SPSP 2013 Symposium S10: Talking Junk about Transposons: Levels of selection and conceptions of functionality in...

SPSP 2013 Symposium S10: Talking Junk about Transposons: Levels of selection and conceptions of functionality in...

Tweeted from the 4th biennial conference of the Society for Philosophy of Science in Practice in Toronto, Ontario, Canada, on June 28, 2013, during Concurrent Sessions V

  1. As an audience member in this session, I had much less relevant background knowledge than I did in some others.  But I was pretty aware, from goings on in the science blogosphere, that there has been some amount of disagreement about what to say about "junk DNA," the ENCODE project's findings, and the coverage of it all by science journalists.
  2. Waiting for Symposium on "Talking Junk abt Trasposons: Levels of Selection & conceptions of functionality..." #SPSP2013 #SPSP2013Toronto
  3. Note that there are tweets below where I ended up with ECODE instead of ENCODE.  All hail Tpyos!
  4. ENCODE: Encyclopedia of DNA Elements. Mult analyses in 147 cell types, looking at various analyses of genome #SPSP2013 #SPSP2013Toronto
  5. Claim: ~80% of human genome participates in some form of biochemical function/activity #SPSP2013 #SPSP2013Toronto
  6. TRG says media reports seem to track claims of ENCODE researchers pretty closely #SPSP2013 #SPSP2013Toronto
  7. You might want to have a look at the posts on ENCODE by Brendan Maher and Ed Yong, both of which include lots of links.
  8. Myth 1: Concept of "junk DNA" based on ignorance (we don't know what it does, must be junk) #SPSP2013 #SPSP2013Toronto
  9. Myth 3: Concept caused biologist to ignore possible functions for most of genome until recently #SPSP2013 #SPSP2013Toronto
  10. Biochemical activity = biochem function = biological function? #SPSP2013 #SPSP2013Toronto
  11. Per ENCODE, function if: transcribed into RNA OR reasonably close to porotein-binding site OR has some struct mod #SPSP2013 #SPSP2013Toronto
  12. Other scientists criticize ENCODE's way of defining "functioning" here; in literature, in press #SPSP2013 #SPSP2013Toronto
  13. No real correspondence between amt of DNA, # of genes, complexity of organism ("C-value paradox", 1971) #SPSP2013 #SPSP2013Toronto
  14. 1972 - "Junk DNA" coined. Initially not widely accepted (If not functional, would've been deleted by now) #SPSP2013 #SPSP2013Toronto
  15. In 1970s, discovery of various types of non-coding DNA (functions considered for each of them) #SPSP2013 #SPSP2013Toronto
  16. Science Q (2005): "Why are some genomes really big and others quite compact?" #SPSP2013 #SPSP2013Toronto
  17. Evolution by gene duplication; often results in coding of pseudo-genes #SPSP2013 #SPSP2013Toronto
  18. "Selfish DNA" papers written as response to widespread assumption that non-coding DNA must be functional #SPSP2013 #SPSP2013Toronto
  19. "Caution: this sign has sharp edges (and also bridge is out)" sign as good analogy #SPSP2013 #SPSP2013Toronto
  20. View the sign here.
  21. By late '80s, early '90s more uptake of "junk DNA" & "selfish DNA" ideas #SPSP2013 #SPSP2013Toronto
  22. Mid-90s to present: "Long dismissed as junk ... but not really junk!" appears regularly in sci lit, media reports #SPSP2013 #SPSP2013Toronto
  23. ECODE didn't take an evolutionary perspective, include philosopher on team. Might have helped in "function" talk #SPSP2013 #SPSP2013Toronto
  24. Compelling narratives (we're starting to discover lots of things we didn't know before) #SPSP2013 #SPSP2013Toronto
  25. Training of people (medical genetics, computational biology, not usually evo biol) can drive the narrative #SPSP2013 #SPSP2013Toronto
  26. Adaptationist biases also make "junk DNA" harder to tolerate conceptually #SPSP2013 #SPSP2013Toronto
  27. Q: How did science permit an inflammatory term like "junk DNA" to persist? Non-coding is more neutral #SPSP2013 #SPSP2013Toronto
  28. Ohno used "junk" to mean "had a function, now it doesn't". Drifted to mean "crap DNA" more or less #SPSP2013 #SPSP2013Toronto
  29. Next up: Tyler Elliott, "Reviving an old approach to eukaryotic transposable element evolution" #SPSP2013 #SPSP2013Toronto
  30. "Controlling elements" in corn, "insertion sequences" in E. coli, virus-like mobile DNA in Drosophila #SPSP2013 #SPSP2013Toronto
  31. Transposable Elements (TEs) make up sig proportion of eukaryotic genomes #SPSP2013 #SPSP2013Toronto
  32. Function of repeats? Ubiquitous->must contribute *something* to host #SPSP2013 #SPSP2013Toronto
  33. Heavy interest in how they contribute to evolution of the organism. Evolvability thru mutations, rearrangements #SPSP2013 #SPSP2013Toronto
  34. Selfish DNA hypothesis: TEs can persist w/out contributing beneficially to host. Intra-genomic selection #SPSP2013 #SPSP2013Toronto
  35. Foundational for understanding evolution at the level of the elements #SPSP2013 #SPSP2013Toronto
  36. Hurdles in understanding: Elements nested in multilevel framework, making interpretation of behavior complex #SPSP2013 #SPSP2013Toronto
  37. Misconceptions abt selfish DNA hypothesis & content of papers, cited widely but seemingly poorly understood #SPSP2013 #SPSP2013Toronto
  38. Exaptation: many examples of components of elements contributing positively to host; contradicts selfish DNA? #SPSP2013 #SPSP2013Toronto
  39. TE pop gen models: interested in element spread & copy # increase in host population #SPSP2013 #SPSP2013Toronto
  40. Genome ecology: shows confusion betw ecology & evolution at TE level; TE ecology & TE evolution shld be separated #SPSP2013 #SPSP2013Toronto
  41. Element-level perspective would explore TEs as an evolving population #SPSP2013 #SPSP2013Toronto
  42. Refocus as complement (not wholesale replacement) to other approaches to help resolve current Qs in TE biology #SPSP2013 #SPSP2013Toronto
  43. Pokey transposons in Daphnia; how do selection pressures influence? How about variation, competition between TEs? #SPSP2013 #SPSP2013Toronto
  44. Building a framework: collect info relevant to evo at TE level to build conceptual framework for future work #SPSP2013 #SPSP2013Toronto
  45. Invitation to ask further Qs on Twitter of @TransposableMan Go for it, tweeps (but expect time lag) #SPSP2013 #SPSP2013Toronto
  46. Had my #SPSP2013 talk live-tweeted by @docfreeride this afternoon, first time that's ever happened!
  47. Next, Stefan Linquist, "Function-talk in transposon biology" #SPSP2013 #SPSP2013Toronto
  48. Selected effects (by natural selection) vs. causal role function (non-historical & interest relative) #SPSP2013 #SPSP2013Toronto
  49. The tweets to come are going to have a bunch of abbreviations:

    SE = selected effect functions
    CR = causal role functions
    TE = transposable elements
  50. Philosophers of biology recognizes both concepts of function at work, but there are boundary disputes #SPSP2013 #SPSP2013Toronto
  51. SE functions in evol expl'ns, CR functions in mechanistic explns. Or not ... #SPSP2013 #SPSP2013Toronto
  52. Even for developing proximate explns of transposable elements, SEs are more useful #SPSP2013 #SPSP2013Toronto
  53. Arg from Doolittle contra ENCODE that Selected effect defn of function is better #SPSP2013 #SPSP2013Toronto
  54. 4 research traditions in TE boil: organism centric, selfish element, neofunctionalist, genome ecology #SPSP2013 #SPSP2013Toronto
  55. McClintock seemed to have a causal role view of function (wanted to explain patterns in gene expression) #SPSP2013 #SPSP2013Toronto
  56. McClintock's discussions of evolutionary significance are rare & surprisingly unsophisticated #SPSP2013 #SPSP2013Toronto
  57. View that TEs have function only if they benefit the organism makes more sense under CR than SE view #SPSP2013 #SPSP2013Toronto
  58. Selfish element conception of function? Origin-function can differ from maintenance-functions #SPSP2013 #SPSP2013Toronto
  59. Diff traditions of TE research operate w/ diff function concepts #SPSP2013 #SPSP2013Toronto
  60. CR functions are promiscuous. Can result in odd-sounding functions. #SPSP2013 #SPSP2013Toronto
  61. Sol'n 1: let scientists decide on appropriate functional ascriptions #SPSP2013 #SPSP2013Toronto
  62. ECODE highlights the danger of this sol'n; plenty of strategic reasons to apply misleading CR functions #SPSP2013 #SPSP2013Toronto
  63. sol'n 2: CR functions informative only to extent that analyzing capacities simpler & diff than analyzed capacity #SPSP2013 #SPSP2013Toronto
  64. Why are some TEs stress-induced? "Function is to generate novel phenotypes." #SPSP2013 #SPSP2013Toronto
  65. CR framework renders "invisible" certain alternative explanations #SPSP2013 #SPSP2013Toronto
  66. Disruption hypothesis: stress conditions compromise normal suppression mechanisms of host #SPSP2013 #SPSP2013Toronto
  67. Looks like a mechanistic explanation, but wouldn't think about it w/out SE way of thinking #SPSP2013 #SPSP2013Toronto
  68. abandon-ship hypothesis: stress of viral infection is an opportunity for horizontal transfer (again, SE thinking) #SPSP2013 #SPSP2013Toronto
  69. SE framework more mechanistically informative than CR, at least in context of transposon biology #SPSP2013 #SPSP2013Toronto
  70. Point here is not to say "natural selection is one broad mechanism". #SPSP2013 #SPSP2013Toronto
  71. Want to understand what's happening in organism during its lifetime. #SPSP2013 #SPSP2013Toronto
  72. Are their insights you get just from CR function that you can't get from SE? (If not stick to SE function in bio) #SPSP2013 #SPSP2013Toronto
  73. Thanks to @TRyanGregory, @TransposableMan, and Stefan Linquist for a very informative session!

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