Understanding Complexity in Biological Systems: From Simple Description to Synthetic Design
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1 Understanding Complexity in Biological Systems: From Simple Description to Synthetic Design Dr. George Poste Chief Scientist, Complex Adaptive Systems Initiative and Del E. Webb Chair in Health Innovation Arizona State University Presentation: Transcending Our Origins Origins 5 th Anniversary Celebration and Workshop Arizona State University 5 April 2014
2 Biological Diversity and Variation: Endless Forms Most Beautiful 2
3 Biological Diversity and Variation: Endless Forms Most Beautiful 3
4 Biological Diversity and Variation: Endless Forms Most Beautiful Form and Function diversity, (species) variation (individuals) specialization (cells) adaptation evolution reproduction 4
5 Biological Diversity and Variation: Endless Forms Most Beautiful Instructional Information code components assembly molecular signaling networks stability resilience plasticity and evolvability reproduction 5
6 Understanding Biological Organization: The Construction of Increasing Hierarchical Complexity and Mapping the Underlying Instructional Information common genetic (digital) code in all life forms tool box of protein motifs for combinatorial assembly ( molecular lego ) assembly of structurally and functionally diverse proteins protein interactions and nanoscale intracellular structures molecular signaling networks cells and tissues organs organism
7 Systems and Synthetic Biology: Exploring Biospace Understanding the Coding Systems for Highly-Specific Programs of Regulated Information Flow and Processing in Dynamic Biological Systems Digital Biology: It from Bits
8 Digital Biology and Synthetic Biology It from Bits It Bits
9 Digital Biology and Molecular Medicine Mapping Instructional Coding Landscapes and Information Networks stable information signaling networks (health) disrupted (dysregulated) information signaling networks (disease) reprogramming information networks (stem cells and regenerative medicine) engineering novel gene constructs (code) to program biological information networks
10 Darwinian Evolution.the inheritance of profitable variation
11 Synthetic Biology: Accelerated and Directed Evolution Creating artificial life with DNA synthesis. That s sort of the equivalent of machine-language programming. If you want to change the world in some big way, use biological molecules. Bill Gates Wired 2010
12 Life as Evolving Software DNA as a universal programming language origin of life is the origin of software (G. Chaitin) all that counts is the information the rest will take care of itself via programmed self-assembly (S. Brenner) immense, combinatorial space (DNA and gene regulatory networks as software) generation of biological diversity (inventiveness, plasticity, adaptation, evolvability) phylogeny is software archeology
13 Synthetic Biology to program and assemble biological functions and organisms based on knowledge of the rule sets underlying hierarchical biological organization - reprogramming existing biological signaling pathways and networks exploring biospace - design, simulation and construction of novel functions/organisms - novel biotic (living): abiotic (inert materials) combinations
14 Advanced Manufacturing Digital Programming of 3-D Fabrication and New Assembly Technologies 14
15 Emerging Technologies for Precision Modification of Genomes and Their Coding Instructions (Biological Software) Cost-Effective Synthetic Production of DNA Genome Editing Construction of Cellular Chassis For Designed Genes
16 Mapping Possibility Space
17 Mapping Possibility Space The Power of Combinatorial Molecular Interactions and Self-Assembly of Complex Molecular Networks number of theoretical possibilities for synthetic assembly far exceeds the narrow space sampled in evolutionary time (existing and extinct species) DNA and RNA nucleotide sequence permutations amino acid sequence permutations gene regulatory networks (gene-gene interactions, RNA-mediated gene regulation) protein-protein interaction networks
18 Exploring Biospace The Power of Combinatorial Interactions and Molecular Assembly 22,000 genes two genes cooperate to create a function =(22,000 x 21,999)/2 = 241,989,000 potential combinations 100 genes generate a complex function = potential combinations number of theoretical possibilities for synthetic assembly (biospace) far exceed narrow molecular space sampled in evolutionary time to date
19 Synthetic Biology: Engineering Novel Organisms with Novel Functions Programmable Microbial Genomes A New Industrial Ecology and Novel Biosyntheses reversal of abnormal microbiome (dysbiosis) in human
20 Synthetic Biology and Engineering Enhanced Traits in Food, Feed and Fiber Products
21 Regenerative Medicine: The Union of Synthetic Biology and Tissue Engineering 21
22 Convergence Natural Digital Software: DNA Artificial Digital Software: Programming Languages 3 4 x 10 9 years old years old
23 Digital Biology and Synthetic Biology the reduction of biological complexity to modularity to rebuild complexity using silicon to make DNA that makes something with no evolutionary counterpart silicon encodes digital DNA for e.transfer to any location
24 The Matternet internet for objects digital coding of fabrication specifications to distributed, point-of-need (PON) synthesis units digital omics and synthetic biology broader concept of digital 3D printing/manufacturing of diverse materials
25 The Digital-Biological Converter We can now send biology at the speed of light J. Craig Venter
26 Oh, God help us! We re in the hands of engineers. Dr. Ian Malcolm Chaotician : Jurassic Park
27 Digital Biology Biodiversity and Natural Evolution Synthetic Biology, Directed (accelerated) Evolution and Novel Biodiversity
28 Synthetic Biology and New Metrics for Biodiversity diversity = net rate of addition of novel genomes versus net rate of genome extinctions rethinking biodiversity the sum total of novel genome sequences (natural or synthetic) or simply the number of distinct species?
29 Advances in Genome Biology and Flights of Imagination Theoretical Scenarios versus Current Technological Capabilities
30 De-extinction: the Revive and Restore Project Science (2013) 340, 32
31 Not Immediately Available! Source: Wired Site: geekologie.com
32 The Expansion of Conceptual Horizons in Biology Living Systems mapping molecular information networks and the origin of biological complexity and biodiversity Life in Simulation computational biology and exploration of new architectures for biological signaling (information) networks Synthetic Systems production of novel structures and functions with no known evolutionary precedent or precursor
33 Technology Convergence and Synthetic Biology: Biology and Medicine Meet Engineering and Computing Automation/Miniaturization and Robotic Production Suites and Advanced Machine Learning Tools Modeling and Simulation of Biological Networks Exabyte and Zettabyte Computing Scale Advanced Computing, New Analytical Tools and Machine Intelligence
34 The Evolution of Biological Complexity: A Contemporary Synthesis Evolutionary Theory Variation Selection Evolution Natural Systems Complexity Emergence Synthetic Systems Information Theory
35 Mapping the Coding Information for Organizational Complexity, Diversity and Variation in Biological Systems design and organization of complex adaptive biological systems evolution, ecology and fitness landscapes biomimetic engineering and synthetic biology modification of human performance and capabilities
36 Mapping the Coding Information for Organizational Complexity, Diversity and Variation in Biological Systems organization of complex adaptive biological systems evolution, ecology and fitness landscapes biomimetic engineering and synthetic biology modification of human performance and capabilities form and function instructional codes and information content mapping existing biospace exploring novel biospace (possibility space) oversight and regulation modulation or augmentation (nonheritable) enhancement (heritable)
37 Synthetic Biology and Expanded, Novel Biodiversity Complex Ethical, Legal and Social Implications and New Dual-Use Dilemmas modulated augmented enhanced systems health agriculture ecosystems industrial applications national security
38 Synthetic Biology and Expanded, Novel Biodiversity: Complex Ethical, Legal and Social Implications and New Dual-Use Dilemmas Impact on Human Identity and Societal Structure health agriculture ecosystems modulated augmented enhanced systems industrial applications national security Oversight: Regulation and Legislation
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