Drawing an elephant with four complex parameters

Mayer, J. Michael; Khairy, Khaled; Howard, Jonathon

doi:10.1119/1.3254017

Cited by 131 publications

(80 citation statements)

References 5 publications

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“…3(b) in the Comment). Even just a few parameters are enough to fit an elephant [8]! And second, the authors' fitting method is not a physical theory since it has no predictive power at all −precisely because of its dependence on many adjustable parameters.…”

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confidence: 99%

Reply to “Comment on ‘Ratchet universality in the presence of thermal noise’ ”

Martínez

Chacón

2013

Phys. Rev. E

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The Comment by Quintero et al. does not dispute the central result of our paper [Phys. Rev. E 87, 062114 (2013)] which is a theory explaining the interplay between thermal noise and symmetry breaking in the ratchet transport of a Brownian particle moving on a periodic substrate subjected to a temporal biharmonic excitation γ [η sin (ωt) + α (1 − η) sin (2ωt + ϕ)]. In the Comment, the authors claim, on the sole basis of their numerical simulations for the particular case α = 2, that "there is no such universal force waveform and that the evidence obtained by the authors otherwise is due to their particular choice of parameters." Here we demonstrate by means of theoretical arguments and additional numerical simulations that all the conclusions of our original article are preserved. The foregoing Comment by Quintero et al.[1] offers some criticisms on certain particular (numerical) aspects of our previous paper [2], in which we studied theoretically and numerically a universal model -a Brownian particle moving on a periodic substrate subjected to a biharmonic excitation,where γ is an amplitude factor, and the parameters (η ∈ [0, 1] , α > 0) and ϕ account for the relative amplitude and initial phase difference of the two harmonics, respectively, while ξ (t) is a Gaussian white noise with zero mean and ξ (t) ξ (t + s) = δ (s), and σ = 2k b T with k b

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confidence: 99%

Reply to “Comment on ‘Ratchet universality in the presence of thermal noise’ ”

Martínez

Chacón

2013

Phys. Rev. E

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“…A famous quote among physicists, attributed to John von Neumann, is 'with four parameters I can fit an elephant, and with five I can make it wiggle its trunk' [3]. Joe Howard and colleagues actually wrote such an elephant-fitting simulation in a very enjoyable recent paper [4], and, because you wondered, with a fifth parameter the trunk does indeed wiggle. This means that, provided enough tweakable parameters are introduced, a model simulation can in principle fit any behavior.…”

Section: Meaningful Models -Any Model Is Not Better Than No Modelmentioning

confidence: 96%

After the Greeting: Realizing the Potential of Physical Models in Cell Biology

Paluch

2015

Trends in Cell Biology

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Biophysics is increasingly taking center stage in cell biology as the tools for precise quantifications of cellular behaviors expand. Interdisciplinary approaches, combining quantitative physical modeling with cell biology, are of growing interest to journal editors, funding agencies, and hiring committees. However, despite an ever-increasing emphasis on the importance of interdisciplinary research, the student trained in biology may still be at a loss as to what it actually means. I discuss here some considerations on how to achieve meaningful and high-quality interdisciplinary work.

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“…Annotated code for the procedure described above can be found in a repository at https:// github.com/dispersing/2DKernSim/blob/master/2DKern Sim.R. For the sake of balancing model overfitting (sensu Mayer et al 2010) and biological meaningfulness, deterministic model selection was limited to two exponential functions that have been shown to have biologically meaningful parameters (see Wichmann et al 2009;Bullock et al 2011). For both pdfs ðxðrÞ; f ðrÞÞ we chose the following models:…”

Section: Seed Dispersalmentioning

confidence: 99%

Scatter-hoarding rodents disperse seeds to safe sites in a fire-prone ecosystem

Moore

Wall

2015

Plant Ecol

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Fire can potentially decimate soil seed banks, even for species that are abundant in fire-prone areas. Many plants, like the widespread and dominant members of the genus Arctostaphylos in the fire-prone California Floristic Province, have seeds that (i) have no clear adaptions for dispersal and (ii) experience lethal fire temperatures if present on or near the soil surface. In this study, we aim to resolve these juxtaposed observations by mechanistically determining how one species, Arctostaphylos patula, is dispersed. To distinguish among dispersal modalities and determine the seed shadow, deposition patterns, and the conditions under which seeds germinate, we employed full-shrub exclosure treatments to monitor fruit removal, used a mark-relocation technique by radioactively labeling seeds, identified dispersers using motion-sensor cameras, and surveyed seedlings following fire to relate natural germination patterns to measured patterns from our experiment. Seed removal from exclosure treatments that allowed rodents access to shrubs was higher than those that prevented rodent access to shrubs, and cameras at radioactively labeledseed stations failed to detect the presence of any other disperser; thus implicating rodents as the primary disperser of A. patula seeds. This evidence is corroborated by our finding from tracking radioactively labeled seeds that the depth at which rodents bury seeds completely overlaps with the depth from which we observed seedlings germinate following two fire events. Our study extends the boundary of what is understood as a scatter-hoarding seed dispersal syndrome and identifies a mechanism that allows populations of Arctostaphylos to exist in spite of recurrent fires that can be lethal to seeds and hazardous to plant populations.

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Drawing an elephant with four complex parameters

Abstract: We define four complex numbers representing the parameters needed to specify an elephantine shape. The real and imaginary parts of these complex numbers are the coefficients of a Fourier coordinate expansion, a powerful tool for reducing the data required to define shapes.

Cited by 131 publications

References 5 publications

Reply to “Comment on ‘Ratchet universality in the presence of thermal noise’ ”

Reply to “Comment on ‘Ratchet universality in the presence of thermal noise’ ”

After the Greeting: Realizing the Potential of Physical Models in Cell Biology

Scatter-hoarding rodents disperse seeds to safe sites in a fire-prone ecosystem

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