Posts about open access paper

Nature Uses Stem Cells from Fetus to Repair Health of Mother

Science shows us so many amazing things. Scientists have learned mice use stem cells from the fetus to repair damage to the mother in the event of things like heart attacks. And there is evidence people do the same thing. Very cool. Nature beat us to the idea of using stem cells to treat health problems.

Helpful Mouse Fetuses Naturally Send Stem Cells to Mom to Fix Her Damaged Heart

When the scientists examined the female mice’s heart tissue two weeks after the heart attacks, they found lots of glowing green tissue—cells that came from the fetus—in the mom’s heart. Mice who had heart attacks had eight times as many cells from the fetus in their hearts as mice who hadn’t had a heart attack did, meaning the high volume of fetal cells was a response to the heart attack.

What’s more, the embryo’s stem cells had differentiated into various types of heart tissue, including cardiomyocytes, the rhythmically contracting muscle cells that produce a heartbeat.

The hearts of two women who suffered from severe heart weakness were later found to contain cells derived from the cells of a male fetus years after they gave birth to their sons.

The same thing seems to hold true for other organs. When pregnant women have damage in other organs, including the brain, lung, and liver, earlier studies have shown, fetal cells show up there, too.

It makes sense for a fetus to try and aid the mother but it is amazing the evolution found such solutions. Given how many challenges the fetus creates for the mother giving some benefits can help increase the odds of a health birth.

Related: Researchers Explain How Rotifers Thrive Despite Forgoing SexMaking Embryonic Stem CellsStructure and Function of RibosomeWhy People Often Get Sicker When They’re Stressed

Faster Than Light Speed Anomaly Reported by CERN

The OPERA result is based on the observation of over 15000 neutrino events measured at Gran Sasso, and appears to indicate that the neutrinos travel at a velocity 20 parts per million above the speed of light, nature’s cosmic speed limit. Given the potential far-reaching consequences of such a result, independent measurements are needed before the effect can either be refuted or firmly established. This is why the OPERA collaboration has decided to open the result to broader scrutiny. The collaboration’s result is available on the preprint server arxiv.org.

The OPERA measurement is at odds with well-established laws of nature, though science frequently progresses by overthrowing the established paradigms. For this reason, many searches have been made for deviations from Einstein’s theory of relativity, so far not finding any such evidence. The strong constraints arising from these observations makes an interpretation of the OPERA measurement in terms of modification of Einstein’s theory unlikely, and give further strong reason to seek new independent measurements.

“This result comes as a complete surprise,” said OPERA spokesperson, Antonio Ereditato of the University of Bern. “After many months of studies and cross checks we have not found any instrumental effect that could explain the result of the measurement. While OPERA researchers will continue their studies, we are also looking forward to independent measurements to fully assess the nature of this observation.”

“When an experiment finds an apparently unbelievable result and can find no artefact of the measurement to account for it, it’s normal procedure to invite broader scrutiny, and this is exactly what the OPERA collaboration is doing, it’s good scientific practice,” said CERN Research Director Sergio Bertolucci. “If this measurement is confirmed, it might change our view of physics, but we need to be sure that there are no other, more mundane, explanations. That will require independent measurements.” This is a great reminder of the proper application of the scientific inquiry process. Our understanding moves forward based on evidence and incredible results require a high burden of proof before we accept them.

In order to perform this study, the OPERA Collaboration teamed up with experts in metrology from CERN and other institutions to perform a series of high precision measurements of the distance between the source and the detector, and of the neutrinos’ time of flight. The distance between the origin of the neutrino beam and OPERA was measured with an uncertainty of 20 cm over the 730 km travel path. The neutrinos’ time of flight was determined with an accuracy of less than 10 nanoseconds by using sophisticated instruments including advanced GPS systems and atomic clocks. The time response of all elements of the CNGS beam line and of the OPERA detector has also been measured with great precision.

“We have established synchronization between CERN and Gran Sasso that gives us nanosecond accuracy, and we’ve measured the distance between the two sites to 20 centimetres,” said Dario Autiero, the CNRS researcher who will give this afternoon’s seminar. “Although our measurements have low systematic uncertainty and high statistical accuracy, and we place great confidence in our results, we’re looking forward to comparing them with those from other experiments.”

“The potential impact on science is too large to draw immediate conclusions or attempt physics interpretations. My first reaction is that the neutrino is still surprising us with its mysteries.” said Ereditato. “Today’s seminar is intended to invite scrutiny from the broader particle physics community.”

The OPERA experiment was inaugurated in 2006, with the main goal of studying the rare transformation (oscillation) of muon neutrinos into tau neutrinos. One first such event was observed in 2010, proving the unique ability of the experiment in the detection of the elusive signal of tau neutrinos.

This is great stuff, wether it turns out to be an amazing result that changes our understanding of physics or even if it doesn’t (if it turns out the apparent result is not what it seems). It is great to see us attempt to learn. My guess is that we find some explanation for the anomaly that does avoids something traveling faster than the speed of light.

Brian Cox on the BBC 6: “This is the way science works, we go away and do it again and check, and then do it again and check. If it is confirmed then it will be the most significant discovery in physics in the last, at least, 100 years.”

Related: full press releaseThe Sun is a Miasma of Incandescent PlasmaGravity and the Scientific MethodMore Mysterious Space PhenomenonNeutrino particle traveling faster than light? Two ways it could rewrite physics

Large Crabs Invading Antarctic as Waters Warm

photo of giant red king crab

Giant red king crabs

Large crabs are invading the Antarctic environment and due to their numbers and practices could cause havoc. They look yummy though. And eating them would be doing nature a favor unlike the overfishing of the oceans. Abstract of the open access article, A large population of king crabs in Palmer Deep on the west Antarctic Peninsula shelf and potential invasive impacts:

Lithodid crabs (and other skeleton-crushing predators) may have been excluded from cold Antarctic continental shelf waters for more than 14 Myr [million years]. The west Antarctic Peninsula shelf is warming rapidly and has been hypothesized to be soon invaded by lithodids. A remotely operated vehicle survey in Palmer Deep, a basin 120 km onto the Antarctic shelf, revealed a large, reproductive population of lithodids, providing the first evidence that king crabs have crossed the Antarctic shelf. DNA sequencing and morphology indicate the lithodid is Neolithodes yaldwyni Ahyong & Dawson, previously reported only from Ross Sea waters. We estimate a N. yaldwyni population density of 10 600 km−2 and a population size of 1.55 × 106 in Palmer Deep, a density similar to lithodid populations of commercial interest around Alaska and South Georgia. The lithodid occurred at depths of more than 850 m and temperatures of more than 1.4°C in Palmer Deep, and was not found in extensive surveys of the colder shelf at depths of 430–725 m. Where N. yaldwyni occurred, crab traces were abundant, megafaunal diversity reduced and echinoderms absent, suggesting that the crabs have major ecological impacts. Antarctic Peninsula shelf waters are warming at approximately 0.01°C yr−1; if N. yaldwyni is currently limited by cold temperatures, it could spread up onto the shelf (400–600 m depths) within 1–2 decades. The Palmer Deep N. yaldwyni population provides an important model for the potential invasive impacts of crushing predators on vulnerable Antarctic shelf ecosystems.

Related: Giant Star Fish and More in Antarctica2,000 Species New to Science (600 of them crabs) from One IslandAntarctic Fish “Hibernate” in Winter

Is Dark Matter an Illusion?

Open access letter asks – Is dark matter an illusion created by the gravitational polarization of the quantum vaccum? by Dragan Slavkov Hajdukovic, CERN

Assuming that a particle and its antiparticle have the gravitational charge of the opposite sign, the physical vacuum may be considered as a fluid of virtual gravitational dipoles. Following this hypothesis, we present the first indications that dark matter may not exist and that the phenomena for which it was invoked might be explained by the gravitational polarization of the quantum vacuum by the known baryonic matter.

Let us start with a major unresolved problem. The measured galaxy rotation curves remain roughly constant at large radii. Faster than expected orbits, require a larger central force, which, in the framework of our theory of gravity, cannot be explained by the existing baryonic matter. The analogous problem persists also at the scale of clusters of galaxies.

The favoured solution is to assume that our current theory of gravity is correct, but every galaxy resides in a halo of dark matter made of unknown non-baryonic particles (for a brief review on dark matter see for instance: Einasto, 2010). A full list of the proposed dark matter particles would be longer than this letter; let us mention only weekly interacting massive particles and axions. In spite of the significant efforts dark particles have never been detected…

The scientific inquiry process continues to be used to try and explain the evidence we gather. Unsettled areas of science show how difficult the discovery process is. Once we have settled on theories it is so easy to explain why basic truths of evolution, geology, chemistry… result in what the evidence shows. But getting to the scientific consensus is a challenging process.


Dark Matter Is an Illusion, New Antigravity Theory Says

Physicist David Evans called the new study a “very interesting theoretical exercise,” but he said he isn’t ready to abandon dark matter just yet. “The evidence for dark matter is now very compelling,” said Evans, of the University of Birmingham, who leads the U.K. team for the ALICE detector at CERN’s Large Hadron Collider.

For example, in 2006 astronomers unveiled a photo of two colliding galaxies known as the Bullet cluster that purportedly showed the separation of matter from dark matter. A similar effect was observed in the Pandora cluster earlier this summer, said Evans, who was not involved in the study.

Hajdukovic said he is currently expanding his theory to account for these observations. His preliminary calculations, he said, suggest that “what is observed in the Bullet cluster and more recently at the Pandora cluster may be understood in the framework of the gravitational polarization of the quantum vacuum.”

CERN physicist Michael Doser agreed that Hajdukovic’s ideas are “unorthodox” but did not immediately dismiss the new theory…
“In a few years,” Doser said, “we should definitely be in a position to confirm or refute [Hajdukovic's] hypothesis.”

Related: The Mystery of Empty SpaceWhy do we Need Dark Energy to Explain the Observable Universe?Dark Matter Experiment ResultsLooking for Signs of Dark Matter Over Antarctica

Cutting the Boarding Time of Planes in Half

I thought I wrote about this several years ago, but I guess I didn’t (I can’t find it, if I did). Experimental test of airplane boarding methods:

The Ste en method, on the other hand, orders the passengers in such a way that adjacent passengers in line are sitting in corresponding seats two rows apart from each other (e.g., 12A, 10A, 8A, 6A, etc.). This method trades a small number of aisle interferences at the front of the cabin, for the benefit of having multiple passengers stowing their luggage simultaneously. Other methods, such as Wilma and the Reverse Pyramid also realize parallel use of the aisle in a natural way as adjacent passengers are frequently sitting in widely separated rows.

We have seen experimentally that there is a marked difference in the time required to board an aircraft depending upon the boarding method used. The evidence strongly supports the heuristic argument from Ste en that methods that parallelize the boarding process by more efficiently utilizing the aisle (having more passengers stow their luggage simultaneously) will board more quickly than those that do not. The relative benefit of the application of this theory will grow with the length of the aircraft. Here, we used a 12-row mock airplane, but a more typical airplane with twice that number of rows will gain more by the implementation of parallelized boarding methods.

How this improvement scales with the cabin length is different for each method. For the Ste en method, the benefit will scale almost linearly. If the airplane is twice as long, the time savings will be nearly twice as much since the density of luggage-stowing passengers will remain the same and the boarding will still be maximally parallel. For Wilma and random boarding the benefit will not be as strong since the benefits of parallel boarding are randomly distributed along the length of the cabin instead of being regularly distributed.

I am not optimistic that airlines will even test out this method. People tend to think companies apply sensible, proven concepts and methods. But that is much less likely to be done than people think. The failure of many places to use simple queuing theory improvement (customers should form one line and be served the next available person not form many individual lines) is one example of failures by companies to apply decades old proven better methods. The poor adoption of multivariate designed experiments is another. Applying better ideas is a process that is not done very efficiently in business, health care, education or even science and engineering – in fact in any human endeavor. This is a waste that impacts each of us every day. It is also an opportunity for you to gain advantages just by applying all the good ideas lying around that others are ignoring. You need to test the ideas out in your setting (using the PDSA cycle in an organizational context a good method).

Related: Engineering the Boarding of AirplanesSuccessful Emergency Plane Landing in the Hudson RiverChecklists Save LivesImproving Engineering Education

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.

Further inspired by Köhler’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).

Related: Orangutan Attempts to Hunt Fish with SpearBird Using Bait to Catch FishCrows Transferring Their Understanding to Novel ProblemCapuchin Monkeys Using Stone ToolsFighting Elephant Poaching With SciencePhoto of Fish Using a Rock to Open a Clam
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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.

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).

image showing the results of cultures treated with DRACO v. those not treated

Related: Science Explained: RNA Interference8 Percent of the Human Genome is Old Virus GenesVirus Engineered To Kill Deadly Brain Tumors
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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.”

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.

Related: Gravity and the Scientific MethodGravity May Emerge from Quantum InformationDoes Time ExistWebcast of Astronaut Testing Gravity on the Moonsupport open science

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.

Related: Robots That Start as Babies Master Walking Faster Than Those That Start as AdultsFriday Fun: Robocup 2010, Robot FootballToyota Develops Thought-controlled Wheelchair
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New Analysis of Primordial Soup Experiment Half a Century Later

Open access paper: Primordial synthesis of amines and amino acids in a 1958 Miller H2S-rich spark discharge experiment

Archived samples from a previously unreported 1958 Stanley Miller electric discharge experiment containing hydrogen sulfide (H2S) were recently discovered and analyzed using high-performance liquid chromatography and time-of-flight mass spectrometry. We report here the detection and quantification of primary amine-containing compounds in the original sample residues, which were produced via spark discharge using a gaseous mixture of H2S, CH4, NH3, and CO2. A total of 23 amino acids and 4 amines, including 7 organosulfur compounds, were detected in these samples.

The major amino acids with chiral centers are racemic within the accuracy of the measurements, indicating that they are not contaminants introduced during sample storage. This experiment marks the first synthesis of sulfur amino acids from spark discharge experiments designed to imitate primordial environments. The relative yield of some amino acids, in particular the isomers of aminobutyric acid, are the highest ever found in a spark discharge experiment.

The simulated primordial conditions used by Miller may serve as a model for early volcanic plume chemistry and provide insight to the possible roles such plumes may have played in abiotic organic synthesis. Additionally, the overall abundances of the synthesized amino acids in the presence of H2S are very similar to the abundances found in some carbonaceous meteorites, suggesting that H2S may have played an important role in prebiotic reactions in early solar system environments.

Related: All present-day Life on Earth Has A Single AncestorLife Untouched by the SunAmazing Designs of LifeAlbert Einstein, Marylin Monroe Hybrid Image

Friday Fun: Aerodynamics for Sports

“Impossible” Soccer Kick Leads to New Physics Equation

The amazing goal — which left French goalkeeper Fabien Barthez too stunned to react — was scored during a friendly match in the run up to the 1998 World Cup. A group of French scientists, perhaps desperate to prove that at least the laws of physics weren’t actively rooting against their national team, have been able to figure out the trajectory of the ball and, with it, an equation to describe its unusual path.

It all comes down to the fact that, when a sphere spins, its trajectory is a spiral. Usually, gravity and the relatively short distance the ball travels cover up this spiral trajectory, but Carlos was a mere 115 feet away and kicked the ball hard enough to reveal its true spiral-like path.

In this open access paper, the spinning ball spiral, the authors explore the science behind ball paths in different situations.

one can identify sports dominated by aerodynamics (table tennis, golf and tennis) and sports dominated by gravity (basketball and handball). In between, we find sports where both gravity and aerodynamics play a comparable role (soccer, volleyball and baseball). Indeed, in the first category of sports, the spin is systematically used, while it is not relevant in the second category, and it only appears occasionally in the third one, in order to produce surprising trajectories.

Related: Friday Fun: Amazing GoalThe Science of the Football SwerveEngineering a Better Football

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