Reed Bender, Karina Kofman, Blaise Agüera y Arcas
et al.
The question of "what is life?" has challenged scientists and philosophers for centuries, producing an array of definitions that reflect both the mystery of its emergence and the diversity of disciplinary perspectives brought to bear on the question. Despite significant progress in our understanding of biological systems, psychology, computation, and information theory, no single definition for life has yet achieved universal acceptance. This challenge becomes increasingly urgent as advances in synthetic biology, artificial intelligence, and astrobiology challenge our traditional conceptions of what it means to be alive. We undertook a methodological approach that leverages large language models (LLMs) to analyze a set of definitions of life provided by a curated set of cross-disciplinary experts. We used a novel pairwise correlation analysis to map the definitions into distinct feature vectors, followed by agglomerative clustering, intra-cluster semantic analysis, and t-SNE projection to reveal underlying conceptual archetypes. This methodology revealed a continuous landscape of the themes relating to the definition of life, suggesting that what has historically been approached as a binary taxonomic problem should be instead conceived as differentiated perspectives within a unified conceptual latent space. We offer a new methodological bridge between reductionist and holistic approaches to fundamental questions in science and philosophy, demonstrating how computational semantic analysis can reveal conceptual patterns across disciplinary boundaries, and opening similar pathways for addressing other contested definitional territories across the sciences.
Mixing maternal and paternal genomes is the base of plant sexual reproduction, but some so-called 'haploid inducer lines' lead to the formation of seeds bearing well-developed embryos with solely the maternal genome. A recent study adds a new piece to the puzzle of this enigmatic in planta haploid embryo induction process.
The more we learn about the cytoplasm of cells, the more we realise that the cytoplasm is not uniform but instead is highly inhomogeneous. In any inhomogeneous solution, there are concentration gradients, and particles move either up or down these gradients due to a mechanism called diffusiophoresis. I estimate that inside metabolically active cells, the dynamics of particles can be strongly accelerated by diffusiophoresis, provided that they are at least tens of nanometres across. The dynamics of smaller objects, such as single proteins are largely unaffected.
We prove that the HOMFLYPT polynomial of a link, colored by partitions with a xed number of rows is a q-holonomic function. Specializing to the case of knots colored by a partition with a single row, it proves the existence of an (a;q) super-polynomial of knots in 3-space, as was conjectured by string theorists. Our proof uses skew Howe duality that reduces the evaluation of web diagrams and their ladders to a Poincare-Birkho- Witt computation of an auxiliary quantum group of rank the number of strings of the ladder diagram.
The design of high quality factor (Q) optical cavities in two dimensional photonic crystal (PC) slab waveguides based upon a momentum space picture is presented. The results of a symmetry analysis of defect modes in hexagonal and square host photonic lattices are used to determine cavity geometries that produce modes which by their very symmetry reduce the vertical radiation loss from the PC slab. Further improvements in the Q are achieved through tailoring of the defect geometry in Fourier space to limit coupling between the dominant momentum components of a given defect mode and those momentum components which are either not reflected by the PC mirror or which lie within the radiation cone of the cladding surrounding the PC slab. Numerical investigations using the finite-difference time-domain (FDTD) method predict that radiation losses can be significantly suppressed through these methods, culminating with a graded square lattice design whose total Q approaches 10;5 with a mode volume of approximately 0.25 cubic half-wavelengths in vacuum.
Site-directed mutagenesis refers to a man-made molecular biology method that is used to make genetic alterations in the DNA sequence of a gene of interest. But based on our recently published experimental findings, we propose that natural site-directed mutagenesis might exist in the eukaryotic cells, which is triggered by harmful agents and co-directed by special transcription hotspots and mutation-contained intranuclear primers.
Till now, in biological sciences, the term, transcription, mainly refers to DNA to RNA transcription. But our recently published experimental findings obtained from Plasmodium falciparum strongly suggest the existence of DNA to DNA transcription in the genome of eukaryotic cells, which could shed some light on the functions of certain noncoding DNA in the human and other eukaryotic genomes.
Kinetic theory and thermodynamics are applied to DNA polymerases with exonuclease activity, taking into account the dependence of the rates on the previously incorportated nucleotide. The replication fidelity is shown to increase significantly thanks to this dependence at the basis of the mechanism of exonuclease proofreading. In particular, this dependence can provide up to a hundred-fold lowering of the error probability under physiological conditions. Theory is compared with numerical simulations for the DNA polymerases of T7 viruses and human mitochondria.