1. Life is Tough! Species share many features in common to help survive and reproduce successfully Species share many features in common to help survive and reproduce successfully This is the “story” of those shared strategies! This is the “story” of those shared strategies!

2. Strategies of Living Systems: Features Common to all Life Forms 17 November 2015 Introduction to life Introduction to life Themes/characteristics of living organisms Themes/characteristics of living organisms Classification of life’s different species (1.8 million and counting) Classification of life’s different species (1.8 million and counting) Case study: bacteria and virus Case study: bacteria and virus

3. Characteristics of all Living Organisms Hierarchy theory, emergent properties and the infrastructure we call the cell Hierarchy theory, emergent properties and the infrastructure we call the cell Continuity of life: function of “information” Continuity of life: function of “information” Openness of biological systems Openness of biological systems Regulatory capacity of living systems Regulatory capacity of living systems Capacity to reproduce Capacity to reproduce Capacity to acquire, utilize, and store energy Capacity to acquire, utilize, and store energy Diversity and similarity of living organisms Diversity and similarity of living organisms

4. Hierarchical Nature of Living Systems Community Population Population Organism Organism Organ Organ Tissue Tissue Cell Cell Organelles Organelles Macromolecules Macromolecules Atoms Atoms Functional unit in biology = Cell Analogue to atom in chemistry and physics and ecosystems in ecology Hierarchy theory and emergent properties

5. Cell: Structure and Function Organism’s basic unit of structure and function Organism’s basic unit of structure and function Lowest level of structure capable of performing all of life’s activities (e.g., irritability, reproduce, grow, develop, etc.) Lowest level of structure capable of performing all of life’s activities (e.g., irritability, reproduce, grow, develop, etc.) Cell Theory Cell Theory Ubiquitous (plant, animal and microbe) Ubiquitous (plant, animal and microbe) All cells from previous cells (no cells are created from scratch) All cells from previous cells (no cells are created from scratch) Why called a theory versus a law? Why called a theory versus a law?

6. General Cell Infrastructure Reproduction …. Energy Utilization … Response to the Environment … Information Rich … Hierarchy

7. Characteristics of all Living Organisms Hierarchy theory, emergent properties and the infrastructure we call the cell Hierarchy theory, emergent properties and the infrastructure we call the cell Continuity of life: function of “information” Continuity of life: function of “information” Openness of biological systems Openness of biological systems Regulatory capacity of living systems Regulatory capacity of living systems Capacity to reproduce Capacity to reproduce Capacity to acquire, utilize, and store energy Capacity to acquire, utilize, and store energy Diversity and similarity of living organisms Diversity and similarity of living organisms

8. Continuity of Life and “Information” Order in any system via instructions as a template (e.g., Constitution, Bill of Rights, legal contracts, language, …) Order in any system via instructions as a template (e.g., Constitution, Bill of Rights, legal contracts, language, …) In living systems, instructions codified in the DNA In living systems, instructions codified in the DNA Instructions: precise, sequential order of nucleotides (ATCG; the alphabet of “instructions”) Instructions: precise, sequential order of nucleotides (ATCG; the alphabet of “instructions”) Example: RAT versus TAR versus ART Example: RAT versus TAR versus ART A = adenineC= cytosine A = adenineC= cytosine G = guanineT = thymine G = guanineT = thymine Nucleotides

9. Open Systems living organisms: open, allowing interaction with the environment All living organisms: open, allowing interaction with the environment Process stimuli Process stimuli Respond to stimuli Respond to stimuli “Open” versus a “closed” system “Open” versus a “closed” system Examples Examples Orientation of leaves to sun Orientation of leaves to sun Eyes Eyes Microbes and single cell organisms (e.g., amoeba) Microbes and single cell organisms (e.g., amoeba)

10. Characteristics of all Living Organisms Hierarchy theory and emergent properties Hierarchy theory and emergent properties Infrastructure: “it is the cell” Infrastructure: “it is the cell” Continuity of life: function of “information” Continuity of life: function of “information” Openness of biological systems Openness of biological systems Regulatory capacity of living systems Regulatory capacity of living systems Capacity to reproduce Capacity to reproduce Capacity to acquire, utilize, and store energy Capacity to acquire, utilize, and store energy Diversity and similarity of living organisms Diversity and similarity of living organisms

11. Regulatory Systems Interplay of organisms with the environment: requires a balanced regulatory system Interplay of organisms with the environment: requires a balanced regulatory system Outcome: homeostasis Outcome: homeostasis Set point, effectors, feedbacks, control centers and sensors Set point, effectors, feedbacks, control centers and sensors Analogy: thermostat for heat control Analogy: thermostat for heat control Examples Examples Enzymes in cells Enzymes in cells Thermostatic control of body temperature Thermostatic control of body temperature Gene regulation: activation and deactivation Gene regulation: activation and deactivation Heart rate and exercise (getting oxygen an removing wastes) Heart rate and exercise (getting oxygen an removing wastes)

12. Regulatory Systems: Cybernetics Feedbacks (+ and -), homeostasis and cybernetics Feedbacks (+ and -), homeostasis and cybernetics Control Center/ Sensor Set Point Effector Positive Feedback Negative Feedback

13. Universality of Reproduction Reproduction: regenerative process of making new organisms (not necessarily copies) Reproduction: regenerative process of making new organisms (not necessarily copies) Methods Methods Sexual Sexual Asexual (microbes; cell division/mitosis) Asexual (microbes; cell division/mitosis) Examples Examples Siblings versus twins Siblings versus twins Geranium plants Geranium plants Dolly (the sheep) Dolly (the sheep) Me and thee! Me and thee!

14. Characteristics of all Living Organisms Hierarchy theory, emergent properties and the infrastructure we call the cell Hierarchy theory, emergent properties and the infrastructure we call the cell Continuity of life: function of “information” Continuity of life: function of “information” Openness of biological systems Openness of biological systems Regulatory capacity of living systems Regulatory capacity of living systems Capacity to reproduce Capacity to reproduce Capacity to acquire, utilize, and store energy Capacity to acquire, utilize, and store energy Diversity and similarity of living organisms Diversity and similarity of living organisms

15. Energy Utilization Three activities: acquisition, utilization, and storage Three activities: acquisition, utilization, and storage Energy acquisition (C-C bonds) Energy acquisition (C-C bonds) Energy capture (autotrophs; heterotrophs) Energy capture (autotrophs; heterotrophs) First law of Thermodynamics First law of Thermodynamics Energy utilization Energy utilization Laws of Thermodynamics (1 st and 2 nd laws).. Releasing energy from C-C bonds) Laws of Thermodynamics (1 st and 2 nd laws).. Releasing energy from C-C bonds) ATP (adenosine triphosphate) and ADP (adenosine diphosphate) ATP (adenosine triphosphate) and ADP (adenosine diphosphate) Energy storage Energy storage Chemical bonds (C-C covalent bonds) Chemical bonds (C-C covalent bonds) Carbohydrates, glycogen and lipids (C-C-C-C-C) Carbohydrates, glycogen and lipids (C-C-C-C-C) Muscle Tissue Wheat Plants

16. Energy Utilization In Metabolism Catabolism Biosynthesis ADP ATP Analogue: Legos on the floor and building a structure Biosynthesis = constructing complex carbon molecules Catabolism = deconstructing complex carbon molecules

17. Characteristics of all Living Organisms Hierarchy theory and emergent properties Hierarchy theory and emergent properties Infrastructure: “it is the cell” Infrastructure: “it is the cell” Continuity of life: function of “information” Continuity of life: function of “information” Openness of biological systems Openness of biological systems Regulatory capacity of living systems Regulatory capacity of living systems Capacity to reproduce Capacity to reproduce Capacity to acquire, utilize, and store energy Capacity to acquire, utilize, and store energy Diversity and similarity of living organisms Diversity and similarity of living organisms

18. Two Sides of a Coin: Diversity and Similarity Diversity: a hallmark of living systems Diversity: a hallmark of living systems 1.8 M known species of plants, animals and microbes 1.8 M known species of plants, animals and microbes 10 M+ thought to exist (perhaps even as high as 50M) 10 M+ thought to exist (perhaps even as high as 50M) Similarity: a hallmark of living systems Similarity: a hallmark of living systems Striking similarity at the molecular level (DNA): kinship to worms, squirrels, birds and pigs (your DNA is ~90% pig!) Striking similarity at the molecular level (DNA): kinship to worms, squirrels, birds and pigs (your DNA is ~90% pig!) Examples Examples Biochemistry Biochemistry Structure and morphology Structure and morphology Me and Thee

19. Similarity of Life: Identical DNA 20% 14% 82% 95% Pig = 90% 55% 70% 100%

20. Strategies of Living Systems: Features Common to all Life Forms Introduction to life Introduction to life Themes/characteristics of living organisms Themes/characteristics of living organisms Classification of life’s different species (1.8 million and counting fast!) Classification of life’s different species (1.8 million and counting fast!) Case study: bacteria and virus Case study: bacteria and virus

21. Classifying Living Systems Hi! How are you today?

22. Classifying Life Kingdoms Kingdoms Monera Monera Protista Protista Fungi Fungi Plants Plants Animals Animals How is this done? How is this done?

23. Cataloging Life Linnean classification Linnean classification Shared characteristics Shared characteristics Hierarchy Hierarchy Kingdom Kingdom (previous slide) Phylum Phylum Class Class Order Order Family Family Genus Genus Species Species Binomial nomenclature Binomial nomenclature Homo sapiens vs. Homo neanderthalensis

24. Classifying Humankind Kingdom: Animals Kingdom: Animals Phylum: Chordates Phylum: Chordates Class: Mammals Class: Mammals Order: Primates Order: Primates Family: Hominid Family: Hominid Who else in in your “Family”? Who else in in your “Family”? Genus: Homo Genus: Homo Species: sapiens Species: sapiens Ardipithecus ramidus and Homo neanderthalensis

25. Classifying Life Kingdoms Kingdoms Monera Monera Protista Protista Fungi Fungi Plants Plants Animals Animals

26. Bacteria Flagella Flagella Information (DNA) Information (DNA) Capsule Capsule Plasma Membrane Plasma Membrane Cytoplasm Cytoplasm Cell Wall Cell Wall Spores (reproduce) Spores (reproduce)

27. Vascular Plants Phylum: vascular plants Phylum: vascular plants Structure - strategy? Structure - strategy? Roots, stems and leaves Roots, stems and leaves Control water loss Control water loss Intercept light Intercept light Autotrophs Autotrophs Reproduction - strategy? Reproduction - strategy? Gymnosperms (e.g., conifers) Gymnosperms (e.g., conifers) Angiosperms (e.g., flowering plants) Angiosperms (e.g., flowering plants)

28. Diversity of Animal Kind Invertebrates Vertebrates Gravity dictated strategy) Role of Gravity as a Strategy?

29. Case Study: Bacteria Flagella Flagella Information Information Capsule Capsule Plasma Membrane Plasma Membrane Cytoplasm Cytoplasm Cell Wall Cell Wall Spores Spores

30. Some Examples of Bacteria Clostridium (botulism) Salmonella (salmonella food poisoning)

31. Habitats of Bacteria Strategy for Survival?

32. Case Study: Virus Strange form of life Nucleic acids in head/capsule Lack metabolism for energy acquisition, storage and utilization Lack membranes Parasitic (means what?) Visible only with electron microscopy Role in disease … huge part of human history and misery

33. Some Examples of Viruses InfluenzaHerpes

34. Ebola Hemorrhagic Fever (virus)

35. Strategies of Living Systems Introduction to life Introduction to life Themes/characteristics of living organisms Themes/characteristics of living organisms Classification of life’s different species Classification of life’s different species Case study: bacteria and virus Case study: bacteria and virus All organism share common strategies for survival, but each “solves” the problem with variation on a common theme All organism share common strategies for survival, but each “solves” the problem with variation on a common theme

36. Life is Tough! Species share many features in common to help survive and reproduce successfully Species share many features in common to help survive and reproduce successfully This is the story of those shared strategies! This is the story of those shared strategies!