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

Ethanol export dynamics changing

first_imgShare Facebook Twitter Google + LinkedIn Pinterest Just four years ago, more than 80% of U.S. ethanol exports went to Brazil, Canada and the European Union. That has changed significantly by 2015.Exports to the United Arab Emirates (UAE), the Philippines and India experienced the strongest growth in 2014. While the UAE is largely importing U.S. ethanol to blend with its gasoline that is later re-exported, and India is importing for industrial purpose, the Philippines has a blend mandate in place. Domestic production in the Philippines has been unable to meet its 10% blend mandate making imports necessary.Currently, the United States has a 55% market share in the Philippines and the Council is hopeful there is room to capture more. To help nurture this market, the U.S. Grains Council and its partners, Renewable Fuels Association, Growth Energy and USDA’s Foreign Agricultural Service, have planned a busy summer with missions heading to the Philippines and other growing markets like China, Indonesia, India and Japan.last_img read more

Spotted lanternflies a growing concern

first_imgShare Facebook Twitter Google + LinkedIn Pinterest An invasive pest that was initially contained within Pennsylvania has spread to Delaware and Virginia, and insect experts worry the next stop will be Ohio.Spotted lanternflies suck sap from fruit crops and trees, which can weaken them and contribute to their death. Native to China, the insect was first found in the United States in 2014 in Pennsylvania.At this time, spotted lanternflies are still relatively far from the Ohio border. They have been found in the southeastern part of Pennsylvania, near Philadelphia. However, they can be spread long distances by people who move infested material or items containing egg masses.“The natural spread would take a long time, but it would be very easy to be moved through firewood or trees that are being relocated,” said Amy Stone, an educator with Ohio State University Extension.If it arrives in Ohio, the spotted lanternfly has the potential to do serious damage to the grape, apple, hops and logging industries, Stone said.The lanternfly’s preferred meal is from the bark of Ailanthus or tree of heaven, which is typically not intentionally planted but instead grows on abandoned property and along rivers and highways.Compared to the spotted wing drosophila or the brown marmorated stink bug, which seize on fruit and vegetable crops, the spotted lanternfly has a more limited palate so it likely would not do as much damage, said Celeste Welty an OSU Extension entomologist.“Everybody’s fear is any new invasive pest will be like those two. But it seems to me, it’s not as much of a threat,” Welty said.And unlike the spotted wing drosophila and the brown marmorated stink bug, the lanternfly is easy to spot because the adult bug is about 1 inch long and, with its wings extended, about 2 inches wide, Welty said.For now, all that can be done to stem the spread of lanterflies is to stay watchful for their presence and any damage they may inflict. On trees, they zero in on the bark, particularly at the base of the tree. Lanternflies can cause a plant to ooze or weep and have a fermented odor. They can also cause sooty mold or a buildup of sticky fluid on plants as well as on the ground beneath infested plants.An app developed by the CFAES School of Environment and Natural Resources allows users to report invasive species if they suspect that they have come across them. The app, which is called the Great Lakes Early Detection Network, features details about invasive species that people should be on the lookout for.If someone sees a lanternfly, he or she should contact the Ohio Department of Agriculture at 614-728-6201.last_img read more

Jive Software Buys Filtrbox: A Purchase All About The Social Web

first_imgRelated Posts Jive Software has acquired Filtrbox, a Boulder-based startup that monitors the social Web to help clients understand and better participate in online conversations.Terms of the deal were not disclosed.Jive sought a social media monitoring company to bring into its Social Business Software (SBS) platform. The goal is to extend the social footprint of the Jive platform. Jive sees the market becoming far more oriented around conversations on social networks such as Twitter and Facebook. These conversations affect everything from product development to sales strategies. Monitoring is critical to following and capitalizing on the conversation flow. Jive looked at several companies in the space before deciding to approach Filtrbox. The choice came down to the Filtrbox user experience; its collaboration features; the scalable architecture and the social intelligence baked into the product.The Filtrbox architecture may be the greatest value to Jive. Filtrbox Founder Ari Newman said its architecture is a hybrid that leverages the cloud. He would not say much more about it though its business model reflects a cloud based approach. Massive Non-Desk Workforce is an Opportunity fo… alex williams Tags:#enterprise#news#NYT#Products 3 Areas of Your Business that Need Tech Now Services that leverage the cloud effectively let users scale up and down, depending on demand. Many charge on a per use basis. Newman said Filtrbox charges $10,000 per year for up to six users. Customers get unlimited use of the platform.How companies leverage the cloud will determine how they fare in the market. The ability to crunch large amounts of data is vital for understanding the real-time nature of how conversations flow. Jive seems to understand this and appears to be moving more toward a cloud-based strategy.Initially, Jive will market Filtrbox through its Jive Market Engagement solution along side Radian6. Jive and Radian6 formed a partnership back in September. Here’s what Jeremiah Owyang and his colleague, R “Ray” Wang had to say about the partnership.Radian6 and Filrtrbox are essentially in the same space. it is unclear how the relationship between Jive and Radian6 will be affected by the Filtrbox purchase.Filtrbox will be fully integrated into the Jive SBS platform in the second quarter of this year.Need to stay up to date on the ways the web is changing? Read The Real-Time Web and its Future to develop an in-depth understanding of the real-time Web and the thought leaders and companies shaping the market. Based on more than 50 interviews with industry leaders like Chris Messina and John Borthwick and insights into companies like Twitter, Warner Brothers and Nozzl Media, it’s a must read for information technology decision makers, innovators and thought leaders. IT + Project Management: A Love Affair Cognitive Automation is the Immediate Future of…last_img read more

Mobile OS Adoption: A Tale of Two Graphs

first_imgWhen it comes to statistics, it seems that you can find anyone to back whatever opinion you might have. Just yesterday, Android was named the number one smartphone platform worldwide…when you look at shipments. Today, however, we’ve come across a stat that is equally good and bad for everyone involved, because everyone is the same. According to Nielsen,  “the competition between smartphone operating systems is a heated one” with a three-way tie between Blackberry, Android and iOS.“When it comes to the installed base, that is, U.S. mobile consumers who already own smartphones, it is a three-way tie between Blackberry RIM, the smartphone pioneer, Apple’s IOS, which revolutionized the smartphone and popularized mobile apps, and Android OS, the operating system created by Google which has been taking the market by storm,” writes the company on its blog. Take a look at the graph for the three mobile platforms: Here, the image almost looks identical, but with each platform continuing its curve. Android takes the lead among new smartphone owners with 43%, Apple hangs around with 26% and Blackberry rounds up the pack with 20%.What do you think? Will the second image soon stand in place for the first when it comes to mobile OS adoption? Why IoT Apps are Eating Device Interfaces Related Posts Of course, what the company doesn’t note is the obvious trajectories for these three companies. Blackberry is on a continual downslope, Android is on a upslope, while Apple has been hovering in a sine wave fashion around the 30% mark for the past two years. As it notes, however, “Analyzing the preferences of those who purchased a smartphone in the past six months paints a different picture.” Role of Mobile App Analytics In-App Engagementcenter_img Tags:#mobile#Statistics#web The Rise and Rise of Mobile Payment Technology mike melanson What it Takes to Build a Highly Secure FinTech …last_img read more

Inspiration! Roundup of 8 Unique Artisan Profile Videos

first_imgBe inspired by these beautifully shot documentary profiles of passionate artisanal craftsmanship.The following videos celebrate the skilled craftmanship of artisans creating work in an old-world style.  Each of these unique vignettes is a source of inspiration, both in the unusual stories being told and in the way each of the videos was beautifully shot and produced.  Spectacular sound design, editing and cinematography give each video a fresh, impassioned spirit.Great Wooden Boatsby Philip Bloom –  Beautiful process video shot by cinematography trailblazer, Philip Bloom.  The video was shot with the RED Epic using almost all natural light.  Wonderful slow motion shots as well! Shinya Kimura – Motorcycle Engineerby Henrik Hansen – Dynamically shot and edited, this inspiring account of a Tokyo motorcycle maker stirs up the senses!  Shot on the Canon 5D & 7D. Guitar Manby Simon Clark & Alison Farmer – Peter Stevens creates guitars with hand tools in a traditional style.  This voiceover driven profile excels in it’s beautiful simplicity. The Distillerby Made by Hand – This is the first video in a series celebrating the people who create handmade goods.  Follow distiller Brad Estabrooke as he shares his process for creating an artisanal gin. The Mast Brothers – Chocolatiersby The Scout  – Get to know Brooklyn’s Mast Brothers and their chocolate business in this fantastic documentary short.  Shot on the Sony EX1 with Indie Dolly and Zacuto camera supports. Esquivel – Shoesby David Hubert  – See how a pair of handmade shoes is created in this stunning promo.  Interesting sound design and engaging macro photography (Canon 5D MarkII) make for a terrific concept video.Birth of a Bookby Glen Milner – Brilliant profile of the making of a book using traditional printing methods.  Lots of gorgeous macro video work showing this unique process. The Sword Makerby Etsy – In Etsy.com’s ongoing series on artisans, they capture one of the last remaining Japanese swordsmiths at work.last_img read more

REBECCA’S GDO POSTCARD FROM THE EDGE…

first_imgIn the second installment of our behind the scenes look at the life and times of the Nation’s Game Development Officers, the Northern Territory’s Rebecca Houston delivers her “Postcard from the Edge” from Australia’s Top End.Last month Queensland’s North Queensland GDO Glenn ‘Richo’ Richardson was featured, this month, Rebecca ‘Chewbeckker’ Houston gives us a sneak peak of her life as a GDO in “The Territory”.Rebecca Houston is promoting Touch Football in some of Australia’s most remote communities, and loving it. The 27-year-old has been in the Game Development Officer role for a little over a year, having moved to Darwin from South-East Queensland when her boyfriend Luke joined the Northern Territory Police Force. Even though she is still relatively new to her job, Houston has an accomplished background in Touch Football.Houston played with Crushers in the Women’s Open SEQTL from 1999-2005, and the Gold Coast Sharks in the National Touch League from 1998-2005. She won an NTL Open Mixed title with ‘Sharkies’ in 2001, and in 2004 she represented the Queensland State of Origin Mixed Open team. Renowned as one of the best ‘finishers’ in the business, the speedster has played a pivotal role in the Barbarians Women’s Open Team’s surge into the semi-finals at the National Touch League for the last two years and continues to prove her mettle under the pressure at the Elite level.The bubbly and dedicated Redlands girl has adjusted well to life as a GDO.Initially moving away from her close knit family and the bright lights of Brisbane was a big adjustment, but the positive and enthusiastic extrovert jumped at the chance to make a career out of the game she has played since she was a teenager in the local Redlands competition.Rebecca has made friends easily and impressed all those around her with her eagerness to work, and willingness to embrace the people and lifestyle in the Territory.Northern Territory Branch Manager Isobel Appo is one person who has keenly observed Rebecca’s progress and is full of praise for the GDO.“Rebecca has done very well. Her AusTouch programs and Junior initiatives have gone over well in the Territory. She has a great rapport with the kids, and her hard work, sense of humour, and genuine desire to help people shines through. She has earned a lot of respect and acceptance in the communities in which she works,” Mrs. Appo said.Rebecca is doing a great job passing on the skills she has honed over her years at the top level to kids in communities that have often never even heard of any kind of football other than AFL. Rebecca recently visited Kalkarindji, Yarralin and Timber Creek in the Katherine Region to run Austouch clinics for 60 children over three days. “By visiting the communities, you get a lot of satisfaction from going out there and teaching them a sport that they’ve never really seen before. Most of the time out in the communities they’ve only seen AFL, so they play AFL. They’ve seen a little bit of Rugby League on the television and that’s about it. So your biggest battle is getting them to pass the ball backwards. Once you get them passing the ball backwards they start to understand what they’re doing and they start to get really excited, it’s a good feeling,” Houston said. Rebecca enjoys the travelling that is part of her Game Development Officer duties. She said she is always welcomed into any community that she visits and appreciates the laid back lifestyle on offer in the Territory. “Everyone loves playing sport, it doesn’t matter what sport it is, people get into it. The kids are always smiling and make you feel so welcome. There is so much natural athleticism and skill as well in the Indigenous communities, and of course it’s very rewarding to give people opportunities that they might not otherwise get in the remote localities,” Houston said.Having covered several communities across the Top End, Houston said she has noticed something about the kids from rural communities compared to the Darwin-based children. “They’re a lot less cheeky!” Houston said with a smile. In June Houston will be travelling to isolated communities in remote Arnhem Land. “I’ve been up to Gove before, but I haven’t been to see their community sport teams so that’ll be good.” Houston said.Houston is dedicated to getting more children involved in Touch Football. Without her work developing Touch Football at the grassroots level the game in the Northern Territory would be struggling for a base. A junior competition that has been established in Darwin is evidence of her work.“We originally had four teams and this year we’ve got eight teams, from under-13s to under-16s. Next year we hope to grow it again so it’s definitely getting bigger. The main thing I want to do is just keep growing it for the children and getting them involved. If we don’t get the kids involved then our sport doesn’t grow and we cease to exist.” Rebecca said.By the end of this year Houston is planning to have a junior competition established in the Katherine region. Her Austouch clinics will hopefully have planted the Touch Football seed in some of tomorrow’s stars. But Houston knows that the kids can only develop their Touch Football skills if competitions are set up for them.“I’m going down to Katherine in August. They are starting a school competition, so hopefully they can get a little bit more interest there for their club so that they can start a junior competition themselves. It would be very rewarding. It is good to say that you’ve started something outside of Darwin, it means that you’re not just focusing on one area and that’s a good outcome for the sport.” Houston said.The Northern Territory is going ahead in leaps and bounds, with the formation of several junior competitions, AusTouch programs, and next month’s NT Junior Development Camp set to further consolidate the Top End’s position as a leading light for junior development in Touch Football in this Country.With the rapid growth of the sport in junior ranks in the Territory, Rebecca Houston is sure to have her hands full for some time to come.last_img read more

Market Challenges Cut Milahas Quarterly Earnings

first_imgzoom Qatar-based marine transport and logistics conglomerate Qatar Navigation (Milaha) has seen its net profit drop by some 33 percent for the first quarter of the year ended March 31, 2017.Namely, the company ended the quarter with a net profit of QAR 236 million (USD 64.8 million), significantly lower than QAR 352 million (USD 96.6 million) reported in the same period in 2016.Milaha’s operating revenues also decreased to QAR 648 million for the first three months of the year, compared to QAR 767 million reached a year earlier, representing a decrease of 15 percent, while its operating profit dropped by 27 percent to QAR 185 million from QAR 256 million in the respective periods.“We are continuing to face the same market challenges as in 2016, but we remain confident in our ability to drive growth and capitalize on new opportunities while exercising financial discipline,” H.E. Sheikh Ali bin Jassim Al Thani, Chairman of Milaha’s Board of Directors, said.Additionally, Milaha Maritime & Logistics’ net profit declined by QAR 14 million, mainly as a result of continued rate pressure in the company’s container shipping unit, while Milaha Gas & Petrochem’s net profit plunged by QAR 46 million mainly driven by a global downturn in shipping rates that impacted all major sectors.Similarly, Milaha Offshore reported a drop in its profit as well, which decreased by QAR 25 million, with QAR 22 million of that related to impairments.“Given the difficult environment we are working in, we posted solid operational results. We will continue moving ahead with our multi-year growth strategy to build a stronger and more sustainable business,” Abdulrahman Essa Al-Mannai, Milaha’s President and CEO, said.last_img read more