AlphaFold can predict the exact shape of proteins to precisions within the width of an atom.

 

Starting in the 1950s, the complete structures of proteins were determined by tedious laboratory experiments. Experimental techniques that can map out the structure of proteins in the lab, such as cryo-electron microscopy, nuclear magnetic resonance, and x-ray crystallography, can take hundreds of thousands of dollars and years of trial and error for each protein. 

  

A protein is a precise amino acid sequence that automatically folds itself up with many complex twists into a typical shape. The final structure determines how the protein behaves. Proteins' action is the key to the basic mechanisms of life, how we digest food, how hormones regulate behavior, and how our immune system fights disease. Efforts to develop vaccines for covid-19 have focused on the virus’s spike protein, for example. The way the coronavirus snags onto human cells depends on the shape of this protein and the shapes of the proteins on the outside of those cells. Therefore, finding the folded protein structures is an essential and vigorous research area.

The latest version of DeepMind’s deep-learning system, called AlphaFold, can find a protein’s shape in a few days with high accuracy. The new AlphaFold computational methods predicted the structure of dozens of proteins with a margin of error of just 1.6 angstroms—that’s 0.16 nanometers, less than the size of an atom. 

The breakthrough is a game-changer in pharmaceutical research, new drug design, and disease understanding. Many drugs are designed by simulating their 3D molecular structure, which requires knowing the structure of those proteins, which is true for only a quarter of the roughly 20,000 human proteins. AlphaFold will revolutionize this research. In the longer term, predicting protein structure will also help design synthetic proteins, such as enzymes that digest waste or produce biofuels. 

Read the whole article: Nature 588, 203-204 (2020)

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Essential Genes Evolve in Genome’s Junkyard

 

Essential genes are often thought to be frozen in evolutionary time-evolving only very slowly because their changing or elimination would lead to the organism's death. Hundreds of millions of years of evolution separate insects and mammals, but experiments show that the Hox genes guiding the development of the body plans in Drosophila fruit flies and mice can be swapped without a hitch because they are so similar. This remarkable evolutionary conservation is a foundational concept in genome research. But a new study turns this rationale for genetic conservation on its head. 

Rapidly changing heterochromatin drives the evolution of new essential genes. Young genes are just as likely as old ones to encode essential functions. The most rapidly evolving ones were much more likely to encode essential functions than the more slowly evolving ones. These transcription factors did not localize to euchromatin, the part of the genome where most genes are located, but in the heterochromatin — the regions of densely packed DNA that are mainly kept in a silent state because they contain most of the noncoding DNA and other so-called genomic junk.

Genes commonly evolve by duplication and divergence. A study examined the role of relatively abundant and functionally important de novo genes. These are newly evolved genes, without a possible parent gene. Under the right environmental conditions, stretches of DNA, without any function can provide some advantages, and thus start evolving under selection. Scientists found that overexpressing these proto-gene sequences enhanced growth, proving their potential for the evolution of new functions. 

The new insight could prove important in identifying genes relevant to various medical conditions and biological mysteries. Essential genes that are potential therapeutic targets can be hiding in the heterochromatin, hidden among genomic junk.

Read the whole article: Innovation of heterochromatin functions drives rapid evolution of essential ZAD-ZNF genes in Drosophila.

De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences

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Evolution of a more upright posture in mammals and birds cooccurred with warm-bloodedness: The benefits of a 252 million years old posture shift.

 

During the Triassic, from 250 to 200 million years ago, the ancestors of both mammals and birds became warm-blooded at the same time. Life was recovering from the Permian-Triassic mass extinction, the greatest mass extinction of all time. It killed as much as 95 percent of life, and the very few survivors were repeatedly hit by global warming and ocean acidification. 

Warm bloodedness is an energy-requiring condition, but it permits the ability to compete better for resources and escape predators. Paleontologists identified warm-bloodedness and evidence for the early origin of feathers or hair in dinosaur and bird ancestors 250 million years ago. The origin of warm-bloodedness is connected to the exact time of the mass extinction. 

Several special features are linked to warm-bloodedness. One is the bones inside the nose and snout, called the turbinates. These bones increase the distance that air travels into the body, allowing it to warm up on the way in. There is also the bony palate, which separates the mouth from the nose and allows for continuous breathing, even while eating. Another, which is rarely preserved in the fossil records, is the presence of fur, which acts as insulation.

At the same time, an almost instantaneous posture shift happened in both mammal and bird ancestors. Amphibians and reptiles are sprawlers, holding their limbs partly sideways. Before the crisis, most reptiles had sprawling posture; afterward, they walked upright. This may have been the first sign of a new pace of life in the Triassic. Erect postures, with the limbs immediately below their bodies, allowed birds and mammals to run faster and further. However, to fuel inner temperature control, warm-blooded animals have to eat much more than cold-blooded animals. Warm bloodedness was a dramatic evolutionary innovation, which led to emotional regulation, making it possible to take care of offspring, learn, and form consciousness. 

Read more about how our mammal ancestors became warm-blooded on Phys.org.

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Quantum entanglement between distant large objects

 

Entanglement is a link between two sister particles or objects, making them behave as a single entity. Researchers at the Niels Bohr Institute, University of Copenhagen, entangled a mechanical oscillator—a vibrating dielectric membrane—with an atom cloud's spin (magnetic orientation).  These very different entities were possible to entangle by connecting them with photons, particles of light. Atoms can be useful in processing quantum information, and the membrane—or mechanical quantum systems in general—can be useful for the storage of quantum information.

Professor Eugene Polzik, who led the effort, states that: "With this new technique, we are on route to pushing the boundaries of the possibilities of entanglement. The bigger the objects, the further apart they are, . . . the more interesting entanglement becomes from both fundamental and applied perspectives. With the new result, entanglement between very different objects has become possible."

The experiment might be a step towards limitless precision of measurements of motion.

The work, "Entanglement between distant macroscopic mechanical and spin systems" was published in Nature Physics.  

Read the whole article in Phys.org

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Quantum gravity: fact or fiction?

 

A new scientific paper suggests using the interference of gravity waves to measure quantum gravity. Interference is a quantum phenomenon where the combination of two or more electromagnetic waves form a resultant wave, the sum of the original waves (i.e., bigger or smaller). 

In the experiment, laser light is shone on an electron. If the electron absorbs the photon's energy, then the electron's spin changes either up or down. During quantum superposition, the electron spin is both up and down. Choosing an electron that is part of a large body, such as a diamond, the entire object—with a vast mass for quantum phenomena—would be in quantum superposition.

By applying a magnetic field, it is possible to separate the two quantum states. When these quantum states are brought together again by turning off the magnetic field, they create an interference pattern. "The nature of this interference depends on the distance the two separate quantum states have traveled. And this can be used to measure gravity waves." These waves are space contractions so that their passing affects the distance between the two separated states and, thus, the interference pattern. The hope is that entanglement between two large objects could be used to determine whether gravity is a quantum phenomenon.  

Entanglement is a quantum phenomenon. When two objects interacting only through gravity show entanglement, gravity is also a quantum phenomenon. The experiment is a long shot with our current technology. Read more on the journal website.

Reference: 

Ryan J Marshman et al., Mesoscopic interference for metric and curvature & gravitational wave detection, New Journal of Physics (2020). DOI: 10.1088/1367-2630/ab9f6c

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Ambition: The Art of Leadership

Ambition is choosing the challenging path, the difficult problem, or forming a higher goal. It is the insight to formulate a long-term vision and the courage to take bold steps. Like gradually moving up on the mountain, every conquered challenge improves your confidence and belief in your abilities. Because our focus follows our attention, we often live up to our expectations, even if we aim high. Intrinsic motivation is the fuel for successful performance, learning, and creativity. Ambition has an essential role in personality development and wellness throughout the lifespan.

Ambition without leadership is worthless, the theory must be put into practice. Leadership is the physical framework, the primary tool, and the nitty-gritty of purpose. Leaders project purpose and flair. Leadership is an essential quality for everybody with a family or even with a circle of friends. Great leaders motivate achievement without manipulation, restrictions. They can resolve conflicts and tolerate honest mistakes, which often inspires commitment and enthusiasm within the organization. Most of the success points on this list are characteristic of great leaders. Professional and personal coherence is the key to both happiness and leadership. Their habit of generosity with compliments and their ability to apologize quickly help to reverse any blunder or mistake. 

The world is in constant flux, change is necessary at every level. In the corporate world, ideas are guarded like a great treasure. Giving over ownership to the group encourages productive contribution, independent of position. Their generous yet focused approach extends to every area of life; they seek excellence in their practice of hobbies, taking meaningful or extreme vacations. They encourage discipline, progress, innovation, and change. The motivation to connect with others, allows them to take decisive actions, and find appropriate words in uncertain situations.

My straightforward handbook, The Power of Joy, gives you the tools and advice you need to liberate yourself from your negativity and become the best version of yourself.

                                                              

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An experimental test to confirm the fermionic mind hypothesis.

The fermionic mind hypothesis (FMH) recognizes that the conscious brain is a self-regulating system. Sensory perception is an energy/information exchange with the environment, which generates mental changes. Intelligent responses to stimulus require that the mind adopts the physical laws for its operation. This is the main idea of the fermionic mind hypothesis. You can test the hypothesis for yourself in the comfort of your own home. You should not experiment if your emotional or physical wellbeing can be in danger. (Disclaimer: The author is not responsible for emotional discomfort or injuries triggered by this experiment.)

The experimental setup:

A well-defined emotional distance characterizes every relationship, which is regulated by emotions with great precision. Although it is difficult to test the emotional distance, you can easily measure its changes, extending and shortening it, like Tuffy candy. Perceived changes trigger a strong reaction to restore normalcy. 

Your experimental subject must be a person (or a pet) close to you emotionally. The test manipulates the distance between you and a loved one or a trusted friend in a relatively short time. Therefore, if you refrain from dramatic actions, this will not cause long-term damage to the relationship. There are two possible versions of the experiment.

1, Reduce the emotional distance. To achieve this, you have to seek closeness, such as romance, giving favors and gifts more than usual. On the other hand, at the moment your subject indicates a need for separation (you will notice his attempt to push you away), reverse your attitude toward them by acting cold and indifferent.

2. Increase the emotional distance. You will have to act cold and ignorant toward your subject. As soon as your partner attempts to reverse the situation by favors and trying to be "nicer," reverse the course by being warm and affectionate.  

Evaluate the results of your experiment. In maintaining the emotional distance between the two of you, your mind performed an everyday miracle. It gradually modified both partners' feelings and attitudes to keep your relationship balanced. How did your feelings change? How did the behavior of your partner change? Congratulations, you achieved an empowering outside view of yourself and your relationship.  

Read the resource article in Activitas Nervosa Superior.

Read the article on Academia. or on ResearchGate.

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What is the Fermionic Mind Hypothesis?

Understanding consciousness is the next great scientific frontier. 

Biological systems must adapt to their environment. The ability to balance and produce intelligent responses depends on a precise mental model of that environment. The superb adaptation to physical laws means that quantum mechanics, such as decision-making, describes our psychology. Comparison processes, the central pillars of intellect, are also utilized by artificial intelligence: Alphazero can learn by comparing game outcomes. As material systems observe the principle of least action when moving through space, biological systems optimize their action repertoire between the past and the future. Like the stationary action in physics, the mind's predictive intelligent processing is a memory-based temporal energy regulation system. Thus, the least action is based on past experience.

Access to air, water, food, and mating influences behavior between urgency and relaxation. Conscious focus is not under conscious control but governed by internal or external motivation. We cannot suppress our thoughts or emotions, nor can we turn them off at will. We say things we do not mean, lie, and commit crimes because we are slaves to our emotions. The inability to consciously guide behavior leads to remorse, shame, and regret. 

Despite dramatic changes to the mind and body, the mental continuum lasts from infancy to old age. Qualia's unique, intractable qualities remain intimately linked with the self, with conscious attention representing just the visible surface of the particle-like isolation of mental content. The introspectively accessible, phenomenal aspects of the mind are at the very heart of the mind-body problem. The mind is a self-regulating system that forms the smallest unit of intellect. This unity and indivisible wholeness is the essence of consciousness' separation from the environment, expressed by the fermionic mind hypothesis (FMH). 

Why is it important?
Recognizing the energetic nature of emotions can provide tools for individuals to achieve their human potential and inspire new, effective treatments for mental illnesses, such as depression. Comprehending how the mind works can inspire innovative types of quantum computers and deep learning systems.

The book Emotional Reasoning: Insight into the Conscious Experience was published on August 30, 2024. 

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