Category Archives: Science

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Another Reason to Hit the Sack— Humans Can Learn While Asleep

Sleep is a state of being characterized by a lack of consciousness. But are we capable to perceiving sensory stimuli while we are asleep, or we totally oblivious to the world around us? It is known that humans can strengthen previously acquired memories during sleep, but it is not known if we can actually take in new information.

If a Skunk Passes By While We Sleep, Would Our Brain Know It?

Researchers at the University of Israel decided to test the assimilation and acquisition of new non-verbal information during sleep. It is known that we respond to unpleasant smells by producing shorter sniffs, and to pleasant smells by longer, deeper sniffs. The research team used this information to create a unique test. While participants were asleep, they paired odors with musical tones, i.e., an odor-tone pairing was created with the tone being separated by the odor by at least 1 second. To ensure that these were being detected by the participants, their sniffing behavior was studied, and it was ensured that their sniffs were shorter when unpleasant odors were being presented. They also ensured that participants did not wake up in response to these odors; participants who did wake up within 30 minutes of the experiment were excluded from the analysis.

Sleeping might be less wasteful that you thought. [Image Credit: wikipedia]

Upon waking up, the same participants were presented to the tones alone, and it was found that the tones which were paired with unpleasant odors induced a shorter sniffing response in the participants. Moreover, they were unaware of the experiments that had been conducted while they were asleep. This shows that their brains could process at least two things—odor processing, and association of tones with odors while sleep. This shows that our senses are definitely at work while we sleep!

What, and How Much Can We Take In While Asleep?

These participants only learned a simple non-verbal response. More studies will have to be conducted to determine the extent to which we can learn during sleep. Head researcher Anat Ariz says, “There will be clear limits on what we can learn in sleep, but I speculate that they will be beyond what we have demonstrated.” Though it is unlikely that we can learn all our Algebra by listening to recordings while we are asleep, this research could have implications in treating addictive disorders, for example, by using conditioning that pairs addictive drugs with a negative connotation. As Arzi says, perhaps the best way to cure such disorders might be learning at a level of non-awareness.

You can read more about this research here.

Neil Armstrong First Man On the Moon Dies

2012 has been a year of great loss, as the first woman in space, Sally Ride, recently passed and now Neil Armstrong has passed away. His family reports that the 82 year old died from complications of a cardiac procedure.

Neil Armstrong
Portrait of Astronaut Neil A. Armstrong, commander of the Apollo 11 Lunar Landing mission in his space suit, with his helmet on the table in front of him. Behind him is a large photograph of the lunar surface. (courtesy Wikimedia Commons)

Neil Armstrong commanded the Apollo 11 Lunar Landing mission. He successfully landed on the moon on July 20, 1969. It was an event that was watched around the world and his words will forever be etched in the minds of all who heard him say, “That’s one small step for man, one giant leap for mankind”.

Everything you can find on Mr. Armstrong seems to point to his humility and attitude of service. In a February 2000 appearance he is quoted saying, “I am, and ever will be, a white socks, pocket protector, nerdy engineer”. Not hardly what you might expect from the first man on the moon.

“As long as there are history books, Neil Armstrong will be included in them, remembered for taking humankind’s first small step on a world beyond our own,” said NASA Administrator Charles Bolden.

Neil Armstrong will be terribly missed by all who are fans of NASA and I am sure that his friends and family will feel the great loss for years to come.

His family has put up a website to keep people informed. I will end this post with what they posted today as I believe it is the most fitting tribute:

“We are heartbroken to share the news that Neil Armstrong has passed away following complications resulting from cardiovascular procedures.

“Neil was our loving husband, father, grandfather, brother and friend.

“Neil Armstrong was also a reluctant American hero who always believed he was just doing his job. He served his Nation proudly, as a navy fighter pilot, test pilot, and astronaut. He also found success back home in his native Ohio in business and academia, and became a community leader in Cincinnati.

“He remained an advocate of aviation and exploration throughout his life and never lost his boyhood wonder of these pursuits.

“As much as Neil cherished his privacy, he always appreciated the expressions of good will from people around the world and from all walks of life.

“While we mourn the loss of a very good man, we also celebrate his remarkable life and hope that it serves as an example to young people around the world to work hard to make their dreams come true, to be willing to explore and push the limits, and to selflessly serve a cause greater than themselves.

“For those who may ask what they can do to honor Neil, we have a simple request. Honor his example of service, accomplishment and modesty, and the next time you walk outside on a clear night and see the moon smiling down at you, think of Neil Armstrong and give him a wink.”

For more information, please visit NASA’s tribute to him at http://www.nasa.gov/topics/people/features/armstrong_obit.html.

Forget Big Bang! The Universe Might Have Begun With Big Freeze

The Universe didn’t start off with a big bang, but a big whimper. Or so say four physicists from the University of Melbourne and RMIT. They compare the beginning of the Universe with that of freezing of water, indicating that the Universe underwent a rapid phase transition. Before you think this is the next big theory, all set to replace the Big Bang as the new standard cosmological theory, hold on!

Did the Universe just freeze out?

Crystallizing out the Universe

Lead researcher of the group, James Quach, says that the early Universe can be compared with a liquid – something which has no particular shape or form. This liquid froze, “crystallizing” into three spatial and one temporal (time) dimension. In a slightly more technical language, consider a crystal lattice forming as a result of some parameter – say temperature – varying from high to low. As the temperature lowers, the lower energy states of the crystal become more and more important. Quach and his group say that these low energy states form the spatial degrees of freedom of the Universe. They herald in a new theory called ‘quantum graphity’.

The stimulus behind the theory proposal is very simple: dissatisfaction. Physicists are unsure as to how the bang in the Big Bang happened. More precisely, the structure of space-time thought to exist at the time of the Big Bang requires a modern theory of quantum gravity. Basically, Einstein’s equations of general relativity and quantum mechanics cannot be reconciled and this creates the problem. Right now, we have no satisfactory theory of quantum gravity.

Do away with it, says the group. Imagine the Universe as a group of dynamical space-time blocks, like small crystalline blocks floating around in a liquid. As the temperature cools, the blocks coalesce and this gives rise to a bigger crystal, simulating the freezing out of space-time from an existing soup.

Cracks

But what about anisotropy and the visible structure in the Universe? Here is where the water-freezing analogy comes in most handy. When water freezes into ice, cracks develop on the surface. Quach and team describe these cracks as some visible structure. Problem is that they aren’t sure what scale to look at and this scale varies all the way from the microscopic to the ultra macroscopic.

All of this sounds fine and dandy, except that this new model must explain or, better predict, the data seen by the various cosmological experiments. Right now, the group doesn’t seem to have the right scale in mind. More problems arise from asking the question where did the soup that crystallized come from?

The work appears in Physical Review D here: http://arxiv.org/abs/1203.5367

Dinosaur Footprint Discovered in NASA’s Back Yard

While NASA was busy peering into deep space to find the origins of life, an ancient life-form had left an indelible print right in its own back yard. Noted dinosaur hunter, Ray Stanford, went hunting on the property of NASA’s Goddard Space Flight Center based on a “hunch” he had. Incredibly, he found what he was looking for, a cretaceous era dinosaur footprint belonging to a large herbivorous nodosaur.

Pictured below, you can see the imprint left behind by the ancient creature. “This was a large, armored dinosaur,” Stanford said. “Think of it as a four-footed tank. It was quite heavy, there’s a quite a ridge or push-up here. … Subsequently the sand was bound together by iron-oxide or hematite, so it gave us a nice preservation, almost like concrete.”

footprint
This imprint shows the right rear foot of a nodosaur – a low-slung, spiny leaf-eater – apparently moving in haste as the heel did not fully settle in the cretaceous mud, according to dinosaur tracker Ray Stanford. Credit: NASA/Goddard/Ray Stanford

Stanford, a self-taught dinosaur tracker, has a history of significant finds in Maryland. He found the first ever fossilized nodosaur hatchling. Nodosaurs were a relative of the better-known ankylosaurs. They were large plant eaters that lumbered low to the ground. Stanford has also found prints of Maryland dinosaurs that they don’t even have bones for yet. In a Washington Post article, Johns Hopkins University expert David Weishampel speaking about Ray’s collection said, “the best collection of footprints we have from early Cretaceous era of the East Coast”.

Below, you can see an embedded NASA’s Flickr share with pictures and videos.

Right now NASA personnel are treating the area as sensitive, as they do not want anyone to damage or try to steal the fossil. They hope to be able to open some type of public display in the future.

Protein in Semen Stimulates Ovulation in Female Brain

A protein being termed ‘Ovulation-inducing Factor’ has been found in the seminal fluid of a variety of male mammals, which stimulates the female brain to produce eggs (the process of which is called ovulation).

Ovulation-Inducing Factor

The presence of such a protein was first discovered when female camels ovulated soon after injection with semen. This experiment was repeated with llamas and alpacas to see the same results. However, the species in which it was first discovered (rabbits and koalas, besides camels) are called ‘induced ovulators’, meaning that the females produce eggs only upon insemination by the male. In other mammals including horses, pigs and humans, ovulation is spontaneous—meaning that there is a biological cycle in the female which leads to a buildup of hormones leading to the release of the egg. It turned out that OIF was also present in the semen of these spontaneous ovulators. Did OIF actually change ovulation rhythms in them?

It isn’t just sperm that is present in semen. A protein called NGF might stimulate production of eggs for the sperm to fuse with. [Image Credit: biology.ucsd.edu]

The conservation of this protein must have a biological significance, and one way to determine that was to characterize the protein OIF. Researchers isolated this protein from llamas and bulls and tried to identify it in order to determine how its mechanism of action in the female body. By comparing protein structures, they found that this protein is actually a Nerve Growth Factor (NGF), a protein commonly found in nerve cells of the body. To confirm this finding, they isolated NGF from mice and injected it into llamas, and found that ovulation was induced in the llamas.

NGF Acts as a Hormone on the Female Brain

The NGF protein can act on the hypothalamus of the female brain via a system of hormones. What this means is that a substance that is a part of the male body can interfere with the female’s reproductive cycle. Is this true in humans too? We don’t know, but it might mean that we can rely less on birth control methods relying on abstinence during some days of the menstrual cycle. We know that human semen contains NGF, and that NGF can act on female hormones, but the female reproductive cycle is one that is tightly controlled, and further studies will have to be performed to determine the extent to which OIF/NGF can influence ovulation in spontaneous ovulators. In cows, injection of OIF has shown to alter ovarian function and shortens the ovarian cycles of cows.

“The idea that a substance in mammalian semen has a direct effect on the female brain is a new one,” says Gregg Adams, who headed the research team. “This latest finding broadens our understanding of the mechanisms that regulate ovulation and raises some intriguing questions about fertility.” Perhaps a host of fertility-related issues could be traced back to deficiencies in NGF in male semen, or NGF receptors in females.

You can read about this research here.

 

Cliodynamics: Treating History As Science and Why That’s a Bad Idea

Often it has happened in the course of history and it might just repeat itself. Ironically. A beautiful idea it is, but like many before it, it might be completely wrong.

Cliodynamics is the name of this strange game, the game of detecting cycles in history and then using this data to predict the occurrence of similar events in the near future. Named after the Greek muse of history, Clio, and championed by a population dynamics expert at the University of Connecticut, Peter Turchin, Cliodynamics is fast making itself noticeable. Its claim of making future events predictable using the past events has drawn a small crop of believers and a larger group of dissidents. Fear not, it doesn’t use crystal balls; the choice of tools is limited to historical data and complex mathematics. The idea: find patterns in recurrent events and extrapolate into the future.

The endless loop

Where I stand

Personally, I belong to the dissident side. I don’t believe that it can work, but, just for the sake of convincing you, I’ll be the angel’s messenger rather than the devil’s advocate. Let me try, as hard as I can, to convince you that Cliodynamics is a genuinely scientific deal. I can always bash it up after that’s done!

The immediate question is how one can paint the whole tapestry of history – and what’s coming up – with such a broad brush! But that’s exactly what Cliodynamics is promising to cure. Right now, the reasons for collapse of large empires – pick one, say the Roman Empire – are all fuzzy. Various scenarios have been proposed. No one knows for sure. Cliodynamics wants to correct this vague outlook by introducing mathematical models backed up by solid data and then predictions ought to be made using this. History should be “predictive science”, says Peter Turchin, who was studying predator-prey problems in the wild, when he had an idea and turned his expertise in the area towards more sociological models.

On to the numbers

Turchin and a few advocates analyse the long-term trends in society using four parameters – population numbers, social structure, state strength and political instability. The dicey bit is to put proper numbers for these quantities. For abstract quantities like this, the definition is crucial, as that determines the measurement procedure. Often, however, a clear-cut definition is not available. Let’s just gloss over this point for the moment, being sure to return to it later on.

The general trend seems to be that a period of political instability, often accompanied by a period of violence, is preceded by a spell of increase in corruption and unpredictable political alliances or rise of unforeseen groups. While this is a broad trend, the challenge is to actually look into the details and come up with definitive correlations, positive or negative, between trends and the events.

But this is exactly how a historian is supposed to work – how is Turchin’s work different?

Endless Cycles of history

With the help of Sergey Nefedov of the Institute of History and Archeology, Yekaterinburg, Russia, Turchin found two independent cycles, which seem to define the course of history. One is called  the ‘Secular Cycle’ and the other one is the ‘father-and-son’ cycle.

Endless loops? (A Lorentz Attractor)

The Secular cycle lasts for a long time – sometimes as long as 200 to 300 years. Large empires grow, labour laws evolve, elitism escalates and political power transfers hands over this large timescales. Many events appear to be at play and each influences the outcome of history in their own way. Even religions can rise, fall and rise again according to the secular cycle.

The shorter cycle is the ‘father-son’ cycle, which lasts about 50-60 years, i.e. about two generations. An individual – the father – revolts against the working of the society or the class of which he is a member and the son bears the brunt of the backlash in a subdued fashion, relegated to the background by the thought that the opposing forces are too strong to fight back against.

Suspected: Insects Undergoing Some Kind of Photosynthesis

The gardener’s nightmare might be the entomologist’s goldmine. Among the most destructive of all insects are small sap-sucking critters, called Aphids. They are very populous, reproducing via both sexual and asexual means, and are difficult to eliminate using pesticides. Aphids are also colored insects. They generally have a green color, but can also acquire a red color as they can also synthesize red carotenoids (pigment proteins). They are the only animals known to be able to synthesize pigments.

Aphids (Photo Courtesy: University of California)

A process similar to photosynthesis

What wasn’t known was that aphids can actually use these pigments to metabolize using sunlight, much the same way that plants do! Yes, aphids can undergo a process similar to photosynthesis in plants, finds a group of researchers.

This startling finding is due to a group working under entomologist Alain Robichon at the Sophia Agrobiotech Institute in Sophia Antipolis, France. The group worked with green, orange and white aphids. White aphids are found where resources are scarce and they are almost completely devoid of pigments. Green aphids are found in places with cold temperatures, but still enough food to go around.

Counting ATP

The group measured the ATP levels in the aphid bodies. ATP is the ‘energy currency’ of the living organism – this is the molecule that is transferred between cells when an energy transfer has to occur. The results of the measurements were astounding: Carotenoid rich green aphids registered a much higher level than the white carotenoid-devoid ones, suggesting that the green pigment might be instrumental in providing another source of energy production.

Look at the two lines. They represent the optical density (OD), indicative of the ATP/metabolic activity of the pigment. Clearly the green pigment (represented by the solid black line) has higher absorption at all wavelengths.

Moreover, when the orange aphids – containing moderate amounts of carotenoids – were placed in sunlight, they showed intermediate levels of ATP. Interesting. Very interesting indeed.

Not the photosynthesis we know

One has to note that this ‘photosynthesis’ merely refers to the use of sunlight in order to gain energy. This doesn’t refer to the photosynthetic process that goes on in plants, which require the transfer of a positive charge from a water molecule, leading to the expulsion of oxygen (and thus we breathe!). Also, carbon dioxide has not been shown to be essential to the aphids version of the photosynthetic process.

The carotenoid molecules are placed about 0-40 micrometers deep under the cuticle, making them perfect to capture both the incident and the transmitted solar radiation.

Questions, questions

But questions remain – why should the aphids need to synthesize? As mentioned above, aphids in high food resource areas develop strong pigmentation and can also synthesize food for themselves. But doesn’t that defeat the very purpose? Why make when you already have food?

Both the mechanism and the necessity are unclear. These tiny critters had an unknown ace up their sleeves and there might be more.

The paper: http://www.nature.com/srep/2012/120816/srep00579/pdf/srep00579.pdf

Encoding Literature in DNA

In a couple of decades from now, your version of the Bible or Harry Potter (or the best-selling book of the 22nd century, whatever that might be) might just be stored in a small vial of liquid or on small chips. Harvard University researchers have just encoded a book in DNA fragments instead of on physical copy or e-copy.

The Alphabets of DNA

DNA is made up of building blocks called nucleotides, similar to how the English alphabet is made up of building blocks called alphabets. In the language of DNA, there are just 4 alphabets instead of 26, ‘A’, ‘T’, ‘G’ and ‘C’. Moving to information theory, each letter in DNA can thus encode 2 bits of information. Each nucleotide weighs around 250 Dalton (each Dalton weighs 1.66×10-24g). Thus, a single gram of single-stranded DNA could encode 455 exabytes (1 exabyte is 1018 bytes) of information. The previous sentence says ‘single-stranded’ because in nature, DNA molecules form two strands that wrap around each other to form a helix. Even keeping in mind this condition, a single gram of double stranded DNA could still encode around 225 exabytes, not a small number!

The four building blocks of DNA, also called bases (shown in green, red, yellow and blue) can be used as effective storage devices. [Image Credit: restlessmindboosters]

Translating English into DNAese

Encoding a book in DNA essentially means translating English into a code in a language of 4 letters. An html-encoded book called ‘Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves’ containing 53,426 words, 11 JPG images and a Javascript program has not been translated into the language of DNA. While DNA-encoding has been done on smaller scales before, the increasing ease and decreasing cost of DNA sequencing has made it possible to encode larger quantities of text in this biological molecule.

The entire book was translated onto small fragments of DNA called oligonucleotides. Each of these fragments had information from the book, and a small block with information for the ‘address’, where in the book the block belonged to. Thus, a ‘library’ of oligonucleotides is created on a DNA microchip. To ‘read’ the book, this library has to be amplified and sequenced using molecular approaches. These researchers encoded just one bit of information per DNA base instead of the maximum two, made multiple copies of the same oligonucleotide fragment so that errors could be accounted for, and still obtained a whopping density of 5.5 petabits (1015 bits) per millimeter cube.

Current costs of sequencing make this technology prohibitive.  However, the costs of DNA synthesis and sequencing are decreasing exponentially every year, making this a feasible storage molecule for the future. DNA is also stable at room temperature meaning it can be preserved for long periods. While DNA storage and retrieval is slower compared to other methods, its scale offers huge potential. It could thus be used in applications involving archival storage of massive amounts of data.

You can read more about this research here.

Meet MASER, Laser’s High Powered Older Cousin

Lasers have been around for a long time now. They are so ubiquitous, you can find them in computers, hunting rifle scopes, medical devices, and even a child’s play thing. Believe it or not, about 50 years ago, most of the devices that use lasers had not even been conceived of. What you also may not know is that the laser has an older cousin that has been sitting quietly on the shelf for nearly 50 years. It’s name is MASER.

Where LASER is an acronym for Light Amplification by Stimulated Emission of Radiation, MASER is Microwave Amplification by Stimulated Emission of Radiation. So basically, instead of visible light, the MASER produces a concentrated beam of microwaves. Though MASERs were actually developed first, the conditions it took to create them were very difficult to achieve. For instance, they required nearly absolute zero temperatures to operate. New research done by Britain’s National Physics Laboratory (NPL) and Imperial College, London has resulted in a solid-state room temperature MASER. The research has been published in the journal Nature and was led by Dr. Mark Oxborrow.

MASER
The MASER core via NPL Youtube Video

Up until now, MASERS were only a thing of physics labs and research facilities. The only real practical use for them was in atomic clocks. Now that the NPL scientists have been able to remove the extreme environmental conditions from the MASER, more practical applications are likely to be introduced. According to an NPL press release, “MASERs could be used to make more sensitive medical instruments for scanning patients, improved chemical sensors for remotely detecting explosives; lower-noise read-out mechanisms for quantum computers and better radio telescopes for potentially detecting life on other planets.” In the embedded video below, Dr. Oxborrow gives a brief description of the MASER and shows the core they invented to make all of this possible.

[Video Link]

Conventional MASERs work by directing microwaves at crystals such as ruby. Unfortunately, this material requires extremely low temperatures, as well as a lot of costly magnets to work. The NPL scientists discovered a new type of crystal called p-terphenyl crystal. This crystal is “doped” pentacene which allows it to be used to amplify microwaves at room temperature. There are still challenges facing the MASER. One, is to get it to work continuously instead of in pulses. The other, is to get it to operate in a broader range of microwave frequencies to make it more useful. To keep up with the MASER research, visit http://www.npl.co.uk/news/maser.

Inception in Real Life: Scientists Figure Out How To Hack The Human Brain

Even Nolan didn’t think it could be possible when he made Inception, but it turns out that researchers at Usenix Security conference have been speaking of using a computer interface to hack the brain! Yes, it might actually be possible to enter the brain and retrieve information that you’d prefer to keep secret. Like retrieving a combination key to a safe that your dying father might have given you and you have it stored somewhere in the subconscious.

Reading the Mind

The idea is simply this: have your brain mapped by sensors (here, an EEG or Electroencephalograph is used), which pick up crucial brain activity and then sophisticated software can help understand what it is that the brain is trying to do! These are called ‘brain-computer interfaces’ (or BCI’s) for obvious reasons.

These can actually help you mentally control your computer using specific thought patterns.

The BCI from Emotiv technologies.
Controlling a video game using BCI

Machine over Mind

What is interesting is how a computer can browse through your mental database and steal away some pieces of sensitive information. Security researchers from the Universities of Oxford and Geneva and University of California, Berkeley have developed a program to be used by the software that has only one purpose – finding information like home address, debit card PIN and date of birth. They found 28 willing participants, who didn’t know about the hacking (of course, otherwise the whole exercise is futile, right?) and tested this program on them. The success rate varied from a mere 10% to a respectable 40% for different fields of sensitive data.

The four experiments

The technique is a lot like hacking passwords. The key response tracked by the program is known as a P300 response – the brainwave activity that the brain undergoes when it recognizes something familiar, like a known face, own neighbourhood, own debit card PIN and so on! The peaks in the P300 activity were noted and the analysis of this data can give a very good indication of what the right answers are!

The P300 activity. Notice the black peak indicating a high for the target stimulus
The EEG results for a target and a non-target stimulus

Future thoughts – You might know them already!

Yes, cool, innovative and scary! Imagine the chaos which will ensue if the bank manager is kidnapped and crucial information is extracted from his brain using these kinds of hacking techniques. How can a big bank cope with that threat in the not-so-far future? What about the fear of malware – say you use the BCIs to control devices, but some pop-ups show you some random numbers and your P300 activity indicates that this might actually be your PIN? How do you protect yourself against that? The only viable option seems to be to not think about it, but then that is, believe it or not, the hardest thing to do!

Maybe, militarizing your subconscious is the only way to go. Don’t be scared to dream a bit bigger – and a bit weirder.

All pictures taken from the paper below.

Paper: https://www.usenix.org/system/files/conference/usenixsecurity12/sec12-final56.pdf