A comic-strip rendition of the tale of the MMR vaccine controversy - a controversy sparked by the contentious claim that the MMR vaccine could result in autism.
From the Blog of Darryl Cunningham as posted on InkyCircus:
A comic-strip rendition of the tale of the MMR vaccine controversy - a controversy sparked by the contentious claim that the MMR vaccine could result in autism.
From the Blog of Darryl Cunningham as posted on InkyCircus:
Summer is here, and with it comes the persistent flow of relatives living abroad coming to stay at my place for a week or two. Some welcome, others not so much. Anyway, two of my cousins from Bahrain are currently here, and so I decided to take them to Café Zouk one night for dinner.
The menu came, and with it, my usual dilemma of picking a dish to order. Being an ardent lover of food, I sometimes wish I could just order a bit of everything and taste it all – a predisposition that is, however, frowned upon by most. Resigned, I began to read each description of the voluminous menu carefully, trying to take in every detail, each little flavor. The catch however is this: even if one was theoretically capable of imagining tastes, one can never be too sure of the descriptions these restaurants put down in their menu – after all, they don’t say “Never trust the chef” in France for nothing. I found myself wishing there was some absolute database with strictly categorized data about each recipe, so that I could simply look up an appropriate dish by narrowing the criteria to certain ingredients, cooking method, etc. However, even that would be insufficient to select a good dish according to my liking.
Wouldn’t it be great to have your very own robotic taster? A machine that could be programmed with your personalized likes and dislikes. You could simply dab the ‘tongue’ of the robot with a small sample of the food, and it would immediately let you know whether or not you would like it or not. A LCD screen could display various emoticons (commonly used to show emotions in text messages) to indicate how much you would like the food. Or it could provide a comprehensive analysis of the food, giving details about probable ingredients used, cooking method, origin (whether the meal was a Mexican or Chinese recipe, for instance), and so on. Such a device would indeed be of enormous use to chefs and customers alike. Chefs could have a multitude of devices programmed to the tastes of random people, and then find out whether or not the food would appeal to their tastes. Customers could use it to maintain a database of dishes tried at each restaurant so far, and therefore remembering which ones they tried and didn’t like, so they don’t order them again.
Progress towards such a device has already started. In fact, an espresso taster has already been invented. See here to read an abstract for an article published in Analytical Chemistry entitled “When Machine Tastes Coffee: Instrumental Approach To Predict the Sensory Profile of Espresso Coffee”. Our sense of taste can be thought of as a quantifier of all ‘tastable’ chemicals. It is, of course, known that different regions on the tongue are sensitive to different tastes, which means that the taste buds in those regions are specialized. Our taste buds can detect the quantity of various chemicals in food, and this process can easily be replicated in a chemist’s lab, where we can take a sample of food and break it down into its constituent compounds, and detect even those that the tongue cannot. Which then begs the question: So What? Just having a list of long complicated chemical names for soy sauce will not reveal to the layman that it is soy sauce. As a response, a computer could utilize this large database, and detect any commonly used ingredients like ketchup, lemon juice, or even Worcestershire sauce, by comparing the list of found chemicals with an already existing database of all the chemicals in these ingredients.
However, that is still nowhere close to the concept of “tasting”. Tasting food is a different experience for each individual. One man’s meat is another man’s poison. That makes the concept of “universal tasting” not even considerable. However, one could program such a device with personalized likes and dislikes. This in itself is a conundrum. What defines ‘likes’ and ‘dislikes’? For example, I may abhor creamed spinach, but I would love it stir-fried in oyster sauce. I hate pineapple chicken, but love Chicken Tikka, but I would hate even that if there was a large amount of salt in it. Such criteria are very hard to specify to a computer, which follows hard and fast rules. However, even if this problem is not easy to solve, coming up with a reasonable approximation looks like an interesting problem to tackle.
While you do that, I think I’ll have the Thai Chicken Cashews. One of my personal favorites at Zouk and highly recommended! Bon appétit!
Ali Raza's essay on Chaos Theory and Lorentz Systems is now up in the Physics section of the Work tab. This is the third essay in the Physics section. Over the summer, we will become much more regular with our essays than we have been previously.
"...with Chaos Theory, we can find patterns in the randomness and noise and solve what seem like the simplest of problems but are exceedingly complicated. Chaos Theory could be the way out, the intuition which has gone missing from theoretical physics of late."
Navigate to here to read more. As always, comments on the essay are welcome on this post.
Who would have thought that oranges could contract malaria? Well. They can’t. However, there is a disease that has a transmission strategy fairly analogous to malaria in humans and which I like to think of as plant malaria – the disease is called Huanglongbing or to put it in easier terms, citrus greening. It is a bacterial disease that needs a vector for its transport.
What’s complicated about the disease is its detection and treatment. The glaring symptom is the inability for the fruit to change color from green to orange; other symptoms include clogged vessels, a sour taste, brown seeds etc. The symptoms may be confused with a mineral deficiency like the one caused by zinc for example, which does not allow the fruit to change color either. The organism that causes it is a bacterium belonging to a category of bacteria termed “candidatus” (from candidates, incidentally). What makes these bacteria complicated is the fact that they are obligate pathogens and cannot be isolated - i.e. they do not survive outside their hosts, thus making it difficult to study them and hence, finding a cure. So the only solution to the problem at hand is to cut the whole tree before it infects other trees. Its like malaria, pre-quinine discovery.
What makes the disease more dangerous is that it can spread rapidly if the vector is not controlled. To get rid of malaria we target mosquitoes. In much the same way, to save oranges from citrus greening we target the vector which in this case is an insect called Asiatic citrus psyllid. The vector has natural enemies in wasps and ladybird beetles that lay eggs on top of the psyllid eggs by rupturing them so that once their babies hatch they can use psyllid eggs for food. Since the similarities are irrefutable, citrus greening might as well be called citrus malaria.
Research revealing the link between citrus greening and the psyllid was carried out by Dr. Shahid Chohan at the Department of Biosciences at the COMSATS Institute of Information Technology.
270.12, 271.225, 271.226
I put the book back into its place, as I droned on with my work hours, only to realize it was one from a set of ten. A look at the book followed by a simple glance at the shelf would've given away its place. I guess that is the difference between me and Benoit Mandelbrot.
Mandelbrot expected symmetry and similarity, not formulas and equations, to provide answers. At school he would solve math questions by imagining the equations as shapes and would solve them by folding and manipulating them. Of course, as the equations grew more complicated this came up short but he never stopped believing that the small could be analyzed by visualizing the whole. Much along the lines of medieval science.
In the eighteenth century, people believed that small things were merely scaled-down versions of bigger ones. For example when sperm was discovered, science thought it was a small man swimming around. If we zoomed in or zoomed out the world would look more or less the same. Of course, now with our microscopes and telescopes we know better. The sperm is very different from a small man and perhaps more interesting. Atoms are not made of smaller atoms which are made of even smaller atoms, but protons and neutrons which are in turn made of a wide variety of quarks - each with its own unique properties. And so, to describe everything at its own specific scale we came up with equations and formulas to identify these unique objects. Much like the unique identification number on my book. But Mandelbrot never liked equations. He believed in visualising the whole, in geometry and symmetry.
A biologist may say arteries, arterioles and capillaries are entirely different things. An economist might say that the day to day fluctuations give no insight into year-long or ten-year trends. Yet Mandelbrot trained himself to see 'self-symmetry'. Self symmetry describes vaguely similar trends that we choose to ignore, saying that they are, in fact, different systems governed by different laws. And out of this symmetry arose fractal geometry: 'Mandlebrot coined the word fractal himself'.
A new math. The math of nature. A math that described the jagged shape of coastlines. That predicted the patterns of trees, leaves, lightning and erratic consumer behaviour. Fractal geometry describes most chaotic systems to a great detail. No more assuming that the cow is spherical. No more saying biological systems have far too many complexities to be governed by simple math formulae.
According to this article on the Secrets of Longevity in Humans: "Fractal Biology is the Physics of how everything made by nature, including the human body, is a cascade of patterns within patterns that go on for infinity down to (and past) the molecular level. This results in extremely complex organisms which must be studied as a functioning whole and can never be fully understood through being broken down into smaller parts. Once one "level" of Biology is understood, the next "level" down is many multiples more complex, and then the next is multiples of that making it literally impossible to ever fully understand an organism."
And even while the natural system becomes ever more complex, the mathematical function that brought on the complexity found in trees, nervous and circulatory systems, remains uncannily simple. It's the repeated application that gives rise to the complex phenomenon.
From Scientific American as posted at filter blog 3QuarksDaily:
Princeton University's fourth annual "Art of Science" exhibition features scientific imagery focused on the theme of energy.
Princeton graduate student David Nagib's energy-saving chemical apparatus, titled 'Therapeutic Illumination,' won the $154.51 second prize in the 2010 Art of Science competition. The device mimics the process of photosynthesis in order to manufacture medicines and other important molecules. 'Our submission depicts our experimental investigations employing an energy-saving compact fluorescent light bulb to excite a variety of colored photocatalysts,' Nagib says.
Wafa Veljee's Mathematical Biology-inspired article on the differential equations which can be used to model the love between Romeo and Juliet, or any two other arbitrary entities, is now up in the new Mathematics section of the Work tab.
"Friendly advice from a Math major with a non-existent love life: here we ask you to disregard all the movie dialogues which imply that love increases every day. Love might increase everyday but it will probably give rise to an unstable fixed point. An unstable fixed point is like a hill-top..."
Navigate to here to read more. Since there is no comment option in the Work section, comments are welcome on this post.
The next addition to the Work section is Ali Raza's essay on Chaos Theory and Lorentz Systems. It will go up in the Physics tab very soon.
In this post, I’m going to bypass the whole argument of whether evolution is a myth or a reality and just take Darwin’s word for it. Not that I’m in hundred percent agreement with what Darwin had to say, but looking at the theory and what a number of people have to say about it, it does raise some interesting issues.
Darwin’s greatest achievement was not only to give a comprehensive view of the evolutionary process but also a plausible explanation of how it could have happened. He suggested that natural selection was the most important cause of evolution. However, he did not leave out the possibility that there might be other factors contributing to it. What is even more remarkable is that he suggested all of this without knowing anything about the processes of variation and heredity - Mendel only worked out the details later. Variation and heredity are two basic foundations of natural selection and explain perfectly some of the points Darwin had to make.
Darwin’s idea was radical. His theory suggests that evolution is just a natural process and according to one of his earliest critics, Robert Beverly MacKenzie, Darwin is implying that “In order to make a perfect and beautiful machine, it is not requisite to know how to make it.”
Darwin said that evolution by natural selection is an adaptive process or similarly adaptation is a mark of natural selection. Now, we know adaptation to be a quick process. According to Vidyanand Nanjundiah in "The Origin of Species after 150 years - one hundred and fifty years without Darwin are enough" (the phrase "One hundred years without Darwin are enough" was first proclaimed by the Nobel Laureate H. J. Muller in 1959):
“Crucially, natural selection works from one generation to the next: it deals with the short term. When one looks back over a great many generations, successive adaptations are seen to have accumulated and given rise to a major transformation, to what looks like a product of design .But the design is unintended, without purpose. There is no way in which evolution can plan for the future.”
This is because what trait is selected for depends on the organism’s environment. The environment not only includes its physical surroundings but also other individuals, species and populations it might be interacting with. Thus evolution is not an isolated process, it depends on selection pressures (the environment) and chance (Suppose if a certain proportion of the population moves to some new area. In this case only a limited gene pool which is isolated from the rest of the population will evolve separately. In another instance some natural disaster might cause only a certain portion of the population to survive, again limiting the gene pool. This is called genetic drift. Chance can also be explained by variation: many mutations that occur are neutral, that is, they neither confer an advantage nor disadvantage to the organism, so they must evolve independent of the environment). So, what we can conclude is that organisms and species are not necessarily evolving for the better. They are ‘just’ evolving, since evolution is a continuous process. Nanjundiah quotes the palaeontologist Van Valen:
“This implies that as a species evolves, it does not improve itself in any absolute sense. If it does not go extinct (which has been the fate of the vast majority of all species (yet another piece of evidence against betterment), the best it can do is to keep up with all the other species. He sums up the situation in the words of the Red Queen: “It takes all the running you can do, to keep in the same place" (Lewis Carroll, in Through the Looking Glass).”
Keeping all this in mind, now variation and heredity can explain how evolution can take place without foresight. Another of Darwin’s amazing ideas (without knowing the actual process) was that variation and heredity act independently of each other. Variations are the mutations that take place in an organism and they happen for a number of reasons. However, which chromosome goes to which gamete is completely independent of whether it contains a mutation or not. Again which gamete fertilizes with which one is also due to chance.
So what is the future of evolution? The agents of evolution (natural forces) are acting today as they have been acting since the beginning. However, there is a major change in the landscape of today: the appearance of humans. Human beings have become the foremost driving force of change on this planet, thus changing the environment and affecting evolution. The evolution of humans far exceeds that of any other animal, making us a dominant force. According to Nanjundiah:
“It is generally believed that along with the development of culture, natural selection has slowed down or become insignificant in humans. Instead, cultural evolution, which unlike biological evolution is largely Lamarckian, is said to have taken over.”
Lamarckian evolution is the idea that acquired characteristics can be transferred to the offspring. One of the most singular ability of humans is language, or at least the myriad complex ways of communication that have been established. The advances in science and knowledge have also given humans powers beyond any other life form on Earth. According to Daniel Dennet who is the Professor and Director of the Centre of Cognitive Studies at the Tufts University, Medford, Massachusetts, “Now, for the first time in its billion of years of history, our planet is protected by far-seeing sentinels, able to anticipate danger from the distant future – an asteroid on a collision course, or global warming – and devise schemes of doing something about it. The planet has finally grown its own nervous system: us. We are responsible for the future of life on the planet, in a way no other species could ever be.”
A most striking observation can be made from the above paragraph, not only have organisms and species been evolving over time, but Earth, as a planet has been evolving with them. With humans as its nervous system, it’s still a question whether we’re making way for the better or will just end up being an auto-immune disease?
Okay so I know that a post on Ramchandran Plots has already been done. For those of you that have forgotten: peptide bonds are essentially planar, a typical amino acid has freedom of rotation about two of its bonds; that between the alpha carbon and the amino group and the bond between the alpha carbon and the carbonyl group. A Ramachandran Plot is a two dimensional diagram of the allowed values of these angles. Those of you who want to know more can scroll back through the blog posts.
The fact is that for any given chain of amino acids, a lot of three dimensional conformations are possible. which begs the question: why is a particular arrangement favored over others? Let's assume for now that the answer lies in energy and that the least energy conformation is the most stable and hence the most favorable. One way of studying protein folding (and hence stability) is to denature the protein, then remove the denaturing agent and monitoring its refolding in vitro. Those interested can look up Anfinsen's ground breaking study (click here) in this area for which he was awarded the Nobel prize in Chemistry in 1972.
However, if we are looking at protein folding in the context of energy then we can't disregard entropy because in the equilibrium between a large number of possible (and random) conformations and one particular conformation there is a strong thermodynamic push for the protein to stay in the former. How is it then that biological polymers can assume well defined and consistent structures? In actuality, flexible polymers with a large number of possible conformations do not spontaneously fold into a particular well defined structure.
And that's where the Ramachandran Plot comes in once again. A lot of arrangements are disallowed merely on the basis of stearic clashes or in the words of Stryer and co. (our Biochemistry text): 'The rigidity of the peptide unit and the restricted set of allowed psi and phi angles limits the number of structures accessible to the unfolded form sufficiently to allow protein folding to occur.'
So there you go folks: I don't know if you had the same 'Uh DUH' moment that I did upon finding this out but its zero-one so far in the organization vs. entropy death match with the REAL winner being Nature, Mother Earth, Gaia, the Big Poobah in the Sky or Captain Planet, whatever you want to call it. Does the answer seem too simple? That's because we haven't really explored the complexities of the question. Until next time...
And because that's enough science for now and we can't have a post without a picture, I present to you:
One Hrithik Roshan looking creepy and spider-like (possibly in a Pepsi ad). Because really what is a blog without an arachnid person on it? Or shameless peddling of products? Enjoy!
Anybody who knows me every remotely knows about my fascination with Jazz. I consume it voraciously - from the haunting tale of racial brutality in Billie Holliday's "Strange Fruit", the background male chorus set to the musings of Ella Fitzgerald in "I Lost My Yellow Basket", to the vigorous trumpeting of Miles Davis, and even the contemporary revamps of Rihanna by Jamie Cullum. Anybody who knows Jazz even remotely understands that its historical connection to ongoing political change is deeply engrained - not just the racial tensions in Strange Fruit but perhaps even its effect on questions concerning the fate of science in schools.
The Jazz Age of the 1920's was associated, among other things, with moral and ethical degradation in American society by the fundamentalist Bible Belt - much like the '60s hippies, the lifestyle just seemed so shocking to the regular young person's stiff parents. In 1925, a man named John Washington Butler, no doubt influenced by what he felt must qualify as degeneracy, framed the Butler Act in Tennessee because his children returned from school to tell him that the Bible was nothing but hogwash. The subsequent law made it a crime to teach that 'man had descended from a lower order of animals'. Evolution was under threat - the stage had almost imperceptibly and suddenly been set by the Butler Act and the movement of William Jennings Bryan, for a fierce debate in schools across the United States sparked by a wider struggle in society over the maintenance of traditional values and mores.
This debate (the evolution one, not the one where Jazz is awesome) is especially interesting for us biologists given its sensitivity inside and outside the lecture hall. Needless to say, in today's United States, creationists can no longer hope to push forward a law that challenges the teaching of what is largely agreed upon across the board in science, but the evolution (pun intended) of the debate is interesting: in 1925, John Scopes, a physics teacher for the local high school in a sleepy town called Dayton, happened to substitute for the biology teacher, and assigned a chapter on evolution to the students in the classroom. This resulted in an extremely high-profile case which, for most people, represented the aged struggle between religion and science with creationists represented by William Jennings Bryan and the evolutionists by a man named Clarence Darrow. The film and Broadway play, Inherit the Wind, tells the tale with dramatic flair (maybe even a tad too dramatic, felt Stephen Jay Gould according to whom the trial was certainly not the debate of free inquiry vs. dogmatism that it was depicted to be). Scopes was found guilty for violating the law (but not before Darrow famously forced Bryan to admit that creation may have lasted more than 24 hours - the Bible believes the Earth is only about ten thousand years old - for those of you who took Biochemistry, we beg to differ), but on a technicality, the decision was overturned and Scopes returned to the streets a free (thinker) man. The law was never repealed until 1968, when a certain Susan Epperson challenged the law on the basis that it obviously appealed to the Christian faith which of course violates the First Amendment.
The story is fascinating in its own right, as is the fact that the Scopes trial is commonly referred to as the Scopes Monkey Trial. The battle, however, continues. Stephen Jay Gould's essay Trouble in Our Own House tells about how creationists, having lost the battle in Tennessee, came back reinvigorated with a different aim under the umbrella term of creation science, intending this time to give equal time to the Biblical Genesis story in schools where evolution was taught.
One amusing anecdote of the trial challenging the law in Arkansas and Louisiana goes like this: a teacher was testifying about how he used a long piece of string to teach children about the origin of life. A long piece of string was strung from one side of the classroom to the other, and children were placed at variable points on the string to represent the extinction of dinosaurs, early man, the Ice Age and other such important landmarks. When asked how he would give equal time to a faith which believed the Earth was only ten thousand years old and that man was 'created' and placed on Earth, the teacher replied that he would need a much shorter piece of string. Cue raucous audience laughter. Stephen Jay Gould elucidates: "the image that had immediately popped into my mind - the thought of twenty earnest second-graders all scrunched up along one millimeter of string".
Science and religion for many people seem irreconcilable. The Scopes trial, of course, represented but one milestone in the teaching of science which seemed so contrary to publically-held religious beliefs, but it by no means was the last frontier. We can, however, fight hard for the rights of those teachers who felt they had an conscionable duty to their students to teach the truth. We may wonder how such a law would change what was taught in the classroom - we don't, however, need to look much further than the summation Clarence Darrow gave at the trial in 1925 to find what we need to set the ball rolling:
If today you can take a thing like evolution and make it a crime to teach it in the public schools, tomorrow you can make it a crime to teach it in the private schools and next year you can make it a crime to teach it to the hustings or in the church. At the next session you may ban books and newspapers...Ignorance and fanaticism are ever busy and need feeding. Always feeding and gloating for more. Today it is the public school teachers; tomorrow the private. The next day the preachers and the lecturers, the magazines, the books, the newspapers. After a while, Your Honor, it is the setting of man against man and creed against creed until with flying banners and beating drums we are marching backwards to the glorious ages of the sixteenth century when bigots lighted fagots to burn the men who dared to bring any intelligence and enlightenment and culture to the human mind.
The story is instructive, however. Consider for one moment what would happen to the state of education in our madrassahs if science was replaced by something pretending. Considered? Now you may break out the Louis Armstrong CD's.
The Box Move blog is no longer active since the founding team has graduated. The archives will remain online.
The SPROJ Forum for the SSE 2012 batch. Discuss potential Senior Projects here.
Brain Talk is an online resource and forum for all things Psychology and Neuroscience.
MUSIC FOR GEEKS:
Featured: Art Tatum Three Letter Word
ON THE FRINGE:
The story of a how a YouTube video of a blind man biking down a mountain inspired good non-fiction writing on echolocation. You may find it useful for your own writing. Read here.
An awful waste of space?
Amidst NASA's budgetary cuts and scientists' renewed vigor in justifying Space Programs, it is important to shed some light on the background. Click here for a succinct overview of the Search for Extra-Terrestrial Intelligence(SETI) project.
Manto ka Muqaddama
Pakistaniat.com publishes, on the anniversary of Saadat Hasan Manto's death, a sampling of his works, a tribute to him as well as articles chronicling the obscenity trial he was tried for. Read all three parts of the series here.
Not Another 2010 List
The folks over at The Last Word put up their list for the best non-fiction in the past year, including 'The Mind's Eye' which is very hard to find in bookstores, indeed! Read the full list here.
Leslie Kaufman at The New York Times tells us exactly why those birds flying above are dropping to their deaths. Click here to read the article.
Spontaneous Solar Growth!
Reported at MadScience, scientists at MIT have found a way to create solar cells that can regenerate themselves like living organisms. Read more here.
Lessons from Chernobyl
Decades after the radiation disaster at Chernobyl, scientists elucidate how plant life has been thriving in the highly radioactive environment. Read more here.
MIT Scientists revisit Galileo's famous inclined plane experiment, this time with polymer ribbons and discover complex results. Read here.
A Lifetime, Washed Away
Pakistani author Daniyal Mueenuddin writes in the NY Times about the aftermath of the flood and displaced people. Read more here of the article posted by 3QD.
On String theory and Materials Science
Click here to find out how physicists at MIT are using ideas of gauge/gravity duality to explain properties of superconductors.
That's why you're irrational!
Newsweek's Sharon Begley provides a fascinating argument for why evolution may favor irrationality. I particularly liked the examples she picked. Read here.
Just when you wanted a gene kit
The US Food and Drug Administration held hearings n the 19th and 20th of July to talk about the validity of tests which were sold directly to the public which gives consumers direct access to to their genomes. Should it be regulated? Read more here.
On Trees and Prisons
In a 6 minute talk on Ted.com, Nalini Nadkarni (shown above) talks about her ideas of incorporating conservation into prison programs. Watch the talk and read Nadkarni's fascinating biography here.
These Lungs are made in USA
Stem Cell Biology takes huge leaps forward with the new advances made in lung transplants based on using the lungs extracellular architecture. Read more from Nature here.
Economist Special Reports
Ten years after Craig Venter revealed the first working draft of the entire Human Genome, this special report demonstrates how Biology is now at the brink of something brilliant - just recently, the draft of the entire genome of the Neanderthal was revealed. Suck on that, sceptics!
Bobby Satcher, astronaut, the first orthopedic surgeon in space. Read all about his tales here on MITnews.
Craig Venter Creations
Researchers create world's first fully synthetic self replicating, living cell. Massive fuss about limitless monster potential possible. Read the NewScientist article here. Watch the Ted.com talk by Craig Venter here.