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
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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.
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Waiting for Symposium on “Talking Junk abt Trasposons: Levels of Selection & conceptions of functionality…” #SPSP2013 #SPSP2013Toronto
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First up: T. Ryan Gregory, “Junk and the genome” #SPSP2013 #SPSP2013Toronto
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Starts w/ a movie ( goo.gl/lpyla/ ) on ENCODE #SPSP2013 #SPSP2013Toronto
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Note that there are tweets below where I ended up with ECODE instead of ENCODE. All hail Tpyos!
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ENCODE: Encyclopedia of DNA Elements. Mult analyses in 147 cell types, looking at various analyses of genome #SPSP2013 #SPSP2013Toronto
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Claim: ~80% of human genome participates in some form of biochemical function/activity #SPSP2013 #SPSP2013Toronto
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TRG says media reports seem to track claims of ENCODE researchers pretty closely #SPSP2013 #SPSP2013Toronto
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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.
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Major issues: Defn of “function”; 3 myths abt “junk DNA” #SPSP2013 #SPSP2013Toronto
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Myth 1: Concept of “junk DNA” based on ignorance (we don’t know what it does, must be junk) #SPSP2013 #SPSP2013Toronto
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Myth 2: “Junk DNA” idea precluded possibility of function #SPSP2013 #SPSP2013Toronto
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Myth 3: Concept caused biologist to ignore possible functions for most of genome until recently #SPSP2013 #SPSP2013Toronto
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Biochemical activity = biochem function = biological function? #SPSP2013 #SPSP2013Toronto
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Per ENCODE, function if: transcribed into RNA OR reasonably close to porotein-binding site OR has some struct mod #SPSP2013 #SPSP2013Toronto
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Other scientists criticize ENCODE’s way of defining “functioning” here; in literature, in press #SPSP2013 #SPSP2013Toronto
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No real correspondence between amt of DNA, # of genes, complexity of organism (“C-value paradox”, 1971) #SPSP2013 #SPSP2013Toronto
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So, what are big genomes doing? #SPSP2013 #SPSP2013Toronto
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1972 – “Junk DNA” coined. Initially not widely accepted (If not functional, would’ve been deleted by now) #SPSP2013 #SPSP2013Toronto
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Most of the genome is not genes (sol’n to C-value paradox) #SPSP2013 #SPSP2013Toronto
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In 1970s, discovery of various types of non-coding DNA (functions considered for each of them) #SPSP2013 #SPSP2013Toronto
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Science Q (2005): “Why are some genomes really big and others quite compact?” #SPSP2013 #SPSP2013Toronto
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Evolution by gene duplication; often results in coding of pseudo-genes #SPSP2013 #SPSP2013Toronto
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“Selfish DNA” papers written as response to widespread assumption that non-coding DNA must be functional #SPSP2013 #SPSP2013Toronto
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(Molecular equivalent of Gould-Lewontin “Spandrels” paper) #SPSP2013 #SPSP2013Toronto
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“Caution: this sign has sharp edges (and also bridge is out)” sign as good analogy #SPSP2013 #SPSP2013Toronto
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View the sign here.
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By late ’80s, early ’90s more uptake of “junk DNA” & “selfish DNA” ideas #SPSP2013 #SPSP2013Toronto
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Mid-90s to present: “Long dismissed as junk … but not really junk!” appears regularly in sci lit, media reports #SPSP2013 #SPSP2013Toronto
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ECODE didn’t take an evolutionary perspective, include philosopher on team. Might have helped in “function” talk #SPSP2013 #SPSP2013Toronto
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Compelling narratives (we’re starting to discover lots of things we didn’t know before) #SPSP2013 #SPSP2013Toronto
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Training of people (medical genetics, computational biology, not usually evo biol) can drive the narrative #SPSP2013 #SPSP2013Toronto
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Adaptationist biases also make “junk DNA” harder to tolerate conceptually #SPSP2013 #SPSP2013Toronto
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Q: How did science permit an inflammatory term like “junk DNA” to persist? Non-coding is more neutral #SPSP2013 #SPSP2013Toronto
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Ohno used “junk” to mean “had a function, now it doesn’t”. Drifted to mean “crap DNA” more or less #SPSP2013 #SPSP2013Toronto
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Next up: Tyler Elliott, “Reviving an old approach to eukaryotic transposable element evolution” #SPSP2013 #SPSP2013Toronto
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Discovery of “mobile repeats” by B. McClintock in corn #SPSP2013 #SPSP2013Toronto
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“Controlling elements” in corn, “insertion sequences” in E. coli, virus-like mobile DNA in Drosophila #SPSP2013 #SPSP2013Toronto
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Transposable Elements (TEs) make up sig proportion of eukaryotic genomes #SPSP2013 #SPSP2013Toronto
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Function of repeats? Ubiquitous->must contribute *something* to host #SPSP2013 #SPSP2013Toronto
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Heavy interest in how they contribute to evolution of the organism. Evolvability thru mutations, rearrangements #SPSP2013 #SPSP2013Toronto
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Also dissenting views: accessory chromosomes as parasitic #SPSP2013 #SPSP2013Toronto
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Accessory & disruptive to genes, parasitic or symbiotoc #SPSP2013 #SPSP2013Toronto
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Selfish DNA hypothesis: TEs can persist w/out contributing beneficially to host. Intra-genomic selection #SPSP2013 #SPSP2013Toronto
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Foundational for understanding evolution at the level of the elements #SPSP2013 #SPSP2013Toronto
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Hurdles in understanding: Elements nested in multilevel framework, making interpretation of behavior complex #SPSP2013 #SPSP2013Toronto
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Misconceptions abt selfish DNA hypothesis & content of papers, cited widely but seemingly poorly understood #SPSP2013 #SPSP2013Toronto
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Exaptation: many examples of components of elements contributing positively to host; contradicts selfish DNA? #SPSP2013 #SPSP2013Toronto
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TE pop gen models: interested in element spread & copy # increase in host population #SPSP2013 #SPSP2013Toronto
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Emphasis not on evolutionary change in elements, though #SPSP2013 #SPSP2013Toronto
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Genome ecology: shows confusion betw ecology & evolution at TE level; TE ecology & TE evolution shld be separated #SPSP2013 #SPSP2013Toronto
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Element-level perspective would explore TEs as an evolving population #SPSP2013 #SPSP2013Toronto
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Refocus as complement (not wholesale replacement) to other approaches to help resolve current Qs in TE biology #SPSP2013 #SPSP2013Toronto
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Pokey transposons in Daphnia; how do selection pressures influence? How about variation, competition between TEs? #SPSP2013 #SPSP2013Toronto
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Building a framework: collect info relevant to evo at TE level to build conceptual framework for future work #SPSP2013 #SPSP2013Toronto
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Invitation to ask further Qs on Twitter of @TransposableMan Go for it, tweeps (but expect time lag) #SPSP2013 #SPSP2013Toronto
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Had my #SPSP2013 talk live-tweeted by @docfreeride this afternoon, first time that’s ever happened!
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Next, Stefan Linquist, “Function-talk in transposon biology” #SPSP2013 #SPSP2013Toronto
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Selected effects (by natural selection) vs. causal role function (non-historical & interest relative) #SPSP2013 #SPSP2013Toronto
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The tweets to come are going to have a bunch of abbreviations:SE = selected effect functionsCR = causal role functionsTE = transposable elements
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Philosophers of biology recognizes both concepts of function at work, but there are boundary disputes #SPSP2013 #SPSP2013Toronto
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SE functions in evol expl’ns, CR functions in mechanistic explns. Or not … #SPSP2013 #SPSP2013Toronto
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Even for developing proximate explns of transposable elements, SEs are more useful #SPSP2013 #SPSP2013Toronto
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Arg from Doolittle contra ENCODE that Selected effect defn of function is better #SPSP2013 #SPSP2013Toronto
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4 research traditions in TE boil: organism centric, selfish element, neofunctionalist, genome ecology #SPSP2013 #SPSP2013Toronto
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McClintock seemed to have a causal role view of function (wanted to explain patterns in gene expression) #SPSP2013 #SPSP2013Toronto
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McClintock’s discussions of evolutionary significance are rare & surprisingly unsophisticated #SPSP2013 #SPSP2013Toronto
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View that TEs have function only if they benefit the organism makes more sense under CR than SE view #SPSP2013 #SPSP2013Toronto
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Selfish element conception of function? Origin-function can differ from maintenance-functions #SPSP2013 #SPSP2013Toronto
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(not all organism-level benefits are functional) #SPSP2013 #SPSP2013Toronto
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Diff traditions of TE research operate w/ diff function concepts #SPSP2013 #SPSP2013Toronto
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CR functions are promiscuous. Can result in odd-sounding functions. #SPSP2013 #SPSP2013Toronto
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Sol’n 1: let scientists decide on appropriate functional ascriptions #SPSP2013 #SPSP2013Toronto
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ECODE highlights the danger of this sol’n; plenty of strategic reasons to apply misleading CR functions #SPSP2013 #SPSP2013Toronto
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sol’n 2: CR functions informative only to extent that analyzing capacities simpler & diff than analyzed capacity #SPSP2013 #SPSP2013Toronto
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Why are some TEs stress-induced? “Function is to generate novel phenotypes.” #SPSP2013 #SPSP2013Toronto
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Most plausibly understood as CR functional claim #SPSP2013 #SPSP2013Toronto
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CR framework renders “invisible” certain alternative explanations #SPSP2013 #SPSP2013Toronto
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Disruption hypothesis: stress conditions compromise normal suppression mechanisms of host #SPSP2013 #SPSP2013Toronto
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Looks like a mechanistic explanation, but wouldn’t think about it w/out SE way of thinking #SPSP2013 #SPSP2013Toronto
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abandon-ship hypothesis: stress of viral infection is an opportunity for horizontal transfer (again, SE thinking) #SPSP2013 #SPSP2013Toronto
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SE framework more mechanistically informative than CR, at least in context of transposon biology #SPSP2013 #SPSP2013Toronto
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Point here is not to say “natural selection is one broad mechanism”. #SPSP2013 #SPSP2013Toronto
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Want to understand what’s happening in organism during its lifetime. #SPSP2013 #SPSP2013Toronto
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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
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Thanks to @TRyanGregory, @TransposableMan, and Stefan Linquist for a very informative session!
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