SPSP 2013 Plenary session #3: James Griesemer
Tweeted from the 4th biennial conference of the Society for Philosophy of Science in Practice in Toronto, Ontario, Canada, on June 28, 2013.
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Getting set for Plenary 3 at #SPSP2013 #SPSP2013Toronto which will be James Griesemer, “Model Taxa as Platforms for Biological Research”
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That there’s a story (and a set of tweets) for Plenary 1 and also for Plenary 3 raises an obvious question:
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“Why no tweets for Plenary 2?” you ask? Because my laptop was used by the esteemed Rachel Ankeny for her slides #SPSP2013 #SPSP2013Toronto
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Assisting the speaker in achieving the conditions required to project her slides is a good thing, yes?
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Have taken notes in the quad-rule notebook for sessions not tweeted. Will try to tweet or blog them when I can #SPSP2013 #SPSP2013Toronto
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There might be a nap between now and then, however.
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James Griesemer: talking about models/modeling in production & use of platforms for research #SPSP2013 #SPSP2013Toronto
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Wondered why so many math. models? Why model species rather than model taxa? #SPSP2013 #SPSP2013Toronto
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Integration of research approaches in practice development of model research platform #SPSP2013 #SPSP2013Toronto
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Research platforms as material circumstances. #SPSP2013 #SPSP2013Toronto
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Model taxa can be used to represent phenomena & as platforms for constructive scientific activity & prob solving #SPSP2013 #SPSP2013Toronto
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Model taxon doesn’t just fill out a trend in model organism development #SPSP2013 #SPSP2013Toronto
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Model taxon = group of biological species used in modeling #SPSP2013 #SPSP2013Toronto
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Model has diverse meanings; should take all of them seriously (not just representational ones) #SPSP2013 #SPSP2013Toronto
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“Model” has complex history. An original = object/phenomenon that could serve as pattern #SPSP2013 #SPSP2013Toronto
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Dual roles of model in use (representation of a class of things & pattern for making new things) #SPSP2013 #SPSP2013Toronto
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Models don’t just stand for something else. Model organisms facilitate generalization (Representational scope?) #SPSP2013 #SPSP2013Toronto
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Model orgs facilitate problem & domain specification (representational target spells out problems to be explored) #SPSP2013 #SPSP2013Toronto
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NIH 13 model orgs for biomed research (Emerging model org = not on the list) #SPSP2013 #SPSP2013Toronto
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You can check out the NIH model organisms webpage. Current count of model organisms as I type this is still 13 …
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Cold Spring Harbor Protocol on EMOs specifies platforms (background, husbandry, related species, …) #SPSP2013 #SPSP2013Toronto
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Read more about the Cold Spring Harbor Protocols for Emerging Model Organisms here
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(use of model system, genomic approaches, protocols, recipes for growing what you’ve collected from field…) #SPSP2013 #SPSP2013Toronto
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Specifying EMO = placing in context of taxon, materials & methods, troubleshooting to stdize activities #SPSP2013 #SPSP2013Toronto
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What about pathways to model taxa? #SPSP2013 #SPSP2013Toronto
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Model taxon not a recent invention (although the term is) #SPSP2013 #SPSP2013Toronto
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Case studies trace back to 1960s-’80s (at least), before genomics drove model org development #SPSP2013 #SPSP2013Toronto
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Classical, semi-classical, genomic, & shotgun approaches to model taxa construction #SPSP2013 #SPSP2013Toronto
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Classical: orgs of convenience, practical necessity, or specific research interest #SPSP2013 #SPSP2013Toronto
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e.g., Drosophila for Mendellian transmission of traits #SPSP2013 #SPSP2013Toronto
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Wake 2009, “What salamanders have taught us about evolution”: model taxon permits multidimensional approach #SPSP2013 #SPSP2013Toronto
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Diversity of perspectives, methodological approaches, etc., required to get adequate empirical results #SPSP2013 #SPSP2013Toronto
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David Wake’s classical salamander model taxa (Salamanders, Lungless salamanders, Lowland neo-tropical salamander) #SPSP2013 #SPSP2013Toronto
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Webbed feet in salamanders explained by selection on body size, not on feet #SPSP2013 #SPSP2013Toronto
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What looks like adaptive characters are better explained by development. Inferences from adaptive evo not robust #SPSP2013 #SPSP2013Toronto
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Methodological lesson is exportable (need developmental mech, morphology, phylogeny, etc.) #SPSP2013 #SPSP2013Toronto
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Glickman’s classical Hyaenidae model taxon. Experimental system, but a model organism? #SPSP2013 #SPSP2013Toronto
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Dev. of genital anatomy studied by comparative work (looking at other carnivores) #SPSP2013 #SPSP2013Toronto
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Repro system & brain development isn’t always about androgens #SPSP2013 #SPSP2013Toronto
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Familiar molecules behave in unfamiliar ways in mod. system; unfamiliar/unexpected behavior in familiar ones too? #SPSP2013 #SPSP2013Toronto
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Semi-classical: study non-model species of research interest that’s sister taxon tp model org #SPSP2013 #SPSP2013Toronto
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Recency of common descent of sister group implies probable common causes #SPSP2013 #SPSP2013Toronto
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James Hanken’s semi-classical frog model taxon (1 model org, African clawed frog 1 outgroup, Budgett’s frog) #SPSP2013 #SPSP2013Toronto
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Genomic approach: choose taxon that’s abt ro be sequenced that also meets semi-classical requirement #SPSP2013 #SPSP2013Toronto
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Shotgun: sequence lots of species by taxon sampling across large segments of tree of life #SPSP2013 #SPSP2013Toronto
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Props of model taxa: (1) integrate research approaches b/c orgs integrate phenomena of interest #SPSP2013 #SPSP2013Toronto
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But the phenomena are studied w/ diff approaches, by diff specialities #SPSP2013 #SPSP2013Toronto
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(2) Orgs not just genetic but developmental, morphological, behavioral, ecological, … #SPSP2013 #SPSP2013Toronto
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Focus on variation & comparison, not unification & universal generalization #SPSP2013 #SPSP2013Toronto
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Integration is piecemeal & pragmatic (b/c that’s how evolution works) #SPSP2013 #SPSP2013Toronto
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MT can represent variation much better than model orgs #SPSP2013 #SPSP2013Toronto
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Model taxa not very portable (unlike bacteria, yeast, flies); researchers need to go where platform is #SPSP2013 #SPSP2013Toronto
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SHould look for more model taxa, especially in field (harder to study) #SPSP2013 #SPSP2013Toronto
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Look for more patterns of export generalization (connect to case-based reasoning discussions) #SPSP2013 #SPSP2013Toronto
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Using model orgs (or taxa), closeness to humans is just one research interest among many #SPSP2013 #SPSP2013Toronto
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Model Taxa nice b/c variation among species something you can address w/in model (vs. needing to extrapolate) #SPSP2013 #SPSP2013Toronto
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