Quo Vadis? Scientific Discovery in the Age of Artificial Intelligence
PDF

Keywords

artificial intelligence
scientific discovery
AI scientists
research automation
human–AI collaboration

How to Cite

Quo Vadis? Scientific Discovery in the Age of Artificial Intelligence. (2026). Teorie vědy Theory of Science. https://doi.org/10.46938/tv.2026.728

Abstract

This paper examines the growing role of AI in scientific discovery. It first surveys the rapid rise of AI capabilities, especially in reasoning, abstraction, planning, and long-horizon task execution, before turning to scientometric evidence of AI’s diffusion across the sciences. It then proposes a typology of AI systems used in research, ranging from specialised scientific AI through scientific AI assistants and agents to hybrid experimental systems that combine computation and physical experimentation. On this basis, it offers a selective overview of recent achievements in mathematics and computer science, physics, chemistry, the life sciences, and the behavioural and social sciences. It argues that, despite these advances, current systems remain constrained by important technical, epistemic, and institutional limitations, and that their growing use introduces both near-term and longer-term risks. The conclusion further suggests that the advancement of AI in science raises broader questions concerning the division of cognitive labour between human researchers and machines.

PDF

References

Abramson, Josh, Jonas Adler, Jack Dunger, Richard Evans, Tim Green, Alexander Pritzel, Olaf Ronneberger, et al. “Accurate Structure Prediction of Biomolecular Interactions with AlphaFold 3.” Nature 630 (2024): 493–500. https://doi.org/10.1038/s41586-024-07487-w.

Agüera y Arcas, Blaise. “Do Large Language Models Understand Us?” Daedalus 151, no. 2 (2022): 183–97. https://doi.org/10.1162/daed_a_01909.

Alper, Jarod, Michael J. Barany, Alain Chavarri Villarello, Sander Dahmen, Walter Dean, Karthik Ganapathy, Michael Harris, et al. Leiden Declaration on Artificial Intelligence and Mathematics. Zenodo, 2026. https://doi.org/10.5281/zenodo.20302944.

Anthropic. System Card: Claude Mythos Preview. April 7, 2026. https://www-cdn.anthropic.com/7624816413e9b4d2e3ba620c5a5e091b98b190a5.pdf.

Artiles, Alejandro H., Martin Weiss, Levin Brinkmann, Iyad Rahwan, Bernhard Schölkopf, Christopher Pal, Hugo Larochelle, Anirudh Goyal, and Nasim Rahaman. “The Alien Space of Science: Sampling Coherent but Cognitively Unavailable Research Directions.” Preprint, arXiv, 2026. https://doi.org/10.48550/arXiv.2603.01092.

Bacon, Francis. Essayes. Religious Meditations. Places of Perswasion and Disswasion. Seene and Allowed. London: Printed [by John Windet] for Humfrey Hooper, 1597. Internet Archive. Accessed June 12, 2026. https://archive.org/details/bim_early-english-books-1475-1640_essayes-religious-medit_bacon-francis-viscount_1597.

Batatia, Ilyes, Philipp Benner, Yuan Chiang, Alin M. Elena, Dávid P. Kovács, Janosh Riebesell, Xavier R. Advincula, et al. “A Foundation Model for Atomistic Materials Chemistry.” The Journal of Chemical Physics 163, no. 18 (2025): 184110. https://doi.org/10.1063/5.0297006.

Bender, Emily M., Timnit Gebru, Angelina McMillan-Major, and Shmargaret Shmitchell. “On the Dangers of Stochastic Parrots: Can Language Models Be Too Big?” In Proceedings of the 2021 ACM Conference on Fairness, Accountability, and Transparency, 610–23. New York: Association for Computing Machinery, 2021. https://doi.org/10.1145/3442188.3445922.

Binksmith, Adam, and Eli Lifland. “A New Moore’s Law for AI Agents.” AI Digest. Article published March 27, 2025; last updated March 2026. Accessed June 12, 2026. https://theaidigest.org/time-horizons.

Binz, Marcel, Elif Akata, Matthias Bethge, Franziska Brändle, Fred Callaway, Julian Coda-Forno, Peter Dayan, et al. “A Foundation Model to Predict and Capture Human Cognition.” Nature 644 (2025): 1002–9. https://doi.org/10.1038/s41586-025-09215-4.

Brixi, Garyk, Matthew G. Durrant, Jerome Ku, Mohsen Naghipourfar, Michael Poli, Gwanggyu Sun, Greg Brockman, et al. “Genome Modelling and Design across All Domains of Life with Evo 2.” Nature 652 (2026): 1349–61. https://doi.org/10.1038/s41586-026-10176-5.

Center for AI Safety. “Humanity’s Last Exam.” Accessed June 12, 2026. https://lastexam.ai/.

Center for AI Safety, Scale AI, and HLE Contributors Consortium. “A Benchmark of Expert-Level Academic Questions to Assess AI Capabilities.” Nature 649 (2026): 1139–46. https://doi.org/10.1038/s41586-025-09962-4.

Chollet, François, Mike Knoop, Gregory Kamradt, and Bryan Landers. “ARC Prize 2025: Technical Report.” Preprint, arXiv, 2026. https://doi.org/10.48550/arXiv.2601.10904.

Costello, Thomas H., Gordon Pennycook, and David G. Rand. “Durably Reducing Conspiracy Beliefs through Dialogues with AI.” Science 385, no. 6714 (2024): eadq1814. https://doi.org/10.1126/science.adq1814.

Dawid, Anna, and Yann LeCun. “Introduction to Latent Variable Energy-Based Models: A Path Towards Autonomous Machine Intelligence.” Preprint, arXiv, 2023. https://doi.org/10.48550/arXiv.2306.02572.

Ding, Liangping, Cornelia Lawson, and Philip Shapira. “Rise of Generative Artificial Intelligence in Science.” Scientometrics 130 (2025): 5093–114. https://doi.org/10.1007/s11192-025-05413-z.

Ghareeb, Ali E., Benjamin Chang, Ludovico Mitchener, Angela Yiu, Caralyn J. Szostkiewicz, Dmytro Shved, Gavin J. Gyimesi, et al. “A Multi-Agent System for Automating Scientific Discovery.” Nature 655 (2026): 497–505. https://doi.org/10.1038/s41586-026-10652-y.

Glickman, Moshe, and Tali Sharot. “How Human–AI Feedback Loops Alter Human Perceptual, Emotional and Social Judgements.” Nature Human Behaviour 9 (2025): 345–59. https://doi.org/10.1038/s41562-024-02077-2.

Gottweis, Juraj, Wei-Hung Weng, Alexander Daryin, Tao Tu, Petar Sirkovic, Artiom Myaskovsky, Grzegorz Glowaty, et al. “Accelerating Scientific Discovery with Co-Scientist.” Nature 655 (2026): 487–96. https://doi.org/10.1038/s41586-026-10644-y.

Guevara, Alfredo, Alexandru Lupsasca, David Skinner, Andrew Strominger, and Kevin Weil. “Single-Minus Gluon Tree Amplitudes Are Nonzero.” Preprint, arXiv, 2026. https://doi.org/10.48550/arXiv.2602.12176.

Ju, Haocheng, Guoxiong Gao, Jiedong Jiang, Bin Wu, Zeming Sun, Shurui Liu, Leheng Chen, et al. “Automated Conjecture Resolution with Formal Verification.” Preprint, arXiv, 2026. https://doi.org/10.48550/arXiv.2604.03789.

Jumper, John, Richard Evans, Alexander Pritzel, Tim Green, Michael Figurnov, Olaf Ronneberger, Kathryn Tunyasuvunakool, et al. “Highly Accurate Protein Structure Prediction with AlphaFold.” Nature 596 (2021): 583–89. https://doi.org/10.1038/s41586-021-03819-2.

Kantrowitz, Alex. “Google DeepMind CEO Demis Hassabis: AI’s Next Breakthroughs, AGI Timeline, Google’s AI Glasses Bet.” Big Technology Podcast. YouTube video, premiered January 23, 2026. https://www.youtube.com/watch?v=bgBfobN2A7A.

Ke, Zixuan, Fangkai Jiao, Yifei Ming, Xuan-Phi Nguyen, Austin Xu, Do Xuan Long, Minzhi Li, et al. “A Survey of Frontiers in LLM Reasoning: Inference Scaling, Learning to Reason, and Agentic Systems.” Preprint, arXiv, 2025. https://doi.org/10.48550/arXiv.2504.09037.

Knuth, Donald E. “Claude’s Cycles.” Manuscript, February 28, 2026; revised April 14, 2026. Accessed June 11, 2026. https://www-cs-faculty.stanford.edu/~knuth/papers/claude-cycles.pdf.

Ko, Kuang-Ting, Frank Lennartz, David Mekhaiel, Bora Guloglu, Arianna Marini, Danielle J. Deuker, Carole A. Long, et al. “Structure of the Malaria Vaccine Candidate Pfs48/45 and Its Recognition by Transmission Blocking Antibodies.” Nature Communications 13, no. 1 (2022): 5603. https://doi.org/10.1038/s41467-022-33379-6.

Kwa, Thomas, Ben West, Joel Becker, Amy Deng, Katharyn Garcia, Max Hasin, Sami Jawhar, et al. “Measuring AI Ability to Complete Long Tasks.” Preprint, arXiv, 2025. https://doi.org/10.48550/arXiv.2503.14499.

Langley, Pat, Herbert A. Simon, and Gary L. Bradshaw. “Heuristics for Empirical Discovery.” In Computational Models of Learning, edited by Leonard Bolc, 21–54. Berlin and Heidelberg: Springer-Verlag, 1987. https://doi.org/10.1007/978-3-642-82742-6_2.

Lee, Seungpil, Woochang Sim, Donghyeon Shin, Wongyu Seo, Jiwon Park, Seokki Lee, Sanha Hwang, Sejin Kim, and Sundong Kim. “Reasoning Abilities of Large Language Models: In-Depth Analysis on the Abstraction and Reasoning Corpus.” ACM Transactions on Intelligent Systems and Technology 16, no. 6 (2025): Article 137, 1–52. https://doi.org/10.1145/3712701.

Liang, Weixin, Yaohui Zhang, Zhengxuan Wu, Haley Lepp, Wenlong Ji, Xuandong Zhao, Hancheng Cao, et al. “Quantifying Large Language Model Usage in Scientific Papers.” Nature Human Behaviour 9 (2025): 2599–609. https://doi.org/10.1038/s41562-025-02273-8.

Liu, Hung Ming. “AI Mother Tongue: Self-Emergent Communication in MARL via Endogenous Symbol Systems.” Preprint, arXiv, 2025. https://doi.org/10.48550/arXiv.2507.10566.

Lowe, Derek. “Evaluating ‘Co-Scientist,’ a New AI Science System.” In the Pipeline. Science. Article published May 27, 2026. https://www.science.org/content/blog-post/evaluating-co-scientist-new-ai-science-system.

Lu, Chris, Cong Lu, Robert Tjarko Lange, Jakob Foerster, Jeff Clune, and David Ha. “The AI Scientist: Towards Fully Automated Open-Ended Scientific Discovery.” Preprint, arXiv, 2024. https://doi.org/10.48550/arXiv.2408.06292.

Lu, Chris, Cong Lu, Robert Tjarko Lange, Yutaro Yamada, Shengran Hu, Jakob Foerster, David Ha, and Jeff Clune. “Towards End-to-End Automation of AI Research.” Nature 651 (2026): 914–19. https://doi.org/10.1038/s41586-026-10265-5.

National Academies of Sciences, Engineering, and Medicine. The Age of AI in the Life Sciences: Benefits and Biosecurity Considerations. Washington, DC: National Academies Press, 2025. https://doi.org/10.17226/28868.

Nature. “Search.” Accessed June 11, 2026. https://www.nature.com/search.

Novikov, Alexander, Ngân Vũ, Marvin Eisenberger, Emilien Dupont, Po-Sen Huang, Adam Zsolt Wagner, Sergey Shirobokov, et al. “AlphaEvolve: A Coding Agent for Scientific and Algorithmic Discovery.” Preprint, arXiv, 2025. https://doi.org/10.48550/arXiv.2506.13131.

OpenAI. “An OpenAI Model Has Disproved a Central Conjecture in Discrete Geometry.” Article published May 20, 2026. Accessed June 11, 2026. https://openai.com/index/model-disproves-discrete-geometry-conjecture/.

Ramji, Keshav, Tahira Naseem, and Ramón Fernandez Astudillo. “Thinking Without Words: Efficient Latent Reasoning with Abstract Chain-of-Thought.” Preprint, arXiv, 2026. https://doi.org/10.48550/arXiv.2604.22709.

Romera-Paredes, Bernardino, Mohammadamin Barekatain, Alexander Novikov, Matej Balog, M. Pawan Kumar, Emilien Dupont, Francisco J. R. Ruiz, et al. “Mathematical Discoveries from Program Search with Large Language Models.” Nature 625 (2024): 468–75. https://doi.org/10.1038/s41586-023-06924-6.

Sajadieh, Sha, Loredana Fattorini, Raymond Perrault, Yolanda Gil, Vanessa Parli, Lapo Santarlasci, Juan Pava, et al. The AI Index 2026 Annual Report. Stanford, CA: AI Index Steering Committee, Institute for Human-Centered AI, Stanford University, 2026. https://hai.stanford.edu/assets/files/ai_index_report_2026.pdf.

Salvi, Francesco, Manoel Horta Ribeiro, Riccardo Gallotti, and Robert West. “On the Conversational Persuasiveness of GPT-4.” Nature Human Behaviour 9 (2025): 1645–53. https://doi.org/10.1038/s41562-025-02194-6.

Samadder, N. Jewel, Gautam Mankaney, Jessica Stout, Reid Ness, Ziad Younes, Harinath Sheela, Bryson W. Katona, et al. “Ongoing Phase 1b/2 Trial of the Allosteric MEK1/2 Inhibitor REC-4881 as Monotherapy in Familial Adenomatous Polyposis (FAP): Preliminary Safety and Efficacy Data.” Presentation at Digestive Disease Week 2025, San Diego, May 4, 2025. Recursion Pharmaceuticals. https://ir.recursion.com/static-files/cef86a12-64aa-4ff9-9074-2f81fb3efd17.

Schmidhuber, Jürgen. “Gödel Machines: Fully Self-Referential Optimal Universal Self-Improvers.” In Artificial General Intelligence, edited by Ben Goertzel and Cassio Pennachin, 199–226. Berlin and Heidelberg: Springer, 2007. https://doi.org/10.1007/978-3-540-68677-4_7.

Schoenegger, Philipp, Spencer Greenberg, Alexander Grishin, Joshua Lewis, and Lucius Caviola. “AI Can Outperform Humans in Predicting Correlations Between Personality Items.” Communications Psychology 3 (2025): 23. https://doi.org/10.1038/s44271-025-00205-w.

Science Friday. “How AlphaFold Has Changed Biology Research, 5 Years On.” YouTube video, November 18, 2025. Accessed June 11, 2026. https://www.youtube.com/watch?v=n1rr36vHG8A.

Soares, Eduardo, Emilio Vital Brazil, Victor Shirasuna, Dmitry Zubarev, Renato Cerqueira, and Kristin Schmidt. “An Open-Source Family of Large Encoder-Decoder Foundation Models for Chemistry.” Communications Chemistry 8 (2025): 193. https://doi.org/10.1038/s42004-025-01585-0.

Song, Tao, Man Luo, Xiaolong Zhang, Linjiang Chen, Yan Huang, Jiaqi Cao, Qing Zhu, et al. “A Multiagent-Driven Robotic AI Chemist Enabling Autonomous Chemical Research on Demand.” Journal of the American Chemical Society 147, no. 15 (2025): 12534–45. https://doi.org/10.1021/jacs.4c17738.

Song, Zhangde, Jieyu Lu, Yuanqi Du, Botao Yu, Thomas M. Pruyn, Yue Huang, Kehan Guo, et al. “Evaluating Large Language Models in Scientific Discovery.” Preprint, arXiv, version 2, 2026. https://arxiv.org/abs/2512.15567v2.

Stokel-Walker, Chris. “Scientists Invented a Fake Disease. AI Told People It Was Real.” Nature 652 (2026): 559–61. https://doi.org/10.1038/d41586-026-01100-y.

Strachan, James W. A., Dalila Albergo, Giulia Borghini, Oriana Pansardi, Eugenio Scaliti, Saurabh Gupta, Krati Saxena, et al. “Testing Theory of Mind in Large Language Models and Humans.” Nature Human Behaviour 8 (2024): 1285–95. https://doi.org/10.1038/s41562-024-01882-z.

Topaz, Maxim, Nir Roguin, Pallavi Gupta, Zhihong Zhang, and Laura-Maria Peltonen. “Fabricated Citations: An Audit across 2.5 Million Biomedical Papers.” The Lancet 407, no. 10541 (2026): 1779–81. https://doi.org/10.1016/S0140-6736(26)00603-3.

Tsoukalas, George, Anton Kovsharov, Sergey Shirobokov, Anja Surina, Moritz Firsching, Gergely Bérczi, Francisco J. R. Ruiz, et al. “Advancing Mathematics Research with AI-Driven Formal Proof Search.” Preprint, arXiv, 2026. https://doi.org/10.48550/arXiv.2605.22763.

UK AI Security Institute. “Our Evaluation of Claude Mythos Preview’s Cyber Capabilities.” Article published April 13, 2026. https://www.aisi.gov.uk/blog/our-evaluation-of-claude-mythos-previews-cyber-capabilities.

Uren, Tom. “Mythos Fallout, U.S. Government Weighs AI Model Regulation.” Lawfare. Article published May 8, 2026. https://www.lawfaremedia.org/article/mythos-fallout--u.s.-government-weighs-ai-model-regulation.

Wenkel, Frederik, Wilson Tu, Cassandra Masschelein, Hamed Shirzad, Liam Hodgson, Ihab Bendidi, Cian Eastwood, et al. “TxPert: Using Multiple Knowledge Graphs for Prediction of Transcriptomic Perturbation Effects.” Nature Biotechnology (2026). https://doi.org/10.1038/s41587-026-03113-4.

Wiesner, Florian, Zoë J. Gray, Matthias Wessling, and Stephen Baek. “Towards a Physics Foundation Model.” Preprint, arXiv, 2025. https://doi.org/10.48550/arXiv.2509.13805.

Creative Commons License

This work is licensed under a Creative Commons Attribution 4.0 International License.

Copyright (c) 2026 Petr O. Jedlička

Downloads

Download data is not yet available.