A note on the quantum-theoretic basis of primary genetic activity

In previous work (Bull. Math. Biophysics,23, 393–403, 1960) it was shown that, if primary genetic processes are of an essentially microphysical nature, the objects bearing the primary genetic information must act in a catalytic fashion. At the same time it was pointed out that the kind of catalysis involved in the primary genetic process was fundamentally different, in specific ways, from that occurring, e.g., in enzyme systems. The present work demonstrates that, if the information-bearing objects of the general theory are identified with molecules of DNA, and the primary gene products are considered to be RNA of the “messenger” variety, then the predictions of the general theory can be compared with experimental data from various recently isolated polymerase systems, which appear to “copy” a sequence of nucleotides from DNA into RNAin vitro, and with certainin vivo microbial systems. It is found that these data provide detailed support for the conclusions drawn from the general theory. However, it is emphasized that the identification of the information-bearing objects and primary gene products as DNA and RNA respectively, which allows us to compare the theory with the cited data, is by no means the only identification which can be made; i.e., other interpretations of the general theory are certainly not precluded. This research was supported by the United States Air Force through the Air Force Office of Scientific Research of the Air Research and Development Command, under Grant No. AF-AFOSR-9-63.     

On the role of chemical systems in the microphysical aspects of primary genetic mechanisms

It is pointed out that two fundamentally different views of primary genetic processes occur in the literature which are frequently confused. The first is a true communication-theoretic view, which regards the genetic apparatus as containing a real information-source and a transducer which converts that information to useful form. The second view is generally expressed as a template scheme based on the Watson-Crick model; it is shown that in this model there is actually no such thing as genetic information in a communication-theoretic sense. Both views are then discussed on the basis of microphysical principles developed in previous work of the author (Bull. Math. Biophysics,22, 227–255, 1960) in an attempt to find which approach is in closer accord with the biological facts. It is shown that, if the communication-theoretic view is correct, then the information-bearing object must act as a “catalyst,” but it is pointed out that the type of catalysis involved must be of a fundamentally different nature than that occurring in familiar enzyme-catalyzed reactions. On the basis of general considerations of irreversible changes in microphysical measuring systems, it is shown that any type of template must suffer a gradual and irreversible denaturation, which seems to make it unlikely that a template could play a primary role in fundamental genetic processes. This research was supported by the United States Air Force through the Air Force Office of Scientific Research of the Air Research and Development Command, under Contract AF 49(638)-917.     

A note on abstract relational biologies

It is shown that the class of abstract block diagrams of (M, ℜ)-systems which can be constructed out of the objects and mappings of a particular subcategoryG ₀ of the categoryG of all sets depends heavily on the structure ofG ₀, and in particular on the number of sets of mappingsH(A, B) which are empty inG ₀. In the context ofG ₀-systems, there-fore, each particular categoryG ₀ gives rise to a different “abstract biology” in the sense of Rashevsky. A number of theorems illustrating the relation between the structure of a categoryG ₀ and the embeddability of an arbitrary mapping αεG ₀ into an (M, ℜ)-system are proved, and their biological implication is discussed. This research was supported by the United States Air Force through the Air Force Office of Scientific Reserch of the Air Research and Development Command, under Contract No. AF 49(638)-917.     

First results from plasma density measurements in the FTU tokamak by means of a two-frequency pulsed time-of-flight refractometer

A pulsed time-of-flight refractometer was developed and tested to determine the mean plasma density in the T-11M tokamak by measuring the propagation time of nanosecond microwave pulses in plasma. Later, it was also proposed to use such an instrument to measure and control the mean plasma density in the ITER tokamak by probing the plasma with an extraordinary wave, the electric field of which is perpendicular to the magnetic field in plasma, in the transparency window at frequencies of 50–100 GHz. To avoid the effect of the density profile shape on the measurement results in the nonlinear mode of refractometer operation (near the cutoff), a system operating at two different probing frequencies was developed and tested. Such a system provides two values of the time delay, which can be used to estimate the peaking factor of the density distribution α and correctly determine the linear density 〈Nl〉, regardless of the density profile (assuming a smooth density profile of the form of N(ρ) = N(0)(1 − ρ²)^α, where N(0) is the central plasma density and ρ = r/a is the normalized plasma radius). The first experiments on density measurements in the FTU tokamak performed with this refractometer are described, and results from these experiments are presented. The formation of a thin dense plasma layer in the zone of a strong magnetic field (the so-called MARFE layer) at a relatively low (for FTU) plasma density of ∼6 × 10¹⁹ m⁻³ was detected. The thickness of this layer, determined from the refractometry data, agrees well with the data obtained using a digital camera.     

Impact of magnetic field inhomogeneity on electron cyclotron radiative loss in tokamak reactors

The potential importance of electron cyclotron (EC) emission in the local electron power balance in the steady-state regimes of ITER operation with high temperatures, as well as in the DEMO reactor, requires accurate calculation of the one-dimensional (over magnetic surfaces) distribution of the net radiated power density, P _EC(ρ). When the central electron temperature increases to ∼30 keV, the local EC radiative loss comprises a substantial fraction of the heating power from fusion alphas and is close to the total auxiliary NBI heating power, P _EC(0) ≃ 0.3P _α(0) ≃ P _aux(0). In the present paper, the model of EC radiative transport in an axisymmetric toroidal plasma is extended to the case of an inhomogeneous magnetic field B(R, Z). The impact of such inhomogeneity on local and total power losses is analyzed in the framework of this model by using the CYNEQ code. It is shown that, for the magnetic field B, temperature T _e , density n _e , and wall reflection coefficient R _w expected in ITER and DEMO, accurate simulations of the EC radiative loss require self-consistent 1.5D transport analysis (i.e., one-dimensional simulations of plasma transport and two-dimensional simulations of plasma equilibrium). It is shown that EC radiative transport can be described with good accuracy in the 1D approximation with the surface-averaged magnetic field, B(ρ) = 〈B(R, Z)〉 _ms . This makes it possible to substantially reduce the computational time required for time-dependent self-consistent 1.5D transport analysis. Benchmarking of the CYNEQ results with available results of the RAYTEC, EXACTEC, and CYTRAN codes is performed for various approximations of the magnetic field.     

On the reversibility of environmentally induced alterations in abstract biological systems

The environmentally induced alterations in structure of (M, ℜ) which were described previously (R. Rosen,Bull. Math. Biophysics,23, 165–171, 1961) are examined from the standpoint of determining under what circumstances they can be reversed by further environmental interactions. For simplicity we consider only the case of (M, ℜ)-systems possessing one “metabolic” and one “genetic” component. In the case of environmentally induced alteration of the “metabolic” component alone, a necessary and sufficient condition is given for the reversibility of the alteration. In the case of alteration of the “genetic” component, the situation becomes more complex; several partial results are given, but a full analysis is not available at this time. Some possible biological implications of this analysis are discussed. This research was supported by the United States Air Force through the Air Force Office of Scientific Research of the Air Research and Development Command, under Contract no. AF-49(638)-917 and Grant no. AF-AFOSR-9-63.     

AnO(N 2 logN) restriction map comparison and search algorithm

We present anO(R logP) time,O(M+P ² ) space algorithm for searching a restriction map withM sites for the best matches to a shorter map withP sites, whereR, the number of matching site pairs, is bounded byMP. As first proposed by Watermanet al. (1984,Nucl. Acids Res. 12, 237–242) the objective function used to score matches is additive in the number of unaligned sites and the discrepancies in the distances between adjacent aligned sites. Our algorithm is basically a sparse dynamic programming computation in which “candidate lists” are used to model the future contribution of all previously computed entries to those yet to be computed. A simple modification to the algorithm computes the distance between two restriction maps withM andN sites, respectively, inO(MN(logM+logN)) time. This author’s work was supported in part by National Library of Medicine Grant R01-LM4960. This author’s work was supported in part by National Library of Medicine Grant R01-LM5110.     

How Willing Are You to Accept Sexual Requests from Slightly Unattractive to Exceptionally Attractive Imagined Requestors?

In their classic study of differences in mating strategies, Clark and Hatfield (1989, Journal of Psychology and Human Sexuality, 2, 39–54) found that men and women demonstrated a striking difference in interest in casual sex. The current study examined the role of an imagined requestor’s physical attractiveness (slightly unattractive, moderately attractive, and exceptionally attractive) on men’s and women’s willingness to accept three different requests (go out, come to apartment, go to bed) as reflected in answers to a questionnaire. We tested two hypotheses with a sample of 427 men and 443 women from three countries. Hypothesis 1 states that men, relative to women, will demonstrate a greater willingness to accept the “come to apartment” and “go to bed” requests but not the “go out” request for all three levels of requestor attractiveness. This hypothesis reflects Clark and Hatfield’s main findings. Hypothesis 2 states that the physical attractiveness of a potential partner will have a greater effect on women’s than on men’s willingness to accept all three requests, and particularly for the explicit request for casual sex. The results partially supported Hypothesis 1 and fully supported Hypothesis 2. The discussion highlights limitations of the current research and presents directions for future research.     

Theoretical description of hydrogen bonding in oxalic acid dimer and trimer based on the combined extended-transition-state energy decomposition analysis and natural orbitals for chemical valence (ETS-NOCV)

In the present study we have analyzed hydrogen bonding in dimer and trimer of oxalic acid, based on a recently proposed charge and energy decomposition scheme (ETS-NOCV). In the case of a dimer, two conformations, α and β, were considered. The deformation density contributions originating from NOCV’s revealed that the formation of hydrogen bonding is associated with the electronic charge deformation in both the σ—(Δρ_σ) and π-networks (Δρ_π). It was demonstrated that σ-donation is realized by electron transfer from the lone pair of oxygen on one monomer into the empty r_{H - O}^* \rho_{H - O}^* orbital of the second oxalic acid fragment. In addition, a covalent contribution is observed by the density transfer from hydrogen of H-O group in one oxalic acid monomer to the oxygen atom of the second fragment. The resonance assisted component (Δρ_π), is based on the transfer of electron density from the π—orbital localized on the oxygen of OH on one oxalic acid monomer to the oxygen atom of the other fragment. ETS-NOCV allowed to conclude that the σ(O---HO) component is roughly eight times as important as π (RAHB) contribution in terms of energetic estimation. The electrostatic factor (ΔE_elstat) is equally as important as orbital interaction term (ΔE_orb). Finally, comparing β-dimer of oxalic acid with trimer we found practically no difference concerning each of the O---HO bonds, neither qualitative nor quantitative.     

The derivation of D’Arcy Thompson’s theory of transformations from the theory of optimal design

It is shown informally that Cohn’s theory of Optimal Forms can be construed as a comparative theory, and that when this is done the celebrated theory of transformations of D’Arcy Thompson follows as a consequence. The implications of this type of theoretical foundation for the Thompson theory with regard to problems of comparative morphology are discussed, and some suggestions for the further implementation of the theory are described. This research was supported by the United States Air Force through the Air Force Office of Scientific Research of the Air Research and Development Command, under Contract No. AF 49(638)-917.     

A relational theory of the structural changes induced in biological systems by alterations in environment

It is shown that a wide variety of structural alterations in both the “metabolic” and “genetic” apparatus of ( , ℜ)-systems can result from specific changes in the environment of such systems. A number of specific examples are investigated in order to demonstrate the scope of these alterations. Certain biological applications of this discussion are suggested, including a suggestion for a possible interpretation of the mitotic cycle. This research was supported by the United States Air Force through the Air Force Office of Scientific Research of the Air Research and Development Command, under Contract #AF 49 (638)-917.     

Kinetic processes initiated by a nanosecond high-current discharge in hot air

Results from numerical investigations of kinetic processes initiated by a pulsed nanosecond discharge in hot (T ₀ ≥ 1000 K) air at atmospheric pressure are presented. The calculated results on the dynamics of the electron density, the population of the N₂(B³Π _g ) and N₂(C³Π _u ) states, and the atomic oxygen density in the axial discharge region agree with experiment. The method for determining the gas temperature by measuring the rotational structure of the transitions N₂(C³Π _u , ν) → N₂(B³Π _g , ν′) of the 2⁺ nitrogen system is analyzed. It is shown that, in relatively weak reduced electric fields typical of secondary discharge pulses, the electron impact excitation of the N₂(C³Π _u ) state from the ground state N₂(X¹Σ _g ⁺) can be accompanied by its additional step population from the N₂(B³Π _g ), N₂(a′Σ _u ⁻), and other electronic states. This effect substantially influences the rotational distribution of nitrogen molecules in the N₂(C³Π _u , ν) state; moreover, the temperature determined from this distribution can be substantially higher than the true gas temperature.     

An account of intersymbol influences in the information theory: Application to linguistics and biology

A model of the statistical structure of symbol sequences that takes into account correlations between the symbols is proposed. The formulas resulting from this model are tested by using empirical data relating to the English language; a satisfactory agreement between the calculated and empirical values is obtained. A formula δ=αl connecting the redundancy δ of a code with the intensity α of correlations and the mean lengthl of compact groups (“words”) of the code is assumed. It is found that the correlation α between adjacent amino-acid residues in protein molecules is less than 10⁻³. In order to detect this correlation by means of the χ² test, a sample of not less than 25,000 dipeptides is required.     

On the theory of indicator-dilution methods under varying blood-flow conditions

The theory of measurement of flow and volume by indicator dilution techniques is given in conditions of time-variable flow rates. It is shown that the usual Hamilton (1932,Am. J. Physiol.,99, 534–551) methods can be misleading if the flow changes at a rate of close to that of the transport function. Operated with support from the United States Army, Navy, and Air Force.     

Theoretical study of hydrogen bond interactions of fluvastatin with <Emphasis Type="BoldItalic">ι</Emphasis>-carrageenan and <Emphasis Type="Italic">λ</Emphasis>-carrageenan

The binding of the reductase inhibitor drug fluvastatin, hydroxy-3-methylglutaryl coenzyme A, with the hydrophilic ι- or λ-carrageenan polymers, serving as potential controllers of the drug’s release rate, have been studied at the density functional level of theory with the B3LYP exchange correlation functional. Three low energy conformers of fluvastatin have been calculated. The vibrational spectroscopic properties calculated for the most stable conformer were in satisfactory agreement with the experimental data. A series of hydrogen bonded complexes of the most stable conformer of fluvastatin anion with low molecular weight models of the polymers have been fully optimized. In almost all, intermolecular H-bonds are formed between the sulfate groups of ι- or λ-carrageenan and fluvastatin’s hydroxyls, resulting in a red shift of the fluvastatin’s O − H stretching vibrations. Cooperative intramolecular H-bonds within fluvastatin or ι-, λ-carrageenan are also present. The BSSE and ZPE corrected interaction energies were estimated in the range 281–318 kJ mol⁻¹ for ι-carrageenan - fluvastatin and 145–200 kJ mol⁻¹ for λ-carrageenan - fluvastatin complexes. The electron density (ρ _bcp) and Laplacian (∇² ρ _bcp) properties at critical points of the intermolecular hydrogen bonds, estimated by AIM (atoms in molecules) calculations, have a low and positive character (∇² ρ _bcp > 0), consistent with the electrostatic character of the hydrogen bonds. The structural and energetic data observed, as well as the extent of the red shift of the fluvastatin’s O − H stretching vibrations upon complex formation and the properties of electron density show a stronger binding of fluvastatin to ι- than to λ-carrageenan.     

Note on the fusion frequency for stimuli of alternating duration

The case of alternating stimulus patterns of moderately high intensity is considered in terms of the model previously discussed (Landahl, 1957,Bull. Math. Biophysics,19, 157–62). If both of the alternating patterns have the same light-dark ratio, then the relation between the period of the longer and the period of the shorter pattern at the critical flicker frequency is independent of the light-dark ratio and is given by a dimensionless expression which is roughly in agreement with data in which the light-dark ratio is one (C. R. Brown and D. M. Forsyth, 1959,Science,129, 390–91). This research was supported in whole or in part by the U. S. Air Force under Contract AF 49(638)-414 monitored by the Air Force Office of Scientific Research.     

Lectin affinity chromatography of articular cartilage fibromodulin: Some molecules have keratan sulphate chains exclusively capped by α(2-3)-linked sialic acid

Fibromodulin from bovine articular cartilage has been subjected to lectin affinity chromatography by Sambucus nigra lectin which binds α(2-6)- linked N-acetylneuraminic acid, and the structure of the keratan sulphate in the binding and non-binding fractions examined by keratanase II digestion and subsequent high pH anion exchange chromatography. It has been confirmed that the keratan sulphate chains attached to fibromodulin isolated from bovine articular cartilage may have the chain terminating N-acetylneuraminic acid residue α(2-3)- or α(2-6)-linked to the adjacent galactose residue. Although the abundance of α(2-6)-linked N-acetylneuraminic acid (ca. 22%) is such that this could cap one of the four chains in almost all fibromodulin molecules, it was found that ca. 34% of the fibromodulin proteoglycan molecules from bovine articular cartilage were capped exclusively with α(2-3)-linked N-acetylneuraminic acid. The remainder of the fibromodulin proteoglycans, which bound to the lectin had a mixture of α(2-3)- and α(2-6)-linked N-acetylneuraminic acid capping structures. The keratan sulphates attached to fibromodulin molecules capped exclusively with α(2-3)- linked N-acetylneuraminic acid were found to have a higher level of galactose sulphation than those from fibromodulin with both α(2-3)- and α(2-6)-linked N-acetylneuraminic acid caps, which bound to the Sambucus nigra lectin. In addition, both pools contained chains of similar length (ca. 8–9 disaccharides). Both also contained α(1-3)-linked fucose, showing that this feature does not co-distribute with α(2-6)-linked N-acetylneuraminic acid, although these two features are present only in mature articular cartilage. These data show that there are discrete populations of fibromodulin within articular cartilage, which may have differing impacts upon tissue processes.     

The environmental signals of stable carbon isotope in various tree-ring components of Pinus tabulaeformis

Chinese pine (Pinus tabulaeformis) trees were sampled in the Helan Mountain, northwest China. The stable carbon isotope (δ¹³C) values of whole wood, holocellulose and alpha-cellulose in tree rings over 30 years (1968–1997) were measured to study the δ¹³C response of different tree-ring components to past environmental change. There were obvious differences in the δ¹³C values of the three components. The Pearson correlation coefficient between the δ¹³C of alpha-cellulose and that of holocellulose was 0.547 (ρ < 0.01); between alpha-cellulose and whole wood, the coefficient was −0.126 (ρ > 0.10); between holocellulose and whole wood, the coefficient was −0.056. Correlation function analyses indicated that the δ¹³C content of tree-ring alpha-cellulose correlated strongly with the average temperature from June to August (r = 0.427, ρ < 0.05), more than that of holocellulose (0.324, ρ < 0.10) or total wood (−0.245, ρ > 0.10). Significant correlations were observed between δ¹³C of tree-ring alpha-cellulose and the precipitation from the current year’s February to July (r = −0.514, ρ < 0.01) that were much higher than that of holocellulose (−0.481, ρ < 0.05) or total wood (−0.249, ρ > 0.10). A significant correlation (−0.545, ρ < 0.01) was also found between the ring width and the δ¹³C residual chronologies. These results suggest that more past environmental information is retained in the δ¹³C of tree-ring alpha-cellulose. Thus, the δ¹³C of alpha-cellulose of tree rings is the most suitable among the studied parameters for reconstructing the past climatic conditions during the growing season. The δ¹³C values of other organic compounds in Pinus tabulaeformis xylem were affected by the external environment after carbon was fixed from the atmosphere.     

Studies in mathematical biosociology of imitative behavior: I. Effects of income distribution

In connection with previous studies (Rashevsky,Mathematical Biology of Social Behavior, chap. xii), a situation is investigated in which the two mutually exclusive possible behaviors of a society consist of the desire to keep the present socioeconomical situation and the desire to change it inany way. The psychophysiological tendency ϕ towards either of the behaviors is considered to be proportional to the difference between the actual incomei of the individual and his needsi′. Assuming that the distribution functionN ₁(i′) of the needs is a given characteristic of the population, it is shown that the distribution functionN(ϕ) of ϕ in the society can be derived fromN ₁(i′) and from the distributionN ₂(i) of the incomesi. A particular case is worked out as an example. Conditions of stability of a socioeconomic structure are studied in their dependence on the income distribution.     

Ethanol production using nuclear petite yeast mutants

Two respiratory-deficient nuclear petites, FY23Δpet191 and FY23Δcox5a, of the yeast Saccharomyces cerevisiae were generated using polymerase-chain-reaction-mediated gene disruption, and their respective ethanol tolerance and productivity assessed and compared to those of the parental grande, FY23WT, and a mitochondrial petite, FY23ρ⁰. Batch culture studies demonstrated that the parental strain was the most tolerant to exogenously added ethanol with an inhibition constant. K _i, of 2.3% (w/v) and a specific rate of ethanol production, q _p, of 0.90 g ethanol g dry cells⁻¹ h⁻¹. FY23ρ⁰ was the most sensitive to ethanol, exhibiting a K _i of 1.71% (w/v) and q _p of 0.87 g ethanol g dry cells⁻¹ h⁻¹. Analyses of the ethanol tolerance of the nuclear petites demonstrate that functional mitochondria are essential for maintaining tolerance to the toxin with the 100% respiratory-deficient nuclear petite, FY23Δpet191, having a K _i of 2.14% (w/v) and the 85% respiratory-deficient FY23Δcox5a, having a K _i of 1.94% (w/v). The retention of ethanol tolerance in the nuclear petites as compared to that of FY23ρ⁰ is mirrored by the ethanol productivities of these nuclear mutants, being respectively 43% and 30% higher than that of the respiratory-sufficient parent strain. This demonstrates that, because of their respiratory deficiency, the nuclear petites are not subject to the Pasteur effect and so exhibit higher rates of fermentation. Received: 22 September 1997 / Accepted: 7 December 1997