Saturday, April 5, 2014

American Feudalism - 9

MoreDough Castle -- The Eye of Sauron (all photos by Guardian)
The Supreme Five have given the go ahead for the Epigovernment to put their wealthy weight upon the scales of justice, the scales of the news media, the scales of electoral politics, and the scales of our culture.

Basically they repeated the Occupy Wall Street complaint that "money talks", but in doing so in their own Supreme Five Speak they cleared things up by saying that "when money talks our party listens" to the jingle-jangled power rhythms of our bustling plutocracy (The Supremes Are Well Oiled - 3).

"Oh," they continued, "and American money is printed with the ink of 'protected speech' under the First Amendment of the U.S. Constitution, so long as it is printed by our plutocratic 3D printers" to wit:
The right to participate in democracy through political contributions is
Supreme Headquarters
protected by the First Amendment, but that right is not absolute. Congress may regulate campaign contributions to protect against corruption or the appearance of corruption ... It may not, however, regulate contributions simply to reduce the amount of money in politics, or to restrict the political participation of some in order to enhance the relative influence of others.
(McCutcheon v FEC). Oyez, Oyez, oh yeah, oh yeah sayeth the vassals, because now only the Supreme Five can "restrict the political participation of some in order to enhance the relative influence of others."

A serf's home is his master's castle
Legal critics say that this bastard child of Foreign Citizens United v FEC is "protecting speech", not "protected speech."

This is so, because MoreDough Speech has been protecting the vassals who live on the Iron Islands along the Bubble Coast, just east of the terminus of Highway 61.

The "United States" are not so united, America is not so democratic, and the supreme umpire of the private empire is also experiencing one decline after another decline (A Decline Of The American Republic - 3).

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

Money, Pink Floyd

Friday, April 4, 2014

On the Origin of the Genes of Viruses - 4

Machines assembling parts into a complete machine
Today, we take a first glance into the evolution of the ribosome, which is a sophisticated molecular machine that makes and/or assembles other molecular machines, such as RNA and/or DNA, and the like (Wikipedia).

The ribosome has also been called a molecular factory that perhaps can be envisioned metaphorically by the photo to the left.

In this hypothetical look at the evolution of the ribosome (perhaps we should call its earliest manifestations a "robosome"), let's first remember one principle we talked about yesterday, which is that evolution in general is said to proceed from simple to complex.

So, let's boil this down and apply it to molecular machine evolution with this basic principle: all parts of a machine must actually exist before the complete machine itself can actually be made to exist (i.e. assembled).

Whether you are building a model car or a model airplane, or even real ones, you must first have all the parts before you can assemble those parts into a complete vehicle.

The factory in the photo at the top of this post could not assemble a complete entity, in this case an automobile, if any part was missing or did not yet exist.

That is the hypothetical model I am following to articulate how the "robosome" / ribosome must have incrementally evolved part by part, piece by piece, and simple to complex (some viruses still have molecular motors that help with genetic work -- see this).

Before proceeding to the parts, notice that we have a modern example of a primitive or prototypical ribosome:
... at the MRC Laboratory of Molecular Biology in Cambridge, UK, have created synthetic molecules that copy genetic material. The enzyme, tC19Z, that has been synthesised could be an artificial version of one of the first enzymes that ever existed on our planet three billion years ago -- and a clue to how life itself got started. Their goal is to create fully self-replicating RNA molecules in the lab.

The dominant theory of how life started involves the emergence in Earth's early history of a self-replicator -- the original molecule of life was an RNA that could make copies of other RNAs, including itself.

As evolution advanced, this self-replicating molecule ceased to exist, with the majority of Earth's organisms using DNA to store their genetic information while using other enzymes to copy itself.

Led by Philipp Holliger, the Cambridge-based reseach team have tested a theory called the "RNA World Hypothesis", which suggests that life was originally based not on DNA but on a related chemical called RNA, which can carry genetic information and fold-up into three-dimensional shapes and function as an enzyme, the biological catalyst that speeds up certain chemical reactions.

Holliger’s group started with an RNA enzyme called R18, which could make copies of other short pieces of RNA, although in an error-prone manner. "It’s like a keyboard with which you can only write one or two words," says Holliger.

To evolve this initial R18 RNA, the group created 50 million clones, each containing random genetic changes in the RNA sequence, and selected those with the best RNA-copying abilities. And by repeating this process a number of times, they generated progressively more powerful enzymes.

"We took all the beneficial mutations that had accumulated from various selection experiments, sorted out what’s helpful and what’s not, and combined them into a single molecule," explains Holliger.

The RNA enzyme tC19Z, created by Philipp Holliger and colleagues, functions like a self-replicator. Until now, the only known RNA-copying RNA was a molecule called R18, which can only copy RNA segments up to 14 "letters" long, and only works on certain sequences.

Holliger made a vast library of thousands of different versions of the R18 molecule and screened them to see which ones made more copies. After several cycles of copying variants and looking for new improvements, he found several, which he baked into his final synthetic enzyme, tC19Z.

tC19Z can reliably copy RNA sequences up to 95 letters long, a sevenfold increase on R18. Its performance varies depending on the sequence it's copying, but it is much less picky than R18. Holliger compares R18 to a sports car that works only on a smooth, flat road. "We have fitted a four-wheel drive, so it can go off-road a bit," he told
(Biologists Create Self-replicating RNA Molecule, cf. Wikipedia "Ribozyme"). The development of the replication dynamics in that lab went from simple to complex.

Eventually, they ended up with a working model of what is a conceptual form of a partial or primitive ribosome or ribozyme.

Another metaphor, in addition to the photo at the top of this post, might be a garage factory that evolved into the modern Apple Computer factory.

Metaphor aside, there are peer-reviewed papers which articulate the hypothesis of the dynamics of RNA abiotic evolution:
"Discoveries demonstrating that RNA can serve genetic, catalytic, structural, and regulatory roles have provided strong support for the existence of an RNA World that preceded the origin of life as we know it. Despite the appeal of this idea, it has been difficult to explain how macromolecular RNAs emerged from small molecules available on the early Earth." (The origin of the RNA world)
"It is now generally accepted that our familiar biological world was preceded by an RNA world in which ribosome-catalyzed, nucleic-acid coded protein synthesis played no part. If the RNA world was the first biological world there is little that one can learn from biochemistry about prebiotic chemistry, except that the formation and polymerization of nucleotides were once prebiotic processes. If the RNA world was not the first biological world, the above conclusion may not be justified, and one can speculate that the monomers of earlier genetic polymers might be recognizable as important biochemicals. This suggests that the construction of replicating polymers from simple, not necessarily standard, aminoacids should be explored." (Some consequences of the RNA world hypothesis).
"The general notion of an “RNA World” is that, in the early development of life on the Earth, genetic continuity was assured by the replication of RNA and genetically encoded proteins were not involved as catalysts. There is now strong evidence indicating that an RNA World did indeed exist before DNA- and protein-based life. However, arguments regarding whether life on Earth began with RNA are more tenuous. It might be imagined that all of the components of RNA were available in some prebiotic pool, and that these components assembled into replicating, evolving polynucleotides without the prior existence of any evolved macromolecules." (The Origins of the RNA World)
"This year marks the 50th anniversary of a proposal by Alex Rich that RNA, as a single biopolymer acting in two capacities, might have supported both genetics and catalysis at the origin of life. We review here both published and previously unreported experimental data that provide new perspectives on this old proposal." (The “Strong” RNA World Hypothesis: Fifty Years Old)
(see also Wikipedia, "RNA World Hypothesis"). Carbon-based living parts are the essential parts for biotic evolution to assemble into complete entities, so, until carbon-based life existed only abiotic evolution could take place.

Yes, abiotic evolution via abiotic mutation and abiotic-selection (before Darwinian "natural selection" yet existed) is to be explored further in future posts (the next post considers the cosmic abiotic robosome).

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

Thursday, April 3, 2014

On the Origin of the Genes of Viruses - 3

RNA & DNA: post-carbon
This series is an unusual one in the sense of daily sequential posts.

Usually, I mix different subjects from day to day, one day it is politics, another day it is climate change, another day some evolution, and so on.

Anyway, in today's post I have to present my hypothesis again.

It has to do with why there is confusion among scientific researchers and teachers about which came first viruses or cells, which came first RNA or DNA, and which came first abiotic evolution or biotic evolution (The Uncertain Gene - 9).

These and related matters incessantly come up when discussing "the evolution of life" --especially when there is no consensus as to what "life" is.

I attribute seven sources to this confusion, which will be discussed today, to wit:
1) interdisciplinary walls
2) teleology
3) carbon ignorance
4) quantum uncertainty
5) evolution from simple to complex
6) virus ignorance
7) propaganda via evangelism
So, let's go through the list as we look at some examples in papers and in Dredd Blog System posts to show how egregious and ubiquitous the problem is.

I. Interdisciplinary Walls

This is an old and persistent problem within the biological sciences as shown by what is called the great synthesis (and a few other names I won't mention):
The modern synthesis solved difficulties and confusions caused by the specialisation and poor communication between biologists in the early years of the 20th century.
(Wikipedia, "Modern evolutionary synthesis", emphasis added). I have pointed out that particular problem time and again (The Uncertain Gene - 2).

Any wall between disciplines is also a problem in the struggle to fabricate a scientific subject-matter nomenclature that is stable enough to cross over boundaries, for example, boundaries between quantum physics and evolutionary biology (If Cosmology Is "Off," How Can Biology Be "On?").

II. Teleology

The teleology discipline is a study of the use of magic language in scientific papers and discourse (The Uncertain Gene - 3).

The use of the word "selfish" when applied to scientific discussions of machinery, i.e. genes, is an example of teleological language which is not professional, because it is not useful (machines are not selfish or unselfish - duh!).

Nevertheless, this magic language continues unabated even with competent scientists (see propaganda via evangelism below), and is also used even in otherwise competent papers:
Under this concept, the principal lineages of viruses and related selfish agents emerged from the primordial pool of primitive genetic elements, the ancestors of both cellular and viral genes. Thus, notwithstanding the numerous gene exchanges and acquisitions attributed to later stages of evolution, most, if not all, modern viruses and other selfish agents are inferred to descend from elements that belonged to the primordial genetic pool.
(Koonin 2006, emphasis added). No, genes are not alive, not selfish, they are molecular machine parts, that is, they are parts in RNA and DNA molecular machines, which are not alive (The Uncertain Gene - 8).

Regular readers know that Dredd Blog provides an example of a more professional use of nomenclature by using the phrase "the uncertain gene."

That is an exacting nomenclature in the context of quantum mechanical proton tunneling as well as its direct impact on genes (see The Uncertain Gene).

III. Carbon Ignorance

By "ignorance" I mean ignoring the established scientific consensus that carbon evolved within stars after stars evolved then went nova, or otherwise ejected their carbon into space.

After carbon was ejected into space it eventually, in some locations in the cosmos, became parts of the molecules of carbon-based life forms.

Until carbon arrived, the chemical structure of pre-RNA would not have contained carbon, so in future posts that will be discussed, because pre-carbon-RNA would be different from post-carbon-RNA.

IV. Quantum Uncertainty

The RNA molecule, with its many genes, can evolve through mutation without any carbon existing, i.e. without the existence of carbon-based life forms.

One way that could take place was pointed out in the first post of the series:
"In this paper we have pointed out that, since the protons are not classical particles but "wave packets" obeying the laws of modern quantum theory, the genetic code cannot --in spite of all precautions-- be 100% stable. Due to the quantum-mechanical "tunnel effect," there is always a small but finite probability that the protons will change place, alter the genetic code, and give rise to mutations.
(The Uncertain Gene). This can happen to DNA or to RNA, however, RNA was exposed to quantum proton tunneling before DNA was, assuming RNA evolved first of course.

V. Evolution From Simple To Complex

Notice again the graphic of RNA and DNA at the top of the post.

Look at the RNA genetic molecular machine system, and then look at the DNA genetic molecular machine system, and it is readily apparent that the RNA molecule is less complex and simpler than the DNA.

This is another reason to expect or assume that RNA was going through genetic evolution prior to DNA.

VI. Virus Ignorance

Again, what I mean by "ignorance" is our ignoring of viruses because they were defined as not alive, not living, and not a carbon-based life form.

Now, we find out that they are by very, very far the greatest population of entities that contain RNA or DNA:
There are an estimated 1031 viruses on Earth. That is to say: there may be a hundred million times more viruses on Earth than there are stars in the universe.
(On the Origin of the Genes of Viruses). It is a no-brainer to realize that it is about a hundred years late that we now begin to study them in earnest:
Now, with the recent discovery of a truly monstrous virus, scientists are again casting about for how best to characterize these spectral life-forms. The new virus, officially known as Mimivirus (because it mimics a bacterium), is a creature "so bizarre," as The London Telegraph described it, "and unlike anything else seen by scientists . . . that . . . it could qualify for a new domain in the tree of life." Indeed, Mimivirus is so much more genetically complex than all previously known viruses, not to mention a number of bacteria,that it seems to call for a dramatic redrawing of the tree of life.

"This thing shows that some viruses are organisms that have an ancestor that was much more complex than they are now," says Didier Raoult, one of the leaders of the research team at the Mediterranean University in Marseille, France, that identified the virus. "We have a lot of evidence with Mimivirus that the virus phylum is at least as old as the other branches of life and that viruses were involved very early on in the evolutionary emergence of life."

That represents a radical change in thinking about life's origins: Viruses, long thought to be biology's hitchhikers, turn out to have been biology's formative force.

This is striking news, especially at a moment when the basic facts of origins and evolution seem to have fallen under a shroud. In the discussions of intelligent design, one hears a yearning for an old-fashioned creation story, in which some singular, inchoate entity stepped in to give rise to complex life-forms—humans in particular. Now the viruses appear to present a creation story of their own: a stirring, topsy-turvy, and decidedly unintelligent design wherein life arose more by reckless accident than original intent, through an accumulation of genetic accounting errors committed by hordes of mindless, microscopic replication machines. Our descent from apes is the least of it. With the discovery of Mimi, scientists are close to ascribing to viruses the last role that anyone would have conceived for them: that of life's prime mover.
(Unintelligent Design, Discover). Yes, we have formulated our theories of genetic mutation and other evolutionary concepts without seriously considering what is  by very far the greatest population of entities that contain genes.

VII. Propaganda via Evangelism

Bloviating about "selfish genes" for decade upon decade, as if genes were not molecular abiotic entities, as if genes were alive, is not at all laudable.

What is shameful is the hateful rhetoric and propaganda spewed by teleological evangelists who have now made it into several books about the origin of assholes (On The Origin of Assholes).


So, I move on in this series, noting that there is some debate as to whether or not the RNA world preceded the DNA world, and whether the form of the first genetic evolution took place because of viruses or instead because of cells.

For example, consider:
The “RNA world” hypothesis, first promoted in 1986 in a paper in the journal Nature and defended and elaborated on for more than 25 years, posits that the first stages of molecular evolution involved RNA and not proteins, and that proteins (and DNA) emerged later ... “I’m convinced that the RNA world (hypothesis) is not correct,” Caetano-Anollés said. “That world of nucleic acids could not have existed if not tethered to proteins.”
“This is a very engaging and provocative article by one of the most innovative and productive researchers in the field of protein evolution,” said University of California at San Diego research professor Russell Doolittle, who was not involved in the study. Doolittle remains puzzled, however, by “the notion that some early proteins were made before the evolution of the ribosome as a protein-manufacturing system.” He wondered how – if proteins were more ancient than the ribosomal machinery that today produces most of them –“the amino acid sequences of those early proteins were ‘remembered’ and incorporated into the new system.”

Caetano-Anollés agreed that this is “a central, foundational question” that must be answered.

“It requires understanding the boundaries of emergent biological functions during the very early stages of protein evolution,” he said. However, he said, “the proteins that catalyze non-ribosomal protein synthesis – a complex and apparently universal assembly-line process of the cell that does not involve RNA molecules and can still retain high levels of specificity – are more ancient than ribosomal proteins. It is therefore likely that the ribosomes were not the first biological machines to synthesize proteins.”
(Study of ribosome evolution challenges RNA world hypothesis). Caetano-Anollés does not seem to realize that ribosomes, like everything else,  evolved from simple to complex.

Which means that ribosomes which today process molecules with carbon in them (DNA) had to evolve after carbon had evolved.

Thus, pre-ribosomes that process pre-carbon RNA and had no carbon molecules to work with, are the likely candidate ribosomes to have evolved first, and to have been more simple.

Finally, ribosomes that process both RNA and DNA are still that way today ("Ribosomes from bacteria, archaea and eukaryotes ... differ in their size, sequence, structure, and the ratio of protein to RNA") as was mentioned in the previous post of this series (On the Origin of the Genes of Viruses - 2).

That will be the focus of the next post in this series: the evolution of ribosomes.

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

Wednesday, April 2, 2014

On the Origin of the Genes of Viruses - 2

RNA & DNA: post-carbon
Using our "mind's eye", our imagination, can we place ourselves inside the world which was on Earth in an epoch that evolutionary scientists say existed prior to the time when carbon-based life forms first appeared?

A world on Earth where the beginnings of viruses are said to be found in a gene pool before carbon-based life forms existed?

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 world for a long time:
Recent advances in genomics of viruses and cellular life forms have greatly stimulated interest in the origins and evolution of viruses and, for the first time, offer an opportunity for a data-driven exploration of the deepest roots of viruses. Here we briefly review the current views of virus evolution and propose a new, coherent scenario that appears to be best compatible with comparative-genomic data and is naturally linked to models of cellular evolution that, from independent considerations, seem to be the most parsimonious among the existing ones.
The existence of several genes that are central to virus replication and structure, are shared by a broad variety of viruses but are missing from cellular genomes (virus hallmark genes) suggests the model of an ancient virus world, a flow of virus-specific genes ... existence of a complex, precellular, compartmentalized but extensively mixing and recombining pool of genes ...
(The ancient Virus World and evolution of cells, emphasis added). That would be the genes of viruses (e.g. virions, viroids, or other first-time prototypes of viruses) that existed prior to carbon-based single cell life forms.

So, where did these genes come from, these non-living genes, these molecular entities that are still non-living genes, these genes that are still non-living molecular entities in us all in today's world on Earth?

When we look at modern viruses they lack what their host cells do not lack, which is the ribosome (The ribosome ... is a large and complex molecular machine. - Wikipedia, "Ribosome") which now does various types of genetic manipulation of the RNA and/or DNA instead of the viruses themselves doing it with their own internal complex molecular machinery.

The RNA of early viruses before carbon-based life evolved was processed in a different manner than it is now.
Ribosome: a sophisticated molecular machine

The modern virus needs a host with ribosome molecular machinery in order to reproduce.

But, where was the ribosome in the pre-cellular world of viruses we are thinking about today?

The ribosomes of the major cell types differ from one another: "Ribosomes from bacteria, archaea and eukaryotes (the three domains of life on Earth) differ in their size, sequence, structure, and the ratio of protein to RNA" (ibid, Wikipedia, "Ribosomes").

Previously we noted that in addition to the ribosome's molecular machinery, smaller molecular machines associated with genetic dynamics have been discovered:
"We took this approach because so many RNAs are rapidly destroyed soon after they are made, and this makes them hard to detect," Pugh said. "So rather than look for the RNA product of transcription we looked for the 'initiation machine' that makes the RNA. This machine assembles RNA polymerase, which goes on to make RNA, which goes on to make a protein." Pugh added that he and Venters were stunned to find 160,000 of these "initiation machines," because humans only have about 30,000 genes. "This finding is even more remarkable, given that fewer than 10,000 of these machines actually were found right at the site of genes. Since most genes are turned off in cells, it is understandable why they are typically devoid of the initiation machinery."

The remaining 150,000 initiation machines -- those Pugh and Venters did not find right at genes -- remained somewhat mysterious. "These initiation machines that were not associated with genes were clearly active since they were making RNA and aligned with fragments of RNA discovered by other scientists," Pugh said. "In the early days, these fragments of RNA were generally dismissed as irrelevant ["junk"] since they did not code for proteins." Pugh added that it was easy to dismiss these fragments because they lacked a feature called polyadenylation -- a long string of genetic material, adenosine bases -- that protect the RNA from being destroyed. Pugh and Venters further validated their surprising findings by determining that these non-coding initiation machines recognized the same DNA sequences as the ones at coding genes, indicating that they have a specific origin and that their production is regulated, just like it is at coding genes.
(Scientists Discover the Origins, emphasis added). So, the ribosome is not the only molecular machine in the game.

The direction this is going is that ancient viruses replicated themselves with pre-ribosome molecular machinery, "pre-ribosomes" which later ended up in cells.

Once there, this hypothesis goes, the pre-ribosome naturally evolved differently within the different types of cells, into what we currently know as the ribosome.

This is reminiscent of a once-rejected scientific theory which is now no longer rejected by scientific consensus:
Thus "symbionticism" and "symbiogenesis" theory could no longer be ignored, because the evidence was mounting:
Entire genomes with their accompanying protein synthetic systems are transferred throughout the biosphere primarily as bacteria and protists which become symbionts as they irreversibly integrate into pre-existing organisms to form more complex individuals. Individualization is stabilized by simultaneous transmission of once-separate heterologous genetic systems. The origin of new species is hypothesized to correlate with the acquisition, integration and subsequent inheritance of such acquired microbial genomes. These processes were recognized by Mereschkovsky (“Symbiogenesis” in Russian, 1909) and by Wallin (“Symbionticism”, see p. 181, this issue).
(Origins of Species). That paper, written by Dr. Lynn Margulis, Department of Biology, University of Massachusetts, concerns "acquired genomes and individuality."
(Are Microbes The Origin of PTSD?). Another interesting paper concerning the ribosome gives some additional perspective:
The modern ribosome was largely formed at the time of the last common ancestor, LUCA. Hence its earliest origins likely lie in the RNA world. Central to its development were RNAs that spawned the modern tRNAs and a symmetrical region deep within the large ribosomal RNA, (rRNA), where the peptidyl transferase reaction occurs. To understand pre-LUCA developments, it is argued that events that are coupled in time are especially useful if one can infer a likely order in which they occurred. Using such timing events, the relative age of various proteins and individual regions within the large rRNA are inferred. An examination of the properties of modern ribosomes strongly suggests that the initial peptides made by the primitive ribosomes were likely enriched for l-amino acids, but did not completely exclude d-amino acids. This has implications for the nature of peptides made by the first ribosomes. From the perspective of ribosome origins, the immediate question regarding coding is when did it arise rather than how did the assignments evolve. The modern ribosome is very dynamic with tRNAs moving in and out and the mRNA moving relative to the ribosome. These movements may have become possible as a result of the addition of a template to hold the tRNAs. That template would subsequently become the mRNA, thereby allowing the evolution of the code and making an RNA genome useful. Finally, a highly speculative timeline of major events in ribosome history is presented and possible future directions discussed.
(Origin and Evolution of the Ribosome, emphasis added). There are some other indicators for an ancient virus world.

Those data indicate that ancient viruses reproduced prior to the existence of the current modern ribosome:
The discovery of a giant virus that falls ill through infection by another virus is fuelling the debate about whether viruses are alive.

“There’s no doubt this is a living organism,” says Jean-Michel Claverie, a virologist at the the CNRS UPR laboratories in Marseilles, part of France’s basic-research agency. “The fact that it can get sick makes it more alive.”

Giant viruses have been captivating virologists since 2003, when a team led by Claverie and Didier Raoult at CNRS UMR, also in Marseilles, reported the discovery of the first monster2. The virus had been isolated more than a decade earlier in amoebae from a cooling tower in Bradford, UK, but was initially mistaken for a bacterium because of its size, and was relegated to the freezer.
Viruses: Dead & Alive?

Closer inspection showed the microbe to be a huge virus with, as later work revealed, a genome harbouring more than 900 protein-coding genes3 — at least three times more than that of the biggest previously known viruses and bigger than that of some bacteria. It was named Acanthamoeba polyphaga mimivirus (for mimicking microbe), and is thought to be part of a much larger family. “It was the cause of great excitement in virology,” says Eugene Koonin at the National Center for Biotechnology Information in Bethesda, Maryland. “It crossed the imaginary boundary between viruses and cellular organisms.”
Now Raoult, Koonin and their colleagues report the isolation of a new strain of giant virus from a cooling tower in Paris, which they have named mamavirus because it seemed slightly larger than mimivirus. Their electron microscopy studies also revealed a second, small virus closely associated with mamavirus that has earned the name Sputnik, after the first man-made satellite.

With just 21 genes, Sputnik is tiny compared with its mama — but insidious. When the giant mamavirus infects an amoeba, it uses its large array of genes to build a ‘viral factory’, a hub where new viral particles are made. Sputnik infects this viral factory and seems to hijack its machinery in order to replicate. The team found that cells co-infected with Sputnik produce fewer and often deformed mamavirus particles, making the virus less infective. This suggests that Sputnik is effectively a viral parasite that sickens its host — seemingly the first such example.
('Virophage' suggests viruses are alive, emphasis added). Well, what it suggests to me is: 1) that some viruses today may be "alive," others not alive, 2) that some viruses can infect other viruses (replicate within another virus), 3) that some may still replicate via another virus' internal mechanisms, and 4) that this is suspected of being done without the modern sophisticated ribosomal molecular machinery within a cell:
"Thus, it seemed reasonable to speculate that the first polynucleotide molecule was initially an RNA polymer that was able to convey genetic information as well as organize amino acids into specific sequences to make proteins.

This article, published in 1962, was probably the first statement to suggest that RNA was the fundamental nucleic acid involved in the origin of living systems." [p. 11]

"These statements were published over 40 years ago. Today we have a wealth of information that strengthens the role of RNA in the early evolution of life. The discovery of ribozymes by Cech and the more recent discovery of micro-RNAs that have a variety of functions in controlling the development of biological systems suggests that these may be trace evidence of what has been called the "RNA world", meaning an era in early evolution in which RNA played a dominant role in both replication and in carrying out a number of chemical modifications leading to the organization of present-day biological systems." [p. 12]
(The Genetic Code and the Origin of Life, PDF, emphasis added). The graphic, above right (Viruses: Dead & Alive?), shows ~14 billion years of abiotic and biotic evolution, while depicting viruses as bridging the gap from the abiotic realm into the biotic realm  (cf. The Uncertain Gene - 9).

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

Tuesday, April 1, 2014

On The Origin of the Genes of Viruses

Does That Mean a "Living" Origin?
Today, I begin a new series about the origin of genes of viruses.

Before anyone can track down the origin or source of something, there are fundamental prerequisites that should first be dealt with, for example, is what you are looking for dead, or to the contrary is it alive?

One would not get to the proper place if one was told that what they are looking for is not alive if in fact it is alive.

By the same token, one would not get to the proper place of origin if one was told that what they are looking for is alive if in fact it is not alive.

"Living" has criteria different from "non-living," so if we look into a very ancient grave while we are searching for a living person, in general we are off on a fool's errand, and consequently will reap a fool's reward.

So, before we begin the search for the origin of genes, we should ask "is a gene alive or is it a non-living entity?"

But, since this search also involves viruses, in the sense that when we ask "where will we find virus genes", we must also consider where we will find viruses.

That doesn't help much in the sense that the answer is "everywhere":
There are an estimated 1031 viruses on Earth. That is to say: there may be a hundred million times more viruses on Earth than there are stars in the universe. The majority of these viruses infect microbes, including bacteria, archaea, and microeukaryotes, all of which are vital players in the global fixation and cycling of key elements such as carbon, nitrogen, and phosphorus. These two facts combined—the sheer number of viruses and their intimate relationship with microbial life—suggest that viruses, too, play a critical role in the planet’s biosphere.
(Ecosystems & Microbes). Nor does it solve the initial inquiry if we ask "is a virus alive?" because in science that is still as controversial as "what is life?":
For about 100 years, the scientific community has repeatedly changed its collective mind over what viruses are. First seen as poisons, then as life-forms, then biological chemicals, viruses today are thought of as being in a gray area between living and nonliving: they cannot replicate on their own but can do so in truly living cells and can also affect the behavior of their hosts profoundly. The categorization of viruses as nonliving during much of the modern era of biological science has had an unintended consequence: it has led most researchers to ignore viruses in the study of evolution. Finally, however, scientists are beginning to appreciate viruses as fundamental players in the history of life.
(The Uncertain Gene - 9). We can, however, narrow the search by asking "are genes alive?" which would limit our search area:
We found that students held misconceptions about the chemical nature of DNA, with 63 % of students claiming that DNA is alive prior to instruction. The chemical nature of DNA is an important fundamental concept in science fields. We confronted this misconception throughout the semester collecting data from several instructional interventions. Case studies of individual students revealed how various instructional strategies/assessments allowed students to construct and demonstrate the scientifically accepted understanding of the chemical nature of DNA.
(The Uncertain Gene - 8, emphasis in original). Genetic material, including genes of course, is not alive (wait, wait, let me finish).

It is, instead, sophisticated molecular machinery which preceded carbon-based life forms:
“Our cells, and the cells of all organisms, are composed of molecular machines. These machines are built of component parts, each of which contributes a partial function or structural element to the machine. How such sophisticated, multi-component machines could evolve has been somewhat mysterious, and highly controversial.” Professor Lithgow said.
Many cellular processes are carried out by molecular ‘machines’ — assemblies of multiple differentiated proteins that physically interact to execute biological functions ... Our experiments show that increased complexity in an essential molecular machine evolved because of simple, high-probability evolutionary processes, without the apparent evolution of novel functions. They point to a plausible mechanism for the evolution of complexity in other multi-paralogue protein complexes.
The most complex molecular machines are found within cells.
Writing in the journal PLoS Pathogens, the team from Queen Mary's School of Biological and Chemical Sciences show how they studied the molecular machine known as the 'type II bacterial secretion system', which is responsible for delivering potent toxins from bacteria such as enterotoxigenic E. coli and Vibrio cholerae into an infected individual.

Professor Richard Pickersgill, who led the research, said: "Bacterial secretion systems deliver disease causing toxins into host tissue. If we can understand how these machines work, then we can work out how it they might be stopped."
(Do Molecular Machines Deliver Toxins of Power?, emphasis in original). When those scientists mentioned that particular molecular machine nomenclature, I don't think that they were exactly ready for the verification which followed:
"We took this approach because so many RNAs are rapidly destroyed soon after they are made, and this makes them hard to detect," Pugh said. "So rather than look for the RNA product of transcription we looked for the 'initiation machine' that makes the RNA. This machine assembles RNA polymerase, which goes on to make RNA, which goes on to make a protein." Pugh added that he and Venters were stunned to find 160,000 of these "initiation machines," because humans only have about 30,000 genes. "This finding is even more remarkable, given that fewer than 10,000 of these machines actually were found right at the site of genes. Since most genes are turned off in cells, it is understandable why they are typically devoid of the initiation machinery."

The remaining 150,000 initiation machines -- those Pugh and Venters did not find right at genes -- remained somewhat mysterious. "These initiation machines that were not associated with genes were clearly active since they were making RNA and aligned with fragments of RNA discovered by other scientists," Pugh said. "In the early days, these fragments of RNA were generally dismissed as irrelevant ["junk"] since they did not code for proteins." Pugh added that it was easy to dismiss these fragments because they lacked a feature called polyadenylation -- a long string of genetic material, adenosine bases -- that protect the RNA from being destroyed. Pugh and Venters further validated their surprising findings by determining that these non-coding initiation machines recognized the same DNA sequences as the ones at coding genes, indicating that they have a specific origin and that their production is regulated, just like it is at coding genes.
(The Uncertain Gene - 3). So, in this search for the origin of the genes of viruses, we must look for "non-living viruses" which were active prior to the origin of carbon based life forms (see e.g. The Uncertain Gene - 9), that is, non-living viruses which were active subsequent to the origin of molecular machines.

That narrows it down some.

The next post in this series is here.

Evolutionists tell us, based on genetic analysis, that hominids in toto came from Africa ...

Monday, March 31, 2014

Agnotology: The Surge - 8

Never shoot the messenger
James Lovelock, evidently an environmental religionist now, is telling everyone environmentalism is a religion for everyone involved.

I am reminded of Senators who are too old to be there, but just can't get off the stage.

The main reason for that mis-characterization of scientists as clerics has been stated here on Dredd Blog in posts past, thus, since today is the day that the final IPCC report for this current time frame will be released by scientists, let's get down to the nitty gritty reason for these shrill exaggerations:
A recent paper by the biologist Janis L Dickinson, published in the journal Ecology and Society, proposes that constant news and discussion about global warming makes it difficult for people to repress thoughts of death, and that they might respond to the terrifying prospect of climate breakdown in ways that strengthen their character armour but diminish our chances of survival. There is already experimental evidence suggesting that some people respond to reminders of death by increasing consumption. Dickinson proposes that growing evidence of climate change might boost this tendency, as well as raising antagonism towards scientists and environmentalists. Our message, after all, presents a lethal threat to the central immortality project of Western society: perpetual economic growth, supported by an ideology of entitlement and exceptionalism.
(Convergence - Fear of Death Syndrome, quoting Monbiot). That reality holds true as the cultural amygdala and personal amygdala subconsciously package reports of calamity in a manner that promotes personal as well as cultural denial:
There is a large amount of data indicating that the amygdala, a particular structure in the brain, is strongly involved during the learning of "conditioned" fear. However, until now, the underlying neuronal circuits have remained largely unknown.

Now, research ... has been able to identify, for the first time, distinct neuronal circuits within the central nucleus of the amygdala which are specifically involved in acquisition and control of behavioural fear responses.
(The Toxic Bridge To Everywhere, quoting Science Daily). A recent example was a state legislative body mandating that state reports shall not indicate that sea level can rise above eight inches over current levels:
There is virtually universal agreement among scientists that the sea will probably rise a good meter or more before the end of the century, wreaking havoc in low-lying coastal counties. So the members of the developers’ lobbying group NC-20 say the sea will rise only 8 inches, because … because … well, SHUT UP, that’s because why.

That is, the meter or so of sea level rise predicted for the NC Coastal Resources Commission by a state-appointed board of scientists is extremely inconvenient for counties along the coast. So the NC-20 types have decided that we can escape sea level rise – in North Carolina, anyhow – by making it against the law. Or making MEASURING it against the law, anyhow.
(Social Dementia ..., quoting Scientific American). Scientists, however, point out that if all ice caps melt a two hundred feet rise is more accurate (Will This Float Your Boat).

But the subconscious amygdala generates fear which propagandists use to deceive the minds of as many as they can, a dynamic which this series has been detailing (Agnotology: The Surge).

The ignorance generators within society, which Agnotolgy studies, has not only reached the North Carolina legislators, it has also contaminated legislators such as the republicans in the House of Representatives:
Climate change is happening, humans are the cause, and a shocking number — over 56 percent — of congressional Republicans refuse to accept it.

160 elected representatives from the 113th Congress have taken over $55.5 million from the fossil fuel industry that is the driving force behind the carbon emissions that cause climate change. They deny what over 97 percent of climate scientists say is happening — current human activity creates the greenhouse gas emissions that trap heat within the atmosphere and cause climate change. And their constituents are paying the price, with Americans across the nation suffering 419 climate-related national disaster declarations since 2011.
(Anti-Science Climate Denier Caucus). A geography professor turned expert denier is having a denier financial affair with those Luddites (Timothy Ball - presstitute for Oil-Qaeda).

These deceived deniers have been the foundation of the ideology that has brought down empires and societies as far back as our history records go:
A new study sponsored by Nasa's Goddard Space Flight Center has highlighted the prospect that global industrial civilisation could collapse in coming decades due to unsustainable resource exploitation and increasingly unequal wealth distribution.

Noting that warnings of 'collapse' are often seen to be fringe or controversial, the study attempts to make sense of compelling historical data showing that "the process of rise-and-collapse is actually a recurrent cycle found throughout history." Cases of severe civilisational disruption due to "precipitous collapse - often lasting centuries - have been quite common."

The research project is based on a new cross-disciplinary 'Human And Nature DYnamical' (HANDY) model, led by applied mathematician Safa Motesharri of the US National Science Foundation-supported National Socio-Environmental Synthesis Center, in association with a team of natural and social scientists. The study based on the HANDY model has been accepted for publication in the peer-reviewed Elsevier journal, Ecological Economics.

It finds that according to the historical record even advanced, complex civilisations are susceptible to collapse, raising questions about the sustainability of modern civilisation:
"The fall of the Roman Empire, and the equally (if not more) advanced Han, Mauryan, and Gupta Empires, as well as so many advanced Mesopotamian Empires, are all testimony to the fact that advanced, sophisticated, complex, and creative civilizations can be both fragile and impermanent."
By investigating the human-nature dynamics of these past cases of collapse, the project identifies the most salient interrelated factors which explain civilisational decline, and which may help determine the risk of collapse today: namely, Population, Climate, Water, Agriculture, and Energy.
(On The Origin of Catastrophe). Like the officials who ignored the landslide warnings in Washington state, it takes ignorant denial of warnings to lead us into catastrophe.

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

A 1958 video which shows we went into the catastrophe with our "eyes wide open."