OOL Study Substitutes Computer for Chemistry

first_imgUpon reading a recent origin-of-life paper in PNAS,1 you might think the authors ran experiments with real chemicals and real deep-sea rocks.  A more careful look, however, reveals that their model only worked in cyberspace.  This raises interesting questions about the ability of simulations to substitute for empirical evidence.    Their claims were dramatic – accumulation of the building blocks of life by factors of 100 million and more.  The paper makes optimistic, if not enthusiastic, claims that “nucleotides” and other important biochemicals can be highly concentrated in micropores in deep-sea geological formations: “We find that interlinked mineral pores in a thermal gradient provide a compelling high-concentration starting point for the molecular evolution of life.”  This, they advertised, can overcome the “concentration problem” that has plagued other models: how does one get a significant number of prebiotic chemicals close enough together to interact?    From the first-sentence reference to Miller and Urey, who used real lab apparatus and real chemicals, the paper appeared to follow the experimental tradition.  It focused on the problem of concentrating chemicals in a plausible environment.  By positing convection currents inside microscopic pores of rocks around deep-sea vents, the model overcame – by at least two orders of magnitude – a minimum set by the Second Law of Thermodynamics on how many molecules are needed for interaction to be considered probable.    True, the authors used the word “simulated” in the title and 14 times in the paper.  Their references to nucleotides and other “real” chemicals were qualified with indirect references.  Nevertheless, until the “Materials and Methods” section at the end of the paper, it seemed they were talking about real chemicals and physical pores in real rocks.  One of the figures showed photographs from real hydrothermal vents.  They mentioned nucleotides 37 times – including the title.  The body of the paper was filled with references to temperatures, pressures, volumes, and concentrations that looked real.  Actually, the entire model was done within two software programs, Comsol and Femlab.  The nucleotides, pores, and thermometers were virtual, not physical.    They tried to plug in real-world values into the programs and use realistic boundary conditions.  They input known properties of real molecules.  Putative pore sizes were based on photographs of real hydrothermal vents.  The bottom line, though, is that none of the concentration results were observed or measured in the wild.2  The model revolved around simplified geometries of pores as programmed into a computer – and that, of pores in only two dimensions.    Here was their concluding paragraph.  Note the lack of reference to a computer simulation.  Is it real, or is it memo tricks?In conclusion, we propose a type of mechanism, driven solely by a temperature gradient, which strongly accumulates even small protobiological molecules in semiclosed hydrothermal pore systems.  This setting provides a compelling, dissipative microenvironment to promote the first steps in the molecular evolution of life.The line between real and virtual was blurred in another passing thought near the end of the paper:Equally, freshly precipitated mesoscopic mineral grains are subjected to thermal cycling by the convection.  Their catalytic surfaces might generate nucleic acid multimers by thermally triggered periodic condensation and unbinding reactions.  In this context, we note that, in a comparable thermal convection setting, DNA was shown to replicate exponentially by using the, albeit protein-catalyzed, PCR.Critics of origin-of-life studies might be stunned at this line.  PCR, or polymerase chain reaction, is an intelligently-guided reaction, performed by machines in laboratories by scientists with PhDs.  PCR depends on protein catalysts – highly complex molecules from living systems, whose specificity enables them to react with DNA.  By associating a guided process that uses complex biological parts with a theoretical process that is unguided and uses simple abiological parts, can the one be properly compared to the other without assuming what needs to be proved – the origin of complex biological processes?    This paper was presented as part of a colloquium by the National Academy of Sciences last December on “In the Light of Evolution I: Adaptation and Complex Design” (see 05/10/2007 entry), published May 9 on the Proceedings website.1Baaske, Weinert, Duhr, Lemke, Russell and Braun, “Extreme accumulation of nucleotides in simulated hydrothermal pore systems,” Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0609592104, published online before print May 9, 2007.2In addition, they did not test complications, such as whether pores might become clogged with tar and sediments – they just speculated and dismissed the possibilities, viz: “One may ask whether the strong accumulation of solvated organic molecules would lead to the tarring of the pore.  This is not expected because thermophoretic coefficients become small for concentrations in the molar range.”Models are OK, and have a long history in science, but the bluffing-to-proof ratio in this paper was beyond the pale.  These authors might be able to defend it by claiming they “said” it was just a simulation in a computer, but nobody scanning the contents would think so.  Few readers are going to look at the Materials and Methods section (usually boring, unless you’re trying to replicate the results).  This paper gave every appearance of being an empirical, laboratory experiment in the real world.  It was all done with software smoke and model mirrors.    As we saw 12/03/2004, one of the conspirators (Russell) is a master bluffer.  He has a propensity to gloss over major problems and swap out experimental facts for cartoon pictures on a screen.  In his 2004 lecture, he made everything look so simple, so problem-free, life should just pop out of the pore.  If life by the yard is hard, and life by the inch is a cinch, wouldn’t life by the micron be right on?  It’s a foregone conclusion.  The hard part over, little Poregum would just gloriously evolve into us.  Some unbiased, objective scientist he is.  He should read Shapiro’s devastating critique (02/15/2007) of such notions.    Observational facts have a way of tarring up computer models.  Let us ask a simple question: where are these nucleotides supposed to get their ribose?  Doesn’t Russell and gang know that deep-sea vents are the last place one would expect to find ribose?  It is so difficult to imagine it forming by chance, in fact, that Steven Benner (11/05/2004) had to envision it forming in a desert in the presence of borate.  (Not Borat, mind you – no humans allowed, no matter how perverse.  It’s borate.)  Now, since Benner’s surface model falsifies Russell’s deep-sea model, and vice versa (Russell thinks the surface environment is “disastrous” for life), this one little “problem” we raised is enough to gum up the software and send their little computer instantly into BSOD (blue screen of death, pun intended).  We would continue with more real-world pressure, but as Windows users know, one BSOD is enough to ruin your whole day.(Visited 9 times, 1 visits today)FacebookTwitterPinterestSave分享0last_img read more

South Africa’s satellite ‘leads the way’

first_img21 December 2010 A design team from satellite builders SunSpace were able to rectify the problem, however, by means of a unique manoeuvre that involved guiding the satellite to tumble “head-over-heels” in order to scan an image from south to north while orbiting from north to south. SumbandilaSat images are available via the CSIR Satellite Applications Centre catalogue. New image requests can be directed to sales and customer services at the CSIR Satellite Applications Centre (SAC). These images would have cost over R40&nbps;000 each from a commercially operated satellite, but SumbandilaSat is able to deliver such images, each covering an area of 50 by 60 kilometres, to local projects at no cost. Affordable micro-satellite technology Setback, solution The SumbandilaSat images can also be used to map burnt areas, for example, in the Kruger National Park, where fire is part of the natural ecology and is used by SANParks as a management tool to manipulate vegetation to promote biodiversity and influence the balance between grass, shrubs and big trees. SAinfo reporterWould you like to use this article in your publication or on your website? See: Using SAinfo material Managing Kruger Park fires So far, the satellite has delivered 800 images of targets worldwide, of which approximately 54% have been cloud-free – translating to four images on average per day. Three to five images of southern African targets can be captured per week. A constellation of similar satellites is planned to increase the availability of such satellite data for diverse applications. Several African countries will participate in this joint venture, and will eventually share in the data produced by the African Resource Management Constellation, especially for disaster monitoring applications. SANParks currently has to rely on very coarse-resolution satellite images of 500m pixel size for regular mapping of burnt areas. SumbandilaSat provides images at 6.25m pixel resolution and covers an area of 50 by 60 kilometres per image. The satellite imagery can also be used to monitor the recovery of the vegetation in the burnt area and the long-term influence of fire on tree and grass cover. South Africa’s micro-satellite, SumbandilaSat, is living up to its Venda name as it “leads the way” in providing free, frequent high-resolution images capable of revolutionising local earth observation in various fields. Although the imaging capacity of SumbandilaSat is much less than that of commercial high-resolution satellites, the satellite has demonstrated the viability of affordable micro-satellite technology, which is its primary stated mission. Earlier in the mission, a setback was experienced with the performance of the altitude stabilisation system on the satellite. The South African National Space Agency will be tasked with ensuring that society benefits from investments in space-based earth observation technology. During August and September, SumbandilaSat produced five high-resolution images of the south-western part of the Kruger National Park and neighbouring Bushbuckridge, where the Council for Scientific and Industrial Research (CSIR) and SA National Parks (SANParks) are conducting various research projects. The provision of free, frequent high-resolution satellite images of specific areas of interest has the potential to revolutionise local earth observation capabilities in many fields, with natural disasters (like fires and floods) and human activities (like mining, settlements, forestry) being accurately monitored on a regular basis.last_img read more

COP 17 a defining moment: Zuma

first_img28 November 2011South African President Jacob Zuma welcomed more than 15 000 delegates from 190 countries to Durban at the start of the UN Climate Change Conference on Monday with the message that the future of the world was in their hands.Speaking at the opening of the 17th Conference of the Parties (COP 17) to the UN Framework Convention on Climate Change (UNFCCC), Zuma told the delegates that they had no choice but to find a lasting solution to the climate problem.“Climate change can no longer be treated as just an environmental problem … It is a matter of life and death,” he said.Calls for compromise, commitmentThe much-anticipated conference kicked off at Durban’s International Convention Centre with calls for compromise and commitment to curbing global carbon emissions.African leaders also urged rich nations to take responsibility for polluting the atmosphere by channelling funds to developing countries as part of a long-term solution to the problem of global warming.Over the course of the next two weeks, the world’s representatives will need to establish some kind of basis for long-term climate cooperation, and in particular will have to negotiate a second, post-2012 commitment period for the Kyoto Protocol.With relative progress made during COP 16 in Cancun, Mexico last year, the South African talks are being touted as a turning point for implementing most of the crucial decisions made last December.Cancun Agreements ‘must be implemented’Zuma said it was crucial for COP17 to ensure that the Cancun Agreements, which included the establishment of a Green Climate Fund, were implemented.Africa’s vulnerability to climate change potentially meant not only droughts and severe weather patterns but poverty and serious food shortages for the continent.“Severe drought in Somalia is causing serious problems and has displaced many. In the Americas, they are still battling to overcome the impacts five years after Hurricane Katrina,” Zuma said.“Given the urgency, parties should find solutions here in Durban. The expectation is that you must be able to work towards the outcome that is fair, balanced and credible.”While expectations are low for a comprehensive and legally binding agreement, there is hope for practical progress on specific packages concerning mitigation, the Kyoto-Protocol, finance and adaptation.Zuma said developing countries required a quick start through early initial capitalisation and activation of the Green Climate Fund.As it was held in Africa, the conference also needed to prioritise adaptation to save lives in many Island nations.‘Part of the fight against poverty’“We also feel strongly that as an African conference, the COP 17 outcome must recognise that solving the climate problem cannot be separated from fighting poverty,” Zuma said.He added that Africa had committed to reduce carbon emissions by 34 percent by 2020 and by 42 percent by 2025.South Africa had gone a long way to make sure this commitment was met, Zuma said, citing the country’s New Growth Path and the climate accord signed recently by the country’s government, business and labour sectors.Earlier, delegates elected Maite Nkoana-Mashabane, South Africa’s minister of international relations, as the new COP president for the 2011/12, taking over from Mexican Foreign Minister Patricia Espinosa Castellano.Nkoana-Mashabane urged the delegates to use their “boldness and courage” to make Durban a decisive moment to address global warming, adding that the world demanded action and a common solution for generations to come.‘There is a crucial need to build trust’UN Climate Executive Secretary Christiana Figueres said that unresolved political issues needed to be advanced in Durban if the world was to achieve its goals on climate change.“It is my hope that through constructive negotiations we will address these issues … this may only be possible if the results are both fair and workable for all of us,” Figueres said. “There is a crucial need to build trust as part of the outcome of this conference.”Global warming has far-reaching consequences for the world with changes in weather patterns threatening millions of lives and expected to affect food security in developing countries.As with previous Conferences of the Parties, the road to COP 17 has not been easy. Negotiators hope to build upon progress made during the pre-conference period to push for a more inclusive deal that will take into consideration the interests of developing nations.The G77 countries, which include South Africa, remain committed to their long-standing position of achieving a legally binding agreement.But given the ongoing rivalry between developed and developing countries, many analysts say they are unlikely to achieve this any time soon.Developed countries such as the United States and Japan, however, remain entrenched in the long-standing position of refusing to accept their own legally binding targets without also including binding commitments from major emerging economies such as China and India.Source: BuaNewslast_img read more

One more holy cross desecrated

first_imgPANAJI: The desecration of religious artefacts in South Goa district continued on Friday, with another Catholic cross vandalised in Margao in the early hours of the day. A spokesperson for the Goa Police said, “The desecration of the cross occurred in the Calconda area in Margao.” This is the seventh instance of desecration of a religious artefact in South Goa in the last few weeks. Chief Minister Manohar Parrikar had earlier called the desecrations an attempt to disturb the communal harmony of the State. Goa and Daman Archbishop Filipe Neri Ferrao had urged the police to crack the cases, and called on people to maintain peace and harmony.last_img

ISRO to test cryogenic stage onboard GSLV-D5

first_imgIndia will undertake the flight test of its indigenous cryogenic stage onboard homegrown rocket GSLV-D5 which will launch GSAT-14 by the middle of 2012, a top ISRO official has said.A facility for static testing of the cryogenic engine would be ready in another two months at ISRO’s Liquid Propulsions Systems centre (LPSC) at Mahendragiri in Tirunelveli district, Indian Space Research Organisation Chairman K Radhakrishnan said.The new thrust chamber facility for static testing would be a big boon for the LPSC, Radhakrishnan told reporters at the LPSC on Friday after inagurating a two-day National Conference on “Expanding Frontiers in Propulsion Technology”.The maiden flight test of the indigenous cryogenic stage by ISRO onboard Geosynchronous Satellite Launch Vehicle GSLV-D3 ended in a failure in May, 2010 after the stage developed some snag and the rocket plunged into sea minutes after liftoff.Radhakrishnan said India’s advanced communication satellite GSAT-8, launched from Kourou in French Guiana on May 21, would become operational by June end.He also said ISRO would launch another communication satellite GSAT-12, equipped with 12 c-band transponders, onboard Polar Satellite Launch Vehicle PSVL-C17 on July 2.PSLV- C18 would be launched in September from Sriharikota carrying Mega Tropiques satellite, an Indo-French joint venture.On December 11, microwave remote sensing satellite Risat 1 would be launched. It would be able to take clear pictures of sky even if they were covered by clouds.- With PTI inputsFor more news on India, click here.For more news on Business, click here.For more news on Movies, click here.For more news on Sports, click here.advertisementlast_img read more