(Roughly) Daily

Posts Tagged ‘xenobot

“Life is a whim of several billion cells to be you for a while”*…

An AI-designed xenobot (parent organism, C shape, red) sweeping up stem cells that have been compressed into a ball (incipient offspring, green)

The more we understand how cells produce shape and form, Philip Ball explains, the more inadequate the idea of a genomic blueprint looks…

Where in the embryo does the person reside? Morphogenesis – the formation of the body from an embryo – once seemed so mystifying that scholars presumed the body must somehow already exist in tiny form at conception. In the 17th century, the Dutch microscopist Nicolaas Hartsoeker illustrated this ‘preformationist’ theory by drawing a foetal homunculus tucked into the head of a sperm.

This idea finds modern expression in the notion that the body plan is encoded in our DNA. But the more we come to understand how cells produce shape and form, the more inadequate the idea of a genomic blueprint looks, too. What cells follow is not a blueprint; if they can be considered programmed at all, it’s not with a plan of what to make, but with a set of rules to guide construction. One implication is that humans and other complex organisms are not the unique result of cells’ behaviour, but only one of many possible outcomes.

This view of the cell as a contingent, constructional entity challenges our traditional idea of what a body is, and what it can be. It also opens up some remarkable and even disconcerting possibilities about the prospects of redirecting biology into new shapes and structures. Life suddenly seems more plastic and amenable to being reconfigured by design. Understanding the contingency and malleability of multicellular form also connects us to our deep evolutionary past, when single-celled organisms first discovered the potential benefits of becoming multicellular. ‘The cell may be the focus of evolution, more than genes or even than the organism,’ says Iñaki Ruiz-Trillo of the Institute of Evolutionary Biology in Barcelona. Far from the pinnacle of the tree of life, humans become just one of the many things our cells are capable of doing.

In one of the most dramatic demonstrations to date that cells are capable of more than we had imagined, the biologist Michael Levin of Tufts University in Medford, Massachusetts and his colleagues have shown that frog cells liberated from their normal developmental path can organise themselves in distinctly un-froglike ways. The researchers separated cells from frog embryos that were developing into skin cells, and simply watched what the free cells did.

Culturing cells – growing them in a dish where they are fed the nutrients they need – is a mature technology. In general, such cells will form an expanding colony as they divide. But the frog skin cells had other plans. They clustered into roughly spherical clumps of up to several thousand cells each, and the surface cells developed little hairlike protrusions called cilia (also present on normal frog skin). The cilia waved in coordinated fashion to propel the clusters through the solution, much like rowing oars. These cell clumps behaved like tiny organisms in their own right, surviving for a week or more – sometimes several months – if supplied with food. The researchers called them xenobots, derived from Xenopus laevis, the Latin name of the African clawed frog from which the cells were taken.

Levin and colleagues have recently found a new type of behaviour that xenobots can exhibit. They discovered that these pseudo-organisms can even replicate, after a fashion. Xenobots placed in a dish of cells will move to marshal those loose cells into piles that, over the course of a few days, cluster into new xenobots that then take off through the liquid themselves. Left to their own devices, the xenobots typically manage to produce only a single generation of offspring. But the researchers wondered if they could do better. They made computer simulations to search for xenobot shapes that were better at making new xenobots, using an AI program devised by their team member Josh Bongard of the University of Vermont. The simulations suggested that structures like C-shaped half-doughnuts could sweep up cells more efficiently than the spheroidal xenobots could, making larger (spherical) clusters of ‘offspring’.

The work shows that, by combining biological xenobots with the exploratory power of AI, it’s possible to make a kind of ‘living machine’ devised for a purpose. ‘AI can be brought in to exaggerate an innate capability,’ says Bongard. ‘The AI can “program” new behaviours into organisms by rearranging their morphology rather than their genes.’ The researchers wonder if the simulations might identify other shapes that can assemble different structures, or perhaps perform other tasks entirely. ‘One of my primary interests in this project is exactly how ‘far’ from the wild type [the natural, spontaneously arising form of xenobots] an AI can push things,’ says Bongard. ‘We’re now working on incorporating several new behaviours into xenobots via AI-driven design.’

This perspective entails a new way of thinking about cells: not as building blocks assembled according to a blueprint, but as autonomous entities with skills that can be leveraged to make all manner of organisms and living structures. You might conceive of them as smart, reprogrammable, shapeshifting robots that can move, stick together, and signal to one another – and, by those means, build themselves into elaborate artifacts.

This might also be a better way to conceptualise how our own bodies are built during embryogenesis…

The generative potential of cells equipped for multicellular construction was evident almost as soon as this became a lifestyle option, in evolutionary terms. In the Cambrian explosion around 540 million years ago, all manner of strange body shapes appeared, many of which are no longer exhibited by any creatures on Earth. Perhaps we should regard those forgotten ‘endless forms most beautiful’, to borrow Charles Darwin’s resonant phrase, as an illustration of the constructive potential of the metazoan cell – an exuberant expression of the palette of solutions to the problem of cell assembly, which natural selection then stringently pruned.

Acknowledging that the human form is a contingent outcome of the way our cells are programmed for construction raises some mind-bending questions. Are there, for example, human xenobots (perhaps we might call them anthrobots)? If so, are they truly ‘human’? Might there be a kind of organ or tissue that our cells could make but don’t normally get the chance to? Might our still cells ‘remember’ older evolutionary body shapes?…

How our understanding of genetics is changing– a fascinating dispatch from the frontiers of experimental biology: “What on earth is a xenobot?,” from @philipcball in @aeonmag. Eminently worth reading in full.

* Groucho Marx


As we ponder possibility, we might spare a thought for Hans Spemann; he died on this date in 1941. An embryologist, he was awarded the Nobel Prize for Physiology and Medicine in 1935 for his discovery of embryonic induction, an effect involving several parts of the embryo in directing the development of the early group of cells into specific tissues and organs.

In a way that can be said to have foreshadowed the work described above, Spemann showed that the in the earliest stage, tissue may be transplanted to different areas of the embryo, where it then develops based on the new location and not from where it came. (For example, early tissue cut from an area of nervous tissue might be moved to an area of skin tissue where it then grows into the same form as the surrounding skin.)


Written by (Roughly) Daily

September 12, 2022 at 1:00 am

“Do you think that the soul first shows itself by a gnashing of teeth?”*…

In January 2020, as a new plague began to upend life on Earth, a small research team from Tufts, the University of Vermont, and Harvard announced that they, too, had turned life on Earth upside-down. Their discovery wasn’t quite so dramatic at first glance. Any regular person peering through a microscope at their creation would see little more than a few globs of dirty pond water in a petri dish. But those globs were alive; in fact, they were alive in a way that nothing has ever been alive before, in an uncharted space between biology and technology. They called them Xenobots, the world’s first living robot—the world’s first programmable organism.

Xenobot: Xeno as in Xenopus laevis, a voracious frog native to the wetlands of Sub-Saharan Africa; bot, of course, as in robot. It’s an unconventional name for an unconventional organism, so novel that even its makers struggle to conceptualize it. “The terminology that has served us well for many years is just not any good anymore,” concedes Michael Levin, the team’s iconoclastic biologist. His collaborator Josh Bongard, a computer scientist and robotics expert, has called Xenobots “novel living machines.” Sam Kriegman—the team’s postdoc—prefers the term “Computer Designed Organism,” although he’s been trying on “living deepfake” for size recently.

And they’re all right, in a way. Xenobots are deepfakes in the sense that they aren’t what they seem. They’re robots in the sense that they’re autonomous, programmable agents. They’re Computer Designed in the sense that their morphology—the form their tiny bodies take—was designed by an evolutionary computer algorithm in Bongard’s UVM lab. They’re living in the sense that they’re made of embryonic frog cells, and they’re machines in the sense that humans are machines: biological mechanisms made up of constituent parts.

Xenobots are the first living creatures whose immediate evolution occurred inside a computer and not in the biosphere. The result is a simple organism. Xenobots have no brains; the shape of their bodies is what determines how they behave. And yet, Levin and Bongard do not fully understand why Xenobots behave the way they do. “What you’re seeing de novois a completely novel creature with new proto-cognitive capacities, preferences, capabilities, IQ,” Levin explains. “All of those things appear out of nowhere.” Sometimes a Xenobot will head in one direction and then abruptly double back, as though changing its mind. What force guides such behaviors? Can a frog’s cells, in some way, think? Xenobots seem to have “nano free-will,” Levin jokes.

And this is where the can of worms—or tadpoles, maybe—pops open…

The word “robot” recently celebrated its centennial. It comes from the Czech playwright Karel Čapek’s 1920 play “Rossum’s Universal Robots,” about a worker uprising in a robot factory. Čapek’s robots are biological, the result of a vaguely alchemical process involving “albumen” with a “raging thirst for life.” Our conception of a robot as being something metallic, with clanging gears and servo-motors, is more recent baggage, a consequence of the science-fiction stories and films of the mid-twentieth century. In order to understand what Xenobots might mean for our future, we’ll have to divest ourselves from the idea that a robot—or any kind of autonomous being—can be wholly defined by its materiality…

As Norbert Weiner, the father of cybernetics, observed: “Let us remember that the automatic machine is the precise economic equivalent of slave labor. Any labor which competes with slave labor must accept the economic consequences of slave labor.”

Claire Evans (@TheUniverse) explains how “Xenobots may change how we think about intelligence.”

For apposite background, see also “The Link Between Bioelectricity and Consciousness.”

Karel Čapek, R.U.R. (Rossumovi Univerzální Roboti, or in English, Rossum’s Universal Robots)


As we ponder life itself, we might recall (with, perhaps, a touch of nostalgia) that it was on this date in 1959 that Texas Instruments (TI) demonstrated the first working integrated circuit (IC), which had been invented by Jack Kilby. Kilby created the device to prove that resistors and capacitors could exist on the same piece of semiconductor material. His circuit consisted of a sliver of germanium with five components linked by wires. It was Fairchild’s Robert Noyce, however, who filed for a patent within months of Kilby and who made the IC a commercially-viable technology. Both men are credited as co-inventors of the IC. (Kilby won the Nobel Prize for his work in 2000; Noyce, who died in 1990, did not share.)


Written by (Roughly) Daily

March 24, 2021 at 1:01 am

%d bloggers like this: