FUNDAMENTALS OF GENERATIVE MEDICINE VOLUME I: CONCEPTS, SYSTEMS AND PATHWAYS PETER J. D’ADAMO, ND MIFHI Copyright 2010 by Peter J. D’Adamo, ND, MIFHI Printed in the United States by Drum Hill Publishing, LLC. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system or transmitted in any form or by any means without the prior written permission of the publisher. Cover art by Peter D’Adamo. Based on a cellular automaton algorithms devised by Stephen Wolfram. 213 Danbury Road, Wilton CT 06897 USA www.drumhillbooks.com ISBN 978-0-9828720-0-0 FUNDAMENTALS OF GENERATIVE MEDICINE | ii “You will seek not a near, but a distant, objective, and you will not be satisfied with what you have done. All that you may achieve or discover you will regard as a fragment of a larger pattern, which from his separate approach every true scholar is striving to descry.” Aims of the Harvard Society of Fellows (1938) FUNDAMENTALS OF GENERATIVE MEDICINE | iii FUNDAMENTALS OF GENERATIVE MEDICINE | iv TABLE OF CONTENTS THE SIMPLE, THE COMPLEX, AND THE GENERATIVE..............................................................................................................17 I. DEUS EX MACHINA ........................................................................................................................................... 23 THE GAME OF LIFE .....................................................................................................................................................................25 Complexity versus complicated ................................................................................................................................................ 27 How things happen......................................................................................................................................................................... 30 Living Systems Theory.................................................................................................................................................................. 31 Life on the edge of chaos .............................................................................................................................................................. 37 THE GREAT CHAIN OF BEING....................................................................................................................................................41 Naturphilosophie...................................................................................................................................................................45 Vitalism ................................................................................................................................................................................................ 46 Preformationism.............................................................................................................................................................................. 47 Epigenesis........................................................................................................................................................................................... 48 GEMMULES...................................................................................................................................................................................51 Pangenesis and Mendelian Inheritance.......................................................................................................................53 Darwin’s Pangenesis ...................................................................................................................................................................... 54 Medelian inheritance ..................................................................................................................................................................... 56 Lamarckism........................................................................................................................................................................................ 59 Weissman’s New Preformationism ......................................................................................................................................... 60 Wrong turns.............................................................................................................................................................................62 Eugenics............................................................................................................................................................................................... 63 Lysenkoism ........................................................................................................................................................................................ 65 Modern Times..........................................................................................................................................................................67 The Modern Synthesis................................................................................................................................................................... 67 II. VARIATION AND INHERITANCE ................................................................................................................. 69 HELLO WORLD.............................................................................................................................................................................71 What is code?...........................................................................................................................................................................72 Transcription and replication: DNA ........................................................................................................................................ 74 Translation: RNA ............................................................................................................................................................................. 78 Proteins................................................................................................................................................................................................ 83 Chromosomes ................................................................................................................................................................................... 87 Cell Cycles..................................................................................................................................................................................90 Mitosis .................................................................................................................................................................................................. 90 Meiosis.................................................................................................................................................................................................. 93 RIGHT FROM WRONG FROM RIGHT...........................................................................................................................................97 Mutations..................................................................................................................................................................................99 Transposable elements.............................................................................................................................................................. 102 Copy number variations .................................................................................................................................................. 106 Fusion genes ................................................................................................................................................................................... 107 Population Genetics........................................................................................................................................................... 110 Haplotypes and haplogroups................................................................................................................................................... 111 GENETICS AS AN INTERACTIVE SPORT ..................................................................................................................................115 What is Information?........................................................................................................................................................ 116 Cistrons and open reading frames (ORF)........................................................................................................................... 120 RNA splicing.................................................................................................................................................................................... 121 Linkage disequilibrium, pleiotropy and epistasis .......................................................................................................... 123 Pleiotropy......................................................................................................................................................................................... 126 Epistasis...........................................................................................................................................................................................