Linnaeus, Ashburner, Pok é mon

1. Linnaeus, Ashburner, Pokémon Lincoln D. Stein

2. Gotta Catch ’em All! • Pokémon, year 2000 • $492 million Pokémon bubble gum & trading cards • 10 million Pokémon video games sold ($3 billion) • $3 billion in toys & other merchandise • Pokémon movie tops cartoon movie of all time ($85 million gross first week) • 13,000 ft2 retail palace in Rockefeller Center • Weekly “Pokémon Market Report” on Market Place radio broadcast Source: The Internet

3. Pokémon Characteristics • 249 characters in Pokémon Database Source: Pokemon Database (http://www.edbydesign.com/pokemon/pokedata.html)

4. Pokémon Phylogeny Small size Electric Good vs water, flying Bad vs electric, grass, dragon Thunderstone evolution Small size, Sings Good vs none Bad vs rock Moonstone evolution Large size, Tackles, Growels Good vs water Bad vs flying, poison, dragon Normal evolution Large size Tackles, Disables Good vs grass, psychic, bug Bad vs ground, ghost, flying Normal evolution

5. Why was Pokémon so Popular? • Similar to previous collectibles fads • Beany babies • Cabbage-patch dolls • Baseball cards • Nearly all children go through collection phases • Rocks, bugs, stamps coins • An innate urge to collect & classify?

6. Hunter Gatherer Societies • Hadza of Tanzania • Plant species: • Recognize 240 wild plant species • Utilize ~100 • Animal species: • Recognize 280 wild species • Utilize 200 (including 10 species of bee) • Children aid in foraging • Accompany parents from infancy • Begin foraging themselves at age 3 Source: The Internet

7. The Collection Urge is our Hunter-Gatherer Brains at Work

8. Biological Classification • Classification systems are foundation of biology • Aristotle (384-322 BC) Scalae naturae of animals • two-footed versus four-footed; hairy versus feathers; with or without an outer shell • Threophrastus (370-285 BC), plant classification • Annual vs perennial and biennial life cycles; superior vs. inferior ovaries; determinate vs. indeterminate; distinct vs. connate petals. • Herbalists (divers) • Plant classification based on utility • Carl Linnaeus (1707-1778) • Familiar Kingdom, Phylum, Order… system & binomial naming • 1st edition of Systema Naturae – 1 volume, 150 species • 10th edition of System Naturae – 7 volumes, 12,000 species

9. Gene Ontology Consortium (Ashburner, 2000) • Gene products classified along 3 dimensions • 6728 process terms • 5291 function terms • 1122 component terms • 13,000 total

10. What Makes a Good Classification System?

11. Linnaean Classification of Pigs • Kingdom Animalia • Phylum Chordata • Class Mammalia • ORDER Artiodactyla: Even-toed ungulates • SUBORDER Suiformes: pigs, hippos Family suidae Sus scrofa – Wild boar Sus babyrousa – Indonesian pig Sus hylochoerus – Giant forest hog …. • SUBORDER Tylopoda: camels, llamas • SUBORDER Ruminantia: ruminants

12. Borgean Classification of Pigs • those that belong to the Emperor • embalmed ones • those that are trained • suckling pigs • mermaids • fabulous ones • stray dogs • those that are included in this classification • those that tremble as if they were mad • innumerable ones • those drawn with a very fine camel’s hair brush • others • those that have just broken a flower vase • those that resemble flies from a distance Source: Jorge Luis Borges, Funes the Memorius

13. Making a Good Classification System • Good classification systems are • Easy to use • Reproducible • Discriminatory • Natural • Predictive

14. Easy to Use • How easy is the system to learn? • Can intelligent systems be trained to use it? • How many characteristics must be gathered in order to classify? • Simple systems easier than complex ones • One characteristic easier than multiple • Protein similarity vs multiple morphological traits

15. Reproducible • Given several classifiers (human or artificial), how often will they classify the subject in the same way? • Objective criteria better than subjective ones.

16. Discriminatory • Classification system should divide the space well • How many divisions? • Can keep hundreds of classes in head (children w/ Pokémon, Hanza w/edible plants) • Thousands with help from record-keeping. • Systema naturae • GO

17. Natural • Natural vs artificial • Pokemon characteristics • “element,” “evolution,” “height,” “weight,” “good against,” “bad against” • Best classification systems reflect nature • The act of classifying reveals the true nature of the subject

18. Alchemical Classification of Chemicals

19. Periodic Table

20. Morphological Classification of Acute Leukemias

21. Immunophenotype of Acute Leukemias

22. Predictive • There are two types of people, those who classify people into two types, and those who don’t. • Classification system should be predictive. • Categorize object by one set of criteria • Does it share other common properties with its group?

23. Periodic Table

24. Evaluating Classification Schemes • Directly test • Ease of use • how long does it take to train a new curator? • Reproducibility • concordance among curators • Discrimination • are all categories used? How many used more than once? • Natural • how directly does the system reflect nature? • Predictive power • correct prediction of properties once an object is classified

25. Gotta Catch ’em All! brca2 1-phosphatidylinositol 3-kinase ras GPI anchor biosynthesis RAS