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Published work

15 published item(s)

preprint2026arXiv

Language Game: Talking to Non-Human Systems

Language carries thought and coordination among humans but rarely reaches further along the spectrum of diverse intelligence. Yet non-neural systems -- from gene regulatory networks and microbial consortia to fungi -- are increasingly recognized as substrates of computation, decision-making and memory, making dialogue with non-human intelligence newly conceivable. Today such dialogue is attempted only by proxy: a large language model speaks on the system's behalf, so any intelligence on display originates from the model while the system itself remains silent. Here we ask whether the system can speak in its own voice. Following Wittgenstein, who located meaning in use, we treat communication as a game played with the system. Its internal dynamics are frozen as the nonlinear core of a reinforcement-learning policy, with only linear input and output interfaces trained. Through use and reward, the system's states and responses acquire meaning within the game, so playing becomes speaking. Because different architectures playing the same game optimize the same reward, their behaviors can all be read as pursuit of that reward; the game serves as a lingua franca across otherwise irreconcilable representations. Given a human prompt, a language model routes it to the game whose semantics best match it and designs an environmental state for which the desired action is the rational response, letting the system reply through its own behavior. Applied across diverse gene regulatory networks and reinforcement-learning tasks, the framework yields fluent dialogue without altering any system parameter, shows that well-trained agents of disparate origin converge on similar behavior, and reveals that specific GRN properties make a system easier or harder to talk with -- an inductive bias of the reservoir itself. Our framework opens a new route to conversing with any dynamical system on its own terms.

preprint2026arXiv

Positive Alignment: Artificial Intelligence for Human Flourishing

Existing alignment research is dominated by concerns about safety and preventing harm: safeguards, controllability, and compliance. This paradigm of alignment parallels early psychology's focus on mental illness: necessary but incomplete. What we call Positive Alignment is the development of AI systems that (i) actively support human and ecological flourishing in a pluralistic, polycentric, context-sensitive, and user-authored way while (ii) remaining safe and cooperative. It is a distinct and necessary agenda within AI alignment research. We argue that several existing failures of alignment (e.g., engagement hacking, loss of human autonomy, failures in truth-seeking, low epistemic humility, error correction, lack of diverse viewpoints, and being primarily reactive rather than proactive) may be better addressed through positive alignment, including cultivating virtues and maximizing human flourishing. We highlight a range of challenges, open questions, and technical directions (e.g., data filtering and upsampling, pre- and post-training, evaluations, collaborative value collection) for different phases of the LLM and agents lifecycle. We end with design principles for promoting disagreement and decentralization through contextual grounding, community customization, continual adaptation, and polycentric governance; that is, many legitimate centers of oversight rather than one institutional or moral chokepoint.

preprint2022arXiv

Competency of the Developmental Layer Alters Evolutionary Dynamics in an Artificial Embryogeny Model of Morphogenesis

Biological genotypes do not code directly for phenotypes; developmental physiology is the control layer that separates genomes from capacities ascertained by selection. A key aspect is competency, as cells are not a passive material but descendants of unicellular organisms with complex context-sensitive capabilities. We used an evolutionary simulation in the context of minimal artificial embryogeny to probe the effects of different degrees of cellular competency on evolutionary dynamics. Virtual embryos consisted of a single axis of positional information values provided by cells' genomes, operated upon by an evolutionary cycle in which embryos' fitness was proportional to monotonicity of the axial gradient. Evolutionary dynamics were evaluated in two modes: hardwired "mosaic" development (genotype directly encodes phenotype), and a more realistic mode in which cells interact prior to evaluation by the fitness function ("regulative" development). Even minimal competency with respect to improving their position in the embryo results in better performance of the evolutionary search. Crucially, we observed that as competency of cells masks the raw fitness of the genomes, the phenotypic fitness gains are then mostly due to improvements of cells' developmental problem-solving capacities, not the structural genome. This suggests the existence of a powerful ratchet mechanism: evolution progressively becomes locked in to improvements in the intelligence of its agential substrate, with reduced pressure on the structural genome. A feedback loop in which evolution increasingly puts more effort into the developmental software than perfecting the hardware explains the very puzzling divergence of genome from anatomy in species like planaria, identifies a possible drive for scaling intelligence over time, and suggests strategies for engineering novel systems in silico and in bioengineering.

preprint2022arXiv

Neurons as hierarchies of quantum reference frames

Conceptual and mathematical models of neurons have lagged behind empirical understanding for decades. Here we extend previous work in modeling biological systems with fully scale-independent quantum information-theoretic tools to develop a uniform, scalable representation of synapses, dendritic and axonal processes, neurons, and local networks of neurons. In this representation, hierarchies of quantum reference frames act as hierarchical active-inference systems. The resulting model enables specific predictions of correlations between synaptic activity, dendritic remodeling, and trophic reward. We summarize how the model may be generalized to nonneural cells and tissues in developmental and regenerative contexts.

preprint2021arXiv

A free energy principle for generic quantum systems

The Free Energy Principle (FEP) states that under suitable conditions of weak coupling, random dynamical systems with sufficient degrees of freedom will behave so as to minimize an upper bound, formalized as a variational free energy, on surprisal (a.k.a., self-information). This upper bound can be read as a Bayesian prediction error. Equivalently, its negative is a lower bound on Bayesian model evidence (a.k.a., marginal likelihood). In short, certain random dynamical systems evince a kind of self-evidencing. Here, we reformulate the FEP in the formal setting of spacetime-background free, scale-free quantum information theory. We show how generic quantum systems can be regarded as observers, which with the standard freedom of choice assumption become agents capable of assigning semantics to observational outcomes. We show how such agents minimize Bayesian prediction error in environments characterized by uncertainty, insufficient learning, and quantum contextuality. We show that in its quantum-theoretic formulation, the FEP is asymptotically equivalent to the Principle of Unitarity. Based on these results, we suggest that biological systems employ quantum coherence as a computational resource and - implicitly - as a communication resource. We summarize a number of problems for future research, particularly involving the resources required for classical communication and for detecting and responding to quantum context switches.

preprint2021arXiv

Metabolic limits on classical information processing by biological cells

Biological information processing is generally assumed to be classical. Measured cellular energy budgets of both prokaryotes and eukaryotes, however, fall orders of magnitude short of the power required to maintain classical states of protein conformation and localization at the Å, fs scales predicted by single-molecule decoherence calculations and assumed by classical molecular dynamics models. We suggest that decoherence is limited to the immediate surroundings of the cell membrane and of intercompartmental boundaries within the cell, and that bulk cellular biochemistry implements quantum information processing. Detection of Bell-inequality violations in responses to perturbation of recently-separated sister cells would provide a sensitive test of this prediction. If it is correct, modeling both intra- and intercellular communication requires quantum theory.

preprint2021arXiv

Stability of ground state degeneracy to long-range interactions

We show that some gapped quantum many-body systems have a ground state degeneracy that is stable to long-range (e.g., power-law) perturbations, in the sense that any ground state energy splitting induced by such perturbations is exponentially small in the system size. More specifically, we consider an Ising symmetry-breaking Hamiltonian with several exactly degenerate ground states and an energy gap, and we then perturb the system with Ising symmetric long-range interactions. For these models we prove (1) the stability of the gap, and (2) that the residual splitting of the low-energy states below the gap is exponentially small in the system size. Our proof relies on a convergent polymer expansion that is adapted to handle the long-range interactions in our model. We also discuss applications of our result to several models of physical interest, including the Kitaev p-wave wire model perturbed by power-law density-density interactions with an exponent greater than 1.

preprint2021arXiv

Technological Approach to Mind Everywhere (TAME): an experimentally-grounded framework for understanding diverse bodies and minds

Synthetic biology and bioengineering provide the opportunity to create novel embodied cognitive systems (otherwise known as minds) in a very wide variety of chimeric architectures combining evolved and designed material and software. These advances are disrupting familiar concepts in the philosophy of mind, and require new ways of thinking about and comparing truly diverse intelligences, whose composition and origin are not like any of the available natural model species. In this Perspective, I introduce TAME - Technological Approach to Mind Everywhere - a framework for understanding and manipulating cognition in unconventional substrates. TAME formalizes a non-binary (continuous), empirically-based approach to strongly embodied agency. When applied to regenerating/developmental systems, TAME suggests a perspective on morphogenesis as an example of basal cognition. The deep symmetry between problem-solving in anatomical, physiological, transcriptional, and 3D (traditional behavioral) spaces drives specific hypotheses by which cognitive capacities can scale during evolution. An important medium exploited by evolution for joining active subunits into greater agents is developmental bioelectricity, implemented by pre-neural use of ion channels and gap junctions to scale cell-level feedback loops into anatomical homeostasis. This architecture of multi-scale competency of biological systems has important implications for plasticity of bodies and minds, greatly potentiating evolvability. Considering classical and recent data from the perspectives of computational science, evolutionary biology, and basal cognition, reveals a rich research program with many implications for cognitive science, evolutionary biology, regenerative medicine, and artificial intelligence.

preprint2021arXiv

Ungappable edge theories with finite dimensional Hilbert spaces

We construct a new class of edge theories for a family of fermionic Abelian topological phases with $K$-matrices of the form $K = \begin{pmatrix} k_1 & 0 \\ 0 & - k_2 \end{pmatrix}$, where $k_1, k_2 > 0$ are odd integers. Our edge theories are notable for two reasons: (i) they have finite dimensional Hilbert spaces (for finite sized systems) and (ii) depending on the values of $k_1, k_2$, some of the edge theories describe boundaries that cannot be gapped by any local interaction. The simplest example of such an ungappable boundary occurs for $(k_1, k_2) = (1, 3)$, which is realized by the $ν= 2/3$ FQH state. We derive our edge theories by starting with the standard chiral boson edge theory, consisting of two counterpropagating chiral boson modes, and then introducing an array of pointlike impurity scatterers. We solve this impurity model exactly in the limit of infinite impurity scattering, and we show that the energy spectrum consists of a gapped phonon spectrum together with a ground state degeneracy that scales exponentially with the number of impurities. This ground state subspace forms the Hilbert space for our edge theory. We believe that similar edge theories can be constructed for any Abelian topological phase with vanishing thermal Hall coefficient, $κ_H = 0$.

preprint2020arXiv

Classification of interacting Floquet phases with $U(1)$ symmetry in two dimensions

We derive a complete classification of Floquet phases of interacting bosons and fermions with $U(1)$ symmetry in two spatial dimensions. According to our classification, there is a one-to-one correspondence between these Floquet phases and rational functions $π(z) = a(z)/b(z)$ where $a(z)$ and $b(z)$ are polynomials obeying certain conditions and $z$ is a formal parameter. The physical meaning of $π(z)$ involves the stroboscopic edge dynamics of the corresponding Floquet system: in the case of bosonic systems, $π(z) = \frac{p}{q} \cdot \tildeπ(z)$ where $\frac{p}{q}$ is a rational number which characterizes the flow of quantum information at the edge during each driving period, and $\tildeπ(z)$ is a rational function which characterizes the flow of $U(1)$ charge at the edge. A similar decomposition exists in the fermionic case. We also show that $\tildeπ(z)$ is directly related to the time-averaged $U(1)$ current that flows in a particular geometry. This $U(1)$ current is a generalization of the quantized current and quantized magnetization density found in previous studies of non-interacting fermionic Floquet phases.

preprint2020arXiv

Fractonic order in infinite-component Chern-Simons gauge theories

2+1D multi-component $U(1)$ gauge theories with a Chern-Simons (CS) term provide a simple and complete characterization of 2+1D Abelian topological orders. In this paper, we extend the theory by taking the number of component gauge fields to infinity and find that they can describe interesting types of 3+1D "fractonic" order. "Fractonic" describes the peculiar phenomena that point excitations in certain strongly interacting systems either cannot move at all or are only allowed to move in a lower dimensional sub-manifold. In the simplest cases of infinite-component CS gauge theory, different components do not couple to each other and the theory describes a decoupled stack of 2+1D fractional Quantum Hall systems with quasi-particles moving only in 2D planes -- hence a fractonic system. We find that when the component gauge fields do couple through the CS term, more varieties of fractonic orders are possible. For example, they may describe foliated fractonic systems for which increasing the system size requires insertion of nontrivial 2+1D topological states. Moreover, we find examples which lie beyond the foliation framework, characterized by 2D excitations of infinite order and braiding statistics that are not strictly local.

preprint2020arXiv

Rigorous results on topological superconductivity with particle number conservation

Most theoretical studies of topological superconductors and Majorana-based quantum computation rely on a mean-field approach to describe superconductivity. A potential problem with this approach is that real superconductors are described by number-conserving Hamiltonians with long-range interactions, so their topological properties may not be correctly captured by mean-field models that violate number conservation and have short-range interactions. To resolve this issue, reliable results on number-conserving models of superconductivity are essential. As a first step in this direction, we use rigorous methods to study a number-conserving toy model of a topological superconducting wire. We prove that this model exhibits many of the desired properties of the mean-field models, including a finite energy gap in a sector of fixed total particle number, the existence of long range "Majorana-like" correlations between the ends of an open wire, and a change in the ground state fermion parity for periodic vs. anti-periodic boundary conditions. These results show that many of the remarkable properties of mean-field models of topological superconductivity persist in more realistic models with number-conserving dynamics.

preprint2019arXiv

Microscopic definitions of anyon data

We present microscopic definitions of both the $F$-symbol and $R$-symbol -- two pieces of algebraic data that characterize anyon excitations in (2+1)-dimensional systems. An important feature of our definitions is that they are operational; that is, they provide concrete procedures for computing these quantities from microscopic models. In fact, our definitions, together with known results, provide a way to extract a complete set of anyon data from a microscopic model, at least in principle. We illustrate our definitions by computing the $F$-symbol and $R$-symbol in several exactly solvable lattice models and edge theories. We also show that our definitions of the $F$-symbol and $R$-symbol satisfy the pentagon and hexagon equations, thereby providing a microscopic derivation of these fundamental constraints.