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Neutralism versus selectionism: Chargaff's second parity rule, revisited.

ABSTRACT: Of Chargaff's four "rules" on DNA base frequencies, the functional interpretation of his second parity rule (PR2) is the most contentious. Thermophile base compositions (GC%) were taken by Galtier and Lobry (1997) as favoring Sueoka's neutral PR2 hypothesis over Forsdyke's selective PR2 hypothesis, namely that mutations improving local within-species recombination efficiency had generated a genome-wide potential for the strands of duplex DNA to separate and initiate recombination through the "kissing" of the tips of stem-loops. However, following Chargaff's GC rule, base composition mainly reflects a species-specific, genome-wide, evolutionary pressure. GC% could not have consistently followed the dictates of temperature, since it plays fundamental roles in both sustaining species integrity and, through primarily neutral genome-wide mutation, fostering speciation. Evidence for a local within-species recombination-initiating role of base order was obtained with a novel technology that masked the contribution of base composition to nucleic acid folding energy. Forsdyke's results were consistent with his PR2 hypothesis, appeared to resolve some root problems in biology and provided a theoretical underpinning for alignment-free taxonomic analyses using relative oligonucleotide frequencies (k-mer analysis). Moreover, consistent with Chargaff's cluster rule, discovery of the thermoadaptive role of the "purine-loading" of open reading frames made less tenable the Galtier-Lobry anti-selectionist arguments.

SUBMITTER: Forsdyke DR

PROVIDER: S-EPMC8057000 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:In the study of consciousness, neurophenomenology was originally established as a novel research program attempting to reconcile two apparently irreconcilable methodologies in psychology: qualitative and quantitative methods. Its potential relies on Francisco Varela's idea of reciprocal constraints, in which first-person accounts and neurophysiological data mutually inform each other. However, since its first conceptualization, neurophenomenology has encountered methodological problems. These problems have emerged mainly because of the difficulty of obtaining and analyzing subjective reports in a systematic manner. However, more recently, several interview techniques for describing subjective accounts have been developed, collectively known as "second-person methods." Second-person methods refer to interview techniques that solicit both verbal and non-verbal information from participants in order to obtain systematic and detailed subjective reports. Here, we examine the potential for employing second-person methodologies in the neurophenomenological study of consciousness and we propose three practical ideas for developing a second-person neurophenomenological method. Thus, we first describe second-person methodologies available in the literature for analyzing subjective reports, identifying specific constraints on the status of the first-, second- and third- person methods. Second, we analyze two experimental studies that explicitly incorporate second-person methods for traversing the "gap" between phenomenology and neuroscience. Third, we analyze the challenges that second-person accounts face in establishing an objective methodology for comparing results across different participants and interviewers: this is the "validation" problem. Finally, we synthesize the common aspects of the interview methods described above. In conclusion, our arguments emphasize that second-person methods represent a powerful approach for closing the gap between the experiential and the neurobiological levels of description in the study of human consciousness.

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Neutralism versus selectionism: Chargaff's second parity rule, revisited.

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