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first_imgThis story is not about Enron and Exxon, but about introns and exons.  The proportions of the scandals they are causing in evolutionary theory, however, may be comparable.    Introns are spacers between genes.  For several decades now, it has been a puzzle why they are there, and why a complex machine called a spliceosome takes them out and joins the active genetic parts – the exons – together. Only eukaryotes have spliceosomes, though; mitochondria have “group II introns” and some mRNAs may have them.  Their presence and numbers in various groups presents a bewildering array of combinations.  Figuring out a phylogenetic tree for introns has eluded evolutionary geneticists, as has understanding their origin and functions (02/18/2005).  Why do genes come in pieces that have to be reassembled?     William Martin and Eugene Koonin said in Nature1 that “The discovery of introns had a broad effect on thoughts about early evolution.”  Some theories have been falsified, and others remain in the running.  Consider the scope of the problems:A current consensus on introns would be that prokaryotes do indeed have group II introns but that they never had spliceosomes; hence, streamlining in the original sense (that is, loss of spliceosomal introns) never occurred in prokaryotes, although it did occur in some eukaryotes such as yeast or microsporidia.  An expansion of that consensus would be that spliceosomes and spliceosomal introns are universal among eukaryotes, that group II introns originating from the mitochondrion are indeed the most likely precursors of eukaryotic mRNA introns and spliceosomal snRNAs, and that many—conceivably most—eukaryotic introns are as old as eukaryotes themselves.  More recent are the insights that there is virtually no evolutionary grade detectable in the origin of the spliceosome, which apparently was present in its (almost) fully fledged state in the common ancestor of eukaryotic lineages studied so far, and that the suspected source of introns—mitochondria, including their anaerobic forms, hydrogenosomes and mitosomes—was also present in the common ancestor of contemporary eukaryotes (the only ones whose origin or attributes require explanation).    This suggests that intron origin and spread occurred within a narrow window of evolutionary time: subsequent to the origin of the mitochondrion, but before the diversification of the major eukaryotic lineages.  This, in turn, indicates the existence of a turbulent phase of genome evolution in the wake of mitochondrial origin, during which group II introns invaded the host’s chromosomes, spread as transposable elements into hundreds—perhaps thousands—of positions that have been conserved to the present, and fragmented into both mRNA introns and snRNA constituents of the spliceosome.This means that a complex molecular machine, the spliceosome (09/17/2004, 09/12/2002), appeared fully formed almost abruptly, and that the intron invasion took place over a short time and has not changed for hundreds of millions of years.  They submitted a new hypothesis:Here we revisit the possible evolutionary significance of introns in light of mitochondrial ubiquity.  We propose that the spread of group II introns and their mutational decay into spliceosomal introns created a strong selective pressure to exclude ribosomes from the vicinity of the chromosomes—thus breaking the prokaryotic paradigm of co-transcriptional translation and forcing nucleus-cytosol compartmentalization, which allowed translation to occur on properly matured mRNAs only.   (Emphasis added in all quotes.)But this means that the nucleus, nucleolus and other complex structures also had to appear in a very brief period of time.  It means that the engulfed organism that somehow became mitochondria had to transfer its introns rapidly into a genome lacking a nucleus.  It means the nucleus had to evolve quickly to segregate the new mitochondrial genes from the nuclear genes.  A lot had to happen quickly.  “This bipartite cell would not be an immediate success story: it would have nothing but problems instead,” they admitted, but they believed that natural selection would favor the few that worked out a symbiotic relationship with their new invaders.    This is not the end of the problems.  The group II introns would have had to embed themselves with reverse transcriptase and maturase without activating the host’s defenses, then evolve into spliceosome-dependent introns and remain unchanged forever after.  Then those embedded group II introns would undergo mutational decay, interfering with gene expression.  Will this work without some miracles?A problem of a much more severe nature arises, however, with the mutational decay of group II introns, resulting in inactivation of the maturase and/or RNA structural elements in at least some of the disseminated copies.  Modern examples from prokaryotes and organelles suggest that splicing with the help of maturase and RNA structural elements provided by intact group II introns in trans could have initially rescued gene expression at such loci, although maturase action in trans is much less effective than in cis.  Thus, the decay of the maturase gene in disseminated introns poses a requirement for invention of a new splicing machinery.  However, as discussed below, the transition to spliceosome-dependent splicing will also impose an unforgiving demand for inventions in addition to the spliceosome.A spliceosome is not an easy thing to invent; it has five snRNAs and over 200 proteins, making it one of the most complex molecular machines in the cell.  Not only that, they appeared in primitive eukaryotes and have been largely conserved since.  Perhaps the miracles can be made more believable by dividing them into smaller steps:It seems that the protospliceosome recruited the Sm-domain, possibly to replace the maturase, while retaining group II RNA domains (snRNAs) ancestrally germane to the splicing mechanism.  While the later evolution of the spliceosome entailed diversification with the recruitment of additional proteins—leading to greater efficiency—the simpler, ancestral protospliceosome could, in principle, rescue expression of genes containing degenerate group II introns in a maturase-independent manner, but at the dear cost of speed.Will a lateral pass from maturase to incipient spliceosome during a long field run lead to a touchdown?  If a stumbling protospliceosome could survive, in spite of vastly decreased translation rate, it might have been able to run the distance with natural selection’s encouragement, they think.  Players would be falling left and right in this “extremely unhealthy situation,” they say, and “the prospects of any descendants emerging from this situation are bleak.”  How could the game go on, then?  “The only recognizable mechanism operating in favour of this clumsy chimaera is weakened purifying selection operating on its exceptionally small initial population.”  Purifying selection means weeding out losers, not adding new champions.  “Finding a solution to the new problem of slow spliceosomes in the presence of fast and abundant ribosomes required an evolutionary novelty.”    They winnow down the possibilities.  Getting instant spliceosomes smacks too much of an improbable feat.  Getting rid of spliceosomal introns from DNA apparently did not occur.  Their solution?  The invention of the nucleus, where slow spliceosomes could operate without competition from fast ribosomes.    This adds new miracles, however.  The nucleus has highly complex pores that permit only authenticated molecules into the inner sanctum.  They think, however, that it must have happened, somehow: “Progeny that failed to physically separate mRNA processing from translation would not survive, nor would those that failed to invent pore complexes to allow chromosome-cytosol interaction.”  So pick your miracles: since necessity is the mother of invention, “The invention of the nucleus was mandatory to allow the expression of intron-containing genes in a cell whose ribosomes were faster than its spliceosomes.”    The near-miraculous arrival of the nucleus is underscored by other feats it performs: “In addition to splicing, eukaryotes possess elaborate mRNA surveillance mechanisms, in particular nonsense-mediated decay (NMD), to assure that only correctly processed mature mRNAs are translated, while aberrant mRNAs and those with premature termination codons are degraded.”  How could this originate?  Again, necessity must have driven the invention: “The initial intron invasion would have precipitated a requirement for mechanisms to identify exon junctions and to discriminate exons (with frame) from introns (without frame), as well as properly from improperly spliced transcripts.  Thus, NMD might be a direct evolutionary consequence of newly arisen genes-in-pieces.”  But then, if it is verified that some translation occurs in the nucleus, that would be “difficult to reconcile with our proposal.”    They ended with comparing their hypothesis with others.  “Our suggestion for the origin of the nucleus differs from previous views on the topic,” they boasted, “which either posit that the nuclear membrane was beneficial to (not mandatory for) its inventor by protecting chromosomes from shearing at division, or offer no plausible selective mechanism at all.”  At least theirs is simpler and includes some requirements to select for the cells with the best inventors – or the ones with the luckiest miracles.1Martin and Koonin, “Hypothesis: Introns and the origin of nucleus-cytosol compartmentalization,” Nature 440, 41-45 (2 March 2006) | doi:10.1038/nature04531.Was any of this storytelling useful?  The shenanigans they pulled, couched in biochemical jargon, can be summarized by two principles in their own imaginations: (1) since the cell needed these superbly-crafted machines, it had to invent them somehow, and (2) since evolution is a fact, it had to happen somehow.  Do you catch any hint of a mechanism for actually inventing a 200-protein supermachine that would actually work?  Did you find any hint that any cell any time had a “protospliceosome” that only worked half-way?  All this was pure fiction built on childlike faith in evolution.    Presenting a hypothesis in science is fine, but how would they ever test something like this?  They offered a few tests that could discriminate between their just-so story and other just-so stories, but nothing that could explain how a spliceosome, or a nuclear membrane with its elaborate pore complexes, or nonsense-mediated decay could have been invented from scratch just because a cell needed these things.    Would that evolutionists would get off this storytelling kick and do something useful with their lives.  Let’s find a cure for cancer.  Let’s find better sources of energy, and think of ways to reduce risks of disease and terrorism, and use science to improve our lives and our world.  Stringing together uncooperative data into a fictional account of prehistory will accomplish nothing and is wasting time and money in a world desperately in need of the productive possibilities of true science.(Visited 10 times, 1 visits today)FacebookTwitterPinterestSave分享0last_img read more

first_imgShare Facebook Twitter Google + LinkedIn Pinterest By Chris ClaytonDTN Ag Policy EditorWASHINGTON (DTN) — A group of Senate Democrats released a report Tuesday on the Trump administration’s agricultural trade aid program, charging USDA “is picking winners and losers in their attempt to aid farmers affected by President Trump’s turbulent trade agenda.”Led by Senate Agriculture Committee ranking member Debbie Stabenow, D-Mich., and Senate Minority Leader Chuck Schumer, D-N.Y., the report stated Market Facilitation Program payments were unevenly distributed across the country.The report states USDA’s MFP “has treated farmers unfairly by, among other things, sending 95% of the top payment rates to Southern farmers, who have been harmed less than other regions, and helping farms owned by billionaires as well as foreign-owned companies, including awarding $90 million in purchase contracts to a Brazilian company.”The MFP was set up last year after the Trump administration vowed farmers would not be hurt by trade disputes with China and other countries that had sparked retaliatory tariffs.Sen. Debbie Stabenow, D-Mich., ranking member of the Senate Agriculture Committee, spearheaded the report.FARMERS NEED HELP“Farmers need help to stay afloat as this administration’s erratic trade actions continue to harm our agricultural economy,” Stabenow said. “The problem is USDA’s flawed aid formula is a short-term solution that picks winners and losers, while failing to adequately help the farms hit the hardest.”In a letter delivering the report to U.S. Agriculture Secretary Sonny Perdue, the senators wrote, “Instead of taking a careful approach like Congress did in the recent bipartisan 2018 farm bill, the USDA has replaced markets with short-term, inequitable payouts that lack transparency.”The senators urged Perdue “to improve its trade assistance program to better support small farmers and pursue a focused trade policy to rebuild the markets American farmers have lost.”The letter states farmers in the Midwest and Northern Plains were hit with lower national soybean prices and higher transportation costs to reach different markets after the Trump administration began its tariff disputes with trading partners, notably China.HIGH PAYMENTS TO COTTON AREASThe report states Southern crops such as cotton did not have a price decline, but they received much higher payment rates “and the top five states for 2019 MFP are in the South.”Senate Democrats questioned the high payments to cotton-producing areas, noting, “During 2018, cotton prices and exports did not exhibit the sharp declines one would assume based on cotton’s payment rate.”As of last week, USDA stated the MFP payments for the 2019 program had reached just under $6.7 billion to more than 564,000 farmers.In a statement to DTN, a USDA spokesperson defended how the MFP payments for 2019 were set up and were being distributed. Payments were based on trade damage, not region or farm size, a USDA spokesperson stated. Further, payments were more weighted to the Midwest and not the South, USDA stated.USDA RESPONSE“To date, the Midwest region has received more than 60% of the funds and the top five recipient states from the 2019 MFP program are Illinois, Iowa, Kansas, Nebraska and Minnesota, which directly refutes the claims made in this report,” the USDA spokesperson stated. “While we appreciate feedback on this program, the fact of the matter is that USDA has provided necessary funding to help farmers who have been impacted by unjustified retaliatory tariffs. While criticism is easy to come up with, we welcome constructive feedback from any member of Congress with recommendations as to how the program could be better administered.”The Senate Democrats’ report points out that farmers in 2,901 counties have received MFP payments, but there are 193 counties with payment rates of $100 an acre or higher. The vast majority of those counties — 95% — are in Southern states, according to the report. Another 402 counties received the minimum $15 an acre.COUNTY DIFFERENCESThe Democrats’ report points out, “The disparities across county lines, even the Southern states, can be extreme.” Hancock County, Georgia, farmers, for example, received an average payment of $150 an acre, while farmers in neighboring Baldwin County got $15 an acre.Senate Democrats also called out “payments made to billionaires and foreign-owned companies,” which includes $90 million in pork sales for JBS, a Brazilian-owned packer with packing plants in several states. JBS was awarded those sales under a $1.2 billion food purchase program USDA created as part of its trade-aid package.Along with that, the report highlights USDA did not take steps to help smaller or beginning farmers, but instead doubled the payment limit from $125,000 per farmer to $250,000. Limits on millionaires getting farm payments were also ignored, Senate Democrats said, citing that “The family-owned farms of the billionaire governor of West Virginia even earned the maximum payment under the 2018 MFP.”The Senate Democrats’ report comes after House Agriculture Committee Chairman Collin Peterson, D-Minn., also wrote Perdue last week, raising some concerns about “inequities” in the MFP payments.Peterson’s letter stated, “The current (MFP) has created winners and losers among neighbors who find themselves facing the same market situations, meaning that some producers may remain viable while others may be forced out of business.”Peterson raised several issues with the payments. For instance, dairy farmers also question why MFP payments were based on established farm production history, while crop were based on actual production. The letter noted dairy farmers’ actual production is readily available via their milk checks.The Senate Democrats’ report can be viewed at https://www.agriculture.senate.gov/….Chris Clayton can be reached at Chris.Clayton@dtn.comFollow him on Twitter @ChrisClaytonDTN(AG/ES)© Copyright 2019 DTN/The Progressive Farmer. All rights reserved.last_img read more

first_imgCONTRIBUTED PHOTO/STEPHEN TANBACOLOD CITY—Stephan Schrock couldn’t have picked a bigger, more important match to make up for all the time he missed away from Ceres-Negros.On another magical night at a packed Panaad Stadium, OJ Porteria and Manny Ott delivered the goals, while Schrock provided the steel and creativity as the Busmen subdued Home United of Singapore, 2-0, to rule the Asean zonal stage of the AFC Cup.ADVERTISEMENT Robredo should’ve resigned as drug czar after lack of trust issue – Panelo The victory completed a 3-2 win on aggregate and sent the Busmen to the inter-zonal semifinals against Istiklol of Tajikistan starting Aug. 22 in Dushanbe. Ceres will host the second leg on Sept. 12.“We left it all out there on the pitch” said Schrock, who rejoined the team in April, which meant he was only added to the squad for the zonal finals. “We put in the performance of our lives in this final. We deserve to make history for the club, the country and Southeast Asia.”FEATURED STORIESSPORTSSEA Games: Biñan football stadium stands out in preparedness, completionSPORTSPrivate companies step in to help SEA Games hostingSPORTSWin or don’t eat: the Philippines’ poverty-driven, world-beating pool starsPorteria gave the Busmen an early lead on the away goals rule with a close-range volley off an Iain Ramsay cross in the second minute, before Ott’s superb free kick in the 41st minute doubled the advantage.The first half performance, where the hosts won a penalty that was wasted by Fernando Rodriguez and created a couple more clear-cut chances, was in stark contrast over their uninspired display in the 2-1 loss in the first leg last week. NGCP on security risk: Chinese just technical advisers View comments “It was a very important game and I’m just honored to be given a starting place,” Schrock said.“I had to prove that I deserve to start because my teammates have been sacrificing the past six months to get us to this stage. I owe it to my teammates and our supporters.”Sports Related Videospowered by AdSparcRead Next NATO’s aging eye in the sky to get a last overhaul But even with the visitors pushing men forward in the second half, the Busmen proved resolute, preserving a clean sheet for the first time in six matches.The Busmen broke down in tears upon hearing the final whistle and becoming the first team to rule the zonal stage, which started in February.And considering the fact that the club owned by Leorey Yanson was only a provincial powerhouse five years ago, the achievement was nevertheless impressive.Schrock worked tirelessly on both ends, winning 14 duels and creating five chances in a dynamic display that reminded why he was once a regular in the top-flight in Germany.The midfield maestro said he was merely making up for lost time.ADVERTISEMENT Celebrity chef Gary Rhodes dies at 59 with wife by his side MOST READcenter_img LATEST STORIES Lacson: SEA Games fund put in foundation like ‘Napoles case’ Don’t miss out on the latest news and information. Robredo should’ve resigned as drug czar after lack of trust issue – Panelo DILG, PNP back suspension of classes during SEA Games Trump signs bills in support of Hong Kong protesters 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 Gonzales wins as Frayna falterslast_img read more

first_imgzoomImage Courtesy: Pixabay (Pixabay License) The shipping industry could see more slow steaming and transhipment being triggered as part of the IMO 2020 sulphur rule, according to shipping consultancy Drewry.“Shippers rightfully want more transparency regarding how the new fuel surcharge mechanisms will work, but they should be mindful of the potential risks to future service options, competition and rates if they don’t concede anything to carriers.”2020 is going to be a pivotal year for the carrier industry. Failure to recover more of the fuel cost from customers than in the past, estimated to be around 50%, could be ruinous for some lines, many of which are still operating with highly distressed balance sheets, Drewry explained.The consultancy added that there is a general acceptance among shippers that they will have to pay more towards the fuel cost burden, although there are still a number of sticking points regarding the mechanics of how it should be done.On the other side, carriers will argue that a short-term win for shippers could quickly turn into a loss. It is something that shippers might want to consider during negotiations as any cost saving today might raise the likelihood of another carrier bankruptcy, causing unwanted chaos in the supply chain.“The reality is that carriers’ fuel costs will start to differ to a considerable degree as the new fuels are pumped into their ships; the variance to be largely driven by the type of fuel used.”Depending on their success in raising the fuel recovery rate, carriers will inevitably seek to mitigate the anticipated higher operating expenses. One potential side-effect from the new regulations could be greater slow-steaming and use of transhipment.The logic being that as ships sailing speed is reduced and round voyages are extended carriers will drop ports from rotations to ensure that transit times to key points remain competitive, according to Drewry. Fewer direct port calls will induce greater need for transhipment and feeder operations.“The upside from this shift towards more transhipment from a ports and terminals perspective is that this will inflate the global port throughput sum as four container movements at the quayside will be required instead of two as with direct port-to-port calls.”last_img read more

first_imgGurugram: The Gurugram Metropolitan City Bus Limited (GMCBL) has come up with four new routes. These new routes of the city bus service Gurugaman was inaugurated by chief minister Manohar Lal Khattar on Wednesday. One of the new routes (number 119 ) of the city bus service will also cater to the residents of Faridabad as it will ply between IFFCO Chowk and NIT Faridabad. The areas which will be covered by this route include Baliyawas, Mangar, Pali zone, Sainik Colony, Masjid, RK Hospital, Metro Mor, Khushboo Chowk, Bristol Chowk, Sikanderpur metro station and MG Road. Also Read – After eight years, businessman arrested for kidnap & murderThe services from IFFCO Chowk will begin at 7:00 am and commence at 6:00 pm. Commuters will be able to complete the entire journey in one hour and fifteen minutes. From NIT Faridabad, the first bus will depart at 8:30am and the last bus is scheduled for 7.25pm. Similarly, another route will cover the distance between Gurugram bus stand and Palam Vihar. This route will include Sector 12 Chowk, CRPF Camp Chowk, Rajeev Nagar Chowk, Ashok Vihar 2 and 3, Park View Residency and Cosmos Executive Apartment, among others. Also Read – Two brothers held for snatchingsThe duration of this route will be 30 minutes. The first bus will depart from the Gurugram Bus Stand at 7.45am and the last bus at 5:45 pm. From Palam Vihar, the last bus is scheduled for 6.20pm. Meanwhile, commuters will soon be able to take a bus service that will be a loop service between Rajiv Chowk, Huda City Centre and Rajiv Chowk. This route will ply through Medanta, sectors 40, 44, 46, Huda City Centre, Sector 31/40 Housing Board Colony, Jharsa, among others. The fourth bus route will cover the distance between IFFCO Chowk to Dundahera. Almost a year after its launch, on September 2018, the Gurugaman bus service hit a daily ridership of 50,000 last month. According to data shared by the Gurugram Metropolitan City Bus Limited, ridership on the service jumped 67% between May and July, going from about 30,000 passengers Presently, four important routes make up more than half of Gurugaman’s daily ridership — Route 212 (from Basai to Huda City Centre and back), Route 134 (from IFFCO Chowk to IMT Manesar), Route 112 (from Sector 56 to Gurugram Railway station) and Route 111 (from Huda City Centre to Bhondsi). In all, these have a daily average ridership of about 33,000 day to 50,000 per day.last_img read more