Organic codes and their identification : is the histone code a true organic code

Kühn, Stefan (2014-03)

Thesis (MSc)--Stellenbosch University, 2014.

Thesis

ENGLISH ABSTRACT: Codes are ubiquitous in culture|and, by implication, in nature. Code biology is the study of these codes. However, the term `code' has assumed a variety of meanings, sowing confusion and cynicism. The rst aim of this study is therefore to de ne what an organic code is. Following from this, I establish a set of criteria that a putative code has to conform to in order to be recognised as a true code. I then o er an information theoretical perspective on how organic codes present a viable method of dealing with biological information, as a logical extension thereof. Once this framework has been established, I proceed to review several of the current organic codes in an attempt to demonstrate how the de nition of and criteria for identifying an organic code may be used to separate the wheat from the cha . I then introduce the `regulatory code' in an e ort to demonstrate how the code biological framework may be applied to novel codes to test their suitability as organic codes and whether they warrant further investigation. Despite the prevalence of codes in the biological world, only a few have been de nitely established as organic codes. I therefore turn to the main aim of this study which is to cement the status of the histone code as a true organic code in the sense of the genetic or signal transduction codes. I provide a full review and analysis of the major histone post-translational modi cations, their biological e ects, and which protein domains are responsible for the translation between these two phenomena. Subsequently I show how these elements can be reliably mapped onto the theoretical framework of code biology. Lastly I discuss the validity of an algorithm-based approach to identifying organic codes developed by G orlich and Dittrich. Unfortunately, the current state of this algorithm and the operationalised de nition of an organic code is such that the process of identifying codes, without the neccessary investigation by a scientist with a biochemical background, is currently not viable. This study therefore demonstrates the utility of code biology as a theoretical framework that provides a synthesis between molecular biology and information theory. It cements the status of the histone code as a true organic code, and criticises the G orlich and Dittrich's method for nding codes by an algorithm based on reaction networks and contingency criteria.

AFRIKAANSE OPSOMMING: Kodes is alomteenwoordig in kultuur|en by implikasie ook in die natuur. Kodebiologie is die studie van hierdie kodes. Tog het die term `kode' 'n verskeidenheid van betekenisse en interpretasies wat heelwat verwarring veroorsaak. Die eerste doel van hierdie studie is dus om te bepaal wat 'n organiese kode is en 'n stel kriteria te formuleer wat 'n vermeende kode aan moet voldoen om as 'n ware kode erken te word. Ek ontwikkel dan 'n inligtings-teoretiese perspektief op hoe organiese kodes `n manier bied om biologiese inligting te hanteer as 'n logiese uitbreiding daarvan. Met hierdie raamwerk as agtergrond gee ek `n oorsig van 'n aantal van die huidige organiese kodes in 'n poging om aan te toon hoe die de nisie van en kriteria vir 'n organiese kode gebruik kan word om die koring van die kaf te skei. Ek stel die `regulering kode' voor in 'n poging om te wys hoe die kode-biologiese raamwerk op nuwe kodes toegepas kan word om hul geskiktheid as organiese kodes te toets en of dit die moeite werd is om hulle verder te ondersoek. Ten spyte daarvan dat kodes algemeen in die biologiese w^ereld voorkom, is relatief min van hulle onomwonde bevestig as organiese kodes. Die hoofdoel van hierdie studie is om vas te stel of die histoonkode 'n ware organiese kode is in die sin van die genetiese of seintransduksie kodes. Ek verskaf 'n volledige oorsig en ontleding van die belangrikste histoon post-translasionele modi kasies, hul biologiese e ekte, en watter prote endomeine verantwoordelik vir die vertaling tussen hierdie twee verskynsels. Ek wys dan hoe hierdie elemente perfek inpas in die teoretiese raamwerk van kodebiologie. Laastens bespreek ek die geldigheid van 'n algoritme-gebaseerde benadering tot die identi sering van organiese kodes wat deur G orlich en Dittrich ontwikkel is. Dit blyk dat hierdie algoritme en die geoperasionaliseerde de nisie van 'n organiese kode sodanig is dat die proses van die identi sering van kodes sonder die nodige ondersoek deur 'n wetenskaplike met 'n biochemiese agtergrond tans nie haalbaar is nie. Hierdie studie bevestig dus die nut van kodebiologie as 'n teoretiese raamwerk vir 'n sintese tussen molekul^ere biologie en inligtingsteorie, bevestig die status van die histoonkode as 'n ware organiese kode, en kritiseer G orlich en Dittrich se poging om organiese kodes te identi seer met 'n algoritme wat gebaseer is op reaksienetwerke en `n kontingensie kriterium.

Please refer to this item in SUNScholar by using the following persistent URL: http://hdl.handle.net/10019.1/86673
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