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The New Science of Network Archaeology
A new way of excavating the past structure of networks reveals important information about their evolution
The study of networks has exploded in recent years. One of the more important discoveries is that many networks share common growth patterns. So if researchers grow a model network at random using these rules, the model will have the same topological structure as the network under study
For example, the world wide web tends to grow according to a process known as preferential attachment in which new links to a page depend on the number it already has (otherwise known as the rich get richer effect).
By contrast, the growth of networks associated with protein interactions in cells is best described by another process known as “duplication-mutation with complementarity”. Here new nodes become copies of old ones by connecting to all their neighbours, then a process of mutation occurs in which connections can be removed.
And social networks tend to grow according to the same model that describes the way forest fires spread.
That has given network specialists all kinds of insights into network dynamics, how they evolve, the relative importance of specific nodes, how communities change over time and how information propagates through them.
But this information is entirely generic rather than specific to a real network. So a snapshot of the Last.fm social network will tell you who the central players are now and the forest fire model will give you an idea of how this structure evolved. But ask who the central players were three years ago, given the structure that exists today, and network scientists will scratch their feet and stare at the floor.
Now that looks set to change thanks to a new approach from Saket Navlakha and Carl Kingsford at the University of Maryland at College Park. Instead of using these growth patterns to study how networks evolve, their idea is to look at the process in reverse.
“Instead of growing a random network forward according to an evolutionary model, we decompose the actual observed network backwards in time, as dictated by the model,” they say. “The resulting sequence of networks constitute a model-inferred history of the present-day network.” This is network archaeology.
That’s significant because the result depends specifically on the network under investigation, rather than solely on the growth model used to generate it.
They go on to show the power of this idea by inferring the history of several networks. For example, they are able to accurately estimate the time at which users of last.fm joined the network simply by looking at the structure today.
Navlakha and Kingsford quite rightly point out that the possibility of inferring past behaviour from current network structures raises certain privacy issues. These will now need to be addressed by the owners this data.
Perhaps the most important application of network archaeology will be in biology. Over the last few years, molecular biologists have been painstakingly mapping the networks formed by protein interactions in cells. These give a snapshot of the way these networks have evolved.
In principle, comparing the networks of closely related species should give some insight into how they evolved. For example, a search for common structures should reveal ancestral subnetworks. That’s useful but it does not show how the process of evolution.
Network archaeology should provide new insight. Navlakha and Kingsford demonstrate it by taking the network of protein-protein interactions in baker’s yeast and essentially “playing the tape backwards” according to the rules of “duplication-mutation with complementarity”.
They discovered they were able to determine the age of proteins, ie how long it has been since they first entered the network. They were also able to work out how the proteins were duplicated and mutated in the past, or, in other words, how they evolved.
That’s a powerful tool that is likely to generate some interesting new insights into the process of evolution, not to mention the history of the networks. Expect to hear a lot more about it.
Ref: arxiv.org/abs/1008.5166: Network Archaeology: Uncovering Ancient Networks from Present-day Interactions
The Extraordinary Tale of Red Rain, Comets and Extraterrestrials
For years, claims have circulated that red rain which fell in India in 2001, contained cells unlike any found on Earth. Now new evidence that these cells can reproduce is about to set the debate alive
Panspermia is the idea that life exists throughout the universe in comets, asteroids and interstellar dust clouds and that life of Earth was seeded from one or more of these sources. Panspermia holds that we are all extraterrestrials.
While this is certainly not a mainstream idea in science, a growing body of evidence suggests that it should be carefully studied rather than casually disregarded.
For example, various bugs have been shown to survive for months or even years in the harsh conditions of space. And one of the more interesting but lesser known facts about the Mars meteorite that some scientists believe holds evidence of life on Mars, is that its interior never rose above 50 degrees centigrade, despite being blasted from the Martian surface by an meteor impact and surviving a fiery a descent through Earth’s thick atmosphere.
If there is life up there, this evidence suggests that it could survive the trip to Earth.
All that seems well established. Now for the really controversial stuff.
In 2001, numerous people observed red rain falling over Kerala in the southern tip of India during a two month period. One of them was Godfrey Louis, a physicist at nearby Cochin University of Science and Technology. Intrigued by this phenomena, Louis collected numerous samples of red rain, determined to find out what was causing the contamination, perhaps sand or dust from some distant desert.
Under a microscope, however, he found no evidence of sand or dust. Instead, the rain water was filled with red cells that look remarkably like conventional bugs on Earth. What was strange was that Louis found no evidence of DNA in these cells which would rule out most kinds of known biological cells (red blood cells are one possibility but ought to be destroyed quickly by rain water).
Louis published his results in the peer-reviewed journal Astrophysics and Space in 2006, along with the tentative suggestion that the cells could be extraterrestrial, perhaps from a comet that had disintegrated in the upper atmosphere and then seeded clouds as the cells floated down to Earth. In fact, Louis says there were reports in the region of a sonic boom-type noise at the time, which could have been caused by the disintegration of an object in the upper atmosphere.
Since then, Louis has continued to study the cells with an international team including Chandra Wickramasinghe from the University of Cardiff in the UK and one of the leading proponents of the panspermia theory, which he developed in the latter half of the 20th century with the remarkable physicist Fred Hoyle.
Today Louis, Wickramasinghe and others publish some extraordinary claims about these red cells. They say that the cells clearly reproduce at a temperature of 121 degrees C. “Under these conditions daughter cells appear within the original mother cells and the number of cells in the samples increases with length of exposure to 121 degrees C,” they say. By contrast, the cells are inert at room temperature.
That makes them highly unusual, to say the least. The spores of some extremophiles can survive these kinds of temperatures and then reproduce at lower temperatures but nothing behaves like this at these temperatures, as far as we know.
This is an extraordinary claim that will need to be independently verified before it will be more broadly accepted.
And of course, this behaviour does not suggest an extraterrestrial origin for these cells, by any means.
However, Wickramasinghe and co can’t resist hinting at such an exotic explanation. They’ve examined the way these fluoresce when bombarded with light and say it is remarkably similar to various unexplained emission spectra seen in various parts of the galaxy. One such place is the Red Rectangle, a cloud of dust and gas around a young star in the Monocerous constellation.
It would be fair to say that more evidence will be required before Kerala’s red rain can be satisfactorily explained. In the meantime, it looks a fascinating mystery.
Ref: arxiv.org/abs/1008.4960: Growth And Replication Of Red Rain Cells At 121oC And Their Red Fluorescence
The Sinister Link Between Infectious Agents, Bacteria and Protozoa
A new technique for studying the relationship between bacteria and protozoans could boost our understanding of how these organisms spread disease
In 1980, Tim Rowbotham, a microbiologist at the University of Bradford, made an extraordinary discovery about a tiny single-celled protozoa called Acanthamoeba. These organisms are ubiquitous, turning up almost anywhere there is liquid water. Since the 1950s they have been known to cause a number of rare diseases, mainly in humans with impaired immune systems.
What Rowbotham found was that they could be much more dangerous.
It had long been known that protozoa feed on bacteria, gradually munching through great mounds of these bugs. However, Rowbotham discovered that Legionella, the particularly nasty bacteria that causes Legionnaire’s disease, could not only survive being eaten by Acanthamoeba but actually thrived on it. In fact, it turns out that there is some kind of symbiotic relationship between these organisms that even today is not yet fully understood.
Microbiologists are still coming to terms with the implications of this discovery. They have since found that Acanthamoeba can host other nasties too such as H Pylori, the bacteria responsible for stomach ulcers, various strains of the food poisoning bugs Lysteria and E coli, a type of Chlamydiae and MRSA, the superbug currently sweeping through many hospitals.
The fear is that Acanthamoeba harbours these bacterial species, providing a safe haven against attack from antibiotics and contributing to the virulence of these bugs. That could make them an important source of infectious disease that is largely ignored.
So the study of the interaction between Acanthamoeba and the bacteria it supports has become an important area of research. But it is hampered by the difficulty of studying how protozoa interact with bacteria.
Today, Giorgos Tsibidis from the Foundation for Research and Technology in Greece and a couple of mates make a contribution that could help. It takes the form of a computer vision system that can identify individual protozoa, distinguishing them from cysts by virtue of their shape, and follow them as they move. The same system is also able to monitor concentration of bacteria.
They’ve tested the idea by watching the behaviour of Acanthamoeba protozoa grazing on a lawn of Salmonella bacteria. The machine is able to follow the Acanthamoeba as they move and to measure the drop in concentration of the Salmonella bacteria is they are eaten.
That’ll save some postdocs a huge amount of time and could dramatically improve our understanding of protozoan-bacterial interactions. it may even help save a few lives if it turns out that Acanthamoeba play a significant role in the transmission of disease.
Ref: arxiv.org/abs/1008.4662: Automated Two-Dimensional Acanthamoeba Polyphaga Tracking And Calculation Of Salmonella Typhimurium Distribution In Spatio-Temporal Images
Mathematicians Create Objective Quality of Life Index
The US comes second in a new quality of life index designed to be mathematically objective
Here’s a thorny problem: to develop an objective way to rank countries according to the quality of life they offer their citizens.
There are various ways of approaching this problem. For example, the Economist Intelligence Unit compiles its quality of life index using surveys, a useful technique but one that is hard to show is objective. Another widely quoted index, the Life Quality Index is based on life expectancy at birth and the gross domestic product per person but is only able to rank countries by applying a correction factor for each country that some critics say is open to bias.
Is there another way? Andrei Zinovyev at the Institut Curie in Paris and Alexander Gorban at the University of Leicester in the UK think so, using a mathematical technique developed in the mid-90s that can cut through this kind of problem .
They chose several widely-measured and well-studied indices on which to base their index: GDP per capita, life expectancy at birth, infant mortality rate and the incidence of tuberculosis. This data from 2005 is available for 162 countries.
Zinovyev and Gorban then plot this data in four-dimensional space. To create a ranking, the important question is whether there is a linear function that reduces this four-dimensional dataset to a one-dimensional set. Unsurprisingly, the answer turns out to be no. “Any linear mapping will inevitably give strong distortions in one or other region of data space,” they say. That’s what makes this problem tricky.
However, in the mid-90s a group of mathematicians devised a technique for reducing the dimensionality of complex data sets. This technique is essentially equivalent to connecting various data points together with springs and allowing the system to relax; hence it’s name: elastic mapping. The trick is to find an arrangement of springs that “flattens” the data set, or in other words, reduces its dimensionality.
And that’s basically what Zinovyev and Gorban have done, creating what they call the Nonlinear Quality of Life Index in the process.
Here are the top and bottom 5 from 2005:
1. Luxembourg
2. USA
3. Norway
4. Ireland
5. Iceland
.
.
.
158. Zambia
159. Mozambique
160. Zimbabwe
161. Kenya
162. Swaziland
No real surprises there, although there are some interesting features of the list. For example Equatorial Guinea is ranked at 140 although its GDP per capita is more than Saudi Arabia’s ranked at 37. That’s because of Equatorial Guinea’s appalling health statistics: 123 infant mortalities per 10,000 inhabitants, for example, compared to 21 in Saudi Arabia.
For similar reasons, Russia is ranked 71st despite having a GDP per capita that is significantly higher than other countries with a similar ranking.
Every list throws ups anomalies like this. The important point about this one is that it is done objectively and transparently.
That’s important because these kinds of indices are widely used by economists and politicians as a measure of economic and social development and so used to determine spending polices and legislation.
Objectivity is hard to come by when making these kinds of decisions. If the people who matter would agree to use it, this index could help.
Ref: arxiv.org/abs/1008.4063: Nonlinear Quality of Life Index
Rings ‘n’ Fingers
The best of the rest from the Physics arXiv this week:
Toward A Quantitative Understanding of Gas Exchange in the Lung
Testing the No-Hair Theorem with Observations of Black Holes in the Electromagnetic Spectrum
Distinguishing Left- And Right-Handed Molecules By Two-Step Coherent Pulses
The Mathematical Secret of Viking Jewellery
A long-standing puzzle over the craftsmanship behind Viking bracelets and necklaces has finally been solved–mathematically
The beautiful bracelets and necklaces made by Viking artisans leave archaeologists with something of a conundrum. These objects are made from rods of gold and silver which have twisted together into double helices. The puzzle is the regularity of these helices, which are remarkably similar in jewellery found in places as diverse as Ireland, Scotland, the Orkney Islands and Scandinavia.
How could craftsmen have achieved this regularity in such disparate places?
The answer comes today thanks to the work of Kasper Olsen and Jakob Bohr at the Technical University of Denmark. They point out that two wires become maximally twisted when no more rotations can be added with deforming the double helix. They go on to demonstrate the properties of maximally twisted wires. (We looked at a similar but more detailed argument about the properties of old rope a few weeks back.)
Olsen and Bohr then measured the properties of helices in Viking jewellery are twisted. It should come as no surprise to find that Viking jewellery is maximally twisted, which neatly explains why it all looks so similar. “Maximally rotated geometry is universal and therefore independent of the skills of the craftsman,” say Olsen and Bohr.
Problem solved.
Ref: arxiv.org/abs/1008.4306: Hidden Beauty in Twisted Viking Neck Rings
Fine Structure Constant Varies With Direction in Space, Says New Data
A spatial variation in the fine structure constant has profound implications for cosmology
Over the years, many physicists have wondered whether the fundamental constants of nature might have been different when the universe was younger. If so, the evidence ought to be out there in the cosmos where we can see distant things exactly as they were in the past.
One thing that ought to be obvious is whether a number known as the fine structure constant was different. The fine structure constant determines how strongly atoms hold onto their electrons and so is an important factor in the frequencies at which atoms absorb light.
If the fine structure were different earlier in the universe, we ought to be able to see the evidence in the way distant gas clouds absorb light on its way here from even more distant objects such as quasars.
As it turns out, exactly this kind of evidence has emerged in the last ten years or so from studies of absorption spectra carried out with the Keck telescope in Hawaii. These indicate that the fine structure constant must have been smaller when the universe was younger. It’s fair to say, however, that this evidence is controversial–other studies have not always corroborated the result.
That debate looks set to pale into insignificance compared to new claims being made about the fine structure constant. Today, John Webb at the University of South Wales, one of the leading proponents of the varying constant idea, and a few cobbers say they have new evidence from the Very Large Telescope in Chile that the fine structure constant was different when the universe was younger.
But get this. While data from the Keck telescope indicate the fine structure constant was once smaller, the data from the Very Large Telescope indicates the opposite, that the fine structure constant was once larger. That’s significant because Keck looks out into the northern hemsiphere, while the VLT looks south
This means that in one direction, the fine structure constant was once smaller and in exactly the opposite direction, it was once bigger. And here we are in the middle, where the constant as it is (about 1/137.03599…)
That’s a mind blowing result. One of the biggest conundrums that cosmologists face is explaining why the fundamental constants of nature seem fine tuned for life. If the fine structure constant were very different, stars and atoms wouldn’t form and the universe as we know it couldn’t exist. No theory explains why it takes the value it does which leaves scientists at a loss.
The implication from Webb and co’s data is that the fine structure constant is continuously varying throughout space and is merely fine-tuned for life in this corner of the cosmos: the universe’s habitable zone. Elsewhere, presumably well beyond the universe we can see, this constant is entirely different.
That’s likely to put the cat among the pigeons. Webb is no stranger to controversy–he has had to fight tooth and nail to have his data and ideas accepted. But this time round, with such a radical new data on the table, the debate is likely to be fiercer still.
So sit back and enjoy the show.
Refs:
arxiv.org/abs/1008.3907: Evidence For Spatial Variation Of The fiFine Structure Constant
arxiv.org/abs/1008.3957: Manifestations Of A Spatial Variation Of Fundamental Constants On Atomic Clocks, Oklo,
Meteorites, And Cosmological Phenomena
Quantum Entanglement Can Be A Measure Of Free Will, Say Physicists
The same experiments that reveal the nature of entanglement can also be interpreted as a measure of free will, say researchers
The nature of quantum mechanics has forced researchers to reconsider their own role in the process of science. Gone is the Victorian idea that measurement is objective and absolute. Today, we know that in the quantum world, it is impossible to separate the measured from the measurer. But exactly what role measurement plays in the universe, we have yet to fathom.
One intriguing idea is that certain kinds of experiments can tease apart the nature of measurement. And one particularly important class of experiment involves quantum entanglement, the hugely puzzling phenomenon in which widely separated objects share the same existence (or in scientific terms, are described by the same wave function).
Imagine two particles that are entangled in this way. Before any measurement takes place, these particles are in a superposition of states. Then a measurement on one immediately influences the other, somehow determining the outcome of a measurement on it.
Many experiments have shown that this “influence” happens as close to instantaneously as it is possible to measure and certainly cannot be mediated by any lightspeed signal. The same experiments also rule out any hidden correlation between the particles in which the outcome of any measurement is agreed upon in advance. Imagine, for example, some unseen hand that forces experimenters to unknowingly carry out measurements that always make it look as if this spooky action at a distance was taking place.
Today, Jonathan Barrett from the University of Bristol and Nicolas Gisin from the University of Geneva provide us with an interesting new take on this problem. They assume that entanglement does occur as quantum mechanics proscribes and then ask how much free will an experimenter must have to rule out the possibility of hidden interference.
The answer is curious. Barret and Gisin prove that if there is any information shared by the experimenters and the particles they are to measure, then entanglement can be explained by some kind of hidden process that is deterministic.
In practical terms, this means that there can be no shared information between the random number generators that determine the parameters of the experiments to be made, and the particles to be measured.
But the same also holds true for the experimenters themselves. It means there can be no information shared between them and the particles to be measured either. In other words, they must have completely free will.
In fact, if an experimenter lacks even a single bit of free will then quantum mechanics can be explained in terms of hidden variables. Conversely, if we accept the veracity of quantum mechanics, then we are able to place a bound on the nature of free will.
That’s an interesting way of stating the problem of entanglement and suggests a number of promising, related conundrums: what of systems that are partially entangled and others in which more than two particle become entangled.
Free will never looked so fascinating.
Ref: arxiv.org/abs/1008.3612: How Much Free Will Is Needed To Demonstrate Nonlocality?
Synaptic Behaviour Captured By New Memristor Circuit Design
When it comes to copying the real behaviour of synapses, two memristors are better than one, according to a new circuit design
Since the 1970s, electronic engineers have known that there are four fundamental building blocks of electronic circuits: resistors, capacitors, inductors and memristors (essentially variable resistors with memory). Memristors, however, had an air of mythology about them until last year when a group of researchers at HP Labs in California announced they had discovered them for the first time.
Since then, numerous others have claimed to have played with memristance over the years (although none seem to have noticed what they were doing until now). In fact, it turns out that the synapses between neurons behave exactly like memristors. That raises the possibility that memristors can be connected together in a way that truly mimics the wiring of human brains.
One of the defining features of the connections between neurons is that they become stronger when neurons fire together; hence the phrase “neurons that fire together, wire together”, a phenomenon otherwise known as Hebbian learning. Various experiments have shown that this effect is most pronounced early in the learning process, when the increase in connection strength is greatest. Later learning merely reinforces the links
That’s somewhat at odds with the actual behaviour of memristors, say Farnood Merrikh-Bayat and Saeed Bagheri at the University of Tehran in Iran. They say that in a single memristor connecting two neurons, the memristance decreases when a voltage is applied which increases the current which in turn causes the memristance to drop further, in a kind of positive feedback effect.
A lower memristance allows more current to flow so this certainly increases the strength of the connection as expected but there’s a problem. The positive feedback effect means that later signals have a bigger effect on the connection than earlier ones, which is the opposite way round to the way real neurons connect, where earlier signals have the strongest effect.
Merrikh-Bayat and Bagheri have a simple solution: use two memristors in series. Choosing their memristance carefully allows them to reproduce Hebbian-type synapse strengthening more or less exactly.
That may turn out to be a useful insight. The first neuromorphic chips to use memristance to mimic synapse behaviour are already being built. A small change in their design may make a significant difference.
Ref: arxiv.org/abs/1008.3450: Bottleneck Of Using Single Memristor As A Synapse And Its Solution
One Idea Solves Dark Energy and Lithium Abundance Mysteries
A simple idea explains two of cosmology’s biggest problems, but introduces a conundrum of its own.
One of the great outstanding challenges of modern science is to explain the observations that point to the accelerating expansion of the universe.
These come from astronomers who say the most distant supernovas are dimmer and so further away than they should be if the universe were merely expanding. Instead, the expansion must be accelerating, they say.
The conventional explanation for this acceleration is that the universe must be filled with an unseen or dark energy that is forcing this process.
That’s something that many physicists feel uncomfortable with. Conventional calculations of the universe’s vacuum energy arrive at a number that is 120 orders of magnitude smaller than dark energy must have. Then there is the small problem of conservation of energy which dark energy seems to violate. It’s an altogether unsatisfactory state of affairs.
There’s another seemingly unconnected problem that cosmologists are wrestling with: the abundance of elements that must have been created in the Big Bang.
Our models for the Big Bang and how the universe grew in its first few minutes make very precise predictions about the abundance of elements that must have been created in this process.
For example, there must have been lots of hydrogen, deuterium and helium-4. And the measurements of this stuff more or less exactly match the predictions.
However, the theory also predicts that a certain amount of lithium must have formed too. The trouble is that, as far as we can see, the universe contains only about a third of this amount. That has caused more than a little head scratching
Now Marco Regis and Chris Clarkson from the University of Cape Town in South Africa say they can explain this shortfall in lithium. What’s extraordinary, however, is that the same thinking also explains the supernova observations without any need for an accelerated expansion or dark energy.
Their new idea is that the lithium abundance can be explained by abandoning one of the fundamental assumptions of modern cosmology: the Copernican principle. This is the notion that humans have no privileged position in the universe. For cosmologists, this means that the universe must be more or less the same everywhere and on all scales.
Various cosmologists have pointed out that if we abandoned this principle, it would be straightforward to explain the supernova data. It simply means that the universe is not homogeneous on the very largest scale. Instead, we must be sitting at the centre of some kind of giant void in a much larger universe.
Now Regis and Clarkson say the same kind of thinking-that there are various irregularities in the way that stuff is distributed in the universe–can explain the lithium shortfall.
That’s an interesting contribution to this debate. That the same idea seems to explain two seemingly unconnected observations is a powerful reason to look at it more carefully.
On the face of it, there seems little to lose from abandoning the Copernican Principle on this scale. After all, why should stuff in the universe be evenly distributed on this scale?
However, this introduces an uncomfortable problem. Regis and Clarkson’s claim is that the Universe contains a region that is short on lithium. That’s not so hard to accept. What’s difficult to swallow is that if true, the observations indicate that the Earth is at the very centre of it.
That would seem to be an extraordinary coincidence, one that Regis and Clarkson say has a chance of of only 1 in 10^8 of occurring.
But they also point out that this has to be compared with the problems with the standard model of physics which is out by 120 orders of magnitude compared with the thinking behind dark energy.
Take your pick. Either way, it looks as if cosmologists will have to do some mighty hard thinking to get us out of this bind.
Ref: arxiv.org/abs/1003.1043: Do Primordial Lithium Abundances Imply There’s No Dark Energy?
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