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ization and introgression are being recognized as a common mechanism hahn and nakhleh 2016 pease et al 2016 that we might call horizontal transfer even though close relatives are involved in cell type and tissue phylogenies the components also may not be inherited from direct ancestors as in the sister cell model but rather could be co opted from distant cell type or tissue cousins when the assumption of vertical descent holds there is great potential to use existing phylogenetic methods to understand evolution however given that strict bifurcation is commonly violated we may want to explore other models and metaphors for macroevolution one of those metaphors is a public goods model economic classification of goods in economics goods may be classified into a 2x2 matrix forming four categories in practice the categories are usually not discrete alternatives but instead form axes with continuous variation one axis asks how excludable and the other axis asks how rival is a particular good non excludable goods can be ubiquitously accessed whereas excludable goods have restricted access for example the air we breath has low excludability because we cannot prevent anyone from breathing the atmosphere however a theme park is quite excludable only those with a ticket may enter on the other axis highly rivalrous goods are exhaustible but non rival goods are unlimited a parking space is rivalrous because if i park there no one else can in contrast a public radio signal is non rivalrous my listening to 92 9 kjee does not prevent someone else from also listening public goods are defined as both nonrivalrous and nonexcludable the extreme corners of these two axes form four named categories and there are many everyday examples for each category table 1 table 1 the classification of goods excludable high excludable low rivalrous high private goods car apple parking spot common pool goods fish stock public park bench rivalrous low club goods private golf course satellite tv public goods air public radio signal public goods in macroevolution recent papers applied the concept of public goods to macroevolutionary topics like the tree of life and novelties mcinerney et al 2011 considered genetic material genes for short to be a public good and considered biological species to be the consumers in this economic metaphor mcinerney et al 2011 contrast their public good hypothesis of genes with the traditional idea of a universally bifurcating tree of life with vertical transmission from ancestor to descendant species with only vertical transmission genes are highly excludable between species because they can only be present in a genome if inherited from a direct ancestor genes also have low rivalrousness because no matter how many descendents evolve they all can have those genes in their genome non rivalrous excludable goods of the tree of life model are club goods instead mcinerney et al 2011 argue that genes should be considered public goods because horizontal transfer is very common horizontal transfer makes genes much less excludable because they could be transferred from any clade to any other clade erwin 2015 applied the concept of public goods to major innovations during evolution he extends public goods thinking in macroevolution beyond genes to include environmental and ecological goods in particular he suggests that the origins of particular public goods were associated with major transitions in evolution a prime example is the production of oxygen first as a waste product of photosynthetic cyanobacteria once oxygen accumulated in the great oxygenation event it became both non excludable and non rivalrous a public good that was exploited by other organisms the macroevolutionary applications above differ from public goods applications to microevolution especially by ignoring costs frank 2010 defined a public good as an individually costly act that benefits all group members the conflict between cost and benefit is central to microevolutionary topics like altruism or cooperation kin and group selection hamilton 1975 parasite virulence frank 1996 tragedy of the commons scenarios and cases where microbes produce public goods like nitrogen west et al 2002 or iron scavenging molecules kümmerli et al 2009 one link of these microevolutionary topics to macroevolution posits that cooperation between units led to changes in the level of selection that precipitated major transitions in evolution smith and szathmary 1997 unlike the microevolutionary applications where a cost is incurred by individuals producing the good the macroevolutionary applications discussed above are not concerned with costs to the producers the production of oxygen is presumably cost free waste for the photosynthetic organisms that produce it and only a benefit to some organisms that do not produce it like animals oxygen production does not then set the stage for conflict between producers and benefactors that are so central to the microevolutionary topics listed above similarly if genes are public goods for all species through horizontal transfer the costs to producers again are not apparent there would seem to be no direct cost to a species if one its genes are copied into a distant relative perhaps because of this explicit absence of costs and any quantification of benefits very little research in macroevolution uses the mathematical framework of public goods that is so prevalent in microevolution instead the macroevolutionary research simply points out that some critical elements of evolution are nonrivalrous and nonexcludable measuring excludability with treeness arendt d 2008 the evolution of cell types in animals emerging principles from molecular studies nat rev genet 9 868 882 arendt d hausen h purschke g 2009 the division of labour model of eye evolution philosophical transactions of the royal society b biological sciences 364 2809 2817 buschbeck e k friedrich m 2008 evolution of insect eyes tales of ancient heritage deconstruction reconstruction remodeling and recycling evo edu outreach 1 448 462 cavalli sforza l l piazza a 1975 analysis of evolution evolutionary rates independence and treeness theor popul biol 8 127 165 erwin d h 2015 a public goods approach to major evolutionary innovations geobiology 13 308 315 ferrer r p zimmer r k 2012 community ecology and the evolution of molecules of keystone significance biol bull 223 167 177 frank s a 1996 models of parasite virulence q rev biol 71 37 78 frank s a 2010 a general model of the public goods dilemma j evol biol 23 1245 1250 friedrich m 2006 continuity versus split and reconstitution exploring the molecular developmental corollaries of insect eye primordium evolution dev biol 299 310 329 geeta r 2003 structure trees and species trees what they say about morphological development and evolution evol dev 5 609 621 haggerty l s jachiet p a hanage w p fitzpatrick d lopez p o connell m j pisani d wilkinson m bapteste e mcinerney j o 2013 a pluralistic account of homology adapting the models to the data mol biol evol mst228 hahn m w nakhleh l 2016 irrational exuberance for resolved species trees evolution 70 7 17 hamilton w d 1975 innate social aptitudes of man an approach from evolutionary genetics biosocial anthropology 133 155 kümmerli r jiricny n clarke l s west s a griffin a s 2009 phenotypic plasticity of a cooperative behaviour in bacteria j evol biol 22 589 598 mcinerney j o pisani d bapteste e o connell m j 2011 the public goods hypothesis for the evolution of life on earth biol direct 6 41 oakley t h plachetzki d c rivera a s 2007 furcation field splitting and the evolutionary origins of novelty in arthropod photoreceptors arthropod struct dev 36 386 400 oakley t h rivera a s 2008 genomics and the evolutionary origins of nervous system complexity curr opin genet dev 18 479 492 pease j b haak d c hahn m w moyle l c 2016 phylogenomics reveals three sources of adaptive variation during a rapid radiation plos biol 14 e1002379 plachetzki d c oakley t h 2007 key transitions during the evolution of animal phototransduction novelty tree thinking co option and co duplication integr comp biol serb j m oakley t h 2005 hierarchical phylogenetics as a quantitative analytical framework for evolutionary developmental biology bioessays 27 1158 1166 smith j m szathmary e 1997 the major transitions in evolution oup oxford west s a kiers e t simms e l denison r f 2002 sanctions and mutualism stability why do rhizobia fix nitrogen proc biol sci 269 685 694 whitehead a crawford d l 2006 variation within and among species in gene expression raw material for evolution mol ecol 15 1197 1211 wray g a hahn m w abouheif e balhoff j p pizer m rockman m v romano l a 2003 the evolution of transcriptional regulation in eukaryotes mol biol evol 20 1377 1419 posted by todd oakley at 12 39 pm no comments saturday october 15 2016 what grad students need to know about submitting a grant proposal our lab just submitted two doctoral dissertation improvement grants ddigs each time i ve been involved in similar such submissions including when i first submitted a grant to nasa as a grad student in the late 1990s i find that graduate students encounter a number of misunderstandings these can cause obstacles to submitting the grants that could be lessened or avoided if they knew about this in advance i hope i will remember to show this post to my future students and i hope others can find it useful too 1 the institution e g the university officially submits m any grants not the individual student i think this is the root cause of most of the misunderstandings while some student grants are submitted by an individual especially local departmental grants or grants to scientific societies most are submitted by the institution so here at ucsb the university office of research submits a ddig as with any full proposal to nsf or nih since the grants that students submit early in their careers are smaller grants to smaller agencies the students might think that all proposals are submitted by individuals but they are not the fact that the institution submits grants has several important downstream effects 2 your practical deadline will be earlier than the final proposal deadline since the university has to make sure that the proposal does not break any rules staff need to read your proposal and approve it before it is submitted at ucsb our office of research or requests us to give them the full proposal 1 week before the deadline note they still allow some changes to the proposal after their screening as long as they don t affect things that or is looking to approve so you can fix typos change hypotheses rewrite a section as long as you do not do things like add a new experiment that now requires iacuc animal welfare approval add a new experiment on human subjects add a new experiment that requires scuba or other activities that are regulated by the institution the or will also check the grant for compliance and may give feedback about things that don t comply 3 there are other forms and signatures needed besides those required by the grant again because the institution submits the grant they want assurances about the activities proposed in the grant the forms at ucsb ask whether we propose to use human or vertebrate subjects whether we will use scuba whether we will use recombinant genetically engineered organisms whether we are up to date on chemical safety plans and other things note that these activities of course do not prevent us from submitting a grant instead they will trigger other actions that we need to take like completing an iacuc or scuba plan 4 you need to contact your grant administrator early institutions vary in how they handle grants but i believe that usually a department will have a grant administrator or team my lab submits grants through ucsb s marine science institute msi my lab is assigned a grant administrator in msi she acts as a liaison with the ucsb office of research and helps us get everything done that we need to do in msi the grant administrator uploads files to fastlane and will create a formal budget in a spreadsheet based on the budget that we sketch the budget can be complicated because there are a lot of rules that change yearly about overhead salaries and benefits overhead is a tax that the university charges on grants that is used for institutional infrastructure that allows the research to be done based on the above considerations i recommend the following timeline about 1 2 months in advance a read the call for proposals to get an idea of whether your idea fits with the call if you are unsure call the program officer you should also make a note of all the forms you will need to do maybe make a to do list this might include things like a data management plan your advisor s biosketch a specifically formatted cv collaborator letters evidence of permits evidence of your advance to candidacy etc etc about 1 month in advance of deadline b contact your departmental grant administrator tell him or her that you will submit a grant in one month and ask what the first steps are for you for me i usually provide the following the title of the grant proposal the projected start date of the proposed work the duration of the proposed work a sketch of the budget it seems counterintuitive and difficult to know what the budget and title will be so early but these are the things the grant admin needs first this is why i now focus on the big idea and the budgetary pieces first what salary do i need to complete the work what equipment what supplies and services like sequencing services i usually estimate a yearly budget for supplies and then fit details to that later c for nsf get your fastlane id or for other agencies make sure you have any accounts that you need d write the actual the proposal if you can complete a draft with several weeks to spare you can get comments from colleagues in our lab i try to go back and forth on drafts with the student making incremental improvements i estimate i go through 5 10 drafts with each student often it is easier to focus on one section at a time i won t go into writing strategies here this is about the administrative hurdles about 2 weeks before the deadline e complete all forms and administrative paperwork check with your departmental grants administrator to make sure all is done re read the call for propoposals carefully to make sure you have everything done f finalize the proposal incorporating comments from colleagues about 1 week before the deadline g have your grant administrator contact the office of research to review your full proposal just before the deadline h make any final changes to your proposal some may be indicated by or i when you are ready tell your grant administrator they can submit the grant remember the institution applies for the grant so they submit it too grants administrators like to submit a day early to avoid any unforeseen difficulties like server traffic ...