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  • Dim-light sensing cells are most sensitive to colors that maximize signal to noise ratio of light power absorption over the spectral density of the Sun

    Abstract

    Why are dim-light sensing cells in eyes most sensitive to specific colors? There are explanations that delve into the detailed chemistry of how existing dim-light sensing cells work and explanations that chart the genetic lineage of their evolutionary development. However, might there be another level of approximation to an explanation that does not depend on these details? In this article the author hypothesizes that evolution has made dim-light sensing cells most sensitive to colors that make light detection minimally corrupted by the random noise inherent in the quantum mechanism of light absorption because this enhances the fitness of organisms. The author develops a theoretical physics implication of the hypothesis that begins at the quantum scale and applies statistics to zoom out to the biological scale; derives a mathematical expression for the absorbed light power signal-to-noise ratio (SNR)—where the source of noise is the quantum nature of the absorption process—as a function of the dominant color absorbed from sunlight; and ultimately predicts the colors that maximize this SNR in environments ranging from above sea level to the deep ocean. The difference between these predictions and observation is within the variability found between species in similarly lit environments, which range over about 5 nm. The author concludes that the hypothesis and theoretical physics implication is another level of approximation to a true explanation for why dim-light sensing cells of vertebrates in certain environments are most sensitive to specific colors of light, an explanation that complements those that depend on chemical details or genetic lineage.

    I Introduction

    Why are dim-light sensing cells in eyes most sensitive to specific colors? I hypothesize that the particular frequencies of peak absorption of photoreceptors of organisms can be influenced by evolutionary adaptation to the random noise that is superposed on light signals. This hypothesis implies that, among the various sources of noise, the inherent randomness of the quantum mechanics of light absorption can influence the evolution of dim-light photoreceptors in organisms because the associated light power absorption signal-to-noise ratio (SNR) can affect the evolutionary fitness of such organisms. This implication can be tested by determining whether this signal-to-noise ratio can be theoretically maximized and whether any photoreceptors approach this maximum.

    Theoretical predictions can be compared with the experimental work of Shozo Yokoyama et al. [20], who deduced the genetic lineage of visual pigments in rod photoreceptor cells in retina (rhodopsins) in vertebrates. They engineered 11 ancestral rhodopsins and showed that those in early ancestors absorbed light maximally at a wavelength of about 501 nm, from which contemporary rhodopsins with variable peak absorption wavelengths of 480–525 nm evolved on at least 18 separate occasions, concluding that

    based on considerations of ecology, life history, and λmaxs of rhodopsins, dim-light vision can be classified into biologically meaningful deep-sea, intermediate, surface, and red-shifted vision. The corresponding rhodopsins have λmaxs of 479–486, 491–496, 500–507, and 526 nm, respectively, establishing the units of possible selection. Consequently, it is possible that selective force may be able to differentiate even 4–5 nm of max differences of rhodopsins. [20]

    Another historically interesting experiment to compare with theory was performed by J. K. Bowmaker and H. J. A. Dartnall [2], who concluded that the peak absorption wavelength of a sample of 9 rod cells from an eye of a man was 497.5±1.5 nm. They went to great lengths to conduct this experiment.

    Yokoyama et al. refer to a popular alternative hypothesis to mine: that having dim-light sensing cells be most sensitive to wavelengths in a range where “the most abundant light falls” augments the fitness of organisms [20]. Bernard H. Soffer and David K. Lynch demonstrated how pervasive this hypothesis has been in the scientific literature and explain in detail why it is false, although they do not propose my hypothesis as an alternative [17]. In short, this popular hypothesis is false because the wavelength λmax at the maximum of the spectral density as a function of wavelength ^(λ) and the frequency νmax at the maximum of the spectral density as a function of frequency (ν) do not satisfy λmaxνmax=c, the speed of light in vacuum. Figures 1 and 2 show these two functional forms of the spectral density of the Sun. Notice the apparent (illusory) concept of a range of wavelengths or frequencies where “the most abundant light falls” shifts between these two perspectives so that λmaxνmaxc. My hypothesis, on the other hand, holds for both of these perspectives, as I will show.

    Refer to caption
    Figure 1: Sunlight spectral density as a function of frequency. Sunlight spectrum in space as a function of frequency. Data source: American Society for Testing and Materials Terrestrial Reference. Image source: Public Domain by Christopher S. Baird, https://wtamu.edu/~cbaird/sq/2013/07/03/what-is-the-color-of-the-sun/
    Refer to caption
    Figure 2: Sunlight spectral density as a function of wavelength. Sunlight spectrum in space as a function of wavelength. Data source: American Society for Testing and Materials Terrestrial Reference. Image source: Public Domain Image by Christopher S. Baird, https://wtamu.edu/~cbaird/sq/2013/07/03/what-is-the-color-of-the-sun/.

    I tested the theoretical implication of the hypothesis by (1) deriving a functional form of a signal-to-noise ratio (SNR) of light power absorption by an idealized photoreceptor (a classical system made up of many copies of a two-state quantum system) that depends on its peak absorption radial frequency and the spectral density of light illuminating the environment; (2) modeling how the Sun’s solar spectral density is attenuated at various depths of water; (3) maximizing the SNR by finding the zeros of its first derivative with respect to the peak absorption radial frequency; (4) comparing the predictions to experimental observations of rhodopsins in vertebrates that evolved in environments ranging from above sea-level to the deep ocean.

    II Methods

    II.1 Quantum mechanism of light absorption

    I begin where Feynman et al. explain off-resonance absorption of light by molecules in volume III chapter 9 section 5 of [6]. They consider the case that the amplitude of the electric field is small and also the period of time during which photon absorption may happen Δt is small, so that ω0Δt1, where ω0 is the resonant radial frequency of absorption for a molecule with an electric dipole moment. For this case, they derive the conditional probability that such a molecule will absorb a photon of monochromatic light over a time interval Δt is

    P2(EII,Δt|EI)=2π[μ24πϵ02c](Δt)2sin2[(ωω0)Δt/2][(ωω0)Δt/2]2. (1)

    The absorbed photon’s energy raises the molecule’s energy from EI to EII, ω0 is the resonant absorption radial frequency, is the spectral radiance, Δt is the time interval during which the absorption may happen, μ is the electric dipole moment of the molecule, c is the speed of light in vacuum, is the reduced Planck constant, and ϵ0 is the vacuum permittivity. P2(EII,Δt|EI) is plotted in Fig. 3 for a fixed Δt and variable ω.

    Refer to caption
    Figure 3: Photon absorption probability. Absorption probability for a molecule with a single dipole moment as a function of photon frequency ω. Adapted from [6].

    Unlike monochromatic light, sunlight has an intensity (ω) per unit frequency interval, covering a broad range which includes ω0. Then the probability of absorption will become an integral over ω:

    P2(EII,Δt|EI)=2π[μ24πϵ02c](Δt)2𝑑ω(ω)sin2[(ωω0)Δt/2][(ωω0)Δt/2]2. (2)
    Refer to caption
    Figure 4: Solar spectral radiance and absorption probability. The solar spectral radiance (solid line) varies much more slowly than the sharp resonant term (dashed line). Adapted from [6].

    The solar spectral radiance varies much more slowly than the sharp resonance term. The two functions in the integral might appear as shown in Fig. 4. Since the solar spectral radiance is relatively constant over the relevant range of integration, it can be taken out of the integral.

    P2(EII,Δt|EI)=2π[μ24πϵ02c](Δt)2(ω0)𝑑ωsin2[(ωω0)Δt/2][(ωω0)Δt/2]2. (3)

    The mean energy absorbed over a time interval Δt is

    ΔE¯=𝑑ωωP2(EII,Δt|EI), (4)

    or more explicitly,

    ΔE¯=2π[μ24πϵ02c](Δt)2(ω0)𝑑ωωsin2[(ωω0)Δt/2][(ωω0)Δt/2]2. (5)

    This can be simplified by integrating over the interval where the probability peaks ω0±2π/Δt, making a change of variables x=(ωω0)Δt/2, and approximating 𝑑x(x2sin2x) over the finite integration interval by its exact, closed form over to , which equals π. The error of this approximation can be estimated by complex contour integration in the upper-half complex-plane along a semicircle of radius π with an indentation around the origin. The approximation is exact to first order in the radius of the contour. The expression for the mean energy absorbed becomes

    ΔE¯=4π3[μ24πϵ02c](Δtπ)ω0(ω0). (6)

    The mean energy absorbed over a time interval Δt is inversely proportional to the half-width π/Δt of the transition probability distribution’s central peak at ω0. It is also directly proportional to the spectral radiance at the absorption peak.

    The variance of the energy absorbed over a time interval Δt is

    σΔE2=𝑑ω(ωΔE¯)2P2(EII,Δt|EI), (7)

    or more explicitly,

    σΔE2=2π[μ24πϵ02c](Δt)2(ω0)2𝑑ω(ωΔE¯)2sin2[(ωω0)Δt/2][(ωω0)Δt/2]2. (8)

    Following much the same procedure as for the mean energy absorbed leads to the simplified form

    σΔE2=16π2[μ24πϵ02c](πΔt)(ω0)[1+18(1ΔE¯ω0)2(ω0Δt)2]. (9)

    Recall that this analysis began by considering the case where the electric field is small and also the period of time Δt is small, so that ω0Δt1, so the last term in square brackets is approximately equal to one, simplifying the variance to

    σΔE2=16π2[μ24πϵ02c](πΔt)(ω0). (10)

    The variance of the absorbed energy is directly proportional to the half-width π/Δt of the transition probability distribution’s central peak at ω0. It is also directly proportion to the solar spectral radiance at the absorption peak.

    II.2 From quantum to biological scale

    Now I will take the analysis from the quantum scale up to biological scale. After N1 absorption events, the cumulative energy absorbed will reach a value of 𝐄(N)=𝐄(0)+j=1NΔEj. The central limit theorem guarantees that the probability distribution of Δ𝐄𝐄(N)𝐄(0) is Gaussian with a mean and variance

    Δ𝐄¯=NΔE¯,σΔ𝐄2=NσΔE2. (11)

    This is to be expected from a one-dimensional random walk, where the distance walked is analogous to the cumulative energy absorbed. This is why the noise I am considering here is generally referred to as ‘random-walk’ noise.

    Viewed on energy-scales ω0, Δ𝐄(N) looks like a continuous random process. At this energy-scale, the energy absorbed over the time interval ΔτNΔt, defined as Δ𝐄(τ)𝐄(τ+Δτ)𝐄(τ), has a mean and variance of

    Δ𝐄¯=ΔE¯Δτ/Δt,σΔ𝐄2=σΔE2Δτ/Δt. (12)

    So, by Eqs. 6 and 10, the mean energy absorbed and its variance over a time Δτ are

    Δ𝐄¯=2π2[μ24πϵ02c]Δτω0(ω0) (13)

    and

    σΔ𝐄2=162[μ24πϵ02c]Δτ(πΔt)2(ω0). (14)

    The mean power W¯ absorbed over a time interval Δτ is related to the mean energy absorbed by

    W¯Δ𝐄¯Δτ=2π2[μ24πϵ02c]ω0(ω0), (15)

    and the absorption power variance σW2 is

    σW2σΔ𝐄2(Δτ)2=162[μ24πϵ02c]1Δτ(πΔt)2(ω0). (16)

    The signal-to-noise ratio (SNR) of a Gaussian signal is the ratio of its mean squared and its variance (a unitless or dimensionless quantity). The SNR of the absorbed power is then

    SNRW=W¯2σW2=π44[μ24πϵ02c]Δτ(Δtπ)2ω02(ω0). (17)

    II.3 Maximizing the signal-to-noise ratio at and above sea level

    The signal-to-noise ratio of light power absorption SNRW takes on its extreme values where its derivative with respect to ω0 is zero, which is where

    ddω0[ω02(ω0)]=0. (18)

    The spectral density of the environment at and above sea level can be approximated by Planck’s law. This approximation ignores (1) the absorption spectrum of the Earth’s atmosphere and (2) the reflectance spectrum of the Moon, making no distinction between nocturnal and diurnal organisms. According to Planck’s distribution law, the spectral radiance (ω) of a black-body at a temperature T is

    (ω)=ω34π3c21eω/(kBT)1, (19)

    where is the reduced Planck constant, c is the speed of light in vacuum, and kB is the Boltzmann constant.

    Using this functional form for (ω), the left hand side of Eq. 18 is proportional up to a constant scalar multiple to

    ddω[ω2(ω)]z4(1z)(e5z1)2[e5z+1z1], (20)

    where zω/(5kBT). Writing the expression this way makes clear where the singularities of the derivative of SNRW are located: where the denominators e5z1 and z1 equal zero, which are at z=0 and z=1. The zeros of Eq. 20 can be found by analyzing its Laurent series expansions about these singularities. These will be all of the zeros by the uniqueness theorem of Laurent series within their annular domain of convergence and by the fundamental theorem of algebra.

    An analytic function f(z) has a zero of order k at z0 if

    f(z)=(zz0)kg(z), (21)

    and g(z0)0.

    Expanding the exponential functions about z=0 in terms of powers of z, the right hand side of Eq. 20 can be written as

    f0(z)=z3g0(z), (22)

    where

    g0(z)=(452)1+(15/8)z+[1+(5/2)z+]2, (23)

    so g0(0)=4/25, satisfying the condition g0(0)0.

    Expanding the powers of z and the exponential functions about z=1 in terms of powers of (z1), the right hand side of Eq. 20 can be written as

    f1(z)=(z1)3g1(z), (24)

    where

    g1(z)=(152)1+5(z1)+[1+(5/2)(z1)+]2, (25)

    so g1(1)=1/25, satisfying the condition g1(1)0.

    So, the zeros of the first derivative of SNRW with respect to peak absorption radial frequency are indeed at z=0 and z=1 (ω=0 and ω=5kBT/). The higher-order (or general) derivative test can be used to determine whether either of these radial frequencies maximize SNRW.

    Let all the derivatives of f at z0 be zero up to and including the n-th derivative, but with the (n+1)-th derivative being non-zero:

    f(z0)==f(n)(z0)=0andf(n+1)(z0)0. (26)

    The higher-order derivative test guarantees that if n is odd and f(n+1)(z0)<0, then z0 is a local maximum; and if n is odd and f(n+1)(z0)>0, then z0 is a local minimum.

    By Eqs. 22 and 24, the first non-zero derivative at the zeros is

    fz0(3)(z0)=6gz0(z0). (27)

    Recalling that fz0 is the first derivative of SNRW near z0, the value of n in the higher-order derivative test needs to be incremented by one more than is written in Eq. 27, and so is equal to 3, which is odd. So, according to the test, since g0(0)>0 by Eq. 23, z=0 is a local minimum; and since g1(1)<0 by Eq. 25, z=1 is a local maximum. These are the global minimum and maximum since these are the only zeros of the derivative of SNRW, as explained previously.

    Converting back from z to ω via z=ω/5kBT, the analysis above shows that when the spectral density illuminating the environment at or above sea level is approximated by Planck’s law, the global maximum of the SNR is reached when a photoreceptor’s peak radial frequency ω0=5kBT/.

    II.4 Maximizing the signal-to-noise ratio below sea-level

    How does the attenuation of light by water affect the prediction of the optimal peak absorption radial frequency for environments beneath the surface of bodies of water? The diffuse attenuation coefficient for irradiance κ(ω) is the apparent optical property that provides the most direct measure of the penetration of radiant energy in water,

    (ω,δ)=(ω,0)eκ(ω)δ, (28)

    where (ω,δ) is the spectral irradiance at depth δ and (ω,0) is the irradiance at the surface.

    Raymond C. Smith and Karen S. Baker created a consistent set of data on the diffuse attenuation coefficient for irradiance of clear fresh- and salt-water environments for wavelengths in the range 200–800 nm [16]. Based on their data, the diffuse attenuation coefficient can be approximated in a neighborhood of its minimum value κ(ωa) by a quadratic,

    κ(ω)=12a(ωωa)2+κ(ωa), (29)

    where the coefficient a can be fit to their data. Such a fit is shown in Fig. 5. Fitting over all of their data, the coefficient of determination R2 over the range 300–600 nm centered at 450 nm is 0.9961.

    Refer to caption
    Figure 5: Fit of diffuse attenuation coefficient. A quadratic fit of the diffuse attenuation coefficient as a function of wavelength to experimental data measured and compiled by [16].

    Using this approximation for κ(ω) and the attenuated spectral density in Eq. 28, the condition for maximizing the SNR in Eq. 18 is proportional up to a constant scalar multiple to

    ddω[ω2(ω,δ)]z4(1z)(e5z1)2[e5z+1z1+αz(zzaz1)(e5z1)]eκ(ω)δ, (30)

    where

    α5(kBT)2aδ, (31)

    and za is the scaled radial frequency where the diffuse attenuation coefficient κ is locally minimal.

    Compare Eqs. 30 and 20. Notice the additional term in the square brackets that introduces a factor of α.

    Since the zeros of Eq. 30 are sought, it can be simplified by ignoring the exponential decay factor on the far right and grouping factors to emphasize the change in the expression going from the above-sea-level analysis to the below-sea-level analysis,

    ddω[ω2(ω,δ)]z4(e5z1)2{e5z[(1z)α(zza)z](1α(zza)z)}. (32)

    Notice the term in square brackets in Eq. 32. Going from the above-sea-level analysis to the below-sea-level analysis, this term changes according to

    (1z)(1z)α(zza)z, (33)

    because at sea level α=0. To see how this change affects the zero of Eq. 32, the right hand side can be factored into powers of (z1) to analyze it in the neighborhood of the zero of the above-sea-level analysis, z=1. The expression becomes

    (z1)(z1)α[(za1)+(za2)(z1)(z1)2]. (34)

    Near z=1, this expression can be truncated to the first power in (z1), so the expression can be simplified to

    (z1)[1α(za2)]{z1[α(za1)1α(za2)]}. (35)

    The approximate change in the zero, Δz0, from z0=1 to z0=1+Δz0 is characterized by

    (z1)[1α(za2)][z(1+Δz0)]. (36)

    Comparing this form to Eq. 35, the approximate change in the zero when going from the above sea level to the below sea level analysis is

    Δz0=α(za1)1α(za2). (37)

    The approximate change in the zero has the limiting values limδ0Δz0=0 (sea level) and limδΔz0=(za1)/(za2) (deep ocean). By the diffuse attenuation data of Smith and Baker [16], za1.1079, so limδΔz0=0.1209, which corresponds to a limiting shift of the peak absorption wavelength from 499 nm at sea level to 445 nm at extreme depths. Notice that the diffuse attenuation coefficient data of [16] is well approximated by a quadratic over this range as shown in Fig. 5 with a coefficient of determination R2 of 0.9961, so the analysis is valid over the entire range of depths.

    This predicted shift to shorter peak absorption wavelengths at lower and lower depths is consistent with what is observed in various species of fish [20]. Exceptions to this trend are deep sea fish that rely on bioluminescence to illuminate their environment, which have rhodopsins with peak absorption wavelengths of 526 nm. Deep sea fish without bioluminescence have rhodopsins with peak absorption wavelengths in the range 479–486 nm, which are within the predicted range [20].

    III Results and discussion

    The result of the analysis above is that the signal-to-noise ratio of light power absorption, SNRW, of a photoreceptor when considering only the random-walk noise due to the quantum mechanism of light absorption is maximal when the peak absorption radial frequency of the photoreceptor ω0 is a zero of the function ddω[ω2(ω,δ)], where (ω,δ) is the spectral density illuminating the environment as a function of radial frequency and depth of water. Translating from frequency to wavelength, the criteria is that the peak absorption wavelength λ0 is a zero of the function ddλ[^(λ,δ)], where ^(λ,δ) is the solar spectral density as a function of wavelength and depth of water.

    This implication of the hypothesis gives compatible predictions when framed in terms of either wavelength (λ) or frequency (ν), that is, ν0λ0=c, the speed of light in vacuum. The popular alternative hypothesis (that having dim-light sensing cells be most sensitive to wavelengths in a range where the most abundant light falls augments the fitness of organisms) does not give predictions that are compatible between these two framings.

    The spectral density of the environment at and above sea level can be approximated by Planck’s law. This approximation ignores (1) the absorption spectrum of the Earth’s atmosphere and (2) the reflectance spectrum of the Moon, making no distinction between nocturnal and diurnal organisms. With this approximation, the theoretically predicted peak absorption radial frequency of organisms at and above sea-level is ω=5kBT/, where kB is the Boltzmann constant, T is the effective black-body temperature of the environmental light source, and is the reduced Planck constant. Using the effective temperature of the Sun as 5,772.0±0.8 K [12] in this relationship predicts the peak absorption radial frequency with the maximal SNRW to be 3,778.4±0.5×1012radHz, or equivalently, a frequency of 601.34±0.08 THz, or a wavelength of 498.54±0.07 nm.

    This prediction is close to what has been measured for human rod cells by [2], 497.5±1.5 nm, and for early rhodopsins in many vertebrates by [20], 501 nm. The difference between this prediction and observation is within the variability found between rhodopsins of species in similarly lit environments, which range over about 5 nm [20].

    Below sea level, the spectral density is diffusely attenuated as a function of wavelength (frequency). The attenuation shifts the predicted maximal peak absorption wavelength to shorter values at deeper depths below sea level, with a limiting value at extreme depths of about 445 nm. This trend is consistent with what is observed in various species of fish that evolved at different depths and includes the range of peak absorption wavelength of deep sea fish that do not illuminate their environments with bioluminesence, 479–486 nm [20].

    IV Conclusion

    In conclusion, the experiments by [20], [2], and [16] verify the theoretical physics implication of the hypothesis that evolution makes dim-light sensing cells in eyes most sensitive to colors that maximize the light power absorption signal-to-noise ratio—where the noise is due to the inherent randomness of quantum mechanics—because having a greater signal-to-noise ratio enhances the fitness of organisms with such eyes.

    This hypothesis supplants the popular hypothesis that evolution has made dim-light sensing cells most sensitive to colors with wavelengths (frequencies) in a range where the most abundant light falls because this augments the fitness of organisms.

    This hypothesis supports the popular hypothesis that the evolution of the rod occurred very early in the history of life on Earth, since quantum mechanical randomness predates life on Earth. As stated in [9]:

    Although the evolution of the rod and the duplex retina would have taken many generations, it must nevertheless have occurred very early: rods are present in every class of vertebrates including jawless cyclostomes, which split off from the rest of the vertebrates approximately 500 Ma. Moreover, the properties of lamprey rods and cones are very similar to those of rods and cones of gnathostomes. Recent experiments have shown, for example, that light adaptation in lamprey rods and cones is virtually indistinguishable from that in other vertebrates [10]. The early emergence of this new kind of ciliary photoreceptor together with the other retinal cells and synaptic pathways required for dim-light vision permitted the formation of the duplex retina, first postulated 150 years ago by Schultze [14], and now recognized to be a fundamental feature of vertebrate photodetection.

    This hypothesis motivates investigation of the impact that other inherent sources of noise may have on the evolution of photoreceptors, along the lines of inquiry of [4, 13, 18, 19, 3]. Other questions come to mind:

    • Rod responses decay much more slowly than cones: exponential fits to the time course of decay give time constants about 10 times slower in rods than in cones [8]. The expression for the SNRW in Eq. 17 is linear with respect to Δτ, which can be interpreted as the sampling time of a photoreceptor. So, the SNRW increases with greater sampling time, or a slower time course of decay. Presumably, the responsiveness of an organism to its dynamic environment is a countervailing fitness pressure so there is a point of diminishing returns for a slower response. Might this explain the response speed of rods?

    • If rods evolved from cones, as the genetics of their pigments suggests [11, 20, 15], why was the SNR of this source of noise not optimized first?

    • Might cone peak absorption frequencies be influenced by other such sources of noise?

    • Along the lines of inquiry of [7, 5, 1], might the peak absorption frequencies of photosynthesis be explained by investigations similar to this one?

    Acknowledgements
    I would like to thank Kenneth Cohen for his help.

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