The Spanish laboratory that programs bacteria as if they were computers

2023-06-11 20:26:30

Bacteria are normally seen as very simple, basic organisms compared to the complexity of mammals. Let’s not talk about a person anymore. However, and although it may seem otherwise, these microscopic beings contain more circuits and more capacity to process information than our mobile, our laptop and even the most powerful supercomputer that exists.

Because, in reality, life, which has been evolving for millions of years, is very skilled at computing: all beings we know house a system that stores data in the form of DNA (or RNA) that processes the information that reaches it and transforms it. in an answer. A process analogous to when we hit the controls of our game console and the character on the screen performs certain movements. Or like when we enter several words in a search engine and it offers us a detailed list of answers. This is the basis of biocomputing, an area that seeks to understand from the prism of computers how living organisms work and how to ‘program’ them to do what we want.

“Of course, a computer and a bacterium do not work exactly in the same way,” Ángel Goñi-Moreno, who directs the Biocomputing Laboratory from the Center for Plant Biotechnology and Genomics (CBGP, UPM-INIA/CSIC), belonging to the Polytechnic University of Madrid and the Higher Council for Scientific Research. “We don’t want to send emails thanks to bacteria; but to apply them in biological systems where classical computing does not reach, giving them commands to do what we want».

The intention, then, is not that these ‘living chips’ or ‘biological computers’ replace the ones we have inside our devices; the goal is to use nature’s computing to solve some of its problems, such as disease or pollution. Or even apply them to other branches, such as the creation of new smart materials or incorporating them into machines powered by biobatteries. Because nature is millions of years ahead of us.

bacteria programmed to eliminate contamination

Specifically, the group led by Goñi-Moreno is dedicated to studying the computational mechanisms of bacteria and converting them into a kind of ‘computers’ that respond to certain stimuli. For example, they have managed to ‘program’ Pseudomona putidaa bacterium commonly found in soil and of great scientific and industrial interest, to biodegrade polluting compounds (such as toluene or metals such as arsenic) following predefined instructions.

P. Putida under the microscope

biocomputing laboratory CBGP, UPM-INIA/CSIC

«The idea is that these bacteria monitor their environment and, if they encounter a polluting agent, decide whether to kill it or not; or when faced with a complex scenario, with various contaminants, they make autonomous decisions about the best bioremediation strategy. At the moment, we can achieve this in the laboratory, but the goal is to design bacteria that can restore balance to a collapsing ecosystem, “he says.

The entire CBGP, UPM-INIA/CSIC Biocomputing Laboratory team

guillermo navarro

His experiments do not end there. One of the most famous applications of biocomputing is to introduce logic gates (the circuits on which our computers work, which carry the information converted into 1 and 0); Goñi-Moreno’s team, as he explains in a study published in ‘Nature Communcations‘, you are experimenting with a type of logic gate called an ‘inverting gate’ or NOT inside the p putida y Escherichia coli, another very common bacterium (present in our intestines), comparing how this type of logic gates behave depending on the organism. «We have seen that the differences are caused by what we call ‘context dependency’: the same as when, for example, you use a program that works very well on an operating system like Windows, but is not as efficient on a different one, like Linux ».

Each brain organoid, like the one in the photo, barely reaches a few millimeters; however, they are excellent test specimens and with a simple raw material: human skin cells.

F. MORA-BERMÚDEZ ET AL., ELIFE

The ethics behind biocomputers

Using living components to act according to our desires entails, in almost all cases, a whole ethical powder keg. When it comes to bacteria, they may feel further removed from us, perhaps. But there are branches of biocomputing that use human cells to store information or have even created ‘mini-brains’, clusters of neurons grown in the laboratory from human tissue that function as a system that can learn to carry out some tasks. How should we treat these living systems? “It is not classical computing, and it has great potential, but we must try to avoid misunderstandings and be rigorous in what they can and cannot do, at least for now,” says Goñi-Moreno.

In this regard, the National Academies of Sciences, Engineering and Medicine of the United States published a report in 2021 dedicated exclusively to these brain organoids, debating whether they could be conscious, feel emotions or pain. The paper concluded that, as currently created, “does not currently differ from other human neural tissues or cultures in vitro,” although, as technology advances, “revision of this concept may be necessary.”

With this type of research, biological programming is understood in a deeper way and it can be observed for which areas the use of one or another bacterium is more recommendable. For example, it would be more efficient to use E. coli for a medical application; and P. putida for an environmental application”, says Goñi-Moreno.

And all this in a system that is constantly evolving, like life itself. «This has always been considered a handicap, but our group tries to turn it around and try to take advantage of the fact that these types of systems adapt to almost any type of circumstance. The objective is to be able to control it and take advantage of it”, points out Goñi-Moreno, who points out that the focus right now is focused on developing the tools that allow them to program these beings in a predictable and reliable way, “which is saying a lot”, apostille.

In his mind it is that, in the not too distant future, these bacteria will perform complex computation, even beyond the abilities of Turing Machines. «Biocomputers on demand. Ambitious, but we are getting there.”