Friday, April 11, 2014

Scientists Urge Rejection of Keystone XL Pipeline

April 7, 2014

President Barack Obama
The White House
1600 Pennsylvania Avenue NW
Washington, DC 20500

Secretary John Kerry
U.S. Department of State
2201 C Street NW
Washington, DC 20520

Dear President Obama and Secretary Kerry,

As scientists and economists, we are concerned about climate change and its impacts. We urge you to reject the Keystone XL tar sands oil pipeline as a project that will contribute to climate change at a time when we should be doing all we can to put clean energy alternatives in place.

As you both have made clear, climate change is a very serious problem. We must address climate change by decarbonizing our energy supply. A critical first step is to stop making climate change worse by tapping into disproportionately carbon-intensive energy sources like tar sands bitumen. The Keystone XL pipeline will drive expansion of the energy-intensive strip-mining and drilling of tar sands from under Canada’s Boreal forest, increasing global carbon emissions. Keystone XL is a step in the wrong direction.

President Obama, you said in your speech in Georgetown last year that “allowing the Keystone pipeline to be built requires a finding that doing so would be in our nation’s interest. And our national interest will be served only if this project does not significantly exacerbate the problem of carbon pollution.”

We agree that climate impact is important and evidence shows that Keystone XL will significantly contribute to climate change. Fuels produced from tar sands result in more greenhouse gas emissions over their lifecycle than fuels produced from conventional oil, including heavy crudes processed in some Gulf Coast refineries. As the main pathway for tar sands to reach overseas markets, the Keystone XL pipeline would cause a sizeable expansion of tar sands production and also an increase in the related greenhouse gas pollution. The State Department review confirmed this analysis under the scenario that best meets the reality of the opposition to alternative pipeline proposals and the higher costs of other ways of transporting diluted bitumen such as rail. The review found:
“The total lifecycle emissions associated with production, refining, and combustion of 830,000 bpd of oil sands crude oil is approximately 147 to 168 MMTCO2e per year. The annual lifecycle GHG emissions from 830,000 bpd of the four reference crudes examined in this section are estimated to be 124 to 159 MMTCO2e. The range of incremental GHG emissions for crude oil that would be transported by the proposed Project is estimated to be 1.3 to 27.4 MMTCO2e annually.”
To put these numbers into perspective, the potential incremental annual emissions of 27.4 MMTCO2e is more than the emissions that seven coal-fired power plants emit in one year. And over the 50-year expected lifespan of the pipeline, the total emissions from Keystone XL could amount to as much as 8.4 billion metric tons CO2e. These are emissions that can and should be avoided with a transition to clean energy.

The contribution of the Keystone XL tar sands pipeline to climate change is real and important, especially given the commitment of the United States and other world leaders to stay within two degrees Celsius of global warming. And yet, the State Department environmental review chose an inconsistent model for its “most likely” scenarios, using business-as-usual energy scenarios that would lead to a catastrophic six degrees Celsius rise in global warming. Rejecting Keystone XL is necessary for the United States to be consistent with its climate commitments. Six degrees Celsius of global warming has no place in a sound climate plan.

Secretary Kerry, in your speech in Jakarta, you said, “The science of climate change is leaping out at us like a scene from a 3D movie – warning us – compelling us to act.” Rejecting the Keystone XL tar sands pipeline would be a decision based on sound science.

The world is looking to the United States to lead through strong climate action at home. This includes rejecting projects that will make climate change worse such as the Keystone XL tar sands pipeline.


John Abraham, Ph.D.
University of St. Thomas

Philip W. Anderson, Ph.D.
Nobel Prize (Physics 1977)
Emeritus Professor
Princeton University

Tim Arnold, Ph.D.
Assistant Project Scientist Scripps Institution of Oceanography
University of California, San Diego

Kenneth J. Arrow, Ph.D.
Nobel Prize (Economics 1972) Professor emeritus of Economics and of
Management Science and Engineering
Stanford University

Roger Bales, Ph.D.
Professor of Engineering
University of California, Merced

Paul H. Beckwith, M.S.
Part-time professor: climatology/meteorology
Department of Geography
University of Ottawa

Anthony Bernhardt, Ph.D.
Physicist and Program Leader (retired)
Lawrence Livermore National Laboratory

Damien C. Brady, Ph.D.
Assistant Professor of Marine Science Darling Marine Center
University of Maine

Julie A. Brill, Ph.D.
Director, Collaborative Program in Developmental Biology, and Professor, Department of Molecular Genetics
University of Toronto
Senior Scientist, Cell Biology Program
The Hospital for Sick Children

Gary Brouhard, Ph.D.
Department of Biology
McGill University

Ken Caldeira, Ph.D.
Senior Scientist
Carnegie Institution for Science

Grant Cameron, Ph.D.
Coastal Data Information Program (CDIP) Scripps Institution of Oceanography
University of California, San Diego

Shelagh D. Campbell, Ph.D.
Professor, Biological Sciences
University of Alberta

Kai M. A. Chan, Ph.D.
Associate Professor & Tier 2 Canada Research Chair (Biodiversity & Ecosystem Services)
Graduate Advisor, RMES Institute for Resources, Environment & Sustainability
University of British Columbia

Eugene Cordero, Ph.D.
Professor, Department of Meteorology and Climate Science
San Jose State University

Rosemary Cornell, Ph.D.
Professor, Molecular Biology and Biochemistry
Simon Fraser University

Gretchen C. Daily, Ph.D.
Bing Professor of Environmental Science
Stanford University

Timothy Daniel, Ph.D.
U.S. Federal Trade Commission

Miriam Diamond, Ph.D.
Department of Earth Sciences
Cross-appointed to:
Department of Chemical Engineering and Applied Sciences
Dalla Lana School of Public Health
School of the Environment
Department of Physical and Environmental Sciences
University of Toronto

Lawrence M. Dill, Ph.D., FRSC
Professor Emeritus
Simon Fraser University

Simon Donner, Ph.D.
Associate Professor, Department of Geography
University of British Columbia

Roland Droitsch, Ph.D.
KM21 Associates

Nicholas Dulvy, Ph.D.
Professor, Canada Research Chair in Marine Biodiversity
and Conservation Biological Sciences
Simon Fraser University

Steve Easterbrook, Ph.D.
Professor of Computer Science
University of Toronto

Anne Ehrlich, Ph.D.
Biology Department
Stanford University

Paul R. Ehrlich, Ph.D.
Bing Professor of Population Studies and President, Center for Conservation Biology
Stanford University

Henry Erlich, Ph.D.
Center for Genetics
Children’s Hospital Research Institute

Alejandro Frid, Ph.D.
Science Coordinator
Central Coast Indigenous Resource Alliance

Konrad Gajewski, Ph.D.
Laboratory for Paleoclimatology and Climatology
Department of Geography
University of Ottawa

Eric Galbraith, Ph.D.
Assistant Professor
Department of Earth and Planetary Science
McGill University

Geoffrey Gearheart, Ph.D.
Scientist, Center for Marine Biodiversity and Biomedicine Scripps Institution of Oceanography
University of California, San Diego

Alexander J. Glass, Ph.D.
Emeritus Associate Director
Lawrence Livermore National Laboratory

John R. Glover, Ph.D.
Associate Professor, Biochemistry
University of Toronto

Ursula Goodenough, Ph.D.
Professor, Department of Biology
Washington University in St. Louis

Stephanie Green, Ph.D.
David H. Smith Conservation Research Fellow
Oregon State University

Steven Hackett, Ph.D.
Professor of Economics Associated Faculty, Energy Technology & Policy
Humboldt State University

Joshua B. Halpern, Ph.D.
Professor, Department of Chemistry
Howard University

Alexandra Hangsterfer, M.S.
Geological Collections Manager Scripps Institution of Oceanography
University of California, San Diego

James Hansen, Ph.D.
Adjunct Professor
Climate Science, Awareness and Solutions
Columbia University Earth Institute

John Harte, Ph.D.
Professor of Ecosystem Sciences
Energy and Resources Group
University of California, Berkeley

H. Criss Hartzell, Ph.D.
Emory University School of Medicine

Danny Harvey, Ph.D.
Professor, Department of Geography
University of Toronto

Rodrick A. Hay, Ph.D.
Dean and Professor of Geography College of Natural and Behavioral Sciences
California State University Dominguez Hills

Karen Holl, Ph.D.
Professor of Environmental Studies
University of California, Santa Cruz

Robert Howarth, Ph.D.
The David R. Atkinson Professor of
Ecology & Environmental Biology
Cornell University

Jonathan Isham, Jr., Ph.D.
Professor of Economics
Middlebury College

Andrew Iwaniuk, Ph.D.
Associate Professor
University of Lethbridge

Mark Jaccard, Ph.D., FRSC
School of Resource and Environmental Management
Simon Fraser University

Louise E. Jackson, Ph.D.
Professor, Department of Land, Air and Water Resources
University of California Davis

Pete Jumars, Ph.D.
Professor of Marine Sciences
Darling Marine Center
University of Maine

David Keith, Ph.D.
Gordon McKay Professor of Applied Physics
School of Engineering and Applied Sciences (SEAS); and,
Professor of Public Policy, Kennedy School of Government
Harvard University

Jeremy T. Kerr, Ph.D.
University Research Chair in
Macroecology and Conservation Professor of Biology
University of Ottawa

Bryan Killett, Ph.D.
Jet Propulsion Lab

Keith W. Kisselle, Ph.D.
Associate Professor of Biology & Environmental Science Academic Chair of Center for Environmental Studies
Austin College

Janet E. Kübler, Ph.D.
Senior Research Scientist
California State University at Northridge

Sherman Lewis, Ph.D.
Professor Emeritus of Political Science
California State University Hayward

Michael E. Loik, Ph.D.
Associate Professor of Environmental Studies
University of California, Santa Cruz

Michael C. MacCracken, Ph.D.
Chief Scientist for Climate Change Programs
Climate Institute

Scott A. Mandia, M.S.
Professor/Asst. Chair, Department of Physical Sciences
Suffolk County Community College

Michael Mann, Ph.D.
Distinguished Professor and Director of Earth System Science Center
Penn State University

Adam Martiny, Ph.D.
Associate Professor in Marine Science Department of Earth System Science
University of California, Irvine

Damon Matthews, Ph.D.
Associate Professor and
Concordia University Research Chair
Geography, Planning and Environment
Concordia University

James J. McCarthy, Ph.D.
Alexander Agassiz Professor of Biological Oceanography
Harvard University

Susan K. McConnell, Ph.D.
Susan B. Ford Professor Dunlevie Family University Fellow Department of Biology
Stanford University

Dominick Mendola, Ph.D.
Senior Development Engineer Scripps Institution of Oceanography
University of California, San Diego

Faisal Moola, Ph.D.
Adjunct Professor, Faculty of Forestry
University of Toronto; and,
Adjunct Professor, Faculty of Environmental Studies
York University

William Moomaw, Ph.D.
Professor, The Fletcher School
Tufts University

Jens Mühle, Dr. rer. nat.
Scripps Institution of Oceanography
University of California, San Diego

Richard B. Norgaard, Ph.D.
Professor Emeritus of Energy and Resources
University of California, Berkeley

Gretchen North, Ph.D.
Professor of Biology
Occidental College

Dana Nuccitelli, M.S.
Environmental Scientist
Tetra Tech, Inc.

Michael Oppenheimer, Ph.D.
Professor of Geosciences and International Affairs
Princeton University

Wendy J. Palen, Ph.D.
Assistant Professor, Earth to Ocean Research Group
Simon Fraser University

Edward A. Parson, Ph.D.
Dan and Rae Emmett Professor of Environmental Law
Faculty Co-Director
Emmett Center on Climate Change and the Environment
UCLA School of Law

Raymond T. Pierrehumbert, Ph.D.
Louis Block Professor in the Geophysical Sciences
The University of Chicago

Richard Plevin, Ph.D.
Research Scientist NextSTEPS (Sustainable Transportation Energy Pathways) Institute of Transportation Studies
University of California, Davis

John Pollack, M.S.
Meteorologist; and,
National Weather Service forecaster (retired)

Jessica Dawn Pratt, Ph.D.
Education & Outreach Coordinator Center for Environmental Biology
University of California, Irvine

Lynne M. Quarmby, Ph.D.
Professor & Chair
Molecular Biology & Biochemistry
Simon Fraser University

Rebecca Rolph, M.S.
Max Planck Institute for Meteorology
Hamburg, Germany; and,
Klimacampus, University of Hamburg

Thomas Roush, MD
Columbia University School of Public Health (retired)

Maureen Ryan, Ph.D.
Research Associate, Simon Fraser University; and,
Postdoctoral Researcher, University of Washington

Anne K. Salomon, Ph.D.
Assistant Professor
School of Resource and Environmental Management
Simon Fraser University

Casey Schmidt, Ph.D.
Assistant Research Professor Desert Research Institute
Division of Hydrologic Sciences

Peter C. Schulze, Ph.D.
Professor of Biology & Environmental Science Director, Center for Environmental Studies
Austin College

Jason Scorse, Ph.D.
Associate Professor
Monterrey Institute of International Studies
Middlebury College

Jamie Scott, MD, Ph.D.
Professor and Canada Research Chair
Department of Molecular Biology & Biochemistry
Faculty of Science and Faculty of Health Sciences
Simon Fraser University

Michael A. Silverman, Ph.D.
Associate Professor, Department of Biological Sciences
Simon Fraser University

Leonard S. Sklar, Ph.D.
Associate Professor
Earth & Climate Sciences Department
San Francisco State University

Jerome A. Smith, Ph.D.
Research Oceanographer Scripps Institution of Oceanography
University of California, San Diego

Richard C. J. Somerville, Ph.D.
Distinguished Professor Emeritus and Research Professor Scripps Institution of Oceanography
University of California, San Diego

Brandon M. Stephens, M.S.
Graduate Student Researcher Scripps Institution of Oceanography
University of California, San Diego

John M. R. Stone, Ph.D.
Adjunct Professor
Carleton University

David Suzuki, Ph.D.
Emeritus Professor
Sustainable Development Research Institute
University of British Columbia

Jennifer Taylor, Ph.D.
Assistant Professor
University of California, San Diego

Michael S. Tift, M.S.
Doctoral Student Scripps Institution of Oceanography
University of California, San Diego

Cali Turner Tomaszewicz, M.S.
Doctoral Student, Biological Sciences
Department of Ecology, Behavior & Evolution
University of California, San Diego

Till Wagner, Ph.D.
Scientist, Scripps Institution of Oceanography
University of California, San Diego

Barrie Webster, Ph.D.
Professor (retired)
University of Manitoba

Richard Weinstein, Ph.D.
University of Tennessee, Knoxville

Anthony LeRoy Westerling, Ph.D.
Associate Professor of
Environmental Engineering and Geography
University of California, Merced

Mark L. Winston, Ph.D., FRSC
Academic Director and Fellow, Center for Dialogue
Simon Fraser University

George M. Woodwell, Ph.D.
Member, National Academy of Sciences, and
Founder and Director Emeritus
The Woods Hole Research Center

Kirsten Zickfeld, Ph.D.
Professor of Climatology
Simon Fraser University

Thursday, April 10, 2014

On the Origin of the Genes of Viruses - 7

Atoms & molecules don't age?
In previous posts of this series abiotic evolution was highlighted because the concept seems to not be talked about.

Microbiologists and biologists tend to begin with "our planet was formed some 4.56 billion years ago."

I don't like leaving out the previous billions of years of abiotic evolution, so on relevant Dredd Blog posts I mention that just-as-important epoch because the evolution of non-living things is actually the bigger picture  (On the Origin of the Genes of Viruses - 5, On the Origin of the Genes of Viruses - 6).

That molecular machines have evolved for a much longer period of time than biological organisms have is not merely the imagining of a science fiction novel, rather, it is the result of the observation of the machinations of, among many other examples, the modern RNA/DNA associated molecular machines known as the ribosome and the ribozyme.

The macro molecular machine factories which are older than the Earth are still with us and are doing just fine thank you.

We are discussing the observations that have been written down in scientific papers about non-living molecular machines which are utilized by today's viruses:
Virus infection involves coordination of a series of molecular machines, including entry machines, replication machines, assembly machines, and genome packaging machines, leading to the production of infectious virions.
Although viruses had been considered as merely dull, static containers, and protectors of genomes, this false concept was replaced by the realization that viruses are beautiful intricate machines, essential to biological evolution, capable of invading cells, stealthily avoiding the protective barriers of the host, usurping the host's synthetic machinery for their own survival and able to self assemble into complex molecular machines. Indeed it has become apparent that the capabilities of viral machines far exceed those to the simple enzymes first studied in the mid-twentieth century. This book is a partial description of some of the amazing things accomplished by viruses in infecting a host and replicating themselves.
(Viral Molecular Machines). The full understanding of viruses involves not only the molecules that the viral molecular machines are constructed from, but it also involves understanding of the atoms which the molecules are constructed of:
One of the principal goals in biology is to be able to fully understand the mechanisms of an organism in atomic detail. Viruses offer the best opportunities to achieve this goal. Written by leaders in the respective fields, this book examines a variety of viral molecular machines ...
(The Uncertain Gene - 10, quoting from "Viral Molecular Machines", ibid). Atoms, molecules, and molecular machines made from them are not alive, they are abiotic.

We could look for non-living fossils that had to be self-replicating until they began to rely on the dynamics of biotic (living) entities, cells, but that "going looking" has fooled even the experts at times:
Twenty years ago the palaeontological community gasped as geoscientists revealed evidence for the oldest bacterial fossils on the planet. Now, a report in Nature Geoscience shows that the filament structures that were so important in the fossil descriptions are not remnants of ancient life, but instead composed of inorganic material.
(Journal Nature, "Filamentous figments in the Apex Cherts"). But they were not looking for what I am looking for, i.e., early "fossils" of abiotic evolution.

They were looking for the earliest fossils of biotic evolution (we must careful not to "find" what we are looking for before we find it, eh?).

Anyway, so far a micro sized ribozyme in a non-living virus has not yet been detected here on Earth:
Although RNA seems well suited to form the basis for a self-replicating set of biochemical catalysts, it is unlikely that RNA was the first kind of molecule to do so. From a purely chemical standpoint, it is difficult to imagine how long RNA molecules could be formed initially by purely nonenzymatic means. For one thing, the precursors of RNA, the ribonucleotides, are difficult to form nonenzymatically. Moreover, the formation of RNA requires that a long series of 3′ to 5′ phosphodiester linkages form in the face of a set of competing reactions, including hydrolysis, 2′ to 5′ linkages, 5′ to 5′ linkages, and so on. Given these problems, it has been suggested that the first molecules to possess both catalytic activity and information storage capabilities may have been polymers that resemble RNA but are chemically simpler (Figure 6-93). We do not have any remnants of these compounds in present-day cells, nor do such compounds leave fossil records. Nonetheless, the relative simplicity of these “RNA-like polymers” make them better candidates than RNA itself for the first biopolymers on Earth that had both information storage capacity and catalytic activity.
(The RNA World and the Origins of Life). Perhaps it is time to focus now, here on Earth, on finding a fossilized pre-life micro-sized ribosome or ribozyme.

The search for the mystical Earth based non-cellular ribosome and/or ribozyme will have to be limited to very carefully examining old rocks, gems, and the like.

Overcoming the complexity involved when imagining an RNA ribosome and ribozyme that can replicate, and which existed before cells evolved, is daunting.

Especially when considering how it must work:
Prominent current ideas on how life emerged on Earth include an RNA world hypothesis in which RNA performed informational as well as catalytic functions
Hammerhead ribozyme HH9
in the absence of both DNA and protein. Demonstration of a self-replicative system based on ribonucleic acid polymers as both information carriers and catalysts would lend support to such a scenario. A pivotal component of this system would be an RNA dependent RNA polymerase ribozyme capable of replicating its own RNA gene. Recent work from the Holliger group at the Laboratory for Molecular Biology in Cambridge has provided synthetic ribozymes that just might foreshadow the future engineering of such self-replicative systems.
Perhaps the closest parallel to the described ribozymes is found among RNA vira that express RNA dependent RNA polymerases, some of which utilize a primer.

A truly self-replicating RNA polymerase ribozyme based system would require that the ribozyme fully replicate its own RNA gene (unlike present day DNA dependent RNA polymerases that do not transcribe the promoter region), including any ssC19 type docking sites on the template. The encoding RNA gene would have to be relatively unstructured to allow efficient primer extension of the entire sequence, and there would need to be a mechanism for strand separation to enable replicative turnover. Even if these requirements can be met, the present ribozymes capable of maximally synthesizing a 95 nt RNA transcript would still fall short of copying their own gene of 187 nt thus precluding their immediate use for self-sustained replication.
(A ribozyme transcribed by a ribozyme, PDF version). The Hammerhead Ribozyme (HHR) has been found in a surprising number of genomes.

That includes genomes of the virus realm (e.g. The ubiquitous hammerhead ribozyme), and in point of fact it was first found in the viral / sub-viral realm:
The first hammerheads were discovered in viroids and plant satellite RNA viruses where they process RNA transcripts containing multimeric genomes to yield individual genomic RNAs. Representatives of this ribozyme class have been studied extensively for the past 25 years because their small size and fundamental catalytic activity make them excellent models for RNA structure-function research.
(Identification of Hammerhead Ribozymes). The Hammerhead ribozyme HH9, shown in the graphic just above, is RNA based, and is composed of Cytocene, Guanine, Adenine, and Uracil (C,G,A,U).

Similar candidates for pre-cellular virus ribosomes or ribozymes might be found in non-living ancient virus-like entities that were the forerunners of some of these:

"Defective interfering (DI) RNAs are subviral RNAs produced during multiplication of RNA viruses by the error-prone viral replicase. DI-RNAs are parasitic RNAs that are derived from and associated with the parent virus, taking advantage of viral-coded protein factors for their multiplication. Recent advances in the field of DI RNA biology has led to a greater understanding about generation and evolution of DI-RNAs as well as the mechanism of symptom attenuation. Moreover, DI-RNAs are versatile tools in the hands of virologists and are used as less complex surrogate templates to understand the biology of their helper viruses. The ease of their genetic manipulation has resulted in rapid discoveries on cis-acting RNA replication elements required for replication and recombination. DI-RNAs have been further exploited to discover host factors that modulate Tomato bushy stunt virus replication, as well as viral RNA recombination. This review discusses the current models on generation and evolution of DI-RNAs, the roles of viral and host factors in DI-RNA replication, and the mechanisms of disease attenuation." (Defective Interfering RNAs)
satellite virus / helper virus

"Plant viruses often contain parasites of their own, referred to as satellites. Satellite RNAs are dependent on their associated (helper) virus for both replication and encapsidation. Satellite RNAs vary from 194 to approximately 1,500 nucleotides (nt). The larger satellites (900 to 1,500 nt) contain open reading frames and express proteins in vitro and in vivo, whereas the smaller satellites (194 to 700 nt) do not appear to produce functional proteins. The smaller satellites contain a high degree of secondary structure involving 49 to 73% of their sequences, with the circular satellites containing more base pairing than the linear satellites. Many of the smaller satellites produce multimeric forms during replication. There are various models to account for their formation and role in satellite replication. Some of these smaller satellites encode ribozymes and are able to undergo autocatalytic cleavage. The enzymology of satellite replication is poorly understood, as is the replication of their helper viruses. In many cases the coreplication of satellites suppresses the replication of the helper virus genome. This is usually paralleled by a reduction in the disease induced by the helper virus; however, there are notable exceptions in which the satellite exacerbates the pathogenicity of the helper virus, albeit on only a limited number of hosts. The ameliorative satellites are being assessed as biocontrol agents of virus-induced disease. In greenhouse studies, satellites have been known to "spontaneously" appear in virus cultures. The possible origin of satellites will be briefly considered." (Satellite RNAs of plant viruses)

"Viroids are unique infectious agents that are restricted to the plant kingdom, and are composed solely of a non-protein-encoding, small (246–401 nucleotide (nt)), single-stranded circular RNA that is able to replicate autonomously in susceptible hosts ... Viroids have similarities with two other classes of RNA replicon—namely, certain satellite RNAs of plant viruses (Mayo et al, 2005) and the RNA of hepatitis delta virus (HDV; Mason et al, 2005), because their genomes all have a circular structure and they replicate through a rolling-circle mechanism.
- (Viroids: an Ariadne's thread into the RNA labyrinth)

"Prion proteins are the infectious pathogens that cause Mad Cow Disease and Creutzfeldt-Jakob disease. They occur when a normal prion protein becomes deformed and clumped. The naturally occurring prion protein is harmless and can be found in most organisms. In humans, it is found in our brain cell membrane. By contrast, the abnormally deformed prion protein is poisonous for the brain cells. Adriano Aguzzi, Professor of Neuropathology at the University of Zurich and University Hospital Zurich, has spent many years exploring why this deformation is poisonous. Aguzzi's team has now discovered that the prion protein has a kind of "switch" that controls its toxicity." (Flexible tail of the prion protein poisons brain cells)
"Our work supports the hypothesis that a protein can serve as an element of genetic inheritance. This protein–only mechanism of inheritance is propagated in much the same way as hypothesized for the transmission of the protein–only infectious agent in the spongiform encephalopathies; hence these protein factors have been called yeast prions. Our work has focused on [PSI+], a dominant cytoplasmically inherited factor that alters translational fidelity.This change in translation is produced by a self–perpetuating change in the conformation of the translation–termination factor, Sup35. Most recently, we have determined that new elements of genetic inheritance can be created by deliberate genetic engineering, opening prospects for new methods of manipulating heredity. We have also uncovered evidence that other previously unknown elements of protein–based inheritance are encoded in the yeast genome. Finally, we have begun to use yeast as a model system for studying human protein folding diseases, such as Huntington's disease. Proteins responsible for some of these diseases have properties uncannily similar to those that produce protein–based mechanisms of inheritance." -(Investigating protein conformation–based inheritance and disease in yeast).
Although the identity and general properties of prions are now well understood, the mechanism of prion infection and propagation remains mysterious.
One idea, the "Protein X" hypothesis, is that an as-yet unidentified cellular protein (Protein X) enables the conversion of PrPC to PrPSc by bringing a molecule of each of the two together into a complex.
(The Prion Molecule).
While finding molecular machines is quite easy for molecular machinists, even molecular machines with two motors, it is difficult or impossible to determine the age of a molecule or a molecular machine.

This is because they are made of atoms which do not age as living things do.

Perhaps the "fossils" have been right in front of our eyes all along, since they do not die because they are not alive?

The next post in this series is here, the previous post in this series is here.

Wednesday, April 9, 2014

On the Origin of the Genes of Viruses - 6

Our 3rd generation solar system (click to enlarge)
In the previous post of this series, it was noted that scientific sources indicate that no significant carbon was created during the Big Bang.

Instead, abiotic evolution in the interiors of stars formed carbon by means of the abiotic robosome's triple-alpha process, then, in order to be available for later biotic evolution of carbon-based life as we know it, this carbon which was formed by abiotic evolution in the first generation stars, was later ejected in a supernova explosion, to then be scattered into space as dust.

Abiotic gravitational forces acting upon that ejected dust-material eventually, via abiotic evolution, formed a second generation star and solar system, which eventually also went through the supernova explosion to once again eject dust-material into space.

Once again abiotic gravity acted on that ejected material to form a third-generation star system, our solar system.

Whether or not intervals of biotic evolution formed carbon-based-life on any planets near the stars which had been formed by abiotic evolution during the first or second generation solar systems, biotic evolution has done so in this the third generation of an abiotic evolution generated solar system (You Are Here).

In the previous post I characterized that repetitively cycling cosmic system as a cosmic abiotic robosome which assembles, disassembles, and manipulates molecules into stars and planets as does, in principle, a ribosome produced by biotic evolution here on the 3rd generation solar system's planet Earth.

In the fourth post of the series I talked about the ribozyme in terms of it being a similar molecular machine when compared to a ribosome, only the ribozyme is less complex in terms of the assembly, disassembly, and/or manipulation of molecules.

Then, in the previous post of this series I wrote: "In the next post we will look closer to try to find an abiotic genetic replicator (e.g. "robozyme") for ancient RNA-virus genes".

In the macro sense this third generation solar system is produced by a cosmic abiotic robozyme in the sense that the robozyme does not continue the cycle of the cosmic abiotic robosome.

The cosmic robosome which cyclically reproduces solar systems out of molecular material, with an incrementally smaller and smaller star at the center of each successive solar system ... until ...

... the third generation star, in this case our Sun, will not go supernova but instead will
Sun becomes a red-giant & destroys some planets
become a Red Giant that will destroy any carbon-based life that has evolved on any planets near it, and it will even destroy some of the inner planets too (Life According To Science).

Eventually, during this abiotic evolution the Sun will shrink down from a Red Giant into a white dwarf star, and the remaining planets that are formed by this ongoing abiotic evolution will re-align into different orbits that are closer to their then much smaller star.

These super-intervening cosmic dynamics of assembling, manipulating then destroying
White dwarf Sun & remaining planets
molecular clouds and solar systems repetitively is all abiotic evolution, not biotic evolution.

Within those dynamics of the cosmic abiotic robosome as it were, are intervals of subsystem dynamics, that is, biotic evolution taking place on planets which have been formed by the overarching abiotic evolution.

Let's note that further abiotic evolution may take place as the Sun abiotically evolves into a Red Giant, evaporates inner planets, and warms planets that were once outside the zone where biotic evolution takes place.

After that, when the Sun abiotically evolves into a much smaller white dwarf star, and the planets are, through abiotic gravity moved closer to the then cooler Sun, biotic evolution may once again activate after the dynamics of abiotic evolution have made biotic evolution once again possible.

So, to accentuate the differences between abiotic evolution and biotic evolution, I label those sub-system dynamics a cosmic abiotic robozyme as it were, like the sub-system dynamics of a ribozyme, which also manipulates molecules within biotic carbon-based life.

Now that the stage has been set, the next post will narrow the focus to both abiotic evolution and biotic evolution that takes place on planets near the central star.

That is, the evolution which produces an "RNA world" where viruses emerge.

The next post in this series is here, the previous post in this series is here.

It is National Poetry Month.

by Dredd

Call a cosmic robosome
a dizzying molecular machine,
like life's ribosome.

Sky factories extraordinaire,
call it abiotic,
assembling stars & planets.
Circles and orbits,
globes and rings,
again once again,
simple to complex,
little to big to little,
darkness to breathtaking.

Assembling likeness
with forces, plasmas, & quanta,
until the third one charms.

Call a cosmic robozyme
a web in a space of endless,
like life's ribozyme.

Call it ancient,
modern, young, new, or old,
it is all the same.

Tuesday, April 8, 2014

On the Origin of the Genes of Viruses - 5

Cosmic abiotic "robosome"
In the second post of this series I wrote about a "place where only forces, quanta, molecules, and atoms existed, but nevertheless a place that some evolutionary hypotheses say we can explore, because a lot of scientists have been pondering that ["place"] for a long time".

That "place" is depicted in the graphic to the left (click to enlarge).

The "primeval atom" of Big Bang theory generated a molecular cloud which eventually condensed into stars that eventually went nova or supernova to then form another molecular cloud, which eventually condensed into yet another star.

You may have noticed that I labeled the "primeval atom", together with the processes
Ribosome: a molecular machine
and parts in it, as a "cosmic abiotic robosome", which is of course a play on the word "ribosome."

In the previous post of this series it was noted that a ribosome is "a large and complex molecular machine", that is, a molecular machine factory within carbon-based living cells which manipulates and/or produces molecules for various genetic purposes (see graphic to the right).

In abiotic evolution terminology the entity that produced the Big Bang is a cosmic abiotic robosome which eventually produced a molecular cloud that condensed into a star or stars, which also eventually produced subsequent molecular clouds.

But more than that, the condensing of the molecular cloud by the cosmic abiotic robosome also produced planets.

The cosmic abiotic robosome, like the earthly biotic ribosome within carbon-based life forms, has its own way of replicating things:
The very earliest universe was so hot, or energetic, that initially no particles existed or could exist (except perhaps in the most fleeting sense), and the forces we see around us today were believed to be merged into one unified force. Space-time itself expanded during an inflationary epoch due to the immensity of the energies involved. Gradually the immense energies cooled – still to a temperature inconceivably hot compared to any we see around us now, but sufficiently to allow forces to gradually undergo symmetry breaking, a kind of repeated condensation from one status quo to another, leading finally to the separation of the strong force from the electroweak force and the first particles.

In the second phase, this quark–gluon plasma universe then cooled further, the current fundamental forces we know take their present forms through further symmetry breaking – notably the breaking of electroweak symmetry – and the full range of complex and composite particles we see around us today became possible, leading to a gravitationally dominated universe, the first neutral atoms (~ 80% hydrogen), and the cosmic microwave background radiation we can detect today. Modern high energy particle physics theories are satisfactory at these energy levels, and so physicists believe they have a good understanding of this and subsequent development of the fundamental universe around us. Because of these changes, space had also become largely transparent to light and other electromagnetic energy, rather than "foggy", by the end of this phase.

The third phase started after a short dark age with a universe whose fundamental particles and forces were as we know them, and witnessed the emergence of large scale stable structures, such as the earliest stars, quasars, galaxies, clusters of galaxies and superclusters, and the development of these to create the kind of universe we see today. Some researchers call the development of all this physical structure over billions of years "cosmic evolution". Other, more interdisciplinary, researchers refer to "cosmic evolution" as the entire scenario of growing complexity from big bang to humankind, thereby incorporating biology and culture into a grand unified view of all complex systems in the universe to date.
(Chronology of the Universe, Wikipedia, emphasis added). The cosmic abiotic robosome eventually produced carbon as well as the planet Earth:
Formation of the carbon atomic nucleus requires a nearly simultaneous triple collision of alpha particles (helium nuclei) within the core of a giant or supergiant star which is known as the triple-alpha process, as the products of further nuclear fusion reactions of helium with hydrogen or another helium nucleus produce lithium-5 and beryllium-8 respectively, both of which are highly unstable and decay almost instantly back into smaller nuclei. This happens in conditions of temperatures over 100 megakelvin and helium concentration that the rapid expansion and cooling of the early universe prohibited, and therefore no significant carbon was created during the Big Bang. Instead, the interiors of stars in the horizontal branch transform three helium nuclei into carbon by means of this triple-alpha process. In order to be available for formation of life as we know it, this carbon must then later be scattered into space as dust, in supernova explosions, as part of the material which later forms second, third-generation star systems which have planets accreted from such dust. The Solar System is one such third-generation star system.
(Wikipedia, Carbon Formation, emphasis added; cf. NASA). This means that our Sun and our Earth have descended from an ancestor star that exploded and emitted a molecular cloud which then condensed to form a second ancestor star that did the same, i.e. formed a molecular cloud that condensed into the Sun and the planets of our solar system.

Thus, the cosmic abiotic robosome is composed of cosmic "parts" as it were: forces, plasmas, quanta, atoms, molecules, planets, stars, and galaxies.

The ribosome within carbon-based life forms is also composed of many parts as it were (The Uncertain Gene - 8).

In the next post we will look closer to try to find an abiotic genetic replicator (e.g. "robozyme") for ancient RNA-virus genes.

The next post in this series is here, the previous post in this series is here.

It is National Poetry Month. The following poem by Sylvia Plath seems to describe the cosmic abiotic robosome philosophy quite well.

Lady Lazarus
by Sylvia Plath

I have done it again.
One year in every ten
I manage it--

A sort of walking miracle, my skin
Bright as a Nazi lampshade,
My right foot

A paperweight,
My face a featureless, fine
Jew linen.

Peel off the napkin
O my enemy.
Do I terrify?--

The nose, the eye pits, the full set of teeth?
The sour breath
Will vanish in a day.

Soon, soon the flesh
The grave cave ate will be
At home on me

And I a smiling woman.
I am only thirty.
And like the cat I have nine times to die.

This is Number Three.
What a trash
To annihilate each decade.

What a million filaments.
The peanut-crunching crowd
Shoves in to see

Them unwrap me hand and foot--
The big strip tease.
Gentlemen, ladies

These are my hands
My knees.
I may be skin and bone,

Nevertheless, I am the same, identical woman.
The first time it happened I was ten.
It was an accident.

The second time I meant
To last it out and not come back at all.
I rocked shut

As a seashell.
They had to call and call
And pick the worms off me like sticky pearls.

Is an art, like everything else.
I do it exceptionally well.

I do it so it feels like hell.
I do it so it feels real.
I guess you could say I've a call.

It's easy enough to do it in a cell.
It's easy enough to do it and stay put.
It's the theatrical

Comeback in broad day
To the same place, the same face, the same brute
Amused shout:

'A miracle!'
That knocks me out.
There is a charge

For the eyeing of my scars, there is a charge
For the hearing of my heart--
It really goes.

And there is a charge, a very large charge
For a word or a touch
Or a bit of blood

Or a piece of my hair or my clothes.
So, so, Herr Doktor.
So, Herr Enemy.

I am your opus,
I am your valuable,
The pure gold baby

That melts to a shriek.
I turn and burn.
Do not think I underestimate your great concern.

Ash, ash--
You poke and stir.
Flesh, bone, there is nothing there--

A cake of soap,
A wedding ring,
A gold filling.

Herr God, Herr Lucifer

Out of the ash
I rise with my red hair
And I eat men like air.

Monday, April 7, 2014

The Rehabilitation of High Priest Bush II - 2

"Like, if you want my bro to be next preznit"
The alchemists, witchy brewers, and warmongering filth peddlers in McTell News, who work feverishly for the Epigovernment, are all aTwitter and very exuberant over something they can't get over.

They miss the genetic descendants of Oilah Akbar, that is, they miss those who engineered global pollution caused global warming, and who still haphazardly lead Oil-Qaeda, yes, they miss the oil barons who are still prominent in the evolution of the death of our current civilization.

"It ain't no dynasty from Dallas"
The Supreme Five, who, in Foreign Citizens United v FEC and McCutcheon v FEC let loose one of the few restraints remaining on the 1% Plutocracy's ability to outright buy elections, by putting elections on sale at a discount.

It is just another coup in a long line of incremental coups that have been changing America into Amurka (A Tale of Coup Cities, A Tale of Coup Cities - 9).

Not many would have thought that they would ever try to rehabilitate the bushies in the eyes of the public, but Dredd Blog did:
Jeb Bush can't run for president unless and until his Big Brother Bush II is seen in a better light.

MOMCOM is going to try to wash the brains of the people, yes, scrub them so hard that her favorite bushie will be loved by all once again.

Don't misunderestimate High Priest Bush II, or misunderinvestigate this seemingly impossible propaganda task, because they are deceit on steroids.
(Dredd Blog, November 9, 2010; cf. Leadership: The Lost Art). Now that the traffic cop on steroids, Governor Chris Christie of New Jersey, has soiled his pants, Jebber The Whut is going to try to step into his large shoes.

Meanwhile, Karl "We Make Reality" Rove has promised the Jebber that he can win, for a cool billion buckos ("thanks supreme five"), and all the sycophants have nodded their wobble-heads toward heaven, praising Saint Adelson of Las Vegas.

So, the horse-shit race is on.

The next post in this series is here, the previous post in this series is here.

"Pour some sugar on me ..." - Bill Maher (click the YouTube button lower right)