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Assembly theory

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For the communication theory about social interactions, see action assembly theory.
Synthesis of aristolochic acid. Complex molecules require many steps to be synthesized. And the more steps are required to synthesize a particular molecule, the more likely it is of a biological (or technological) origin.

Assembly theory is the name of a hypothesis that proposes to quantify selection and evolution by counting the abundance of repeated identical blocks in an object.

Background

The hypothesis was proposed by chemist Leroy Cronin in 2017 and developed by the team he leads at the University of Glasgow, then extended in collaboration with a team at Arizona State University led by astrobiologist Sara Imari Walker, in a paper released in 2021.

According to the authors, Assembly Theory conceptualizes objects not as point particles, but as entities defined by their possible formation histories. This allows objects to show evidence of selection, within well-defined boundaries of individuals or selected units. The 'assembly index' is the number of steps on a minimal path producing the object. The assembly is defined as "the total amount of selection necessary to produce an ensemble of observed objects"; for an ensemble containing N T {\displaystyle N_{T}} objects in total, N {\displaystyle N} of which are unique, the assembly A {\displaystyle A} is defined to be

A = ∑ i = 1 N ⁡ e a i ( n i − 1 N T ) {\displaystyle A=\mathop {\sum } \limits _{i=1}^{N}{e}^{{a}_{i}}\left({\frac {{n}_{i}-1}{{N}_{\rm {T}}}}\right)} ,

where objects of type i {\displaystyle i} occur n i {\displaystyle n_{i}} times and have assembly index a i {\displaystyle a_{i}} .

For example, the word 'abracadabra' contains 5 unique letters (a, b, c, d and r) and is 11 symbols long. It can be assembled from its constituents as a + b --> ab + r --> abr + a --> abra + c --> abrac + a --> abraca + d --> abracad + abra --> abracadabra, because 'abra' was already constructed at an earlier stage. Because this requires at least 7 steps, the assembly index is 7. The word ‘abracadrbaa’, of the same length, for example, has no repeats so has an assembly index of 10.

Take two binary strings C = [ 01010101 ] {\displaystyle C=} and D = [ 00010111 ] {\displaystyle D=} as another example. Both have the same length N = 8 {\displaystyle N=8} bits, both have the same Hamming weight N 1 = N / 2 = 4 {\displaystyle N_{1}=N/2=4} . However, the assembly index of the first string is a ( C ) = 3 {\displaystyle a(C)=3} ("01" is assembled, joined with itself into "0101", and joined again with "0101" taken from the assembly pool), while the assembly index of the second string is a ( D ) = 6 {\displaystyle a(D)=6} , since in this case only "01" can be taken from the assembly pool.

In general, for K subunits of an object O the assembly index is bounded by log 2 ⁡ ( K ) ≤ a O ≤ K − 1 {\displaystyle \log _{2}(K)\leq a_{O}\leq K-1} .

While other approaches can provide a measure of complexity, the researchers claim that assembly theory's molecular assembly number is the first to be measurable experimentally. Molecules with a high assembly index are very unlikely to form abiotically, and the probability of abiotic formation goes down as the value of the assembly index increases. The assembly index of a molecule can be obtained directly via spectroscopic methods. This method could be implemented in a fragmentation tandem mass spectrometry instrument to search for biosignatures.

The theory was extended to map chemical space with molecular assembly trees, demonstrating the application of this approach in drug discovery.

It is difficult to identify chemical signatures that are unique to life. For example, the Viking lander biological experiments detected molecules that could be explained by either living or natural non-living processes. It appears that only living samples can produce assembly index measurements above ~15. However, another paper demonstrated that abiotic chemical processes could form highly complex crystal structures whose assembly indices exceed this threshold. Authors conclude that "while the proposal of a biosignature based on a molecular assembly index of 15 is an intriguing and testable concept, the contention that only life can generate molecular structures with MA index ≥ 15 is in error".

Critical views

Steven A. Benner, a former Professor from Harvard, has publicly criticized various aspects of Assembly Theory. Benner argues that it is transparently false that non-living systems, and with no life intervention, cannot contain molecules that are complex but people would be misled in thinking that because it was published in Nature journals after peer review, these papers must be right.

A paper published in the Journal of Molecular Evolution refers to Hector Zenil's blog post "that identifies no less than eight fallacies of assembly theory". The paper also refers to the video essay by the same author staying "that summarizes these fallacies, and highlights conceptual/methodological limitations, and the pervasive failure by the proponents of assembly theory to acknowledge relevant previous work in the field of complexity science". The paper concludes that "the hype around Assembly Theory reflects rather unfavorably both on the authors and the scientific publication system in general". The author concludes that what "assembly theory really does is to detect and quantify bias caused by higher-level constraints in some well-defined rule-based worlds"; one "can use assembly theory to check whether something unexpected is going on in a very broad range of computational model worlds or universes".

The group led by Hector Zenil, a former Senior researcher and faculty member from Oxford and Cambridge and currently an Associate Professor in Biomedical Engineering from King's College London, is cited to have reproduced the results of Assembly Theory with traditional statistical algorithms.

Another paper authored by a group of chemists and planetary scientists, including an author affiliated with NASA, published in the journal of the Royal Society Interface demonstrated that abiotic chemical processes have the potential to form crystal structures of great complexity — values exceeding the proposed abiotic/biotic divide of MA index = 15. They conclude that "while the proposal of a biosignature based on a molecular assembly index of 15 is an intriguing and testable concept, the contention that only life can generate molecular structures with MA index ≥ 15 is in error".

The paper also cites the papers and posts of Hector Zenil as questioning whether a single scalar value like the assembly index can be employed to adequately discriminate between living and nonliving systems, and pointing out the noticeable similarities of the Assembly Theory approach to uncited prior efforts to distinguish biotic from abiotic molecular compounds.

In particular, the paper mentions that Zenil and colleagues "may also have anticipated key conclusions of Assembly Theory by exploring connections among causal memory, selection, and evolution".

See also

References

  1. ^ Marshall SM, Mathis C, Carrick E, et al. (24 May 2021). "Identifying molecules as biosignatures with assembly theory and mass spectrometry". Nature Communications. 12 (3033): 3033. Bibcode:2021NatCo..12.3033M. doi:10.1038/s41467-021-23258-x. PMC 8144626. PMID 34031398.
  2. ^ Liu, Yu; Mathis, Cole; Bajczyk, Michał Dariusz; Marshall, Stuart M.; Wilbraham, Liam; Cronin, Leroy (2021). "Exploring and mapping chemical space with molecular assembly trees". Science Advances. 7 (39): eabj2465. Bibcode:2021SciA....7J2465L. doi:10.1126/sciadv.abj2465. PMC 8462901. PMID 34559562.
  3. ^ Marshall, Stuart M.; Murray, Alastair R. G.; Cronin, Leroy (2017). "A probabilistic framework for identifying biosignatures using Pathway Complexity". Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. 375 (2109). arXiv:1705.03460. Bibcode:2017RSPTA.37560342M. doi:10.1098/rsta.2016.0342. PMC 5686400. PMID 29133442.
  4. Sara Imari Walker; Leroy Cronin; Alexa Drew; Shawn Domagal-Goldman; Theresa Fisher; Michael Line; Camerian Millsaps (7 April 2019). "Probabilistic Biosignature Frameworks". In Victoria Meadows; Giada Arney; Britney Schmidt; David J. Des Marais (eds.). Planetary Astrobiology. doi:10.2458/azu_uapress_9780816540068-ch018.
  5. ^ Sharma, Abhishek; Czégel, Dániel; Lachmann, Michael; Kempes, Christopher P.; Walker, Sara I.; Cronin, Leroy (October 2023). "Assembly theory explains and quantifies selection and evolution". Nature. 622 (7982): 321–328. Bibcode:2023Natur.622..321S. doi:10.1038/s41586-023-06600-9. ISSN 1476-4687. PMC 10567559.
  6. Mathis, Cole; Y. Patarroyo, Keith; Cronin, Lee. "Understanding Assembly Indices". Molecular Assembly. Cronin Group. Retrieved 26 March 2024. resulting in an Assembly Index of 7
  7. Schwieterman, Edward W.; Kiang, Nancy Y.; Parenteau, Mary N.; Harman, Chester E.; Dassarma, Shiladitya; Fisher, Theresa M.; Arney, Giada N.; Hartnett, Hilairy E.; Reinhard, Christopher T.; Olson, Stephanie L.; Meadows, Victoria S.; Cockell, Charles S.; Walker, Sara I.; Grenfell, John Lee; Hegde, Siddharth; Rugheimer, Sarah; Hu, Renyu; Lyons, Timothy W. (2018). "Exoplanet Biosignatures: A Review of Remotely Detectable Signs of Life". Astrobiology. 18 (6): 663–708. arXiv:1705.05791. Bibcode:2018AsBio..18..663S. doi:10.1089/ast.2017.1729. PMC 6016574. PMID 29727196.
  8. Plaxco KW, Gross M (12 August 2011). Astrobiology: A Brief Introduction. JHU Press. pp. 285–286. ISBN 978-1-4214-0194-2. Retrieved 16 July 2013.
  9. ^ Hazen, Robert M.; Burns, Peter C.; Cleaves II, H. James; Downs, Robert T.; Krivovichev, Sergey V.; Wong, Michael L. (2024). "Molecular assembly indices of mineral heteropolyanions: some abiotic molecules are as complex as large biomolecules". Journal of the Royal Society Interface. 21 (211). doi:10.1098/rsif.2023.0632. PMC 10878807. This article incorporates text from this source, which is available under the CC BY 4.0 license.
  10. Benner, Steven A. "Assembly Theory and Agnostic Life Finding – The Primordial Scoop". Retrieved 19 September 2023.
  11. ^ Jaeger, Johannes (2024). "Assembly Theory: What It Does and What It Does Not Do". Journal of Molecular Evolution. doi:10.1007/s00239-024-10163-2. PMC 10978598.
  12. Zenil, Hector. "The 8 Fallacies of Assembly Theory – Medium". Retrieved 26 September 2023.
  13. "Lee Cronin's Assembly Theory Disputed & Debunked by Dr. Hector Zenil - YouTube". YouTube. January 2024. Retrieved 13 March 2024.
  14. "Dr Hector Zenil". Retrieved 17 March 2024.
  15. Uthamacumaran, Abicumaran; Abrahão, Felipe S.; Kiani, Narsis; Zenil, Hector (2022). "On the Salient Limitations of the Methods of Assembly Theory and their Classification of Molecular Biosignatures". arXiv. arXiv:2210.00901.
  16. Hazen, Robert M.; Burns, Peter C.; Cleaves II, H. James; Downs, Robert T.; Krivovichev, Sergey V.; Wong, Michael L. (2024). "Molecular assembly indices of mineral heteropolyanions: some abiotic molecules are as complex as large biomolecules". Journal of the Royal Society Interface. 21 (211). doi:10.1098/rsif.2023.0632. PMC 10878807.
  17. Zenil, Hector. "The 8 Fallacies of Assembly Theory – Medium". Retrieved 26 September 2023.
  18. Zenil, Hector; Kiani, Narsis A.; Shang, M-M; Tegnér, Jesper (2018). "Algorithmic complexity and reprogrammability of chemical structure networks". Parallel Processing Letters. 28 (1850005). arXiv:1802.05856. doi:10.1142/S0129626418500056.
  19. Hernández-Orozco, Santiago; Kiani, Narsis A.; Zenil, Hector (2018). "Algorithmically probable mutations reproduce aspects of evolution, such as convergence rate, genetic memory and modularity". Royal Society Open Science. 5 (8). arXiv:1709.00268. doi:10.1098/rsos.180399.
  20. Hazen, Robert M.; Burns, Peter C.; Cleaves II, H. James; Downs, Robert T.; Krivovichev, Sergey V.; Wong, Michael L. (2024). "Molecular assembly indices of mineral heteropolyanions: some abiotic molecules are as complex as large biomolecules". Journal of the Royal Society Interface. 21 (211). doi:10.1098/rsif.2023.0632. PMC 10878807.

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