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a three pound monkey brain august 2008 a three pound monkey brain biology programming linguistics phylogeny systematics 23 august 2008 what is it that you hate about the phylocode mention of the phylocode can incite some pretty strong emotions among biologists some are supportive but there s a lot of vitriol out there consider for example the title of carpenter s 2003 paper a critique of pure folly yes a paper with that title actually got published in a scientific journal why the hate the thing is it s sometimes hard to pin people down on exactly why they dislike it part of the problem is that the phylocode is surrounded by misconceptions much of what s been written about it is shockingly ignorant considering that the code is freely available online and not horribly long certainly shorter than any of the other codes consider benton 2000 who seems to have not even read the then current draft and proceeded to write an entire review based on what he imagined the phylocode to be like this is not to say that all critiques are uninformed but of those that are i find that they fall into two camps they either raise points that have since been addressed in later drafts or they are simple matters of taste as an example of addressed issues the critiques of how the phylocode was going to handle species are now defunct since it won t cover species i myself raised dozens of smaller issues to the authors of the code who then either emended the draft of the code or convinced me that no change was needed and as an example of difference of opinion some people don t see the utility of the crown clade convention adopted by recent drafts some people just don t like phylogenetic nomenclature period the rank based systems which incidentally should not be called linnaean systems per de queiroz 2005 do well enough for many people s purposes and they don t see a reason to change of those who like phylogenetic nomenclature some don t see the advantages of a centralized approach and would rather let it grow freely e g sereno pers comm that s all fine it s good for people to point out flaws if they are later addressed and it s understandable that not all people would agree on matters of opinion but i see so much misinformation out there that i think it has to be the source of much of the dislike out there one popular article is titled what if we decided to rename every living thing on earth when the phylocode has always advocated using existing names when possible pickett s 2005 report on the first ispn meeting is titled the new and improved phylocode now with types ranks and even polyphyly when the phylocode has never had types only specifiers which are similar but operationally different has always allowed ranks and has never allowed polyphyly so let me put a question out there if you dislike the phylocode what is it about it that you dislike and are you sure it s something actually in the code posted by mike keesey at 7 39 pm 17 comments labels nomenclature phylocode systematics 17 august 2008 sets for actionscript it s been a busy couple of months one of the things keeping me busy is of course names on nodes the web application i am developing that will automate phylogenetic nomenclature as part of that project i have developed a mathematics package that i would eventually like to release as its own package one class however is so useful that i have decided to jump the gun and offer it on its own we actionscript programmers all know how useful the array class is it can be used to store a sequence of anything so it can be repurposed as a list a vector an edge all manner of collections well not all manner of collections just ordered collections that allow duplicate elements what if you want a set an unordered collection with no duplicates i find i need sets all the time but i have to use arrays and arrays are not optimal for looking up an element s membership or preventing duplication as lists they re great but as sets they suck for a while i used a class i d made called arrayset that wrapped an array but this was only an improvement in api not in performance then i took a cue from java and created hashset download hashset as the hashset class wraps a dictionary object which it uses as a hash table if an element belongs to the set then that element is a self referential key in the dictionary if it doesn t then there is no such key in the dictionary and hashset extends proxy so you can use bracket notation for many operations you can also use for in and for each in loops here s a quick example create and populate the set var s hashset hashset fromobject 1 2 3 trace s size 3 trace s 1 1 trace s 2 2 trace s 0 undefined trace s has 1 true trace all elements of the set for each var i int in s trace i trace all elements of the set different method for var x in s trace x trace s 1 2 3 s add 1 trace s 1 2 3 s add 4 trace s 1 2 3 4 s remove 1 trace s 2 3 4 delete s 2 trace s 3 4 s 3 undefined trace s 4 and so on full documentation is in the class itself so you can figure out the details for yourself i will mention that hashset also has a number of functions in common with array every filter foreach map some and others that are unique to sets get empty diff intersect prsubsetof subsetof union it also has a few functions that array really ought to have clone equals remove download it and try it the full version is integrated into the mathematics package that i m still tweaking but this is too useful to keep to myself any longer at least i think so let me know what you think posted by mike keesey at 12 34 pm 5 comments labels actionscript flash flex java mathematics names on nodes oop newer posts older posts home subscribe to posts atom philosophy is the art of understanding the universe using a three pound monkey brain what is this blog about for that you d better see the first post the author mike keesey view my complete profile search this blog my other stuff résumé phylopic dragabok flickr names on nodes parry carney friends for life reference material actionscript language reference typescript archives of the dinosaur mailing list the phylocode the tree of life web project blog archive 2014 3 july 1 march 1 february 1 2013 15 october 1 september 1 may 2 april 1 march 3 february 4 january 3 2012 17 december 3 october 1 august 4 may 1 april 1 february 4 january 3 2011 13 december 1 november 2 october 1 september 1 august 2 may 1 march 2 february 2 january 1 2010 34 december 3 october 1 august 3 july 4 june 1 may 7 april 5 march 3 february 5 january 2 2009 26 december 2 november 2 september 1 august 1 july 2 june 2 may 4 march 3 february 7 january 2 2008 48 december 2 november 3 october 4 september 3 august 2 what is it that you hate about the phylocode sets for actionscript june 7 may 6 april 3 march 2 february 6 january 10 2007 17 december 4 november 13 popular posts brand new forum for discussion of phylogenetic nomenclature the title says it all as some of you may know the ispn s online forum has been down for a while daniel madzia of wild prehistory human clades a look at a complex phylogeny most methods of phylogenetic analysis deal with simple trees in these phylogenies every taxonomic unit has a single direct ancestor or using typescript to define json data json has gradually been wearing away at xml s position as the primary format for data communication on the web in some ways that the dinosauricon is dead long live the dinosauricon as some of you may know i used to run a website devoted to dinosaur information and illustration called the di the evolution of cranial capacity in humans and stem humans hey i m actually writing on the blog s title subject today here s a chart i ve been working on for a while t guest post similarities between macaque and human brains despite the title of this blog i ve rarely if ever actually discussed simian brains the title refers to my own brain or more genera extinct or extant it s pretty easy to tell whether something s alive right you might have to jab it with a stick a couple of times to make sure ass mathematical expressions as json and phyloreferencing for names on nodes i did a lot of work with mathml specifically mathml content an application of xml for representing mathematical co hybridizing stem humans or is everyone right analysis of mitochondrial dna shows that the human matrilineage split from the denisovan matrilineage around a million years ago the nuclea posting code in blogs until the previous post i d been hand converting code samples into html for blog entries incredibly tedious amazingly tedious now i simple theme theme images by gaffera powered by blogger