tag:blogger.com,1999:blog-69411512024-03-07T14:37:38.521+10:00Evolving ThoughtsEvolution, culture, philosophy and chocolate! John Wilkins' continuing struggle to come to terms with impermanence...
"Humanus sum, nihil humanum a me alienum puto" - TerenceJohn S. Wilkinshttp://www.blogger.com/profile/04417266986565803683noreply@blogger.comBlogger401125tag:blogger.com,1999:blog-6941151.post-10425699474811982662007-02-07T04:06:00.000+10:002007-02-07T04:06:15.373+10:00The Voltage Gate: Basic Concepts: What Is Ecology?Basic Concepts in Science - A listJohn S. Wilkinshttp://www.blogger.com/profile/04417266986565803683noreply@blogger.com0tag:blogger.com,1999:blog-6941151.post-1149565535080488062006-09-13T14:33:00.000+10:002006-09-13T14:39:35.436+10:00The last ever post hereDear folks. I have defected to Seed Blogs on a promise of fame, fortune and women. So this will be my last ever post at this site. The new link is here, and the news feed in Atom form is here. It's been fun, so drop by for a chat.I will repost some oldies from here to begin with, and continue our discussions.John S. Wilkinshttp://www.blogger.com/profile/04417266986565803683noreply@blogger.com0tag:blogger.com,1999:blog-6941151.post-1149812762800468412006-06-09T10:23:00.000+10:002006-06-09T10:27:03.340+10:00A blogging delayDear readers, for reasons that will shortly become clear, there is a blogging delay here. Hmm... "blogging" in that context sounds like a swear word... "another blogging delay! Dammit!"Stay tuned and in a day or so All Will Be Revealed.John S. Wilkinshttp://www.blogger.com/profile/04417266986565803683noreply@blogger.com0tag:blogger.com,1999:blog-6941151.post-1149492872414749622006-06-05T17:23:00.000+10:002006-06-05T17:34:32.573+10:00Biologically feasible political systemsI often wonder what goes through the minds of those who propose utopian political ideals that turn out to become the worst of all possible dystopias, like Leninism or Maoism, or for that matter the extreme laisse faire capitalist conservatism. For it appears to me that these systems would work just fine, if only they didn't involve any human beings. And that raises an interesting question in my John S. Wilkinshttp://www.blogger.com/profile/04417266986565803683noreply@blogger.com0tag:blogger.com,1999:blog-6941151.post-1149297610288832912006-06-03T11:18:00.000+10:002006-06-03T11:20:10.483+10:00Evolution and irony in the yardA funny story on a site called Community Press about one woman's struggle against dandelions in the yard makes a nice followup to my piece on lawns a while back. In case the link changes, I will give the story here (and here is the direct link):Tales from the imperfect rural wife: Chuck had it all wrong in the survival gameby Paula Cassidy 06.02.06I had just chopped off their heads, but by the John S. Wilkinshttp://www.blogger.com/profile/04417266986565803683noreply@blogger.com0tag:blogger.com,1999:blog-6941151.post-1149224317550933042006-06-02T14:33:00.000+10:002006-06-02T18:10:24.160+10:00The Synthesis and historiographyIn an execrable display of taste, Rob Skipper at hpb etc. has linked to this blog, and discussed the Michael Ghiselin quote I put up a few days ago. He rightly notes the standard story is a bit harsh, and suggests some extra reading (to which I would add the series of papers from a special issue of Journal of the History of Biology last year, in particular Jon Hodge's article).I would like to addJohn S. Wilkinshttp://www.blogger.com/profile/04417266986565803683noreply@blogger.com0tag:blogger.com,1999:blog-6941151.post-1149222642088411402006-06-02T14:27:00.000+10:002006-06-02T14:30:42.106+10:00Not cooking frogsTalking Points Memo links to a number of debunkings of the myth that a frog will stay in a gradually heated pot and so boil. Yet Another Thing Everybody Knows that is false. J.B.S. Haldane called this the Aunt Jobisca Theorem: it is a thing that everyone knows.John S. Wilkinshttp://www.blogger.com/profile/04417266986565803683noreply@blogger.com0tag:blogger.com,1999:blog-6941151.post-1149207266560056002006-06-02T10:09:00.000+10:002006-06-02T10:14:26.560+10:00Possible cause of the Permian extinctionResearchers have found a 300 mile (that's around 480km in real money) crater beneath the Antarctic ice sheet that dates to around the time of the Permian extinction. Bolides seem to be at or near most of the major extinctions. I wonder, idly*, if the impacts themselves aren't the killer blow but rather the subsequent tectonic vulcanism.* Idly = "wild eyed guess with no evidence or real John S. Wilkinshttp://www.blogger.com/profile/04417266986565803683noreply@blogger.com0tag:blogger.com,1999:blog-6941151.post-1149206493893385802006-06-02T10:00:00.000+10:002006-06-02T10:01:33.913+10:00Invade America, and establish democracy there!A while back I was at a dinner sitting next to Pete Richerson, a lovely guy who is an ornithologist who has written with Robert Boyd (who I haven't met, but I'm sure he's just as nice) some of the most sophisticated and sensible material on cultural evolution - it figures anyone who has to deal with the hyperintelligent Corvidae and other passerine birds would be interested in that. But the talk John S. Wilkinshttp://www.blogger.com/profile/04417266986565803683noreply@blogger.com0tag:blogger.com,1999:blog-6941151.post-1149166158129443722006-06-01T22:47:00.000+10:002006-06-01T22:51:04.096+10:00Cooking up a speciesHere's one I was going to leave until I could read the actual paper, because I am both suspicious and skeptical on the one hand and sympathetic to the underlying rationale on the other. And on the gripping hand...Writing this week in the Proceedings of the National Academy of Sciences, scientists say higher temperatures near the equator speed up the metabolisms of the inhabitants, fueling geneticJohn S. Wilkinshttp://www.blogger.com/profile/04417266986565803683noreply@blogger.com0tag:blogger.com,1999:blog-6941151.post-1149136945032830012006-06-01T14:40:00.000+10:002006-06-01T14:42:25.046+10:00The good that men dois oft interred with their bones. The evil lives on after them in their posts and papers...The Explanatory Filter is being revived for SETI. See the post by Pim van Meurs at Panda's Thumb linked above.John S. Wilkinshttp://www.blogger.com/profile/04417266986565803683noreply@blogger.com0tag:blogger.com,1999:blog-6941151.post-1149136058259924722006-06-01T14:26:00.000+10:002006-06-01T14:30:31.123+10:00Microbial species 5: A new beginningWell after reading many papers by various bacteriologists, mycologists, and other non-vertebrates specialists, I have come to the conclusion that there is no single set of conceptions or criteria (that much abused word!) for something being a species in non-sexual organisms, which I am here calling "microbial". Of course, as I noted, microbes can be "sexual" in various ways. They can share genes John S. Wilkinshttp://www.blogger.com/profile/04417266986565803683noreply@blogger.com0tag:blogger.com,1999:blog-6941151.post-1149133748565092872006-06-01T13:47:00.000+10:002006-06-01T22:43:32.506+10:00Quote: Ghiselin on the SynthesisThe notion that "the" Synthesis was somehow complete at one time or another in its history implies that the participants were aiming at some culminating event, like the Resurrection of Christ.The canonical texts are being treated as if they were The Gospel according to Saint Doby, The Gospel according to Saint Ernst, The Gospel according to Saint G. G., The Gospel according to Saint Julian, The John S. Wilkinshttp://www.blogger.com/profile/04417266986565803683noreply@blogger.com0tag:blogger.com,1999:blog-6941151.post-1149130036545621522006-06-01T12:35:00.000+10:002006-06-01T12:47:16.873+10:00Hobbits and toolsIn a hole in the ground there was found a hobbit...The Independent is reporting objections to the recent claims by the Microcephaly Proponents that the hobbits (Homo floresiensis) had brains that were too small to make the stone tools found with them.James Phillips, professor of anthropology at the University of Illinois at Chicago, said that it was wrong to suggest that the stone tools could John S. Wilkinshttp://www.blogger.com/profile/04417266986565803683noreply@blogger.com0tag:blogger.com,1999:blog-6941151.post-1149123223608333152006-06-01T10:52:00.000+10:002006-06-01T10:55:31.926+10:00New cave species found in IsraelIsraeli researchers have described eight new species of crustaceans and invertebrates in a recently discovered limestone cave isolated from the external world. They live in and around an underground lake fed by deep water sources rather than rainfall from above.John S. Wilkinshttp://www.blogger.com/profile/04417266986565803683noreply@blogger.com0tag:blogger.com,1999:blog-6941151.post-1149122540872011552006-06-01T10:40:00.000+10:002006-06-01T10:42:21.103+10:00Creationist UK school expels anyone who doesn't conformThe Guardian reports that parents of students at Sir Peter Vardy's Trinity school, the school that gained some notoriety for being partially government funded but also teaching creationism, are complaining that it is expelling students for any kind of religious or cultural nonconformity, thereby selecting both academically and religiously. The school denies this.John S. Wilkinshttp://www.blogger.com/profile/04417266986565803683noreply@blogger.com0tag:blogger.com,1999:blog-6941151.post-1149050974834025372006-05-31T14:47:00.000+10:002006-05-31T14:54:55.496+10:00A quoteFrancis Bacon wrote of thosethat have pretended to find the truth of all natural philosophy in the Scriptures; scandalizing and traducing all other philosophy as heathenish and profane. But there is no such enmity between God's word and His works; neither do they give honour to the Scriptures, as they suppose, but much imbase them. For to seek heaven and earth in the word of God, (whereof it is John S. Wilkinshttp://www.blogger.com/profile/04417266986565803683noreply@blogger.com0tag:blogger.com,1999:blog-6941151.post-1148874640476297572006-05-29T13:39:00.000+10:002006-05-29T13:50:40.503+10:00Microbial species 4a: monophyly and speciesHere is a nice image that shows that even among eukaryotes, reciprocal monophyly is not always the case for species. It's from a paper in PLOS Computational Biology critical of the DNA Barcoding proposal.Each version shows two species, X and Y. In A, X and Y are reciprocally monophyletic, which means that the coalescent (or last common shared genomic node in the tree, shown by the open stars) is John S. Wilkinshttp://www.blogger.com/profile/04417266986565803683noreply@blogger.com0tag:blogger.com,1999:blog-6941151.post-1148873913992779462006-05-29T13:32:00.000+10:002006-05-29T13:38:34.013+10:00Evolving Thoughts up a treeWell, everybody's doing it (doing it, doing it) so I have to. Yes, if everybody else jumped off a cliff I would too, mum. This is what the HTML tags look like for this site when run through the websitesasgraphs Java Applet. It is also what the mental contents of my my brain look like when viewed through any medium at all.I can't believe Pharyngula's was so tidy. Maybe his HTML is cleaner than John S. Wilkinshttp://www.blogger.com/profile/04417266986565803683noreply@blogger.com0tag:blogger.com,1999:blog-6941151.post-1148863935465307472006-05-29T10:50:00.000+10:002006-05-31T14:53:47.000+10:00State religion encroaching on military freedoms to believeWhile I'm working through the conceptual tangle I've gotten myself in over microbial species. allow me to mention this item from Mike Dunford's The Questionable Authority: apparently the US Army National Cemetery Administration will not permit Wiccans to use a symbol for the headstones of dead veterans.Guys, the reason why there's a separation of church and state in the first place is because of John S. Wilkinshttp://www.blogger.com/profile/04417266986565803683noreply@blogger.com0tag:blogger.com,1999:blog-6941151.post-1148726890595174242006-05-27T20:45:00.000+10:002006-05-27T20:48:10.796+10:00How not to apply evolution to cultureHere is a small piece in the Korea Herald, by Arne Jernelov on how evolution explains cultural excellence. It's all about sexual selection, you see - if you do something that is very hard and very costly, you are attracting mates, and this explains sports, painting, literature and science. It is only coincidental that the author is a scientist (an environmental biochemist). I bet he also plays John S. Wilkinshttp://www.blogger.com/profile/04417266986565803683noreply@blogger.com0tag:blogger.com,1999:blog-6941151.post-1148646818826937012006-05-26T22:30:00.000+10:002006-05-28T01:14:06.026+10:00Microbial species 4: degrees of sexWhen we attempt to apply to organisms that are not obligately sexual (that is, which don't have to have sex to reproduce) concepts that were specified to use with those that are, we have problems. The Recombination Model is one such attempt. Sure, some microbial species exchange genes. Others do it more frequently and more completely. There appears to be a continuum of gene exchange all the way John S. Wilkinshttp://www.blogger.com/profile/04417266986565803683noreply@blogger.com0tag:blogger.com,1999:blog-6941151.post-1148620704031379742006-05-26T15:15:00.000+10:002006-05-26T15:27:35.170+10:00Microbial species 3: Quasispecies and ecologyThe second main approach to a natural conception of microbial species (by which I mean, as opposed to operational, practical or conventional ones, collectively called "artificial" conceptions) is what I will call the Quasispecies Model. According to the concept developed by Manfred Eigen for viral species, a quasispecies ("as-if-species") is a cluster of genomes in a genome space of the John S. Wilkinshttp://www.blogger.com/profile/04417266986565803683noreply@blogger.com0tag:blogger.com,1999:blog-6941151.post-1148522097514563072006-05-25T11:07:00.000+10:002006-05-25T14:23:42.280+10:00Microbial species 2: recombinationThe cluster of genomes of asexual organisms forms what is called a "phylotype" (Denniston 1974, a term coined by C. W. Cotterman in unpublished notes dated 1960; I like to track these things down). Phylotype is a taxon-neutral term, though, that is determined entirely by the arbitrary level of genetic identity chosen. For example, "species" in asexuals might be specified as being 98%+ similarity John S. Wilkinshttp://www.blogger.com/profile/04417266986565803683noreply@blogger.com0tag:blogger.com,1999:blog-6941151.post-1148455603696896292006-05-24T17:19:00.000+10:002006-05-24T17:31:58.843+10:00On microbial speciesOK, this is one of a series of posts in which I will play with ideas that might become a paper.The problem is this: usually we define a species as a group of related organisms that share genes (or a gene pool, which amounts to the same thing). Sometimes we include also ecological considerations (either in the form of natural selection, or in terms of sharing a niche).But many microbial species John S. Wilkinshttp://www.blogger.com/profile/04417266986565803683noreply@blogger.com0