Apple presents MUSCLE A Model Update Strategy for Compatible LLM Evolution.
Apple presents MUSCLE
A model update strategy for compatible LLM evolution.
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In new research, Arizona State University scientists and their colleagues investigated genetic changes occurring in a naturally isolated population of the water flea, Daphnia pulex. This tiny crustacean, barely visible to the naked eye, plays a crucial role in freshwater ecosystems and offers a unique window into natural selection and evolution.
By analyzing co-evolution of mitochondrial and nuclear genomes across insect species, the authors uncover the evolutionary covariation of a group of non-mitochondrially targeted nuclear genes with mitochondrial genes, including the uncharacterized gene CG11837, which regulates insect lifespan.
A long-term study since 1929 has revealed significant insights into barley’s evolution, showing its adaptation to different environments and the substantial impact of natural selection. This research underscores the limitations of evolutionary breeding and highlights the need for further exploration to enhance crop yields.
Utilizing one of the world’s oldest biological experiments, which commenced in 1929, researchers have revealed how barley, a major crop, has been influenced by agricultural pressures and its evolving natural environment. These findings highlight the significance of long-term studies in comprehending the dynamics of adaptive evolution.
The survival of cultivated plants after their dispersal across different environments is a classic example of rapid adaptive evolution. For example, barley, an important neolithic crop, spread widely after domestication over 10,000 years ago to become a staple source of nutrition for humans and livestock throughout Europe, Asia, and Northern Africa over just a few thousand generations. Such rapid expansion and cultivation have subjected the plant to strong selective pressures, including artificial selection for desired traits and natural selection by being forced to adapt to diverse new environments.
LA JOLLA (March 4, 2024)—Charles Darwin described evolution as “descent with modification.” Genetic information in the form of DNA sequences is copied and passed down from one generation to the next. But this process must also be somewhat flexible, allowing slight variations of genes to arise over time and introduce new traits into the population.
But how did all of this begin? In the origins of life, long before cells and proteins and DNA, could a similar sort of evolution have taken place on a simpler scale? Scientists in the 1960s, including Salk Fellow Leslie Orgel, proposed that life began with the “RNA World,” a hypothetical era in which small, stringy RNA molecules ruled the early Earth and established the dynamics of Darwinian evolution.
New research at the Salk Institute now provides fresh insights on the origins of life, presenting compelling evidence supporting the RNA World hypothesis. The study, published in Proceedings of the National Academy of Sciences (PNAS) on March 4, 2024, unveils an RNA enzyme that can make accurate copies of other functional RNA strands, while also allowing new variants of the molecule to emerge over time. These remarkable capabilities suggest the earliest forms of evolution may have occurred on a molecular scale in RNA.
Numerous open questions in gravity theory become apparent from observations in cosmology, such as the cosmic microwave background radiation [1, 2, 3, 4, 5, 6], the large scale structure [7, 8], gravitational waves [9, 10] and supernovae [11]. In order to describe these observations, one needs to study the evolution of both the universe as a whole, modeled by a homogeneous and isotropic background geometry and matter distribution, as well as perturbations of this background. A thorough understanding of such cosmological perturbations and their dynamics imposed by the gravitational interaction is therefore an important necessity for describing and explaining the modern observations in cosmology.
Cosmological perturbations in gravity have been studied for a long time, starting with the case of (pseudo-)Riemannian spacetime geometry, which is employed by the standard formulation of general relativity and the most well-known class of its extensions, in which the gravitational interaction is attributed to the curvature of the metric-compatible, torsion-free Levi-Civita connection [,13,14,15]. This task is significantly simplified by the fact by understanding how perturbations transform under gauge transformations, i.e., infinitesimal diffeomorphisms which retain the nature of the spacetime geometry as a small perturbation of a cosmologically symmetric background. From these gauge transformations, one can derive a set of gauge-invariant perturbation variables, which describe the physical information contained in the metric perturbations as well as the perturbations of the matter variables, so that they become independent of the arbitrary gauge choice. The resulting gauge-invariant perturbation theory is one of the cornerstones of modern cosmology [16,17,18,19].
Despite its overwhelming success in describing observations from laboratory scales up to galactic scales, general relativity is challenged by the aforementioned open questions, as well as the open question how it can be reconciled with quantum theory. This situation motivates the study of modified gravity theories [20]. While numerous theories depart from the standard formulation of general relativity in terms of the curvature of the Levi-Civita connection of a Riemannian spacetime, also other formulations in terms of the torsion or nonmetricity of a flat connection exist and can be used as potential starting points for the construction of modified gravity theories [21, 22]. Focusing on general relativity alone, one finds that these formulations are equivalent in the sense that they lead to field equations which possess the same solutions for the metric irrespective of the geometric properties of the connection under consideration…
Life’s evolutionary timescale is typically calibrated to the oldest fossil occurrences. However, the veracity of fossil discoveries from the early Archaean period has been contested11,12. Relaxed Bayesian node-calibrated molecular clock approaches provide a means of integrating the sparse fossil and geochemical record of early life with the information provided by molecular data; however, constraining LUCA’s age is challenging due to limited prokaryote fossil calibrations and the uncertainty in their placement on the phylogeny. Molecular clock estimates of LUCA13,14,15 have relied on conserved universal single-copy marker genes within phylogenies for which LUCA represented the root. Dating the root of a tree is difficult because errors propagate from the tips to the root of the dated phylogeny and information is not available to estimate the rate of evolution for the branch incident on the root node. Therefore, we analysed genes that duplicated before LUCA with two (or more) copies in LUCA’s genome16. The root in these gene trees represents this duplication preceding LUCA, whereas LUCA is represented by two descendant nodes. Use of these universal paralogues also has the advantage that the same calibrations can be applied at least twice. After duplication, the same species divergences are represented on both sides of the gene tree17,18 and thus can be assumed to have the same age. This considerably reduces the uncertainty when genetic distance (branch length) is resolved into absolute time and rate. When a shared node is assigned a fossil calibration, such cross-bracing also serves to double the number of calibrations on the phylogeny, improving divergence time estimates. We calibrated our molecular clock analyses using 13 calibrations (see ‘Fossil calibrations’ in Supplementary Information). The calibration on the root of the tree of life is of particular importance. Some previous studies have placed a younger maximum constraint on the age of LUCA based on the assumption that life could not have survived Late Heavy Bombardment (LHB) (~3.7–3.9 billion years ago (Ga))19. However, the LHB hypothesis is extrapolated and scaled from the Moon’s impact record, the interpretation of which has been questioned in terms of the intensity, duration and even the veracity of an LHB episode20,21,22,23. Thus, the LHB hypothesis should not be considered a credible maximum constraint on the age of LUCA. We used soft-uniform bounds, with the maximum-age bound based on the time of the Moon-forming impact (4,510 million years ago (Ma) ± 10 Myr), which would have effectively sterilized Earth’s precursors, Tellus and Theia13. Our minimum bound on the age of LUCA is based on low δ98 Mo isotope values indicative of Mn oxidation compatible with oxygenic photosynthesis and, therefore, total-group Oxyphotobacteria in the Mozaan Group, Pongola Supergroup, South Africa24,25, dated minimally to 2,954 Ma ± 9 Myr (ref. 26).
Our estimates for the age of LUCA are inferred with a concatenated and a partitioned dataset, both consisting of five pre-LUCA paralogues: catalytic and non-catalytic subunits from ATP synthases, elongation factor Tu and G, signal recognition protein and signal recognition particle receptor, tyrosyl-tRNA and tryptophanyl-tRNA synthetases, and leucyl-and valyl-tRNA synthetases27. Marginal densities (commonly referred to as effective priors) fall within calibration densities (that is, user-specified priors) when topologically adjacent calibrations do not overlap temporally, but may differ when they overlap, to ensure the relative age relationships between ancestor-descendant nodes. We consider the marginal densities a reasonable interpretation of the calibration evidence given the phylogeny; we are not attempting to test the hypothesis that the fossil record is an accurate temporal archive of evolutionary history because it is not28.
“We think these objects came from the inner and/or outer main asteroid belt, and the implication of that is that this is another mechanism for getting some ice into the inner solar system,” said Aster Taylor.
What are dark comets and how are they responsible for delivering water to the Earth? This is what a recent study published in Icarus hopes to address as a team of international researchers investigated the origins of dark comets and their evolution throughout the history of the solar system, including how much water they could have potentially brought to Earth in the past. This study holds the potential to help astronomers better understand dark comets and the formation and evolution of planetary bodies throughout the solar system.
Dark comets are often described as being a combination of asteroids and classified based on their unique behaviors, specifically their ability to accelerate without the aid of gravitational means, which researchers have previously hypothesized to be invisible gas jets emanating like traditional comets. Additionally, their physical characteristics consist of dark surfaces that could be hiding an icy subsurface, whereas traditional comets exhibit icy characteristics directly on their surface.
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In 2006, just a few years after the fruit fly genome had been sequenced, geneticists at the University of California, Davis, made a startling discovery: Several new genes had cropped up, seemingly out of nowhere.
These “de novo genes” weren’t simply new variants of existing ones; they had sprung forth from the supposedly inert spaces in between the coding sections of DNA—regions long dismissed as the junkyards of the double helix. Since the days of Darwin, such sprightly biological change agents had never before been seen.
A young graduate student at the time, Li Zhao was so intrigued that upon graduating in 2011, she set out to join the lab of David Begun, where the discovery was first made. She soon revealed that these little genetic big bangs happen all the time—over the past decade, she and her team have identified more than 500 de novo genes in the Drosophila lineage alone.
“Of all currently known temperate exoplanets, LHS 1,140 b could well be our best bet to one day indirectly confirm liquid water on the surface of an alien world beyond our Solar System,” said Charles Cadieux.
The search for Earth’s twin just got a little closer as astronomers recently presented findings regarding a potential icy or watery “super-Earth” called LHS 1,140 b, which is located approximately 49 light-years from Earth and whose radius is approximately 1.7 times our planet, along with orbiting within its star’s habitable zone. What makes this finding unique is LHS 1,140 b was previously hypothesized to be a mini-Neptune and astronomers speculate could be completely covered in either ice or water.
The findings were recently accepted to The Astrophysical Journal Letters and hold the potential to help astronomers better understand the formation and evolution of exoplanets, and specifically Earth-sized exoplanets within their star’s habitable zone.
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