Darwin Can’t Find His Tree of Life

first_imgThe “tree of life,” a branching pattern of evolutionary diversification, was the only illustration in Darwin’s Origin of Species.  In 1859, it only existed in his imagination as he speculated, with only circumstantial evidence based on similarities, that all living things descended from a common ancestor.  The fossil record did not show such a tree.  Darwin expected the record would be filled in by subsequent discoveries (but cf. 04/23/2006).  He could not have anticipated the revolution in genomics of the 20th century.  Neo-Darwinists met these discoveries with great anticipation that Darwin’s tree of life would now become visible in the genetic codes impressed in the cell of every organism.  Richard Dawkins predicted in A Devil’s Chaplain (2003, p. 272),…there is, after all, one true tree of life, the unique pattern of evolutionary branchings that actually happened.  It exists.  It is in principle knowable.  We don’t know it all yet.  By 2050 we should – or if we do not, we shall have been defeated only at the terminal twigs, by the sheer number of species.We are now at a stage where enough data have been published, including complete genomes of dozens of plants and animals, such that an assessment is now possible to see if a tree is coming into focus.  In addition, we have decades of comparative studies of proteins from different organisms.  A status report of sorts was published this week by Antonis Rokas and Sean B. Carroll in PLoS Biology.1  Though they began with Dawkins’ optimistic prophecy, the news is not good.  They see multiple bushes, not a tree.  These two evolutionary biologists admit that not only is a tree pattern indecipherable, it may never become visible, even as more data are added:Genome analyses are delivering unprecedented amounts of data from an abundance of organisms, raising expectations that in the near future, resolving the tree of life (TOL) will simply be a matter of data collection.  However, recent analyses of some key clades in life’s history have produced bushes and not resolved trees.  The patterns observed in these clades are both important signals of biological history and symptoms of fundamental challenges that must be confronted.  Here we examine how the combination of the spacing of cladogenetic events and the high frequency of independently evolved characters (homoplasy) limit the resolution of ancient divergences.  Because some histories may not be resolvable by even vast increases in amounts of conventional data, the identification of new molecular characters will be crucial to future progress.This frank admission by two believers in common ancestry demonstrates that molecular genetics has not delivered the hoped-for pattern: “Obtaining an accurate depiction of the evolutionary history of all living organisms has been and remains one of biology’s great challenges.”    In addition to the problem of homoplasy (convergent evolution, or the independent origin of similar traits), the authors point to unexpected groupings that came out of molecular studies.  One study resulted in a grouping of “strikingly different mammals including elephants, aardvarks, manatees, and golden moles” in the same clade.  The pace of change presents another problem: some molecular events were explosively rapid, while others remained undisturbed (conserved) for hundreds of millions of years.  Opposite conclusions are sometimes reached depending on the method used.  Rokas and Carroll give an example of two papers within the same issue of Molecular Biology and Evolution that confirmed and falsified the existence of a certain group.  It’s not simply a matter that some methods are more accurate than others.  “The observed conflicts are not dependent on the optimality criterion used,” they said.  The problem is real, and it’s pervasive.    It’s hard to tell if this paper is an admission of failure and hopelessness, or a call for a brief time out before an optimistic new charge:Here we discuss how and why certain critical parts of the TOL [tree of life] may be difficult to resolve, regardless of the quantity of conventional data available.  We do not mean this essay to be a comprehensive review of molecular systematics.  Rather, we have focused on the emerging evidence from genome-scale studies on several branches of the TOL that sharply contrasts with viewpoints—such as that in the opening quotation—which imply that the assembly of all branches of the TOL will simply be a matter of data collection.  We view this difficulty in obtaining full resolution of particular clades—when given substantial data—as both biologically informative and a pressing methodological challenge.  The recurring discovery of persistently unresolved clades (bushes) should force a re-evaluation of several widely held assumptions of molecular systematics.  Now, as the field is transformed from a data-limited to an analysis-limited discipline, it is an opportune time to do so.Most of the paper is taken up with examples.  For instance, despite what the media have often claimed, there is conflicting evidence linking humans to chimpanzees: “Specifically, analyses of almost 100 genes (under two different optimality criteria) show that ~55% of genes support a human-chimpanzee clade, 40% are evenly split among the two alternative topologies, with the remaining genes being uninformative” – and this is for two species considered so closely related, some political activists are advocating granting human rights to chimpanzees.    To exhibit the scale of the problems, they list four notable “bushes” in the tree of life.  Notice how these are spread all over the evolutionary time scale:(A) The human/chimpanzee/gorilla tree (5-8 million years ago).(B) The elephant/sirenian/hyrax bush (57-65 million years ago).(C) The tetrapod/coelacanth/lungfish bush (370-390 million years ago).(D) The metazoan superbush (>550 million years ago).They did not select these to be isolated examples.  These cases, despite getting the most detailed analysis by molecular phylogenists, are representative of the problems pervading the entire record.  Notice their use of words like “majority” and “large fraction” to indicate the scale of the challenge to Darwinian expectations:Three observations generally hold true across metazoan datasets that indicate the pervasive influence of homoplasy at these evolutionary depths.  First, a large fraction of single genes produce phylogenies of poor quality.  For example, Wolf and colleagues omitted 35% of single genes from their data matrix, because those genes produced phylogenies at odds with conventional wisdom (Figure 2D).  Second, in all studies, a large fraction of characters—genes, PICs or RGCs2—disagree with the optimal phylogeny, indicating the existence of serious conflict in the DNA record.  For example, the majority of PICs conflict with the optimal topology in the Dopazo and Dopazo study.  Third, the conflict among these and other studies in metazoan phylogenetics is occurring at very “high” taxonomic levels—above or at the phylum level.If the best techniques applied to the most detailed data sets show these conflicts, it cannot be expected that poorer methods on smaller data sets will do any better.  Clearly, this is not a crisis that is going to go away with more data.    So are molecular phylogenists “barking up the wrong trees,” they ask?  Is there “systematic bias” in tree-building efforts to date, that can “positively mislead phylogenetic inference”?  (see 06/08/2006).  Some sources of bias, like long-branch attraction, are understood.  If not careful, researchers can create trees out of wishful thinking: “Thus, a priori expectations of obtaining fully resolved topologies combined with the use of large amounts of data (which generate high support values) can make trees out of bushes.”  Researchers might just be engaged in self-fulfilling prophecy.  If this were the only source of bias, it might be possible to account for it, but Rokas and Carroll have shown that no method is consistently resolving one tree out of the bushes.    Now for the recommendations.  Is there any hope?  If so, it is not in more data:“Can we realistically hope to resolve diversification events spanning a few or even tens of millions of years that occurred in deep time?  It is widely accepted that nucleotide data are of limited use for resolving deep divergences because of mutational saturation and homoplasy.  Until the recent expansion in available data, it has not been possible to fully explore what the limits of the protein record might be.  Like others in the field, we also had expectations that scaling up dataset size would be sufficient to resolve interesting groups.  The evidence presented here suggests that large amounts of conventional characters will not always suffice, even if analyzed by state-of-the-art methodology.  Just as it would be futile to use radioisotopes with modest half lives to date ancient rocks, it appears unrealistic to expect conventional linear, homoplasy-sensitive sequences to reliably resolve series of events that transpired in a small fraction of deep time.  Although we have known this from theory, we are now confronted with the actual pattern of molecular evolution.The recommendations are: (1) the “prevalence and causes of homoplasy need to be better understood” and (2) “molecular systematics must now move beyond conventional characters and mine genomic data for new, less-homoplastic characters such as RGCs” [rare genomic changes].  This second plan, though is subject to confusion because of the widespread incidence of horizontal gene transfer and lineage sorting.  Earlier in the paper, Rokas and Carroll expressed frustration that the very stems in the tree of most interest to evolutionists are the very ones with the most problems:Thus, absolutely or relatively short stems present distinct challenges that could be described as the bane of the molecular systematist.  Yet, it is precisely these stems—associated with some of the most interesting episodes in life’s history—that most intrigue the evolutionist.  Analyses of large molecular datasets from clades at different time depths of the TOL illustrate how short stems, whether placed just 6 million or 600 million years in the past, can confound phylogenetic resolution.What to do?  When the tree of life is a lemon tree, make lemonade.  The authors ended by asking, “What’s wrong with bushes?”  Nothing, if you are willing to be called a heretic:A bush in which series of cladogenetic events lie crammed and unresolved within a small section of a larger tree does harbour historical information.  Although it may be heresy to say so, it could be argued that knowing that strikingly different groups form a clade and that the time spans between the branching of these groups must have been very short, makes the knowledge of the branching order among groups potentially a secondary concern.    For example, the lack of phylogenetic resolution at the base of the tetrapod/lungfish/coelacanth clade has not hampered in the least evolutionary research on the anatomical changes that occurred early on in the evolution of the tetrapod lineage.  Similarly, if the origin of most bilaterian phyla was compressed in time, more than 550 million years later it may matter little to know the exact relationships between most phyla to understand the evolution of the molecular tool kit that enabled the evolution of the body plans of the 35 or so animal phyla.    We submit that if the current efforts to assemble the TOL have, by 2050 (if not much sooner), assembled an arborescent bush of life, Dawkins’ prediction will have come to fruition.Translated, this may either mean that evolutionary thinking can proceed without evidence for a tree of life, or that there is still hope that somewhere hidden in the foliage there is a single trunk waiting to be found: the disparate bushes will become a single “arborescent bush of life.”  For now, it’s an article of faith foundering on confusing and contradictory evidence.1 Antonis Rokas, Sean B. Carroll, “Bushes in the Tree of Life,” Public Library of Science Biology, 4(11): e352. DOI: 10.1371/journal.pbio.0040352.2Abbreviations: TOL, tree of life; PIC, parsimony-informative character; RGC, rare genomic change.Folks, do you have any idea how damaging this paper is?  Darwinism has been falsified.  It’s over.  We may as well dance on the grave of Charlie D, because both of the greatest hopes for confirming his tall tale have falsified it: the fossil record and the genetic record.  For Rokas and Carroll to have any hope now is as pathetic as watching a Las Vegas gambler continue on after being told the slot machine is broken and there is no money in it.    Incredibly, these evolutionists do continue on in spite of the lack of evidence.  They do exactly what Charlie himself did: trust their imaginations.  Dawkins believes that the magical tree exists.  He accepts this myth, and the other evolutionists have so devoted their lies, their distortions, and their sacrilegious dishonor so much to it, that no amount of falsification will stop them.  The search must go on, till 2050 or beyond (after they are long dead), so that Charlie’s Myth can inspire a new generation of dreamers.  And Dawkins has the audacity to claim that creationists are the ones believing in fairy tales.    You realize that a series of bushes does not look like evolution; it looks like creation.  The universality of the genetic code ensures that the phyla did not evolve independently.  Since they cannot connect the dots from a universal common ancestor to the plethora of organisms alive today, the dots are imaginary – no better than a Kipling tale.  The evidence is very consistent, by contrast, with a single Creator who made separate groupings of plants and animals that reproduce after their kind (with variability), while still exhibiting a common underlying plan.    The only claim to authority and public trust that the evolutionary biologist can appeal to is empirical evidence.  This is what the Darwinists think makes their beliefs superior to religion.  For example, if you go to a new BBC Education site for kids, it will continue to propound the idea that religious truth is based on faith, while scientific truth is based on empirical evidence.This same site also has a section on Evolution that blatantly presents known falsehoods about evolutionary evidence, including peppered moths, finch beaks and the horse series, while claiming that the fossil record proves evolution.  Each of these icons has been refuted in scientific journals and scholarly books, often written by believers in evolution.  Are the webmasters of Bite-Size Science merely uninformed about this, or are they deliberately deceiving students to promote an agenda?The assumption of empirical support has been the main thing the Darwin Party has preached gives them superiority in truth claims and the right to rule the schools.  Only their myth gets exclusivity in “science” class.  Everyone else’s view must be consigned to the funny farm known as “religious studies.”    That was then.  This is now.  Their assumed empirical evidence has vanished, leaving them with nothing but vivid imaginations to keep their creation myth intact.  Read what Rokas and Carroll have said, and then re-read what Marshall said about the fossil record in the 04/23/2006 entry (ignoring the spin, just examining the evidence).  We no longer need to claim Darwinian evolution has been falsified; they did it for us.  Q.E.D.  Mission accomplished.  Fait accompli.  Done deal.  Way to go.  High five.  Glory to God.  Now, let’s get back on the road to the real Tree of Life.  But this time, let’s follow the Manufacturer’s directions.Boy, was that a bad detour, or what? (11/30/2005).(Visited 42 times, 1 visits today)FacebookTwitterPinterestSave分享0last_img read more

SA firms lead BRICS carbon disclosures

first_img30 April 2013 South Africa has the highest percentage of companies that publicly disclose their greenhouse gas emissions in the BRICS group of countries, according to a carbon ranking index released by the Environmental Investment Organisation (EIO) on Monday. The EIO is a London-based independent research organisation that promotes ecological investment systems. South African mobile telecommunications firm Vodacom came second overall in the EIO’s rankings, while diversified industrial firm Barloworld and miner Kumba Iron Ore placed 11th and 20th respectively. The index examines the emissions and transparency of the 300 largest firms in the BRICS (Brazil, Russia, India, China and South Africa) grouping. It is one of six ranking reports on emissions disclosure around the world. The Environmental Tracking Carbon Ranking series is the only public database of its kind. Over half of the 45 South African companies in the BRICS 300 ranking were found to be reporting complete data, which includes direct emissions as well as emissions resulting from the purchase of electricity, investments, transportation of goods, waste and employees.‘Reliable emissions database’ “As the world shifts towards a low carbon model, it’s extremely important that we have access to a reliable, consistent and cross-comparable greenhouse gas emissions database on the world’s largest companies,” chief executive of the London-based EIO, Sam Gill, said in a statement. A key finding of the index, however, was that none of the 300 BRICS companies surveyed reported emissions across their entire value chains. These are referred to as “scope 3 emissions”, and include emissions from sources not owned or directly controlled by the firm but which it has some influence over, such as business travel, transportation and distribution. “Since the majority of total corporate emissions often come from scope 3 sources, large quantities of emissions are not being accounted for,” Gill said. “This is precisely why the carbon rankings are designed to encourage scope 3 disclosure.” The EIO will also announce the 2013 Environmental Tracking Scope 3 leaders award on Wednesday to recognise the companies leading the field in emissions disclosure. “The rankings make up the first phase of the Environmental Tracking mechanism, with phase two seeing them developed into a series of investable indexes within which companies are weighted according to their position in the public carbon ranking,” the EIO said in a report. “The EIO hopes to make its Environmental Tracking Index Series available to investors later in the year.” SAinfo reporterlast_img read more

Govt to buy potatoes from farmers to stop suicides

first_imgA day after a potato farmer allegedly committed suicide after suffering heavy losses, Chief Minister Mamata Banerjee on Tuesday said her government will purchase 28,000 tonnes of potatoes, required for Anganwadi centres and midday meal programme, directly from farmers. Her announcement comes at a time when potato farmers across the State are facing a severe crisis — at least two of them have committed suicide — due to the sharp drop in prices following this years’ bumper crop.Krishak Dibas“We have decided to buy 28,000 tonnes of potatoes directly from the farmers which we need every month for the Anganwadi centres and the midday meal programme. The government will buy potatoes at ₹4.60 per kg,” she said. Ms. Banerjee was speaking at a government programme on Krishak Dibas (Farmers’ Day) observed by the Trinamool Congress government on March 14 to pay tribute to those who died during the anti-land acquisition movements at Singur in Hooghly district and Nandigram in Purba Medinipur district. As per the projected estimates of the State government, the number of schools (up to Class VIII) to be covered under the midday meal scheme is 83,673 and the number of students is about 1 crore. According to potato merchants, this is the first time that the TMC government is directly purchasing potatoes from farmers.The development comes a day after a potato farmer allegedly committed suicide due to losses in farming in the Anandapur area of Paschim Medinipur district’s Keshpur block. According to his family, Swapan Hajra (45) committed suicide after sustaining “heavy losses” in potato farming. ‘Heavy debt’“He incurred a large debt for cultivating potatoes in four bighas (1.60 acres) of land,” Mr. Hajra’s son Indrajit told journalists.The Opposition, however, is sceptical whether the move will be beneficial for the potato farmers. “This is nothing but a face saving move. If the TMC government is really bothered about the farmers they would have purchased potato from them at a much higher rate,” said CPI-M district secretary of Paschim Medinipur Tarun Roy.last_img read more

Star escapes

first_imgPBA IMAGESAldrech Ramos put order in Star’s tentative finish on Saturday night, draining the dagger triple with 12.8 seconds remaining as the Hotshots held off San Miguel Beer, 109-105, in Game 1 of their Final Four series at Smart Araneta Coliseum.The Hotshots almost blew a 13-point lead going into the final two minutes as they lapsed into miscues and needed Ramos to convert that triple from top of the key off a Paul Lee set-up as Star drew first blood in their best-of-five series.ADVERTISEMENT World’s 50 Best Restaurants launches new drinking and dining guide Heart Evangelista admits she’s pregnant… with chicken Pocari sweat coach expecting more from Rivers in Game 2 Cayetano dares Lacson, Drilon to take lie-detector test: Wala akong kinita sa SEA Games LATEST STORIES “That’s why he’s there,” said Star coach Chito Victolero, referring to the game-sealing bucket. “That’s what I keep telling my players, for them to shoot when they’re open.”Victolero is aware of what to expect on Game 2 set Monday at Mall of Asia Arena in Pasay.FEATURED STORIESSPORTSSEA Games: Biñan football stadium stands out in preparedness, completionSPORTSPrivate companies step in to help SEA Games hostingSPORTSMalditas save PH from shutout“They (Beermen) will keep fighting, they’re a champion team,” he said as he guns for the first Finals appearance of his young coaching career after falling just a win short against Barangay Ginebra in this season’s Philippine Cup.“We (coaching staff) will review the game tape and see what we can still do,” he went on. “San Miguel will never give up.” Ricardo Ratliffe scored 26 points and grabbed 22 rebounds before fouling out in the dying seconds while Allein Maliksi also fired 26.Lee struggled against the San Miguel defense to finish with just four and eight assists.Charles Rhodes had 34 points and reigning three-time MVP June Mar Fajardo had 24 for the Beermen, who beat the Hotshots in the eliminations, 103-97.ADVERTISEMENT 1 dead in Cavite blast, fire Lacson: SEA Games fund put in foundation like ‘Napoles case’center_img Don’t miss out on the latest news and information. WATCH: Firefighters rescue baby seal found in parking garage Sports Related Videospowered by AdSparcRead Next Heart Evangelista admits she’s pregnant… with chicken View comments Robredo: True leaders perform well despite having ‘uninspiring’ boss PLAY LIST 02:49Robredo: 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 City01:07Trump talks impeachment while meeting NCAA athletes02:49World-class track facilities installed at NCC for SEA Games MOST READ What ‘missteps’?last_img read more

Morrison delivers promise to win gold for his grandmother

first_imgBiggest Pogo service provider padlocked for tax evasion Ethel Booba on hotel’s clarification that ‘kikiam’ is ‘chicken sausage’: ‘Kung di pa pansinin, baka isipin nila ok lang’ Hotel says PH coach apologized for ‘kikiam for breakfast’ claim MOST READ Robredo should’ve resigned as drug czar after lack of trust issue – Panelo Ravena wants more after winning record fourth gold medal Don’t miss out on the latest news and information. Samuel Thomas Harper Morrison of the Philippines battles Ardian Prayogo Dinggo of Indonesia in the finals of the men’s -74kg of the 29th Southeast Asian Games taekwondo competition. Morrisson prevailed to win the gold medal. CONTRIBUTED PHOTO/SEA GAMES MEDIA POOLKUALA LUMPUR — Samuel Morrison knew that he could be fighting in his last Southeast Asian Games of his career.That’s why he was overcome with emotions after capturing the gold medal in the -74-kilogram division.ADVERTISEMENT LATEST STORIES Celebrity chef Gary Rhodes dies at 59 with wife by his sidecenter_img READ: Emotional Morrison wins gold in taekwondo, avenges teammate’s loss“I made a promise to my grandmother to win,” said Morrison, 27.FEATURED STORIESSPORTSSEA Games: Biñan football stadium stands out in preparedness, completionSPORTSPrivate companies step in to help SEA Games hostingSPORTSBoxers Pacquiao, Petecio torchbearers for SEA Games openingHis maternal grandmother died during the time he was trying to qualify for the Rio Olympics last year. He didn’t make it to the Games.“That’s why I went to her grave before I flew here,” said Morrison, who was born in Olongapo to an American serviceman and Filipino mother. Lacson: SEA Games fund put in foundation like ‘Napoles case’ Sports Related Videospowered by AdSparcRead Next Trump signs bills in support of Hong Kong protesters NATO’s aging eye in the sky to get a last overhaul PH boxing team determined to deliver gold medals for PH PLAY LIST 05:25PH boxing team determined to deliver gold medals for PH00:45Onyok Velasco see bright future for PH boxing in Olympics02:25PH women’s volleyball team motivated to deliver in front of hometown crowd00:50Trending Articles02:49World-class track facilities installed at NCC for SEA Games03:07PH billiards team upbeat about gold medal chances in SEA Games03:04Filipino athletes share their expectations for 2019 SEA Games01:27Filipino athletes get grand send-off ahead of SEA Games00:36Manny Pacquiao part of 2019 SEA Games opening ceremony His family migrated to Maryland but transferred to the Philippines for good when he was seven.The 2015 SEA Games gold medalist in featherweight graduated from the University of Santo Tomas.He was also a bronze medalist in the Incheon Asian Games in 2014.“I’m already 27 now, so if I can still can I will still fight in the 2019 SEA Games in Manila,” said the 6-foot-1 Morrison.ADVERTISEMENT View commentslast_img read more