Archive | December, 2012

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Doha Climate Conference: Success or Failure?

Posted on 29 December 2012 by Jerry

Conservative pundits from the Heritage Foundation declared the 2012 U.N. Climate Conference in Doha, Qatar a failure.  Supporters point to expanded commitments at a conference that was only expected to be a planning session for a “Big Deal” in 2015.  Was Doha a success or Failure?  You decide.

Detractors cited failure to hit Kyoto Protocol defined emissions objectives, lack of international support (U.S. refusing to ratify and exceptions for developing nations such as China and India) and an unworkable Kyoto structure that placed all emissions targets on a few dozen countries.  They called for the U.S. government to “more accurately determine the severity of climate change and verify U.N. claims.”  They continued saying the U.S. should work “through informal arrangements….undertaking appropriate steps toward a cost-effective reduction in warming.”

In an expansion of the definition of “beggar-thy-neighbor” which is an economics phrase describing how one country gains advantage at the expense of other countries, they said we should not try to mitigate global warming by “going it alone”.  Their suggestion was it was “Better to remove unnecessary regulations on fossil fuels and block any attempts to implement a carbon tax.”  In other words, we should act like global warming is not yet proven, slow our efforts to informal discussions with others and drill baby drill.

Advocates of climate change declared the meeting a success citing the following agreements accomplished at the Doha conference:

  • Attending countries altered the structure of future negotiations from two tracks (one each for developed and developing countries) to just one negotiating forum ostensibly limiting future exceptions for developing nations.
  • The EU and some other countries extended the Kyoto Protocol which was set to expire at the end of 2012, until 2020 and the EU, Australia, and Norway increased their carbon cutting targets. The Kyoto Protocol is the only existing treaty that requires emission cuts.
  • Developed nations gave recognition to poor countries for the “loss and damage” they face from the ravages of climate change.  This first ever concession opens the way for developed nations which have arguably caused climate change to possibly one day compensate poor countries for efforts they must take to repair the “loss and damage” incurred.
  • Attendees at the conference set out a schedule of necessary steps to be taken between now and 2015 as a work plan to prepare for negotiation of the “Big Deal” in Paris.

In the shadow of U.S. economic stresses, political gridlock, and inaction, the world owes a debt of gratitude to the EU, Australia, Norway and other nations for continuing the fight to control global warming.  We can only hope the US finally provides leadership in 2015 (the second Obama term) for the world’s efforts to limit rising temperatures.

On a related topic, scientists are afraid the world has passed the opportunity to limit the climate change temperature rise to only + 2°.  Accordingly the World Bank sponsored a report entitled “Turn Down the Heat” which was prepared by the Potsdam Institute for Climate Impact Research (PIK) and Climate Analytics. The report states the world is on a path to a + 4° temperature rise by the end of the century and predicts additional dire consequences.

Use the following links to obtain more information:  Select first entry “Climate Change Report Warns of Dramatically Warmer World This Century” and read.

Scroll down farther and select 5th entry, “Turn Down the Heat Executive Summary English”, and read.


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Life Evolved to Compete and Cooperate

Posted on 24 December 2012 by Jerry

The conventional wisdom has been that life is about competition and survival of the fittest. This includes cooperation for survival amongst animals that hunt in packs, share food, and collectively care for the young of the group.  Scientific observations have recently shown cooperation between all types of animals such as mice, chimps, elephants and others in situations where there is no apparent selfish reason to motivate their actions.  Now cooperation has been seen between RNA molecules during replication.  This may be at the most fundamental level of life.

Research published in the November 1, 2012 issue of Nature magazine shows that “mixtures of RNA fragments that self-assemble into self-replicating ribozymes spontaneously form cooperative catalytic cycles and networks.  We find that a specific three-membered network has highly cooperative growth dynamics.”  Further when the faster growth of these networks is compared to that achieved by single fragments which self catalyzes a chemical reaction, they show the “intrinsic ability of RNA populations to evolve greater complexity through cooperation…. Our experiments highlight the advantages of cooperative behavior even at the molecular stages of nascent life.”  

An additional article entitled “The cooperative gene” by James Attwater and Philipp Holliger speaks to the original principle of self-organization, a 30 year old theory of cooperation within RNA entities.  They state the theory is that “self replicating RNA entities go beyond simply making copies of themselves and act on other replicators through a cyclic network of reinforcing loops called hyper-cycles.” They describe the recent study’s findings that “show that variants of such RNA fragments can assemble and act on one another to form cooperative self-assembly cycles very much like the proposed hypercycles, in which ribozyme 1 aids assembly of ribozyme 2;  2 aids 3; and 3 aids 1.”  See figure 1 in the second article referenced below.

Use the following links to obtain for information:

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Bright Idea

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Nuclear Power Alternatives to Light-Water Reactors

Posted on 16 December 2012 by Jerry

The path of least resistance leads people to reuse solutions they first developed to solve a problem.  Such was the case with the light-water nuclear reactor developed in the late 1940’s, the design for which represents over 80% (356 of 437) of the world’s operating power reactors.  An article in the December 6, 2012 issue of Nature magazine recounts the history of nuclear power reactors and elaborates on three major, later competing designs which offer less expensive and cleaner power for a developing third world and a world in which increasing greenhouse gas emissions contribute to global warming.

A light-water nuclear reactor uses a fission reaction in the solid nuclear material to create heat which is exposed to normal water to generate steam used to power steam turbines which generate electricity.  As the steam loses heat it turns to water that is recycled back into the steam generators.   In addition to light-water reactors, the article cites the pros and cons of molten-salt reactors, high-temperature reactors, and fast reactors each of which, in the opinion of the article’s author, deserves another look.

The original idea was that the light-water reactors would be coupled with a worldwide network of reprocessing centers that would allow spent fuel rods to be chemically processed to extract still usable fission components like uranium-235 and the fissionable plutonium – 239.  Unfortunately, India in May of 1974 tested a nuclear device made from plutonium produced as this by-product.  Then in March of 1979, the reactor core of Three Mile Island had a partial meltdown which caused a halt to all further development of reactors in the U.S.  This caused the beginning of a worldwide ‘nuclear brown-out’ that lasted over twenty-five years, halted building of reprocessing centers, and saddled the world with huge stockpiles of spent radioactive rods.

A molten-salt reactor uses nuclear fuel in the liquid form of uranium tetraflouride which when blended with lithium and beryllium fluorides creates a liquid coolant used in the reactor.  This keeps the liquid material from achieving the high temperatures that would put the reactor in danger.  As the reactor recycles the liquid mixture extracting more and more fissionable material it keeps the fuel from being poisoned which is when the fuel has accumulated fragments left over after the uranium atoms split which in turn absorb the neutrons required to keep the reactor going.

A high-temperature reactor generates steam up to 1,000°C using helium gas in place of water which rises to only 300°C in light-water reactors.  It also uses a heat-resistant fuel composed of oxides and carbides of uranium that cannot melt down because it is stable up to 1,600°C which is hundreds of degrees hotter than the core would become even if completely without power and coolant.  The design would also dramatically reduce carbon emissions.

The slow neutrons of the light-water reactor often get absorbed into its uranium core creating the long lived plutonium, neptunium, americium, curium or other heavy elements which make fuel disposal so difficult with today’s reactors.  A fast-reactor ejects ‘fast’ neutrons which generally don’t get absorbed by the core.  This avoids the problem of long lived radioactive isotopes.  It can even destroy them in spent fuel.  While fast-reactors have to be cooled by liquid sodium or some other substance that will not slow down the neutrons, they have integrated recycling units which remove fission by-products and put rejuvenated fuel back into the reactor.

The question is do we keep investing in the old technology that is in place to protect our past investment or switch because there are better, safer and more environmentally friendly alternatives?  The costs of construction and operation of a nuclear power plant is multiple billions of dollars irrespective of how it is accounted for and what is included. 

With the prospect of better alternatives from which to choose, nuclear power needs to be in our mix of energy assets.  It is likely our choice is to have the world continue to build the old light-water variety with all of its known problems or switch to a newer, better design.  In any case, we are already spending a considerable amount on unclean alternatives like coal plants which while solving our electricity shortages make a deadly contribution to greenhouse gasses.  A new nuclear power plant architecture that solved historic problems of meltdowns, radioactive waste and greenhouse gasses would be an almost perfect alternative for future power plants.

Use the following links for further information:

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Synthetic Biology Continued: Risks or Benefits?

Posted on 02 December 2012 by Jerry

The synthetic biology controversy continues.  The latest salvo was in the December 2012 Scientific American article entitled “World Changing Ideas: 10 innovations that are radical enough to alter our lives”.  The lead idea is “New Life-Forms, No DNA Required” written by Ferris Jabr.  This optimistic article again raises issues first identified on this blog seven months ago in a posting entitled, “Troubling Progress for Synthetic Biology”.  The Scientific American article largely ignores synthetic biology dangers and offers only modest possible future benefits. 

Citing Philipp Holliger of the Medical Research Council’s Laboratory of Molecular Biology in Cambridge, the article states that when compared to DNA and RNA “Related polymers – at least six more – can do the same function.” That the earth’s flora and fauna rely only on DNA and RNA, Holliger says, is an “accident from the origin of life.” In another article he elaborates this thought by saying “There is nothing ‘Goldilocks’ about DNA and RNA – there is no overwhelming functional imperative for genetic systems or biology to be based on these two nucleic acids.”

The problem with these thoughts is that they ignore DNA and RNA have functioned successfully through fully 3+ billion years and have served as the flexible infrastructure allowing the development of the wide variety of life forms on the planet.  In addition, they survived all of the changes and dangers in Earth’s environment somehow helping the evolutionary process produce all the various and sundry species.  The reality is that “related polymers” and XNAs have not done this and have not naturally occurred anywhere to our knowledge.  It is as if with a sweep of the hand we negate the importance of DNA and RNA and their role in the history of life. At the same time we fail to acknowledge the uniqueness of the life phenomenon and how it integrates with the incredibly complex universe of which it is a part.

The Scientific American article credits Holliger with creating XNA or xeno nucleic acid, his replacement for DNA and RNA by “substituting entirely different molecules, such as cyclohexane and threose.  Just as important, they created enzymes that work with the XNAs to form a complete genetic system.  The enzymes enable XNAs to do something no other artificial nucleic acids can do: they evolve…Holliger reprogrammed natural polymerase enzymes to translate DNA into XNA and back again, establishing a novel system for storing and transmitting genetic information, which is the foundation of evolution.”

In another article written by Holliger entitled “XNA is synthetic DNA that’s stronger than the real thing” he uses an analogy to explain translation of DNA into XNA and back again.  He states “You can think of a DNA strand like a classmate’s lecture notes.  DNA polymerase is the pen that lets you copy these notes directly to a new sheet of paper.  But let’s say your friend’s notes are written in the ‘language’ of XNA.  Ideally, your XNA-based genetic system would have a pen that could copy these notes directly to a new sheet of paper.  What Pinheiro’s team did was create two distinct classes of writing utensil – one pen that copies your friend’s XNA-notes into DNA-notes, and a second pen that converts those DNA notes back into XNA-notes.  Is it the most efficient method of replication? No. But it gets the job done.”

These descriptions contain a contradiction.  In order to produce copies of the XNA, the research team uses the flexibility of DNA in the middle of the copying process.  Its reliance on the flexibility of traditional DNA means they have not formed a complete genetic system.  Instead they were forced to rely on DNA.  They go on to claim their enzymes evolve.  Absent DNA they do not replicate themselves or store their information.  Hence they do not evolve. Again we see an under-appreciated DNA dismissed as completely incidental to the evolution of their XNAs as opposed to the absolutely necessary role it performs.

Anticipating criticism from antagonists of synthetic biology, the article further states, “Holliger emphasizes that XNA-based life-forms are a long way off, but he already recognizes a distinct advantage.  If such a creature escaped into the wild, it would die without a steady supply of XNA-specific enzymes.  And XNA could not weave itself into the genomes of natural organisms, because their native enzymes would not recognize it.  XNA-based bacteria designed to devour oil spills or turn wastewater into electricity, for example, could not interfere with native organisms.” The Scientific American article further asserts, “Alternatively, scientists could enclose XNA within protocells – the origin of a new life-form that could evolve in ways no one can predict.”

When thinking about a creature of his creation escaping “into the wild” Holliger uses the word ‘wild’ as a substitute for the word ‘world’.  People do not live in the wild.  They do live in the world within which these organisms would escape. When contemplating an escape he observes his creature would die without a steady supply of XNA-specific enzymes.  There are several problems with this statement.  If he was able to modify enzymes to work with DNA in copying his XNAs, is it not possible for the same enzymes to mutate to the new form or become truly self-replicating?  Is it also not possible for existing DNA to produce a mutation that allows it to recognize, accept and incorporate these XNAs into the DNA of our normal life forms?  In other words, are our researchers not ignoring the most powerful life processes, mutation and evolution?

Against the obvious risks of what Holliger and others are doing is an array of unimpressive and limited applications they offer to justify the risks they are taking. They suggest XNAs could be injected into the human body to detect early, subtle signs of viruses or other infections.  They indicate that XNA-based bacteria could be designed to devour oil spills or turn wastewater into electricity.  So what happens if these bacteria get underground in oil fields or get loose in the world’s water supplies?  Does anyone really know what will happen with the release of Holliger’s creatures?  No one knows, but are these the types of “earth shaking” developments that would justify the risks?

We know that life forms are incredibly tenacious always seeking survival and replication.  Holliger claims his creature will evolve.  The author of the article mentions “The origin of a new life-form that could evolve in ways that no one can predict.”  This last sentence describes simply the threat Holliger’s creatures represent.

Use the following links to obtain more information:

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