The next leap in synthetic life

"It took geneticist Craig Venter 15 years and US$40 million to synthesize the genome of a bacterial parasite. Today, an academic team made up mostly of undergraduate students reports the next leap in synthetic life: the redesign and production of a fully functional chromosome from the baker’s yeast Saccharomyces cerevisiae.

As a eukaryote, a category that includes humans and other animals, S. cerevisiae has a more complex genome than Venter's parasite. "

“I wasn’t sceptical about whether it could be done,” Boeke says. The question, he explains, was: “How can we make this different from a normal chromosome and put something into it that’s really going to make it worthwhile?”

Nature - First synthetic yeast chromosome revealed
http://www.nature.com/news/first-synthetic-yeast-chromosome-revealed-1.14941

BBC - Scientists hail synthetic chromosome advance
http://www.bbc.com/news/science-environment-26768445

Wiki - Yeast artificial chromosome
http://en.wikipedia.org/wiki/Yeast_artificial_chromosome

Rack your brains over brains running on racks

This month's issue of Nature delivers a special on the brain that really gets you thinking. They take a detailed look at how Europe's Human Brain Project and the US BRAIN initiative are taking shape but the real prize is this interesting write-up on some of the most promising currently existing neuromorphic hardware. Check out Neurogrid, SpiNNaker, BrainScaleS, SyNAPSE and the neural net simulation called Spaun.
http://www.nature.com/news/neuroelectronics-smart-connections-1.14089

Here's a collection of interesting bits from the article that will make you click onwards to read the thing in full.

Just a few years ago, Kwabena Boahen completed a device called Neurogrid that emulates a million neurons, about as many as there are in a honeybee's brain. Now applications for 'neuromorphic technology' are finally in sight.

In 2012 Boahen contacted Chris Eliasmith, who is responsible for Spaun: a design for a computer model of the brain that includes the parts responsible for vision, movement and decision-making. Previously, a simulation of Spaun on a conventional computer had shown that, with 2.5 million simulated neurons plus a simulated retina and hand, it could copy handwritten digits, recall the items in a list, work out the next number in a given sequence and carry out several other cognitive tasks. But the Spaun simulation ran about 9,000 times slower than real time, taking 2.5 hours to simulate 1 second of behaviour.

Boahen contacted Eliasmith with the obvious proposition: build a physical version of Spaun using real-time neuromorphic hardware. “I got very excited,” says Eliasmith, for whom the match seemed perfect. “You've got the peanut butter, we've got the chocolate!”

With funding from the US Office of Naval Research, Boahen and Eliasmith have put together a team that plans to build a small-scale prototype in three years and a full-scale system in five. For sensory input they will use neuromorphic retinas and cochleas developed at the INI, says Boahen. For output, they have a robotic arm. But the cognitive hardware will be built from scratch.

The system is explicitly designed for real-world applications. On a five-year timescale, says Boahen, “we envision building fully autonomous robots that interact with their environments in a meaningful way, and operate in real-time while [their brains] consume as much electricity as a cell phone”. Such devices would be much more flexible and adaptive than today's autonomous robots, and would consume considerably less power.

In the longer term, Boahen adds, the project could pave the way for compact, low-power processors in any computer system, not just robotics. If researchers really have managed to capture the essential ingredients that make the brain so efficient, compact and robust, then it could be the salvation of an industry about to run into a wall as chips get ever smaller.

“But we won't know for sure,” Boahen says, “until we try.”

> http://www.nature.com/news/neuroelectronics-smart-connections-1.14089
> Neurogrid; http://www.stanford.edu/group/brainsinsilicon/neurogrid.html
> SpiNNaker; http://apt.cs.man.ac.uk/projects/SpiNNaker/
> BrainScaleS - http://brainscales.kip.uni-heidelberg.de/
> SyNAPSE - http://www.research.ibm.com/cognitive-computing/neurosynaptic-chips.shtml
> Spaun; http://nengo.ca/build-a-brain/spaunvideos

Neuroscience - today and tomorrow

Nature takes a look at the technologies that will enable us to unravel some of the mind's mysteries.
http://www.nature.com/news/neuroscience-solving-the-brain-1.13382 - Researchers want to understand the ways in which brain circuitry changes — through the constant growth and retreat of synapses — as life rolls by.

"Reaching this goal will require innovative new technologies, ranging from nanotechnologies to genetics to optics, that can capture the electrical activity coursing through neurons, prod those neurons to find out what they do, map the underlying anatomical circuits in fine detail and process the exabytes of information all this work will spit out. “Think about it,” says neuroscientist Konrad Kording of Northwestern University in Chicago, Illinois. “The human brain produces in 30 seconds as much data as the Hubble Space Telescope has produced in its lifetime.”

the most daunting part of the brain challenge lies in storing and handling data. One cubic millimetre of brain tissue will generate an estimated 2,000 terabytes of electron-microscopy information using Lichtman and Denk's new microscope, for example. Denk estimates that an entire mouse brain could produce 60 petabytes and a human brain about 200 exabytes. This amount of data will rival the entire digital content of today's world, “including Facebook and all the big data stores”, says Lichtman."

I was particularly impressed with the predictions made by IMEC, a nanoelectronics research organization. They recently unveiled a prototype 'neuroprobe'. One-centimetre long and as thin as a dollar bill, the probe packs in 52 thin wires and switches that neuroscientists can flip seamlessly between 456 silicon electrodes.

When inserted into a mouse brain, the electrodes dotted across the imec probe can span — and record from — all layers of the animal's brain simultaneously, from the cortex to the thalamus in the brainstem. This could help neuroscientists to unpick the circuitry that connects them. “This prototype can be scaled up,” says Peter Peumans, director of bio- and nanoelectronics at imec. Within three years, he says, the neuroprobes will have up to 2,000 electrodes and more than 200 wires.

It's a pretty good read if you are looking for an update on the current and future state of Neuroscience.
http://www.nature.com/news/neuroscience-solving-the-brain-1.13382

Looking for more brainy links?
> Make up your mind
http://goo.gl/O80gGP .
> How does the world look through the eyes of neuroscience?http://goo.gl/MFHj5v .
> Old Brains Learning New Tricks
http://goo.gl/IZYnTR .
> Inception
http://goo.gl/qFXsgl .

Read this if you want to have the time of your life

http://www.nature.com/news/biomarkers-and-ageing-the-clock-watcher-1.15014

Steve Horvath, a geneticist and biostatistician at UCLA, has developed a cellular biological clock that has impressed researchers with its accuracy, how easy it is to read and the fact that it ticks at the same rate in many parts of the body — with some intriguing exceptions that might provide clues to the nature of ageing and its maladies.

Horvath's clock emerges from epigenetics, the study of chemical and structural modifications made to the genome that do not alter the DNA sequence but that are passed along as cells divide and can influence how genes are expressed. As cells age, the pattern of epigenetic alterations shifts, and some of the changes seem to mark time. To determine a person's age, Horvath explores data for hundreds of far-flung positions on DNA from a sample of cells and notes how often those positions are methylated.

“I wanted to develop a method that would work in many or most tissues. It was a very risky project,” Horvath says. But now the gamble seems to be paying off. By the time his findings were finally published last year1, the clock's median error was 3.6 years, meaning that it could guess the age of half the donors to within 43 months for a broad selection of tissues. That accuracy improves to 2.7 years for saliva alone, 1.9 years for certain types of white blood cell and 1.5 years for the brain cortex. The clock shows stem cells removed from embryos to be extremely young and the brains of centenarians to be about 100.

The reviews came back in the spring: more disbelief, and another rejection. Horvath didn't blame the reviewers for being sceptical. “Everyone who develops biomarkers knows what to expect: a very strong biomarker gives you a correlation of, say, 0.6 or 0.7.” For example, the correlation between age and the length of telomeres is less than 0.5. For Horvath's clock algorithm, that figure is 0.96. He confesses that he had trouble believing it himself until other researchers independently confirmed the tight association.

“Such tight correlations suggest there is something seemingly immutable going on in cells,” says Elizabeth Blackburn of the University of California, San Francisco, who won a Nobel prize for her research on telomeres — caps on the ends of chromosomes that shorten with age. It could be a clue to undiscovered biology, she suggests. And there may be medical implications in cases in which epigenetic estimates do not match a person's birth certificate.

http://www.nature.com/news/biomarkers-and-ageing-the-clock-watcher-1.15014


Picture; Compact Object (1962) by Natsuyuki Nakanishi
A plastic egg with bones, watch and clock parts, hair, eggshells, lens bits, ...

Times as artificial constructs born form synthetics. A plastic egg giving birth to both flesh and time, to the real, the material, and the ephemeral and elusive. Can one exist without the other? Is time internalized mechanically by the flesh, or is it the other way around? Time made flesh... by the machine? Our time isn't really all that similar to physical or even biological time. Ours ticks at different rates from day to day, from cradle to the grave. From atomic vibrations measuring millions of intervals in a single second, to the number of pressure waves transmitted by your local church bell, not all times are made equal. Then again, pulsars are very good clocks but they do not tell time the way Chicxulub did when it reshaped Mexico's Yucatan peninsula.

The experiments stoking fusion's fire

Are these about to set the world ablaze or will they fizzle and fade? If we are serious about finding out we better start throwing money at them.

You might have heard of the most popular fusion design, tokamaks like JET (Joint European Torus) and ITER (International Thermonuclear Experimental Reactor), devices that look like giant donuts and utilize giant magnets to confine and accelerate plasma. Or perhaps you've heard of NIF's (National Ignition Facility) laser initiated approach which counts on a massive 192 barrel laser cannon to focus all its energy on a tiny pellet in order to compress it to such a degree as to achieve ignition. Those two approaches have received the most attention and as a result have sucked up most of fusion's funding in the last few decades. They do look promising and are worth every penny spent but a variety of new approaches has been picking up steam which too are deserving of a much closer look and thus the funds to do so.

Nature digs into some of them with this excellent article that shines a bit of light on the secretive start-ups that claim to have found the answer to our energy woes. There's Tri Alpha's linear design trying to get things going by having 2 directly opposite plasma cannons fire at each other in sync as well as Helion Energy's somewhat similar colliding-beam reactor and last but not least they also talk a bit about General Fusion's approach which hopes to literally hammer their plasma into obedience.

http://www.nature.com/news/plasma-physics-the-fusion-upstarts-1.15592

If you think that's an exhaustive listing, you'd be wrong. Another big one is Lawrenceville Plasma Physics's Focus Fusion idea but there's also various teams hoping to work on different types of stellarators as well as the so called triple-threat methods. So many avenues worth exploring yet so few funds to do so. Luckily the private sector is chipping in a bit because else these would all have been shot down before even having had a chance of making it to the door. The fact that VCs, including some really big names, are investing in these should raise eyebrows as they don't typically start pumping money into something unless the road to market is somewhat mapped. Is it possible that fusion will follow the google model and reach the world from someone's garage? It might not seem likely but the chance definitely exists for all those billions invested in traditional designs to be bypassed by one really good innovative idea.

Lockheed - Solve for X: Charles Chase on energy for everyone
Google Talks - Focus Fusion: The Fastest Route to Cheap, Clean Energy
TED - Michel Laberge: How synchronized hammer strikes could generate nuclear fusion

Related posts
> A Star in a Bottle (ITER - Tokamak)

> National Ignition Facility (NIF - laser based confinement)
https://plus.google.com/108487783243149848473/posts/UHEhKLCyxLs

> Nuclear man; the humane power station (fission poetry?)
https://plus.google.com/108487783243149848473/posts/6LKW1s5yW2h

Photo below; General fusion's current experimental prototype on top and what they hope to build below. At the center of the containment vessel, within the spun liquid metal's vortex, plasma rings (think smoke rings) composed of the deuterium-tritium fuel are injected from both above and below which merge to form a single magnetized plasma target. The protruding cylinders you see in the pictures house the pistons used to batter the liquid metal into a fusion susceptible environment. When they are all fired at the same time they send a shockwave through the spinning lead-lithium mixture that gets stronger as it travel towards the center of the vessel where it rapidly collapses the vortex cavity with the plasma in it generating a fusion burst. Quite the turn on wouldn't you say? :)

Are chemputers about to mix things up?

The race to build machines that can synthesize any organic compound is heating up. Below you can find some very interesting snippets from a nature article on "robo-chemists" but you are better off reading the article in full. Note that the synthesis machines discussed are way more complex than ones currently in use or the more advanced chemprinters in development. The machines themselves would certainly be marvels of engineering but the hardest part will lie in the development of their brains, the software that would understand chemistry well enough to predict what'll work and what won't.

http://www.nature.com/news/organic-synthesis-the-robo-chemist-1.15661

Organic chemists typically plan their work on paper, sketching hexagons and carbon chains on page after page as they think through the sequence of reactions they will need to make a given molecule. Then they try to follow that sequence by hand — painstakingly mixing, filtering and distilling, stitching together molecules as if they were embroidering quilts.

But a growing band of chemists is now trying to free the field from its artisanal roots by creating a device with the ability to fabricate any organic molecule automatically. “I would consider it entirely feasible to build a synthesis machine which could make any one of a billion defined small molecules on demand,” declares Richard Whitby, a chemist at the University of Southampton, UK.

A British project called Dial-a-Molecule is laying the groundwork. Led by Whitby, the £700,000 (US$1.2-million) project began in 2010 and currently runs until May 2015. So far, it has mostly focused on working out what components the machine would need, and building a collaboration of more than 450 researchers and 60 companies to help work on the idea.

Some reckon it would take decades to develop an automated chemist as adept as a human — but a less capable, although still useful, device could be a lot closer. “With adequate funding, five years and we're done,” says Bartosz Grzybowski, a chemist at Northwestern University in Evanston, Illinois, who has ambitious plans for a synthesis machine of his own.

Grzybowski has spent the past decade building a system called Chematica and designed it to take a holistic view of synthesis: it not only hunts for the best reaction to use at each step, but also considers the efficiency of every possible synthetic route as a whole. This means that a poor yield in one step can be counterbalanced by a succession of high-yielding reactions elsewhere in the sequence. “In 5 seconds we can screen 2 billion possible synthetic routes,” says Grzybowski.

When Grzybowski first unveiled the network behind Chematica in 2005 (ref. 3), “people said it was bullshit”, he laughs. But that changed in 2012, when he and his team published a trio of landmark papers showing Chematica in action. For example, the program discovered a slew of 'one pot' syntheses in which reagents could be thrown into a vessel one after the other, without all the troublesome separation and purification of products after each step. Chematica can also look up information about the cost of starting materials and estimate the labour involved in each reaction, allowing it to predict the cheapest route to a particular molecule. When Grzybowski's lab tested 51 cut-price syntheses suggested by Chematica5, it collectively trimmed costs by more than 45%.

As long as programmes like Chematica rely on databases of published studies, says Whitby, they will struggle to design reliable synthetic routes to unknown compounds. To build a synthesis machine, “we need to be able to predict when a reaction is going to work — but more importantly we need to be able to predict when it's going to fail”.

Unfortunately, those failures are rarely recorded in the literature. “We only publish the successes, a cleaned-up version of what happens in the lab,” says Whitby. “We also lose a lot of information: what really was the temperature, what was the stirring speed, how much solvent did you use?” One solution is to record those successes and failures using electronic laboratory notebooks (ELNs), computer systems for logging raw experimental data that are widely used in industry but still rare in academia. “A lot of people ask, 'Who reads all these data?' The point is that machines use them — they can search the data,” explains Mat Todd, a chemist at the University of Sydney in Australia.

“If we really did know the history of every chemical reaction that had ever been done, we'd have amazing predictive capabilities,” says Todd. Many of those dreaming of a synthesis machine agree that widespread data harvesting will require a huge cultural shift. “That's absolutely the biggest barrier,”. “In chemistry, we don't have that culture of sharing, and I think it's got to change.”

http://www.nature.com/news/organic-synthesis-the-robo-chemist-1.15661

If curiosity kills the cat, the solution is to pretend not to care.

http://www.nature.com/news/entangled-photons-make-a-picture-from-a-paradox-1.15781

Normally, you have to collect particles that come from the object to image it, says Anton Zeilinger, a physicist at the Austrian Academy of Sciences in Vienna who led the work. “Now, for the first time, you don’t have to do that."

One advantage of this imaging technique is that the two photons need not be of the same energy, Zeilinger says, meaning that the light that touches the object can be of a different colour than the light that is detected. For example, a quantum imager could probe delicate biological samples by sending low-energy photons through them while building up the image using visible-range photons and a conventional camera. (!)

According to the laws of quantum physics, if no one detects which path a photon took, the particle effectively has taken both routes, and a photon pair is created in each path at once, says Gabriela Barreto Lemos, a physicist at Austrian Academy of Sciences and a co-author on the latest paper.

In the first path, one photon in the pair passes through the object to be imaged, and the other does not. The photon that passed through the object is then recombined with its other ‘possible self’ — which travelled down the second path and not through the object — and is thrown away. The remaining photon from the second path is also reunited with itself from the first path and directed towards a camera, where it is used to build the image, despite having never interacted with the object.

The researchers imaged a cut-out of a cat, a few millimetres wide, as well as other shapes etched into silicon. The team probed the cat cut-out using a wavelength of light which they knew could not be detected by their camera. "That's important, it's the proof that it's working," says Zeilinger.

http://www.nature.com/news/entangled-photons-make-a-picture-from-a-paradox-1.15781

Information is central to quantum mechanics. In particular, quantum interference occurs only if there exists no information to distinguish between the superposed states. The mere possibility of obtaining information that could distinguish between overlapping states inhibits quantum interference. Here we introduce and experimentally demonstrate a quantum imaging concept based on induced coherence without induced emission.

The experiment is fundamentally different from previous quantum imaging techniques, such as interaction-free imaging or ghost imaging, because now the photons used to illuminate the object do not have to be detected at all and no coincidence detection is necessary. This enables the probe wavelength to be chosen in a range for which suitable detectors are not available. To illustrate this, we show images of objects that are either opaque or invisible to the detected photons.

Paper: http://www.nature.com/nature/journal/v512/n7515/full/nature13586.html

From 2014-08-31

Sex redefined - Escaping the binary prison

This collection of hard hitting snippets from an excellent Nature article worth reading in full makes clear how the societal boundaries between the sexes are beginning to break down under the weight of reality. Hopefully mainstream knowledge of work like this will ultimately help us move away from having to conform to expectations surrounding both sex and gender.

As a staunch advocate of transhumanism I can draw a lot of inspiration from the LGBT community who is in many ways our advance guard. For decades they have been trying to establish the right to construe one's own identity instead of being forced into one of the two rigidly defined prefabricated package deals. They have done so in the face of enormous adversity which makes their perseverance especially admirable. Considering that the LGBT community has trouble getting the world to accept them for who they are, it's nigh impossible to imagine a world embracing people for who or what they want to be. If people are forced to make their case by explaining that they were born this way and thus don't have a choice, this does not bode well for the expanded cognitive and morphological rights transhumanism hopes to enshrine.

I can only hope that some day soon my home country of Belgium follows Germany's excellent example and will too introduce a third gender. It's rather infuriating that we currently lack both the common decency and the basic courtesy to implement even the barest minimum.

http://www.nature.com/news/sex-redefined-1.16943

As a clinical geneticist, Paul James is accustomed to discussing some of the most delicate issues with his patients. But in early 2010, he found himself having a particularly awkward conversation about sex.

A 46-year-old pregnant woman had visited his clinic at the Royal Melbourne Hospital in Australia to hear the results of an amniocentesis test to screen her baby's chromosomes for abnormalities. The baby was fine — but follow-up tests had revealed something astonishing about the mother. Her body was built of cells from two individuals, probably from twin embryos that had merged in her own mother's womb. And there was more. One set of cells carried two X chromosomes, the complement that typically makes a person female; the other had an X and a Y. Halfway through her fifth decade and pregnant with her third child, the woman learned for the first time that a large part of her body was chromosomally male.

doctors have long known that some people straddle the boundary — their sex chromosomes say one thing, but their gonads (ovaries or testes) or sexual anatomy say another. Parents of children with these kinds of conditions — known as intersex conditions — often face difficult decisions about whether to bring up their child as a boy or a girl. Some researchers now say that as many as 1 person in 100 has some form of DSD.

When genetics is taken into consideration, the boundary between the sexes becomes even blurrier. new technologies in DNA sequencing and cell biology are revealing that almost everyone is, to varying degrees, a patchwork of genetically distinct cells, some with a sex that might not match that of the rest of their body. Some studies even suggest that the sex of each cell drives its behaviour, through a complicated network of molecular interactions.

These discoveries do not sit well in a world in which sex is still defined in binary terms. Few legal systems allow for any ambiguity in biological sex, and a person's legal rights and social status can be heavily influenced by whether their birth certificate says male or female.

That the two sexes are physically different is obvious, but at the start of life, it is not. Five weeks into development, a human embryo has the potential to form both male and female anatomy.

For many years, scientists believed that female development was the default programme, and that male development was actively switched on by the presence of a particular gene on the Y chromosome. In 1990, researchers made headlines when they uncovered the identity of this gene which they called SRY. Just by itself, this gene can switch the gonad from ovarian to testicular development. For example, XX individuals who carry a fragment of the Y chromosome that contains SRY develop as males.

By the turn of the millennium, however, the idea of femaleness being a passive default option had been toppled by the discovery of genes that actively promote ovarian development and suppress the testicular programme.

These discoveries have pointed to a complex process of sex determination, in which the identity of the gonad emerges from a contest between two opposing networks of gene activity. Changes in the activity or amounts of molecules (such as WNT4) in the networks can tip the balance towards or away from the sex seemingly spelled out by the chromosomes. “It has been, in a sense, a philosophical change in our way of looking at sex; that it's a balance,”

Studies in mice suggest that the gonad teeters between being male and female throughout life, its identity requiring constant maintenance. In 2009, researchers reported deactivating an ovarian gene called Foxl2 in adult female mice; they found that the granulosa cells that support the development of eggs transformed into Sertoli cells, which support sperm development. Two years later, a separate team showed the opposite: that inactivating a gene called Dmrt1 could turn adult testicular cells into ovarian ones. “That was the big shock, the fact that it was going on post-natally,” says Vincent Harley, a geneticist who studies gonad development at the MIMR-PHI Institute for Medical Research in Melbourne.

Many people never discover their condition unless they seek help for infertility, or discover it through some other brush with medicine. Last year, for example, surgeons reported that they had been operating on a hernia in a man, when they discovered that he had a womb. The man was 70, and had fathered four children.

Studies of DSDs have shown that sex is no simple dichotomy. But things become even more complex when scientists zoom in to look at individual cells. The common assumption that every cell contains the same set of genes is untrue. Some people have mosaicism: they develop from a single fertilized egg but become a patchwork of cells with different genetic make-ups. This can happen when sex chromosomes are doled out unevenly between dividing cells during early embryonic development.

Biologists may have been building a more nuanced view of sex, but society has yet to catch up. True, more than half a century of activism from members of the lesbian, gay, bisexual and transgender community has softened social attitudes to sexual orientation and gender. Many societies are now comfortable with men and women crossing conventional societal boundaries in their choice of appearance, career and sexual partner. But when it comes to sex, there is still intense social pressure to conform to the binary model.

This pressure has meant that people born with clear DSDs often undergo surgery to 'normalize' their genitals. Such surgery is controversial because it is usually performed on babies, who are too young to consent, and risks assigning a sex at odds with the child's ultimate gender identity — their sense of their own gender.

In most countries, it is legally impossible to be anything but male or female. Yet if biologists continue to show that sex is a spectrum, then society and state will have to grapple with the consequences, and work out where and how to draw the line. Many transgender and intersex activists dream of a world where a person's sex or gender is irrelevant. Although some governments are moving in this direction, Greenberg is pessimistic about the prospects of realizing this dream — in the United States, at least. “I think to get rid of gender markers altogether or to allow a third, indeterminate marker, is going to be difficult.”

So if the law requires that a person is male or female, should that sex be assigned by anatomy, hormones, cells or chromosomes, and what should be done if they clash? “My feeling is that since there is not one biological parameter that takes over every other parameter, at the end of the day, gender identity seems to be the most reasonable parameter,” says Vilain. In other words, if you want to know whether someone is male or female, it may be best just to ask.

http://www.nature.com/news/sex-redefined-1.16943


> http://en.wikipedia.org/wiki/Sex
> http://en.wikipedia.org/wiki/Intersex
> http://en.wikipedia.org/wiki/Disorders_of_sex_development
> http://en.wikipedia.org/wiki/Gender
> http://en.wikipedia.org/wiki/Gender_identity
> http://en.wikipedia.org/wiki/Gender_role
> http://en.wikipedia.org/wiki/Androgyny
> http://en.wikipedia.org/wiki/Third_gender

photo; Andreja Pejić, self-described as living in between genders.

Where there's a will, there's a way

Many of you have likely heard a thing or two about the recent Nobel prizes awarded for the development of the blue LED (physics), the discovery of cells that constitute a positioning system in the brain (Physiology/Medicine), and the super-resolution fluorescence microscopy technique (chemistry). If not, I've included some links below that will bring you up to speed.

One article I particularly enjoyed was one from nature that, apart from digging into the incredibly awesome science behind the discovery of the specialized brain cells that enable us to navigate our surroundings, also took some time to cast a light on the lives of the husband and wife team largely responsible for the breakthrough.

http://www.nature.com/news/neuroscience-brains-of-norway-1.16079

If anyone knows how we navigate home, it is the Mosers. They shot to fame in 2005 with their discovery of grid cells deep in the brains of rats. These intriguing cells, which are also present in humans, work much like the Global Positioning System, allowing animals to understand their location.

In 2007, while still only in their mid-40s, they won a competition by the Kavli Foundation of Oxnard, California, to build and direct one of only 17 Kavli Institutes around the world. The Mosers are now minor celebrities in their home country, and their institute has become a magnet for other big thinkers in neuroscience.

The Mosers' work has also given them traction at one of the most challenging twenty-first-century research frontiers: how the brain computes. Just as computers use programming languages such as Java, the brain seems to have its own operating languages — a bewildering set of codes hidden in the rates and timing with which neurons fire as well as the rhythmic electrical activities that oscillate through brain circuits. These codes allow the brain to represent features of the external world — such as sound, light, smell and position in space — in a language that it can understand and compute. With their grid-cell work, the Mosers have been the first to crack one such code deep in the brain; now the challenge for the field is to find all the rest.

The Mosers grew up on different Norwegian islands in the North Atlantic, where summer days seem eternal and the long winter nights are brightened only by the dancing Northern Lights. They were both from non-academic families and they went to the same school. But they didn't get to know each other until 1983, when both were at the University of Oslo, both were wondering what to study and both were starting to realize that their true passion was for neuroscience and the brain.

Suddenly, everything sparked: romance between the two of them, intellectual curiosity and the beginnings of their mission in life — to find out how the brain generates behaviour. The Mosers visited one of the university's more famous faculty members, electrophysiologist Per Andersen, and asked to do their undergraduate projects with him. Andersen was studying the activity of neurons in the hippocampus — a brain area associated with memory — and the two students wanted to try to link this precise activity of cells with the behaviour of animals. Andersen, like most neuroscientists at the time, was sceptical about making such a big leap across the black box of the brain. But the pair wouldn't leave his office until he gave in and offered them an apparently simple project: how much of the hippocampus could you cut away before a rat could no longer remember new environments?
...

In 1984, while still undergraduates, the couple got engaged on top of the dormant volcano Mount Kilimanjaro in Tanzania. (The bitter temperature at the peak forced them to rush their exchange of rings, the quicker to get their gloves back on.) The pair had decided how their joint lives should be: children early, postdoc experience abroad and then their own lab together, somewhere in the world. These plans panned out — just a little faster than they had anticipated.
...

Not every couple would find it easy to work together in such apparent harmony. The Mosers ascribe their ability to do so in large part to their patient temperaments and shared interests — in science and beyond. Both love outdoor activities: May-Britt runs every other day across the rugged hills around their coastal home, and Edvard hikes at weekends. They share an obsession with volcanoes — hence their engagement at the top of one — and have climbed many of the globe's most spectacular peaks.
...

Edvard and May-Britt Moser: A journey into entorhinal cortex

It took some months before it dawned on them that they needed the rats to run around bigger boxes, so that the pattern would be stretched out and easier to see. At that point, it came into view: a near-perfect hexagon lattice, like a honeycomb. At first they refused to believe it. Such simplicity and regularity was the last thing they had expected — biology is usually a lot messier than this.

There were no physical hexagons traced on the floor; the shapes were abstractly created in the rat's brain and imposed on its environment, such that a single neuron fired whenever it crossed one of the points of the hexagon. The discovery was exciting for more than its pleasing pattern. This representation of space in brain-language was one of the long-sought codes by which the brain represents the world around us. “It was a long-drawn-out eureka moment,” recalls Edvard.

The Mosers also found that the different cells in the entorhinal cortex generate grids of many different types, like overlapping honeycombs — big, small and in every orientation and position relative to the box's border. And they ultimately came to see that the brain's grid cells are arranged according to a precise mathematical rule.

The cells that generate smaller grids, with narrower spacing, are at the top of the entorhinal cortex, and those that generate bigger grids are at the bottom. But it is even more exact than that: cells that make grids of the same size and orientation seem to cluster into modules. The modules are arranged in steps down the length of the entorhinal cortex, and the size of the grid represented by each module expands by a constant factor of 1.4 with every step.

The discoveries also astonished and thrilled theoreticians, because the hexagonal pattern is the optimal arrangement for achieving the highest-possible spatial resolution with a minimum number of grid cells. This saves energy, showing how beautifully efficient the brain can sometimes be. “Whoever would have believed that such a beautiful hexagonal representation existed so deep in the brain?” says Andreas Herz, a computational neuroscientist at the University of Munich in Germany.

Mindblowing stuff. There's a lot more where that came from so check out the article in full!

http://www.nature.com/news/neuroscience-brains-of-norway-1.16079

> http://www.nature.com/news/nobel-for-microscopy-that-reveals-inner-world-of-cells-1.16097 .
> http://www.nature.com/news/through-the-nanoscope-a-nobel-prize-gallery-1.16129 .
> http://www.nature.com/news/nobel-for-blue-led-that-revolutionized-lighting-1.16092 .

Microbes given a new lease on shelf life

http://www.nature.com/news/gm-microbes-created-that-can-t-escape-the-lab-1.16758

Critics of genetic engineering have long worried about the risk of modified organisms escaping into the environment. A biological-containment strategy described this week in Nature has the potential to put some of those fears to rest and to pave the way for greater use of engineered organisms in areas such as agriculture, medicine and environmental clean-up.

The new approach gives GMOs an Achilles heel. The researchers who have produced the organism have built in vital dependency on an artificial nutrient. If the nutrient is withdrawn, or the organism spreads to where it is no longer available, then the organism cannot survive.

The research marks an elegant step forward for the growing field of synthetic biology. In the first paper, Farren Isaacs and his colleagues at Yale University in New Haven, Connecticut, describe how they have produced various GMOs whose growth is restricted by the expression of multiple essential genes that depend on synthetic amino acids (A. J. Rovner et al. Nature http://dx.doi.org/10.1038/nature14095; 2015). In the second, separate study, George Church at Harvard Medical School in Boston, Massachusetts, and his colleagues redesigned essential enzymes in a GMO to make it metabolically dependent on synthetic amino acids (D. J. Mandell et al. Nature http://dx.doi.org/10.1038/nature14121; 2015). The modifications are made throughout the genome to make it harder for the altered sequences to be ejected.

The new technique originated in the laboratory of George Church. Two years ago, Church and his team (which included Isaacs) reported the synthesis of a strain of Escherichia coli that had a reprogrammed genetic code3. Instead of recognizing a particular DNA triplet known as the amber stop codon as an order to terminate protein synthesis, the recoded bacterium read the same instruction as a directive to incorporate a new kind of amino acid into its proteins.

Church and Isaacs have independently made this engineered microbe reliant on unnatural amino acids. The Isaacs team used genomic sequencing to identify sites in essential bacterial proteins where the microbes could incorporate synthetic amino acids without affecting overall function, whereas Church’s group started with the protein structures and added elements to help integrate and accommodate the artificial amino acids. “This is really the culmination of a decade of work,” says Church.

These organisms are also more resistant to viruses than their natural counter­parts because of the mismatch between the genetic code of the virus and that of its host3. Looking ahead, Church and his team are working to co-opt seven different codons, instead of just one.

The research in both papers is with bacteria, but there seems no reason why the techniques they describe could not be used to engineer more-complex, multicellular organisms — including crops — in the same way.

So what is the downside? Much of the controversy over genetic modification relates to early, clumsy, attempts by big business to commercialize crops, and to gain control over where, when and how they were grown to maximize profit. A crop that needs constant nourishment with a bespoke foodstuff — unavailable elsewhere and with manufacture protected under probable patents — could be presented as a way of tying vulnerable farmers still closer to largely unloved seed companies.

http://www.nature.com/news/gm-microbes-created-that-can-t-escape-the-lab-1.16758