biological systems also physical systems? Shant Shahbazian Faculty - PowerPoint PPT Presentation

The age of the “synthetic” biology: Are biological systems also physical systems? Shant Shahbazian Faculty of physics, Department of complex and biological systems, Shahid Beheshti University Prepared by Shant Shahbazian for the seminar of "What is life" at the Institute for research in fundamental sciences (IPM) (2-Nov-2016) 1

What is life: The physical aspects of the living cell • Order emerges from disorder • Mutations are quantum leaps • Negative entropy is the source of non-equilibrium state of living systems • An aperiodic crystal is the physical basis of heredity • The living systems do not elude the “laws of physics” Prepared by Shant Shahbazian for the seminar of "What is life" at the Institute for research in fundamental sciences (IPM) (2-Nov-2016) 2

Are biological systems also physical systems? Yes for Schrödinger as a physicist! Since “in principle” every structure or event in a living system obeys the known laws of physics But, in practice how this “in principle” understanding may help for “actual” understanding ? Prepared by Shant Shahbazian for the seminar of "What is life" at the Institute for research in fundamental sciences (IPM) (2-Nov-2016) 3

The anatomy of the physical “understanding” • Every physical system must be decomposed into subsystems • The nature of the interactions of subsystems must be deduced • The state of physical system is derived from these two elements • The evolution (usually time- dependent) of the state of system governs a physical law • When all these are available, we have a physical model • Solar system as a classic example Prepared by Shant Shahbazian for the seminar of "What is life" at the Institute for research in fundamental sciences (IPM) (2-Nov-2016) 4

The “effective” understanding in physics • Physical system may be decomposed into various types of subsystems • The nature of the interactions are different for various decomposition schemes • Usually there is a decomposition scheme that is perceived to be effective • Everything redundant has been discarded from the effective model • There is a hierarchical structure in model building • The kinetic theory of gases is a classic example 5 Prepared by Shant Shahbazian for the seminar of "What is life" at the Institute for research in fundamental sciences (IPM) (2-Nov-2016)

What “in principle ” is not yet understandable • There are systems or events that the physical laws governing their evolution is not yet known • The particle physics at ultrahigh energies • The internal structure of the back holes • The start of the universe some • The nature of dark matter • The nature of dark energy • Search in underlying theories is ongoing in these areas though they govern phenomena much beyond the everyday life and probably irrelevant to biology… 6 Prepared by Shant Shahbazian for the seminar of "What is life" at the Institute for research in fundamental sciences (IPM) (2-Nov-2016)

What is not yet understandable “effectively” • There are systems or events that the laws (physical theories) governing their evolution is known, but the effective modeling has not yet been achieved • The mechanism behind high-temperature superconductivity and the nature of turbulence in hydrodynamics are examples • Searching effective models is ongoing in these areas… • In principle understating does not guarantee effective understating and without the latter, physicists are not usually claiming a physical” understanding 7 Prepared by Shant Shahbazian for the seminar of "What is life" at the Institute for research in fundamental sciences (IPM) (2-Nov-2016)

Are biological systems also physical systems? Conditional yes! If we are able to construct “effective models” for various types of biological systems Prepared by Shant Shahbazian for the seminar of "What is life" at the Institute for research in fundamental sciences (IPM) (2-Nov-2016) 8

Theories of complexity: Effective biological modeling • Extending the model construction business to biology: Theoretical and computational biology • Computational neuroscience • Genetic population • System biology • Modeling ecological systems • Network biology • Modeling immunological system • Searching effective models is ongoing in various areas of biology: From the molecular biology to the biology of ecosystems Prepared by Shant Shahbazian for the seminar of "What is life" at the Institute for research in fundamental sciences (IPM) (2-Nov-2016) 9

How successful are current effective models in biology? • In some areas, like neurobiology, the effective models have been quite efficient • In other areas, like the origin of life at the Earth, or the evolution of the global ecosystem of the Earth, things are less clear… • Are there inherent limitations to the biological modeling? Prepared by Shant Shahbazian for the seminar of "What is life" at the Institute for research in fundamental sciences (IPM) (2-Nov-2016) 10

Take home lesson: What I can model, I understand Let’s make a pause and take a twist! Prepared by Shant Shahbazian for the seminar of "What is life" at the Institute for research in fundamental sciences (IPM) (2-Nov-2016) 11

Are biological systems also chemical systems? Strange question! Isn’t true that chemical systems are just a small subset of the physical systems? Let’s look at the problem from an alternative viewpoint! Prepared by Shant Shahbazian for the seminar of "What is life" at the Institute for research in fundamental sciences (IPM) (2-Nov-2016) 12

The anatomy of the “understanding” in chemistry: Molecular structures • Every chemical system is composed of molecules, they are the natural units of chemistry • Each molecule has a molecular structure , which is code for the constituent atoms and the chemical bonds linking them • Every chemical phenomena, like a chemical reaction, is finally conceived as a transformation of molecular structures Prepared by Shant Shahbazian for the seminar of "What is life" at the Institute for research in fundamental sciences (IPM) (2-Nov-2016) 13

The anatomy of the “understanding” in chemistry: Chemical synthesis • Every reasonable molecular structure drawn on a paper is a potential chemical system • Every potential chemical system is realized in laboratory starting from known simple molecular structures and using chemical reactions to reach more complex molecular structures • The procedure is called the chemical synthesis • The synthesis of complex natural products is an example 14 Prepared by Shant Shahbazian for the seminar of "What is life" at the Institute for research in fundamental sciences (IPM) (2-Nov-2016)

The new dimension of the chemical synthesis: “Creation” • From the space of all molecular structures not all have been realized in nature • The ultimate goal of the chemical synthesis is realizing all potential molecular structures as actual chemical systems • In this procedure new chemical systems are materialized without no previous known existence in nature • The art of chemical synthesis is the de novo creation … 15 Prepared by Shant Shahbazian for the seminar of "What is life" at the Institute for research in fundamental sciences (IPM) (2-Nov-2016)

The chemical synthesis as the “chess” game of chemistry • To start the game of chess you must know all the pieces and the rules governing their moves • However, what makes the chess an intellectual game is the strategies used for winning • The known molecules and reactions are the pieces of the synthetic chemist and it is an intellectual game for him/her to design strategies for synthesizing a new complex molecule • The grandmasters of chemistry are whom able to make new plans to climb in the space of molecular structures, they understand chemistry … Prepared by Shant Shahbazian for the seminar of "What is life" at the Institute for research in fundamental sciences (IPM) (2-Nov-2016) 16

Take home lesson: What I can create, I understand or What I cannot create, I do not understand last words of Richard Feynman (15 February 1988), recalled by his sister! Prepared by Shant Shahbazian for the seminar of "What is life" at the Institute for research in fundamental sciences (IPM) (2-Nov-2016) 17

Are biological systems also chemical systems? Conditional yes! If we are able to reconstruct biological systems from their constituent molecules and more, if we may “design” novel biological systems without any previous existence… Prepared by Shant Shahbazian for the seminar of "What is life" at the Institute for research in fundamental sciences (IPM) (2-Nov-2016) 18

Synthetic biology starts when descriptive biology stops… Prepared by Shant Shahbazian for the seminar of "What is life" at the Institute for research in fundamental sciences (IPM) (2-Nov-2016) 19