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Tree of Life in the Genes? Not Yet

first_imgNow that we have hundreds of animal genomes in the bank (the GenBank), is Darwin’s tree of life becoming visible?  If the image is present, it is extremely weak, said Michael J. Sanderson of the Department of Ecology and Evolutionary Biology at University of Arizona.  Writing for Science,1 he showed that only a small fraction of genomes show even minimal support for a phylogenetic (evolutionary) tree.    His report was accompanied by a circle diagram with 876 taxonomic orders represented by small rectangles along the rim.  He shaded blue those that contained a minimal phylogenetic signal, and yellow those that did not.  The entire circle was almost all yellow.  One has to look hard for blue rectangles.  This is after “improvements in algorithms and high-performance computing technology have dramatically increased the scale of feasible phylogenetic inference; and unconventional sources of data, including whole genomes, expressed sequence tag libraries, and barcode sequences, have altered the landscape of large-scale phylogenetics with an infusion of new evidence.”  The distribution of species in GenBank (the database of gene sequences) is remarkably broad, he said.  If there was ever a time to see Darwin’s tree of life come to light in the genes, it should be now.    In light of the flood of evidence, how can the phylogenetic signal be so weak?  “Construction of a high-resolution phylogenetic tree containing all eukaryotic species in the database is a grand challenge that is substantially more tractable than inferring the entire tree of life, but to succeed, strategies will have to overcome serious sampling impediments,” he said.  “Quantifying the distribution and strength of phylogenetic evidence currently in the database is a prerequisite for this effort.”  So that’s what he set out to do.  And that’s what turned out to look pretty weak.    Sanderson looked at 1127 higher taxa for evidence of a phylogenetic signal.  He had to set his standards pretty low.  He figured if there were at least four operational taxonomic units [OTUs] that were similar between two taxa, for instance, then an evolutionary relationship could be inferred.  His choice of tree-building software also was rigged to produce a “fast but conservative” result.  “Any clade in the resulting tree will have had at least 50% bootstrap support in maximum parsimony ‘fast’ bootstrap analyses with two different sequence alignment algorithms,” he explained.2  “Although this protocol biases the confidence assessment slightly downward, the bias is small.”  Is that a matter of human opinion?    There were more hints the standards were loose.  “For comparative purposes and to aid in the visualization of results, an arbitrary cutoff value of 1.5 was selected as minimal phylogenetic support,” he continued.  “This is equivalent, for example, to the information content of two independent loci, each resolving three-quarters of clades to at least a bootstrap value of 51%.”  This sounds close to the tipping point for inferring no relationship at all.    After manipulating his protocols, summing, and averaging, the evolutionary signal came out surprisingly low, even with the loose standards.  Here is the upshot:Among individual OTUs [operational taxonomic units], Homo sapiens had the maximum support value of 293.9, but the distribution of scores had a long tail leading to 6402 OTUs with no support at all (most of which, 6079, simply were not found in any phylogenetically informative clusters).  The top 10 were all mammals; the top 25 were mammals, angiosperms (tomato, potato, tobacco, rice, and wheat), Drosophila melanogaster, and Drosophila simulans, all with support scores above 60 units.  Of the 171,703 OTUs for which scores were calculated, only 12% achieved minimal phylogenetic support.  The mean support was 0.84, less than the equivalent of each taxon being found in at least one well-resolved and -supported phylogenetic tree.So only 12% reached the already-low bar for evolutionary signal – that means 88% did not.  At the level of orders, the scores were skewed even lower.  The maximum score was 10 in primates, and 0.0 in 75 other orders.  He tried to draw an inference between orders that were species-rich and species poor, but many of the orders outside of primates and arthropods did not even reach minimal phylogenetic support regardless of species richness.    So what did Sanderson conclude from his investigation of the strength of the signal of Darwin’s tree of life in the genes?  Basically, he said more work is needed.  “An accurate high-resolution phylogeny will require substantial increases in sequence data to bring that score to a level comparable to that of the best-supported higher taxa.”  He thinks more data targeted at the right clusters of genes might help.  Better algorithms in the tree-building software might help, too.  Maybe the signal will become clearer when genes from undiscovered species in poorly-resolved branches become available.  “In the meantime, sampling protocols guided by quantitative assessments of the phylogenetic distribution of data will improve the efficiency of emerging phylogenomic strategies for building the tree of life of known organisms.”  Translated, this almost sounds like he is claiming that better data-massaging methods might just begin to help develop strategies for beginning to find ways to begin to visualize Darwin’s tree.  In colloquial terms, it’s going to take a lot of work to fix this picture.1.  Michael J. Sanderson, “Phylogenetic Signal in the Eukaryotic Tree of Life,” Science, 4 July 2008: Vol. 321. no. 5885, pp. 121-123, DOI: 10.1126/science.1154449.2.  For more on the meanings of bootstrap, maximum parsimony and other phylogenetic tree-building terms, see the entries from 04/26/2008, 01/26/2008, 03/30/2004, 10/15/2003, and 11/06/2002.Charlie’s hanging from his own tree.  Why give him more rope?  It will only make the carcass horizontal instead of vertical.(Visited 23 times, 1 visits today)FacebookTwitterPinterestSave分享0last_img read more

Dan Uetrecht, June 8

first_imgShare Facebook Twitter Google + LinkedIn Pinterest Things are going really well. The crop looks really good. I think we are one inch of rain away from having a perfect spring. We are a little dry and if we could just get a good soaker it would be perfect. Hopefully we’ll get it. We are supposed to heat up today. The weather has been really nice with some 70- and 80-degree days with low humidity. Now we’re supposed to get hot and humid and that should kick up some thunderstorms.For emergence it has been perfect. We didn’t have any beating rains. Everyone down this way said that this year was as good for getting the crop out of the ground without any issues as they have ever seen. The crop looks healthy.Around Wilmington and up towards Court House they have been getting some rains and things are really going. We could use some rain but we are still doing well.I think we’ll be running wheat in two or three weeks. We put fungicide down to protect it. I did find a little head scab in our wheat but not much. I think it will be a good crop but not a great crop. Two months ago I said there was no way we’d be running wheat in June. Now I think we will be. We hope to get second cutting hay done before we start baling straw.I plant about 50 acres of cover crops after wheat and the rest of the wheat acres will go to double-crop beans. The last couple years, double-crop beans have been phenomenal down here. We need late rains and a late frost for a good double-crop situation.This corn has gotten so big. I went out today and the corn is pushing waist high. We got done sidedressing last week and we just finished post- spraying all of our soybeans. We had to come back on all of our beans because we had problems with grass. We got a good burndown on the broadleaves.The markets have taken a little hit and this is the timeframe where you can get one more spike up or it could be on the downward spiral and it will be interesting to see what prices do in the next couple weeks.last_img read more

Consumer Electronics 2.0: MIT’s Henry Holtzman on The Internet of Things

first_imgWhy Tech Companies Need Simpler Terms of Servic… Related Posts Internet of Things Concepts & IssuesI asked Henry Holtzman what other concepts are interesting him currently, as well as what issues are still to be overcome in the emerging Internet of Things. He talked about using sensors as an “additional sense,” by putting a tag reader on people. Not dissimilar to another Media Lab project we wrote about recently, a wearable internet system which aims to become a “sixth sense.” Holtzman said that possible uses for sensors on people include: finding objects (for example your keys), raising an alert (e.g. a safety warning), a memory assist device, being a bridge between what you do in the real world and what gets recorded on your social network (e.g. Facebook updating when you’re in certain locations; which we mentioned here). As for issues: while currently light and temperature sensors are popular, Holtzman thinks that we need to do better job with location. But this is where RFID comes in.One big issue that Holtzman is concerned about is identity. He told me that mobile phones that interact with objects using NFC (Near Field Communication) will need to work out how to federate around the same ID for a user. This is perhaps similar to the identity issues that the browser-based Web has.Privacy and security are two other important issues that Holtzman has been focusing on of late.It was great to speak with Henry Holtzman – someone with extensive experience, both theoretical and practical, in the Internet of Things. Let us know your own thoughts in the comments. Top Reasons to Go With Managed WordPress Hosting richard macmanus A Web Developer’s New Best Friend is the AI Wai…center_img During my visit to MIT earlier this year I met up with Henry Holtzman, Chief Knowledge Officer of the MIT Media Lab. We discussed the Internet of Things, which Holtzman has been actively involved in since the 90s. Holtzman said that consumer apps for Web-connected objects are becoming more common; he refers to this as an emerging “ecology of devices.” There are many real world objects being connected to the Internet nowadays, he said, and they are beginning to act in concert. Read on to find out which Internet of Things products have most impressed Henry Holtzman lately, plus we explore some of his own projects.Editor’s note: This story is part of a series we call Redux, where we’ll re-publish some of our best posts of 2009. As we look back at the year – and ahead to what next year holds – we think these are the stories that deserve a second glance. It’s not just a best-of list, it’s also a collection of posts that examine the fundamental issues that continue to shape the Web. We hope you enjoy reading them again and we look forward to bringing you more Web products and trends analysis in 2010. Happy holidays from Team ReadWriteWeb!I started off by remarking that the Internet of Things is ramping up in 2009. Holtzman replied that it’s been many years in the making – for example he did a project back in 1997 involving putting RFID tags onto Pokemon figures. Indeed Holtzman created a commercial company in 1998 to output Internet of Things products. Consumer Electronics 2.0A Wired article from February 2000 outlines how Holtzman founded Presto Technologies in 1998, with fellow MIT Lab professors Andrew Lippman (see our recent post featuring Lippman) and Michael Hawley. The Presto network embedded RFID tags in objects. It was an early version of Internet of Things. The vision for Presto was to make it an e-commerce tool – “products become roving portals for the companies that make them,” according to the 2000 Wired article. While it was too early for that vision to transpire fully, Presto is still operating. One of its current products, PrestoPass, allows consumers to make purchases “by simply waving a card, key tag, or even a wristwatch.” Nowadays Holtzman refers to this trend as “consumer electronics 2.0.” He cites an MIT spin-off company, Ambient Devices, as one to watch in this area. One of their products is the Ambient Clock, which can hook up to your Google Calendar.Henry Holtzman’s Favorite 2009 ProductsAs we’ve been reporting here on ReadWriteWeb this year, there are plenty of Internet of Things products making their presence felt in 2009. I asked Holtzman which products from the current era have particularly impressed him? He replied that he really likes Violet, the company behind the Nabaztag (a cute robot rabbit that can deliver anything from ambient information, through lights and sounds, to verbal information). We reviewed Violet back in May. Tags:#Features#Internet of Things#NYT#Trends#web Touchatag (formally known as Tikitag) is another company to have impressed Holtzman. As we wrote in February, Touchatag allows you to program your own RFID tags so that they can do anything you want. Holtzman said that he’s been very impressed by the decisions the company has made, for example using adhesives. He also likes their ‘web 2.0 savvy’ – they host everything, but let the users create the content. 8 Best WordPress Hosting Solutions on the Marketlast_img read more

Two U.P. constables arrested in Pilakhuwa custodial torture case

first_imgMore than six weeks after a security guard Pradeep Tomar allegedly died because of torture at a police post in Pilakhuwa town of Hapur district, two constables have been arrested.Also read ‘Custodial’ death sparks tension in U.P. town“Manish Singh and Sonu Kumar were arrested on Wednesday. They were produced before a magistrate and have been sent to jail,” said Rajesh Kumar Singh, Circle Officer, Hapur (city), who is investigating the case.He refused to comment on the constables’ role in the case. “It is still a matter of investigation.” He said two other accused, SHO Yogesh Baliyan and sub-inspector Ajab Singh, who were under suspension, were still on the run.Deputy Superintendent of Police Santosh Mishra, who was also named in the FIR and transferred to Garhmukteshwar after the incident, has already been given a clean chit in the case.Mr. Tomar, 35, died on the intervening night of October 13 after he was picked by the police from the Chhijarasai toll booth in Pilakhuwa. The police had claimed he was picked up for questioning in connection with a murder case. However, Mr. Tomar’s family, including his 10-year-old son who was allegedly present when his father was picked up, claimed that he was tortured by the police personnel.Based on the complaint of the deceased’s brother Kuldeep, an FIR was registered against six police personnel under stringent Sections of the Indian Penal Code.last_img read more

Heat complete another season series over Mavs with 95-88 win

first_imgNEXT BLOCK ASIA 2.0 introduces GURUS AWARDS to recognize and reward industry influencers Read Next Trending Articles PLAY LIST 00:50Trending Articles00:59Sports venues to be ready in time for SEA Games01:27Filipino athletes get grand send-off ahead of SEA Games01:29Police teams find crossbows, bows in HK university01:35Panelo suggests discounted SEA Games tickets for students02:49Robredo: True leaders perform well despite having ‘uninspiring’ boss02:42PH underwater hockey team aims to make waves in SEA Games01:44Philippines marks anniversary of massacre with calls for justice01:19Fire erupts in Barangay Tatalon in Quezon City LATEST STORIES View comments The Mavericks hit the road for four games over nine nights, starting Wednesday at Phoenix. MOST READ Harrison Barnes had 20 points and Wesley Matthews 19 for the Mavericks (16-35), who have dropped four games in a row and seven of eight overall.This is the 14th time in their 30 seasons that the Heat, who beat Dallas 113-101 at home on Dec. 22, have swept the regular-season series. These teams twice met in the NBA Finals, with Miami getting its first championship in 2006 and the Mavs winning their only title in 2011.FEATURED STORIESSPORTSWATCH: Drones light up sky in final leg of SEA Games torch runSPORTSLillard, Anthony lead Blazers over ThunderSPORTSMalditas save PH from shutoutMiami (29-21) led 51-41 when Josh Richardson hit a 3-pointer with 41 seconds left in the first half. But the Mavs trimmed that in half when rookie Dennis Smith Jr. made a defended buzzer-beating 3-pointer from about 27 feet to make it 51-46. James Johnson had a hand up in front of Smiths’ face with Whiteside coming from the side.Richardson had 14 points for the Heat, while Gragic had 13 and Kelly Olynyk 12. Brace for potentially devastating typhoon approaching PH – NDRRMC Typhoon Kammuri accelerates, gains strength en route to PH 2 ‘newbie’ drug pushers fall in Lucena sting Kammuri turning to super typhoon less likely but possible — Pagasa Smith scored 14 for Dallas, and Nowitzki 10.TIP-INSHeat: Whiteside had his 18th double-double this season. … For the second game in a row, Miami won to complete a season sweep. The Heat beat Charlotte on Saturday night to complete a four-game series sweep. … The only team the Heat have swept more in the regular season is Sacramento at 15 times. The lost to the Kings already this season.Mavericks: Nowitziki has now played 49,941 minutes, only 59 shy of becoming only the sixth player in NBA history with 50,000 career minutes. Elvin Hayes had exactly 50,000 career minutes, and former Mavs guard Jason Kidd is fourth on the league’s career list at 50,111. “It’s a very staggering accomplishment and done with such grace and such little hype that it’s probably very much taken for granted,” coach Rick Carlisle said. … G J.J. Barea missed his second straight game because of a left oblique strain.UP NEXTMiami still has three games left on its four-game trip, and play Cleveland on Wednesday night.ADVERTISEMENT Giannis, Delly spark Bucks in 107-95 win over 76ers Miami Heat center Hassan Whiteside (21) works against Dallas Mavericks guard Wesley Matthews (23) for a shot-attempt in the first half of an NBA basketball game Monday, Jan. 29, 2018, in Dallas. (AP Photo/Tony Gutierrez)DALLAS — Hassan Whiteside had 25 points and 14 rebounds as the Miami Heat completed another season series sweep of the Dallas Mavericks with a 95-88 victory Monday night.The Heat never trailed after Goran Dragic had a steal that led to Tyler Johnson’s tiebreaking 3-pointer to make it 38-35 just under 4 1/2 minutes left in the first half. Their lead went to double-digits again after Whiteside had consecutive baskets midway through the third quarter.ADVERTISEMENT John Lloyd Cruz a dashing guest at Vhong Navarro’s wedding Globe Business launches leading cloud-enabled and hardware-agnostic conferencing platform in PH Don’t miss out on the latest news and information. Slow and steady hope for near-extinct Bangladesh tortoiseslast_img read more