arXiv subjects

Michael Jirasek

Publications and source records attributed to Michael Jirasek.

4 recordsLinked to original sources

arXiv2025

Quantifying the Emergence of Selection Prior to Biological Evolution

Selection is central to biological evolution, yet there has been no general experimental framework for quantifying selection in chemical systems before life. Here we demonstrate that selection in a prebiological chemical system can be directly quantified. Assembly Theory predicts that selection corresponds to a transition from undirected to directed exploration of chemical possibility space, measurable through the amount of Assembly, A, which integrates molecular assembly index with observed copy number. By analysing peptide ensembles produced under diverse polymerisation conditions, we show that undirected reactions explore sequence space almost uniformly, yielding exploration ratios of 0.85-0.95, whereas reactions influenced by evolved proteases generate markedly lower ratios (0.51-0.75) and elevated A, consistent with selective reinforcement of specific assembly pathways. Across multiple environments and amino-acid combinations, the exploration ratio and ensemble assembly A robustly distinguish directed from undirected exploration, establishing a general, experimentally tractable metric for detecting and measuring selection in chemical evolution.

q-bio.MN↗

arXiv2025

Constructing the Molecular Tree of Life using Assembly Theory and Mass Spectrometry

Here we demonstrate the first biochemistry-agnostic approach to map evolutionary relationships at the molecular scale, allowing the construction of phylogenetic models using mass spectrometry (MS) and Assembly Theory (AT) without elucidating molecular identities. AT allows us to estimate the complexity of molecules by deducing the amount of shared information stored within them when . By examining 74 samples from a diverse range of biotic and abiotic sources, we used tandem MS data to detect 24102 analytes (9262 unique) and 59518 molecular fragments (6755 unique). Using this MS dataset, together with AT, we were able to infer the joint assembly spaces (JAS) of samples from molecular analytes. We show how JAS allows agnostic annotation of samples without fingerprinting exact analyte identities, facilitating accurate determination of their biogenicity and taxonomical grouping. Furthermore, we developed an AT-based framework to construct a biochemistry-agnostic phylogenetic tree which is consistent with genome-based models and outperforms other similarity-based algorithms. Finally, we were able to use AT to track colony lineages of a single bacterial species based on phenotypic variation in their molecular composition with high accuracy, which would be challenging to track with genomic data. Our results demonstrate how AT can expand causal molecular inference to non-sequence information without requiring exact molecular identities, thereby opening the possibility to study previously inaccessible biological domains.

q-bio.PE↗

arXiv2024

Validation of the Scientific Literature via Chemputation Augmented by Large Language Models

Chemputation is the process of programming chemical robots to do experiments using a universal symbolic language, but the literature can be error prone and hard to read due to ambiguities. Large Language Models (LLMs) have demonstrated remarkable capabilities in various domains, including natural language processing, robotic control, and more recently, chemistry. Despite significant advancements in standardizing the reporting and collection of synthetic chemistry data, the automatic reproduction of reported syntheses remains a labour-intensive task. In this work, we introduce an LLM-based chemical research agent workflow designed for the automatic validation of synthetic literature procedures. Our workflow can autonomously extract synthetic procedures and analytical data from extensive documents, translate these procedures into universal XDL code, simulate the execution of the procedure in a hardware-specific setup, and ultimately execute the procedure on an XDL-controlled robotic system for synthetic chemistry. This demonstrates the potential of LLM-based workflows for autonomous chemical synthesis with Chemputers. Due to the abstraction of XDL this approach is safe, secure, and scalable since hallucinations will not be chemputable and the XDL can be both verified and encrypted. Unlike previous efforts, which either addressed only a limited portion of the workflow, relied on inflexible hard-coded rules, or lacked validation in physical systems, our approach provides four realistic examples of syntheses directly executed from synthetic literature. We anticipate that our workflow will significantly enhance automation in robotically driven synthetic chemistry research, streamline data extraction, improve the reproducibility, scalability, and safety of synthetic and experimental chemistry.

cs.AI↗

arXiv2023

Determining Molecular Complexity using Assembly Theory and Spectroscopy

Determining the complexity of molecules has important applications from molecular design to understanding the history of the process that led to the formation of the molecule. Currently, it is not possible to experimentally determine, without full structure elucidation, how complex a molecule is. Assembly Theory has been developed to quantify the complexity of a molecule by finding the shortest path to construct the molecule from building blocks, revealing its molecular assembly index (MA). In this study, we present an approach to rapidly and exhaustively calculate the MA of molecules from the spectroscopic measurements. We demonstrate that molecular complexity (MA) can be experimentally estimated using three independent techniques: nuclear magnetic resonance (NMR), tandem mass spectrometry (MS/MS), and infrared spectroscopy (IR), and these give consistent results with good correlations with the theoretically determined values from assembly theory. By identifying and analysing the number of absorbances in IR spectra, carbon resonances in NMR, or molecular fragments in tandem MS, the molecular assembly of an unknown molecule can be reliably estimated from experimental data. This represents the first experimentally quantifiable approach to defining molecular assembly, a reliable metric for complexity, as an intrinsic property of molecules and can also be performed on complex mixtures. This paves the way to use spectroscopic and spectrometric techniques to unambiguously detect alien life in the solar system, and beyond on exoplanets.

q-bio.QM↗