This repository contains a detailed, evidence-based, figure-by-figure critical commentary on the article “The origin of hepatocellular carcinoma depends on metabolic zonation” by Guo et al. (Science, 2025; eadv7129). The purpose of this commentary is to provide a rigorous, transparent, and meticulously documented evaluation of the methodological, statistical, conceptual, and visual limitations of the original study. Given the significant scientific implications of attributing hepatocellular carcinoma (HCC) initiation to specific metabolic zones within the liver lobule, any such claim warrants extensive scrutiny. This repository aims to facilitate informed discussion by consolidating an unbiased, data-driven assessment of the original figures, supplementary materials, and analytical choices. The commentary identifies several major concerns across the primary and supplementary figures. These include inconsistent zonal boundary definitions, lack of validation for lineage-tracing tools, mosaic or incomplete reporter expression patterns, ambiguous tumor mapping procedures, and overinterpretation of bulk metabolomics and single-cell RNA-seq data. In multiple instances, figure panels display inconsistent staining, patchy fluorescent labeling, or visual features that undermine the interpretation presented in the manuscript. Particular attention is devoted to issues of Cre driver fidelity, stability of metabolic zonation under physiological and pathological conditions, and the consequences of pseudo-replication in single-cell statistical analyses. The repository also documents internal inconsistencies within the original article, such as discrepancies between textual claims and figure-based evidence, conceptual oversimplifications of hepatocyte zonation, and the use of 2D histological sections to infer 3D spatial origins of tumors. Where relevant, the commentary cross-references specific phrases from the published article to highlight points where the evidence shown in the figures does not support the narrative. Additionally, the document notes apparent technical irregularities in several supplementary panels, including inconsistencies in brightness, scale bar representation, labeling density, and potential image stitching or cropping artifacts. While not implying misconduct, these irregularities warrant clarification in the interest of scientific transparency. By aggregating these observations into a structured critical analysis, this repository provides a comprehensive resource for researchers, clinicians, and scholars interested in liver zonation, hepatocyte biology, tumorigenesis, spatial transcriptomics, lineage tracing, and liver cancer pathophysiology. The commentary emphasizes the importance of robust spatial quantification, 3D mapping, reproducible lineage-tracing validation, and proper statistical treatment of single-cell datasets when addressing fundamental biological questions such as tumor cell-of-origin. This Zenodo record includes the complete commentary in Markdown form, enabling reuse, citation, and open peer discussion. The goal is to support transparent scientific dialogue, strengthen methodological standards in spatial biology, and encourage more rigorous evaluation of claims linking metabolic zonation to cancer initiation.