Distinguishing between "Function" and "Effect" in Genome Biology

Abstract

Much confusion in genome biology results from conflation of possible meanings of the word “function.” We suggest that, in this connection, attention should be paid to evolutionary biologists and philosophers who have previously dealt with this problem. We need only decide that although all genomic structures have effects, only some of them should be said to have functions. Although it will very often be difficult or impossible to establish function (strictly defined), it should not automatically be assumed. We enjoin genomicists in particular to pay greater attention to parsing biological effects.

Identification of introns harboring functional sequence elements through positional conservation

“…The mere presence of a TFBS within an intron is not an indication of functionality 3, 17 , as TFBS are greatly over-represented in the genome and only a small fraction of them has a true biological significance 18, 19 . To avoid this, we only considered TFBS that coincide with human active genomic segments as mapped by the ENCODE project 20–23 .…”

Assessment of Circulating LncRNAs Under Physiologic and Pathologic Conditions in Humans Reveals Potential Limitations as Biomarkers

“…This was another key consideration because ideal biomarkers should not only report changes in disease activity, but also be readily measurable and reproducible, and this is a characteristic that has not been clearly addressed for plasma lncRNAs in previous studies. Furthermore, the abundance of non-coding RNA species in cells have been shown to roughly correlate with their level of phylogenetic conservation18, which has been suggested to be a good proxy for function1920. In parallel, understanding the relative abundance of lncRNAs in circulation may thus provide similar clues about their functional significance.…”

L’apophénie d’ENCODE ou Pangloss examine le génome humain

“…En revanche, les conclusions des articles de 2014 semblent bien insipides. Qu'on en juge par la platitude de la conclusion de la comparaison des transcriptomes humains / drosophiles / nématodes : « nos résultats soulignent l'importance de comparer des organismes modèles distants avec les humains afin de distinguer les principes la transmission de son patrimoine génétique [14]. Mais ENCODE utilise une définition plus inattendue : le fragment d'ADN doit être transcrit et/ou impliqué dans des interactions avec des protéines connues pour leurs rôles dans la régulation de la transcription, et ce dans au moins un des types cellulaires testés.…”