Friday, June 29, 2007

Survivor – Biochemistry lab

(My laptop is having some serious trouble, so there is a good chance it might die and I might not be able to blog at all for the next week. Hope I can save it).

I’m not big on reality TV shows, but over the years have caught an episode or two of the immensely popular Survivor shows, where a whole bunch of annoying people are left on a “deserted” island or something, and have to survive using the minimal tools they have, foraging for food and using their wits.

Well, I don’t know about deserted islands, but let us say I had to choose to be abandoned all alone somewhere. And that somewhere cannot have any other people in it, nor would there be any food, but I had to use the resources available, as well as knowledge of the environment to survive.

There is only one place I can think of where I think I’ll be able to do just fine. And that would be a well equipped biochemistry/biology lab.

No, the high-speed university internet connection is NOT the reason why I choose the lab to be abandoned in. And it isn’t because I’m a workaholic science geek, so I’d work myself out of boredom and to death. It is purely because just about everything you’d need to survive (and possibly even thrive, with only your lost sanity as collateral damage) is available in plenty in a well equipped biochemistry lab.

There are three things you need to survive. Water, shelter and food (in that order of importance). Throw in sanitation, and life is good.

Let’s start with water. There’s plenty of water in labs, since they can’t function without a steady supply. There are plenty of deionizers to further purify the water, so it will be absolutely free of any microbes and perfectly potable.

As far as shelter goes, labs aren’t too bad. Most of them have the temperatures set at a comfortable 25 degrees centigrade. Now, you might think that isn’t fair, but too many biochemists swear by assays and reactions at “room temperature” (read ~ 25 C), which means you cannot turn off the heat or air conditioning (as the case may be). If you did, I will argue that it isn’t a fully functional biochemistry lab any more. So, shelter is taken care of, and quite nicely.

Then there’s the other important factor; food. And surprisingly, biochemistry labs are fabulous sources of food, with spectacular choice. First, there is plenty of glucose, sucrose or sodium chloride (salt) in the chemical reagent shelf. So, emergency drips of glucose or saline is just no problem. But you cannot survive on salt and sugar alone, and the body would waste away too quickly. What you need are carbohydrates, proteins, minerals and vitamins.

No problem. The solution lies in the availability of plenty of media all around the lab. The richest (and nastiest) source of nutrition is probably Luria-Bertani (LB) broth, a potent mixture of yeast extract, tryptone (which is a specially formulated enzymatic digestion of a protein called casein) and salt. Yeast extract, like the name suggest, is obtained from yeast. It contains a whole bunch of proteins, vitamins and other components that yeast cells release when inactivated. A superbly rich food. Now, usually LB is used to grow bacteria but hey, if it is good for the bacteria, it probably is good for me.

But if that stuff seems too nasty, there’s always the option of using cell culture media. The various media are made of a precise balance of salts, minerals, vitamins, and proteins (from serum). Using this, various types of cells (even human cells) can grow quite well. So, this should provide plenty of nutritious food for growth (though it probably tastes terrible). To top it all, you could find most minerals and vitamins you need, which you can carefully titrate into your diet.

And then, if eating all of this gets too nasty, at least most labs are also very well stocked in powdered milk. Powdered milk is used almost daily to make a blocking solution which is widely used in numerous experiments (particularly in blocking membranes in Western Blots). So there’s always going to be something reasonably tasty, and evenings can be spent sipping warm milk with sugar. Oh yes, I forgot. Heating food wouldn’t be a problem at all, since there are plenty of microwaves or Bunsen burners around to do the job.

Sanitation isn’t too much of a problem either. There are plenty of autoclaves to sanitize (sterilize) anything you want. Washing isn’t a problem, since there is a steady supply of water, and soap is always around. But if the purist insists that soap isn’t essential for a biochemistry lab, so it shouldn’t be there, there is no problem at all. Soap can be easily made. Soap is usually a foamy combination of fatty acids, a polyol, a tiny amount of sodium hydroxide and water, and some saponification. So it shouldn’t be too hard to make those from some 12-20 carbon chain fatty acids, and all the other ingredients on the bench.

Life in science might be tough but hey, at least I can say I work in a place where I can be abandoned for days, and still come out alive and kicking.

Monday, June 25, 2007

A couple of quotable quotes

This one deserves to be engraved somewhere prominent:

"If something is fun, as someone else said, it is either immoral, expensive or fattening"

(P.G. Wodehouse in "The girl in blue")


This one cannot ever be erazed from my memory.

"How does a black buffalo eat green grass, have red blood and yet give white milk? That pa is the wonder of god"

(An old high school teacher of mine, and a constant source of rib-cracking amusement amongst us students).

Friday, June 22, 2007

What is pain?

In a previous post Curious cat asked what pain was. The question is simple, but the answer certainly is not. I vaguely recalled sitting through some pharmacology lectures on pain, so thought I could make a post out of it.

Except, when I started looking up what pain was I found out that the whole phenomenon of pain is far, far more complex than what I can bottle down in a single article. However, I think my reductionist and simplistic knowledge of pain might suffice in providing a broad, very general outline of pain, so here goes.

Our sensory system is complex, and pain is amongst our most complex senses. The sensory systems (smell, taste, feeling (and pain), sight) all evolved primarily to help the organism survive better, by locating food better or sensing enemies or predators better and so on. Pain is one of the most obvious warning systems the body has. When something hurts, your body immediately responds by trying to get away from the pain.
Pain is also differentiated into acute and chronic pain. Acute pain is sudden, and is limited to a short time. For example, a stubbed toe hurts, but the pain subsides as soon. Chronic pain though can last a long time, and is indicative of a more serious ailment which may not be obvious, but could be extremely damaging.

But how is pain actually perceived at a molecular level? There are numerous nerve fibers throughout the body that sense pain, and these nerve fibers transmit information to the spinal chord, which in turn relays the information to the brain. These nerve cell receptors, which are unspecialized nerve endings that actually initiate the sensing of pain, are called “nociceptors”. The nociceptors themselves form two or three major classes (depending on how you classify them). There are mechanosensitive nociceptors (which sense pressure), mechanothermal nociceptors (temperature and pressure) and polynodal nociceptors. The nociceptors themselves are made up of A-fiber nociceptors, which mediate that fast, prickly sensation of pain, or C-fiber nociceptors, which conduct pain more slowly, and are responsible for the throbbing or burning sensation of pain. Now, many sensory nerve endings respond to nonpainful mechanical or thermal stimuli, but nociceptors are designed only to respond to high levels of mechanical or thermal stress, which subsequently cause pain. The threshold of activation of these nociceptors is very high, and they don’t respond when say you are exposed to lukewarm water, or to cool temperatures (like in the post describing the receptor for cool temperatures).

At a more molecular level, these different types of nociceptors all express different classes of ion channels, which provide the molecular specificity for sensing different pain. To give a molecular idea of how pain is perceived through these different channels, I’ll use a very recent example from a paper in Nature. Here, researchers describe the role of a very specific channel called Nav1.8. This is a “voltage gated sodium channel” that excites the nociceptors under extreme cold. Ion channels are proteins that form pores across cell membranes, and then specifically allow certain ions across. By doing so, they can maintain an electrochemical or voltage gradient across either side of the membrane. By opening and closing, the ion channels allow specific ions across, and thus change the electrochemical gradient. This results in an electrical impulse. In a nerve cell (including these nociceptor cells), when this happens, the cell releases molecules called neurotransmitters at the end point of the nerve, called a synapse. These neurotransmitter molecules can then go across to the next nerve cell at the synapse, and then pass on the information to the next nerve cell, and finally the information reaches the brain and is processed.

So, coming back to Nav1.8, this is a channel specific for Sodium ions, and only allows sodium ions across. Now, different stimuli open different ion channels, and this particular channel, found in nociceptors, responds to extreme cold. When exposed to extreme cold (which will cause pain), these channels remain open, and pass this information on to the brain. When the researchers started work on this ion channel, it was not known what role it played in extreme cold perception. So, what they did was to knock-out this protein in mice (just like the other experiments in the previous post on cold). Normal mice, when kept on a cold plate (at zero degrees Centigrade) will hop about, lift their feet, and be extremely uncomfortable. But in the mice where this Nav1.8 protein was removed, they would be impervious to cold, and calmly stand and freeze.

Similarly, for different stimuli (which can cause pain), there remain different proteins that sense them, and relay the information to the brain, usually saying “ouch” in different ways. Because pain works through these specific receptors and neurotransmitters, drugs can be designed to block them (opiods, including opium and morphine, work by blocking these neurotransmitters), and so we can “treat” pain.

But pain is also perhaps the most subjective of all senses. The threshold for pain varies dramatically for different people. Some people can tolerate extreme pain, others can’t. This mental component of pain is far more complex (I hardly understand it fully, so cannot explain it well in this article), and a lot of pain is indeed purely from the mind. But given how important pain is to all of us, I think we’ll always remain interested in knowing how it happens.

Friday, June 15, 2007

A bibliophile’s dilemma

I don’t even remember when I fell in love with books.

I’m one of those people with an outrageous memory, and distinctly recall even my early childhood, and I remember (and have been told by my parents) that I was a fairly early reader. Some of my memories are associated with the houses I lived in, and with every house (including the house I lived in when I was around 3 or 4 years old, before moving to Malleshwaram in Bangalore for the next three years) there have been books associated with them. In kindergarden and firstgrade I had ploughed through Noddy, collections of other Enid Blyton stories with toys as major characters, and Dr. Seuss, which I found in the house of my first grade teacher, which was also the school for us 20 kids. I read my first Asterix comic in second grade, and am still amazed at the timelessness, richness and absolute brilliance of that series, which I reread constantly, and learn something new each time. I must have been one of the few kids in school who read the textbooks (particularly the History, Geography and English books) before each school year started, for fun. And the books kept piling on, blurring as they increased in number and diversity. I need to read a book, or a section of a book, just about every single day.

But this isn’t about books loved and read. It’s about being a bibliophile. Ever since I can remember, I actually loved the books themselves. I love holding books, I love the smell of old books, I love looking at books on bookshelves, I love placing my books on bookshelves, and arranging them in some kind of topical order. And then I’d go and rearrange the topically arranged books into sub-sections, tallest books closest to the end of the bookshelf. I hate creasing books, or using dog-ears to mark the page. I hate leaving a book open and upturned. Books are almost living creatures, to be cherished.

I almost feel like some kind of reborn librarian.

But this love for books can make life rather difficult. I cannot resist buying books. When I lived in Seattle, I would spend many hours in the numerous used bookstores all around campus, picking up little treasures while soaking up the smell of varnish, ink and paper. I spend hours on the internet looking at books on Amazon, from classic authors to personal favorites. “Why buy a book when you can borrow it from the library?” is a constant question. But that’s the whole point. A book isn’t complete unless it rests on your bookshelf.

Our present apartment is tiny, and there really isn’t too much place for bookshelves, even if they are 8 feet tall. The bookshelves in the living room are all groaning with the weight they have to bear, with misshapen shelves, books piled atop each other, and the distinct possibility of the entire units collapsing. But I cannot come around to taking out the books, putting them in a box, and then putting them away in a closet. Nor can I keep away from visiting the nearest half price bookstore, or buying more books.

Now, logic states that doing that would be the most efficient way to go about things. Space is at a premium. Clearly, I cannot read all the books all the time. If I read a book, it is unlikely that I will revisit it for months, or perhaps even years (unless it is a favorite constantly reached out for). Perhaps even never read it again. So, once I’ve read a book, it can be safely put away. Or it could even be sold, at a used bookstore or on Ebay or Amazon.

But nooooooo, I cannot do that. The book has to be on a bookshelf. I mean, dang it, the book deserves a home doesn’t it? A nice, respectable spot it can call it’s home? Living amongst kin?

If I argue with my wife about this (who very astutely and correctly points out that once read they can be stored away in boxes in a closet), I know my argument has no sound legs to stand on.

But on that rainy Sunday afternoon, when even the thought of TV detests me, I know I can always reach out and find a classic in my own collection that I haven’t read, or can reach out and discover something new in something old.

Or I could just rearrange all the books on the bookshelf, chronologically or alphabetically or by author or by subject, and at the end of it all stand triumphant, and glow with satisfaction.

Tuesday, June 12, 2007

A cold, cold feeling

Our sensory systems are incredibly fascinating. Readers of this blog might remember earlier posts on taste or smell or body temperature and longevity. Through our sensory systems we smell, see, hear, feel, and experience cold or heat. The Texas summer heat is beginning to get serious, so I thought it was high time for a “cool” post. Now, all of us experience feeling hot or cold, and thermosensing is an essential part of our own survival. But have you ever wondered how the body actually senses cold??

For many, many years researchers had hypothesized that the detection of temperature would occur through specialized protein sensors in the body, which would most likely be ion channels. Ion channels are proteins that form pores across cell membranes, and specifically allow ions to flow through them, thus controlling an electrochemical gradient. By doing so, the electrical gradients formed can control many biological processes, from vision to muscle contraction and your heartbeat. Vertebrate organisms have evolved numerous diverse ion channels, all with specific functions, in order to enable these diverse processes. Now, the specific channels that responded to hot or cold temperatures were largely unknown, and it was unclear what made a “sensory cell”.

Unknown, that is, until the so called TRP channels were discovered. The TRP (or transient receptor potential) channels were first discovered in fruit flies, where they played an important role in fruit fly vision. The TRP channels respond to a specific stimulus (different for each channel), which could be some molecule that (say) caused a sweet or sour taste, or sensed physical stress (touch), or bound a pheromone. When the TRP channel sensed this stimulus, it would open or close, and thus modify the movement of ions across the membrane. This electrical potential created would reach the brain and tell us what the stimulus was. While the first TRP channel was discovered in flies, it wasn’t long before dozens of genes (28, to be precise) encoding 28 different TRP channel proteins were found in mammals (from mice to men). Two important TRP channels (with respect to thermosensing) were TRPV1 and TRPV2, which were shown to be the sensors for capsaicin (hot peppers) or sense heat. Researchers immediately proposed that some similar TRP channel would be the primary sensor of cold.

About four years ago, a TRP receptor called the TRPM8 receptor was identified. This receptor was activated (and opened, to let ions through) in the presence of chemical cooling agents like menthol (which you love in your toothpaste, though it does absolutely nothing to clean your teeth). Some researchers immediately proposed that this protein was indeed the “cold sensor”, but many other researchers (with some supporting data) suggested that this receptor played only a minor role in sensing cold.

The issue has been more or less put to rest now, with some excellent work from David Julius’s lab, published in a recent issue of Nature (1). In order to see if TRPM8 was actually the sensor for cold, the researchers made knock-out mice for TRPM8, by introducing a stop-codon in the TRPM8 gene in the mice. By doing so, the gene no longer coded for a functional TRPM8 protein, and the researchers were able to verify that the mice carrying this mutation no longer had the TRPM8 protein in their sensory neurons. The next step was to show that the absence of this TRPM8 protein would make the mice insensitive to cold.

Proteins like TRP channels have a specific function that can not only be observed as an effect in an organism, but can actually be biochemically measured. Being ion channels, they allow the influx of specific ions (in this case calcium ions) that can be quantitatively measured in the specific cells that express the channel. So, the researchers used normal (or “wild type”) mice, as well as the mutant TRPM8 knock-out mice in their studies, and first removed specific sensory neurons from the mice. These neurons were then subjected to a battery of tests with capsaicin (for hot sensation) or menthol (for cold sensation). While the neurons from normal mice showed responses for both capsaicin and menthol (showing that the receptors for both these compounds were present and working), the mutant mice responded only to capcaisin (showing that removing this one protein, TRPM8 alone, was sufficient to prevent almost all electrochemical responses to menthol). Having clearly shown that TRPM8 caused the major response to menthol, they then decided to test if removing TRPM8 alone would be sufficient for the mice to no longer sensitively respond to cold temperatures.

In their next experiments, the researchers tested if the mutant mice themselves were compromised in their ability to sense the cold. In just one of their (many different) tests, they used normal mice or mutant mice, and placed them in a box where the floor had different properties at different ends. One end was kept at a normal temperature, while the other end was systematically cooled. The animals were allowed to explore both sides, and the time spent on either side was carefully measured. Normal mice preferred the side that was kept at 30 degrees centigrade. In sharp contrast, the mutant mice didn’t care on which side they were on, until the temperature dropped really low, to below 15 degrees centigrade. Also, the normal mice would always only cautiously explore the cold surface, while the mutant mice would confidently walk on the cold surface (not really knowing it was cold).

Collectively the studies have now shown definitively that just one single protein, TRPM8, plays the major role in sensing cold. Of course, at temperatures below 15 degrees, both normal and mutant mice largely behaved similarly, suggesting that there are more sensors for extreme cold. But the simplicity of the system for such complex regulation is strikingly elegant.

So, the next time you swish mouthwash in your mouth, feel that cool, cool sensation and wonder why it’s cooling, remember TRPM8.

Full reference: (1) Nature 2007; doi:10.1038/nature05910

Friday, June 08, 2007

Intuition, “common sense” and resistance to science

Sometimes, even if science has shown beyond most reasonable doubt that a certain thing is a certain way, it is extremely hard to believe it. This is because we think it goes against what we see, and “seeing is believing”, as the saying goes. I’ve often thought about this, and have come up with my own ideas on why this is so. But that’s hardly a scientific study.

I happened to come across this fascinating mini-review in Science (unfortunately, subscription is required to read the entire article) where the authors do go into details on the “childhood origins of adult resistance to science” (don’t worry, there’s nothing Freudian in that). The article starts with data from various polls, talking about human (in this case American) tendencies to disbelieve evolution or natural selection, and believe in unproven medical treatment, or ghosts or angels, astrology and divination. Now, I think almost all of us have, to varying degrees, some of these beliefs. But the implications of a population that is not just scientifically ignorant, but resistant to science (that goes against their belief) is significant.

The authors go on to extensively review studies from developmental psychology, and say why this resistance to many scientific ideas is universal. It all starts from what kids know, and what they learn. Kids, even babies, “know” a lot without being actively taught it. They know solid objects will fall to the ground, for example, or that people have different emotions. So, say that they know unsupported objects fall to the ground, it is difficult for them to actually comprehend that the world can be round. Things fall off round objects. At this stage, kids cannot comprehend the scale of the earth (and our own relative scale), or the concept of gravity. Apparently, it takes kids many years (around ages 8 or 9) to be able to accurately draw out the earth. In essence, people reject scientific ideas because it appears to be counter-intuitive.

A second level of resistance to science comes purely from cultural factors. Some information is specifically asserted or defined in each culture. For example, the resistance to understanding evolution is prominent in America, and particularly amongst certain groups of people. This is because it has been specifically asserted otherwise. Now, not everyone is qualified to study or understand some more advanced scientific concepts (the authors of this review give string theory as an example). So, it is typical for people to believe in what they are told by people they trust, which typically should be perceived experts in that field. This is what adults are expected to do. Interestingly but not surprisingly, many studies have shown that children do the exact same thing, and will believe things that are told to them by people they trust; parents, teachers, or peers. Importantly, when the data is conflicting (in their own minds), children will tend to believe people they trust, and not necessarily the data itself. (Sidetrack; I cannot remember the number of times I’ve told people something, to be completely disbelieved, till they went and found the exact same information in a textbook, journal or wikipedia. Why do some people distrust me?). Again, not surprisingly, most people who do not believe in something (say natural selection) really have no clue about it, and cannot explain the basic concepts of the thing they don’t believe in. So, their disbelief is not based on any objective evaluation of facts.

To quote the authors: “These developmental data suggest that resistance to science will arise in children when scientific claims clash with early emerging, intuitive expectations. This resistance will persist through adulthood if the scientific claims are contested within a society, and it will be especially strong if there is a nonscientific alternative that is rooted in common sense and championed by people who are thought of as reliable and

I’m reminded of this little incident some years ago, when I was flying to India. There was this elderly gentleman sitting next to me. He was a pastor from Kerala, with a PhD in theology. We talked about this and that, and then there was this little ad on the television screen. It was about some zoo, and (as is wholly appropriate in a zoo) there were monkeys and birds and animals and fish prancing around onscreen.

Out of nowhere, the gentleman said “just look at how beautiful and different they all are. And people say god didn’t make them but they evolved. How is it possible.

While I thought of a suitable reply, he added as an afterthought, with a shocked look on his face as he realized the consequences of his thought; “you don’t believe in that evolution stuff do you?

I half-thought about explaining how evolution works and why the earth is much, much older than his mind could fathom, but decided it was completely futile in this case, and that I had to sit next to him for the next 4 hours, so I just said yes, and left it at that.

But he was such a perfect example for this entire post.

Thursday, June 07, 2007

Tough luck...

Apologies for not posting over the past 4-5 days. I have some fascinating posts in my mind, but it is just a question of finding time to type them out, since work has been rather busy.

Here's a sob story from work. I painstakingly prepare some cells for a major experiment. Then I harvest them and lyse and suspend them in some sucrose solutions and load them onto an elaborate density gradient that I wanted. At nearly the end of the day, I put them into tubes and start the ultracentrifugation run.

I finish the run, open the centrifuge, and find that the *#&$^$ tube has cracked, and with it I've lost my sample.

There goes two days of work, and all I'm left with is a dirty centrifuge rotor which I have to clean out.

Hardly leaves me with time to blog, does it

Saturday, June 02, 2007

Marine reserves and national parks

The April 2007 issue of the National Geographic magazine had an extensive series about the looming problems of over fishing across the world, with fish “harvests” beginning to show extremely worrying trends. To people across the world following fishing trends, this isn’t new. The fishing industry of Newfoundland has been struggling for years, with plummeting yields. Fishermen across the world (particularly in Asia and Africa) now complain that they have to travel farther and into deeper waters to get any fish. The problems are complex, starting from trawlers that use massive nets, and just discard over 40% of their catch (which die in vain), keeping only lucrative species for commercial sale. The net result is that marine ecosystems across the world are facing severe strain from overfishing.

Now, we don’t think of fish as something that really needs to be protected. There aren’t any cute and cuddly panda-fish or tiger-fish or polar bear-fish that can act as iconic mascots of conservation. Yet, fish and seafood provide a substantial proportion of the protein intake of a major percentage of the world’s population, and determine the livelihood of millions of people. And though we don’t ever think about it, the health of the oceans will affect the health of the entire world (the oceans cover a major proportion of the world’s surface, and hold a majority of all life on the planet).

Anyway, coming back to the protection of fish, I first read about the concept of marine national parks in this issue of NG. And it looks like that little country down under, New Zealand, has taken the leadership role in protecting its marine ecosystems. More importantly, this is having substantial economic benefits as well.

New Zealand has almost all of the world’s ”no take” marine reserves. And by no take, it means that these reserves do not allow any fishing activity (commercial or recreational) what so ever. But what is the use of a marine reserve? It was hardly surprising that a lot of fishermen at first strongly opposed this idea, since they would have been denied fishing rights in that area. But the marine reserves have actually gone on to improve fishing beyond imagination.

Usually, fishing (particularly modern fishing) is extremely destructive to marine ecosystems. The most lucrative species are the larger fish (like tuna, shark, mackerel and the like), which are key predators on top of the food pyramid keeping the balance of that ecosystem. In their absence smaller fish and other creatures start to proliferate rapidly, some more so than others. This results in the eventual complete destruction of coral reefs and local marine ecosystems, finally leaving behind what I imagine a marine desert would be like. But what a marine park (which prevents all human activity) does is this: it acts as a central resource for the entire marine region beyond. In this protected area, fish breed without disturbance, and the complete ecosystem (from plankton to kelp to algae to crustaceans through fish and mammals) retains a balance. The “spillover” effect and larval export – where millions of eggs and larvae drift beyond the reserve and replenish neighboring areas– is massive. In effect the reserve serves as a replenishing ground for the entire area, and in the end the fishing industry all around benefits.

There are also obvious benefits to the recreational and tourism industry, and marine reserves in New Zealand have hundreds of thousands of visitors annually, providing a substantial economic benefit.

To think of marine reserves as the “libraries” of the sea, where all the life of the seas are showcased, preserved and promoted is a new concept. But it certainly is a new concept in the right direction, and one that will leave this planet in better shape for subsequent generations. Conservation, contrary to popular imagination, is not bad for economics, but in the long run is essential for economic well being.

(And while the George W. Bush government has been routinely criticized for severely damaging the parks and wildlife services and national parks across the country, Bush’s visionary designation of the Hawaiian Marine reserve, the world’s largest marine reserve, deserves all the praise it can get).