# Explicit Tracking of Uncertainty Increases the Power of Quantitative Rule-of-Thumb Reasoning in Cell Biology

@article{Johnston2014ExplicitTO, title={Explicit Tracking of Uncertainty Increases the Power of Quantitative Rule-of-Thumb Reasoning in Cell Biology}, author={Iain G. Johnston and Benjamin C Rickett and Nick S. Jones}, journal={Biophysical Journal}, year={2014}, volume={107}, pages={2612 - 2617} }

Back-of-the-envelope or rule-of-thumb calculations involving rough estimates of quantities play a central scientific role in developing intuition about the structure and behavior of physical systems, for example in so-called Fermi problems in the physical sciences. Such calculations can be used to powerfully and quantitatively reason about biological systems, particularly at the interface between physics and biology. However, substantial uncertainties are often associated with values in cell…

## 17 Citations

Hierarchical Bayesian Uncertainty Quantification for a Model of the Red Blood Cell

- Physics
- 2021

Simulations of blood flows in microfluidic devices and physiological systems are gaining importance in complementing experimental and clinical studies. The predictive capabilities of these…

New and notable: uncertainty quantification.

- Mathematics, MedicineBiophysical journal
- 2014

It is shown that simple calculations are not so simple when there is uncertainty in the underlying input data, using an on-line CALADIS calculator where the uncertainty in a variable or parameter is represented using a probability density function.

Evolution of Cell-to-Cell Variability in Stochastic, Controlled, Heteroplasmic mtDNA Populations.

- Medicine, BiologyAmerican journal of human genetics
- 2016

A mathematical theory is developed describing the evolution of stochastic mtDNA populations for any type of cellular control, showing that cell-to-cell variability in mtDNA and mutant load inevitably increases with time, according to rates that the authors derive and which are notably independent of the mechanistic details of feedback signaling.

Evolution of cell-to-cell variability in stochastic, controlled, heteroplasmic mtDNA populations

- Biology
- 2016

A mathematical theory is developed describing the evolution and variability in stochastic mtDNA populations for any type of cellular control, showing that cell-to-cell variability in mtDNA, and mutant load, inevitably increases with time, according to rates which are notably independent of the mechanistic details of feedback signalling.

Stochastic survival of the densest and mitochondrial DNA clonal expansion in ageing

- Biology
- 2020

This work presents a spatial model that produces travelling waves of mutants even if mutants are preferentially eliminated, and introduces the mechanism of stochastic survival of the densest, an alternative to replicative advantage, that may underpin other evolutionary phenomena.

Survival of the densest accounts for the expansion of mitochondrial mutations in ageing

- Biology
- 2020

A spatial model is presented that produces a wave of expanding mutations with wave speed consistent with experimental data, unlike a standard model based on replicative advantage, and introduces the mechanism of stochastic survival of the densest, an alternative to replicativeadvantage that may underpin other phenomena, like the evolution of altruism.

What is the function of mitochondrial networks? A theoretical assessment of hypotheses and proposal for future research

- Biology, MedicineBioEssays : news and reviews in molecular, cellular and developmental biology
- 2015

The possibilities that (i) selective mitophagy is not required for quality control because selective fusion is sufficient; (ii) increased connectivity may have non‐linear effects on the diffusion rate of proteins; and (iii) fused networks can act to dampen biochemical fluctuations are described.

Multiple hypothesis correction is vital and undermines reported mtDNA links to diseases including AIDS, cancer, and Huntingdon’s

- Biology, MedicineMitochondrial DNA. Part A, DNA mapping, sequencing, and analysis
- 2016

It is shown that statistics matching those claimed to illustrate significant links can arise, with a high probability, when no such link exists, and that these claims should thus be discarded until results of suitable statistical reliability are provided.

Multiple hypothesis correction is vital and undermines reported mtDNA links to diseases including AIDS, cancer, and Huntingdon’s

- Biology
- 2015

It is shown that statistics matching those claimed to illustrate significant links can arise, with a high probability, when no such link exists, and that these claims should thus be discarded until results of suitable statistical power are provided.

Energetic costs of cellular and therapeutic control of stochastic mitochondrial DNA populations

- Computer Science, BiologyPLoS Comput. Biol.
- 2019

Stochastic modelling is used to derive general results for the impact of cellular control on mt DNA populations, the cost to the cell of different mtDNA states, and the optimisation of therapeutic control of mtDNA populations.

## References

SHOWING 1-10 OF 13 REFERENCES

SnapShot: Key Numbers in Biology

- Biology, MedicineCell
- 2010

This compilation is based on the BioNumbers wiki project where these and the values of several thousand other biological properties are provided together with their experimental context and references to the primary literature.

A feeling for the numbers in biology

- Biology, PhysicsProceedings of the National Academy of Sciences
- 2009

The confluence of two different approaches to biological numbers is described and their synergism is illustrated in several particularly appealing case studies that reveal the impact that an emphasis on numbers can have on important biological questions.

Equivalence of methods for uncertainty propagation of real-valued random variables

- Computer Science, MathematicsInt. J. Approx. Reason.
- 2004

This paper compares four methods for the reliable propagation of uncertainty through calculations involving the binary operations of addition, multiplication, subtraction and division and shows that they converge to equivalent methods when they are restricted to cumulative distribution functions on the positive reals.

Guesstimation: Solving the World's Problems on the Back of a Cocktail Napkin

- 2008

Guesstimation is a book that unlocks the power of approximation--it's popular mathematics rounded to the nearest power of ten! The ability to estimate is an important skill in daily life. More and…

Quantifying origins of cell-to-cell variations in gene expression.

- Biology, MedicineBiophysical journal
- 2008

It is shown that a dynamic description is much more reliable to discriminate extrinsic and intrinsic sources of noise than it is on grounds of cell-cycle averaged descriptions and that a quantitative description of gene expression noise is indeed possible on the basis of idealized stochastic processes.

BioNumbers—the database of key numbers in molecular and cell biology

- Computer Science, MedicineNucleic Acids Res.
- 2010

The database characteristics and implementation are described, the use of the use is demonstrated, its use is discussed, and future directions for its development are discussed.

All of Statistics: a Concise Course in Statistical Inference

- Computer Science
- 2005

This book is for people who want to learn probability and statistics quickly and is suitable for graduate or advanced undergraduate students in computer science, mathematics, statistics, and related disciplines.

Street-Fighting Mathematics: The Art of Educated Guessing and Opportunistic Problem Solving

- Computer Science, Mathematics
- 2010

Street-Fighting Mathematics is an antidote to the rigor mortis brought on by too much mathematical rigor, teaching us how to guess answers without needing a proof or an exact calculation.

An Introduction to MCMC for Machine Learning

- Computer ScienceMachine Learning
- 2004

This purpose of this introductory paper is to introduce the Monte Carlo method with emphasis on probabilistic machine learning and review the main building blocks of modern Markov chain Monte Carlo simulation.

BioNumber of the Month. http://www.weizmann.ac.il/ plants/Milo/index.php?page_name1⁄4BioNumberOfTheMonth

- 2009