FUNGAL COMPUTERS

Posted on 2023/03/22 by secret santa

“Recording electrical activity of split gill fungi Schizophyllum commune”

MYCOLOGICAL ELECTRONICS
https://popsci.com/unconventional-computing-lab-mushroom/
Inside the lab that’s growing mushroom computers
by Charlotte Hu / February 27, 2023

“Upon first glance, the Unconventional Computing Laboratory looks like a regular workspace, with computers and scientific instruments lining its clean, smooth countertops. But if you look closely, the anomalies start appearing. A series of videos shared with PopSci show the weird quirks of this research: On top of the cluttered desks, there are large plastic containers with electrodes sticking out of a foam-like substance, and a massive motherboard with tiny oyster mushrooms growing on top of it.

The researchers there have been working on stuff like this for awhile: It was founded in 2001 with the belief that the computers of the coming century will be made of chemical or living systems, or wetware, that are going to work in harmony with hardware and software. Why? Integrating these complex dynamics and system architectures into computing infrastructure could in theory allow information to be processed and analyzed in new ways. And it’s definitely an idea that has gained ground recently, as seen through experimental biology-based algorithms and prototypes of microbe sensors and kombucha circuit boards. In other words, they’re trying to see if mushrooms can carry out computing and sensing functions.

“Electrical potential difference between two neighbouring fruits. (a) Position of electrodes when measuring potential different between fungal bodies. (b) Part of experimental set-up. (c) Exemplar plot of electrical potential.”

With fungal computers, mycelium—the branching, web-like root structure of the fungus—acts as conductors as well as the electronic components of a computer. (Remember, mushrooms are only the fruiting body of the fungus.) They can receive and send electric signals, as well as retain memory. “I mix mycelium cultures with hemp or with wood shavings, and then place it in closed plastic boxes and allow the mycelium to colonize the substrate, so everything then looks white,” says Andrew Adamatzky, director of the Unconventional Computing Laboratory at the University of the West of England in Bristol, UK. “Then we insert electrodes and record the electrical activity of the mycelium. So, through the stimulation, it becomes electrical activity, and then we get the response.” He notes that this is the UK’s only wet lab—one where chemical, liquid, or biological matter is present—in any department of computer science.

“Preparing to record dynamics of electrical resistance
of hemp shaving colonized by oyster fungi”

The classical computers today see problems as binaries: the ones and zeros that represent the traditional approach these devices use. However, most dynamics in the real world cannot always be captured through that system. This is the reason why researchers are working on technologies like quantum computers (which could better simulate molecules) and living brain cell-based chips (which could better mimic neural networks), because they can represent and process information in different ways, utilizing a series of complex, multi-dimensional functions, and provide more precise calculations for certain problems. Already, scientists know that mushrooms stay connected with the environment and the organisms around them using a kind of “internet” communication. You may have heard this referred to as the wood wide web. By deciphering the language fungi use to send signals through this biological network, scientists might be able to not only get insights about the state of underground ecosystems, and also tap into them to improve our own information systems.

“An illustration of the fruit bodies of Cordyceps fungi. Irina Petrova Adamatzky””

Mushroom computers could offer some benefits over conventional computers. Although they can’t ever match the speeds of today’s modern machines, they could be more fault tolerant (they can self-regenerate), reconfigurable (they naturally grow and evolve), and consume very little energy. Before stumbling upon mushrooms, Adamatzky worked on slime mold computers—yes, that involves using slime mold to carry out computing problems—from 2006 to 2016. Physarum, as slime molds are called scientifically, is an amoeba-like creature that spreads its mass amorphously across space. Slime molds are “intelligent,” which means that they can figure out their way around problems, like finding the shortest path through a maze without programmers giving them exact instructions or parameters about what to do. Yet, they can be controlled as well through different types of stimuli, and be used to simulate logic gates, which are the basic building blocks for circuits and electronics.

“Recording electrical potential spikes of hemp shaving colonized by oyster fungi”

Much of the work with slime molds was done on what are known as “Steiner tree” or “spanning tree” problems that are important in network design, and are solved by using pathfinding optimization algorithms. “With slime mold, we imitated pathways and roads. We even published a book on bio-evaluation of the road transport networks,” says Adamatzky “Also, we solved many problems with computation geometry. We also used slime molds to control robots.” When he had wrapped up his slime mold projects, Adamatzky wondered if anything interesting would happen if they started working with mushrooms, an organism that’s both similar to, and wildly different from, Physarum. “We found actually that mushrooms produce action potential-like spikes. The same spikes as neurons produce,” he says. “We’re the first lab to report about spiking activity of fungi measured by microelectrodes, and the first to develop fungal computing and fungal electronics.”

“An example of how spiking activity can be used to make gates”

In the brain, neurons use spiking activities and patterns to communicate signals, and this property has been mimicked to make artificial neural networks. Mycelium does something similar. That means researchers can use the presence or absence of a spike as their zero or one, and code the different timing and spacing of the spikes that are detected to correlate to the various gates seen in computer programming language (or, and, etc).

Further, if you stimulate mycelium at two separate points, then conductivity between them increases, and they communicate faster, and more reliably, allowing memory to be established. This is like how brain cells form habits. Mycelium with different geometries can compute different logical functions, and they can map these circuits based on the electrical responses they receive from it. “If you send electrons, they will spike,” says Adamatzky. “It’s possible to implement neuromorphic circuits… We can say I’m planning to make a brain from mushrooms.”

“Hemp shavings in the shaping of a brain, injected with chemicals”

So far, they’ve worked with oyster fungi (Pleurotus djamor), ghost fungi (Omphalotus nidiformis), bracket fungi (Ganoderma resinaceum), Enoki fungi (Flammulina velutipes), split gill fungi (Schizophyllum commune) and caterpillar fungi (Cordyceps militaris). “Right now it’s just feasibility studies. We’re just demonstrating that it’s possible to implement computation, and it’s possible to implement basic logical circuits and basic electronic circuits with mycelium,” Adamatzky says. “In the future, we can grow more advanced mycelium computers and control devices.”

“Note the gel-like layer of SCOBY (symbiotic culture of bacteria and yeast)”

KOMBUCHA ELECTRONICS
https://arstechnica.com/science/2023/02/kombucha-electronics-sure-why-not/
by Jennifer Ouellette / 2/22/2023

“Cheap, light, flexible, yet robust circuit boards are critical for wearable electronics, among other applications. In the future, those electronics might be printed on flexible circuits made out of bacterial cultures used to make the popular fermented black tea drink called kombucha, according to a recent paper posted to the arXiv preprint server. As we’ve reported previously, making kombucha merely requires combining tea and sugar with a kombucha culture known as a SCOBY (symbiotic culture of bacteria and yeast), aka the “mother”—also known as a tea mushroom, tea fungus, or a Manchurian mushroom. It’s akin to a sourdough starter.

A SCOBY is a firm, gel-like collection of cellulose fiber (biofilm), courtesy of the active bacteria in the culture creating the perfect breeding ground for the yeast and bacteria to flourish. Dissolve the sugar in non-chlorinated boiling water, then steep some tea leaves of your choice in the hot sugar-water before discarding them. Once the tea cools, add the SCOBY and pour the whole thing into a sterilized beaker or jar. Then cover the beaker or jar with a paper towel or cheesecloth to keep out insects, let it sit for two to three weeks, and voila! You’ve got your own home-brewed kombucha. A new “daughter” SCOBY will be floating right at the top of the liquid (technically known in this form as a pellicle). Beyond the popularity of the beverage, kombucha cultures hold promise as a useful biomaterial. For instance, in 2016, an Iowa State professor of apparel, merchandising, and design named Young-A Lee gained attention for her proof-of-concept research in using dried SCOBY as a sustainable leather substitute for biodegradable SCOBY-based clothing, shoes, or handbags.

“fresh SCOBY (symbiotic culture of bacteria and yeast) used in kombucha”

In 2021, scientists at Massachusetts Institute of Technology and Imperial College London created new kinds of tough “living materials” that could one day be used as biosensors, helping purify water or detect damage to “smart” packing materials. Experiments last year by researchers at Montana Technological University (MTU) and Arizona State University (ASU) showed that membranes grown from kombucha cultures were better at preventing the formation of biofilms—a significant challenge in water filtration—than current commercial membranes. “Nowadays kombucha is emerging as a promising candidate to produce sustainable textiles to be used as eco-friendly bio wearables,” co-author Andrew Adamatzky, of the University of the West of England in Bristol, told New Scientist. “We will see that dried—and hopefully living—kombucha mats will be incorporated in smart wearables that extend the functionality of clothes and gadgets. We propose to develop smart eco-wearables which are a convergence of dead and alive biological matter.”

Adamatzky previously co-authored a 2021 paper demonstrating that living kombucha mats showed dynamic electrical activity and stimulating responses, as well as a paper last year describing the development of a bacterial reactive glove to serve as a living electronic sensing device. Inspired by the potential of kombucha mats for wearable electronics, he and his latest co-authors have now demonstrated that it’s possible to print electronic circuits onto dried SCOBY mats. The team used commercially sourced kombucha bacteria to grow their mats, then air-dried the cultures on plastic or paper at room temperature. The mats don’t tear easily and are not easily destroyed, even when immersed in water for several days. One of the test mats even survived oven temperatures up to 200° C (392° F), although the mats will burn when exposed to an open flame.

Andrew Adamatzky et al., 2023

Adamatzky et al. were able to print conductive polymer circuits onto the dried kombucha mats with an aerosol jet printer and also successfully tested an alternative method of 3D printing a circuit out of a conductive polyester/copper mix. They could even attach small LEDs to the circuits with an epoxy adhesive spiked with silver, which were still functioning after repeatedly being bent and stretched. According to Adamatzky et al., unlike the living kombucha mats he worked with previously, the dried SCOBY mats are non-conductive, confining the electrical current to the printed circuit. The mats are also lighter, cheaper, and more flexible than the ceramic or plastic alternatives. Potential applications include wearable heart rate monitors, for instance, and other kombucha-based devices. “Future research will be concerned with printing advanced functional circuits, capable for detecting—and maybe recognizing—mechanical, optical, and chemical stimuli,” the authors concluded.”

DOI: arXiv [preprint], 2023. 10.48550/arXiv.2302.03984

PREVIOUSLY