Libraries Galore on Friday

I have been working on the Argo data.

It shows that the solar heat arriving on the Earth can't radiate back into space because of green house gases.

So, the heat had to go somewhere, but was found hiding (like the Malaysian Airliner in the southern oceans) by floating buoys that had instruments to measure those things.

The Argo format is a popular scientific format ("netCDF") which is more difficult to process than .csv files or flat database files, and the like.

In studying that Argo data, and writing analytical programs, I have fallen behind in posting.

In the mean time, I though I would share a reference list, a sort of library I have collected for reference purposes.

It is for those who want to do some reading from a smorgasbord of issues of scientific interest:

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Neurons

How neurons fire (How Exactly) Note synapses carefully ("a chemical soup") - Lakoff; cf. The Brain: Neurobiology)

How stress changes that (Hypothesis: How Toxins of Power Are Neutralized or Removed video of Eschel Ben-Jacob at bottom)

Psychology Today (excerpts about stress)

(Stress:It's Worse Than You Think, Stress - Psy Today, Stress - APA, What Is The Stress Response - SP, Robert Sapolsky: The Psychology of Stress)

Ethology (a branch of politics - animal behavior)

Misc.

Canyon Under Antarctica

How long do stars Live?

(HIV Dynamics - paper). So what is a retrovirus, what is HIV, and what does science say about it:

To understand what HIV is, let’s break it down:

H – Human – This particular virus can only infect human beings.

I – Immunodeficiency – HIV weakens your immune system by destroying important cells that fight disease and infection. A “deficient” immune system can’t protect you.

V – Virus – A virus can only reproduce itself by taking over a cell in the body of its host.

(What is HIV?). HIV is a virus that infects only humans?

Interesting.

How does it determine a human cell from another primate's cell, or any other organism's cell for that matter?

"DNA — deoxyribonucleic acid; the molecular carrier of hereditary information; usually occurs as a double-stranded, double helical structure comprised of the four bases adenine thymine, guanine, and cytosine; DNA organization is similar to that of a language document, divided into words (codons), sentences (genes), paragraphs (operons), volume (chromosomes)" (Microbes-Mind).

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Climatology:

Is 7.2 deg. F (4C) Hot or Warm?

Ocean Die Off In California Waters (accord: Professor's Diary)

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You Are Here Psychology

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Some interesting videos:

Lakoff:

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Sapolsky:

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Midbody @ Cell Division - Toxin Source?

Psychopathic Personality, "Bridging the Gap Between Scientific Evidence and Public Policy"

Does Studying Economics Breed Greed

Memory Morph

Microbial Garden

New Human Brain Cells Daily

Virus origin of Schizophrenia?

Slime Mold Problem Solving

Viral Genes In Humans

Mammals Made By Viruses

Microbes Produce What Scientists call Toxins

White Folk Skull Shape & Size changing

Views of Populace Unscientific

Do Plants Think?

Neurotransmitters & T. gondii 

Evolution of cats 

Cat virus origins/evolution

Stop The War On Microbes

Stem Cells Stay Alive 17 days after person dies 

Complex Communication System Between Proteins in Cells (video)

Harvard Magazine Protein Communication In Cells

Medical Treatment with Microbes

Microbes Found In Lake Under Antarctica

Diabetes (Unhealthy Civilization):

Ninety-five percent of diabetes is lifestyle-induced Type 2 diabetes. The world's bestselling blockbuster diabetes drug Avandia has killed nearly 200,000 people from heart attacks since it was introduced in 1999 -- the very disease that kills most diabetics. The solution to our diabetes epidemic will not come from within the health care system. It will not come at the end of a pill bottle or the blade of a scalpel. We cannot bypass the fact that this is a lifestyle disease and cannot be solved by better or more medication.

That lifestyle which brought us unhealthiness is described by this statement: "[o]ver23% of all the goods and services made since 1AD were produced from 2001 to 2010" (Economist).

Stem Cell Basics

Adult stem cells are rare. Their primary functions are to maintain the steady state functioning of a cell—called homeostasis—and, with limitations, to replace cells that die because of injury or disease [44, 58]. For example, only an estimated 1 in 10,000 to 15,000 cells in the bone marrow is a hematopoietic (bloodforming) stem cell (HSC) [105]. Furthermore, adult stem cells are dispersed in tissues throughout the mature animal and behave very differently, depending on their local environment. For example, HSCs are constantly being generated in the bone marrow where they differentiate into mature types of blood cells. Indeed, the primary role of HSCs is to replace blood cells [26] (see Chapter 5. Hematopoietic Stem Cells). In contrast, stem cells in the small intestine are stationary, and are physically separated from the mature cell types they generate. Gut epithelial stem cells (or precursors) occur at the bases of crypts—deep invaginations between the mature, differentiated epithelial cells that line the lumen of the intestine. These epithelial crypt cells divide fairly often, but remain part of the stationary group of cells they generate [93].

Leukemia  (@ Host-microbe interactions).

Host-microbe communication (signaling / messaging) should be suspect in the degeneration of hematopoiesis stem cells which leads to myeloid leukemia.

"Hematopoiesis produces multiple immune cell types that perceive and respond to microbial stimuli." ...

"Another emerging theme suggests that microbial cells and their products can influence zebrafish immune cell production and function. Many microbial pathogenesis studies in zebrafish have focused on embryonic stages when hematopoietic development is especially dynamic (Fig. 1), raising the possibility that immune challenges during these stages could alter the proliferation, differentiation, and/or maintenance of hematopoietic immune cells. "

"Host responses to microbial encounters frequently involve communication between multiple host cell lineages and tissues. It is therefore important to not only identify the signaling mechanisms that facilitate a host response, but also the temporal and spatial pattern in which those signaling events occur."


Herpes Virus (HSV)


The herpes virus remains in the spinal cord area until it detects that the time is right, then it travels to the face of its host to cause a breakout:

How does HSV enter the body?

The virus gains entry into the body, not through intact skin, but through mucous membranes, such as the oral region, vagina, tip of the penis, or the eye. The virus will first replicate (make copies of itself) inside surface cells at these sites, eventually killing the infected surface cells. In a person with normal immunity, the immune system is quickly mobilized to contain the primary infection.

However, before this happens, the virus gains entry to the nerve cell end-plates (structures that help us to feel things like pain and temperature), present at the skin surface. The end-plates connect to the more deeply located nerve cell body through an elongated nerve fibre or axon. This cell in turn is connected to “serially coupled” layers of internal nerve cells, which eventually lead to a ganglion, which is a collection of nerve cell bodies just like a node in an electricity grid. Through such intricate connections the nerve cells eventually lead into and communicate with the central nervous system or the brain. The axons are protected by “myelin blankets”, just like the insulating material around electrical wires, but the endings are bare, as are the nodes where one nerve cell extension connects with the next (synapse). It is thought that the virus sheds its envelope as soon as it has entered the nerve and uses the axon as a conduit, hiding from immune system attack, as if it were inside a “Trojan Horse”.

HSV has specifically chosen the nerve cell body and ultimately the ganglion (HSV-1 resides in the trigeminal ganglion; HSV-2 resides in the sacral ganglia) as a site where it remains dormant. It is from these locations that the virus may reactivate from its dormant state to the respective innervated (nerve-cell-serviced) body areas. This is why dormant virus from the trigeminal ganglion (oral or facial area) reactivates in the oral or facial region, whereas the dormant virus from the sacral ganglion (lower back/spine area) reactivate to the genital area or the buttock.

The Emotional Brain

Ugly Delusions, Salon

Ayn Rand, Monbiot

Want to Understand Republicans? First Understand Evolution

The Science of Truthiness: Why Conservatives Deny Global Warming

How the Right-Wing Brain Works and What That Means for Progressives

Cyanobacteria

Origin of Viruses

The Origin and Evolution of Viruses

Despite recent advances in our understanding of diverse aspects of virus evolution, particularly at the epidemiological scale, revealing the ultimate origins of viruses has proven to be a more intractable problem. Herein I review some current ideas on the evolutionary origins of viruses, and assess how well these theories accord with what we know about the evolution of contemporary viruses. I note the growing evidence for the theory that viruses arose before the Last Universal Cellular Ancestor (LUCA). This ancient origin theory is supported by the presence of capsid architectures that are conserved among diverse viral taxa, including among RNA and DNA viruses, and the strongly inverse relationship between genome size and mutation rate across all replication systems, such that pre-LUCA genomes were probably both small and highly error prone and hence RNA virus-like. I also highlight the advances that are needed to come to a better understanding of virus origins, most notably the ability to accurately infer deep evolutionary history from the phylogenetic analysis of conserved protein structures.

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Journal Viruses, What does virus evolution tell us about virus origins?

Edward C. Holmes (Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, Mueller Laboratory, University Park, PA 16802, USA; Fogarty International Center, National Institutes of Health, Bethesda, MD 20892. USA.

Some of the oxygen we breathe today is being produced because of viruses infecting micro-organisms in the world’s oceans, scientists heard Wednesday 2 April 2008 at the Society for General Microbiology’s 162nd meeting held at the Edinburgh International Conference Centre.

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Astrobiology Magazine

About half the world’s oxygen is being produced by tiny photosynthesizing creatures called phytoplankton in the major oceans. These organisms are also responsible for removing carbon dioxide from our atmosphere and locking it away in their bodies, which sink to the bottom of the ocean when they die, removing it forever and limiting global warming.

“In major parts of the oceans, the micro-organisms responsible for providing oxygen and locking away carbon dioxide are actually single celled bacteria called cyanobacteria,” says Professor Nicholas Mann of the University of Warwick. “These organisms, which are so important for making our planet inhabitable, are attacked and infected by a range of different types of viruses.”

The researchers have identified the genetic codes of these viruses using molecular techniques and discovered that some of them are responsible for providing the genetic material that codes for key components of photosynthesis machinery [in cyanobacteria].

Viruses may also help to spread useful genes for photosynthesis from one strain of bacteria to another.

The study provides new insight into the role that viruses play in both the processes of evolution, and in making our planet a habitable environment for living organisms.

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Hypothesis:
 
The ancient Virus World and evolution of cells
Eugene V Koonin*, Tatiana G Senkevich and Valerian V Dolja

Several genes coding for key proteins involved in viral replication and morphogenesis as well as the major capsid protein of icosahedral virions are shared by many groups of RNA and DNA viruses but are missing in cellular life forms.

On the basis of this key observation and the data on extensive genetic exchange between diverse viruses, we propose the concept of the ancient virus world. The virus world is construed as a distinct contingent of viral genes that continuously retained its identity throughout the entire history of life. 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. 

In this pool, RNA viruses would evolve first, followed by retroid elements, and DNA viruses. The Virus World concept is predicated on a model of early evolution whereby emergence of substantial genetic diversity antedates the advent of full-fledged cells, allowing for extensive gene mixing at this early stage of evolution.

We outline a scenario of the origin of the main classes of viruses in conjunction with a specific model of precellular evolution under which the primordial gene pool dwelled in a network of inorganic compartments. Somewhat paradoxically, under this scenario, we surmise that selfish genetic elements ancestral to viruses evolved prior to typical cells, to become intracellular parasites once bacteria and archaea arrived at the scene.

Selection against excessively aggressive parasites that would kill off the host ensembles of genetic elements would lead to early evolution of temperate virus-like agents and primitive defense mechanisms, possibly, based on the RNA interference principle.

The emergence of the eukaryotic cell is construed as the second melting pot of virus evolution from which the major groups of eukaryotic viruses originated as a result of extensive recombination of genes from various bacteriophages, archaeal viruses, plasmids, and the evolving eukaryotic genomes.

Again, this vision is predicated on a specific model of the emergence of eukaryotic cell under which archaeo-bacterial symbiosis was the starting point of eukaryogenesis, a scenario that appears to be best compatible with the data.

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The earliest version of the hypothesis:

Several genes coding for key proteins involved in viral replication and morphogenesis as well as the major capsid protein of icosahedral virions are shared by many groups of RNA and DNA viruses but are missing in cellular life forms.

On the basis of this key observation and the data on extensive genetic exchange between diverse viruses, we propose the concept of the ancient virus world. The virus world is construed as a distinct contingent of viral genes that continuously retained its identity throughout the entire history of life. 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.;

In this pool, RNA viruses would evolve first, followed by retroid elements, and DNA viruses. The Virus World concept is predicated on a model of early evolution whereby emergence of substantial genetic diversity antedates the advent of full-fledged cells, allowing for extensive gene mixing at this early stage of evolution.

We outline a scenario of the origin of the main classes of viruses in conjunction with a specific model of precellular evolution under which the primordial gene pool dwelled in a network of inorganic compartments. Somewhat paradoxically, under this scenario, we surmise that selfish genetic elements ancestral to viruses evolved prior to typical cells, to become intracellular parasites once bacteria and archaea arrived at the scene.

Selection against excessively aggressive parasites that would kill off the host ensembles of genetic elements would lead to early evolution of temperate virus-like agents and primitive defense mechanisms, possibly, based on the RNA interference principle.

The emergence of the eukaryotic cell is construed as the second melting pot of virus evolution from which the major groups of eukaryotic viruses originated as a result of extensive recombination of genes from various bacteriophages, archaeal viruses, plasmids, and the evolving eukaryotic genomes.

Again, this vision is predicated on a specific model of the emergence of eukaryotic cell under which archaeo-bacterial symbiosis was the starting point of eukaryogenesis, a scenario that appears to be best compatible with the data.

("The ancient Virus World and evolution of cells", 2006, by Eugene V Koonin, Tatiana G Senkevich, and Valerian V Dolja). These folks are or were from:

National Center for Biotechnology Information, National Library of Medicine, USA (Koonin)

Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894, USA (Senkevich)

Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA (Dolja)

(ibid).

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A natural link from virus to cyanobacteria and oxygen:

The researchers have identified the genetic codes of these viruses using molecular techniques and discovered that some of them are responsible for providing the genetic material that codes for key components of photosynthesis machinery [in cyanobacteria].

Viruses may also help to spread useful genes for photosynthesis from one strain of bacteria to another.

The study provides new insight into the role that viruses play in both the processes of evolution, and in making our planet a habitable environment for living organisms.

(Astrobiology Magazine, emphasis added). The list of scientists going with the virus-first hypothesis is growing:

I note the growing evidence for the theory that viruses arose before the Last Universal Cellular Ancestor (LUCA). This ancient origin theory is supported by the presence of capsid architectures that are conserved among diverse viral taxa, including among RNA and DNA viruses, and the strongly inverse relationship between genome size and mutation rate across all replication systems, such that pre-LUCA genomes were probably both small and highly error prone and hence RNA virus-like. I also highlight the advances that are needed to come to a better understanding of virus origins, most notably the ability to accurately infer deep evolutionary history from the phylogenetic analysis of conserved protein structures.

(What does virus evolution tell us about virus origins?, Edward C. Holmes, Journal of Virology, J. Virol. doi:10.1128/JVI.02203-10, Mar. 2011).

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There.

That is now out of my draft files.

Have a good weekend.