What is an individual? Biologists are looking for clues in information theory.

Beijing time, July 23 ( BEIJING ) In order to identify strange extraterrestrial organisms and solve the mysteries of our earth , scientists are looking for an objective definition of the basic unit of life . In the Edikara era more than 500 million years ago (the last period of The Ancient Zeus, followed by the beginning of the Cambrian period of the apparent zeus), the Earth’s seabed is covered by a surreal world of life.

There, the weird molluscs have an incredible body shape: some are like a circle with a mezzanine, some are a disc with ribs, some are segmented tubes, some are like inverted clocks, and some are spindle-shaped or slender cones. They may have been the first large multicellular organisms on Earth, but soon went extinct, leaving no modern descendants, and in ancient sandstone and quartz slabs, we can also find some extremely strange traces of fossils, the remains of these exotic creatures.

What is an individual? Biologists are looking for clues in information theory.

Leaf-shaped life is a peculiar marine animal that lived in the Edikara period. Some studies have tried to determine which factors led to the growth of their ferns, and the thinking is similar to recent mathematical theories about biological individuality.

Because of this strangeness, palaeontologists are even debating the most basic question about these creatures: How did they evolve? How do they eat and reproduce? For a fossil individual, we don’t even know where it comes from and where it’s going. Are these animals a single organism, or are they a community of smaller individuals, like monk-hat jellyfish? Where do their gel-like bodies end up? What is their living environment like?

The task of distinguishing biological individuals is difficult, not only for scientists who want to figure out the information recorded by fossil fragments, but also for researchers in other fields. Researchers looking for life on other planets or satellites are bound to face similar problems. Even on today’s earth, it is clear that nature is so careless about “limits”: viruses rely on host cells for self-replication; bacteria share and exchange genes, and higher species often interbreed; thousands of mucous bacteria gather to form deformities, spreading spores; workers and bees may be non-reproductive members of the swarm’s “super-organisms”; and lichen fungus and cyanobacteria are symbiotic; Bacterial cells are at least as many as human “own” cells, and gut microbes are inextricably linked to our development, physiology, and survival.

John Dupree, director of the Centre for Life Sciences Research at the University of Exeter in the UK, says the organisms are “so closely linked that you don’t know whether they should be one or two or more”.

However, such a distinction is extremely important for scientists. Ecologists need to identify individuals to untangle complex symbiotic relationships and interconnectedrelationships to define a community. Evolutionary biologists are looking at the mechanisms of natural selection and how it selects individuals to ensure reproductive success, and they need to figure out what constitutes these selected individuals.

The same applies to the more abstract biology of individual concepts, such as in some larger framework of behavior or activity, where large numbers of entities tend to appear in different patterns. Molecular biologists must determine which genes interact as an independent network of thousands of genes to produce specific traits. Neuroscientists must determine when the neurons in the brain bind together into tight entities to represent stimulus signals.

“In a way, (biology) is a science about individuals, ” says Melanie Mitchell, a computer scientist at the Santa Fe Institute in the United States.

But what does an individual mean? This concept is often overlooked. “So far, our concept of ‘individual’ is very similar to the concept of ‘heap,'” says Maxwell Ramstead, a postdoctoral researcher at McGill University in Canada. But ‘a bunch’ is not a precisely defined concept. Not that there are more than 13 grains of sand, it goes from ‘a batch’ to a ‘pile’. “

Manfred Laubischler, a theoretical biologist at Arizona State University in the United States, says the lack of such a basic definition is partly because “biology as an area is not yet fully theoretical.” To a large extent, this is still an experience-driven discipline. “

Now, some scientists are working to change that. Based on a set of principles and measurement methods, they began to formalize the concept of individuals in the hope of guiding biology into a new era.

Verbs, not nouns.

When it comes to the definition of biological individuals, we tend to rely on things that can be observed and measured. Cells are wrapped in cell membranes, animals are wrapped in skin; we can sequence DNA and divide different genes in these sequences. Most importantly, our definition gives the organism and the characteristics associated with it some privilege: it is a physically separated entity from the environment, it has DNA, can be copied, and subject to natural selection.

However, this is not the only way to observe life, nor is it necessarily the best way. “I’ve always said that if Darwin were a microbiologist, we would have a very different evolution,” said David Krakauer, director of the Santa Fe Institute and an evolutionary theorist. This theory will have a very different premise. “

What is an individual? Biologists are looking for clues in information theory.

David Krakauer, an evolutionary theorist and director of the Santa Fe Institute, has spent his career thinking about how to establish a deeper connection between physics and evolution.

Krakauer is exploring a more natural and objective way to identify biological units, which he hopes is an operational measure that quantifies individual characteristics, based on the internal dynamics of the system under study, without deviations or limitations from the outside environment.

Jessica Flack, also from the Santa Fe Institute, is an expert on group phenomena. Flake’s frustration is that the concept of “individual” is often applied arbitrarily in the study of natural selection and other biological processes. So she teamed up with Krakauer for most of the last decade to develop “a more open, basic and effective definition that does not assume that we know the answer, or that we know too many answers a priori”.

What is an individual? Biologists are looking for clues in information theory.

Jessica Flack, also from the Santa Fe Institute, is an expert on group phenomena. Flake’s frustration is that the concept of “individual” is often applied arbitrarily in the study of natural selection and other biological processes. She has worked with colleagues to develop a more standardized approach to identifying these units.

The core idea of this effective definition is that individuals should not be thought of in spatial terms, but in time terms. In other words, the individual should be seen as something that exists steadily and dynamically in time. “It’s another way of looking at the individual, ” says Mitchell, who was not involved in the work. ” “

This is not a novel approach. At the beginning of the 19th century, the French zoologist George Scuveyer described life as a vortex: “The flow rate is fast or slow, complexity is more or less, the direction is constant, and always carries a similar kind of molecule, but the individual molecules keep coming in and leaving; “Many philosophers and biologists have embraced this “process view”. In particular, this view holds that life and other biological systems do not exist as fixed objects or matter, but as patterns of flow and interrelationships, in a changing river.

Unfortunately, “once genetic theory dominates, it becomes the biology of things,” says Scott Gilbert, a developmental biologist at Swarthmore College in the United States. But now things have changed, “20th-century biology is a biology of things,” Gilbert says. “

Scientists have developed tools to study these processes in a standardized and accurate way. “Many of these things can be expressed in the language of the object spent in biology,” said Eric Smith, who studies the origin of life at the Santa Fe Institute. “

The multiple dimensions of an individual.

Krakauer and Flake, as well as other colleagues such as Nihat Oy of the Max Planck Institute for Mathematical Sciences, have realized that they need to turn to information theory and formalize the so-called “some kind of verb” of individual theory. In their view, an individual is a collection of “measures that preserve the integrity of time” that propagates information close to the maximum value in time.

In a paper published in The Theory of Biological Sciences in March, they set out this formal system, based on three principles. The first principle holds that individuals can exist at any level of biological tissue, from subcellular to social;

Chris Kempes, a physical biologist at the Santa Fe Institute who wasn’t involved in the work, said, “It’s not a binary function that suddenly jumps.” “In this physicist, the Santa Fe team’s theory has some appeal. The emphasis on quantification rather than classification can provide more useful help to biology, in part because it can bypass complex definitional questions, such as whether a virus is biological or can be considered an individual, Kempes said. “The real question is, how does the virus survive?” He said, “How many individual characteristics does the virus have?” “

Next, Krakauer and Flake, among others, began defining “lenses” to find these individuals in complex and noisy environments. “Imagine building a microscope that allows me to see the information travel forward in a timely manner, ” says Krakauer. They describe a mathematical framework that breaks down the flow of information into different parts and evaluates individuals based on different combinations of environmental impacts and internal dynamics to predict the future state of the system.

Based on the change gradient of the information flow, the team distinguished three types of individuals. The first category is an organic individual, an entity shaped by environmental factors but highly self-organizing. Almost all the information that defines such individuals is internal and based on its own a priori state. Through this “lens”, you can see humans, mammals and birds, says Krakauer.

The second category is the individual in the form of a group, involving more complex relationships between internal and external factors. An ant colony, or a cobweb, may also be considered such an individual. This individual is a distributed system “partially built” by environmental factors, but still retains some of its own structures.

The third type of individual is almost entirely environmentally driven. If environmental factors were removed, the entities would fall apart, Krakauer said. It’s a bit like a tornado, which dissipates quickly under the wrong temperature and humidity conditions. Krakauer added that the earliest life on Earth may have been like this.

The researchers call their new theory “individual information theory” and say it provides a very common way to understand the basic cells of living things. Krakauer said they hope the theory will inspire new algorithms that “allow you to extract living things from the environment, just like images from the ground”. Such an algorithm can be applied to the flow of data collected over time to determine the correlation between the information that indicates the individual’s presence.

According to Krakauer, in individual information theory, individuals can be cells, tissues, organisms, communities, companies, political institutions, online groups, artificial intelligence or cities, or even ideas or theories. “What we want to do is to discover a complete set of life forms that go far beyond what we usually call life,” he said. “

These individuals may be entities that we’ve never considered because they don’t fit the scale, function, or spatial distribution we’re familiar with — these entities are “inconsistent with our general intuition of individuals,” Flake said.

“Our senses are very limited. What we can deal with in the brain is ultimately limited, even if it’s pretty impressive,” said Martin Beale, a researcher at Araya, an artificial intelligence company in Tokyo. “He is developing a mathematical method for identifying individual subjects in an artificial system.

Life is not as we know it.

This new method of identifying individuals can bring many useful uses. Perhaps some gene networks and signaling molecules play an individual role at the cellular level, while others are dispersed between cells. Perhaps the cause of cancer can be understood to be that some cells gain a higher degree of individuality than neighbouring cells.

What is an individual? Biologists are looking for clues in information theory.

In this cell-based mucosal, hundreds of free-living amoeba gather together, sacrificing themselves to form stalks so that other cells can spread spores. Throughout the kingdom of life, the effective definition of individuality seems to be erratic.

Scientists such as Krakauer and Kempes hope to use this measurement-based theory to solve the problem of the origin of life. “Planetary objects have rich, complex environments, and chemistry is a huge combination of spaces, ” Kempes said. . . We may be surprised to find that the way life originates is unusually diverse. He wanted to use krakauer et al.’s measurements to determine the basic attributes or general principles common to different life origin stories.

“People want to focus on what we all know of in common with life, ” Kempes added, “but the history of evolution we’ve experienced on this planet, and the origin of life that we happen to experience on this planet, are very special.” This is not a general way of thinking about life. “This thinking certainly does nare not help us identify life outside the solar system, because it may be completely beyond human understanding, as the Polish writer Stanislaw Lyme imagined in his 1961 novel “The Star of Solaris.”

A broader definition of individual sedituated not only to help scientists find new types of life, but also to explore how different boundary conditions will affect the individuality of the entity and its relationship to its surroundings. For example, how much “individuality” is an ecosystem? What happens to this individuality if a species disappears or a key environmental factor changes? What does it mean if the boundaries of a creature are not defined by its skin, but by their surroundings? The answers to these questions may affect conservation efforts and our understanding of the degree of interdependence between organisms, species and their natural environments. If researchers can better understand the factors that affect the individuality of a system, they may have a better understanding of evolutionary shifts, such as the emergence of multicellular organisms.

“I think this definition of the basic amount gives us a sudden insight into dynamics that we haven’t seen before and an understanding of the process that we haven’t thought of before,” Kempes said. This change is as if defining and understanding temperature helps to form new physical theories.

Stay individual.

In the view of other scientists who study the concept of “individuals”, Krakauer and Flake’s theories do not necessarily provide the best or most useful framework. For example, according to Ramstead of McGill University, the framework of Krakauer et al. applies equally to any system, and this is not entirely an advantage. He agreed with the initial assumptions of the research groups and their use of the theory of information, but noted that their definition required something extra — a method based on the flow of information that distinguishes biological entities from entities in non-living systems, such as hurricanes.

Ramsted speculates that the team’s approach does not take into account how individuals maintain their own boundaries. “Organisms are not individualized, ” he says. ” For him, the information used in Krakauer and Flake’s framework may be “unknowable” for organisms. “I don’t know if organisms can use the information metrics they define to sustain themselves,” he said. “

What is an individual? Biologists are looking for clues in information theory.

Lichen is a composite organism that consists of photosynthesis algae or blue bacteria that grow in mycelium. However, these partnerships are so close and unique that they operate like a single organism.

As an alternative, Ramsted is working with Carl Friston, a renowned neuroscientist at University College London, to develop a theory based on free energy principles for biological self-organization proposed by Friston. Ramsted argues that this idea is consistent with the formal system of Krakauer and Flake, but the narrative of how biological entities remain individualized is usefully constrained.

The free energy principle asserts that any self-organizing system looks like it has made predictions about its environment and attempts to minimize the error of these predictions. For organisms, this means that they are to some extent constantly measuring their own sensory and perceived experiences according to expectations.

“You can literally interpret organisms as guesswork about the structure of the environment, ” Ramsted said. Over time, the organism defines itself as an individual independent of its surroundings by maintaining the integrity of these expectations.

Ancient fractal form.

The Santa Fe team’s theory is “an important proof of principle,” Says Laubickler, “and this tissue program creates some reasonable order in the biological ‘wild west’.” However, the researchers acknowledge that they are still a long way from creating useful algorithms that can put these concepts into practice.

Still, some biologists have found ways to make the most of information to individualize. Their work gives us some confidence in how the theories pursued by Krakauer, Flake, and Ramsted will one day be applied.

Researcher Jennifer Oyar Cahill of the University of Essex in the United Kingdom focused on the study of life during the Edicara period. “Studying fossils or life forms from a very long time is almost like studying extraterrestrial biology on Earth, ” she said. So to some extent, the real problem we face is how to identify individuals? “

Cahill said the solutions she and her colleagues developed were linked to the concepts described by Krakauer and Flake, especially as the information they emphasized persisted over time.

In Cahill’s recent study of leaf-like life, this fern-like animal can grow to more than 1.8 meters high, its central stem is attached to the sea floor, and fractal leaf branches radiate from the central stem. Early analysis often classified these animals with sea pens (also known as sea slugs, which belong to the hedgehogs, the coral spheroids), a more common invertebrate that resembled goose pens. Since the sea pen is actually a group of organisms, consisting of a group of independent, tentacle-like corals, scientists believe that the same is true of leaf-shaped life. Until about 10 years ago, researchers suggested that leaf-shaped classes might have a specific growth procedure that allows individuals to produce fractals.

What is an individual? Biologists are looking for clues in information theory.

The sea pen looks like a separate animal, but is actually made up of a group of tentacles.

This study can also be considered from the perspective of information theory. Cahill studied the fractal forms of the animal, which reflect its growing history, like concentric rings on tree trunks. “It’s been tested by time; we can see that it retains the information of the past,” Cahill said.

These growth histories are also records of information flows in the environment in which leafy form life is located, such as the diffusion of dissolved organic carbon in the surrounding seawater. By studying the persistence of this information, Cahill and his colleagues made assumptions about how leafy morphological classes change over their lifetimes. The environment supports their development, significantly affecting their size and shape – although, as defined by the Santa Fe study group, the balance of internal and external forces makes them interconnected organisms, not group organisms. Borrowing the language of Krakauer and Flake’s paper, Cahill said: “Even in some of the oldest known animals, we can see traces of inner, organic individuals, as well as traces of environmental decisions.” “

What is an individual? Biologists are looking for clues in information theory.

Researchers at the University of Essex studied the strange forms of life that flourished on the seabed 600 million years ago. “It’s almost like you’re studying extraterrestrial biology on Earth,” she said. “

Such attempts to exploit the flow of information, both in theory and in practice, are equivalent to cutting the connections of nature, says Mr Cahill. On the other hand, these attempts “outline the beginnings of certain ideas and concepts that may become a potential basis for new areas of biology”.

Lauby-Hillagrees. “Life sciences or biology need to grow into a science discipline,” he said. “