The scientists who are creating a bio-internet of things

The internet of things connects devices across the globe. Now researchers are considering how bacteria can join the network.
by Emerging Technology from the arXiv


 
Imagine designing the perfect device for the internet of things. What functions must it have? For a start,  

• it must be able to communicate, both with other devices and with its human overlords. 
• It must be able to store and process information. 
• And it must monitor its environment with a range of sensors. 
• Finally, it will need some kind of built-in motor.

There is no shortage of devices that have many of these features. Most are based on widely available, low-cost devices such as Raspberry Pis, Arduino boards, and the like.

But another set of machines with similar functions is much more plentiful, say Raphael Kim and Stefan Poslad at Queen Mary University of London in the UK. They point out that bacteria communicate effectively and have built-in engines and sensors, as well as powerful information storage and processing architecture.

And that raises an interesting possibility, they say. Why not use bacteria to create a biological version of the internet of things? Today, in a call to action, they lay out some of the thinking and the technologies that could make this possible.

The way bacteria store and process information is an emerging area of research, much of it focused on the bacterial workhorse Escherichia coli. These (and other) bacteria store information in ring-shaped DNA structures called plasmids, which they transmit from one organism to the next in a process called conjugation.
 


Last year, Federico Tavella at the University of Padua in Italy and colleagues built a circuit in which one strain of immotile E. coli transmitted a simple “Hello world” message to a motile strain, which carried the information to another location.

This kind of information transmission occurs all the time in the bacterial world, creating a fantastically complex network. But Tavella and co’s proof-of-principle experiment shows how it can be exploited to create a kind of bio-internet, say Kim and Poslad.

E. coli make a perfect medium for this network. They are motile—they have a built-in engine in the form of waving, thread-like appendages called flagella, which generate thrust. They have receptors in their cell walls that sense aspects of their environment—temperature, light, chemicals, etc. They store information in DNA and process it using ribosomes. And they are tiny, allowing them to exist in environments that human-made technologies have trouble accessing.

E. coli are relatively easy to manipulate and engineer as well. The grassroots movement of DIY biology is making biotechnology tools cheaper and more easily available. The Amino Lab, for example, is a genetic engineering kit for schoolchildren, allowing them to reprogram E. coli to glow in the dark, among other things.

This kind of biohacking is becoming relatively common and shows the remarkable potential of a bio-internet of things. Kim and Poslad talk about a wide range of possibilities. “Bacteria could be programmed and deployed in different surroundings, such as the sea and ‘smart cities’, to sense for toxins and pollutants, gather data, and undertake bioremediation processes,” they say.

Bacteria could even be reprogrammed to treat diseases. “Harbouring DNA that encode useful hormones, for instance, the bacteria can swim to a chosen destination within the human body, [and] produce and release the hormones when triggered by the microbe’s internal sensor,” they suggest.

Of course, there are various downsides. While genetic engineering makes possible all kinds of amusing experiments, darker possibilities give biosecurity experts sleepless nights. It’s not hard to imagine bacteria acting as vectors for various nasty diseases, for example.

It’s also easy to lose bacteria. One thing they do not have is the equivalent of GPS. So tracking them is hard. Indeed, it can be almost impossible to track the information they transmit once it is released into the wild.

And therein lies one of the problems with a biological internet of things. The conventional internet is a way of starting with a message at one point in space and re-creating it at another point chosen by the sender. It allows humans, and increasingly devices, to communicate with each other across the planet.

Kim and Poslad’s bio-internet, on the other hand, offers a way of creating and releasing a message but little in the way of controlling where it ends up. The bionetwork created by bacterial conjugation is so mind-bogglingly vast that information can spread more or less anywhere. Biologists have observed the process of conjugation transferring genetic material from bacteria to yeast, to plants, and even to mammalian cells.

Evolution plays a role too. All living things are subject to its forces. No matter how benign a bacterium might seem, the process of evolution can wreak havoc via mutation and selection, with outcomes that are impossible to predict.

Then there is the problem of bad actors influencing this network. The conventional internet has attracted more than its fair share of individuals who release malware for nefarious purposes. The interest they might have in a biological internet of things is the stuff of nightmares.

Kim and Poslad acknowledge some of these issues, saying that creating a bacteria-based network presents fresh ethical issues. “Such challenges offer a rich area for discussion on the wider implication of bacteria driven Internet of Things systems,” they conclude with some understatement.

That’s a discussion worth having sooner rather than later.

Ref: arxiv.org/abs/1910.01974 : The Thing with E. coli: Highlighting Opportunities and Challenges of Integrating Bacteria in IoT and HCI.

ORIGINAL: MIT Technology Review

By Michael Schiffer / unsplash
Nov 1, 2019

Carlo Ratti's orange squeezer serves juice in bioplastic cups made from the peel

Italian studio Carlo Ratti Associati has developed an orange juice bar that turns the waste fruit peel into 3D-printed bioplastic cups to drink the contents from, as an example of the circular economy in practice.

Created for global energy company Eni, Feel the Peel is a prototype orange-squeezing machine that aims to bring circular design into everyday life.

The 3.10-metre-tall experimental juice bar is topped by a circular dome filled with 1,500 oranges. When someone orders a juice, the oranges slide down into the squeezer where they are cut in half and juiced.

After being juiced, the leftover orange peel falls into a see-through compartment at the bottom of the machine. The collected rinds are then dried and milled to make "orange dust", which is mixed with polylactic acid (PLA) to form a bioplastic material.

Related story

Carlo Ratti grows Gaudí-inspired structures with a kilometre of mushroom mycelium

Grown from a fungus material, the structures were shredded and returned to the soil as compost after the design festival, in a fully circular fashion.

This material is then heated and melted to form a filament, which is fed through a 3D printer incorporated into the machine.

Visitors can watch the printing process as it builds up concentric layers of the filament, before using the finished product to drink the freshly-squeezed juice.

The cup can then be recycled after use, with the material continually broken down and remade into further cups in theory.

The move to a circular economy – which involves designing out waste and pollution from the production and consumption process, and regenerating natural systems – is being encouraged by the Ellen MacArthur Foundation and others.

Last month, MacArthur launched an initiative to persuade 20 million designers to shift from linear to circular principles in their work.

"The principle of circularity is a must for today's objects," said founder Carlo Ratti. "Working with Eni, we tried to show circularity in a very tangible way, by developing a machine that helps us to understand how oranges can be used well beyond their juice."

According to Ratti, the next iterations of Feel the Peel might include new functions, such as printing fabric for clothing from orange peel. 

The Circular Juice Bar will be installed at the Singularity University Summit in Milan from 8 to 9 October 2019, before touring around Italy in the following months in a bid to "demonstrate a new approach to environmental circularity in daily life".

Feel the Peel is not the first collaboration between Carlo Ratti Associati and Eni that explores circular design. The pair previously teamed up to present a series of arched architectural structures made from mushroom mycelium at Milan Design Week 2019.

Grown from a fungus material, the structures were shredded and returned to the soil as compost after the design festival, in a fully circular fashion.

ORIGINAL: Dezeen
Natashah Hitti
10 September 2019

I have a dream that the powerful take the climate crisis seriously. The time for their fairytales is over

IN A HIGHLY ANTICIPATED SPEECH IN CONGRESS AFTER TRAVELLING HALF THE WAY ACROSS THE ATLANTIC BY BOAT, GRETA THUNBERG URGES US SENATORS TO LEARN FROM THE SACRIFICES OF MARTIN LUTHER KING AND OTHER CIVIL RIGHTS ACTIVISTS IN THE FIGHT AGAINST CLIMATE CHANGE. HERE IS THE TRANSCRIPT

• Greta Thunberg
• 8 hours ago

My name is Greta Thunberg, I am 16 years old and I’m from Sweden. I am grateful for being with you here in the USA. A nation that, to many people, is the country of dreams.

I also have a dream: that governments, political parties, and corporations grasp the urgency of the climate and ecological crisis and come together despite their differences - as you would in an emergency - and take the measures required to safeguard the conditions for a dignified life for everybody on earth.

Because then - we millions of school striking youth - could go back to school.

I have a dream that the people in power, as well as the media, start treating this crisis like the existential emergency it is. So that I could go home to my sister and my dogs. Because I miss them.

In fact, I have many dreams. But this is the year 2019. This is not the time and place for dreams. This is the time to wake up. This is the moment in history when we need to be wide awake.

And yes, we need dreams, we can not live without dreams. But there’s a time and place for everything. And dreams can not stand in the way of telling it like it is.

Greta Thunberg inspires climate activists everywhere: in pictures

And yet, wherever I go I seem to be surrounded by fairytales. Business leaders, elected officials all across the political spectrum spending their time making up and telling bedtime stories that soothe us, that make us go back to sleep.

These are “feel-good” stories about how we are going to fix everything. How wonderful everything is going to be when we have “solved” everything. But the problem we are facing is not that we lack the ability to dream or to imagine a better world. The problem now is that we need to wake up. It’s time to face the reality, the facts, the science.

And the science doesn’t mainly speak of “great opportunities to create the society we always wanted”. It tells of unspoken human sufferings, which will get worse and worse the longer we delay action - unless we start to act now. And yes, of course, a sustainable transformed world will include lots of new benefits. But you have to understand. This is not primarily an opportunity to create new green jobs, new businesses or green economic growth. This is above all an emergency, and not just any emergency. This is the biggest crisis humanity has ever faced.

And we need to treat it accordingly so that people can understand and grasp the urgency. Because you can not solve a crisis without treating it as one. Stop telling people that everything will be fine when in fact, as it looks now, it won’t be very fine. This is not something you can package and sell or ”like” on social media.

Stop pretending that you, your business idea, your political party or plan will solve everything. We must realize that we don’t have all the solutions yet. Far from it. Unless those solutions mean that we simply stop doing certain things.

Changing one disastrous energy source for a slightly less disastrous one is not progress. Exporting our emissions overseas is not reducing our emission. Creative accounting will not help us. In fact, it’s the very heart of the problem.

Some of you may have heard that we have 12 years from 1 January 2018 to cut our emissions of carbon dioxide in half. But I guess that hardly any of you have heard that there is a 50 percent chance of staying below a 1.5 degree Celsius of global temperature rise above pre-industrial levels. Fifty percent chance.

And these current, best available scientific calculations do not include nonlinear tipping points as well as most unforeseen feedback loops like the extremely powerful methane gas escaping from rapidly thawing arctic permafrost. Or already locked in warming hidden by toxic air pollution. Or the aspect of equity; climate justice.

So a 50 percent chance - a statistical flip of a coin - will most definitely not be enough. That would be impossible to morally defend. Would anyone of you step onto a plane if you knew it had more than a 50 percent chance of crashing? More to the point: would you put your children on that flight?

And why is it so important to stay below the 1.5 degree limit? Because that is what the united science calls for, to avoid destabilizing the climate so that we stay clear of setting off an irreversible chain reaction beyond human control. Even at 1 degree of warming, we are seeing an unacceptable loss of life and livelihoods.

So where do we begin? Well, I would suggest that we start looking at chapter 2, on page 108 in the IPCC report that came out last year. Right there it says that if we are to have a 67 per cent chance of limiting the global temperature rise to below 1.5 degrees Celsius, we had, on 1 January 2018, about 420 Gtonnes of CO2 left to emit in that carbon dioxide budget. And of course, that number is much lower today. As we emit about 42 Gtonnes of CO2 every year if you include land use.

With today’s emissions levels, that remaining budget is gone within less than 8 and a half years. These numbers are not my opinions. They aren’t anyone’s opinions or political views. This is the current best available science. Though a great number of scientists suggest even these figures are too moderate, these are the ones that have been accepted by all nations through the IPCC.

And please note that these figures are global and therefore do not say anything about the aspect of equity, clearly stated throughout the Paris Agreement, which is absolutely necessary to make it work on a global scale. That means that richer countries need to do their fair share and get down to zero emissions much faster, so that people in poorer countries can heighten their standard of living, by building some of the infrastructures that we have already built. Such as roads, hospitals, schools, clean drinking water, and electricity.

The USA is the biggest carbon polluter in history. It is also the world’s number one producer of oil. And yet, you are also the only nation in the world that has signaled your strong intention to leave the Paris Agreement. Because quote ”it was a bad deal for the USA”.

Four-hundred and twenty GTons of CO2 left to emit on 1 January 2018 to have a 67 percent chance of staying below 1.5 degrees of global temperature rise. Now that figure is already down to less than 360 GTons.

These numbers are very uncomfortable. But people have the right to know. And the vast majority of us have no idea these numbers even exist. In fact, not even the journalists that I meet seem to know that they even exist. Not to mention the politicians. And yet they all seem so certain that their political plan will solve the entire crisis.

But how can we solve a problem that we don’t even fully understand? How can we leave out the full picture and the current best available science?

I believe there is a huge danger in doing so. And no matter how political the background to this crisis may be, we must not allow this to continue to be a partisan political question. The climate and ecological crisis are beyond party politics. And our main enemy right now is not our political opponents. Our main enemy now is physics. And we can not make “deals” with physics.

Everybody says that making sacrifices for the survival of the biosphere - and to secure the living conditions for future and present generations - is an impossible thing to do.

Americans have indeed made great sacrifices to overcome terrible odds before.

Think of the brave soldiers that rushed ashore in that first wave on Omaha Beach on D Day. Think of Martin Luther King and the 600 other civil rights leaders who risked everything to march from Selma to Montgomery. Think of President John F. Kennedy announcing in 1962 that America would “choose to go to the moon in this decade and do the other things, not because they are easy, but because they are hard…”

Perhaps it is impossible. But looking at those numbers - looking at the current best available science signed by every nation - then I think that is precisely what we are up against.

But you must not spend all of your time dreaming or see this as some political fight to win.

And you must not gamble your children’s future on the flip of a coin.

Instead, you must unite behind the science.

You must take action.

You must do the impossible.

Because giving up can never ever be an option.

ORIGINAL: The Independent
by Greta Thumberg
2019/09/19

Greta Thunberg speech at the National Assembly in Paris 2019-07-23

Transcript:

"I have some good news and some bad news regarding the climate emergency. I will start with the good news.

The world, as a small number of people have been saying lately, will not end in 11 years.

The bad news, however, is that around the year 2030, if we continue with business as usual, we will likely be in a position where we may pass a number of tipping points. And then we might no longer be able to undo the irreversible climate breakdown.

A lot of people, a lot of politicians, business leaders, journalists say they don't agree with what we are saying. They say we children are exaggerating, that we are alarmists. To answer this I would like to refer to page 108, chapter 2 in the latest IPCC report. There you will find all our "opinions" summarized because there you find a remaining carbon dioxide budget. Right there it says that: if we are to have a 67% chance of limiting the global temperature rise to below 1.5 degrees, we had on January 1st, 2018, 420 gigatons of carbon dioxide left in our CO2 budget. And of course, that number is much lower today. We emit about 42 gigatons of CO2 every year.

At current emissions levels, that remaining budget is gone within roughly eight and a half years. These numbers are as real as it gets, though a great number of scientists suggests that they are too generous, these are the ones that have been accepted by all nations through the IPCC.

And not once, not one single time have I heard any politician, journalists or business leader even mention these numbers. It is almost like you don't even know they exist, as if you haven't even read the latest IPCC reports on which the future of our civilization is depending.

Or maybe you are simply not mature enough to tell it like it is. Because even that burden you leave to us children. We become the bad guys who have to tell people these uncomfortable things because no one else wants to or dares to. And just for quoting and acting on these numbers, these scientific facts, we receive unimaginable amounts of hate and threats. We are being mocked and lied about by elected officials, members of Parliament's, business leaders, journalists. What I really would like to ask all of those who question our so-called "opinions" or think that we are extreme: - Do you have a different budget for at least a reasonable chance of staying below the 1.5 degrees of warming limit? Is there another intergovernmental panel on climate change? Is there a secret Paris agreement that we don't know about? One that not includes the aspect of equity? Because these are the numbers that count, this is the current best available science. You can't simply make up your own facts just because you don't like what you hear.

There is no middle ground when it comes to the climate and ecological emergency. Of course, you could argue that we should go for a more risky pathway, such as the alternative of 580 gigatons of CO2 from January 1st, 2018, which gives us a 50/50 percent chance of limiting the global temperature rise to below 1.5 degrees. That amount of carbon dioxide will run out in about 12 years of current business as usual. But why should we do that, why should we accept taking that risk, leaving the future living conditions for humankind to a 50/50 flip of a coin. 420 gigatons left of CO2 to emit. And now that number is down to less than 360 gigatons. And please note that these figures are global and therefore do not say anything about the aspect of equity, clearly stated throughout the Paris agreement, which is absolutely necessary to make it work on a global scale. That means that richer countries need to get down to zero emissions faster, so the people in poorer parts of the world can heighten their standard of living by building some of the infrastructures that we have already built, such as roads, hospitals, electricity, schools and providing clean drinking water.

And because you have ignored these facts, because you and pretty much all of the media to this very minute, keep ignoring them, people do not know what is going on. If you respect science, if you understand science, then this is it. 420 gigatons of CO2 left to emit on January 1st to have a 67% chance of staying below 1.5 degrees of global temperature rise, according to the IPCC.

In the Paris agreement, we have only signed up for staying below 1.5 to 2 degrees of temperature rise. And that, of course, gives us a bigger remaining carbon dioxide budget. But the latest IPCC report shows that aiming instead for below 1.5 degrees would significantly reduce the climate impacts, and that would most certainly save countless human lives.

This is what it's all about, this is all that we are saying. But I will also tell you this: -You cannot solve the crisis without treating it as a crisis, without seeing the full picture. You cannot leave the responsibility to individuals, politicians, the market or other parts of the world to take. This has to include everything and everyone.

Once you realize how painfully small the size of our remaining carbon dioxide budget is, once you realize how fast it is disappearing, once you realize that basically nothing is being done about it and once you realize that almost no one is even aware of the fact that carbon dioxide budgets even exists, then tell me what exactly do you do? And how do we do it without sounding alarmist? That is the question we must ask ourselves, and the people in power.

The science is clear and all we children are doing is communicating and acting on that united science. Now political leaders in some countries are starting to talk. They are starting to declare climate emergencies and announcing dates for so-called climate neutrality. And declaring a climate emergency is good. But only setting up these vague, distant dates and saying things which give the impression of that things are being done and that action is on the way, will most likely do more harm than good. Because of the changes required are still nowhere in sight. Not in France, not in the EU, nowhere. And I believe that the biggest danger is not our inaction. The real danger is when companies and politicians are making it look like real action is happening, when in fact almost nothing is being done, apart from clever accounting and creative PR.

The climate and ecological emergency is right here, right now. But it has only just begun, it will get worse. 420 gigatons of CO2 left to emit on January 1st 2018 to have a 67 percent chance of staying below a 1.5 degrees of global temperature rise. And now that figure is already down to less than 360 gigatons.

At current emissions levels that remaining budgets is gone within roughly eight and a half years. In fact, since I started this speech the world has emitted about 800,000 tons of carbon dioxide. And if anyone still has excuses not to listen, not to act, not to care, I ask you once again: -Is there another Intergovernmental Panel on Climate Change? Is there a secret Paris agreement that we don't know about? One that does not include the aspect of equity? Do you have a different budget for at least a reasonable chance of staying below 1.5 degrees of global temperature rise? Some people have chosen not to come here today, some people have chosen not to listen to us, and that is fine, we are after all just children. You don't have to listen to us, but you do have to listen to the United science, the scientists. And that is all we ask, just unite behind the science!"

ORIGINAL: https://fridaysforfuture.org/greta-speeches#greta_speech_july23_2019Fridays for Future

These Artificial Leaves Can Absorb 10 Times More CO2 From The Air Than Real Leaves

Plants possess a natural ability to purify the air and produce energy while doing so. The ability is called photosynthesis and it is the process whereby plants use water and carbon dioxide from the air to produce carbohydrates using energy from the sun. Scientists have found a way to make this happen artificially. The thing is, they hadn’t been able to get these artificial leaves to work outside the lab because the lab leaves use pure, pressurized carbon dioxide from tanks, which is different than getting it out of the air.

An artificial, bio-inspired leaf. Carbon dioxide (red and black balls) enter the leaf as water (white and red balls) evaporates from the bottom of the leaf. An artificial photosystem (purple circle at the center of the leaf) made of a light absorber coated with catalysts converts carbon dioxide to carbon monoxide and converts water to oxygen (shown as double red balls) using sunlight.” (Image: Meenesh Singh).

But now, researchers from the University of Illinois at Chicago have proposed a design solution that could change everything. Their idea just might be the leaves’ ticket out of the lab and into the environment. Their findings are reported in the journal ACS Sustainable Chemistry & Engineering .“

Meenesh Singh, assistant professor of chemical engineering in the UIC College of Engineering and corresponding author on the paper, said:

“So far, all designs for artificial leaves that have been tested in the lab use carbon dioxide from pressurized tanks. In order to implement successfully in the real world, these devices need to be able to draw carbon dioxide from much more dilute sources, such as air and flue gas, which is the gas given off by coal-burning power plants.”

The only way that these artificial leaves will be able to collect and concentrate carbon dioxide (a potent greenhouse gas) from the air around us to drive their artificial photosynthetic reactions is if they are unhooked from the pressurized carbon dioxide supply.

Image: Meenesh Singh

Here’s how Singh and his colleague Aditya Prajapati, a graduate student in his lab, propose to solve this problem:

• The traditional artificial leaf is placed inside a water-filled capsule constructed out of a semi-permeable membrane.
• When the sunlight warms the water, it evaporates through the membrane – when that happens it gets the capsule to suck in carbon dioxide (co2).
• The CO2 that’s been sucked in then gets converted into carbon monoxide (CO) and oxygen by the artificial leaf inside the capsule.
• The carbon monoxide (CO) could be siphoned from the device and used to create synthetic fuels ranging from gasoline to methanol;
• And the oxygen could be released back into the environment or collected.

In other words, all they have to do is envelope the artificial leaf technology (that has already been developed and works but only in the lab) within this specialized membrane and the whole unit will be able to function outside, like a natural leaf. Furthermore, according to their research, they believe that an artificial leaf built around their design would be 10 times more efficient at converting CO2 to fuel than natural leaves.

Their calculations reveal that 360 of their artificial leaves, each 1.7 meters long and 0.2 meters wide, would generate about half a ton of CO daily, which can be used as a basis for synthetic fuels. If those leaves were to be spread out over 500 square meters, then they could reduce the CO2 levels in the air within 100 meters of the space by 10 percent in just one day.

Singh concludes:

“Our conceptual design uses readily available materials and technology, that when combined can produce an artificial leaf that is ready to be deployed outside the lab where it can play a significant role in reducing greenhouse gases in the atmosphere.”

ORIGINAL: Intelligent Living

by Andrea D. Steffen
February 22, 2019

Chemical Computing, the Future of Artificial Intelligence

In 1951, the Russian chemist Boris Belousov sent to a scientific journal a study in which he described an astonishing discovery: while trying to simulate a metabolic process in the laboratory, he had discovered a chemical reaction that occurred and then reversed itself on its own, alternating between a yellow colour and a colourless state. Belousov couldn’t find any journal willing to publish his results, since they appeared to violate a fundamental law of nature.

However, his work—which only came to light in 1959 through a brief presentation at a symposium—has become, half a century later, the foundation stone of a new discipline: chemical computing. This technological path is an alternative to quantum computing and conventional computing, capable of processing in parallel based on the same operating principles as our brain, promising futuristic applications, such as integrating in our body in the form of intelligent biosensors.

Portrait of Boris Belousov. Source: Wikimedia

Computing is based on the use of logic gates, which process a data input—usually in binary code—to produce a result or output. In the chips of our current computers, this function is carried out thanks to semiconductors, materials with a binary response capacity operating through the movement of electrons. However, this is not the only possible system; quantum computing, currently in the experimental phase, uses properties of subatomic particles that can also take alternative values, with greater versatility than semiconductors.

Until the discovery of Belousov, no one would have suspected that chemical reactions could act as logic gates. According to the second law of thermodynamics, these processes are linear, spontaneously moving towards equilibrium through an increase in entropy, a measure of the energy of chaos; what is done cannot be undone, at least on its own. For this reason, Belousov’s work was rejected and ignored, until a decade later it was recovered, extended and made known by the biophysicist Anatol Zhabotinsky.

THE FIRST CHEMICAL OSCILLATOR

The Belousov-Zhabotinsky reaction was the first chemical oscillator, a non-linear reaction that moves alternately in one direction and then the opposite as the process itself modifies the concentrations of the ions present, and which only stops when the reagents are consumed. In a Petri dish, these reactions produce waves of colours that diffuse from different points and act as inputs; the interaction between these input data can produce as an output a new wave—a 1, in binary code.

But this ability of chemical systems to compute by acting as logic gates is not something invented by humans, but was discovered, since it exists in nature. “We are already using chemical computers, because our brains and bodies employ communication via the diffusion of mediators, neuromodulators, hormones, etc.,” says computer scientist Andrew Adamatzky, director of the International Center of Unconventional Computing at the University of the West of England in Bristol. “We are chemical computers,” he summarises.

The Belousov-Zhabotinsky reaction is a non-linear reaction that moves alternately in one direction and then the opposite. Credit: Jkrieger

For decades it was believed that the brain’s computational capacity lay in the neuron as a minimal unit, and that its subcellular parts were limited to acting as simple transmitters of the decisions made by the cell in terms of the inputs received. Today it is known that this is not the case, and that discrete parts of the neuron, such as

• the dendrites (the branches that receive the signals), 
• the axon (which sends the impulse to other neurons), and 
• the synapse (the space that communicates between them) 

are independently modulable, and therefore capable of computing by themselves. As this modulation is exerted through chemical agents, the brain is not an electrical computer, but an electrochemical one.

THE BRAIN, A PARALLEL COMPUTER

The great versatility of each neuron confers on the brain a valuable quality. “The brain and chemical computers are parallel computers,” explains biophysicist Vladimir Vanag, from the Centre for Nonlinear Chemistry at the Immanuel Kant Baltic Federal University (Russia). Parallel computing is not within the reach of conventional microprocessors (though it is for quantum ones). In practice, this advantage that chemical computing possesses overcomes one of its drawbacks—its slower speed.

(a) The array of the BZ microdroplets in a 1D capillary. (b) Spacetime plot for the dynamics of the BZ MDs at GNF with coefficient g e = 0.11. The total size of the space-time plot is equal to 1875 mm  424 s. Short horizontal bars depict spikes for each of the 15 BZ MDs. The averaged diameter d of a single MD equals 125 mm. The red arrow depicts the averaged period of oscillations, T 0 = 159 s. The slope of the blue line characterizes the ''velocity'' spike propagation, 1.68 mm s À1. Some droplets in snapshot (a) look lighter since they are in the oxidized state of the catalyst, the others look darker since they correspond to the reduced state of the catalyst. White dashes in droplets with index numbers (from 1 to 15) display the image reading area to record the ox-red state of the droplets. Compared with the great speed of electronic chips, chemical computing is limited by the speed of the diffusion of reactions in the medium. Researchers like Adamaztky are working on breaking this barrier: “Systems can be scaled down to the nano-scale and then everything will be fast,” he says. However, he notes that certain applications will not require higher speeds: “When reaction-diffusion computers are embedded in the human body, their speed of processing information will perfectly match natural processes.”

But in any case, Vanag explains with an example how parallel computing compensates for any speed limit: if a micro-oscillator—equivalent to a processor—occupies a cubic volume of 100 microns on each side, a single cubic centimetre could contain a million of them, all working in parallel. Thus, “we can increase the number of micro-oscillators by many orders of magnitude and overcome the speed of conventional computers,” he says. Say goodbye to Moore’s law; with chemical computing, a small increase in volume is enough to multiply the processing capacity. This is the secret of the human brain, slower than any computer, but more powerful than all of them.

The brain is slower than any computer, but much more powerful. Credit: Pixbay

A NEW ARTIFICIAL-INTELLIGENCE

In addition, chemical computing brings other crucial advantages. “It should work without electricity,” says Vanag. “No viruses, autonomous regime of working, and extremely high efficiency.” And all this while using just a few cheap chemical reagents. Thanks to these qualities, chemical computing is emerging as a promising alternative to simulate the human brain. By building bottom-up systems, starting with small oscillator networks and adding more and more layers of complexity, scientists are learning how cognitive functions such as image recognition or decision making appear.

Of course, a consequence of this chemical recreation of the brain would be the possibility of obtaining new artificial-intelligence systems, but radically different from what we usually envision: imagine robots made of gel, without a defined shape, capable of dividing themselves into smaller ones so that each one of them works independently. Perhaps they’ll even be embedded in our own bodies, analysing our biological parameters, curing our diseases. “But this is a fantasy,” concludes Vanag. “At the moment.”

Javier Yanes

@yanes68

ORIGINAL: OpenMind

David Attenborough: 'The Garden of Eden is no more'. Read his Davos speech in full

Hilde Schwab and Sir David Attenborough at the 25th Annual Crystal Awards.
Image: World Economic Forum / Manuel Lopez

Thank you, Professor Klaus Schwab, Hilde Schwab and the World Economic Forum for this generous award and inviting me to Davos.

I am quite literally from another age.

I was born during the Holocene- the name given to the 12,000-year period of climatic stability that allowed humans to settle, farm and create civilisations.

Those conditions fostered our unique minds, giving rise to international trade in ideas as well as goods making us the globally-connected species we are today.

Much of what will be discussed here is the consequence of that stability.

Global businesses, international co-operation and the striving for higher ideals these are all possible because for millennia, on a global scale, nature has largely been predictable and stable.

Now in the space of one human lifetime - indeed in the space of my lifetime all that has changed.

The Holocene has ended. The Garden of Eden is no more.

We have changed the world so much that scientists say we are now in a new geological age - The Anthropocene - The Age of Humans.

When you think about it, there is perhaps no more unsettling thought. The only conditions modern humans have ever known are changing and changing fast.

It is tempting and understandable to ignore the evidence and carry on as usual or to be filled with doom and gloom.

But there is also a vast potential for what we might do.

We need to move beyond guilt or blame and get on with the practical tasks at hand.

We did not get to this point deliberately – and it has happened astonishingly quickly.

When I made my first television programmes most of audiences had never even seen a pangolin - indeed few pangolin had ever seen a TV camera!

When in 1979 I made a series tracing the history of life on earth, I was aware of environmental problems but I didn’t imagine we were fundamentally changing nature.

In 1999, whilst making the Blue Planet series about marine life, we filmed coral-bleaching, but I still didn’t appreciate the magnitude of the damage that had already started.

Now however we have evidence, knowledge and the ability to share it on a scale unimaginable even just a few years ago.

Movements and ideas can spread at astonishing speed.

The audience for that first series, 60 years ago, was restricted to a few million viewers in southern England.

My next series - Our Planet- which is about to be launched, will go instantly to hundreds of millions of people in almost every country on Earth via Netflix.

And the evidence supporting the series will be free to view by everyone with an internet connection via WWF.

If people can truly understand what is at stake, I believe they will give permission to business and governments to get on with the practical solutions.

And as a species we are expert problem-solvers. But we haven’t yet applied ourselves to this problem with the focus it requires.

We can create a world with clean air and water, unlimited energy, and fish stocks that will sustain us well into the future.

But to do that we need a plan.

Over the next 2 years there will be United Nations decisions on Climate Change, Sustainable Development and a New Deal for Nature. Together these will form our species’ plan for a route through the Anthropocene.

What we do in the next few years will profoundly affect the next few thousand years.

I look forward very much to the discussions and insights this week

Thank you again for this great honour.

ORIGINAL: WEForum

El poder de la opción B para romper estereotipos

La Dra. Alexandra Olaya Castro es física teórica, y es conocida por su trabajo en física cuántica biomolecular, en particular por su investigación sobre los efectos cuánticos en la fotosíntesis. En 2016 fue galardonada con la Medalla Maxwell del Institute of Physics, una de las mayores distinciones de la física teórica, siendo la primera latinoamericana en obtenerla.

En esta conferencia de TEDxBogotaMujeres, Alexandra Olaya Castro habla sobre estereotipos y propone enfrentarse a ellos para intentar eliminarnos, es decir, propone optar por “la opción B”. En primer lugar, habla de su historia personal, de cómo consiguió estudiar, doctorarse y ganar la Medalla Maxwell procediendo de una familia humilde de Colombia. Y en segundo lugar, habla de su investigación, de la física cuántica biomolecular, y de cómo tomó “la opción B” para investigar en un área interdisciplinar, rompiendo estereotipos en la ciencia.

Yo veo a los estereotipos como agujeros negros sociales, que atrapan la luz de mentes brillantes, de mentes talentosas, de mentes que pueden transformar. 

ORIGINAL: Mujeres Con Ciencia

Edición realizada por Marta Macho Stadler

8 abril, 2018

Test Tube Artificial Neural Network Recognizes "Molecular Handwriting"

Conceptual illustration of a droplet containing an artificial neural network made of DNA that has been designed to recognize complex and noisy molecular information, represented as 'molecular handwriting.' Credit: Olivier Wyart

Qian Lab - "Winner Take All" Method Enables DNA Computing

Test tube chemistry using synthetic DNA molecules can be utilized in complex computing tasks to exhibit artificial intelligence

Researchers at Caltech have developed an artificial neural network made out of DNA that can solve a classic machine learning problem: correctly identifying handwritten numbers. The work is a significant step in demonstrating the capacity to program artificial intelligence into synthetic biomolecular circuits.

The work was done in the laboratory of Lulu Qian, assistant professor of bioengineering. A paper describing the research (paywall) appears online on July 4 and in the July 19 print issue of the journal Nature.

"Though scientists have only just begun to explore creating artificial intelligence in molecular machines, its potential is already undeniable," says Qian. "Similar to how electronic computers and smart phones have made humans more capable than a hundred years ago, artificial molecular machines could make all things made of molecules, perhaps including even paint and bandages, more capable and more responsive to the environment in the hundred years to come."

Artificial neural networks are mathematical models inspired by the human brain. Despite being much simplified compared to their biological counterparts, artificial neural networks function like networks of neurons and are capable of processing complex information. The Qian laboratory's ultimate goal for this work is to program intelligent behaviors (the ability to compute, make choices, and more) with artificial neural networks made out of DNA.

"Humans each have over 80 billion neurons in the brain, with which they make highly sophisticated decisions. Smaller animals such as roundworms can make simpler decisions using just a few hundred neurons. In this work, we have designed and created biochemical circuits that function like a small network of neurons to classify molecular information substantially more complex than previously possible," says Qian.

To illustrate the capability of DNA-based neural networks, Qian laboratory graduate student Kevin Cherry chose a task that is a classic challenge for electronic artificial neural networks: recognizing handwriting.

Human handwriting can vary widely, and so when a person scrutinizes a scribbled sequence of numbers, the brain performs complex computational tasks in order to identify them. Because it can be difficult even for humans to recognize others' sloppy handwriting, identifying handwritten numbers is a common test for programming intelligence into artificial neural networks. These networks must be "taught" how to recognize numbers, account for variations in handwriting, then compare an unknown number to their so-called memories and decide the number's identity.

WHY DNA?

Key to creating biomolecular circuits out of DNA are the strict binding rules between molecules of DNA. A single-stranded DNA molecule is composed of smaller molecules called nucleotides—abbreviated A, T, C, and G—arranged in a string, or sequence. The nucleotides in a single-stranded DNA molecule can bond with those of another single strand to form double-stranded DNA, but the nucleotides bind only in very specific ways: An A nucleotide with a T or a C nucleotide with a G.

Taking advantage of these predictable binding rules, Qian and her colleagues can design short strands of DNA to undergo predictable chemical reactions in a test tube and thereby compute tasks, such as molecular pattern recognition. In 2011, Qian and her colleagues created the first artificial neural network made of DNA molecules that could recognize four simple patterns.

In the work described in the Nature paper, Cherry, who is the first author on the paper, demonstrated that a neural network made out of carefully designed DNA sequences could carry out prescribed chemical reactions to accurately identify "molecular handwriting." Unlike visual handwriting that varies in geometrical shape, each example of molecular handwriting does not actually take the shape of a number. Instead, each molecular number is made up of 20 unique DNA strands chosen from 100 molecules, each assigned to represent an individual pixel in any 10 by 10 pattern. These DNA strands are mixed together in a test tube.

"The lack of geometry is not uncommon in natural molecular signatures yet still requires sophisticated biological neural networks to identify them: for example, a mixture of unique odor molecules comprises a smell," says Qian.

Given a particular example of molecular handwriting, the DNA neural network can classify it into up to nine categories, each representing one of the nine possible handwritten digits from 1 to 9.

First, Cherry built a DNA neural network to distinguish between handwritten 6s and 7s. He tested 36 handwritten numbers and the test tube neural network correctly identified all of them. His system theoretically has the capability of classifying over 12,000 handwritten 6s and 7s—90 percent of those numbers taken from a database of handwritten numbers used widely for machine learning—into the two possibilities.

Crucial to this process was encoding a "winner take all" competitive strategy using DNA molecules, developed by Qian and Cherry. In this strategy, a particular type of DNA molecule dubbed the annihilator was used to select a winner when determining the identity of an unknown number.

"The annihilator forms a complex with one molecule from one competitor and one molecule from a different competitor and reacts to form inert, unreactive species," says Cherry. "The annihilator quickly eats up all of the competitor molecules until only a single competitor species remains. The winning competitor is then restored to a high concentration and produces a fluorescent signal indicating the networks' decision." 

Next, Cherry built upon the principles of his first DNA neural network to develop one even more complex, one that could classify single digit numbers 1 through 9. When given an unknown number, this "smart soup" would undergo a series of reactions and output two fluorescent signals, for example, green and yellow to represent a 5, or green and red to represent a 9.

Qian and Cherry plan to develop artificial neural networks that can learn, forming "memories" from examples added to the test tube. This way, Qian says, the same smart soup can be trained to perform different tasks.

"Common medical diagnostics detect the presence of a few biomolecules, for example cholesterol or blood glucose." says Cherry. "Using more sophisticated biomolecular circuits like ours, diagnostic testing could one day include hundreds of biomolecules, with the analysis and response conducted directly in the molecular environment."

The paper is titled "Scaling up molecular pattern recognition with DNA-based winner-take-all neural networks." Funding was provided by the National Science Foundation, the Burroughs Wellcome Fund, and the Shurl and Kay Curci Foundation.

Related:

• Computing with Biochemical Circuits Made Easy
• Caltech Researchers Create the First Artificial Neural Network Out of DNA
• Caltech Researchers Build Largest Biochemical Circuit Out of Small Synthetic DNA Molecules

ORIGINAL: Caltech

by Lori Dajose

07/05/2018