From owner-biophys@hgmp.mrc.ac.uk Fri May 16 05:25:14 2003 Return-Path: X-Original-To: biophys-outgoing Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with SMTP id 831507D205 for ; Fri, 16 May 2003 05:25:14 +0100 (BST) X-Original-To: biophys-list@hgmp.mrc.ac.uk Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 0E9217D3FF for ; Fri, 16 May 2003 05:25:14 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id E5D047D205 for ; Fri, 16 May 2003 05:25:10 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.11.6+Sun/8.8.8) id h4G4PAf00227 for biophys-list@hgmp.mrc.ac.uk; Fri, 16 May 2003 05:25:10 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Douglas Otis X-Newsgroups: bionet.biophysics Subject: Re: Introns Message-ID: References: X-Newsreader: Forte Agent 1.93/32.576 English (American) MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lines: 106 Date: Fri, 16 May 2003 04:21:00 GMT X-Complaints-To: abuse@sonic.net To: biophys@hgmp.mrc.ac.uk Sender: owner-biophys@hgmp.mrc.ac.uk Precedence: bulk Dear Enzo Di Giulio, I have a different view regarding the beginning of life. Actually this does not appear to be a new idea. I have these ideas expressed on a website http://www.rigidether.org Doug On Sun, 4 May 2003 08:59:08 +0200, "Enzo Di Giulio" wrote: > > > Introns: a hypothesis on their origin, function, elimination. > > > Rather than being molecular junk, introns may have a meaningful role in the >structure of DNA. > In the following the 'story' of introns is sketched on the basis of the >'theory of electroscalenes' (E.S.T.). This theory investigates on the >electrostatic features of the heteroatomic molecules of biochemistry, using >the schemata of abstract entities: clusters of linked electric charges (with >links capable of rotating around their axis, for flexibility). The name >scalene means that for these structures to be interesting, they must be >irregular (not symmetrical). A scalene is a sort of electrical skeleton of a >molecule, its charges coinciding (approximately) with charge concentrations >along the molecular architecture. > Natural environments are ionic solutions, therefore electric fields are of >the diffuse charge type: the potential (x,y,z) is a solution of the Poisson >equation, rather than the Laplace equation that rules common dielectric >fields. This leads to a fundamental property: provided parameters satisfy >some conditions, the electrical forces acting on the scalene can zero in at >a definite point in space and the scalene can sit in equilibrium in this >'address'. Even at the two-dimension level, that is accessible to simple >mathematics, a number of properties of natural systems can thus be given >reasonable justification. In particular, the theory can account for the >specificity of some reactions. > Long linear scalenes can simulate natural polymers like polynucleotides and >polypeptide. 'Polyscalenes' of orderly structure possess an address in >particular fields: they can be used to represent genes. > > Primitive seawaters contained all sort of soluble molecules, waiting to >meet their chemical fate. In times when earthquakes and volcanic eruptions >were intense and frequent, strong electric fields accompanied the mutual >sliding of rock layers. In the diffuse charge environment of sea waters this >gave way to active sites that acted on specific molecules catalyzing >chemical conversions. > Polymer science knows the way ionic catalysts cen select specific monomers >to generate long chain of specific structure. Under the influence of >electric fields, it was then possible to collect a great number of monomer >units in homo- or co-polymers that dispersed in the seawater environment. >The copolymers of particular purins and pyrimidines with short phosphor >units and the copolymers of a restricted number of alpha amino acids were so >robust to survive degradation for long stretches of time: enough to reach >the shelter, as explained below, of lipid bubbles. > This chemical selection of nucleic acids and polypeptides following the >creation of specific catalytic sites is the origin of the complex process of >development of living structures. > The peculiar properties of lipids generated hollow spheres that realized >the separation of an inside from the outside. The membranes attracted >lipo-soluble molecules. The presence of electric charges on their surface >generated in the inside an electric field. As can be shown, this field has a >zero-intensity zone at the center of the structure: a zone (widely >coinciding with the cell nucleus) that can be called a 'crater'. This crater >acted as an attractor on charge-carrying polymers. Polynucleotides and >polypeptide were sucked in, with negatively charged nucleic acids 'falling' >in the crater and rolling up in a compact mass. > As ionic polymerization never produces perfect isotactic polymers, the >chains contained non-isotactic sequences. Polynucleic chains consisted of >orderly sequences with helically disposed monomer triplets, alternating with >non-isotactic sequences. In the cellular fields, the first (exons) would lie >along lines of force, the second (introns) remained as free-bending linking >elements. > Is this the beginning of a cell. > In a complete cell orderly polynucleotide sequences may be caught up by >cellular fields displaying particular patterns (depending on the development >stage of the cell). If specifity conditions are met the macromolecules >protrude from the central mass, sliding along a line of force till they >reach their address. Their linear configuration makes them accessible to >replication enzymes. These sequences are the expressed genes (exons). They >are linked to the 'next' exon and/or the central mass by strings of flexible >introns. In conjunction with the cellular field, variable with the cell >stage, they determine the kind of cell that is active at any time. > The function of introns is then to connect the regular sequences forming >genes into one and the same linear element (chromosome). The problem of a >code realizable with chemical means has been solved by nature by this >superposition of tasks in a random-access, ribbon-like structure. > > After replication, the structure must get rid of excess units and send to >the ribosomes a sequence of 'genes only'. This comes about spontaneously: on >the spot where it is formed, a messenger RNA molecule finds itself in an >'alien' field, and to diminish the moment acting on the molecule it rolls up >to a closed curve. ( This can be seen in two dimensions calculating the >total moment when the units are bent with an angle of increasing value, till >the sequence rolls up to a closed polygon: the moment decreases >progressively to become zero in the full 'circle'). Then the end of one >exon and the beginning of the next are brought to close proximity (a >'capital omega' effect) and join, while the free intron sequence detaches >itself and is quickly demolished. The orderly sequences (RNA-copies of >genes) travel along lines of force that, like rails of a railway, pass >through the nuclear membrane pores and lead to the ribosome. > > .