On the origin of biological similarity

The principles of biological similarity have not been adequately defined. Previous studies have not been fully successful, mainly because the search for such principles centered around the idea that a few of them would apply to all animals, just as Newton's principles of mechanical similarity apply to all inanimate objects. However, this is not possible, so that the search has led up a number of blind alleys, ending with a failure to provide a fundamental and unified explanation—as contrasted with empirical justification—for the scaling of basal metabolic rate of many kinds of animals (e.g. mammals, birds, fish, certain small metazoa) according to a $\text{3}\text{4}\text{-}\text{power}$ of body mass, M, rather than as $\text{M}{}^{\mathrm{<mtext>2</mtext><mtext>3</mtext>}}$ (“surface law”) or M^1·0; moreover, none of the previous theories can account for the fact that other kinds of animals (e.g. insects, snakes, hibernating mammals) do not obey the $\text{M}{}^{\mathrm{<mtext>3</mtext><mtext>4</mtext>}}\text{-}\text{rule}$. Two basic characteristics of all animals are that in the water they are on “the verge of floating” and that movement is interwoven with the nature of animal life itself. These observations lead to the principle of constancy of body density ($\text{ρ ? 1}$) and to the principle of similarity in some defined sense of the muscular apparatus—the universal generator of movement—across species, but only within classes of animals that have evolved similar methods of locomotion. Because muscle tissues are subject to elastic (“spring-type”) contraction forces, a general elastic similarity principle holds for muscle diameter, d, vs. a linear body dimension, L, i.e., d² ∝ L³ (Galileo-Rashevsky principle; this principle is valid also for the dimensions of the trunk of animals without exoskeleton subject to a gravitational load, e.g. for land mammals but not for sea mammals). A final principle which, combined with the above, leads to the $\text{M}\text{3}\text{4}\text{-}\text{rule}$ for muscle-power generation, is that time is scaled as the linear dimension, T ∝ L (in contrast to Newton's second principle of mechanical similarity for physical objects, $\text{T ∝ L}{}^{\mathrm{<mtext>1</mtext><mtext>2</mtext>}}$). This principle was introduced in the past either as an arbitrary assumption (Lambert & Teissier) or based on the empirical finding of constancy of muscle shortening velocity ($\text{∝}\text{L}\text{T}$ across mammalian species (Hill-McMahon). However, this principle cannot be valid for the classes of animals which do not obey the $\text{M}{}^{\mathrm{<mtext>3</mtext><mtext>4</mtext>}}\text{-}\text{rule}$. This principle is derived here from the more fundamental principle of constancy, across similar species, of mechanical stress (force over cross-section) endured by contracting muscles. In species such as snakes, however, in which locomotion is generated in a different way, friction forces assume an important role and scaling of time as with mechanical similarity, $\text{T ∝ L}{}^{\mathrm{<mtext>1</mtext><mtext>2</mtext>}}$, is obtained by assuming a similar velocity of the animals along their axis as size increases; using this scaling, the deviation of snakes from the $\text{M}{}^{\mathrm{<mtext>3</mtext><mtext>4</mtext>}}\text{-}\text{rule}$ is explained. Interestingly, though, such scaling may have limited the maximal body size of snakes. A yet different principle seems to be operating in insects, leading to the scaling: $\text{T ∝ L}{}^{\mathrm{<mtext>?</mtext><mtext>1</mtext><mtext>3</mtext>}}$ and a faster than body mass increase of basal metabolic rate. Finally, neither heat loss nor surface-related transport appear to be limiting and setting factors for metabolic rate—indeed “surface arguments” are entirely unbased. Only in some situations where the $\text{M}{}^{\mathrm{<mtext>3</mtext><mtext>4</mtext>}}\text{-}\text{rule}$ is not obeyed because of heat loss considerations (e.g. dogs adapted to the tropics or to the arctic cold) is a surface argument relevant.     

On the physical origin of biological handedness

In the racemic conglomerate crystallization of over 1000 samples of D, L-sodium-ammonium tartrate the effect of³²P beta irradiation on the weight, optical activity, and crystallite size was measured. Both weight and optical activity showed a statistical dependence on the intensity of beta irradiation. The crystallite size is also affected by the presence of³²P. Asymmetric crystals are suggested to have been potential mediators between asymmetric parity violating forces and molecular asymmetry so that stereo-selective prebiotic chemical reactions involving crystals need not be considered chance processes.No measurable difference in the energy content of optical isomers was found. An upper limit for the direct contribution of weak interactions to electromagnetic ones has been calculated. The mechanism of stereoselective crystal seeding by beta particles is discussed.     

Ontogeny, phylogeny and the origin of biological information.

Accepting the evidence that evolution is largely finished and that sexual reproduction is incapable of supporting macroevolution, indicates that macroevolutionary changes were produced presexually through the cytological events associated with the first meiotic division. This reproductive mode is ideally suited to the production of new structural rearrangements of preexisting genetic information in instantaneous homozygous form. These new arrangements (position effects) produce new and discrete species. Thus, speciation results not from new genetic information, but rather from information already present (preformed). The several parallels that exist between epigenesis and preformation in both ontogeny (development) and phylogeny (evolution) are discussed. I propose that both of these phenomena have proceeded through the selective activation (derepression) of an enormous potential supply of information already present at the onset of each of these biological phenomena. Acceptance of these possibilities can serve to liberate us in our quest for the ultimate truth concerning these two closely related phenomena.     

On the physical origin of biological handedness.

In the racemic conglomerate crystallization of over 1,000 samples of D,L-sodium-ammonium tartrate the effect of 32P beta irradiation on the weight, optical activity, and crystallite size was measured. Both weight and optical activity showed a statistical dependence on the intensity of beta irradiation. The crystallite size is also affected by the presence of 32P. Asymmetric crystals are suggested to have been potential mediators between asymmetric parity violating forces and molecular asymmetry so that stereo-selective prebiotic chemical reactions involving crystals need not be considered 'chance' processes. No measurable difference in the energy content of optical isomers was found. An upper limit for the direct contribution of weak interactions to electromagnetic ones has been calculated. The mechanism of stereoselective crystal seeding by beta particles is discussed.     

On the origin of biological chirality via natural beta-decay

Experimental evidence that longitudinally polarized electrons having the handedness characteristic of terrestrial beta-decay electrons preferentially remove D-leucine from a racemic mixture, coupled with the probable presence of¹⁴C in pre-biotic molecules, offers a plausible hypothesis for the origin of biomolecular handedness.     

On the origin of distribution patterns of motifs in biological networks

Background

Data from high-throughput experiments of protein-protein interactions are commonly used to probe the nature of biological organization and extract functional relationships between sets of proteins. What has not been appreciated is that the underlying mechanisms involved in assembling these networks may exhibit considerable probabilistic behaviour.

Results

We find that the probability of an interaction between two proteins is generally proportional to the numerical product of their individual interacting partners, or degrees. The degree-weighted behaviour is manifested throughout the protein-protein interaction networks studied here, except for the high-degree, or hub, interaction areas. However, we find that the probabilities of interaction between the hubs are still high. Further evidence is provided by path length analyses, which show that these hubs are separated by very few links.

Conclusion

The results suggest that protein-protein interaction networks incorporate probabilistic elements that lead to scale-rich hierarchical architectures. These observations seem to be at odds with a biologically-guided organization. One interpretation of the findings is that we are witnessing the ability of proteins to indiscriminately bind rather than the protein-protein interactions that are actually utilized by the cell in biological processes. Therefore, the topological study of a degree-weighted network requires a more refined methodology to extract biological information about pathways, modules, or other inferred relationships among proteins.     

The origin of biological homochirality

The single handedness of biological molecules has fascinated scientists and laymen alike since Pasteur's first painstaking separation of the enantiomorphic crystals of a tartrate salt over 150 years ago. More recently, a number of theoretical and experimental investigations have helped to delineate models for how one enantiomer might have come to dominate over the other from what presumably was a racemic prebiotic world. Mechanisms for enantioenrichment that include either chemical or physical processes, or a combination of both, are discussed in the context of experimental studies in autocatalysis and in the phase behaviour of chiral molecules.     

Evolution of biological information

How do genetic systems gain information by evolutionary processes? Answering this question precisely requires a robust, quantitative measure of information. Fortunately, 50 years ago Claude Shannon defined information as a decrease in the uncertainty of a receiver. For molecular systems, uncertainty is closely related to entropy and hence has clear connections to the Second Law of Thermodynamics. These aspects of information theory have allowed the development of a straightforward and practical method of measuring information in genetic control systems. Here this method is used to observe information gain in the binding sites for an artificial ‘protein’ in a computer simulation of evolution. The simulation begins with zero information and, as in naturally occurring genetic systems, the information measured in the fully evolved binding sites is close to that needed to locate the sites in the genome. The transition is rapid, demonstrating that information gain can occur by punctuated equilibrium.     

New insights into the origin of biological chirality

Life is characterized by a selectivity for asymmetric molecules. A great deal of theoretical and experimental work has yet to explain why living organisms utilize only L-amino acids in proteins and D-sugars in RNA and DNA. Also unknown is how a form of life based on asymmetric molecules evolved from an environment containing a racemic mixture of prebiotic molecules. By what mechanism did this selectivity for asymmetric molecules take place?     

Levels of biological organization and the origin of novelty

The concept of novelty in evolutionary biology pertains to multiple tiers of biological organization from behavioral and morphological changes to changes at the molecular level. Identifying novel features requires assessments of similarity (homology and homoplasy) of relationships (phylogenetic history) and of shared developmental and genetic pathways or networks. After a brief discussion of how novelty is used in recent literature, we discuss whether the evolutionary approach to homology and homoplasy initially formulated by Lankester in the 19th century informs our understanding of novelty today. We then discuss six examples of morphological features described in the recent literature as novelties, and assess the basis upon which they are regarded as novel. The six are: origin of the turtle shell, transition from fish fins to tetrapod limbs, origination of the neural crest and neural crest cells, cement glands in frogs and casquettes in fish, whale bone-eating tubeworms, and the digestion of plant proteins by nematodes. The article concludes with a discussion of means of acquiring novel genetic information that can account for novelty recognized at higher levels. These are co-options of existing genetic circuitry, gene duplication followed by neofunctionalization, gene rearrangements through mobile genetic elements, and lateral gene transfer. We conclude that on the molecular level only the latter category provides novel genetic information, in that there is no homologous precursor. However, novel phenotypes can be generated through both neofunctionalization and gene rearrangements. Therefore, assigning phenotypic or genotypic "novelty" is contingent on the level of biological organization addressed.     

Proline autocatalysis in the origin of biological enantioenriched chirality

Biological enantioenriched chirality is a phenomenon that in living organisms, amino acids and carbohydrates typically have the same absolute configuration. Perhaps one of the earliest attempts to delineate the origins of this phenomenon was a theory known as asymmetric autocatalysis, a reaction in which the structures of the chiral catalyst and the product are the same, and in which the chiral product acts as a chiral catalyst for its own production. In theory, this would mean that small asymmetries in the product will propagate rapidly. However, autocatalysis also relies on the cross‐inhibition of chiral states, something that would not likely be possible on primordial Earth. But recently, theories on asymmetric autocatalysis have begun to resurface as more recent findings indicate that other mechanisms exist to stabilize the homochiral states. In this study, I propose an autocatalytic cycle, and using density functional theory, prove that (1) it is plausible on primordial Earth, and (2) it propagates arbitrary asymmetries in proline. Thus, facilitating asymmetry in proline and allowing access to a wide variety of asymmetric proline‐catalyzed reactions, including those involved in the synthesis of amino acids and carbohydrates from achiral precursors.     

On the origin of plastids

The buoyant density in CsCl of ribosomes from chloroplasts of the green algaChlorella pyrenoidosa and two species of higher plants,Pisum sativum andChenopodium album, has been studied. From the relative protein content it was calculated that 70S ribosomes from chloroplasts are much smaller than 80S cytoplasmic ribosomes (3.0–3.1×10⁶ and 4.0×10⁶ daltons) and slightly larger than 70S ribosomes from abcteriaE. coli 2.5×10⁶ daltons). Chloroplast ribosomes from pea seedlings were analyzed by two-dimensional polyacrylamide gel electrophoresis. They appear to contain 71 proteins. This indicates that chloroplast ribosomes contain a larger number of proteins than do the ribosomes fromE. coli and other species of Enterobacteriaceae. Further study will permit a probable evaluation of the validity of Mereschkowsky's hypothesis that the photosynthetic plastids of eukaryotic plant cells are the evolutionary descendants of endosymbiotic blue-green algae.