Skip to main page content
U.S. flag

An official website of the United States government

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Review
. 2021 Dec 22;14(1):14.
doi: 10.3390/v14010014.

How Well Does Evolution Explain Endogenous Retroviruses?-A Lakatosian Assessment

Ruben N Jorritsma  1
Affiliations
Review

How Well Does Evolution Explain Endogenous Retroviruses?-A Lakatosian Assessment

Ruben N Jorritsma. Viruses. .

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.

Keywords: endogenization-amplification theory (EAT); endogenous retroviruses (ERVs); evolution; evolutionary research programme; long terminal repeats (LTRs); methodology of scientific research programmes (MSRP); phylogenetics.

PubMed Disclaimer

Conflict of interest statement

The author declares no conflict of interest.

Figures

Figure 1
Figure 1
A research programme consists of a hard core of static beliefs, a heuristic, and a protective belt containing all other knowledge. The protective belt is dynamic and adapts in such a way that observations can be explained without affecting the hard core.
Figure 2
Figure 2
An ideal phylogenetic tree of LTRs of an orthologous ERV in five species. When the ERV integrates in the common ancestor, the 5′ and 3′ LTRs are identical. They then drift apart as they incur mutations. The two LTRs each keep an independent record of subsequent speciation events. All 5′ LTRs have been diverging from all 3′ LTRs since integration, whereas the 5′ LTRs amongst themselves have only been diverging since the various speciation events. All 5′ LTRs should thus clade together, as should all 3′ LTRs. The outgroup consists of a related ERV at another locus.
See this image and copyright information in PMC

Similar articles

See all similar articles

References

    1. Popper K.R. The Logic of Scientific Discovery. Hutchinson & Co; London, UK: 1959.
    1. Kuhn T.S. The Structure of Scientific Revolutions. University of Chicago Press; Chicago, IL, USA: 1962.
    1. Lakatos I. In: The Methodology of Scientific Research Programmes: Volume 1: Philosophical Papers. Worrall J., Currie G., editors. Volume 1 Cambridge University Press; Cambridge, UK: 1980.
    1. Darlington C. The plasmagene theory of the origin of cancer. Br. J. Cancer. 1948;2:118. doi: 10.1038/bjc.1948.17. - DOI - PMC - PubMed
    1. Temin H.M. The DNA provirus hypothesis. Science. 1976;192:1075–1080. doi: 10.1126/science.58444. - DOI - PubMed

Publication types

LinkOut - more resources