Tag Archives: Biology

Electronic gene control could let us plug bacteria into devices

Pink bacterium with purple background

We don’t usually welcome bugs in digital technology, but that’s about to change. Researchers have developed a way to control bacterial genes at the flick of a switch using electricity.

Synthetic biologists are eager to find ways to connect engineered organisms to electronics, so we can make living components for devices.

The ability of custom-made microbes to sense the environment and make biological molecules would be particularly valuable for devices that work inside the body, says William Bentley at the University of Maryland.

“If you want to discover what’s going on in the gastrointestinal tract or the oral cavity, if you can connect to electronics you have a way of interpreting what’s going on and you may be able to manipulate it,” he says.

For example, a device could use an organism to sense chemicals produced by harmful bacteria in the body and secrete an antibiotic when it detects them.

To get specific genes in bacteria to respond to electrical stimulation, Bentley’s team took advantage of what are called redox molecules. These biological molecules are found in all cells and can pick up and pass on electrons. They are said to have a reduced state when they gain electrons, and an oxidised state when they lose electrons.

The team also made use of naturally occurring genetic components in E. coli that respond to oxidative stress, which occurs when too many molecules in the cell are o apply electrical input, the researchers submerged an electrode in a liquid containing the bacteria. When the electrode supplies a positive charge, certain redox molecules get oxidised and trigger the genetic mechanisms that respond to oxidative stress.

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When science meets aboriginal oral history

In Inuit oral history, the Tuniit loom both large and small.

They inhabited the Arctic before the Inuit came, and they were a different stock of people — taller and stronger, with the muscularity of polar bears, the stories say. A Tuniit man could lift a 1,000 pound seal on his back, or drag a whole walrus. Others say the Tuniit slept with their legs in the air to drain the blood from their feet and make them lighter, so they could outrun a caribou.

But despite their superior strength and size, the Tuniit were shy. They were “easily put to flight and it was seldom heard that they killed others,” according to one storyteller in the book “Uqalurait: An Oral History of Nunavut.” The Inuit took over the best hunting camps and displaced the conflict-averse Tuniit. Soon enough, these strange people disappeared from the land.

This week, the prestigious journal Science published an unprecedented paleogenomic study that resolves long-held questions about the people of the prehistoric Arctic. By analyzing DNA from 169 ancient human specimens from Canada, Alaska, Siberia, and Greenland, the researchers concluded that a series of Paleo-Eskimo cultures known as the Pre-Dorset and Dorset were actually one population who lived with great success in the eastern Arctic for 4,000 years — until disappearing suddenly a couple generations after the ancestors of the modern Inuit appeared, around 1200 A.D. There is no evidence the two groups interbred.

The Dorset are almost certainly the Tuniit of Inuit oral history.

“The outcome of the genetic analysis is completely in agreement, namely that the Paleo-Eskimos are a different people,” says Eske Willerslev, a co-author of the Science study.

It’s not the first time his genomic research has synchronized neatly with indigenous oral traditions.

In February, when Willerslev and colleagues announced they had sequenced the genome of a 12,500-year-old skeleton found in Montana, the results showed that nearly all South and North American indigenous populations were related to this ancient American. Shane Doyle, a member of the Crow tribe of Montana, said at the time: “This discovery basically confirms what tribes have never really doubted — that we’ve been here since time immemorial, and that all the artifacts and objects in the ground are remnants of our direct ancestors.” The sequenced genome of an Aboriginal from Australia also revealed findings in line with the local communities’ oral histories, Willerslev says.

“Scientists are sitting around and academically discussing different theories about peopling of Americas, and you have all these different views on how many migrations, and who is related to,” he says. “Then when we actually undertake the most sophisticated genetic analysis we can do today, and this is state of the art, genetically — we could have just have listened to them in the first place.”

He was laughing when he said that. But he and many others are serious when they say that scientists need to revaluate the weight they give traditional indigenous knowledge

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Tiny, Vast Windows Into Human DNA by Carl Zimmer

In the history of biology, two little animals loom large.

In the early 1900s, scientists began studying Drosophila melanogaster, the common fruit fly. Research on these fast-breeding insects revealed that genes lie on chromosomes, which turned out to be true for other animals, including us. For more than a century, scientists have continued to glean clues from the lowly fly to other mysteries of biology, like why we sleep and how heart disease develops.

In the 1960s, another unassuming animal joined biology’s pantheon: a tiny worm called Caenorhabditis elegans. The biologist Sydney Brenner realized that its body, made up of just a couple of thousand cells, offered an singular opportunity to learn how a single egg gives rise to a complete animal. Today, many scientists are studying the worm for clues to how our own brains are wired and why we age.

Now the two species are providing even deeper insights in biology. A team of hundreds of scientists has exhaustively recorded the choreography of their genes as the animals develop from eggs to adults.

“It’s not just this gene or that gene,” said Robert H. Waterston, a geneticist at the University of Washington who is among the scientists working on the project, called modENCODE. “We can get a picture of the whole.”

Dr. Waterston and his colleagues published overviews of the modENCODE results in five papers last week in Nature. In their initial analysis, they find a striking similarity between the choreography of genes in flies and worms and that of our own DNA. Exploring that similarity may provide scientists with new insights into genetic disorders and diseases like cancer.

In 1998, Dr. Waterston and a large group of fellow scientists cataloged all 19,000 protein-coding genes in C. elegans, along with a rough guide to the rest of its DNA. In 2000, researchers did the same for D. melanogaster. These two efforts were a huge help to scientists studying the biology of the animals. But these two efforts revealed little about what the genes actually do in an organism. It was as if they had inventoried all the instruments in an orchestra but weren’t able to see the sheet music.

A gene contains information that a cell can use to make a particular molecule. But an animal may only use a given gene at a particular time in its life, or in a particular organ.

Cellular DNA is coiled around spool-like molecules called histones. When DNA is tucked away, gene-reading molecules cannot reach it. By adding certain compounds, known as histone marks, to the histones, a cell opens up a stretch of DNA.

When a gene is exposed this way, a protein called a transcription factor latches onto it, recruiting other molecules to “read” it and produce a new protein or RNA molecule. Sometimes, a single transcription factor may switch on dozens of other genes. And sometimes, those genes encode transcription factors of their own, enabling a cell to produce hundreds of kinds of molecules at once.

The modENCODE team took on an enormous task: to create a detailed picture of this molecular dance. For the past five years, hundreds of biologists have been recording DNA activity in flies and worms, and systematically comparing the results to what they see in humans.

To study genes in humans, the scientists focused on a wide variety of cells, like neurons, blood cells and liver cells. In the experiments on flies and worms, the scientists examined the entire bodies of the animals as they matured from eggs.

The scientists cataloged the parts of the genome that cells were using. They also mapped the histone marks and located the transcription factors latching onto the DNA. Because the scientists used the same methods to gather data from all three species, they were able to compare them on a scale never before attempted.

Flies, worms and humans come from distant branches on the evolutionary tree. The last common ancestor lived 700 million years ago. Despite the tremendous differences among the three species, the modENCODE team found some striking parallels in the workings of their DNA.

In all three, it turned out, many genes tended to turn on and off in the same pattern, following a predictable rhythm. All told, the researchers found 16 such sets of genes, each containing hundreds of genes working together. While it’s not clear yet what these genes are doing in all three species, the scientists did observe that a dozen clusters were especially active at some stages of development in the worm and the fly. They may be essential for transforming an egg into an adult animal.

The scientists also found that histone marks control DNA in much the same way in all three species. If certain marks were present around a gene, the scientists usually could predict how active it was, whether fly, worm or human.

“The neat thing is that it works — it really works well,” Mark Gerstein of Yale University, a modENCODE team member, said of the group’s predictive model.

Read on (NYT)


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Peter Godfrey-Smith Takes On The Philosophy Of Biology

Peter Godfrey-Smith’s Philosophy of Biology (Princeton University Press), may not sound like the kind of book even science enthusiasts want to crack open for pleasure, but it’s a great way to get up to speed on all the issues that working biologists love to debate amongst themselves.

Godfrey-Smith is a professor in the Philosophy Program at City University of New York. His more academic books include, Darwinian Populations and Natural Selection (Oxford University Press), and Theory and Reality: An Introduction to the Philosophy of Science (University of Chicago Press). His main areas of interest include the philosophy of mind and pragmatism.

In just 200 pages, Philosophy of Biology includes short, succinct chapters on mechanisms and models, natural selection, genes, adaptation and function, species and the Tree of Life, evolution and social behavior, and information.

But as I mentioned in my last post, the question for many science geeks is: why even bother with a book on philosophy at all–let alone the philosophy of science?

What good is it?

So, I asked Scott Carson, an associate professor of philosophy at Ohio University*, what he tells his students at the start of each semester.

Carson’s main areas of interest are the history of evolutionary biology and the biomedical sciences, and among his publications is this fascinating essay he co-authored on how quantum indeterminacy may effect evolution.

“Typically,” he said via email, “I tell my students that philosophy of science is important because we live in a society that is very much a product of what Bas Van Fraassen called ‘The Scientific Image’. That is, we are, as persons, largely shaped by the culture that surrounds us and we are presently surrounded by a culture that is increasingly impacted by science and technology.

“If we are to be intelligent and well-informed members of the society and culture in which we find ourselves, it is essential that we understand not only the results of scientific research, but the foundations of science itself.”

In Carson’s view, this will put us in a better position to evaluate questions about the nature of the authority of the sciences and the reliability of the conclusions and recommendations made by scientists.

“Ideally a philosopher of science is not someone who hopes to make any positive contributions to the working sciences,” he said, “but someone who is interested in answering philosophical questions that are informed by the discoveries of the sciences and who wants to describe and assess scientific practice as accurately as possible.”

In terms of the current book, he added, “I think you will find that this is very close to what Godfrey-Smith believes is the proper function of the philosopher of science.”

Read on @Forbes

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How the zebra got its stripes, with Alan Turing

3.turing72-03 © Job Boot for Mosaic


n 1952 a mathematician published a set of equations that tried to explain the patterns we see in nature, from the dappled stripes adorning the back of a zebra to the whorled leaves on a plant stem, or even the complex tucking and folding that turns a ball of cells into an organism. His name was Alan Turing.

More famous for cracking the wartime Enigma code and his contributions to mathematics, computer science and artificial intelligence, it may come as a surprise that Turing harboured such an interest. In fact, it was an extension of his fascination with the workings of the mind and the underlying nature of life.

The secret glory of Turing’s wartime success had faded by the 1950s, and he was holed up in the grimly industrial confines of the University of Manchester. In theory he was there to develop programs for one of the world’s first electronic computers – a motley collection of valves, wires and tubes – but he found himself increasingly side-lined by greasy-fingered engineers who were more focused on nuts and bolts than numbers. This disconnection was probably intentional on Turing’s part, rather than deliberate exclusion on theirs, as his attention was drifting away from computing towards bigger questions about life.

It was a good time to be excited about biology. Researchers around the world were busy getting to grips with the nature of genes, and James Watson and Francis Crick would soon reveal the structure of DNA in 1953. There was also a growing interest in cybernetics – the idea of living beings as biological computers that could be deconstructed, hacked and rebuilt. Turing was quickly adopted into a gang of pioneering scientists and mathematicians known as the Ratio Club, where his ideas about artificial intelligence and machine learning were welcomed and encouraged.

Against this backdrop Turing took up a subject that had fascinated him since before the war. Embryology – the science of building a baby from a single fertilised egg cell – had been a hot topic in the early part of the 20th century, but progress sputtered to a halt as scientists realised they lacked the technical tools and scientific framework to figure it out. Perhaps, some thinkers concluded, the inner workings of life were fundamentally unknowable.

Turing viewed this as a cop-out. If a computer could be programmed to calculate, then a biological organism must also have some kind of underlying logic too.

He set to work collecting flowers in the Cheshire countryside, scrutinising the patterns in nature. Then came the equations – complex, unruly beasts that couldn’t be solved by human hands and brains. Luckily the very latest computer, a Ferranti Mark I, had just arrived in Manchester, and Turing soon put it to work crunching the numbers. Gradually, his “mathematical theory of embryology”, as he referred to it, began to take shape.

Like all the best scientific ideas, Turing’s theory was elegant and simple: any repeating natural pattern could be created by the interaction of two things – molecules, cells, whatever – with particular characteristics. Through a mathematical principle he called ‘reaction–diffusion’, these two components would spontaneously self-organise into spots, stripes, rings, swirls or dappled blobs.

In particular his attention focused on morphogens – the then-unknown molecules in developing organisms that control their growing shape and structure. The identities and interactions of these chemicals were, at the time, as enigmatic as the eponymous wartime code. Based on pioneering experiments on frog, fly and sea urchin embryos from the turn of the 20th century – involving painstakingly cutting and pasting tiny bits of tissue onto other tiny bits of tissue – biologists knew they had to be there. But they had no idea how they worked.


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