The definitions of information and meaning two possible boundaries between physics and biology.

The standard approach to the definition of the physical quantities has not produced satisfactory results with the concepts of information and meaning. In the case of information we have at least two unrelated definitions, while in the case of meaning we have no definition at all. Here it is shown that both information and meaning can be defined by operative procedures, but it is also pointed out that we need to recognize them as a new type of natural entities. They are not quantities (neither fundamental nor derived) because they cannot be measured, and they are not qualities because are not subjective features. Here it is proposed to call them nominable entities, i.e., entities which can be specified only by naming their components in their natural order. If the genetic code is not a linguistic metaphor but a reality, we must conclude that information and meaning are real natural entities, and now we must also conclude that they are not equivalent to the quantities and qualities of our present theoretical framework. This gives us two options. One is to extend the definition of physics and say that the list of its fundamental entities must include information and meaning. The other is to say that physics is the science of quantities only, and in this case information and meaning become the exclusive province of biology. The boundary between physics and biology, in short, is a matter of convention, but the existence of information and meaning is not. We can decide to study them in the framework of an extended physics or in a purely biological framework, but we cannot avoid studying them for what they are, i.e., as fundamental components of the fabric of Nature.     

微量元素蛋白质组的比较基因组学研究

微量元素指需要量很少（人体中含量在0．01％以下）,但却是所有生物体所必需的元素。它们参与了生物体中各种复杂的生物过程,因此不同生物必须依赖相应的微量元素才能生存。过去大量的工作主要放在微量元素代谢通路和微量元素结合蛋白的实验研究上,由此凸显出微量元素对生命的重要性。然而,微量元素的计算生物学研究工作却非常有限。着重介绍当前利用比较基因组学的理论和方法来研究不同微量元素的利用、代谢、功能和进化方面问题的最新进展。对于所讨论的元素,大多数利用它们的蛋白已经基本确定,并且这些蛋白对于特定元素的依赖性也是非常保守的。通过比较基因组学分析,有助于帮助我们进一步认识微量元素领域很多基本问题（如在古菌、细菌和真核生物中的代谢、功能和动态进化规律等）及其重要特征。     

Organisational closure in biological organisms

The central aim of this paper consists in arguing that biological organisms realize a specific kind of causal regime that we call "organisational closure"; i.e., a distinct level of causation, operating in addition to physical laws, generated by the action of material structures acting as constraints. We argue that organisational closure constitutes a fundamental property of biological systems since even its minimal instances are likely to possess at least some of the typical features of biological organisation as exhibited by more complex organisms. Yet, while being a necessary condition for biological organization, organisational closure underdetermines, as such, the whole set of requirements that a system has to satisfy in order to be taken as a paradigmatic example of organism. As we suggest, additional properties, as modular templates and control mechanisms via dynamical decoupling between constraints, are required to get the complexity typical of full-fledged biological organisms.     

Kant's concept of natural purpose and the reflecting power of judgement

This paper examines how in the 'Critique of teleological judgment' Kant characterized the concept of natural purpose in relation to and in distinction from the concepts of nature and the concept of purpose he had developed in his other critical writings. Kant maintained that neither the principles of mechanical science nor the pure concepts of the understanding through which we determine experience in general provide adequate conceptualizations of the unique capacities of organisms. He also held that although the concept of natural purpose was derived through reflection upon an analogy to human purposive activity in artistic production and moral action, it articulates a unique notion of intrinsic purposiveness. Kant restricted his critical reflections on organisms to phenomena that can be given to us in experience, criticizing speculations on their first origins or final purpose. But I argue that he held that the concept of natural purpose is a product of the reflecting power of judgment, rather than an empirical concept, and represents only the relation of things to our power of judgment. Yet it is necessary for the identification of organisms as organized and self-organizing, and as subject to unique norms and causal relations between parts and whole.     

Ecology,physiology, allometry and dimensionality

Many ecologically important empirical laws governing physiological rates can be derived from a small set of assumptions. The body size of an organism, the density of tissue and the caloric content of tissue comprise a fundamental set of dimensional quantities. Dimensional arguments can account for a wide variety of ecophysiological observations such as the difference between the size dependence of respiration in terrestrial and aquatic organisms and the independence of net growth efficiency on body size.     

Organic Codes: A Unifying Concept for Life

Although the knowledge about biological systems has advanced exponentially in recent decades, it is surprising to realize that the very definition of Life keeps presenting theoretical challenges. Even if several lines of reasoning seek to identify the essence of life phenomenon, most of these thoughts contain fundamental problem in their basic conceptual structure. Most concepts fail to identify either necessary or sufficient features to define life. Here, we analyzed the main conceptual frameworks regarding theoretical aspects that have been supporting the most accepted concepts of life, such as (i) the physical, (ii) the cellular and (iii) the molecular approaches. Based on an ontological analysis, we propose that Life should not be positioned under the ontological category of Matter. Yet, life should be better understood under the top-level ontology of “Process”. Exercising an epistemological approach, we propose that the essential characteristic that pervades each and every living being is the presence of organic codes. Therefore, we explore theories in biosemiotics and code biology in order to propose a clear concept of life as a macrocode composed by multiple inter-related coding layers. This way, as life is a sort of metaphysical process of encoding, the living beings became the molecular materialization of that process. From the proposed concept, we show that the evolutionary process is a fundamental characteristic for life’s maintenance but it is not necessary to define life, as many organisms are clearly alive but they do not participate in the evolutionary process (such as infertile hybrids). The current proposition opens a fertile field of debate in astrobiology, epistemology, biosemiotics, code biology and robotics.

     

The brain-machine disanalogy revisited.

Michael Conrad was a pioneer in investigating biological information processing. He believed that there are fundamental lessons to be learned from the structure and behavior of biological brains that we are far from understanding or have implemented in our computers. Accumulation of advances in several fields have confirmed his views in broad outline but not necessarily in some of the strong forms he had tried to establish. For example, his assertion that programmable computers are intrinsically incapable of the brain's efficient and adaptive behavior has not received much examination. Yet, this is clearly a direction that could afford much insight into fundamental differences between brain and machine. In this paper, we pay tribute to Michael, by examining his pioneering thoughts on the brain-machine disanalogy in some depth and from the hindsight of a decade later. We argue that as long as we stay within the frame of reference of classical computation, it is not possible to confirm that programmability places a fundamental limitation on computing power, although the resources required to implement a programmable interface leave fewer resources for actual problem-solving work. However, if we abandon the classical computational frame and adopt one in which the user interacts with the system (artificial or natural) in real time, it becomes easier to examine the key attributes that Michael believed place biological brains on a higher plane of capability than artificial ones. While we then see some of these positive distinctions confirmed (e.g. the limitations of symbol manipulation systems in addressing real-world perception problems), we also see attributes in which the implementation in bioware constrains the behavior of real brains. We conclude by discussing how new insights are emerging, that look at the time-bound problem-solving constraints under which organisms have had to survive and how their so-called 'fast and frugal' faculties are tuned to the environments that coevolved with them. These directions open new paths for a multifaceted understanding of what biological brains do and what we can learn from them. We close by suggesting how the discrete event modeling and simulation paradigm offers a suitable medium for exploring these paths.     

Bacteria as a new model system for aging studies: investigations using light microscopy

Aging-the decline in an individual's condition over time-is at the center of an active research field in medicine and biology. Some very basic questions have, however, remained unresolved, the most fundamental being: do all organisms age? Or are there organisms that would continue to live forever if not killed by external forces? For a long time it was believed that aging only affected organisms such as animals, plants, and fungi. Bacteria, in contrast, were assumed to be potentially immortal and until recently this assertion remained untested. We used phase-contrast microscopy (on an Olympus BX61) to follow individual bacterial cells over many divisions to prove that some bacteria show a distinction between an aging mother cell and a rejuvenated daughter, and that these bacteria thus age. This indicates that aging is a more fundamental property of organisms than was previously assumed. Bacteria can now be used as very simple model system for investigating why and how organisms age.     

Kant’s concept of natural purpose and the reflecting power of judgement

This paper examines how in the ‘Critique of teleological judgment’ Kant characterized the concept of natural purpose in relation to and in distinction from the concepts of nature and the concept of purpose he had developed in his other critical writings. Kant maintained that neither the principles of mechanical science nor the pure concepts of the understanding through which we determine experience in general provide adequate conceptualizations of the unique capacities of organisms. He also held that although the concept of natural purpose was derived through reflection upon an analogy to human purposive activity in artistic production and moral action, it articulates a unique notion of intrinsic purposiveness. Kant restricted his critical reflections on organisms to phenomena that can be given to us in experience, criticizing speculations on their first origins or final purpose. But I argue that he held that the concept of natural purpose is a product of the reflecting power of judgment, rather than an empirical concept, and represents only the relation of things to our power of judgment. Yet it is necessary for the identification of organisms as organized and self-organizing, and as subject to unique norms and causal relations between parts and whole.     

Biodiversity as insurance: from concept to measurement and application

Biological insurance theory predicts that, in a variable environment, aggregate ecosystem properties will vary less in more diverse communities because declines in the performance or abundance of some species or phenotypes will be offset, at least partly, by smoother declines or increases in others. During the past two decades, ecology has accumulated strong evidence for the stabilising effect of biodiversity on ecosystem functioning. As biological insurance is reaching the stage of a mature theory, it is critical to revisit and clarify its conceptual foundations to guide future developments, applications and measurements. In this review, we first clarify the connections between the insurance and portfolio concepts that have been used in ecology and the economic concepts that inspired them. Doing so points to gaps and mismatches between ecology and economics that could be filled profitably by new theoretical developments and new management applications. Second, we discuss some fundamental issues in biological insurance theory that have remained unnoticed so far and that emerge from some of its recent applications. In particular, we draw a clear distinction between the two effects embedded in biological insurance theory, i.e. the effects of biodiversity on the mean and variability of ecosystem properties. This distinction allows explicit consideration of trade-offs between the mean and stability of ecosystem processes and services. We also review applications of biological insurance theory in ecosystem management. Finally, we provide a synthetic conceptual framework that unifies the various approaches across disciplines, and we suggest new ways in which biological insurance theory could be extended to address new issues in ecology and ecosystem management. Exciting future challenges include linking the effects of biodiversity on ecosystem functioning and stability, incorporating multiple functions and feedbacks, developing new approaches to partition biodiversity effects across scales, extending biological insurance theory to complex interaction networks, and developing new applications to biodiversity and ecosystem management.     

An introductory review of information theory in the context of computational neuroscience

This article introduces several fundamental concepts in information theory from the perspective of their origins in engineering. Understanding such concepts is important in neuroscience for two reasons. Simply applying formulae from information theory without understanding the assumptions behind their definitions can lead to erroneous results and conclusions. Furthermore, this century will see a convergence of information theory and neuroscience; information theory will expand its foundations to incorporate more comprehensively biological processes thereby helping reveal how neuronal networks achieve their remarkable information processing abilities.     

Does Biology Need an Organism Concept?

Among biologists, there is no general agreement on exactly what entities qualify as ‘organisms’. Instead, there are multiple competing organism concepts and definitions. While some authors think this is a problem that should be corrected, others have suggested that biology does not actually need an organism concept. We argue that the organism concept is central to biology and should not be abandoned. Both organism concepts and operational definitions are useful. We review criteria used for recognizing organisms and conclude that they are not categorical but rather continuously variable. Different organism concepts are useful for addressing different questions, and it is important to be explicit about which is being used. Finally, we examine the origins of the derived state of organismality, and suggest that it may result from positive feedback between natural selection and functional integration in biological entities.     

Morphological variation of species through time

Ten measurements, taken from each of 700 shells or four biologically distinct shallow marine gastropod species, were used to define the appropriate phenotypes in multidimensional space. Canonical discriminant analysis was performed on the data and a set of allocatory rules was derived. These allocatory rules, derived from extant specimens, were than applied to 644 fossil specimens of three of these biological species. Fossil individuals occupy the appropriate phenotypic space as defined by their modern descendants. The variation of fossil sample means about the modern means is illustrated. This variation is in the form of oscillations around the modern mean values and is correlated with climate. The distinction between taxonomic and biological species is discussed. The results of a number of previous studies are re-examined in the light of this discussion. It is argued that biological groupings can only be reliably determined when the appropriate data are available for extant organisms. Extant organisms, which have good fossil records, should therefore from the basis of paleontological evolutionary studies.     

How to be a chaste species pluralist-realist: the origins of species modes and the synapomorphic species concept

The biological species (biospecies) concept applies only to sexually reproducing species, which means that until sexual reproduction evolved, there were no biospecies. On the universal tree of life, biospecies concepts therefore apply only to a relatively small number of clades, notably plants andanimals. I argue that it is useful to treat the various ways of being a species (species modes) as traits of clades. By extension from biospecies to the other concepts intended to capture the natural realities of what keeps taxa distinct, we can treat other modes as traits also, and so come to understand that theplurality of species concepts reflects the biological realities of monophyletic groups.We should expect that specialists in different organisms will tend to favour those concepts that best represent the intrinsic mechanisms that keep taxa distinct in their clades. I will address the question whether modes ofreproduction such as asexual and sexual reproduction are natural classes, given that they are paraphyletic in most clades.     

A unifying view of 21st century systems biology

The idea that multi-scale dynamic complex systems formed by interacting macromolecules and metabolites, cells, organs and organisms underlie some of the most fundamental aspects of life was proposed by a few visionaries half a century ago. We are witnessing a powerful resurgence of this idea made possible by the availability of nearly complete genome sequences, ever improving gene annotations and interactome network maps, the development of sophisticated informatic and imaging tools, and importantly, the use of engineering and physics concepts such as control and graph theory. Alongside four other fundamental “great ideas” as suggested by Sir Paul Nurse, namely, the gene, the cell, the role of chemistry in biological processes, and evolution by natural selection, systems-level understanding of “What is Life” may materialize as one of the major ideas of biology.     

Biological races in humans

Races may exist in humans in a cultural sense, but biological concepts of race are needed to access their reality in a non-species-specific manner and to see if cultural categories correspond to biological categories within humans. Modern biological concepts of race can be implemented objectively with molecular genetic data through hypothesis-testing. Genetic data sets are used to see if biological races exist in humans and in our closest evolutionary relative, the chimpanzee. Using the two most commonly used biological concepts of race, chimpanzees are indeed subdivided into races but humans are not. Adaptive traits, such as skin color, have frequently been used to define races in humans, but such adaptive traits reflect the underlying environmental factor to which they are adaptive and not overall genetic differentiation, and different adaptive traits define discordant groups. There are no objective criteria for choosing one adaptive trait over another to define race. As a consequence, adaptive traits do not define races in humans. Much of the recent scientific literature on human evolution portrays human populations as separate branches on an evolutionary tree. A tree-like structure among humans has been falsified whenever tested, so this practice is scientifically indefensible. It is also socially irresponsible as these pictorial representations of human evolution have more impact on the general public than nuanced phrases in the text of a scientific paper. Humans have much genetic diversity, but the vast majority of this diversity reflects individual uniqueness and not race.     

The cell biology of aging

One of the original hypotheses of organismal longevity posits that aging is the natural result of entropy on the cells, tissues, and organs of the animal—a slow, inexorable slide into nonfunctionality caused by stochastic degradation of its parts. We now have evidence that aging is instead at least in part genetically regulated. Many mutations have been discovered to extend lifespan in organisms of all complexities, from yeast to mammals. The study of metazoan model organisms, such as Caenorhabditis elegans, has been instrumental in understanding the role of genetics in the cell biology of aging. Longevity mutants across the spectrum of model organisms demonstrate that rates of aging are regulated through genetic control of cellular processes. The regulation and subsequent breakdown of cellular processes represent a programmatic decision by the cell to either continue or abandon maintenance procedures with age. Our understanding of cell biological processes involved in regulating aging have been particularly informed by longevity mutants and treatments, such as reduced insulin/IGF-1 signaling and dietary restriction, which are critical in determining the distinction between causes of and responses to aging and have revealed a set of downstream targets that participate in a range of cell biological activities. Here we briefly review some of these important cellular processes.     

Statistical Versus Biological Hypothesis Testing: Response to Steidl

ABSTRACT In spite of the wide use and acceptance of information theoretic approaches in the wildlife sciences, debate continues on the correct use and interpretation of Akaike's Information Criterion as compared to frequentist methods. Misunderstandings as to the fundamental nature of such comparisons continue. Here we agree with Steidl's argument about situation-specific use of each approach. However, Steidl did not make clear the distinction between statistical and biological hypotheses. Certainly model selection is not statistical, or null, hypothesis testing; importantly, it represents a more effective means to test among competing biological, or research, hypotheses. Employed correctly, it leads to superior strength of inference and reduces the risk that favorite hypotheses are uncritically accepted.     

The cell as nexus: connections between the history, philosophy and science of cell biology

Although the cell is commonly addressed as the unit of life, historians and philosophers have devoted relatively little attention to this concept in comparison to other fundamental concepts of biology such as the gene or species. As a partial remedy to this neglect, we introduce the cell as a major point of connection between various disciplinary approaches, epistemic strategies, technological vectors and overarching biological processes such as metabolism, growth, reproduction and evolution. We suggest that the role of the cell as a nexus forms the basis for a new philosophical and historical appreciation of cell biology. This perspective focuses less on the cell as a well-defined, stable object and places more emphasis on its role as a mediator of fundamental biological processes.