Abstract
One of the most sophisticated philosophies of science is the methodology of scientific research programmes (MSRP), developed by Imre Lakatos. According to MSRP, scientists are working within so-called research programmes, consisting of a hard core of fixed convictions and a flexible protective belt of auxiliary hypotheses. Anomalies are accommodated by changes to the protective belt that do not affect the hard core. Under MSRP, research programmes are appraised as ‘progressive’ if they successfully predict novel facts but are judged as ‘degenerative’ if they merely offer ad hoc solutions to anomalies. This paper applies these criteria to the evolutionary research programme as it has performed during half a century of ERV research. It describes the early history of the field and the emergence of the endogenization-amplification theory on the origins of retroviral-like sequences. It then discusses various predictions and postdictions that were generated by the programme, regarding orthologous ERVs in different species, the presence of target site duplications and the divergence of long terminal repeats, and appraises how the programme has dealt with data that did not conform to initial expectations. It is concluded that the evolutionary research programme has been progressive with regard to the issues here examined.
Highlights
Viruses 2022, 14, 14 provided some color commentary to the discoveries of molecular biologists, explaining their findings after the fact but never anticipating or participating in them? This paper examines these questions with respect to the discovery and further characterization of endogenous retroviruses (ERVs) in vertebrate genomes
It was not until 1964 that Howard Temin proposed the DNA provirus hypothesis, which states that the RNA of the Rous Sarcoma Virus acts as a template for the synthesis of DNA, which is integrated in the host genome and in turn provides a template for new viral RNA [5]
If ERVs have been endogenized and amplified over evolutionary history, as claimed by endogenization-amplification theory (EAT), and if much of this evolutionary history is shared between different species, as claimed by the thesis of common descent, we should expect that closely related species share the same ERV elements at orthologous loci
Summary
Two 20th century philosophers of science have strongly shaped how scientists, to this day, view what science is and how it works. Less well known is that the seemingly opposing views of Popper and Kuhn have been synthesized by the Hungarian philosopher Imre Lakatos [3] This synthesis is called the methodology of scientific research programmes (MSRP). On the other hand, a research programme the forward momentum of the positive heuristic, Lakatos demands that thesegenerally changes features degenerative have rational are basis for switching to another, lead to the prediction adjustments, of novel facts.scientists. If they do, theachanges ‘theoretically progressive’, more researchare programme. This section will briefly outline the history of ERV research and the emergence of this theory of endogenization and amplification
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