Category Archives: Research

Bacteria Offer Line of Attack on Cystic Fibrosis

MIT researchers have found that the pigments responsible for the blue-green stain of the mucus that clogs the lungs of cystic fibrosis (CF) patients are primarily signaling molecules that allow large clusters of the opportunistic infection agent, Pseudomonas aeruginosa, to organize themselves into structured communities.
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P. aeruginosa appears as a classic opportunistic infection, easily shrugged off by healthy people but a grave threat to those with CF, which chokes the lungs of its victims with sticky mucus.

“We have a long way to go before being able to test this idea, but the hope is that if survival in the lung is influenced by phenazine — or some other electron-shuttling molecule or molecules — tampering with phenazine trafficking might be a potential way to make antibiotics more effective,” said Newman, whose lab investigates how ancestral bacteria on the early Earth evolved the ability to metabolize minerals.

Bird Brain

Bird-brains smarter than your average ape

In a recent study 20 individuals from the great ape species were unable to transfer their knowledge from the trap-table and trap-tube or vice versa, despite the fact that both these puzzles work in the same way. Strikingly the crows in The University of Auckland study were able to solve the trap-table problem after their experience with the trap-tube.

“The crows appeared to solve these complex problems by identifying causal regularities,” says Professor Russell Gray of the Department of Psychology. “The crows’ success with the trap-table suggests that the crows were transferring their causal understanding to this novel problem by analogical reasoning. However, the crows didn’t understand the difference between a hole with a bottom and one without. This suggests the level of cognition here is intermediate between human-like reasoning and associative learning.”

“It was very surprising to see the crows solve the trap-table,” says PhD student Alex Taylor. “The trap table puzzle was visually different from the trap-tube in its colour, shape and material. Transfer between these two distinct problems is not predicted by theories of associative learning and is something not even the great apes have so far been able to do.”

How We Found the Missing Memristor

How We Found the Missing Memristor By R. Stanley Williams

For nearly 150 years, the known fundamental passive circuit elements were limited to the capacitor (discovered in 1745), the resistor (1827), and the inductor (1831). Then, in a brilliant but underappreciated 1971 paper, Leon Chua, a professor of electrical engineering at the University of California, Berkeley, predicted the existence of a fourth fundamental device, which he called a memristor. He proved that memristor behavior could not be duplicated by any circuit built using only the other three elements, which is why the memristor is truly fundamental.
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the memristor’s potential goes far beyond instant-on computers to embrace one of the grandest technology challenges: mimicking the functions of a brain. Within a decade, memristors could let us emulate, instead of merely simulate, networks of neurons and synapses. Many research groups have been working toward a brain in silico: IBM’s Blue Brain project, Howard Hughes Medical Institute’s Janelia Farm, and Harvard’s Center for Brain Science are just three. However, even a mouse brain simulation in real time involves solving an astronomical number of coupled partial differential equations. A digital computer capable of coping with this staggering workload would need to be the size of a small city, and powering it would require several dedicated nuclear power plants.

Dolphins Using Tools to Hunt

photo of a dolphin with a sponge it uses to hunt

Photograph of dolphin with a sponge it uses to hunt, courtesy of Ewa Krzyszczyk, PLoS, high resolution.

Cool open access research from PLoS One, Why Do Dolphins Carry Sponges?

Tool use is rare in wild animals, but of widespread interest because of its relationship to animal cognition, social learning and culture. Despite such attention, quantifying the costs and benefits of tool use has been difficult, largely because if tool use occurs, all population members typically exhibit the behavior. In Shark Bay, Australia, only a subset of the bottlenose dolphin population uses marine sponges as tools, providing an opportunity to assess both proximate and ultimate costs and benefits and document patterns of transmission.

We compared sponge-carrying (sponger) females to non-sponge-carrying (non-sponger) females and show that spongers were more solitary, spent more time in deep water channel habitats, dived for longer durations, and devoted more time to foraging than non-spongers; and, even with these potential proximate costs, calving success of sponger females was not significantly different from non-spongers. We also show a clear female-bias in the ontogeny of sponging. With a solitary lifestyle, specialization, and high foraging demands, spongers used tools more than any non-human animal. We suggest that the ecological, social, and developmental mechanisms involved likely (1) help explain the high intrapopulation variation in female behaviour, (2) indicate tradeoffs (e.g., time allocation) between ecological and social factors and, (3) constrain the spread of this innovation to primarily vertical transmission.

The dolphins use the sponge to push along the ocean floor and disturb fish, that are hidden. Once the fish start swimming away the dolphin abandons the sponge and catches and eats the fish. Then the dolphin goes back and gets the sponge and continues.

The Chip That Designs Itself

The chip that designs itself by Clive Davidson , 1998

Adrian Thompson, who works at the university’s Centre for Computational Neuroscience and Robotics, came up with the idea of self-designing circuits while thinking about building neural network chips. A graduate in microelectronics, he joined the centre four years ago to pursue a PhD in neural networks and robotics.
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To get the experiment started, he created an initial population of 50 random circuit designs coded as binary strings. The genetic algorithm, running on a standard PC, downloaded each design to the Field Programmable Gate Arrays (FPGA) and tested it with the two tones generated by the PC’s sound card. At first there was almost no evidence of any ability to discriminate between the two tones, so the genetic algorithm simply selected circuits which did not appear to behave entirely randomly. The fittest circuit in the first generation was one that output a steady five-volt signal no matter which tone it heard.

By generation 220 there was some sign of improvement. The fittest circuit could produce an output that mimicked the input – wave forms that corresponded to the 1KHz or 10KHz tones – but not a steady zero or five-volt output.

By generation 650, some evolved circuits gave a steady output to one tone but not the other. It took almost another 1,000 generations to find circuits that could give approximately the right output and another 1,000 to get accurate results. However, there were still some glitches in the results and it took until generation 4,100 for these to disappear. The genetic algorithm was allowed to run for a further 1,000 generations but there were no further changes.

See Adrian Thompson’s home page (Department of Informatics, University of Sussex) for more on evolutionary electronics. Such as Scrubbing away transients and Jiggling around the permanent: Long survival of FPGA systems through evolutionary self-repair:

Mission operation is never interrupted. The repair circuitry is sufficiently small that a pair could mutually repair each other. A minimal evolutionary algorithm is used during permanent fault self-repair. Reliability analysis of the studied case shows the system has a 0.99 probability of surviving 17 times the mean time to local permanent fault arrival. Such a system would be 0.99 probable to survive 100 years with one fault every 6 years.

Very cool.

Related: Evolutionary Design – Invention Machine – Evo-Devo

One Sneeze, 150 Colds for Commuters

One sneeze, 150 colds for commuters

An analysis of the germs unleashed from a single commuter’s sneeze showed that within minutes they are being passed on via escalator handrails or seats on trains and underground carriages. At the busiest stations, one sneeze not smothered by a tissue or handkerchief will provide enough germs to infect another 150 commuters.
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A single sneeze expels 100,000 droplets of germs into the air at 90mph. Individual droplets get transferred to handles, rails and other areas frequently held or touched. Up to 10 per cent of all commuters will come into contact with an area infected by that one sneeze, Dr Henderson calculated.
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Researchers asked 1,300 workers about their health and found 99 per cent of commuters suffered at least one cold last winter. In contrast, just 58 per cent of those who work from home and 88 per cent of those who walk to work regularly caught a cold last winter.

It is amazing (or maybe not but I find it amazing) how well cold viruses have evolved to have us sneeze and send out personal virus jet packs to spread them all over and let them infect others. It is sad how impolite some people are as they go around potentially infecting hundreds of other people. Partially their ignorance of basic science may also be to blame for their behavior. It is too bad others have to suffer due to their bad manners and ignorance.

Harnessing Light to Drive Nanomachines

A team led by researchers has shown that the force of light indeed can be harnessed to drive machines – when the process is scaled to nano-proportions. Their work opens the door to a new class of semiconductor devices that are operated by the force of light. They envision a future where this process powers quantum information processing and sensing devices, as well as telecommunications that run at ultra-high speed and consume little power.

The energy of light has been harnessed and used in many ways. The “force” of light is different — it is a push or a pull action that causes something to move. “While the force of light is far too weak for us to feel in everyday life, we have found that it can be harnessed and used at the nanoscale,” said team leader Hong Tang, assistant professor at Yale. “Our work demonstrates the advantage of using nano-objects as ‘targets’ for the force of light – using devices that are a billion-billion times smaller than a space sail, and that match the size of today’s typical transistors.”

Full Press release

2,000 Species New to Science from One Island

photo of squat lobster

Photograph by Dr Tin-Yam Chan, University of Keelung

153 scientists from 20 countries fanned out across the remote South Pacific island of Espiritu Santo, examining mountains, forests, caves, reefs, and water for all living organisms. In five months, they collected 10,000 species. Some 2,000 of these may be new to science.

This squat lobster, found in waters 150 meters (492 feet) deep, is one of the new species. Eighty percent of the world’s species remain to be discovered, notes French scientist Philippe Bouchet, one of the expedition’s leaders.

A World of Crabs from One Tiny Island

About 600 of these were crab species. The two-horn box crab is able to crack and peel open snails’ shells using a sharp “tooth” on its right claw to cut open shells and long, slender “fingers” on the left claw to yank out its prey.

Do Breast Tumors go Away on Their Own?

Authors of a new study hope to begin a debate challenging the conventional wisdom about early detection of breast cancer. In an article in today’s Archives of Internal Medicine, they ask: Do breast tumors ever go away on their own?

Researchers of this controversial article note that one type of cancer found through screening — a rare childhood tumor, called neuroblastoma — sometimes disappears. In the new article, researchers try to learn if the same phenomenon occurs with invasive breast cancers found with mammograms

The Natural History of Invasive Breast Cancers Detected by Screening Mammography

Conclusions: Because the cumulative incidence among controls never reached that of the screened group, it appears that some breast cancers detected by repeated mammographic screening would not persist to be detectable by a single mammogram at the end of 6 years. This raises the possibility that the natural course of some screen-detected invasive breast cancers is to spontaneously regress.

As with so much medical research the results are not completely clear. Studies need to be followed by more studies, which often lead to more studies. As long as progress is being made this is a perfectly reasonable course of scientific inquiry. And even if progress is not being made this can be perfectly reasonable – finding answers can be hard.

HHMI on Science 2.0: Information Revolution

The Howard Hughes Medical Institute does great things for science and for open science. They have an excellent article in their HHMI Bulletin – Science 2.0: You Say You Want a Revolution?

Cross-pollination among research disciplines is in fact at the core of many other popular science blogs. Michael Eisen, an HHMI investigator at the University of California, Berkeley, is an avid blog reader who particularly enjoys John Hawks’ site on paleoanthropology, genetics, and evolution. A recent post there discussed a new sequencing of Neanderthal mitochondrial DNA. “It’s like a conduit into another whole world,” says Eisen.
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The current extreme of collaboration via Science 2.0 is OpenWetWare.org. Begun in 2003 by Austin Che, who was then a computer science and biology graduate student at MIT, this biological-engineering Website uses the wiki model to showcase protocols and lab books: everything is open and can be edited by any of its 4,000 members.
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“Most publishers wish open access would go away,” says Brown. It won’t. Major research-funding organizations, including NIH, HHMI, and the Wellcome Trust, now require their grantees to post their findings on openaccess Websites such as PLoS or PubMed Central within 12 months of publication in traditional journals. Publishers are pushing back, however, and in September, the House Judiciary Committee began holding hearings on whether the federal government should be allowed to require grantees to submit accepted papers to a free archive.