World’s first commercial biological computer launched by Australian start up Cortical Labs

Good news! Brain vs. silicon! The website of this company is a little wild and does not provide much background or additional information.

"... The technology is based on fusing the lab-grown cells with hard silicon. The goal is to create a new form of artificial intelligence (AI), called Synthetic Biological Intelligence (SBI). ...

The company hopes to have units and racks of CL1 manufactured and ready to ship by the end of June this year. Cortical Labs is also offering Wetware-as-a-Service (WaaS), allowing remote access to the biological computers to build applications. ...

CL1’s lab-cultivated cells are grown across a silicon chip that has pins used to send electrical impulses into the web of neurons and receive impulses back. This creates a high bandwidth connection between the organic network and digital set ups. ..."

World’s first commercial biological computer launched by Australian start up

Actual neurons, living on a silicon chip.

CL1

Genetically engineered bacteria solve computational problems

Amazing stuff! A promising approach!

"... Now a research team from the Saha Institute of Nuclear Physics in India has used genetically modified bacteria to create a cell-based biocomputer with problem-solving capabilities. The researchers created 14 engineered bacterial cells, each of which functioned as a modular and configurable system. They demonstrated that by mixing and matching appropriate modules, the resulting multicellular system could solve nine yes/no computational decision problems and one optimization problem. ..."

From the abstract:

"Here, we report a modular multicellular system created by mixing and matching discrete engineered bacterial cells. This system can be designed to solve multiple computational decision problems. The modular system is based on a set of engineered bacteria that are modeled as an ‘artificial neurosynapse’ that, in a coculture, formed a single-layer artificial neural network-type architecture that can perform computational tasks. As a demonstration, we constructed devices that function as a full subtractor and a full adder. The system is also capable of solving problems such as determining if a number between 0 and 9 is a prime number and if a letter between A and L is a vowel. Finally, we built a system that determines the maximum number of pieces of a pie that can be made for a given number of straight cuts. This work may have importance in biocomputer technology development and multicellular synthetic biology."

Genetically engineered bacteria solve computational problems – Physics World

Multicellular artificial neural network-type architectures demonstrate computational problem solving (no public access, but article above contains link to the PDF file)

Graphical abstract:

For First Time, DNA Tech Offers Both Data Storage and Computing Functions

The research on DNA based computers continues!

"... DNA is rather fragile to work with, it can be hard to reliably write to, read from, move and process information on it. But the new study claims to have developed a new system that can solve those problems. The key is a soft polymer material that acts like a scaffold for the DNA, which can be dehydrated for long term storage and rehydrated for retrieval. ...
To write data to the DNA, algorithms first convert it into sequences of nucleic acids – the familiar ACGT letters of DNA code. Specific pieces of information can be retrieved using RNA molecules that copy the data from the DNA, and then sequencing that RNA. That means you don’t have to destroy the DNA to read back from it, unlike some existing DNA data techniques. ..."

"Researchers f... have demonstrated a technology capable of a suite of data storage and computing functions – repeatedly storing, retrieving, computing, erasing or rewriting data – that uses DNA rather than conventional electronics. Previous DNA data storage and computing technologies could complete some but not all of these tasks. ..."

From the abstract:

"... Here we present a DNA-based store and compute engine that captures these primordial capabilities. This system comprises multiple image files encoded into DNA and adsorbed onto ~50-μm-diameter, highly porous, hierarchically branched, colloidal substrate particles comprised of naturally abundant cellulose acetate. Their surface areas are over 200 cm2 mg−1 with binding capacities of over 1012 DNA oligos mg−1, 10 TB mg−1 or 104 TB cm−3. This ‘dendricolloid’ stably holds DNA files better than bare DNA with an extrapolated ability to be repeatedly lyophilized and rehydrated over 170 times compared with 60 times, respectively. Accelerated ageing studies project half-lives of ~6,000 and 2 million years at 4 °C and −18 °C, respectively. The data can also be erased and replaced, and non-destructive file access is achieved through transcribing from distinct synthetic promoters. The resultant RNA molecules can be directly read via nanopore sequencing and can also be enzymatically computed to solve simplified 3 × 3 chess and sudoku problems. Our study establishes a feasible route for utilizing the high information density and parallel computational advantages of nucleic acids."

DNA "computer" solves sudoku and stores millions of GB for millennia "A full DNA computer is a step closer, thanks to a new technology that could store petabytes of data in DNA for thousands or even millions of years. The system can also process data, as demonstrated by solving sudoku puzzles."

For First Time, DNA Tech Offers Both Data Storage and Computing Functions (original news release)

A primordial DNA store and compute engine (no public access)

Liquid biological Computer Made From DNA Comprises Billions of Circuits

Amazing stuff! Silicon is not the only stuff computers are made of! This could be a breakthrough!

"... In recent years engineers have explored a subtly new role for the molecule's unique capabilities, as the basis for a biological computer. Yet in spite of the passing of 30 years since the first prototype, most DNA computers have struggled to process more than a few tailored algorithms.

A team researchers from China has now come up with a DNA integrated circuit (DIC) that's far more general purpose. Their liquid computer's gates can form an astonishing 100 billion circuits, showing its versatility with each capable of running its own program.

DNA computing has the potential to create machines that offer significant leaps in speeds and capacities, and – as with quantum computing – there are various approaches that can be taken. Here, scientists wanted to build something that was more adaptable than previous efforts, with a broader range of potential uses. ...

What's more, the experimental systems showed little in the way of signal attenuation, or the gradual loss of the strength of a signal as it travels. That's another key part of being able to build DNA computers that can scale and adapt. ..."

From the abstract:

"The past decades have witnessed the evolution of electronic and photonic integrated circuits, from application specific to programmable. Although liquid-phase DNA circuitry holds the potential for massive parallelism in the encoding and execution of algorithms, the development of general-purpose DNA integrated circuits (DICs) has yet to be explored. Here we demonstrate a DIC system by integration of multilayer DNA-based programmable gate arrays (DPGAs). We find that the use of generic single-stranded oligonucleotides as a uniform transmission signal can reliably integrate large-scale DICs with minimal leakage and high fidelity for general-purpose computing. Reconfiguration of a single DPGA with 24 addressable dual-rail gates can be programmed with wiring instructions to implement over 100 billion distinct circuits. Furthermore, to control the intrinsically random collision of molecules, we designed DNA origami registers to provide the directionality for asynchronous execution of cascaded DPGAs. We exemplify this by a quadratic equation-solving DIC assembled with three layers of cascade DPGAs comprising 30 logic gates with around 500 DNA strands. We further show that integration of a DPGA with an analog-to-digital converter can classify disease-related microRNAs. The ability to integrate large-scale DPGA networks without apparent signal attenuation marks a key step towards general-purpose DNA computing."

Liquid Computer Made From DNA Comprises Billions of Circuits : ScienceAlert

DNA-based programmable gate arrays for general-purpose DNA computing (no public access)

Computing functions were matched to DNA molecules in a test tube.

Designing and Programming Living Computers challenging the predominant Silicon computer hardware paradigm

Silicon based hardware still dominates computing, but is it always superior to other forms of computing? At present, computer hardware e.g. consumes a lot more energy than our human brain. Machine learning often needs millions of samples, hours if not days of computation etc.

This is very exciting research into biological computers! Escherichia coli again is the superstar of this research!

"The genetic material was inserted into the bacterial cell in the form of a plasmid: a relatively short DNA molecule that remains separate from the bacteria’s “natural” genome. Plasmids also exist in nature, and serve various functions. The research group designed the plasmid’s genetic sequence to function as a simple computer, or more specifically, a simple artificial neural network. This was done by means of several genes on the plasmid regulating each other’s activation and deactivation according to outside stimuli. ...
But our cells are also computers, of a different sort. There, the presence or absence of a molecule can act as a switch. Genes activate, trigger or suppress other genes, forming, modifying, or removing molecules. Synthetic biology aims (among other goals) to harness these processes, to synthesize the switches and program the genes that would make a bacterial cell perform complex tasks. Cells are naturally equipped to sense chemicals and to produce organic molecules. Being able to “computerize” these processes within the cell could have major implications for biomanufacturing and have multiple medical applications. ...

The group were able to create flexible bacterial cells that can be dynamically reprogrammed to switch between reporting whether at least one of a test chemicals, or two, are present (that is, the cells were able to switch between performing the OR and the AND functions). Cells that can change their programming dynamically are capable of performing different operations under different conditions. (Indeed, our cells do this naturally.) Being able to create and control this process paves the way for more complex programming, making the engineered cells suitable for more advanced tasks. Artificial Intelligence algorithms allowed the scientists to produce the required genetic modifications to the bacterial cells at a significantly reduced time and cost.

Going further, ... living cells: they are capable of responding to gradients. Using artificial intelligence algorithms, the group succeeded in harnessing this natural ability to make an analog-to-digital converter – a cell capable of reporting whether the concentration of a particular molecule is “low”, “medium”, or “high.” Such a sensor could be used to deliver the correct dosage of medicaments, including cancer immunotherapy and diabetes drugs. ..."

From the abstract:

"Computational properties of neuronal networks have been applied to computing systems using simplified models comprising repeated connected nodes, e.g., perceptrons, with decision-making capabilities and flexible weighted links. Analogously to their revolutionary impact on computing, neuro-inspired models can transform synthetic gene circuit design in a manner that is reliable, efficient in resource utilization, and readily reconfigurable for different tasks. To this end, we introduce the perceptgene, a perceptron that computes in the logarithmic domain, which enables efficient implementation of artificial neural networks in Escherichia coli cells. We successfully modify perceptgene parameters to create devices that encode a minimum, maximum, and average of analog inputs. With these devices, we create multi-layer perceptgene circuits that compute a soft majority function, perform an analog-to-digital conversion, and implement a ternary switch. We also create a programmable perceptgene circuit whose computation can be modified from OR to AND logic using small molecule induction. Finally, we show that our approach enables circuit optimization via artificial intelligence algorithms."

Designing and Programming Living Computers Technion and MIT collaborate to transform bacterial cells into living artificial neural circuits. Applications include biomanufacturing and therapeutics

Synthetic neuromorphic computing in living cells (open access)

Fig. 1: Perceptgene theory and implementation