Scientists have created enzymes with enhanced ability to select between left- and right-handed molecules, using an “evolutionary” process, claims Manfred Reetz in a Perspective article in PNAS:1A fundamentally new approach to asymmetric catalysis in organic chemistry is described based on the in vitro evolution of enantioselective enzymes. It comprises the appropriate combination of gene mutagenesis and expression coupled with an efficient high-throughput screening system for evaluating enantioselectivity (enantiomeric excess assay). Several such cycles lead to a “Darwinistic” process, which is independent of any knowledge concerning the structure or the mechanism of the enzyme being evolved. The challenge is to choose the optimal mutagenesis methods to navigate efficiently in protein sequence space. As a first example, the combination of error-prone mutagenesis, saturation mutagenesis, and DNA-shuffling led to a dramatic enhancement of enantioselectivity of a lipase acting as a catalyst in the kinetic resolution of a chiral ester. Mutations at positions remote from the catalytically active center were identified, a surprising finding, which was explained on the basis of a novel relay mechanism. The scope and limitations of the method are discussed, including the prospect of directed evolution of stereoselective hybrid catalysts composed of robust protein hosts in which transition metal centers have been implanted.Basically, researchers built enzymes top-down instead of bottom-up. Instead of the old “rational design” method, trying to construct an active site to perform the function needed, they started with the function they wanted, and iteratively selected any “mutants” that came closest to doing the job, without stipulating how they did it. The “surprising finding” he spoke of was that a distant mutation, far from the active site, actually improved the performance of the enzyme.1Manfred T. Reetz, “Controlling the enantioselectivity of enzymes by directed evolution: Practical and theoretical ramifications,” Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0306866101, published online before print April 12, 2004.He put “Darwinistic” in quotes, because it was not really Darwinistic, it was Designistic. The scientists played the role of designer by carefully selecting the results and directing the outcome. This paper, like others before it, gives two false impressions: (1) that Darwinism achieved the high specificity of proteins in the past, and (2) that Darwinian theory is a boon to science in the present. This is nothing but name-dropping. Charlie had nothing to do with it. If this were Darwinism, there would be no “directed evolution” (an oxymoron), because there would be no direction. Here, the scientists had a goal: they wanted enantioselective enzymes. Their “mutation and selection” process was results-driven by artificial selection, a form of intelligent design. Yet Reetz illogically claims, without any evidence or support (only belief), “Enzymes are products of evolution, and might therefore be expected to function with high enantioselectivity only with natural substrates under physiological conditions.” Then, in the very next breath, he falsifies this evolutionary prediction: “However, it is well known that this is not the case, because a surprisingly large number of unnatural compounds are converted with high enantioselectivity, even in organic solvents.” So does this convert him to ID theory? No, he just waltzes into the problem at hand: “Nevertheless, the problem of substrate specificity persists. In such cases several approaches to enhance enzyme stereoselectivity have been described, including site-specific mutagenesis based on theoretical considerations…” la te da, blah blah, and so on, and so forth, so we’ll design an enzyme with a creative method and give Charlie the glory. The difference between this method and the traditional bottom-up approach Reetz calls “rational design” can be compared to the difference between engineering and management. The engineer knows the physical laws and properties of the widget he is designing, and organizes the parts specifically toward the solution. The manager just says, “Build me a widget that flies.” An upper manager might devise a contest between engineers to see who can come up with the best design. All the manager cares about is the results: will it fly? He weeds out the losers and rewards the winners. The winner gets more resources to refine the design until an optimal design is produced. Even if the engineer uses trial and error and chance, given enough trials a working prototype will emerge as long as intelligence is directing the process toward a goal. In a similar way, these researchers did not need to know all the details of the structure of the enzyme they wanted to create; they just mutated ingredients and selected the few that worked, then iterated the process until the best design was filtered out of the pile. They managed the process rather than engineering it. Only Dilbert would nominate his manager for a Darwin award. Another thing. The “surprising” discovery Reetz made also argues against Darwinism. His team found that a remote amino acid, far from the active site, was essential to the function. He was so surprised by this he called it a paradigm-shifting finding: “This observation leads to a change in paradigm, because all previous attempts to influence enantioselectivity of an enzyme by using site-specific mutagenesis had focused on amino acid substitutions near the active center. Such protein engineering was designed to “carve” an appropriate chiral pocket at the active center, in line with Fischer’s “lock-and-key” hypothesis or modified versions such as Koshland’s induced fit. Later, he adds, “… our studies show that the long-standing dogma regarding the necessity of amino acid substitutions exclusively at the active site to influence enantioselectivity no longer holds.” What this means is that an enzyme is designed all the way through, not just at the active site. The “lock and key” fit of an enzyme to its substrate is amazing enough, but to think that distant amino acids actually affect the workings of the molecular machine calls into question the belief that proteins can be mutated at will, as long as they are far from the active site. This underscores the improbability of getting all the amino acids in the right order, as described in our online book, Evolution: Possible or Impossible? Let’s give credit where credit is due. This experiment is all about design. Calling this “Darwinistic” is like calling Boeing a manufacturer of tornados in junkyards.(Visited 44 times, 1 visits today)FacebookTwitterPinterestSave分享0
Marthinus van Schalkwyk and performersat the 2009 opening of the Nelson MandelaBay visitor information centre.(Image: Port Elizabeth Daily Photo) Van Schalkwyk addresses the delegatesat a climate change convention in Montreal.(Image: IISD) MEDIA CONTACTS • Vusi MonaPresidency, Head of Communications+27 82 047 2260.RELATED ARTICLES• Climate-friendly development• SA tourism outstrips world rates• Tourism remains strong in SA• Clean-up drive along SA bordersJanine ErasmusSouth Africa’s Presidency has put forward the country’s minister of tourism, Marthinus van Schalkwyk, as a candidate to head the UN Framework Convention on Climate Change (UNFCCC).The Presidency announced in March that after consideration, it had nominated Van Schalkwyk to take over from the outgoing executive secretary Yvo de Boer, who has been at the head of the organisation since 2006.Earlier in 2010 De Boer announced his retirement from the UN position to join consultancy giant KPMG as their global advisor on sustainability and climate. He will take up his new post on 1 July 2010.Van Schalkwyk is regarded as a strong contender for the position, having gained extensive experience in dealing with climate-related issues in his previous post as minister of environmental affairs and tourism.The Presidency reported that it had received requests from a number of outside parties – including governments, corporations and NGOs in both the developed and developing world – for Van Schalkwyk to be made available for nomination for this prestigious post.President Jacob Zuma and Van Schalkwyk have already met to discuss the matter.The final decision lies with UN secretary-general Ban Ki-Moon.A tough jobShould his bid be successful, the minister will face a tough job in getting the 192 members of the UNFCCC to agree on the effects of climate change and unite to implement strategies to counter the global phenomenon.In the wake of the 2009 climate conference held in Copenhagen, which failed to produce any realistic or legally binding emission-reduction target between participating nations, Van Schalkwyk will have his work cut out for him to bring the members of the UNFCCC into accord. De Boer is of the opinion that a new climate deal will not be struck before 2011.Van Schalkwyk will also have to restore the faith of developing nations, who also widely condemned the failure of the Copenhagen talks to provide any real hope of assistance for them from developed nations.However, as environmental affairs minister, a post which he held until after the general elections of 2009, Van Schalkwyk earned respect as a fighter for developing nations, and for leading South Africa in a number of progressive climate change initiatives that elevated the country as a champion for good environmental practices.Among his achievements are the implementation of a Black Economic Empowerment scorecard and charter for tourism, the launch of a new environmental protection fleet to counteract illegal fishing, the enforcing of the 2004 Air Quality Act, and the banning of the use, import and export, and manufacturing of asbestos and asbestos-containing materials.In 2008 he assumed the rotating presidency of the biennial African Ministerial Conference on the Environment, a gathering of African ministers of the environment, at its 12th session, which took place in Johannesburg.“Our message for this gathering is that we are ready to assist in shaping and building a cohesive African environmental agenda,” said Van Schalkwyk in his acceptance speech.He therefore has the understanding and the experience needed to effectively punt the needs of developing nations, ensuring they do not get pushed aside in the global climate debate.Towards the end of next year South Africa hosts the 2011 Conference of the Parties, an annual meeting of the members of the UNFCCC. To have a South African at the helm of global climate negotiations would be fitting, and, said the Presidency, “an honour and a privilege”.Saving the planetThe UNFCCC arose out of the 1992 UN environment summit, known as the Earth Summit, which took place in Rio de Janeiro. The treaty was established with the main aim of stabilising the world’s greenhouse gas emissions, and came into force in March 1994.The UNFCCC’s 192 parties are classified as Annex I or Annex II members. Annex I countries are seen as industrialised economies or economies in transition. Annex II countries have developed economies and are able to help developing countries financially with initiatives that fall under the UNFCCC.To date, 40 Annex I and 23 Annex II countries have become parties. There are also a number of non-Annex 1 parties, of which South Africa is one – these are mostly developing nations who are dependent on assistance from wealthier nations.The UNFCCC itself has no compulsory carbon emission limits to which members are expected to adhere, but its main instrument, the 1997 Kyoto Protocol, does set legally binding targets for carbon emission reduction for its own 184 members.The UNFCCC secretariat is based in Bonn, Germany.
Tripura Chief Minister Biplab Kumar Deb on Tuesday said ducks help recycle water and increase oxygen levels in water bodies besides boosting the rural economy.Addressing an inaugural event of a traditional boat race at Rudrasagar, an artificial lake about 50 km from Agartala, he announced he would distribute 50,000 ducklings of local species to fishermen who live nearby and other villagers across Tripura.‘Healthy droppings’“When 50,000 white ducks swim in water, they will look beautiful and increase oxygen levels in the water bodies,” he said. This, he added, will help the fish get more oxygen. The Chief Minister also said droppings of the ducks would make the fish grow faster organically.Experts in Tripura said movement does aerate water bodies, but there is no scientific evidence to attribute the aeration job to swimming ducks.Mr. Deb also criticised the previous Left Front government for damaging old village culture of rearing ducks and poultry. “CPI(M) activists would force people to attend their frequent rallies, hardly giving them time to for rearing fowls. I want every rural family in Tripura to rear four-five ducks, which will help meet protein and vitamin requirements of children,” he said.The CPI(M) said it was expected of Mr. Deb to make outlandish observations.