Darwinian Phylogenists Do the Funky Chicken

first_imgAfter all this reluctant criticism, Ronquist manages to find something to compliment, in closing:Although it is easy to criticize a book that tries to cover so much, in this case doing so is like throwing stones in a glass house.  Every phylogeneticist can probably find some points they understand better than Felsenstein, but I can think of no one who could provide a better and more comprehensive summary of the current methods for building evolutionary trees.  It will be a long time before there will be a comparable book; perhaps the field is now growing too fast for there to ever be one.  The publication of Inferring Phylogenies is a milestone for evolutionary biology in general and phylogenetics in particular.1Fredrick Ronquist, “Phylogenetics: A Broad Look at Tree-Building,” Science Volume 303, Number 5659, Issue of 6 Feb 2004, pp. 767-768.Sometimes you have to just stand back and let the Darwin Party members do it to each other.  Does anyone have confidence in evolutionary tree-building after this indecent exposure?  When an expert in the field omits significant parts of the story (why? because he feels they are invalid?), characterizes it as a battle over the most prestigious authorities, and describes one of the chief methodologies to be as mystical as casting chicken bones and using magical incantations, what are we supposed to conclude?  Don’t they realize it’s confusing to the peasants when the shamans are exorcising one another?For more on phylogenetic tree-building, see 11/26/2002 and 06/13/2003 entries, and follow the Chain Links on “Genes and DNA.”(Visited 10 times, 1 visits today)FacebookTwitterPinterestSave分享0 Fredrik Ronquist is active in phylogenetic systematics, the art of drawing evolutionary trees from DNA comparisons.  And he admires Joseph Felsenstein, an “icon in the field.”  But when he reviewed Felsenstein’s new book, Inferring Phylogenies (Sinauer, 2004) in the Feb. 5 issue of Science,1 he had mixed feelings about the author’s biases and his choice of humor.    Ronquist has much to praise about the iconic master’s work, concluding “I can think of no one who could provide a better and more comprehensive summary of the current methods for building evolutionary trees.”  Nevertheless, his criticisms are revealing about the state of this art:What is it about, anyway?  The book seems to omit a rather important part of phylogenetic systematics:What I found most surprising about the book is that it is not at all about systematics.  Readers will find no coverage of many basic concepts in phylogenetic systematics–such as synapomorphy, symplesiomorphy, sistergroups, outgroups, and monophyly.While Felsenstein covers many subjects like “techniques for statistical testing of evolutionary trees,” uses of phylogenies, and “nearly every quantitative approach to tree-building that has been tried,” Ronquist is most surprised there is no coverage of these important terms and concepts in a 684-page definitive treatise by an expert in the field.No help on classification.Another topic that many phylogenetic systematists consider important but the book glosses over is how one should convert phylogenetic trees into classifications of organisms.  According to Felsenstein, “The delimitation of higher taxa is no longer a major task of systematics, as the availability of estimates of the phylogeny removes the need to use these classifications.”  Even a cursory look at the literature would prove that many active systematists disagree; indeed, the discussion of classification and naming principles seems to be as vigorous as ever.  This neglect of the classification issue is all the more remarkable because Felsenstein devotes an entire chapter–one of the more original and important contributions in the book–to the drawing of trees (specifically, to algorithms for drawing diagrams of trees).  After all, drawing trees is just another way of communicating the results of a phylogenetic analysis.  Often a diagram is better, but sometimes a name is necessary.  I do not think we will ever see papers with titles like “The biology of .”Controversy is bitter.In a field that has been plagued by outrageously bitter controversy, the book is remarkably balanced on the whole.  For example, consider Felsenstein’s summary of the debates on statistical inconsistency.  It reveals when parsimony is inconsistent and suffers from “long-branch attraction,” but it makes no secret of the fact that likelihood methods can also be misled by similar phenomena when the model used for inference is incorrect.  The attempt to provide balanced coverage probably will not stop ardent parsimony advocates from being disappointed.This is because Ronquist feels Fenselstein was unfair in his choice of algorithms to exalt, and ones to ignore.The Bayesian Funky Chicken.  “The book’s coverage of Bayesian inference of phylogenies is surprisingly short and critical,” Ronquist complains.  Bayesian inference is a fancy mathematical form of educated guessing by applying values to likely causes, but it suffers from GIGO: garbage in, garbage out.  Ronquist disagrees with the author’s criticisms, and is not amused by the joking description Fenselstein gives to this technique as applied to evolutionary tree-building:I find the author’s complaints about prior distributions partly misdirected.  For instance, Mau and Newton’s prior on clocklike trees is described as “technically inadmissible” and “an impossible distribution” because it is an improper probability distribution.  But improper priors are often unproblematic in Bayesian inference, and there is an entire school of “objective Bayesians” who routinely use them.  The comment on the choice of proposal distributions is more funny than helpful: “At the moment the choice of a good proposal distribution involves the burning of incense, casting of chicken bones, use of magical incantations, and invoking the opinions of more prestigious colleagues.”last_img read more

Beware of Starstuff

first_imgStars can be dangerous.  They spew out deadly particles, unless you are protected from them in a safety bubble – like Earth has.  The Earth’s magnetic field and atmosphere only let in the life-giving part of sunlight.  Studies of other stars, and our own moon, show that things could be far worse.Record flare:  A little star 16 light-years away in Lacerta just went whoosh!  On April 25, it “unleashed what is considered the brightest burst of light ever seen in the universe from a normal star,” reported Space.com.  If that is normal, be glad our sun is abnormal (see 03/07/2007).  A NASA scientist said, “Flares like this would deplete the atmospheres of life-bearing planets, sterilizing their surfaces.”  Science Daily called this star “the mouse that roared.”  For an artist conception of a planet near a roaring star, see Astronomy Picture of the Day for 5/21/2008.Electric dust:  Future moon astronauts will have new challenges only briefly experienced by the Apollo crews.  NASA Science reported that the moon flies through Earth’s magnetotail once a month.  That’s a stream of charged particles from the sun that flows around Earth’s magnetic field and hits the full moon.  The Apollo astronauts never felt the full brunt of this stream.    Physicists believe that electrons from the sun can charge moon dust and make it levitate above the surface.  Not only that, it can start moving from one hemisphere to the other in a kind of lunar wind, depending on charge differences.  The Apollo astronauts learned a little about the hazards of moon dust.  It scratched visors, got into everything, stuck like glue and smelled like gunpowder.  Future astronauts living through magnetotail crossings may get the full brunt of hazards that electrified dust will throw at them.Question: if dust like this has been dancing around the moon for billions of years, would it alter the appearance of lunar features?Our waterful, airful world is such a blessing, we often take it for granted.  Skeptics can argue all they want that if it weren’t this way we wouldn’t be here arguing about it.  Don’t be such an ingrate.  Thank God for that blue sky with its ozone and magnetic shield.  It’s not just a necessity for survival; it’s a blessing that didn’t have to be.(Visited 12 times, 1 visits today)FacebookTwitterPinterestSave分享0last_img read more

South Africa, Malaysia sign science memorandum

first_img29 April 2014 A memorandum of understanding on science and technology co-operation was signed by South Africa’s Minister of Science and Technology, Derek Hanekom, and Ewon Ebin, the Malaysian Minister of Science, Technology and Innovation (STI), the Department of Science and Technology said in a statement last week. “The agreement is aimed at enhancing socioeconomic development in both countries through STI co-operation, and will provide a tremendous opportunity for both countries to share knowledge and experience,” the department said. Hanekom said the agreement would strengthen human capital development through the initiation of joint research projects and programmes between role players in the science and technology communities of both countries. Ebin described the agreement as “a strategic first step in fostering a smart partnership between our countries, reinforcing our commitment to promoting and developing co-operation in the field of science and technology”. “It has created a win-win situation for Malaysia and South Africa in terms of human resource development, technological and research development, economic growth and advancing ICT,” he said.Economic transformation Malaysia has been successful in transforming its agriculture-based economy since its independence in 1957, the department said. Over the years, the emphasis has shifted from rubber, tin and palm oil, to biotechnology, nanotechnology, pharmaceuticals and other high-tech industries. It has given priority to information and communication technologies. South Africa is on a similar trajectory, as it moves from a resource-based to a knowledge-based economy, the department said. “Like South Africa, Malaysia is one of the most bio-diverse countries in the world. It is a leader in bio-prospecting, and has had some success in commercialising local research results, so there are opportunities for knowledge sharing in this area.” Both South Africa and Malaysia identified specific areas of co-operation for discussion at the first South Africa-Malaysian joint committee meeting in Pretoria last week. The meeting was aimed at developing an action plan for bilateral co-operation over the next two years. Areas of focus include Antarctic research, ICT, energy security, innovation for inclusive development, sustainable human settlements, innovation and commercialisation, astronomy and the bioeconomy. The Council for Scientific and Industrial Research’s Meraka Institute, a unit focused on ICT, and its Malaysian counterpart, MIMOS, also signed a memorandum of agreement last week. The co-operation between the two institutes will include exchange programmes related to technology development and commercialisation. SAinfo reporterlast_img read more