Life consists of the ability to move and generate electricity; to take up nutrients and expel wastes; to perform chemical syntheses of organic molecules at ambient temperatures and pressures, and therefore grow; to reproduce itself with near-perfect fidelity; and to sense and respond to changes in the external environment to maintain itself. The cell is the lowest level of organization that has the ability to perform all these processes and thus is the basic unit of life. To get an idea of the nature of cells based on first principles, I describe the discovery of cells, their dimensions, their chemical composition, and the energetics of cells.

This chapter focuses on the various adaptive and developmental responses that plants undergo in response to their environment. When the cells receive the stimulus from the environment, they respond through changes in their biophysical, biochemical, physiological, morphological, or developmental processes. These responses may include germination, flowering, osmoregulation, turgor regulation, chloroplast movement, phototaxis, leaf movements, gravitropism, senescence, abscission, and the processes involved in plant defense. A stimulus contains energy, and a signal transduction chain converts the energy of the primary stimulus, which may be light, gravity, chemical, heat, or electrical energy, to the energy of an intracellular molecule that can be coupled to the biochemical machinery in the cell. The energy of the stimulus is transferred to a receptor, which often takes advantage of the potential energy already present, typically in the form of Ca2+ difference across the plasma membrane, to activate the cell. The competence of the cell to respond to a given stimulus is dependent on the receptors in the cell, and the response that the cell undergoes depends on its response elements.

Maxwell’s electromagnetic wave theory has provided the foundation for life- changing and life-saving technologies from smartphones to magnetic resonance imaging. This is especially intriguing given that Maxwell’s electromagnetic wave is inconsistent with the fundamental scientific principles of causality and conservation of energy, as well as the assumption of the Kirchhoff diffraction integral, which is the fundamental equation used in optics to relate the object to the image. These contradictions exist because Maxwell arbitrarily considered the waves that represent the magnetic and electric fields to be in-phase. In this article, I show that the reintroduction of the “evil” magnetic vector potential resolves the contradictions by giving a first principle approach to the claim that the waves that represent the magnetic and electric fields are a quadrature out-of-phase.

In the cells of Chara corallina, permeant monohydric alcohols including methanol, ethanol and 1-propanol increased the hydraulic resistance of the membrane (Lpm−1). We found that the relative value of the hydraulic resistance (rLpm−1) was linearly dependent on the concentration (Cs) of the alcohol. The relationship is expressed in the equation: rLpm−1 = ρmCs + 1, where ρm is the hydraulic resistance modifier coefficient of the membrane. Ye et al. (2004) showed that membrane-permeant glycol ethers also increased Lp−1. We used their data to estimate Lpm−1 and rLpm−1. The values of rLpm−1 fit the above relation we found for alcohols. When we plotted the ρm values of all the permeant alcohols and glycol ethers against their molecular weights (MW), we obtained a linear curve with a slope of 0.014 M−1/MW and with a correlation coefficient of 0.99. We analyzed the influence of the permeant solutes on the relative hydraulic resistance of the membrane (rLpm−1) as a function of the external (π0) and internal (πi) osmotic pressures. The analysis showed that the hydraulic resistance modifier coefficients (ρm) were linearly related to the MW of the permeant solutes with a slope of 0.012 M−1/MW and with a correlation coefficient of 0.84. The linear relationship between the effects of permeating solutes on the hydraulic resistance modifier coefficient (ρm) and the MW can be explained in terms of the effect of the effective osmotic pressure on the hydraulic conductivity of water channels. The result of the analysis suggests that the osmotic pressure and not the size of the permeant solute as proposed by (Ye et al., J Exp Bot 55:449–461, 2004) is the decisive factor in a solute’s influence on hydraulic conductivity. Thus, characean water channels (aquaporins) respond to permeant solutes with essentially the same mechanism as to impermeant solutes.

The hydraulic resistance (the reciprocal of the hydraulic conductivity Lp) Lp−1 was measured in cells of Chara corallina by the method of transcellular osmosis. Treatment of cells with 100 mM KCl decreased Lp−1 significantly. Subsequent treatment of the cells with 70 mM CaCl2 recovered the decreased Lp−1 to the original value. To know whether K+ or Ca2+/Mg2+ acts on the cell wall and/or the membrane, the hydraulic resistances of the cell wall (Lpw−1) and that of the membrane (Lpm−1) were determined in one and the same cell. For this, a pair of cells (twin cells) were made from an internodal cell, one used for measurement of Lp−1 and the other used for the measurement of Lpw−1. From Lp−1 and Lpw−1, Lpm−1 was calculated. Both Lp−1 and Lpw−1 were decreased by K+, while Lpm−1 was not affected by K+. The same result was obtained with 5 mM EGTA. Lpw−1 was decreased more than it was by KCl but Lpm−1 remained constant after EGTA treatment. The recovery of the K+-decreased Lp−1 with Ca2+ can be explained exclusively by the recovery of Lpw−1 with Ca2+. The Ca2+ recovery of Lpw−1 was observed in the intact cell wall but not in the cell wall tube isolated from an internodal cell. The different response to Ca2+ between the intact cell wall and the isolated cell wall was discussed in relation to the tension in the cell wall which may be an important factor for the ionic regulation of hydraulic conductivity.

Hydraulic resistances (reciprocals of hydraulic conductivities) of the cell (Lp−1), the cell wall (Lpw−1), the membrane (Lpm−1), the plasma membrane (Lppm−1), and the tonoplast (Lptp−1) were determined in individual internodal cells of Chara corallina and their dependence on the cell age was studied. The thickness of the cell wall (d) was adopted as an index of the cell age, since the cell wall of spring-grown young cells (sg-cells) was found to be significantly thinner than that of winter-spent old cells (ws-cells). Both Lpw−1 and Lpm−1 were found to increase with cell age. Since Lpm−1 is the sum of Lppm−1 and Lptp−1, their dependence on the wall thickness was studied. It was found that both Lppm−1 and Lptp−1 increase with cell age using d as a proxy and that the former is distinctly higher than the latter. The ratio Lppm−1/Lptp−1 amounts to 30 for 5 μm of d, indicating that the tonoplast is a negligible barrier to osmotic water flow. The ratio decreases with the increase in d and amounts to 5.0 for 11 μm of d, showing that the tonoplast ages faster than the plasma membrane. The physiological meaning of the age dependence of hydraulic resistance of the tonoplast was discussed in terms of the role of the vacuole in the osmoregulation of the cytoplasm.

Michael Faraday discovered that linearly polarized light could be rotated by a magnetic field as it propagated through a piece of "heavy glass." Since the effect could not be observed in air, Faraday assumed that the magnetic field acted on the glass and that the glass influenced the magnetic properties of light itself. According to the standard theory, the magnetic field causes the glass, which has a single refractive index in the absence of a magnetic field, to become optically active as a result of the Lorentz force acting on the electrons in the glass. As a result, the glass develops one refractive index for right circularly polarized (RCP) light and another refractive index for left circularly polarized (LCP) light. This results in the rotation of the azimuth of polarization. While the discovery of the Faraday effect was important evidence for the electromagnetic theory of light, the magnetic property of light itself that responds to the changes in the refractive index remains enigmatic. Here we suggest that if light be described as being composed of equal and opposite moving charges within each binary photon, the magnetic field would act both on the glass and on the light itself. The binary photon model proposes that the photon is not an elementary particle but a complex of two particles that are conjugate in terms of mass, electric charge, and sense of rotation, whose movements generate a linearly polarized transverse electric field and a circularly polarized magnetic field that is orthogonal to the electric field and phase shifted by one quarter wavelength. The binary photon contains an electric dipole and a magnetic moment, which logically seem to be a sine qua non for the carrier of the electromagnetic force. As a result of the electromagnetic properties of the binary photon, the force exerted on the binary photons by the applied magnetic field used to demonstrate the Faraday effect would result in the transformation of binary photons with a single wavelength into binary photons with two different wavelengths. The binary photons with two different wavelengths would no longer experience the same refractive index as they propagated through the glass because by necessity, the glass required to show the Faraday effect with a relatively short geometrical path length must have high dispersion and a low Abbe number. As a result of the high dispersion and low Abbe number, the transformed binary photons with the shorter wavelength would experience a higher refractive index and the transformed binary photons with the longer wavelength would experience a lower refractive index. Consequently, as they propagated through the glass, the shorter wavelength binary photons would be retarded relative to the longer wavelength binary photons and the azimuth of polarization would be rotated. The model of the binary photon and its response to a magnetic field describes and explains the magnetic properties of light proposed by Faraday and the requirement for high dispersion glass to observe the Faraday effect. In addition, the electromagnetic properties of the binary photon have the required number of degrees of freedom to account for other magneto-optical phenomena such as the Zeeman effect.

Images of sub-resolution fluorescent microspheres taken with a laser scanning confocal microscope do not appear as spheres but as prolate ellipsoids relative to the optical axis of a microscope. The full width at half maximum (FWHM) intensity of the major axis of the ellipsoid is greater than the FWHM intensity of the minor axis of the ellipsoid by pi n/NA, where pi is a factor that depends on the geometry of the binary photon and N/NA is a factor that depends on the geometry of the optical system. The standard equations of confocal microscopy are inadequate describers and predictors of these results. However, the lateral and axial resolution equations that are based on Rayleigh's criterion and derived from the Kirchhoff diffraction equation whose assumptions are met by the binary photon are not only better describers and predictors but also explainers of the quantitative spatial aspects of the images. The accuracy of the equations that are based on the model of the binary photon in predicting the FWHM of the images of the fluorescent microspheres support the claim that binary photons, which exhibit wave-particle duality as a consequence of the motions of two oppositely-charged particles that give rise to wave-like electromagnetic fields may be the fundamental and irreducible component of light.

The quantum mechanical photon is described as a mathematical point-like elementary bosonic particle that is characterized by its energy (h omega), linear momentum (h), and angular momentum (h), and that propagates a circularly-polarized electromagnetic force at the speed of light (c). The quantum mechanical photon is also considered to be its own antiparticle. With this model of the photon, it is impossible, in principle, to visualize how the photon transfers energy, linear momentum, angular momentum, or the electromagnetic force to matter, and how a photon interacts with nearby photons resulting in interference effects. I have explained the enigmatic properties of the quantum mechanical photon with the model of the binary photon, which postulates that that photon is not an elementary particle and its own antiparticle, but a composite entity composed of a particle of matter and its conjugate antiparticle of antimatter. These conjugate particles are known as semiphotons. Unlike the quantum mechanical photon, the binary photon has extension is space, giving intelligibility and understandability to concepts such as the energy distribution within a photon, the cross-section of a photon, the angular momentum of a photon, the rotational energy of a photon, and the electromagnetic fields of a photon. In this contribution, I depict the wave functions, which are solutions to the Schrodinger equation for a boson, in three-dimensional Euclidean space. The wave functions describe the paths of the corpuscular semiphotons in three-dimensional Euclidean space and unidirectional and absolute Newtonian time. The wave functions that describe the movement of semiphotons give intelligibility and understandability to the wave-particle duality, and they yield the mechanical properties of the binary photon. By assuming that the binary photon is electrically neutral as a consequence of the semiphotons having equal and opposite charge, I show that the propagating binary photon produces a transverse sinusoidal electric field and a three-dimensional magnetic field that are orthogonal to each other and a quadrature out-of-phase with each other. The phase characteristics of the electric and magnetic fields are consistent with Faraday's law and the Ampere-Maxwell law, but inconsistent with Maxwell's electromagnetic waves, which were derived upon the assumption that light is electrically neutral due to the absence of charge (del center dot E = 0). By endowing the quantum of light with equal and opposite charge and using Maxwell's equations, the model of the binary photon offers an alternative way to address the principle of relativity that demands that there are no preferred frames in reckoning the speed of light. In this contribution, I provide animations that are not only consistent with the canonical mechanical and electromagnetic properties of light, but in addition, they give Anschaulichkeit, intelligibility, and understandability to the nature of light. Many people consider that science is the body of existing knowledge and scientists add to this knowledge in a straightforward, logical manner. This commonly accepted viewpoint is at variance with what another Nobelist, Szent-Gyorgyi, said, "A discovery must be, by definition, at variance with existing knowledge." The fact that well-meaning people and good scientists can have such opposing views shows that C. P. Snow's division of our society into two cultures of arts and science is wrong; there are two cultures in science itself. However, there is truly but one culture in which art, literature, music, and science are one, for all the basic attributes of the arts-of beauty, aesthetics, simplicity and the wonderment of the human condition-can be expressed in many ways, but are an essential part of our civilization.

The wavelength of light is thought to shorten as light goes from a rarer medium (air or vacuum) to a denser medium (water or glass) and to lengthen as light goes from a denser medium to a rarer medium. Since the linear momentum of light is equal to the ratio of Planck's constant to the wavelength of light, the change of wavelength would mean that the linear momentum would increase as light goes from a rarer medium to a denser medium and decrease as light goes from a denser medium to a rarer medium. Since the light that exits a refracting medium is indistinguishable from the light that enters the refracting medium, this would be in direct conflict with the conservation of linear momentum, which otherwise is a fundamental principle of nature. Here we show, using the model of the binary photon that the intrinsic wavelength, which is equal to the circumference of the path of the semiphotons projected on the transverse plane, is invariant as it propagates through media of different refractive indices. This wavelength is related to the intrinsic and invariant energy, linear momentum, and angular momentum. The intrinsic wavelength is related to the intrinsic frequency by the dispersion relation: lambda v = c. The binary photon is an oscillating rotor whose rotation and oscillation are invariant. The binary photon is a rotating oscillator that produces a linearly polarized electric field and a circularly polarized magnetic field that are a quarter of a wavelength out-of-phase with each other. Because of the change in velocity of the propagating invariant rotating oscillator, the electromagnetic fields contract in the direction of propagation when light propagates from a rarer to a denser medium and expand in the direction of propagation when light propagates from a denser medium to a rarer medium. The change in the wavelength in a refracting medium gives rise to the Minkowski momentum and the change in velocity in a refracting medium gives rise to the Abraham momentum. Individually the Minkowski and Abraham momenta are not conserved but the geometrical mean of these two momenta is equal to the intrinsic and conserved linear momentum. Like the Minkowski and Abraham momenta, the wavelength of the electric and magnetic fields is not an intrinsic wavelength but a contingent wavelength that depends on the refractive index of the refracting medium. The contracted and expanded fields interfere in three dimensions in the refracting medium just as they do in a vacuum. The intrinsic properties of the binary photon are sufficient to explain diffraction in a refracting medium consistent with the conservation of linear momentum. We also show that a study of diffraction in a refracting medium reveals that the binary photon has intrinsic, conserved, and invariant properties described by its intrinsic wavelength and frequency as well as reversible social properties, such as the crowding of binary photons along the axis of propagation that are described by its contingent wavelength and frequency.

This chapter discusses the various theories related to the origin of life on earth. The belief in spontaneous generation of large plants and animals began to wane throughout the 17th and 18th centuries. According to some scientists, as no one has yet created life in the laboratory, this means that life cannot be created but must come from existing life. Thus if life can only originate from life, then life on Earth must have originated in outer space and come to Earth on meteorites in the form of cosmozoa, microbes, spores, or seeds. This theory is called panspermia. This leads to another assumption that life arose from lifeless matter in the earth. According to Harold Urey, who had been studying the atmosphere of Jupiter, the atmosphere of the early Earth, like that of Jupiter's, may have been reducing, and thus may have consisted largely of hydrogen, methane, ammonia, and water. Experiments conducted by Stanley Miller, in which a gaseous mixture of methane, ammonia, hydrogen, and water was connected to a flask of boiling water, resulted in the production of glycine and alanine. This result indicated that amino acids may have been present on the early Earth before the advent of life. Under prebiotic conditions, amino acids can polymerize into polypeptides without the aid of enzymes or a template. Even more complex structures like proteinoid microspheres can form under prebiotic conditions. Such proteinoid microspheres may have joined together with phospholipids, which can also be synthesized under prebiotic conditions to form the first plasma membranes in a process of self-assembly.

The results presented in the previous 20 chapters generally started with a scientist asking an important biological question and then performing various experiments and observations to gather data that made it possible to answer the question in a rigorous and productive manner. The question was of paramount importance, and the technology was used and/or developed intelligently when it was appropriate to answer the question. By contrast, the approach of the omic sciences presented in this chapter is to accumulate information concerning the genome, transcriptome, proteome, metabolome, and phenome in a high-throughput unbiased manner and then use bioinformatic techniques to determine which parts are of importance. Until the important parts have been determined with the rigor demonstrated in the previous chapters, the technology seems to be used for technology's sake. While the applications of the technology have not provided any new fundamental knowledge of plant cell biology, the study of the development of the technology by creative scientists provides a great pedagogical tool to understand how to ask questions and achieve results to further our fundamental knowledge of science and technology.

Kirchhoff’s diffraction equation, which has been used for over a century to design optical instruments, exactly describes observed optical phenomena. This is a curious fact given that the derivation of Kirchhoff’s equation from the Helmholtz equation requires that the Dirichlet and Neumann boundary conditions are satisfied for an arbitrary surface simultaneously in ordinary space. According to Sommerfeld and Poincaré, this should be impossible if light is an electromagnetic wave as described by Maxwell where the magnetic and electrical fields are in phase. Given Maxwell’s theory of light as an electromagnetic wave, the Dirichlet and Neumann boundary conditions could be satisfied only if light vanished identically in the image space, which is clearly contrary to experience. By contrast, the Dirichlet and Neumann boundary conditions are satisfied simultaneously by the binary photon, which is composed of electrical and magnetic fields that are out-of-phase by a quarter of a wavelength. Consequently, one field satisfies the Dirichlet boundary condition while the other field simultaneously and in ordinary space satisfies the Neumann boundary condition. A complex plane wave where the magnetic and electrical fields are a quadrature out-of-phase is also a solution to the standard and a relativistic form of Maxwell’s wave equation. To derive the scalar Kirchhoff diffraction integral from the binary photon, I have developed two functions U and G that are based on the magnetic and electrical properties of light, respectively. The two functions are twice differentiable. I have obtained their

In this chapter I discuss the relationship between interference microscopy and phase-contrast microscopy and how both types of microscopy convert a difference in phase in transparent and would-be invisible specimens into a difference in intensity that is visible. I discuss the various methods used to produce two coherent beams and the methods used to recombine them. The interference microscope can be used qualitatively to produce contrast in transparent and would-be invisible specimens or quantitatively to measure the refractive index or the mass of a specimen. I discuss how colors are produced in nature, including interference colors. I also discuss how the transmission–interference microscope and the reflection–interference microscope have been used by biologists.

Organisms as diverse as bacteria, fungi, plants, and animals manifest a property called “polarity.” The literature shows that polarity emerges as a consequence of different mechanisms in different lineages. However, across all unicellular and multicellular organisms, polarity is evident when cells, organs, or organisms manifest one or more of the following: orientation , axiation , and asymmetry . Here, we review the relationships among these three features in the context of cell division and the evolution of multicellular polarity primarily in plants (defined here to include the algae). Data from unicellular and unbranched filamentous organisms (e.g., Chlamydomonas and Ulothrix ) show that cell orientation and axiation are marked by cytoplasmic asymmetries. Branched filamentous organisms (e.g., Cladophora and moss protonema) require an orthogonal reorientation of axiation, or a localized cell asymmetry (e.g., “tip” growth in pollen tubes and fungal hyphae). The evolution of complex multicellular meristematic polarity required a third reorientation of axiation. These transitions show that polarity and the orientation of the future plane(s) of cell division are dyadic dynamical patterning modules that were critical for multicellular eukaryotic organisms.

The mechanical properties of a binary photon can be described by transverse and longitudinal wave functions that give the positions and velocities of the semiphotons that make up a binary photon. The electromagnetic properties of the binary photon can be determined with the aid of Gauss's law of electricity by assuming that the two semiphotons have equal and opposite electrical charge, and consequently, they act as sources and sinks to produce electric and magnetic fields. The binary photon has a large transverse polarized electric field and a smaller longitudinal electric field. Magnetic fields are associated with the two electric fields. The associated electric and magnetic fields are a quarter of a wavelength out-of-phase, which is consistent with Faraday's law and the Ampere-Maxwell law. By assuming that light was electrically neutral due to the absence of charge, Maxwell proposed that the electric and magnetic fields produced by electrically-neutral light were orthogonal and in-phase. By contrast, the out-of-phase electric and magnetic fields found within the binary photon are a consequence of assuming that the electrical neutrality of light is due to the possession of equal and opposite charges. The strengths of the electric and magnetic fields are related to the wavelength of the binary photon. The transverse electric field (E-y) of the monochromatic binary photon is linearly polarized, the longitudinal electric field (z) is unpolarized, and the magnetic fields (B-xz, B-xy) are best represented by circulations or curls. The quantized three-dimensional electric and magnetic fields of a binary photon are able to interact with the quantized three-dimensional electric and magnetic fields of another binary photon as observed interference phenomena demand. However, complete destructive interference is only attainable if a given beam contains equal numbers of binary photons with oppositely-directed angular momenta. In retrospect, this makes sense since randomly arranged emitters will emit binary photons with opposite angular momenta with equal numbers. This suggests that the direction of angular momentum may be a hidden variable of light. The binary photon interprets the wave-particle duality of quantum mechanics in a way that makes it possible to visualize simultaneously the wave and particle properties of light as waves and two particles, where the electromagnetic waves are produced by two electrically-charged particles. This differs from the standard model where light is visualized as a wave or a particle. The visualizability of the semiphotons and the electromagnetic fields they generate within the binary photon makes Born and Heisenberg's claim that the microscopic quantum mechanical world must be fundamentally indeterminate, acausal, and unpicturable unwarranted.