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BIOLOGY Bios = Greek for: “life” Logos = Greek for: “word” “rational account” “study of” “ science of ”

Biology and Biomedical Informatics Robert Arp, Ph.D. Ontology Research Group (ORG) www.org.buffalo.edu National Center for Biomedical Ontology (NCBO) www.bioontology.org. BIOLOGY Bios = Greek for: “life” Logos = Greek for: “word” “rational account” “study of” “ science of ”.

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BIOLOGY Bios = Greek for: “life” Logos = Greek for: “word” “rational account” “study of” “ science of ”

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  1. Biology andBiomedical InformaticsRobert Arp, Ph.D.Ontology Research Group (ORG)www.org.buffalo.eduNational Center for Biomedical Ontology (NCBO)www.bioontology.org

  2. BIOLOGYBios = Greek for:“life”Logos = Greek for:“word”“rational account”“study of”“science of”

  3. BIOLOGYSo, biology is ascience, the sciencethat studies life andliving things.What is science?

  4. Some Important Scientific Literature • Journals Scientific American (all lay persons should subscribe to this) Skeptic (ditto for this) Nature (technical) Science (technical) • Books What is This Thing Called Science, by Chalmers (McGraw-Hill) Scientific Method in Practice, by Gauch (Cambridge) Science: A History, by Gribbin (Penguin) Evolution: What the Fossils Say…, by Prothero (Columbia)

  5. Science:the systematic attempt on the part of researchers to develop theories to explain the phenomena of our experience so as to classify, describe, organize, explain, explore, predict and, ultimately, control the phenomena.

  6. Science:the systematic attempt on the part of researchers to develop theories to explain the phenomena of our experience so as to classify, describe, organize, explain, explore, predict and, ultimately, control the phenomena.

  7. phenomena of our experience…Things that are publicly observable, 5 senses-able, testable, repeatedly, directly:Things that are publicly observable, 5 senses-able, testable, repeatedly, indirectly: molecules, cells, crystals, cats, dogs, ecosystem, solar system, Milky Way gravity, electromagnetism, strong force, weak force, subatomic particles

  8. Can you, I, anyone, and everyone experience it or sense it with one of the 5 senses directly or indirectly, repeatedly, by testing it in a controlled environment?Yes = scientificNo = non-scientific 5

  9. NOT the 4 Ms:M ind…in terms of “soul”M orality…right and wrongM eaning…purpose in lifeM agnificent Beings…god or gods…these are outside the realm of the phenomena of our experience (OK to study and believe in, but not in science proper)

  10. NOT these other Mseither:M iracles…M artians… or other aliensM ind-control… like ESPMagic……these are outside the realm of the phenomena of our experience (OK to de-bunk, but not in science proper)

  11. Intelligent Design:- The universe was createdby some superior intelligentmind (SSIM)- Life itself was created by SSIM- The highly complex things in the universe (e.g., eyes, flagellums, blood clotting) could not have evolved and had to be created by SSIM

  12. Intelligent Design:- The universe was created by somesuperior intelligent mind (SSIM)- Life itself was created by SSIM- The highly complex things in the universe (e.g., eyes, flagellums, blood clotting) could not have evolved and had to be created by SSIM • Unfortunately for Intelligent Design: • Not part of the phenomena of our experience • Can’t be publicly observed, repeated, tested either directly or indirectly • There just is no science of Intelligent Design False, too…

  13. Some Literature on Intelligent Design • Science, Evolution, and Creationism, by the National Academy of Sciences • Evolution vs. Creationism, by Scott (University of California) • The Edge of Evolution: The Search for the Limits of Darwinism, by Behe (InterVarsity) • Debating Design: From Darwin to DNA, edited by Dembski & Ruse (Cambridge)

  14. Intelligent Design:Does it belong in ascience classroom?Or, is it more appropriate for a religion or history class?How about… the study of souls? …what’s right and wrong?…the meaning of life?

  15. Science:the systematic attempt on the part of researchers to develop theories to explain the phenomena of our experience so as to classify, describe, organize, explain, explore, predict and, ultimately, control the phenomena.

  16. THESCIENTIFIC METHOD

  17. systematic attempt on the part of researchers…Scientific Method1 = ask relevant question2 = do background search3 = construct hypothesis4 = test hypothesis with experiment5 = analyze results of experiment6a = if hypothesis is confirmed (true) = go to 76b = if hypothesis is not confirmed (false) or partially true7 = report results8 = use results to construct more hypotheses

  18. Car won’t start

  19. Car won’t start Hypotheses?

  20. Car won’t start Hypotheses? Battery?

  21. Car won’t start Hypotheses? Battery? How do you test this Hypothesis?

  22. Science:the systematic attempt on the part of researchers to develop theories to explain the phenomena of our experience so as to classify, describe, organize, explain, explore, predict and, ultimately, control the phenomena.

  23. to develop theories to explain…Theory:- essentially a truth, body of facts- coherent system- confirmed hypotheses- laws (WHAT GOES UP… DOPPLER EFFECT…)- deductions from these laws- overall… reliable predictions

  24. to develop theories to explain…Theory:- essentially a truth, body of facts- coherent system- confirmed hypotheses- laws (WHAT GOES UP… DOPPLER EFFECT…)- deductions from these laws- overall… reliable predictions E.g., Atomic, Big Bang, Evolution

  25. And reliable predictions lead to:- Developing better drugs to fight disease…- Developing early warning systems for tornadoes, floods, earthquakes…- Safer highways…- Spaceships and exploration…and the list goes on and on…

  26. So much for Science…What is Biology?

  27. Biology:the systematic attempt on the part of researchers to develop theories to explain the organic (living) phenomena of our experience so as to classify, describe, organize, explain, explore, predict and, ultimately, control the phenomena.

  28. Some Biology Literature • Journals • Journal of Biology (technical) • PLoS Biology (http://biology.plosjournals.org/) • Science Magazine (all science, too) • Books • Biology, by Raven et al. (McGraw-Hill) • Biology: Life on Earth, by Audesirk et al. (Prentice-Hall) • The Epic History of Biology, by Serafini (Basic)

  29. biochemistrymolecular biologymicrobiologycellular biologyphysiologybotanyzoologyecologyevolutionary biology…

  30. …and many more branchesand sub-branches

  31. …to explain theorganic (living) phenomena of our experience One Goal of Biology

  32. So… what is Life?- Replication…DNA, RNA- Encapsulation…cell wall, barrier- Self-Movement…growth, repair- Adaptation…homeostasis- Use of Energy in Multiple Ways- Hierarchically-Organized System ?

  33. So… what is Life?- Replication…DNA, RNA- Encapsulation…cell wall, barrier- Self-Movement…growth, repair- Adaptation…homeostasis, fitness- Use of Energy in Multiple Ways- Hierarchically-Organized System D. Koshland, “The Seven Pillars of Life” In Science (2002) 295: 2215-2216

  34. - is a single cell alive?- the organelles that make up a cell? (Mitochondrion, Golgi Apparatus)- a virus?- a prion? (abnormal protein)- the ecosystem itself?

  35. Biology:the systematic attempt on the part of researchers to develop theories to explain the organic (living) phenomena of our experience so as to classify, describe, organize, explain, explore, predict and, ultimately, control the phenomena.

  36. classify, describe, organize…Homo sapiens (species)is_aHomo (genus)is_ahominid (family)is_aprimate (order)is_aplacental (subclass)is_amammal (class)is_avertebrate (subphylum)is_achordate (phylum)is_aanimal (kingdom)is_aeukaryote (domain)

  37. What I Do:BIOMEDICAL INFORMATICSThe science associated with the collection, categorization, management, storage, processing, retrieval, and dissemination of biomedical knowledge and information using computational tools with the overall goal to improve patient care, medical education, and health science research… classify, describe, organize…

  38. What I Do:BIOMEDICAL INFORMATICS Combination of:BiologyMedicineHealth CareComputer ScienceInformation Science classify, describe, organize…

  39. Some Biomedical Informatics Literature • Chen, H., Fuller, S., Friedman, C., & Hersh, W. (2005). Medical informatics: Knowledge management and data mining in biomedicine. The Netherlands: Springer. • Goldstein, D., Groen, P., Ponkshe, S., & Wine, M. (2007). Medical informatics 20/20: Quality and electronic health records through collaboration, open solutions, and innovation. New York: Jones & Bartlett. • Polanski, A., & Kimmel, M. (2007). Bioinformatics. London: Springer. • van Bemmel, J., & Musen, M. (Eds.). (1997). Handbook of medical informatics. The Netherlands: Springer. • Xiong, J. (2006). Essential bioinformatics. Cambridge: Cambridge University Press.

  40. New York State Center of Excellence in Bioinformatics& Life SciencesUniversity at Buffalo

  41. Information Science science associated with the collection, categorization, management, storage, processing, retrieval, and dissemination of knowledge and information, often times using computational tools… think librarian, but a librarian with computational skills… OVERALL GOAL: KNOWLEDGE SHARING

  42. What I Do:BIOMEDICAL INFORMATICS More specifically, I help biomedical researchers:(A) classify their data and information in their labs(B) build links between and among all of their labs so that they can share the data and information with each other classify, describe, organize…

  43. What I Do:BIOMEDICAL INFORMATICS More specifically, I help biomedical researchers:(A) classify their data and information in their labs(B) build links between and among all of their labs so that they can share the data and information with each other classify, describe, organize… with domain ontologies with formal ontologies

  44. Domain:Area of study like biology, law, psychology, or any other science or discipline you would find at a university

  45. Domain Ontology:A classification kind of like:Periodic Table of the ElementsKingdoms of Biologyin some domain (like biology, law, psychology, or any other science or discipline you would find at a university)

  46. …Only more complex in terms of the objects and their relationships to one another

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