SPU-22: The Unity of Science from the Big Bang to the Brontosaurus and Beyond

1. SPU-22: The Unity of Science from the Big Bang to the Brontosaurus and Beyond Lecture 22 23 April 2014 Science Center Lecture Hall A

2. Today’s Tales Additions to some past topics: general and specific Origin of life Tree of life Origin of polar bears Origin of whales

3. Comments On Topics Treated Decision as to which topics to touch on (and how deeply) in treating such an incredibly broad field is partly personal and somewhat quixotic

4. Clear Conclusion Prime lesson from recent lectures: Key to advances in science is often asking of fundamental questions Examples include: Darwin/Wallace, Mendel, Miescher, Avery, W & C, Gamow, Nirenberg,… [Note: This key applies to most other fields as well.]

5. Move To: “Simple” Organisms In trying to understand whole organisms, biologists study just few, relatively simple types. Why specialize in such apparently narrow manner? Reason also simple: intrinsic complexity requires many complementary studies by many groups Choices partly practical: fruit flies (“drosophila melanogaster”), simple worms (“c. elegans”), zebrafish, and mice. Each has traits desirable for understanding intrinsic complexity

6. More Complex Biology Subjects Importance sometimes trumps drive for simplicity (previous slide) Prime example is brain science: research is exploding via intertwined investigations -- experiments, taxonomy, models, and simulations Funds available for biomedical research dwarf those for everything else. Research, like most other endeavors, follows the funds

7. Mutations: Causes and Consequences Errors in replication Damage to DNA by environment (high energy light: x-rays and ultraviolet; toxic chemicals of all sorts) Example of process of damage: cytosine converted to uracil via water damage, which pairs with adenine not guanine. Repair mechanisms quite complicated Connection with evolution

8. Trace Elements In Cell: Case Of Selenium Important for cell growth and function Helps detoxify cell and protect from oxidative damage What is “right” amount of selenium? Culture with various levels; see who thrives and who dies Plus much more: roles in thyroid de-iodinization; carries iron to cell

9. Unanswered Question in Biology and Evolution Number of questions to be addressed is almost limitless. One (amusing?) example: Why has Nature taken the trouble to produce c. 450,000 species of beetles? (Will beetles or bacteria rule the world?)

10. Origin Of Life How to define? Where arose? How to produce? (Stanley Miller experiment for one location) Is ours really an RNA world?

11. What Is Life? Define by properties: - store and transmit information - “express” that information - evolve (descent with modification)

12. Creating Life: A Nontrivial Enterprise (Obviously!) Inorganic raw materials Relevant chemical reactions need appropriate sources of energy Building blocks must self assemble Built blocks must be protected from “bad” environments

13. Bewildering Diversity Of Life Here Could we possibly be alone? There are about 1022 stars and perhaps about twice as many planets: Formation of life must be truly arcane to think that just one planet had “right” conditions to develop life and its evolution

14. Life Delivered To Earth From Afar? Concept of panspermia Delivery accidental or purposeful? Survival of interstellar journey feasible or not?

15. Life Delivered Via Impact? Murchison meteorite (1969) was quite massive (>100 kg) (see next slide) Analyses of internal parts disclosed amino acids Real or contamination from earth? Real: These amino acids were roughly half left-handed and half right-handed (mirror images); in biological material on earth, almost all amino acids are left-handed (see next slide plus one)

16. Note: What Is “Meteorite”? Macroscopic object reaching surface of earth from elsewhere in solar system Contrast with meteor: Object from elsewhere in solar system that disintegrates in earth’s atmosphere with at most dust reaching surface

17. Handedness Of Amino Acids

18. Back To Life Assuming came from afar begs question: How did it originate? (Know even less about other possible abodes than our own.)

19. So, How Could Life Start Here? Early conundrum: proteins or DNA? DNA: stores and transmits information; does no “biological”work Protein: does enormous amount of biological work, but cannot store and transmit information [Somewhat similar to classic question: chicken first or egg?]

20. RNA To Rescue Need for entity that combines traits of DNA and proteins Early 1980s discovery that RNA fills bill: RNA molecule can catalyze chemical reaction. Single-stranded RNA molecule with complicated folds and sites (locations) that can catalyze chemical reactions: ribozymes

21. Evidence For RNA Being Ancient Involved in critical machinery for replication and functioning of cells Basic currency for energy in cell (e.g., ATP) [What is ATP? See next slide] How can RNA be produced abiotically? Outstanding question spawning whole field of study to address means for evolving RNA in “test tube” (in vitro) situations

22. Adenosine Triphosphate

23. DNA Advantages Over RNA Double strand stronger Greater heat resistance (recall Griffith) Greater stability against chemical de-gradation (acids and bases) How did DNA evolve from RNA, if it did? Good question!

24. How Biological Materials May Have Been Produced On Earth Stanley Miller’s (1953) experiment: boiled water passed through atmosphere of methane, ammonia, and hydrogen in presence of electric sparks [why these and no oxygen? See next slide]; resultant vapors condensed. Week later: condensate contained, e.g., glycine and alanine – two amino acids Publication problem; Urey intercession Later experiments able to produce nucleotides, sugars, and over 20 amino acids! Field seemed to die or at least hibernate: What to do next not clear then and apparently still not clear

25. Oxygen In Atmosphere Over Time

26. Stanley Miller (1930-2007)

27. How Biological Materials May Have Been Produced On Earth (Concluded) What about undersea location for origin of life? “Extremophiles” live near thermal vents at mid-ocean ridges (see next slide): Origin there? If so, very different process from Miller’s approach

28. Extremophiles at Thermal Vent

29. Tree Of Life What is it? (See next two slides.) Why is it important? (Basically, we want to know…) How do we construct it? (With difficulty and aid from fossils and DNA analyses)

30. Tree Of Life Showing Three Domains

31. Tree Of (Early) Life • all what is wrong

32. Estimates Of Evolutionary Relations From DNA Analyses Basic assumption: Greater number of differences between sequences of bases, greater evolutionary separation Apply to relatively stable section of DNA Good choice: part that codes for rRNA; this part present in all living organisms so far studied

33. Resultant Tree Of Life Detailed analysis with many decisions of somewhat subtle variety yields comprehensive tree of life (see next slide for simplified sketch) Problem: Use of other sequences yields rather different trees Rapid increase in DNA sequencing of other organisms is expected to vastly improve matters (costs decrease; speed increases; see next slide plus one) Very much work in progress

34. Sketch Of Tree Of Life

35. Cost To Sequence Human Genome

36. How To Keep Time Pace of evolution difficult to determine Molecular clocks developed; based on principle of change occurring at constant rate, far from reliable assumption Calibration against fossil record is one solution; most reliable, obviously, but only when available

37. Inferring Oldest Fossils No known survivors of earliest life forms (sigh) Evidence of oldest life must be indirect, virtual guarantor of controversy Example of indirect evidencefrom shapes of carbon nanoscale grains found in biological, but not abiotic materials; sample from western Greenland; dated ~3.7 billion years old. Published 12/14

38. Move To Examples of Use of DNA And Fossils To Trace Evolution (Placements On Tree Of Life) Polar bears Whales

39. Evolution Of Polar Bears Little known about species history of polar bears. Why? Paucity of fossil record Current warming trend dangerous for polar bears Knowledge of history might, just might, help in planning strategy to prevent polar-bear extinction (via, e.g., fatally low genetic diversity)

40. Three Contemporary Polar Bears

41. Why Extinction Threat For Polar Bears? Disappearance of ice in Arctic Relatively new and dangerous predator: humans Indirect effects of predator: disappearance of ice in Arctic chemical pollution Above combination unprecedented

42. How To Determine History? Absent fossils, DNA trail only game in town. Different attempts yielded increased estimates for separate existence of polar bears; latest 4 – 5 million years (first attempt yielded ~ 100+ kiloyears; second 600 kiloyears, with high confidence: tricky analyses) Found interbreeding (“hybridization”) with brown bears; expected during interglacial periods: opportunistic mating as ranges overlapped. Could be savior (again) Prospects bright for further insights into past

43. Whales Biggest creatures in today’s world From whence did they come? How was this big deal resolved?

44. Origin Of Whales Whales, dolphins, and porpoises are mammals Aristotle in fourth century BCE is reputed to have pointed out that whales breathe air, have hair, and nurse their young Classification not exactly universally accepted by public, witness Ishmael in Herman Melville’s, “Moby Dick” (1851): “a spouting fish with a horizontal tail”

45. Why Do We Think Whales Had Land Ancestors? Fossil record of mammals on land goes back 200 million years (see next slide) Fossil record of and (molecular inferences for) whales goes back only 50 million years Conclusion: Transformation of four-footed land animal into fully aquatic whale is truly remarkable event in evolutionary history. How did it come about?

46. Earliest Mammal Fossil Yet Known

47. What Are Some Key Questions To Address? How long did transition take for whale ancestors to evolve from freshwater to saltwater-adapted creatures? When did whales become fully marine? Was transition gradual or abrupt? Did adaptation to ingestion of seawater and to marine diet occur at same or different (if so how different) times? Answers not yet all known; progress has been speeding up

48. One Example: Determination Of Epoch Of Freshwater To Saltwater Adaptation Enter ever-useful isotopes. Oxygen 18 is depleted relative to 16O in freshwater compared to in oceans. How do we understand that fact? Water with 16O is preferentially evaporated (it is less dense) and water with 18O is preferentially precipitated. So what?

49. Separation Of Water By Isotope Water evaporated over oceans travels inland and condenses. Further inland precipitation, lower concentration of 18O relative to 16O in (fresh) water. Similar arguments apply to carbon isotopes in carbon dioxide Examination of isotopes of dated fossils of various ancestors allows one to distinguish freshwater from ocean ancestors of modern whales