Laws, causation, and explanation in the special sciences

There is the general philosophical question concerning the relationship between physics, which is often taken to be our fundamental and all-encompassing science, on one hand and the special sciences, such as biology and psychology, each of which deals with phenomena in some specially restricted domain, on the other. This paper deals with a narrower question: Are there laws in the special sciences, laws like those we find, or expect to find, in basic physics? Three arguments that are intended to show that there are no such laws are presented and examined. The paper ends with brief remarks concerning the implications of these arguments for explanation and causation in the special sciences.     

The non-universality of the genetic code: the universal ancestor was a progenote

The coevolution theory of genetic code origin (Wong, J.T. 1975, Proc. Natl Acad. Sci. U.S.A.72, 1909-1912) is assumed here to be substantially correct. This theory is based on the strict parallelism of the biosynthetic relationships between amino acids and the organization of the genetic code and postulates that these relationships were mediated by tRNA-like molecules on which the biosynthetic transformations between precursor and product amino acids took place. These transformations underlay the mechanism that gave rise to genetic code organization. One of the pathways which represents these transformations found in current organisms, and which are thus probably molecular fossils, is the Met-tRNA(fMet)-->fMet-tRNA(fMet)pathway. This pathway is present only in the Bacteria domain. This along with other observations and arguments leads us to believe that this pathway is a clear violation of the universality of the genetic code. Furthermore, the presence of this pathway only in the Bacteria domain seems to imply that the translation apparatus was still rapidly evolving when this pathway was fixed. This, in turn, appears to imply that the last universal common ancestor was a progenote. Finally, the implications that the finding of this pathway has for the stereochemical theory of genetic code origin are discussed.     

Speciation and bifurcations

The interrelations of physics and biology are discussed. It is shown that Darwin can be considered as one of the founders of the important field of contemporary physics called physics of dissipative structures or synergetics. The theories of gradual and punctual evolution are presented. The contradiction between these theories can be solved on the basis of molecular theory of evolution and on the basis of the phenomenological physical treatment. The general physical properties of living systems, considered as open systems being far from equilibrium, are listed and simple non-linear mathematical models describing gradual and punctual speciation are suggested. The usual pictures which present these two kinds of speciation can possess physico-mathematical sense. Punctuated speciation means bifurcation, a kind of non-equilibrium phase transition.     

Physical explanations and biological explanations,empirical laws and a priori laws

Philosophers intent upon characterizing the difference between physics and biology often seize upon the purported fact that physical explanations conform more closely to the covering law model than biological explanations. Central to this purported difference is the role of laws of nature in the explanations of these two sciences. However, I argue that, although certain important differences between physics and biology can be highlighted by differences between physical and biological explanations, these differences are not differences in the degree to which those explanations conform to the covering law model, which fits biology about as well as it does physics.     

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.     

Are attractors 'strange', or is life more complicated than the simple laws of physics?

Interesting and intriguing questions involve complex systems whose properties cannot be explained fully by reductionist approaches. Last century was dominated by physics, and applying the simple laws of physics to biology appeared to be a practical solution to understand living organisms. However, although some attributes of living organisms involve physico-chemical properties, the genetic program and evolutionary history of complex biological systems make them unique and unpredictable. Furthermore, there are and will be 'unobservable' phenomena in biology which have to be accounted for.     

Theory of degenerate coding and informational parameters of protein coding genes

The theory of degenerate coding is presented in a way enabling further application to molecular biology. There are two kinds of redundancy of a degenerate code. The first is due to the excess in codon length and the second to the code degeneracy. If the code is asymmetrically degenerate, the second kind of redundancy can be profitable for control of error rate. This control can be performed just by selective synonymous codon usage. Utilisation of the genetic code is partially influenced by this theoretical possibility. In particular the degree of error protectivity is well correlated with deviation from equiprobability in synonymous codon usage. The biological significance of this fact is discussed.     

Physicochemical Optimization in the Genetic Code Origin as the Number of Codified Amino Acids Increases

We have assumed that the coevolution theory of genetic code origin (Wong JT, Proc Natl Acad Sci USA 72:1909–1912, 1975) is essentially correct. This theory makes it possible to identify at least 10 evolutionary stages through which genetic code organization might have passed prior to reaching its current form. The calculation of the minimization level of all these evolutionary stages leads to the following conclusions. (1) The minimization percentages increased linearly with the number of amino acids codified in the codes of the various evolutionary stages when only the sense changes are considered in the analysis. This seems to favor the physicochemical theory of genetic code origin even if, as discussed in the paper, this observation is also compatible with the coevolution theory. (2) For the first seven evolutionary stages of the genetic code, this trend is less clear and indeed is inverted when we consider the global optimisation of the codes due to both sense changes and synonymous changes. This inverse correlation between minimization percentages and the number of amino acids codified in the codes of the intermediate stages seems to favor neither the physicochemical nor the stereochemical theories of genetic code origin, as it is in the early and intermediate stages of code development that these theories would expect minimization to have played a crucial role, and this does not seem to be the case. However, these results are in agreement with the coevolution theory, which attributes a role to the physicochemical properties of amino acids that, while important, is nevertheless subordinate to the mechanism which concedes codons from the precursor amino acids to the product amino acids as the primary factor determining the evolutionary structuring of the genetic code. The results are therefore discussed in the context of the various theories proposed to explain genetic code origin. Received: 25 October 1998 / Accepted: 19 February 1999     

Robustness: confronting lessons from physics and biology

The term robustness is encountered in very different scientific fields, from engineering and control theory to dynamical systems to biology. The main question addressed herein is whether the notion of robustness and its correlates (stability, resilience, self‐organisation) developed in physics are relevant to biology, or whether specific extensions and novel frameworks are required to account for the robustness properties of living systems. To clarify this issue, the different meanings covered by this unique term are discussed; it is argued that they crucially depend on the kind of perturbations that a robust system should by definition withstand. Possible mechanisms underlying robust behaviours are examined, either encountered in all natural systems (symmetries, conservation laws, dynamic stability) or specific to biological systems (feedbacks and regulatory networks). Special attention is devoted to the (sometimes counterintuitive) interrelations between robustness and noise. A distinction between dynamic selection and natural selection in the establishment of a robust behaviour is underlined. It is finally argued that nested notions of robustness, relevant to different time scales and different levels of organisation, allow one to reconcile the seemingly contradictory requirements for robustness and adaptability in living systems.     

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.     

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.     

Are There Laws of Genome Evolution?

Research in quantitative evolutionary genomics and systems biology led to the discovery of several universal regularities connecting genomic and molecular phenomic variables. These universals include the log-normal distribution of the evolutionary rates of orthologous genes; the power law-like distributions of paralogous family size and node degree in various biological networks; the negative correlation between a gene's sequence evolution rate and expression level; and differential scaling of functional classes of genes with genome size. The universals of genome evolution can be accounted for by simple mathematical models similar to those used in statistical physics, such as the birth-death-innovation model. These models do not explicitly incorporate selection; therefore, the observed universal regularities do not appear to be shaped by selection but rather are emergent properties of gene ensembles. Although a complete physical theory of evolutionary biology is inconceivable, the universals of genome evolution might qualify as "laws of evolutionary genomics" in the same sense "law" is understood in modern physics.     

Studies on Order in Prebiological Systems at the Laboratory of Chemical Evolution

The basic tenet of investigations in the Laboratory of Chemical Evolution (LCE) under Cyril Ponnamperuma was that biology is a recapitulation of prebiology, and that protobiology is an outcome of simple molecular interactions, engendered by the physics and chemistry of the molecules themselves. Studies were undertaken to continue research into understanding the determining physical and chemical parameters of molecular interactions leading to increasing complexity in pre- and proto-biological systems. Among other, related work, research was performed on the origin of the genetic code, the origin of order in prebiotic polymers, and related studies on the origins of optical activity in biological macromolecules. Highlights of some these studies are presented here.     

The organic codes. The basic mechanism of macroevolution.

The origin of the genetic code coincided with the origin of life, while the human codes of cultural evolution emerged almost four billion years later. Modern biology does not recognize any other organic code in nature, and is bound therefore to conclude that the whole of cellular evolution consisted of informational changes. Semantic transformations, natural conventions and biological meaning are things that officially do not exist in the organic world, and play no part in our reconstruction of development and evolution. And yet the properties of organic codes are beginning to emerge in various biological processes. Here it is shown that splicing, signal transduction and pattern formation can be accounted for precisely by the existence of organic codes. It is also shown that those processes were instrumental in bringing about major changes in the history of life, and it is concluded that every main step of macroevolution corresponded to the origin of a new organic code.     

Gould on Laws in Biological Science

Are there laws in evolutionary biology? Stephen J. Gould has argued that there are factors unique to biological theorizing which prevent the formulation of laws in biology, in contradistinction to the case in physics and chemistry. Gould offers the problem of ’’complexity‘‘ as just such a fundamental barrier to biological laws in general, and to Dollo‘s Law in particular. But I argue that Gould fails to demonstrate: (1) that Dollo‘s Law is not law-like, (2) that the alleged failure of Dollo‘s Law demonstrates why there cannot be laws in biological science, and (3) that ’’complexity‘‘ is a fundamental barrier to nomologicality.     

Shifting to structures in physics and biology: a prophylactic for promiscuous realism

Within the philosophy of science, the realism debate has been revitalised by the development of forms of structural realism. These urge a shift in focus from the object oriented ontologies that come and go through the history of science to the structures that remain through theory change. Such views have typically been elaborated in the context of theories of physics and are motivated by, first of all, the presence within such theories of mathematical equations that allow straightforward representation of the relevant structures; and secondly, the implications of such theories for the individuality and identity of putative objects. My aim in this paper is to explore the possibility of extending such views to biological theories. An obvious concern is that within the context of the latter it is typically insisted that we cannot find the kinds of highly mathematised structures that structural realism can point to in physics. I shall indicate how the model-theoretic approach to theories might help allay such concerns. Furthermore, issues of identity and individuality also arise within biology. Thus Dupré has recently noted that there exists a 'General Problem of Biological Individuality' which relates to the issue of how one divides 'massively integrated and interconnected' systems into discrete components. In response Dupré advocates a form of 'Promiscuous Realism' that holds, for example, that there is no unique way of dividing the phylogenetic tree into kinds. Instead I shall urge serious consideration of those aspects of the work of Dupré and others that lean towards a structuralist interpretation. By doing so I hope to suggest possible ways in which a structuralist stance might be extended to biology.     

The geometrization of biology

The twentieth century has witnessed a geometrization of physics, that is, a reduction of the basic concepts of physics to geometric concepts. The topological approach to biology, recently proposed and to some extent developed by the author, is a small step in the direction of geometrization of biology, but is unable to achieve the main purpose of such a geometrization of biology, namely, the reduction to geometric concepts of such purely biological concepts as ingestion, digestion, assimilation, etc. To achieve this purpose we must find geometric structures or spaces, in which different geometric properties stand to each other in the same formal logical relation, as the different concepts of biology stand to each other. If this were possible, then a set of geometric theorems could be “translated” by an appropriate “glossary” into a set of biological laws. While not offering a solution to this problem, the present paper illustrates the possibility of such an approach on several examples. Certain new types of topological spaces are introduced, which are used for illustration purposes only. It is shown, however, how from a theorem about such spaces a verifiable biological prediction could be made, if these spaces were to be taken seriously. A possible application to biology of E. Artin's theory of braids is outlined.     

DNA Codes and Information: Formal Structures and Relational Causes

Recently the terms "codes" and "information" as used in the context of molecular biology have been the subject of much discussion. Here I propose that a variety of structural realism can assist us in rethinking the concepts of DNA codes and information apart from semantic criteria. Using the genetic code as a theoretical backdrop, a necessary distinction is made between codes qua symbolic representations and information qua structure that accords with data. Structural attractors are also shown to be entailed by the mapping relation that any DNA code is a part of (as the domain). In this framework, these attractors are higher-order informational structures that obviate any "DNA-centric" reductionism. In addition to the implications that are discussed, this approach validates the array of coding systems now recognized in molecular biology.     

分子人类学与现代人的起源*

1953年Watson & Crick 对于DNA双螺旋结构模型的提出及对其遗传机理的解释,标志着现代分子生物学的诞生。其后短短50年的时间里,分子生物学在各个学科之间广泛渗透,相互促进,不断深入和发展。在以研究人类的起源和进化为首要任务的人类学领域,由于现代分子生物学理论和方法的应用,诞生了分子人类学这一全新的结合型分支学科,为人类学的发展提供了科学可信的研究方法和具发展前景的研究方向。系统地介绍了分子人类学的发展历史、研究方法及原理;另外,结合分子人类学在古人类学研究中的应用,讨论了关于现代人起源的“非洲起源说”和“多地区连续演化说”。Abstract: Since Watson & Crick put forward the double-helix model of DNA structure and hereditary mechanism in 1953, it is generally accepted that this event marks the birth of modern molecular biology. This new field of biology has experienced a flourishing development in the past 50 years. On one hand, the development of molecular biology has been deeply influencing many relative fields; on the other hand, its own proceeding pace has been accelerated by the reaction from the other fields. Anthropology is one of the fields most deeply impacted by the theory and method of molecular biology. Most importantly, molecular anthropology was born as a result of combination of molecular biology, anthropology as well as paleoanthropology. This new branch provides reliable method and vital direction for paleoanthropology. This paper systematically reviews the history, principle and method of molecular anthropology. Two hypotheses on the origin of modern human, which include “out-of-African theory” and “theory of multiregional evolution” are also discussed for the purpose of showing how molecular anthropology is applied in paleoanthropology.