Science

Profluent, a California-based artificial intelligence (AI)-first protein design company, announced its AI model that can generate CRISPR-like proteins that do not occur in nature on Tuesday. CRISPR or Clustered Regularly Interspaced Short Palindromic Repeats is a complex containing important proteins that scientists can use for precise gene editing in organisms. The company claims the usage of AI can create a vast number of such proteins that can help in creating bespoke cures for diseases which, at present, remain incurable.

Ali Madani, the founder and CEO of Profluent announced the AI model in a series of posts on X (formerly known as Twitter). The company has also made a blog post detailing the initiative and a pre-print version of its research paper has been published on bioRxiv. Besides announcing the DNA editor-generating AI model, the company also launched OpenCRISPR-1, one of the AI-created gene editors, as an initial open-source release licencing it for both ethical research and commercial uses.

Why OpenCRISPR AI Model matters

While CRISPR is a major focus of scientists, the research is limited due to the protein Cas9, which acts as a gene editor, and its equivalent being only available in nature. As a result, scientists spend a significant amount of time discovering different types of gene editors and their impact. Profluent claims its AI model, which is powered by an in-house large language model (LLM) trained on “massive scale sequence and biological context”, can now generate millions of diverse CRISPR-like proteins that do not occur in nature. In theory, these synthetic gene editors can play a pivotal role in finding cures for diseases previously thought to be incurable.

In its blog post, the company said, “OpenCRISPR-1 gene editor maintains the prototypical architecture of a Type II Cas9 nuclease but is more than 400 mutations away from SpCas9 and nearly 200 mutations away from any other known natural CRISPR-associated protein.”

What is CRISPR

CRISPR, put simply, is a complex or system found in bacteria and some other unicellular organisms. This complex contains the Cas9 (or similar proteins like Cas12 and Cas13) proteins that have a specific ability to make precise cuts in gene strands of DNA to enable editing. It was first discovered in 1987, and ever since scientists have been researching it extensively. The technology has vast applications and has already been used to artificially create crop variants that have a higher yield, are resistant to diseases, and are drought tolerant.

It is also used to change the DNA of mosquitoes so that they cannot spread diseases like malaria. Experiments are being conducted to cure patients suffering from diseases such as sickle-cell anaemia. It is also theorised that the technology can be used to edit the DNA of the embryo to create babies who are naturally resistant to diseases and possess genes that promote higher physical and mental abilities.

The following is an extract from our Lost in Space-Time newsletter. Each month, we hand over the keyboard to a physicist or mathematician to tell you about fascinating ideas from their corner of the universe. You can sign up for Lost in Space-Time for free here.

Is the universe a game? Famed physicist Richard Feynman certainly thought so: “‘The world’ is something like a great chess game being played by the gods, and we are observers of the game.” As we observe, it is our task…

A research team led by Prof. Zhang Guoqing from the University of Science and Technology of China (USTC) of the Chinese Academy of Sciences (CAS) has discovered a highly reactive photo-induced charge-transfer complex (PCTC) between amine and imide. Their findings are published in the journal Chem.

Charge transfer between molecules, a critical process in both natural and synthetic systems, plays a fundamental role in photosynthesis, respiration, and various organic synthesis and energy conversion applications.

Despite extensive research, creating stable, light-responsive charge-transfer complexes in artificial systems remains challenging. The discovery of PCTCs addresses this challenge, offering new insights into complex photochemical processes.

The researchers first discovered that aromatic imides and alkyl amines, which did not interact significantly in their ground state, form stable PCTCs when exposed to UV light. This interaction resulted in a highly fluorescent complex resembling a Meisenheimer complex.

The use of various spectroscopic techniques, including high-resolution mass spectrometry and time-resolved spectroscopy, confirmed the formation and stability of these complexes.

The researchers conducted a series of experiments to explore the formation mechanism. They observed that the interaction between naphthalimide and triethylamine in solution resulted in no significant changes in the absorption or emission spectra in the absence of light.

However, upon UV irradiation, new spectral features emerged, indicating the formation of the PCTC. These features included a distinct absorption band and enhanced fluorescence, which were absent in the individual components.

Moreover, researchers applied PCTC to initiate the polymerization of acrylic esters under UV light, demonstrating its potential in creating new polymeric materials with unique properties. Additionally, the complex showed efficacy in reducing carbon dioxide, a crucial reaction for addressing environmental challenges and developing sustainable energy sources.

One of the most intriguing applications of the PCTC was its ability to store UV energy and release it in the dark. This capability enabled processes traditionally dependent on continuous light exposure to proceed in the absence of light.

The discovery of highly reactive PCTCs between amines and imides under UV light not only enhances our understanding of photo-induced charge-transfer processes but also opens up new avenues for practical applications in polymer science, environmental technology, and energy storage.

NASA’s Mars InSight Lander may be resting on the Red Planet in retirement, but data from the robotic explorer is still leading to seismic discoveries on Earth.

In one of the latest studies using data from the spacecraft, an international team of scientists led by a Brown University researcher found that Mars may be getting bombarded by space rocks at more frequent rates than previously thought. Impact rates could be two to 10 times higher than previously estimated, depending on the size of the meteoroids, according to the study published in Science Advances.

“It’s possible Mars is more geologically active than we thought, which holds implications for the age and evolution of the planet’s surface,” said lead researcher Ingrid Daubar, an associate professor of Earth, environmental and planetary sciences at Brown.

“Our results are based on a small number of examples available to us, but the estimate of the current impact rate suggests the planet is getting hit much more frequently than we can see using imaging alone.”

As part of the study, the research team used InSight’s highly sensitive onboard seismometer to identify eight new impact craters from meteoroids not previously seen from orbit.

The frequency of these cosmic collisions challenges existing notions about how often meteoroids hit the Martian surface and suggests a need to revise current Martian cratering models to incorporate higher impact rates, especially from smaller meteoroids.

The findings could ultimately reshape current understandings of the Martian surface—as batterings from small meteoroids continue to sculpt it—and the impact history of not just Mars, but other planets.

“This is going to require us to rethink some of the models the science community uses to estimate the age of planetary surfaces throughout the entire solar system,” Daubar said.

Six of the craters the researchers detected were near the site where the stationary InSight Lander set down. The two distant impacts they identified from the data were the two biggest impacts ever detected by scientists, even after decades of watching from orbit. The larger impacts, each leaving a crater roughly the size of a football field, came just 97 days apart, underscoring the higher frequency of these types of geological events.

“This size impact, we would expect to happen maybe once every couple of decades, maybe even once in a lifetime, but here we have two of them that are just over 90 days apart,” Daubar said.

“It could just be a crazy coincidence, but there’s a really, really small likelihood that it’s just coincidence. What’s more likely is that either the two big impacts are related, or the impact rate is a lot higher for Mars than what we thought it was.”

NASA’s InSight’s mission was active from November 2018 to December 2022. One of its main objectives was measuring the planet’s seismological shaking. Previously, new impacts on Mars were spotted with before-and-after images taken from cameras in orbit around the planet. The seismometer provided a new tool to find and detect these impacts, many of which might have otherwise gone unnoticed.

“Planetary impacts are happening all across the solar system all the time,” Daubar said.

“We’re interested in studying that on Mars because we can then compare and contrast what’s happening on Mars to what’s happening on the Earth. This is important for understanding our solar system, what’s in it and what the population of impacting bodies in our solar system looks like—both as hazards to the Earth and also historically to other planets.”

The rates are also important for assessing potential hazards that impacts pose for future exploration missions as NASA sends rovers or even human missions to space.

To pinpoint when and where the impacts occurred on Mars, Daubar and the research team analyzed seismic signals from InSight and then compared that seismic data with images taken by NASA’s Mars Reconnaissance Orbiter.

The team visually confirmed eight of the events as new craters by examining before-and-after images. This dual approach of using seismic data and orbital imagery allowed them to confirm the seismic signals were caused by impacts and cross-check their findings to ensure accuracy.

The InSight lander collected seismic data from its landing until its solar panels, as expected, were covered in dust to the extent that the lander could no longer generate power.

The current study by Daubar and the research team ties into a companion paper in Nature Communications that uses even more data from InSight to look at all the very high frequency seismic events the lander detected.

The companion paper, also published on June 28, 2024, assumes all these events were caused by impacts and finds the resulting estimated rate falls in line with what the researchers from Daubar’s team calculated independently, further strengthening each team’s findings.

“It’s possible that more events that InSight picked up during its mission were actually impacts,” Daubar said. “Next steps are to do more detailed orbital searches to try to confirm this using machine learning techniques. If we can confirm even more impacts, we might be able to find other seismic signals that were caused by impacts, too.”

Along with Brown, the study also involved researchers from the Institut Supérieur de l’Aéronautique et de l’Espace, University of Oxford, Imperial College London, U.S. Geological Survey, ETH Zürich, University of Arizona, NASA’s Jet Propulsion Laboratory, and Université Paris Cité.

A research team led by Prof. Wang Pengfei from Xi’an Institute of Optics and Precision Mechanics (XIOPM) of the Chinese Academy of Sciences revealed the relationship between F/O ratio and the structure of fluorophosphate glass through conducting comprehensive research on Raman spectroscopy and nuclear magnetic resonance (NMR) spectroscopy.

The results were published in the Journal of Non-Crystalline Solids.

The performance of fluorophosphate glass is closely related to its structure. However, the conclusions drawn from all the studies on the structure of fluorophosphate glass so far cannot be universally applied to glasses with different components.

Given that F^– and O^– are the only two existing anions and play a dominant role in the structure, studying the common structural features of glasses based on F/O ratio is an efficient approach.

In this study, researchers prepared a series of glass samples based on the fluorophosphate system with an F/O ratio range of 1 to 7. They studied the content changes of different Qⁿ groups under different F/O ratio by Raman and NMR spectra. Then, they concluded quantitative relationship between F/O ratio and Qⁿ characteristics through comparative analysis of reported NMR spectra.

When the F/O ratio is below 0.3, Q² content is highest, while the unit presence of Q⁰ is very small, and the percentage is less than 10%. When the F/O ratio is in the range of 0.3 to 1, the Qⁿ units with the highest content is composed of Q² or Q¹ units.

With the increase of the F/O ratio, the content of Q¹ increased significantly, while the content of Q⁰ remained relatively stable within this range. When the F/O ratio is in the range of 1 to 4, the Qⁿ units with the highest content include Q⁰ or Q¹ units.

When the F/O ratio is more than 4, the Qⁿ units with the highest content are composed of Q⁰. With the increase of oxygen content ratio, the growth rate of Q⁰ slows down and approaches saturation.

This study reveals the general rule of the effect of F/O ratio on the structure of fluorophosphate glass, which provides an effective way to predict the structure and properties of glass by composition.

Our present-day moon has an interior structure containing a central metallic core, overlain by a mantle comprised of minerals such as olivine and pyroxene (e.g. Ol+Px mantle) underneath a shell of crust. Such a picture of the moon’s interior has been formed from analyses of returning lunar samples and records of deep seismic events collected during missions to the moon.

Despite the wealth of literature, there is still a longstanding debate as to the existence of garnet (Gt) within the deeper part of the lunar mantle. Reflecting upon the existence of garnet, the pivotal question first posited 50 years ago has remained unanswered: are laboratory measured sound velocities in realistic lunar aggregates containing garnet compatible with the seismic profiles of the deep lunar interior?

To provide answers to this question, Ehime’s researchers first synthesized garnet-rich lunar rock assemblages (Ol+Px+Gt sample) at high pressures and high temperatures using the multi-anvil press apparatus “ORANGE-2000” at the Geodynamics Research Center.

The findings are published in the journal Earth and Planetary Science Letters.

These samples were then transported to SPring-8, the Large-scale Synchrotron Radiation Facility, located in Hyogo Prefecture, where experiments were carried out at the high pressure and high temperature beamline BL04B1. Here the researchers subjected the lunar rock assemblage to pressure and temperature conditions similar to those of the moon’s deep interior while they measured the propagation speed of sound waves in the lunar rock assemblage.

Combining the results of their experiment with a modeling component, the researchers concluded that the sound velocities in lunar assemblages containing large amounts of garnet were compatible with the seismic and density profiles of the moon’s deep interior, between depths of 740–1,260 km.

Furthermore, they found that rock assemblages containing little to no garnet are unlikely to explain the observed seismic velocities and densities of the lunar mantle at those depths.

These intriguing results have significant implications for the moon and its interior dynamics, including its composition and formation, the interior temperature, as well as implications for the lunar core and the now defunct lunar dynamo.

A recent study, conducted in the midst of last year’s widespread protests in Israel, has uncovered extreme polarization in public opinion regarding the judicial reform introduced by Prime Minister Benjamin Netanyahu’s government.

The study, published in Communications Psychology by researchers at Bar-Ilan University, highlights the significant role of motivated reasoning in shaping people’s views on this controversial issue.

In January 2023, Israel’s newly elected government proposed a judicial reform aimed at curtailing the Supreme Court’s power over the government. While some groups expressed support, many others saw it as a weakening of democratic institutions.

The reform was pushed forward despite a lack of widespread voter support. Protests erupted across the country, reflecting deep concerns about the reform’s potential negative impacts on various sectors, including health care and academic freedom.

The study, conducted among the general Jewish population in Israel in the midst of the protests, involved two rounds of surveys in March and May 2023. It found that opinions about the reform were extremely polarized, with most individuals either strongly supporting or opposing it.

This polarization was driven by motivated reasoning, where people’s pre-existing beliefs significantly influenced their views. This thought process leads people to arrive at conclusions that align with what they already believe.

The study was led by Dr. Dora Simunovic, of Constructor University in Germany and Bar-Ilan University in Israel, and Dr. Anna Dorfman and Dr. Maayan Katzir, of the Department of Psychology and Conflict Management, Resolution and Negotiation Program at Bar-Ilan University.

Key findings include:

• Trust Dynamics: Reform supporters showed high trust in the government and mistrust in the judiciary, while opponents exhibited the opposite.
• Views on Protests: Reform opponents viewed extreme protest measures as legitimate, whereas supporters justified the use of forceful means, such as stun grenades and water cannons to disperse demonstrations.
• Democratic Principles: Reform supporters, who won the electoral majority, prioritized Majority Rule as a core democratic principle, while opponents valued the protection of Minority Rights and Independent Media more highly.
• False Consensus: Both supporters and opponents believed their camp represented the majority, reflecting the psychological phenomenon of False Consensus.

“We were surprised by how quickly polarization over this newly emerging issue developed and the strong false consensus effect we observed,” said researcher Dr. Maayan Katzir.

“People were convinced that their camp was the majority, no matter what their actual opinion was. This is a serious issue, because when each side is certain that they represent the majority, they are less willing to compromise, which maintains and deepens polarization.”

Dr. Dora Simunovic, the study’s lead author, explains that motivated reasoning affects everybody, regardless of partisanship, religion, education, and other characteristics. She adds, “The phenomenon of false consensus is concerning because it suggests that both sides feel emboldened by their perceived majority status, reducing the likelihood of compromise.”

The study underscores the importance of understanding how motivated reasoning affects opinions on controversial topics and the potential for rapid polarization in societies, like Israel, with segregated education streams. Future research will explore how these educational differences influence national identity and democratic understanding.

“We need to look at how people understand what democracy is, because distorted and biased understanding of democracy can lead to support of undemocratic policies and actions,” concludes Dr. Dorfman.

Can you remember your last in-person exam? You’re waiting outside the venue with your identification, pens and back-up pens. Everyone is nervously looking at their notes or avoiding eye contact.

The doors open and you enter a cavernous space of numbered tables in rows. You find your seat and, waiting to start, glance around the vast space that surrounds you.

Our research suggests this environment may have an effect on your ability to perform at your best.

In our new study, we looked at the impact of ceiling heights on the exam performance of Australian students.

Exams have a long history

Exams date back more than 1,300 years and are still one of the most common forms of assessment for school and university. They are often conducted in large spaces for efficiency in supervision and space use. This often includes gymnasiums, auditoriums, showgrounds, halls and exhibition buildings.

While the pandemic led a shift to online exams, growing concern over AI and other forms of cheating has seen a renewed emphasis on this traditional style of in-person assessment (even if research shows “high stakes” exams are not good for learning or the prevention of cheating).

Our research

In our previous 2022 lab-based study, we found if rooms were larger, there was an impact on brain activity associated with our ability to concentrate.

This led us to wonder whether, in everyday life, large rooms have an impact on cognitive performance (or how well our brains can perform tasks)—and therefore whether traditional large exam halls have an impact on students’ results.

To test this, in our new study, we compared students’ exam results across different sizes of rooms.

We looked at the results from 15,400 psychology undergraduates at one Australian university over eight years (2011–19), and across three campuses.

We matched exam scores and the room dimensions where the examinations were held. This included rooms with ceiling heights between 2.79 meters to 9.50m, and internal floor areas between 38m² to 1,562m².

As we relied on non-experimental data (things in their natural state), we were careful to account for other variables that might account for the results.

We factored in students’ coursework scores as well as variables such as their gender, age, past exam experience and the unit of study. We also looked at geographic location, as admission requirements were different across campuses. All of these helped us understand what might affect our results.

To do our analysis, we used a statistical model called a “linear mixed model.” This meant we could add these different variables to try and understand the extent to which they predict something (in this case, exam performance).

What we found

The “significance” score for coursework was less than 0.001 and for ceiling height it was 0.002. A score below 0.05 means the result is unlikely to happen by chance, so we can be confident there’s a real effect.

This means a students’ prior coursework scores had a bigger impact on their exam score. But we still found ceiling height was a significant predictor of their results. In other words, even after accounting for other factors, higher ceiling heights were a significant predictor of the students’ exam scores.

This suggests study habits matter but so too do the dimensions of the room in which you sit the exam.

Why is this?

Our fresh findings suggest several questions ripe for further research. These include:

• is room insulation and climate control (which affect the air temperature, quality and circulation) a reason for room size making a difference? Research shows factors such as temperature affect cognitive performance.
• does room context have an impact? If we know big halls and gyms are usually designed for large social gatherings and sporting events, does this make us feel less comfortable or bring back past memories, and therefore make us less likely to perform at our best?
• does being in a space with more people sitting close by means you are more or less likely to cheat? How does this affect your score?
• what happens when students are randomly allocated to rooms of different sizes? At present there are other factors such as special consideration which will determine exam room allocation and conditions.

We also need to consider what is happening now for online exams. This has introduced new variability around the environmental conditions for students. Here, a student may have an advantage if they feel cozy and relaxed at home, or perhaps they may struggle to concentrate due to other environmental and social factors at home.

Given we only studied students in one discipline (psychology) we also need to replicate these findings in different areas and groups of students.

What else?

This work also feeds into our broader research about how building design can effect what our brains need to do.

There is already significant community awareness of how buildings can impact upon our physical health—and building codes and regulations to make sure they meet these standards.

But as our research shows, the way spaces are designed can have an impact on the way we think and how well we perform a task. This could be applied beyond exams to how we learn or do our jobs in the broader world.

This article is republished from The Conversation under a Creative Commons license. Read the original article.