Analogies between physics and biology

Considerations about fundamental relations between physics and biology are continued. So the base of this new hypothesis is finished and can be discussed.     

The synthesis of physics and biology

The hypothesis of a qualitative new field permits the prediction of a new fundamental constant. With this constant a relation between c and h can be found. The new constant permits not only a system of physics but also a new transition from physics into biology.     

Bridging the gap between physics and biology.

The work is devoted to the historical development of physics and biology. Various aspects of their interactions are shown: antagonism, mutual penetration and a lot of bridges, built or being built between them. The gradual "evolution of the world picture" from going away of the "pre-scientific" animated Universe and the appearance of mechanicism and vitalism to the development of systems and field approaches is traced. The last part of the paper is concerned with some present-day works at the joint between physics and biology.     

Metrology in physics,chemistry, and biology

The association of physics and chemistry with metrology (the science of measurements) is well documented. For practical purposes, basic metrological measurements in physics are governed by two components, namely, the measure (i.e., the unit of measurement) and the measurand (i.e., the entity measured), which fully account for the integrity of a measurement process. In simple words, in the case of measuring the length of a room (the measurand), the SI unit meter (the measure) provides a direct answer sustained by metrological concepts. Metrology in chemistry, as observed through physical chemistry (measures used to express molar relationships, volume, pressure, temperature, surface tension, among others) follows the same principles of metrology as in physics. The same basis percolates to classical analytical chemistry (gravimetry for preparing high-purity standards, related definitive analytical techniques, among others). However, certain transition takes place in extending the metrological principles to chemical measurements in complex chemical matrices (e.g., food samples), as it adds a third component, namely, indirect measurements (e.g., AAS determination of Zn in foods). This is a practice frequently used in field assays, and calls for additional steps to account for traceability of such chemical measurements for safeguarding reliability concerns. Hence, the assessment that chemical metrology is still evolving.     

Note on a combinatorial problem in topological biology

In connection with a previous paper, an expression is derived for the number of possibilities in whichn distinguishable elements can be distributed intom≤n classes, so that each class contains at least one element.     

The principle of complementarity in biology

Zusammenfassung Es wird der Nachweis versucht, dass es — ebenso wie in der Physik — auch in der Biologie komplementäre Erkenntnissysteme gibt. Wie Welle und Korpuskel in der Physik, so sind innerhalb der Biologie u.a. Form und Funktion, Innenwelt und Umwelt sowie auch vor allem Vererbung und Anpassung komplementäre Begriffsgefüge. Das wird im einzelnen diskutiert und nachgewiesen.Für die Erkenntnis der Wirklichkeit im Ganzen folgt daraus, dass systematisch aufgebaute Erkenntnisgefüge nur in Teilbereichen des Wirklichen möglich sind — nur in der klassischen Mechanik, der Elektrodynamik, der vergleichenden Anatomie, der Genetik usw. — Das Wirkliche in seiner Gesamthet hingegen besitzt keine systematische sondern nur eine historisch-dialektische Struktur. Metaphysisch bedeutet das, dass das Wesen der Wirklichkeit in schöpferischer Freiheit im Sinne etwaGoethes, aber nicht in sturer Notwendigkeit (dira necessitas im SinneSpinozas) besteht.

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Contenido Se demuestra que — como en laFisica — tambien en la Biologia existen complementarios sistemas de conocimiento. Como onda y corpúsculo dentro de la Fisica, asi son dentro de la Biologia entre otros forma y función, mundo internoy ambientey en primer lugar también herencia y adaptación principios complementarios. Esto será discutido y demonstrado en sus particularidades.Para el conocimiento de la realidad como totalidad sigue de tales consideraciones la conclusión que conocimientos sistematicamente construidos son posibles solo en esferas particulares de la realidad — como p.e. en la mecánica racional, en la electrodinámica, en la anatomia comparada, en la genética etc. —. Lo real en su totalidad posee al contrario ninguna estructura sistemática sino solo un históricadialectica. Metafisicamente hablado significa esto que la esencia de la realidad consiste en una libertad creativa en el sentido deGoethe, pero de ninguna manera en una necesidad absoluta en el sentido deSpinoza.

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Lecture delivered August 1953 at the Biological Department of the University of Texas in Austin (Texas) U.S.A.     

Modelling DNA stretching for physics and biology

We have used internal coordinate molecular mechanics calculations to study how the DNA double helix deforms upon stretching. Results obtained for polymeric DNA under helical symmetry constraints suggest that two distinct forms, an unwound ribbon and a narrow fibre, can be formed as a function of which ends of the duplex are pulled. Similar results are also obtained with DNA oligomers. These experiments lead to force curves which exhibit a plateau as the conformational transition occurs. This behaviour is confirmed by applying an increasing force to DNA and observing a sudden length increase at a critical force value. It is finally shown some DNA binding proteins can also stretch DNA locally, to conformations related to those created by nanomanipulation.This revised version was published online in October 2005 with corrections to the Cover Date.     

Reduction of biology to fundamental physics

It was shown that, while interpreting life as a physical phenomenon, fundamental physics allows for the following alternatives: relativity of animate and inanimate upon canonical transformations; the impossibility of the change from animate to inanimate state of isolated systems; the abandonment of attempts to reduce biology to the physics of isolated systems. The possibility of reducing biology to phenomenological physics was considered. A number of equations for the general phenomenological dynamics of density matrix was proposed.     

Higher-order chromatin structure: bridging physics and biology

Advances in microscopy and genomic techniques have provided new insight into spatial chromatin organization inside of the nucleus. In particular, chromosome conformation capture data has highlighted the relevance of polymer physics for high-order chromatin organization. In this context, we review basic polymer states, discuss how an appropriate polymer model can be determined from experimental data, and examine the success and limitations of various polymer models of higher-order interphase chromatin organization. By taking into account topological constraints acting on the chromatin fiber, recently developed polymer models of interphase chromatin can reproduce the observed scaling of distances between genomic loci, chromosomal territories, and probabilities of contacts between loci measured by chromosome conformation capture methods. Polymer models provide a framework for the interpretation of experimental data as ensembles of conformations rather than collections of loops, and will be crucial for untangling functional implications of chromosomal organization.     

On the application of statistical physics to evolutionary biology

There is a close analogy between statistical thermodynamics and the evolution of allele frequencies under mutation, selection and random drift. Wright's formula for the stationary distribution of allele frequencies is analogous to the Boltzmann distribution in statistical physics. Population size, 2N, plays the role of the inverse temperature, 1/kT, and determines the magnitude of random fluctuations. Log mean fitness, , tends to increase under selection, and is analogous to a (negative) energy; a potential function, U, increases under mutation in a similar way. An entropy, S_H, can be defined which measures the deviation from the distribution of allele frequencies expected under random drift alone; the sum gives a free fitness that increases as the population evolves towards its stationary distribution. Usually, we observe the distribution of a few quantitative traits that depend on the frequencies of very many alleles. The mean and variance of such traits are analogous to observable quantities in statistical thermodynamics. Thus, we can define an entropy, S_Ω, which measures the volume of allele frequency space that is consistent with the observed trait distribution. The stationary distribution of the traits is ; this applies with arbitrary epistasis and dominance. The entropies S_Ω, S_H are distinct, but converge when there are so many alleles that traits fluctuate close to their expectations. Populations tend to evolve towards states that can be realised in many ways (i.e., large S_Ω), which may lead to a substantial drop below the adaptive peak; we illustrate this point with a simple model of genetic redundancy. This analogy with statistical thermodynamics brings together previous ideas in a general framework, and justifies a maximum entropy approximation to the dynamics of quantitative traits.     

Toward an optimal design principle in relational biology

A vulnerability criterion is posed for a biological system within the context of representing the system as a relational set, i.e., a collection of components whose interdependency is described by means of a set of binary relations. The criterion provides a numerical value for each representation and therefore a means for comparing one representation against another. Choice of the criterion is such that the larger a numerical value a representation has then the less vulnerable to destruction is the system represented. Other things being equal, it is argued that the representation which endows the system with the least vulnerability is more likely to be a valid representation. A selection criterion is thereby achieved for narrowing down the choice ofa priori representations.