Assembly Theory Research Articles

Predicting the first steps of evolution in randomly assembled communities

Microbial communities can self-assemble into highly diverse states with predictable statistical properties. However, these initial states can be disrupted by rapid evolution of the resident strains. When a new mutation arises, it competes for resources with its parent strain and with the other species in the community. This interplay between ecology and evolution is difficult to capture with existing community assembly theory. Here, we introduce a mathematical framework for predicting the first steps of evolution in large randomly assembled communities that compete for substitutable resources. We show how the fitness effects of new mutations and the probability that they coexist with their parent depends on the size of the community, the saturation of its niches, and the metabolic overlap between its members. We find that successful mutations are often able to coexist with their parent strains, even in saturated communities with low niche availability. At the same time, these invading mutants often cause extinctions of metabolically distant species. Our results suggest that even small amounts of evolution can produce distinct genetic signatures in natural microbial communities.

Assembly Theory is an approximation to algorithmic complexity based on LZ compression that does not explain selection or evolution

We formally prove the equivalence between Assembly Theory (AT) and Shannon Entropy via a method based upon the principles of statistical compression that belongs to the LZ family of popular compression algorithms. Such popular lossless compression algorithms behind file formats such as ZIP and PNG have been shown to empirically reproduce the results that AT considers its cornerstone. The same results have also been reported before AT in successful application of other complexity measures in the areas covered by AT such as separating organic from non-organic molecules and in the context of the study of selection and evolution. We demonstrate that the assembly index is equivalent to the size of a minimal context-free grammar. The statistical compressibility of such a method is bounded by Shannon Entropy and other equivalent traditional LZ compression schemes, such as LZ77 and LZW. We also demonstrate that AT, and the algorithms supporting its pathway complexity, assembly index, and assembly number, define compression schemes and methods that are subsumed into algorithmic information theory. We conclude that the assembly index and the assembly number do not lead to an explanation or quantification of biases in generative (physical or biological) processes, including those brought about by (abiotic or biotic) selection and evolution, that could not have been arrived at using Shannon Entropy, or that have not been already reported before using classical information theory or algorithmic complexity.

Autocatalytic Sets and Assembly Theory: A Toy Model Perspective.

Assembly Theory provides a promising framework to explain the complexity of systems such as molecular structures and the origins of life, with broad applicability across various disciplines. In this study, we explore and consolidate different aspects of Assembly Theory by introducing a simplified Toy Model to simulate the autocatalytic formation of complex structures. This model abstracts the molecular formation process, focusing on the probabilistic control of catalysis rather than the intricate interactions found in organic chemistry. We establish a connection between probabilistic catalysis events and key principles of Assembly Theory, particularly the probability of a possible construction path in the formation of a complex object, and examine how the assembly of complex objects is impacted by the presence of autocatalysis. Our findings suggest that this presence of autocatalysis tends to favor longer consecutive construction sequences in environments with a low probability of catalysis, while this bias diminishes in environments with higher catalysis probabilities, highlighting the significant influence of environmental factors on the assembly of complex structures.

“Activism is not a one-lane highway”: the digital modalities of Alliance for Choice and abortion decriminalisation

ABSTRACT In 2019, abortion was decriminalised in Northern Ireland (NI) after decades of campaigning against the almost-total ban. Abortion activists in NI used multiple tools for change, utilising a feminist law-making strategy that also encompassed ‘cheeky’ witnessing [Fletcher, R. (2020). Cheeky witnessing. Feminist Review, 124(1), 124–141. https://doi.org/10.1177/0141778919896342] and movement-building alongside mutual-aid approaches to care. This paper outlines the significant contribution of alternative creative modes of dialogue from the insider perspective of core Alliance for Choice activists. The key element of the campaign towards decriminalisation in NI, was inspired and influenced by the global networks of abortion campaigns also utilising digital networks to challenge problematic abortion discourse with an abundance of creative content. It also required daily visual online output that complimented and coalesced the wider campaign, in a digital space that [Butler, J. (2018). Notes toward a performative theory of assembly. Harvard University Press] contends is a version of the public street. This paper offers a unique insight into the creative production and careful navigation required for campaigning towards decriminalisation in the NI. It examines the complexity of the digital space and its challenges and opportunities for abortion activists. It offers lessons for other campaigns against abortion restrictions and other social justice movements.

Predicting the First Steps of Evolution in Randomly Assembled Communities.

Microbial communities can self-assemble into highly diverse states with predictable statistical properties. However, these initial states can be disrupted by rapid evolution of the resident strains. When a new mutation arises, it competes for resources with its parent strain and with the other species in the community. This interplay between ecology and evolution is difficult to capture with existing community assembly theory. Here, we introduce a mathematical framework for predicting the first steps of evolution in large randomly assembled communities that compete for substitutable resources. We show how the fitness effects of new mutations and the probability that they coexist with their parent depends on the size of the community, the saturation of its niches, and the metabolic overlap between its members. We find that successful mutations are often able to coexist with their parent strains, even in saturated communities with low niche availability. At the same time, these invading mutants often cause extinctions of metabolically distant species. Our results suggest that even small amounts of evolution can produce distinct genetic signatures in natural microbial communities.

Assembly Theory of Binary Messages

Using assembly theory, we investigate the assembly pathways of binary strings (bitstrings) of length N formed by joining bits present in the assembly pool and the bitstrings that entered the pool as a result of previous joining operations. We show that the bitstring assembly index is bounded from below by the shortest addition chain for N, and we conjecture about the form of the upper bound. We define the degree of causation for the minimum assembly index and show that, for certain N values, it has regularities that can be used to determine the length of the shortest addition chain for N. We show that a bitstring with the smallest assembly index for N can be assembled via a binary program of a length equal to this index if the length of this bitstring is expressible as a product of Fibonacci numbers. Knowing that the problem of determining the assembly index is at least NP-complete, we conjecture that this problem is NP-complete, while the problem of creating the bitstring so that it would have a predetermined largest assembly index is NP-hard. The proof of this conjecture would imply P ≠ NP since every computable problem and every computable solution can be encoded as a finite bitstring. The lower bound on the bitstring assembly index implies a creative path and an optimization path of the evolution of information, where only the latter is available to Turing machines (artificial intelligence). Furthermore, the upper bound hints at the role of dissipative structures and collective, in particular human, intelligence in this evolution.

Minimizing Entropy and Complexity in Creative Production from Emergent Pragmatics to Action Semantics.

New insights into intractable industrial challenges can be revealed by framing them in terms of natural science. One intractable industrial challenge is that creative production can be much more financially expensive and time consuming than standardized production. Creative products include a wide range of goods that have one or more original characteristics. The scaling up of creative production is hindered by high financial production costs and long production durations. In this paper, creative production is framed in terms of interactions between entropy and complexity during progressions from emergent pragmatics to action semantics. An analysis of interactions between entropy and complexity is provided that relates established practice in creative production to organizational survival in changing environments. The analysis in this paper is related to assembly theory, which is a recent theoretical development in natural science that addresses how open-ended generation of complex physical objects can emerge from selection in biology. Parallels between assembly practice in industrial production and assembly theory in natural science are explained through constructs that are common to both, such as assembly index. Overall, analyses reported in the paper reveal that interactions between entropy and complexity underlie intractable challenges in creative production, from the production of individual products to the survival of companies.

Investigating and Quantifying Molecular Complexity Using Assembly Theory and Spectroscopy

Investigating and Quantifying Molecular Complexity Using Assembly Theory and Spectroscopy

Say Nope to the Pope: performance and resistance in the creative interventions during the 2018 papal visit to Ireland

ABSTRACT In September 1979, the newly elected head of the Catholic Church, Pope John Paul II, made a historic pastoral visit to Ireland where he celebrated an open-air mass in Dublin’s Phoenix Park to an estimated 1,250,000 people, a third of the country’s population. In August 2018, Pope Francis returned to Ireland, though the second papal visit was met with a series of protests and a lower-than-expected turn-out at the public mass in Phoenix Park. In the intervening years Ireland underwent broad social changes and the credibility of the Catholic Church, once the bedrock of morality in Ireland, was eroded by scandals revealing the depths of clerical sex abuse and abuse in Catholic-run institutions. This article considers the creative protests and interventionist actions that marked the 2018 Papal visit, using Judith Butler’s Notes Toward A Performative Theory of Assembly (2015) to think through these public actions. Focusing specifically on Say Nope to the Pope and the associated events of Stand 4 Truth, it explores these public performances of protest grounded in solidarity and resistance.

A Theory of Assembly: From Museums to Memes by Kyle Parry (review)

A Theory of Assembly: From Museums to Memes by Kyle Parry (review)

Pelatihan Kemampuan Komunikasi Oleh Mahasiswa Ibm Bekasi Di Masa Pandemi Dalam Perspektif Teori Action Assembly (Studi Fenomenologi Pada Karang Taruna)

This research has a problem formulation about, How is the communication skills training by IBM Bekasi students in the Covid 19 period, in the perspective of the Action Assembly theory (Phenomenology Study on Youth Organization). In the perspective of assembly action theory. This research uses a qualitative approach. Likewise, the research methods are both qualitative in nature. Data collection is obtained through observation and in-depth interviews with key informants, while informant data is obtained through literature study from sources such as photo documentation, printed media, journals, and others. The results of the study, in factual conditions, phenomenology regarding training designed by IBM Bekasi students, has been processing assertion messages, by (1) students describing the existing conditions as they are, (2) expressing the intent and purpose of working together with youth organizations to empower youth with communication skills training. (3) expressed a desire for an appropriate and beneficial training time for Karang Taruna, IBM Bekasi Students, and the local community.

Molecular assembly indices of mineral heteropolyanions: some abiotic molecules are as complex as large biomolecules.

Molecular assembly indices, which measure the number of unique sequential steps theoretically required to construct a three-dimensional molecule from its constituent atomic bonds, have been proposed as potential biosignatures. A central hypothesis of assembly theory is that any molecule with an assembly index ≥15 found in significant local concentrations represents an unambiguous sign of life. We show that abiotic molecule-like heteropolyanions, which assemble in aqueous solution as precursors to some mineral crystals, range in molecular assembly indices from 2 for H2CO3 or Si(OH)4 groups to as large as 21 for the most complex known molecule-like subunits in the rare minerals ewingite and ilmajokite. Therefore, values of molecular assembly indices ≥15 do not represent unambiguous biosignatures.

Mean landscape‐scale incidence of species in discrete habitats is patch size dependent

AbstractAimA pervasive negative relationship between the species richness of an assemblage and the mean global range size of the species it contains has recently been identified. Here, we test for an effect of habitat patch size on the mean landscape‐scale incidence (estimating local range size) of constituent species independent of variation in richness.LocationGlobal.Time PeriodContemporary.Major Taxa StudiedVarious.MethodsWe devised a new standardized patch‐scale metric, Mean Species Landscape‐scale Incidences per Patch (MSLIP). Positive values indicate a patch contains more widespread (high‐incidence) species than expected relative to their frequency in the landscape; negative values indicate the presence of more narrow‐range (low‐incidence) species. For 202 metacommunity datasets (archipelagos, habitat islands and fragments) we regressed MSLIP on patch size, testing four hypotheses: (i) no effect (zero slope), (ii) more widespread species in smaller patches (negative slope), (iii) more narrow‐range species in smaller patches (positive slope), (iv) a composite effect (curvilinear/unimodal).ResultsThere was a generally negative curvilinear relationship between MSLIP and patch size, consistent with smaller and larger patches respectively containing more high‐ and low‐incidence species than expected. At intermediate patch sizes, mean species incidence approximates that of the overall landscape. Relative richness mediated this relationship; species‐rich sites of any size increasingly favoured low‐incidence species, species‐poor sites high‐incidence species. Results were consistent for taxonomic groups, and metacommunity types, except aquatic habitat islands.Main ConclusionsThe dependence of mean species incidence on both patch size and relative richness has implications for biodiversity and community assembly theory, or when seeking to understand ecological processes sensitive to species composition (e.g., ecosystem functioning, trophic web structures). We propose the ‘patch size where the MSLIP regression intersects zero’ as a benchmark distinguishing smaller from larger patches, with the expectation small patches preferentially support more high‐incidence and large patches more low‐incidence species.

Physical solidarity as feeling the feeling

ABSTRACT This provocation reflects on the experience of taking a class in contemporary African dance in Senegal, arguing that it represents a physicalisation of solidarity. The class included dance students from Europe and the African continent who came together through moving rhythmically despite having no common verbal language. Drawing on Sara Ahmed’s proposals about solidarity and Judith Butler’s theory of performative assembly, this intervention argues that the aesthetic underlying these students’ dancing was one that challenged dominant aesthetic values and the power relations underling them to generate solidarity as feeling the feeling of this challenge. This is a short provocation that was prepared for the roundtable discussion on ‘Decolonisation and Solidarity’ as part of the conference, Borderlines IX: Seeking Solidarity and Wonder Through Performance, which took place at De Montfort University in Leicester, UK, on 30 June and 1 July 2022.

Assembly mechanisms of microbial communities in plastisphere related to species taxonomic types and habitat niches

A lot of plastic floats are presented in the kelp cultivation zone, enabling us to effectively evaluate the differences between surface water (SW) and plastic-attached (PA) microbial communities. In this study, we explored the microbial communities (both bacteria and protists) in SW and PA niches during the kelp cultivation activities. Effects of habitat niches on the diversity and composition of microbial communities were found. Beta partitioning and core taxa analyses showed species turnover and local species pool governed the microbial community assembly, and they contributed more to bacteria and protists, respectively. Based on the results of null model, bacterial communities presented a more deterministic and homogeneous assembly compared to protistan communities. Moreover, microbial communities in PA niche had higher species turnover and homogenizing assembly compared to the SW niche. The results of this study supplemented the theory of microbial community assembly and expanded our understanding of protists in plastisphere.

Mechanics of assembling two-dimensional materials on a solid substrate by droplet drying

Assembly of two-dimensional (2D) nanomaterials by droplet drying offers a straightforward and low-cost route to obtain their bulk forms for widespread applications in manufacturing and printing of functional structures and devices. However, unlike rigid nanoparticles that usually do not experience mechanical deformation, 2D nanomaterials are easily deformed and folded during assembly by evaporative drying, and traditional assembly theory that can address these fundamental deformation mechanisms is currently lacking. In the present study, we have developed an energy-based rotational spring-mechanical slider mechanics model to describe the mechanical deformation and assembly of 2D material graphene on a solid substrate during the evaporation of its droplet solution. In the development of theory, the mechanical folding deformation of 2D material graphene itself is modeled by the rotational spring, and the folding-induced interior interactions of graphene itself and its assembly interactions with neighboring ones and solid substrate all due to van der Waal force are modeled by the mechanical sliders. The surface wettability of substrate and the evaporative modes of droplet on substrate including constant contact angle (CCA), constant contact radius (CCR), and their combination are also incorporated into the mechanics model. In parallel, large-scale molecular dynamics (MD) simulations with the development of coarse-grained model of 2D graphene and its virtual force field interaction with liquid is performed and show remarkable agreement with theoretical predictions on both assembly patterns and dimensional sizes. The effect of graphene size and its interaction strength with substrate on assembly is also elucidated. This work uncovers fundamental assembly mechansim of mechanically deformable nanomaterials by solution drying, and also provides immediate application guidance to ink-based printing techniques for manufacturing deformable nanomaterials-enabled devices with controlled patterns on substrates.

Assembly theory explains and quantifies selection and evolution

Scientists have grappled with reconciling biological evolution1,2 with the immutable laws of the Universe defined by physics. These laws underpin life’s origin, evolution and the development of human culture and technology, yet they do not predict the emergence of these phenomena. Evolutionary theory explains why some things exist and others do not through the lens of selection. To comprehend how diverse, open-ended forms can emerge from physics without an inherent design blueprint, a new approach to understanding and quantifying selection is necessary3–5. We present assembly theory (AT) as a framework that does not alter the laws of physics, but redefines the concept of an ‘object’ on which these laws act. AT 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. We introduce a measure called assembly (A), capturing the degree of causation required to produce a given ensemble of objects. This approach enables us to incorporate novelty generation and selection into the physics of complex objects. It explains how these objects can be characterized through a forward dynamical process considering their assembly. By reimagining the concept of matter within assembly spaces, AT provides a powerful interface between physics and biology. It discloses a new aspect of physics emerging at the chemical scale, whereby history and causal contingency influence what exists.

Applying community assembly theory to restoration: overcoming dispersal and abiotic filters is key to diversifying California grassland

Ecologists have explored community assembly through the framework of ecological filters, which predicts that species must overcome a series of challenges (i.e. pass through “filters”) to successfully establish in a given community. In the context of restoration, these filters (dispersal, abiotic, and biotic) can be manipulated to alter the resulting plant community by favoring native species or disadvantaging non‐native invasive species. We conducted two studies manipulating assembly filters at two California grassland sites previously dominated by non‐native species. At Site 1, we explored how variations in sequential seeding of native grasses and forbs (to overcome dispersal and biotic filters caused by priority effects) influenced the resulting community. At Site 2, we explored how thatch removal (to overcome the abiotic filter of light limitation) and herbicide‐based weed control (to overcome the biotic filter of competition from non‐native species) influenced the addition of native forbs into a partially restored grassland. Native forbs at Site 1 did not suffer from arriving after grasses, but native grasses benefited when given 1 year priority over forbs. At Site 2, dethatching increased native forb cover in a high rainfall year. Herbicide application reduced non‐native grass cover in dethatched plots without negatively affecting native cover. Native forb and grass cover were significant predictors of non‐native grass cover. However, they accounted for only 29% of the variation observed, suggesting there are other influential factors not considered in this study. Our results suggest that forbs can be incorporated into established native grasslands more successfully after dethatching.

Together in the future wilderness: CAConrad’s queer appearances

In the performance and written work of trans nonbinary poet CAConrad, queerness is explicitly a practice of anticipatory relation through which we must not only dream but also begin to enact better possible futures in common with the world’s living and nonliving others. Reading works from Conrad’s Ecodeviance: (Soma)tics for the Future Wilderness (2014), this article argues that the poet’s performative conjunction of queerness, ecological consciousness and anti-war activism at the shareable sites of the body and the poem aligns with, and even exceeds, Judith Butler’s call for an extension of the political order or realm of appearance beyond the representational order as conceived by Hannah Arendt. I show how Conrad’s practice critically distinguishes queer visibility from queer appearance, insisting that a liveable future demands and deserves the oppositional relation made possible by bodies appearing queerly together, over against visibility’s complicity with the status quo. If Butler works ‘toward a performative theory of assembly’ (emphasis added), trying to theorize the body as not merely a ‘sign’ of vulnerability or injury but as politically potent in itself, I suggest that Conrad is already leading the way with their provocative, alliance-oriented experiments in both public and print.

Relaxational dynamics of the T-number conversion of virus capsids.

We extend a recently proposed kinetic theory of virus capsid assembly based on Model A kinetics and study the dynamics of the interconversion of virus capsids of different sizes triggered by a quench, that is, by sudden changes in the solution conditions. The work is inspired by in vitro experiments on functionalized coat proteins of the plant virus cowpea chlorotic mottle virus, which undergo a reversible transition between two different shell sizes (T = 1 and T = 3) upon changing the acidity and salinity of the solution. We find that the relaxation dynamics are governed by two time scales that, in almost all cases, can be identified as two distinct processes. Initially, the monomers and one of the two types of capsids respond to the quench. Subsequently, the monomer concentration remains essentially constant, and the conversion between the two capsid species completes. In the intermediate stages, a long-lived metastable steady state may present itself, where the thermodynamically less stable species predominate. We conclude that a Model A based relaxational model can reasonably describe the early and intermediate stages of the conversion experiments. However, it fails to provide a good representation of the time evolution of the state of assembly of the coat proteins in the very late stages of equilibration when one of the two species disappears from the solution. It appears that explicitly incorporating the nucleation barriers to assembly and disassembly is crucial for an accurate description of the experimental findings, at least under conditions where these barriers are sufficiently large.