The Old Man and the Game of Trust

An Old Man Putting Dry Rice on the Hearth 1881 Vincent van GoghLet us play a game, you and I.

I will give you some money – here, have this note. Of course it’s not a joke. You can take that 100$ bill and walk out of here. No one’ll say a thing. Or come after you.

Or you could do something nice. You see young Joe over there? You don’t know him? Of course you don’t. Doesn’t matter, he’s a good lad. Let me tell you what you can do. You can give him a small share of that 100$ you got. And I’ll say what, however much you decide to give him, I’ll give him twice the amount you do, so that he now has a tight little bundle. And now that he has so much money, I’m sure he’d be feeling grateful, and give you back some of that cash. So, on your part it’s not really a gift, but an investment, one that could make you a nice little packet in the end.

How will you know that he won’t take the money and run, you ask? Well, I can’t answer that. It’s up to the goodness of your heart, and your trust in the goodness of your fellow man. As I said, I won’t make your choice for you. You decide how much you want to give, and he decides how much he wants to give back.

You’ll give him 10$, you say? Fine, fine, I’m sure he’ll appreciate it. By and by, you see this little bottle? Why don’t you take a sniff of that? Nothing that’ll harm you, I promise. All natural, all the goodness of the earth in this little bottle – a perfume of my own invention. And while you smell that and think over how much you want to give young Joe here, let me tell you a little story.

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‘Netting’ bacteria with DNA: strategies of a social amoeba

Life has survived for more than three billion years because it is robust, and almost no mutations can easily outwit the defense mechanisms built up through eons of exposure to potential pathogens.
–Lawrence M. Krauss

Every second, every minute of your life, your body is under attack. This may be strange to think about, but millions of bacteria, as well as myriad other parasites, are attempting at this very moment to invade the sanctum of your body. Do not be offended, these creatures do not do this out of any sense of malice. They are simply driven by the two greatest necessities of life – survival and reproduction.

Dictyostelium Aggregation
Dictyostelium discoideum

Ever since the first cells arose in the hot, steamy, soup that was our earth’s oceans billions of years ago, organisms have competed fiercely for the same limited resources. Some cells devised ways to halt the growth of or outright kill other cells, while others entered complex beneficial (mutualistic) or harmful (parasitic) interactions with each other. With time, two kinds of life forms emerged – parasites, who attack other organisms to their own benefit and the other’s loss, and hosts, who suffer from the parasites’ attack. A much larger class is that of pathogens – any organism that can directly cause disease in a host is called a pathogen. Host defense mechanisms have, therefore, evolved over eons to outsmart parasites and pathogens. Plants have specialized signaling systems to fight invading bacteria, and multicellular animals like human beings have an immune system with several tiers of defense to combat infection. Yet, at the same time, the parasites have been evolving too, devising sneakier and subtler ways of evading the host’s defense pathways to gain entry and live undetected. Life can, in fact, be described as a continuous arms race between hosts and their parasites, where neither gains the upper hand on the other, even after centuries of creating sophisticated arsenals for the purpose.

This continuous struggle has given rise to some truly ingenious forms of biological innovation. A recent study from Xuezhi Zhang and colleagues, working in a collaboration between the University of Geneva, Switzerland, and Baylor College of Medicine, USA, sheds light on a remarkable and evolutionarily ancient line of defense employed by a class of social amoeba. Simply put, the defense consists of casting a net formed of DNA molecules over bacteria and killing them slowly with poisons embedded in the net.

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Ancient DNA: A story writ in genes

The Dinosaur Debacle

Picture a day millions of years past, in a land as yet untouched by the vagaries of man.

jurassic park photoDense forests stretch in every direction from where you stand, and the air you breathe is hot and humid. Now watch, as a magnificent beast, several feet tall, thunders through the undergrowth in determined pursuit of its prey. Years later, men stumbling upon its bones would name it a dinosaur. The little mouse-like creature it is chasing disappears into a burrow, but not before its mate is snatched up in the dinosaur’s crushing jaws. While the predator stands enjoying its meal, it barely notices the little spot of irritation on its shoulder, where a resourceful mosquito sits feasting on the giant’s blood. As the dinosaur moves on, the mosquito flies off to a nearby pine tree, where it rests for a moment before its next meal. Yet this rest would prove to be fatal, as a drop of the tree’s resin, oozing out from a wound in the tree bark, engulfs the hapless mosquito. The resin solidifies, and over millions and millions of years, turns slowly into amber. In the present day, fossil-hunters discover the piece of amber with the perfectly preserved mosquito inside. It would have been dismissed as a curiosity, if it weren’t for some scientists, who, while examining the fossil, discover a drop of dinosaur blood stuck in the mosquito’s tiny stomach. From this drop of blood, they extract DNA, the molecular blueprint of life. Using this DNA, they are able to build a dinosaur genome artificially, and then clone and produce living dinosaurs, enough to fill an island. Enough, in fact, to form a dinosaur theme park. And thus is a story born, that of Stephen Spielberg’s masterpiece and one of the most iconic films of the 20th century – Jurassic Park.

Mosquito in amber
Mosquito in amber by Oregon State University

Spielberg’s movie, which is based on a book by Michael Crichton, is founded on some very real scientific outpourings of that era. In the 1990s, a number of research groups from around the world reported the extraction of intact DNA from ancient insect fossils preserved in amber. While, to the best of my knowledge, no drop of dinosaur blood with dinosaur DNA was ever recovered from an amber fossil, there were enough and widespread studies of fossilized insect DNA sequences that suggested that this was possible. Yet, in the back of many scientific minds, there was a glimmer of doubt, perhaps fanned by the astounding success rates of such studies. Ancient DNA is notoriously difficult to obtain and analyze, and yet reports of doing exactly so continued to pour in in spades. In 1997, Jeremy Austin and colleagues, of the Natural History Museum, London, decided to try and see whether these studies could be replicated.

Amber Insect Fossil

They took more samples than all the other studies before this had had combined, and used a large number of extraction and amplification methods to try and obtain authentic ancient insect DNA. The results were surprising. Most of the samples did not yield sufficient amount of analyzable DNA, and those that did so were inevitably found to be contaminated with modern DNA. This and other studies later went on to establish that it is virtually impossible to retrieve usable DNA from amberized fossil remains, and all of the sensational reports that had come earlier had failed the key test of scientific validity – reproducibility.

In my opinion, this little story demonstrates everything that is exciting and problematic in the field of ancient DNA research, a field that hit its 30th year in 2014.

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Thank you for your support and Happy New Year !

Hi everyone!

happy new yearI started this blog with the aim of bringing to your notice some of the most exciting scientific studies being performed around the world today. Science is a public endeavor, meant for the common good, and hence hiding it behind a wall of jargon and esoteric literature makes little sense . Here, at the Scientific Lens, I hope to contribute a little bit towards demystifying the process of doing science, and to share the most interesting scientific breakthroughs of the day. I started writing in Septmeber, 2015, and since then this blog has received nearly 5000 views, much more than anything I had hoped for. I wanted to take this opportunity to thank you for your continuing support, and to wish you a very happy new year.

Here’re the top stories on this blog published in 2015, and I hope you enjoyed reading them –

  1. Freud, cocaine and the dopamine hypothesis of depression – A recent study, from researchers at the University of Geneva, Switzerland, attempted to test once and for all whether or not dopamine is sufficient for the progression to addiction.
  2. ‘Sonogenetics’ – using sound waves to activate brain cells – Scientists have discovered a way to control brain cells using ultrasonic sound waves.
  3. The Story behind this year’s Nobel Prize in Physiology and Medicine – The Nobel Prize in Physiology or Medicine 2015 was divided, one half jointly to William C. Campbell and Satoshi Ōmura “for their discoveries concerning a novel therapy against infections caused by roundworm parasites” and the other half to Youyou Tu “for her discoveries concerning a novel therapy against Malaria”.
  4. The Oldest Stars in our galaxy – Australian astronomers claim to have found some of the oldest stars in the galaxy hiding in the bulge of the Milky Way
  5. The Secret lives of Bees – Research reveals that honey bees reconsolidate their memories while sleeping and can be tricked into foraging by caffeine. Some bees cultivate a fungus for their larvae, and others use vibrations to tell potential mates apart.
  6. Demystifying the brain – what the brain does and does not do – Our brain is a marvel of evolutionary complexity that allows us to think, dream and philosophize – here is a look at what functions it performs, and why certain species are content to exist without the benefit of one.
  7. Demystifying the brain – the brains of our ancestors – Nothing in biology makes sense except in the light of evolution.
    –Theodosius Dobzhansky (1900-1975)
  8. Underwater adhesives, disappearing frogs and electric eels – Mussel-inspired glue design, extinction rates of amphibians, electric eels tracking their prey, molecular oxygen found on comet 67P, and more
  9. New Horizons, mysterious male neurons and Remote-controlled T-cells – New information about Pluto, Two new neurons were discovered in C. elegans, and CAR-T cells can now be remote controlled to fight cancer
  10. Why do some birds mimic human speech?
  11. Nobel Prize, ancient humans and the autism debate – A collection of stories, including the analysis of the bone structure of an ancient human species, the announcement of the 2015 Nobel prizes and a study demonstrating (yet again) that vaccines do not cause autism.
  12. New planets, 1000 genomes and tricky parasites – Weekly review of science stories around the world, including the discovery of a new Jupiter-like planet, the completion of the 1000 genomes project, and the way the HIV protein outsmarts it host.

If you have time, you can also give the introduction post – ‘Let’s talk about Science‘, a read through. Things were a bit slow in December, but I promise a bunch of interesting posts in the coming month – a study showed how corals use moonlight to decide the time to spawn, another showed how gut microbiota drive behaviour in a bunch of cockroaches, and female elephants were shown to inherit their social status from their mothers. Neuroscientist Russel Poldrack scanned his own brain several times a week over a period of 18 months, providing the most comprehensive data set yet achieved for daily variations in the state of a human brain, and lion populations were observed to be on a steady decline on the African mainland. I hope to bring you these stories and more in the coming year, and hope for your continued support throughout this journey.

Wishing you a scientifically sound 2016, and may it bring you plenty of joy and prosperity!

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The Oldest Stars in our Galaxy

UniverseThe Universe sprang into being about 13.8 billion years ago, expanding exponentially from a point of infinite density and infinite temperature. Such a point is called a singularity, and this event is popularly known as the ‘Big Bang’. Before this point, time and space did not exist, so the word ‘before’ itself ceases to hold meaning. Within the space of a second, the first elementary particles were formed, and the universe shifted from a state of pure energy to one containing matter as well as energy. Within 20 minutes, the universe had cooled down enough to allow protons and neutrons to combine through nuclear fusion, and the nuclei of the first atoms graced the universe. These were the nuclei of hydrogen (simply a proton), helium, and a tiny bit of lithium. The first true atoms, with positively charged nuclei surrounded by negatively charged electrons, would not arise till about 300,000 years later.

The first stars were created about 100 – 200 million years after the big bang, when areas of large matter densities began to cool and undergo gravitational collapse. These first stars were composed primarily of hydrogen and helium, the first elements in the universe, with perhaps a trace of lithium. These stars were probably massive, many hundreds of times the mass of our sun, significantly hotter, and relatively-short lived. Higher molecular weight elements (rather confusingly called ‘metals’ by astronomers) were formed within these stars as a result of thermonuclear reactions, and when these stars exploded as supernovae, these metals were flung far and wide, finding their way into clouds from which the next generation of stars took birth. As a result, newer stars (our own sun being one of these) are much more metal-rich than those formed during the dawn of the universe.

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Freud, Cocaine and the Dopamine Hypothesis of Addiction

Sigmund Freud LIFE
Sigmund Freud
Sigmund Freud, the venerable father of psychoanalysis, had a lesser known distinction up his sleeve. He produced one of the first comprehensive scientific analyses of the drug Cocaine, published in 1884 under the title ‘Über Coca’. In this remarkable manuscript, amidst sections such as a detailed description of the cocaine plant (Erythroxylon coca, for the curious), Freud inserted his meticulous observations on the effects of cocaine on the human body. As he was quite free in admitting, he based his remarks on the “some dozen times” he consumed the ‘coca’ himself, ostensibly for research purposes. Once the effects wore off, Freud reported no lasting side effects, and was quite positive in denying any craving or addiction like symptoms.

It seems to me noteworthy – and I discovered this in myself and in other observers who were capable of judging such things – that a first dose or even repeated doses of coca produce no compulsive desire to use the stimulant further; on the contrary, one feels a certain unmotivated aversion to the substance.

– Sigmund Freud, Über Coca

Till the end of his days, Freud remained convinced about the beneficial nature of cocaine, and strongly advocated its use for medicinal purposes. In an idea that was surprisingly ahead of his time, though ultimately misguided, he even suggested that cocaine be used as a substitution therapy for de-addicting patients from morphine or alcohol.

Freud isn’t alone among illustrious personalities in having dabbled with cocaine, heroin, morphine or any of the other well-known drugs of abuse. Recreational drug use has always been common, particularly among certain social, occupational or age groups, drug prohibition laws notwithstanding. And a really curious fact that is rarely talked about in scientific literature is that many of these users somehow escape without any negative consequences, and never develop the compulsive addiction that makes these drugs so deadly to the population at large.

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The Secret Lives of Bees

If you have ever felt a yearning for a perfect picture of domestic bliss, take one look inside a simple beehive. The life of the social bee is a life of contentment and diligence, of strict order and unfailing discipline, of stratified classes and organized division of labor, and above all, of a collective mind which puts the survival of the colony above the survival of the individual. Bees are close relatives of wasps and ants, and are found on every continent except Antarctica. They also tend to exhibit some of most sophisticated behaviors in the animal world. In many species of social bees (honeybees being the best known example), hives consist of a reproductive queen, male drones whose only function is to mate with the queen, and several sterile, female worker bees. This week’s Current Biology carries a bunch of interesting studies concerning bees, which bring to light the layers of complexity that underlie the routine behaviors of these remarkable creatures. We are going to take a brief look at each of these studies.

Tricking a bee with a cup of coffee

honey bee photo
Photo by eleZeta

Honeybees feed on nectar, a sweet tasting, sugar-rich substance produced by several species of flowering plants. Nectar carried back to the nests is used to prepare honey, which is stored as food for the young ones, and as surplus rations for the winter. The plants are benefitted by this, as pollen sticking to hairy bristles on the honeybee’s body helps cross-pollinate flowers. The nectar serves as incentive to get the bees to help in this process. So far this seems like a win-win situation for the plant and the bee (a relationship known as ‘mutualism’ in ecology), but nothing in biology is that simple. In light of recent evidence, it now appears that the plants are not as keen as the bees on providing an honest deal, and can trick the bees in a rather ingenious way.

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The Story Behind this year’s Nobel Prize in Physiology and Medicine

Part 1: Going back to Nature

The year is 1967. Thirty-two year old Satoshi Ōmura, in his lab at the prestigious Kitasato University in Japan, is giving serious thought to the direction his research career is going to take. In the two years he has spent at the University, he has studied the structure of multiple antibiotics using nuclear magnetic resonance (NMR) spectroscopy, uncovering information that might go a long way towards elucidating their mode of action. Since the discovery of Penicillin in 1928, the initial rush of antibiotic discovery has died down, and interest has shifted towards figuring out the structure and function of existing antibiotics, so that new drugs can be synthesized chemically based on this data. It is rewarding work for Ōmura, who is a year away from receiving his PhD, but he is not entirely satisfied. More than anything, he is not convinced that the store of medically relevant novel compounds present in the microbial world has been exhausted.

He believes the search is only just beginning.

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Underwater adhesives, Disappearing frogs and Electric Eels

Hello Folks! As promised, here is part II of our roundup of the most interesting breakthroughs in the world of science in the last couple of weeks. If you missed Part I, you can read it here. You will learn about mysterious brain cells of male roundworms, methods for remote-controlling cancer-fighting immune cells, the latest findings concerning Pluto by the New Horizons spacecraft, and much more.

And now, for the rest.

A glue inspired by nature

<a href="https://pixabay.com/users/Mhy/">Mhy</a> / Pixabay

Making glues that work underwater has long been a challenge for chemical engineers. Since a long time, researchers have been trying to exploit their knowledge of marine mussels to overcome this problem. Mussels stick to rocks in shallow waters using thread-like processes and can withstand battering by heavy waves without losing their grip. They do this by using a family of proteins, called mussel foot proteins (mfps) which they secrete near their points of contact with the rocks. A lot of interest, therefore, lies in uncovering the special properties of mfps that allow them to adhere underwater. Chemically, the main suspects are modified amino acids called catechols, the presence of large numbers of positive and negative charges in the same protein, and non-polar, hydrophobic elements interspersed throughout. Researchers at University of California, Santa Barbara, decided to strip away all the extraneous stuff and design a single small molecule that would incorporate all these components. This they achieved by chemically modifying a zwitterionic (having both positive and negative charges) detergent molecule to include the important catechol group alongside a few other small modifications. When this new material was tested for its stickiness, is was found to be highly adhesive, much stronger than the mfp proteins themselves, and could easily stick underwater forming a thin, uniform layer. According to the scientists, this might have important applications in the field of nanofabrication.

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New Horizons, Mysterious male neurons, and Remote-controlled T-cells

Hi everyone! I missed making a post on the last two Sundays, so today I’m bringing you a bunch of interesting discoveries that occurred over the last two weeks. Or rather, I am bringing you half of those stories, because there are simply too many to include in one post. I’ll be posting Part II in a day or two, so stay tuned for that.

Let’s begin!

Pluto Spills its secrets

A close-up of Pluto’s surface, taken by New Horizons

The New Horizons spacecraft was launched from Cape Canaveral on January 19, 2006 with a mission to make a close flyby of objects in the Kuiper belt, the dark outer frontier of our solar system. By far, the most interesting target was Pluto, the erstwhile planet, of which we only had data from distant astronomical observations till now. New Horizons took about thirteen months to reach Jupiter and then used Jupiter’s gravity to get a boost in speed before making a beeline for Pluto. On July 14, 2015, it made its closest approach to Pluto, after having transmitted images and data relating to it for a period of almost six months. This month, the results from the flyby were published in the journal Science, exposing a wealth of new information.

For starters, Pluto seems to be unusually geologically active for a planet of its size and status. Its surface is dotted with craters alongside deep features like mountains that can only be formed as a result of tectonic activity and the presence of hard bedrock. The surface of Pluto is covered with nitrogen, carbon monoxide and methane ice, which do not fit the requirement for hard bedrock, and hence this suggests the presence of a harder substance below the surface layer – most likely water-ice. Also, certain parts of Pluto’s surface show really few craters, suggesting that these regions were formed relatively recently – strong evidence for continuing geological activity. Intriguingly, in certain places, the scientists even reported seeing ‘glacier-like’ features.

PIA18179 d-Pluto270-Hubble2003-20100204Pluto-01 Stern 03 Pluto Color TXTAnother surprising discovery was the extent of Pluto’s atmosphere – with an almost 150 Km deep atmospheric ‘haze’ clearly visible above the surface. The surface pressure is low, about 10 microbar (for comparison, atmospheric pressure at the earth’s surface is approximately 1 bar, about 100,000 times that of Pluto). Methane and Nitrogen were among the gases detected. In addition to studying Pluto, New Horizons also took high resolution photos of Pluto’s biggest moon, Charon. Charon also shows evidence of tectonic activities, and has several large craters on its surface. New Horizon also sent back information about two more moons of Pluto – Hydra and Nyx – which are tiny, irregularly shaped satellites, whose highly reflective surfaces indicate that they are mostly covered with water-ice.
Till the New Horizons flyby, the highest resolution image we had of Pluto is the one shown on the top left, taken from the Hubble Space Telescope. Compare it to the latest images released by NASA (top right), if you want to know how much the recent flyby has added to our knowledge of this controversial member of our solar system.

Mysterious male neurons of C. elegans

Caenherrobditis elegans is a small soil-living roundworm (also called a nematode) found in temperate zones. In 1974, the famous South African geneticist Sydney Brenner, proposed the use of C. elegans as a model system for studying development in multicellular organisms.

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