A Contemporary Message from Mendel's Logical Empiricism

Mendel: From genes to genome

Two hundred years after the birth of Gregor Mendel, it is an appropriate time to reflect on recent developments in the discipline of genetics, particularly advances relating to the prescient friar's model species, the garden pea (Pisum sativum L.). Mendel's study of seven characteristics established the laws of segregation and independent assortment. The genes underlying four of Mendel's loci (A, LE, I, and R) have been characterized at the molecular level for over a decade. However, the three remaining genes, influencing pod color (GP), pod form (V/P), and the position of flowers (FA/FAS), have remained elusive for a variety of reasons, including a lack of detail regarding the loci with which Mendel worked. Here, we discuss potential candidate genes for these characteristics, in light of recent advances in the genetic resources for pea. These advances, including the pea genome sequence and reverse-genetics techniques, have revitalized pea as an excellent model species for physiological-genetic studies. We also discuss the issues that have been raised with Mendel's results, such as the recent controversy regarding the discrete nature of the characters that Mendel chose and the perceived overly-good fit of his segregations to his hypotheses. We also consider the relevance of these controversies to his lasting contribution. Finally, we discuss the use of Mendel's classical results to teach and enthuse future generations of geneticists, not only regarding the core principles of the discipline, but also its history and the role of hypothesis testing.

Gregor Mendel at the source of genetics and systems biology

Gregor Mendel is generally presented as the ‘ignored and solitary founder of genetics’. This Moravian friar would have worked in strict isolation on the heredity of peas in the garden of his monastery, and his experiments would have been ignored by his contemporaries, before being ‘rediscovered’ independently by three botanists in 1900, 34 years after their publication. Historians have contributed to replace the genesis of Mendel’s work in the context of his time, questioning the mythical image that prevailed in academic circles and the public perception. This paper recalls that Mendel benefitted from a very favourable context for the development of his experiments at St Thomas Monastery in Brno and was not isolated from the scientific community of his time. Although the notions on which his work was based were already present in scientific publications, this does not diminish the importance of Mendel’s contribution to the development of modern biology. We provide a detailed analysis of the results of his experiments on the development of hybrid plants that he presented in two lectures at the Brno Society of Natural History in 1865, demonstrating that beyond his major contribution to the foundation of genetics, Mendel was one of the pioneers of systems biology.

Virtual Gene Concept and a Corresponding Pragmatic Research Program in Genetical Data Science

Mendel proposed an experimentally verifiable paradigm of particle-based heredity that has been influential for over 150 years. The historical arguments have been reflected in the near past as Mendel's concept has been diversified by new types of omics data. As an effect of the accumulation of omics data, a virtual gene concept forms, giving rise to genetical data science. The concept integrates genetical, functional, and molecular features of the Mendelian paradigm. I argue that the virtual gene concept should be deployed pragmatically. Indeed, the concept has already inspired a practical research program related to systems genetics. The program includes questions about functionality of structural and categorical gene variants, about regulation of gene expression, and about roles of epigenetic modifications. The methodology of the program includes bioinformatics, machine learning, and deep learning. Education, funding, careers, standards, benchmarks, and tools to monitor research progress should be provided to support the research program.