Interesting Science This Week. Week 7

In our modern liberal society, a great deal of effort has gone into eliminating the differences in how women are treated from men. In nature, however, male and female sexes have well defined roles in ensuring that perpetuation and evolution of life is not interrupted. Recently published research has indicated that the distinct biological roles of the two sexes also contributes to determining the lethality of infections by bacteria and viruses. It was well known that many bacterial and viral infections tend to be deadlier in men than in women. Men who are infected by TB causing bacteria, for example, are 1.5 times more likely to die due to infection than women. Similarly, many cancers are more likely to lead to death in men than in women. This difference in susceptibility to pathogenic infections among men and women was hypothesized to be due to the different sex hormones. However, in a recent paper published in the journal Nature Communications, researchers from Royal Holloway University of London have reported the results of their work that shows that the observed difference in lethality of bacterial or viral infections could be because it might be evolutionarily advantageous for the pathogen to keep the infected women alive. This, the researchers argue, is because women can transmit the pathogen to a wider population of hosts through pregnancy and nursing. To support their hypothesis, the scientists have examined the case of Human T-cell Lymphotorpic Virus Type-1 (HTLV-1) that causes Adult T-cell Leukemia (ATL), a type of blood cancer and is highly prevalent among Japanese and Caribbean populations. While the infection by HTLV-1 virus is equally lethal in both men and women in the Caribbean population, it is more lethal among Japanese men than women. The scientists have explained that this difference is because the Japanese women breastfeed for longer duration than Caribbean women. This incentivizes the virus to evolve such that they are less virulent in the body of Japanese women since that will help them survive longer. How the pathogen identifies the sex of its host is an interesting puzzle that needs to be unravelled through further research.   

*****************************************************************************

Bats are probably one of the most vilified animals in our popular culture, along with Owls. Every horror or thriller movie has atleast one scene starring these flying mammals. Usually these scenes feature a large number of bats rushing out of a cave or some such desolate space accompanied by a lot of noise just as one of the characters is trying to enter. A group of researchers from Israel have now come out with a study where they have tried to understand if there is any meaning and purpose to these sounds that the bats make.  The results of this study have recently been published in the journal Scientific reports. To conduct this study, the scientists collected a group of Egyptian fruit bats in a room and continuously recorded their sounds and actions for 75 days. They then used a computer program to analyze thousands of sounds and correlated them to actions from the video recordings. From these analyses, the researchers identified that most of the sounds that the bats made were not random but had a specific context in the everyday life of the animals. Not only did these sounds have a purpose, they were also directed at a specific member of the group. The bat sounds also had different intonations depending on the sex of the recipient of the sound. Most interestingly, the scientists discovered that more than 70% of the sounds that they analyzed could be attributed to just 4 different behavioural contexts - quarelling over food, bickering about the sleeping spot, raising alarm when another member of the group came too close to a bat  and a female protesting against the attempts of a male bat to have sex. Apart from contributing to the understanding of the social behaviour of the bats, this work has the potential of forming the foundation to explore the vocal communication among other animals. 

************************************************************************************

Do take a minute to leave your feedback in the comments; it helps me stay engaged 

And do remember to check back in next weekend; there will be more interesting science in this corner of the internet. 

Interesting Science This Week. Week-6

The basic idea of of immunization is to inject inactivated pathogens or their parts which then activates and prepares the body's immune system to fight infection by live pathogen in future. Development of innate immunity in the body involves production of specific proteins called antibodies which will identify the pathogen during an infection. After antibody binding to the pathogen, a group of proteins called the Complement system assists in further processing and eventual clearance of the pathogen from the body. 

Malaria is one of the deadliest diseases in the world inflicting greatest damage in the developing and under-developed countries. As per WHO, there were 214 million cases of malaria in 2015 resulting in 438,000 deaths. In India itself there were more than 1 million malaria cases and 287 deaths, according to the data available with National Vector Borne Disease Control Programme. In keeping with the seriousness of this disease, efforts have been going on for several years now to develop a vaccine against malaria. The efforts till now have been without much success because prospective vaccines that worked in blocking the parasite in laboratory conditions were not effective when tested in humans. But in recently published research, scientists seem to have identified the reason behind the failure of these vaccines in animal trials. It appears that the malaria pathogen, Plasmodium falciparum, exploits the immune response generated in response to the vaccine to further its infection. The pathogen uses the components of the complement system to enhance its ability to enter the red blood cells (RBC) inside which it replicates. The presence of antibodies in the blood only further enhances the exploitation of complement system by P.falciparum. It was further shown that complement deficiency in mice resulted in decreased efficacy of infection by the pathogen. These results are a very important observation that could inform the future design of strategies towards a successful development of anti-malaria vaccine.      

*************************************************************************************************

Most people know regular exercise is required for good physical health. What is less well known is that exercise also helps with mental health. Regular exercise helps keep the brain active, improve memory and learning and helps in dealing with conditions such as depression. One of the many factors which contributes to this effect of exercise on mental health is the increased production of a protein in brain called Brain Derived Neurotrophic Factor (BDNF) after exercise. BDNF is a growth factor required for growth, maturation and upkeep of nerve cells. This protein also actively participates in the formation and maintenance of connections between nerve cells (called Synapses) which are required for learning and long-term memory. How exercise contributes to increasing the synthesis of this protein was, however, not known. A group of American researchers have addressed this missing link between exercise and mental health in a recently published report. They found that in mice exercise resulted in increased production of beta-hydroxybutyrate, a metabolite produced in the liver when fatty acids are used as energy source instead of glucose. The beta-hydroxybutyrate that reaches brain through blood activates the DNA in brain cells that codes for BDNF to be translated into protein molecules which then help with improved brain function.

****************************************************************************************************  
The cells in our body can be divided into two types based on the number of sets of chromosomes they contain - diploid and haploid cells. Diploid cells contain two sets of chromosomes (each set contains 23 chromosomes) each derived from one of the parent. Most of the cells in our body are diploid. Only haploid cells in the body are the gametes (or the sex cells, sperm in males and egg or ova in females) that are involved in reproduction. These cells contain only one set of chromosomes. Scientists have been trying to grow these gametes in laboratories for a while now in order to better understand their biological development process. Sperms have already been cultured successfully in petridishes before. In a report published in the journal PNAS, scientists have now reported successfully growing a mature, functional ovum (egg) from mice in laboratory conditions. These lab cultured eggs, fertilized with sperm and implanted into surrogate mothers, lead to the birth of healthy mice. Apart from serving as a critical tool in studies to understand the development of ova, the technique reported in this publication can also be useful in future for treatment of female infertility. 

*******************************************************************************************************
There is a new map of brain. After more than 100 years since the publication of the first map in 1907 identifying different regions of brain to various functions, scientists have now published the new map where they have identified 97 new areas in addition to the 83 previously known using the data available from the Human Connectome Project. New York Times has published a report on this development (which you can find here). For the technically inclined, you can find the original paper published in the journal Nature here.

*****************************************************************************************************
Thanks for reading. Do take a minute to leave your feedback in the comments.

Interesting Science This Week. Week-5

Bacteria in your stomach is making you fat. That is the conclusion from a recent study published in the journal Nature. It is reported that the gut microbiome, a collective term for bacteria and other microbes that reside in the stomach of humans and other animals, could be responsible for the development of obesity in those constantly exposed to high fat diet. The researchers found that mice regularly fed on high fat diet showed an increase in the concentration of acetate in plasma, feces and brain. Acetate is a short-chain fatty acid produced as a result of digestion of fats. When the mice were either treated with antibiotics or were maintained in a sterile environment, they failed to produce increased acetate even with high fat diet which led the researchers to conclude that the acetate was produced by the action of gut bacteria. The acetate so produced by bacteria reaches the brain, possibly through blood, and induces the brain to send a signal to pancreas to increase the production insulin which in turn leads to fat accumulation and consequently to obesity. Acetate was also found to cause an increase in hunger hormone, ghrelin, which causes the animals to consume even more food, further exacerbating the obesity. It remains to be seen if these observations on the link between gut microbiota and obesity can be extrapolated to humans. But if these observations hold true in humans, it could pave way for further more drug-targets to fight obesity.

*******************************************************************************************************
There is some good news for those of us tortured by mosquito bites. Research has found a very effective method to keep those malaria carriers away; take a chicken along when going to bed. According to a recently published report, when scientists took a host census of malaria carrying mosquito Anopheles arabiensis, it was found that the insects fed on humans indoors and on cattle, goats, sheep etc. outdoors. But the mosquito totally avoided going anywhere near chickens. The researchers have identified 11 compounds from chicken feathers which when spread near a sleeping human were effective in keeping the mosquito away. Since it is going to take some time before the actual chicken mosquito-repellent is purified and marketed to general public, having some chicken companions in bedroom could, in the meanwhile, help you get a good night's sleep.

******************************************************************************************************
It was traditionally thought that brain was separated from immune system but recent studies have shown that immune system defects can effect learning and memory. In a recently published study the same research group has now shown that immune system could also have an effect on the social behavior of the animal. It was found that a molecule called interferon-gamma, which is normally produced as an immune response to infection by bacteria, virus and other pathogens, is crucial for social behavior. Blocking the production of this molecule in mice resulted in them becoming less social. The researchers also found that this molecule was produced by various organisms including flies, zebrafish, mice, rats etc. when they were social. 

******************************************************************************************************
In laboratory setting, a technique called electroporation is widely used to introduce DNA and other molecules into cells. In this technique, the cells are subjected to short electric pulses which causes formation of temporary perforations in the membrane surrounding the cell (called Plasma Membrane) through which DNA can enter the cell. The plasma membrane is eventually repaired and the perforations are sealed returning the cell to its normal health. The electroporation is also used in cancer therapy in conjunction with chemo-therapeutic drugs. It is observed that electroporation is more effective by being more damaging to malignant cells than normal cells. But the reason behind the efficacy of treatment strategies that include electroporation in specifically targeting malignant cells is not known. In a paper published in the Journal of Membrane Biology, data is presented that shows that the plasma membrane of cancer cells is resealed more slowly than normal cells following electroporation. This slow repair of plasma membrane ensures that drugs or DNA have more time in which to enter the cancerous cells than normal cells, increasing the efficacy of treatment.   

*******************************************************************************************************
Edit: Realized a little late. This is my 50th blogpost. Thank you all for the support. Keep reading. Do share your feedback in the comments.

Interesting Science This Week. Week-4

Have you ever been to a hospital for a health check-up and wondered, while the doctors and nurses were poking needles and probes all over your body, if there was an easy, less painful way to do things? Worry not, the science gods have answered your prayers. According to a recently published research report, the state of a person's health can be predicted from his/her facial features. For the study, a group of researchers from China looked at 3D scan images of the faces of more than 300 people (both male and female) in the 17 to 77 age range. For each age group and each gender, the scientists generated average 3D images of faces and from comparing their facial features such as eye slopes and nose width generated a map of changes in facial features with ageing. When the average 3D faces of a particular age group was compared to real faces, it was found that on average the chronological age of a person differed from their facial age by about 6 years. The most interesting finding in this study was that biological parameters such as the blood profile of a person coincided more with their facial age than the chronological age. What that means is that, you might be 50 years old but if the machinery inside your body resembles that of a 45 year old or of a 55 year old, it is going to show on your face. The face, it seems, is the mirror to not just the mind. 

******************************************************************************************************
Please do take a minute to leave your feedback in the comments.

Interesting Science This Week. Week-3

Every time one ventures to watch a movie in India now a days, you are subjected to the gory images of cancerous tissues, patients etc and are warned about the relation between use of tobacco and incidence of cancer. You are probably aware that cancer happens because of changes to the DNA in a cell which then goes berserk, looses all regulation and starts diving abnormally. The cancerous cells in a tissue eventually move out in a process called metastasis and spread to other parts of the body damaging the tissue there. This sequence of events is now pretty common knowledge. But have you heard of super-metastasis where the cancerous cells move out of one body and infect another? This is a rare process that has till now been discovered only in two animals where the cancerous cells are transmitted by bodily contact, either through bite (Tasmanian devil) or through sexual mating (dogs). But in a recently published report in the journal Nature, scientists have shown that the transmission of cancerous cells can happen even through water. This phenomenon was observed in a class of molluscs called Bivalves including mussels, cockles and golden carpet shell clams.

• Metzger et al., Nature, 2016. DOI: 10.1038/nature18599  

*********************************************************************

It's monsoon time in India and the puddles of water seen everywhere offer abundant breeding grounds for nature's master disease carriers, the mosquitoes. But what makes mosquitoes so efficient in being able to spread pathogens? The answer is, according to recent research findings, our own immune system. The most common reminder of having spent a good night futilely trying to fend off the mosquitoes are the red welts seen on the body next morning. The research suggests it is the inflammatory reaction resulting in these welts that aids the efficient spread of pathogens injected by the mosquito bite. The inflammatory response is due to a local reaction that serves to warn the body that skin, which is the first defensive barrier against infections, has been breached. This activates the body's immune response and leukocytes (also called white blood cells) are mobilized to the site of inflammation in order to contain the infection. Researchers have found that, the immune cells that reach the spot of mosquito bite themselves get inadvertently infected and contribute to rapid spread of infection to rest of the body. This hijacking of the immune cells by pathogens might be due to help from certain molecules present in the saliva of mosquitoes that get injected at the point of bite. This conclusion is based on the observation that injection of the same pathogen into the body with a needle did not produce an infection of comparable intensity as when injected by a mosquito bite. Researchers also suggest that the ability of mosquito bites to promote infections can be ameliorated by suppressing the initial inflammatory reaction. 

• Pingen et al., Immunity, 2016. DOI: 10.1016/j.immuni.2016.06.002 

 ************************************************************************************************

 There is a nice write-up published in Quanta Magazine detailing the research about a class of micro organisms called the Lithoautotrophs, or the rock-eaters, that survive by consuming only electrons as their source of energy. As such, these microbes can be described as "electricity-eaters".

• https://www.quantamagazine.org/20160621-electron-eating-microbes-found-in-odd-places/

 **************************************************************************************************

Please take a minute to leave your feedback in the comments. 

***************************************************************************************************

Interesting Science This Week. Week-2.

As kids we heard the story of a crow that strategizes by using pebbles to bring the level of water in a pot to the brim so it can drink. We have also heard parrots that were trained to speak like humans. For a very long time in human history, messenger pigeons served as the only reliable means of long distance communication. More recently, pigeons were shown to be almost as good as trained doctors in detecting cancer and scientists have made visual recording of the ability of crows to make hooked tools. Have you ever wondered how birds, with such small heads, can manage such feats that animals with much larger brains cannot accomplish? A group of scientists have now found the answer. In their recently publish work based on studying the brains of 28 species of birds, Seweryn OlKowicz and colleagues have found that the bird brains contain at least twice as many nerve cells (neurons) as a similarly sized mammalian brain and the nerve cells are packed at a much higher density. They also discovered that most of the extra neurons in birds are found in the forebrain responsible for learning, planning, etc. So much so that the number of neurons found in the forebrains of some of these birds was more than or comparable to those found in monkeys with much larger sized brains. 

• Olkowicz et al., PNAS, 2016, DOI:10.1073/pnas.1517131113
• Levenson et al., PLOS, 2015, DOI:10.1371/journal.pone.0141357
• Troscianko and Rutz, Biology Letters, 2015, DOI:10.1098/rsbl.2015.0777 

*****************************************************************************************
The red color of our blood is due to a complex protein called Hemoglobin that transports oxygen and carbondioxide between lungs and various tissues of the body. Hemoglobin is made up of 4 subunits each of which transports a oxygen molecule. Each Hemoglobin subunit in turn is made up of a protein chain that surrounds a non-proteinaceous part called Heme. Each Heme moiety consists of an iron ion (which is the part that actually binds oxygen) within an organic ring called Porphyrin. Heme is synthesized in the red blood cells in a multi-step process involving about 8 different enzymes. In people suffering from a group of rare genetic diseases called Porphyrias, there is an accumulation of porphyrin in the cells due to a defect at one or more steps in the Heme bio-synthetic pathway. People suffering from porphyria often develop irritation, burns or blisters in the skin upon even medium duration exposure to sunlight. In severe cases, porphyria can lead to even neurological disorders. Yet, there is currently no real cure for this condition. In a recent work published in the journal eLife, a group of scientists from United States and Canada have reported the discovery of a type of flatworm (Schmidtea mediterranea) that naturally accumulates porphyrin in its skin cells. These worms, which are naturally brown colored, lose their color and turn white when exposed to sunlight for a prolonged period of time due to cell death induced by accumulated porphyrin. It is also reported that the natural color of the worms is restored after returning to dark. Scientists expect that these worms could be used as model organisms to study the biological processes leading to the development of porphyria in humans as well as to analyze the efficacy of potential drugs that could be used in treatment of porphyrias. 

• Stubenhaus et al., eLife, 2016, DOI: 10.7554/eLife.14175 

************************************************************************

'Frogman of India' S.D.Biju is back in news. In a recent report published in the journal PeerJ, Dr. Biju and colleagues report the discovery of a new mating position in the frogs. They have made this report based on their work on Bombay Night Frogs (Nyctibatrachus humayuni), a type of frog that is endemic to the Western Ghats of south India. There were 6 different types of amplexus (mating positions) that were previously known among the amphibians; with the discovery of this position, called the Dorsal Straddle, the number increases to 7. The researchers also report the discovery of female mating calls in this species of frogs that is rare occurrence among the amphibians. 

• Willaert et al., PeerJ, 2016, DOI: 10.7717/peerj.2117 

***************************************************************************
Earlier this year we heard the first ever recording of the 'sound of the Universe' when the LIGO scientific collaboration unveiled the discovery of Gravitational Waves. Now the team has reported the discovery of second such event in an article published in Physics Review Letters. The signal was identified on 26th December 2015 and involved the collapse of two stars that are much smaller than the two involved in the first discovered event. While the two stars that collapsed to produce the gravitational waves during the event detected in September of last year were 36 and 29 times more massive than our own Sun, the two stars involved in this event were only 14 and 7.5 times more massive. 

• Abbott et al., PRL, 2016, DOI: 10.1103/PhysRevLett.116.241103

*********************************************************************************

Interesting Science This Week. Week - 1

Starting this week, I am planning on writing a recurring post every week. The objective of these posts will be describe some of the interesting research development that I had come across in the scientific literature during the course of that week to general public. While the intention is to explain the research in as simple language as possible, I do not intend to dumb it down to the extent that it is done in main stream media where one comes across reports that claim drinking red wine can prevent cancer or diabetes or stroke or heart-attack or whatever. Also it requires to be pointed out that these blog-posts will essentially be about research that I find interesting. So, the content will almost entirely be biology. Also considering the demand on my time, I will limit each posts to at the most 3 or 4 findings from that week and a brief summary in each case. I will attach relevant original research references for anyone interested in knowing more details. Here is the first week's post. 

*************************************************************************************

There are two types of tumors that are formed in the body. Benign tumors, as the name suggests, aren't generally dangerous. They are compact, grow slowly, tend to remain in the organ where they are formed and do not spread to other organs. Malignant tumors, on the other hand, are responsible for causing cancer in the body. The cell mass of these tumors is generally loose, grows uncontrollably and the cells tend to spread to other tissues where they cause the formation of more tumors. The process of tumor cells spreading to other organs is called metastasis. Metastatic cells of tumors, also stem-cell like cancer cells (SCLCCs) or tumor-repopulating cells (TRCs), tend to be softer and more deformable than the differentiated cells in the tumor. The TRCs are also more resistant to drugs than differentiated tumor cells which reduces the efficacy of chemotherapy and prevents complete elimination of cancer, often leading to relapse. In a recent paper published in the journal Cell Research, a procedure has been described that could potentially help in combating this drug resistance in TRCs. The researchers in this work produced microparticles packaged with anti-tumor drugs from tumor cells in which programmed cell death was induced. Microparticles are 0.1 - 1 micrometer size vesicles derived from the plasma membrane of induced cells (1 micrometer = 1/1000000 of a meter). In subsequent analysis it was found that these drug-packaged microparticles are able to selectively induce death in TRCs than differentiated tumor cells because of their greater deformability. Microparticle treatment was also able to prevent development of drug resistance. In clinical trials, treatment of cancer patients with these microparticles was able to eliminate the cancer cells in malignant fluids to a large extent providing hope for their future therapeutic utility in combating the drug resistance of SCLCCs. 

1. Ma et. al., Cell Research (2016) 26:713–727. doi:10.1038/cr.2016.53

***********************************************************************************

Please do let me know your thoughts in the comments. It actually encourages me to know that people actually read the stuff that I put out. 

Gene editing can now change an entire species -- forever | Jennifer Kahn

Lasker Award 2014

The names of the recipients of the Albert Lasker Basic Medical Research award for the year 2014 have been announced. This year's award is in recognition of the work done by Peter Walter and Kazutoshi Mori to uncover the process of Unfolded Protein Response (UPR) in the Endoplasmic Reticulum (ER).

1. Short talk by Peter Walter about the UPR at iBiology 
2. Award announcement . Also has links to videos about the work and description of the work.  
3. Home page of Lasker Foundation has the information about the other biomedical awards announced for this year. 

Talking about Talks

In popular culture, the stereotype of a scientist is that of an introvert and a recluse. I do not know if this is based on the observation of real life lab-rats or its the product of a writer's imagination. Either way, it has come to be accepted by the larger populace outside the academic world. But, from looking at my own colleagues and the wider research fraternity, this stereotype is as bad as every New York cab driver being an Indian. The fact is that the reclusive, loner scientist is probably an endangered species being driven to the brink of extinction by a growing culture of academic cliques and the increasing prominence of collaborative research. It is now important that you network with the right people, employ the appropriate jargon and attend the popular conferences. The funding agencies and grants' review committees tend to be more sympathetic towards projects with an inter-disciplinary character which might require that you need to have at least a working relation with folks who have an entirely different way of looking at a problem. Then there are the hiring committees that ensure that you humour and stay in touch with every supervisor and every committee member that you had ever worked with, so that you can furnish some 10 or 15 reference letters with your application. So, in this new and improved (?) world of academic research, being good at communication is as important (if not more) as knowing science. And one of the most important means of scientific communication is to talk about your work. You give talks at lab meeting, at departmental seminars, at student/post-doc association meetings, at conferences, at job interviews, etc etc etc. Considering that giving talks is such an important, and frequent, part of an academic's life, its a real surprise that many researchers are not good at it. 
As a graduate student, I worked at an isolated, multi-disciplinary research centre and had very few opportunities to listen to talks from external researchers. But when I started my first postdoc position at a medical college in the Tri-Institution area of New York, it was like going from being starved to being obese; there was at least one (but usually more) talk every week. I have attended talks by some of the best researchers, working on almost every possible problem in life sciences, sitting in the same room with Nobel laureates, sometimes more than one (as a grad student, I remember going to a seminar by Sydney Brenner and being so overwhelmed at seeing a Nobel laureate that I didn't hear anything he spoke). Now, as a postdoc at a conventional university with all the different faculties ranging from humanities to engineering, I get to attend talks on such variety of topics from the effects of Indian residential schools to monitoring bike traffic to develop a better signalling system. Of the hundreds of  talks that I might have attended, there are only a handful that really had my attention throughout. But this is in no way a comment on the quality or novelty of the work discussed but on the style of presentation. Recently, there was a "job seminar" in the department (I really look forward to attending those as an opportunity to collect tips for my own performance when the time comes). I was a little extra interested since the candidate had an Indian name, was from Harvard and had done some excellent work. But during the seminar, she looked nervous and overwhelmed by the occasion and overall the performance was a let down. On another occasion, the candidate's talk was so monotonous and understated that it was really hard to feel the excitement of the work. Recently, there was another seminar by a very senior scientist. Again the work was excellent but for some reason, the presenter tried hard to avoid eye contact with the audience; most of the time he looked at some empty space towards the end of the seminar hall. Good writing or talking may not make up for bad work, but bad writing or talking can certainly let down some really good work. That was the lesson I learnt from that experience. Whenever I myself give a seminar on my work, I try to keep the presentation the way I like to hear; informal, without too much jargon, assuming no one knows anything about my work and overall having the feel of a conversation rather than a sermon. My first real research presentation was during the first meeting of my doctoral committee. I had made what I thought was a bunch of good powerpoint slides, reviewing a lot of literature on the Gap Junctions (a lot of which I only barely understood then) and describing the plans for my PhD project. In my mind, I had a clear picture of how I was going to talk and explain my project. But I was so nervous that as soon as I was asked to talk, I could not recognize anything from the presentation I myself had prepared.  At the end of that disastrous presentation, my supervisor gave me an advice that I still use while preparing for a seminar to this day. Preparing for a talk is not about making powerpoint slides. Its about planning what you are going to say about each figure on each slide. A good way to do that is to write down or type down exactly what you are going to speak about each slide. This helps to keep the talk compact by staying focussed and to stay away from rambling about aimlessly. The one mantra that has served me well through the many academic talks all these years is that "good talks are well practiced talks". 

Update (5:10PM 16 June 2014):

Wanted to add a quick note. Whether the science in your talk is good or not, whether your presentation is good or not, it is always important to watch your manners. I had once attended a workshop at IISc, Bangalore. Most of us  participating were grad students. One of the workshop speakers was a young professor from JNCASR, Bangalore. During the seminar, while he was still talking, raised his leg onto a desk, placed his foot facing the audience and started tying his shoe lace. I do not know if he was in some unbearable discomfort that he needed to retie his shoe laces then and there. But I thought that was improper and extremely arrogant behavior from someone who at least at that time was like a teacher for us. 

"THAT" moment

I have read this somewhere but don't really remember where. That the greatest motivation for a scientist and the reward they work for is the experience of that one night when he (or she) alone knows a particular secret hidden in the nature's treasure trove before they reveal it to the rest of the world next morning. It is to experience that feeling of discovery that we slog day and night. I have heard people talk of it in research pep talks. I've wanted to experience it and have been waiting for it ever since I started doing research. Through years of being a grad student and a postdoc; and I started my PhD in 2004. I call it the eureka moment. That moment when you see something in your experiments that you hadn't expected when you started. A pleasant surprise. I think that moment for me has come now. 

I am sure you've noticed that I said "think". You see, the way academic research works these days, you can't just jump out of your bathtub and start celebrating butt-naked. And it's never a moment. There is a long gestation period before you can be sure that you have got something good with you. A period when you have to repeat the experiment a number of times, so the observation is reproducible. You also have to think if you have got all the controls right and haven't missed anything. You have to do a number of supporting experiments that can explain the unexpected. Your work then has to be reviewed and approved by your "peers", who you hope don't have a conflict of interest in approving your observation. After all this, you have to be approved by a copy editor somewhere who wants to make sure that you have got your fonts right, the spacing right, the size of images right, their color right, the spellings and grammar right, etc., etc., etc. Only then will your work be published for consumption by the tax paying public that has funded the entire process. By then you would have lost all the enthusiasm to open the cork and it will be time to be back at the bench so you can continue with your efforts to save the humanity (from itself?). And wait for the next eureka moment. 

Minor efforts, Major effects

Towards the end of this blog post, the blogger describes how her employer, IISER-Pune, has taken steps to address a few minor, but non-trivial, issues that could worry a prospective employee, especially the ones that are not natives of the town/state. This is a particularly important, and probably a peculiar, issue relevant to India considering the multitude of languages and cultures in our country that change dramatically from state to state and sometimes even within a state. An outsider might have to deal with not only a bit of a culture shock but also subtle discrimination. This reminds me of my own experience as a PhD student that was diametrically opposite of what folks at IISER-Pune experienced. And the issues at hand were pretty much the same. 

I grew up in Visakhapatnam, a coastal town in Andhra Pradesh. When I got a PhD position in Chennai, it was my first big move away from my native town. Also included in the "move to a new place" package were the issues pertaining to a new culture, language and life in a metro. The institute where I did my PhD was a center affiliated to Anna University and established on a Public-Private-Partnership (PPP) model with pretty ambitious goals for research excellence. In tune with its stated objectives, the center has a very cosmopolitan composition, both in personnel and the research pursued. People of non-Chennai and/or non-Tamil background composed a good chunk of the staff and student population. One of the unintended (and certainly unwanted for someone in my situation) side story of this PPP experiment was that the PhD students did not have access to the University's hostel facilities.  And unlike the Pune folks, people entrusted with the job of running our center did not deem it an important enough issue to pay attention to. Consequently, the students were left to fend for themselves with their broken Tamil and shallow pockets. The challenge was not finding a decent place that was close enough to the campus. There were plenty of such places. The problem though was with the people who owned these places and insisted on renting them out only to "vegetarians" and "families". Luckily for me, both my roommates belonged to this "vegetarian" category. So, we were only half disqualified to be tenants on account of our failure to get married. In the almost 5 years that I spent there, we rented 4 different places. Each time we had to spend considerable time and energy in the process of finding each one of those and in trying to convince the landlords that we did not intend to burn the place down. It is important for me to clarify that I do not blame the landlords of that locality for thinking the way they do. I am sure they have valid reasons derived from their past experiences for imposing those conditions on their future tenants and every property owner has a right to decide who to rent their place out to or not to. But the point I am trying to make is that knowing how things were in the community, the administrators could have done things differently to ease the life a little for the students rather than leave them to their fate. It could have earned them a life time's goodwill for sure.

Another such example of administrative apathy was with regard to our stipends. Some of us had fellowships directly from CSIR. The way these fellowships were administered was something like this. At the beginning of the fellowship year (sometime around June, I think) we had to submit a claim form telling them how much to pay us (as if they didn't know that already) along with a progress report and a certificate from the supervisor confirming our continuation in the program and recommending the release of stipend. These forms are submitted to a particular office in the university. Once this office receives the forms from all the fellows in the university, they forward them to the CSIR in New Delhi who process them and release the funds to the university which then pays us every month. It usually took about 6 months before this entire process was completed and some money showed up in our bank accounts during which time we were without a pay. This could have been fine for someone living in university accommodation and eating in university mess. As mentioned above, we did not have half of this luxury. So, the system forced us to develop a grasshopper like personality to escape an ant like fate during the dry months. Again, things could have been done differently. Since, the CSIR was going to transfer funds to the university, our stipend could have been payed by the university in the interim. As it turns out this mile was too long for them to walk. 

In none of the above instances, were the authorities concerned breaking any rules. They can't even be accused of dereliction of duty. They were just not prepared to walk the extra few centimeters to make our lives a little bit easier. And this is not something limited only to our university. From what I know, this is what happens in most universities in India. In some places, things are even worse. I have heard from people who had to spend money from their pockets to buy chemicals and plastics or to get their samples analysed on specialized instruments. I probably had a relatively better Indian PhD experience. Mostly because I was part of the above mentioned PPP experiment. Though I was part of the university system, I was also detached from it. I was also fortunate to have done my PhD with supervisors who, above everything else, were great human beings. Working from within the system they did their best to protect me and tried to minimize the influence of  the negative experiences. Most importantly, they did not let any of this compromise the quality of my research. Not every researcher in Indian university system is that fortunate. Often one hears the leaders of Indian science lament the decline of research in Indian universities. For all their eminence and experience, one doesn't get a feeling that  they are looking at the right problems and suggesting the right solutions.  Maybe because, like most of our politicians, they too haven't gone through the systems and hence haven't experienced the problems first hand. Hopefully India will soon have leaders, both in politics and in science, who have grown through the system and have experienced the problems to provide real solutions. 
Were you a researcher associated  with a state university in India? Do you have similar experiences to share? 

Communicating research

The big cola companies Pepsi and Coca-Cola are constantly at war with each other for dominance of the un-healthy foods market. And the weapons of choice employed in this battle to capture the public mindscape are the TV and print commercials. Sometimes these ads are witty and interesting to watch, but most times they down right nasty where one company takes potshots at the other’s products (here’s an example). This was what I was reminded of while reading a recent report in Science which the journal claimed were the results of an year-long “sting” operation carried out to expose the ugly underbelly of Open Access research publishing (here is the link; but I am not sure if the full text can be accessed without a subscription to Science). In my opinion, this was not an honest “sting” Operation and Science was taking a cheap-shot at the Open Access movement that is starting to threaten the subscription access model that journals like Science have been employing to exploit (I’m tempted to say extort) the research community. If the study was objective, the fake paper should have also been submitted to the traditional subscription-access journals from the stables of Nature, Springer, Wiley and Science itself. The sample selection for the study is clearly biased and was done to fit into a pre-determined outcome. In fact, it could be a textbook case of how not to design a research study. Anyway, the point of this post is not to criticize the Science report (there is plenty of that already in the blogosphere, like this for example), but to present my views on communicating research findings.

Just like religious books had once served a  useful purpose in setting order in society before the advent of Democratic governments and constitutions, the subscription-driven, peer review backed research journals too had played a very important role in furthering the cause of research communities in a pre-internet world. The basic idea behind the origin of journals was the need to communicate latest research findings to the widest possible academic audience. So, a system developed where by the research from all over the world will be collected, published in the form of a book and distributed to everyone that wanted to read. Since printing and distributing these research records involved considerable expense, a fee was collected from those who wanted to read them. But evolution of the world wide web has made the hard copy journals irrelevant. Now almost everyone discovers and keeps to date with the latest developments in the research world on the internet. The open access journals that publish online and provide access to their content to everyone free of charge are fast overtaking the traditional publications. But even the open access journals, though an improvement, have not been able to shake off all the deficiencies. Specifically, the reliance on the age old practice of peer-review to judge the quality of research to be published still continues. My biggest problem with the anonymous peer-review practice is the conflict of interest that arises due to the fact that these reviewers are by rule competitors. The entire process is built on the foundation of abstract ideas like honesty and trust.

Also, though there is no charge to read the articles published in open access journals, they do charge the authors to publish their findings. I basically think even this is unnecessary expense of scarce research funds that could be expended on doing the research. Since the very idea of research publications is to communicate one’s work to the wider community, there are many alternate ways available today to accomplish that. And most of them come at almost no expense to either the author or the reader. For example, I plan on using this blog space to regularly publish my research findings and then publicize/communicate them to my peers using social media avenues like Twitter, ResearchGate, Mendeley etc. Since the content on blogs and other social media sites are indexed by search engines such as Google, it won't be difficult for those interested to find and access the information on the internet, just the way they do now. Of course, I will have to wait to establish myself as a principal investigator before implementing this plan and taking the liberty to challenge the established tradition of research communication. But I have a very strong feeling that something similar or a variation of this approach will be embraced by the wider research community in the very near future. And we can all spend more energy on doing, rather than writing and presenting, novel science.