Albert Newen and Carlos Montemayor describe consciousness as having three distinct forms, each serving a different role: 1. basic arousal, 2. general alertness, and 3. a reflexive (self-)consciousness. According to Newen, basic arousal was the first to emerge in evolutionary history. “Evolutionarily, basic arousal developed first, with the base function of putting the body in a state of ALARM in life-threatening situations so that the organism can stay alive,” he explains. Pain plays a crucial role here. “Pain is an extremely efficient means for perceiving damage to the body and to indicate the associated threat to its continued life. This often triggers a survival response, such as fleeing or freezing.”

How Attention and Learning Evolved

A later evolutionary development is general alertness. This form of consciousness allows an individual to focus on one important signal while filtering out others. For example, if someone is talking to you and you suddenly notice smoke, your attention shifts immediately to the smoke as you look for its source. As Carlos Montemayor explains, “This makes it possible to learn about new correlations: first the simple, causal correlation that smoke comes from fire and shows where a fire is located. But targeted alertness also lets us identify complex, scientific correlations.”

Self Awareness and Social Life

Humans and some other animals go a step further by developing reflexive (self-)consciousness. In its more advanced form, this ability allows individuals to think about themselves, remember the past, and anticipate the future. It also makes it possible to build a mental image of oneself and use that image to guide decisions and plans. Newen notes, “Reflexive consciousness, in its simple forms, developed parallel to the two basic forms of consciousness. In such cases conscious experience focuses not on perceiving the environment, but rather on the conscious registration of aspects of oneself.” These aspects include bodily states, perceptions, sensations, thoughts, and actions.

A simple example of reflexive consciousness is recognizing oneself in a mirror. Human children usually develop this ability around 18 months of age. It has also been observed in certain animals, including chimpanzees, dolphins, and magpies. At its core, reflexive conscious experience supports social integration and coordination with others, helping individuals function within groups.

What Birds Perceive

Research by Gianmarco Maldarelli and Onur Güntürkün suggests that birds may also possess basic forms of conscious perception. Their work highlights three main areas where birds show strong similarities to mammals: sensory consciousness, underlying brain structures, and forms of self-consciousness.

Evidence of Sensory Experience in Birds

Studies of sensory consciousness show that birds do more than automatically react to stimuli. They appear to have subjective experiences. When pigeons are shown visually ambiguous images, they alternate between different interpretations, much like humans do. Research on crows provides further evidence. Certain nerve signals in their brains reflect what the animal perceives rather than the physical stimulus itself. When a crow sometimes consciously detects a stimulus and sometimes does not, specific nerve cells respond in line with that internal experience.

Bird Brains and Conscious Processing

Bird brains also contain structures that support conscious processing, even though their anatomy differs from that of mammals. Güntürkün explains, “The avian equivalent to the prefrontal cortex, the NCL, is immensely connected and allows the brain to integrate and flexibly process information.” He adds, “The connectome of the avian forebrain, which presents the entirety of the flows of information between the regions of the brain, shares many similarities with mammals. Birds thus meet many criteria of established theories of consciousness, such as the Global Neuronal Workspace theory.”

Signs of Self Perception in Birds

More recent experiments indicate that birds may also show forms of self-perception. While some corvid species pass the classic mirror test, other studies use alternative approaches that better reflect birds’ natural behaviors. These experiments reveal additional forms of self-consciousness in different species. Güntürkün notes, “Experiments indicate that pigeons and chickens differentiate between their reflection in a mirror and a real fellow member of their species, and react to these according to context. This is a sign of situational, basic self-consciousness.”

Taken together, these findings suggest that consciousness did not emerge recently or exclusively in humans. Instead, it appears to be an ancient and widespread feature of evolution. Birds demonstrate that conscious processing can occur without a cerebral cortex and that very different brain structures can arrive at similar functional outcomes.

New theoretical work suggests that the fundamental behavior of nature could arise directly from the structure of spacetime, pointing to geometry as the common origin of physical interactions.

Hidden Dimensions and Seven-Dimensional Geometry

In a paper published in Nuclear Physics B, physicist Richard Pincak and collaborators examine whether the properties of matter and forces can emerge from the geometry of unseen dimensions beyond everyday space.

Their research proposes that the universe includes additional dimensions that are not directly observable. These dimensions may be compact and folded into complex seven-dimensional shapes called G₂-manifolds. Until now, such geometric structures were typically treated as fixed and unchanging. The new study instead explores what happens when these shapes are allowed to evolve over time through a mathematical process known as the G₂-Ricci flow, which gradually alters their internal geometry.

Twisting Geometry and Stable Structures

“As in organic systems, such as the twisting of DNA or the handedness of amino acids, these extra-dimensional structures can possess torsion, a kind of intrinsic twist,” explains Pincak. This torsion introduces a built-in rotation within the geometry itself.

When the researchers modeled how these twisted shapes change over time, they found that the geometry can naturally settle into stable patterns called solitons. “When we let them evolve in time, we find that they can settle into stable configurations called solitons. These solitons could provide a purely geometric explanation of phenomena such as spontaneous symmetry breaking.”

Rethinking the Origin of Mass

In the Standard Model of particle physics, mass arises through interactions with the Higgs field, which gives weight to particles such as the W and Z bosons. The new theory suggests a different possibility. Instead of relying on a separate field, mass may result from torsion within extra-dimensional geometry itself.

“In our picture,” Pincak says, “matter emerges from the resistance of geometry itself, not from an external field.” In this view, mass reflects how spacetime responds to its own internal structure rather than the influence of an added physical ingredient.

Cosmic Expansion and a Possible New Particle

The researchers also connect geometric torsion to the curvature of spacetime on large scales. This relationship could help explain the positive cosmological constant associated with the accelerating expansion of the universe.

Beyond these cosmological implications, the team speculates about the existence of a previously unknown particle linked to torsion, which they call the “Torstone.” If real, it could potentially be detected in future experiments.

Extending Einstein’s Geometric Vision

The broader ambition of the work is to push Einstein’s idea further. If gravity arises from geometry, the authors ask whether all fundamental forces might share the same origin. As Pincak puts it, “Nature often prefers simple solutions. Perhaps the masses of the W and Z bosons come not from the famous Higgs field, but directly from the geometry of seven-dimensional space.”

The article published in the journal Nuclear Physics B.

The research was supported by R3 project No.09I03-03-V04-00356.

The study, published in the journal Nanoscale, focused on uncovering and blocking a specific molecular interaction that herpes viruses rely on to gain access to cells. The work brought together researchers from the School of Mechanical and Materials Engineering and the Department of Veterinary Microbiology and Pathology.

“Viruses are very smart,” said Jin Liu, corresponding author of the study and a professor in the School of Mechanical and Materials Engineering. “The whole process of invading cells is very complex, and there are a lot of interactions. Not all of the interactions are equally important — most of them may just be background noise, but there are some critical interactions.”

Understanding the Viral Fusion Process

The team examined a viral “fusion” protein that herpes viruses use to merge with and enter cells, a process responsible for many infections. Scientists still have limited insight into how this large and complex protein changes shape to make cell entry possible, which helps explain why vaccines for these widespread viruses have been difficult to develop.

To tackle this challenge, researchers turned to artificial intelligence and detailed molecular simulations. Professors Prashanta Dutta and Jin Liu analyzed thousands of potential interactions within the protein to identify a single amino acid that plays an essential role in viral entry. They created an algorithm to examine interactions among amino acids, the basic components of proteins, and then applied machine learning to sort through them and pinpoint the most influential ones.

Using AI to Pinpoint a Critical Weak Spot

After identifying the key amino acid, the research team moved to laboratory experiments led by Anthony Nicola from the Department of Veterinary Microbiology and Pathology. By introducing a targeted mutation to this amino acid, they found that the virus could no longer successfully fuse with cells. As a result, the herpes virus was blocked from entering the cells altogether.

According to Liu, the use of simulations and machine learning was essential because experimentally testing even a single interaction can take months. Narrowing down the most important interaction ahead of time made the experimental work far more efficient.

“It was just a single interaction from thousands of interactions. If we don’t do the simulation and instead did this work by trial and error, it could have taken years to find,” said Liu. “The combination of theoretical computational work with the experiments is so efficient and can accelerate the discovery of these important biological interactions.”

What Researchers Still Need to Learn

Although the team confirmed the importance of this specific interaction, many questions remain about how the mutation changes the structure of the full fusion protein. The researchers plan to continue using simulations and machine learning to better understand how small molecular changes ripple through the entire protein.

“There is a gap between what the experimentalists see and what we can see in the simulation,” said Liu. “The next step is how this small interaction affects the structural change at larger scales. That is also very challenging for us.”

The research was carried out by Liu, Dutta, and Nicola along with PhD students Ryan Odstrcil, Albina Makio, and McKenna Hull. Funding for the project was provided by the National Institutes of Health.

“The hepatic portal vein drains much of the blood from the intestine to the liver. Therefore, it’s the first place to receive products from the gut microbiome. In the liver, they can be conjugated, transformed, or eliminated, and then enter the systemic circulation,” explains Vitor Rosetto Muñoz, first author of the study and postdoctoral researcher at the Ribeirão Preto School of Physical Education and Sports at the University of São Paulo (EEFERP-USP) in Brazil.

“By analyzing the blood leaving the intestine and the peripheral blood circulating throughout the body, we were able to more accurately observe the enrichment of these metabolites derived from the gut microbiome in each location and, consequently, how they can modify hepatic metabolism and metabolic health,” adds Muñoz. He completed this work during an internship at the Joslin Diabetes Center at Harvard Medical School in the United States with support from a FAPESP scholarship under the guidance of researcher Carl Ronald Kahn.

Gut Microbiome Diversity and Metabolic Disease Risk

Over the past several years, scientists have increasingly recognized that the gut microbiome acts as a key link between genetics, environmental factors, and the development of metabolic disorders. Studies have shown that people and animals with obesity, type 2 diabetes, glucose intolerance, or insulin resistance often have distinct gut microbial compositions compared to those without these conditions.

Even so, researchers still struggle to determine which specific bacteria or microbial products drive these differences or how they interact with intestinal tissues. To explore this question, the recently published study examined metabolites in the blood of mice that varied in their susceptibility to obesity and diabetes. Samples were taken from the hepatic portal vein, which carries blood from the intestine to the liver, and from peripheral blood, which travels from the liver to the heart before circulating through the body.

“Normally, studies tend to look at metabolites present in fecal material or peripheral blood, but they don’t accurately reflect what’s first reaching the tissue of the liver, which is an important metabolic organ linked to different diseases,” says the researcher.

Environmental and Genetic Effects on Metabolite Profiles

In healthy mice, the team detected 111 metabolites enriched in the hepatic portal vein and 74 in peripheral blood. When mice genetically predisposed to obesity and type 2 diabetes were fed a hyperlipidemic diet (rich in fat), the number of metabolites enriched in the hepatic portal vein dropped from 111 to 48. This finding indicates that environmental factors, such as diet, can strongly influence the distribution of these compounds.

The metabolite profiles in these susceptible mice also differed from those observed in a strain of mice naturally resistant to metabolic syndrome. This contrast suggests that genetic background plays a central role in shaping which metabolites appear in the hepatic portal vein.

“This shows that both the environment and the host’s genetics can interact in complex ways with the gut microbiome. As a result of these interactions, different combinations of metabolites may be sent to the liver and subsequently to the peripheral circulation. These metabolites likely play an important role in mediating the conditions that lead to obesity, diabetes, and metabolic syndrome,” says Muñoz.

Testing Microbiome Disruption and Metabolite Effects

To identify which bacteria and microbial byproducts contribute to these metabolite patterns, the researchers treated obesity and diabetes susceptible mice with an antibiotic designed to target specific intestinal microorganisms. As expected, the treatment altered the microbiome and changed the balance of metabolites in both peripheral blood and the hepatic portal vein.

One outcome was an increase in metabolites such as mesaconate, which participates in the Krebs cycle, a fundamental energy-producing pathway in cells.

Using this insight, the scientists exposed hepatocytes (liver cells) to mesaconate and its isomers, which are chemical compounds with the same molecular formula but different structures. The treatments improved insulin signaling and regulated genes involved in hepatic fat accumulation (lipogenesis) and fatty acid oxidation, both of which are crucial processes for maintaining metabolic health.

“The metabolites found in the blood of these two sites, therefore, play important roles in mediating the effects of the microbiome on liver metabolism and the pathogenesis of type 2 diabetes insulin resistance, which is related to eating a high-fat diet,” says Muñoz.

Next Steps in Mapping Gut Driven Metabolic Pathways

The scientists now aim to characterize each metabolite in greater detail and determine how they are produced. This deeper understanding of microbial influences on metabolism may eventually lead to the identification of molecules that could serve as new therapeutic options for metabolic diseases.