搜索结果：The Biological bulletin

There are innumerable 'biological complexity measure's. While some patterns emerge from these attempts to represent biological complexity, a single measure to encompass the seemingly countless features of biological systems, still eludes the students of Biology. It is the pursuit of this paper to discuss the feasibility of finding one complete and objective measure for biological complexity. A theoretical construct (the 'Thread-Mesh model') is proposed here to describe biological reality. It segments the entire biological space-time in a series of different biological organizations before modeling the property space of each of these organizations with computational and topological constructs. Acknowledging emergence as a key biological property, it has been proved here that the quest for an objective and all-encompassing biological complexity measure would necessarily end up in failure. Since any study of biological complexity is rooted in the knowledge of biological reality, an expression for possible limit of human knowledge about ontological biological reality, in the form of an uncertainty principle, is proposed here. Two theorems are proposed to model the fundamental limitatio

We review the trade-offs between speed, fluctuations, and thermodynamic cost involved with biological processes in nonequilibrium states, and discuss how optimal these processes are in light of the universal bound set by the thermodynamic uncertainty relation (TUR). The values of the uncertainty product $\mathcal{Q}$ of TUR, which can be used as a measure of the precision of enzymatic processes realized for a given thermodynamic cost, are suboptimal when the substrate concentration $[S]$ is at the Michaelis constant ($K_\text{M}$), and some of the key biological processes are found to work around this condition. We illustrate the utility of $\mathcal{Q}$ in assessing how close the molecular motors and biomass producing machineries are to the TUR bound, and for the cases of biomass production (or biological copying processes) we discuss how their optimality quantified in terms of $\mathcal{Q}$ is balanced with the error rate in the information transfer process. We also touch upon the trade-offs in other error-minimizing processes in biology, such as gene regulation and chaperone-assisted protein folding. A spectrum of $\mathcal{Q}$ recapitulating the biological processes surveyed he

Morphogenesis, the process of growth and shape formation in biological tissues, is driven by complex interactions between mechanical, biochemical, and genetic factors. Traditional models of biological growth often rely on the concept of homeostatic Eshelby stress, which defines an ideal target state for the growing body. Any local deviation from this state triggers growth and remodelling, aimed at restoring balance between mechanical forces and biological adaptation. Despite its relevance in the biomechanical context, the nature of homeostatic stress remains elusive, with its value and spatial distribution often chosen arbitrarily, lacking a clear biological interpretation or understanding of its connection to the lower scales of the tissue. To bring clarity on the nature of homeostatic stress, we shift the focus from Eshelby stress to growth incompatibility, a measure of geometric frustration in the tissue that is the primary source of residual stresses in the developing body. Incompatibility, measured by the Ricci tensor of the growth metric at the continuous level, can be potentially regulated at the cell level through connections with the surrounding cells, making it a more mea

The function of the organism hinges on the performance of its information-processing networks, which convey information via molecular recognition. Many paths within these networks utilize molecular codebooks, such as the genetic code, to translate information written in one class of molecules into another molecular "language" . The present paper examines the emergence and evolution of molecular codes in terms of rate-distortion theory and reviews recent results of this approach. We discuss how the biological problem of maximizing the fitness of an organism by optimizing its molecular coding machinery is equivalent to the communication engineering problem of designing an optimal information channel. The fitness of a molecular code takes into account the interplay between the quality of the channel and the cost of resources which the organism needs to invest in its construction and maintenance. We analyze the dynamics of a population of organisms that compete according to the fitness of their codes. The model suggests a generic mechanism for the emergence of molecular codes as a phase transition in an information channel. This mechanism is put into biological context and demonstrated

Many biological processes can be thought of as the result of an underlying dynamics in which the system repeatedly undergoes distinct and abortive trajectories with the dynamical process only ending when some specific process, purpose, structure or function is achieved. A classic example is the way in which microtubules attach to kinetochores as a prerequisite for chromosome segregation and cell division. In this example, the dynamics is characterized by apparently futile time histories in which microtubules repeatedly grow and shrink without chromosomal attachment. We hypothesize that for biological processes for which it is not the initial conditions that matter, but rather the final state, this kind of exploratory dynamics is biology's unique and necessary solution to achieving these functions with high fidelity. This kind of cause and effect relationship can be contrasted to examples from physics and chemistry where the initial conditions determine the outcome. In this paper, we examine the similarities of many biological processes that depend upon random trajectories starting from the initial state and the selection of subsets of these trajectories to achieve some desired func

Provided that there is no theoretical frame for complex engineered systems (CES) as yet, this paper claims that bio-inspired engineering can help provide such a frame. Within CES bio-inspired systems play a key role. The disclosure from bio-inspired systems and biological computation has not been sufficiently worked out, however. Biological computation is to be taken as the processing of information by living systems that is carried out in polynomial time, i.e., efficiently; such processing however is grasped by current science and research as an intractable problem (for instance, the protein folding problem). A remark is needed here: P versus NP problems should be well defined and delimited but biological computation problems are not. The shift from conventional engineering to bio-inspired engineering needs bring the subject (or problem) of computability to a new level. Within the frame of computation, so far, the prevailing paradigm is still the Turing-Church thesis. In other words, conventional engineering is still ruled by the Church-Turing thesis (CTt). However, CES is ruled by CTt, too. Contrarily to the above, we shall argue here that biological computation demands a more ca

Many biological functions are executed by molecular machines, which consume energy and convert it into mechanical work. Biological machines have evolved to transport cargo, facilitate folding of proteins and RNA, remodel chromatin and replicate DNA. A common aspect of these machines is that their functions are driven out of equilibrium. It is a challenge to provide a general framework for understanding the functions of biological machines, such as molecular motors, molecular chaperones, and helicases. Using these machines as prototypical examples, we describe a few general theoretical methods providing insights into their functions. Although the theories rely on coarse-graining of these complex systems they have proven useful in not only accounting for many in vitro experiments but also addressing questions such as how the trade-off between precision, energetic costs and optimal performances are balanced. However, many complexities associated with biological machines will require one to go beyond current theoretical methods. Simple point mutations in the enzyme could drastically alter functions, making the motors bi-directional or result in unexpected diseases or dramatically restr

Graph Theoretic Process Network Synthesis is described as an introduction to biological networks. Genetic, protein and metabolic systems are considered. The theoretical work of Kauffman is discussed and amplified by critical property excursions. The scaling apparent in biological systems is shown. Applications to evolution and reverse engineering are construed. The use of several programs, such as the Synprops, Design of molecules, Therm and Knapsack are suggested as instruments to study biological process network synthesis. The properties of robust self-assembly and Self-Organizing synthesis are important contributors to the discussion. The bar code of life and intelligent design is reviewed. The need for better data in biological systems is emphasized.

Primates exhibit a robust deviation from canonical allometric scaling: at fixed body mass, their lifespans exceed those of non-primate mammals by factors of two to three. A rhesus macaque (8 kg) lives 25-40 years, whereas a cat of similar mass rarely exceeds 18 years. This statistically significant clade-level excess cannot be explained by standard metabolic or ecological models. We provide a thermodynamic explanation within the Principle of Biological Time Equivalence (PBTE), where lifespan is determined by a finite cycle budget governed by entropy production. We show that primates reduce entropy production per physiological cycle through increased neural energy allocation. The neural power fraction acts as a control parameter, extending the effective lifetime cycle count. Three mechanisms, predictive regulation, enhanced repair, and behavioral buffering, jointly suppress dissipation. This yields a quantitative neuro-metabolic multiplier that explains primate longevity and provides testable predictions linking brain energetics, entropy production, and lifespan.

Biological systems possess negative entropy. In them, one form of order produces another, more organized form of order. We propose a formal scheme to calculate robustness of an entire biological system by quantifying the negative entropy present in it. Our Methodology is based upon a computational implementation of two-person non-cooperative finite zero-sum game between positive (physico-chemical) and negative (biological) entropy, present in the system(TCA cycle, for this work). Biochemical analogue of Nash equilibrium, proposed here, could measure the robustness in TCA cycle in exact numeric terms, whereas the mixed strategy game between these entropies could quantitate the progression of stages of biological adaptation. Synchronization profile amongst macromolecular concentrations (even under environmental perturbations) is found to account for negative entropy and biological robustness. Emergence of synchronization profile was investigated with dynamically varying metabolite concentrations. Obtained results were verified with that from the deterministic simulation methods. Categorical plans to apply this algorithm in Cancer studies and anti-viral therapies are proposed alongsid

Throughout our history, we, humans, have sought to better control and understand our environment. To this end, we have extended our natural senses with a host of sensors-tools that enable us to detect both the very large, such as the merging of two black holes at a distance of 1.3 billion light-years from Earth, and the very small, such as the identification of individual viral particles from a complex mixture. This dissertation is devoted to studying the physical mechanisms that govern a tiny, yet highly versatile sensor: the biological nanopore. Biological nanopores are protein molecules that form nanometer-sized apertures in lipid membranes. When an individual molecule passes through this aperture (i.e., "translocates"), the temporary disturbance of the ionic current caused by its passage reveals valuable information on its identity and properties. Despite this seemingly straightforward sensing principle, the complexity of the interactions between the nanopore and the translocating molecule implies that it is often very challenging to unambiguously link the changes in the ionic current with the precise physical phenomena that cause them. It is here that the computational methods

Mobile devices encroach on almost every part of our lives, including work and leisure, and contain a wealth of personal and sensitive information. It is, therefore, imperative that these devices uphold high security standards. A key aspect is the security of the underlying operating system. In particular, Android plays a critical role due to being the most dominant platform in the mobile ecosystem with more than one billion active devices and due to its openness, which allows vendors to adopt and customize it. Similar to other platforms, Android maintains security by providing monthly security patches and announcing them via the Android security bulletin. To absorb this information successfully across the Android ecosystem, impeccable coordination by many different vendors is required. In this paper, we perform a comprehensive study of 3,171 Android-related vulnerabilities and study to which degree they are reflected in the Android security bulletin, as well as in the security bulletins of three leading vendors: Samsung, LG, and Huawei. In our analysis, we focus on the metadata of these security bulletins (e.g., timing, affected layers, severity, and CWE data) to better understand

Nowadays people realize that it is difficult to find information simply and quickly on the bulletin boards. In order to solve this problem, people propose the concept of bulletin board search engine. This paper describes the priscrawler system, a subsystem of the bulletin board search engine, which can automatically crawl and add the relevance to the classified attachments of the bulletin board. Priscrawler utilizes Attachrank algorithm to generate the relevance between webpages and attachments and then turns bulletin board into clear classified and associated databases, making the search for attachments greatly simplified. Moreover, it can effectively reduce the complexity of pretreatment subsystem and retrieval subsystem and improve the search precision. We provide experimental results to demonstrate the efficacy of the priscrawler.

The control of gene expression involves complex mechanisms that show large variation in design. For example, genes can be turned on either by the binding of an activator (positive control) or the unbinding of a repressor (negative control). What determines the choice of mode of control for each gene? This study proposes rules for gene regulation based on the assumption that free regulatory sites are exposed to nonspecific binding errors, whereas sites bound to their cognate regulators are protected from errors. Hence, the selected mechanisms keep the sites bound to their designated regulators for most of the time, thus minimizing fitness-reducing errors. This offers an explanation of the empirically demonstrated Savageau demand rule: Genes that are needed often in the natural environment tend to be regulated by activators, and rarely needed genes tend to be regulated by repressors; in both cases, sites are bound for most of the time, and errors are minimized. The fitness advantage of error minimization appears to be readily selectable. The present approach can also generate rules for multi-regulator systems. The error-minimization framework raises several experimentally testable hy

We plan to simulate a private and unlinkable exchange of messages by using a Public bulletin board and Mix networks in Opportunistic networks. This Opportunistic network uses a secure and privacy-friendly asynchronous unidirectional message transmission protocol. By using this protocol, we create a Public bulletin board in a network that makes individuals send or receive events unlinkable to one another . With the design of a Public bulletin board in an Opportunistic network, the clients can use the benefits of this Public bulletin board in a safe environment. When this Opportunistic network uses the protocol, it can guarantee an unlinkable communication based on the Mix networks. The protocol can work with the Public bulletin board exclusively with acceptable performance. Also, this simulation can be used for hiding metadata in the bidirectional message exchange in some messengers such as WhatsApp. As we know, one of the main goals of a messenger like WhatsApp is to protect the social graph. By using this protocol, a messenger can protect social graph and a central Public bulletin board.

In this issue we announce a fascinating series of works on the comparison of various types of convergence of sequences of functions. Some of these properties are provably related to some of the properties which were introduced in the earlier issues of the SPM Bulletin, and many problems remain open. Section 2, written by Lev Bukovský, contains a brief survey of some of the major open problems in this area. This issue gives the first example of the importance of the transmission of knowledge between the recipients of this bulletin: One of the announcements implies a solution to one of the problems posed in an independent paper announced here. looking forward to receive more announcements from other recipients and readers of the bulletin.

Are biological self-organising systems more ``intelligent'' than artificial intelligence (AI)? If so, why? I address this question using a mathematical framework that defines intelligence in terms of adaptability. Systems are modelled as stacks of abstraction layers (\emph{Stack Theory}) and compared by how effectively they delegate agentic control down their stacks. I illustrate this using computational, biological, military, governmental, and economic systems. Contemporary AI typically relies on static, human-engineered stacks whose lower layers are fixed during deployment. Put provocatively, such systems resemble inflexible bureaucracies that adapt only top-down. Biological systems are more intelligent because they delegate adaptation. Formally, I prove a theorem (\emph{The Law of the Stack}) showing that adaptability at higher layers is bottlenecked by adaptability at lower layers. I further show that, under standard viability assumptions, maximising adaptability is equivalent to minimising variational free energy, implying that delegation is necessary for free-energy minimisation. Generalising bioelectric accounts of cancer as isolation from collective informational structures

This issue contains, in addition to the usual contents, a special festive announcement: A book. This book by Banakh and Zdomsky seems to be the first in a planned series by these authors. We believe that the book will become a cornerstone in many future mathematical investigations, in particular in the field of infinite-combinatorial topology. The book's preliminary version is available online, as seen in the announcement, and the readers of the SPM Bulletin are encouraged to take a look and make comments. Zdomsky has also made two detailed contributions to this issue. This is the ideal form of a contribution to the SPM Bulletin, and we urge all contributors to consider this possibility from time to time. 1 Editor's note; 2 Research announcements; 2.1 On subclasses of weak Asplund spaces; 2.2 The number of translates of a closed nowhere dense set required to cover a Polish group; 2.3 More on convexity numbers of closed sets in R^n; 2.4 A new book: Coherence of Semifilters; 3 Characterization of topological spaces with (strictly) o-bounded free topological group; 4 An equivalent of SPM Bulletin 2's Problem of the month; 5 Boise Extravaganza In Set Theory (March 25--27, 2005); 6 Prob

The Web Bulletin Board (WBB) is a key component of verifiable election systems. It is used in the context of election verification to publish evidence of voting and tallying that voters and officials can check, and where challenges can be launched in the event of malfeasance. In practice, the election authority has responsibility for implementing the web bulletin board correctly and reliably, and will wish to ensure that it behaves correctly even in the presence of failures and attacks. To ensure robustness, an implementation will typically use a number of peers to be able to provide a correct service even when some peers go down or behave dishonestly. In this paper we propose a new protocol to implement such a Web Bulletin Board, motivated by the needs of the vVote verifiable voting system. Using a distributed algorithm increases the complexity of the protocol and requires careful reasoning in order to establish correctness. Here we use the Event-B modelling and refinement approach to establish correctness of the peered design against an idealised specification of the bulletin board behaviour. In particular we show that for n peers, a threshold of t > 2n/3 peers behaving correc