiricism that we must tread without resorting to dogmatism. We simply don't know whether some "deep" underlying principles will appear in the same way that they have in fundamental physics. Regardless, we can make progress. We can try to do science and reduce the number of facts that constitute an understanding of the world.
Wednesday, March 28, 2012
Predictions
http://en.wikipedia.org/wiki/Discovery_of_Neptune
(this is a real picture of Neptune taken by Voyager)
Its been a long time since my last post...but what a way to return
http://io9.com/5894600/watch-a-series-of-seven-brilliant-lectures-by-richard-feynman
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