Jerman I., Stern A. (1996). Publisher: Znanstveno publicisticno sredisce. (Scientific Publishing Center), Ljubljana. Language: Slovene.
It is a fact that radical changes of biological paradigms has been the rule throughout the history of biology. In Ancient Greece two radically different, opposing, views were established: the Aristotelian vitalistic and Democritean mechanistic (reductionistic). According to the first view, organisms had some special property and were thus definitely disjoined from the inanimate world. According to the second view, the living beings were only special cases of atomic nature, led by inexorable mechanical laws. In the age of Galileo and Newton biology was not a special science yet, but natural scientists, studying living beings (Harvey, Maupertuis, Buffon, etc.), believed that there was no basic difference between the animate and inanimate worlds. "Biological" paradigm of the time thus was mainly in tune with Democritean view. At the close of the 18th century, in the time of Lamarck and Cuvier, a great paradigm shift took place where life obtained a new dimension: an inner organization with a kind of a purpose. The parts of organisms were seen as having functions in relation to the whole; the first true organistic biology began. It was also the beginning of biology as a separate science of natural sciences; which was mainly in line with the Aristotelian thought. Around the middle of the 19th century, after great successes of the cellular biologists, Darwin-Wallace theory of biological evolution, Bernard's experimental biology and the successes of biochemists, paradigm again shifted into reductionistic realms where it still remains.
Modern mechanistic-reductionistic (for short: M-R) paradigm of biology means conceptual and methodological orientation according to which the causes for phenomena of life must be sought in the living being's constituent parts and their interactions. In the first half of this century its triumphant position was not endangered either by still unsolved problems of the origin of life (for instance the question of the optically active compounds within organisms), nor by the questions of embryonic development, e.g., the famous discovery of Hans Driesch regarding the capability of two separated halves of a zygote of the sea-urchin to develop into a whole organism. The M-R paradigm found its true prosperity in the second half of this century when it found itself in complete conformity with the astonishing discoveries of molecular biology. The conception of life as a complex molecular phenomenon which is revolving around the axis of the (miraculous) molecule of DNA arose. The understanding of life had thus shifted to become a knowledge of the complicated web of chemical processes - and in particular, this is a very clear point of reductionist theory in modern biology. This reduction (even though it can not be complete, because life is a very complicated phenomenon) is threefold: a) the reduction of biologyas a science to physics and chemistry (as a specialized branch), b) life is reduced to complex chemical and physical processes and c) a living being is reduced to a complex aggregation of countless molecules. Through such treatment, a living being as a whole loses its autonomy, and the same happens to biology as a specific natural science. The loss of autonomy is somewhat hidden behind the complexity of even simple organisms and the complexity of biology. It renders impossible a real (practical) reduction of life to physico-chemical laws and processes thus giving the illusion of autonomy. A special form of modern reductionism arose under the name of sociobiology, which tried to reduce social phenomena to biological ones.
As stated at the beginning - an organistic paradigm is gradually taking shape. It may be understood as a concept which treats processes and structural elements in living organisms as an emergent entity with new, to its structural elements irreducible, qualities - a whole. This whole is seen as possessing properties and laws, which are not possible to derive or foretell just from knowing the properties and laws of its partial or elementary processes and structural elements. Contrary to the M-R paradigm the organistic one is based on the irreducibility of the whole to its constituent parts. The irreducible laws and properties of the whole are the source of its autonomy. According to the logic of the emergent organicism, the laws of the whole are, in a sense, superior to the laws of its constituent parts. This logic was clearly elaborated by Michael Polanyi. He showed that the laws of a lower hierarchical order can make possible a very significant, sometimes immensely great set of processes. But in organisms (or even in machines or languages) this set is reduced and structured by the laws of a higher order. Thus it is the latter laws that determine the behavior of the whole, the laws of a lower order represent only a necessary condition (material cause) for the functioning of the whole. This principle is called downward causation.
Actually, modern organicism started with the work of Ludwig von Bertalanffy in the first part of this century. He tried to explain life and organisms in terms of hierarchically ordered systems capable of self-perpetuation. He stressed the relationships among an organism's parts instead of the parts themselves and advocated emergent organismic laws. Organisms were thus seen as dynamic and active wholes. The advocates of the so called organic evolution, e.g., Popper and Bateson, held similar views. They refused the "Darwinistic" idea that organisms have no active role in the evolution of their species. They hypothesized that organisms create new selective pressures by their own preferences; that they are in some measure capable to create their own evolutionary possibilities and selection of them. Something of this kind was already clear to Darwin when he spoke about sexual selection.
The most elaborated modern organistic theory is biological structuralism, which was strongly advocated by the British biologist Brian Goodwin. Here the organism is treated as an autonomous whole with its own causal powers. The latter does not correspond to the Aristotelian teleological cause but to the formal one. The organismic whole is thus primary, its parts being derived from it through differentiation during the ontogeny. Biological structuralists strongly oppose neo-Darwinism, since it presents a picture of an organism as an impotent mediator between a freaky environment and a variable genome. The evolution of life (at least above the species level), is not led by selection but by the laws of a living state. The latter is processed at the point of dynamic stability and there the organism is shaped in a similar way as a sinking vortex in a bath. The origin of a new biological type can be seen as a shift of a living state of related organisms from one stable point to another. As far as the generation of an organism's form is concerned, the actuating agent is the so-called morphogenetic field. It is not only postulated as an idea but it has also been mathematically modeled and experimentally verified. Its basis is a visco-elastic cellular field and possibly other fields encountered within organisms. Genes are important, because their products influence morphogenetic fields, but they are not all that counts. Actually, not only genes are transmitted from generation to generation but also many other various components of the living state. Thus it is no more suitable to speak of the genotype and the phenotype. This dualism is resolved in the monism of the living state with its morphogenetic field. Since the evolution of organisms is not led only by the sheer hazard of spontaneous variability and selection pressures, but mainly by organismic laws, taxonomy should reflect these laws and thus be rational. There are many indicators that evolution is led by some order instead of by pure chance alone.
Beside biological structuralism another (mainly) organistic biology
is taking shape; it is based on quantum mechanics and is called quantum
(mechanic) biology. Its basic recognition is that living processes have
a quantum mechanical nature, be it because many biological processes begin
at the level of molecules with their quantum mechanical behavior or because
of some special electromagnetic fields. This form of biology also is strongly
antireductionistic.
If we want to understand the nature of a basic biological entity, we
delve deeply into the mysterious origins of life. Contemporary science
concerned with these origins can tell us much. It tells us that life is
not a unique event in the whole cosmos, but an orderly process, stemming
from the self-organizing capacities of matter under suitable conditions.
There are two basic kinds of hypotheses: life originated in cellular forms
with self-organizing abilities (Oparin, Fox) or it originated through autocatalytic
molecular cycles (Eigen, Kauffman) capable of further development in the
direction of increasing informational complexity. According to the latter
hypotheses there had to be some bridge - some kind of organization of matter
that is no longer present - which joined purely molecular evolution with
the most primitive forms of life. In Eigen's theory it was a so-called
hypercyclic organization of molecular autocatalytic cycles, while in Kauffman's
theory it was autocatalytic sets of proteins or RNAs.
To start with, all replicators belonging to quite a long period of time after the origin of life can be considered concrete, at least in a certain sense - namely, each one of those which succeeded in replication transferred its message to its descendants through an unequivocal physical contact between them. This fact also holds true for all replicators that reside in unicelular organisms, including the present-day ones. But at the beginning of multicellular life only very few replicators remained active with any real continuity. Almost without exception the genes in somatic cells die with the death of organisms and are thus also parts of active replicators' vehicles. Something very similar can be said about the great majority of germ-line replicators - namely, just a very small number of them truly gets replicated; and for the rest, everything is just the same as with the dead-end replicators. Both of these only share the same structure with the concrete replicators, and may thus be called abstract replicators. It is not clear, how the majority of active replicators forwent their continuity and became servers of the minuscule rest of them, with whom they share only their abstract structure. And, to make the story still more radical, there is trouble even with those few concrete replicators from the germ line that succeeded to reproduce: after a fortunate conception they are no more a part of a parent's body - thus they are no longer its replicators. Therefore, more or less, active replicators as selfish genes and basic biological entities, as far as multicellular organisms are concerned, are always abstract entities. Hence it is difficult to maintain that dead-end replicators are manipulated by concrete replicators as if they were their "slaves". The second possibility is that the former are "altruistic" to the latter, since they share the same structure. Certain discoveries in the realm of biological altruism and even mathematical calculations demonstrate that this could be so. It seems that biology offers us something unusual for the modern sciences, namely that abstract entities have some reality and physical effect! However, this phenomenon may also be interpreted in a more nominalistic manner: as the end of the conception of the active biological replicator or the selfish gene.
Beside its fading into pure abstraction, the concept of the selfish gene has other weak points, namely, it has no known cohesive factor. It is not clear how it - as a concrete entity - could really unite all other concrete units of the same structure, which Dawkins would call replicas of the same selfish gene. The difficulty lies also within the three criteria for establishing the concept of the selfish gene: copying fidelity, longevity and fecundity. None of these criteria is stated as absolute. In terms of the first criterion, it means that the DNA sequence only needs to perform a relatively high level of copying fidelity in order to contend for the epithet of the gene. On the other hand Dawkins demands that a certain gene should be absolutely unchangeable, for even a minor mutation ends its existence and places it into the realm of a new gene. These two demands cannot be reconciled with each other. If we allow some changeability, then we have to relinquish the central idea of the concept, i.e., the notion of the selfish gene itself. And, after the first criterion has fallen, the other two, i.e., longevity and fecundity, also lose sense - namely, if something is changeable, it is just as indurable; and if it ceases to exist, it most definitely cannot remain fertile. It also holds that when we allow changes it is no longer clear where the gene remains the same and where it mutates into something else. The selfish gene therefore either has no evolution (for the latter connotes changeability), or it has no clear identity. Both possibilities are inadequate and yet they are a logical consequence of Dawkins' theory.
If the notion of the selfish gene, as a modern most emphasized notion of the basic biological entity, demonstrated itself as very problematic, from the semantic, ontological and even from the logical standpoint, let us see what happens if we go back to the conventional notion of the gene. After the discovery of the role and structure of DNA it seemed that it was clear what a gene was, but the further development of genetics thoroughly complicated and obscured its original simplicity. Today it is not clear what genes really are. They may represent many widely different functional parts of a DNA molecule, for instance regulatory, structural and segregation genes, etc. In Eukaryota they are frequently interrupted by introns, and may even have alternative splicing schemes, according to which one and the same DNA sequence may result in different proteins. A similar thing happens in overlapping genes. It is therefore difficult to adhere strictly to and identify the gene with a definite DNA sequence. This fact is at least implicitly in the minds of geneticists when they prefer to name the gene according to its function. But here the problem is that this function may only be potential. For instance, the gene for red efflorescence may be completely unexpressed in green leafs and roots. The notion of the gene as a functional entity is thus very elusive. And even more. The gene is not a fixed entity at all. It is continuously changing: it is subject to different types of mutation; it may be changed through transposition (this implies the change of its position), recombination or gene conversion. They are also prone to the so-called molecular clock, i.e., to steadily change through mutation, consequently their continuity is limited. And according to recent understandings of molecular evolution, it may not be the smallest unit of evolution at all. Genes are further composed of modules, corresponding to functional and structural units in proteins and are expressed mostly in exons. Besides mutation (whose expression is limited in harmony with the complexity of the species) their evolution consists mainly through exon insertion and duplication.
On the other hand it is also very questionable, how much autonomy the
genes really have. The fluidity of genome through transposition and other
means suggests some other factor, above the level of the genes, that is
responsible for biological order and forms. The autonomy of the genes is
thus restricted. Another indication of limited autonomy is the phenomenon
of adaptive mutation (Cairns), where the mutation rate to wild types (revertants)
is conditioned by the environment. Third, it is also known that the DNA
genes may be synthesized from cellular RNA (retroposition). Fourth, the
expression of the genes depends strongly on different cellular proteins.
Fifth, the autonomy of the genes is also threatened by prions - types of
viruses without known nucleic acids. Here it seems that proteins succeeded
to replicate themselves. From the standpoint of the germ line, it is known
that certain retroviruses are able to penetrate the famous Weismann's barrier,
thus certain influences from a somatic line or various environments can
become inherited. And lastly, through the induction of phenocopies, we
are able to mimic mutations and thus the action of the genes. It is consequently
clear that we need a new, consistent notion of the gene, first considering
its conventional molecular nature; and second, we need a notion that not
only includes inheritance and continuity but which is much more autonomous
than the molecular (DNA) gene alone.
But if we want to deal with the genes on the level of organisms, we should build the concept of the organismic gene. An organismic gene - in diploid multicelular species it consists of components A and B - comprises all templates of continuous-molecular genes A together with their homologues B at the same locus and in the same organism. Thus there are two criteria for the organismic gene: the same origin of molecular replicas (for instance from the zygote) and its limitation to a concrete organism. In the diploid zygote its organismic gene includes only two continuous-molecular genes, namely A and B. But through embryogenetic divisions it becomes multiplied into countless replicas. Yet these replicas, though of the same origin, are not necessarily equal in their structure: many somatic mutations may make the structure of an organismic gene disperse somewhat. On the other hand, even replicas with equal structure can be fully expressed in certain tissues and completely unexpressed in others. They may also be active at certain ontogenetic stages and completely inactive in the same tissue in later stages, or vice versa. Thus the organismic gene is a very complex structure. In line with the idea of the organismic gene we may also define the organismic genome; it includes all organismic genes together with their above mentioned complex structures. Neither the organismic gene nor genome can account for its true inheritance, since they are limited to one organism; if we want to include this very important phenomenon of heredity, we must build the next concept, the concept of the species gene. Analogous to the organismic gene, the species gene comprises all continuous-molecular genes limited to some biological species; there should be their origin. A species gene is still more complicated than an organismic one. It may be differentiated into many mutant forms and many alleles; it may also be - either temporarily or permanently - active in some organisms, while being inactive in others. The species gene does not include only inheritance, i.e., transmission from parents to their offspring, but also molecular evolution, a steady change of the gene structure. In analogy to the organismic genome we may also define the species genome, which is superficially similar to the concept of the gene pool. Yet the two are different, since the species genome comprises all genes in a species, while the gene pool includes only genes from sexually reproducing organisms.
At the end of this path we should also define genes which are capable of spanning phylogenetic distances. They may be called phylogenetic genes (p-genes). To limit them into some rational framework we must have certain criteria. According to one of them, the p-gene is limited to the genes in two successive species. According to another, the p-gene comprises genes included in the same concerted evolution and amenable to gene conversion. The concept of the p-gene is perhaps the most natural, but still somewhat limited, since concerted evolution needs multigene families. More suitable, yet less natural, is the concept of the p-gene as a member of a gene family or superfamily.
If we come back to our search for the basic biological entity, we may now conclude that the concepts of species and phylogenetic genes come close to it. They are well defined and do not have semantic and logical problems which characterized the selfish gene concept. Still, they are only pieces of DNA and have questionable autonomy. Hence they are only relatively suitable and we should still seek a more perfected biological entity.
Dynamic information is a case of many biological processes, called biological flows. The latter are seen as primarily dynamic entities. As such, they are problematic from the standpoint of classical logic and its many derivatives, since any dynamic connotes contradiction, it denotes something and yet, at the same time, something else into which it is changing. It is thus very difficult to handle dynamic entities, yet scientists (particularly biologists) are already doing this. It is time to build a new logic capable of handling dynamic entities. Flows are ever in transition, nothing has definite limits and a definite identity; everything is interconnected. Flows are thus very inclusive. Besides, any flow includes a past, present and a future. The past means some remnants in the whole flow which still has some influence on its present form; the future denotes the embryo of its unfolding forms. The three are connected. Any two entities in the flow share a so-called transitional identity, which may be more or less strong, according to the strength of their binding potentials.
Biological flows actively build biological structures - cells, tissues, organs, organisms. Every biological structure is included into some biological flow. The genes are thus the carriers of replicative (autocatalytic) and informative (catalytic) flows. This is the dynamic correspondent to the concept of genetic information. Informative flows in their cyclic interconnections unite the whole organism; they compose an organismic flow. Concerning genetics and evolution we can identify two types of biological flow: a mutational flow corresponding to basic molecular evolution, and the evolutionary flow of the species, called a phylogenetic flow. For a basic biological entity we may now identify the genetic-organismic flow, including the organismic genome and its informative flows. However, for an explanation of evolution of biological species the concept of the phylogenetic flow is more appropriate than the one of the genetic-organismic flow. Because of their inclusive nature these flows are much more autonomous than genes, considered in materialistic concepts.
The theory of coherent oscillations stems from the British biophysicist Herbert Fröhlich. In short, on the basis of special electrical characteristics of the living cell, the theory supposes the existence of coherent oscillations (originating from the Bose condensation) of molecular dipoles which together with the endogenous EM field create coherent EM field at the frequency 10 - 100 GHz. These oscillations are supposed to be the basis for the intramolecular as well as for the intercellular order. In a neoplasm such order is broken and uncontrolled growth follows. Experimentally this theory was verified in various ways, either through microdielectrophoresis (which showed somewhat lower frequencies) or erythrocyte rouleaux formation and through interference and resonance effects with exogenous low intensity mm EM waves. However, a direct evidence for "Fröhlich's" radiation still awaits discovery. Fröhlich's theory was further elaborated, in terms of a quantum filed theory, by the group around del Giudice. According to this view, the endogenous bioelectromagnetic field is organized into tiny filaments, of the diameter similar to microtubules. The filamentous field is supposed to organize biochemical reactions through resonance induction. It should be mainly limited to the interior of the organism, leaking only a little - hence its radiation could also be termed ultraweak.
Many authors are concentrating on quantum mechanical and peculiar electrical characteristics of biological molecules. Hameroff speaks about computing capabilities of the cytoskeleton (microtubular and microtrabecular network), connected with the filamentous field. Through the cytoskeleton the filamentous field could influence the flow of the intracellular stuff, cells' perception and direct the axis of the mitotic spindle. Other authors refer to the intramolecular coherence of enzymes. Through their phonons biological molecules should be able to examine the cellular interiors and thereby make correct orientations. Certain authors even speak about the intelligence of some bigger biomolecules (proteins) like bacteriorhodopsin.
Very important is the thermodynamic theory of biological coherence tackled by British biologist Mae-Wan Ho. Many biological processes are characterized by a cascade of processes, beginning on the levels of molecules and ending on the level of the whole organism; for instance a muscle contraction or the vertebrates vision. These processes are highly coordinated and at the beginning, since there are only a few molecules, a statistical approach of conventional thermodynamics, even a non-equilibrium one, is inappropriate. In the new biological thermodynamics the concept of free energy is replaced by the more important concept of stored energy. Life demands such big inner coordinations that its processes should be very tightly connected and organized, supposedly through quantum coherence. The thermodynamics of organisms is the thermodynamics of an organized complexity. The energy of organisms is mostly stored in a long-term way. The living state demands that the elements of life (for instance molecules) behave in a highly collective manner like the phenomena of superfluidity and superconductivity. In this new outlook, organisms are a special case of a solid state of matter because of very tight connections between polar molecules. Free energy is stored into different vibrational modes as described by Fröhlich and del Giudice. The basic order of life has therefore nothing to do with the Brownian motion. There are also strong indications for the solid state theory of the living state: for instance centrifugation of Euglena sp. yielded no macromolecules in the upper phase, while these abounded in the case where centrifugation was done after homogenization. Biological research should therefore be as non-invasive as possible. Ho discloses further indications for the coherent nature of the living state, her own discovery of bands of colors when the living organism is exposed to polarized light in an unconventionally used polarization microscope - and this effect was never achieved when dead organisms were examined. This phenomenon strongly demonstrates a long-range coherent order in organisms which vanishes at death. It is important also from the thermodynamic standpoint, since in coherent processes the transference of energy may be almost without losses; if their coherence is perfect the entropy is zero.
Because of the importance of its dynamics we can include the field concept into the concept of the coherent flow. This flow is truly cohesive and is transmitted from generation to generation. It also comprises genes and all their information processing. Transmitted from parents to their offspring is a complex and highly ordered wave structure of the coherent flow; it is natural that within the framework of the new biology we should speak of wave genes and wave genomes, the first being a substructure of the second. Instead of nucleotides we have a wave pattern; it still depends on material genes and their nucleotide sequences, but also on other vital factors of the cell, including the all-organizing coherent field.
Now we may ask what is life in light of the new biology. In conventional biology, life is usually defined as some process with the capabilities of self replication of its own systems, the production of its own material and structures from a substance of a different kind, and the separation of its systems from the environment. The stress is upon autocatalysis (which includes inheritance) and the highly organized transformation of substances. The new biology affirms this, too, but it goes further; it sees life more as a process of being an organized whole, as Popp and Ho put it. The term organized whole should be understood as a coherent organismic field. This definition is still not very elaborate, indicating only the basic idea. But it leaves open the doors to more comprehensive and penetrating definitions of life, when more is known about the details of biological coherence; and it shows how the paradigm of the new biology differs from the one of conventional biology.
In the view of the new biology life is a flow of a predominantly coherent nature. Through its wave structure it establishes a dynamic structure - a body of the organism. It exists on three levels: on the level of physiology (physiological flow), on the level of ontogeny (ontogenetic flow) and on the level of phylogeny (evolutionary flow). The first two are characterized by the coherent field while the phenomenon of coherence is still not certain on the third level. We can identify also a fourth level of life, the level of flows where organisms interchange their flows with other organisms, and can be called symbiotic flow. All these flows can coexist together. But physiological flow alone suffices for life.
According to the theory of del Giudice, a new empirically testable hypothesis of the emergence of life can be put forward. In contemporary hypotheses (Eigen, Kauffman) suitable molecules and their interaction are the focus. Nobody among the renowned researchers exploring the origin of life asks whether there should be some underlying order different from the order of Brownian movement. But perchance, just certain supramolecular order, proposed by Fröhlich and others, is needed to establish life. In harmony with this view, life would have appeared in systems with a certain density of dipoles and the inflow of free energy. In such a system coherent oscillations would have emerged, which would have given rise to ordered processes on the molecular level. The latter might have been organized in coacervates, microspheres or other cellular formations. Cells with more coherent fields should have been more stable and should reproduce more efficiently. In something akin to the battle for life (even if perhaps this was not yet life) the field should have become coherent enough and at the same time it would have supported cooperation between proteins and nucleic acids. Thus life could emerge as a sort of the materialization of the primeval coherent field formed in cellular structures with a sufficient density of dipoles.
Another very important field, which functions like a taboo in neo-Darwinistic biology is the question of how much organisms, or better, the basic living entity, can influence the evolution of its own species. If organisms are really led only by material genes as a kind of computer programs, which are selected by a whimsical environment, organisms have indeed only negligible influence on their own evolution. But if their essence is the coherent field with its implicit potentials for change, organisms can have some causal powers in directing their evolution. There is also ample evidence for this. On the level of molecular evolution, it is the phenomenon of molecular and meiotic drive and the phenomenon of the evoked transposition, where organisms adapt their genomes to an environmental challenge. From the graph theory it is further known that the genetic system of Eucaryotes is too complicated to be able to be optimally adapted to the environment. The fourth strong field which speaks in favor of organisms' causal powers over their evolution also comes from molecular genetics - it is the phenomenon of the already mentioned adaptive mutation, discovered by Cairns and studied by many researchers today.
This new outlook on life can also give new insights into consciousness and perception, especially when we take into consideration the perceptive and adaptive capabilities of molecules. Consciousness is thus not something miraculously appearing in sufficiently organized matter - perhaps higher vertebrate brain - but it is, in a certain sense, present in some primeval form also on the level of molecules and through the cascade process of organismic information flow it transforms itself into organism's perception and registration.
Last though not least, through new biology we may shed new light on one of the most puzzling phenomena of modern biology, namely on biological altruism. We may see what is the common entity which enables organisms to sacrifice their own good or even life for the sake of others, mainly relatives. This problem is, as far as relatives are concerned, mathematically well solved in modern population genetics through the coefficient of kinship. But here altruism is reduced to gene selfishness, therefore it is based on the already criticized selfish gene theory. The concept of the wave gene can be of better help here as well.