Biology subjects

Newman, S. J.

Publications and source records attributed to Newman, S. J..

5 recordsLinked to original sources

bioRxiv2021

Explainable machine learning models of major crop traits from satellite-monitored continent-wide field trial data

Four species of grass generate half of all human-consumed calories1. However, abundant biological data on species that produce our food remains largely inaccessible, imposing direct barriers to understanding crop yield and fitness traits. Here, we assemble and analyse a continent-wide database of field experiments spanning ten years and hundreds of thousands of machine-phenotyped populations of ten major crop species. Training an ensemble of machine learning models, using thousands of variables capturing weather, ground-sensor, soil, chemical and fertiliser dosage, management, and satellite data, produces robust cross-continent yield models exceeding R2 = 0.8 prediction accuracy. In contrast to black box analytics, detailed interrogation of these models reveals fundamental drivers of crop behaviour and complex interactions predicting yield and agronomic traits. These results demonstrate the capacity of machine learning models to build unified, interpretable, and explainable models of crop behaviour, and highlight the powerful role of data in the future of food.

plant biology↗

bioRxiv2019

Supercentenarians and the oldest-old are concentrated into regions with no birth certificates and short lifespans

The observation of individuals attaining remarkable ages, and their concentration into geographic sub-regions or blue zones, has generated considerable scientific interest. Proposed drivers of remarkable longevity include high vegetable intake, strong social connections, and genetic markers. Here, we reveal new predictors of remarkable longevity and supercentenarian status. In the United States, supercentenarian status is predicted by the absence of vital registration. The state-specific introduction of birth certificates is associated with a 69-82% fall in the number of supercentenarian records. In Italy, England, and France, which have more uniform vital registration, remarkable longevity is instead predicted by poverty, low per capita incomes, shorter life expectancy, higher crime rates, worse health, higher deprivation, fewer 90+ year olds, and residence in remote, overseas, and colonial territories. In England and France, higher old-age poverty rates alone predict more than half of the regional variation in attaining a remarkable age. Only 18% of exhaustively validated supercentenarians have a birth certificate, falling to zero percent in the USA, and supercentenarian birthdates are concentrated on days divisible by five: a pattern indicative of widespread fraud and error. Finally, the designated blue zones of Sardinia, Okinawa, and Ikaria corresponded to regions with low incomes, low literacy, high crime rate and short life expectancy relative to their national average. As such, relative poverty and short lifespan constitute unexpected predictors of centenarian and supercentenarian status and support a primary role of fraud and error in generating remarkable human age records.

developmental biology↗

bioRxiv2018

Late-life mortality plateaus through error, not evolution

This study highlights how the mortality plateau in Barbi et al. [1] can be generated by low frequency, randomly distributed age misreporting errors. Furthermore, sensitivity of the late-life mortality plateau in Barbi et al. [1] to the particular age range selected for regression is illustrated. Collectively, the simulation of age misreporting errors in late-life human mortality data and a less specific model choice than that of Barbi et al. [1] highlight a clear alternative hypothesis to the cessation of ageing.

evolutionary biology↗

bioRxiv2017

Global patterns of human ageing

Ageing is a common, but not universal1-3, degradation of biological systems. Ageing in human populations is marked by a highly constrained, log-linear acceleration of the probability of mortality with age4. This acceleration determines the onset and duration of human morbidity5 and the upper limits of human life. Recent studies have revealed remarkable taxonomic diversity in mortality-derived ageing rates1,3. However, the extent of intraspecific variation in ageing rates is assumed to be negligible2. Here we show the considerable diversity of human ageing rates, across 81,000 population-specific longitudinal measures of the ageing rate derived from 330 billion life-years of mortality data. These data reveal remarkable flexibility and unexpected trends in the pattern of human ageing. Populations with lo ...

developmental biology↗

bioRxiv2017

The dynamic upper limit of human lifespan

We respond to claims by Dong et al. that human lifespan is limited below 125 years. Using the log-linear increase in mortality rates with age to predict the upper limits of human survival we find, in contrast to Dong et al., that the limit to human lifespan is historically flexible and increasing. This discrepancy can be explained by Dong et al.s use of data with variable sample sizes, age-biased rounding errors, and log(0) instead of log(1) values in linear regressions. Addressing these issues eliminates the proposed 125-year upper limit to human lifespan.

physiology↗