Physics,biology, and sociology: A reappraisal

To the extent that all biological phenomena are perceivable only through their physical manifestations, it may be justified to assume that all biological phenomena will be eventually represented in terms of physics; perhaps not of present day physics, but of some “extended” form of it. However, even if this should be correct, it must be kept in mind that representing individual biological phenomena in terms of physics is not the same as deducing from known physical laws the necessity of biological phenomena. Drawing an analogy from pure mathematics, it is possible that while every biological phenomenon may be represented in terms of physics, yet biological statements represent a class of “undecidable” statements within the framework of physics. Such a conjecture is reinforced by the history of physics itself and illustrated on several examples. The 19th century physicists tried in vain todeduce electromagnetic phenomena from mechanical ones. A similar situation may exist in regard to biological and social sciences. Quite generally, the possibility of representing a class B phenomena in terms of class A phenomena does not imply that the phenomena of class B can be deduced from those of class A. The consequences of the above on the relation between physics, biology, and sociology are studied. A tentative postulational formulation of basic biological principles are given and some consequences are discussed. It is pointed out that not only can the study of biological phenomena throw light on some physical phenomena, but that the study of social phenomena may be of value for the understanding of the structures and functions of living organisms. The possibility of a sort of “socionics” is indicated.     

Again on language of biology]

Some time ago I proposed in an Editorial in this journal some considerations on the language of biology. I concluded that, to realize an autonomy of such a language (and therefore of biology), we have to develop a valid language for biology. In such a context, it seemed to me that the term "metaphors" referred to the concepts concerning the information carried by genetic code, was a reasonable one. However, Barbieri's article in this issue of Rivista di Biologia / Biology Forum calls for a reply. Of course, we do not know very much in this field, even if we have some evidence that a sequence of bases on a DNA is not determined only by chance. In any case we can exclude that nature in this occasion has "invented" a code. Nature doesn't "invent" anything: it only follows its rules, that we name "laws of nature". Barbieri quotes the Morse code, but forgets to say that such a code is "conventional" in the sense that it is valid only because it is the result of an "agreement" between Morse and the users of that code. There is nothing more unnatural than a "code": with whom nature should actually have to "reach an agreement"? As a matter of fact, we interpret as "information" what happens by law of nature. Also Barbieri's thesis that genes and proteins are molecular artifacts, assembled by external agents, whereas generally molecules are determined by their bonds, i.e. by internal factors, is a disputable one. It is examined how much an external structure plays a role in ordinary chemical reactions. The "information" of physics is not a semantic information. For such information we can refer to history of literature, telegraphic offices, genetics or biochemistry.     

Biochemistry on a Leash: The Roles of Tether Length and Geometry in Signal Integration Proteins

We use statistical mechanics and simple ideas from polymer physics to develop a quantitative model of proteins whose activity is controlled by flexibly tethered ligands and receptors. We predict how the properties of tethers influence the function of these proteins and demonstrate how their tether length dependence can be exploited to construct proteins whose integration of multiple signals can be tuned. One case study to which we apply these ideas is that of the Wiskott-Aldrich Syndrome Proteins as activators of actin polymerization. More generally, tethered ligands competing with those free in solution are common phenomena in biology, making this an important specific example of a widespread biological idea.     

Biological scaling and physics

Kleiber’s law in biology states that the specific metabolic rate (metabolic rate per unit mass) scales as M^-1/2 in terms of the massM of the organism. A long-standing puzzle is the (-1/4) power in place of the usual expectation of (-1/3) based on the surface to volume ratio in three-dimensions. While recent papers by physicists have focused exclusively on geometry in attempting to explain the puzzle, we consider here a specific law of physics that governs fluid flow to show how the (-1/4) power arises under certain conditions. More generally, such a line of approach that identifies a specific physical law as involved and then examines the implications of a power law may illuminate better the role of physics in biology.     

Quantitative cell biology: the essential role of theory

Quantitative biology is a hot area, as evidenced by the recent establishment of institutes, graduate programs, and conferences with that name. But what is quantitative biology? What should it be? And how can it contribute to solving the big questions in biology? The past decade has seen very rapid development of quantitative experimental techniques, especially at the single-molecule and single-cell levels. In this essay, I argue that quantitative biology is much more than just the quantitation of these experimental results. Instead, it should be the application of the scientific method by which measurement is directed toward testing theories. In this view, quantitative biology is the recognition that theory and models play critical roles in biology, as they do in physics and engineering. By tying together experiment and theory, quantitative biology promises a deeper understanding of underlying mechanisms, when the theory works, or to new discoveries, when it does not.     

Fundamental and functional aspects of mesoscopic architectures with examples in physics,cell biology,and chemistry

How small can a macroscopic object be made without losing its intended function? Obviously, the smallest possible size is determined by the size of an atom, but it is not so obvious how many atoms are required to assemble an object so small, and yet that performs the same function as its macroscopic counterpart. In this review, we are concerned with objects of intermediate nature, lying between the microscopic and the macroscopic world. In physics and chemistry literature, this regime in-between is often called mesoscopic, and is known to bear interesting and counterintuitive features. After a brief introduction to the concept of mesoscopic systems from the perspective of physics, we discuss the functional aspects of mesoscopic architectures in cell biology, and supramolecular chemistry through many examples from the literature. We argue that the biochemistry of the cell is largely regulated by mesoscopic functional architectures; however, the significance of mesoscopic phenomena seems to be quite underappreciated in biological sciences. With this motivation, one of our main purposes here is to emphasize the critical role that mesoscopic structures play in cell biology and biochemistry.     

Overcoming the Newtonian paradigm: The unfinished project of theoretical biology from a Schellingian perspective

Defending Robert Rosen's claim that in every confrontation between physics and biology it is physics that has always had to give ground, it is shown that many of the most important advances in mathematics and physics over the last two centuries have followed from Schelling's demand for a new physics that could make the emergence of life intelligible. Consequently, while reductionism prevails in biology, many biophysicists are resolutely anti-reductionist. This history is used to identify and defend a fragmented but progressive tradition of anti-reductionist biomathematics. It is shown that the mathematico–physico–chemical morphology research program, the biosemiotics movement, and the relational biology of Rosen, although they have developed independently of each other, are built on and advance this anti-reductionist tradition of thought. It is suggested that understanding this history and its relationship to the broader history of post-Newtonian science could provide guidance for and justify both the integration of these strands and radically new work in post-reductionist biomathematics.     

Fundamental and functional aspects of mesoscopic architectures with examples in physics, cell biology, and chemistry

How small can a macroscopic object be made without losing its intended function? Obviously, the smallest possible size is determined by the size of an atom, but it is not so obvious how many atoms are required to assemble an object so small, and yet that performs the same function as its macroscopic counterpart. In this review, we are concerned with objects of intermediate nature, lying between the microscopic and the macroscopic world. In physics and chemistry literature, this regime in-between is often called mesoscopic, and is known to bear interesting and counterintuitive features. After a brief introduction to the concept of mesoscopic systems from the perspective of physics, we discuss the functional aspects of mesoscopic architectures in cell biology, and supramolecular chemistry through many examples from the literature. We argue that the biochemistry of the cell is largely regulated by mesoscopic functional architectures; however, the significance of mesoscopic phenomena seems to be quite underappreciated in biological sciences. With this motivation, one of our main purposes here is to emphasize the critical role that mesoscopic structures play in cell biology and biochemistry.     

A new hypothesis for molecular behavior

In order to understand the living cell, biologists need workable explanations of molecular phenomena. From data in the literature, it is possible to construct a mathematical hypothesis: molecular behavior in the continuum can be represented by a set of simple, logarithmic functions. These functions apply not only to biology, but also to chemistry and to physics.Although empirical in its origins, this hypothesis satisfies criteria which are often associated with good theories. It is comprehensive in its application, and it is mathematically simple. It is easily tested; and it is accurate, when tested. Because it can be correlated with classical atomic and molecular theory, the hypothesis can be used to make strong predictions. The proposal also appears to be consistent with quantum mechanics.     

Between history and physics

Biology has traditionally occupied a middle ground between the determinism of classical physics and the uncertainties of history. These issues are analyzed with respect to statistical laws which are applied to the prebiotic domain and strategy laws which characterize evolutionary biology. The differences in approach between biology and physics are discussed in detail. The origin of life is discussed in the context of physical chemical laws. A scenario for biogenesis is presented in terms of known molecular hardware. Evolutionary biology is then examined with respect to the kinds of laws that are possible in a domain where thermal fluctuations (mutations) have macroscopic effects. Game theory is employed to demonstrate the kinds of theory appropriate to this historical domain. The transition point between physics and history is the origin and development of the code. This is discussed and it is concluded that we are not yet able to assign the code to either the deterministic domain or to the arena of history.     

Systems Biology: The elements and principles of Life

Systems Biology has a mission that puts it at odds with traditional paradigms of physics and molecular biology, such as the simplicity requested by Occam’s razor and minimum energy/maximal efficiency. By referring to biochemical experiments on control and regulation, and on flux balancing in yeast, we show that these paradigms are inapt. Systems Biology does not quite converge with biology either: Although it certainly requires accurate ‘stamp collecting’, it discovers quantitative laws. Systems Biology is a science of its own, discovering own fundamental principles, some of which we identify here.     

The rest is silence.

Over the past several years, RNAi and its related phenomena have emerged not only as a powerful experimental tool but also as a new mode of gene regulation. Through a combination of genetic and biochemical approaches we have learned much about the mechanisms underlying dsRNA responses. However, many of the most intriguing aspects of dsRNA-induced gene silencing have yet to be illuminated. What has become abundantly clear is that the complex and highly conserved biology underlying RNA interference is critical both for genome maintenance and for the development of complex organisms. However, it seems probable that we have only begun to reveal the diversity of biological roles played by RNAi-related processes.     

Physical models of biological information and adaptation

The bio-informational equivalence asserts that biological processes reduce to processes of information transfer. In this paper, that equivalence is treated as a metaphor with deeply anthropomorphic content of a sort that resists constitutive-analytical definition, including formulation within mathematical theories of information. It is argued that continuance of the metaphor, as a quasi-theoretical perspective in biology, must entail a methodological dislocation between biological and physical science. It is proposed that a general class of functions, drawn from classical physics, can serve to eliminate the anthropomorphism. Further considerations indicate that the concept of biological adaptation is central to the general applicability of the informational idea in biology; a non-anthropomorphic treatment of adaptive phenomena is suggested in terms of variational principles.     

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.     

Save the planet: eliminate biodiversity

Recent work in the philosophy of biology has attempted to clarify and defend the use of the biodiversity concept in conservation science. I argue against these views, and give reasons to think that the biodiversity concept is a poor fit for the role we want it to play in conservation biology on both empirical and conceptual grounds. Against pluralists, who hold that biodiversity consists of distinct but correlated properties of natural systems, I argue that the supposed correlations between these properties are not tight enough to warrant treating and measuring them as a bundle. I additionally argue that deflationary theories of biodiversity don’t go far enough, since a large proportion of what we value in the environment falls outside bounds of what could reasonably be called “diversity”. I suggest that in current scientific practice biodiversity is generally an unnecessary placeholder for biological value of all sorts, and that we are better off eliminating it from conservation biology, or at least drastically reducing its role.     

The mathematical biophysics of Nicolas Rashevsky

N. Rashevsky (1899-1972) was one of the pioneers in the application of mathematics to biology. With the slogan: mathematical biophysics : biology :: mathematical physics ; physics, he proposed the creation of a quantitative theoretical biology. Here, we will give a brief biography, and consider Rashevsky's contributions to mathematical biology including neural nets and relational biology. We conclude that Rashevsky was an important figure in the introduction of quantitative models and methods into biology.