COMPLEX SYSTEMS, LIFE, & their ORIGIN PCES 5.61 The t true c comple lexity of real l solid lids and liq liquids is is frig ightening t g to contempla late. T They do NOT lo look lik like s sim imple le models o of crystals ls and m mole lecule les. I Instead there is is an amazin zing g hie ierarchy of patterns t that d develo lop in in them, a and in in their dynamics. Physi sicists an and mat athemat atician ans have nam amed so some o of these f feat atures. T . They tal alk, eg., of ‘ ‘chaos’, o or ‘ ‘turbule lence’, r referring t g to hie ierarchical l structures in in flu luid ids. R Real l solid lids & & liq liquid ids m move between a vast number o of possible le states, im impossible le t to predict. M Many in inanimate structures, a and a all ll bio iolo logic gical s systems, a are n not in in thermal equili ilibriu ium – they a are driv iven by energy gy e eit ither from outsid ide ( (typic ically ly b but n not a alw lways the the sun) n), or from i int nternal c che hemical r reactions. This allo llows t them t to evolve a and, under c certain in cir ircumstances, f form e ever more comple lex structures a as t tim ime goes o on. The e exis istence o of autocataly lysis m makes t the formation o of comple lex s structures (in including w what w we call ll lif life) in inevit itable le in in our univ iverse. L Lif ife orig iginated o on earth b by a serie ies o of accidents, w whic ich were continge gent upon n specific c cond nditions o on the n the p plane net – thus lif life els lsewhere w will lik ill likely ly lo look VERY dif ifferent. Comple lex m mole lecule les form e even in in space, o on, eg., in interstell llar g grain ins. Bio iolo logical s systems on earth, & & some artif ificia ial l structures lik like p pla lastics, a are a at le least p partia iall lly made f from ‘ ‘soft matter’, w wit ith la large ‘ ‘flo loppy’ m mole lecules, unstable t to too m much he heat, but d t dependent on n the the s sun’ n’s ene nergy a and nd/or radioactivity. Even a at the very lo lowest t temperatures, quantum tunneli ling s g stil ill l driv ives s some complex m motion. . Quantum m mechanics i s is essential to underst stan and t the structures s formed in in bio iolo logy.
COMPLEX MICROSTRUCTURE in SOLIDS PCES 5.62 Even in simple inanimate solids, complex hierarchical structure forms naturally. Simple objects like w indow glass have an elaborate structure w hich is not apparent from the completely disordered spatial arrangement of the atoms. Crystals of course look highly ordered, but only microscopic crystals are common in Nature (a rock is a conglomerate of millions of microcrystals) The hierarchical structure of ‘glassy states’ Even in interstellar space one finds ‘interstellar in a disordered solid grains’ and polycrystalline dust particles, w ith an organized internal & surface structure – also found on rocks and sand on earth. One w ay complex molecules may have formed on early earth w as on such surfaces, w hich both catalyzed and formed a template for their rapid synthesis. Interstellar grains, discussed later, are Typically C plus impurities, like the graphite in pencils, The surface of a lump of graphite, w ith its w ith a ‘sheetlike’ atomic structure acting as a template. layered structure visible. Interstellar grains and dust look similar. On earth, solid objects – rocks - formed initially by cooling of the hot liquid earth. Thermal energy drove chemical reactions – & it still does, along w ith energy from radioactive decay, & the sun. But even at extremely low temperatures, w here conventional chemical reactions have stopped, quantum tunneling still allow s things to change in time – the same thing can happen, very slow ly, even in the depths of space, far from stars. So quantum mechanics drives change, & structure Experiments on mylar and on SiO 2 glass, show ing how formation, everyw here in the universe. the capacitance is still changing even at only 2.5 mK above absolute zero! Most solids show this behaviour.
LARGE-SCALE PATTERN FORMATION PCES 5.63 in SOLIDS & LIQUIDS At our ‘macroscopic’ scale, one sees patterns forming – these may be affected by the microscopic structure, but they arise because of complicated ‘collective’ motions involving many sub-units together. The patterns include w aves, vortices, and also much more complicated structures. ABOVE: dendrite formation BELOW: grow ing snow flakes There is of course no purpose or design here – these structures arise from very simple interactions betw een the sub-units, w ith the addition of external energy. But in the real world they act as the templates or basic architectures used by most of the animate & inanimate objects that w e see around us – ranging from simple fluid flow s to the structures of plants and animals. ABOVE & below : Vortex w akes Beginning in the 1960’s, both biologists & physicists began to speak of the ‘emergent properties’ of large systems – properties w hich did not exist at the small scale, w hich ABOVE: Period doubling to chaos – cannot easily be predicted & w hich the oscillation modes of a system often not depend on the form of the increase in number as an interaction is changed microscopic interactions.
SOFT MATTER PCES 5.64 Solids a are ha hard because o of f qu quantum m mechanics, , whi hich creates strong bond nds. . However l larger, m more compl mplex mo x molec ecules are e ver ery ‘ ‘flopp ppy’. On Only carbo bon- bas ased lar arge ge m molecules can can e even hold t toge gether, because e C-C b bon onds are v very st stron ong. Lon Long cha hain structures w with r repeated C C uni nits form pol olymers w s which can asse ssemble i into o a mess ssy disorder dered ed net etwork l k like rubber ber. Repetition o of very PG de Gennes (1932-2007) long ng s sequ quences of f an n ‘a ‘alphabet’ o ’ of f a few different amino aci acids, in pairs of f cha hains w whi hich can n be link nked or ‘u ‘unz nzipped’, , gives D DNA NA & & the ‘genetic ic c code’. P Protein ins a are malle leable le assemblie ies of compl mplex f x folde ded chain in struct ctures. . Chain of ethylene molecules (polythene) The general physical properties of ‘soft matter’: rubber, polymers, emulsions like yoghurt, etc., are now w ell understood (de Gennes & others). How ever in living things molecules are constantly changing, & the essence of this is not in the structure of the molecules or their constituents, but in the inter-connected processes they are involved in. One talks of ‘dissipative structures’ far from thermal equilibrium, exchanging material & info in a connected network of processes. Living organisms are amongst such systems. Our know ledge of these is limited – but biologists & nanoscientists are starting to modify these structures to make new ones of their ow n. Such work raises profound ethical questions, & may be very dangerous, to us and other living things. Structure of RAS-RID protein Artificial DNA/nanopore system
PCES 5.65 MOLECULES ENCODING LIFE on EARTH A key step in the evolution of life on earth w as the evolution of RNA and DNA molecules. In our current understanding of ‘life as w e know it’, life needs a copying mechanism to carry information about a living object to Its descendants. Note this isn’t SUFFICIENT for life – even computer programs have it. But it’s NECESSARY, otherw ise A virus dissociating: no organizational structure can be maintained over time. the very long RNA molecule is starting The RNA molecule can replicate, & also catalyzes itself – to unravel. its formation in the early history of the earth w as crucial, & many viruses still have a genetics based on RNA. How ever the error rate in passing dow n info is high, leading to a very high mutation rate, and loss of info – so this method does not work except for very simple systems, w here these mutations are not so important (this is w hy viruses mutate so fast). The DNA double The DNA replication mechanism is common to all helix molecule species of life on earth, & to some viruses – it first appeared roughly 4 Gya ago. The key is to have 2 chains of long molecules (each one basically an RNA), made from amino acids, w hich pair off and can be zipped/unzipped together. A copying error now show s up because the zip doesn’t work properly - the error can be corrected. Now huge amounts of info can be transmitted to descendants. A small mutation rate is essential - new variations can then be tried – but it must be kept very small. The DNA unzipping – the ‘base The sequence of amino acids encodes info – A DNA fingerprint, pair’ amino acids are labelled by from a crime lab – it it is then ‘expressed’ w hen the chain unzips to letters A,C,T,G. An unzipped half Uniquely identifies w ill then attract base pairs that make proteins (ie., to make the organism). The the organism from match up to form a new DNA DNA is the ‘instructional plan’ for living things. w hich it comes. double helix (replication)
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