21 October 2010

The work of integrating living cells into electrical systems has begun. To Do: Redefine "human"

Berkeley Lab scientists open electrical link to living cells

An engineered Escherichia coli strain (yellow) attaches to solid iron oxide (black). Scientists at the Molecular Foundry took the first step toward electronically interfacing microbes with inorganic materials, without disrupting cell viability. Credit: Image courtesy of Heather Jensen

The Terminator. The Borg. The Six Million Dollar Man. Science fiction is ripe with biological beings armed with artificial capabilities. In reality, however, the clunky connections between living and non-living worlds often lack a clear channel for communication. Now, scientists with the Lawrence Berkeley National Laboratory (Berkeley Lab) have designed an electrical link to living cells engineered to shuttle electrons across a cell's membrane to an external acceptor along a well-defined path. This direct channel could yield cells that can read and respond to electronic signals, electronics capable of self-replication and repair, or efficiently transfer sunlight into electricity.

"Melding the living and non-living worlds is a canonical image in science fiction," said Caroline Ajo-Franklin, a staff scientist in the Biological Nanostructures Facility at Berkeley Lab's Molecular Foundry. "However, in most attempts to interface living and non-living systems, you poke cells with a sharp hard object, and the cells respond in a predictable way – they die. Yet, in Nature many organisms have evolved to interact with the rocks and minerals that are part of their environment. Here, we took inspiration from Nature's approach and actually grew the connections out of the cell."

"We were interested in finding a pathway that wouldn't kill the living systems we were studying," said Heather Jensen, a graduate student at University of California, Berkeley whose thesis work is part of this publication. "By using a living system in electronics, we can one day create biotechnologies that can repair and self-replicate."

…"This recent breakthrough is part of a larger Department of Energy project on domesticating life at the cellular and molecular level. By directly interfacing synthetic devices with living organisms, we can harness the vast capabilities of life in photo- and chemical energy conversion, chemical synthesis, and self-assembly and repair," said Jay Groves, a faculty scientist at Berkeley Labs and professor of chemistry at University of California, Berkeley.

The researchers plan to implement this genetic cassette in photosynthetic bacteria, as cellular electrons from these bacteria can be produced from sunlight—providing cheap, self-replicating solar batteries. These metal-reducing bacteria could also assist in producing pharmaceutical drugs, Ajo-Franklin adds, as the fermentation step in drug manufacturing requires energy-intensive pumping of oxygen. In contrast, these engineered bacteria breathe using rust, rather than oxygen, saving energy.

20 October 2010

Kipling was right about why the leopard got its spots

Patterns like the leopard's rosettes evolve in cats which use forest habitats.
Why do leopards have rosette shaped markings but tigers have stripes? Rudyard Kipling suggested that it was because the leopard moved to an environment "full of trees and bushes and stripy, speckly, patchy-blatchy shadows" but is there any truth in this just-so story?

Researchers at the University of Bristol investigated the flank markings of 35 species of wild cats to understand what drives the evolution of such beautiful and intriguing variation. They captured detailed differences in the visual appearance of the cats by linking them to a mathematical model of pattern development.

They found that cats living in dense habitats, in the trees, and active at low light levels, are the most likely to be patterned, especially with particularly irregular or complex patterns. This suggests that detailed aspects of patterning evolve for camouflage. Analysis of the evolutionary history of the patterns shows they can evolve and disappear relatively quickly.

The research also explains why, for example, black leopards are common but black cheetahs unknown. Unlike cheetahs, leopards live in a wide range of habitats and have varied behavioural patterns. Having several environmental niches that different individuals of the species can exploit allows atypical colours and patterns to become stable within a population.

Although a clear link between environment and patterning was established, the study also highlighted some anomalies. For example, cheetahs have evolved or retained spotted patterns despite a strong preference for open habitats, while a number of cats, such as the bay cat and the flat-headed cat, have plain coats despite a preference for closed environments. Why this should be remains unclear.

The study also highlighted just how few species of cats have vertical stripes. Of the 35 species examined, only tigers always had vertically elongated patterns and these patterns were not associated with a grassland habitat, as might be expected. However, tigers seem to be very well camouflaged so this raises the question why vertical stripes are not more common in cats and other mammals. 

Will Allen of Bristol's School of Experimental Psychology, who led the research, said: "The method we have developed offers insights into cat patterning at many levels of explanation and we are now applying it to other groups of animals."


19 October 2010

The closer you look, the more there is to see: Bacteria are talking to each other and they may be thinking, too. Inside our bodies.

Some 100,000 Myxococcus xanthus cells amassed into a fruiting body with spores, above. Experimental competitions showed that some strains of this social bacterium exploited others

Bacteria use chemicals to talk to each other and to nonbacterial cells as well. These exchanges work much as human language does, says Herbert Levine of the University of California, San Diego’s Center for Theoretical Biological Physics. With colleagues from Tel Aviv University, Levine proposed in the August 2004 Trends in Microbiology that bacteria “maintain linguistic communication,” enabling them to engage in intentional behavior both singly and in groups. In other words, they have “social intelligence.”

…Researchers have found several reasons to believe that bacteria affect the mental health of humans. For one thing, bacteria produce some of the same types of neurotransmitters that regulate the function of the human brain. The human intestine contains a network of neurons, and the gut network routinely communicates with the brain. Gut bacteria affect that communication. “The bugs are talking to each other, and they’re talking to their host, and their host talks back,” Young says. The phrase “gut feeling” is probably, literally true.…

…Giovannoni stops short of claiming that bacteria are actually thinking. But the litany of bacterial talents does nibble at conventional assumptions about thinking: Bacteria can distinguish “self” from “other,” and between their relatives and strangers; they can sense how big a space they’re in; they can move as a unit; they can produce a wide variety of signaling compounds, including at least one human neurotransmitter; they can also engage in numerous mutually beneficial relationships with their host’s cells. Even more impressive, some bacteria, such as Myxococcus xanthus, practice predation in packs, swarming as a group over prey microbes such as E. coli and dissolving their cell walls.…

Read the whole article:

18 October 2010

Financially-troubled Japanese railway pins turnaround hopes on uniformed monkeys

"The monkeys, aged seven months and three months, were dressed in blue uniforms made from traditional local fabrics complete with mini hats before being formally appointed station masters and “special city residents” by the local mayor. The pair will now go on duty at the station located on the Hojo-cho line, which currently operates Japan’s first biodiesel fuel train. The monkeys belong to a local resident who proposed the unusual arrangement in order to help revive the fortunes of the financially troubled railway line, according to the Mainichi newspaper.

12 October 2010

What are ants telling us?

The anthill:  model for utopia or dystopia?

E.O. Wilson, who knows as much about ants as anybody, thinks we ought to worry, based on the way he sees ants dealing with resource shortages.
  Or maybe we ought not to worry about whether or not we act like ants and instead focus on our behavior. What do you think?
 From a recent article about Wilson:
…He has joked that Karl Marx had it right about socialism, he just got the wrong species. In his writings he is wont to emphasise the beneficence of ants, how an ant with a full stomach will regurgitate liquid food for those without, and how the old will venture into battle so that the young can survive. That may confirm some of the findings of “Mutual Aid”, the pioneering 1902 study of altruism in animals by the Russian anarchist Prince Pyotr Kropotkin. But is this really socialism? To the casual observer the ant colony looks more like a Nazi ideal, where the weak are shed and fed upon, and those who have the slightest scent of another colony are sprayed with a chemical marking them out for death. It makes one glad to be human.
When Wilson unveiled sociobiology in 1975, it met with an angry response. Feminists, Marxists and Christians were opposed; so was Stephen Jay Gould, another Harvard biologist. But Wilson’s belief in sociobiology has not wavered. He leans forward and folds his hands together. “History is almost certainly colony against individual and colony against colony. If group selection is correct, what you would expect to find is an intense human desire to form groups that attack other groups; bands of brothers, teams.” Then comes the rider. “As shortages in oil and other energy sources increase, we will see insect traits. Group conflict is so deeply endemic that we will never diminish it until we confront it.”…
…We were not driven from Eden. Instead, we destroyed most of it.

They work together, share food and send their elders into battle to protect the young. And the world authority on them thinks they have a lot to teach us. J.M. Ledgard goes to Harvard to discuss ants, and more, with E.O. Wilson ...
From INTELLIGENT LIFE Magazine, Autumn 2010
More Intelligent Life (http://moreintelligentlife.com)

06 October 2010

Surprisingly social lizards & ferocious robins

Seems that every time they look a bit closer at nonhumans, researchers find our fellow Earthlings more complex, more "like us" than humans expected.  Seems reasonable to assume that we continue to underestimate them. 

The latest example: " Researchers at the University of California, Santa Cruz, have found that a species of lizard in the Mojave Desert lives in family groups and shows patterns of social behavior more commonly associated with mammals and birds. Their investigation of the formation and stability of family groups in desert night lizards (Xantusia vigilis) provides new insights into the evolution of cooperative behavior."

Robin song is suited to cooler air, to mornings and evenings in spring and summer and the shorter day length later. It has a sharp-edged clarity, with liquid runs and etched phrases enhanced by the sounding woods. Here there is some leaf cover surrounding still, open, well-lit spaces which act as studios for the singing birds. Robins have a reputation for ferocity with each other and a lack of fear with us. They also have a sweetness of song which reaches points where joy and melancholy merge. This is where the mood is shaped which, with the fragrance of leaf-rot and rain, fruits and earth, create what we feel as autumn.