Category Archives: Research

Insightful Problem Solving in an Asian Elephant

Another example of very cool animal behavior. This Asian Elephant, seemed to consider the problem, devise a solution and then go get a stool to reach food that could not be reached without a tool.

Insightful Problem Solving in an Asian Elephant

The “aha” moment or the sudden arrival of the solution to a problem is a common human experience. Spontaneous problem solving without evident trial and error behavior in humans and other animals has been referred to as insight. Surprisingly, elephants, thought to be highly intelligent, have failed to exhibit insightful problem solving in previous cognitive studies. We tested whether three Asian elephants (Elephas maximus) would use sticks or other objects to obtain food items placed out-of-reach and overhead. Without prior trial and error behavior, a 7-year-old male Asian elephant showed spontaneous problem solving by moving a large plastic cube, on which he then stood, to acquire the food. In further testing he showed behavioral flexibility, using this technique to reach other items and retrieving the cube from various locations to use as a tool to acquire food. In the cube’s absence, he generalized this tool utilization technique to other objects and, when given smaller objects, stacked them in an attempt to reach the food. The elephant’s overall behavior was consistent with the definition of insightful problem solving. Previous failures to demonstrate this ability in elephants may have resulted not from a lack of cognitive ability but from the presentation of tasks requiring trunk-held sticks as potential tools, thereby interfering with the trunk’s use as a sensory organ to locate the targeted food.
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Further inspired by KÃ¶hler’s chimpanzee studies, in experiment 4 we conducted 8 additional sessions to investigate whether Kandula would stack items to reach food. For these sessions, the baited branches were hung at a height that could be reached by stacking three butcher block cutting boards or by the use of other objects. In addition, the elephant was given sticks and other enrichment items. Kandula first touched several items and then moved two items, a plastic disk and a block under the suspended branches, placing one front foot on each in an unsuccessful attempt to reach for the branch. He solved the problem in an unexpected novel manner, moving and standing on the object closest in size to the absent cube, a large ball. Standing on unstable platforms such as this had not been previously observed. He repeated this behavior 9 times during this session. During the session’s last minutes, Kandula picked up a block ~2 m from the food and placed it directly on top of a block that he placed under the food in a previous attempt. He stood on the stacked blocks and attempted to reach the food but was unsuccessful. He stacked two blocks again in the second and sixth sessions but each time his trunk was several inches from the food.

This is very cool research. I do wonder why they didn’t provide more videos (and in a more user-friendly format than .mov files). I made them available via YouTube.

It seems like a very interesting area to have more experiments with more elephants (and continuing to work with Kandula: he seems to be very curious elephant, good for him).

MIT Scientists Find New Drug That Could Cure Nearly Any Viral Infection

New drug could cure nearly any viral infection

The drug works by targeting a type of RNA produced only in cells that have been infected by viruses. “In theory, it should work against all viruses,” says Todd Rider, a senior staff scientist in Lincoln Laboratory‘s Chemical, Biological, and Nanoscale Technologies Group who invented the new technology.
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There are a handful of drugs that combat specific viruses, such as the protease inhibitors used to control HIV infection, but these are relatively few in number and susceptible to viral resistance.

Rider drew inspiration for his therapeutic agents, dubbed DRACOs (Double-stranded RNA Activated Caspase Oligomerizers), from living cells’ own defense systems. When viruses infect a cell, they take over its cellular machinery for their own purpose — that is, creating more copies of the virus. During this process, the viruses create long strings of double-stranded RNA (dsRNA), which is not found in human or other animal cells.

As part of their natural defenses against viral infection, human cells have proteins that latch onto dsRNA, setting off a cascade of reactions that prevents the virus from replicating itself. However, many viruses can outsmart that system by blocking one of the steps further down the cascade.

Rider had the idea to combine a dsRNA-binding protein with another protein that induces cells to undergo apoptosis (programmed cell suicide) — launched, for example, when a cell determines it is en route to becoming cancerous. Therefore, when one end of the DRACO binds to dsRNA, it signals the other end of the DRACO to initiate cell suicide.

Combining those two elements is a “great idea” and a very novel approach, says Karla Kirkegaard, professor of microbiology and immunology at Stanford University. “Viruses are pretty good at developing resistance to things we try against them, but in this case, it’s hard to think of a simple path pathway to drug resistance,” she says.

Each DRACO also includes a “delivery tag,” taken from naturally occurring proteins, that allows it to cross cell membranes and enter any human or animal cell. However, if no dsRNA is present, DRACO leaves the cell unharmed.

Very cool stuff and potentially hugely beneficial. Just a reminder: this works against viruses – not bacteria (just as antibiotics do not work against viruses).

Quantum Information Theory Postulated As Source of Emergent Theory of Gravity

I love the advances we have made using our understanding of science and engineering, like the internet, air conditioning and antibiotics. I also love the discussion of research where we really have only educated guesses about what the scientific inquiry process is telling us about the way things are. This research from the University of York is very interesting.

Escaping gravity’s clutches: the black hole breakout

Professor Braunstein says: “Our results didn’t need the details of a black hole’s curved space geometry. That lends support to recent proposals that space, time and even gravity itself may be emergent properties within a deeper theory. Our work subtly changes those proposals, by identifying quantum information theory as the likely candidate for the source of an emergent theory of gravity.”
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Dr Patra adds: “We cannot claim to have proven that escape from a black hole is truly possible, but that is the most straight-forward interpretation of our results. Indeed, our results suggest that quantum information theory will play a key role in a future theory combining quantum mechanics and gravity.”

It is too bad the University of York supports closed science and allows work to be withheld from the public to support outdated publishers business models. Luckily scientists often support open science and publish material openly – I have provided a link for those interested in science instead of the link the University of York gives to a publishers closed system.

Black Hole Evaporation Rates without Spacetime

Verlinde recently suggested that gravity, inertia, and even spacetime may be emergent properties of an underlying thermodynamic theory. This vision was motivated in part by Jacobson’s 1995 surprise result that the Einstein equations of gravity follow from the thermodynamic properties of event horizons. Taking a first tentative step in such a program, we derive the evaporation rate (or radiation spectrum) from black hole event horizons in a spacetime-free manner. Our result relies on a Hilbert space description of black hole evaporation, symmetries therein which follow from the inherent high dimensionality of black holes, global conservation of the no-hair quantities, and the existence of Penrose processes. Our analysis is not wedded to standard general relativity and so should apply to extended gravity theories where we find that the black hole area must be replaced by some other property in any generalized area theorem.

Biologists Identified a New Way in Which Bacteria Hijack Healthy Cells

Associate professor of biological sciences Zhao-Qing Luo, foreground, and graduate student Yunhao Tan identified a new way in which bacteria modify healthy cells during infection. Shown on the computer screen are cells infected with a mutant strain of the bacteria Legionella pneumophila used in their research.

Purdue University biologists identified a new way in which bacteria hijack healthy cells during infection, which could provide a target for new antibiotics. Zhao-Qing Luo, the associate professor of biological sciences who led the study, said the team discovered a new enzyme used by the bacterium Legionella pneumophila – which causes Legionnaires’ disease – to control its host cell in order to take up residence.

“Legionnaires’ disease is a severe form of pneumonia, and this finding could lead to the design of a new therapy that saves lives,” Luo said. “At the same time it also provides great insight into a general mechanism of both bacterial infection and cell signaling events in higher organisms including humans.”

Successful infection by Legionella pneumophila requires the delivery of hundreds of proteins into the host cells that alter various functions to turn the naturally hostile environment into one tailor-made for bacterial replication. These proteins tap into existing communication processes within the cells in which an external signal, such as a hormone, triggers a cascade of slight modifications to proteins that eventually turns on a gene that changes the cell’s behavior, he said.

“Pathogens are successful because they know how information in our cells is relayed and they amplify some signals and block others in order to evade the immune system and keep the cell from defending itself,” Luo said. “Despite our understanding of this, we do not know much about how the proteins delivered by the bacteria accomplish this – how they work. This time we were able to pinpoint an enzyme and see how it disrupted and manipulated a specific signaling pathway in order to create a better environment for itself.”

The signaling pathway involved was only recently identified, and the discovery by Luo and graduate student Yunhao Tan also provides a key insight into its process. The signaling pathway involves a new form of protein modification called AMPylation in order to relay instructions to change cell behavior and has been found to be used by almost all organisms, Luo said.

The bacterium affects the host cell’s functions differently during different phases of the infection process, tapping into signaling pathways to turn on and off certain natural cellular activities. SidD stops the AMPylation process four hours after the start of infection in order to reverse an earlier modification that would be detrimental to the cell if left in place, he said.

Read the full press release.

NASA’s Mars Curiosity Rover

Curiosity is the name of the new rover from NASA. It will be launched to continue the exploration of Mars so successfully done by Spirit and Opportunity (2 previous Mars rovers that did some amazing work and laster years longer than expected). The rover is NASA’s Mars Science Laboratory, a mobile robot for investigating Mars’ past or present ability to sustain microbial life.

photo of NASA's Mars Rover: Curiosity

Once on the surface, the rover will be able to roll over obstacles up to 75 centimeters (29 inches) high and travel up to 90 meters per hour. On average, the rover is expected to travel about 30 meters per hour, based on power levels, slippage, steepness of the terrain, visibility, and other variables.

The rover is about the size of a small SUV — 10 feet long (not including the arm), 9 feet wide and 7 feet tall. It weighs 900 kilograms (2,000 pounds)

The rover will carry a radioisotope power system that generates electricity from the heat of plutonium’s radioactive decay. This power source gives the mission an operating lifespan on Mars’ surface of a full martian year (687 Earth days) or more, while also providing significantly greater mobility and operational flexibility, enhanced science payload capability, and exploration of a much larger range of latitudes and altitudes than was possible on previous missions to Mars.

More Dark Matter Experiment Results

A dark-matter experiment deep in the Soudan mine of Minnesota now has detected a seasonal signal variation similar to one an Italian experiment has been reporting for more than a decade.

The new seasonal variation, recorded by the Coherent Germanium Neutrino Technology (CoGeNT) experiment, is exactly what theoreticians had predicted if dark matter turned out to be what physicists call Weakly Interacting Massive Particles (WIMPs).

“We cannot call this a WIMP signal. It’s just what you might expect from it,” said Juan Collar, associate professor in physics at the University of Chicago. Collar and John Orrell of Pacific Northwest National Laboratory, who lead the CoGeNT collaboration, are submitting their results in two papers to Physical Review Letters.

WIMPS might have caused the signal variation, but it also might be a random fluctuation, a false reading sparked by the experimental apparatus itself or even some exotic new phenomenon in atomic physics, Collar said.

Dark matter accounts for nearly 90 percent of all matter in the universe, yet its identity remains one of the biggest mysteries of modern science. Although dark matter is invisible to telescopes, astronomers know it is there from the gravitational influence it exerts over galaxies.

Theorists had predicted that dark matter experiments would detect an annual modulation because of the relative motion of the Earth and sun with respect to the plane of the Milky Way galaxy.
Continue reading →

H-index Rank for Countries: for Science Publications

The SCImago Journal and Country Rank provides journal and country scientific indicators. As stated in previous posts, these types of rankings have limitations but they are also interesting. The table shows the top 6 countries by h-index and then some others I chose to list (the top 6 repeat from my post in 2008 – Country H-index Rank for Science Publications). The h-index provides a numeric indication of scientific production and significance (by looking at the citations given papers by other papers). Read more about the h-index (Hirsh index).

Country	h-index	h-index (2007)	% of World Population	total Cites
USA	1,139	793	4.5%	87,296,701
United Kingdom	689	465	.9%	21,030,171
Germany	607	408	1.2%	17,576,464
France	554	376	1.0%	12,168,898
Canada	536	370	.5%	10,375,245
Japan	527	372	1.8%	14,341,252
Additional countries of interest
18) China	279	161	19.4%	5,614,294
21) South Korea	258	161	.7%	2,710,566
22) Brazil	239	148	2.8%	1,970,704
25) India	227	146	17.5%	2,590,791
31) Singapore	196		.01%	871,512

Evolution of Altruism in Robots

The webcast explores robots evolving cooperative behavior. A Quantitative Test of Hamilton’s Rule for the Evolution of Altruism (open access paper)

One of the enduring puzzles in biology and the social sciences is the origin and persistence of altruism, whereby a behavior benefiting another individual incurs a direct cost for the individual performing the altruistic action. This apparent paradox was resolved by Hamilton’s theory, known as kin selection, which states that individuals can transmit copies of their own genes not only directly through their own reproduction but also indirectly by favoring the reproduction of kin, such as siblings or cousins. While many studies have provided qualitative support for kin selection theory, quantitative tests have not yet been possible due to the difficulty of quantifying the costs and benefits of helping acts. In this study, we conduct simulations with the help of a simulated system of foraging robots to manipulate the costs and benefits of altruism and determine the conditions under which altruism evolves.

By conducting experimental evolution over hundreds of generations of selection in populations with different costs and benefits of altruistic behavior, we show that kin selection theory always accurately predicts the minimum relatedness necessary for altruism to evolve. This high accuracy is remarkable given the presence of pleiotropic and epistatic effects, as well as mutations with strong effects on behavior and fitness. In addition to providing a quantitative test of kin selection theory in a system with a complex mapping between genotype and phenotype, this study reveals that a fundamental principle of natural selection also applies to synthetic organisms when these have heritable properties.

5% of the Universe is Normal Matter, What About the Other 95%?

Dark Matters from PHD Comics on Vimeo.

Great discussion and illustration of the state of our understanding of physics, matter, dark matter and the rest of the stuff our universe has from PhD comics. What is the universe made of? 5% of it is normal matter (the stardust we are made of), 20% dark matter and the other 75% – we have no idea!

Dark Cosmos is a nice book on some of these ideas. It is 5 years old so missing some of the latest discoveries.

Cancer Vaccines

A reader commented on a previous post (MIT Engineers Design New Type of Nanoparticle for Vacines) asking about how vaccines can fight cancer. Preventative vaccines can build up immune response to viruses which cause cancer. So the vaccine actually works against the virus which prevents the virus from causing cancer.

The U.S. Food and Drug Administration (FDA) has approved two vaccines, GardasilÂ® and CervarixÂ®, that protect against infection by the two types of human papillomavirus (HPV) – types 16 and 18 – that cause approximately 70% of all cases of cervical cancer worldwide. At least 17 other types of HPV are responsible for the remaining 30% of cervical cancer cases. HPV types 16 and/or 18 also cause some vaginal, vulvar, anal, penile, and oropharyngeal cancers.

Many scientists believe that microbes cause or contribute to between 15% and 25% of all cancers diagnosed worldwide each year, with the percentages being lower in developed than developing countries.

Vaccines can also help stimulate the immune system to fight cancers.

B cells make antibodies, which are large secreted proteins that bind to, inactivate, and help destroy foreign invaders or abnormal cells. Most preventive vaccines, including those aimed at hepatitis B virus (HBV) and human papillomavirus (HPV), stimulate the production of antibodies that bind to specific, targeted microbes and block their ability to cause infection. Cytotoxic T cells, which are also known as killer T cells, kill infected or abnormal cells by releasing toxic chemicals or by prompting the cells to self-destruct (a process known as apoptosis).

Other types of lymphocytes and leukocytes play supporting roles to ensure that B cells and killer T cells do their jobs effectively. These supporting cells include helper T cells and dendritic cells, which help activate killer T cells and enable them to recognize specific threats.

Cancer treatment vaccines are designed to work by activating B cells and killer T cells and directing them to recognize and act against specific types of cancer. They do this by introducing one or more molecules known as antigens into the body, usually by injection. An antigen is a substance that stimulates a specific immune response. An antigen can be a protein or another type of molecule found on the surface of or inside a cell.