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

Reflections on “Communicating Effectively During Transitions” Webinar

first_imgDr. Patty Stewart Griffith is a licensed clinical psychologist who has worked for more than 26 years in Los Angeles and Minneapolis providing mental health services ­ and also direct psychological services to hospitals, human service organizations, and the military. She has provided mental health services for the past 23 years to PICA Head Start, which serves 2500 children and families a year. She also has provided direct ongoing mental health services for U.S Military service members for the past 7 years. by Patty Steward Griffith, PsyD, MA, LPSometimes I feel that as mental health providers we are often out of breath, running to catch up with the ever changing and dynamic needs of service members and their families. And, although each military family is different and special, broader themes emerge in our work with the military culture that could best be explored through the research of social scientists in order to better serve our military families.The August 18, 2015 MFLN Family Transitions webinar “Communicating Effectively During Transitions – Managing Turbulence and Dilemmas” with Steven Wilson and Leanne Knobloch is a prime example of the investigative work being conducted that offers a contextual understanding for common challenges faced by service members and their families. Especially relevant for mental health providers was the methodology of the research. This webinar was beneficial in that participants were able to walk away with concrete data and tools for their toolbox to support better communication during transitions. The strategies shared for achieving meaningful and productive communication are helpful to both families and practitioners..One resource that was shared, VA Coaching into Care, seems to be an excellent resource, because bringing in a third party to navigate the VA health care system can help families avoid the potentially painful conflict of trying to coax a resistant service member into unwanted treatment. The social stigma that surrounds asking for mental health support still exists within the military culture. This a complicated dilemma and understandable to individuals serving in the military. Many military men and women would rather confide in their unit buddies about mental health issues, than speak to a stranger who may or may not “get it.”In my experience when working with military families as a mental health provider, through the Yellow Ribbon Program and then with rotational work with the military, I have found that chaplains are incredibly helpful and important in easing the transition for our military men and women to find their way to civilian or military behavioral health help. The chaplains are trusted and quite often the first responder for an individual’s mental health issues.Outside of the somewhat protective bubble of the Yellow Ribbon events, providers working with trusted military individuals are essential for creating strong and helpful relationships with families. I have worked with some remarkable women and men of military families within communities who have quietly been providing excellent support and services to military families for decades. They have been extraordinary role models and teachers. The military community in outstate rural areas often depend upon the expertise and wisdom of these individuals.I have worked on the clinical side of the psychological service spectrum for more than 20 years. Since 2009 I have worked with other mental health providers at innovative Yellow Ribbon programs events nearly every weekend in a 5 state area. We provided confidential support and also trained service members and families about post deployment issues, children and deployment, effective communication, the new normal, predeployment preparation, strong bonds couples’ work and more. These workshops served as conversation starters and provided useful shared information as well. This has been a casual and effective way to provide services to interested families and individuals. Having the communication data from this webinar would have been ideal then, and will now be a good addition to workshops, and for therapeutic work with military families.Something that Steven Wilson spoke about in regard to clear and thoughtful communication with a family member or provider talking to a post deployment service member was the statement, “I can’t ever know what you have gone through.” . This really resonated with me. This statement is both honest and somewhat open ended. Sometimes this kind of comment will pave the way for more conversation in a relationship or therapy session. It is, without being prying or judgmental, a neutral statement that can promote better communication and potentially develop trust with the family member or provider.At the end of the day, having excellent care for military families with sound, research-based strategies is what I believe mental health providers strive to offer. The research presented in this communication webinar supports this vision.last_img read more