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arXiv:2210.00901cs.IT

On the Salient Limitations of the Methods of Assembly Theory and their Classification of Molecular Biosignatures

Abicumaran Uthamacumaran, Felipe S. Abrahão, Narsis A. Kiani, Hector Zenil

Abstract

We demonstrate that the assembly pathway method underlying assembly theory (AT) is an encoding scheme widely used by popular statistical compression algorithms. We show that in all cases (synthetic or natural) AT performs similarly to other simple coding schemes and underperforms compared to system-related indexes based upon algorithmic probability that take into account statistical repetitions but also the likelihood of other computable patterns. Our results imply that the assembly index does not offer substantial improvements over existing methods, including traditional statistical ones, and imply that the separation between living and non-living compounds following these methods has been reported before.

arXiv comments
Journal reference
npj Systems Biology and Applications, volume 10, number 82, year 2024
DOI
doi:10.1038/s41540-024-00403-y
Subjects
cs.ITInformation Theory

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Linked by 3 identifiable commenters in 4 comments across 3 threads, from May 2023 to Oct 2023.

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Discussed in comments3 threads

  1. How purposeless physics underlies purposeful life 1 comment

    • Please, be mindful of the criticisms to Assembly Theory too: https://arxiv.org/abs/2210.00901, https://hectorzenil.medium.com/the-8-fallacies-of-assembly-t..., https://primordialscoop.org/2023/03/24/assembly-theory-and-a...

      JIsalazarView on HNParent context

  2. Assembly theory explains and quantifies selection and evolution 1 comment

    • Yes. But it seems perhaps they haven't even done those things correctly. The project seems to have a slight case of Wolframesque overreach https://arxiv.org/abs/2210.00901 The 8 Fallacies of Assembly Theory https://hectorzenil.medium.com/test-8f0be54817c4

      goodmachineView on HNParent context

  3. A New Theory for the Assembly of Life in the Universe 2 comments

    • Fascinating stuff. However: annihilating critique here "What they have proposed is a limited special case of an RLE-Huffman coding algorithm, which means their paper introduces a simpler version of what was already considered one of the simplest coding algorithms in computer…

      goodmachineView on HNParent context

    • > https://arxiv.org/abs/2210.00901 Granted, I'm not very familiar with the math behind things like compression and I skimmed a few sections, but this seems to be a criticism of the authors' methods and not the general idea. They show that there are other ways to produce these…

      cowboysauceView on HNParent context

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